view card202.json @ 7:4d2777aa99db draft

planemo upload

{"2":{"model_id":"2","model_name":"CblA-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"1188":{"protein_sequence":{"accession":"ACT97415.1","sequence":"MKAYFIAILTLFTCIATVVRAQQMSELENRIDSLLNGKKATVGIAVWTDKGDMLRYNDHVHFPLLSVFKFHVALAVLDKMDKQSISLDSIVSIKASQMPPNTYSPLRKKFPDQDFTITLRELMQYSISQSDNNACDILIEYAGGIKHINDYIHRLSIDSFNLSETEDGMHSSFEAVYRNWSTPSAMVRLLRTADEKELFSNKELKDFLWQTMIDTETGANKLKGMLPAKTVVGHKTGSSDRNADGMKTADNDAGLVILPDGRKYYIAAFVMDSYETDEDNANIIARISRMVYDAMR"},"dna_sequence":{"accession":"GQ343019","fmin":"132","fmax":"1023","strand":"+","sequence":"ATGAAAGCATATTTCATCGCCATACTTACCTTATTCACTTGTATAGCTACCGTCGTCCGGGCGCAGCAAATGTCTGAACTTGAAAACCGGATTGACAGTCTGCTCAATGGCAAGAAAGCCACCGTTGGTATAGCCGTATGGACAGACAAAGGAGACATGCTCCGGTATAACGACCATGTACACTTCCCCTTGCTCAGTGTATTCAAATTCCATGTGGCACTGGCCGTACTGGACAAGATGGATAAGCAAAGCATCAGTCTGGACAGCATTGTTTCCATAAAGGCATCCCAAATGCCGCCCAATACCTACAGCCCCCTGCGGAAGAAGTTTCCCGACCAGGATTTCACGATTACGCTTAGGGAACTGATGCAATACAGCATTTCCCAAAGCGACAACAATGCCTGCGACATCTTGATAGAATATGCAGGAGGCATCAAACATATCAACGACTATATCCACCGGTTGAGTATCGACTCCTTCAACCTCTCGGAAACAGAAGACGGCATGCACTCCAGCTTCGAGGCTGTATACCGCAACTGGAGTACTCCTTCCGCTATGGTCCGACTACTGAGAACGGCTGATGAAAAAGAGTTGTTCTCCAACAAGGAGCTGAAAGACTTCTTGTGGCAGACCATGATAGATACTGAAACCGGTGCCAACAAACTGAAAGGTATGTTGCCAGCCAAAACCGTGGTAGGACACAAGACCGGCTCTTCCGACCGCAATGCCGACGGTATGAAAACTGCAGATAATGATGCCGGCCTCGTTATCCTTCCCGACGGCCGGAAATACTACATTGCCGCCTTCGTCATGGACTCATACGAGACGGATGAGGACAATGCGAACATCATCGCCCGCATATCACGCATGGTATATGATGCGATGAGATGAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39659","NCBI_taxonomy_name":"mixed culture bacterium AX_gF3SD01_15","NCBI_taxonomy_id":"663108"}}}},"ARO_accession":"3002999","ARO_id":"39433","ARO_name":"CblA-1","ARO_description":"CblA-1 beta-lactamase is a class A beta-lactamase found in Bacteroides uniformis that is species-specific.","ARO_category":{"39432":{"category_aro_accession":"3002998","category_aro_cvterm_id":"39432","category_aro_name":"CblA beta-lactamase","category_aro_description":"CblA beta-lactamases are class A beta-lactamases that confer resistance to cephalosporins.","category_aro_class_name":"AMR Gene Family"},"41256":{"category_aro_accession":"3004129","category_aro_cvterm_id":"41256","category_aro_name":"cephaloridine","category_aro_description":"Cephaloridine is a semisynthetic, broad-spectrum, first-generation cephalosporin with antibacterial activity. Cephaloridine binds to and inactivates penicillin-binding proteins (PBPs) located on the inner membrane of the bacterial cell wall. PBPs are enzymes involved in the terminal stages of assembling the bacterial cell wall and in reshaping the cell wall during growth and division. Inactivation of PBPs interferes with the cross-linkage of peptidoglycan chains necessary for bacterial cell wall strength and rigidity. This results in the weakening of the bacterial cell wall and causes cell lysis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4":{"model_id":"4","model_name":"SHV-52","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1393":{"protein_sequence":{"accession":"AEJ08681.1","sequence":"MRYIRLCIISLLAALPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMISTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLAIVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"HQ845196","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCGCCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATAAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATTTGCTGCTGGCCATCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTAGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001109","ARO_id":"37489","ARO_name":"SHV-52","ARO_description":"SHV-52 is a beta-lactamase that has been found in clinical isolates.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5":{"model_id":"5","model_name":"dfrF","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"677":{"protein_sequence":{"accession":"AAD01868.1","sequence":"MIGLIVARSKNNVIGKNGNIPWKIKGEQKQFRELTTGNVVIMGRKSYEEIGHPLPNRMNIVVSTTTEYQGDNLVSVKSLEDALLLAKGRDVYISGGYGLFKEALQIVDKMYITEVDLNIEDGDTFFPEFDINDFEVLIGETLGEEVKYTRTFYVRKNELSRFWI"},"dna_sequence":{"accession":"AF028812","fmin":"392","fmax":"887","strand":"+","sequence":"ATGATAGGTTTGATTGTTGCGAGGTCAAAGAATAATGTTATAGGCAAGAATGGTAATATACCATGGAAAATAAAGGGAGAACAAAAGCAATTTAGAGAGTTAACAACGGGTAATGTGGTTATTATGGGGCGAAAGTCTTATGAAGAAATCGGTCATCCGTTGCCTAATAGAATGAATATTGTTGTTTCCACCACAACAGAGTATCAAGGAGATAATTTAGTTTCAGTTAAATCATTAGAAGATGCATTATTATTGGCTAAAGGACGAGATGTATACATATCTGGTGGATATGGACTATTTAAGGAAGCTTTGCAAATAGTAGATAAAATGTATATCACAGAAGTAGATTTAAATATTGAAGATGGAGATACATTCTTTCCAGAATTTGATATCAATGATTTTGAAGTTTTGATAGGGGAAACACTTGGTGAGGAAGTGAAATATACGAGAACATTTTATGTAAGGAAAAATGAATTGAGTAGATTTTGGATTTAGG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3002867","ARO_id":"39301","ARO_name":"dfrF","ARO_description":"dfrF is a chromosome-encoded dihydrofolate reductase found in Streptococcus pyogenes","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36408":{"category_aro_accession":"3000269","category_aro_cvterm_id":"36408","category_aro_name":"brodimoprim","category_aro_description":"Brodimoprim is a structural derivative of trimethoprim and an inhibitor of bacterial dihydrofolate reductase. The 4-methoxy group of trimethoprim is replaced with a bromine atom.","category_aro_class_name":"Antibiotic"},"36423":{"category_aro_accession":"3000284","category_aro_cvterm_id":"36423","category_aro_name":"tetroxoprim","category_aro_description":"Tetroxoprim is a trimethoprim derivative that inhibits bacterial dihydrofolate reductase.","category_aro_class_name":"Antibiotic"},"36476":{"category_aro_accession":"3000337","category_aro_cvterm_id":"36476","category_aro_name":"iclaprim","category_aro_description":"Iclaprim is a bactericidal compound that inhibits dihydrofolate reductase. It is used against clinically important Gram-positive pathogens, including methicillin-sensitive Staphylococcus aureus and methicillin-resistant S. aureus.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7":{"model_id":"7","model_name":"CTX-M-130","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1703":{"protein_sequence":{"accession":"AFJ59957.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAERRHDVLASAARIIAEGL"},"dna_sequence":{"accession":"JX017365","fmin":"244","fmax":"1120","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGCGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGACGCCACGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001989","ARO_id":"38389","ARO_name":"CTX-M-130","ARO_description":"CTX-M-130 is a beta-lactamase. From the Lahey list of CTX-M beta-lactamases.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8":{"model_id":"8","model_name":"NDM-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1103":{"protein_sequence":{"accession":"AEX08599.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASVRAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"JN967644","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGATGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGTGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002356","ARO_id":"38756","ARO_name":"NDM-6","ARO_description":"NDM-6 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"9":{"model_id":"9","model_name":"ACT-35","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1584":{"protein_sequence":{"accession":"BAP68758.1","sequence":"MMKKSLCCALLLGISCSALATPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVVEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYYILEALQ"},"dna_sequence":{"accession":"LC004922","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCACGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTAGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTGTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAACGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAGGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTGCCCGTGGTAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACTATATCCTCGAGGCGCTACAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001855","ARO_id":"38255","ARO_name":"ACT-35","ARO_description":"ACT-35 is a beta-lactamase. From the Lahey list of ACT beta-lactamases.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"10":{"model_id":"10","model_name":"CARB-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1661":{"protein_sequence":{"accession":"AAF61417.1","sequence":"MNVRKHKASFFSVVITFLCLTLSLNANATDSVLEAVTNAETELGARIGLAVHDLETGKRWEHKSNERFPLSSTFKTLACANVLQRVDLGKERIDRVVRFSESNLVTYSPVTEKHVGKKGMSLAELCQATLSTSDNSAANFILQAIGGPKALTKFLRSIGDDTTRLDRWETELNEAVPGDKRDTTTPIAMVTTLEKLLIDETLSIKSRQQLESWLKGNEVGDALFRKGVPSDWIVADRTGAGGYGSRAITAVMWPPNRKPIVAALYITETDASFEERNAVIAKIGEQIAKTVLMENSRN"},"dna_sequence":{"accession":"AF135373","fmin":"11","fmax":"908","strand":"+","sequence":"ATGAACGTACGTAAACACAAGGCTAGTTTTTTTAGCGTAGTAATTACTTTTTTATGTCTCACGCTATCATTAAATGCTAATGCAACAGACTCAGTACTTGAAGCGGTTACCAATGCTGAAACTGAATTAGGCGCTAGAATTGGTCTAGCTGTGCATGATTTGGAAACGGGAAAACGTTGGGAACATAAATCTAATGAACGTTTTCCTCTAAGTAGTACCTTTAAAACACTTGCCTGTGCAAACGTTCTTCAAAGAGTTGATCTAGGTAAAGAAAGAATTGATAGAGTTGTGAGATTCTCTGAAAGCAATCTCGTTACATACTCACCTGTAACAGAAAAACATGTGGGTAAAAAAGGGATGTCGCTCGCAGAGCTGTGTCAGGCCACATTATCAACCAGTGATAATTCAGCTGCCAATTTTATTCTACAAGCGATTGGTGGACCTAAGGCTCTAACGAAATTTTTGCGTTCCATTGGCGACGATACTACGCGCCTTGATCGCTGGGAAACAGAACTTAACGAAGCGGTGCCTGGAGATAAGCGAGACACGACAACACCAATTGCAATGGTAACGACACTTGAAAAGTTACTAATTGACGAAACACTATCTATCAAATCTCGTCAACAACTAGAATCTTGGCTTAAAGGTAATGAGGTTGGCGATGCATTGTTTCGTAAAGGCGTTCCAAGTGACTGGATAGTAGCAGATAGAACAGGCGCTGGTGGTTATGGGTCGCGTGCTATTACTGCGGTGATGTGGCCTCCAAATCGCAAGCCTATCGTAGCCGCTCTATACATTACAGAGACAGACGCCTCGTTTGAAGAAAGAAATGCTGTCATTGCAAAAATTGGTGAGCAAATAGCGAAGACAGTATTAATGGAGAATAGCCGTAACTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36918","NCBI_taxonomy_name":"Acinetobacter calcoaceticus subsp. anitratus","NCBI_taxonomy_id":"107673"}}}},"ARO_accession":"3002244","ARO_id":"38644","ARO_name":"CARB-5","ARO_description":"CARB-5 is a beta-lactamase found in Acinetobacter calcoaceticus","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"11":{"model_id":"11","model_name":"Erm(34)","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"162":{"protein_sequence":{"accession":"AAP74657.1","sequence":"MTKKMNKYNGKKLSRGEPPNFSGQHFMHNKRLLKEIVDKADVSVRDTVLELGAGKGALTTILSERADRVLAVEYDQKCIEALQWKLVGSKNVSILHQDIMKVALPTEPFVVVSNIPYSITTAIMKMLLNNPKNKLQRGAIVMEKGAAKRFTSVSPKDAYVMAWHMWFDIHYERGISRSSFSPPPKVDSALVRIVRKQHPLFPYKEAKAMHDFLSYALNNPRAPLDQVLRGIFTAPQAKKVRQAIGVKPETPVAMLHARQWAMVCDAMVRHVPKVYWPRRKR"},"dna_sequence":{"accession":"AY234334","fmin":"0","fmax":"846","strand":"+","sequence":"ATGACGAAAAAAATGAACAAGTATAATGGGAAAAAACTTAGCCGTGGAGAACCTCCCAATTTTAGCGGTCAGCATTTTATGCACAATAAACGGCTACTGAAGGAAATTGTTGATAAAGCTGACGTCTCTGTTCGTGATACGGTTTTAGAGCTGGGAGCAGGAAAAGGCGCGTTGACGACGATTTTAAGCGAACGCGCGGACCGGGTTCTAGCCGTCGAGTATGACCAAAAATGTATTGAAGCGCTGCAATGGAAACTAGTTGGGTCAAAAAACGTGTCCATTCTCCATCAAGATATTATGAAGGTGGCATTGCCAACGGAACCGTTTGTTGTTGTTTCCAACATCCCTTATTCGATCACAACGGCAATCATGAAAATGCTGTTAAACAATCCAAAAAACAAACTACAACGAGGGGCAATTGTAATGGAGAAAGGAGCAGCAAAGCGGTTTACAAGCGTTTCGCCGAAAGACGCTTATGTGATGGCTTGGCATATGTGGTTTGACATCCACTATGAAAGGGGAATTTCCAGAAGTTCATTTTCGCCGCCGCCGAAAGTCGATTCTGCCCTTGTCCGCATTGTCCGCAAACAGCATCCCCTTTTTCCATATAAAGAGGCGAAAGCGATGCATGACTTTTTATCGTACGCACTAAACAACCCTAGAGCACCCCTTGATCAGGTATTACGAGGAATTTTTACCGCCCCTCAAGCAAAAAAAGTGCGGCAGGCAATCGGCGTCAAACCTGAGACACCAGTGGCCATGCTTCATGCCAGGCAGTGGGCGATGGTTTGTGACGCGATGGTTCGGCATGTTCCAAAAGTGTATTGGCCAAGGCGAAAGAGATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36882","NCBI_taxonomy_name":"Bacillus clausii","NCBI_taxonomy_id":"79880"}}}},"ARO_accession":"3000600","ARO_id":"36739","ARO_name":"Erm(34)","ARO_description":"ErmD confers MLSb phenotype.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35946":{"category_aro_accession":"0000027","category_aro_cvterm_id":"35946","category_aro_name":"roxithromycin","category_aro_description":"Roxithromycin is a semi-synthetic, 14-carbon ring macrolide antibiotic derived from erythromycin. It is used to treat respiratory tract, urinary and soft tissue infections. Roxithromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35974":{"category_aro_accession":"0000057","category_aro_cvterm_id":"35974","category_aro_name":"telithromycin","category_aro_description":"Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36315":{"category_aro_accession":"3000176","category_aro_cvterm_id":"36315","category_aro_name":"dirithromycin","category_aro_description":"Dirithromycin is an oxazine derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome to inhibit bacterial protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin 1A is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"vernamycin B-gamma","category_aro_description":"Vernamycin B-gamma is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"12":{"model_id":"12","model_name":"TEM-126","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1567":{"protein_sequence":{"accession":"AAT45742.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERETTTPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AY628199","fmin":"203","fmax":"1064","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGAAACCACGACGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000988","ARO_id":"37368","ARO_name":"TEM-126","ARO_description":"TEM-126 is an extended-spectrum beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"13":{"model_id":"13","model_name":"LRA-12","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1445":{"protein_sequence":{"accession":"ACH58990.1","sequence":"MNVQNCMVKAVSVSIILFASLSLAAQKVKEPTVSNADWSKPYRPFRIAGNLYYIGTYDLACYLITTKQGNIIVNTGLAASALQIKNNIKALGFKLTDTKILLTTQAHYDHLGAMAEIKKITGAKLMADEGDATVMADGGSSDYAFGGHGSMFEPIIADRLLHDKDTIQLGDTKLVMLHHPGHTKGSCSFLFDTKDEQRSYRILIANMPTIVIEKKFSEVSSYPGIAKDYAYTLQAMKNLSFDIWVASHASQFSMHSKHKPGDGYNPKSFMDRKGYDESLDKLQKEYEKHLNEN"},"dna_sequence":{"accession":"EU408351","fmin":"16572","fmax":"17454","strand":"+","sequence":"ATGAATGTTCAAAATTGTATGGTAAAAGCCGTTTCCGTTAGCATCATTTTATTTGCATCCCTTTCCCTTGCTGCGCAAAAGGTAAAGGAACCAACCGTTAGTAACGCAGACTGGTCAAAGCCGTACCGGCCCTTTAGAATTGCCGGCAATTTATATTACATCGGTACATATGATCTCGCTTGTTATCTTATTACTACTAAACAGGGTAATATCATTGTCAATACCGGGCTGGCGGCTTCTGCATTACAAATAAAAAATAATATCAAAGCGTTAGGCTTTAAGTTAACTGACACCAAAATACTCTTAACAACACAGGCCCATTATGACCATTTGGGTGCAATGGCTGAAATTAAGAAAATAACAGGCGCAAAGCTCATGGCAGATGAGGGCGATGCGACGGTAATGGCTGATGGAGGCAGTTCTGATTACGCCTTCGGCGGGCATGGCAGTATGTTTGAACCTATAATAGCAGACCGCCTGCTGCATGATAAGGATACCATTCAGTTAGGGGATACAAAATTGGTGATGTTGCATCATCCCGGTCACACGAAGGGTTCCTGCAGTTTTTTATTTGATACAAAAGATGAGCAACGATCTTACAGGATATTAATCGCCAACATGCCTACCATCGTTATTGAAAAAAAATTTAGTGAAGTAAGTAGTTATCCCGGCATTGCTAAAGACTATGCCTATACTTTACAGGCAATGAAAAATCTTTCTTTTGATATATGGGTTGCATCTCATGCCAGCCAGTTTAGTATGCATAGCAAACACAAGCCGGGCGATGGGTATAATCCCAAGTCTTTTATGGACAGGAAGGGTTATGATGAATCTTTGGATAAGCTGCAAAAAGAGTATGAAAAGCACTTGAATGAAAATTGAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39084","NCBI_taxonomy_name":"uncultured bacterium BLR12","NCBI_taxonomy_id":"506514"}}}},"ARO_accession":"3002511","ARO_id":"38911","ARO_name":"LRA-12","ARO_description":"LRA-12 is a beta-lactamase isolated from soil samples in Alaska","ARO_category":{"41390":{"category_aro_accession":"3004226","category_aro_cvterm_id":"41390","category_aro_name":"subclass B3 LRA beta-lactamase","category_aro_description":"Beta-lactamases that are part of the LRA gene family and are classified as B3 (metallo-) beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"14":{"model_id":"14","model_name":"TEM-72","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1651":{"protein_sequence":{"accession":"AAF19151.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTTPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASKRGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AF157553","fmin":"147","fmax":"1008","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTAAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36917","NCBI_taxonomy_name":"Morganella morganii","NCBI_taxonomy_id":"582"}}}},"ARO_accession":"3000938","ARO_id":"37318","ARO_name":"TEM-72","ARO_description":"TEM-72 is an extended-spectrum beta-lactamase found in Proteus mirabilis and Morganella morganii.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"15":{"model_id":"15","model_name":"TEM-59","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"931":{"protein_sequence":{"accession":"AAD45935.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMGDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAE"},"dna_sequence":{"accession":"AF062386","fmin":"30","fmax":"862","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGGGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3000928","ARO_id":"37308","ARO_name":"TEM-59","ARO_description":"TEM-59 is an inhibitor-resistant beta-lactamase that has been found in clinical isolates.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"16":{"model_id":"16","model_name":"KPC-10","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1633":{"protein_sequence":{"accession":"ACS35345.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVRWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"GQ140348","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCGGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3002320","ARO_id":"38720","ARO_name":"KPC-10","ARO_description":"KPC-10 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"18":{"model_id":"18","model_name":"OXA-212","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1048":{"protein_sequence":{"accession":"AEV91551.1","sequence":"MKTLQSGLIALITTFGSACTTISPSVETAKNQQQQSAQQQIQQAFDQLQTTGVIVVKDKHSLHSYGNDLSRAQTPYIPASTFKMLNALIGLEHGKATSTEVFKWDGQKRSFPTWEKDMTLGQAMQASAVPVYQELARRIGLDLMKKEVQRIGYGNQQIGTVVDNFWLVGPLQITPVQEVLFVEKLANTQLAFKPDVQHAVQDMLLIEQKPNYKLYAKSGWGMDLEPQVGWWAGWVETSTGEKVYFALNMHMKTGISASVREQLVKQSLTALGII"},"dna_sequence":{"accession":"JN861780","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAAAACTTTACAGTCGGGCCTCATCGCCCTCATTACAACCTTCGGTTCCGCATGTACCACAATAAGCCCCTCGGTAGAAACAGCTAAAAACCAACAGCAACAAAGTGCGCAGCAGCAGATCCAACAGGCCTTCGATCAACTCCAAACCACTGGGGTGATTGTCGTTAAAGATAAGCATAGCTTACACAGCTACGGCAATGACTTGAGCCGTGCTCAGACACCCTATATACCCGCCTCTACCTTTAAAATGCTGAATGCCTTAATCGGACTAGAACATGGTAAAGCAACCAGCACCGAGGTATTTAAATGGGATGGTCAAAAGCGCAGCTTCCCTACTTGGGAAAAAGACATGACTTTAGGGCAAGCCATGCAAGCATCTGCCGTTCCCGTTTATCAGGAGCTAGCACGGCGCATTGGCCTAGACCTGATGAAAAAAGAAGTGCAGCGCATTGGATATGGCAATCAACAGATTGGCACCGTTGTCGATAATTTTTGGTTAGTCGGTCCACTGCAAATTACGCCTGTTCAAGAAGTCCTTTTTGTAGAGAAGCTGGCCAATACACAACTCGCTTTTAAACCCGATGTACAACATGCAGTACAAGACATGCTGCTGATTGAACAAAAACCGAATTATAAACTCTATGCCAAATCTGGTTGGGGCATGGACCTAGAACCGCAAGTGGGCTGGTGGGCAGGCTGGGTCGAAACTTCAACAGGTGAAAAAGTGTATTTTGCTTTGAATATGCATATGAAAACAGGGATTTCAGCCAGCGTGCGTGAGCAACTGGTCAAACAAAGTCTGACAGCACTGGGGATAATTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39092","NCBI_taxonomy_name":"Acinetobacter johnsonii","NCBI_taxonomy_id":"40214"}}}},"ARO_accession":"3001711","ARO_id":"38111","ARO_name":"OXA-212","ARO_description":"OXA-212 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"19":{"model_id":"19","model_name":"IMP-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1091":{"protein_sequence":{"accession":"CAB94707.1","sequence":"MKKLFVLCVCFLCSITAAGARLPDLKIEKLEEGVYVHTSFEEVNGWGVVSKHGLVVLVNTDAYLIDTPFTATDTEKLVNWFVERGYKIKGTISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKDGKVQAKNSFSGVSYWLVKNKIEVFYPGPGHTQDNVVVWLPEKKILFGGCFVKPDGLGNLGDANLEAWPKSAKILMSKYVKAKLVVSSHSEIGDASLLKRTWEQAVKGLNESKKPSQPSN"},"dna_sequence":{"accession":"AJ243491","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAAGAAATTATTTGTTTTATGTGTATGCTTCCTTTGTAGCATTACTGCCGCGGGAGCGCGTTTGCCTGATTTAAAAATCGAGAAGCTTGAAGAAGGTGTTTATGTTCATACATCGTTCGAAGAAGTTAACGGTTGGGGTGTTGTTTCTAAACACGGTTTGGTGGTTCTTGTAAACACTGACGCCTATCTGATTGACACTCCATTTACTGCTACAGATACTGAAAAGTTAGTCAATTGGTTTGTGGAGCGCGGCTATAAAATCAAAGGCACTATTTCCTCACATTTCCATAGCGACAGCACAGGGGGAATAGAGTGGCTTAATTCTCAATCTATTCCCACGTATGCATCTGAATTAACAAATGAACTTCTTAAAAAAGACGGTAAGGTGCAAGCTAAAAACTCATTTAGCGGAGTTAGTTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCCGGCCCGGGGCACACTCAAGATAACGTAGTGGTTTGGTTACCTGAAAAGAAAATTTTATTCGGTGGTTGTTTTGTTAAACCGGACGGTCTTGGTAATTTGGGTGACGCAAATTTAGAAGCTTGGCCAAAGTCCGCCAAAATATTAATGTCTAAATATGTTAAAGCAAAACTGGTTGTTTCAAGTCATAGTGAAATTGGGGACGCATCACTCTTGAAACGTACATGGGAACAGGCTGTTAAAGGGCTAAATGAAAGTAAAAAACCATCACAGCCAAGTAACTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3002193","ARO_id":"38593","ARO_name":"IMP-2","ARO_description":"IMP-2 is a beta-lactamase found in Acinetobacter baumannii","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"20":{"model_id":"20","model_name":"CMY-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1034":{"protein_sequence":{"accession":"CAA63264.1","sequence":"MQQRQSILWGAVATLMWAGLAHAGEASPVDPLRPVVDASIQPLLKEHRIPGMAVAVLKDGKAHYFNYGVANRESGAGVSEQTLFEIGSVSKTLTATLGAYAVVKGAMQLDDKASRHAPWLKGSAFDSITMGELATYSAGGLPLQFPEEVDSSEKMRAYYRQWAPVYSPGSHRQYSNPSIGLFGHLAASSLKQPFAPLMEQTLLPGLGMHHTYVNVPKQAMASYAYGYSKEDKPIRVNPGMLADEAYGIKTSSADLLRFVKANIGGVDDKALQQAISLTHQGHYSVGGMTQGLGWESYAYPVTEQTLLAGNSAKVILEANPTAAPRESGSQVLFNKTGSTNGFGAYVAFVPARGIGIVMLANRNYPNEARIKAAHAILAQLAG"},"dna_sequence":{"accession":"X92508","fmin":"332","fmax":"1481","strand":"+","sequence":"ATGCAACAACGACAATCCATCCTGTGGGGGGCCGTGGCCACCCTGATGTGGGCCGGTCTGGCCCATGCAGGTGAGGCTTCACCGGTCGATCCCCTGCGCCCCGTGGTGGATGCCAGCATCCAGCCGCTGCTCAAGGAGCACAGGATCCCGGGCATGGCGGTGGCCGTGCTCAAGGATGGCAAGGCCCACTACTTCAATTACGGGGTGGCCAACCGGGAGAGCGGGGCCGGCGTCAGCGAGCAGACCCTGTTCGAGATAGGATCCGTGAGCAAGACCCTGACTGCGACCCTGGGGGCCTATGCGGTGGTCAAGGGAGCGATGCAGCTGGATGACAAGGCGAGCCGGCACGCGCCCTGGCTCAAGGGATCCGCCTTTGACAGCATCACCATGGGGGAGCTTGCCACCTACAGCGCCGGAGGCCTGCCACTGCAATTCCCCGAGGAGGTGGATTCATCCGAGAAGATGCGCGCCTACTACCGCCAGTGGGCCCCTGTCTATTCGCCGGGCTCCCATCGCCAGTACTCCAACCCCAGCATAGGGCTGTTCGGCCACCTGGCGGCGAGCAGCCTGAAGCAGCCGTTTGCCCCCTTGATGGAGCAGACCCTGCTGCCCGGGCTCGGCATGCACCACACCTATGTCAATGTGCCGAAGCAGGCCATGGCGAGTTATGCCTATGGCTATTCGAAAGAGGACAAGCCCATCCGTGTCAACCCTGGCATGCTGGCGGACGAGGCCTATGGCATCAAGACCAGCTCGGCGGATCTGCTGCGTTTTGTGAAGGCCAACATCGGCGGGGTTGATGACAAGGCGTTGCAGCAGGCCATCTCCCTGACCCACCAAGGGCATTACTCGGTAGGCGGGATGACCCAGGGGCTGGGTTGGGAGAGTTACGCCTATCCCGTCACCGAGCAGACATTGCTGGCGGGCAATTCGGCCAAGGTGATCCTCGAAGCCAATCCGACGGCGGCGCCCCGGGAGTCGGGGAGCCAGGTGCTCTTCAACAAGACCGGCTCGACCAATGGCTTTGGCGCCTATGTGGCCTTCGTGCCGGCCAGGGGGATCGGCATCGTCATGCTGGCCAATCGCAACTACCCCAACGAGGCGCGCATCAAGGCGGCCCACGCCATCCTGGCGCAGTTGGCCGGTTGAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002012","ARO_id":"38412","ARO_name":"CMY-1","ARO_description":"CMY-1 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"21":{"model_id":"21","model_name":"OXA-329","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1212":{"protein_sequence":{"accession":"AGW16411.1","sequence":"MYKKALIVATSILFLSACSSNTVKQHQIHSISANKNSEAIKSLFDQAQTTGVLVIKRGQTEEIYGNDLKRASTAYVPASTFKMLNALIGLEHHKAITTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNANIGSKVDDFWLVGPLKITPQQETQFAYQLAHKMLPFSKDVQEQVQSMVFIEEKNGRKIYAKSGWGWDIEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"KF203103","fmin":"0","fmax":"822","strand":"+","sequence":"ATGTATAAAAAAGCCCTTATCGTTGCAACAAGTATCCTATTTTTATCCGCCTGTTCTTCCAATACGGTAAAACAACATCAAATACACTCTATTTCTGCCAATAAAAATTCAGAAGCAATTAAATCACTTTTTGATCAAGCACAGACCACGGGAGTTTTGGTGATTAAGCGAGGGCAAACAGAAGAAATTTATGGCAATGATCTTAAAAGAGCATCAACCGCCTATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTAATTGGACTTGAACATCATAAGGCAATTACAACTGAAGTATTTAAATGGGATGGGCAAAAACGTTTATTTCCTGATTGGGAAAAGGACATGACACTGGGTGATGCCATGAAAGCTTCTGCAATCCCAGTTTACCAAGAATTAGCCCGACGAATTGGTCTGGATCTTATGTCTAAAGAGGTAAAGCGAATTGGTTTCGGTAATGCTAACATTGGCTCAAAAGTAGATGATTTCTGGCTTGTTGGTCCTCTAAAAATTACACCTCAACAAGAAACCCAATTTGCTTATCAATTAGCCCATAAAATGCTTCCATTTAGTAAAGATGTACAAGAACAAGTTCAATCAATGGTGTTCATAGAAGAAAAAAATGGACGTAAAATTTATGCAAAAAGCGGTTGGGGATGGGATATTGAGCCACAAGTTGGTTGGTTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTGGCATTCTCACTTAATTTAGAAATGAAAAAAGGAACTCCTAGCTCTATTCGCAAAGAAATTGCTTATAAAGGCTTAGAACAACTGGGTATCTTATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3001517","ARO_id":"37917","ARO_name":"OXA-329","ARO_description":"OXA-329 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"22":{"model_id":"22","model_name":"ACT-10","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"940":{"protein_sequence":{"accession":"AEV91214.1","sequence":"MMKKSVCCALLLSTSCSVLAAPMSEKQLAEVVERTVTPLMKAQAIPGIAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWKGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAITTRVFKPLKLDHTWINVPKTEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVKDMASWVMVNMKPDSLEDSSLRKGFTLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVEGSDNKVALAPLPAREVNPPAPPVNASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"JN848330","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCGTTTGCTGCGCCCTGCTGCTCAGCACCTCCTGCTCGGTATTGGCTGCCCCGATGTCAGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAAAGCTCAGGCCATTCCGGGTATAGCGGTGGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAATAAACCTGTCACCCCACAAACCTTATTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTCGGCGGCGATGCCATTGCTCGGGGTGAAATATCGCTGGGCGATCCGGTGACAAAATACTGGCCTGAGCTGACAGGCAAGCAGTGGAAGGGGATCCGCATGCTGGATCTGGCAACCTATACCGCAGGAGGTTTGCCGTTACAGGTACCGGATGAGGTCACGGATAACGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATAACGACGCGGGTCTTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAACGGAAGAGGCGCATTACGCCTGGGGATACCGCGACGGTAAGGCGGTACACGTTTCGCCAGGAATGCTGGACGCTGAAGCCTATGGCGTAAAAACCAACGTGAAGGATATGGCAAGCTGGGTGATGGTCAACATGAAGCCGGACTCGCTTGAGGATAGTTCACTCAGGAAAGGCTTTACCCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGGTTAGGCTGGGAAATGCTTAACTGGCCGGTCGATGCCAAAACCGTGGTTGAAGGTAGCGACAATAAGGTGGCGCTGGCACCGTTGCCTGCGAGAGAAGTGAATCCACCGGCGCCCCCGGTCAACGCATCCTGGGTCCATAAAACCGGCTCTACCGGCGGGTTTGGCAGCTACGTGGCGTTTATTCCCGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCCAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36783","NCBI_taxonomy_name":"Serratia marcescens","NCBI_taxonomy_id":"615"}}}},"ARO_accession":"3001832","ARO_id":"38232","ARO_name":"ACT-10","ARO_description":"ACT-10 is a beta-lactamase. From the Lahey list of ACT beta-lactamases.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"23":{"model_id":"23","model_name":"OXA-371","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1301":{"protein_sequence":{"accession":"BAO09635.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGEKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVKPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"AB871653","fmin":"11870","fmax":"12695","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAATGGGATGGGGAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTCTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTAAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001557","ARO_id":"37957","ARO_name":"OXA-371","ARO_description":"OXA-371 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"24":{"model_id":"24","model_name":"fusB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"375"}},"model_sequences":{"sequence":{"3451":{"protein_sequence":{"accession":"AAL12234.1","sequence":"MKTMIYPHQYNYIRSVILRLKNVYKTVNDKETVKVIQSETYNDINEIFGHIDDDIEESLKVLMNIRLSNKEIEAILNKFLEYVVPFELPSPQKLQKVFKKVKKIKIPQFEEYDLKVSSFVGWNELASNRKYIIYYDEKKQLKGLYGEISNQVVKGFCTICNKESNVSLFMKKSKTNSDGQYVKKGDYICRDSIHCNKQLTDINQFYNFIDKLD"},"dna_sequence":{"accession":"AY047358","fmin":"1710","fmax":"2352","strand":"+","sequence":"ATGAAAACAATGATTTATCCTCACCAATATAATTATATCAGATCGGTTATTTTAAGATTGAAAAATGTATATAAAACGGTAAATGATAAAGAAACCGTCAAAGTTATTCAATCGGAAACCTATAATGATATTAATGAGATTTTTGGTCATATAGATGACGATATTGAAGAATCTTTAAAAGTATTAATGAACATCAGATTATCAAACAAAGAAATTGAAGCAATACTTAATAAATTTTTAGAATATGTAGTACCTTTTGAACTACCTAGTCCGCAAAAACTTCAGAAAGTATTTAAGAAAGTTAAAAAAATAAAAATACCTCAATTTGAAGAATATGATTTGAAGGTAAGTTCATTTGTAGGATGGAATGAACTTGCATCAAATCGGAAATATATAATATATTACGATGAAAAAAAACAATTAAAAGGACTTTATGGAGAAATTTCTAATCAGGTTGTAAAGGGGTTCTGCACAATTTGTAATAAAGAATCTAATGTTTCATTATTCATGAAAAAGTCAAAAACCAATTCGGATGGTCAATATGTAAAAAAAGGTGACTATATATGTCGAGATAGCATTCATTGTAATAAACAATTAACAGATATTAATCAGTTTTATAATTTTATTGATAAACTAGATTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3003552","ARO_id":"40155","ARO_name":"fusB","ARO_description":"FusB encodes a 2-domain zinc-binding protein that binds the ribosomal translocase EF-G, causing it to dissociate from the ribosome. This action increases the ribosomal turnover rate and confers resistance to fusidic acid.","ARO_category":{"39459":{"category_aro_accession":"3003025","category_aro_cvterm_id":"39459","category_aro_name":"fusidic acid inactivation enzyme","category_aro_description":"Enzymes that confer resistance to fusidic acid by inactivation","category_aro_class_name":"AMR Gene Family"},"37139":{"category_aro_accession":"3000759","category_aro_cvterm_id":"37139","category_aro_name":"fusidic acid","category_aro_description":"Fusidic acid is the only commercially available fusidane, a group of steroid-like antibiotics. It is most active against Gram-positive bacteria, and acts by inhibiting elongation factor G to  block protein synthesis.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"25":{"model_id":"25","model_name":"CTX-M-121","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1085":{"protein_sequence":{"accession":"AFA51699.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPITEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGGYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"JN790862","fmin":"244","fmax":"1120","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTACCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGGCTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001980","ARO_id":"38380","ARO_name":"CTX-M-121","ARO_description":"CTX-M-121 is a beta-lactamase found in Escherichia coli","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"26":{"model_id":"26","model_name":"VEB-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1406":{"protein_sequence":{"accession":"AAS48620.1","sequence":"MKIVKRILLVLLSLFFTVVYSNAQTDNLTLKIENVLKAKNARIGVAIFNSNEKDTFKINNDFHFPMQSVMKFPIALAVLSEIDKGNLSFEQKIEITPQDLLPKTWSPIKEEFPNGTTLTIEQILNYTVSESDNIGCDILLKLIGGTDSVQKFLNANHFTDISIKANEEQMHKDWNTQYQNWATPTAMNKLLIDTYNNKNQLLSKKSYDFIWKIMRETTTGSNRLKGQLPKNTIVAHKTGTSGINNGIAAATNDVGVITLPNGQLIFISVFVAESKETSEINEKIISDIAKITWNYYLNK"},"dna_sequence":{"accession":"AY536519","fmin":"37","fmax":"937","strand":"+","sequence":"ATGAAAATCGTAAAAAGGATATTATTAGTATTGTTAAGTTTATTTTTTACAGTTGTGTATTCAAATGCTCAAACTGACAACTTAACTTTGAAAATTGAGAATGTTTTAAAGGCAAAAAATGCCAGAATAGGAGTAGCAATATTCAACAGCAATGAGAAGGATACTTTTAAGATTAATAACGACTTCCATTTCCCGATGCAAAGCGTTATGAAATTTCCGATTGCTTTAGCCGTTTTGTCTGAGATAGATAAAGGGAATCTTTCTTTTGAACAAAAAATAGAGATTACCCCTCAAGACCTTTTGCCTAAAACGTGGAGTCCGATTAAAGAGGAATTCCCTAATGGAACAACTTTGACGATTGAACAAATACTAAATTATACAGTATCAGAGAGCGACAATATTGGTTGTGATATTTTGCTAAAATTAATCGGAGGAACTGATTCTGTTCAAAAATTCTTGAATGCTAATCATTTCACTGATATTTCAATCAAAGCAAACGAAGAACAAATGCACAAGGATTGGAATACCCAATATCAAAATTGGGCAACCCCAACAGCGATGAACAAACTGTTAATAGATACTTATAATAATAAGAACCAATTACTTTCTAAAAAAAGTTATGATTTTATTTGGAAAATTATGAGAGAAACAACAACAGGAAGTAACCGATTAAAAGGACAATTACCAAAGAATACAATTGTTGCTCATAAAACAGGGACTTCCGGAATAAATAATGGAATTGCAGCAGCCACTAATGATGTTGGGGTAATTACTTTACCGAATGGACAATTAATTTTTATAAGCGTATTTGTTGCAGAGTCCAAAGAAACTTCGGAAATTAATGAAAAGATTATTTCAGACATTGCAAAAATAACGTGGAATTACTATTTGAATAAATAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3002372","ARO_id":"38772","ARO_name":"VEB-3","ARO_description":"VEB-3 is a beta-lactamase found in Enterobacter cloacae","ARO_category":{"36182":{"category_aro_accession":"3000043","category_aro_cvterm_id":"36182","category_aro_name":"VEB beta-lactamase","category_aro_description":"VEB beta-lactamases or Vietnamese extended-spectrum beta-lactamases are class A beta-lactamases that confer high-level resistance to oxyimino cephalosporins and to aztreonam","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"27":{"model_id":"27","model_name":"lnuA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"4280":{"protein_sequence":{"accession":"CAL44992.1","sequence":"MKNNNVTEKDLFYILDLFEHMKVTYWLDGGWGVDVLTGKQQREHRDIDIDFDAQHTQKVIQKLEDIGYKIEVDWMPSRMELKHEEYGYLDIHPINLNDDGSITQANPEGGNYVFQNDWFSETNYKGRKIPCISKEAQLLFHSGYDLTEKDHFDIKNLKSIT"},"dna_sequence":{"accession":"AM399080","fmin":"1664","fmax":"2150","strand":"-","sequence":"TTATGTTATTGATTTTAAATTTTTTATATCAAAATGGTCTTTTTCTGTTAAATCATAACCAGAATGAAAAAGAAGTTGAGCTTCTTTTGAAATACATGGTATTTTTCGACCTTTGTAATTAGTTTCTGAAAACCAGTCATTTTGGAAAACATAATTACCACCTTCTGGGTTTGCTTGGGTAATTGATCCATCATCATTTAGATTTATAGGATGAATATCTAAATACCCATATTCTTCATGCTTAAGTTCCATACGTGAAGGCATCCAATCAACTTCTATTTTGTATCCGATATCTTCTAATTTTTGTATAACTTTTTGAGTGTGTTGAGCGTCAAAATCTATATCTATATCTCTGTGTTCTCTTTGTTGTTTTCCAGTTAATACATCTACCCCCCAGCCACCATCTAACCAATAAGTTACTTTCATGTGTTCAAATAAATCTAAAATATAAAATAAATCTTTTTCTGTTACATTATTATTTTTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39565","NCBI_taxonomy_name":"Staphylococcus chromogenes","NCBI_taxonomy_id":"46126"}}}},"ARO_accession":"3002835","ARO_id":"39269","ARO_name":"lnuA","ARO_description":"lnuA is a plasmid-mediated nucleotidyltransferase found in Staphylococcus chromogenes","ARO_category":{"36360":{"category_aro_accession":"3000221","category_aro_cvterm_id":"36360","category_aro_name":"lincosamide nucleotidyltransferase (LNU)","category_aro_description":"Resistance to the lincosamide antibiotic by ATP-dependent modification of the 3' and\/or 4'-hydroxyl groups of the methylthiolincosamide sugar.","category_aro_class_name":"AMR Gene Family"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"28":{"model_id":"28","model_name":"OXA-45","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1463":{"protein_sequence":{"accession":"CAD58780.1","sequence":"MRGKHTVILGAALSALFAGAAGAQMLECTLVADAASGQELYRKGACDKAFAPMSTFKVPLAVMGYDAGILVDAHNPRWDYKPEFNGYKFQQKTTDPTIWEKDSIVWYSQQLTRKMGQKRFAAYVAGFGYGNGDISGEPGKSNGLTHSWLGSSLKISPEGQVRFVRDLLSAKLPASKDAQQMTVSILPHFAAGDWAVQGKTGTGSFIDARGAKAPLGWFIGWATHEERRVVFARMTAGGKKGEQPAGPAARDAFLKALPDLAKRF"},"dna_sequence":{"accession":"AJ519683","fmin":"281","fmax":"1076","strand":"+","sequence":"ATGCGCGGTAAACACACTGTCATTCTGGGCGCGGCACTGTCGGCGCTTTTTGCCGGCGCGGCTGGCGCGCAGATGCTCGAATGCACGCTGGTCGCCGATGCCGCGAGCGGTCAGGAGCTTTACCGCAAGGGTGCCTGTGACAAGGCCTTCGCGCCAATGTCGACGTTCAAGGTGCCGTTGGCCGTCATGGGCTACGATGCTGGCATTCTTGTGGACGCGCATAATCCGCGCTGGGACTACAAGCCGGAATTCAATGGCTACAAATTCCAGCAGAAAACCACCGACCCTACGATCTGGGAAAAGGACTCGATCGTCTGGTATTCGCAGCAATTGACCCGCAAGATGGGGCAAAAACGCTTTGCCGCATACGTGGCCGGGTTCGGCTATGGCAATGGCGATATCTCCGGTGAGCCCGGTAAGAGCAACGGCCTGACGCATTCATGGCTGGGCTCCTCGCTGAAGATTTCTCCGGAAGGACAGGTGCGGTTCGTACGCGATCTGCTGTCGGCGAAACTGCCGGCTTCGAAAGACGCCCAGCAAATGACGGTTTCCATCCTGCCGCATTTCGCGGCCGGTGATTGGGCTGTGCAGGGCAAGACCGGCACCGGCTCGTTCATCGACGCCAGGGGTGCGAAGGCGCCGCTCGGATGGTTCATCGGCTGGGCGACGCACGAGGAACGCCGCGTCGTCTTCGCCCGCATGACTGCGGGCGGGAAGAAGGGCGAGCAACCCGCCGGACCGGCTGCCCGCGACGCCTTCCTCAAGGCATTGCCGGATCTCGCGAAAAGGTTCTGAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001794","ARO_id":"38194","ARO_name":"OXA-45","ARO_description":"OXA-45 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"30":{"model_id":"30","model_name":"OXA-226","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1927":{"protein_sequence":{"accession":"ACM67635.1","sequence":"MAIRIFAILFSIFSLATFAHAQEGTLERSDWRKFFSEFQAKGTIVVADERQADRAMLVFDPVRSKKRYSPASTFKIPHTLFALDAGAVRDEFQIFRWDGVNRGFAGHNQDQDLRSAMRNSTVWVYELFAKEIGDDKARRYLKKIDYGNADPSTSNGDYRIEGSLAISAQEQIAFLRKLYRNELPFRVEHQRLVKDLMIVEAGRNWILRAKTGWEGRMGWWVGWVEWPTGSVFFALNIDTPNRMDDLFKREAIVRAILRSIEALPPNPAVNSDAAR"},"dna_sequence":{"accession":"FJ617207","fmin":"0","fmax":"828","strand":"+","sequence":"ATGGCAATCCGAATCTTCGCGATACTTTTCTCCATTTTTTCTCTTGCCACTTTCGCGCATGCGCAAGAAGGCACGCTAGAACGTTCTGACTGGAGGAAGTTTTTCAGCGAATTTCAAGCCAAAGGCACGATAGTTGTGGCAGACGAACGCCAAGCGGATCGTGCCATGTTGGTTTTTGATCCTGTGCGATCGAAGAAACGCTACTCGCCTGCATCGACATTCAAGATACCTCATACACTTTTTGCACTTGATGCAGGCGCTGTTCGTGATGAGTTCCAGATTTTTCGATGGGACGGCGTTAACAGGGGCTTTGCAGGCCACAATCAAGACCAAGATTTGCGATCAGCAATGCGGAATTCTACTGTTTGGGTGTATGAGCTATTTGCAAAGGAAATTGGTGATGACAAAGCTCGGCGCTATTTGAAGAAAATCGACTATGGCAACGCCGATCCTTCGACAAGTAATGGCGATTACAGGATAGAAGGCAGCCTTGCAATCTCGGCGCAGGAGCAAATTGCATTTCTCAGGAAGCTCTATCGTAACGAGCTGCCCTTTCGGGTAGAACATCAGCGCTTGGTCAAGGATCTCATGATTGTGGAAGCCGGTCGCAACTGGATACTGCGTGCAAAGACGGGCTGGGAAGGCCGTATGGGTTGGTGGGTAGGATGGGTTGAGTGGCCGACTGGCTCCGTATTCTTCGCACTGAATATTGATACGCCAAACAGAATGGATGATCTTTTCAAGAGGGAGGCAATCGTGCGGGCAATCCTTCGCTCTATTGAAGCGTTACCGCCCAACCCGGCAGTCAACTCGGACGCTGCGCGATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001800","ARO_id":"38200","ARO_name":"OXA-226","ARO_description":"OXA-226 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"31":{"model_id":"31","model_name":"CTX-M-155","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1666":{"protein_sequence":{"accession":"AIS67611.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTAPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASGAKIVTDGL"},"dna_sequence":{"accession":"KM211508","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGCACCGCGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGGCGCTAAAATCGTCACCGACGGTTTGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3003163","ARO_id":"39740","ARO_name":"CTX-M-155","ARO_description":"From the Lahey list of beta-lactamases.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"32":{"model_id":"32","model_name":"DHA-15","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"910":{"protein_sequence":{"accession":"AIT76106.1","sequence":"MKKSLSATLISALLAFSAPGFSAADNVAAVVDSTIKPLMAQQDIPGMAVAVSVKGKPYYFNYGFADIQAKQPVTENTLFELGSVSKTFTGVLGAVSVAKKEMALNDPAAKYQPELALPQWKGITLLDLATYTAGGLPLQVPDAVKSRADLLNFYQQWQPSRKPGYMRLYANSSIGLFGALTANAAGMPYEQLLTARILAPLGLSHTFITVPESAQSQYAYGYKNKKPVRVSPGQLDAESYGVKSASKDMLRWAEMNMEPSRAGNADLEMAMYLAQTRYYKTAAINQGLGWEMYDWPQQKDMIINGVTNEVALQPHPVTDNQVQPYNRASWVHKTGATTGFGAYVAFIPEKQVAIVILANKNYPNTERVKAAQAILSALE"},"dna_sequence":{"accession":"KM087853","fmin":"0","fmax":"1140","strand":"+","sequence":"ATGAAAAAATCGTTATCTGCAACACTGATTTCCGCTCTGCTGGCGTTTTCCGCCCCGGGGTTTTCTGCCGCTGATAATGTCGCGGCGGTGGTGGACAGCACCATTAAACCGCTGATGGCACAGCAGGATATTCCCGGGATGGCGGTTGCCGTCTCCGTAAAGGGTAAGCCCTATTATTTCAATTATGGTTTTGCCGATATTCAGGCAAAACAGCCGGTCACTGAAAATACACTATTTGAGCTCGGATCTGTAAGTAAAACTTTCACAGGTGTGCTGGGTGCGGTTTCTGTGGCGAAAAAAGAGATGGCGCTGAATGATCCGGCGGCAAAATACCAGCCGGAGCTGGCTCTGCCGCAGTGGAAGGGGATCACATTGCTGGATCTGGCTACCTATACCGCAGGCGGACTGCCGTTACAGGTGCCGGATGCGGTAAAAAGCCGTGCGGATCTGCTGAATTTCTATCAGCAGTGGCAGCCGTCCCGGAAACCGGGCTATATGCGTCTGTATGCAAACAGCAGTATCGGCCTGTTTGGTGCTCTGACCGCAAACGCGGCGGGGATGCCGTATGAGCAGTTGCTGACTGCACGGATCCTGGCACCGCTGGGGTTATCTCACACCTTTATTACTGTGCCGGAAAGTGCGCAAAGCCAGTATGCGTACGGTTATAAAAACAAAAAACCGGTCCGCGTGTCGCCGGGACAGCTTGATGCGGAATCTTACGGCGTGAAATCCGCCTCAAAAGATATGCTGCGCTGGGCGGAAATGAATATGGAGCCGTCACGGGCCGGTAATGCGGATCTGGAAATGGCAATGTATCTCGCCCAGACCCGCTACTATAAAACCGCCGCGATTAACCAGGGGCTGGGCTGGGAAATGTATGACTGGCCGCAGCAGAAAGATATGATCATTAACGGTGTGACCAACGAGGTCGCATTGCAGCCGCATCCGGTAACAGACAACCAGGTTCAGCCGTATAACCGTGCTTCCTGGGTGCATAAAACGGGCGCAACAACTGGTTTCGGCGCCTATGTCGCCTTTATTCCGGAAAAACAGGTGGCGATTGTGATTCTGGCGAATAAAAACTACCCGAATACCGAAAGAGTCAAAGCTGCACAGGCTATTTTGAGTGCACTGGAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002146","ARO_id":"38546","ARO_name":"DHA-15","ARO_description":"DHA-15 is a beta-lactamase. From the Lahey list of DHA beta-lactamases.","ARO_category":{"36207":{"category_aro_accession":"3000068","category_aro_cvterm_id":"36207","category_aro_name":"DHA beta-lactamase","category_aro_description":"DHA beta-lactamases are plasmid-mediated AmpC \u03b2-lactamases that confer resistance to cephamycins and oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"33":{"model_id":"33","model_name":"msrE","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"950"}},"model_sequences":{"sequence":{"149":{"protein_sequence":{"accession":"YP_724476.1","sequence":"MSLIIKARNIRLDYAGRDVLDIDELEIHSYDRIGLVGDNGAGKSSLLKVLNGEIVLAEATLQRFGDFAHISQLGGIEIETVEDRAMLSRLGVSNVQNDTMSGGEETRAKIAAAFSQQVHGILADEPTSHLDLNGIDLLIGQLKAFDGALLVISHDRYFLDMVVDKIWELKDGKITEYWGGYSDYLRQKEEERQHQAVEYELMMKERERLESAVQEKRQQANRLDNKKKGEKSKNSTESAGRLGHAKMTGTKQRKLYQAAKSMEKRLAALEDIQAPEHLRSIRFRQSSALELHNKFPITADGLSLKFGSRTIFDDANFIIPLGAKVAITGSNGTGKTSLLKMISERADGLTISPKAEIGYFTQTGYKFNTHKSVLSFMQEECEYTVAEIRAVLASMGIGANDIQKNLSDLSGGEIIKLLLSKMLLGKYNILLMDEPGNYLDLKSIAALETMMKSYAGTIIFVSHDKQLVDNIADIIYEIKDHKIIKTFERDC"},"dna_sequence":{"accession":"NC_007682","fmin":"20649","fmax":"22125","strand":"+","sequence":"ATGAGTTTAATTATTAAAGCGAGAAACATACGCTTGGATTATGCTGGGCGTGATGTTTTGGATATTGATGAATTGGAAATTCACTCTTATGACCGTATTGGTCTTGTGGGTGATAACGGAGCAGGAAAGAGTAGTTTACTCAAAGTACTTAATGGCGAAATTGTTTTAGCCGAAGCGACATTACAGCGTTTTGGTGATTTTGCACATATCAGCCAACTGGGCGGAATCGAAATAGAAACGGTCGAAGACCGGGCAATGTTATCTCGCCTTGGTGTTTCCAATGTACAAAACGACACAATGAGTGGCGGAGAGGAAACTCGTGCAAAAATTGCTGCCGCATTTTCCCAACAAGTACATGGCATTCTAGCGGATGAACCAACCAGCCACCTTGATCTCAATGGAATAGATCTACTTATTGGTCAACTTAAAGCATTTGATGGAGCATTACTTGTTATCAGTCATGACCGATATTTTCTTGATATGGTTGTAGACAAGATATGGGAGTTAAAAGACGGTAAAATTACGGAATATTGGGGTGGTTACTCGGATTACTTGCGTCAAAAAGAAGAAGAGCGACAACACCAAGCCGTAGAATATGAGCTGATGATGAAGGAACGGGAGCGATTAGAATCTGCTGTGCAAGAAAAACGCCAGCAAGCTAATCGATTAGACAATAAGAAAAAAGGAGAAAAATCCAAAAACTCTACCGAAAGTGCTGGACGACTTGGGCATGCAAAAATGACTGGCACCAAGCAAAGAAAACTGTATCAGGCAGCTAAGAGTATGGAAAAGCGTTTGGCTGCATTAGAAGATATTCAAGCACCAGAGCATTTGCGTTCTATTCGTTTTCGTCAAAGTTCAGCCCTAGAACTGCACAATAAGTTCCCGATTACGGCAGATGGTCTGAGCTTAAAATTTGGTAGCCGTACTATCTTTGATGACGCTAACTTTATAATACCGCTTGGCGCTAAAGTCGCTATAACTGGATCGAATGGAACAGGGAAAACGTCCTTGTTAAAAATGATATCAGAACGTGCTGATGGATTAACCATATCTCCAAAAGCTGAAATTGGCTACTTTACACAAACAGGATATAAATTTAACACGCATAAATCTGTGCTCTCCTTTATGCAGGAAGAGTGCGAGTACACAGTTGCGGAAATTCGTGCAGTATTGGCTTCAATGGGGATCGGAGCGAATGATATTCAAAAAAACTTATCCGACTTATCGGGAGGTGAAATCATCAAACTGCTTTTATCCAAAATGCTTTTAGGAAAATATAATATTTTGCTTATGGATGAACCAGGAAACTATCTTGACCTAAAAAGTATTGCCGCATTAGAAACAATGATGAAGTCCTATGCAGGAACTATTATCTTCGTATCTCATGACAAGCAATTGGTCGATAATATTGCTGACATTATCTACGAGATCAAAGACCACAAAATCATCAAGACTTTTGAGAGAGATTGTTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3003109","ARO_id":"39685","ARO_name":"msrE","ARO_description":"MsrE is an ABC-efflux pump expressed to Klebsiella pneumoniae that confers resistance to erythromycin and streptogramin B antibiotics. It is associated with plasmid DNA. It is also 100% identical to ABC-F type ribosomal protection protein Msr(E) which is in multiple species.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"34":{"model_id":"34","model_name":"OXY-6-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1060":{"protein_sequence":{"accession":"CAI43424.1","sequence":"MLKSSWRKSALMAAAAVPLLLASGSLWASADAIQQKLADLEKRSGGRLGVALINTTDDSQTLYRGDERFAMCSTGKVMAAAAVLKQSESHPDVVNKRLEIKKSDLVVWSPITEKHLQSGMTLAELSAAALQYSDNTAMNKMISYLGGPEKVTAFAQSIGDVTFRLDRTEPALNSAIPGDKRDTTTPLAMAESLRKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPASWAVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKSRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"AJ871876","fmin":"0","fmax":"876","strand":"+","sequence":"ATGTTGAAAAGTTCGTGGCGTAAAAGCGCCCTGATGGCCGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGTTCATTATGGGCCAGTGCCGATGCTATCCAGCAAAAGCTGGCTGATTTAGAAAAACGGTCCGGTGGCCGGCTGGGCGTGGCGCTGATTAACACGACGGATGATTCGCAAACCCTTTATCGCGGCGATGAACGTTTTGCCATGTGCAGCACCGGTAAAGTGATGGCCGCCGCCGCGGTGTTAAAGCAGAGCGAAAGCCATCCCGATGTGGTGAATAAAAGGCTGGAGATTAAAAAATCGGATTTAGTGGTCTGGAGCCCGATTACCGAAAAACATCTGCAAAGCGGAATGACCCTGGCGGAACTCAGCGCGGCGGCGCTGCAGTACAGCGACAATACCGCGATGAATAAGATGATTAGCTACCTTGGCGGACCGGAAAAGGTGACCGCATTCGCCCAGAGCATCGGGGACGTTACTTTTCGTCTCGATCGTACGGAGCCGGCGCTGAACAGCGCGATTCCCGGCGATAAGCGCGATACCACCACTCCGTTGGCGATGGCCGAAAGCCTGCGCAAGCTGACGCTGGGCAATGCGCTGGGCGAACAGCAGCGCGCCCAGTTAGTGACGTGGCTAAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCAGGCCTGCCCGCAAGCTGGGCGGTCGGGGATAAAACCGGCGCCGGAGATTACGGCACCACCAACGATATCGCGGTGATCTGGCCGGAAAATCATGCCCCGCTGGTGTTAGTGACCTATTTTACCCAGCCGCAGCAGGATGCGAAAAGCCGCAAAGAGGTGTTAGCCGCGGCGGCGAAAATCGTGACCGAAGGGCTGTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002415","ARO_id":"38815","ARO_name":"OXY-6-3","ARO_description":"OXY-6-3 is a beta-lactamase found in Klebsiella oxytoca","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"35":{"model_id":"35","model_name":"FosA2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"341":{"protein_sequence":{"accession":"ACC85616.1","sequence":"MLQSLNHLTLAVSDLQKSVTFWHELLGLTLHARWNTGAYLTCGDLWVCLSYDEARGYVPPQESDYTHYAFTVAAEDFEPFSHKLEQAGVTVWKQNKSEGASFYFLDPDGHKLELHVGSLAARLAACREKPYAGMVFTSDEA"},"dna_sequence":{"accession":"EU487198","fmin":"216","fmax":"642","strand":"+","sequence":"ATGCTGCAATCACTCAACCATCTGACCCTCGCGGTCAGCGACCTGCAAAAAAGCGTTACCTTCTGGCACGAGCTGCTGGGGCTGACGCTGCACGCCCGCTGGAATACCGGGGCCTATCTTACCTGCGGCGATCTGTGGGTCTGCCTGTCCTATGACGAGGCGCGCGGTTACGTGCCGCCGCAGGAGAGCGACTATACCCATTACGCGTTTACCGTTGCGGCGGAAGATTTTGAGCCGTTCTCGCACAAGCTGGAGCAGGCGGGCGTTACCGTCTGGAAGCAAAACAAAAGTGAGGGGGCATCGTTCTATTTTCTCGACCCGGACGGGCACAAGCTGGAGCTGCACGTGGGCAGCCTCGCCGCGCGGCTGGCGGCGTGCCGGGAGAAACCCTATGCCGGAATGGTCTTCACCTCAGACGAGGCTTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3002804","ARO_id":"39238","ARO_name":"FosA2","ARO_description":"An enzyme that confers resistance to fosfomycin in Enterobacter cloacae by breaking the epoxide ring of the molecule. It depends on the cofactors Manganese (II) and Potassium and uses Glutathione (GSH) as the nucleophilic molecule.","ARO_category":{"36272":{"category_aro_accession":"3000133","category_aro_cvterm_id":"36272","category_aro_name":"fosfomycin thiol transferase","category_aro_description":"Catalyzes the addition of a thiol group from a nucleophilic molecule to fosfomycin.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"38":{"model_id":"38","model_name":"APH(3')-Va","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"371":{"protein_sequence":{"accession":"AAA26699.1","sequence":"MDDSTLRRKYPHHEWHAVNEGDSGAFVYQLTGGPEPQPELYAKIAPRAPENSAFDLSGEADRLEWLHRHGIPVPRVVERGADDTAAWLVTEAVPGVAAAEEWPEHQRFAVVEAMAELARALHELPVEDCPSDRRLDAAVAEARRNVAEGLVDLDDLQEERAGWTGDQLLAELDRTRPEKEDLVVCHGDLCPNNVLLDPGTCRVTGVIDVGRLGVADRHADIALAARELEIDEDPWFGPAYAERFLERYGAHRVDKEKLAFYQLLDEFF"},"dna_sequence":{"accession":"K00432","fmin":"306","fmax":"1113","strand":"+","sequence":"ATGGACGACAGCACGTTGCGCCGGAAGTACCCGCACCACGAGTGGCACGCAGTGAACGAAGGAGACTCGGGCGCCTTCGTCTACCAGCTCACCGGCGGCCCCGAGCCCCAGCCCGAGCTCTACGCGAAGATCGCCCCCCGCGCCCCCGAGAACTCCGCCTTCGACCTGTCCGGCGAGGCCGACCGGCTGGAGTGGCTCCACCGCCACGGGATCCCCGTCCCCCGCGTCGTCGAGCGCGGTGCCGACGACACCGCCGCGTGGCTCGTCACGGAGGCCGTCCCCGGCGTCGCGGCGGCCGAGGAGTGGCCCGAGCACCAGCGGTTCGCCGTGGTCGAGGCGATGGCGGAGCTGGCCCGCGCCCTCCACGAGCTGCCCGTGGAGGACTGCCCCTCCGACCGGCGCCTCGACGCGGCGGTCGCCGAGGCCCGGCGGAACGTCGCCGAGGGCTTGGTGGACCTCGACGACCTGCAGGAGGAGCGGGCCGGGTGGACCGGCGACCAGCTCCTGGCGGAGCTCGACCGCACCCGTCCCGAGAAGGAGGACCTGGTCGTCTGCCATGGCGACCTGTGCCCCAACAACGTCCTGCTCGACCCCGGGACCTGCCGGGTCACCGGCGTGATCGACGTCGGCCGCCTCGGGGTCGCCGACCGCCACGCCGACATCGCCTTGGCCGCCCGCGAGCTGGAGATCGACGAGGACCCCTGGTTCGGCCCCGCCTACGCCGAGCGGTTCCTGGAGCGGTACGGCGCCCACCGCGTCGACAAGGAGAAGCTGGCCTTCTACCAGCTTCTCGACGAGTTCTTCTAGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36838","NCBI_taxonomy_name":"Streptomyces fradiae","NCBI_taxonomy_id":"1906"}}}},"ARO_accession":"3002649","ARO_id":"39049","ARO_name":"APH(3')-Va","ARO_description":"APH(3')-Va is a chromosomal-encoded aminoglycoside phosphotransferase in Streptomyces fradiae","ARO_category":{"36265":{"category_aro_accession":"3000126","category_aro_cvterm_id":"36265","category_aro_name":"APH(3')","category_aro_description":"Phosphorylation of 2-deoxystreptamine aminoglycosides on the hydroxyl group at position 3'","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"39":{"model_id":"39","model_name":"AAC(3)-Ia","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"3369":{"protein_sequence":{"accession":"AAG15269.1","sequence":"MGIIRTCRLGPDQVKSMRAALDLFGREFGDVATYSQHQPDSDYLGNLLRSKTFIALAAFDQEAVVGALAAYVLPRFEQPRSEIYIYDLAVSGEHRRQGIATALINLLKHEANALGAYVIYVQADYGDDPAVALYTKLGIREEVMHFDIDPSTAT"},"dna_sequence":{"accession":"U12338","fmin":"5055","fmax":"5520","strand":"+","sequence":"ATGGGCATCATTCGCACATGTAGGCTCGGCCCTGACCAAGTCAAATCCATGCGGGCTGCTCTTGATCTTTTCGGTCGTGAGTTCGGAGACGTAGCCACCTACTCCCAACATCAGCCGGACTCCGATTACCTCGGGAACTTGCTCCGTAGTAAGACATTCATCGCGCTTGCTGCCTTCGACCAAGAAGCGGTTGTTGGCGCTCTCGCGGCTTACGTTCTGCCCAGGTTTGAGCAGCCGCGTAGTGAGATCTATATCTATGATCTCGCAGTCTCCGGCGAGCACCGGAGGCAGGGCATTGCCACCGCGCTCATCAATCTCCTCAAGCATGAGGCCAACGCGCTTGGTGCTTATGTGATCTACGTGCAAGCAGATTACGGTGACGATCCCGCAGTGGCTCTCTATACAAAGTTGGGCATACGGGAAGAAGTGATGCACTTTGATATCGACCCAAGTACCGCCACCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002528","ARO_id":"38928","ARO_name":"AAC(3)-Ia","ARO_description":"AAC(3)-Ia is an aminoglycoside acetyltransferase encoded by plasmids, transposons, integrons in S. marcescens, E. coli, Acinetobacter baumannii, Klebsiella pneumoniae, Klebsiella oxytoca, P. aeruginosa, Salmonella typhimurium and Proteus mirabilis","ARO_category":{"36461":{"category_aro_accession":"3000322","category_aro_cvterm_id":"36461","category_aro_name":"AAC(3)","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 3.","category_aro_class_name":"AMR Gene Family"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"40":{"model_id":"40","model_name":"QnrB58","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"532":{"protein_sequence":{"accession":"AFR46589.1","sequence":"MTPLLYKKTGTNMALALVGEKIDRNRFTGEKIDNSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNASALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAIIG"},"dna_sequence":{"accession":"JX259319","fmin":"0","fmax":"681","strand":"+","sequence":"ATGACGCCATTACTGTATAAAAAAACAGGTACAAATATGGCTCTGGCACTCGTTGGCGAAAAAATTGACAGAAACCGTTTCACCGGTGAGAAAATTGATAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCGATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATGCCAGTGCGCTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGCGCAAGTTTTATGAATATGATCACTACTCGCACCTGGTTTTGTAGTGCATATATCACTAACACAAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGCTGGAAAAGTGTGAGCTGTGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGGGACTTAGATATTCGGGGCGTTGATTTACAAGGCGTTAAGTTGGACAACTACCAGGCATCGTTGCTCATGGAACGTCTTGGCATCGCGATTATTGGCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002771","ARO_id":"39205","ARO_name":"QnrB58","ARO_description":"QnrB58 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"41":{"model_id":"41","model_name":"rmtH","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"3309":{"protein_sequence":{"accession":"AGH19769.1","sequence":"MTIEQAAADILSSKKYQLLCPDTVVRILTQEWGRHKKPKQAVERTRERLHGICGAYLAPQVEKQASTALAAGDVQKALALHASTRERLDTYPQLYQFVFENNLPARVLDIACGLNPLMLHRQGVASVWGCDIHQGLGNVLTPYAQKHGWDFTFALHDVLCAPVAASGDMALVFKLLPLLEREQPGAALALLRTLDAPVICVSFPTRSLGGRGKGMHQHYATWFEGLVAPHFTVQHHTLIGDELLYRIQPNPA"},"dna_sequence":{"accession":"KC544262","fmin":"665","fmax":"1424","strand":"+","sequence":"ATGACCATTGAACAGGCAGCGGCCGACATCCTCTCCTCAAAAAAATATCAACTGCTGTGCCCGGATACCGTGGTGCGCATCCTCACGCAGGAGTGGGGACGCCACAAAAAGCCCAAGCAGGCGGTGGAGCGCACCCGCGAGCGGCTGCACGGCATCTGCGGTGCCTACCTGGCCCCCCAGGTGGAAAAGCAGGCAAGCACCGCACTGGCTGCGGGCGATGTGCAAAAAGCGCTGGCACTGCATGCCTCCACCCGTGAGCGGCTGGATACCTATCCCCAGCTGTATCAGTTTGTGTTTGAAAACAATCTGCCCGCCCGTGTGCTGGATATCGCCTGCGGCTTAAACCCGCTGATGCTGCACCGCCAGGGGGTGGCATCGGTTTGGGGGTGTGATATCCATCAGGGGCTGGGCAATGTGCTAACCCCCTATGCCCAAAAACACGGGTGGGATTTTACCTTTGCCCTGCACGATGTGCTGTGCGCACCGGTGGCGGCCAGCGGCGATATGGCACTGGTGTTTAAACTGCTGCCCCTTTTGGAAAGAGAGCAGCCCGGCGCAGCCCTTGCGCTGCTGCGCACATTGGATGCCCCGGTGATCTGCGTCAGCTTCCCCACCCGCAGCTTGGGCGGCAGGGGTAAGGGGATGCACCAGCACTACGCCACCTGGTTTGAGGGCCTGGTCGCCCCGCATTTTACCGTGCAGCACCACACCCTTATCGGGGACGAGCTGCTTTACCGCATCCAGCCAAACCCAGCTTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3003198","ARO_id":"39781","ARO_name":"rmtH","ARO_description":"rmtH is a 16s ribosomal RNA methyltransferase found in Klebsiella pneumoniae strain MRSN2404 that was isolated from the chronic wound of a soldier wounded in Iraq in 2006. It confers high resistance to all aminoglycosides","ARO_category":{"41435":{"category_aro_accession":"3004271","category_aro_cvterm_id":"41435","category_aro_name":"16S rRNA methyltransferase (G1405)","category_aro_description":"Methyltransferases that methylate the G1405 position of 16S rRNA, which is part of an aminoglycoside binding site.","category_aro_class_name":"AMR Gene Family"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"42":{"model_id":"42","model_name":"OXY-6-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"897":{"protein_sequence":{"accession":"CAI43422.1","sequence":"MLKSSWRKSALMAAAAVPLLLASGSLWASADAIQQKLADLEKRSGGRLGVALINTADDSQTLYRGDERFAMCSTGKVMAAAAVLKQSESHPDVVNKRLEIKKSDLVVWSPITEKHLQSGMTLAELSAAALQYSDNTAMNKMISYLGGPEKVTAFAQSIGDVTFRLDRTEPALNSAIPGDKRDTTTPLAMAESLRKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPASWAVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKSRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"AJ871874","fmin":"0","fmax":"876","strand":"+","sequence":"ATGTTGAAAAGTTCGTGGCGTAAAAGCGCCCTGATGGCCGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGTTCATTATGGGCCAGTGCCGATGCTATCCAGCAAAAGCTGGCTGATTTAGAAAAACGGTCCGGTGGCCGGCTGGGCGTGGCGCTGATTAACACGGCGGATGATTCGCAAACCCTTTATCGCGGCGACGAACGTTTTGCCATGTGCAGCACCGGTAAAGTGATGGCCGCCGCCGCGGTGTTAAAGCAGAGCGAAAGCCATCCCGATGTGGTGAATAAAAGGCTGGAGATTAAAAAATCGGATTTAGTGGTCTGGAGCCCGATTACCGAAAAACATCTGCAAAGCGGAATGACCCTGGCGGAACTCAGCGCGGCGGCGCTGCAGTACAGCGACAATACCGCGATGAATAAGATGATTAGCTACCTTGGCGGACCGGAAAAGGTGACCGCATTCGCCCAGAGCATCGGGGACGTTACTTTTCGTCTCGATCGTACGGAGCCGGCGCTGAACAGCGCGATACCCGGCGATAAGCGCGATACCACCACCCCGTTGGCGATGGCCGAAAGCCTGCGCAAGCTGACGCTGGGCAATGCGCTGGGCGAACAGCAGCGCGCCCAGTTAGTGACGTGGCTAAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCAGGCCTGCCCGCAAGCTGGGCGGTCGGGGATAAAACCGGCGCCGGAGATTACGGCACCACCAACGATATCGCGGTGATCTGGCCGGAAAATCATGCCCCGCTGGTGTTAGTGACCTATTTTACCCAGCCGCAGCAGGATGCGAAAAGCCGCAAAGAGGTGTTAGCCGCGGCGGCGAAAATCGTGACCGAAGGGCTGTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002413","ARO_id":"38813","ARO_name":"OXY-6-1","ARO_description":"OXY-6-1 is a beta-lactamase found in Klebsiella oxytoca","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"44":{"model_id":"44","model_name":"golS","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"290"}},"model_sequences":{"sequence":{"627":{"protein_sequence":{"accession":"NP_459349.1","sequence":"MNIGKAAKASKVSAKMIRYYEQIGLIPAASRTDSGYRAYTQADVNQLHFIRRARDLGFSVAEISDLLNLWNNQSRQSADVKRLAQTHIDELDRRIQNMQHMAQTLKALIHCCAGDALPDCPILHTLGQPDDSEPEARTGAVLRRPRRHGLAKRL"},"dna_sequence":{"accession":"NC_003197","fmin":"400859","fmax":"401324","strand":"+","sequence":"ATGAACATCGGTAAAGCAGCTAAAGCATCGAAAGTCTCGGCCAAAATGATTCGCTACTATGAACAGATTGGTCTGATTCCCGCGGCAAGTCGGACGGATTCCGGCTATCGGGCCTATACCCAGGCTGATGTTAATCAATTGCATTTTATACGCCGCGCGCGCGACCTCGGTTTTTCAGTTGCTGAAATCAGCGACTTACTGAATCTTTGGAATAACCAGTCGCGGCAAAGCGCTGACGTCAAACGCCTGGCGCAGACGCACATTGATGAACTGGACAGACGTATCCAGAACATGCAGCACATGGCGCAAACCCTCAAAGCGCTGATTCACTGCTGCGCCGGCGACGCGCTGCCAGATTGCCCCATTCTGCATACGCTTGGACAACCTGACGATAGCGAGCCGGAGGCGCGTACCGGAGCGGTATTGCGACGTCCTCGTCGCCACGGACTGGCAAAGCGTCTGTAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35734","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium str. LT2","NCBI_taxonomy_id":"99287"}}}},"ARO_accession":"3000504","ARO_id":"36643","ARO_name":"golS","ARO_description":"GolS is a regulator activated by the presence of gold, and promotes the expression of the MdsABC efflux pump.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"45":{"model_id":"45","model_name":"mdtP","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"875"}},"model_sequences":{"sequence":{"3303":{"protein_sequence":{"accession":"BAE78082.1","sequence":"MINRQLSRLLLCSILGSTTLISGCALVRKDSAPHQQLKPEQIKLADDIHLASSGWPQAQWWKQLNDPQLDALIQRTLSGSHTLAEAKLREEKAQSQADLLDAGSQLQVAALGMLNRQRVSANGFLSPYSMDAPALGMDGPYYTEATVGLFAGLDLDLWGVHRSAVAAAIGAHNAALAETAAVELSLATGVAQLYYSMQASYQMLDLLEQTHDVIDYAVKAHQSKVAHGLEAQVPFHGARAQILAVDKQIVAVKGQITETRESLRALIGAGASDMPEIRPVALPQVQTGIPATLSYELLARRPDLQAMRWYVQASLDQVDSARALFYPSFDIKAFFGLDSIHLHTLFKKTSRQFNFIPGLKLPLFDGGRLNANLEGTRAASNMMIERYNQSVLNAVRDVAVNGTRLQTLNDEREMQAERVEATRFTQRAAEAAYQRGLTSRLQATEARLPVLAEEMSLLMLDSRRVIQSIQLMKSLGGGYQAGPVVEKK"},"dna_sequence":{"accession":"AP009048","fmin":"4303042","fmax":"4304509","strand":"-","sequence":"TTATTTTTTCTCGACGACGGGACCTGCCTGATACCCGCCGCCCAGCGATTTCATCAACTGAATGCTTTGGATCACCCGGCGGCTGTCCAGCATCAGTAATGACATCTCTTCGGCAAGCACTGGCAACCGGGCTTCGGTGGCCTGTAAGCGGCTGGTTAAGCCGCGCTGATAGGCGGCCTCGGCAGCGCGCTGGGTAAAGCGCGTGGCTTCCACGCGTTCAGCCTGCATTTCTCGCTCGTCGTTGAGCGTTTGCAGACGCGTGCCGTTGACGGCAACGTCACGCACCGCGTTCAGTACTGACTGGTTGTAACGTTCAATCATCATGTTGCTGGCGGCGCGCGTGCCTTCGAGATTGGCATTCAACCGTCCACCGTCAAACAGCGGCAATTTCAGACCCGGGATGAAGTTGAACTGGCGACTGGTTTTTTTGAATAAGGTATGCAGATGGATGGAGTCCAGACCGAAAAACGCTTTGATATCAAAGCTCGGATAGAACAACGCCCGCGCGGAATCCACCTGATCTAATGACGCCTGAACATACCAGCGCATGGCTTGCAGATCCGGGCGTCTGGCGAGCAACTCATAAGAGAGTGTCGCCGGAATGCCGGTCTGGACTTGCGGTAATGCCACCGGTCTGATCTCCGGCATATCGCTGGCTCCCGCGCCAATCAATGCACGCAGAGATTCTCGCGTTTCGGTGATTTGCCCTTTGACGGCAACAATTTGTTTATCGACCGCCAGAATCTGTGCCCGCGCGCCGTGGAAAGGCACTTGCGCTTCCAGACCGTGCGCCACTTTACTCTGGTGCGCTTTCACCGCGTAATCAATCACATCGTGAGTTTGTTCTAACAGATCGAGCATCTGATAGCTGGCCTGCATACTGTAATAAAGCTGCGCTACGCCCGTGGCCAGCGATAGCTCTACTGCTGCGGTTTCTGCCAGCGCGGCATTATGCGCGCCAATGGCGGCGGCAACCGCTGAGCGATGCACACCCCACAAATCAAGATCCAGTCCGGCAAACAAACCTACTGTGGCTTCCGTATAGTACGGCCCGTCCATACCCAGTGCTGGCGCATCCATTGAATAAGGGCTTAAAAAGCCGTTCGCCGAGACACGTTGGCGGTTGAGCATCCCTAACGCTGCGACCTGTAATTGTGAACCGGCATCTAACAAATCGGCCTGGGACTGCGCTTTTTCTTCCCGCAGTTTCGCTTCGGCGAGGGTGTGTGAACCACTTAGCGTCCGTTGGATCAGCGCATCCAGCTGCGGGTCATTGAGTTGTTTCCACCACTGCGCCTGCGGCCAGCCGGAGCTGGCAAGATGAATATCGTCGGCCAGTTTGATTTGTTCCGGTTTGAGCTGTTGATGAGGTGCAGAATCCTTACGTACCAGGGCACAGCCGGAAATCAGCGTCGTGCTGCCGAGAATGCTGCACAACAGCAGACGTGAAAGTTGACGATTGATCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36839","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. W3110","NCBI_taxonomy_id":"316407"}}}},"ARO_accession":"3003550","ARO_id":"40152","ARO_name":"mdtP","ARO_description":"Multidrug resistance efflux pump. Could be involved in resistance to puromycin, acriflavine and tetraphenylarsonium chloride","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavin","category_aro_description":"Acriflavin is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35965":{"category_aro_accession":"0000047","category_aro_cvterm_id":"35965","category_aro_name":"puromycin","category_aro_description":"Puromycin is an aminonucleoside antibiotic, derived from Streptomyces alboniger, that causes premature chain termination during ribosomal protein translation.","category_aro_class_name":"Antibiotic"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36193":{"category_aro_accession":"3000054","category_aro_cvterm_id":"36193","category_aro_name":"acridine dye","category_aro_description":"Acridine dyes are cell permeable, basic molecules with an acridine chromophore. These compounds intercalate DNA. The image shown represents the core structure of the acridine family, with specific dyes containing varying substituents.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"46":{"model_id":"46","model_name":"CMY-114","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"943":{"protein_sequence":{"accession":"AIT76099.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDYVTDKAELLRFYQNWQPQWTPGAKRLYANSSIGLFGALVVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"KM087846","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCGCTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGCATGGCCGTGGCAATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGTTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATTACGTTACGGATAAAGCCGAATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGTGGTAAAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACAGGATCCACAGGCGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTAATGTTGGCAAACAAAAGCTACCCCAACCCGGCTCGCGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002125","ARO_id":"38525","ARO_name":"CMY-114","ARO_description":"CMY-114 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"47":{"model_id":"47","model_name":"OXA-60","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1381":{"protein_sequence":{"accession":"AAQ08905.1","sequence":"MLSRYSKTLAFAVVACTLAISTATAHAELVVRNDLKRVFDDAGVSGTFVLMDITADRTYVVDPARAARSIHPASTFKIPNSLIAFDTGAVRDDQEVLPYGGKPQPYEQWEHDMALPEAIRLSAVPIYQEVARRVGFERMQAYVDAFDYGNRQLGSAIDQFWLRGPLEISAFEEARFTSRMALKQLPVKPRTWDMVQRMLLIEQQGDAALYAKTGVATEYQPEIGWWAGWVERAGHVYAFALNIDMPREGDMAKRIPLGKQLMRALEVWPAP"},"dna_sequence":{"accession":"AF525303","fmin":"2770","fmax":"3586","strand":"+","sequence":"ATGCTGTCTCGCTACTCGAAGACCCTCGCGTTTGCCGTGGTGGCCTGCACGCTCGCAATAAGCACCGCCACCGCTCATGCCGAGCTGGTCGTGCGCAATGACCTCAAGCGCGTGTTCGACGACGCCGGCGTCTCCGGCACCTTCGTGCTGATGGACATCACCGCCGACCGTACCTATGTCGTCGATCCGGCGCGTGCCGCGCGGAGCATCCATCCGGCTTCGACGTTCAAGATTCCGAACAGCCTGATCGCCTTCGACACCGGGGCCGTGCGCGACGATCAGGAAGTGCTGCCCTACGGCGGCAAGCCGCAGCCTTACGAGCAGTGGGAGCACGACATGGCGTTACCCGAGGCGATTCGCCTGTCGGCCGTGCCGATCTATCAGGAAGTCGCGCGCCGCGTTGGCTTCGAGCGCATGCAGGCTTATGTCGATGCGTTCGACTACGGCAATCGCCAGCTCGGCAGCGCGATCGACCAGTTCTGGCTGCGTGGCCCGCTGGAGATTTCCGCTTTCGAAGAAGCACGCTTCACCAGCCGCATGGCGCTCAAGCAGTTGCCGGTGAAGCCGCGCACGTGGGACATGGTCCAGCGCATGCTGTTGATCGAGCAGCAGGGCGATGCCGCGCTATATGCCAAGACCGGCGTCGCCACCGAATACCAGCCGGAGATCGGTTGGTGGGCCGGCTGGGTGGAGCGTGCGGGGCATGTCTATGCATTCGCGCTGAACATCGACATGCCGCGCGAGGGCGATATGGCCAAGCGCATTCCGCTGGGCAAGCAGTTGATGCGGGCGCTCGAGGTGTGGCCGGCACCGTGAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36921","NCBI_taxonomy_name":"Ralstonia pickettii","NCBI_taxonomy_id":"329"}}}},"ARO_accession":"3001808","ARO_id":"38208","ARO_name":"OXA-60","ARO_description":"OXA-60 is a beta-lactamase found in Ralstonia pickettii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"48":{"model_id":"48","model_name":"OXA-90","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1306":{"protein_sequence":{"accession":"CAJ77809.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"AM231719","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCCCTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTAGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001650","ARO_id":"38050","ARO_name":"OXA-90","ARO_description":"OXA-90 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"50":{"model_id":"50","model_name":"SME-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"1396":{"protein_sequence":{"accession":"AAG29813.1","sequence":"MSNKVNFKTASFLFSVCLALSAFNAHANKSDAAAKQIKKLEEDFDGRIGVFAIDTGSGNTFGYRSDERFPLCSSFKGFLAAAVLERVQQKKLDINQKVKYESRDLEYHSPITTKYKGSGMTLGDMASAALQYSDNGATNIIMERFLGGPEGMTKFMRSIGDNEFRLDRWELELNTAIPGDKRDTSTPKAVANSLNKLALGNVLNAKEKAIYQNWLKGNTTGDARIRASVPADWVVGDKTGSCGAYGTANDYAVIWPKNRAPLIVSIYTTRKSKDDKHSDKTIAEASRIAIQAID"},"dna_sequence":{"accession":"AF275256","fmin":"0","fmax":"885","strand":"+","sequence":"ATGTCAAACAAAGTAAATTTTAAAACGGCTTCATTTTTGTTTAGTGTTTGTTTAGCTTTGTCGGCATTTAATGCTCATGCTAACAAAAGTGATGCTGCGGCAAAACAAATAAAAAAATTAGAGGAAGACTTTGATGGGAGGATTGGCGTCTTTGCAATAGATACAGGATCGGGTAATACATTTGGGTATAGATCAGATGAGCGGTTCCCTTTATGCAGTTCATTTAAAGGTTTTTTGGCGGCTGCTGTTTTAGAGAGAGTGCAACAAAAAAAACTAGATATCAACCAAAAGGTTAAATATGAGAGTAGGGATCTAGAATATCATTCACCTATTACAACAAAATATAAAGGCTCAGGTATGACATTAGGTGATATGGCTTCTGCTGCATTGCAATATAGCGACAATGGGGCAACAAATATAATTATGGAACGATTTCTTGGCGGTCCTGAGGGGATGACTAAATTTATGCGTTCTATTGGAGATAATGAGTTTAGGTTAGATCGCTGGGAACTGGAACTTAACACTGCAATCCCAGGAGATAAACGTGACACTTCAACGCCAAAAGCTGTTGCAAATAGTTTGAATAAACTAGCTTTGGGGAATGTTCTCAATGCTAAAGAGAAAGCGATTTATCAAAATTGGTTAAAAGGTAATACAACTGGTGATGCTCGAATTCGTGCTAGTGTTCCTGCTGATTGGGTTGTAGGTGACAAAACTGGGAGCTGTGGGGCATATGGTACTGCGAATGATTATGCCGTCATTTGGCCTAAAAATAGAGCACCATTAATTGTCTCTATATATACAACACGAAAATCGAAAGATGATAAGCACAGTGATAAAACTATTGCGGAAGCATCACGTATTGCAATTCAGGCAATTGATTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36783","NCBI_taxonomy_name":"Serratia marcescens","NCBI_taxonomy_id":"615"}}}},"ARO_accession":"3002380","ARO_id":"38780","ARO_name":"SME-2","ARO_description":"SME-2 is a beta-lactamase found in Serratia marcescens","ARO_category":{"36194":{"category_aro_accession":"3000055","category_aro_cvterm_id":"36194","category_aro_name":"SME beta-lactamase","category_aro_description":"SME beta-lactamases are chromosome-mediated class A beta-lactamases that hydrolyze carbapenems in Serratia marcescens.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"51":{"model_id":"51","model_name":"AAC(3)-IIIc","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"9":{"protein_sequence":{"accession":"AAA25683.1","sequence":"MFSRWSKPLVLAAVTRASLAADLAALGLAAGDAVMVHAAVSKVGRLLDGPDTIIAALSDAGRPAGTILAYADWEARYEDLVDEDGRVPQEWREHIPPFDPRRSRAIRDNGVLPEFLRTTPGALRSGNPGASMVGLGARAEWFTADHPLDYGYGEGSPLARLVEAGGKVLMLGAPLDTLTLLHHAEHLADIPGKRIRRIEVPLATPTGTQWRMIEEFDTGDPIVEGLAEDYFAEIVTAFLAGGRGRQGLIGTAPSVLVDAAAITAFGVAWLESRFGSPSS"},"dna_sequence":{"accession":"L06161","fmin":"105","fmax":"945","strand":"+","sequence":"ATGTTCTCTCGTTGGTCGAAACCTCTCGTGCTTGCCGCCGTGACCCGCGCCTCGCTCGCCGCTGATCTCGCCGCGCTTGGCCTTGCCGCGGGCGATGCGGTCATGGTCCATGCCGCCGTCAGCAAGGTCGGCCGCCTGCTCGACGGTCCCGACACGATCATCGCCGCTCTGTCCGACGCCGGTCGGCCTGCCGGCACCATCCTCGCCTATGCCGATTGGGAAGCGCGCTACGAGGACCTCGTGGACGAGGACGGCCGCGTGCCGCAGGAATGGCGCGAGCACATCCCACCCTTCGATCCGCGGCGCTCACGCGCGATCCGCGACAATGGCGTGCTTCCGGAATTCCTGCGGACGACACCGGGTGCGTTGCGCAGCGGCAATCCCGGCGCCTCGATGGTCGGGCTCGGCGCCAGAGCGGAATGGTTCACCGCAGACCATCCCCTCGACTACGGCTATGGCGAGGGTTCGCCGCTGGCCAGGCTGGTCGAAGCCGGCGGCAAGGTGCTGATGCTCGGGGCGCCGCTCGACACGCTGACCCTGCTGCACCATGCCGAGCATCTGGCCGACATCCCCGGCAAGCGCATCCGGCGGATCGAGGTGCCGCTGGCGACGCCGACCGGCACGCAATGGCGCATGATCGAGGAATTCGATACCGGCGATCCGATCGTCGAAGGTTTGGCCGAGGACTACTTCGCCGAGATCGTGACGGCGTTCCTTGCCGGCGGCCGAGGACGGCAGGGCTTGATCGGCACCGCGCCATCCGTGCTGGTCGATGCTGCCGCAATCACGGCTTTCGGCGTCGCCTGGCTGGAATCGCGCTTCGGCTCGCCCTCATCCTGAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002538","ARO_id":"38938","ARO_name":"AAC(3)-IIIc","ARO_description":"AAC(3)-IIIc is an aminoglycoside acetyltransferase in P. aeruginosa","ARO_category":{"36461":{"category_aro_accession":"3000322","category_aro_cvterm_id":"36461","category_aro_name":"AAC(3)","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 3.","category_aro_class_name":"AMR Gene Family"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"52":{"model_id":"52","model_name":"OXY-2-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1220":{"protein_sequence":{"accession":"AAL79541.1","sequence":"MIKSSWRKIAMLAAAVPLLLASGALWASTDAIHQKLTDLEKRSGGRLGVALINTADNSQILYRGDERFAMCSTSKVMAAAAVLKQSESNKEVVNKRLEINAADLVVWSPITEKHLQSGMTLAELSAATLQYSDNTAMNLIIGYLGGPEKVTAFARSIGDATFRLDRTEPTLNTAIPGDERDTSTPLAMAESLRKLTLGDALGEQQRAQLVTWLKGNTTGGQSIRAGLPESWVVGDKTGAGDYGTTNDIAVIWPEDHAPLILVTYFTQPQQDAKNRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"AF473577","fmin":"0","fmax":"873","strand":"+","sequence":"ATGATAAAAAGTTCGTGGCGTAAAATTGCAATGCTAGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGCGCACTGTGGGCCAGTACCGATGCTATCCATCAGAAGCTGACAGATCTCGAGAAGCGTTCAGGCGGCAGGTTGGGCGTGGCGCTAATCAACACGGCAGATAATTCTCAAATCTTATATCGCGGCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCCGCCGCCGCGGTATTAAAACAGAGCGAAAGCAATAAAGAGGTGGTAAATAAAAGGCTGGAGATTAACGCAGCCGATTTGGTGGTCTGGAGTCCGATTACCGAAAAACATCTCCAGAGCGGAATGACGCTGGCTGAGCTAAGCGCGGCGACGCTGCAATATAGCGACAATACGGCGATGAATCTGATCATCGGCTACCTTGGCGGGCCGGAAAAAGTCACCGCCTTCGCCCGCAGTATCGGCGATGCCACCTTTCGTCTCGATCGTACGGAGCCCACGCTGAATACCGCCATCCCGGGCGATGAGCGTGATACCAGCACGCCGCTGGCGATGGCTGAAAGCCTGCGCAAGCTGACGCTTGGCGATGCGCTGGGCGAACAGCAACGCGCCCAGTTAGTCACCTGGCTGAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCGGGCCTGCCTGAAAGCTGGGTGGTCGGCGATAAAACCGGCGCCGGAGATTACGGCACCACCAATGATATTGCGGTTATCTGGCCGGAAGATCACGCTCCGCTGATATTAGTCACCTACTTTACCCAGCCGCAGCAGGATGCGAAAAACCGCAAAGAGGTGTTAGCCGCAGCGGCAAAAATCGTGACCGAAGGGCTTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002397","ARO_id":"38797","ARO_name":"OXY-2-2","ARO_description":"OXY-2-2 is a beta-lactamase found in Klebsiella oxytoca","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"53":{"model_id":"53","model_name":"MOX-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1286":{"protein_sequence":{"accession":"ACS44783.1","sequence":"MQQRQSILWGALATLMWAGLAHAGDKAATDPLRPVVDASIRPLLKEHRIPGMAVAVLKDGKAHYFNYGVADRERAVGVSEQTLFEIGSVSKTLTATLGAYAVVQGGFELDDKASLFAPWLKGSAFDNITMGELATYSAGGLPLQFPEEVDSLEKMQAYYRQWTPAYSRGSHRQYANPSIGLFGYLAASSMKQPFDRLMEQTMLPGLGLYHTYLNVPEQPMGHYAYGYWKEDKPFRVTPAMLAEEPYGIKTSSADLLRFVKANISGVDNAAMQQAIDLTHQGQYAVGEMTQGLGWERYPYPVSEQTLLAGNSPAMIYNANPAAPAPAAAGHPVLFKKTGSTNGFGAYVAFVPAKGIGVVMLANRNYPNEGTLKAGHAILTQLAR"},"dna_sequence":{"accession":"GQ152600","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCAACAACGACAATCCATCCTGTGGGGCGCTCTGGCCACCCTGATGTGGGCCGGTTTGGCCCATGCCGGTGACAAGGCGGCGACCGATCCCCTGCGCCCCGTGGTGGATGCCAGCATCCGGCCGCTGCTCAAGGAGCACAGGATCCCGGGCATGGCGGTGGCCGTGCTCAAGGATGGCAAGGCCCACTATTTCAACTACGGTGTGGCCGATCGGGAGCGCGCGGTCGGTGTCAGCGAGCAGACCCTGTTCGAGATAGGCTCCGTGAGCAAGACCCTGACCGCGACGCTGGGGGCCTACGCCGTGGTGCAGGGGGGCTTCGAGCTCGATGACAAGGCGAGTCTGTTCGCCCCCTGGCTCAAGGGATCCGCCTTTGACAACATCACCATGGGGGAGCTGGCTACCTACAGCGCGGGCGGCTTGCCGCTGCAATTCCCCGAGGAGGTGGATTCGCTCGAGAAGATGCAGGCCTACTACCGCCAGTGGACCCCAGCCTACTCGCGGGGTTCCCATCGCCAGTACGCCAACCCCAGCATCGGGCTTTTTGGCTATCTGGCGGCGAGCAGCATGAAGCAGCCGTTCGATCGCTTGATGGAGCAGACGATGCTGCCGGGGCTTGGCCTGTACCATACCTACCTCAATGTGCCCGAGCAGCCCATGGGGCACTACGCCTACGGTTACTGGAAGGAGGACAAGCCATTCCGCGTCACTCCCGCCATGCTGGCGGAGGAGCCTTACGGCATCAAGACCAGCTCGGCGGATCTGCTGCGCTTCGTGAAGGCGAACATCAGCGGGGTGGATAATGCGGCCATGCAGCAGGCCATCGATCTGACTCACCAGGGCCAGTATGCGGTGGGGGAGATGACCCAGGGACTGGGCTGGGAGCGTTACCCCTATCCCGTCAGCGAGCAGACGCTGCTGGCGGGCAACTCCCCGGCGATGATTTACAATGCCAACCCGGCGGCGCCCGCGCCCGCTGCGGCAGGGCACCCTGTGCTCTTCAAAAAGACCGGCTCGACCAATGGCTTCGGGGCCTATGTGGCCTTCGTGCCGGCCAAAGGGATCGGCGTCGTCATGCTGGCCAATCGCAACTACCCCAACGAGGGCACGCTCAAGGCGGGCCACGCCATCCTGACGCAACTGGCCAGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36936","NCBI_taxonomy_name":"Aeromonas caviae","NCBI_taxonomy_id":"648"}}}},"ARO_accession":"3002188","ARO_id":"38588","ARO_name":"MOX-5","ARO_description":"MOX-5 is a beta-lactamase. From the Lahey list of MOX beta-lactamases.","ARO_category":{"36222":{"category_aro_accession":"3000083","category_aro_cvterm_id":"36222","category_aro_name":"MOX beta-lactamase","category_aro_description":"MOX beta-lactamases are plasmid-mediated AmpC-type beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"54":{"model_id":"54","model_name":"TEM-34","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1160":{"protein_sequence":{"accession":"AGE11905.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMVSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"KC292503","fmin":"4334","fmax":"5195","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGGTGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36927","NCBI_taxonomy_name":"Haemophilus parainfluenzae","NCBI_taxonomy_id":"729"}}}},"ARO_accession":"3000904","ARO_id":"37284","ARO_name":"TEM-34","ARO_description":"TEM-34 is an inhibitor-resistant beta-lactamase that has been found in clinical isolates.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"55":{"model_id":"55","model_name":"OXA-69","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"813":{"protein_sequence":{"accession":"YP_001713983.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGEKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NC_010410","fmin":"2175316","fmax":"2176141","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAATGGGATGGGGAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTCTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35535","NCBI_taxonomy_name":"Acinetobacter baumannii AYE","NCBI_taxonomy_id":"509173"}}}},"ARO_accession":"3001617","ARO_id":"38017","ARO_name":"OXA-69","ARO_description":"OXA-69 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"56":{"model_id":"56","model_name":"TEM-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4407":{"protein_sequence":{"accession":"AAO33760.1","sequence":"FFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNR"},"dna_sequence":{"accession":"AF527798.1","fmin":"0","fmax":"785","strand":"+","sequence":"TTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000879","ARO_id":"37259","ARO_name":"TEM-7","ARO_description":"TEM-7 is an extended-spectrum beta-lactamase that has been found in clinical isolates.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"57":{"model_id":"57","model_name":"SHV-24","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1637":{"protein_sequence":{"accession":"BAA84973.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARGTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AB023477","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGGCACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001082","ARO_id":"37462","ARO_name":"SHV-24","ARO_description":"SHV-24 is an extended-spectrum beta-lactamase found in E. coli.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"58":{"model_id":"58","model_name":"QnrB47","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"147":{"protein_sequence":{"accession":"AFU25658.1","sequence":"MTLALVGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLRDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"JX440358","fmin":"130","fmax":"775","strand":"+","sequence":"ATGACTCTGGCATTAGTTGGCGAAAAAATTGACAGAAATCGCTTCACCGGTGAGAAAGTTGAAAATAGTACATTTTTTAACTGCGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGCCAGTTCTATGATCGCGAAAGTCAGAAAGGATGCAATTTTAGTCGCGCAATGCTGAGAGATGCCATTTTCAAAAGCTGTGATTTATCAATGGCAGATTTCCGCAACGTCAGCGCATTGGGCATTGAAATTCGCCACTGCCGTGCACAAGGCGCAGATTTCCGCGGTGCAAGCTTTATGAATATGATCACCACGCGCACCTGGTTTTGCAGCGCATATATCACTAATACCAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAGCTATGGGAAAACCGCTGGATGGGGACTCAGGTACTGGGTGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTAGGTGACTTAGATATTCGGGGTGTTGATTTACAAGGCGTTAAGTTAGACAACTACCAGGCATCGTTGCTCATGGAGCGGCTTGGCATCGCTGTGATTGGTTAGC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002762","ARO_id":"39196","ARO_name":"QnrB47","ARO_description":"QnrB47 is a plasmid-mediated quinolone resistance protein found in Escherichia coli","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"59":{"model_id":"59","model_name":"OXA-256","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1685":{"protein_sequence":{"accession":"CCE94500.1","sequence":"MKTFAAYVIIACLSSTALAGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPDAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG"},"dna_sequence":{"accession":"HE616889","fmin":"1826","fmax":"2627","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTATCGCGTGTCTTTCGAGTACGGCATTAGCTGGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTCTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATGACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCGACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAGCAATGGGAAAGAGACTTGACCTTAAGAGGGGCAATACAAGTTTCAGCTGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCCTATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAAGGCCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATATTTAAATAAATTGTCAGCATCTAAAGAAAACCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCGGCACCTGAATATCTAGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGGTGGGTTGAGAAGGAGACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAGTAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGAAAGTGAGGGCATCATTGGTGGCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001502","ARO_id":"37902","ARO_name":"OXA-256","ARO_description":"OXA-256 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"60":{"model_id":"60","model_name":"QnrS6","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"296":{"protein_sequence":{"accession":"AEG74318.1","sequence":"METYRHTYRHHSFSHQDLSDITFTACTFIRCDFRRANLRDATFINCKFIEQGDIEGCHFDVADLRDASFQQCQLAMANFSNANCYGIELRECDLKGANFSRANFANQVSNRMYFCSAFITGCNLSYANMERVCLEKCELYENRWIGTHLAGASLKESDLSRGVFSEDVWGQFSLQGANLCHAELDGLDPRKVDTSGIKIASWQQEQLLEALGIVVFPD"},"dna_sequence":{"accession":"HQ631376","fmin":"0","fmax":"657","strand":"+","sequence":"ATGGAAACCTACCGTCACACATATCGACACCACAGTTTTTCACATCAAGATCTAAGTGATATTACTTTCACTGCTTGCACCTTTATCCGATGCGATTTTCGACGTGCTAACTTGCGTGATGCGACATTTATTAACTGCAAGTTCATTGAACAGGGTGATATCGAAGGTTGCCATTTTGATGTCGCAGACCTTCGCGATGCAAGTTTCCAACAATGCCAGCTTGCGATGGCAAACTTTAGTAACGCCAATTGCTACGGTATTGAGTTACGTGAGTGTGATTTAAAAGGGGCCAACTTTTCCCGAGCAAACTTTGCCAATCAAGTGAGTAATCGTATGTACTTTTGCTCAGCCTTTATTACTGGATGTAACCTGTCTTATGCCAATATGGAGCGGGTCTGTTTAGAAAAATGTGAGCTGTATGAAAATCGCTGGATAGGGACTCACCTCGCGGGCGCATCACTGAAAGAGTCAGACTTAAGTCGAGGTGTTTTTTCTGAAGATGTCTGGGGACAGTTTAGCCTACAGGGTGCTAATTTATGTCACGCCGAACTCGACGGTTTAGATCCTCGAAAAGTCGATACATCAGGTATCAAAATTGCCAGCTGGCAACAAGAACAGCTTCTCGAAGCGTTGGGTATTGTTGTTTTTCCTGACTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36810","NCBI_taxonomy_name":"Aeromonas hydrophila","NCBI_taxonomy_id":"644"}}}},"ARO_accession":"3002795","ARO_id":"39229","ARO_name":"QnrS6","ARO_description":"QnrS6 is a plasmid-mediated quinolone resistance protein found in Aeromonas hydrophila","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"61":{"model_id":"61","model_name":"OXA-330","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1377":{"protein_sequence":{"accession":"AGW16412.1","sequence":"MYKKALIVATSILFLSACSSNLVKQHQIHSISANKSSEEIKSLFDQAQTTGVLVIKRGQTEEIYGNDLKRASTAYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNANIGSKVDNFWLVGPLKITPQQETQFAYQLAHKTLPFSKNVQEQVQSMVFIEKKNGSKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTSSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"KF203104","fmin":"0","fmax":"822","strand":"+","sequence":"ATGTATAAAAAAGCCCTTATCGTTGCAACAAGTATCCTATTTTTATCCGCCTGTTCTTCTAATTTAGTAAAACAACATCAAATACACTCTATTTCTGCCAATAAAAGTTCAGAAGAAATTAAATCACTGTTTGATCAAGCACAGACGACGGGTGTTTTGGTGATTAAGCGAGGGCAAACAGAAGAAATTTATGGCAATGATCTTAAAAGAGCATCAACCGCCTATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTAATTGGACTTGAACATCATAAGGCAACTACAACTGAAGTATTTAAATGGAATGGGCAAAAACGTTTATTTCCTGATTGGGAAAAGGACATGACACTGGGTGATGCCATGAAAGCTTCTGCAATTCCAGTTTACCAAGAATTAGCCCGACGAATTGGACTTGACCTTATGTCCAAAGAGGTGAAAAGAATTGGTTTCGGTAATGCTAACATTGGTTCAAAAGTAGATAATTTTTGGCTCGTTGGCCCTCTAAAAATTACACCTCAACAAGAAACCCAATTTGCTTATCAATTAGCCCATAAAACGCTTCCATTTAGCAAAAATGTACAAGAGCAAGTTCAATCAATGGTGTTCATAGAGAAAAAAAATGGAAGTAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTTGAACCACAAGTTGGTTGGCTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTGGCATTCTCACTTAATTTAGAAATGAAAAAAGGAACTTCTAGCTCTATTCGCAAAGAAATTGCTTATAAAGGCTTAGAACAACTGGGTATCTTATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3001518","ARO_id":"37918","ARO_name":"OXA-330","ARO_description":"OXA-330 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"62":{"model_id":"62","model_name":"CMY-42","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1422":{"protein_sequence":{"accession":"ADM21467.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHSSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"HM146927","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACAGTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002053","ARO_id":"38453","ARO_name":"CMY-42","ARO_description":"CMY-42 is a plasmid-borne AmpC cephalosporinase gene found in Escherichia coli","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35927":{"category_aro_accession":"0000008","category_aro_cvterm_id":"35927","category_aro_name":"cefoxitin","category_aro_description":"Cefoxitin is a cephamycin antibiotic often grouped with the second generation cephalosporins. Cefoxitin is bactericidal and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. Cefoxitin's 7-alpha-methoxy group and 3' leaving group make it a poor substrate for most beta-lactamases.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"63":{"model_id":"63","model_name":"AAC(6')-Ib","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"231":{"protein_sequence":{"accession":"AFJ11384.1","sequence":"MTNSNDSVTLRLMTEHDLAMLYEWLNRSHIVEWWGGEEARPTLADVQEQYLPSVLAQESVTPYIAMLNGEPIGYAQSYVALGSGDGWWEEETDPGVRGIDQSLANASQLGKGLGTKLVRALVELLFNDPEVTKIQTDPSPSNLRAIRCYEKAGFEKQGTVTTPDGPAVYMVQTRQAFERTRSDA"},"dna_sequence":{"accession":"JQ808129","fmin":"633","fmax":"1188","strand":"+","sequence":"GTGACCAACAGCAACGATTCCGTAACACTGCGCCTCATGACTGAGCATGACCTTGCGATGCTCTATGAGTGGCTAAATCGATCTCATATCGTCGAGTGGTGGGGCGGAGAAGAAGCACGCCCGACACTTGCTGACGTACAGGAACAGTACTTGCCAAGCGTTTTAGCGCAAGAGTCCGTCACTCCATACATTGCAATGCTGAATGGAGAGCCGATTGGGTATGCCCAGTCGTACGTTGCTCTTGGAAGCGGGGACGGATGGTGGGAAGAAGAAACCGATCCAGGAGTACGCGGAATAGACCAGTCACTGGCGAATGCATCACAACTGGGCAAAGGCTTGGGAACCAAGCTGGTTCGAGCTCTGGTTGAGTTGCTGTTCAATGATCCCGAGGTCACCAAGATCCAAACGGACCCGTCGCCGAGCAACTTGCGAGCGATCCGATGCTACGAGAAAGCGGGGTTTGAGAAGCAAGGTACCGTAACCACCCCAGATGGTCCAGCCGTGTACATGGTTCAAACACGCCAGGCATTCGAGCGAACACGCAGTGATGCCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002546","ARO_id":"38946","ARO_name":"AAC(6')-Ib","ARO_description":"AAC(6')-Ib is an aminoglycoside acetyltransferase encoded by plasmids, transposons, integrons in K. pneumoniae, P. mirabilis, P. aeruginosa, S. enterica, K. oxytoca, S. maltophilia, E. cloacae and V. cholerae","ARO_category":{"36461":{"category_aro_accession":"3000322","category_aro_cvterm_id":"36461","category_aro_name":"AAC(3)","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 3.","category_aro_class_name":"AMR Gene Family"},"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"64":{"model_id":"64","model_name":"CMY-70","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1180":{"protein_sequence":{"accession":"AFU25635.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYQGKPYYFTWGKADIANNRPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTQYWPELTGKQWQGISLLHLATYTAGGLPLQVPDDVTDKAALLRFYQNWQPQWAPGAKRLYANSSIGLFGALAVKPSGMSYEEAMSKRVLHPLKLAHTWITVPQSEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMTRWVQANMDASQVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPVKADSIISGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"JX440350","fmin":"1026","fmax":"2172","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCGCTGCTGCTGACAGCTTCTTTCTCCACGTTTGCCGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCGCTGATGCAGGAGCAGGCAATTCCGGGTATGGCCGTTGCGATTATCTATCAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCGTCCAGTCACGCAACAAACGCTGTTTGAACTCGGATCGGTCAGTAAAACGTTCAACGGTGTGCTGGGCGGCGATGCTATAGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGCAGTACTGGCCTGAACTGACTGGTAAGCAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTACACGGCAGGCGGCCTGCCGCTTCAGGTTCCGGACGACGTTACGGATAAAGCCGCGTTACTACGCTTTTATCAAAACTGGCAGCCGCAATGGGCCCCAGGCGCTAAACGTCTTTATGCTAACTCCAGCATTGGTCTGTTTGGCGCCCTGGCAGTGAAACCCTCAGGCATGAGCTACGAAGAGGCGATGTCCAAACGCGTCCTGCACCCCTTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAGCGAACAAAAAGATTATGCCTGGGGTTATCGCGAAGGAAAGCCAGTGCATGTATCCCCTGGCCAACTTGATGCCGAAGCATACGGGGTGAAATCGAGCGTTATCGATATGACCCGTTGGGTTCAGGCCAACATGGACGCCAGCCAGGTTCAGGAGAAAACGCTCCAGCAGGGCATCGAGCTTGCGCAGTCACGTTACTGGCGTATTGGCGATATGTACCAGGGCCTGGGCTGGGAGATGCTGAACTGGCCGGTGAAGGCCGACTCGATAATTAGCGGTAGCGACAGCAAAGTGGCACTGGCAGCGCTTCCTGCCGTTGAGGTAAACCCGCCCGCGCCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGCGGATTCGGCAGCTACGTTGCTTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAGAGCTACCCAAACCCTGTTCGCGTCGAGGCCGCCTGGCGCATTCTTGAAAAACTGCAGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39584","NCBI_taxonomy_name":"Citrobacter braakii","NCBI_taxonomy_id":"57706"}}}},"ARO_accession":"3002083","ARO_id":"38483","ARO_name":"CMY-70","ARO_description":"CMY-70 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"65":{"model_id":"65","model_name":"GES-21","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1338":{"protein_sequence":{"accession":"AFK80745.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVLERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMSDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"JQ772478","fmin":"140","fmax":"1004","strand":"+","sequence":"ATGCGCTTCATTCACGCTCTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCCTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGAGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAAAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAGT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3002350","ARO_id":"38750","ARO_name":"GES-21","ARO_description":"GES-21 is a beta-lactamase. From the Lahey list of GES beta-lactamases.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"66":{"model_id":"66","model_name":"SHV-41","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1790":{"protein_sequence":{"accession":"AAN04883.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATFGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AF535129","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGTATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCTTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAACACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001099","ARO_id":"37479","ARO_name":"SHV-41","ARO_description":"SHV-41 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"67":{"model_id":"67","model_name":"OXA-391","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1462":{"protein_sequence":{"accession":"AHN53381.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDKKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KJ427797","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATAAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTACGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001577","ARO_id":"37977","ARO_name":"OXA-391","ARO_description":"OXA-391 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"68":{"model_id":"68","model_name":"TEM-132","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2031":{"protein_sequence":{"accession":"AAR84298.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDHWEPELNEAVPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGKRGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AY491682","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCATTGGGAACCGGAGCTGAATGAAGCCGTACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTAAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000996","ARO_id":"37376","ARO_name":"TEM-132","ARO_description":"TEM-132 is an extended-spectrum beta-lactamase found in E. coli and Klebsiella pneumoniae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"69":{"model_id":"69","model_name":"aadA23","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"280":{"protein_sequence":{"accession":"CAH10847.1","sequence":"MTIEISNQLSEVLSVIERHLESTLLAVHLYGSAVDGGLKPYSDIDLLVTVTVRLDETTRRALINDLLETSASPGESEILRAVEVTIVVHDDIIPWRYPAKRELQFGEWQRNDILAGIFEPATIDIDLAILLTKAREHSVALVGPAAEELFDPVPEQDLFEALNETLTLWNSPPDWAGDERNVVLTLSRIWYSAVTGKIAPKDVAADWAMERLPAQYQPVILEARQAYLGQEEDRLASRADQLEEFVHYVKGEITKVVGK"},"dna_sequence":{"accession":"AJ809407","fmin":"118","fmax":"898","strand":"+","sequence":"GTGACCATCGAAATTTCGAACCAACTATCAGAGGTGCTAAGCGTCATTGAGCGCCATCTGGAATCAACGTTGCTGGCCGTGCATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCATACAGCGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCGAGCTTTGATCAACGACCTTTTGGAAACTTCGGCTTCCCCTGGAGAGAGCGAGATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGCCTTAGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCTGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAGTAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATGGAGCGCCTGCCGGCCCAGTATCAGCCCGTCATACTTGAAGCTAGACAGGCTTATCTTGGACAAGAAGAAGATCGCTTGGCCTCGCGCGCAGATCAGTTGGAAGAATTTGTCCACTACGTGAAAGGCGAGATCACCAAGGTAGTCGGCAAATAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35709","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Agona","NCBI_taxonomy_id":"58095"}}}},"ARO_accession":"3002620","ARO_id":"39020","ARO_name":"aadA23","ARO_description":"aadA23 is an integron-encoded aminoglycoside nucleotidyltransferase gene in S. enterica","ARO_category":{"41439":{"category_aro_accession":"3004275","category_aro_cvterm_id":"41439","category_aro_name":"ANT(3'')","category_aro_description":"Nucleotidylylation of streptomycin at the hydroxyl group at position 3''","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"70":{"model_id":"70","model_name":"NDM-10","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1749":{"protein_sequence":{"accession":"AGT37351.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEISPTIDQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPSFGAVTSNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDRTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"KF361506","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCAGCCCGACGATTGACCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGAGTTTCGGGGCAGTCACTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGATGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACCGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39097","NCBI_taxonomy_name":"Klebsiella pneumoniae subsp. pneumoniae","NCBI_taxonomy_id":"72407"}}}},"ARO_accession":"3002360","ARO_id":"38760","ARO_name":"NDM-10","ARO_description":"NDM-10 is a beta-lactamase. From the Lahey list of NDM beta-lactamases.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"71":{"model_id":"71","model_name":"QnrB66","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"157":{"protein_sequence":{"accession":"AGL43627.1","sequence":"MALALVGEKINRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNSSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"KC580655","fmin":"0","fmax":"645","strand":"+","sequence":"ATGGCTCTGGCACTCGTTGGCGAAAAAATTAACAGAAACCGTTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCGATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATTCCAGTGCGCTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGCGCAAGCTTTATGAATATGATCACCACGCGCACCTGGTTTTGTAGCGCATATATCACGAATACCAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAGCTGTGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCGAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTGACTTAGATATTCGGGGCGTTGATTTACAAGGCGTTAAGCTGGACAACTACCAGGCGTCGTTGCTCATGGAGCGGCTTGGCATCGCGGTGATTGGTTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002778","ARO_id":"39212","ARO_name":"QnrB66","ARO_description":"QnrB66 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"72":{"model_id":"72","model_name":"SHV-42","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1874":{"protein_sequence":{"accession":"AAN04884.1","sequence":"MRYIRLCIISLLATLPLAVHSSPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITVSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AF535130","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACTCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACCCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCGTGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001100","ARO_id":"37480","ARO_name":"SHV-42","ARO_description":"SHV-42 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"73":{"model_id":"73","model_name":"OXA-35","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"975":{"protein_sequence":{"accession":"AAK49460.1","sequence":"MKTFAAYVITACLSSTALASSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNNLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLSLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLFLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKGTEVYFFAFNMDIDNENKLPLRKSIPTKIMASEGIIGG"},"dna_sequence":{"accession":"AF315786","fmin":"1313","fmax":"2114","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTACTGCGTGTCTTTCAAGTACGGCATTAGCTAGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTTTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATAACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAACAATGGGAAAGAGACTTGAGCTTAAGAGGGGCAATACAAGTTTCAGCGGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCATATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAGGGTCAGCTAAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATTTTTAAATAAATTGTCAGCATCAAAAGAAAATCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCTGCGCCTGAATATCTTGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGTTGGGTTGAGAAGGGAACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAATAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGCAAGTGAGGGCATCATTGGTGGCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001429","ARO_id":"37829","ARO_name":"OXA-35","ARO_description":"OXA-35 is a beta-lactamase found in P. aeruginosa","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"74":{"model_id":"74","model_name":"SHV-18","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1636":{"protein_sequence":{"accession":"AAF64386.1","sequence":"MRYFRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGSVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAAKRGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AF132290","fmin":"87","fmax":"948","strand":"+","sequence":"ATGCGTTATTTTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCAGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGCCAAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGGATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001076","ARO_id":"37456","ARO_name":"SHV-18","ARO_description":"SHV-18 is an extended-spectrum beta-lactamase found in Acinetobacter baumannii and Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"75":{"model_id":"75","model_name":"fusH","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"950"}},"model_sequences":{"sequence":{"201":{"protein_sequence":{"accession":"CAA90432.1","sequence":"MLNKGIRTRRARGALAGGTVLTAAAALLTAVPAAQAISGEPPAATDHAFTARLHIGEGDTLRGCSAALVHQQWLLTATSCFAATPGGEVKSGKPALKSTATLGGKTLGIVEVVPRDDRDVAMVRLAEPVTTVEPVRLAADAPVAAETLLGAGFGRTRTEWAPDQLHTGEFRVDSVTGTTVELTGQDGVSVCKGDTGGPALRGTGGEVELAAVHSRSWQGGCFGETETRTGAVDARADGLADWVTDVRNRDRTQSADVDGDGRADLVVLRSNGDVVVHRNLGDSFAAGRVMSGGWGLFVTWKDLGRLYFADVDGDRKADMIVHTSDGNIEVRFNHGTYWDQGTHWSGGWGRFIDGSDLGRLYFADVDGDGRADMIVHTGDGNVEVRFNHGTYWDQGTHWSGGWGRFVTWKDLGRLYFADVDGDGRADMIVHTGDGNVEVRFNHGTYWDQGTHWSGGWGRFVDGSDLGSLEFGDATGDGKADLLVRTKDGKVALRTNHGTYWDQGKFMITL"},"dna_sequence":{"accession":"Z50108","fmin":"238","fmax":"1768","strand":"+","sequence":"TTGCTCAACAAAGGAATCCGCACGCGGCGGGCTCGCGGGGCACTGGCCGGCGGCACGGTCCTGACGGCCGCCGCCGCCCTGCTCACCGCGGTGCCGGCCGCGCAGGCGATTTCCGGCGAGCCCCCGGCCGCGACCGACCACGCCTTCACCGCCCGGCTGCACATCGGCGAGGGCGACACCCTCCGCGGCTGTTCCGCCGCTCTGGTGCACCAGCAGTGGCTGCTGACCGCCACGAGCTGTTTCGCCGCCACCCCGGGTGGCGAGGTCAAGTCGGGCAAGCCCGCGCTGAAGTCGACGGCGACCCTGGGCGGCAAGACCCTCGGCATAGTCGAGGTCGTTCCGCGCGACGACCGGGACGTGGCCATGGTCCGGCTCGCCGAACCCGTCACCACGGTCGAGCCCGTGCGGCTGGCCGCGGACGCCCCCGTGGCGGCCGAGACCCTGCTCGGTGCAGGGTTCGGGCGGACCCGGACGGAGTGGGCCCCGGACCAGTTGCACACCGGCGAGTTCCGAGTGGACTCCGTCACCGGCACCACCGTGGAGCTGACCGGTCAGGACGGGGTGTCCGTGTGCAAGGGCGACACCGGCGGCCCGGCCCTGCGCGGCACGGGTGGTGAGGTCGAGCTGGCCGCCGTGCACAGCCGGTCCTGGCAGGGCGGGTGCTTCGGCGAGACGGAGACCCGGACCGGCGCGGTGGACGCCAGGGCCGACGGCCTGGCGGACTGGGTGACGGACGTCCGCAACCGCGACCGGACGCAGTCGGCCGACGTCGACGGCGACGGCAGGGCCGACCTCGTCGTCCTGCGCTCGAACGGCGACGTCGTCGTCCACCGCAACCTGGGCGACAGCTTCGCCGCCGGCCGGGTCATGTCCGGCGGCTGGGGCCTCTTCGTGACCTGGAAGGACCTGGGCCGGCTCTATTTCGCCGACGTCGACGGCGACCGCAAGGCCGACATGATCGTCCACACCAGCGACGGCAACATCGAGGTCCGCTTCAACCACGGCACCTACTGGGACCAGGGCACGCACTGGTCCGGCGGCTGGGGCCGCTTCATCGACGGCAGCGACCTGGGCCGGCTCTACTTCGCCGATGTGGACGGCGACGGCAGGGCGGACATGATCGTCCACACCGGCGACGGCAACGTCGAGGTGCGCTTCAACCACGGCACGTACTGGGACCAGGGGACGCACTGGTCGGGCGGCTGGGGCCGCTTCGTGACCTGGAAGGACCTGGGCCGGCTCTACTTCGCCGATGTCGACGGCGACGGCAGGGCGGACATGATCGTCCACACCGGCGACGGCAACGTAGAGGTCCGCTTCAACCACGGCACGTACTGGGACCAGGGCACGCACTGGTCCGGCGGCTGGGGCCGCTTCGTCGACGGCAGCGACCTGGGGTCCCTCGAGTTCGGCGACGCCACCGGTGACGGCAAGGCCGACCTGCTCGTCCGCACCAAGGACGGGAAGGTCGCCCTCCGTACCAACCACGGCACCTACTGGGACCAGGGCAAGTTCATGATCACGCTCTGAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39569","NCBI_taxonomy_name":"Streptomyces lividans","NCBI_taxonomy_id":"1916"}}}},"ARO_accession":"3003026","ARO_id":"39460","ARO_name":"fusH","ARO_description":"fusH is a highly specific fusidic acid esterase found in Streptomyces lividans","ARO_category":{"39459":{"category_aro_accession":"3003025","category_aro_cvterm_id":"39459","category_aro_name":"fusidic acid inactivation enzyme","category_aro_description":"Enzymes that confer resistance to fusidic acid by inactivation","category_aro_class_name":"AMR Gene Family"},"37139":{"category_aro_accession":"3000759","category_aro_cvterm_id":"37139","category_aro_name":"fusidic acid","category_aro_description":"Fusidic acid is the only commercially available fusidane, a group of steroid-like antibiotics. It is most active against Gram-positive bacteria, and acts by inhibiting elongation factor G to  block protein synthesis.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"76":{"model_id":"76","model_name":"SHV-79","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"921":{"protein_sequence":{"accession":"CAJ47134.2","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEVLPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM176554","fmin":"30","fmax":"891","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGTGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATCGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001133","ARO_id":"37513","ARO_name":"SHV-79","ARO_description":"SHV-79 is a broad-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"77":{"model_id":"77","model_name":"TEM-47","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1573":{"protein_sequence":{"accession":"CAA71322.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASKRGSRGIIAALGPDGKPSRIVVIYMTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"Y10279","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTAAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACATGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000916","ARO_id":"37296","ARO_name":"TEM-47","ARO_description":"TEM-47 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"78":{"model_id":"78","model_name":"TEM-16","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1722":{"protein_sequence":{"accession":"CAA46346.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDHWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"X65254","fmin":"175","fmax":"1036","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCATTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000887","ARO_id":"37267","ARO_name":"TEM-16","ARO_description":"TEM-16 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"79":{"model_id":"79","model_name":"VIM-37","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1655":{"protein_sequence":{"accession":"AGC50807.1","sequence":"MLKVISSLLVYMTASVMAVASPLAHSGEPSGEYPTVNEIPVGEVRLYQIADGVWSHISTQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEAEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSANVLYGGCAVHELSRTSAGNVADADLAEWPTSVERIQKHYPEAEVVIPGHGLPGGLDLLQHTANVVKAHKNRSVAE"},"dna_sequence":{"accession":"JX982636","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTACATGACCGCGTCTGTCATGGCTGTCGCAAGTCCGTTAGCCCATTCCGGGGAGCCGAGTGGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGAGAGGTCCGACTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCTCAACGCAGTCGTTTGATGGCGCGGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAAAAGCAAATTGGACTTCCCGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGCAGAGGGGAACGAGATTCCCACGCATTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGCTCTTCTATCCTGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAACGTGCTATACGGTGGTTGTGCCGTTCATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCGTTGAGCGGATTCAAAAACACTACCCGGAAGCAGAGGTCGTCATTCCCGGGCACGGTCTACCGGGCGGTCTAGACTTGCTCCAGCACACAGCGAACGTTGTCAAAGCACACAAAAATCGCTCAGTCGCCGAGTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002307","ARO_id":"38707","ARO_name":"VIM-37","ARO_description":"VIM-37 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"80":{"model_id":"80","model_name":"ACT-29","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1095":{"protein_sequence":{"accession":"AIT76085.1","sequence":"MMKKSLCCALLLSTSCSVLAAPMSEKQLAEMVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAITTRVFKPLKLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVKDMASWVMVNMKPDSLQDSSLRKGITLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVEGSDNKVALAPLPAREVNPPAPPVNASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"KM087832","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCTCTTTGCTGCGCCCTGCTGCTCAGCACATCCTGCTCGGTATTGGCTGCACCGATGTCAGAAAAACAGCTGGCTGAGATGGTGGAACGTACCGTTACGCCGCTGATGAAAGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGTAAAGCCGATGTCGCGGCGAATAAACCTGTCACTCCACAAACCTTATTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGCGGCGATGCCATTGCTCGCGGTGAAATATCGCTGGGCGATCCGGTGACAAAATACTGGCCTGAGCTGACAGGCAAGCAGTGGCAGGGGATCCGCATGCTGGATCTGGCAACCTATACCGCAGGAGGTTTGCCGTTACAGGTACCGGATGAGGTCACGGATAACGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGTATGAGCTATGAGCAGGCCATAACGACGCGGGTCTTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCCAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGCGACGGTAAGGCGGTACACGTTTCGCCAGGAATGCTGGACGCTGAAGCCTATGGCGTAAAAACCAACGTGAAGGATATGGCAAGCTGGGTGATGGTCAATATGAAGCCGGACTCGCTTCAGGATAGTTCACTCAGGAAAGGCATTACCCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGGTTAGGCTGGGAAATGCTTAACTGGCCGGTCGATGCCAAAACCGTGGTTGAAGGTAGCGACAATAAGGTGGCACTGGCACCGTTGCCTGCGAGAGAAGTGAATCCACCGGCTCCCCCGGTCAATGCGTCCTGGGTCCATAAAACCGGCTCTACCGGCGGGTTTGGCAGCTACGTGGCATTTATTCCCGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTACAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36926","NCBI_taxonomy_name":"Enterobacter asburiae","NCBI_taxonomy_id":"61645"}}}},"ARO_accession":"3001849","ARO_id":"38249","ARO_name":"ACT-29","ARO_description":"ACT-29 is a beta-lactamase. From the Lahey list of ACT beta-lactamases.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"81":{"model_id":"81","model_name":"FOX-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1109":{"protein_sequence":{"accession":"CAA71947.1","sequence":"MQQRRAFALLTLGSLLLAPCTYASGEAPLTATVDGIIQPMLKEYRIPGIAVAVLKDGKAHYFNYGVANRESGQRVSEQTLFEIGSVSKTLTATLGAYAAVKGGFVLDDKVSQHAPWLKGSALDGVTMAELATYSAGGLPLQFPDKVDSNDKMQTYYRSWSPVYPAGTHRQYSNPSIGLFGHLAANSLGQPFEQLMSQTLLPKLGLHHTYIQVPESAMANYAYGYSKEDKPIRVTPGVLAAEAYGIKTGSADLLKFAEANMGYQGDALVKSAIALTHTGFYSVGEMTQGLGWESYDYPVTEQVLLAGNSPAVSFQANPVTRFAVPKAMGEQRLYNKTGSTGGFGAYVAFVPARGIAIVMLANRNYPIEARVKAAHAILSQLAE"},"dna_sequence":{"accession":"Y11068","fmin":"16","fmax":"1165","strand":"+","sequence":"ATGCAACAACGACGTGCGTTCGCGCTACTGACGCTGGGTAGCCTGCTGCTAGCCCCTTGTACTTATGCCAGCGGGGAGGCCCCGCTGACCGCCACTGTGGACGGCATTATCCAGCCGATGCTCAAGGAGTATCGGATCCCGGGGATAGCGGTCGCCGTACTGAAAGATGGCAAGGCCCACTATTTCAACTATGGGGTTGCCAACCGCGAGAGTGGCCAGCGCGTCAGCGAGCAGACCCTGTTCGAGATTGGCTCGGTCAGCAAGACCCTGACCGCGACCCTCGGTGCCTATGCTGCGGTCAAGGGGGGCTTTGTGCTGGATGACAAGGTGAGCCAGCACGCCCCCTGGCTCAAAGGTTCCGCCTTGGATGGTGTGACCATGGCCGAGCTTGCCACCTACAGTGCGGGTGGTTTGCCGCTGCAGTTCCCCGATAAGGTGGATTCGAATGACAAGATGCAAACTTACTATCGGAGCTGGTCACCGGTTTATCCGGCAGGGACTCATCGCCAGTATTCCAACCCCAGCATAGGCCTGTTTGGTCACCTGGCCGCAAATAGTCTGGGCCAGCCATTTGAGCAACTGATGAGCCAGACCCTGCTGCCCAAGCTGGGTTTGCACCACACCTATATCCAGGTGCCGGAGTCGGCCATGGCGAACTATGCCTACGGCTATTCGAAGGAAGATAAGCCCATCCGGGTCACTCCGGGCGTGCTGGCGGCCGAGGCTTACGGGATCAAGACCGGCTCGGCGGATCTGCTGAAGTTTGCCGAGGCAAACATGGGGTATCAGGGAGATGCCCTGGTAAAAAGCGCAATCGCGCTGACCCACACCGGTTTCTACTCGGTGGGGGAAATGACCCAGGGGCTGGGCTGGGAGAGTTACGACTATCCCGTCACCGAGCAGGTGCTGCTGGCGGGCAACTCCCCGGCGGTGAGCTTCCAGGCCAATCCGGTTACGCGCTTTGCGGTGCCCAAAGCGATGGGCGAGCAGCGGCTCTATAACAAGACGGGCTCGACTGGCGGCTTTGGCGCCTATGTGGCGTTCGTGCCCGCCAGAGGGATCGCCATCGTCATGCTGGCCAATCGCAACTATCCCATCGAGGCCAGGGTGAAGGCGGCTCACGCCATCCTGAGTCAGTTGGCCGAGTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002157","ARO_id":"38557","ARO_name":"FOX-3","ARO_description":"FOX-3 is a beta-lactamase found in Klebsiella oxytoca","ARO_category":{"36206":{"category_aro_accession":"3000067","category_aro_cvterm_id":"36206","category_aro_name":"FOX beta-lactamase","category_aro_description":"FOX beta-lactamases are plasmid-encoded AmpC-type beta-lactamase which conferred resistance to broad-spectrum cephalosporins and cephamycins","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"82":{"model_id":"82","model_name":"PER-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1061":{"protein_sequence":{"accession":"ACE77058.1","sequence":"MNVIIKAVVTASTLLMVSFSSFETSAQSPLLKEQIESIVIGKKATVGVAVWGPDDLEPLLINPFEKFPMQSVFKLHLAMLVLHQVDQGKLDLNQTVIVNRAKVLQNTWAPIMKAYQGDEFSVPVQQLLQYSVSHTDNVACDLLFELVGGPAALHDYIQSMGIKETAVVANEAQMHADDQVQYQNWTSMKGAAEILKKFEQKTQLSETSQALLWKWMVETTTGPERLKGLLPAGTVVAHKTGTSGIKAGKTAATNDLGIILLPDGRPLLVAVFVKDSAESSRTNEAIIAQVAQTAYQFELKKLSALSPN"},"dna_sequence":{"accession":"EU748544","fmin":"0","fmax":"927","strand":"+","sequence":"ATGAATGTCATTATAAAAGCTGTAGTTACTGCCTCGACGCTACTGATGGTATCTTTTAGTTCATTCGAAACCTCAGCGCAATCCCCACTGTTAAAAGAGCAAATTGAATCCATAGTCATTGGAAAAAAAGCCACTGTAGGCGTTGCAGTGTGGGGGCCTGACGATCTGGAACCTTTACTGATTAATCCTTTTGAAAAATTCCCAATGCAAAGTGTATTTAAATTGCATTTAGCTATGTTGGTACTGCATCAGGTTGATCAGGGAAAGTTGGATTTAAATCAGACCGTTATCGTAAACAGGGCTAAGGTTTTACAGAATACCTGGGCTCCGATAATGAAAGCGTATCAGGGAGACGAGTTTAGTGTTCCAGTGCAGCAACTGCTGCAATACTCGGTCTCGCACACCGATAACGTGGCCTGTGATTTGTTATTTGAACTGGTTGGTGGACCAGCTGCTTTGCATGACTATATCCAGTCTATGGGTATAAAGGAGACCGCTGTGGTCGCAAATGAAGCGCAGATGCACGCCGATGATCAGGTGCAGTATCAAAACTGGACCTCGATGAAAGGTGCTGCAGAGATCCTGAAAAAGTTTGAGCAAAAAACACAGCTGTCTGAAACCTCGCAGGCTTTGTTATGGAAGTGGATGGTCGAAACCACCACAGGACCAGAGCGGTTAAAAGGTTTGTTACCAGCTGGTACTGTGGTCGCACATAAAACTGGTACTTCGGGTATCAAAGCCGGAAAAACTGCGGCCACTAATGATTTAGGTATCATTCTGTTGCCTGATGGACGGCCCTTGCTGGTTGCTGTTTTTGTGAAAGACTCAGCCGAGTCAAGCCGAACCAATGAAGCTATCATTGCGCAGGTTGCTCAGACTGCGTATCAATTTGAATTGAAAAAGCTTTCTGCCCTAAGCCCAAATTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36943","NCBI_taxonomy_name":"Proteus vulgaris","NCBI_taxonomy_id":"585"}}}},"ARO_accession":"3002366","ARO_id":"38766","ARO_name":"PER-4","ARO_description":"PER-4 is a beta-lactamase. From the Lahey list of PER beta-lactamases.","ARO_category":{"36195":{"category_aro_accession":"3000056","category_aro_cvterm_id":"36195","category_aro_name":"PER beta-lactamase","category_aro_description":"PER beta-lactamases are plasmid-mediated extended spectrum beta-lactamases found in the Enterobacteriaceae family.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"83":{"model_id":"83","model_name":"IMP-47","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"3319":{"protein_sequence":{"accession":"AAK13430.1","sequence":"MKKLFVLCVCFLCSITAAGAALPDLKIEKLEEGVYVHTSFEEVNGWGVVSKHGLVVLVNTDAYLIDTPFTATDTEKLVNWFVERGYKIKGTISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKDGKVQAKNSFSGVSYWLVKNKIEVFYPGPGHTQDNVVVWLPEKKILFGGCFVKPDGLGNLGDANLEAWPKSAKILMSKYGKAKLVVSSHSEIGDASLLKRTWEQAVKGLNESKKPSQPSN"},"dna_sequence":{"accession":"AF322577","fmin":"2081","fmax":"2822","strand":"+","sequence":"ATGAAGAAATTATTTGTTTTATGTGTATGCTTCCTTTGTAGCATTACTGCCGCAGGAGCGGCTTTGCCTGATTTAAAAATCGAGAAGCTTGAAGAAGGTGTTTATGTTCATACATCGTTCGAAGAAGTTAACGGTTGGGGTGTTGTTTCTAAACACGGTTTGGTGGTTCTTGTAAACACTGACGCCTATCTGATTGACACTCCATTTACTGCTACAGATACTGAAAAGTTAGTCAATTGGTTTGTGGAGCGCGGCTATAAAATCAAAGGCACTATTTCCTCACATTTCCATAGCGACAGCACAGGGGGAATAGAGTGGCTTAATTCTCAATCTATTCCCACGTATGCATCTGAATTAACAAATGAACTTCTTAAAAAAGACGGTAAGGTGCAAGCTAAAAACTCATTTAGCGGAGTTAGTTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCCGGCCCGGGGCACACTCAAGATAACGTAGTGGTTTGGTTACCTGAAAAGAAAATTTTATTCGGTGGTTGTTTTGTTAAACCGGACGGTCTTGGTAATTTGGGTGACGCAAATTTAGAAGCTTGGCCAAAGTCCGCCAAAATATTAATGTCTAAATATGGTAAAGCAAAACTGGTTGTTTCAAGTCATAGTGAAATTGGGGACGCATCACTCTTGAAACGTACATGGGAACAGGCTGTTAAAGGGCTAAATGAAAGTAAAAAACCATCACAGCCAAGTAACTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002238","ARO_id":"38638","ARO_name":"IMP-47","ARO_description":"IMP-47 is a beta-lactamase. From the Lahey list of IMP beta-lactamases.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"84":{"model_id":"84","model_name":"GIM-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"952":{"protein_sequence":{"accession":"CAF05908.1","sequence":"MKNVLVFLILLVALPALAQGHKPLEVIKIEDGVYLHTSFKNIEGYGLVDSNGLVVLDNNQAYIIDTPWSEEDTKLLLSWATDRGYQVMASISTHSHEDRTAGIKLLNSKSIPTYTSELTKKLLAREGKPVPTHYFKDDEFTLGNGLIELYYPGAGHTEDNIVAWLPKSKILFGGCLVRSHEWEGLGYVGDASISSWADSIKNIVSKKYPIQMVVPGHGKVGSSDILDHTIDLAESASNKLMQPTAEASAD"},"dna_sequence":{"accession":"AJ620678","fmin":"0","fmax":"753","strand":"+","sequence":"ATGAAAAATGTATTAGTGTTTTTAATATTACTTGTAGCGTTGCCAGCTTTAGCTCAGGGTCATAAACCGCTAGAAGTTATAAAAATTGAAGATGGAGTATATCTTCATACCTCCTTTAAGAATATTGAAGGCTATGGGTTAGTTGATTCGAATGGGTTGGTAGTTCTGGATAATAATCAAGCCTATATTATCGACACACCTTGGTCTGAAGAAGACACGAAGTTGTTATTATCCTGGGCGACTGACAGGGGATACCAGGTTATGGCTAGCATCTCAACTCATTCTCATGAAGATCGCACTGCTGGTATCAAGTTGCTAAATTCAAAGTCAATTCCTACATACACATCAGAGTTAACTAAAAAGCTTCTTGCCCGTGAAGGAAAGCCGGTTCCTACCCACTACTTTAAAGACGACGAATTCACACTGGGAAATGGGCTTATAGAGCTCTACTATCCAGGTGCTGGGCATACAGAGGATAATATTGTTGCTTGGTTACCCAAAAGCAAAATACTATTTGGTGGCTGCCTCGTGAGGAGTCATGAGTGGGAAGGCTTAGGTTACGTAGGCGACGCCTCAATTAGCTCTTGGGCTGACTCAATTAAAAATATTGTATCGAAAAAATATCCCATTCAAATGGTCGTTCCGGGGCATGGCAAAGTTGGAAGTTCAGATATATTAGATCACACCATTGATCTTGCTGAATCAGCTTCTAACAAATTAATGCAACCGACCGCTGAAGCGTCGGCTGATTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3000845","ARO_id":"37225","ARO_name":"GIM-1","ARO_description":"GIM-1 is an integron-encoded B1 beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"39772":{"category_aro_accession":"3003195","category_aro_cvterm_id":"39772","category_aro_name":"GIM beta-lactamase","category_aro_description":"The GIM beta-lactamases are isolated from Pseudomonas aeruginosa. They are located in a distinct integron structure. They confers high broad spectrum resistant, including all \u00df-lactams, aminoglycosides and quinolones.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"85":{"model_id":"85","model_name":"IMP-42","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"2048":{"protein_sequence":{"accession":"BAM62793.1","sequence":"MSKLSVFFIFLFCSIATAAESLPDLKIEKLDEGVYVHTSFEEVNRWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNESKKPSKPSN"},"dna_sequence":{"accession":"AB753456","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAGCAAGTTATCTGTATTCTTTATATTTTTGTTTTGCAGCATTGCTACCGCAGCAGAGTCTTTGCCAGATTTAAAAATTGAAAAGCTTGATGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACAGGTGGGGCGTTGTTCCTAAACATGGTTTGGTGGTTCTTGTAAATGCTGAGGCTTACCTAATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAGCGTGGCTATAAAATAAAAGGCAGCATTTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCGATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTGCTTAAAAAAGACGGTAAGGTTCAAGCCACAAATTCATTTAGCGGAGTTAACTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCGGGACACACTCCAGATAACGTAGTGGTTTGGTTGCCTGAAAGGAAAATATTATTCGGTGGTTGTTTTATTAAACCGTACGGTTTAGGCAATTTGGGTGACGCAAATATAGAAGCTTGGCCAAAGTCCGCCAAATTATTAAAGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAAGTCACAGTGAAGTTGGAGACGCATCACTCTTGAAACTTACATTAGAGCAGGCGGTTAAAGGGTTAAACGAAAGTAAAAAACCATCAAAACCAAGCAACTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39070","NCBI_taxonomy_name":"Acinetobacter soli","NCBI_taxonomy_id":"487316"}}}},"ARO_accession":"3002233","ARO_id":"38633","ARO_name":"IMP-42","ARO_description":"IMP-42 is a beta-lactamase found in Pseudomonas and Acinetobacter spp.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"86":{"model_id":"86","model_name":"TEM-102","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"923":{"protein_sequence":{"accession":"AAK82652.1","sequence":"MSIQHFRVALIPFFAAFCLPVFVRPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAAVGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AY040093","fmin":"68","fmax":"929","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGTACGCCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGACGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACGACTTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGGGGGTCTCGCGGTATCATTGCAGCAGTCGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39077","NCBI_taxonomy_name":"Plasmid pWW100","NCBI_taxonomy_id":"167474"}}}},"ARO_accession":"3000965","ARO_id":"37345","ARO_name":"TEM-102","ARO_description":"TEM-102 is an extended-spectrum beta-lactamase that has been found in clinical isolates.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"87":{"model_id":"87","model_name":"TEM-116","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2030":{"protein_sequence":{"accession":"NP_052129.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"NC_002156","fmin":"1429","fmax":"2290","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTATTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3000979","ARO_id":"37359","ARO_name":"TEM-116","ARO_description":"TEM-116 is a broad-spectrum beta-lactamase found in many species of bacteria.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"88":{"model_id":"88","model_name":"CMY-55","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1116":{"protein_sequence":{"accession":"ADK55605.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGEAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"HM544040","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACATGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGAAGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002066","ARO_id":"38466","ARO_name":"CMY-55","ARO_description":"CMY-55 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"89":{"model_id":"89","model_name":"vanYA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"3278":{"protein_sequence":{"accession":"AAA65958.1","sequence":"MKKLFFLLLLLFLIYLGYDYVNEALFSQEKVEFQNYDQNPKEHLENSGTSENTQEKTITEEQVYQGNLLLINSKYPVRQESVKSDIVNLSKHDELINGYGLLDSNIYMSKEIAQKFSEMVNDAVKGGVSHFIINSGYRDFDEQSVLYQEMGAEYALPAGYSEHNSGLSLDVGSSLTKMERAPEGKWIEENAWKYGFILRYPEDKTELTGIQYEPWHIRYVGLPHSAIMKEKNFVLEEYMDYLKEEKTISVSVNGEKYEIFYYPVTKNTTIHVPTNLRYEISGNNIDGVIVTVFPGSTHTNSRR"},"dna_sequence":{"accession":"M97297","fmin":"9052","fmax":"9963","strand":"+","sequence":"ATGAAGAAGTTGTTTTTTTTATTGTTATTGTTATTCTTAATATACTTAGGTTATGACTACGTTAATGAAGCACTGTTTTCTCAGGAAAAAGTCGAATTTCAAAATTATGATCAAAATCCCAAAGAACATTTAGAAAATAGTGGGACTTCTGAAAATACCCAAGAGAAAACAATTACAGAAGAACAGGTTTATCAAGGAAATCTGCTATTAATCAATAGTAAATATCCTGTTCGCCAAGAAAGTGTGAAGTCAGATATCGTGAATTTATCTAAACATGACGAATTAATAAATGGATACGGGTTGCTTGATAGTAATATTTATATGTCAAAAGAAATAGCACAAAAATTTTCAGAGATGGTCAATGATGCTGTAAAGGGTGGCGTTAGTCATTTTATTATTAATAGTGGCTATCGAGACTTTGATGAGCAAAGTGTGCTTTACCAAGAAATGGGGGCTGAGTATGCCTTACCAGCAGGTTATAGTGAGCATAATTCAGGTTTATCACTAGATGTAGGATCAAGCTTGACGAAAATGGAACGAGCCCCTGAAGGAAAGTGGATAGAAGAAAATGCTTGGAAATACGGGTTCATTTTACGTTATCCAGAGGACAAAACAGAGTTAACAGGAATTCAATATGAACCATGGCATATTCGCTATGTTGGTTTACCACATAGTGCGATTATGAAAGAAAAGAATTTCGTTCTCGAGGAATATATGGATTACCTAAAAGAAGAAAAAACCATTTCTGTTAGTGTAAATGGGGAAAAATATGAGATCTTTTATTATCCTGTTACTAAAAATACCACCATTCATGTGCCGACTAATCTTCGTTATGAGATATCAGGAAACAATATAGACGGTGTAATTGTGACAGTGTTTCCCGGATCAACACATACTAATTCAAGGAGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002955","ARO_id":"39389","ARO_name":"vanYA","ARO_description":"vanYA, also known as vanY, is a vanY variant found in the vanA gene cluster","ARO_category":{"36216":{"category_aro_accession":"3000077","category_aro_cvterm_id":"36216","category_aro_name":"vanY","category_aro_description":"VanY is a D,D-carboxypeptidase that cleaves removes the terminal D-Ala from peptidoglycan for the addition of D-Lactate. The D-Ala-D-Lac peptidoglycan subunits have reduced binding affinity with vancomycin compared to D-Ala-D-Ala.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"35948":{"category_aro_accession":"0000029","category_aro_cvterm_id":"35948","category_aro_name":"teicoplanin","category_aro_description":"Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation  and transpeptidation.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"91":{"model_id":"91","model_name":"gadX","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"615":{"protein_sequence":{"accession":"YP_491919.1","sequence":"MQSLHGNCLIAYARHKYILTMVNGEYRYFNGGDLVFADASQIRVDKCVENFVFVSRDTLSLFLPMLKEEALNLHAHKKVSSLLVHHCSRDIPVFQEVAQLSQNKNLRYAEMLRKRALIFALLSVFLEDEHFIPLLLNVLQPNMRTRVCTVINNNIAHEWTLARIASELLMSPSLLKKKLREEETSYSQLLTECRMQRALQLIVIHGFSIKRVAVSCGYHSVSYFIYVFRNYYGMTPTEYQERSAQRLSNRDSAASIVAQGNFYGTDRSAEGIRL"},"dna_sequence":{"accession":"NC_007779","fmin":"3974604","fmax":"3975429","strand":"+","sequence":"ATGCAATCACTACATGGGAATTGTCTAATTGCGTATGCAAGACATAAATATATTCTCACCATGGTTAATGGTGAATATCGCTATTTTAATGGCGGTGACCTGGTTTTTGCGGATGCAAGCCAAATTCGAGTAGATAAGTGTGTTGAAAATTTTGTATTCGTGTCAAGGGACACGCTTTCATTATTTCTCCCGATGCTCAAGGAGGAGGCATTAAATCTTCATGCACATAAAAAAGTTTCTTCATTACTCGTTCATCACTGTAGTAGAGATATTCCTGTTTTTCAGGAAGTTGCGCAACTATCGCAGAATAAGAATCTTCGCTATGCAGAAATGCTACGTAAAAGAGCATTAATCTTTGCGTTGTTATCTGTTTTTCTTGAGGATGAGCACTTTATACCGCTGCTTCTGAACGTTTTACAACCGAACATGCGAACACGAGTTTGTACGGTTATCAATAATAATATCGCCCATGAGTGGACACTAGCCCGAATCGCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCAATTAAGCGAGTTGCAGTATCCTGTGGATATCACAGCGTGTCGTATTTCATTTACGTCTTTCGAAATTATTATGGGATGACGCCCACAGAGTATCAGGAGCGATCGGCGCAGAGATTGTCGAACCGTGACTCGGCGGCAAGTATTGTTGCGCAAGGGAATTTTTACGGCACTGACCGTTCTGCGGAAGGAATAAGATTATAGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36839","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. W3110","NCBI_taxonomy_id":"316407"}}}},"ARO_accession":"3000508","ARO_id":"36647","ARO_name":"gadX","ARO_description":"GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35930":{"category_aro_accession":"0000011","category_aro_cvterm_id":"35930","category_aro_name":"cloxacillin","category_aro_description":"Cloxacillin is a semisynthetic, isoxazolyl penicillin derivative in the beta-lactam class of antibiotics. It interferes with peptidogylcan synthesis and is commonly used for treating penicillin-resistant Staphylococcus aureus infections.","category_aro_class_name":"Antibiotic"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"92":{"model_id":"92","model_name":"CTX-M-42","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1742":{"protein_sequence":{"accession":"AAY84742.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTETTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"DQ061159","fmin":"346","fmax":"1222","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGACGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001904","ARO_id":"38304","ARO_name":"CTX-M-42","ARO_description":"CTX-M-42 is a beta-lactamase found in Escherichia coli","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"93":{"model_id":"93","model_name":"SHV-105","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1941":{"protein_sequence":{"accession":"ACI22621.1","sequence":"MRYFRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGSVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIDDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASKRGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"FJ194944","fmin":"46","fmax":"907","strand":"+","sequence":"ATGCGTTATTTTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCAGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGACGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCAAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGGATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001154","ARO_id":"37534","ARO_name":"SHV-105","ARO_description":"SHV-105 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"94":{"model_id":"94","model_name":"CMY-79","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1897":{"protein_sequence":{"accession":"AFK73446.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDDITDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQDKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPVPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"JQ733576","fmin":"1027","fmax":"2173","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCACTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGACATTACGGATAAAGCCGCATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGCGGTGAAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAACTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTGCACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGATAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGTACCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACAGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATAGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGCGTCGAGGCGGCCTGGCGCATTCTTGAAAAACTGCAATAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002092","ARO_id":"38492","ARO_name":"CMY-79","ARO_description":"CMY-79 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"95":{"model_id":"95","model_name":"CMY-56","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1196":{"protein_sequence":{"accession":"ADT91162.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKTDSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"HQ322613","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAACTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002067","ARO_id":"38467","ARO_name":"CMY-56","ARO_description":"CMY-56 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"96":{"model_id":"96","model_name":"OXA-426","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1216":{"protein_sequence":{"accession":"AJA32744.1","sequence":"MNIKALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDFARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQEVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KM588354","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATTTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTAGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAGAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003149","ARO_id":"39726","ARO_name":"OXA-426","ARO_description":"OXA-426 is a beta-lactamase found in clinical isolates of Acinetobacter baumannii. It is carbapenem resistant","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"97":{"model_id":"97","model_name":"vanXYC","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"39":{"protein_sequence":{"accession":"AAF61331.1","sequence":"MNTLQLINKNHPLKKNQEPPHLVLAPFSDHDVYLQPEVAKQWERLVRATGLEKDIRLVDGYRTEKEQRRLWEYSLKENGLAYTKQFVALPGCSEHQIGLAIDVGLKKQEDDDLICPHFRDSAAADLFMQQMMNYGFILRYPEDKQEITGISYEPWHFRYVGLPHSQVITAQKWTLEEYHDYLAQTVRQFA"},"dna_sequence":{"accession":"AF162694","fmin":"2438","fmax":"3011","strand":"+","sequence":"ATGAACACATTACAATTGATCAATAAAAACCATCCATTGAAAAAAAATCAAGAGCCCCCGCACTTAGTGCTAGCTCCTTTTAGCGATCACGATGTTTACCTGCAGCCAGAAGTGGCAAAACAATGGGAACGACTCGTACGAGCAACCGGACTAGAAAAGGACATTCGTCTGGTAGATGGGTATCGTACGGAAAAAGAACAGCGACGCTTGTGGGAGTATTCTCTAAAAGAAAACGGGTTAGCTTATACCAAACAATTCGTTGCTTTGCCAGGTTGCAGTGAACATCAAATCGGTCTGGCCATTGATGTAGGACTAAAGAAACAAGAAGATGATGATCTTATCTGCCCTCATTTTCGAGATAGTGCTGCTGCTGATTTATTTATGCAGCAGATGATGAATTATGGCTTTATTCTACGCTATCCGGAAGATAAACAAGAGATCACCGGTATCAGTTATGAACCTTGGCATTTTCGTTATGTCGGGCTTCCCCATAGCCAAGTCATCACTGCCCAAAAATGGACTCTGGAAGAATACCATGATTACTTGGCTCAGACAGTGAGGCAGTTCGCATGAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36781","NCBI_taxonomy_name":"Enterococcus gallinarum","NCBI_taxonomy_id":"1353"}}}},"ARO_accession":"3002966","ARO_id":"39400","ARO_name":"vanXYC","ARO_description":"vanXYC is a vanXY variant found in the vanC gene cluster","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36635":{"category_aro_accession":"3000496","category_aro_cvterm_id":"36635","category_aro_name":"vanXY","category_aro_description":"VanXY is a protein with both D,D-carboxypeptidase and D,D-dipeptidase activity, found in Enterococcus gallinarum. It cleaves and removes the terminal D-Ala of peptidoglycan subunits for the incorporation of D-Ser by VanC. D-Ala-D-Ser has low binding affinity with vancomycin.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"98":{"model_id":"98","model_name":"CMY-48","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1896":{"protein_sequence":{"accession":"ADP02979.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"HM569226","fmin":"1039","fmax":"2185","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCGCTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGCGGTGAAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGTTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACAGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATAGTGATGCTGGCAAACAAAAGCTATCCTAACCCGGCTCGCGTAGAGGCGGCCTGGCGCATTCTTGAAAAACTGCAATAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002059","ARO_id":"38459","ARO_name":"CMY-48","ARO_description":"CMY-48 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"99":{"model_id":"99","model_name":"QnrB38","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"715":{"protein_sequence":{"accession":"AEL00461.1","sequence":"MALALIGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAILKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKAVLEKCELWENRWMGTQVLGATLSGSDLSGGEFSSFDWRTANFTHCDLTNSELGDLDIRGVDLQGVKLDSYQAALLMERLGIAVIG"},"dna_sequence":{"accession":"JN173060","fmin":"2306","fmax":"2951","strand":"+","sequence":"ATGGCTCTGGCATTAATTGGCGAAAAAATTGACAGAAACCGCTTCACCGGTGAAAAAGTTGAAAATAGCACTTTTTTTAACTGTGATTTTTCGGGTGCCGACCTTAGCGGTACTGAATTTATCGGCTGTCAGTTCTATGATCGAGAAAGCCAGAAAGGGTGCAATTTCAGTCGCGCAATACTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAACGTCAGTGCGTTGGGCATAGAAATTCGCCACTGCCGCGCACAGGGTGCAGATTTTCGCGGCGCAAGTTTCATGAATATGATCACCACGCGCACCTGGTTTTGCAGCGCATATATCACTAATACCAATCTAAGCTACGCCAACTTTTCGAAGGCCGTGCTTGAAAAGTGCGAATTGTGGGAAAATCGCTGGATGGGAACTCAGGTACTGGGTGCGACGTTGAGTGGTTCCGATCTCTCCGGTGGCGAGTTTTCGTCGTTCGACTGGCGGACGGCAAATTTCACGCACTGTGATTTGACCAATTCAGAACTGGGTGATTTAGATATTCGGGGCGTCGATTTACAAGGTGTCAAATTGGACAGCTATCAGGCCGCATTGCTCATGGAACGTCTTGGCATCGCTGTCATTGGCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002753","ARO_id":"39187","ARO_name":"QnrB38","ARO_description":"QnrB38 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"101":{"model_id":"101","model_name":"TEM-109","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1397":{"protein_sequence":{"accession":"AAT46413.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMLSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDHWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AY628175","fmin":"210","fmax":"1071","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGCTGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCATTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000972","ARO_id":"37352","ARO_name":"TEM-109","ARO_description":"TEM-109 is an inhibitor-resistant, extended-spectrum beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"102":{"model_id":"102","model_name":"TLA-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"3316":{"protein_sequence":{"accession":"CAG27800.1","sequence":"MNIKYFKFAEKFILLVLIMSFSSLAFCKSDDSLEQRINSIISGKKASVGVAVAGIEDNFSLSINGKKNFPMMSVYKLHIVLAVLNKVDGGSLKLDEKIPLNKKDLHPGTWSPLRDKYPNGGVSIPLSEIIEYTITQSDNNGCDILIALAGGTEAVKRYIISKGISDFDIRATEKECHESWNVQYSNWSTPVSAVALLKKFNDRKILSSVSTEYLMNVMIHTSTGNKRIKGLIPPSADVAHKTGTSGIRNGITPGTNDIGIVTLPNGKHFAIAVFVSDSRENNAANERIIAEISKAAWDYFVKMN"},"dna_sequence":{"accession":"AJ698325","fmin":"14502","fmax":"15417","strand":"-","sequence":"TCAATTCATTTTAACAAAATAATCCCAAGCAGCCTTTGATATTTCAGCAATTATTCTTTCATTTGCCGCATTGTTCTCGCGGGAATCCGACACAAAAACTGCAATCGCAAAATGCTTCCCGTTCGGCAGCGTGACTATTCCGATATCATTAGTTCCTGGAGTAATTCCGTTTCGAATTCCAGATGTTCCGGTTTTATGCGCAACATCAGCACTTGGCGGAATCAGACCCTTTATTCTTTTATTGCCGGTTGAAGTATGAATCATTACATTCATCAGATATTCAGTTGATACAGAAGAAAGGATTTTTCTGTCATTAAACTTCTTTAGAAGAGCCACCGCAGAAACCGGCGTTGACCAGTTCGAATACTGAACATTCCATGACTCGTGGCATTCTTTCTCTGTTGCTCTGATATCAAAATCAGAAATTCCTTTTGATATAATATATCTCTTAACAGCTTCAGTTCCGCCCGCAAGAGCAATCAAAATATCACAGCCGTTGTTGTCGCTTTGAGTGATTGTATATTCTATAATTTCTGAAAGCGGAATGCTCACTCCGCCATTCGGATATTTGTCGCGCAGAGGACTCCAAGTTCCGGGATGAAGATCTTTTTTATTAAGCGGAATTTTTTCATCAAGCTTCAAACTGCCGCCGTCAACTTTGTTCAAAACAGCAAGCACGATATGCAATTTATAAACGCTCATCATCGGAAAATTTTTCTTTCCGTTTATGCTCAGCGAAAAATTATCTTCTATGCCCGCAACAGCAACACCGACTGATGCTTTTTTTCCTGATATGATTGAATTGATGCGCTGTTCGAGAGAATCATCAGACTTGCAGAAAGCTAAAGAAGAAAAAGACATTATAAGAACTAATAAAATGAATTTTTCTGCAAATTTAAAATATTTTATATTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3003203","ARO_id":"39787","ARO_name":"TLA-2","ARO_description":"TLA-2 is a beta-lactamase is present on a plasmid isolated from an unidentified bacterial strain from a waste water treatment plant. The enzyme mostly hydrolyzes cephalosporins.","ARO_category":{"39785":{"category_aro_accession":"3003201","category_aro_cvterm_id":"39785","category_aro_name":"TLA beta-lactamase","category_aro_description":"The TLA beta-lactamases are resistant to expanded-spectrum cephalosporins, aztreonam, ciprofloxacin, and ofloxacin but was susceptible to amikacin, cefotetan, and imipenem.","category_aro_class_name":"AMR Gene Family"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"103":{"model_id":"103","model_name":"SHV-12","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1470":{"protein_sequence":{"accession":"CAI76927.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASKRGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAA"},"dna_sequence":{"accession":"AJ920369","fmin":"23","fmax":"860","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCAAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001071","ARO_id":"37451","ARO_name":"SHV-12","ARO_description":"SHV-12 is an extended-spectrum beta-lactamase found in Acinetobacter baumannii.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35979":{"category_aro_accession":"0000062","category_aro_cvterm_id":"35979","category_aro_name":"ceftriaxone","category_aro_description":"Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"104":{"model_id":"104","model_name":"OXA-61","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1464":{"protein_sequence":{"accession":"AAT01092.1","sequence":"MKKITLFLLFLNLVFGQDKILNNWFKEYNTSGTFVFYDGKTWASNDFSRAMETFSPASTFKIFNALIALDSGVIKTKKEIFYHYRGEKVFLSSWAQDMNLSSAIKYSNVLAFKEVARRIGIKTMQEYLNKLHYGNAKISKIDTFWLDNSLKISAKEQAILLFRLSQNSLPFSQEAMNSVKEMIYLKNMENLELFGKTGFNDGQKIAWIVGFVYLKDENKYKAFALNLDIDKFEDLYKREKILEKYLDELVKKVKNDG"},"dna_sequence":{"accession":"AY587956","fmin":"0","fmax":"774","strand":"+","sequence":"ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGATATTAAATAATTGGTTTAAAGAGTATAATACAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTCAAGGGCTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTCTAATTGCACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGAAAAAGTATTTTTATCTTCTTGGGCGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGGCAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAAACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGACAACTCACTAAAAATAAGCGCTAAAGAACAAGCAATTTTGCTTTTTAGACTTTCACAAAATAGCTTACCTTTTTCTCAAGAAGCAATGAATAGTGTTAAGGAAATGATTTATTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGGGCAAAAAATTGCTTGGATTGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGGCTTTCGCGCTAAATTTAGATATTGATAAATTTGAAGATTTATATAAAAGAGAAAAAATTTTAGAAAAATATTTAGATGAACTTGTAAAAAAAGTTAAAAATGATGGCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3001773","ARO_id":"38173","ARO_name":"OXA-61","ARO_description":"OXA-61 is a beta-lactamase found in Campylobacter jejuni","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"105":{"model_id":"105","model_name":"CARB-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1585":{"protein_sequence":{"accession":"AAC09012.1","sequence":"MKLLLVFSLLIPSMVFANSSKFQQVEQDAKVIEASLSAHIGISVLDTQTGEYWDYNGNQRFPLTSTFKTIACAKLLYDAEQGEINPKSTIEIKKADLVTYSPVIEKQVGQAITLDDACFATMTTSDNAAANIILNALGGPESVTDFLRQIGDKETRLDRIEPELNEGKLGDLRDTTTPNAIVNTLNELLFGSTLSQDGQKKLEYWMVNNQVTGNLLRSVLPEGWNIADRSGAGGFGARSITAVVWSEAQSPIIVSIYLAQTEASIADRNDAIVKIGRSIFEVYSSQSR"},"dna_sequence":{"accession":"U14749","fmin":"690","fmax":"1557","strand":"+","sequence":"ATGAAGCTTTTACTGGTATTTTCGCTTTTAATACCGTCTATGGTGTTTGCAAATAGTTCAAAGTTTCAACAGGTTGAACAAGATGCTAAGGTAATTGAAGCATCTCTTTCTGCGCATATAGGGATTTCTGTTCTTGATACTCAAACTGGAGAGTATTGGGATTACAATGGCAATCAGCGTTTTCCTTTGACAAGTACTTTTAAAACAATAGCTTGTGCTAAATTATTATATGATGCTGAGCAAGGGGAAATAAACCCTAAGAGTACAATTGAGATCAAAAAAGCAGATCTTGTGACCTATTCTCCCGTAATAGAAAAGCAAGTAGGACAAGCAATAACGCTCGATGATGCGTGTTTTGCAACTATGACGACAAGTGATAATGCAGCAGCAAATATCATCCTAAATGCCCTAGGAGGTCCTGAAAGCGTGACGGATTTTCTAAGACAAATCGGAGATAAAGAAACCCGTCTAGACCGTATTGAACCTGAATTAAATGAAGGCAAGCTTGGTGATTTGAGGGATACGACAACTCCTAATGCAATAGTGAATACTTTAAATGAATTATTATTTGGTTCCACATTGTCTCAAGATGGCCAGAAAAAATTAGAGTATTGGATGGTGAATAATCAAGTCACTGGTAATTTATTGCGGTCAGTATTGCCAGAGGGATGGAATATTGCGGATCGTTCAGGTGCTGGCGGATTTGGTGCTCGGAGTATTACAGCCGTTGTTTGGAGTGAAGCTCAATCCCCAATCATAGTTAGTATCTATCTAGCGCAAACAGAGGCTTCAATAGCAGATCGAAATGATGCAATTGTTAAAATTGGTCGTTCAATTTTTGAAGTTTATTCATCACAATCGCGTTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002243","ARO_id":"38643","ARO_name":"CARB-4","ARO_description":"CARB-4 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"106":{"model_id":"106","model_name":"catB9","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"386":{"protein_sequence":{"accession":"AAL68645.1","sequence":"MNFFTSPFSGIPLDQQVTNPNIIVGKHSYYSGYYHGHSFDDCVRYLHPERDDVDKLVIGSFCSIGSGAVFMMAGNQGHRSDWISTFPFFYQDNDNFADARDGFTRSGDTIIGHDVWIGTEAMIMPGVKIGHGAIIASRSVVTKDVAPYEVVGSNPAKHIKFRFSDVEIAMLLEMAWWNWPESWLKESMQSLCSSDIEGLYLNWQSKART"},"dna_sequence":{"accession":"AF462019","fmin":"26","fmax":"656","strand":"+","sequence":"ATGAACTTCTTTACGTCTCCATTTTCTGGGATTCCCTTAGATCAGCAAGTAACAAATCCGAACATTATTGTGGGAAAACACAGTTATTATTCTGGTTATTATCACGGGCACAGTTTCGATGATTGTGTGCGATATTTACATCCAGAAAGAGATGACGTTGATAAGTTAGTCATAGGGAGTTTTTGTTCTATAGGCTCTGGTGCTGTATTTATGATGGCCGGTAATCAAGGGCATCGCAGTGATTGGATAAGTACATTCCCATTTTTCTATCAGGATAATGATAATTTTGCAGATGCACGCGATGGTTTTACGCGTTCAGGAGACACAATTATTGGTCATGATGTGTGGATTGGCACTGAGGCTATGATAATGCCTGGGGTTAAAATTGGACATGGAGCGATAATCGCCAGTCGTTCAGTAGTGACTAAGGATGTTGCACCTTATGAAGTGGTCGGTTCAAATCCTGCTAAACATATCAAGTTTAGATTTTCTGATGTGGAAATAGCGATGTTACTTGAAATGGCATGGTGGAATTGGCCAGAATCGTGGTTGAAAGAGAGTATGCAGTCTCTGTGTTCATCAGACATTGAAGGGCTTTATCTCAATTGGCAGTCAAAAGCACGCACATAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36789","NCBI_taxonomy_name":"Vibrio cholerae","NCBI_taxonomy_id":"666"}}}},"ARO_accession":"3002681","ARO_id":"39115","ARO_name":"catB9","ARO_description":"catB9 is a chromosome-encoded variant of the cat gene found in Vibrio cholerae","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. cat is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Bacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini","category_aro_class_name":"AMR Gene Family"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"107":{"model_id":"107","model_name":"TEM-43","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1403":{"protein_sequence":{"accession":"AAC32889.2","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDHWEPELNEAIPNDERDTTTPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"U95363","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCATTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000912","ARO_id":"37292","ARO_name":"TEM-43","ARO_description":"TEM-43 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"108":{"model_id":"108","model_name":"PDC-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"1940":{"protein_sequence":{"accession":"ACQ82813.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRRYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"FJ666071","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCGCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTATGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002507","ARO_id":"38907","ARO_name":"PDC-8","ARO_description":"PDC-8 is a extended-spectrum beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"109":{"model_id":"109","model_name":"ErmE","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"384":{"protein_sequence":{"accession":"CAB60001.1","sequence":"MSSSDEQPRPRRRNQDRQHPNQNRPVLGRTERDRNRRQFGQNFLRDRKTIARIAETAELRPDLPVLEAGPGEGLLTRELADRARQVTSYEIDPRLAKSLREKLSGHPNIEVVNADFLTAEPPPEPFAFVGAIPYGITSAIVDWCLEAPTIETATMVTQLEFARKRTGDYGRWSRLTVMTWPLFEWEFVEKVDRRLFKPVPKVDSAIMRLRRRAEPLLEGAALERYESMVELCFTGVGGNIQASLLRKYPRRRVEAALDHAGVGGGAVVAYVRPEQWLRLFERLDQKNEPRGGQPQRGRRTGGRDHGDRRTGGQDRGDRRTGGRDHRDRQASGHGDRRSSGRNRDDGRTGEREQGDQGGRRGPSGGGRTGGRPGRRGGPGQR"},"dna_sequence":{"accession":"X51891","fmin":"189","fmax":"1335","strand":"+","sequence":"GTGAGCAGTTCGGACGAGCAGCCGCGCCCGCGTCGCCGCAACCAGGATCGGCAGCACCCCAACCAGAACCGGCCGGTGCTGGGCCGTACCGAGCGGGACCGCAACCGGCGCCAGTTCGGGCAGAACTTCCTCCGCGACCGCAAGACCATCGCGCGCATCGCCGAGACAGCCGAGCTGCGGCCCGATCTGCCGGTGCTGGAAGCCGGCCCCGGCGAAGGGCTGCTCACCAGGGAACTCGCCGACCGCGCGCGTCAGGTGACGTCGTACGAGATCGACCCCCGGCTGGCGAAGTCGTTGCGGGAGAAGCTTTCCGGCCACCCGAACATCGAAGTCGTCAACGCCGACTTCCTCACCGCCGAACCGCCGCCCGAGCCGTTCGCCTTCGTCGGCGCGATCCCCTACGGCATCACCTCGGCGATCGTGGACTGGTGCCTGGAGGCGCCGACGATCGAGACGGCGACGATGGTCACGCAGCTGGAGTTCGCCCGGAAGCGGACCGGCGATTACGGCCGCTGGAGCCGCCTCACGGTGATGACCTGGCCGCTGTTCGAGTGGGAGTTCGTCGAGAAGGTCGACCGCCGGCTGTTCAAGCCGGTGCCCAAGGTCGACTCGGCGATCATGCGGCTGCGCAGGCGCGCCGAACCGCTGCTGGAAGGCGCGGCGCTCGAACGCTACGAGTCGATGGTCGAGCTGTGCTTCACCGGCGTCGGCGGCAACATCCAGGCGTCGCTTCTGCGCAAGTACCCGAGGCGCCGCGTCGAGGCGGCGCTCGACCACGCGGGGGTCGGGGGCGGCGCCGTGGTCGCCTACGTCCGGCCGGAGCAGTGGCTCCGGCTGTTCGAGCGGCTGGATCAGAAGAACGAACCGAGGGGTGGGCAGCCCCAGCGGGGCAGGCGAACCGGCGGACGGGACCACGGGGACCGGCGAACCGGCGGGCAGGATCGCGGCGATCGGCGAACCGGCGGCCGCGACCACAGGGACCGGCAAGCCAGCGGCCACGGCGATCGTCGCAGCAGCGGACGCAATCGCGACGACGGACGAACCGGCGAGCGCGAGCAGGGGGACCAAGGCGGGCGGCGGGGGCCGTCCGGGGGTGGACGGACCGGCGGACGTCCAGGGCGACGCGGCGGACCCGGGCAGCGGTAGT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36902","NCBI_taxonomy_name":"Saccharopolyspora erythraea NRRL 2338","NCBI_taxonomy_id":"405948"}}}},"ARO_accession":"3000326","ARO_id":"36465","ARO_name":"ErmE","ARO_description":"ErmE is a methyltransferase found in the erythromycin producer Saccharopolyspora erythraea. Like other Erm enzymes, it catalyzes the methylation of A2058 of the 23S ribosomal RNA. The gene is found within the erythromycin biosynthetic cluster and is responsible for self-resistance.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35946":{"category_aro_accession":"0000027","category_aro_cvterm_id":"35946","category_aro_name":"roxithromycin","category_aro_description":"Roxithromycin is a semi-synthetic, 14-carbon ring macrolide antibiotic derived from erythromycin. It is used to treat respiratory tract, urinary and soft tissue infections. Roxithromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35974":{"category_aro_accession":"0000057","category_aro_cvterm_id":"35974","category_aro_name":"telithromycin","category_aro_description":"Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36315":{"category_aro_accession":"3000176","category_aro_cvterm_id":"36315","category_aro_name":"dirithromycin","category_aro_description":"Dirithromycin is an oxazine derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome to inhibit bacterial protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin 1A is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"vernamycin B-gamma","category_aro_description":"Vernamycin B-gamma is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"110":{"model_id":"110","model_name":"AAC(6')-Iu","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"27":{"protein_sequence":{"accession":"AAD03493.1","sequence":"MNILPISESQLSDWLALRSLLWPDHEEAHLQEMRQLLKQTDTLQLLAYSETQHAIAMLEASIRHEYVNGTQTSPVAFLEGIYVLPEYRRSGIATQLVQCVEEWAKQFACTEFASDAALDNTISHAMHRALGFHETERVVYFKKNIS"},"dna_sequence":{"accession":"AF031329","fmin":"0","fmax":"441","strand":"+","sequence":"ATGAATATTTTGCCGATATCTGAATCACAATTATCAGATTGGCTAGCATTAAGAAGCTTACTCTGGCCTGATCATGAAGAAGCACATTTACAGGAAATGCGCCAACTACTTAAACAAACCGATACTTTACAGTTATTGGCGTATTCGGAAACGCAACATGCGATAGCAATGTTGGAAGCATCGATTCGGCATGAATATGTGAATGGTACGCAAACCTCACCCGTGGCTTTTCTTGAAGGGATTTATGTATTGCCTGAATATCGACGTTCAGGCATCGCGACCCAGTTGGTTCAGTGCGTAGAGGAATGGGCGAAACAATTTGCATGTACTGAGTTTGCTTCAGATGCAGCGCTTGACAATACGATTAGCCATGCAATGCATCGAGCACTGGGTTTTCATGAAACTGAACGCGTGGTTTATTTTAAGAAAAATATCAGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39516","NCBI_taxonomy_name":"Acinetobacter genomosp. 17BJ","NCBI_taxonomy_id":"70348"}}}},"ARO_accession":"3002565","ARO_id":"38965","ARO_name":"AAC(6')-Iu","ARO_description":"AAC(6')-Iu is a chromosomal-encoded aminoglycoside acetyltransferase in Acinetobacter genomosp. 17","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"112":{"model_id":"112","model_name":"FosA5","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"3293":{"protein_sequence":{"accession":"AJE60855.1","sequence":"MLSGLNHLTLAVSQLAPSVAFYQQLLGMMLHARWDSGAYLSCGDLWLCLSLDPQRRVTPPEESDYTHYAFSISEADFASFAARLEAAGVAVWKLNRSEGASHYFLDPDGHKLELHVGSLAQRLAACREQPYKGMVFFAE"},"dna_sequence":{"accession":"KP143090","fmin":"1199","fmax":"1619","strand":"-","sequence":"TCACTCAGCAAAAAACACCATCCCCTTATACGGCTGCTCGCGGCAGGCGGCCAGACGCTGGGCGAGACTGCCGACGTGCAGCTCCAGCTTATGGCCATCGGGATCGAGGAAATAGTGCGAAGCGCCTTCGCTACGGTTCAGCTTCCAGACCGCTACGCCGGCAGCCTCAAGGCGGGCGGCGAAGCTAGCAAAATCGGCTTCGCTAATACTAAACGCATAATGGGTGTAGTCGCTCTCTTCCGGCGGAGTAACGCGCCGCTGCGGATCCAGCGACAGGCACAGCCACAGATCGCCGCAGGAGAGATAAGCCCCGCTGTCCCAGCGGGCATGCAGCATCATGCCCAGCAGCTGCTGATAAAACGCCACGCTCGGCGCCAGCTGGCTGACTGCCAGGGTCAGGTGATTCAGTCCACTCAGCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3003209","ARO_id":"39793","ARO_name":"FosA5","ARO_description":"fosA5 is a fosfomycin resistance gene isolated from clinical strain of Escherichia coli E265. It is susceptible to amikacin, tetracycline and imipenem, and resistant to sulphonamide, cephalosporins, gentamicin, ciprofloxacin, chloramphenicol and streptomycin","ARO_category":{"36272":{"category_aro_accession":"3000133","category_aro_cvterm_id":"36272","category_aro_name":"fosfomycin thiol transferase","category_aro_description":"Catalyzes the addition of a thiol group from a nucleophilic molecule to fosfomycin.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"113":{"model_id":"113","model_name":"VEB-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1576":{"protein_sequence":{"accession":"ABN80430.1","sequence":"MKIVKRILLVLLSLFFTVEYSNAQTDNLTLKIENVLKAKNARIGVAIFNSNEKDTLKINNDFHFPMQSVMKFPIALAVLSEIDKGNLSFEQKIEITPQDLLPKMWSPIKEEFPNGTTLTIEQILNYTVSESDNIGCDILLKLIGGTDSVQKFLNANHFTDISIKANEEQMHKDWNTQYQNWATPTAMNKLLIDTYNNKNQLLSKKSYDFIWKIMRETTTGSNRLKGQLPKNTIVAHKTGTSGINNGIAAATNDVGVITLPNGQLIFISVFVAESKETSEINEKIISDIAKITWNYYLNK"},"dna_sequence":{"accession":"EF420108","fmin":"37","fmax":"937","strand":"+","sequence":"ATGAAAATCGTAAAAAGGATATTATTAGTATTGTTAAGTTTATTTTTTACAGTTGAGTATTCAAATGCTCAAACTGACAACTTAACTTTGAAAATTGAGAATGTTTTAAAGGCAAAAAATGCCAGAATAGGAGTAGCAATATTCAACAGCAATGAGAAGGATACTTTGAAGATTAATAACGACTTCCATTTCCCGATGCAAAGCGTTATGAAATTTCCGATTGCTTTAGCCGTTTTGTCTGAGATAGATAAAGGGAATCTTTCTTTTGAACAAAAAATAGAGATTACCCCTCAAGACCTTTTGCCTAAAATGTGGAGTCCGATTAAAGAGGAATTCCCTAATGGAACAACTTTGACGATTGAACAAATACTAAATTATACAGTATCAGAGAGCGACAATATTGGTTGTGATATTTTGCTAAAATTAATCGGAGGAACTGATTCTGTTCAAAAATTCTTGAATGCTAATCATTTCACTGATATTTCAATCAAAGCAAACGAAGAACAAATGCACAAGGATTGGAATACCCAATATCAAAATTGGGCAACCCCAACAGCGATGAACAAACTGTTAATAGATACTTATAATAATAAGAACCAATTACTTTCTAAAAAAAGTTATGATTTTATTTGGAAAATTATGAGAGAAACAACAACAGGAAGTAACCGATTAAAAGGACAATTACCAAAGAATACAATTGTTGCTCATAAAACAGGGACTTCCGGAATAAATAATGGAATTGCAGCAGCCACTAATGATGTTGGGGTAATTACTTTACCGAATGGACAATTAATTTTTATAAGCGTATTTGTTGCAGAGTCCAAAGAAACTTCGGAAATTAATGAAAAGATTATTTCAGACATTGCAAAAATAACGTGGAATTACTATTTGAATAAATAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002375","ARO_id":"38775","ARO_name":"VEB-5","ARO_description":"VEB-5 is a beta-lactamase. From the Lahey list of VEB beta-lactamases.","ARO_category":{"36182":{"category_aro_accession":"3000043","category_aro_cvterm_id":"36182","category_aro_name":"VEB beta-lactamase","category_aro_description":"VEB beta-lactamases or Vietnamese extended-spectrum beta-lactamases are class A beta-lactamases that confer high-level resistance to oxyimino cephalosporins and to aztreonam","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"114":{"model_id":"114","model_name":"dfrA13","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"491":{"protein_sequence":{"accession":"CAA90683.1","sequence":"MNPESVRIYLVAAMGANRVIGNGPDIPWKIPGEQKIFRRLTESKVVVMGRKTFESIGKPLPNRHTVVLSRQAGYSAPGCAVVSTLSHVSPSTAEHGKELYVARGAEVYALALPHANGVFLSEVHQTFEGDAFFPVLNAAEFEVVSSETIQGTITYTHSVYARRNG"},"dna_sequence":{"accession":"Z50802","fmin":"717","fmax":"1215","strand":"+","sequence":"ATGAACCCGGAATCGGTCCGCATTTATCTGGTCGCTGCCATGGGTGCCAATCGGGTTATTGGCAATGGTCCCGATATCCCCTGGAAAATCCCAGGTGAGCAGAAGATTTTTCGCAGGCTCACCGAGAGCAAAGTGGTCGTTATGGGCCGCAAGACATTTGAGTCCATAGGCAAGCCCTTACCAAACCGCCACACAGTGGTGCTCTCGCGCCAAGCTGGTTATAGCGCTCCTGGTTGTGCAGTTGTTTCAACGCTGTCACACGTATCGCCATCGACAGCCGAACACGGCAAAGAACTCTACGTAGCGCGCGGAGCCGAGGTATATGCGCTGGCGCTACCGCATGCCAACGGCGTCTTTCTATCTGAGGTACATCAAACCTTTGAGGGTGACGCCTTCTTCCCAGTGCTTAACGCAGCAGAATTCGAGGTTGTCTCATCCGAAACCATTCAAGGCACAATCACGTACACGCACTCCGTCTATGCGCGTCGTAACGGCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3003012","ARO_id":"39446","ARO_name":"dfrA13","ARO_description":"dfrA13 is an integron-encoded dihydrofolate reductase found in Escherichia coli","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36408":{"category_aro_accession":"3000269","category_aro_cvterm_id":"36408","category_aro_name":"brodimoprim","category_aro_description":"Brodimoprim is a structural derivative of trimethoprim and an inhibitor of bacterial dihydrofolate reductase. The 4-methoxy group of trimethoprim is replaced with a bromine atom.","category_aro_class_name":"Antibiotic"},"36423":{"category_aro_accession":"3000284","category_aro_cvterm_id":"36423","category_aro_name":"tetroxoprim","category_aro_description":"Tetroxoprim is a trimethoprim derivative that inhibits bacterial dihydrofolate reductase.","category_aro_class_name":"Antibiotic"},"36476":{"category_aro_accession":"3000337","category_aro_cvterm_id":"36476","category_aro_name":"iclaprim","category_aro_description":"Iclaprim is a bactericidal compound that inhibits dihydrofolate reductase. It is used against clinically important Gram-positive pathogens, including methicillin-sensitive Staphylococcus aureus and methicillin-resistant S. aureus.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"115":{"model_id":"115","model_name":"TEM-87","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1575":{"protein_sequence":{"accession":"AAG44570.1","sequence":"MSIKHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLHCWEPELNEAIPNDERDTTTPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AF250872","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTAAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTCATTGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3000954","ARO_id":"37334","ARO_name":"TEM-87","ARO_description":"TEM-87 is an extended-spectrum beta-lactamase found in Proteus mirabilis.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"116":{"model_id":"116","model_name":"QnrB18","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"424":{"protein_sequence":{"accession":"CAP45903.1","sequence":"MTPLLYKKTGTNMALALVGEKIDRNRFTGEKIDNSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNASALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"AM919399","fmin":"0","fmax":"681","strand":"+","sequence":"ATGACGCCATTACTGTATAAAAAAACAGGTACAAATATGGCTCTGGCACTCGTTGGCGAAAAAATTGACAGAAACCGTTTCACCGGTGAGAAAATTGATAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCGATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATGCCAGTGCGCTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGCGCAAGTTTTATGAATATGATCACTACTCGCACCTGGTTTTGTAGTGCATATATCACTAACACAAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGCTGGAAAAGTGTGAGCTGTGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGGGACTTAGATATTCGGGGCGTTGATTTACAAGGCGTTAAGTTGGACAACTACCAGGCATCGTTGCTCATGGAGCGACTTGGCATCGCGGTGATTGGTTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002733","ARO_id":"39167","ARO_name":"QnrB18","ARO_description":"QnrB18 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"118":{"model_id":"118","model_name":"LRA-9","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"4284":{"protein_sequence":{"accession":"ACH58989.1","sequence":"MKLRYLLAAALLMTTASAFGADAPKRLPVNITNKEWLMPFPGFKIVGNMYYVGTYDLGCYLIDTGAGLILVNTGIMGSYPLMKASIESLGFKTSDIKIITATHGHSDHVGDIALFKKDAPGATVYMSERDVESLESGGNFDYRRPAPEGRGGLVYDPIHVDVKTKPGDHIKLGNVDMTVLQAYGHTPGATSFSFQQTDAGKTYNVLIVNMNGINAGVKLLGSPHYPTIVEDFKNTIDMQATYKPDIWVSSHSGQFNLHQVYKPGDAYNPARFGDLAAYQKKIATAKANYEKQLAEERAAAK"},"dna_sequence":{"accession":"EU408350","fmin":"11679","fmax":"12585","strand":"-","sequence":"TCACTTCGCCGCGGCGCGTTCTTCCGCGAGCTGCTTTTCGTAATTCGCCTTCGCGGTCGCGATCTTCTTCTGATAGGCCGCGAGGTCGCCGAAGCGCGCCGGATTGTACGCATCGCCCGGCTTATAGACCTGGTGCAGGTTGAACTGCCCGGAATGCGACGACACCCAGATATCGGGCTTGTAGGTCGCCTGCATGTCGATCGTGTTCTTGAAGTCCTCGACGATGGTCGGATAATGCGGCGAGCCCAACAGCTTCACGCCCGCGTTGATGCCGTTCATGTTGACGATGAGGACGTTGTAGGTCTTGCCCGCATCCGTCTGCTGGAACGAGAAGCTCGTCGCGCCCGGCGTGTGGCCATAAGCCTGCAGCACGGTCATGTCGACATTGCCGAGCTTGATGTGATCGCCAGGCTTCGTCTTCACGTCGACATGGATGGGATCGTAGACGAGGCCGCCGCGGCCTTCGGGCGCGGGCCGGCGGTAATCGAAATTGCCGCCGGATTCGAGGCTCTCCACATCGCGCTCGCTCATATACACGGTGGCGCCCGGCGCATCCTTCTTGAACAGCGCGATATCGCCGACATGGTCCGAATGGCCGTGGGTTGCGGTGATGATCTTGATGTCGCTGGTCTTGAAGCCGAGGGATTCGATGCTCGCCTTCATCAGCGGATAGGAACCCATGATCCCGGTGTTGACGAGGATCAGGCCGGCGCCCGTATCGATCAGATAGCAGCCCAGATCATAGGTGCCGACGTAATACATGTTGCCGACGATCTTGAAGCCGGGGAACGGCATCAGCCATTCTTTGTTGGTGATGTTGACCGGCAGGCGCTTGGGCGCGTCCGCGCCGAACGCGCTGGCCGTGGTCATCAGAAGCGCGGCGGCGAGCAGATATCGCAATTTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39083","NCBI_taxonomy_name":"uncultured bacterium BLR9","NCBI_taxonomy_id":"506525"}}}},"ARO_accession":"3002488","ARO_id":"38888","ARO_name":"LRA-9","ARO_description":"LRA-9 is a beta-lactamase isolated from soil samples in Alaska","ARO_category":{"41390":{"category_aro_accession":"3004226","category_aro_cvterm_id":"41390","category_aro_name":"subclass B3 LRA beta-lactamase","category_aro_description":"Beta-lactamases that are part of the LRA gene family and are classified as B3 (metallo-) beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"119":{"model_id":"119","model_name":"VIM-12","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"934":{"protein_sequence":{"accession":"AAZ73123.1","sequence":"MLKVISSLLVYMTASVMAVASPLAHSGEPSGEYPTVNEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEAEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSANVLYGGCAVHELSSTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"DQ143913","fmin":"1774","fmax":"2575","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTACATGACCGCGTCTGTCATGGCTGTCGCAAGTCCGTTAGCCCATTCCGGGGAGCCGAGTGGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGAGAGGTCCGACTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCGGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAAAAGCAAATTGGACTTCCCGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGCAGAGGGGAACGAGATTCCCACGCATTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGCTCTTCTATCCTGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAACGTGCTATACGGTGGTTGTGCCGTTCATGAGTTGTCAAGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAGC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002282","ARO_id":"38682","ARO_name":"VIM-12","ARO_description":"VIM-12 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"120":{"model_id":"120","model_name":"aadA4","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"408":{"protein_sequence":{"accession":"AAN34365.1","sequence":"MGEFFPAQISEQLSHARGVIERHLAATLDTIHLFGSALDGGLKPDSNIDLLVTVSAAPNDSLRQALMLDLLKVSSPPGNGGPWRPLEVTVVARSEVVPWRYPARRGLQFGEWLRHDILSGTFEPAVLDHDLAILLTKARQHSLALLGPSAVTFFEPVPNEHFSKALFDTIAQWNSESDWKGDERNVVLALARIWYSASTGLIAPKDVAAAWVSERLPAEHRPIICKARAAYLGSEDDDLAMRVEETAAFVRYAKATIERILR"},"dna_sequence":{"accession":"AY138986","fmin":"0","fmax":"789","strand":"+","sequence":"ATGGGTGAATTCTTTCCTGCACAAATTTCCGAGCAGCTATCCCACGCTCGCGGGGTGATCGAGCGCCATCTAGCTGCAACGCTGGACACAATCCACCTGTTCGGATCTGCGCTCGATGGAGGGTTGAAGCCGGACAGCAACATCGACTTGCTCGTGACCGTCAGCGCCGCACCTAACGATTCGCTCCGGCAGGCACTAATGCTCGACCTGCTAAAAGTCTCATCACCGCCAGGCAATGGCGGACCATGGCGACCGCTGGAGGTGACTGTTGTCGCTCGAAGCGAAGTAGTGCCCTGGCGCTATCCGGCGCGACGTGGGCTTCAGTTCGGTGAGTGGCTCCGCCACGACATCCTCTCCGGAACGTTCGAGCCTGCCGTTCTGGATCACGATCTTGCGATTTTGCTGACCAAGGCGAGGCAACACAGCCTTGCACTGCTAGGTCCATCCGCAGTCACGTTCTTCGAGCCGGTGCCGAACGAGCATTTTTCCAAGGCGCTTTTCGACACGATTGCCCAGTGGAATTCAGAGTCGGATTGGAAGGGTGACGAGCGGAACGTCGTTCTTGCTCTTGCTCGCATTTGGTACAGTGCTTCAACGGGTCTCATTGCTCCTAAGGACGTTGCTGCCGCATGGGTATCGGAGCGTTTGCCTGCCGAGCATCGGCCCATCATTTGCAAGGCACGCGCGGCGTACCTGGGTAGCGAGGACGACGACCTAGCAATGCGCGTCGAAGAGACGGCTGCGTTCGTTCGATATGCCAAAGCAACGATTGAGAGAATCTTGCGTTGAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3002604","ARO_id":"39004","ARO_name":"aadA4","ARO_description":"aadA4 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids and chromosomes in Bordetella parapertussis and E. coli","ARO_category":{"41439":{"category_aro_accession":"3004275","category_aro_cvterm_id":"41439","category_aro_name":"ANT(3'')","category_aro_description":"Nucleotidylylation of streptomycin at the hydroxyl group at position 3''","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"121":{"model_id":"121","model_name":"mdtF","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1850"}},"model_sequences":{"sequence":{"286":{"protein_sequence":{"accession":"AAC76539.1","sequence":"MANYFIDRPVFAWVLAIIMMLAGGLAIMNLPVAQYPQIAPPTITVSATYPGADAQTVEDSVTQVIEQNMNGLDGLMYMSSTSDAAGNASITLTFETGTSPDIAQVQVQNKLQLAMPSLPEAVQQQGISVDKSSSNILMVAAFISDNGSLNQYDIADYVASNIKDPLSRTAGVGSVQLFGSEYAMRIWLDPQKLNKYNLVPSDVISQIKVQNNQISGGQLGGMPQAADQQLNASIIVQTRLQTPEEFGKILLKVQQDGSQVLLRDVARVELGAEDYSTVARYNGKPAAGIAIKLAAGANALDTSRAVKEELNRLSAYFPASLKTVYPYDTTPFIEISIQEVFKTLVEAIILVFLVMYLFLQNFRATIIPTIAVPVVILGTFAILSAVGFTINTLTMFGMVLAIGLLVDDAIVVVENVERVIAEDKLPPKEATHKSMGQIQRALVGIAVVLSAVFMPMAFMSGATGEIYRQFSITLISSMLLSVFVAMSLTPALCATILKAAPEGGHKPNALFARFNTLFEKSTQHYTDSTRSLLRCTGRYMVVYLLICAGMAVLFLRTPTSFLPEEDQGVFMTTAQLPSGATMVNTTKVLQQVTDYYLTKEKDNVQSVFTVGGFGFSGQGQNNGLAFISLKPWSERVGEENSVTAIIQRAMIALSSINKAVVFPFNLPAVAELGTASGFDMELLDNGNLGHEKLTQARNELLSLAAQSPNQVTGVRPNGLEDTPMFKVNVNAAKAEAMGVALSDINQTISTAFGSSYVNDFLNQGRVKKVYVQAGTPFRMLPDNINQWYVRNASGTMAPLSAYSSTEWTYGSPRLERYNGIPSMEILGEAAAGKSTGDAMKFMADLVAKLPAGVGYSWTGLSYQEALSSNQAPALYAISLVVVFLALAALYESWSIPFSVMLVVPLGVVGALLATDLRGLSNDVYFQVGLLTTIGLSAKNAILIVEFAVEMMQKEGKTPIEAIIEAARMRLRPILMTSLAFILGVLPLVISHGAGSGAQNAVGTGVMGGMFAATVLAIYFVPVFFVVVEHLFARFKKA"},"dna_sequence":{"accession":"U00096","fmin":"3660413","fmax":"3663527","strand":"+","sequence":"ATGGCTAACTATTTTATTGATCGCCCGGTTTTTGCCTGGGTACTTGCCATTATTATGATGCTTGCAGGTGGTCTGGCGATCATGAACTTACCGGTTGCGCAGTATCCGCAGATTGCGCCACCGACCATTACCGTCAGCGCTACCTATCCAGGTGCCGATGCGCAAACGGTAGAAGACTCGGTCACTCAGGTGATTGAGCAAAATATGAATGGGCTTGATGGCCTGATGTACATGTCTTCAACCAGTGATGCGGCGGGCAATGCCTCTATCACTCTGACCTTCGAGACTGGGACATCTCCTGATATCGCACAGGTTCAAGTGCAAAATAAACTGCAACTCGCTATGCCTTCATTACCTGAAGCAGTGCAGCAGCAGGGGATTAGCGTCGATAAGTCGAGCAGTAATATCCTGATGGTAGCGGCGTTTATTTCTGATAACGGCAGCCTCAACCAGTACGATATCGCGGACTATGTAGCGTCTAATATCAAAGACCCGCTAAGCCGTACCGCGGGCGTTGGTAGCGTACAACTCTTTGGTTCCGAGTATGCCATGCGTATCTGGCTGGACCCGCAAAAACTCAATAAATATAACCTGGTACCTTCCGATGTTATTTCCCAGATTAAGGTGCAAAACAACCAGATTTCCGGTGGTCAACTGGGTGGCATGCCACAGGCGGCAGACCAGCAGCTAAACGCCTCGATCATTGTGCAGACGCGTCTGCAAACGCCGGAAGAATTTGGCAAAATCCTGTTGAAAGTTCAGCAAGATGGTTCGCAAGTGCTGCTGCGTGATGTCGCTCGCGTCGAACTTGGGGCGGAAGATTATTCCACCGTGGCACGCTATAACGGCAAACCTGCTGCCGGGATCGCCATCAAACTGGCTGCCGGAGCAAACGCCCTGGATACCTCGCGGGCAGTCAAAGAGGAACTGAACCGCTTATCAGCCTATTTCCCGGCAAGTCTGAAGACGGTTTATCCTTACGACACCACGCCGTTTATCGAAATTTCTATTCAGGAAGTTTTCAAAACACTGGTTGAGGCTATCATCCTAGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGTGCCACAATCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTGACTATGTTCGGGATGGTGCTGGCGATAGGGTTACTGGTGGATGACGCCATCGTGGTGGTGGAGAACGTCGAGCGTGTCATTGCGGAAGATAAGCTACCGCCGAAGGAAGCGACGCATAAATCGATGGGGCAGATCCAACGTGCGCTGGTCGGTATTGCCGTTGTTCTTTCCGCAGTGTTTATGCCGATGGCCTTTATGAGCGGTGCAACCGGGGAGATCTACCGCCAGTTCTCCATCACGCTGATCTCCTCCATGCTGCTTTCAGTATTTGTGGCAATGAGCCTGACCCCTGCCCTGTGCGCCACCATTCTGAAAGCCGCGCCGGAAGGCGGTCACAAACCTAACGCCCTGTTCGCACGCTTCAACACGCTGTTTGAAAAATCAACTCAACACTATACCGATAGCACCCGCTCGCTGTTGCGTTGTACCGGTCGCTACATGGTGGTCTACCTGCTGATTTGCGCCGGGATGGCGGTGCTGTTCCTGCGCACGCCGACCTCTTTCTTACCAGAAGAGGATCAGGGGGTATTTATGACCACCGCGCAGTTACCTTCCGGTGCCACCATGGTTAACACCACGAAAGTGCTGCAACAGGTGACGGATTATTATCTGACTAAAGAGAAAGATAATGTCCAGTCGGTGTTTACCGTTGGCGGCTTTGGCTTCAGCGGTCAGGGGCAAAACAACGGCCTGGCGTTTATCAGTCTCAAGCCGTGGTCTGAACGTGTCGGTGAGGAAAACTCGGTTACCGCGATCATTCAGCGGGCAATGATTGCGTTAAGCAGTATCAATAAAGCCGTCGTCTTCCCGTTCAACTTACCCGCGGTGGCTGAACTGGGTACCGCGTCAGGTTTTGATATGGAACTGCTGGACAACGGTAACCTGGGGCACGAAAAACTAACCCAGGCGCGAAACGAGCTGTTATCACTGGCAGCGCAATCACCGAATCAGGTCACCGGGGTACGCCCGAACGGCCTGGAAGATACGCCGATGTTCAAAGTGAACGTCAACGCTGCGAAAGCTGAAGCGATGGGCGTGGCGCTGTCTGATATCAACCAGACAATTTCCACCGCCTTCGGCAGCAGCTACGTGAACGACTTCCTCAACCAGGGGCGGGTGAAAAAAGTGTATGTCCAGGCAGGCACGCCGTTCCGTATGTTGCCGGATAACATCAACCAATGGTATGTACGCAACGCCTCTGGCACGATGGCACCGCTTTCTGCCTACTCGTCTACCGAATGGACCTATGGTTCACCGCGACTGGAACGCTACAACGGCATCCCGTCAATGGAGATTTTAGGTGAAGCGGCGGCCGGGAAAAGTACCGGTGACGCCATGAAATTTATGGCAGACCTGGTCGCTAAACTTCCGGCAGGCGTCGGCTACTCATGGACCGGACTATCGTATCAGGAAGCGTTATCCTCAAATCAGGCTCCTGCGCTGTATGCGATTTCACTGGTCGTGGTGTTCCTCGCCCTCGCCGCACTCTATGAGAGCTGGTCAATTCCGTTCTCGGTGATGTTGGTTGTTCCGTTAGGCGTCGTTGGCGCATTACTGGCCACCGATCTGCGCGGCTTAAGTAATGACGTCTACTTCCAGGTTGGTTTGCTGACCACCATCGGGCTTTCCGCCAAAAACGCCATCCTGATTGTCGAATTTGCCGTTGAGATGATGCAGAAAGAAGGGAAAACGCCGATAGAGGCAATCATCGAAGCGGCGCGGATGCGTTTACGCCCAATCCTGATGACCTCTCTGGCCTTTATTCTCGGCGTGCTGCCGCTGGTTATCAGTCATGGTGCCGGTTCTGGCGCGCAAAACGCGGTAGGTACCGGCGTGATGGGCGGGATGTTTGCCGCAACAGTGCTGGCAATTTACTTCGTTCCGGTCTTTTTCGTTGTAGTGGAACATCTCTTTGCCCGCTTTAAAAAAGCGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3000796","ARO_id":"37176","ARO_name":"mdtF","ARO_description":"MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35930":{"category_aro_accession":"0000011","category_aro_cvterm_id":"35930","category_aro_name":"cloxacillin","category_aro_description":"Cloxacillin is a semisynthetic, isoxazolyl penicillin derivative in the beta-lactam class of antibiotics. It interferes with peptidogylcan synthesis and is commonly used for treating penicillin-resistant Staphylococcus aureus infections.","category_aro_class_name":"Antibiotic"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"122":{"model_id":"122","model_name":"VIM-34","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1408":{"protein_sequence":{"accession":"AFN88953.1","sequence":"MLKVISSLLVYMTASVMAVASPLAHSGEPSGEYPTVNEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAISTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEAEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSANVLYGGCAVHELSSTSAGNVADADLAEWPTSVERIQKHYPEAEVVIPGHGLPGGLDLLQHTANVVKAHKNRSVAE"},"dna_sequence":{"accession":"JX013656","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTACATGACCGCGTCTGTCATGGCTGTCGCAAGTCCGTTAGCCCATTCCGGGGAGCCGAGTGGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGAGAGGTCCGACTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCGGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAAAAGCAAATTGGACTTCCCGTAACGCGTGCAATCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGCAGAGGGGAACGAGATTCCCACGCATTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGCTCTTCTATCCTGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAACGTGCTATACGGTGGTTGTGCCGTTCATGAGTTGTCAAGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCGTTGAGCGGATTCAAAAACACTACCCGGAAGCAGAGGTCGTCATTCCCGGGCACGGTCTACCGGGCGGTCTAGACTTGCTCCAGCACACAGCGAACGTTGTCAAAGCACACAAAAATCGCTCAGTCGCCGAGTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002304","ARO_id":"38704","ARO_name":"VIM-34","ARO_description":"VIM-34 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"123":{"model_id":"123","model_name":"SHV-64","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"992":{"protein_sequence":{"accession":"ABA06586.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVLLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASKRGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"DQ174304","fmin":"4","fmax":"865","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTACTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGTCCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCAAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001119","ARO_id":"37499","ARO_name":"SHV-64","ARO_description":"SHV-64 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"124":{"model_id":"124","model_name":"IND-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1261":{"protein_sequence":{"accession":"BAJ05825.1","sequence":"MKKSIRFFIVSILLSPFASAQVKDFVIEPPIKNNLHIYKTFGVFGGKEYSANSMYLVTKKGVVLFDVPWEKVQYQSLMDTIKKRHNLPVVAVFATHSHDDRAGDLSFFNNKGIKTYATAKTNEFLKKDGKATSTEIIKTGKPYRIGGEEFVVDFLGEGHTADNVVVWFPKYNVLDGGCLVKSNSATDLGYIKEANVEQWPKTINKLKAKYSKATLIIPGHDEWKGGGHVEHTLELLNKK"},"dna_sequence":{"accession":"AB529520","fmin":"0","fmax":"720","strand":"+","sequence":"ATGAAAAAAAGCATCCGTTTTTTTATTGTTTCGATATTGTTGAGCCCTTTTGCAAGTGCGCAGGTAAAAGATTTTGTAATAGAACCACCCATCAAAAATAACCTGCATATTTATAAAACTTTTGGAGTATTTGGTGGTAAAGAATATTCTGCAAATTCAATGTATCTGGTTACTAAAAAAGGAGTTGTTCTCTTTGACGTTCCATGGGAAAAAGTACAGTACCAAAGCCTCATGGATACCATTAAAAAACGTCATAATTTACCGGTTGTAGCGGTATTTGCCACACACTCCCATGATGACCGCGCCGGTGACCTTAGCTTTTTCAATAATAAAGGGATTAAAACATATGCAACTGCCAAAACCAACGAGTTCTTGAAAAAAGACGGAAAAGCAACATCCACAGAAATCATCAAAACCGGAAAACCGTACCGCATTGGCGGAGAAGAATTTGTGGTAGATTTTCTTGGTGAAGGGCATACTGCTGATAATGTAGTGGTATGGTTCCCTAAATACAATGTATTGGATGGTGGCTGTCTTGTAAAAAGTAATTCAGCTACTGATTTAGGATATATTAAGGAAGCCAATGTAGAACAGTGGCCCAAAACTATAAATAAATTAAAAGCCAAATATTCTAAAGCAACATTAATTATTCCGGGACATGATGAATGGAAAGGCGGTGGACATGTTGAACACACTTTAGAACTTCTGAATAAAAAATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36916","NCBI_taxonomy_name":"Chryseobacterium indologenes","NCBI_taxonomy_id":"253"}}}},"ARO_accession":"3002263","ARO_id":"38663","ARO_name":"IND-7","ARO_description":"IND-7 is a beta-lactamase found in Chryseobacterium indologenes","ARO_category":{"36199":{"category_aro_accession":"3000060","category_aro_cvterm_id":"36199","category_aro_name":"IND beta-lactamase","category_aro_description":"IND beta-lactamases are class B carbapenem-hydrolyzing beta-lactamases","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"125":{"model_id":"125","model_name":"SHV-182","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"2124":{"protein_sequence":{"accession":"AJO16042.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYTPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"KP050489","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACACGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGTATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001364","ARO_id":"37764","ARO_name":"SHV-182","ARO_description":"From the Lahey list of beta-lactamases.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"126":{"model_id":"126","model_name":"TEM-183","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1647":{"protein_sequence":{"accession":"ADR71220.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWLIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"HQ529916","fmin":"110","fmax":"971","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGCTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001045","ARO_id":"37425","ARO_name":"TEM-183","ARO_description":"TEM-183 is a broad-spectrum beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"127":{"model_id":"127","model_name":"clbB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"4285":{"protein_sequence":{"accession":"YP_002773985.1","sequence":"MKLTSKYETIRRILSECKQPEYRYAQIMDAIFKQNIGEYERMTILPKFLRDELNRILGPNVCSIAPVKELTSKQVSKVLFAIPGDEQVEAVRLTYERGWKSYCISTQCGCGFRCKFCATGTIGLKRNLTADEITDQLLYFRLNGHSLDSISFMGMGEALANPHIFEAMTILTDPYLFGLGHRRITISTIGLLPGIDKLTREFPQVNLTFSLHSPFDDQRSELMPINDRFPVRDVLIALDRHIRETGRKVYIAYILLRGVNDSTAHAEAVAELLRGRGAWEHLYHVNLIPFNSTEVTPDSYRQSDPSRIKAFVRILKSRGISVTVRTQFGSDINAACGQLYRSE"},"dna_sequence":{"accession":"NC_012491","fmin":"4758175","fmax":"4759207","strand":"-","sequence":"TTATTCAGAGCGGTATAACTGGCCGCATGCCGCGTTTATGTCCGATCCGAATTGAGTTCGGACCGTGACGCTTATCCCCCTTGACTTCAAGATCCGAACAAACGCTTTAATCCGCGAAGGATCGGATTGCCGATAGCTGTCTGGCGTAACTTCGGTCGAATTGAATGGAATCAGGTTAACGTGGTAGAGATGTTCCCAAGCTCCCCTTCCCCTTAGCAACTCGGCAACTGCTTCCGCATGCGCTGTCGAGTCGTTTACTCCACGAAGAAGAATATACGCAATATATACCTTTCTCCCTGTTTCCCTGATGTGACGATCCAATGCTATCAGTACGTCACGGACTGGAAATCGGTCGTTGATCGGCATCAGCTCGCTTCGCTGATCGTCGAACGGTGAATGCAGCGAGAAGGTTAGATTGACCTGGGGGAACTCCCGAGTCAGCTTGTCAATCCCCGGCAACAGGCCGATCGTGGAAATCGTAATTCGTCGATGTCCTAAACCGAAGAGATACGGGTCGGTCAATATCGTCATGGCCTCAAAAATATGCGGGTTGGCGAGCGCCTCTCCCATGCCCATGAATGAGATGCTGTCCAAAGAGTGGCCGTTCAAACGAAAGTACAGCAATTGGTCGGTAATTTCGTCGGCGGTCAGATTTCGTTTCAGACCAATGGTACCGGTAGCACAAAACTTGCACCTGAATCCGCAGCCGCACTGTGTGGAAATACAATACGATTTCCACCCCCGTTCATAAGTAAGTCGTACGGCCTCGACCTGTTCGTCGCCCGGAATCGCAAACAGCACCTTGCTAACCTGTTTCGACGTGAGCTCCTTTACCGGAGCGATACTGCAAACGTTCGGTCCAAGTATCCGATTCAACTCGTCGCGCAAAAATTTGGGTAGGATGGTCATCCGTTCGTATTCGCCGATGTTTTGCTTGAAAATGGCGTCCATAATCTGAGCATACCGATACTCAGGCTGCTTGCATTCGGACAAGATTCGCCGAATCGTTTCATATTTCGAGGTTAGTTTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39604","NCBI_taxonomy_name":"Brevibacillus brevis NBRC 100599","NCBI_taxonomy_id":"358681"}}}},"ARO_accession":"3002815","ARO_id":"39249","ARO_name":"clbB","ARO_description":"clbB is a plasmid-encoded cfr gene found in Bacillus brevis","ARO_category":{"36341":{"category_aro_accession":"3000202","category_aro_cvterm_id":"36341","category_aro_name":"Cfr 23S ribosomal RNA methyltransferase","category_aro_description":"Cfr genes produce enzymes which catalyze the methylation of the 23S rRNA subunit at position 8 of adenine-2503. Methylation of 23S rRNA at this site confers resistance to some classes of antibiotics, including streptogramins, chloramphenicols, florfenicols, linezolids and clindamycin.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"35989":{"category_aro_accession":"0000072","category_aro_cvterm_id":"35989","category_aro_name":"linezolid","category_aro_description":"Linezolid is a synthetic antibiotic used for the treatment of serious infections caused by Gram-positive bacteria that are resistant to several other antibiotics. It inhibits protein synthesis by binding to domain V of the 23S rRNA of the 50S subunit of bacterial ribosomes.","category_aro_class_name":"Antibiotic"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37015":{"category_aro_accession":"3000671","category_aro_cvterm_id":"37015","category_aro_name":"tiamulin","category_aro_description":"Tiamulin is a pleuromutilin derivative currently used in veterinary medicine. It binds to the 23 rRNA of the 50S ribosomal subunit to inhibit protein translation.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"36218":{"category_aro_accession":"3000079","category_aro_cvterm_id":"36218","category_aro_name":"oxazolidinone antibiotic","category_aro_description":"Oxazolidinones are a class of synthetic antibiotics discovered the the 1980's.  They inhibit protein synthesis by binding to domain V of the 23S rRNA of the 50S subunit of bacterial ribosomes.  Linezolid is the only member of this class currently in clinical use.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"128":{"model_id":"128","model_name":"srmB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1050"}},"model_sequences":{"sequence":{"189":{"protein_sequence":{"accession":"CAA45050.1","sequence":"MSIAQYALHDITKRYHDCVVLDRVGFSIKPGEKVGVIGDNGSGKSTLLKILAGRVEPDNGALTVVAPGGVGYLAQTLELPLDATVQDAVDLALSDLRELEAAMREAEAELGESDENGSERELSAGLQRYAALVEQYQARGGYEADVRVEVALHGLGLPSLDRDRKLGTLSGGERSRLALAATLASSPELLLLDEPTNDLDDRAMEWLEDHLAGHRGTVIAVTHDRVFLDRLTTTILEVDSGSVTRYGNGYEGYLTAKAVERERRLREYEEWRAELDRNRGLITSNVARMDGIPRKMSLSVFGHGAYRRRGRDHGAMVRIRNAKQRVAQLTENPVHAPADPLSFAARIDTAGPEAEEAVAELTDVRVAGRLAVDSLTIRPGERLLVTGPNGAGKSTLLRVLSGELEPDGGSVRVGCRVGHLRQDETPWAPGLTVLRAFAQGREGYLEDHAEKLLSLGLFSPSDLRRRVKDLSYGQRRRIEIARLVSDPMDLLLLDEPTNHLTPVLVEELEQALADYRGAVVVVTHDRRMRSRFTGARLTMGDGRIAEFSAG"},"dna_sequence":{"accession":"X63451","fmin":"0","fmax":"1653","strand":"+","sequence":"GTGTCGATTGCGCAATACGCCCTACACGACATCACGAAGCGCTACCACGACTGTGTCGTGCTCGACCGGGTCGGTTTCAGCATCAAGCCGGGCGAGAAGGTCGGCGTGATCGGCGACAACGGTTCCGGCAAGTCCACGCTGCTCAAGATCCTCGCCGGCCGCGTGGAGCCCGACAACGGCGCGCTCACCGTGGTCGCTCCCGGCGGCGTCGGCTACCTGGCGCAGACACTGGAACTGCCCCTCGACGCCACCGTCCAGGACGCCGTCGACCTGGCCCTGTCCGACCTGCGCGAGCTCGAAGCGGCGATGCGCGAGGCCGAGGCGGAGCTGGGCGAGAGCGACGAGAACGGCTCCGAGCGCGAGCTGTCCGCCGGCCTCCAGCGCTACGCCGCTCTGGTCGAGCAGTACCAGGCGCGTGGCGGCTACGAGGCCGACGTGCGCGTGGAGGTCGCGCTGCACGGCCTCGGACTGCCGAGCCTGGACCGCGACCGCAAGCTCGGAACCCTCTCCGGTGGCGAACGCTCCCGCCTCGCGCTCGCCGCGACCCTCGCCTCGTCGCCGGAGCTGCTGCTCCTGGACGAACCGACCAACGACCTCGACGACCGGGCGATGGAATGGCTGGAGGACCACCTGGCCGGCCACCGCGGCACGGTGATCGCGGTCACCCACGACCGGGTCTTCCTCGACCGGCTCACCACCACGATCCTGGAGGTCGACTCCGGCAGCGTCACCCGCTACGGCAACGGCTACGAGGGCTACCTGACGGCCAAGGCCGTGGAACGCGAGCGGCGGCTGCGGGAGTACGAGGAGTGGCGTGCCGAACTCGACCGCAACCGCGGGCTGATCACCTCCAACGTGGCGCGGATGGACGGCATCCCGCGCAAGATGTCCCTCTCCGTGTTCGGCCACGGCGCCTACCGCAGGCGAGGGCGCGACCACGGCGCGATGGTGCGGATCCGCAACGCGAAGCAACGCGTGGCGCAGCTGACCGAGAACCCGGTCCACGCTCCCGCCGACCCGTTGTCCTTCGCCGCCCGCATCGACACCGCGGGCCCGGAGGCGGAGGAGGCGGTGGCCGAACTCACCGACGTGCGCGTCGCGGGTCGGCTCGCCGTGGACTCCCTGACGATCCGGCCCGGCGAACGGCTGCTCGTCACAGGTCCCAACGGTGCGGGCAAGTCCACCTTGTTGCGGGTGCTGTCCGGGGAACTGGAGCCGGACGGCGGCTCGGTGCGCGTCGGCTGCCGGGTCGGTCATCTGCGGCAGGACGAGACGCCCTGGGCGCCCGGACTGACCGTGCTGCGGGCCTTCGCCCAGGGCCGGGAGGGCTACCTGGAGGACCACGCGGAGAAACTGCTGTCGCTCGGCCTGTTCAGCCCGTCCGACCTGCGGCGACGCGTGAAGGATCTGTCCTACGGGCAGCGCCGCCGGATCGAGATCGCCCGGCTGGTGAGCGACCCGATGGACCTGCTGCTGCTGGACGAGCCCACCAACCACCTCACCCCGGTGCTGGTGGAGGAGTTGGAGCAGGCACTCGCGGACTACCGCGGCGCCGTCGTGGTCGTCACCCACGACCGTCGGATGCGGTCCCGGTTCACCGGCGCCCGGCTGACCATGGGAGACGGGCGCATCGCCGAGTTCAGCGCCGGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36864","NCBI_taxonomy_name":"Streptomyces ambofaciens","NCBI_taxonomy_id":"1889"}}}},"ARO_accession":"3002828","ARO_id":"39262","ARO_name":"srmB","ARO_description":"srmB is an efflux pump found in Streptomyces ambofaciens that confers resistance to spiramycin","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"129":{"model_id":"129","model_name":"FosX","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"3611":{"protein_sequence":{"accession":"CWV56762.1","sequence":"MISGLSHITLIVKDLNKTTAFLQNIFNAEEIYSSGDKTFSLSKEKFFLIAGLWICIMEGDSLQERTYNHIAFQIQSEEVDEYTERIKALGVEMKPERPRVQGEGRSIYFYDFDNHLFELHAGTLEERLKRYHE"},"dna_sequence":{"accession":"FFFO01000009.1","fmin":"81760","fmax":"82162","strand":"+","sequence":"ATGATTTCAGGATTAAGCCATATCACTTTAATTGTGAAAGATTTGAATAAAACAACTGCTTTCTTACAGAATATTTTTAATGCAGAAGAAATCTATTCTAGTGGCGACAAAACATTTTCGCTTTCCAAAGAAAAATTTTTTCTAATAGCTGGTTTGTGGATTTGCATTATGGAAGGAGATTCTTTACAAGAGCGAACTTACAATCATATTGCTTTCCAAATTCAATCCGAGGAAGTGGATGAATATACTGAGCGGATTAAAGCTCTCGGTGTGGAAATGAAACCAGAACGTCCCAGAGTCCAAGGTGAAGGACGTTCCATTTATTTTTATGATTTTGATAATCATCTGTTTGAATTACACGCTGGTACATTAGAAGAACGCTTAAAAAGGTATCACGAATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36757","NCBI_taxonomy_name":"Listeria monocytogenes","NCBI_taxonomy_id":"1639"}}}},"ARO_accession":"3000198","ARO_id":"36337","ARO_name":"FosX","ARO_description":"FosX is an enzyme used to confer resistance to fosfomycin. It's dependent on the cofactor, manganese (II), and uses water to generate a vicinal diol.","ARO_category":{"36272":{"category_aro_accession":"3000133","category_aro_cvterm_id":"36272","category_aro_name":"fosfomycin thiol transferase","category_aro_description":"Catalyzes the addition of a thiol group from a nucleophilic molecule to fosfomycin.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"130":{"model_id":"130","model_name":"CTX-M-112","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1818":{"protein_sequence":{"accession":"AEM44652.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"JF274246","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGGGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36954","NCBI_taxonomy_name":"Shigella sp. SH257","NCBI_taxonomy_id":"1074435"}}}},"ARO_accession":"3001972","ARO_id":"38372","ARO_name":"CTX-M-112","ARO_description":"CTX-M-112 is a beta-lactamase found in Shigella spp.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"131":{"model_id":"131","model_name":"CTX-M-50","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1169":{"protein_sequence":{"accession":"AAV97955.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVPLIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"AY847146","fmin":"82","fmax":"958","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCCCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001912","ARO_id":"38312","ARO_name":"CTX-M-50","ARO_description":"CTX-M-50 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"132":{"model_id":"132","model_name":"TEM-198","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1571":{"protein_sequence":{"accession":"BAL68178.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQAIMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AB700703","fmin":"161","fmax":"1022","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAATTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001057","ARO_id":"37437","ARO_name":"TEM-198","ARO_description":"TEM-198 is a beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"133":{"model_id":"133","model_name":"arr-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"250"}},"model_sequences":{"sequence":{"682":{"protein_sequence":{"accession":"AGC29882.1","sequence":"MIKDWIPTTHENCKKMQGPFYHGTKAKLSVGELLTTGFNTHFEEGRTLKHVYFSAMLEPAIWGAELAVSLSGLDGRGYIYLVEPTGPFEDDPNLTNKKFPGNPTMSYRTSEPLQIVGVVEEWEGHSAEALKAMLDSLENLERNGLHVIYD"},"dna_sequence":{"accession":"KC199968","fmin":"0","fmax":"453","strand":"+","sequence":"ATGATTAAAGATTGGATTCCAACCACACATGAAAATTGTAAAAAAATGCAGGGACCGTTTTATCATGGCACCAAAGCTAAATTATCGGTAGGTGAACTCCTAACAACTGGGTTCAACACTCATTTTGAAGAGGGTCGCACACTCAAGCACGTTTATTTTTCAGCTATGCTTGAGCCAGCAATTTGGGGGGCTGAACTCGCTGTTTCACTGTCTGGTCTAGATGGCCGGGGATACATATACTTAGTTGAACCAACTGGACCTTTCGAGGATGACCCGAATCTTACCAATAAAAAATTTCCAGGAAATCCAACAATGTCCTATCGAACTTCTGAGCCTCTCCAGATTGTGGGGGTCGTTGAAGAGTGGGAGGGACACTCCGCTGAAGCCCTGAAAGCGATGCTGGATTCCTTGGAGAATCTAGAGCGCAATGGACTTCATGTCATATATGATTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002853","ARO_id":"39287","ARO_name":"arr-8","ARO_description":"arr-8 is an integron-encoded ribosyltransferase found in Klebsiella oxytoca","ARO_category":{"36529":{"category_aro_accession":"3000390","category_aro_cvterm_id":"36529","category_aro_name":"rifampin ADP-ribosyltransferase (Arr)","category_aro_description":"Enzyme responsible for the ADP-ribosylative inactivation of rifampin at the 23-OH position using NAD+.","category_aro_class_name":"AMR Gene Family"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36656":{"category_aro_accession":"3000517","category_aro_cvterm_id":"36656","category_aro_name":"rifaximin","category_aro_description":"Rifaximin is a semi-synthetic rifamycin used to treat traveller's diarrhea. Rifaximin inhibits RNA synthesis by binding to the beta subunit of bacterial RNA polymerase.","category_aro_class_name":"Antibiotic"},"36669":{"category_aro_accession":"3000530","category_aro_cvterm_id":"36669","category_aro_name":"rifabutin","category_aro_description":"Rifabutin is a semisynthetic rifamycin used in tuberculosis therapy. It inhibits DNA-dependent RNA synthesis.","category_aro_class_name":"Antibiotic"},"36673":{"category_aro_accession":"3000534","category_aro_cvterm_id":"36673","category_aro_name":"rifapentine","category_aro_description":"Rifapentine is a semisynthetic rifamycin that inhibits DNA-dependent RNA synthesis. It is often used in the treatment of tuberculosis and leprosy.","category_aro_class_name":"Antibiotic"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"134":{"model_id":"134","model_name":"rgt1438","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"4286":{"protein_sequence":{"accession":"AFO53532.1","sequence":"MRMLLTTYGSRGDVEPLAGLAAGLRKLGVEARVCAPPDEEFAALPARAGVPLIPLGPPVRPVVAGERPPTPQDAFRLAAELVTARFDTLTEAAEGCQAVLATGLMPAGVRDVAEKLGIPYVFACFHIYGLPSRHFPPGARPGTPPAPDGTDHRELWEQDARSVNALYGDALNRHRTGIGLPPVRNVRDHVLTDRPWLAADPVLCPAEGMTEFDLVQTGPWFLPDERPLPAGLEEFLGAGAPPVYVGFGSMGAYAPEGIARVAVEACRAQGRRVVLARGWAGLTPDDGGADCFAVGEVNQQALFRRVAAVVHHGGAGTTTTAARAGAPQVVVPRIADQPYWAERVRDLGIGSAHPDPVVTFDSLSAALTTALAPEVRARARTVAGTIRTDGASVAARLLVETADRAGRPVSP"},"dna_sequence":{"accession":"JX028276","fmin":"35585","fmax":"36821","strand":"-","sequence":"TCACGGGGACACCGGCCGCCCCGCCCGGTCGGCGGTCTCGACGAGGAGCCGCGCGGCCACCGAGGCACCGTCCGTGCGGATGGTGCCCGCCACCGTCCGTGCCCGTGCCCGGACTTCGGGTGCCAGAGCCGTCGTCAGCGCGGCGGACAGGGAGTCGAAGGTCACCACCGGGTCGGGATGAGCCGAGCCGATGCCGAGGTCCCTCACCCTCTCGGCCCAGTACGGCTGGTCCGCGATCCTCGGAACCACCACCTGGGGCGCCCCCGCGCGGGCGGCCGTCGTCGTGGTCCCCGCCCCGCCGTGGTGCACCACGGCGGCCACCCGGCGGAACAGCGCCTGCTGGTTGACCTCGCCGACCGCGAAGCAGTCGGCACCGCCGTCGTCCGGAGTCAGCCCGGCCCACCCGCGAGCGAGGACCACACGGCGCCCCTGCGCACGGCAGGCTTCGACGGCCACCCGGGCGATGCCCTCCGGAGCGTAGGCGCCCATGCTGCCGAAGCCCACGTACACCGGTGGTGCCCCGGCGCCGAGGAACTCCTCCAGCCCGGCGGGCAGCGGACGTTCGTCCGGCAGGAACCACGGTCCGGTCTGTACGAGGTCGAACTCCGTCATCCCCTCCGCGGGACACAGCACCGGGTCCGCTGCGAGCCACGGCCGGTCGGTGAGGACGTGGTCCCGGACGTTCCGCACGGGCGGCAGGCCGATCCCGGTGCGGTGACGGTTGAGGGCGTCGCCGTACAGCGCGTTCACGCTCCGGGCGTCCTGTTCCCACAACTCCCGGTGGTCGGTCCCGTCCGGTGCGGGCGGGGTGCCCGGACGCGCGCCCGGAGGAAAGTGCCGCGACGGCAGCCCGTAGATGTGGAAGCAGGCGAAGACGTAGGGAATCCCCAGCTTCTCGGCCACGTCGCGGACACCGGCCGGCATCAACCCCGTGGCCAGCACCGCCTGACAACCCTCGGCCGCCTCGGTGAGCGTGTCGAAGCGGGCGGTGACCAGTTCGGCGGCGAGCCGGAAGGCGTCCTGAGGTGTCGGTGGCCGCTCACCGGCCACCACCGGACGCACCGGCGGGCCGAGCGGAATCAGCGGAACGCCCGCACGCGCCGGCAACGCCGCGAACTCCTCGTCCGGCGGCGCGCACACCCGCGCCTCCACGCCCAACTTTCGCAATCCCGCCGCGAGTCCGGCCAGCGGCTCGACATCTCCGCGCGATCCGTACGTGGTCAGCAGCATGCGCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39592","NCBI_taxonomy_name":"Streptomyces sp. WAC1438","NCBI_taxonomy_id":"1214076"}}}},"ARO_accession":"3002883","ARO_id":"39317","ARO_name":"rgt1438","ARO_description":"rgt1438 is a glycosyltransferase that confers rifampin resistance in Streptomyces","ARO_category":{"36582":{"category_aro_accession":"3000443","category_aro_cvterm_id":"36582","category_aro_name":"rifampin glycosyltransferase","category_aro_description":"The enzymatic inactivation of rifampin by glycosylation at the 23-OH position.","category_aro_class_name":"AMR Gene Family"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36656":{"category_aro_accession":"3000517","category_aro_cvterm_id":"36656","category_aro_name":"rifaximin","category_aro_description":"Rifaximin is a semi-synthetic rifamycin used to treat traveller's diarrhea. Rifaximin inhibits RNA synthesis by binding to the beta subunit of bacterial RNA polymerase.","category_aro_class_name":"Antibiotic"},"36669":{"category_aro_accession":"3000530","category_aro_cvterm_id":"36669","category_aro_name":"rifabutin","category_aro_description":"Rifabutin is a semisynthetic rifamycin used in tuberculosis therapy. It inhibits DNA-dependent RNA synthesis.","category_aro_class_name":"Antibiotic"},"36673":{"category_aro_accession":"3000534","category_aro_cvterm_id":"36673","category_aro_name":"rifapentine","category_aro_description":"Rifapentine is a semisynthetic rifamycin that inhibits DNA-dependent RNA synthesis. It is often used in the treatment of tuberculosis and leprosy.","category_aro_class_name":"Antibiotic"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"135":{"model_id":"135","model_name":"SME-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"1642":{"protein_sequence":{"accession":"AHV85514.1","sequence":"MSNKVNFKTASFLFSVCLALSAFNAHANKSDAAAKQIKKLEEDFDGRIGVFAIDTGSGNTFGYRSDERFPLCSSFKGFLAAAVLERVQQKKLDINQKVKYESRDLEYHSPITPKYKGSGMTLGDMASAALQYSDNGATNIIMERFLGGPEGMTKFMRSIGDNEFRLDRWELELNTAIPGDKRDTSTPKAVANSLNKLALGNVLNAKVKAIYQNWLKGNTTGDARIRASVPADWVVGDKTGSCGAYGTANDYAVIWPKNRAPLIVSIYTTRKSKDDKHSDKTIAEASRIAIQAID"},"dna_sequence":{"accession":"KJ188748","fmin":"0","fmax":"885","strand":"+","sequence":"ATGTCAAACAAAGTAAATTTTAAAACGGCTTCATTTTTGTTTAGTGTTTGTTTAGCTTTGTCGGCATTTAATGCTCATGCTAACAAAAGTGATGCTGCGGCAAAACAAATAAAAAAATTAGAGGAAGACTTTGATGGGAGGATTGGCGTCTTTGCAATAGATACAGGATCGGGTAATACATTTGGGTATAGATCAGATGAGCGGTTCCCTTTATGCAGTTCATTTAAAGGTTTTTTGGCGGCTGCTGTTTTAGAGAGGGTGCAACAAAAAAAACTAGATATCAACCAAAAGGTTAAATATGAGAGTAGGGATCTAGAATATCATTCACCTATTACACCAAAATATAAAGGCTCAGGTATGACATTAGGTGATATGGCTTCTGCTGCATTGCAATATAGCGACAATGGGGCAACAAATATAATTATGGAACGATTTCTTGGCGGTCCTGAGGGGATGACTAAATTTATGCGTTCTATTGGAGATAATGAGTTTAGGTTAGATCGCTGGGAACTGGAACTTAACACTGCAATCCCAGGAGATAAACGTGACACTTCAACGCCAAAAGCTGTTGCAAATAGTTTGAATAAACTAGCTTTGGGGAATGTTCTCAATGCTAAAGTGAAAGCGATTTATCAAAATTGGTTAAAAGGTAATACAACTGGTGATGCTCGAATTCGTGCTAGTGTTCCTGCTGATTGGGTTGTAGGTGACAAAACTGGGAGCTGTGGGGCATATGGTACTGCGAATGATTATGCCGTCATTTGGCCTAAAAATAGAGCACCATTAATTGTCTCTATATATACAACACGAAAATCGAAAGATGATAAGCACAGTGATAAAACTATTGCGGAAGCATCACGTATTGCAATTCAGGCAATTGATTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36783","NCBI_taxonomy_name":"Serratia marcescens","NCBI_taxonomy_id":"615"}}}},"ARO_accession":"3002383","ARO_id":"38783","ARO_name":"SME-5","ARO_description":"SME-5 is a beta-lactamase. From the Lahey list of SME beta-lactamases.","ARO_category":{"36194":{"category_aro_accession":"3000055","category_aro_cvterm_id":"36194","category_aro_name":"SME beta-lactamase","category_aro_description":"SME beta-lactamases are chromosome-mediated class A beta-lactamases that hydrolyze carbapenems in Serratia marcescens.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"136":{"model_id":"136","model_name":"CMY-9","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1363":{"protein_sequence":{"accession":"BAB72158.1","sequence":"MQQRQSILWGAVATLMWAGLAHAGEASPVDPLRPVVDASIQPLLKEHRIPGMAVAVLKDGKAHYFNYGVANRESGASVSEQTLFDIGSVSKTLTATLGAYAVVKGAMQLDDKASRHAPWLKGSVFDSITMGELATYSAGGLPLQFPEEVDSSEKMRAYYRQWAPVYSPGSHRQYSNPSIGLFGHLAASSLKQPFAQLMEQTLLPGLGMHHTYVNVPKQAMASYAYGYSKEDKPIRVNPGMLADEAYGIKTSSADLLAFVKANIGGVDDKALQQAISLTHKGHYSVGGMTQGLGWESYAYPVTEQTLLAGNSAKVILEANPTAAPRESGSQVLFNKTGSTNGFGAYVAFVPARGIGIVMLANRNYPIPARVKAAHAILAQLAG"},"dna_sequence":{"accession":"AB061794","fmin":"6017","fmax":"7166","strand":"+","sequence":"ATGCAACAACGACAATCCATCCTGTGGGGGGCCGTGGCCACCCTGATGTGGGCCGGTCTGGCCCATGCAGGTGAGGCTTCACCGGTCGATCCCCTGCGCCCCGTGGTGGATGCCAGCATCCAGCCGCTGCTCAAGGAGCACAGGATCCCGGGCATGGCGGTGGCCGTGCTCAAGGATGGCAAGGCCCACTATTTCAATTACGGGGTGGCCAACCGGGAGAGCGGGGCCAGCGTCAGCGAGCAGACCCTGTTCGATATAGGATCCGTGAGCAAGACCCTGACTGCGACCCTGGGGGCCTATGCGGTGGTCAAGGGAGCGATGCAGCTGGATGACAAGGCGAGCCGGCACGCGCCCTGGCTCAAGGGATCCGTCTTTGACAGCATCACCATGGGGGAGCTTGCCACCTACAGCGCCGGAGGCCTGCCACTGCAATTCCCCGAGGAGGTGGATTCATCCGAGAAGATGCGCGCCTACTACCGCCAGTGGGCCCCTGTCTATTCGCCGGGCTCCCATCGCCAGTACTCCAACCCCAGCATAGGGCTGTTCGGCCACCTGGCGGCGAGCAGCCTGAAGCAGCCATTTGCCCAGTTGATGGAGCAGACCCTGCTGCCCGGGCTCGGCATGCACCACACCTATGTCAATGTGCCGAAGCAGGCCATGGCGAGTTATGCCTATGGCTATTCGAAAGAGGACAAGCCCATCCGGGTCAACCCTGGCATGCTGGCGGACGAGGCCTACGGCATCAAGACCAGCTCGGCGGATCTGCTCGCCTTCGTGAAGGCCAACATCGGCGGGGTTGATGACAAGGCGTTGCAGCAGGCCATCTCCCTGACCCACAAAGGGCATTACTCGGTAGGCGGGATGACCCAGGGGCTGGGTTGGGAGAGTTACGCCTATCCCGTCACCGAGCAGACATTGCTGGCGGGCAATTCGGCCAAGGTGATCCTCGAAGCCAATCCGACGGCGGCTCCCCGGGAGTCGGGGAGCCAGGTGCTCTTCAACAAGACCGGCTCGACCAATGGCTTTGGCGCCTATGTGGCCTTCGTGCCGGCCAGGGGGATCGGCATCGTCATGCTGGCCAATCGCAACTATCCCATCCCGGCCAGGGTGAAGGCGGCCCACGCCATCCTGGCGCAGTTGGCCGGTTGAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002020","ARO_id":"38420","ARO_name":"CMY-9","ARO_description":"CMY-9 is a beta-lactamase found in Escherichia coli","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"137":{"model_id":"137","model_name":"APH(2'')-Ie","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"18":{"protein_sequence":{"accession":"AAX38178.1","sequence":"MTTYTFDQVEEAIEQLYPDFTINTIEISGEGNDCIAYEINGNFIFKFPKHSRASINLLNEVTVLKTIHNELSLPIPEVVFTGMPSEMCQMSFAGFTKIKGVPLTPLLLKNLPKQSQDQAAKDLARFLSELHSINISGFKSNLVLDFREKINEDNKKIKKLLSRELKGHQMKKVDDFYRDILDNEIYFKYYPCLIHNDFSSDHILFDTEKNTICGIIDFGDAAISDPDNDFISLMEDDEEYGMEFVSKILNHYKHKDIPTVLEKYMMKEKYWSFEKIIYGKEYGYMDWYEEGLNEIRSIKIK"},"dna_sequence":{"accession":"AY939911","fmin":"3535","fmax":"4441","strand":"+","sequence":"ATGACAACTTATACTTTCGACCAGGTAGAAGAGGCAATAGAGCAGTTATATCCTGATTTTACTATCAATACAATAGAGATTTCAGGAGAAGGCAATGACTGTATTGCATATGAAATAAACGGGAATTTTATTTTTAAATTTCCAAAGCATTCAAGAGCTTCGATTAATCTCTTGAATGAAGTAACCGTACTCAAAACAATCCACAATGAATTATCACTACCCATTCCCGAGGTGGTTTTTACAGGAATGCCATCAGAAATGTGCCAAATGTCTTTCGCAGGTTTTACAAAAATTAAAGGAGTACCTTTGACACCTCTTCTACTCAAAAATCTGCCGAAGCAATCTCAAGATCAGGCAGCTAAGGACCTGGCCCGATTTTTAAGTGAACTTCACAGCATAAATATCTCTGGATTCAAAAGTAATCTGGTATTAGATTTTCGAGAGAAGATAAATGAAGATAATAAAAAAATCAAAAAGTTACTATCCAGGGAATTAAAGGGTCACCAGATGAAGAAAGTGGATGATTTTTACAGGGATATTCTAGACAACGAAATCTACTTCAAATACTATCCTTGTCTTATTCATAACGATTTCAGCAGCGATCATATTTTATTTGATACCGAAAAAAATACCATTTGTGGAATAATCGATTTTGGAGATGCAGCTATTTCTGATCCCGACAATGATTTTATAAGTTTGATGGAAGATGATGAAGAGTACGGCATGGAATTCGTATCAAAAATATTGAACCATTACAAACATAAGGATATACCGACAGTTTTGGAAAAATATATGATGAAAGAAAAATACTGGTCGTTCGAAAAGATTATCTATGGAAAGGAATATGGTTATATGGATTGGTATGAAGAGGGATTAAATGAAATCAGAAGCATTAAAATTAAATAGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36767","NCBI_taxonomy_name":"Enterococcus casseliflavus","NCBI_taxonomy_id":"37734"}}}},"ARO_accession":"3002634","ARO_id":"39034","ARO_name":"APH(2'')-Ie","ARO_description":"APH(2'')-Ie is a plasmid or transposon-encoded aminoglycoside phosphotransferase in E. faecium and E. casseliflavus","ARO_category":{"36267":{"category_aro_accession":"3000128","category_aro_cvterm_id":"36267","category_aro_name":"APH(2'')","category_aro_description":"Phosphorylation of 2-deoxystreptamine aminoglycosides on the hydroxyl group at position 2''","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"138":{"model_id":"138","model_name":"cml","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"755":{"protein_sequence":{"accession":"CAA42594.1","sequence":"MPLPLYLLAVAVCAMGTSEFMLAGLVPDIASDLGVTVGTAGTLTSAFATGMIVGAPLVAALARTWPRRSSLLGFILAFAAAHAVGAGTTSFPVLVACRVVAALANAGFLAVALTTAAALVPADKQGRALAVLLSGTTVATVAGVPGGSLLGTWLGWRATFWAVAVCCLPAAFGVLKAIPAGRATAAATGGPPLRVELAALKTPRLLLAMLLGALVNAATFASFTFLAPVVTDTAGLGDLWISVALVLFGAGSFAGVTVAGRLSDRRPAQVLAVAGPLLLVGWPALAMLADRPVALLTLVFVQGALSFALGSTLITRVLYEAAGAPTMAGSYATAALNVGAAAGPLVAATTLGHTTGNLGPLWASGLLVAVALLVAFPFRTVITTAAPADATR"},"dna_sequence":{"accession":"X59968","fmin":"507","fmax":"1686","strand":"+","sequence":"ATGCCTCTTCCGCTGTACCTGCTCGCCGTGGCCGTCTGCGCCATGGGCACCTCGGAGTTCATGCTCGCCGGTCTCGTGCCGGACATCGCCTCGGATCTCGGCGTCACCGTCGGGACCGCAGGCACGCTCACCTCCGCCTTCGCGACCGGCATGATCGTCGGCGCTCCCCTCGTGGCGGCGCTGGCCCGCACCTGGCCCAGGCGTTCCAGCCTCCTCGGATTCATCCTCGCCTTCGCGGCGGCACACGCCGTGGGAGCCGGCACCACGAGCTTCCCCGTCCTGGTGGCCTGCCGGGTCGTGGCCGCGCTCGCGAACGCGGGATTCCTCGCGGTCGCACTGACGACTGCCGCCGCACTGGTCCCTGCCGACAAGCAGGGACGCGCGCTGGCCGTGCTGCTGTCCGGCACGACGGTGGCCACGGTCGCCGGCGTCCCCGGCGGGTCACTCCTCGGCACGTGGCTCGGCTGGCGGGCCACGTTCTGGGCCGTCGCCGTCTGCTGCCTGCCCGCGGCGTTCGGCGTGCTGAAGGCAATCCCCGCCGGACGTGCGACGGCAGCGGCGACCGGTGGGCCGCCGCTGCGAGTCGAGCTCGCCGCGCTCAAGACCCCCCGGTTGCTGCTGGCGATGCTGCTGGGCGCGCTGGTGAACGCGGCAACCTTCGCGAGCTTCACCTTCCTGGCCCCCGTCGTGACCGACACCGCAGGGCTGGGCGACCTGTGGATCTCTGTCGCCCTGGTGCTCTTCGGCGCCGGTTCCTTCGCCGGCGTCACCGTCGCCGGACGACTGTCCGACCGACGCCCCGCCCAGGTGCTCGCCGTCGCCGGTCCGCTGCTGCTCGTCGGCTGGCCCGCGCTGGCGATGCTGGCCGACCGGCCGGTCGCCCTGCTGACCCTCGTGTTCGTCCAAGGCGCACTGTCGTTCGCGCTGGGCAGCACGCTGATCACGCGGGTCCTCTACGAGGCGGCGGGAGCACCCACCATGGCCGGTTCGTACGCGACCGCCGCCCTCAACGTGGGCGCCGCGGCCGGACCGCTCGTCGCCGCGACCACTCTCGGCCACACGACCGGCAACCTCGGGCCGCTGTGGGCGAGCGGGCTCCTGGTCGCCGTCGCGCTGCTCGTCGCGTTCCCCTTCCGCACGGTGATCACGACGGCCGCACCCGCCGACGCGACCCGGTGAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39551","NCBI_taxonomy_name":"Streptomyces lividans 1326","NCBI_taxonomy_id":"1200984"}}}},"ARO_accession":"3002690","ARO_id":"39124","ARO_name":"Streptomyces lividans cmlR","ARO_description":"cmlR is a plasmid or chromosome-encoded chloramphenicol resistance determinant (putative transmembrane protein) that is found in Escherichia coli and Streptomyces lividans","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"139":{"model_id":"139","model_name":"QnrB10","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"88":{"protein_sequence":{"accession":"ABG56269.1","sequence":"MLSLLYKNTGIDMTLALVGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"DQ631414","fmin":"0","fmax":"681","strand":"+","sequence":"ATGTTGTCATTACTGTATAAAAACACAGGCATAGATATGACTCTGGCATTAGTTGGCGAAAAAATTGACAGAAACCGCTTCACCGGTGAGAAAGTTGAAAATAGTACATTTTTTAACTGCGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGCCAGTTCTATGATCGCGAAAGTCAGAAAGGGTGCAATTTTAGTCGCGCAATGCTGAAAGATGCCATTTTCAAAAGCTGTGATTTATCAATGGCAGATTTCCGCAACGTCAGCGCATTGGGCATTGAAATTCGCCACTGTCGCGCACAAGGCGCAGATTTTCGCGGTGCAAGCTTTATGAATATGATCACCACGCGCACCTGGTTTTGCAGCGCATATATCACTAATACCAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAGCTATGGGAAAACCGCTGGATGGGGACTCAGGTACTGGGTGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCCGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTAGGTGACTTAGATATTCGGGGTGTTGATTTACAAGGCGTTAAGTTAGACAACTACCAGGCATCGTTGCTCATGGAGCGACTTGGCATCGCTGTGATTGGTTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002724","ARO_id":"39158","ARO_name":"QnrB10","ARO_description":"QnrB10 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"140":{"model_id":"140","model_name":"AAC(6')-IIb","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"497":{"protein_sequence":{"accession":"AAA25680.1","sequence":"MHPGVVTLRPMTEDDIGMLHEWLNRPHIVEWWGGERPSLEEVKEDYRPSALAEEGVTPYIGLLDGTPFAFAQSYVALGSGGGWWEEETDPGVRGIDQSIADSGLLGRGYGTRLVQALVDLLFADPQVSKVQTDPSPNNMRAIRCYEKAGFRKVKVVSTPDGPAMYMLHERPLVNGLRSAA"},"dna_sequence":{"accession":"L06163","fmin":"531","fmax":"1074","strand":"+","sequence":"ATGCATCCCGGCGTTGTTACTCTGCGTCCGATGACCGAAGACGACATCGGTATGCTTCACGAATGGTTGAATCGGCCGCACATTGTCGAATGGTGGGGTGGTGAGCGGCCCTCGCTCGAAGAGGTGAAAGAGGACTATCGGCCCAGCGCGTTGGCCGAAGAAGGAGTGACGCCGTACATCGGTTTGCTTGACGGAACTCCATTCGCGTTCGCACAGTCGTACGTTGCGCTCGGGTCGGGTGGTGGATGGTGGGAGGAAGAGACCGATCCTGGTGTCCGCGGAATCGATCAATCAATCGCCGATTCCGGGCTTCTCGGAAGAGGTTACGGCACTCGGCTGGTGCAGGCGCTTGTTGATTTGCTGTTCGCCGACCCGCAGGTATCCAAGGTTCAGACGGACCCCTCCCCGAACAACATGCGCGCGATACGCTGCTATGAGAAGGCAGGCTTCCGGAAGGTCAAGGTCGTTTCAACACCGGATGGGCCGGCCATGTACATGTTGCACGAGCGTCCGTTGGTGAACGGTTTGCGCAGTGCGGCCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36937","NCBI_taxonomy_name":"Pseudomonas fluorescens","NCBI_taxonomy_id":"294"}}}},"ARO_accession":"3002595","ARO_id":"38995","ARO_name":"AAC(6')-IIb","ARO_description":"AAC(6')-IIb is an integron-encoded aminoglycoside acetyltransferase in P. fluorescens","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"141":{"model_id":"141","model_name":"vanRB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"3453":{"protein_sequence":{"accession":"AAB05622.1","sequence":"MSIRILLVEDDDHICNTVRAFLAEARYEVDACTDGNEAHTKFYENTYQLVILDIMLPGMNGHELLREFRAQNDTPILMMTALSDDENQIRAFDAEADDYVTKPFKMRILLKRVEALLRRSGALAKEFRVGRLTLLPEDFRVLCDGTELPLTRKEFEILLLLVQNKGRTLTHEIILSRIWGYDFDGDGSTVHTHIKNLRAKLPENIIKTIRGVGYRLEESL"},"dna_sequence":{"accession":"U35369","fmin":"177","fmax":"840","strand":"+","sequence":"ATGTCGATACGAATTCTACTTGTCGAGGATGATGATCATATCTGCAATACAGTAAGGGCGTTTTTGGCTGAAGCAAGATATGAGGTGGATGCCTGCACAGATGGAAACGAAGCACACACCAAGTTCTATGAAAACACCTATCAACTGGTTATTCTTGATATTATGCTGCCCGGTATGAATGGGCATGAACTTCTACGTGAATTTCGGGCGCAAAATGATACCCCCATTCTGATGATGACAGCCCTGTCGGATGACGAAAACCAAATCCGGGCGTTTGATGCAGAGGCAGACGACTATGTAACAAAGCCATTCAAGATGCGGATTTTACTAAAGCGGGTGGAAGCCCTGTTACGGCGCAGCGGTGCGCTGGCAAAGGAATTTCGTGTGGGCAGGCTGACACTTCTGCCGGAGGATTTTAGGGTACTTTGTGACGGTACGGAGCTGCCCCTGACACGAAAAGAATTTGAAATCCTTTTGCTGCTGGTGCAGAACAAAGGCAGAACCTTAACCCATGAAATCATTTTGTCCCGCATATGGGGATATGACTTTGACGGTGATGGCAGCACAGTCCACACTCATATCAAAAATCTGCGGGCGAAGCTGCCGGAAAATATCATCAAAACCATCCGCGGTGTAGGTTACCGATTGGAGGAATCATTATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3002921","ARO_id":"39355","ARO_name":"vanRB","ARO_description":"vanRB is a vanR variant found in the vanB gene cluster","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36713":{"category_aro_accession":"3000574","category_aro_cvterm_id":"36713","category_aro_name":"vanR","category_aro_description":"VanR is a OmpR-family transcriptional activator in the VanSR regulatory system. When activated by VanS, it promotes cotranscription of VanA, VanH, and VanX.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"143":{"model_id":"143","model_name":"cphA7","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"1656":{"protein_sequence":{"accession":"CAA40386.1","sequence":"MMKGWMKCGLAGAVVLMASFWGGSVRAAGMSLTQVSGPVYVVEDNYYVQENSMVYFGAKGVTVVGATWTPDTARELHKLIKRVSRKPVLEVINTNYHTDRAGGNAYWKSIGAKVVSTRQTRDLMKSDWAEIVAFTRKGLPEYPDLPLVLPNVVHDGDFTLQEGKVRAFYAGPAHTPDGIFVYFPDEQVLYGNCILKEKLGNLSFADVKAYPQTLERLKAMKLPIKTVIGGHDSPLHGPELIDHYEALIKAAPQS"},"dna_sequence":{"accession":"X57102","fmin":"147","fmax":"912","strand":"+","sequence":"ATGATGAAAGGTTGGATGAAGTGTGGATTGGCCGGCGCCGTGGTGCTGATGGCGAGTTTCTGGGGTGGCAGCGTGCGGGCGGCGGGGATGTCGCTGACGCAGGTGAGCGGCCCTGTGTATGTGGTAGAGGACAACTACTACGTGCAGGAAAATTCCATGGTCTATTTCGGGGCCAAGGGCGTGACTGTGGTGGGGGCGACCTGGACGCCGGACACCGCCCGCGAGCTGCACAAGCTGATCAAACGGGTCAGCCGCAAGCCGGTGCTGGAGGTGATCAACACCAACTACCACACCGACCGGGCTGGCGGTAACGCCTACTGGAAGTCCATCGGTGCCAAGGTGGTGTCGACCCGCCAGACCCGGGATCTGATGAAGAGCGACTGGGCCGAGATTGTTGCCTTTACCCGCAAGGGGCTGCCGGAGTACCCGGATCTGCCGCTGGTGCTGCCCAACGTGGTGCACGATGGCGACTTCACGCTGCAAGAGGGCAAGGTGCGCGCCTTCTACGCGGGCCCGGCCCATACGCCGGACGGCATCTTTGTCTACTTCCCCGACGAGCAGGTGCTCTATGGCAACTGCATTCTCAAGGAGAAGCTGGGCAACCTGAGCTTTGCCGATGTGAAGGCCTATCCACAGACGCTTGAGCGGCTGAAAGCGATGAAGCTGCCGATCAAGACGGTGATCGGCGGTCACGACTCACCGCTGCACGGCCCCGAGCTGATTGATCACTACGAAGCGCTGATCAAGGCCGCACCCCAGTCATAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36810","NCBI_taxonomy_name":"Aeromonas hydrophila","NCBI_taxonomy_id":"644"}}}},"ARO_accession":"3003103","ARO_id":"39669","ARO_name":"cphA7","ARO_description":"cphA7 is an Ambler Class B MBL; subclass B2 originally isolated from Aeromonas jandaei. This enzyme has specific activity against carbapenems and is active as a mono-zinc protein.","ARO_category":{"36720":{"category_aro_accession":"3000581","category_aro_cvterm_id":"36720","category_aro_name":"CphA beta-lactamase","category_aro_description":"CphA is an Ambler Class B MBL; subclass B2 originally isolated from Aeromonas hydrophilia.  This enzyme has specific activity against carbapenems and is active as a mono-zinc protein.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"144":{"model_id":"144","model_name":"IMP-12","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1824":{"protein_sequence":{"accession":"CAD12765.1","sequence":"MKKLFVLCIFLFLSITASGEVLPDLKIEKLEEGVYLHTSFEEVSGWGVVTKHGLVVLVNNDAYLIDTPFTNKDTEKLVAWFVGRGFTIKGSVSSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKNGKVQATNSFSGVSYWLVKNKIEIFYPGPGHTQDNVVVWLPENKILFGGCFVKPDGLGNLDDANLKAWPKSAKILMSKYGKAKLVVSGHSEIGNASLLKLTWEQAVKGLKESKKPLLPSN"},"dna_sequence":{"accession":"AJ420864","fmin":"155","fmax":"896","strand":"+","sequence":"ATGAAGAAATTATTTGTTTTATGCATTTTTTTGTTTTTAAGTATTACTGCCTCAGGTGAGGTTTTGCCTGATTTGAAAATTGAGAAGCTTGAAGAGGGTGTTTATCTTCATACATCTTTTGAAGAGGTTAGCGGTTGGGGTGTTGTTACTAAACATGGTTTGGTAGTTCTTGTAAATAATGACGCCTATCTAATTGACACTCCATTTACAAATAAAGATACTGAAAAATTAGTTGCTTGGTTTGTAGGGCGCGGCTTTACAATAAAGGGAAGTGTTTCCTCACATTTTCATAGCGACAGTACGGGTGGAATAGAGTGGCTTAATTCTCAATCTATTCCCACGTATGCATCTGAGTTAACAAATGAACTTCTGAAAAAGAACGGTAAGGTGCAAGCTACAAATTCATTTAGCGGGGTTAGTTATTGGCTAGTTAAAAATAAAATTGAAATTTTTTATCCCGGCCCAGGACATACTCAAGATAACGTAGTGGTTTGGCTACCTGAAAACAAAATTTTATTCGGTGGTTGTTTTGTTAAACCGGACGGTCTTGGTAATTTGGATGACGCAAATTTAAAAGCTTGGCCAAAGTCCGCAAAAATATTAATGTCTAAATATGGTAAAGCAAAGTTAGTTGTTTCAGGTCATAGTGAAATTGGGAACGCATCACTCTTGAAACTTACTTGGGAGCAGGCTGTTAAAGGGCTAAAAGAAAGTAAAAAACCATTACTGCCAAGTAACTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36803","NCBI_taxonomy_name":"Pseudomonas putida","NCBI_taxonomy_id":"303"}}}},"ARO_accession":"3002203","ARO_id":"38603","ARO_name":"IMP-12","ARO_description":"IMP-12 is a beta-lactamase found in Pseudomonas putida","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"145":{"model_id":"145","model_name":"OXA-229","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"804":{"protein_sequence":{"accession":"AFM55000.1","sequence":"MKFKMKGLFCVILSSLAFSGCVYDSKLQRPVISERETEIPLLFDQAQTQAVFVTYDGIHLKSYGNDLSRAKTEYIPASTFKMLNALIGLQNAKATNTEVFHWNGEKRAFSAWEKDMTLAEAMQASAVPVYQELARRIGLELMREEVKRVGFGNAEIGQQVDNFWLVGPLKISPEQEVQFAYQLAMKQLPFDSNVQQQVKDMLYIERRGDSKLYAKSGWGMDVEPQVGWYTGWVEQPNGKVTAFALNMNMQAGDDPTERKQLTLSILDKLGLFFYLR"},"dna_sequence":{"accession":"JQ422052","fmin":"1099","fmax":"1930","strand":"+","sequence":"ATGAAGTTTAAAATGAAAGGTTTATTTTGTGTCATCCTCAGTAGTTTGGCATTTTCAGGTTGTGTTTATGATTCAAAACTACAACGCCCAGTCATATCAGAGCGAGAAACTGAGATTCCTTTATTATTTGATCAAGCACAGACTCAAGCTGTGTTTGTTACTTATGATGGGATTCATCTAAAAAGTTATGGTAATGATCTAAGCCGAGCAAAGACTGAATATATTCCTGCATCTACATTTAAGATGTTGAATGCTTTAATTGGCTTGCAAAATGCAAAAGCAACCAATACTGAAGTATTTCATTGGAATGGTGAAAAGCGCGCTTTTTCAGCATGGGAAAAAGATATGACTTTGGCAGAAGCGATGCAGGCTTCAGCTGTTCCCGTATATCAGGAGCTTGCTCGACGTATTGGCTTGGAATTGATGCGTGAAGAAGTGAAGCGTGTAGGTTTTGGCAATGCGGAGATTGGTCAGCAAGTCGATAATTTTTGGTTGGTGGGGCCTTTAAAAATCTCTCCTGAACAAGAAGTTCAATTTGCCTATCAACTGGCAATGAAGCAATTGCCTTTTGATTCAAATGTACAGCAACAAGTCAAAGATATGCTTTATATCGAGAGACGTGGTGACAGTAAACTGTATGCTAAAAGTGGTTGGGGAATGGATGTTGAACCTCAAGTGGGTTGGTATACGGGATGGGTTGAACAACCCAATGGCAAGGTGACTGCATTTGCGTTAAATATGAACATGCAAGCAGGTGATGATCCAACTGAACGTAAACAATTAACCTTAAGTATTTTGGACAAATTGGGTCTATTTTTTTATTTAAGATAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39090","NCBI_taxonomy_name":"Acinetobacter bereziniae","NCBI_taxonomy_id":"106648"}}}},"ARO_accession":"3001692","ARO_id":"38092","ARO_name":"OXA-229","ARO_description":"OXA-229 is a beta-lactamase found in A. bereziniae","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"146":{"model_id":"146","model_name":"OXA-98","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1769":{"protein_sequence":{"accession":"CAK50801.1","sequence":"MNIKALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"AM279652","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACGCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001646","ARO_id":"38046","ARO_name":"OXA-98","ARO_description":"OXA-98 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"147":{"model_id":"147","model_name":"OXA-27","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4236":{"protein_sequence":{"accession":"AAG35609.2","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETPSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKADINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKPQVGWLTGWVEQPDGKIVAFALKMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"AF201828.2","fmin":"115","fmax":"937","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTCATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAGCGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGACCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCCCAATTAGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAAAATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001422","ARO_id":"37822","ARO_name":"OXA-27","ARO_description":"OXA-27 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"148":{"model_id":"148","model_name":"SHV-92","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1793":{"protein_sequence":{"accession":"ABH04327.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMISTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLAIVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"DQ836922","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATAAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATTTGCTGCTGGCCATCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTAGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001144","ARO_id":"37524","ARO_name":"SHV-92","ARO_description":"SHV-92 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"149":{"model_id":"149","model_name":"aadA12","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"57":{"protein_sequence":{"accession":"ACJ47200.1","sequence":"MRVAVTIEISNQLSEVLSVIERHLESTLLAVHLYGSAVDGGLKPYSDIDLLVTVTVRLDETTRRALINDLLETSASPGESEILRAVEVTIVVHDDIIPWRYPAKRELQFGEWQRNDILAGIFEPATIDIDLAILLTKAREHSVALVGPAAEELFDPVPEQDLFEALNETLTLWNSPPDWAGDERNVVLTLSRIWYSAITGKIAPKDVAADWAIKRLPAQYQPVLLEAKQAYLGQKEDHLASRADHLEEFIRFVKGEIIKSVGK"},"dna_sequence":{"accession":"FJ381668","fmin":"56","fmax":"848","strand":"+","sequence":"ATGAGGGTAGCGGTGACCATCGAAATTTCGAACCAACTATCAGAGGTGCTAAGCGTCATTGAGCGCCATCTGGAATCAACGTTGCTGGCCGTGCATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCATACAGCGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCGAGCTTTGATCAACGACCTTTTGGAAACTTCGGCTTCCCCTGGAGAGAGCGAGATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCTGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAATAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATAAAACGCCTACCTGCCCAGTATCAGCCCGTCTTACTTGAAGCTAAGCAAGCTTATCTGGGACAAAAAGAAGATCACTTGGCCTCACGCGCAGATCACTTGGAAGAATTTATTCGCTTTGTGAAAGGCGAGATCATCAAGTCAGTTGGTAAATGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002612","ARO_id":"39012","ARO_name":"aadA12","ARO_description":"aadA12 is an integron-encoded aminoglycoside nucleotidyltransferase gene in E. coli, Yersinia enterocolitica and S. enterica","ARO_category":{"41439":{"category_aro_accession":"3004275","category_aro_cvterm_id":"41439","category_aro_name":"ANT(3'')","category_aro_description":"Nucleotidylylation of streptomycin at the hydroxyl group at position 3''","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"150":{"model_id":"150","model_name":"catB3","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"3699":{"protein_sequence":{"accession":"YP_006965431.1","sequence":"MTNYFDSPFKGKLLSEQVKNPNIKVGRYSYYSGYYHGHSFDDCARYLFPDRDDVDKLIIGSFCSIGSGASFIMAGNQGHRYDWASSFPFFYMQEEPAFSSALDAFQKAGNTVIGNDVWIGSEAMVMPGIKIGHGAVIGSRSLVTKDVEPYAIVGGNPAKKIKKRFTDEEISLLLEMEWWNWSLEKIKAAMPMLCSSNIVGLHKYWLEFAV"},"dna_sequence":{"accession":"NC_019368.1","fmin":"58200","fmax":"58833","strand":"+","sequence":"ATGACCAACTACTTTGATAGCCCCTTCAAAGGCAAGCTGCTTTCTGAGCAAGTGAAGAACCCCAATATCAAAGTTGGGCGGTACAGCTATTACTCTGGCTACTATCATGGGCACTCATTCGATGACTGCGCACGGTATCTGTTTCCGGACCGTGATGACGTTGATAAGTTGATCATCGGTAGTTTCTGCTCTATCGGGAGTGGGGCTTCCTTTATCATGGCTGGCAATCAGGGGCATCGGTACGACTGGGCATCATCTTTCCCGTTCTTTTATATGCAGGAAGAACCTGCATTCTCAAGCGCACTCGATGCCTTCCAAAAAGCAGGTAATACTGTCATTGGCAATGACGTTTGGATCGGCTCTGAGGCAATGGTCATGCCCGGAATCAAGATCGGGCACGGTGCGGTGATAGGCAGCCGCTCGTTGGTGACAAAAGATGTGGAGCCTTACGCTATCGTTGGCGGCAATCCCGCTAAGAAGATTAAGAAACGCTTCACCGATGAGGAAATTTCATTGCTTCTGGAGATGGAGTGGTGGAATTGGTCACTGGAGAAGATCAAAGCGGCAATGCCCATGCTGTGCTCGTCTAATATTGTTGGCCTGCACAAGTATTGGCTCGAGTTTGCCGTCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3002676","ARO_id":"39110","ARO_name":"catB3","ARO_description":"catB3 is a plasmid or chromosome-encoded variant of the cat gene found in Salmonella typhimurium, Acinetobacter baumannii and Escherichia coli","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. cat is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Bacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini","category_aro_class_name":"AMR Gene Family"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"151":{"model_id":"151","model_name":"OKP-A-15","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1200":{"protein_sequence":{"accession":"ACN65419.1","sequence":"MRYVRLCLFSLIAALPLAVFASPPPLEQITRSESQLAGRVGYVEMDLLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIRYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKSVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMAATLRKLLTSHTLSARSQQQLLQWMVDDQVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPNGKAERIVVIYLRDTPATMAERNQQIARIGAALIEHWQR"},"dna_sequence":{"accession":"FJ755841","fmin":"0","fmax":"846","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTTTCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCCGCCGCTTGAGCAAATTACACGCAGCGAAAGTCAGCTGGCGGGCCGCGTGGGCTATGTTGAAATGGATCTGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGAGACGAACAGCTGGATCGGCGGATCCGCTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGAGCGTTGGCGGCCCCGCGGGATTGACCGCTTTTTTGCGCCAGATCGGTGACAACGTCACCCGCCTCGACCGCTGGGAAACGGAGCTCAATGAAGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCAGCCAGCATGGCCGCCACCCTGCGCAAGCTGCTAACCAGCCACACTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGACCAGGTAGCCGGTCCGCTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGCGAGCGGGGCTCACGTGGCATTGTCGCCCTGCTCGGCCCGAACGGCAAAGCGGAGCGCATCGTGGTGATCTATCTGCGGGATACGCCGGCGACCATGGCCGAGCGTAACCAGCAGATCGCCAGAATAGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002432","ARO_id":"38832","ARO_name":"OKP-A-15","ARO_description":"OKP-A-15 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"152":{"model_id":"152","model_name":"cpxA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"890"}},"model_sequences":{"sequence":{"4287":{"protein_sequence":{"accession":"NP_312864.1","sequence":"MIGSLTARIFAIFWLTLALVLMLVLMLPKLDSRQMTELLDSEQRQGLMIEQHVEAELANDPPNDLMWWRRLFRAIDKWAPPGQRLLLVTTEGRVIGAERSEMQIIRNFIGQADNADHPQKKKYGRVELVGPFSVRDGEDNYQLYLIRPASSSQSDFINLLFDRPLLLLIVTMLVSTPLLLWLAWSLAKPARKLKNAADEVAQGNLRQHPELEAGPQEFLAAGASFNQMVTALERMMTSQQRLLSDISHELRTPLTRLQLGTALLRRRSGESKELERIETEAQRLDSMINDLLVMSRNQQKNALVSETIKANQLWSEVLDNAAFEAEQMGKSLTVNFPPGPWPLYGNPNALESALENIVRNALRYSHTKIEVGFAVDKDGITITVDDDGPGVSPEDREQIFRPFYRTDEARDRESGGTGLGLAIVETAIQQHRGWVKAEDSPLGGLRLVIWLPLYKRS"},"dna_sequence":{"accession":"NC_002695","fmin":"4903561","fmax":"4904935","strand":"-","sequence":"TTAACTCCGCTTATACAGCGGCAACCAAATCACCAGCCGTAAACCGCCCAGCGGGCTGTCTTCTGCTTTCACCCAGCCACGATGCTGCTGAATGGCGGTTTCAACAATCGCCAGTCCCAAACCTGTACCGCCAGATTCACGATCGCGCGCTTCATCGGTCCGATAGAACGGACGGAAAATCTGTTCGCGATCTTCCGGGCTAACGCCAGGACCATCGTCGTCCACCGTAATGGTGATACCGTCTTTATCTACCGCAAAGCCCACTTCAATCTTCGTATGGGAATAACGCAGGGCATTACGAACAATGTTTTCCAGCGCACTCTCCAGGGCGTTCGGGTTGCCGTACAGCGGCCACGGCCCAGGCGGGAAGTTAACTGTCAACGACTTGCCCATTTGCTCGGCTTCGAACGCCGCGTTATCCAGCACTTCACTCCACAACTGATTGGCTTTGATGGTCTCGCTAACCAGCGCGTTTTTTTGCTGATTACGTGACATCACCAACAGGTCGTTAATCATGCTGTCCAGACGTTGCGCTTCGGTTTCAATACGCTCCAGTTCCTTGCTTTCACCACTACGACGGCGCAGTAACGCCGTACCCAGTTGCAGACGCGTCAGCGGGGTGCGCAGCTCGTGAGAGATATCAGAAAGCAGACGCTGCTGAGAGGTCATCATGCGCTCCAGCGCGGTGACCATCTGGTTAAAACTGGCACCTGCGGCAAGGAATTCCTGTGGCCCCGCTTCCAGTTCCGGGTGCTGGCGTAAGTTTCCCTGGGCAACTTCATCGGCAGCGTTTTTCAGCTTACGCGCCGGTTTTGCCAGACTCCAGGCCAACCACAACAGCAGCGGCGTACTGACCAACATGGTGACAATCAGCAGTAATAGCGGGCGGTCAAACAGTAAGTTAATGAAATCGGATTGAGAACTGCTGGCCGGACGAATCAGATAAAGTTGGTAATTATCTTCGCCATCACGCACGGAGAACGGACCGACCAGTTCCACGCGGCCATACTTTTTCTTCTGCGGATGATCGGCGTTATCGGCCTGACCAATAAAGTTACGAATGATCTGCATTTCGCTGCGTTCAGCGCCGATCACGCGGCCTTCGGTGGTCACCAATAACAAACGCTGTCCTGGCGGTGCCCACTTATCAATCGCCCGGAACAGACGCCGCCACCACATTAAATCGTTGGGCGGATCGTTCGCCAGCTCCGCTTCAACATGCTGCTCAATCATCAGACCCTGACGCTGTTCGCTATCCAGAAGCTCGGTCATCTGGCGTGAATCGAGCTTGGGTAACATCAAAACCAACATCAACACCAGCGCCAGCGTCAGCCAGAAGATGGCGAAGATGCGCGCGGTTAAGCTGCCTATCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36747","NCBI_taxonomy_name":"Escherichia coli O157:H7 str. Sakai","NCBI_taxonomy_id":"386585"}}}},"ARO_accession":"3000830","ARO_id":"37210","ARO_name":"cpxA","ARO_description":"CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR, which promotes efflux complex expression.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"153":{"model_id":"153","model_name":"adeF","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"4252":{"protein_sequence":{"accession":"CAJ77856.1","sequence":"MNISKFFIDRPIFAGVLSVLILLAGLLSVFQLPISEYPEVVPPSVVVRAQYPGANPKVIAETVASPLEESINGVEDMLYMQSQANSDGNLTITVNFKLGIDPDKAQQLVQNRVSQAMPRLPEDVQRLGVTTLKSSPTLTMVVHLTSPDNRYDMTYLRNYAVLNVKDRLARLQGVGEVGLFGSGDYAMRVWLDPQKVAQRNLTATEIVNAIREQNIQVAAGTIGASPSNSPLQLSVNAQGRLTTEQEFADIILKTAPDGAVTRLGDVARVELAASQYGLRSLLDNKQAVAIPIFQAPGANALQVSDQVRSTMKELSKDFPSSIKYDIVYDPTQFVRASIKAVVHTLLEAITLVVVVVILFLQTWRASIIPLLAVPVSIIGTFALMLAFGYSINALSLFGMVLAIGIVVDDAIVVVENVERNIEAGLNPREATYRAMREVSGPIIAIALTLVAVFVPLAFMTGLTGQFYKQFAMTIAISTVISAFNSLTLSPALAALLLKGHDAKPDALTRIMNRVFGRFFALFNRVFSRASDRYSQGVSRVISHKASAMGVYAALLGLTVGISYIVPGGFVPAQDKQYLISFAQLPNGASLDRTEAVIRKMSDTALKQPGVESAVAFPGLSINGFTNSSSAGIVFVTLKPFDERKAKDLSANAIAGALNQKYSAIQDAYIAVFPPPPVMGLGTMGGFKLQLEDRGALGYSALNDAAQNFMKAAQSAPELGPMFSSYQINVPQLNVDLDRVKAKQQGVAVTDVFNTMQIYLGSQYVNDFNRFGRVYQVRAQADAPFRANPEDILQLKTRNSAGQMVPLSSLVNVTQTYGPEMVVRYNGYTSADINGGPAPGYSSSQAEAAVERIAAQTLPRGIKFEWTDLTYQKILAGNAGLWVFPISVLLVFLVLAAQYESLTLPLAVILIVPMGILAALTGVWLTAGDNNIFTQIGLMVLVGLACKNAILIVEFARELEMQGATAFKAAVEASRLRLRPILMTSIAFIMGVVPLVTSTGAGSEMRHAMGVAVFFGMIGVTFFGLFLTPAFYVLIRTLNSKHKLHSAAVHEAPLASPHDH"},"dna_sequence":{"accession":"CT025801.2","fmin":"0","fmax":"3180","strand":"+","sequence":"ATGAATATTTCTAAATTTTTTATTGATCGGCCGATCTTTGCTGGTGTGCTATCAGTCTTGATTTTACTCGCCGGTCTCCTTTCGGTATTTCAGTTACCGATTTCTGAATATCCCGAGGTTGTTCCACCATCTGTGGTGGTACGCGCCCAATATCCGGGTGCAAACCCAAAAGTGATTGCTGAAACGGTTGCATCTCCGCTCGAAGAGTCAATCAACGGCGTCGAAGACATGCTGTATATGCAATCTCAAGCAAACAGCGACGGTAACCTAACCATTACGGTGAACTTTAAGCTCGGTATCGACCCAGACAAAGCCCAACAATTGGTTCAAAACCGTGTGTCTCAGGCCATGCCCCGTTTACCTGAAGATGTACAGCGCTTAGGTGTAACCACACTAAAAAGCTCACCTACTTTAACTATGGTAGTGCATCTGACCTCACCAGATAATCGCTATGACATGACCTACTTACGTAACTATGCGGTGCTCAACGTGAAAGACCGTTTAGCGCGTTTACAAGGGGTTGGTGAAGTCGGATTATTTGGTTCTGGTGACTACGCGATGCGTGTATGGCTTGACCCGCAAAAAGTAGCGCAGCGTAACCTCACCGCGACCGAAATTGTGAATGCAATCCGTGAACAAAATATTCAGGTTGCAGCGGGTACAATCGGTGCATCACCAAGTAATTCACCTTTACAGCTTTCAGTCAATGCTCAAGGTCGTTTAACTACTGAACAAGAATTCGCAGATATCATTTTAAAAACTGCACCAGATGGCGCGGTTACCCGATTGGGTGATGTTGCTCGTGTCGAACTTGCAGCCTCTCAATATGGCTTACGTTCATTGCTTGATAATAAACAAGCGGTCGCGATTCCAATTTTCCAAGCACCGGGTGCGAATGCTTTACAAGTTTCCGATCAAGTGCGTAGCACAATGAAGGAGCTTTCAAAAGATTTCCCATCTTCAATTAAATACGACATTGTTTATGACCCGACTCAATTCGTACGTGCAAGTATTAAAGCGGTCGTTCATACCTTACTTGAAGCAATTACACTGGTTGTTGTGGTCGTTATTTTATTCTTGCAAACATGGCGTGCCTCAATCATTCCATTGCTTGCCGTACCGGTTTCAATTATTGGTACATTCGCGCTCATGCTCGCTTTTGGTTACTCAATCAATGCGCTATCACTGTTCGGAATGGTACTTGCCATCGGGATTGTCGTCGATGACGCGATTGTGGTCGTCGAAAATGTCGAGAGGAATATTGAAGCAGGCTTAAACCCAAGGGAGGCGACTTACCGTGCCATGCGAGAAGTCAGTGGACCGATTATTGCCATTGCTTTAACACTTGTTGCAGTATTCGTACCTCTTGCCTTTATGACAGGCTTAACAGGGCAATTCTATAAACAATTTGCCATGACCATTGCCATTTCAACGGTTATTTCGGCATTTAACTCGCTTACCCTATCTCCTGCTTTGGCAGCGCTGTTACTGAAAGGACATGATGCTAAACCGGATGCCTTAACACGTATTATGAATCGTGTATTCGGTCGTTTCTTTGCACTGTTTAACCGTGTGTTTTCACGTGCTTCAGACCGTTATAGTCAAGGCGTCAGCCGTGTCATTTCCCATAAAGCTTCGGCAATGGGTGTCTATGCAGCACTCTTAGGTTTAACCGTTGGTATTTCCTATATTGTTCCAGGTGGTTTCGTTCCTGCGCAGGACAAACAATATTTAATTAGCTTTGCGCAGCTACCAAACGGCGCATCATTAGATCGTACCGAAGCGGTCATTCGTAAAATGAGTGACACTGCACTTAAACAACCTGGTGTAGAAAGTGCAGTTGCCTTTCCTGGCCTATCAATTAACGGTTTCACCAATAGCTCAAGTGCCGGTATTGTCTTTGTGACTTTAAAGCCATTTGATGAACGTAAGGCAAAAGACTTATCTGCAAATGCAATTGCAGGTGCGCTCAACCAGAAATATTCAGCTATTCAAGATGCCTATATCGCGGTTTTCCCACCGCCACCAGTGATGGGCTTAGGTACTATGGGCGGCTTTAAACTACAACTTGAAGACCGAGGTGCCTTAGGCTATTCAGCCTTGAACGATGCTGCACAAAACTTTATGAAGGCAGCACAATCAGCCCCTGAACTGGGTCCAATGTTCTCAAGTTATCAAATTAACGTACCTCAACTCAACGTAGATCTGGACCGTGTAAAAGCTAAACAGCAAGGCGTTGCTGTGACAGATGTTTTCAATACTATGCAGATTTATTTAGGTTCTCAGTACGTTAACGACTTTAACCGCTTTGGACGTGTTTATCAGGTTCGTGCACAAGCCGATGCGCCTTTCCGTGCTAACCCTGAAGATATTTTGCAGCTTAAAACCCGTAATAGTGCCGGACAAATGGTGCCATTATCTTCATTGGTGAATGTAACTCAAACCTATGGTCCTGAAATGGTCGTTCGTTATAACGGTTACACATCAGCAGATATTAACGGTGGCCCTGCCCCAGGTTATTCATCTAGCCAAGCAGAAGCTGCGGTTGAACGTATTGCTGCACAAACTCTACCGCGTGGTATCAAGTTTGAATGGACAGATTTAACTTATCAAAAAATCTTGGCTGGTAATGCTGGACTTTGGGTATTCCCTATTAGCGTATTACTCGTGTTCTTAGTGTTAGCTGCTCAGTATGAAAGCTTAACCCTACCATTAGCAGTTATCTTAATTGTACCAATGGGAATCTTAGCGGCTCTGACAGGTGTCTGGTTGACAGCTGGAGATAACAACATCTTTACTCAAATCGGTCTAATGGTACTGGTCGGGCTAGCCTGTAAAAATGCCATCTTAATTGTCGAATTTGCGAGGGAACTTGAAATGCAAGGTGCGACTGCCTTTAAAGCAGCCGTTGAAGCAAGTCGTCTACGTTTACGCCCAATTTTAATGACCTCTATTGCATTTATTATGGGTGTAGTGCCACTGGTTACTTCAACTGGCGCAGGTTCTGAAATGCGACATGCGATGGGTGTTGCCGTATTCTTCGGTATGATCGGTGTAACATTCTTTGGTTTATTCCTCACCCCGGCCTTTTACGTTCTGATTCGTACCCTCAACAGCAAACATAAACTGCATTCTGCGGCAGTTCATGAAGCGCCGTTAGCTAGCCCACATGATCATTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35535","NCBI_taxonomy_name":"Acinetobacter baumannii AYE","NCBI_taxonomy_id":"509173"}}}},"ARO_accession":"3000777","ARO_id":"37157","ARO_name":"adeF","ARO_description":"AdeF is the membrane fusion protein of the multidrug efflux complex AdeFGH.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"154":{"model_id":"154","model_name":"mgrA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"270"}},"model_sequences":{"sequence":{"4288":{"protein_sequence":{"accession":"YP_003281576.1","sequence":"MSDQHNLKEQLCFSLYNAQRQVNRYYSNKVFKKYNLTYPQFLVLTILWDESPVNVKKVVTELALDTGTVSPLLKRMEQVDLIKRERSEVDQREVFIHLTDKSETIRPELSNASDKVASASSLSQDEVKELNRLLGKVIHAFDETKEK"},"dna_sequence":{"accession":"NC_013450","fmin":"694852","fmax":"695296","strand":"-","sequence":"TTATTTTTCCTTTGTTTCATCAAATGCATGAATGACTTTACCTAATAAGCGATTAAGTTCTTTAACTTCATCTTGAGATAAAGAAGAAGCTGAAGCGACTTTGTCAGATGCATTACTTAATTCTGGTCTAATAGTTTCACTTTTGTCAGTCAAGTGAATAAATACTTCACGTTGATCGACTTCGGAACGTTCACGCTTAATTAAGTCTACTTGTTCCATTCGTTTTAATAATGGTGATACTGTACCAGTATCGAGTGCTAATTCAGTTACGACTTTCTTGACGTTTACAGGAGATTCATCCCATAAAATTGTTAAGACAAGAAATTGTGGGTATGTTAGATTGTACTTCTTAAAAACTTTGTTAGAGTAGTAGCGATTAACTTGTCTTTGAGCATTGTACAAACTAAAGCATAGCTGTTCTTTTAAATTATGTTGATCAGACAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35647","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus ED98","NCBI_taxonomy_id":"681288"}}}},"ARO_accession":"3000815","ARO_id":"37195","ARO_name":"mgrA","ARO_description":"MgrA, also known as NorR, is a regulator for norA, norB, and tet38. It is a positive regulator for norA expression, but is a direct repressor for norB and an indirect repressor of tet38.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35934":{"category_aro_accession":"0000015","category_aro_cvterm_id":"35934","category_aro_name":"methicillin","category_aro_description":"Derived from penicillin to combat penicillin-resistance, methicillin is insensitive to beta-lactamases (also known as penicillinases) secreted by many penicillin-resistant bacteria. Methicillin is bactericidal, and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavin","category_aro_description":"Acriflavin is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35985":{"category_aro_accession":"0000068","category_aro_cvterm_id":"35985","category_aro_name":"daptomycin","category_aro_description":"Daptomycin is a novel lipopeptide antibiotic used in the treatment of certain infections caused by Gram-positive organisms. Daptomycin interferes with the bacterial cell membrane, reducing membrane potential and inhibiting cell wall synthesis.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"36989":{"category_aro_accession":"3000645","category_aro_cvterm_id":"36989","category_aro_name":"cefotaxime","category_aro_description":"Cefotaxime is a semisynthetic cephalosporin taken parenterally. It is resistant to most beta-lactamases and active against Gram-negative rods and cocci due to its aminothiazoyl and methoximino functional groups.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36193":{"category_aro_accession":"3000054","category_aro_cvterm_id":"36193","category_aro_name":"acridine dye","category_aro_description":"Acridine dyes are cell permeable, basic molecules with an acridine chromophore. These compounds intercalate DNA. The image shown represents the core structure of the acridine family, with specific dyes containing varying substituents.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"155":{"model_id":"155","model_name":"TEM-195","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1402":{"protein_sequence":{"accession":"AFC75525.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSRNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDCWEPELNEAIPHDERDTTMPAAVATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"JN935137","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCGGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTCACCGCTTTTTTGCACAACATGGGGGATCATGTCACCCGCCTTGATTGTTGGGAACCGGAGCTGAATGAAGCCATACCACACGACGAGCGTGACACCACGATGCCTGCTGCAGTGGCCACCACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001055","ARO_id":"37435","ARO_name":"TEM-195","ARO_description":"TEM-195 is a beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"156":{"model_id":"156","model_name":"AAC(6')-Iaf","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"672":{"protein_sequence":{"accession":"BAH66386.1","sequence":"MDYSICDIAESNELILEAAKILKKSFLDVGNESWGDIKKAIEEVEECIEHPNICLGICLDDKLIGWTGLRPMYDKTWELHPMVIKTEYQGKDFGKVLLRELETRAKGRGIIGIALGTDDEYQKTSLSMIDINERNIFDEIENIKNINNHPYEFYKKCGYMIVGIIPNANGKRKPDIWMWKDIS"},"dna_sequence":{"accession":"AB462903","fmin":"1199","fmax":"1751","strand":"+","sequence":"TTGGACTATTCAATATGCGATATAGCTGAATCAAATGAATTAATCCTTGAAGCAGCAAAGATTCTTAAGAAAAGCTTTCTTGATGTTGGAAATGAATCATGGGGAGATATTAAAAAAGCTATTGAAGAAGTTGAAGAATGTATAGAACATCCAAATATATGCTTGGGAATATGTCTGGATGATAAACTGATTGGCTGGACCGGATTAAGGCCGATGTACGATAAGACCTGGGAACTTCATCCCATGGTTATAAAAACTGAATATCAAGGCAAGGATTTTGGGAAAGTACTACTAAGAGAACTAGAGACGAGAGCGAAGGGTAGGGGAATTATCGGAATAGCTCTTGGAACTGATGATGAATATCAGAAAACTAGTTTGTCTATGATTGATATAAACGAACGAAATATCTTCGATGAAATCGAGAATATAAAGAACATTAATAATCATCCATATGAGTTTTATAAGAAATGTGGTTATATGATCGTTGGAATAATCCCTAATGCTAATGGAAAAAGGAAACCAGATATATGGATGTGGAAAGATATTAGCTAGG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002574","ARO_id":"38974","ARO_name":"AAC(6')-Iaf","ARO_description":"AAC(6')-Iaf is an aminoglycoside acetyltransferase encoded by plasmids and integrons in P. aeruginosa","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"157":{"model_id":"157","model_name":"dfrA21","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"383":{"protein_sequence":{"accession":"CAP69659.1","sequence":"MNPESVRIYLVAAMGANRVIGNGPDIPWKIPGEQKIFRRLTESKVVVMGRKTFESIGKPLPNRHTVVLSRQARYSAPGCAVVSTLSQAIAIAAEHGKELYVAGGAEVYALALPHANGVFLSEVHQTFEGDAFFPVLNAAEFEVVSSETIQGTITYTHSVYARRNG"},"dna_sequence":{"accession":"AM932669","fmin":"105","fmax":"603","strand":"+","sequence":"ATGAACCCGGAATCGGTCCGCATTTATCTGGTCGCTGCCATGGGTGCCAATCGGGTTATTGGCAATGGTCCCGATATCCCCTGGAAAATCCCAGGTGAGCAGAAGATTTTTCGCAGGCTCACCGAGAGCAAAGTGGTCGTTATGGGCCGCAAGACATTTGAGTCCATAGGCAAGCCCTTACCAAACCGCCACACAGTGGTGCTCTCGCGCCAAGCTCGTTATAGCGCTCCTGGTTGTGCAGTTGTTTCAACGCTGTCACAGGCTATCGCCATCGCAGCCGAACACGGCAAAGAACTCTACGTAGCCGGCGGAGCCGAGGTATATGCGCTGGCGCTACCGCATGCCAACGGCGTCTTTCTATCTGAGGTACATCAAACCTTTGAGGGTGACGCCTTCTTCCCAGTGCTTAACGCAGCAGAATTCGAGGTTGTCTCATCCGAAACCATTCAAGGCACAATCACGTACACGCACTCCGTCTATGCGCGTCGTAACGGCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35739","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Bredeney","NCBI_taxonomy_id":"134047"}}}},"ARO_accession":"3003017","ARO_id":"39451","ARO_name":"dfrA21","ARO_description":"dfrA21 is an integron-encoded dihydrofolate reductase found in Salmonella enterica","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36408":{"category_aro_accession":"3000269","category_aro_cvterm_id":"36408","category_aro_name":"brodimoprim","category_aro_description":"Brodimoprim is a structural derivative of trimethoprim and an inhibitor of bacterial dihydrofolate reductase. The 4-methoxy group of trimethoprim is replaced with a bromine atom.","category_aro_class_name":"Antibiotic"},"36423":{"category_aro_accession":"3000284","category_aro_cvterm_id":"36423","category_aro_name":"tetroxoprim","category_aro_description":"Tetroxoprim is a trimethoprim derivative that inhibits bacterial dihydrofolate reductase.","category_aro_class_name":"Antibiotic"},"36476":{"category_aro_accession":"3000337","category_aro_cvterm_id":"36476","category_aro_name":"iclaprim","category_aro_description":"Iclaprim is a bactericidal compound that inhibits dihydrofolate reductase. It is used against clinically important Gram-positive pathogens, including methicillin-sensitive Staphylococcus aureus and methicillin-resistant S. aureus.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"158":{"model_id":"158","model_name":"myrA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"204":{"protein_sequence":{"accession":"BAA03674.1","sequence":"MHPDLLPHLRCPVCGQPLHQADAAPPRALRCPAGHSFDIARQGYVNLLTGRAPHVGDTAEMIAAREEFLAAGHYDPFSAALATAAARAVPRRVRPGDGVGEPVAYPDLVVDAGAGTGRHLAAVLDAVPTAVGLALDVSKPALRRAARAHPRAGAAVCDTWGRLPLADATVAVLVNVFAPRNGPEFRRVLRPDGALLVVTPTAEHLVELVDRLGLLRVDPAKDARVADSLTRHFEPAGQSTHRHRLQLTRKEVLTLVGMGPSAWHTDPARLTARVAALSEPVTVTAAVRLARYRPI"},"dna_sequence":{"accession":"D16099","fmin":"409","fmax":"1297","strand":"+","sequence":"GTGCACCCCGACCTGCTCCCCCACCTCCGCTGCCCGGTCTGCGGCCAGCCGCTGCACCAGGCCGACGCGGCACCACCACGCGCCCTGCGCTGCCCGGCCGGGCACAGCTTCGACATCGCCCGACAGGGTTACGTCAACCTGCTCACGGGCCGGGCACCGCACGTCGGCGACACCGCCGAGATGATCGCCGCCAGGGAGGAGTTTCTGGCCGCCGGGCACTACGACCCGTTCTCGGCGGCACTCGCCACCGCGGCCGCGCGGGCGGTGCCACGTCGTGTCCGGCCCGGCGACGGCGTGGGCGAACCGGTGGCGTACCCGGATCTGGTGGTGGACGCCGGAGCCGGTACCGGCCGGCACCTCGCCGCAGTGCTCGACGCGGTGCCGACCGCCGTCGGCCTGGCGCTGGACGTCTCGAAGCCCGCACTACGCCGGGCGGCCCGGGCGCATCCCCGGGCCGGCGCGGCCGTCTGCGACACCTGGGGCCGGTTGCCGCTGGCCGATGCCACGGTCGCAGTACTGGTCAACGTCTTCGCCCCGCGCAACGGGCCGGAATTCCGTCGGGTGCTCCGGCCGGACGGCGCCCTGCTCGTGGTGACACCGACCGCCGAACACCTGGTCGAGCTGGTGGACCGGCTGGGGCTGCTGCGGGTCGACCCGGCCAAGGACGCCCGGGTGGCCGACAGCCTCACGAGACACTTCGAACCGGCCGGGCAGAGCACCCACCGGCACCGGCTTCAGCTGACCCGGAAGGAGGTGCTGACCCTGGTTGGTATGGGGCCGAGCGCCTGGCACACCGACCCGGCCCGGCTCACCGCGCGGGTCGCAGCCCTGTCCGAGCCGGTCACGGTCACCGCCGCTGTCCGGCTCGCCCGTTACCGCCCGATCTGAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39571","NCBI_taxonomy_name":"Micromonospora griseorubida","NCBI_taxonomy_id":"28040"}}}},"ARO_accession":"3001300","ARO_id":"37699","ARO_name":"myrA","ARO_description":"myrA is a methyltransferase found in Micromonospora griseorubida and confers resistance to mycinamicin, tylosin and lincosamides. Specifically, this enzyme adds a methyl group to guanosine 748 (E. coli numbering) of 23S ribosomal RNA. MyrA is found in the mycinamicin biosynthetic cluster and is one mechanism by which M. griseorubida protects itself from self-destruction when producing this macrolide.","ARO_category":{"37697":{"category_aro_accession":"3001298","category_aro_cvterm_id":"37697","category_aro_name":"non-erm 23S ribosomal RNA methyltransferase (G748)","category_aro_description":"Non-erm 23S ribosomal RNA methyltransferases modify guanosine 748 (E. coli numbering) to confer resistance to some macrolides and lincosamides","category_aro_class_name":"AMR Gene Family"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"159":{"model_id":"159","model_name":"vgaALC","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"412":{"protein_sequence":{"accession":"ABH10964.1","sequence":"MKILLEGLHIKHYVQDRLLLNINRLKIYQNDRIGLIGKNGSGKTTLLHILYKKIVPEEGIVKQFSHCELIPQLKLIESTKSGGEVTRNYIRQALDKNPELLLADEPTTNLDNNYIEKLEQDLKNWHGAFIIVSHDRAFLDNLCTTIWEIDEGRITEYKGNYSNYVEQKELERHREELEYEKYEKEKKRLEKAINIKEQKAQRATKKPKNLSSSEGKIKVTKPYFASKQKKLRKTVKSLETRLEKLERVEKRNELPPLKMDLVNLESVKNRTIIRGEDVSGTIEGRVLWKAKSFSIRGGDKMAIIGSNGTGKTTFIKKIVHGNPGISLSPSVKIGYFSQKIDTLELDKSILENVQSSSQQNETLIRTILARMHFFRDDVYKPISVLSGGERVKVALTKVFLSEVNTLVLDEPTNFLDMEAIEAFESLLKEYNGSIIFVSHDRKFIEKVATRIMTIDNKEIKIFDGTYEQFKQAEKPTRNIKEDKKLLLETKITEVLSRLSIEPSEELEQEFQNLINEKRNLDK"},"dna_sequence":{"accession":"DQ823382","fmin":"0","fmax":"1569","strand":"+","sequence":"ATGAAAATACTGTTAGAGGGACTTCATATAAAACATTATGTTCAAGATCGTTTATTGTTGAACATAAATCGCCTAAAGATTTATCAGAATGATCGTATTGGTTTAATTGGTAAAAATGGAAGTGGAAAAACAACGTTACTTCACATATTATATAAAAAAATTGTGCCTGAAGAAGGTATTGTAAAACAATTTTCACATTGTGAACTTATTCCTCAATTGAAGCTCATAGAATCAACTAAAAGTGGTGGTGAAGTAACACGAAACTATATTCGGCAAGCGCTTGATAAAAATCCAGAACTGCTATTAGCAGATGAACCAACAACTAACTTAGATAATAACTATATAGAAAAATTAGAACAGGATTTAAAAAATTGGCATGGAGCATTTATTATAGTTTCACATGATCGCGCTTTTTTAGATAACTTATGTACTACTATATGGGAAATTGACGAGGGGAGAATAACTGAATATAAGGGGAATTATAGTAACTATGTTGAACAAAAAGAATTAGAAAGACATCGAGAAGAATTAGAATATGAAAAATATGAAAAAGAAAAGAAACGATTGGAAAAAGCTATAAATATAAAAGAACAGAAAGCTCAACGAGCAACTAAAAAACCGAAAAACTTAAGTTCATCTGAAGGCAAAATAAAAGTAACAAAGCCATACTTTGCAAGTAAGCAAAAGAAGTTACGAAAAACTGTAAAATCTCTAGAAACCAGACTAGAAAAACTTGAAAGGGTCGAAAAGAGAAACGAACTTCCTCCACTTAAAATGGATTTAGTGAACTTAGAAAGTGTAAAAAATAGAACTATAATACGTGGTGAAGATGTCTCGGGTACAATTGAAGGACGGGTATTGTGGAAAGCAAAAAGTTTTAGTATTCGCGGAGGAGACAAGATGGCAATTATCGGATCTAATGGTACAGGAAAGACAACGTTTATTAAAAAAATTGTGCATGGGAATCCTGGTATTTCATTATCGCCATCTGTCAAAATCGGTTATTTTAGCCAAAAAATAGATACATTAGAATTAGATAAGAGTATTTTAGAAAATGTTCAATCTTCTTCACAACAAAATGAAACTCTTATTCGAACTATTCTAGCTAGAATGCATTTTTTTAGAGATGATGTTTATAAACCAATAAGTGTCTTAAGTGGTGGAGAGCGAGTTAAAGTAGCACTAACTAAAGTATTCTTAAGTGAAGTTAATACGTTGGTACTAGATGAACCAACAAACTTTCTTGATATGGAAGCTATAGAGGCGTTTGAATCTTTGTTAAAGGAATATAATGGCAGTATAATCTTTGTATCTCACGATCGTAAATTTATCGAAAAAGTAGCCACTCGAATAATGACAATTGATAATAAAGAAATAAAAATATTTGATGGCACATATGAACAATTTAAACAAGCTGAAAAGCCAACAAGGAATATTAAAGAAGATAAAAAACTTTTACTTGAGACAAAAATTACAGAAGTACTCAGTCGATTGAGTATTGAACCTTCGGAAGAATTAGAACAAGAGTTTCAAAACTTAATAAATGAAAAAAGAAATTTAGATAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36827","NCBI_taxonomy_name":"Staphylococcus haemolyticus","NCBI_taxonomy_id":"1283"}}}},"ARO_accession":"3002830","ARO_id":"39264","ARO_name":"vgaALC","ARO_description":"vgaALC is an efflux protein expressed in staphylococci that confers resistance to streptogramin A antibiotics and related compounds. It is associated with plasmid DNA.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37716":{"category_aro_accession":"3001317","category_aro_cvterm_id":"37716","category_aro_name":"pleuromutilin","category_aro_description":"Pleuromutilin is a natural product antibiotic produced by Clitopilus passeckerianus. Related antibiotics of clinical significance, such as tiamulin and retapamulin, are semi-synthetic derivatives of this compound.","category_aro_class_name":"Antibiotic"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"160":{"model_id":"160","model_name":"OXA-236","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1374":{"protein_sequence":{"accession":"AFH36332.1","sequence":"MKTLILLPLLSCLSLTACSLPVSNSSSQITSTQSIQTIAKLFDQAQSSGVLVIQRGPHLQVYGNDLSRAHTEYIPASTFKILNALIGLQHGKATTNEIFKWDGKKRSFAAWEKDMTLGQAMQASAVPVYQELARRIGLELMQQEVQRIRFGNQQIGQHIDNFWLVGPLKITPVQEVEFASALAQEQLAFDPQVQQQVKAMLLLQERQDYRLYAKSGWGMDVEPQVGWLTGWIETPQDEIVAFSLNMQMQSNMDPAIRLKILQQALAELALYPKAEG"},"dna_sequence":{"accession":"JQ820242","fmin":"0","fmax":"831","strand":"+","sequence":"ATGAAAACTCTTATTTTGTTGCCTTTACTTAGTTGCTTGAGCCTGACAGCCTGTAGCTTGCCTGTTTCAAATTCGTCCTCTCAAATCACTTCAACTCAATCTATTCAAACCATTGCCAAATTATTTGATCAGGCACAAAGCTCTGGCGTTTTAGTAATTCAACGGGGCCCACATCTACAGGTCTATGGCAATGATTTGAGTCGTGCACATACCGAATATATTCCTGCTTCAACCTTTAAAATACTCAATGCCCTGATTGGCCTGCAACATGGTAAAGCCACGACCAATGAAATCTTTAAATGGGATGGCAAGAAGCGCAGTTTTGCAGCCTGGGAAAAAGACATGACTCTCGGCCAAGCCATGCAAGCTTCTGCTGTACCCGTCTATCAGGAACTGGCACGTCGCATTGGTCTGGAACTAATGCAACAGGAAGTGCAACGCATTCGATTTGGTAATCAGCAGATTGGTCAGCATATCGACAACTTCTGGTTAGTCGGACCTTTGAAAATCACCCCGGTACAAGAAGTCGAATTTGCCTCTGCGCTTGCTCAAGAGCAACTTGCCTTTGATCCTCAAGTCCAGCAACAAGTCAAAGCCATGTTACTGTTACAGGAGCGACAAGATTATCGACTATATGCCAAATCTGGTTGGGGTATGGATGTGGAGCCGCAAGTCGGCTGGCTCACCGGCTGGATCGAAACACCTCAGGACGAAATCGTGGCATTTTCACTGAATATGCAGATGCAAAGTAATATGGATCCGGCGATCCGTCTTAAAATTTTGCAGCAGGCCTTGGCCGAATTAGCGCTTTATCCGAAAGCTGAAGGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001677","ARO_id":"38077","ARO_name":"OXA-236","ARO_description":"OXA-236 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"161":{"model_id":"161","model_name":"SHV-56","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1639":{"protein_sequence":{"accession":"ACB73258.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADRTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"EU586041","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAGGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATCGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001112","ARO_id":"37492","ARO_name":"SHV-56","ARO_description":"SHV-56 is an inhibitor-resistant beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"162":{"model_id":"162","model_name":"KPC-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1870":{"protein_sequence":{"accession":"ACI95258.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGGYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"FJ234412","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGGGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002318","ARO_id":"38718","ARO_name":"KPC-8","ARO_description":"KPC-8 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"163":{"model_id":"163","model_name":"OXA-376","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1534":{"protein_sequence":{"accession":"AHL30276.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEYHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KF986257","fmin":"20","fmax":"845","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGTACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAACGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001562","ARO_id":"37962","ARO_name":"OXA-376","ARO_description":"OXA-376 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"164":{"model_id":"164","model_name":"vanN","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"650"}},"model_sequences":{"sequence":{"684":{"protein_sequence":{"accession":"AEP40500.1","sequence":"MKKIALIFGGTSAEYEVSLKSAASVLSVLENLNVEIYRIGIASNGKWYLTFSDNETIANDLWLQDKKLNEITPSFDGRGFYDQAEKVYFKPDVLFPMLHGGTGENGTLQGVFECMQIPYVGCGVASSAICMNKYLLHQFAKSVGVMSTPTQLISSTDEQQVIKNFTELYGFPIFIKPNEAGSSKGISKVHTEAELTKALTEAFQFSQTVILQKAVSGVEIGCAILGNDQLLVGECDEVSLATDFFDYTEKYQMTTAKLTVPAKIPVATSREIKRQAQLLYQLLGCQGLARIDFFLTEAGEILLNEINTMPGFTNHSRFPAMMAATGITYQELISTLITLAEDK"},"dna_sequence":{"accession":"JF802084","fmin":"559","fmax":"1591","strand":"+","sequence":"ATGAAAAAAATCGCCTTAATTTTTGGTGGTACTTCAGCAGAATATGAAGTATCCCTCAAATCAGCAGCTAGTGTTTTGTCTGTATTAGAAAATCTAAATGTTGAAATTTACAGAATTGGCATAGCTTCGAACGGAAAATGGTATTTAACCTTTAGTGATAATGAAACTATTGCAAATGACTTATGGTTACAAGATAAAAAATTAAATGAGATCACTCCCTCCTTCGATGGGAGAGGGTTTTATGACCAAGCAGAAAAAGTATATTTTAAACCAGATGTCTTATTTCCGATGCTACACGGTGGCACTGGAGAAAATGGTACATTACAAGGAGTTTTTGAATGTATGCAAATTCCTTATGTTGGTTGCGGCGTTGCCTCCTCTGCCATTTGTATGAATAAATATCTATTACATCAGTTTGCAAAAAGTGTCGGAGTGATGAGTACGCCTACACAGCTGATCTCATCGACGGACGAACAACAAGTAATCAAAAATTTTACTGAGTTGTACGGTTTTCCTATATTTATCAAACCAAATGAAGCTGGTTCTTCAAAGGGAATCAGCAAAGTTCATACCGAAGCAGAGTTAACTAAAGCGCTGACCGAAGCGTTCCAATTCAGTCAGACAGTCATTTTACAAAAAGCTGTTTCTGGAGTAGAGATCGGTTGCGCCATCCTAGGAAATGATCAATTGCTTGTTGGGGAATGTGATGAAGTATCCTTAGCGACCGACTTTTTTGATTATACGGAAAAATATCAAATGACTACAGCAAAGTTGACCGTTCCAGCAAAAATTCCAGTGGCAACTAGTAGAGAAATCAAGCGTCAAGCACAATTACTGTATCAATTACTTGGATGTCAGGGCTTAGCTCGCATTGATTTTTTTCTAACAGAAGCAGGTGAAATTCTCTTAAATGAAATCAATACAATGCCAGGCTTTACCAATCATTCTAGATTTCCAGCCATGATGGCAGCTACGGGTATCACTTATCAGGAGCTTATTTCAACATTAATTACTTTAGCGGAGGATAAATAGC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002912","ARO_id":"39346","ARO_name":"vanN","ARO_description":"VanN is a D-Ala-D-Ala ligase homolog that can synthesize D-Ala-D-Ser, an alternative substrate for peptidoglycan synthesis that reduces vancomycin binding affinity in Enterococcus faecium","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"39340":{"category_aro_accession":"3002906","category_aro_cvterm_id":"39340","category_aro_name":"van ligase","category_aro_description":"van ligases synthesize alternative substrates for peptidoglycan synthesis that reduce vancomycin binding affinity.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"165":{"model_id":"165","model_name":"VIM-29","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"935":{"protein_sequence":{"accession":"AFP99885.1","sequence":"MLKVISSLLVYMTASVMAVASPLAHSGEPSGEYPTVNEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEAEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSAKVLYGGCAVHELSSTSAGNVADADLAEWPTSVERIQKRYPEAEVVIPGHGLPGGLDLLQHTANVVKAHKNRSVAE"},"dna_sequence":{"accession":"JX311308","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTACATGACCGCGTCTGTCATGGCTGTCGCAAGTCCGTTAGCCCATTCCGGGGAGCCGAGTGGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGAGAGGTCCGACTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCGGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAAAAGCAAATTGGACTTCCCGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGCAGAGGGGAACGAGATTCCCACGCATTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGCTCTTCTATCCTGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAAAGTGCTATACGGTGGTTGTGCCGTTCATGAGTTGTCAAGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCGTTGAGCGGATTCAAAAACGCTACCCGGAAGCAGAGGTCGTCATTCCCGGGCACGGTCTACCGGGCGGTCTAGACTTGCTCCAGCACACAGCGAACGTTGTCAAAGCACACAAAAATCGCTCAGTCGCCGAGTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002299","ARO_id":"38699","ARO_name":"VIM-29","ARO_description":"VIM-29 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"43":{"model_id":"43","model_name":"tet(42)","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"734":{"protein_sequence":{"accession":"ACD35503.1","sequence":"MTSPTSLTRRDQNRAWIMLIVLTMLTVIGMTVVLPVLPFVVLQYVSHESDLAIWVGVLEAINGLCAFLVAPFLGRLSDRFGRRPVIIVAAFGAAFSMALFGFGGALWVLVLARVIQGLTAGDLPALFAYLADITPPEQRAKRFGLLGALSGIGTMIGPAIGGLLAAISIQLPVFLTAAVALTIAILSIFLLPESLKPGNRITAIKLRDVQPFAVFKEAFGRKELRGLMIGFGLLALPFGFFVNNFSVLALDSIQWGPTQIGLLTAAVGIIDILIQGVLLGILLPRIGERGVIVSGIVAQMIGLAALAVVASVFAQPWVFIVGALMLAAGQGASQAAMDGAMSNAVGDDEQGWLGGATQSLNAAMGTAAPLIAGALYALVSHAAPYWLGVALMIVAVTVVSRAHIANTAKRPAGETTGDAPAALVETAG"},"dna_sequence":{"accession":"EU523697","fmin":"686","fmax":"1973","strand":"+","sequence":"ATGACTTCACCCACCTCTCTCACGCGACGGGACCAGAACCGCGCGTGGATCATGCTCATCGTGCTCACGATGCTCACCGTCATCGGAATGACGGTCGTCCTCCCGGTCCTGCCCTTCGTCGTGCTCCAGTACGTCTCGCACGAGAGCGACCTGGCCATCTGGGTCGGCGTGCTCGAAGCGATCAACGGCCTCTGCGCCTTCCTGGTCGCGCCCTTCCTCGGACGTCTCTCAGACCGCTTCGGACGTCGACCCGTGATCATCGTCGCGGCATTCGGTGCGGCCTTCTCGATGGCGCTGTTCGGATTCGGCGGCGCCCTCTGGGTGCTCGTGCTCGCTCGCGTCATCCAGGGCCTCACCGCGGGCGATCTACCCGCCCTCTTCGCCTACCTGGCCGACATCACCCCGCCGGAGCAGCGCGCCAAGCGCTTCGGCCTCCTCGGTGCGCTCTCGGGGATCGGCACCATGATCGGTCCAGCCATCGGAGGACTGCTCGCCGCGATCAGCATCCAGCTCCCGGTGTTCCTGACCGCCGCCGTCGCCCTCACGATCGCGATCCTCAGCATCTTCCTCCTCCCGGAGAGCCTGAAGCCGGGCAACAGGATCACCGCGATCAAGCTGCGCGACGTGCAGCCCTTCGCCGTCTTCAAGGAGGCCTTCGGACGCAAGGAGCTGCGCGGGCTGATGATCGGCTTCGGCCTGCTCGCGCTGCCGTTCGGCTTCTTCGTGAACAACTTCAGCGTGCTCGCCCTGGACTCCATCCAGTGGGGACCGACCCAGATCGGACTCCTGACCGCGGCCGTCGGCATCATCGACATCCTCATCCAGGGCGTGCTGCTGGGCATCCTGCTTCCGCGCATCGGCGAGCGCGGAGTGATCGTGAGCGGCATCGTCGCGCAGATGATCGGTCTCGCGGCCCTCGCCGTCGTGGCTTCCGTCTTCGCGCAGCCGTGGGTGTTCATCGTCGGCGCCCTGATGCTGGCCGCCGGCCAGGGGGCGTCCCAGGCCGCGATGGACGGGGCGATGTCCAACGCCGTCGGCGACGACGAGCAGGGCTGGCTCGGCGGAGCCACCCAGTCGTTGAATGCGGCGATGGGCACGGCAGCCCCGCTCATCGCCGGTGCGCTCTACGCACTGGTCAGCCACGCGGCCCCGTACTGGCTCGGGGTCGCGCTCATGATCGTGGCGGTGACCGTCGTCAGCCGCGCGCACATCGCGAACACCGCGAAGCGCCCGGCCGGCGAGACGACGGGCGACGCTCCCGCGGCACTCGTGGAGACGGCTGGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37079","NCBI_taxonomy_name":"Micrococcus sp. SMCC G887","NCBI_taxonomy_id":"526920"}}}},"ARO_accession":"3000572","ARO_id":"36711","ARO_name":"tet(42)","ARO_description":"Tet42 is a tetracycline efflux pump found in both Gram-negative (Pseudomonas) and Gram-positive (Microbacterium, Bacillus, Staphylococcus, Paenibacillus) bacteria.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"17":{"model_id":"17","model_name":"tet(45)","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"3314":{"protein_sequence":{"accession":"ADE08374.2","sequence":"ENRGKAFGIIGSIVTMGEGVGPSVGGVIAEYAHWSYILLLPVVTIITVPFLAKLLKQEEVIKGSFDTKGIIFMSVGIVFFIMFTTCYRVSFLVVSIICFLIFVKNIRKVSNPFINPSLGKNVSFMIGIICGGLIFGTVAGFISMVPYMMKDVYQLSTAAIGSGIIFPGAMSVIVFGYIGGLLVDKKGSLFVLTTGVAFLSISFLVAALFIETTPWLITIILIFVFGGLSFTKTVISTIVSSSLEQKEAG"},"dna_sequence":{"accession":"GU584222","fmin":"0","fmax":"747","strand":"+","sequence":"AGAAAATAGGGGTAAAGCATTTGGTATTATTGGGTCCATTGTAACTATGGGAGAAGGTGTCGGACCATCTGTTGGTGGAGTGATTGCCGAATATGCCCATTGGTCTTATATACTGCTTTTGCCTGTTGTAACGATTATCACTGTTCCATTCCTTGCAAAATTATTGAAACAGGAAGAGGTAATAAAAGGATCTTTTGATACTAAAGGAATAATATTTATGTCCGTAGGCATTGTATTTTTTATAATGTTTACGACATGTTATAGAGTTTCCTTTCTAGTCGTTAGCATAATATGTTTCTTAATATTTGTTAAGAATATTAGGAAAGTGTCTAATCCTTTTATTAATCCTTCGCTAGGAAAAAATGTCTCATTTATGATTGGAATCATTTGTGGAGGACTTATATTTGGAACCGTAGCAGGATTTATTTCTATGGTCCCTTATATGATGAAAGATGTCTATCAATTAAGTACTGCTGCAATTGGAAGTGGGATTATTTTTCCTGGGGCAATGAGTGTTATTGTTTTCGGTTATATTGGGGGATTGCTTGTTGATAAGAAAGGTTCACTATTTGTATTAACAACTGGAGTTGCATTTCTTTCTATAAGCTTTTTAGTAGCTGCCCTTTTTATAGAAACAACGCCTTGGCTTATAACAATTATATTAATTTTTGTTTTTGGGGGGCTTTCTTTTACGAAAACAGTTATATCCACCATTGTTTCAAGTAGTTTGGAACAAAAGGAAGCTGG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3003196","ARO_id":"39779","ARO_name":"tet(45)","ARO_description":"tet45 is a tetracycline efflux pump found in Bhargavaea cecembensis strain previously isolated from a poultry-litter-impacted soil.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"142":{"model_id":"142","model_name":"tet(E)","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"587":{"protein_sequence":{"accession":"AAA71915.1","sequence":"MNRTVMMALVIIFLDAMGIGIIMPVLPALLREFVGKANVAENYGVLLALYAMMQVIFAPLLGRWSDRIGRRPVLLLSLLGATLDYALMATASVVWVLYLGRLIAGITGATGAVAASTIADVTPEESRTHWFGMMGACFGGGMIAGPVIGGFAGQLSVQAPFMFAAAINGLAFLVSLFILHETHNANQVSDELKNETINETTSSIREMISPLSGLLVVFFIIQLIGQIPATLWVLFGEERFAWDGVMVGVSLAVFGLTHALFQGLAAGFIAKHLGERKAIAVGILADGCGLFLLAVITQSWMVWPVLLLLACGGITLPALQGIISVRVGQVAQGQLQGVLTSLTHLTAVIGPLVFAFLYSATRETWNGWVWIIGCGLYVVALIILRFFHPGRVIHPINKSDVQQRI"},"dna_sequence":{"accession":"L06940","fmin":"0","fmax":"1218","strand":"+","sequence":"ATGAACCGCACTGTGATGATGGCACTGGTCATCATTTTTTTAGATGCTATGGGGATTGGCATAATTATGCCTGTCTTGCCGGCGTTATTACGGGAGTTTGTTGGAAAGGCTAATGTTGCAGAGAACTACGGTGTTTTATTGGCGCTGTATGCAATGATGCAAGTGATTTTTGCCCCTCTTCTCGGCCGCTGGTCAGATCGCATAGGTCGTCGCCCTGTATTGTTACTTTCACTTTTAGGTGCAACACTGGACTACGCATTAATGGCAACAGCCAGCGTAGTGTGGGTGTTGTATTTGGGACGCTTAATTGCTGGTATTACCGGTGCGACTGGAGCTGTTGCAGCCTCAACAATTGCCGATGTCACACCTGAGGAATCCAGGACACATTGGTTTGGTATGATGGGTGCCTGTTTTGGTGGCGGTATGATTGCTGGACCAGTCATTGGTGGTTTTGCCGGTCAACTTTCGGTACAGGCACCGTTTATGTTCGCTGCTGCTATTAACGGGCTGGCATTTCTGGTCTCCCTATTCATTTTACATGAGACCCATAATGCTAATCAGGTTAGTGACGAGTTAAAGAATGAAACAATCAATGAAACCACATCCTCCATACGCGAGATGATCTCCCCATTATCGGGATTGTTAGTTGTCTTTTTCATCATTCAATTGATTGGCCAAATCCCCGCAACATTATGGGTTTTATTCGGAGAAGAGCGCTTCGCATGGGATGGCGTAATGGTCGGTGTTTCATTGGCTGTGTTCGGGCTGACACACGCACTGTTTCAAGGACTTGCTGCTGGTTTTATCGCTAAACATTTGGGAGAACGGAAAGCTATAGCGGTTGGCATTTTGGCTGACGGTTGTGGCCTATTTTTATTGGCGGTCATTACACAAAGCTGGATGGTTTGGCCGGTTTTGCTGTTACTAGCTTGTGGTGGCATCACACTTCCCGCCTTGCAGGGAATTATATCTGTTCGTGTCGGTCAGGTAGCACAGGGACAATTACAAGGGGTGCTGACCAGTTTGACCCACCTGACAGCTGTAATCGGTCCACTTGTTTTTGCATTTTTGTATAGTGCAACCCGCGAAACGTGGAATGGATGGGTATGGATAATTGGCTGCGGATTATATGTAGTTGCATTGATTATACTGAGGTTTTTCCATCCAGGTAGGGTAATCCACCCGATAAATAAGAGCGATGTACAGCAGAGAATTTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000173","ARO_id":"36312","ARO_name":"tet(E)","ARO_description":"TetE is a tetracycline efflux pump found in many Gram-negative bacteria, especially those in water environments. The gene is found on large plasmids.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"49":{"model_id":"49","model_name":"tsnR","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"4186":{"protein_sequence":{"accession":"AAA99931.1","sequence":"MANLDVIVDRSDPAVQRIVDVTKHSRSVVRTVLIEDIEPLTQSIRAGVEFTEVYGLDTVPFPGDLLAACEKRGIRVRLLSAAVANQVFKTEKKPKVFGIAKVPPAGRFADLESLSGDVVLLDGVKIVGNIGAIVRTRSALGAAGIVLVDSGLGTIADRRLIRASRGYVFSLPIVLATRDEALAFFRDGGMRPVVFEADGKLSIGELDGIDERLVLVFGSEKTGPSGEFAGVATESVSIPMNPAAESLNVSVSAGIALHRRARRNLSRPRG"},"dna_sequence":{"accession":"L39157.1","fmin":"345","fmax":"1158","strand":"+","sequence":"GTGGCCAATCTTGACGTTATTGTCGACCGTTCCGACCCCGCGGTGCAGCGCATCGTCGATGTGACCAAGCATTCCCGGTCCGTCGTGCGAACGGTGCTGATCGAGGACATCGAGCCCCTGACGCAGAGCATCCGCGCCGGGGTCGAGTTCACCGAGGTCTACGGTCTCGACACCGTGCCGTTCCCGGGTGATCTGCTCGCCGCCTGCGAAAAGCGCGGAATTCGGGTGCGGCTGCTCTCCGCCGCGGTCGCGAATCAGGTTTTCAAGACCGAGAAGAAGCCCAAGGTCTTCGGTATCGCGAAGGTTCCGCCGGCCGGCCGTTTCGCCGACCTGGAGAGCCTTTCCGGCGATGTCGTCCTGCTCGACGGCGTGAAGATCGTCGGCAACATCGGCGCCATCGTGCGGACGCGTTCGGCGCTCGGCGCCGCCGGCATCGTCCTGGTCGACAGCGGCCTCGGCACCATCGCGGACCGCCGGCTCATCCGCGCCAGCCGCGGCTACGTGTTCTCCCTGCCGATCGTGCTCGCGACGCGCGACGAGGCGCTGGCCTTCTTCCGTGACGGCGGGATGCGGCCCGTGGTCTTCGAGGCGGACGGCAAGCTGTCCATCGGAGAGCTCGACGGCATCGACGAGCGGCTCGTGCTCGTGTTCGGCAGCGAGAAGACCGGCCCGTCGGGCGAGTTCGCCGGGGTCGCCACCGAGTCGGTGTCCATCCCGATGAACCCCGCCGCCGAGTCGCTCAACGTCTCGGTGTCGGCCGGCATCGCCCTGCACCGGCGGGCCCGCCGCAACCTCTCGCGCCCGCGCGGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41352","NCBI_taxonomy_name":"Streptomyces laurentii","NCBI_taxonomy_id":"39478"}}}},"ARO_accession":"3003060","ARO_id":"39494","ARO_name":"tsnR","ARO_description":"tsnR is a 23S ribosomal RNA methyltransferase that methylates adenosine-1067 to confer resistance to thiostrepton","ARO_category":{"39499":{"category_aro_accession":"3003065","category_aro_cvterm_id":"39499","category_aro_name":"non-erm 23S ribosomal RNA methyltransferase (A1067)","category_aro_description":"Non-erm 23S ribosomal RNA methyltransferases modify adenosine 1067 to confer resistance to peptide antibiotics","category_aro_class_name":"AMR Gene Family"},"37030":{"category_aro_accession":"3000686","category_aro_cvterm_id":"37030","category_aro_name":"thiostrepton","category_aro_description":"Thiostrepton is a cyclic peptide active against Gram-positive bacteria. It is produced by streptomyces bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"166":{"model_id":"166","model_name":"TEM-77","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1960":{"protein_sequence":{"accession":"CAB65358.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMLSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSSGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AJ012256","fmin":"208","fmax":"1069","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGCTGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTAGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3000943","ARO_id":"37323","ARO_name":"TEM-77","ARO_description":"TEM-77 is an inhibitor-resistant beta-lactamase found in E. coli and Proteus mirabilis.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"167":{"model_id":"167","model_name":"CMY-39","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1099":{"protein_sequence":{"accession":"BAF95726.1","sequence":"MMKKSLCCALLLTAPLSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADITNNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWAPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWIKVPQSEQKDYAWGYREGKAVHVSPGQLDAEAYGVKSSVIDMARWVQVNMDASRVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"AB372224","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCCCTTTATCCACGTTTGCCGCCGCCAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCTGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCACCAATAACCACCCAGTCACGCAGCAAACTCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTACACGGCAGGCGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCGTTTTTATCAAAACTGGCAGCCGCAATGGGCCCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTAAAGTTCCGCAAAGCGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGGCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGTCAACATGGACGCCAGCCGCGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCAATCATCAACGGTAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACTGGAGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002050","ARO_id":"38450","ARO_name":"CMY-39","ARO_description":"CMY-39 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"168":{"model_id":"168","model_name":"VIM-17","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1330":{"protein_sequence":{"accession":"ABW90721.1","sequence":"MFKLLSKLLVYLTASMMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"EU118148","fmin":"1010","fmax":"1811","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATGATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAGC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002287","ARO_id":"38687","ARO_name":"VIM-17","ARO_description":"VIM-17 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"169":{"model_id":"169","model_name":"IMP-33","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1416":{"protein_sequence":{"accession":"AEU17778.1","sequence":"MKKLFVLCVCFFCSITAAGSSLPDLKIEKLEEGVFVHTSFEEVNGWGVVTKHGLVVLVNTDAYLIDTPFTATDTEKLVNWFVERGYKIKGTISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKSGKVQAKYSFSEVSYWLVKNKIEVFYPGPGHTQDNLVVWLPESKILFGGCFVKPHGLGNLGDANLEAWPKSAKILMSKYGKAKLVVSSHSEKGDASLLKRTWEQALKGLKESKKTSSPSN"},"dna_sequence":{"accession":"JN848782","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAAGAAATTATTTGTTTTATGTGTATGCTTCTTTTGTAGCATTACTGCCGCAGGATCGTCTTTACCTGATTTAAAAATTGAGAAGCTTGAAGAAGGTGTTTTTGTTCATACATCGTTCGAAGAAGTTAACGGTTGGGGGGTTGTTACTAAACACGGTTTGGTGGTGCTTGTAAACACAGACGCCTATCTAATTGACACTCCATTTACTGCTACAGACACTGAAAAATTAGTCAATTGGTTTGTGGAGCGCGGCTATAAAATCAAAGGCACTATTTCATCACATTTCCATAGCGACAGCACAGGAGGAATAGAGTGGCTTAATTCTCAATCTATTCCCACGTATGCATCTGAATTAACAAATGAACTTTTGAAAAAATCCGGTAAGGTACAAGCTAAATATTCATTTAGCGAAGTTAGCTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCTGGCCCAGGTCACACTCAAGATAACCTAGTGGTTTGGTTGCCTGAAAGTAAAATTTTATTCGGTGGTTGCTTTGTTAAACCTCACGGTCTTGGCAATTTAGGTGACGCAAATTTAGAAGCTTGGCCAAAGTCCGCCAAAATATTAATGTCTAAATATGGCAAAGCAAAGCTTGTTGTTTCAAGTCATAGTGAGAAAGGGGACGCATCACTATTGAAACGTACATGGGAACAAGCTCTTAAAGGGCTTAAAGAAAGTAAAAAAACATCATCACCAAGTAACTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002224","ARO_id":"38624","ARO_name":"IMP-33","ARO_description":"IMP-33 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"170":{"model_id":"170","model_name":"IMP-19","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1014":{"protein_sequence":{"accession":"ABM67078.1","sequence":"MKKLFVLCVCFLCSITAAGAALPDLKIEKLEEGVYVHTSFEEVNGWGVVSKHGLVVLVNTDAYLIDTPFTATDTEKLVNWFVERGYKIKGTISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKDGKVQAKNSFSGVSYWLVKNKIEVFYPGPGHTQDNVVVWLPEKKILFGGCFVKPDGLGNLGDANLEAWPKSAKILMSKYVKAKLVVSSHSEIGDASLLKRTWEQAVKGLNESKKPSQPSN"},"dna_sequence":{"accession":"EF118171","fmin":"3181","fmax":"3922","strand":"+","sequence":"ATGAAGAAATTATTTGTTTTATGTGTATGCTTCCTTTGTAGCATTACTGCCGCAGGAGCGGCTTTGCCTGATTTAAAAATCGAGAAGCTTGAAGAAGGTGTTTATGTTCATACATCGTTCGAAGAAGTTAACGGTTGGGGTGTTGTTTCTAAACACGGTTTGGTGGTTCTTGTAAACACTGACGCCTATCTGATTGACACTCCATTTACTGCTACAGATACTGAAAAGTTAGTCAATTGGTTTGTGGAGCGCGGCTATAAAATCAAAGGCACTATTTCCTCACATTTCCATAGCGACAGCACAGGGGGAATAGAGTGGCTTAATTCTCAATCTATTCCCACGTATGCATCTGAATTAACAAATGAACTTCTTAAAAAAGACGGTAAGGTGCAAGCTAAAAACTCATTTAGCGGAGTTAGTTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCCGGCCCGGGGCACACTCAAGATAACGTAGTGGTTTGGTTACCTGAAAAGAAAATTTTATTCGGTGGTTGTTTTGTTAAACCGGACGGTCTTGGTAATTTGGGTGACGCAAATTTAGAAGCTTGGCCAAAGTCCGCCAAAATATTAATGTCTAAATATGTTAAAGCAAAACTGGTTGTTTCAAGTCATAGTGAAATTGGGGACGCATCACTCTTGAAACGTACATGGGAACAGGCTGTTAAAGGGCTAAATGAAAGTAAAAAACCATCACAGCCAAGTAACTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36936","NCBI_taxonomy_name":"Aeromonas caviae","NCBI_taxonomy_id":"648"}}}},"ARO_accession":"3002210","ARO_id":"38610","ARO_name":"IMP-19","ARO_description":"IMP-19 is a beta-lactamase found in Aeromonas caviae","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"171":{"model_id":"171","model_name":"TEM-78","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2038":{"protein_sequence":{"accession":"AAF05612.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMVSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRREPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERDRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AF190693","fmin":"208","fmax":"1069","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGGTGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTCGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAGATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000944","ARO_id":"37324","ARO_name":"TEM-78","ARO_description":"TEM-78 is an inhibitor-resistant beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"173":{"model_id":"173","model_name":"arr-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"250"}},"model_sequences":{"sequence":{"524":{"protein_sequence":{"accession":"ABV26705.1","sequence":"MTNDWIPTSHDNCSQVAGPFYHGTKAKLTVGDLLSPGHPSHFEQGRKLKHIYFAALMEPAIWGAELAMSLSSLEGRGHIYIVEPLGPFEDDPNLTNKKFPGNPTKSYRTTEPLRIVGIVEDWQGHSPEVLQGMLASLEDLQRRGLAIIED"},"dna_sequence":{"accession":"EF660562","fmin":"1671","fmax":"2124","strand":"+","sequence":"ATGACGAATGACTGGATTCCCACTTCGCATGACAACTGCTCGCAAGTAGCGGGGCCGTTCTATCACGGCACCAAAGCCAAACTCACGGTTGGTGACTTGCTTTCCCCAGGACACCCGTCTCACTTTGAGCAAGGTCGCAAGCTCAAACACATCTACTTTGCCGCCCTGATGGAACCAGCCATCTGGGGAGCGGAGCTTGCGATGTCGCTGTCAAGCCTAGAGGGGCGCGGCCACATCTACATCGTTGAACCGCTCGGCCCATTTGAGGACGACCCGAACCTTACAAACAAGAAATTCCCGGGAAATCCAACCAAGTCCTATCGCACCACTGAGCCGCTGCGGATTGTTGGGATCGTAGAAGACTGGCAAGGCCACTCACCGGAGGTGTTACAGGGCATGTTGGCGTCTCTGGAGGATCTTCAGCGTCGTGGCCTCGCCATCATTGAGGACTAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002849","ARO_id":"39283","ARO_name":"arr-4","ARO_description":"arr-4 is an integron-encoded ribosyltransferase found in Pseudomonas aeruginosa","ARO_category":{"36529":{"category_aro_accession":"3000390","category_aro_cvterm_id":"36529","category_aro_name":"rifampin ADP-ribosyltransferase (Arr)","category_aro_description":"Enzyme responsible for the ADP-ribosylative inactivation of rifampin at the 23-OH position using NAD+.","category_aro_class_name":"AMR Gene Family"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36656":{"category_aro_accession":"3000517","category_aro_cvterm_id":"36656","category_aro_name":"rifaximin","category_aro_description":"Rifaximin is a semi-synthetic rifamycin used to treat traveller's diarrhea. Rifaximin inhibits RNA synthesis by binding to the beta subunit of bacterial RNA polymerase.","category_aro_class_name":"Antibiotic"},"36669":{"category_aro_accession":"3000530","category_aro_cvterm_id":"36669","category_aro_name":"rifabutin","category_aro_description":"Rifabutin is a semisynthetic rifamycin used in tuberculosis therapy. It inhibits DNA-dependent RNA synthesis.","category_aro_class_name":"Antibiotic"},"36673":{"category_aro_accession":"3000534","category_aro_cvterm_id":"36673","category_aro_name":"rifapentine","category_aro_description":"Rifapentine is a semisynthetic rifamycin that inhibits DNA-dependent RNA synthesis. It is often used in the treatment of tuberculosis and leprosy.","category_aro_class_name":"Antibiotic"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"174":{"model_id":"174","model_name":"CfxA2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"4289":{"protein_sequence":{"accession":"AAD23513.1","sequence":"MEKNRKKQIVVLSIALVCIFILVFSLFHKSATKDSANPPLTNVLTDSISQIVSACPGEIGVAVIVNNRDTVKVNNKSVYPMMSVFKVHQALALCNDFDNKGISLDTLVNINRDKLDPKTWSPMLKDYSGPVISLTVRDLLRYTLTQSDNNASNLMFKDMVNVAQTDSFIATLIPRSSFQIAYTEEEMSADHNKAYSNYTSPLGAAMLMNRLFTEGLIDDEKQSFIKNTLKECKTGVDRIAAPLLDKEGVVIAHKTGSGYVNENGVLAAHNDVAYICLPNNISYTLAVFVKDFKGNESQASQYVAHISAVVYSLLMQTSVKS"},"dna_sequence":{"accession":"AF118110","fmin":"71","fmax":"1037","strand":"-","sequence":"TTAAGATTTTACTGAAGTTTGCATTAATAAAGAATATACTACAGCTGATATATGCGCAACATATTGTGACGCTTGTGATTCATTTCCCTTGAAATCCTTAACAAATACCGCTAAGGTATAACTGATATTATTAGGCAGACATATATAGGCAACATCATTGTGAGCTGCAAGAACACCATTTTCATTAACATAACCTGAACCTGTCTTATGCGCTATAACAACCCCTTCTTTATCAAGAAGTGGAGCTGCTATCCTATCTACACCTGTTTTGCATTCTTTTAACGTATTCTTAATGAAACTTTGTTTCTCATCATCGATAAGACCTTCAGTAAACAAACGATTCATCAACATTGCAGCACCAAGAGGAGATGTATAGTTAGAGTAAGCCTTGTTATGGTCAGCCGACATTTCCTCTTCCGTATAAGCTATCTGAAAACTTGAACGAGGAATGAGTGTGGCTATAAAACTATCTGTTTGAGCGACATTAACCATATCCTTAAACATAAGGTTGCTTGCATTGTTGTCACTCTGAGTAAGAGTATAACGCAGCAAATCTCTCACTGTCAATGATATGACTGGCCCTGAATAATCTTTCAGCATAGGACTCCAAGTCTTTGGGTCAAGTTTATCCCTATTTATATTTACTAAGGTATCAAGTGAAATTCCTTTATTGTCAAAGTCATTACAAAGAGCTAATGCCTGATGAACCTTAAACACACTCATCATAGGATAAACACTCTTATTATTGACCTTAACCGTATCTCTGTTATTAACAATAACCGCCACACCAATTTCGCCAGGACAAGCTGAGACAATTTGAGAAATGCTATCAGTCAAAACATTTGTTAAAGGAGGATTTGCGCTATCTTTTGTCGCTGATTTATGGAACAATGAAAATACCAAGATGAAAATGCAAACTAAAGCTATACTCAAAACTACGATTTGTTTTTTTCTGTTTTTTTCCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39547","NCBI_taxonomy_name":"Prevotella intermedia","NCBI_taxonomy_id":"28131"}}}},"ARO_accession":"3003002","ARO_id":"39436","ARO_name":"CfxA2","ARO_description":"cfxA2 beta-lactamase is a class A beta-lactamase found in Prevotella intermedia","ARO_category":{"39434":{"category_aro_accession":"3003000","category_aro_cvterm_id":"39434","category_aro_name":"CfxA beta-lactamase","category_aro_description":"cfxA beta-lactamases are class A beta-lactamases","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"175":{"model_id":"175","model_name":"CTX-M-24","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1477":{"protein_sequence":{"accession":"AAN38836.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAERRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"AY143430","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGCGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001886","ARO_id":"38286","ARO_name":"CTX-M-24","ARO_description":"CTX-M-24 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"176":{"model_id":"176","model_name":"CMY-25","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1282":{"protein_sequence":{"accession":"ACA30420.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVTDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"EU515249","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACTGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACAGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAACCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002036","ARO_id":"38436","ARO_name":"CMY-25","ARO_description":"CMY-25 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"177":{"model_id":"177","model_name":"IMP-51","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"2108":{"protein_sequence":{"accession":"BAQ56016.1","sequence":"MKKLSVFFMFLFCSIAASGEALPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNTDAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKDGKVQAKNSFSGASYWLVKKKIEIFYPGPGHTPDNVVVWLPEHRVLFGGCFVKPYGLGNLGDANLEAWPKSAKLLVSKYGKAKLVVPGHSEVGDASLLKRTLEQAVKGLNESKKLSKPSN"},"dna_sequence":{"accession":"LC031883","fmin":"5071","fmax":"5812","strand":"+","sequence":"ATGAAAAAGTTATCAGTATTCTTTATGTTTTTGTTTTGTAGCATTGCTGCCTCAGGAGAGGCTTTGCCAGATTTAAAAATTGAGAAGCTTGACGAAGGCGTTTATGTTCATACTTCGTTTGAGGAAGTTAACGGCTGGGGCGTGGTTCCTAAACACGGCTTGGTGGTTCTTGTAAATACTGACGCTTATTTGATTGACACTCCATTTACAGCTAAAGATACTGAAAAGTTAGTTACTTGGTTTGTAGAGCGCGGCTATAAAATAAAAGGCAGTATCTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCAATCTATTCCAACATATGCATCTGAATTAACAAATGAACTTCTTAAAAAAGACGGTAAGGTACAAGCTAAAAATTCATTTAGCGGAGCCAGCTATTGGTTAGTTAAGAAAAAGATTGAAATTTTTTATCCTGGCCCAGGGCACACTCCAGATAACGTAGTGGTTTGGCTACCTGAACATAGAGTTTTGTTTGGTGGTTGTTTTGTTAAACCGTATGGTCTAGGTAATTTGGGTGACGCAAATTTAGAAGCTTGGCCAAAGTCTGCCAAATTATTAGTGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAGGTCACAGTGAAGTTGGAGATGCATCACTCTTGAAACGTACATTAGAACAGGCTGTTAAAGGATTAAACGAAAGTAAAAAGCTATCAAAACCAAGTAACTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3003659","ARO_id":"40269","ARO_name":"IMP-51","ARO_description":"From Lahey's list of beta-lactamases, no additional information available","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"178":{"model_id":"178","model_name":"vanHA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"3279":{"protein_sequence":{"accession":"AAA65955.1","sequence":"MNNIGITVYGCEQDEADAFHALSPRFGVMATIINANVSESNAKSAPFNQCISVGHKSEISASILLALKRAGVKYISTRSIGCNHIDTTAAKRMGITVDNVAYSPDSVADYTMMLILMAVRNVKSIVRSVEKHDFRLDSDRGKVLSDMTVGVVGTGQIGKAVIERLRGFGCKVLAYSRSRSIEVNYVPFDELLQNSDIVTLHVPLNTDTHYIISHEQIQRMKQGAFLINTGRGPLVDTYELVKALENGKLGGAALDVLEGEEEFFYSDCTQKPIDNQFLLKLQRMPNVIITPHTAYYTEQALRDTVEKTIKNCLDFERRQEHE"},"dna_sequence":{"accession":"M97297","fmin":"6018","fmax":"6986","strand":"+","sequence":"ATGAATAACATCGGCATTACTGTTTATGGATGTGAGCAGGATGAGGCAGATGCATTCCATGCTCTTTCGCCTCGCTTTGGCGTTATGGCAACGATAATTAACGCCAACGTGTCGGAATCCAACGCCAAATCCGCGCCTTTCAATCAATGTATCAGTGTGGGACATAAATCAGAGATTTCCGCCTCTATTCTTCTTGCGCTGAAGAGAGCCGGTGTGAAATATATTTCTACCCGAAGCATCGGCTGCAATCATATAGATACAACTGCTGCTAAGAGAATGGGCATCACTGTCGACAATGTGGCGTACTCGCCGGATAGCGTTGCCGATTATACTATGATGCTAATTCTTATGGCAGTACGCAACGTAAAATCGATTGTGCGCTCTGTGGAAAAACATGATTTCAGGTTGGACAGCGACCGTGGCAAGGTACTCAGCGACATGACAGTTGGTGTGGTGGGAACGGGCCAGATAGGCAAAGCGGTTATTGAGCGGCTGCGAGGATTTGGATGTAAAGTGTTGGCTTATAGTCGCAGCCGAAGTATAGAGGTAAACTATGTACCGTTTGATGAGTTGCTGCAAAATAGCGATATCGTTACGCTTCATGTGCCGCTCAATACGGATACGCACTATATTATCAGCCACGAACAAATACAGAGAATGAAGCAAGGAGCATTTCTTATCAATACTGGGCGCGGTCCACTTGTAGATACCTATGAGTTGGTTAAAGCATTAGAAAACGGGAAACTGGGCGGTGCCGCATTGGATGTATTGGAAGGAGAGGAAGAGTTTTTCTACTCTGATTGCACCCAAAAACCAATTGATAATCAATTTTTACTTAAACTTCAAAGAATGCCTAACGTGATAATCACACCGCATACGGCCTATTATACCGAGCAAGCGTTGCGTGATACCGTTGAAAAAACCATTAAAAACTGTTTGGATTTTGAAAGGAGACAGGAGCATGAATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002942","ARO_id":"39376","ARO_name":"vanHA","ARO_description":"vanHA, also known as vanH, is a vanH variant in the vanA gene cluster","ARO_category":{"36015":{"category_aro_accession":"3000006","category_aro_cvterm_id":"36015","category_aro_name":"vanH","category_aro_description":"VanH is a D-specific alpha-ketoacid dehydrogenase that synthesizes D-lactate. D-lactate is incorporated into the end of the peptidoglycan subunits, decreasing vancomycin binding affinity.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"35948":{"category_aro_accession":"0000029","category_aro_cvterm_id":"35948","category_aro_name":"teicoplanin","category_aro_description":"Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation  and transpeptidation.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"179":{"model_id":"179","model_name":"QnrA5","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"588":{"protein_sequence":{"accession":"AAZ04784.1","sequence":"MDIIDKVFQQEDFSRQDLSDSRFRRCRFYQCDFSHCQLRDASFEDCSFIESGAVEGCHFSYADLRDASFKACRLSLANFSGANCFGIEFRECDLKGANFSRARFYNQISHKMYFCSAYISGCNLAYANLSGQCLEKCELFENNWSNANLSGASLMGSDLSCGTFSRDCWQQVNLRGCDLTFADLDGLDPRRVNLEGVKICAWQQEQLLEPLGVIVLPD"},"dna_sequence":{"accession":"DQ058663","fmin":"0","fmax":"657","strand":"+","sequence":"ATGGATATTATTGATAAAGTTTTTCAGCAAGAGGATTTCTCACGCCAGGATTTGAGTGACAGCCGTTTTCGCCGCTGCCGCTTTTATCAGTGTGACTTCAGCCATTGCCAGCTAAGGGATGCCAGTTTCGAGGATTGCAGTTTCATTGAAAGCGGCGCCGTCGAAGGGTGCCACTTCAGCTATGCCGATCTGCGCGATGCCAGTTTCAAGGCCTGCCGCCTGTCTTTGGCCAATTTCAGCGGTGCCAACTGCTTTGGCATAGAGTTCAGGGAGTGCGATCTCAAGGGCGCCAATTTTTCCCGGGCCCGTTTTTACAATCAAATCAGCCATAAGATGTACTTCTGCTCGGCTTATATCTCAGGCTGCAACCTGGCCTATGCCAATTTGAGCGGCCAATGCCTGGAAAAGTGCGAGCTGTTTGAAAACAACTGGAGCAATGCCAACCTCAGCGGCGCTTCCTTGATGGGCTCCGACCTCAGCTGCGGCACCTTCTCCCGCGACTGCTGGCAGCAGGTAAACCTGCGGGGCTGTGACCTGACTTTTGCCGATCTGGATGGGCTCGATCCCAGACGGGTCAACCTCGAAGGGGTCAAGATCTGTGCCTGGCAGCAGGAGCAACTGCTGGAACCCTTGGGAGTCATAGTGCTGCCGGATTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36891","NCBI_taxonomy_name":"Shewanella algae","NCBI_taxonomy_id":"38313"}}}},"ARO_accession":"3002711","ARO_id":"39145","ARO_name":"QnrA5","ARO_description":"QnrA5 is a plasmid-mediated quinolone resistance protein found in Shewanella algae","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"180":{"model_id":"180","model_name":"DHA-19","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1258":{"protein_sequence":{"accession":"AIT76102.1","sequence":"MKKSLSATLISALLAFSAPGFSAADNVAAVVDSTIKPLMAQQDIPGMAVAVSVKGKPYYFNYGFADVQAKQPVTENTLFELGSVSKTFTGVLGAVSVAKKEMALNDPAAKYQPELALPQWKGITLLDLATYTAGGLPLQVPDAVKSRADLLNFYQQWQPSWKPGDMRLYANSSIGLFGALTANAAGMPYEQLLTARILAPLGLSHTFITVPESAQSQYAYGYKNKKPVRVSPEQLDAESYGVKSASKDMLRWAEMNMEPSRAGNADLEMAMYLAQTRYYKTAAINQGLGWEMYDWPQQKDMIINGVTNEVALQPHPVTDNQVQPYNRASWVHKTGATTGFGAYVAFIPEKQVAIVILANKNYPNTERVKAAQAILSALE"},"dna_sequence":{"accession":"KM087849","fmin":"0","fmax":"1140","strand":"+","sequence":"ATGAAAAAATCGTTATCTGCAACACTGATTTCCGCTCTGCTGGCGTTTTCCGCCCCGGGGTTTTCTGCCGCTGATAATGTCGCGGCGGTGGTGGACAGCACCATTAAACCGCTGATGGCACAGCAGGATATTCCCGGGATGGCGGTTGCCGTCTCCGTAAAGGGTAAGCCCTATTATTTCAATTACGGTTTTGCCGATGTTCAGGCAAAACAGCCTGTCACTGAAAATACACTATTTGAGCTCGGATCTGTAAGTAAAACTTTCACAGGTGTGCTGGGTGCGGTTTCCGTGGCGAAAAAAGAGATGGCGCTGAATGATCCGGCGGCAAAATATCAGCCGGAGCTGGCTCTGCCGCAGTGGAAGGGGATCACGCTGCTGGATCTGGCCACCTATACCGCAGGCGGGCTGCCGTTACAGGTACCGGATGCGGTGAAAAGCCGTGCGGATCTGCTGAATTTCTATCAGCAGTGGCAGCCATCATGGAAACCGGGCGATATGCGTCTGTATGCAAACAGCAGTATCGGCCTGTTTGGTGCTCTGACCGCCAACGCGGCGGGGATGCCGTATGAGCAGTTGCTGACTGCACGGATCCTGGCACCGCTGGGGTTATCTCACACCTTTATTACTGTGCCGGAAAGTGCGCAAAGCCAGTATGCGTACGGTTATAAAAACAAAAAACCGGTCCGCGTGTCGCCGGAACAGCTTGATGCGGAATCTTACGGCGTGAAATCCGCCTCAAAAGATATGCTGCGCTGGGCGGAAATGAATATGGAGCCGTCACGGGCCGGTAATGCGGATCTGGAAATGGCAATGTATCTTGCACAGACCCGCTACTATAAAACCGCCGCGATTAACCAGGGGCTGGGCTGGGAAATGTATGACTGGCCGCAGCAGAAAGATATGATCATTAACGGCGTGACCAACGAGGTCGCATTGCAGCCGCACCCGGTAACAGACAACCAGGTTCAGCCGTATAACCGTGCTTCCTGGGTGCATAAAACGGGGGCAACAACTGGTTTCGGCGCCTATGTGGCCTTTATTCCGGAAAAACAGGTGGCGATTGTGATTCTGGCGAATAAAAACTACCCGAATACCGAAAGAGTCAAAGCCGCACAGGCTATTTTGAGTGCACTGGAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36917","NCBI_taxonomy_name":"Morganella morganii","NCBI_taxonomy_id":"582"}}}},"ARO_accession":"3002150","ARO_id":"38550","ARO_name":"DHA-19","ARO_description":"DHA-19 is a beta-lactamase. From the Lahey list of DHA beta-lactamases.","ARO_category":{"36207":{"category_aro_accession":"3000068","category_aro_cvterm_id":"36207","category_aro_name":"DHA beta-lactamase","category_aro_description":"DHA beta-lactamases are plasmid-mediated AmpC \u03b2-lactamases that confer resistance to cephamycins and oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"181":{"model_id":"181","model_name":"GES-14","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1984":{"protein_sequence":{"accession":"ADC91899.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMSDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGARNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"GU207844","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGAGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGCCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3002343","ARO_id":"38743","ARO_name":"GES-14","ARO_description":"GES-14 is a beta-lactamase found in Acinetobacter baumannii","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"182":{"model_id":"182","model_name":"arlS","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"880"}},"model_sequences":{"sequence":{"4290":{"protein_sequence":{"accession":"YP_499945.1","sequence":"MTKRKLRNNWIIVTTMITFVTIFLFCLIIIFFLKDTLHNSELDDAERSSSDINNLFHSKPVKDISALDLNASLGNFQEIIIYDEHNNKLFETSNDNTVRVEPGYEHRYFDRVIKKRYKGIEYLIIKEPITTQDFKGYSLLIHSLENYDNIVKSLYIIALAFGVIATIITATISYVFSTQITKPLVSLSNKMIEIRRDGFQNKLQLNTNYEEIDNLANTFNEMMSQIEESFNQQRQFVEDASHELRTPLQIIQGHLNLIQRWGKKDPAVLEESLNISIEEMNRIIKLVEELLELTKGDVNDISSEAQTVHINDEIRSRIHSLKQLHPDYQFDTDLTSKNLEIKMKPHQFEQLFLIFIDNAIKYDVKNKKIKVKTRLKNKQKIIEITDHGIGIPEEDQDFIFDRFYRVDKSRSRSQGGNGLGLSIAQKIIQLNGGSIKIKSEINKGTTFKIIF"},"dna_sequence":{"accession":"NC_007795","fmin":"1360280","fmax":"1361636","strand":"-","sequence":"TTAAAATATGATTTTAAACGTTGTTCCTTTGTTAATTTCACTTTTAATTTTAATCGATCCTCCGTTTAATTGAATGATTTTTTGAGCAATAGATAATCCGAGTCCATTACCGCCTTGACTTCTTGAACGAGATTTATCCACTCGATAAAAGCGATCAAAAATGAAATCTTGATCTTCCTCTGGAATACCAATTCCATGATCTGTAATTTCAATTATTTTTTGCTTATTTTTTAACCTTGTCTTAACTTTAATTTTCTTATTCTTCACATCATATTTGATTGCATTATCAATAAAGATTAAAAATAATTGTTCGAATTGATGAGGTTTCATTTTAATTTCTAGATTTTTAGATGTCAGATCCGTATCAAATTGATAATCAGGATGCAATTGTTTTAATGAGTGTATTCGCGAGCGAATTTCATCATTAATATGCACGGTCTGTGCTTCAGAAGAAATGTCATTTACATCTCCTTTAGTCAATTCAAGTAATTCTTCGACTAATTTTATGATACGATTCATTTCTTCAATAGAAATATTTAACGATTCTTCTAATACTGCTGGGTCTTTTTTTCCCCATCGCTGAATCAAATTTAAATGACCTTGAATAATTTGTAATGGTGTTCGTAATTCATGTGACGCATCTTCAACAAATTGTCTTTGTTGATTAAATGATTCTTCAATTTGGCTCATCATCTCATTAAACGTATTTGCTAAATTATCTATTTCTTCATAATTTGTATTTAATTGCAATTTATTTTGAAAACCATCTCGTCGAATCTCAATCATTTTATTTGATAAACTGACAAGCGGTTTAGTAATTTGTGTTGAAAATACATAACTGATTGTGGCAGTTATAATTGTTGCAATCACTCCAAATGCCAGCGCAATGATATACAATGATTTTACGATGTTATCATAATTTTCTAGTGAATGAATTAACAAGCTATACCCTTTGAAATCTTGCGTTGTAATTGGTTCTTTAATAATTAAATATTCAATGCCTTTATAGCGTTTTTTTATTACGCGGTCAAAATAACGGTGTTCATAACCTGGTTCAACTCTCACTGTGTTATCATTCGATGTCTCAAATAATTTATTATTATGCTCATCATAAATAATTATCTCTTGAAAATTACCTAAAGATGCATTCAAGTCTAATGCAGATATATCTTTAACAGGCTTAGAATGAAATAAATTATTAATATCGCTTGAGCTTCGTTCTGCATCATCAAGCTCACTATTATGCAGTGTATCTTTCAAGAAAAAAATAATAATTAAACAAAACAAAAATATCGTGACAAACGTAATCATCGTGGTAACAATAATCCAGTTATTGCGCAATTTACGTTTTGTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35511","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus NCTC 8325","NCBI_taxonomy_id":"93061"}}}},"ARO_accession":"3000839","ARO_id":"37219","ARO_name":"arlS","ARO_description":"ArlS is a protein histidine kinase that phosphorylates ArlR, a promoter for norA expression.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavin","category_aro_description":"Acriflavin is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36193":{"category_aro_accession":"3000054","category_aro_cvterm_id":"36193","category_aro_name":"acridine dye","category_aro_description":"Acridine dyes are cell permeable, basic molecules with an acridine chromophore. These compounds intercalate DNA. The image shown represents the core structure of the acridine family, with specific dyes containing varying substituents.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"183":{"model_id":"183","model_name":"adeS","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"596":{"protein_sequence":{"accession":"ADM92606.1","sequence":"MKSKLGISKQLFIALTIVNLSVTLFSIVLGYIIYNYAIEKGWISLSSFQQEDWTSFHFVDWIWLATVIFCGCIISLVIGMRLAKRFIVPINFLVEAAKKISHGDLSARAYDNRIHSAEMSELLYNFNDMAQKLEVSVKNAQVWNAAIAHELRTPITILQGRLQGIIDGVFKPDEVLFKSLLNQVEGLSHLVEDLRTLSLVENQQLRLNYELFDLKAVVEKVLKAFEDRLDQAKLVPELDLTSTPVYCDRRRIEQVLIALIDNAIRYSNAGKLKISSEVVADNWILKIEDEGPGIATEFRDDLFKPFFRLEESRNKEFGGTGLGLAVVHAIIVALKGTIKYSNQGSKSVFTIKISMGHEEMG"},"dna_sequence":{"accession":"HM440348","fmin":"775","fmax":"1861","strand":"+","sequence":"ATGAAAAGTAAGTTAGGAATTAGTAAGCAACTTTTTATTGCCTTAACTATTGTGAATTTAAGCGTTACGCTATTTTCTATAGTATTGGGTTATATCATTTATAACTATGCGATTGAAAAAGGCTGGATTAGCTTAAGCTCATTTCAACAAGAAGATTGGACCAGTTTTCATTTTGTAGACTGGATCTGGTTAGCCACTGTTATCTTCTGTGGCTGTATTATTTCATTAGTGATTGGCATGCGCCTCGCAAAGCGTTTTATTGTGCCAATTAACTTCTTAGTCGAAGCAGCAAAAAAAATTAGTCACGGCGACCTCTCTGCTAGAGCTTACGATAATAGAATTCACTCCGCCGAAATGTCGGAGCTTTTATATAATTTTAATGATATGGCTCAAAAGCTAGAGGTTTCCGTCAAAAATGCGCAGGTTTGGAATGCAGCTATCGCACATGAGTTAAGAACGCCTATAACGATATTACAAGGTCGTTTACAGGGAATTATTGATGGCGTTTTTAAACCTGATGAAGTCCTATTTAAAAGCCTTTTAAATCAAGTTGAAGGTTTATCTCACTTAGTCGAAGACTTACGGACTTTAAGCTTAGTAGAGAACCAGCAACTCCGGTTAAATTATGAATTGTTTGACTTGAAGGCGGTAGTTGAAAAAGTTCTTAAAGCATTTGAAGATCGTTTGGATCAAGCTAAGCTAGTACCAGAACTTGACCTAACGTCCACTCCTGTATATTGCGACCGCCGTCGTATTGAGCAAGTTTTAATTGCTTTAATTGATAATGCGATTCGCTATTCAAATGCAGGCAAACTTAAAATCTCTTCAGAAGTGGTTGCAGACAACTGGATATTAAAAATTGAGGATGAAGGCCCCGGCATTGCAACCGAGTTTCGGGACGATTTATTTAAGCCTTTCTTTAGATTAGAAGAATCAAGGAATAAAGAATTTGGCGGCACAGGTTTAGGTCTTGCTGTTGTACATGCAATTATTGTGGCACTGAAAGGCACTATTAAATATAGCAATCAAGGCTCGAAAAGTGTTTTCACCATAAAAATTTCTATGGGTCATGAAGAGATGGGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3000549","ARO_id":"36688","ARO_name":"adeS","ARO_description":"AdeS is a sensor kinase in the AdeRS regulatory system of AdeABC. It is essential for AdeABC expression.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"184":{"model_id":"184","model_name":"OCH-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1426":{"protein_sequence":{"accession":"CAC04522.1","sequence":"MRKSTTLLIGFLTTAAIIPNSGALAASKVNDGDLRRIVDETVRPLMAEQKIPGMAVAITIDGKSHFFGYGVASKESGQKVTEDTIFEIGSVSKTFTAMLGGYGLATGAFSLSDPATKWAPELAGSSFDKITMRDLGTYTPGGLPLQFPDAVTDDSSMLAYFKKWKPDYPAGTQRRYSNPSIGLFGYLAARSMDKPFDVLMEQKLLPAFGLKNTFINVPASQMKNYAYGYSKANKPIRVSGGALDAQAYGIKTTALDLARFVELNIDSSSLEPDFQKAVAATHTGYYHVGANNQGLGWEFYNYPTALKTLLEGNSSDMALKSHKIEKFDTPRQPSADVLINKTGSTNGFGAYAAFIPAKKTGIVLLANRNYPIDERVKAAYRILQALDNKQ"},"dna_sequence":{"accession":"AJ401618","fmin":"1971","fmax":"3144","strand":"+","sequence":"ATGAGAAAATCTACGACACTTTTGATCGGTTTCCTCACCACTGCCGCTATTATCCCGAATAGCGGCGCGCTGGCTGCGAGCAAGGTGAATGATGGCGACTTGCGCCGTATTGTCGATGAAACGGTGCGCCCGCTCATGGCCGAGCAGAAAATCCCCGGCATGGCGGTTGCCATAACCATCGACGGCAAGAGCCACTTCTTCGGTTATGGTGTGGCATCGAAAGAAAGCGGGCAAAAAGTCACTGAAGACACGATTTTCGAGATCGGTTCGGTCAGCAAGACCTTCACTGCAATGCTTGGCGGTTACGGGCTGGCGACAGGCGCGTTCTCCCTGTCCGATCCCGCGACCAAATGGGCTCCTGAACTGGCAGGCAGCAGCTTCGACAAGATCACCATGCGTGATCTTGGGACCTACACGCCGGGCGGATTGCCCCTCCAGTTTCCCGATGCTGTCACCGATGACAGTTCGATGCTGGCATATTTCAAGAAATGGAAGCCGGACTATCCGGCAGGGACGCAGCGTCGCTATTCGAATCCCAGCATCGGCCTGTTCGGCTATCTGGCGGCACGAAGCATGGACAAGCCGTTCGACGTTTTGATGGAGCAAAAGCTTCTGCCTGCATTCGGCCTGAAGAACACCTTCATCAATGTGCCGGCAAGCCAGATGAAGAACTACGCCTACGGCTATTCCAAAGCCAACAAGCCGATCCGGGTATCGGGCGGGGCGCTGGATGCACAAGCCTATGGCATCAAGACCACCGCGCTTGATCTTGCCCGCTTCGTCGAACTGAACATCGACAGCTCATCTCTGGAGCCTGATTTCCAGAAAGCCGTCGCCGCAACGCATACCGGTTACTACCATGTCGGAGCGAACAATCAGGGACTTGGCTGGGAGTTCTACAACTATCCGACTGCGCTCAAGACGCTTCTTGAGGGCAACTCGTCGGACATGGCGCTGAAGTCGCACAAAATCGAGAAATTCGATACACCTCGCCAACCGTCAGCTGATGTGCTGATCAATAAGACAGGCTCAACCAACGGCTTTGGCGCTTATGCGGCCTTTATTCCTGCGAAGAAGACCGGAATTGTTCTGCTTGCCAACCGGAATTATCCGATCGATGAGCGCGTAAAGGCTGCCTATCGGATATTGCAGGCGCTCGACAACAAGCAATAGG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37077","NCBI_taxonomy_name":"Ochrobactrum anthropi","NCBI_taxonomy_id":"529"}}}},"ARO_accession":"3002514","ARO_id":"38914","ARO_name":"OCH-1","ARO_description":"OCH-1 beta-lactamase is an Ambler class C chromosomal-encoded beta-lactamases in Ochrobactrum anthropi","ARO_category":{"36233":{"category_aro_accession":"3000094","category_aro_cvterm_id":"36233","category_aro_name":"OCH beta-lactamase","category_aro_description":"OCH beta-lactamases are Ambler class C chromosomal-encoded beta-lactamases in Ochrobactrum anthropi","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"185":{"model_id":"185","model_name":"OXA-232","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1129":{"protein_sequence":{"accession":"AGD91915.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIAAWNRDHDLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATQQIAFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTSIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"JX423831","fmin":"2676","fmax":"3474","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCAGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGTGATATCGCCGCTTGGAATCGTGACCATGACTTAATTACCGCGATGAAGTACTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGTGAGGCACGTATGAGTAAAATGCTGCACGCCTTCGATTATGGCAATGAGGATATCTCGGGCAATGTAGACAGTTTTTGGCTCGATGGTGGTATTCGCATTTCGGCTACCCAGCAAATCGCTTTTTTACGCAAGCTGTATCACAACAAGCTGCACGTTTCTGAGCGTAGTCAGCGCATCGTGAAACAAGCCATGCTGACCGAAGCCAATGGCGACTATATTATTCGGGCTAAAACGGGATACTCGACTAGTATCGAACCTAAGATTGGCTGGTGGGTTGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAGAAAATTATTCCCTAGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001778","ARO_id":"38178","ARO_name":"OXA-232","ARO_description":"OXA-232 is a beta-lactamase found in Enterobacteriaceae","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"186":{"model_id":"186","model_name":"OXA-12","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1123":{"protein_sequence":{"accession":"AAA83417.1","sequence":"MSRLLLSGLLATGLLCAVPASAASGCFLYADGNGQTLSSEGDCSSQLPPASTFKIPLALMGYDSGFLVNEEHPALPYKPSYDGWLPAWRETTTPRRWETYSVVWFSQQITEWLGMERFQQYVDRFDYGNRDLSGNPGKHDGLTQAWLSSSLAISPEEQARFLGKMVSGKLPVSAQTLQYTANILKVSEVEGWQIHGKTGMGYPKKLDGSLNRDQQIGWFVGWASKPGKQLIFVHTVVQKPGKQFASIKAKEEVLAALPAQLKKL"},"dna_sequence":{"accession":"U10251","fmin":"180","fmax":"975","strand":"+","sequence":"ATGTCTCGCCTGCTTCTTTCCGGCCTGCTGGCTACCGGTCTGCTCTGTGCAGTACCGGCCTCCGCCGCCAGCGGCTGTTTTCTCTATGCCGATGGCAACGGTCAGACCCTCTCCAGCGAAGGGGACTGCTCCAGCCAGCTGCCGCCCGCATCCACCTTCAAGATCCCGCTGGCGCTGATGGGTTATGACAGTGGCTTTCTGGTGAATGAAGAGCATCCGGCGCTGCCCTACAAGCCGAGCTATGACGGCTGGCTGCCCGCCTGGCGCGAAACCACTACCCCGCGCCGCTGGGAAACCTATTCGGTGGTCTGGTTCTCCCAGCAGATCACCGAGTGGCTGGGGATGGAGCGCTTCCAGCAATACGTCGACCGCTTCGACTACGGCAACCGGGATCTCTCCGGCAATCCGGGCAAGCATGACGGTCTGACCCAAGCCTGGCTCAGCTCGAGCCTCGCCATCAGTCCGGAGGAGCAGGCTCGCTTCCTCGGCAAGATGGTGAGCGGCAAGCTGCCGGTCTCGGCGCAGACCCTGCAGTACACCGCCAATATCCTCAAGGTGAGCGAGGTCGAGGGCTGGCAGATCCACGGCAAGACCGGCATGGGCTACCCGAAGAAACTGGATGGCAGCCTCAACCGCGATCAGCAGATCGGCTGGTTCGTCGGCTGGGCCAGCAAACCGGGCAAGCAGCTCATTTTCGTTCATACCGTGGTGCAGAAACCGGGCAAGCAATTCGCCTCTATCAAGGCGAAAGAAGAGGTGCTGGCCGCCCTGCCCGCGCAACTCAAGAAACTCTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36957","NCBI_taxonomy_name":"Aeromonas sobria","NCBI_taxonomy_id":"646"}}}},"ARO_accession":"3001407","ARO_id":"37807","ARO_name":"OXA-12","ARO_description":"OXA-12 is a beta-lactamase found in Aeromonas jandaei","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"187":{"model_id":"187","model_name":"OXA-348","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"808":{"protein_sequence":{"accession":"AGW83446.1","sequence":"MYKKALIVATSILFLSACSSNMVKQHQIHSISANKNSEEIKSLFDQAQTTGVLVIKRGQTEEIYGNDLKRASTDYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPDWEKDMTLSDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNANIGSKVDDFWLVGPLKITPQQETQFAYQLAHKTLPFSKNVQEQVQSMVFIEEKNGSKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"KF297577","fmin":"0","fmax":"822","strand":"+","sequence":"ATGTATAAAAAAGCCCTTATCGTTGCAACAAGTATCCTATTTTTATCCGCCTGTTCTTCCAATATGGTCAAACAACATCAAATACACTCTATTTCTGCCAATAAAAATTCAGAAGAAATTAAATCACTGTTTGATCAAGCACAGACCACTGGAGTTTTGGTGATTAAGCGAGGGCAAACAGAAGAAATTTATGGCAATGATCTTAAAAGAGCATCAACCGACTATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTAATTGGACTTGAACATCATAAGGCAACTACAACTGAAGTATTTAAATGGAATGGGCAAAAACGTTTATTTCCTGATTGGGAAAAGGACATGACACTGAGCGATGCCATGAAAGCTTCTGCAATTCCAGTTTACCAAGAATTAGCCCGACGGATTGGTCTGGATCTTATGTCCAAAGAGGTGAAACGAATTGGTTTCGGTAATGCTAACATTGGCTCAAAAGTAGATGATTTTTGGCTTGTTGGCCCTCTAAAAATTACACCTCAACAAGAAACCCAATTTGCTTATCAATTAGCCCATAAAACTCTTCCATTTAGCAAAAATGTACAAGAACAAGTTCAATCGATGGTGTTCATAGAGGAAAAAAATGGAAGTAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTTGAACCGCAAGTTGGTTGGTTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTGGCATTTTCACTTAATTTAGAAATGAAAAAAGGAACTCCTAGCTCTATTCGCAAAGAAATTGCTTATAAAGGCTTAGAACAACTGGGTATTTTATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3001535","ARO_id":"37935","ARO_name":"OXA-348","ARO_description":"OXA-348 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"188":{"model_id":"188","model_name":"SHV-89","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1641":{"protein_sequence":{"accession":"ABA60809.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITVSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"DQ193536","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCGTGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATCGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001141","ARO_id":"37521","ARO_name":"SHV-89","ARO_description":"SHV-89 is a broad-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"189":{"model_id":"189","model_name":"CTX-M-19","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1009":{"protein_sequence":{"accession":"AAK55534.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTESTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"AF325134","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAATCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001881","ARO_id":"38281","ARO_name":"CTX-M-19","ARO_description":"CTX-M-19 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"190":{"model_id":"190","model_name":"OXA-195","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2003":{"protein_sequence":{"accession":"AEB98921.1","sequence":"MNIKALFLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWVVGPLKITPQQEAQFAYKLANKTLPSSQKVQDEVQSMLFIEEKNGNKMYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"HQ425493","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAACATTAAAGCACTCTTCCTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGGTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATCTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAGAAGAATGGAAACAAAATGTACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36949","NCBI_taxonomy_name":"Acinetobacter nosocomialis","NCBI_taxonomy_id":"106654"}}}},"ARO_accession":"3001480","ARO_id":"37880","ARO_name":"OXA-195","ARO_description":"OXA-195 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"191":{"model_id":"191","model_name":"OXA-199","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1047":{"protein_sequence":{"accession":"AFC95894.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEYKSQGVVALWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVGSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"JN704570","fmin":"4038","fmax":"4836","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAATATAAATCACAGGGCGTAGTTGCGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGGCAGTTTCTGGCTCGACGGTGGTATTCGAATTTCGGCCACTGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATGCTGACCGAAGCCAATGGCGACTATATTATTCGGGCTAAAACTGGATACTCGACTAGAATCGAACCTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39674","NCBI_taxonomy_name":"Shewanella xiamenensis","NCBI_taxonomy_id":"332186"}}}},"ARO_accession":"3001814","ARO_id":"38214","ARO_name":"OXA-199","ARO_description":"OXA-199 is a beta-lactamase found in Shewanella spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"192":{"model_id":"192","model_name":"CTX-M-38","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1352":{"protein_sequence":{"accession":"AAV70602.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAARIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"AY822595","fmin":"22","fmax":"898","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGAATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001900","ARO_id":"38300","ARO_name":"CTX-M-38","ARO_description":"CTX-M-38 is a beta-lactamase found in Escherichia coli","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"193":{"model_id":"193","model_name":"TEM-121","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1154":{"protein_sequence":{"accession":"AAQ01671.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGTGKRGSSGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AY271267","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAACCGGTAAGCGTGGGTCTAGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000983","ARO_id":"37363","ARO_name":"TEM-121","ARO_description":"TEM-121 is an inhibitor-resistant, extended-spectrum beta-lactamase found in E. coli and Enterobacter aerogenes.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"194":{"model_id":"194","model_name":"SHV-61","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"2026":{"protein_sequence":{"accession":"CAI30650.2","sequence":"MRYIRRCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AJ866284","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCGGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001116","ARO_id":"37496","ARO_name":"SHV-61","ARO_description":"SHV-61 is a broad-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"195":{"model_id":"195","model_name":"CTX-M-58","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1705":{"protein_sequence":{"accession":"ABM97538.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAVAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVDGTMSLAELSAAALQYSDNVAMNKLISHVGGPASVTAFARQLGDETFRLDRTETTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTNGL"},"dna_sequence":{"accession":"EF210159","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGTCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGAAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGTGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACTTGGTTAACTATAATCCGATTGCGGAAAAGCACGTCGATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTTCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGACGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGTAATCTGACGCTGGGTAAAGCATTGGGTGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCAACGGTTTGTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001919","ARO_id":"38319","ARO_name":"CTX-M-58","ARO_description":"CTX-M-58 is a beta-lactamase found in Escherichia coli","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"197":{"model_id":"197","model_name":"CTX-M-56","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1629":{"protein_sequence":{"accession":"ABN48311.1","sequence":"MMTQSIRRSMLTVMATLPLLFSSATLHAQANSVQQQLEALEKSSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKQSESDKHLLNQRVEIKKSDLVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSASIRAGLPKSWVVGDKTGSGDYGTTNDIAVIWPENHAPLVLVTYFTQPEQKAENRRDILAAAAKIVTHGF"},"dna_sequence":{"accession":"EF374097","fmin":"0","fmax":"876","strand":"+","sequence":"ATGATGACTCAGAGCATTCGCCGCTCAATGTTAACGGTGATGGCGACGCTACCCCTGCTATTTAGCAGCGCAACGCTGCATGCGCAGGCGAACAGCGTGCAACAGCAGCTGGAAGCCCTGGAGAAAAGTTCGGGAGGTCGGCTTGGCGTTGCGCTGATTAACACCGCCGATAATTCGCAGATTCTCTACCGTGCCGATGAACGTTTTGCGATGTGCAGTACCAGTAAGGTGATGGCGGCCGCGGCGGTGCTTAAACAGAGCGAGAGCGATAAGCACCTGCTAAATCAGCGCGTTGAAATCAAGAAGAGCGACCTGGTTAACTACAATCCCATTGCGGAGAAACACGTTAACGGCACGATGACGCTGGCTGAGCTTGGCGCAGCGGCGCTGCAGTATAGCGACAATACTGCCATGAATAAGCTGATTGCCCATCTGGGTGGTCCCGATAAAGTGACGGCGTTTGCTCGCTCGTTGGGTGATGAGACCTTCCGTCTGGACAGAACCGAGCCCACGCTCAATACCGCCATTCCAGGCGACCCGCGTGATACCACCACGCCGCTCGCGATGGCGCAGACCCTGAAAAATCTGACGCTGGGTAAAGCGCTGGCGGAAACTCAGCGGGCACAGTTGGTGACGTGGCTTAAGGGCAATACTACCGGTAGCGCGAGCATTCGGGCGGGTCTGCCGAAATCATGGGTAGTGGGCGATAAAACCGGCAGCGGAGATTATGGCACCACCAACGATATCGCGGTTATCTGGCCGGAAAACCACGCACCGCTGGTTCTGGTGACCTACTTTACCCAACCGGAGCAGAAGGCGGAAAACCGTCGGGATATTCTGGCTGCGGCGGCGAAAATCGTAACCCACGGTTTCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001918","ARO_id":"38318","ARO_name":"CTX-M-56","ARO_description":"CTX-M-56 is a beta-lactamase found in Escherichia coli","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"198":{"model_id":"198","model_name":"TEM-138","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1242":{"protein_sequence":{"accession":"AAW47922.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPIDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AY853593","fmin":"214","fmax":"1075","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAATCGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35672","NCBI_taxonomy_name":"Salmonella enterica","NCBI_taxonomy_id":"28901"}}}},"ARO_accession":"3001002","ARO_id":"37382","ARO_name":"TEM-138","ARO_description":"TEM-138 is an extended-spectrum beta-lactamase found in Salmonella enterica.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"199":{"model_id":"199","model_name":"SRT-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"725"}},"model_sequences":{"sequence":{"1718":{"protein_sequence":{"accession":"BAA23130.1","sequence":"MTKMNRLAAALIAALILPTAQAAQQQDIDAVIQPLMKKYGVPGMAIAVSVDGKQQIYPYGVASKQTGKPITEQTLFEVGSLSKTFTATLAVYAQQQGKLSFNDPASRYLPELRGSAFDGVSLLNLATHTSGLPLFVPDDVTNDAQLMAYYRAWQPKHPAGSYRVYSNLGIVMLGMIAAKSLDQPFIQAMEQGMLPALGMSHTYVQVPAAQMANYAQGYSKDDKPVRVNPGPLDAKSYGIKSNARDLIRYLDANLQQVKVAHAWRDALAATHVGYYKAGAFTQDLMWENYPYPVKLSRLIEGNNAGMIMNGTPATAITPPQPELRAGWYNKTGSTGGFSTYAVFIPAKNIAVVMLANKWFPNDDRVEAAYHIVQALEKR"},"dna_sequence":{"accession":"AB008454","fmin":"153","fmax":"1290","strand":"+","sequence":"ATGACGAAAATGAACCGCCTGGCGGCCGCGCTGATCGCCGCACTGATCTTGCCGACCGCGCAGGCCGCGCAGCAGCAGGATATCGACGCCGTTATTCAGCCGCTGATGAAAAAATATGGCGTACCGGGCATGGCGATCGCCGTGTCGGTCGACGGCAAACAGCAGATTTACCCGTATGGCGTCGCCTCGAAGCAGACCGGCAAACCGATCACCGAGCAGACGCTGTTCGAAGTGGGCTCGCTGAGCAAAACCTTTACCGCGACGCTGGCGGTCTATGCGCAGCAGCAGGGCAAGCTGTCGTTCAACGATCCGGCCAGCCGCTATCTGCCCGAGCTGCGCGGCAGCGCCTTCGACGGCGTCAGCCTGCTGAATCTGGCGACGCATACCTCCGGCCTGCCGCTGTTCGTGCCGGACGACGTCACCAACGACGCCCAGCTGATGGCCTACTACCGGGCCTGGCAGCCGAAACACCCGGCGGGCAGCTACCGCGTCTATTCCAACCTCGGCATCGTCATGCTGGGCATGATCGCCGCCAAGAGCCTCGACCAGCCGTTTATCCAGGCGATGGAACAGGGGATGCTGCCGGCGCTGGGCATGAGCCACACCTACGTTCAGGTGCCGGCGGCGCAGATGGCTAACTATGCGCAGGGTTACAGCAAGGACGATAAGCCGGTGCGGGTCAATCCCGGCCCGCTGGACGCCAAATCTTACGGCATCAAGTCCAACGCTCGCGATCTGATTCGCTATCTGGACGCCAACCTGCAGCAGGTGAAGGTGGCGCACGCGTGGCGCGACGCGCTGGCCGCGACGCACGTCGGGTATTACAAGGCGGGCGCGTTCACGCAGGATCTGATGTGGGAGAACTACCCGTATCCGGTGAAACTGTCGCGTTTGATTGAAGGCAACAACGCCGGGATGATCATGAACGGCACGCCGGCCACCGCCATCACGCCACCGCAGCCGGAATTGCGCGCCGGCTGGTATAACAAAACCGGCTCCACCGGCGGCTTCTCCACCTACGCGGTATTTATCCCGGCGAAAAATATCGCCGTGGTGATGCTGGCCAACAAGTGGTTCCCGAACGACGATCGCGTCGAGGCGGCTTACCACATCGTCCAGGCGCTGGAGAAGCGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36783","NCBI_taxonomy_name":"Serratia marcescens","NCBI_taxonomy_id":"615"}}}},"ARO_accession":"3002493","ARO_id":"38893","ARO_name":"SRT-1","ARO_description":"SRT-1, isolated from Serratia marcescens, confers resistance to cephalosporins but not carbapenems, penems and monobactams.","ARO_category":{"36234":{"category_aro_accession":"3000095","category_aro_cvterm_id":"36234","category_aro_name":"SRT beta-lactamase","category_aro_description":"SRT beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"200":{"model_id":"200","model_name":"LEN-14","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"4404":{"protein_sequence":{"accession":"AAP93847.1","sequence":"SLLATLPLAVYAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGLEQLDRRIHYRQQDLVDYSPVSEKHLTDGMTIGELCAAAITLSDNCAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRW"},"dna_sequence":{"accession":"AY265889","fmin":"0","fmax":"458","strand":"+","sequence":"TCTCCCTGTTAGCCACCCTGCCACTGGCGGTATACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCGGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTACCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACTGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3002477","ARO_id":"38877","ARO_name":"LEN-14","ARO_description":"LEN-14 is a beta-lactamase. From the Pasteur Institute list of LEN beta-lactamases.","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"201":{"model_id":"201","model_name":"OCH-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1582":{"protein_sequence":{"accession":"CAC17623.1","sequence":"MRKSTTLLIGFLTTAAIIPNNGALAASKANDGDLRRIVDETVRPLMAEQKIPGMAVAITIDGKSHFFGYGVASKESGQKVTEDTIFEIGSVSKTFTAMLGGYGLATGAFTLSDPATKWAPELADSSFDKITMLDLGTYTPGGLPLQFPDAVSDDSSMLAYFKKWKPDYPAGTQRRYSNPSIGLFGYLAARSMDKPFDVLMEQKLLPAFGLKNTFINVPESQMKNYAYGYSKANKPIRVSGGALDAQAYGIKTTALDLARFVELNIDSSSLEPDFQKAVAATHTGYYRVDANNQGLGWEFYNYPTALKTLLEGNSSDMALKSHKIEKFDTPSQPSADVWLNKTGSTNGFGAYAAFIPAKKIGIVLLANRNYPIDERVKAAYRILQALDNKQ"},"dna_sequence":{"accession":"AJ295341","fmin":"0","fmax":"1173","strand":"+","sequence":"ATGAGAAAATCTACGACACTTTTGATCGGTTTCCTCACCACTGCCGCTATTATCCCGAATAATGGCGCGCTGGCTGCGAGCAAGGCGAATGATGGCGACTTGCGCCGTATTGTCGATGAAACGGTGCGCCCGCTCATGGCCGAGCAGAAAATCCCCGGCATGGCCGTCGCTATAACCATCGACGGCAAGAGCCACTTCTTCGGTTATGGTGTGGCATCGAAGGAAAGCGGGCAAAAAGTCACCGAAGACACGATTTTCGAGATCGGCTCGGTCAGCAAGACCTTCACTGCAATGCTCGGCGGCTACGGGCTGGCGACAGGCGCGTTCACTCTGTCCGATCCCGCGACCAAATGGGCCCCCGAACTGGCAGACAGCAGCTTCGACAAGATCACCATGCTTGATCTTGGGACCTACACGCCGGGCGGATTGCCCCTCCAGTTTCCCGATGCTGTCTCCGATGACAGTTCGATGCTGGCATATTTCAAGAAATGGAAGCCGGACTATCCGGCAGGCACGCAGCGTCGCTATTCGAATCCCAGCATCGGCCTGTTCGGCTATCTGGCGGCACGAAGCATGGACAAGCCGTTCGACGTTTTGATGGAGCAAAAGCTTCTGCCTGCATTCGGCCTGAAGAACACCTTCATCAATGTGCCGGAAAGCCAGATGAAGAACTACGCCTACGGCTATTCCAAAGCCAACAAGCCGATCCGGGTATCGGGCGGGGCGCTGGATGCACAAGCCTATGGCATCAAGACCACCGCGCTTGATCTTGCCCGCTTCGTCGAACTGAACATCGACAGCTCATCTCTGGAGCCTGATTTCCAGAAAGCCGTCGCCGCAACGCATACCGGTTACTACCGTGTCGATGCGAACAATCAGGGGCTTGGCTGGGAGTTCTACAACTATCCGACCGCGCTCAAGACGCTTCTTGAGGGCAACTCGTCGGACATGGCGCTGAAGTCGCACAAAATCGAGAAATTCGATACACCTAGCCAACCGTCAGCTGATGTGTGGCTCAACAAGACAGGCTCAACCAACGGCTTTGGCGCTTATGCGGCCTTTATTCCTGCGAAGAAGATCGGAATTGTTCTGCTTGCCAACCGGAACTATCCGATTGATGAGCGCGTAAAGGCTGCCTATCGGATATTGCAGGCGCTCGACAACAAGCAATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37077","NCBI_taxonomy_name":"Ochrobactrum anthropi","NCBI_taxonomy_id":"529"}}}},"ARO_accession":"3002516","ARO_id":"38916","ARO_name":"OCH-3","ARO_description":"OCH-3 beta-lactamase is an Ambler class C chromosomal-encoded beta-lactamases in Ochrobactrum anthropi","ARO_category":{"36233":{"category_aro_accession":"3000094","category_aro_cvterm_id":"36233","category_aro_name":"OCH beta-lactamase","category_aro_description":"OCH beta-lactamases are Ambler class C chromosomal-encoded beta-lactamases in Ochrobactrum anthropi","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"202":{"model_id":"202","model_name":"SHV-101","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1620":{"protein_sequence":{"accession":"ABV72593.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDGRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"EU155018","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGGTCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATATATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001150","ARO_id":"37530","ARO_name":"SHV-101","ARO_description":"SHV-101 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"203":{"model_id":"203","model_name":"OXY-2-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1695":{"protein_sequence":{"accession":"AAL17873.1","sequence":"MIKSSWRKIAMLAAAVPLLLASSALWASTDAIHQKLTDLEKRSGGRLGVALINTADNSQILYRGDERFAMCSTSKVMAAAAVLKQSESNKEVVNKRLEINAADLVVWSPITEKHLQSGMTLAELSAATLQYSDNTAMNLIIGYLGGPEKVTAFARSIGDATFRLDRTEPTLNTAIPGDERDTSTPLAMAESLRKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPESWVVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKNRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"AY055205","fmin":"181","fmax":"1054","strand":"+","sequence":"ATGATAAAAAGTTCGTGGCGTAAAATTGCAATGCTAGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCAGCGCACTGTGGGCCAGTACCGATGCTATCCATCAGAAGCTGACAGATCTCGAGAAGCGTTCAGGCGGCAGGTTGGGCGTGGCGCTAATCAACACGGCAGATAATTCTCAAATCTTATATCGCGGCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCCGCCGCCGCGGTATTAAAACAGAGCGAAAGCAATAAAGAGGTGGTAAATAAAAGGCTGGAGATTAACGCAGCCGATTTGGTGGTCTGGAGTCCGATTACCGAAAAACATCTCCAGAGCGGAATGACGCTGGCTGAGCTAAGCGCGGCGACGCTGCAATATAGCGACAATACGGCGATGAATCTGATCATCGGCTACCTTGGCGGGCCGGAAAAAGTCACCGCCTTCGCCCGCAGTATCGGCGATGCCACCTTTCGTCTCGATCGTACGGAGCCCACGCTGAATACCGCCATCCCGGGCGATGAGCGTGATACCAGCACGCCGCTGGCGATGGCTGAAAGCCTGCGCAAGCTGACGCTTGGCAATGCGCTGGGCGAACAGCAACGCGCCCAGTTAGTCACCTGGCTGAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCGGGCCTGCCTGAAAGCTGGGTGGTCGGCGATAAAACCGGCGCCGGAGATTACGGCACCACCAATGATATTGCGGTTATCTGGCCGGAAAATCACGCTCCGCTGGTATTAGTCACCTACTTTACCCAGCCGCAGCAGGATGCGAAAAACCGCAAGGAGGTGTTAGCCGCAGCGGCAAAAATCGTGACCGAAGGGCTTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002403","ARO_id":"38803","ARO_name":"OXY-2-8","ARO_description":"OXY-2-8 is a beta-lactamase found in Klebsiella oxytoca","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"204":{"model_id":"204","model_name":"VIM-43","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"2129":{"protein_sequence":{"accession":"AJP67511.1","sequence":"MLKVISSLLVYMTASVMAVASPLVHSGEPSGEYPTVNEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEAEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSANVLYGGCAVHELSRTSAGNVADADLAEWPTSVERIQKHYPEAEVVIPGHGLPGGLDLLQHTANVVKAHKNRSVAE"},"dna_sequence":{"accession":"KP096412","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTACATGACCGCGTCTGTCATGGCTGTCGCAAGTCCGTTAGTCCATTCCGGGGAGCCGAGTGGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGAGAGGTCCGACTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCGGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAAAAGCAAATTGGACTTCCCGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGCAGAGGGGAACGAGATTCCCACGCATTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGCTCTTCTATCCTGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAACGTGCTATACGGTGGTTGTGCCGTTCATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCGTTGAGCGGATTCAAAAACACTACCCGGAAGCAGAGGTCGTCATTCCCGGGCACGGTCTACCGGGCGGTCTAGACTTGCTCCAGCACACAGCGAACGTTGTCAAAGCACACAAAAATCGCTCAGTCGCCGAGTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3003179","ARO_id":"39756","ARO_name":"VIM-43","ARO_description":"From the Lahey list of beta-lactamases.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"205":{"model_id":"205","model_name":"APH(4)-Ia","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"221":{"protein_sequence":{"accession":"CAA24743.1","sequence":"MKKPELTATSVEKFLIEKFDSVSDLMQLSEGEESRAFSFDVGGRGYVLRVNSCADGFYKDRYVYRHFASAALPIPEVLDIGEFSESLTYCISRRAQGVTLQDLPETELPAVLQPVAEAMDAIAAADLSQTSGFGPFGPQGIGQYTTWRDFICAIADPHVYHWQTVMDDTVSASVAQALDELMLWAEDCPEVRHLVHADFGSNNVLTDNGRITAVIDWSEAMFGDSQYEVANIFFWRPWLACMEQQTRYFERRHPELAGSPRLRAYMLRIGLDQLYQSLVDGNFDDAAWAQGRCDAIVRSGAGTVGRTQIARRSAAVWTDGCVEVLADSGNRRPSTRPRAKE"},"dna_sequence":{"accession":"V01499","fmin":"230","fmax":"1256","strand":"+","sequence":"ATGAAAAAGCCTGAACTCACCGCGACGTCTGTCGAGAAGTTTCTGATCGAAAAGTTCGACAGCGTCTCCGACCTGATGCAGCTCTCGGAGGGCGAAGAATCTCGTGCTTTCAGCTTCGATGTAGGAGGGCGTGGATATGTCCTGCGGGTAAATAGCTGCGCCGATGGTTTCTACAAAGATCGTTATGTTTATCGGCACTTTGCATCGGCCGCGCTCCCGATTCCGGAAGTGCTTGACATTGGGGAATTCAGCGAGAGCCTGACCTATTGCATCTCCCGCCGTGCACAGGGTGTCACGTTGCAAGACCTGCCTGAAACCGAACTGCCCGCTGTTCTGCAGCCGGTCGCGGAGGCCATGGATGCGATCGCTGCGGCCGATCTTAGCCAGACGAGCGGGTTCGGCCCATTCGGACCGCAAGGAATCGGTCAATACACTACATGGCGTGATTTCATATGCGCGATTGCTGATCCCCATGTGTATCACTGGCAAACTGTGATGGACGACACCGTCAGTGCGTCCGTCGCGCAGGCTCTCGATGAGCTGATGCTTTGGGCCGAGGACTGCCCCGAAGTCCGGCACCTCGTGCACGCGGATTTCGGCTCCAACAATGTCCTGACGGACAATGGCCGCATAACAGCGGTCATTGACTGGAGCGAGGCGATGTTCGGGGATTCCCAATACGAGGTCGCCAACATCTTCTTCTGGAGGCCGTGGTTGGCTTGTATGGAGCAGCAGACGCGCTACTTCGAGCGGAGGCATCCGGAGCTTGCAGGATCGCCGCGGCTCCGGGCGTATATGCTCCGCATTGGTCTTGACCAACTCTATCAGAGCTTGGTTGACGGCAATTTCGATGATGCAGCTTGGGCGCAGGGTCGATGCGACGCAATCGTCCGATCCGGAGCCGGGACTGTCGGGCGTACACAAATCGCCCGCAGAAGCGCGGCCGTCTGGACCGATGGCTGTGTAGAAGTACTCGCCGATAGTGGAAACCGACGCCCCAGCACTCGTCCGAGGGCAAAGGAATAGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002655","ARO_id":"39055","ARO_name":"APH(4)-Ia","ARO_description":"APH(4)-Ia is a plasmid-encoded aminoglycoside phosphotransferase in E. coli","ARO_category":{"36294":{"category_aro_accession":"3000155","category_aro_cvterm_id":"36294","category_aro_name":"APH(4)","category_aro_description":"Phosphorylation of hygromycin on the hydroxyl group at position 4","category_aro_class_name":"AMR Gene Family"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"206":{"model_id":"206","model_name":"FomA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"614":{"protein_sequence":{"accession":"BAA32493.1","sequence":"MTPDFLAIKVGGSLFSRKDEPGSLDDDAVTPFARNFARLAETYRGRMVLISGGGAFGHGAIRDHDSTHAFSLAGLTEATFEVKKRWAEKLRGIGVDAFPLQLAAMCTLRNGIPQLRSEVLRDVLDHGALPVLAGDALFDEHGKLWAFSSDRVPEVLLPMVEGRLRVVTLTDVDGIVTDGAGGDTILPEVDARSPEQAYAALWGSSEWDATGAMHTKLDALVTCARRGAECFIMRGDPGSDLEFLTAPFSSWPAHVRSTRITTTASA"},"dna_sequence":{"accession":"AB016934","fmin":"6575","fmax":"7376","strand":"+","sequence":"ATGACGCCCGATTTCTTGGCCATCAAGGTTGGCGGCAGCCTGTTCTCCCGCAAGGACGAACCCGGCAGCCTGGACGACGACGCGGTGACGCCGTTCGCCAGGAACTTCGCCCGGCTCGCCGAGACCTACCGGGGCCGGATGGTTCTCATCAGCGGCGGCGGCGCCTTCGGCCACGGGGCCATCCGTGACCACGACAGCACGCACGCGTTCTCCCTCGCCGGCCTGACCGAGGCCACCTTCGAGGTGAAGAAGCGGTGGGCCGAGAAGCTCCGCGGGATCGGCGTGGACGCCTTCCCGCTCCAGCTGGCGGCCATGTGCACGCTCCGCAACGGCATACCGCAGCTCCGGTCCGAGGTCCTCCGGGACGTCCTCGACCACGGCGCGCTGCCCGTCCTCGCCGGCGACGCCCTGTTCGACGAGCACGGAAAGCTGTGGGCGTTCTCCAGCGACCGCGTCCCCGAGGTCCTCCTGCCCATGGTCGAGGGGCGCCTCCGGGTCGTCACCCTGACCGACGTCGACGGCATCGTGACCGACGGCGCCGGCGGCGACACGATCCTGCCCGAGGTCGACGCCCGGTCCCCCGAGCAGGCGTACGCCGCGCTCTGGGGCAGCAGCGAATGGGACGCCACCGGCGCCATGCACACCAAGCTCGACGCACTGGTCACCTGCGCCCGCCGCGGTGCCGAGTGCTTCATCATGCGGGGCGACCCCGGCAGCGACCTGGAGTTCCTGACCGCCCCCTTCTCCTCCTGGCCGGCGCACGTGCGGTCCACCAGGATCACCACGACTGCTTCTGCGTAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39587","NCBI_taxonomy_name":"Streptomyces wedmorensis","NCBI_taxonomy_id":"43759"}}}},"ARO_accession":"3000423","ARO_id":"36562","ARO_name":"FomA","ARO_description":"In the presence of ATP and magnesium (II), fosfomycin gets phosphorylated at the phosphate group resulting in a diphosphate group which inactivates the antibiotic.","ARO_category":{"41410":{"category_aro_accession":"3004246","category_aro_cvterm_id":"41410","category_aro_name":"Fom phosphotransferase family","category_aro_description":"Two members of the Fom family have been identified, FomA and FomB. FomB must interact with FomA confer resistance to fosfomycin, however FomA is capable of conferring resistance alone.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"207":{"model_id":"207","model_name":"GES-12","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1823":{"protein_sequence":{"accession":"CBG22732.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMGDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGACANGARNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"FN554543","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGGGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTGCCTGCGCCAACGGGGCCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3002341","ARO_id":"38741","ARO_name":"GES-12","ARO_description":"GES-12 is a beta-lactamase found in Acinetobacter baumannii","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"208":{"model_id":"208","model_name":"CMY-105","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1623":{"protein_sequence":{"accession":"AHL39330.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDEVTDKAELLRFYQNWQPQWTPGAKRLYANSSIGLFGALVVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"KJ207205","fmin":"1039","fmax":"2185","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCACTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGCATGGCCGTGGCAATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAATTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGAAGTTACGGATAAAGCCGAATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGTGGTAAAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACAGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATAGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGCGTCGAGGCGGCCTGGCGCATTCTTGAAAAACTGCAATAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002117","ARO_id":"38517","ARO_name":"CMY-105","ARO_description":"CMY-105 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"209":{"model_id":"209","model_name":"AAC(3)-Ib\/AAC(6')-Ib''","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"271":{"protein_sequence":{"accession":"AAL82588.1","sequence":"MSIIATVKIGPDEISAMRAVLDLFGKEFEDIPTYSDRQPTNEYLANLLHSETFIALAAFDRGTAIGGLAAYVLPKFEQARSEIYIYDLAVASSHRRLGVATALISHLKRVAVELGAYVIYVQADYGDDPAVALYTKLGVREDVMHFDIDPLTNSNDSVTLRLMTEHDLAMLYEWVNRSHIVEWWGGEEARPTLADVQEQYLPSVLAQESVTPYIAMLNGEPIGYAQSYVALGGGDGWWEEETDPGVRGIDQSLANASQLGKGLGTKLVRALVELLFNDPEVTKIQTDPSPSNLRAIRCYEKAGFERQGTVTTPDGPAVYMVQTRQAFERTRSDA"},"dna_sequence":{"accession":"AF355189","fmin":"1434","fmax":"2439","strand":"+","sequence":"ATGAGCATCATTGCAACCGTCAAGATCGGCCCTGACGAAATTTCAGCCATGAGGGCTGTGCTCGATCTCTTCGGCAAAGAGTTTGAGGACATTCCAACCTACTCTGATCGCCAGCCGACCAATGAGTATCTTGCCAATCTTCTGCACAGCGAGACGTTCATCGCGCTCGCTGCTTTTGACCGCGGAACAGCAATAGGTGGGCTCGCAGCCTACGTTCTACCCAAGTTCGAGCAAGCGCGAAGCGAGATCTACATTTATGACTTGGCAGTCGCTTCCAGCCATCGAAGGCTAGGAGTCGCAACTGCCCTGATTAGCCACCTGAAGCGTGTGGCGGTTGAACTTGGCGCGTATGTAATCTATGTGCAAGCAGACTACGGTGACGATCCGGCAGTCGCTCTCTACACAAAGCTTGGAGTTCGGGAAGACGTCATGCACTTCGACATTGATCCATTGACCAACAGCAACGATTCCGTCACACTGCGCCTCATGACTGAGCATGACCTTGCGATGCTCTATGAGTGGGTAAATCGATCTCATATCGTCGAGTGGTGGGGCGGAGAAGAAGCACGCCCGACACTTGCTGACGTACAGGAACAGTACTTGCCAAGCGTTTTAGCGCAAGAGTCCGTCACTCCATACATTGCAATGCTGAATGGAGAGCCGATTGGGTATGCCCAGTCGTACGTTGCTCTTGGAGGCGGGGACGGATGGTGGGAAGAAGAAACCGATCCAGGAGTACGCGGAATAGACCAGTCACTGGCGAATGCATCACAACTGGGCAAAGGCTTGGGAACCAAGCTGGTTCGAGCTCTGGTTGAGTTGCTGTTCAATGATCCCGAGGTCACCAAGATCCAAACGGACCCGTCGCCGAGCAACTTGCGAGCGATCCGATGCTACGAGAAAGCGGGGTTTGAGAGGCAAGGTACCGTAACCACCCCAGATGGTCCAGCCGTGTACATGGTTCAAACACGCCAGGCATTCGAGCGAACACGCAGTGATGCCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002600","ARO_id":"39000","ARO_name":"AAC(3)-Ib\/AAC(6')-Ib''","ARO_description":"AAC(3)-Ib\/AAC(6')-Ib'' is an integron-encoded aminoglycoside acetyltransferase in P. aeruginosa","ARO_category":{"36461":{"category_aro_accession":"3000322","category_aro_cvterm_id":"36461","category_aro_name":"AAC(3)","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 3.","category_aro_class_name":"AMR Gene Family"},"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"210":{"model_id":"210","model_name":"SHV-35","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1315":{"protein_sequence":{"accession":"AAL68926.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDKQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGGRGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AY070258","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACAAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGGGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001093","ARO_id":"37473","ARO_name":"SHV-35","ARO_description":"SHV-35 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"211":{"model_id":"211","model_name":"TEM-206","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2035":{"protein_sequence":{"accession":"AGK82336.1","sequence":"MSIQHFRVTLIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"KC783461","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCACCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001383","ARO_id":"37783","ARO_name":"TEM-206","ARO_description":"From the Lahey list of beta-lactamases. Not yet released.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"213":{"model_id":"213","model_name":"OXA-21","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"803":{"protein_sequence":{"accession":"CAA71699.2","sequence":"MAIRIFAILFSTFVFGTFAHAQEGMRERSDWRKFFSEFQAKGTIVVADERQTDRVILVFDQVRSEKRYSPASTFKIPHTLFALDAGAARDEFQVFRWDGIKRSFAAHNQDQDLRSAMRNSTVWIYELFAKEIGEDKARRYLKQIDYGNADPSTSNGDYWIDGNLAIAAQEQIAFLRKLYHNELPFRVEHQRLVKDLMIVEAGRNWILRAKTGWEGRMGWWVGWVEWPTGPVFFALNIDTPNRMDDLFKREAIVRAILRSIEALPPNPAVNSDAAR"},"dna_sequence":{"accession":"Y10693","fmin":"0","fmax":"828","strand":"+","sequence":"ATGGCAATCCGAATCTTCGCAATACTTTTCTCCACTTTTGTTTTTGGCACGTTCGCGCATGCACAAGAAGGCATGCGCGAACGTTCTGACTGGCGGAAGTTTTTCAGCGAATTTCAAGCCAAAGGCACGATAGTTGTGGCAGACGAACGCCAAACAGATCGTGTCATATTGGTTTTTGATCAGGTGCGGTCAGAGAAACGCTACTCGCCGGCCTCGACATTCAAGATTCCACATACACTTTTTGCACTTGACGCAGGCGCTGCACGTGATGAGTTTCAAGTTTTCCGATGGGACGGCATCAAAAGAAGCTTTGCAGCTCACAACCAAGACCAAGACTTGCGATCAGCAATGCGGAATTCTACTGTCTGGATTTATGAGCTATTTGCAAAAGAGATCGGTGAAGACAAGGCTCGACGCTATTTGAAGCAAATCGACTATGGCAACGCCGATCCTTCGACAAGTAATGGCGATTACTGGATAGATGGCAATCTTGCTATCGCGGCACAAGAACAGATTGCATTTCTCAGGAAGCTCTATCATAACGAGTTGCCCTTTCGGGTAGAACATCAGCGCTTGGTCAAGGACCTCATGATTGTGGAAGCCGGTCGCAACTGGATACTGCGCGCAAAGACGGGCTGGGAAGGCCGCATGGGTTGGTGGGTAGGATGGGTTGAGTGGCCGACTGGCCCCGTATTTTTCGCACTGAATATTGATACGCCAAACAGGATGGATGACCTTTTCAAAAGGGAGGCAATAGTGCGGGCAATCCTTCGCTCTATCGAAGCGTTGCCGCCCAACCCGGCAGTCAACTCGGACGCAGCGCGATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001416","ARO_id":"37816","ARO_name":"OXA-21","ARO_description":"OXA-21 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"214":{"model_id":"214","model_name":"SHV-121","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1621":{"protein_sequence":{"accession":"AEI83429.1","sequence":"MRYIRLCIISLLAALPLVVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITVSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"HQ661362","fmin":"71","fmax":"932","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCGCCCTGCCGCTGGTGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCGTGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001168","ARO_id":"37548","ARO_name":"SHV-121","ARO_description":"SHV-121 is a beta-lactamase that has been found in clinical isolates. Identical to SHV-136.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"215":{"model_id":"215","model_name":"bcrC","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"2050":{"protein_sequence":{"accession":"AAA99503.1","sequence":"MSFSELNIDAFRFINDLGKEYSMLNPVVYFLAEYMMYFLALGLVVYWLTRTTKNRLMVIYAVIAFVVAEILGKIMGSLHSNYQPFATLPNVNKLIEHEIDNSFPSDHTILFFSIGFLIFLFHKKTGWLWLVLAFAVGISRIWSGVHYPLDVAAGALLGVLSALFVFWTAPKLSFIHQMLSLYEKVEQRIVPSKNKSNDKSKNF"},"dna_sequence":{"accession":"L20573","fmin":"2064","fmax":"2676","strand":"+","sequence":"ATGTCTTTTTCAGAATTAAATATTGATGCTTTTCGTTTCATTAATGATTTGGGAAAAGAGTATTCGATGCTGAATCCGGTCGTTTACTTTCTAGCCGAATATATGATGTACTTTCTCGCATTAGGTCTTGTCGTTTATTGGCTGACCCGGACGACAAAAAACAGATTGATGGTCATTTATGCAGTCATCGCATTTGTGGTTGCCGAAATTCTCGGGAAAATCATGGGCTCTCTGCATTCCAACTATCAACCGTTTGCAACGCTTCCGAATGTCAACAAGCTGATAGAGCATGAAATTGACAATTCGTTTCCGAGCGACCATACGATTTTGTTTTTTTCAATTGGTTTTTTAATCTTTCTGTTTCACAAAAAGACGGGCTGGCTGTGGCTTGTACTTGCGTTTGCCGTGGGAATTTCCCGCATTTGGTCGGGCGTTCACTATCCGCTCGACGTTGCGGCGGGAGCCCTTCTTGGCGTGTTGTCAGCTCTGTTTGTATTCTGGACAGCACCGAAGCTGTCATTTATTCATCAAATGCTGTCCCTTTATGAAAAGGTGGAACAGCGGATTGTTCCTTCCAAAAACAAATCGAACGATAAATCGAAGAACTTTTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36834","NCBI_taxonomy_name":"Bacillus licheniformis","NCBI_taxonomy_id":"1402"}}}},"ARO_accession":"3003250","ARO_id":"39834","ARO_name":"bcrC","ARO_description":"bcrC is an undecaprenyl pyrophosphate phosphatase that has a role in bacitracin resistance if it is overexpressed. It is isolated from Bacillus subtilis.","ARO_category":{"39982":{"category_aro_accession":"3003398","category_aro_cvterm_id":"39982","category_aro_name":"undecaprenyl pyrophosphate related proteins","category_aro_description":"Undecaprenyl phosphate is a universal lipid carrier of glycan biosynthetic intermediates for carbohydrate polymers that are exported to the bacterial cell envelope. Antibiotics that targets this compound or proteins associated with the production of this compound leads to cell death.","category_aro_class_name":"AMR Gene Family"},"36973":{"category_aro_accession":"3000629","category_aro_cvterm_id":"36973","category_aro_name":"bacitracin A","category_aro_description":"Bacitracin A is the primary component of bacitracin. It contains many uncommon amino acids and interferes with bacterial cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36974":{"category_aro_accession":"3000630","category_aro_cvterm_id":"36974","category_aro_name":"bacitracin B","category_aro_description":"Bacitracin B is a component of bacitracin, an antibiotic mixture that interferes with bacterial cell wall synthesis. It differs from Bacitracin A with a valine instead of an isoleucine in its peptide.","category_aro_class_name":"Antibiotic"},"36975":{"category_aro_accession":"3000631","category_aro_cvterm_id":"36975","category_aro_name":"bacitracin F","category_aro_description":"Bacitracin F is a component of bacitracin, an antibiotic mixture that interferes with bacterial cell wall synthesis. It is formed when the thiazoline ring of bacitracin A is oxidatively deaminated.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"216":{"model_id":"216","model_name":"LEN-9","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"4405":{"protein_sequence":{"accession":"WP_032735535.1","sequence":"MRYVRLCVISLLATLPLVVYAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGLEQLDRRIHYRQQDLVDYSPVSEKHLVDGMTIGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPPGWFIADKTGAGERGARGIVALLGPDGKPERIVVIYLRDTPASMAERNQHIAGIGAALIEHWQR"},"dna_sequence":{"accession":"NG_050780.1","fmin":"100","fmax":"961","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCACCCTGCCACTGGTGGTATACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGTCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGCCGGGCTGGTTTATCGCCGACAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37059","NCBI_taxonomy_name":"Klebsiella","NCBI_taxonomy_id":"570"}}}},"ARO_accession":"3002459","ARO_id":"38859","ARO_name":"LEN-9","ARO_description":"LEN-9 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"217":{"model_id":"217","model_name":"vanXA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"375"}},"model_sequences":{"sequence":{"3281":{"protein_sequence":{"accession":"AAA65957.1","sequence":"MEIGFTFLDEIVHGVRWDAKYATWDNFTGKPVDGYEVNRIVGTYELAESLLKAKELAATQGYGLLLWDGYRPKRAVNCFMQWAAQPENNLTKESYYPNIDRTEMISKGYVASKSSHSRGSAIDLTLYRLDTGELVPMGSRFDFMDERSHHAANGISCNEAQNRRRLRSIMENSGFEAYSLEWWHYVLRDEPYPNSYFDFPVK"},"dna_sequence":{"accession":"M97297","fmin":"8016","fmax":"8624","strand":"+","sequence":"ATGGAAATAGGATTTACTTTTTTAGATGAAATAGTACACGGTGTTCGTTGGGACGCTAAATATGCCACTTGGGATAATTTCACCGGAAAACCGGTTGACGGTTATGAAGTAAATCGCATTGTAGGGACATACGAGTTGGCTGAATCGCTTTTGAAGGCAAAAGAACTGGCTGCTACCCAAGGGTACGGATTGCTTCTATGGGACGGTTACCGTCCTAAGCGTGCTGTAAACTGTTTTATGCAATGGGCTGCACAGCCGGAAAATAACCTGACAAAGGAAAGTTATTATCCCAATATTGACCGAACTGAGATGATTTCAAAAGGATACGTGGCTTCAAAATCAAGCCATAGCCGCGGCAGTGCCATTGATCTTACGCTTTATCGATTAGACACGGGTGAGCTTGTACCAATGGGGAGCCGATTTGATTTTATGGATGAACGCTCTCATCATGCGGCAAATGGAATATCATGCAATGAAGCGCAAAATCGCAGACGTTTGCGCTCCATCATGGAAAACAGTGGGTTTGAAGCATATAGCCTCGAATGGTGGCACTATGTATTAAGAGACGAACCATACCCCAATAGCTATTTTGATTTCCCCGTTAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002949","ARO_id":"39383","ARO_name":"vanXA","ARO_description":"vanXA, also known as vanX, is a vanX variant found in the vanA gene cluster","ARO_category":{"36020":{"category_aro_accession":"3000011","category_aro_cvterm_id":"36020","category_aro_name":"vanX","category_aro_description":"VanX is a D,D-dipeptidase that cleaves D-Ala-D-Ala but not D-Ala-D-Lac, ensuring that the latter dipeptide that has reduced binding affinity with vancomycin is used to synthesize peptidoglycan substrate.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"35948":{"category_aro_accession":"0000029","category_aro_cvterm_id":"35948","category_aro_name":"teicoplanin","category_aro_description":"Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation  and transpeptidation.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"218":{"model_id":"218","model_name":"npmA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"273":{"protein_sequence":{"accession":"BAF80809.1","sequence":"MLILKGTKTVDLSKDELTEIIGQFDRVHIDLGTGDGRNIYKLAINDQNTFYIGIDPVKENLFDISKKIIKKPSKGGLSNVVFVIAAAESLPFELKNIADSISILFPWGTLLEYVIKPNRDILSNVADLAKKEAHFEFVTTYSDSYEEAEIKKRGLPLLSKAYFLSEQYKAELSNSGFRIDDVKELDNEYVKQFNSLWAKRLAFGRKRSFFRVSGHVSKH"},"dna_sequence":{"accession":"AB261016","fmin":"3068","fmax":"3728","strand":"+","sequence":"TTGTTAATACTCAAAGGAACAAAGACGGTTGATTTATCAAAAGATGAATTGACAGAAATAATAGGTCAGTTTGATCGTGTGCATATAGATTTGGGTACTGGAGACGGTAGAAATATATATAAACTTGCAATTAATGATCAAAACACTTTCTATATCGGAATAGATCCGGTAAAAGAAAACTTGTTTGATATATCCAAAAAAATTATAAAGAAGCCCTCAAAAGGAGGGCTATCTAATGTGGTGTTTGTTATTGCAGCTGCAGAGTCTCTCCCTTTTGAATTGAAAAACATTGCTGATTCAATTTCCATTTTGTTTCCTTGGGGGACATTGCTTGAATATGTAATTAAACCGAATAGAGATATTCTTTCGAATGTTGCAGATTTGGCTAAAAAAGAAGCTCACTTTGAATTTGTGACCACATACTCAGATTCATACGAAGAAGCGGAAATAAAAAAAAGAGGACTTCCTCTTTTAAGTAAGGCCTATTTTTTGAGCGAACAATACAAAGCTGAATTATCAAACTCAGGTTTTCGCATTGATGATGTTAAGGAATTGGACAATGAGTATGTAAAACAGTTTAATTCTCTTTGGGCAAAGCGATTAGCTTTTGGGCGAAAACGTTCTTTCTTTCGAGTTTCTGGCCATGTTTCAAAACATTAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002665","ARO_id":"39065","ARO_name":"npmA","ARO_description":"NpmA is a plasmid-mediated aminoglycoside-resistance 16S rRNA methyltransferase by interfering with aminoglycoside binding with the A site of 16S rRNA through N-1 methylation at position A1408.","ARO_category":{"41436":{"category_aro_accession":"3004272","category_aro_cvterm_id":"41436","category_aro_name":"16S rRNA methyltransferase (A1408)","category_aro_description":"Methyltransferases that methylate the A1408 position of 16S rRNA, which is part of an aminoglycoside binding site.","category_aro_class_name":"AMR Gene Family"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"219":{"model_id":"219","model_name":"OKP-A-12","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"962":{"protein_sequence":{"accession":"CAP12354.2","sequence":"MRYVRLCLISLIAALPLAAFASPQPLEQVTRSESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIRYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKSVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMAATLRKLLTSHALSARSQQQLLQWMVDDQVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPNGKAERIVVIYLRDTPATMAERNQQIARIGAALIEHWQR"},"dna_sequence":{"accession":"AM850916","fmin":"18","fmax":"879","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGCATTCGCCAGCCCTCAGCCGCTCGAGCAAGTTACACGCAGCGAAAGTCAGCTGGCGGGCCGCGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCACTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGAGACGAACAGCTGGATCGGCGGATCCGCTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGTGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGAGCGTTGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAGCTCAATGAAGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCAGCCAGCATGGCCGCCACCCTGCGCAAGCTGCTAACCAGCCACGCGCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGACCAGGTGGCCGGCCCGCTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGCGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGAACGGCAAAGCGGAGCGCATCGTGGTGATCTATCTGCGGGATACGCCGGCGACCATGGCCGAACGTAACCAGCAGATCGCCAGAATAGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002429","ARO_id":"38829","ARO_name":"OKP-A-12","ARO_description":"OKP-A-12 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"220":{"model_id":"220","model_name":"TEM-92","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1961":{"protein_sequence":{"accession":"AAF66653.1","sequence":"MSIKHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTTPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AF143804","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTAAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3000959","ARO_id":"37339","ARO_name":"TEM-92","ARO_description":"TEM-92 is an extended-spectrum beta-lactamase found in Proteus mirabilis.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"221":{"model_id":"221","model_name":"CMY-100","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1194":{"protein_sequence":{"accession":"AHA80101.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYQGKPYYFTWGKADIANNRPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTQYWPELTGKQWQGISLLHLATYTAGGLPLQVPDDVTDKAALLHFYQNWQPQWASGAKRLYANSSIGLFGALAVKPSGMSYEEAMTKRVLHPLKLAHTWITVPQSEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMTRWVQANMDASQVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPVKADSIISGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"KF526113","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCGCTGCTGCTGACAGCTTCTTTCTCCACGTTTGCCGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCGCTGATGCAGGAGCAGGCAATTCCGGGCATGGCCGTTGCGATTATCTATCAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCGTCCAGTCACTCAACAAACGCTGTTTGAACTCGGTTCGGTCAGTAAAACGTTCAACGGTGTGCTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGCAGTACTGGCCTGAACTGACGGGTAAGCAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTACACGGCAGGCGGCCTGCCGCTTCAGGTTCCGGACGACGTTACGGATAAAGCCGCATTACTACACTTTTATCAAAACTGGCAGCCGCAATGGGCCTCAGGCGCTAAACGTCTTTATGCTAACTCCAGCATTGGTCTGTTTGGCGCCCTGGCGGTGAAACCTTCAGGCATGAGCTACGAAGAGGCGATGACCAAACGCGTCCTGCACCCCTTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAGCGAACAAAAAGATTATGCCTGGGGTTATCGCGAAGGAAAGCCAGTGCATGTATCCCCTGGCCAACTTGATGCCGAAGCCTACGGGGTGAAATCGAGCGTTATCGATATGACCCGTTGGGTTCAGGCCAACATGGACGCCAGCCAGGTTCAGGAGAAAACGCTCCAGCAGGGAATCGAGCTTGCGCAGTCACGTTACTGGCGTATTGGCGATATGTACCAGGGCCTGGGTTGGGAGATGCTGAACTGGCCGGTGAAGGCCGACTCGATAATTAGCGGTAGCGACAGCAAAGTAGCACTGGCAGCGCTTCCTGCCGTTGAGGTAAACCCGCCCGCGCCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGCGGATTTGGCAGCTACGTTGCTTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAGAGCTACCCAAACCCTGTTCGCGTCGAGGCCGCCTGGCGCATTCTTGAAAAACTGCAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002112","ARO_id":"38512","ARO_name":"CMY-100","ARO_description":"CMY-100 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"222":{"model_id":"222","model_name":"JOHN-1 beta-lactamase","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1483":{"protein_sequence":{"accession":"AAK38324.1","sequence":"MRKLASIILFLAAVSNSLGQSKNSPLQISHLTGDFYVYRTFNDYKGTKISANAMYVVTDKGVVLFDAPWDKTQFQPLLDSIKAKHNKEVVMLFGTHSHEDRAGGFDFYKKKGIKTYSIKLTDDILKKNKEPRAEFIISNDTTFTVGNHTFEVYYPGKGHAPDNIVAWFKKEKILYGGCFVKSAEALDLGYLGDADVKEWQKSIKKVQAKFKKPDYIISGHDDWTSKESLNHTLKLVDEYLAQKSAGKK"},"dna_sequence":{"accession":"AY028464","fmin":"442","fmax":"1189","strand":"+","sequence":"ATGCGAAAATTAGCTTCGATAATTTTATTCTTAGCCGCGGTTTCAAATAGTTTGGGACAATCTAAGAATTCGCCATTACAAATAAGTCATCTTACAGGTGACTTTTATGTTTATAGAACTTTTAATGATTACAAAGGAACTAAGATTTCTGCCAATGCTATGTATGTTGTTACAGATAAAGGCGTTGTGCTTTTTGATGCGCCTTGGGATAAAACACAGTTTCAGCCGTTATTAGACAGCATAAAAGCAAAACACAATAAAGAGGTTGTGATGCTTTTTGGCACGCATTCTCATGAAGATCGTGCAGGAGGATTTGATTTTTACAAGAAAAAAGGAATCAAAACGTACTCAATTAAACTGACTGATGATATTCTTAAAAAGAATAAGGAACCAAGAGCAGAATTTATAATTTCAAATGATACAACATTTACTGTTGGAAATCATACTTTTGAAGTTTATTACCCAGGAAAAGGACATGCTCCTGATAATATTGTAGCATGGTTTAAAAAAGAGAAAATTCTTTACGGAGGCTGTTTTGTAAAAAGTGCAGAAGCATTAGATTTAGGTTATCTGGGTGATGCTGATGTTAAAGAATGGCAGAAATCTATAAAAAAAGTGCAGGCAAAATTCAAAAAACCGGATTATATAATTTCGGGACATGATGACTGGACTAGTAAAGAATCTTTAAATCATACTTTGAAATTGGTTGACGAGTATTTGGCTCAAAAATCTGCCGGAAAAAAGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39076","NCBI_taxonomy_name":"Flavobacterium johnsoniae UW101","NCBI_taxonomy_id":"376686"}}}},"ARO_accession":"3000840","ARO_id":"37220","ARO_name":"JOHN-1","ARO_description":"JOHN-1 is an Ambler class B carbapenem-hydrolysing beta-lactamase from Flavobacterium johnsoniae.","ARO_category":{"41366":{"category_aro_accession":"3004202","category_aro_cvterm_id":"41366","category_aro_name":"JOHN beta-lactamase","category_aro_description":"JOHN beta-lactamases hydrolyse penicillins, narrow- and expanded-spectrum cephalosporins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"223":{"model_id":"223","model_name":"GES-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1708":{"protein_sequence":{"accession":"BAD06399.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRTAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVKWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMGDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"AB113580","fmin":"1329","fmax":"2193","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAACGGCGCAGCGCTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCAAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGGGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAGT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002332","ARO_id":"38732","ARO_name":"GES-3","ARO_description":"GES-3 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"224":{"model_id":"224","model_name":"MIR-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"1733":{"protein_sequence":{"accession":"AAO42602.1","sequence":"MMTKSLSCALLLSVASAAFAAPMSETQLAEVVERTVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEIALGDPVAKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDTASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEEAHYAWGYREGKAVHVSPGMLDAEAYGVKTNVKDMASWVIANMKPDSLQAPSLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYHILDALQ"},"dna_sequence":{"accession":"AY227752","fmin":"88","fmax":"1234","strand":"+","sequence":"ATGATGACAAAATCCCTAAGCTGTGCCCTGCTGCTCAGCGTCGCCAGCGCTGCATTCGCCGCACCGATGTCCGAAACACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTAATTTATCAGGGTCAGCCACACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGCGGCGATGCCATTGCCCGGGGTGAAATAGCGCTGGGCGATCCGGTAGCAAAATACTGGCCTGAGCTCACGGGCAAGCAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTATACCGCAGGCGGTCTGCCGTTACAGGTGCCGGATGAGGTCACGGATACCGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCTAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTTAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAACCCCTCAAGCTGGACCATACCTGGATTAACGTCCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGAGGGTAAAGCGGTCCACGTTTCGCCAGGGATGCTGGACGCGGAAGCCTATGGCGTAAAAACTAACGTGAAGGATATGGCGAGCTGGGTGATAGCCAACATGAAGCCGGATTCTCTTCAGGCTCCCTCACTCAAGCAAGGCATTGCTCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCTATGTATCAGGGGTTAGGCTGGGAGATGCTCAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCATTGCCCGTGGCAGAAGTGAATCCACCCGCGCCGCCGGTCAAGGCCTCCTGGGTCCATAAAACAGGCTCGACGGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGACGCGCTACAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3002168","ARO_id":"38568","ARO_name":"MIR-2","ARO_description":"MIR-2 is a beta-lactamase. From the Lahey list of MIR beta-lactamases.","ARO_category":{"36197":{"category_aro_accession":"3000058","category_aro_cvterm_id":"36197","category_aro_name":"MIR beta-lactamase","category_aro_description":"MIR beta-lactamases are plasmid-mediated beta-lactamases that confer resistance to oxyimino- and alpha-methoxy beta-lactams","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"225":{"model_id":"225","model_name":"CTX-M-88","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1553":{"protein_sequence":{"accession":"ACP18863.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRHDVLASAAKIVTDGL"},"dna_sequence":{"accession":"FJ873739","fmin":"0","fmax":"875","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCACGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35655","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Infantis","NCBI_taxonomy_id":"595"}}}},"ARO_accession":"3001948","ARO_id":"38348","ARO_name":"CTX-M-88","ARO_description":"CTX-M-88 is a beta-lactamase. From the Lahey list of CTX-M beta-lactamases.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"226":{"model_id":"226","model_name":"OXA-113","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1832":{"protein_sequence":{"accession":"ABW70410.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKTTTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWVVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"EF653400","fmin":"434","fmax":"1259","strand":"+","sequence":"ATGAACATTAAAGCCCTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTCTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGACAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGGTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001644","ARO_id":"38044","ARO_name":"OXA-113","ARO_description":"OXA-113 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"227":{"model_id":"227","model_name":"OKP-B-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1521":{"protein_sequence":{"accession":"CAJ19611.1","sequence":"MRYVRLCLISLIAALPLAVFASPQPLEQIKISESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKIVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMATTLRKLLTTPSLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPDGKAERIVVIYLRDTAATMVERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM051152","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCAGCCGCTTGAGCAGATTAAAATCAGCGAAAGTCAGCTGGCGGGCCGGGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGCGACGAACAGCTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGATCGTCGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGAACTCAATGAGGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCGGCCAGCATGGCCACCACCCTGCGCAAGCTGCTAACCACCCCCTCTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTTGACGACCGGGTGGCCGGCCCGTTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGTGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAAGCGGAGCGTATCGTGGTGATCTATCTGCGGGATACCGCGGCGACCATGGTCGAGCGTAACCAGCAGATCGCCGGGATAGGCGCGGCGCTGATCGAGCACTGGCAGCGCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002436","ARO_id":"38836","ARO_name":"OKP-B-3","ARO_description":"OKP-B-3 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"228":{"model_id":"228","model_name":"sdiA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"470"}},"model_sequences":{"sequence":{"4304":{"protein_sequence":{"accession":"NP_460903.1","sequence":"MQENDFFTWRRAMLLRFQEMAAAEDVYTELQYQTQRLEFDYYALCVRHPVPFTRPKISLRTTYPPAWVTHYQSENYFAIDPVLKPENFRQGHLHWDDVLFHEAKAMWDAAQRFGLRRGVTQCVMLPNRALGFLSFSRSSLRCSSFTYDEVELRLQLLARESLSALTRFEDDMVMAPEMRFSKREKEILKWTAEGKTSSEIAIILSISENTVNFHQKNMQKKFNAPNKTQIACYAAATGLI"},"dna_sequence":{"accession":"NC_003197","fmin":"2039654","fmax":"2040377","strand":"-","sequence":"TCATATCAGACCTGTCGCCGCAGCGTAGCAGGCAATCTGTGTTTTATTTGGCGCATTGAATTTCTTCTGCATATTTTTCTGATGGAAGTTAACGGTATTTTCAGAAATCGACAGAATAATGGCGATCTCCGATGAGGTCTTCCCTTCCGCCGTCCACTTCAGAATCTCTTTCTCACGTTTACTGAAACGCATTTCAGGCGCCATCACCATGTCGTCTTCAAATCTTGTCAGCGCCGAAAGACTCTCCCGCGCCAGCAGTTGCAACCTCAGCTCCACTTCGTCGTAGGTAAACGAGGAGCAGCGTAAACTGCTACGGGAGAAAGATAAAAAGCCCAGCGCCCGGTTCGGCAACATCACACACTGGGTTACGCCTCTGCGTAATCCGAAACGCTGGGCGGCATCCCACATCGCCTTCGCTTCATGAAATAGCACGTCATCCCAATGTAAATGACCCTGCCTGAAATTTTCCGGCTTTAATACCGGATCGATCGCGAAATAGTTTTCGGACTGGTAATGCGTTACCCACGCCGGAGGATAAGTGGTACGAAGCGATATTTTAGGCCGGGTAAAGGGGACGGGATGACGAACACACAGGGCATAATAATCAAATTCCAGCCGCTGTGTCTGATATTGCAATTCAGTATAAACATCCTCTGCTGCCGCCATCTCCTGAAAGCGTAACAACATTGCGCGTCGCCAGGTGAAGAAATCATTTTCCTGCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35734","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium str. LT2","NCBI_taxonomy_id":"99287"}}}},"ARO_accession":"3000826","ARO_id":"37206","ARO_name":"sdiA","ARO_description":"SdiA is a cell division regulator that is also a positive regulator of AcrAB only when it's expressed from a plasmid. When the sdiA gene is on the chromosome, it has no effect on expression of acrAB","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"229":{"model_id":"229","model_name":"vanTmL","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"301":{"protein_sequence":{"accession":"ABX54689.1","sequence":"MKKQNTGVNNFRLIAAAMVVAIHCFPFQTISKELDTLVTLTVFRIAVPFFFMVSGYYLLGPIPSSATNTYQINNYIKKQLKVYTFAIVLYLPLAFYSQSITLDMSIISFIKQLLFNGFFYHLWFFPAWVLGLLIVQFLLKRMNIQTVLFITFVAYLIGLGGDSWWGIVKQVPFFFRFYNAIFQLFGYTRNGLFYAPLFFALGAYLYKMNIKNFNSARNNYLLLLFSIEMILESYFLHLFNIPKHDSMYLFLPFVMTLVFIKIYNWSPKNNLLNSSQLSLGVYLIHPYIIAVIHSISIYVSIFTNSIINYLSVLLISYLTIRLILKRKEW"},"dna_sequence":{"accession":"EU250284","fmin":"2574","fmax":"3564","strand":"+","sequence":"ATGAAAAAACAAAATACGGGTGTAAATAATTTCCGTTTAATCGCTGCTGCCATGGTAGTAGCGATTCATTGCTTTCCATTTCAAACAATCAGTAAAGAACTAGATACATTGGTTACGCTAACTGTCTTTCGTATTGCCGTTCCTTTTTTCTTCATGGTTTCTGGGTACTACCTACTAGGTCCAATTCCAAGTTCAGCCACAAATACTTATCAAATTAATAACTATATAAAGAAACAGCTTAAAGTTTATACTTTCGCTATAGTTCTGTATCTACCTTTAGCGTTTTATAGTCAATCTATCACTTTGGATATGTCAATTATTAGTTTTATAAAACAACTACTTTTTAACGGTTTTTTTTACCATCTTTGGTTTTTCCCTGCATGGGTATTAGGATTATTAATTGTTCAATTTTTATTAAAAAGAATGAATATACAGACTGTATTGTTTATAACATTTGTGGCTTATTTAATAGGACTAGGAGGGGATAGTTGGTGGGGAATAGTTAAACAAGTTCCCTTTTTTTTCAGATTTTACAATGCTATATTTCAATTATTTGGTTATACACGAAATGGTCTATTTTATGCGCCGTTATTCTTTGCACTGGGAGCATATCTATACAAGATGAATATTAAAAACTTTAATTCCGCAAGAAATAACTATCTTTTACTGCTTTTTAGTATAGAAATGATTTTAGAAAGTTATTTCTTACATCTCTTTAACATTCCTAAACATGACAGTATGTATTTGTTTTTACCGTTTGTAATGACTTTGGTGTTTATCAAAATATACAATTGGTCACCAAAAAATAATTTATTGAACAGCTCTCAGCTATCTCTAGGAGTATATCTTATACATCCATATATCATCGCAGTAATTCACTCTATCTCAATTTACGTTTCTATTTTTACTAATAGCATAATTAATTATTTAAGTGTGCTATTGATAAGTTACCTAACTATAAGACTAATACTAAAAAGGAAGGAATGGTAGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3002973","ARO_id":"39407","ARO_name":"vanTmL","ARO_description":"vanTmL is a vanT variant found in the vanL gene cluster. vanTmL codes for the membrane-binding domain of vanTL","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36511":{"category_aro_accession":"3000372","category_aro_cvterm_id":"36511","category_aro_name":"vanT","category_aro_description":"VanT is a membrane bound serine racemase, converting L-serine to D-serine. It is associated with VanC, which incorporated D-serine into D-Ala-D-Ser terminal end of peptidoglycan subunits that have a decreased binding affinity with vancomycin. It was isolated from Enterococcus gallinarum.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"230":{"model_id":"230","model_name":"OXA-422","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"892":{"protein_sequence":{"accession":"AIY30331.1","sequence":"MNKYFTCYVVASPFLSGCTVQHNLINETPSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKPQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"KM433671","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCCTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGACCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCCCAATTAGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003160","ARO_id":"39737","ARO_name":"OXA-422","ARO_description":"From the Lahey list of beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"231":{"model_id":"231","model_name":"OXA-178","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1046":{"protein_sequence":{"accession":"ADI58622.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDSKKRLFPEWEKDMTLGDAMKASAILVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"HM113564","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATAGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCTAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001472","ARO_id":"37872","ARO_name":"OXA-178","ARO_description":"OXA-178 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"232":{"model_id":"232","model_name":"imiH","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"1808":{"protein_sequence":{"accession":"CAD69003.1","sequence":"MMKGWMKCGLAGAVVLMASFWGGSVRAAGMSLTQVSGPVYVVEDNYYVQENSMVYFGAKGVTVVGATWTPDTARELHKLIKRVSRQPVLEVINTNYHTDRAGGNAYWKSIGAKVVSTRQTRDLMKSDWAEIVAFTRKGLPEYPDLPLVLPNVVHDGDFTLQEGKLRAFYAGPAHTPDGIFVYFPDQLVLYGNCILKEKLGNLSFADVKAYPQTLERLKAMKLPIKTVVGGHDSPLHGPELIDHYEALIKAAPQS"},"dna_sequence":{"accession":"AJ548797","fmin":"923","fmax":"1688","strand":"+","sequence":"ATGATGAAAGGTTGGATGAAGTGTGGATTGGCCGGCGCCGTGGTGCTGATGGCGAGTTTCTGGGGTGGCAGCGTGCGGGCGGCGGGGATGTCGCTGACGCAGGTGAGCGGCCCTGTGTATGTGGTAGAGGACAACTACTACGTGCAGGAAAATTCCATGGTCTATTTCGGGGCCAAGGGCGTGACTGTGGTGGGGGCGACCTGGACGCCGGACACCGCCCGCGAGCTGCACAAGCTGATCAAACGGGTCAGCCGCCAGCCGGTGCTGGAGGTGATCAACACCAACTACCACACCGACCGGGCTGGCGGTAACGCCTACTGGAAGTCCATCGGTGCCAAGGTGGTATCGACCCGCCAGACCCGGGATCTGATGAAGAGCGACTGGGCCGAGATCGTTGCCTTTACCCGCAAGGGGTTGCCGGAGTACCCGGATCTGCCCCTGGTGCTGCCCAACGTGGTGCACGATGGCGACTTCACCCTGCAAGAGGGCAAGCTGCGCGCCTTCTACGCGGGCCCGGCCCACACGCCGGACGGCATCTTTGTCTACTTCCCCGACCAGCTGGTGCTCTATGGCAACTGCATCCTCAAGGAGAAGCTGGGCAACCTGAGCTTTGCCGATGTGAAGGCCTATCCGCAGACACTTGAGCGGCTGAAAGCGATGAAGCTGCCGATCAAGACGGTGGTGGGCGGTCACGACTCGCCACTGCACGGCCCCGAGCTTATCGATCACTACGAAGCGCTGATCAAGGCCGCACCCCAGTCATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36810","NCBI_taxonomy_name":"Aeromonas hydrophila","NCBI_taxonomy_id":"644"}}}},"ARO_accession":"3003094","ARO_id":"39647","ARO_name":"imiH","ARO_description":"imiH is an Ambler Class B MBL; subclass B2 originally isolated from Aeromonas hydrophila. This enzyme has specific activity against carbapenems.","ARO_category":{"36720":{"category_aro_accession":"3000581","category_aro_cvterm_id":"36720","category_aro_name":"CphA beta-lactamase","category_aro_description":"CphA is an Ambler Class B MBL; subclass B2 originally isolated from Aeromonas hydrophilia.  This enzyme has specific activity against carbapenems and is active as a mono-zinc protein.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"233":{"model_id":"233","model_name":"LEN-21","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1732":{"protein_sequence":{"accession":"CAP12349.2","sequence":"MRYVRLCVISLLATLPLAVDAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGVEQLVRRIHYRQQDLVDYSPVSEKHLVDGMTIGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGARGIVALLGPDGKPERIVVIYLRDTPASMAERNQHIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM850911","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCACCCTGCCACTGGCGGTAGACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCAGGGGTCGAACAACTGGTTCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGTCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGACAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002468","ARO_id":"38868","ARO_name":"LEN-21","ARO_description":"LEN-21 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"234":{"model_id":"234","model_name":"QnrS8","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"387":{"protein_sequence":{"accession":"AHE41345.1","sequence":"METYNHTYRHHNFSHKDLSDLTFTACTLIRSDFRRANLRDTTFVNCKFIEQGDIEGCHFDVADLRDASFQQCQLAMANFSNANCYGIEFRACDLKGANFSRTNFAHQVSNRMYFCSAFISGCNLSYANMERVCLEKCELFENRWIGTNLAGASLKESDLSRGVFSEDVWGQFSLQGANLCHAELDGLDPRKVDTSGIKIAAWQQELILEALGIVVYPD"},"dna_sequence":{"accession":"KF730652","fmin":"0","fmax":"657","strand":"+","sequence":"ATGGAAACCTACAATCATACATATCGGCACCACAACTTTTCACATAAAGACTTAAGTGATCTCACCTTCACCGCTTGCACACTCATTCGCAGCGACTTTCGACGTGCTAACTTGCGTGATACGACATTCGTCAACTGCAAGTTCATTGAACAGGGTGATATCGAAGGCTGCCACTTTGATGTCGCAGATCTTCGTGATGCAAGTTTCCAACAATGCCAACTTGCGATGGCAAACTTCAGTAATGCCAATTGCTACGGTATAGAGTTCCGTGCGTGTGATTTAAAAGGTGCCAACTTTTCCCGAACAAACTTTGCCCATCAAGTGAGTAATCGTATGTACTTTTGCTCAGCATTTATTTCTGGATGTAATCTTTCCTATGCCAATATGGAGAGGGTTTGTTTAGAAAAATGTGAGTTGTTTGAAAATCGCTGGATAGGAACGAACCTAGCGGGTGCATCACTGAAAGAGTCAGACTTAAGTCGAGGTGTTTTTTCCGAAGATGTCTGGGGGCAATTTAGCCTACAGGGTGCCAATTTATGCCACGCCGAACTCGACGGTTTAGATCCCCGCAAAGTCGATACATCAGGTATCAAAATTGCAGCCTGGCAGCAAGAACTGATTCTCGAAGCACTGGGTATTGTTGTTTATCCTGACTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002797","ARO_id":"39231","ARO_name":"QnrS8","ARO_description":"QnrS8 is a plasmid-mediated quinolone resistance protein found in Klebsiella pneumoniae","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"235":{"model_id":"235","model_name":"OXA-181","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1371":{"protein_sequence":{"accession":"AEP16366.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIAAWNRDHDLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATQQIAFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"JN205800","fmin":"4140","fmax":"4938","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCAGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGTGATATCGCCGCTTGGAATCGTGACCATGACTTAATTACCGCGATGAAGTACTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGTGAGGCACGTATGAGTAAAATGCTGCACGCCTTCGATTATGGCAATGAGGATATCTCGGGCAATGTAGACAGTTTTTGGCTCGATGGTGGTATTCGCATTTCGGCTACCCAGCAAATCGCTTTTTTACGCAAGCTGTATCACAACAAGCTGCACGTTTCTGAGCGTAGTCAGCGCATCGTGAAACAAGCCATGCTGACCGAAGCCAATGGCGACTATATTATTCGGGCTAAAACGGGATACTCGACTAGAATCGAACCTAAGATTGGCTGGTGGGTTGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAGAAAATTATTCCCTAGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001784","ARO_id":"38184","ARO_name":"OXA-181","ARO_description":"OXA-181 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"35994":{"category_aro_accession":"0000077","category_aro_cvterm_id":"35994","category_aro_name":"tazobactam","category_aro_description":"Tazobactam is a compound which inhibits the action of bacterial beta-lactamases.","category_aro_class_name":"Adjuvant"},"35996":{"category_aro_accession":"0000079","category_aro_cvterm_id":"35996","category_aro_name":"clavulanate","category_aro_description":"Clavulanic acid is a beta-lactamase inhibitor (marketed by GlaxoSmithKline, formerly Beecham) combined with penicillin group antibiotics to overcome certain types of antibiotic resistance. It is used to overcome resistance in bacteria that secrete beta-lactamase, which otherwise inactivates most penicillins.","category_aro_class_name":"Adjuvant"},"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"35995":{"category_aro_accession":"0000078","category_aro_cvterm_id":"35995","category_aro_name":"piperacillin","category_aro_description":"Piperacillin is an acetylureidopenicillin and has an extended spectrum of targets relative to other beta-lactam antibiotics. It inhibits cell wall synthesis in bacteria, and is usually taken with the beta-lactamase inhibitor tazobactam to overcome penicillin-resistant bacteria.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"236":{"model_id":"236","model_name":"ACT-19","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1583":{"protein_sequence":{"accession":"AHM76779.1","sequence":"MMKKSFCCALLLAISGSALAAPVSEKQLAEVVANTVTPLMKTQAIPGMAVAVIYQGKPHYYTFGEADIAAKKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTKFWPELTGKQWQGIRMLDLATYTAGGLPLQVPEEVTDNASLLRFYQHWQPQWKPGTTRLYANASIGLFGALAVKPSGMRYEQAMTKRVFKPLRLNHTWINVPKAEAAHYAWGYRDGKAVHISPGMLDAEAYGVKTNVQDMANWVMANMAPENIADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEAKMVIEGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYHILDALQ"},"dna_sequence":{"accession":"KF992029","fmin":"748","fmax":"1894","strand":"+","sequence":"ATGATGAAAAAATCCTTTTGCTGCGCCCTGCTGCTCGCCATCTCTGGCTCTGCTCTCGCCGCGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAACCCAGGCTATTCCAGGCATGGCGGTGGCCGTTATCTATCAGGGAAAACCGCACTATTACACGTTTGGCGAAGCCGATATTGCGGCCAAAAAACCTGTTACGCCACAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCCCTGGACGATCCGGTGACCAAATTCTGGCCTGAACTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCAACCTACACCGCGGGCGGCCTGCCGCTACAGGTACCGGAAGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAACACTGGCAACCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAATGCCAGCATCGGACTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGCGCTATGAGCAGGCCATGACGAAGCGGGTCTTCAAGCCGCTCAGGCTGAACCATACCTGGATTAACGTTCCGAAAGCGGAAGCGGCGCATTACGCCTGGGGTTATCGTGACGGTAAAGCGGTCCACATTTCACCGGGTATGCTGGACGCAGAGGCCTATGGCGTGAAAACTAACGTGCAGGATATGGCGAACTGGGTGATGGCGAACATGGCGCCGGAGAACATTGCTGATGCCTCACTCAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGCATCGGGTCAATGTATCAGGGCCTGGGCTGGGAAATGCTCAACTGGCCCGTGGAGGCCAAAATGGTGATCGAGGGCAGCGACAATAAGGTGGCACTGGCGCCGTTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACAGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAATCCGGCACGCGTTGAGGCGGCATACCATATCCTCGACGCACTACAGTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001840","ARO_id":"38240","ARO_name":"ACT-19","ARO_description":"ACT-19 is a beta-lactamase. From the Lahey list of ACT beta-lactamases.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"238":{"model_id":"238","model_name":"SHV-137","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1388":{"protein_sequence":{"accession":"AEI83430.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAALTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPHNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"HQ661363","fmin":"71","fmax":"932","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGCATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGCATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001181","ARO_id":"37561","ARO_name":"SHV-137","ARO_description":"SHV-137 is a beta-lactamase.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"239":{"model_id":"239","model_name":"OXA-83","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1937":{"protein_sequence":{"accession":"ABC26007.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASALPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"DQ309277","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTCTTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001623","ARO_id":"38023","ARO_name":"OXA-83","ARO_description":"OXA-83 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"240":{"model_id":"240","model_name":"vanRF","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"202":{"protein_sequence":{"accession":"AAR84672.1","sequence":"MKNITILIADDDAEIADLVAIHLEKEGYRVIKVSDGQETIDVIQNQPIDLLILDIMMPKMDGFEVTRRIREKHNMPIIFLSAKTSDFDKVQGLVIGADDYMTKPFIPIELVARVNAQLRRFMKLNQPKTKQNSNLEFGGLTISPEQRTVTLYGKNIELTPKEFEILFLLASNPNKVYRAEDIFQKVWGDAYYEGGNTVMVHIRTLRKKLEEDKRKNKLIQTVWGVGYKFNG"},"dna_sequence":{"accession":"AF155139","fmin":"1511","fmax":"2207","strand":"+","sequence":"ATGAAAAATATAACAATATTAATAGCTGATGATGATGCTGAAATTGCTGATTTGGTTGCTATACATTTAGAGAAAGAAGGGTATCGTGTCATTAAGGTATCGGATGGGCAAGAAACCATTGATGTTATCCAGAACCAACCCATTGATTTACTGATTTTGGATATTATGATGCCGAAAATGGATGGATTTGAAGTGACACGTCGCATTCGCGAAAAACATAATATGCCCATTATTTTTTTGAGCGCTAAAACGTCTGATTTTGATAAAGTGCAGGGACTCGTGATTGGAGCAGACGATTATATGACGAAACCATTTATACCCATTGAATTGGTAGCTCGGGTAAATGCACAGCTGCGACGCTTTATGAAGTTGAATCAACCTAAAACCAAACAGAACTCAAACTTGGAATTTGGAGGATTAACGATTTCTCCTGAACAACGTACAGTTACTCTATATGGTAAGAATATTGAGTTAACACCGAAAGAGTTTGAAATTTTATTTTTATTAGCCAGTAATCCAAATAAAGTTTATCGTGCAGAAGATATTTTTCAGAAGGTATGGGGGGATGCATACTATGAAGGTGGGAATACCGTTATGGTTCATATTCGTACTTTGCGGAAAAAACTTGAAGAGGATAAACGAAAAAACAAATTGATACAAACTGTATGGGGGGTAGGTTATAAATTCAATGGGTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39542","NCBI_taxonomy_name":"Paenibacillus popilliae ATCC 14706","NCBI_taxonomy_id":"1212764"}}}},"ARO_accession":"3002925","ARO_id":"39359","ARO_name":"vanRF","ARO_description":"vanRF is a vanR variant found in the vanF gene cluster","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36713":{"category_aro_accession":"3000574","category_aro_cvterm_id":"36713","category_aro_name":"vanR","category_aro_description":"VanR is a OmpR-family transcriptional activator in the VanSR regulatory system. When activated by VanS, it promotes cotranscription of VanA, VanH, and VanX.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"241":{"model_id":"241","model_name":"ACT-30","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1263":{"protein_sequence":{"accession":"AIT76086.1","sequence":"MMKKSLCCALLLGLSCSALAAPVSEKQLAEVVANTVTPLMIAQSVPGMAVAVIYQGKSHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYARGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPEKVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQVGIVMLANKSYPNPARVEAAYHILDALQ"},"dna_sequence":{"accession":"KM087833","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCTCTTTGCTGCGCCCTGCTGCTCGGCCTCTCTTGCTCTGCTCTCGCCGCGCCAGTATCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGATAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAATCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCAGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAAGGTTGCCGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAAGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTACCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCATGGGTCCATAAAACGGGTTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGGTCGGTATTGTAATGCTCGCGAATAAAAGCTATCCGAATCCGGCACGCGTTGAGGCGGCATACCATATCCTCGACGCGCTACAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001850","ARO_id":"38250","ARO_name":"ACT-30","ARO_description":"ACT-30 is a beta-lactamase. From the Lahey list of ACT beta-lactamases.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"242":{"model_id":"242","model_name":"SHV-152","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1232":{"protein_sequence":{"accession":"AFQ23958.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTARRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"JX121119","fmin":"0","fmax":"858","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCCGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001191","ARO_id":"37571","ARO_name":"SHV-152","ARO_description":"SHV-152 is a beta-lactamase.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"243":{"model_id":"243","model_name":"OXA-9","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1219":{"protein_sequence":{"accession":"AAA98406.1","sequence":"MKKILLLHMLVFVSATLPISSVASDEVETLKCTIIADAITGNTLYETGECARRVSPCSSFKLPLAIMGFDSGILQSPKSPTWELKPEYNPSPRDRTYKQVYPALWQSDSVVWFSQQLTSRLGVDRFTEYVKKFEYGNQDVSGDSGKHNGLTQSWLMSSLTISPKEQIQFLLRFVAHKLPVSEAAYDMAYATIPQYQAAEGWAVHGKSGSGWLRDNNGKINESRPQGWFVGWAEKNGRQVVFARLEIGKEKSDIPGGSKAREDILVELPVLMGNK"},"dna_sequence":{"accession":"M55547","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAAAAAAATTTTGCTGCTGCATATGTTGGTGTTCGTTTCCGCCACTCTCCCAATCAGTTCCGTGGCTTCTGATGAGGTTGAAACGCTTAAATGCACCATCATCGCAGACGCCATTACCGGAAATACCTTATATGAGACCGGAGAATGTGCCCGTCGTGTGTCTCCGTGCTCGTCTTTTAAACTTCCATTGGCAATCATGGGGTTTGATAGTGGAATCTTGCAGTCGCCAAAATCACCTACGTGGGAATTGAAGCCGGAATACAACCCGTCTCCGAGAGATCGCACATACAAACAAGTCTATCCGGCGCTATGGCAAAGCGACTCTGTTGTCTGGTTCTCGCAGCAATTAACAAGCCGTCTGGGAGTTGATCGGTTCACGGAATACGTAAAGAAATTTGAGTACGGTAATCAAGATGTTTCCGGTGACTCGGGGAAGCATAACGGCTTGACCCAGTCATGGCTGATGTCGTCGCTCACCATATCTCCCAAGGAGCAAATTCAGTTTCTTCTACGCTTTGTCGCGCATAAGCTGCCTGTATCCGAAGCGGCTTATGACATGGCGTATGCCACAATCCCGCAGTACCAGGCAGCCGAAGGATGGGCTGTACATGGAAAAAGCGGCAGCGGCTGGCTTCGGGACAATAACGGCAAGATAAATGAAAGTCGTCCGCAGGGCTGGTTCGTGGGCTGGGCTGAAAAAAACGGACGGCAAGTTGTTTTCGCCCGATTGGAAATAGGAAAGGAAAAGTCCGATATTCCCGGCGGGTCTAAAGCACGAGAGGATATTCTCGTGGAATTACCCGTGTTGATGGGTAACAAATGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001404","ARO_id":"37804","ARO_name":"OXA-9","ARO_description":"OXA-9 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"244":{"model_id":"244","model_name":"SHV-164","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"988":{"protein_sequence":{"accession":"CCK86744.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGEQGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"HE981194","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACCCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGAGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACAGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATCGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001347","ARO_id":"37747","ARO_name":"SHV-164","ARO_description":"From the Lahey list of beta-lactamases.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"245":{"model_id":"245","model_name":"cmlA5","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"695":{"protein_sequence":{"accession":"AAM77075.1","sequence":"MRSKNFSWRYSLAATVLLLSPFDLLASLGMDMYLPAVPFMPNALGTTASTIQLTLTTYLVMIGAGQLLFGPLSDRLGRRPVLLGGGLAYVVASMGLALTSSAEVFLGLRILQACGASACLVSTFATVRDIYAGREESNVIYGILGSMLAMVPAVGPLLGALVDMWLGWRAIFAFLGLGMIAASAAAWRFWPETRVQRVAGLQWSQLLLPVKCLNFWLYTLCYAAGMGSFFVFFSIAPGLMMGRQGVSQLGFSLLFATVAIAMVFTARFMGRVIPKWGSPSVLRMGMGCLIAGAVLLAITEIWASQSVLGFIAPMWLVGIGVATAVSVSPNGALRGFDHVAGTVTAVYFCLGGVLLGSIGTLIISLLPRNTAWPVVVYCLTLATVVLGLSCVSRVKGSRGQGEHDVVALQSAESTSNPNR"},"dna_sequence":{"accession":"AY115475","fmin":"3337","fmax":"4597","strand":"+","sequence":"GTGCGCTCAAAAAACTTTAGTTGGCGGTACTCCCTTGCCGCCACGGTGTTGTTGTTATCACCGTTCGATTTATTGGCATCACTCGGCATGGACATGTACTTGCCAGCAGTGCCGTTTATGCCAAACGCGCTTGGTACGACAGCGAGCACAATTCAGCTTACGCTGACAACGTACTTGGTCATGATTGGTGCCGGTCAGCTCTTGTTTGGACCGCTATCGGACCGACTGGGGCGCCGCCCCGTTCTACTGGGAGGTGGCCTCGCCTACGTTGTGGCGTCAATGGGCCTCGCTCTTACGTCATCGGCTGAAGTCTTTCTGGGGCTTCGGATTCTTCAGGCTTGTGGTGCCTCGGCGTGCCTTGTTTCCACATTTGCAACAGTACGTGACATTTACGCAGGTCGCGAGGAAAGTAATGTCATTTACGGCATACTCGGATCCATGCTGGCCATGGTCCCGGCGGTAGGCCCATTGCTCGGAGCGCTCGTCGACATGTGGCTTGGGTGGCGGGCTATCTTTGCGTTTCTAGGTTTGGGCATGATCGCTGCATCTGCAGCAGCGTGGCGATTCTGGCCTGAAACCCGGGTGCAACGAGTTGCGGGCTTGCAATGGTCGCAGCTGCTACTCCCCGTTAAGTGCCTGAACTTCTGGTTGTACACGTTGTGTTACGCCGCTGGAATGGGTAGCTTCTTCGTCTTTTTCTCCATTGCGCCCGGACTAATGATGGGCAGGCAAGGTGTGTCTCAGCTTGGCTTCAGCCTGCTGTTCGCCACAGTGGCAATTGCCATGGTGTTTACGGCTCGTTTTATGGGGCGTGTGATACCCAAGTGGGGCAGCCCAAGTGTCTTGCGAATGGGAATGGGATGCCTGATAGCTGGAGCAGTATTGCTTGCCATCACCGAAATATGGGCTTCGCAGTCCGTGTTAGGCTTTATTGCTCCAATGTGGCTAGTGGGTATTGGTGTCGCCACAGCGGTATCTGTGTCGCCCAATGGCGCTCTTCGAGGATTCGACCATGTTGCTGGAACGGTCACGGCAGTCTACTTCTGCTTGGGCGGTGTACTGCTAGGAAGCATCGGAACGTTGATCATTTCGCTGTTGCCGCGCAACACGGCTTGGCCGGTTGTCGTGTACTGTTTGACCCTTGCAACAGTCGTGCTCGGTCTGTCTTGTGTTTCCCGAGTGAAGGGCTCTCGCGGCCAGGGGGAGCATGATGTGGTCGCGCTACAAAGTGCGGAAAGTACATCAAATCCCAATCGTTGAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3002695","ARO_id":"39129","ARO_name":"cmlA5","ARO_description":"cmlA5 is a plasmid or transposon-encoded chloramphenicol exporter that is found in Escherichia coli","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"246":{"model_id":"246","model_name":"CTX-M-126","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1476":{"protein_sequence":{"accession":"BAL72196.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEATLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"AB703103","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAAGCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAGCAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001985","ARO_id":"38385","ARO_name":"CTX-M-126","ARO_description":"CTX-M-126 is a beta-lactamase. From the Lahey list of CTX-M beta-lactamases.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"247":{"model_id":"247","model_name":"TEM-158","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1569":{"protein_sequence":{"accession":"ABQ00181.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMLSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERDRQIAEIGASLIKHW"},"dna_sequence":{"accession":"EF534736","fmin":"213","fmax":"1074","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGCTGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAGATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001024","ARO_id":"37404","ARO_name":"TEM-158","ARO_description":"TEM-158 is an inhibitor-resistant, extended-spectrum beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"248":{"model_id":"248","model_name":"OKP-B-9","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1998":{"protein_sequence":{"accession":"CAJ19618.1","sequence":"MRYVRLCLISLIAALPLAVFASPQPLEQIKISESQLAGRVGYIEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKSVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMATTLRRLLTTPSLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPDGKAERIVVIYLRDTAATMVERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM051159","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCAGCCGCTTGAGCAGATTAAAATCAGCGAAAGTCAGCTGGCGGGCCGGGTGGGCTATATTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGCGACGAACAGCTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGAGCGTCGGCGGCCCTGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGAACTCAATGAGGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCGGCCAGCATGGCCACCACCCTGCGCAGGCTGCTAACCACCCCCTCTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGACCGGGTGGCCGGCCCGTTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGTGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAAGCGGAGCGTATCGTGGTGATCTATCTGCGGGATACCGCGGCGACCATGGTCGAGCGTAACCAGCAGATCGCCGGGATAGGCGCGGCGCTGATCGAGCACTGGCAGCGCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002442","ARO_id":"38842","ARO_name":"OKP-B-9","ARO_description":"OKP-B-9 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"251":{"model_id":"251","model_name":"APH(3')-VIIa","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"326":{"protein_sequence":{"accession":"AAA76822.1","sequence":"MKYIDEIQILGKCSEGMSPAEVYKCQLKNTVCYLKKIDDIFSKTTYSVKREAEMMMWLSDKLKVPDVIEYGVREHSEYLIMSELRGKHIDCFIDHPIKYIECLVNALHQLQAIDIRNCPFSSKIDVRLKELKYLLDNRIADIDVSNWEDTTEFDDPMTLYQWLCENQPQEELCLSHGDMSANFFVSHDGIYFYDLARCGVADKWLDIAFCVREIREYYPDSDYEKFFFNMLGLEPDYKKINYYILLDEMF"},"dna_sequence":{"accession":"M29953","fmin":"295","fmax":"1048","strand":"+","sequence":"ATGAAATATATCGATGAAATTCAAATTCTGGGAAAATGTTCAGAGGGTATGTCTCCAGCAGAAGTATATAAATGCCAGCTTAAAAATACTGTATGCTATCTGAAAAAAATTGACGATATATTTTCAAAAACCACATACAGCGTGAAAAGAGAAGCTGAGATGATGATGTGGTTATCCGATAAACTGAAAGTACCAGATGTAATCGAATACGGAGTACGAGAACATTCAGAATATTTGATCATGAGTGAGTTAAGGGGGAAACACATAGATTGCTTTATTGATCATCCAATAAAATATATTGAGTGCTTGGTAAACGCACTTCATCAGCTACAAGCAATAGATATAAGAAACTGCCCATTTTCATCCAAAATAGATGTTCGATTAAAAGAACTAAAATATCTTTTGGATAACAGAATTGCCGATATTGATGTATCGAATTGGGAAGATACAACAGAATTTGATGATCCAATGACGTTATATCAGTGGCTTTGCGAAAATCAACCTCAAGAAGAACTGTGTCTCTCTCATGGAGATATGAGCGCTAATTTTTTTGTATCTCATGATGGAATATATTTTTATGATTTGGCAAGATGTGGAGTTGCAGACAAATGGTTGGATATAGCATTTTGTGTCAGAGAGATTCGAGAATATTATCCTGATTCTGATTATGAAAAATTCTTTTTTAACATGTTGGGACTTGAACCGGATTATAAAAAAATTAACTATTACATTTTATTAGATGAGATGTTTTAGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3002654","ARO_id":"39054","ARO_name":"APH(3')-VIIa","ARO_description":"APH(3')-VIIa is a plasmid-encoded aminoglycoside phosphotransferase in C. jejuni","ARO_category":{"36265":{"category_aro_accession":"3000126","category_aro_cvterm_id":"36265","category_aro_name":"APH(3')","category_aro_description":"Phosphorylation of 2-deoxystreptamine aminoglycosides on the hydroxyl group at position 3'","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"252":{"model_id":"252","model_name":"APH(9)-Ia","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"514":{"protein_sequence":{"accession":"AAB58447.1","sequence":"MLKQPIQAQQLIELLKVHYGIDIHTAQFIQGGADTNAFAYQADSESKSYFIKLKYGYHDEINLSIIRLLHDSGIKEIIFPIHTLEAKLFQQLKHFKIIAYPFIHAPNGFTQNLTGKQWKQLGKVLRQIHETSVPISIQQQLRKEIYSPKWREIVRSFYNQIEFDNSDDKLTAAFKSFFNQNSAAIHRLVDTSEKLSKKIQPDLDKYVLCHSDIHAGNVLVGNEESIYIIDWDEPMLAPKERDLMFIGGGVGNVWNKPHEIQYFYEGYGEINVDKTILSYYRHERIVEDIAVYGQDLLSRNQNNQSRLESFKYFKEMFDPNNVVEIAFATEQ"},"dna_sequence":{"accession":"U94857","fmin":"0","fmax":"996","strand":"+","sequence":"ATGCTAAAACAACCAATTCAAGCTCAACAACTTATCGAACTTTTGAAAGTGCATTATGGAATTGATATTCATACAGCACAATTCATCCAGGGTGGTGCTGATACGAATGCATTTGCATATCAAGCAGATTCAGAATCCAAGTCTTATTTCATAAAGCTAAAATACGGCTATCATGATGAAATTAATTTATCGATAATCCGTCTTTTACATGATTCTGGAATAAAAGAAATTATTTTTCCTATCCATACACTTGAAGCAAAATTATTCCAGCAACTAAAGCATTTTAAAATAATTGCGTATCCATTTATTCATGCGCCCAATGGTTTCACCCAAAATTTAACAGGAAAACAGTGGAAACAGCTTGGAAAAGTATTAAGACAAATTCATGAAACATCAGTTCCCATCTCGATTCAACAACAATTAAGAAAAGAAATATACTCCCCTAAATGGCGTGAAATAGTCAGATCCTTTTATAATCAAATTGAATTTGATAATTCAGATGATAAGCTCACGGCTGCCTTTAAATCTTTTTTTAACCAAAATAGTGCTGCAATTCATCGATTAGTTGATACTTCAGAAAAACTATCTAAAAAAATTCAACCTGATTTAGATAAATACGTACTATGTCATTCTGATATACATGCGGGCAATGTGTTAGTCGGTAATGAAGAGTCGATTTACATTATTGATTGGGATGAGCCTATGTTAGCTCCAAAAGAACGTGATTTGATGTTCATAGGTGGTGGCGTTGGTAATGTATGGAATAAACCCCATGAAATCCAATATTTTTATGAAGGTTATGGTGAAATAAATGTCGATAAAACAATTTTGTCTTATTACAGGCATGAACGAATTGTCGAAGATATCGCAGTATACGGGCAAGACTTGCTTTCACGTAATCAAAACAATCAGTCCAGACTTGAAAGTTTTAAATATTTTAAAGAAATGTTTGATCCAAACAACGTTGTTGAAATAGCTTTTGCTACAGAGCAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36899","NCBI_taxonomy_name":"Legionella pneumophila 130b","NCBI_taxonomy_id":"866628"}}}},"ARO_accession":"3002662","ARO_id":"39062","ARO_name":"APH(9)-Ia","ARO_description":"APH(9)-Ia is a chromosomal-encoded aminoglycoside phosphotransferase in L. pneumophila","ARO_category":{"36292":{"category_aro_accession":"3000153","category_aro_cvterm_id":"36292","category_aro_name":"APH(9)","category_aro_description":"Phosphorylation of spectinomycin on the hydroxyl group at position 9","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"253":{"model_id":"253","model_name":"vanXYG","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"123":{"protein_sequence":{"accession":"ABA71732.1","sequence":"MMKTIELEKEEIYCGNLLLVNKNYPLRDNNVKGLVPADIRFPNILMKRDVANVLQLIFEKISAGNSIVPVSGYRSLEEQTAIYDGSLKDNGEDFTRKYVALPNHSEHQTGLAIDLGLNKKDIDFIRPDFPYDGICDEFRRAAPDYGFTQRYARDKEEITGISHEPWHFRYVGYPHSKIMQENGFSLEEYTQFIKAYLEDNKYLFEQAHRAEIEIYYVPAKDDKTLIKIPENCVYQISGNNIDGFVVTIWRKTDD"},"dna_sequence":{"accession":"DQ212986","fmin":"7030","fmax":"7795","strand":"+","sequence":"ATGATGAAAACGATTGAGCTTGAAAAGGAAGAAATTTATTGTGGAAATTTGCTGCTCGTCAACAAAAATTATCCGCTACGAGATAACAATGTAAAGGGTTTAGTTCCTGCTGATATACGCTTTCCAAATATTCTTATGAAGCGTGATGTGGCAAATGTTTTGCAGCTTATTTTTGAAAAAATCTCGGCAGGTAACTCTATCGTTCCTGTAAGCGGTTATCGCTCATTAGAAGAACAGACAGCCATATATGACGGCTCTCTCAAAGATAATGGAGAGGATTTTACAAGAAAATATGTTGCTCTGCCCAATCATAGTGAACATCAAACAGGTCTTGCCATTGATTTAGGACTGAATAAAAAGGATATAGACTTTATCCGTCCCGATTTTCCCTATGACGGTATTTGCGATGAATTTAGGAGAGCTGCCCCAGACTATGGCTTTACCCAGCGTTATGCAAGGGATAAAGAAGAAATAACAGGGATTTCACACGAGCCGTGGCATTTTCGATATGTAGGATACCCACACTCAAAAATTATGCAGGAAAATGGTTTTTCACTTGAAGAATACACACAATTTATAAAAGCCTATCTGGAAGATAACAAATATCTTTTTGAGCAGGCTCACAGAGCTGAGATTGAAATATATTATGTTCCTGCAAAAGACGACAAAACGCTGATAAAAATACCAGAAAATTGTGTTTATCAGATTTCTGGTAATAACATAGACGGTTTTGTTGTGACCATATGGAGGAAAACAGATGACTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3003069","ARO_id":"39549","ARO_name":"vanXYG","ARO_description":"vanXYG is a vanXY variant found in the vanG gene cluster","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36635":{"category_aro_accession":"3000496","category_aro_cvterm_id":"36635","category_aro_name":"vanXY","category_aro_description":"VanXY is a protein with both D,D-carboxypeptidase and D,D-dipeptidase activity, found in Enterococcus gallinarum. It cleaves and removes the terminal D-Ala of peptidoglycan subunits for the incorporation of D-Ser by VanC. D-Ala-D-Ser has low binding affinity with vancomycin.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"254":{"model_id":"254","model_name":"OXA-150","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1923":{"protein_sequence":{"accession":"ACX31142.1","sequence":"MNIKALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKHVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"GQ853681","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATTCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCATGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTGTTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001455","ARO_id":"37855","ARO_name":"OXA-150","ARO_description":"OXA-150 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"256":{"model_id":"256","model_name":"CMY-21","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"957":{"protein_sequence":{"accession":"AAZ66866.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGELAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGKLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"DQ139328","fmin":"160","fmax":"1306","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGAGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGAAAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002032","ARO_id":"38432","ARO_name":"CMY-21","ARO_description":"CMY-21 is a beta-lactamase found in Escherichia coli","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"257":{"model_id":"257","model_name":"ACT-37","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1735":{"protein_sequence":{"accession":"AJG06172.1","sequence":"MMKKSFCCALLLAISGAALAAPVSEKQLAEVVANTVTPLMKAQAIPGMAVAVIYQGKPHYYTFGEADIAAKKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVIKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPEEVTDNASLLRFYQHWQPQWKPGTTRLYANASIGLFGALAVKPSGMRYEQAMTKRVFKPLRLNHTWINVPKAEAAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEAKTVIEGSDNKVALAPLPVAEVNPPVPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYHILDALQ"},"dna_sequence":{"accession":"KM926622","fmin":"238","fmax":"1384","strand":"+","sequence":"ATGATGAAAAAATCCTTTTGCTGCGCCCTGCTGCTCGCCATCTCTGGCGCTGCTCTCGCCGCGCCAGTATCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGGCTATTCCAGGCATGGCGGTGGCCGTTATCTATCAGGGAAAACCGCACTATTACACGTTTGGCGAAGCCGATATTGCGGCCAAAAAACCCGTTACGCCACAAACCCTGTTCGAGCTAGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGATGATCCGGTGATCAAATACTGGCCTGAACTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCAACCTACACCGCGGGCGGCCTGCCGCTACAGGTACCGGAAGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAACACTGGCAACCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAATGCCAGCATCGGACTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGCGCTATGAGCAGGCCATGACGAAGCGGGTCTTCAAGCCGCTCAGGCTGAACCATACCTGGATTAACGTTCCGAAAGCGGAAGCGGCGCATTACGCCTGGGGTTATCGTGACGGTAAAGCGGTCCACGTTTCACCGGGTATGCTGGACGCAGAGGCCTATGGCGTGAAAACTAACGTGCAGGATATGGCGAACTGGGTGATGGCGAACATGGCGCCGGAGAACGTTGCTGATGCCTCACTCAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGCCTGGGCTGGGAAATGCTCAACTGGCCCGTGGAGGCCAAAACAGTGATCGAGGGCAGCGACAATAAGGTGGCACTGGCGCCGTTGCCCGTGGCAGAAGTGAATCCACCGGTTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAATCCGGCACGCGTTGAGGCGGCATACCATATCCTCGACGCACTACAGTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3003172","ARO_id":"39749","ARO_name":"ACT-37","ARO_description":"From the Lahey list of beta-lactamases.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"258":{"model_id":"258","model_name":"OXA-208","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1926":{"protein_sequence":{"accession":"CCA94644.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"FR853176","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001486","ARO_id":"37886","ARO_name":"OXA-208","ARO_description":"OXA-208 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"260":{"model_id":"260","model_name":"ErmN","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"4244":{"protein_sequence":{"accession":"CAA66307.2","sequence":"MPSRPRTDSPHRHEGPAGPARLDRDEARRVWGQNFFRSAGSARRFARQLTGAESAGNDSVTVEVGPGAGRITKELVRDGHPIVAVEVDPHWADRLAELELPNLTVVNDDFTTWPLPDGPLRFIGNLPFGTGTRMLRRCLALGPDRCREGVFLLQKQYTRKRTGAYGGNLFNAQWEPWYTFRRGLGFPRQEFAPVPGSDTETLLVRSRPRPLAPWSRHAAYQRFVEDVFNTSRLTIGEAARALDRRAGPGWLRGARVPPGLRVKDITAEQWADLFHACTPPPARRISPQRRR"},"dna_sequence":{"accession":"X97721.2","fmin":"159","fmax":"1035","strand":"+","sequence":"ATGCCGTCCCGGCCACGTACCGATTCGCCCCACCGGCACGAGGGGCCGGCCGGCCCGGCCCGTCTCGACCGGGACGAGGCCCGCCGTGTATGGGGCCAGAATTTCTTCCGCTCGGCGGGTTCGGCCCGCCGTTTCGCCCGGCAGTTGACCGGCGCGGAATCGGCCGGAAACGACTCGGTCACCGTCGAGGTGGGTCCCGGGGCCGGCCGTATCACCAAGGAGTTAGTGAGGGACGGTCATCCGATCGTCGCGGTGGAGGTGGACCCCCATTGGGCCGACCGCCTCGCCGAACTGGAACTGCCGAACCTCACCGTCGTCAACGACGACTTCACGACCTGGCCGCTGCCCGACGGGCCGCTGCGGTTCATCGGCAATCTGCCCTTCGGCACCGGCACCAGGATGCTCCGCCGCTGCCTCGCCCTCGGCCCGGACCGCTGCCGCGAAGGCGTGTTCCTTCTCCAGAAGCAGTACACGCGCAAGCGCACCGGTGCCTACGGCGGCAATCTCTTCAACGCCCAGTGGGAGCCCTGGTACACGTTCCGCCGCGGACTGGGCTTCCCCCGGCAGGAGTTCGCCCCGGTCCCGGGCTCCGACACCGAGACCCTGCTGGTGAGATCGCGCCCGCGCCCGCTGGCGCCCTGGTCCCGCCATGCCGCCTACCAGCGGTTCGTGGAGGACGTGTTCAACACCTCCCGGCTCACCATCGGTGAGGCCGCCCGCGCGCTGGACCGCCGGGCCGGCCCGGGCTGGCTCCGGGGCGCGCGGGTGCCTCCCGGGTTGCGGGTCAAGGACATCACGGCCGAGCAGTGGGCCGATCTCTTCCACGCGTGCACCCCGCCGCCCGCCCGGCGCATCTCGCCGCAGCGGAGGCGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36838","NCBI_taxonomy_name":"Streptomyces fradiae","NCBI_taxonomy_id":"1906"}}}},"ARO_accession":"3000592","ARO_id":"36731","ARO_name":"ErmN","ARO_description":"ErmN is a methyltransferase found in the tylosin producer Streptomyces fradiae. Like other Erm enzymes, it catalyzes the methylation of A2058 of the 23S ribosomal RNA. Specifically, this enzyme transfers only one methyl group. The gene is found in the tylosin biosynthetic cluster and is responsible for self-resistance to tylosin.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35946":{"category_aro_accession":"0000027","category_aro_cvterm_id":"35946","category_aro_name":"roxithromycin","category_aro_description":"Roxithromycin is a semi-synthetic, 14-carbon ring macrolide antibiotic derived from erythromycin. It is used to treat respiratory tract, urinary and soft tissue infections. Roxithromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35974":{"category_aro_accession":"0000057","category_aro_cvterm_id":"35974","category_aro_name":"telithromycin","category_aro_description":"Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36315":{"category_aro_accession":"3000176","category_aro_cvterm_id":"36315","category_aro_name":"dirithromycin","category_aro_description":"Dirithromycin is an oxazine derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome to inhibit bacterial protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin 1A is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"vernamycin B-gamma","category_aro_description":"Vernamycin B-gamma is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"261":{"model_id":"261","model_name":"CMY-65","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1994":{"protein_sequence":{"accession":"AEI52842.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDDVTDKAELLRFYQNWQPQWTPGAKRLYANSSIGLFGALVVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"JF780936","fmin":"63","fmax":"1209","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCACTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGAATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGTGGTAAAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACAGGATCCACAGGCGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTAATGTTGGCAAACAAAAGCTACCCCAACCCGGCTCGCGTCGAGGCGGCCTGGCGCATTCTTGAAAAACTGCAATAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39093","NCBI_taxonomy_name":"Citrobacter sp. 913","NCBI_taxonomy_id":"1037358"}}}},"ARO_accession":"3002078","ARO_id":"38478","ARO_name":"CMY-65","ARO_description":"CMY-65 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"262":{"model_id":"262","model_name":"VIM-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1084":{"protein_sequence":{"accession":"AAS13759.1","sequence":"MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSARRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"AY524987","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGGCACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCGGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCAGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002278","ARO_id":"38678","ARO_name":"VIM-8","ARO_description":"VIM-8 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"263":{"model_id":"263","model_name":"dfrA24","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"66":{"protein_sequence":{"accession":"CAI99385.1","sequence":"MTYQLDVSKILSFDLEAIVAATENGGIGYKGDLPWRLQGDLKRFREITQGGIVIMGAGTYKSLPSPLKDRINIVITKKSEISWTACYDVRVVNSPEDALRMVGRIIDEKEEQGRDRPRVFVIGGASIYQALMPFVSTLHWTEVHVEQLPEEIGLDTYIEDFLSLRGTSTPKRKSNLVLPPTPTTP"},"dna_sequence":{"accession":"AJ972619","fmin":"82","fmax":"640","strand":"+","sequence":"ATGACCTATCAGTTGGACGTGAGCAAAATTCTGTCGTTTGACCTGGAGGCCATCGTTGCTGCTACTGAGAACGGCGGCATCGGTTACAAAGGTGACCTCCCATGGCGTCTACAAGGCGATCTGAAGCGTTTTCGCGAAATCACCCAAGGCGGTATAGTCATCATGGGTGCAGGCACGTATAAGAGCCTCCCAAGTCCTCTGAAAGACCGCATCAATATCGTCATCACCAAGAAGTCAGAGATTTCTTGGACGGCTTGCTATGACGTGCGTGTGGTCAACAGTCCAGAAGACGCTTTGCGCATGGTTGGTCGCATTATCGACGAGAAAGAAGAGCAAGGTCGTGATCGACCTCGTGTATTCGTTATCGGCGGGGCTTCGATCTATCAGGCACTGATGCCTTTCGTTTCTACGCTCCACTGGACTGAGGTGCATGTTGAACAACTGCCAGAGGAAATCGGTCTCGATACGTATATCGAAGACTTCCTTTCTCTGCGTGGGACTTCTACACCGAAGAGAAAGTCGAATCTGGTTTTACCACCCACACCTACCACACCCTGAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002856","ARO_id":"39290","ARO_name":"dfrA24","ARO_description":"dfrA24 is an integron-encoded dihydrofolate reductase found in Escherichia coli","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36408":{"category_aro_accession":"3000269","category_aro_cvterm_id":"36408","category_aro_name":"brodimoprim","category_aro_description":"Brodimoprim is a structural derivative of trimethoprim and an inhibitor of bacterial dihydrofolate reductase. The 4-methoxy group of trimethoprim is replaced with a bromine atom.","category_aro_class_name":"Antibiotic"},"36423":{"category_aro_accession":"3000284","category_aro_cvterm_id":"36423","category_aro_name":"tetroxoprim","category_aro_description":"Tetroxoprim is a trimethoprim derivative that inhibits bacterial dihydrofolate reductase.","category_aro_class_name":"Antibiotic"},"36476":{"category_aro_accession":"3000337","category_aro_cvterm_id":"36476","category_aro_name":"iclaprim","category_aro_description":"Iclaprim is a bactericidal compound that inhibits dihydrofolate reductase. It is used against clinically important Gram-positive pathogens, including methicillin-sensitive Staphylococcus aureus and methicillin-resistant S. aureus.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"264":{"model_id":"264","model_name":"lsaE","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"850"}},"model_sequences":{"sequence":{"3296":{"protein_sequence":{"accession":"AFU35065.1","sequence":"MSLINVSNLTFSYEGSYDNIFENVSFQIDTDWKLGFIGRNGRGKTTFLNLLLGKYAYSGNISSTVKFEYFPYDVEDKSLYTIEVMKSICTECMDWEIFREISLLDVQEDALYRPFNTLSNGEQTKVLLAALFLTASCFLLIDEPTNHLDIDARNVVQNYLKRKKGFILVSHDRSLLDQCVDHILSINKTNIEIQKGNFTSWWENKTLQDNFELAENKKLLKEIGRLSYAAKRSSNWSNKVEKSKYGTTNSGSKLDKGYVGHKAAKAMKRAKNIESRHQEAVLQKSELLHNIEQYDDLKISPLEFHKECLIEANDLSLSYGDKEVCSNLNFRVNIGDRVAIIGKNGSGKSSILKLINGDDIKFTGNFMLASGLKISYISQDTSYLKGNLSEFAYNNKIDETLFKTILRKLDFNREQFDKNMVDFSAGQKKKVLIAKSLCESAHLYIWDEPLNYIDIFSRIQIEKMILEYCPTLLFVEHDDAFCNNICTKNINLGL"},"dna_sequence":{"accession":"JX560992","fmin":"11387","fmax":"12872","strand":"+","sequence":"ATGTCCTTAATAAATGTTTCAAATCTAACTTTTTCATATGAAGGAAGTTATGACAATATTTTTGAAAATGTAAGTTTTCAGATAGATACAGATTGGAAACTCGGTTTTATTGGAAGAAACGGACGCGGTAAAACTACTTTCTTAAATTTACTGCTTGGCAAATATGCGTATTCCGGCAATATAAGTTCTACAGTTAAGTTTGAGTATTTTCCTTATGATGTGGAAGATAAGAGTCTATATACAATTGAAGTAATGAAGAGTATTTGTACGGAATGTATGGATTGGGAGATTTTTCGTGAAATATCATTGCTTGATGTTCAAGAAGATGCTTTATATCGTCCGTTTAATACATTGTCAAATGGTGAGCAAACGAAGGTCCTTCTTGCAGCTTTATTCCTTACAGCGAGTTGTTTCCTGCTTATTGATGAACCTACAAACCATCTTGACATCGATGCACGTAATGTAGTGCAAAACTATTTGAAACGCAAGAAGGGGTTTATTTTGGTATCTCATGATAGAAGCTTACTTGATCAATGTGTTGACCATATACTATCTATCAATAAAACGAATATCGAAATCCAAAAGGGAAATTTTACTTCTTGGTGGGAGAACAAAACGTTACAAGATAATTTTGAACTGGCAGAAAACAAGAAACTCCTTAAAGAAATAGGAAGGTTGTCTTATGCAGCAAAACGTAGTTCAAACTGGTCAAATAAAGTAGAAAAAAGTAAATATGGAACAACAAATTCTGGTTCAAAACTGGATAAGGGTTATGTTGGACATAAGGCTGCAAAAGCGATGAAACGTGCCAAAAATATTGAGTCAAGACATCAGGAAGCCGTTTTACAAAAATCAGAACTGCTCCACAACATTGAACAATATGATGACTTAAAAATTTCACCACTTGAATTTCACAAAGAGTGCTTAATAGAAGCGAATGATTTATCATTGTCTTATGGAGATAAAGAAGTATGCAGTAATCTTAATTTCAGAGTCAATATTGGTGATAGAGTTGCCATTATCGGAAAAAATGGGAGTGGTAAGTCTAGTATCCTAAAATTGATTAATGGAGATGATATTAAATTTACCGGAAATTTTATGCTAGCAAGTGGACTAAAAATTTCTTATATTTCGCAAGATACTTCATATTTAAAAGGTAATCTATCTGAATTTGCCTATAATAATAAGATCGATGAAACTCTATTTAAAACGATTCTTCGTAAACTGGATTTTAATAGAGAGCAGTTTGATAAGAACATGGTGGATTTTAGTGCTGGTCAGAAAAAGAAAGTACTAATTGCTAAAAGCCTTTGTGAAAGTGCACATTTGTATATATGGGATGAGCCATTGAACTATATTGATATTTTTTCACGTATCCAAATTGAAAAAATGATTTTGGAATATTGTCCTACACTATTGTTTGTGGAGCATGATGATGCTTTTTGCAATAACATTTGTACGAAAAATATTAATTTAGGTTTGTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3003206","ARO_id":"39790","ARO_name":"lsaE","ARO_description":"lsaE is a ABC transporter gene found in porcine MRSA isolates. It confers resistance to pleuromutilin, lincosamide, and streptogramin A","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"37716":{"category_aro_accession":"3001317","category_aro_cvterm_id":"37716","category_aro_name":"pleuromutilin","category_aro_description":"Pleuromutilin is a natural product antibiotic produced by Clitopilus passeckerianus. Related antibiotics of clinical significance, such as tiamulin and retapamulin, are semi-synthetic derivatives of this compound.","category_aro_class_name":"Antibiotic"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"265":{"model_id":"265","model_name":"SHV-128","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"900":{"protein_sequence":{"accession":"ADE58494.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELRAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASKRGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGTGAAPIEHWQR"},"dna_sequence":{"accession":"GU932590","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAGCTCCGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCAAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGACTGGCGCGGCGCCGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001175","ARO_id":"37555","ARO_name":"SHV-128","ARO_description":"SHV-128 is an extended-spectrum beta-lactamase that has been found in clinical isolates.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"266":{"model_id":"266","model_name":"QnrB13","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"213":{"protein_sequence":{"accession":"ABX72042.1","sequence":"MTPLLYKKTGTNMALALVGEKIDRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNASALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRRVDLQGVKLDNYQASLLMERLGIAIIG"},"dna_sequence":{"accession":"EU273755","fmin":"0","fmax":"681","strand":"+","sequence":"ATGACGCCATTACTGTATAAAAAAACAGGTACAAATATGGCTCTGGCACTCGTTGGCGAAAAAATTGACAGAAACCGCTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCGATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATGCCAGTGCGCTTGGCATTGAAATTCGCCACTGTCGTGCGCAAGGCGCAGATTTCCGCGGCGCAAGCTTTATGAATATGATCACTACTCGCACCTGGTTTTGCAGCGCATATATCACTAACACAAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAATGTGAGCTGTGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTTTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTGACTTAGATATTCGGCGCGTTGATTTACAAGGCGTTAAGTTGGACAACTACCAGGCATCGTTGCTCATGGAACGTCTTGGCATCGCGATTATTGGCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002727","ARO_id":"39161","ARO_name":"QnrB13","ARO_description":"QnrB13 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"267":{"model_id":"267","model_name":"OXA-43","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1303":{"protein_sequence":{"accession":"CAD32565.1","sequence":"MKFRHALSSAFVLLGCIAASAHAKTICTAIADAGTGKLLVQDGDCGRRASPASTFKIAISLMGYDAGFLRNEHDPVLPYRDSYIAWGGEAWKQPTDPTRWLKYPVVWYSQQVAHHLGAQRFAQYAKAFGYGNADVSGDPGQNNGLDRAWIGSSLQISPLEQLEFLGKMLNRKLPVSPTAVDMTERIVESTTLADGTVVHGKTGVSYPLLADGTRDWARGSGWFVGWIVRGKQTLVFARLTQDERKQPVSAGIRTREAFLRDLPRLLAAR"},"dna_sequence":{"accession":"AJ488303","fmin":"0","fmax":"810","strand":"+","sequence":"ATGAAATTCCGACACGCGCTGTCGAGCGCATTCGTTTTGCTGGGTTGCATCGCCGCGTCGGCGCATGCGAAGACGATCTGCACGGCGATCGCCGATGCGGGCACGGGCAAGCTGCTGGTGCAGGACGGCGATTGCGGCCGCCGCGCATCGCCCGCGTCGACGTTCAAGATCGCGATCAGCCTGATGGGCTACGACGCAGGCTTCCTGCGCAACGAGCATGACCCGGTGCTGCCGTATCGCGACAGTTACATCGCGTGGGGTGGCGAAGCATGGAAGCAGCCGACCGATCCGACGCGCTGGCTCAAGTATCCGGTCGTGTGGTATTCGCAGCAGGTGGCGCACCATCTCGGCGCGCAGCGCTTCGCGCAGTATGCGAAGGCGTTCGGCTACGGCAATGCGGACGTGTCCGGCGATCCCGGCCAGAACAACGGCCTCGATCGCGCGTGGATCGGCTCGTCGCTGCAGATCTCGCCGCTCGAACAATTGGAATTCCTCGGCAAGATGCTCAATCGCAAGCTGCCCGTGTCGCCCACAGCCGTCGACATGACGGAGCGGATCGTCGAATCGACGACGCTTGCCGACGGAACGGTGGTGCACGGCAAGACCGGCGTGTCCTATCCGCTGCTGGCCGACGGCACACGCGACTGGGCGCGTGGATCCGGCTGGTTTGTCGGCTGGATCGTGCGTGGCAAGCAGACGCTGGTGTTCGCGCGCCTCACGCAGGACGAGCGCAAGCAGCCCGTTTCAGCCGGCATACGGACGCGCGAGGCCTTCCTGCGCGACTTGCCCCGGCTTCTCGCCGCGCGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36923","NCBI_taxonomy_name":"Burkholderia pseudomallei","NCBI_taxonomy_id":"28450"}}}},"ARO_accession":"3001770","ARO_id":"38170","ARO_name":"OXA-43","ARO_description":"OXA-43 is a beta-lactamase found in Burkholderia pseudomallei","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"268":{"model_id":"268","model_name":"CfxA6","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"1744":{"protein_sequence":{"accession":"ACT97371.1","sequence":"MSNYSVAELRNMKKNRKKQIVVLCIALVCIFILVFSLSHKSATKGSANPPLTDVLTDSISQIVSACPGEIGVAVIINNTDTVSVNNKSIYPMMSVFKVHQALALCNDFDKKGLSLDTLVKINREKLDPKTWSPMMKDYSAPVISLTVRDLLRYTLSQSDNNASNIMFKNMLNTAQTDSFIAKLIPRSSFQIAYTEEEMSADHDKAYSNYTSPLGAAMLMNRLFTESLISNEKQDFIKNALKECKTGIDRIVAPLLDKEGVVIAHKTGSGNVNENGILAAQNDVAYICLPNKVCYTLAVFVKDFKGNESQASQFVAHISAVVYSLLINTALN"},"dna_sequence":{"accession":"GQ342996","fmin":"797","fmax":"1793","strand":"+","sequence":"ATGTCAAACTATAGTGTTGCGGAATTAAGAAACATGAAAAAAAACAGAAAAAAGCAAATCGTAGTTTTGTGTATAGCTTTAGTTTGCATCTTCATCTTGGTGTTCTCATTGTCCCATAAATCAGCTACAAAAGGTAGCGCGAATCCTCCATTAACAGATGTTTTGACTGATAGCATTTCTCAGATTGTCTCGGCTTGTCCTGGTGAAATTGGTGTGGCGGTTATTATTAATAACACAGATACGGTTAGTGTTAATAATAAAAGCATTTATCCTATGATGAGTGTATTTAAGGTTCATCAGGCATTAGCTCTTTGCAATGATTTTGACAAAAAAGGCCTTTCCCTTGATACCTTGGTAAAGATAAATAGGGAAAAACTTGATCCAAAGACATGGAGCCCTATGATGAAAGATTATTCAGCACCAGTTATATCGTTGACAGTAAGAGATCTGTTGCGCTATACTCTTTCCCAGAGCGACAATAATGCAAGCAATATCATGTTTAAGAATATGCTCAATACTGCACAAACAGACAGTTTTATAGCGAAACTCATACCACGTTCGAGTTTTCAGATAGCTTATACAGAAGAGGAAATGTCCGCTGACCATGACAAAGCTTACTCTAATTACACATCTCCTCTTGGTGCTGCAATGTTGATGAATCGTTTGTTTACAGAAAGTCTTATCAGTAATGAGAAACAAGATTTCATTAAGAATGCATTGAAAGAATGTAAAACAGGTATAGATAGGATAGTAGCTCCACTTCTTGATAAAGAAGGGGTTGTAATAGCACATAAGACAGGTTCTGGTAATGTCAATGAAAATGGTATTCTTGCAGCTCAGAATGATGTAGCCTATATATGTCTGCCTAATAAGGTCTGCTATACCTTAGCTGTATTTGTTAAGGATTTCAAGGGAAATGAATCACAAGCGTCACAATTTGTTGCGCATATATCAGCGGTAGTATATTCTTTATTAATCAATACTGCGTTAAATTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39661","NCBI_taxonomy_name":"uncultured organism","NCBI_taxonomy_id":"155900"}}}},"ARO_accession":"3003097","ARO_id":"39650","ARO_name":"CfxA6","ARO_description":"cfxA6 beta-lactamase is a class A beta-lactamase found in an uncultured bacterium","ARO_category":{"39434":{"category_aro_accession":"3003000","category_aro_cvterm_id":"39434","category_aro_name":"CfxA beta-lactamase","category_aro_description":"cfxA beta-lactamases are class A beta-lactamases","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"269":{"model_id":"269","model_name":"CMY-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1976":{"protein_sequence":{"accession":"AAD50818.2","sequence":"MQQRQSILWGAVATLMWAGLAHAGEASPVDPLRPVVDASIQPLLKEHRIPGMAVAVLKDGKAHYFNYGVANRESGASVSEQTLFEIGSVSKTLTATLGAYAVVKGAMQLDDKASRHAPWLKGSVFDSITMGELATYSAGGLPLQFPEEVDSSEKMRAYYRQWAPVYSPGSHRQYSNPSIGLFGHLAASSLKQPFAQLMEQTLLPGLGMHHTYVNVPKQAMASYAYGYSKEDKPIRVNPGMLADEAYGIKTSSADLLAFVKANIGGVDDKALQQAISLTHKGHYSVGGMTQGLGWESYAYPVTEQTLLAGNSAKVILEANPTAAPRESGSQVLFNKTGSTNGFGAYVAFVPARGIGIVMLANRNYPIPARVKAAHAILAQLAG"},"dna_sequence":{"accession":"AF167990","fmin":"612","fmax":"1761","strand":"+","sequence":"ATGCAACAACGACAATCCATCCTGTGGGGGGCCGTGGCCACCCTGATGTGGGCCGGTCTGGCCCATGCAGGTGAGGCTTCACCGGTCGATCCCCTGCGCCCCGTGGTGGATGCCAGCATCCAGCCGCTGCTCAAGGAGCACAGGATCCCGGGCATGGCGGTGGCCGTGCTCAAGGATGGCAAGGCCCACTATTTCAATTACGGGGTGGCCAACCGGGAGAGCGGGGCCAGCGTCAGCGAGCAGACCCTGTTCGAGATAGGATCCGTGAGCAAGACCCTGACTGCGACCCTGGGGGCCTATGCGGTGGTCAAGGGAGCGATGCAGCTGGATGACAAGGCGAGCCGGCACGCGCCCTGGCTCAAGGGATCCGTCTTTGACAGCATCACCATGGGGGAGCTTGCCACCTACAGCGCCGGAGGCCTGCCACTGCAATTCCCCGAGGAGGTGGATTCATCCGAGAAGATGCGCGCCTACTACCGCCAGTGGGCCCCTGTCTATTCGCCGGGCTCCCATCGCCAGTACTCCAACCCCAGCATAGGGCTGTTCGGCCACCTGGCGGCGAGCAGCCTGAAGCAGCCATTTGCCCAGTTGATGGAGCAGACCCTGCTGCCCGGGCTCGGCATGCACCACACCTATGTCAATGTGCCGAAGCAGGCCATGGCGAGTTATGCCTATGGCTATTCGAAAGAGGACAAGCCCATCCGGGTCAACCCTGGCATGCTGGCGGACGAGGCCTACGGCATCAAGACCAGCTCGGCGGATCTGCTCGCCTTCGTGAAGGCCAACATCGGCGGGGTTGATGACAAGGCGTTGCAGCAGGCCATCTCCCTGACCCACAAAGGGCATTACTCGGTAGGCGGGATGACCCAGGGGCTGGGTTGGGAGAGTTACGCCTATCCCGTCACCGAGCAGACATTGCTGGCGGGCAATTCGGCCAAGGTGATCCTCGAAGCCAATCCGACGGCGGCTCCCCGGGAGTCGGGGAGCCAGGTGCTCTTCAACAAGACCGGCTCGACCAATGGCTTTGGCGCCTATGTGGCCTTCGTGCCGGCCAGGGGGATCGGCATCGTCATGCTGGCCAATCGCAACTATCCCATCCCGGCCAGGGTGAAGGCGGCCCACGCCATCCTGGCGCAGTTGGCCGGTTGAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002019","ARO_id":"38419","ARO_name":"CMY-8","ARO_description":"CMY-8 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"270":{"model_id":"270","model_name":"LEN-20","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1657":{"protein_sequence":{"accession":"CAP12348.2","sequence":"MRYVRLCVISLLATLPLAVDAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGLEQLDRRIHYRQQDLVDYSPVSEKHLTDGMTVGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPPGWFIADKTGAGERGARGIVALLGPDGKPERIVVIYLRDTPVSMAERNQHIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM850910","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCACCCTGCCACTGGCGGTAGACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTACCGACGGGATGACGGTCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGCCGGGCTGGTTTATCGCCGACAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGTGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002467","ARO_id":"38867","ARO_name":"LEN-20","ARO_description":"LEN-20 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"271":{"model_id":"271","model_name":"CMY-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1179":{"protein_sequence":{"accession":"CAA75402.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYARGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"Y15130","fmin":"0","fmax":"1143","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCAGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTACAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3002015","ARO_id":"38415","ARO_name":"CMY-4","ARO_description":"CMY-4 is a beta-lactamase found in Proteus mirabilis","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"272":{"model_id":"272","model_name":"QnrB36","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"591":{"protein_sequence":{"accession":"AEL00458.1","sequence":"MTLALVGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDTIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"JN173058","fmin":"36","fmax":"681","strand":"+","sequence":"ATGACTCTGGCATTAGTTGGCGAAAAAATTGACAGAAATCGCTTCACCGGTGAGAAAGTTGAAAATAGTACATTTTTTAACTGCGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGCCAGTTCTATGATCGCGAAAGTCAGAAAGGATGCAATTTTAGTCGCGCAATGCTGAAAGATACCATTTTCAAAAGCTGTGATTTATCAATGGCAGATTTCCGCAACGTCAGCGCATTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGTGCAAGCTTTATGAATATGATCACCACGCGCACCTGGTTTTGCAGCGCATATATCACTAATACCAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAGCTATGGGAAAACCGCTGGATGGGGACTCAGGTACTGGGTGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTAGGTGACTTAGATATTCGGGGTGTTGATTTACAAGGCGTTAAGTTAGACAACTACCAGGCATCGTTGCTCATGGAGCGGCTTGGCATCGCTGTGATTGGTTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002751","ARO_id":"39185","ARO_name":"QnrB36","ARO_description":"QnrB36 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"273":{"model_id":"273","model_name":"VEB-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1728":{"protein_sequence":{"accession":"ACO56763.1","sequence":"MKIVKRILLVLLSLFFTVEYSNAQTDNLTLKIENVLKAKNARIGVAIFNSNEKDTLKINNDFHFPMQSVMKFPIALAVLSEIDKGNLSFEQKIEITPQDLLPKTWSPIKEEFPNGTTLTIEQILNYTVSESDNIGCDILLKLIGGTDSVQKFLNANHFTDISIKANEEQMHKDWNTQYQNWATPTAMNKLLIDTYNNKNQLLSKKSYDFIWKIMRETTTGSNRLKGQLPKNTIVAHKTGTSGINNGITAATNDVGVITLPNGQLIFISVFVAESKETSEINEKIISDIAKITWNYYLNK"},"dna_sequence":{"accession":"FJ825622","fmin":"0","fmax":"900","strand":"+","sequence":"ATGAAAATCGTAAAAAGGATATTATTAGTATTGTTAAGTTTATTTTTTACAGTTGAGTATTCAAATGCTCAAACTGACAACTTAACTTTGAAAATTGAGAATGTTTTAAAGGCAAAAAATGCCAGAATAGGAGTAGCAATATTCAACAGCAATGAGAAGGATACTTTGAAGATTAATAACGACTTCCATTTCCCGATGCAAAGCGTTATGAAATTTCCGATTGCTTTAGCCGTTTTGTCTGAGATAGATAAAGGGAATCTTTCTTTTGAACAAAAAATAGAGATTACCCCTCAAGACCTTTTGCCTAAAACGTGGAGTCCGATTAAAGAGGAATTCCCTAATGGAACAACTTTGACGATTGAACAAATACTAAATTATACAGTATCAGAGAGCGACAATATTGGTTGTGATATTTTGCTAAAATTAATCGGAGGAACTGATTCTGTTCAAAAATTCTTGAATGCTAATCATTTCACTGATATTTCAATCAAAGCAAACGAAGAACAAATGCACAAGGATTGGAATACCCAATATCAAAATTGGGCAACCCCAACAGCGATGAACAAACTGTTAATAGATACTTATAATAATAAGAACCAATTACTTTCTAAAAAAAGTTATGATTTTATTTGGAAAATTATGAGAGAAACAACAACAGGAAGTAACCGATTAAAAGGACAATTACCAAAGAATACAATTGTTGCTCATAAAACAGGGACTTCCGGAATAAATAATGGAATTACAGCAGCCACTAATGATGTTGGGGTAATTACTTTACCGAATGGACAATTAATTTTTATAAGCGTATTTGTTGCAGAGTCCAAAGAAACTTCGGAAATTAATGAAAAGATTATTTCAGACATTGCAAAAATAACGTGGAATTACTATTTGAATAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3002376","ARO_id":"38776","ARO_name":"VEB-7","ARO_description":"VEB-7 is a beta-lactamase. From the Lahey list of VEB beta-lactamases.","ARO_category":{"36182":{"category_aro_accession":"3000043","category_aro_cvterm_id":"36182","category_aro_name":"VEB beta-lactamase","category_aro_description":"VEB beta-lactamases or Vietnamese extended-spectrum beta-lactamases are class A beta-lactamases that confer high-level resistance to oxyimino cephalosporins and to aztreonam","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"274":{"model_id":"274","model_name":"OXA-174","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2002":{"protein_sequence":{"accession":"ADI58618.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWVVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEKLGIL"},"dna_sequence":{"accession":"HM113560","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGGTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAAAAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001658","ARO_id":"38058","ARO_name":"OXA-174","ARO_description":"OXA-174 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"275":{"model_id":"275","model_name":"OKP-B-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1366":{"protein_sequence":{"accession":"CAJ19610.1","sequence":"MRYVRLCLISLIAALPLAVFASPQPLEQIKISEGQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKSVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMATTLRKLLTTPSLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPDGKAERIVVIYLRDTAATMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM051151","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCAGCCGCTTGAGCAGATTAAAATCAGCGAAGGTCAGCTGGCGGGCCGGGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGCGACGAACAGCTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGAGCGTCGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTCAATGAGGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCGGCCAGCATGGCCACCACCCTGCGCAAGTTGCTAACCACCCCCTCTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGACCGGGTGGCCGGCCCGTTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGTGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAAGCGGAGCGTATCGTGGTGATCTATCTGCGGGATACCGCAGCGACCATGGCCGAACGTAACCAGCAGATCGCCGGGATAGGCGCGGCGCTGATCGAGCACTGGCAGCGCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002435","ARO_id":"38835","ARO_name":"OKP-B-2","ARO_description":"OKP-B-2 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"277":{"model_id":"277","model_name":"TEM-91","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1888":{"protein_sequence":{"accession":"BAB16308.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDCWEPELNEAIPNDERDTTTPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGKRGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AB049569","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATTGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTAAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000958","ARO_id":"37338","ARO_name":"TEM-91","ARO_description":"TEM-91 is an extended-spectrum beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"278":{"model_id":"278","model_name":"imiS","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"1892":{"protein_sequence":{"accession":"CAA71441.1","sequence":"MMKGWIKCGLAGAVVLMASFWGGSVRAAGMSLTQQVSGPVYVVEDNYYVQENSMVYFGAKGVTVVGATWTPDTARELHKLIKRVSRKPVLEVINTNYHTDRAGGNAYWKSIGAKVISTRQTRDLMKSDWAEIVAFTRKGLPEYPDLPLVLPNVVHEGDFTLQEGKLRAFYLGPAHSPDGIFVYFPDQQVLYGNCILKEKLGNLSFADVKAYPQTLERLKAMKLPIKTVVGGHDSPLHGPELIDHYEALIKAASQS"},"dna_sequence":{"accession":"Y10415","fmin":"125","fmax":"893","strand":"+","sequence":"ATGATGAAGGGTTGGATAAAGTGCGGGCTGGCCGGGGCCGTGGTGCTGATGGCGAGTTTTTGGGGGGGCAGCGTGCGGGCGGCGGGGATGTCGCTGACGCAGCAGGTGAGCGGCCCTGTTTACGTCGTAGAGGACAACTACTACGTGCAGGAAAATTCCATGGTCTATTTCGGGGCCAAGGGAGTGACTGTGGTGGGGGCGACCTGGACGCCGGATACCGCCCGCGAGCTGCACAAGCTGATCAAACGGGTCAGCCGCAAGCCGGTGCTGGAGGTGATCAACACCAACTACCACACCGACCGGGCAGGCGGTAACGCCTACTGGAAGTCCATCGGTGCCAAGGTGATATCGACCCGCCAGACCCGGGATCTGATGAAGAGCGACTGGGCCGAGATTGTCGCCTTTACCCGCAAGGGGCTGCCGGAGTACCCGGACTTGCCGCTGGTGCTGCCCAACGTGGTGCACGAAGGCGACTTCACGCTGCAAGAAGGCAAGCTGCGCGCCTTCTACCTGGGCCCGGCTCACAGCCCGGACGGCATCTTTGTTTACTTCCCCGACCAGCAGGTGCTTTATGGCAACTGCATCCTCAAGGAGAAGCTGGGCAACCTGAGCTTTGCCGATGTGAAGGCTTATCCGCAGACACTTGAGCGGCTGAAAGCGATGAAGCTGCCGATCAAGACGGTGGTGGGCGGTCACGACTCACCGCTGCACGGCCCGGAGCTTATCGATCACTACGAAGCGCTGATCAAGGCGGCTTCACAATCATAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39677","NCBI_taxonomy_name":"Aeromonas veronii","NCBI_taxonomy_id":"654"}}}},"ARO_accession":"3003095","ARO_id":"39648","ARO_name":"imiS","ARO_description":"imiS is an Ambler Class B MBL; subclass B2 originally isolated from Aeromonas veronii. This enzyme has specific activity against carbapenems.","ARO_category":{"36720":{"category_aro_accession":"3000581","category_aro_cvterm_id":"36720","category_aro_name":"CphA beta-lactamase","category_aro_description":"CphA is an Ambler Class B MBL; subclass B2 originally isolated from Aeromonas hydrophilia.  This enzyme has specific activity against carbapenems and is active as a mono-zinc protein.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"279":{"model_id":"279","model_name":"CTX-M-107","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4326":{"protein_sequence":{"accession":"AEM44650.1","sequence":"VKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDRTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVT"},"dna_sequence":{"accession":"JF274244.1","fmin":"0","fmax":"864","strand":"-","sequence":"TTGGTGACGATTTTAGCCGCCGACGCTAATACATCGCGACGGCTTTCTGCCTTAGGTTGAGGCTGGGTGAAGTAAGTGACCAGAATCAGCGGCGCACGATCTTTTGGCCAGATCACCGCGATATCGTTGGTGGTGCCATAGCCACCGCTGCCGGTTCTATCCCCCACAACCCAGGAAGCAGGCAGTCCAGCCTGAATGCTCGCTGCACCGGTGGTATTGCCTTTCATCCATGTCACCAGCTGCGCCCGTTGGCTGTCGCCCAATGCTTTACCCAGCGTCAGATTCCGCAGAGTTTGCGCCATTGCCCGAGGTGAAGTGGTATCACGCGGATCGCCCGGAATGGCGGTGTTTAACGTCGGCTCGGTACGGTCGAGACGGAACGTTTCGTCTCCCAGCTGTCGGGCGAACGCGGTGACGCTAGCCGGGCCGCCAACGTGAGCAATCAGCTTATTCATCGCCACGTTATCGCTGTACTGTAGCGCGGCCGCGCTAAGCTCAGCCAGTGACATCGTCCCATTGACGTGCTTTTCCGCAATCGGATTATAGTTAACAAGGTCAGATTTTTTGATCTCAACTCGCTGATTTAACAGATTCGGTTCGCTTTCACTTTTCTTCAGCACCGCGGCCGCGGCCATCACTTTACTGGTGCTGCACATCGCAAAGCGCTCATCAGCACGATAAAGTATTTGCGAATTATCTGCTGTGTTAATCAATGCCACACCCAGTCTGCCTCCCGACTGCCGCTCTAATTCGGCAAGTTTTTGCTGTACGTCCGCCGTTTGCGCATACAGCGGCACACTTCCTAACAACAGCGTGACGGTTGCCGTCGCCATCAGCGTGAACTGACGCAGTGATTTTTTAACC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39656","NCBI_taxonomy_name":"Shigella sp. SH219","NCBI_taxonomy_id":"1074433"}}}},"ARO_accession":"3001967","ARO_id":"38367","ARO_name":"CTX-M-107","ARO_description":"CTX-M-107 is a beta-lactamase found in Shigella spp.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"280":{"model_id":"280","model_name":"CTX-M-11","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1588":{"protein_sequence":{"accession":"AAF93177.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAGLERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSPAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRHVLAS"},"dna_sequence":{"accession":"AY005110","fmin":"0","fmax":"846","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGGATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACCGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCCGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCCATGTATTAGCGTCG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001874","ARO_id":"38274","ARO_name":"CTX-M-11","ARO_description":"CTX-M-11 is a beta-lactamase. From the Lahey list of CTX-M beta-lactamases.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"281":{"model_id":"281","model_name":"CMY-110","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1913":{"protein_sequence":{"accession":"BAO05497.1","sequence":"MMKKSICCALLLTASFSKFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWGIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"AB872957","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCGCTGCTGCTGACAGCCTCTTTCTCCAAGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGCATGGCCGTGGCAATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAATTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGCGGTGAAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGTTACTGGGGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACAGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATAGTGATGCTGGCAAACAAAAGCTATCCTAACCCGGCTCGCGTAGAGGCGGCCTGGCGCATTCTTGAAAAACTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002071","ARO_id":"38471","ARO_name":"CMY-110","ARO_description":"CMY-110 is a beta-lactamase found in Escherichia coli","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"282":{"model_id":"282","model_name":"CTX-M-125","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1410":{"protein_sequence":{"accession":"AFO69261.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAEHRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"JQ724542","fmin":"174","fmax":"1050","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGCACCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001984","ARO_id":"38384","ARO_name":"CTX-M-125","ARO_description":"CTX-M-125 is a beta-lactamase found in Escherichia coli","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"283":{"model_id":"283","model_name":"CMY-85","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1117":{"protein_sequence":{"accession":"AHL39322.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVKSSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYLEGKPLHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQLGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"KJ207202","fmin":"548","fmax":"1694","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCGCTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGCGGTGAAATCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAACTATGCCTGGGGCTATCTCGAAGGGAAGCCTTTGCACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCTGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACAGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATAGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGCGTCGAGGCGGCCTGGCGCATTCTTGAAAAACTGCAATAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002098","ARO_id":"38498","ARO_name":"CMY-85","ARO_description":"CMY-85 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"284":{"model_id":"284","model_name":"smeD","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"570":{"protein_sequence":{"accession":"CAC14594.1","sequence":"MLLSRIRPFALSLAIAATVAACGGQPQAPEQGPGDVTVVTLKSETVGLTRELPGRTNAFLVAEVRPQVNGIVAKRLFTEGGMVKAGEPLYQLDDASYRAQANNARAQLARAEATANAARLSAKRITELAKVDAVSQQDLENAVAAQKQAEADVGAAKASLDAANVTLGYARITAPISGRIGKSSVTQGALVSAGQANALATVQQLDPIYVDLTQSSAELLQLRRELAAGRLQDNQTLPVSILMEDGSTFEHKGTLEFSEVSVDPTTGSFGLRVKVDNPDGLLMPGMYVRAVIGGGVRSDAVLVPMQGIARDPKGDTTAMVVGKDNKVEVRPVKVSRTVGDKWLVEDGLKAGDKVIVEGLQKIGPGMPVKATEKGDAPAKPAAAAQPAAPAGDAK"},"dna_sequence":{"accession":"AJ252200","fmin":"81","fmax":"1266","strand":"+","sequence":"ATGTTGCTGAGCCGAATCCGACCCTTTGCACTGTCGCTGGCAATCGCCGCGACCGTGGCTGCCTGCGGCGGCCAACCCCAGGCCCCCGAGCAGGGCCCGGGTGACGTCACCGTGGTCACGCTGAAGTCCGAGACCGTGGGCCTGACCCGCGAACTGCCGGGCCGTACCAATGCCTTCCTGGTCGCCGAAGTGCGCCCGCAGGTCAATGGCATCGTGGCCAAGCGCCTGTTTACCGAGGGCGGCATGGTCAAGGCCGGCGAGCCGCTGTACCAGCTCGACGATGCCAGCTACCGGGCCCAGGCCAACAACGCCCGCGCCCAGCTGGCCCGCGCCGAAGCCACCGCCAATGCCGCGCGCCTGAGTGCCAAGCGCATCACCGAGCTGGCCAAGGTCGATGCGGTCAGCCAGCAGGACCTGGAGAACGCCGTCGCCGCGCAGAAGCAGGCCGAGGCCGACGTCGGTGCCGCCAAGGCCTCGCTGGATGCGGCCAACGTCACCCTGGGCTACGCCCGCATCACCGCGCCGATCAGCGGCCGCATCGGCAAGTCCAGCGTCACCCAGGGTGCGCTGGTCAGCGCCGGCCAGGCCAACGCACTGGCCACCGTGCAGCAGCTGGACCCGATCTATGTCGACCTGACCCAGTCCTCGGCCGAGCTGCTGCAGCTGCGCCGCGAACTGGCCGCCGGCCGCCTGCAGGACAACCAGACCCTGCCGGTCAGCATCCTGATGGAAGACGGCAGCACCTTCGAGCACAAGGGCACTCTGGAGTTCTCCGAAGTCAGCGTTGATCCGACCACCGGCAGCTTCGGCCTGCGCGTGAAGGTGGACAACCCGGACGGCCTGCTGATGCCGGGCATGTACGTGCGTGCGGTGATCGGCGGCGGCGTGCGCAGCGACGCGGTGCTGGTGCCGATGCAGGGCATCGCGCGCGATCCGAAGGGCGACACCACCGCGATGGTGGTCGGCAAGGACAACAAGGTCGAAGTGCGCCCGGTCAAGGTCAGCCGCACGGTCGGCGACAAGTGGCTGGTCGAGGACGGCCTGAAGGCCGGTGACAAGGTCATCGTCGAAGGCCTGCAGAAGATCGGCCCCGGCATGCCGGTCAAGGCCACCGAGAAGGGCGACGCACCGGCCAAGCCGGCGGCAGCCGCCCAGCCTGCCGCCCCGGCCGGCGACGCGAAGTAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37076","NCBI_taxonomy_name":"Stenotrophomonas maltophilia","NCBI_taxonomy_id":"40324"}}}},"ARO_accession":"3003055","ARO_id":"39489","ARO_name":"smeD","ARO_description":"smeD is the membrane fusion protein of the smeDEF multidrug efflux complex in Stenotrophomonas maltophilia","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"285":{"model_id":"285","model_name":"TEM-11","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1488":{"protein_sequence":{"accession":"AAW66604.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDHWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AY874537","fmin":"177","fmax":"1038","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCATTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3000883","ARO_id":"37263","ARO_name":"TEM-11","ARO_description":"TEM-11 is an extended-spectrum beta-lactamase found in Proteus mirabilis.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"286":{"model_id":"286","model_name":"SHV-162","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"830":{"protein_sequence":{"accession":"AFQ23968.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGSVGMVEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"JX121129","fmin":"0","fmax":"858","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCAGCGTAGGCATGGTAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCAGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGGATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001201","ARO_id":"37581","ARO_name":"SHV-162","ARO_description":"SHV-162 is a beta-lactamase.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"287":{"model_id":"287","model_name":"TEM-67","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1248":{"protein_sequence":{"accession":"AAD33116.2","sequence":"MSIQHFRVALIPFFAAFCIPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSCGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AF091113","fmin":"450","fmax":"1311","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCATTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTTGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3000934","ARO_id":"37314","ARO_name":"TEM-67","ARO_description":"TEM-67 is an inhibitor-resistant beta-lactamase found in Proteus mirabilis.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"288":{"model_id":"288","model_name":"CMY-60","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1625":{"protein_sequence":{"accession":"AEM97672.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFIGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"JF460794","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTATCGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002073","ARO_id":"38473","ARO_name":"CMY-60","ARO_description":"CMY-60 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"289":{"model_id":"289","model_name":"OXA-85","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"814":{"protein_sequence":{"accession":"AAP69916.1","sequence":"MLLFMFSIISFGNENQFMKEIFERKGLNGTFVVYDLKNDKIDYYNLDRANERFYPASSFKIFNTLIGLENGIVKNVDEMFYYYDGSKVFLDSWAKDSNLRYAIKVSQVPAYKKLARELGKERMQEGLNKLNYGNKEIGSEIDKFWLEGPLKISAMEQVKLLNLLSQSKLPFKLENQEQVKDITILEKKDDFILHGKTGWATDNIVVPIGWFVGWIETSDNIYSFAINLDISDSKFLPKREEIVREYFKNINVIK"},"dna_sequence":{"accession":"AY227054","fmin":"0","fmax":"765","strand":"+","sequence":"ATGTTATTATTTATGTTCTCGATTATTTCTTTTGGTAATGAAAATCAATTTATGAAAGAGATTTTTGAAAGAAAAGGTTTAAACGGAACTTTTGTTGTTTATGATTTAAAAAATGATAAAATTGATTATTATAATTTGGATAGAGCTAATGAGAGATTTTATCCTGCTTCATCATTTAAAATTTTTAATACTTTGATAGGATTAGAAAATGGGATAGTAAAAAATGTTGATGAAATGTTTTATTATTATGATGGTTCTAAAGTTTTTCTTGATTCATGGGCAAAAGATTCGAATTTAAGATATGCAATAAAGGTATCTCAAGTTCCAGCTTATAAAAAGCTTGCAAGAGAATTGGGAAAAGAAAGAATGCAAGAAGGATTAAATAAATTAAATTATGGAAATAAGGAAATAGGTAGTGAGATTGATAAGTTTTGGTTAGAAGGTCCATTAAAAATAAGTGCAATGGAACAAGTTAAATTATTAAATCTATTATCACAATCAAAACTTCCTTTTAAATTAGAAAATCAAGAACAAGTAAAAGATATTACGATTTTAGAGAAAAAAGATGATTTTATTTTACATGGAAAAACTGGGTGGGCTACTGATAATATAGTTGTTCCTATTGGTTGGTTTGTAGGTTGGATAGAAACTTCTGATAATATATATTCATTTGCTATTAATTTAGATATTTCTGATAGTAAATTTTTACCTAAACGTGAAGAAATTGTAAGAGAATATTTCAAAAATATAAATGTTATAAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36931","NCBI_taxonomy_name":"Fusobacterium nucleatum","NCBI_taxonomy_id":"851"}}}},"ARO_accession":"3001780","ARO_id":"38180","ARO_name":"OXA-85","ARO_description":"OXA-85 is a beta-lactamase found in Fusobacterium nucleatum","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"290":{"model_id":"290","model_name":"vatD","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"462":{"protein_sequence":{"accession":"AAK84316.1","sequence":"MKMYPIEGNKSVQFIKPILEKLENVEVGEYSYYDSKNGETFDKQILYHYPILNDKLKIGKFCSIGPGVTIIMNGANHRMDGSTYPFNLFGNGWEKHMPKLDQLPIKGDTIIGNDVWIGKDVVIMPGVKIGDGAIVAANSVVVKDIAPYMLAGGNPANEIKQRFDQDTINQLLDIKWWNWPIDIINENIDKILDNSIIREVIWKK"},"dna_sequence":{"accession":"AF368302","fmin":"2716","fmax":"3331","strand":"+","sequence":"ATGAAAATGTATCCTATAGAAGGAAACAAATCAGTACAATTTATCAAACCTATTTTAGAAAAATTAGAAAATGTTGAGGTTGGAGAATACTCATATTATGATTCTAAGAATGGAGAAACTTTTGATAAGCAAATTTTATATCATTATCCAATCTTAAACGATAAGTTAAAAATAGGTAAATTTTGCTCAATAGGACCAGGTGTAACTATTATTATGAATGGAGCAAATCATAGAATGGATGGCTCAACATATCCATTTAATTTATTTGGTAATGGATGGGAGAAACATATGCCAAAATTAGATCAACTACCTATTAAGGGGGATACAATAATAGGTAATGATGTATGGATAGGAAAAGATGTTGTAATTATGCCAGGAGTAAAAATCGGGGATGGTGCAATAGTAGCTGCTAATTCTGTTGTTGTAAAAGATATAGCGCCATACATGTTAGCTGGAGGAAATCCTGCTAACGAAATAAAACAAAGATTTGATCAAGATACAATAAATCAGCTGCTTGATATAAAATGGTGGAATTGGCCAATAGACATTATTAATGAGAATATAGATAAAATTCTTGATAATAGCATCATTAGAGAAGTCATATGGAAAAAATGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002843","ARO_id":"39277","ARO_name":"vatD","ARO_description":"vatD is a transposon-mediated acetyltransferase found in Enterococcus faecium","ARO_category":{"36592":{"category_aro_accession":"3000453","category_aro_cvterm_id":"36592","category_aro_name":"streptogramin vat acetyltransferase","category_aro_description":"vat (Virginiamycin acetyltransferases) enzymes catalyze the transfer of an acetyl group from acetyl-CoA to the secondary alcohol of streptogramin A compounds, thus inactivating virginiamycin-like antibiotics and conferring resistance to these compounds.","category_aro_class_name":"AMR Gene Family"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"291":{"model_id":"291","model_name":"APH(3')-Ia","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4294":{"protein_sequence":{"accession":"CAE51638.1","sequence":"MSHIQRETSCSRPRLNSNLDADLYGYRWARDNVGQSGATIYRLYGKPNAPELFLKHGKGSVANDVTDEMVRLNWLTAFMPLPTIKHFIRTPDDAWLLTTAIPGKTAFQVLEEYPDSGENIVDALAVFLRRLHSIPVCNCPFNSDRVFRLAQAQSRMNNGLVDASDFDDERNGWPVEQVWKEMHKLLPFSPDSVVTHGDFSLDNLIFDEGKLIGCIDVGRVGIADRYQDLAILWNCLGEFSPSLQKRLFQKYGIDNPDMNKLQFHLMLDEFF"},"dna_sequence":{"accession":"BX664015","fmin":"103017","fmax":"103833","strand":"-","sequence":"TCAGAAAAACTCATCGAGCATCAAATGAAACTGCAATTTATTCATATCAGGATTATCAATACCATATTTTTGAAAAAGCCGTTTCTGTAATGAAGGAGAAAACTCACCGAGGCAGTTCCATAGGATGGCAAGATCCTGGTATCGGTCTGCGATTCCGACTCGTCCAACATCAATACAACCTATTAATTTCCCCTCGTCAAAAATAAGGTTATCAAGTGAGAAATCACCATGAGTGACGACTGAATCCGGTGAGAATGGCAAAAGCTTATGCATTTCTTTCCAGACTTGTTCAACAGGCCAGCCATTACGCTCGTCATCAAAATCACTAGCATCAACCAAACCGTTATTCATTCGTGATTGCGCCTGAGCGAGACGAAATACGCGATCGCTGTTAAAAGGACAATTACAAACAGGAATCGAATGCAACCGGCGCAGGAACACTGCCAGCGCATCAACAATATTTTCACCTGAATCAGGATATTCTTCTAATACCTGGAATGCTGTTTTCCCGGGGATCGCAGTGGTGAGTAACCATGCATCATCAGGAGTACGGATAAAATGCTTGATGGTCGGAAGAGGCATAAATGCCGTCAGCCAGTTTAGTCTGACCATCTCATCTGTAACATCATTGGCAACGCTACCTTTGCCATGTTTCAGAAACAACTCTGGCGCATTGGGCTTCCCATACAATCGATAGATTGTCGCACCTGATTGCCCGACATTATCGCGAGCCCATCTATACCCATATAAATCAGCATCCAGGTTGGAATTTAATCGCGGCCTCGAGCAAGACGTTTCCCGTTGAATATGGCTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36783","NCBI_taxonomy_name":"Serratia marcescens","NCBI_taxonomy_id":"615"}}}},"ARO_accession":"3002641","ARO_id":"39041","ARO_name":"APH(3')-Ia","ARO_description":"APH(3')-Ia is a transposon-encoded aminoglycoside phosphotransferase in E. coli and S. enterica. It is identical at the protein sequence to APH(3')-Ic, an aminoglycoside phosphotransferase encoded by plasmids, transposons and genomic islands in K. pneumoniae, A. baumannii, S. marcescens, Corynebacterium spp., Photobacterium spp. and Citrobacter spp.","ARO_category":{"36265":{"category_aro_accession":"3000126","category_aro_cvterm_id":"36265","category_aro_name":"APH(3')","category_aro_description":"Phosphorylation of 2-deoxystreptamine aminoglycosides on the hydroxyl group at position 3'","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37044":{"category_aro_accession":"3000700","category_aro_cvterm_id":"37044","category_aro_name":"lividomycin A","category_aro_description":"Lividomycin A is a pentasaccharide antibiotic which interferes with bacterial protein synthesis.","category_aro_class_name":"Antibiotic"},"37045":{"category_aro_accession":"3000701","category_aro_cvterm_id":"37045","category_aro_name":"lividomycin B","category_aro_description":"Lividomycin B is a derivative of lividomycin A with a removed mannose group (demannosyllividomycin A). Livodomycins interfere with bacterial protein synthesis.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"292":{"model_id":"292","model_name":"TEM-17","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1157":{"protein_sequence":{"accession":"CAA74912.2","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"Y14574","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAACAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTTTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATTTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36958","NCBI_taxonomy_name":"Capnocytophaga ochracea","NCBI_taxonomy_id":"1018"}}}},"ARO_accession":"3000888","ARO_id":"37268","ARO_name":"TEM-17","ARO_description":"TEM-17 is an extended-spectrum beta-lactamase found in Capnocytophaga ochracea.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"293":{"model_id":"293","model_name":"SHV-180","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"3768":{"protein_sequence":{"accession":"AJO16040.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGHVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMTATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"KP050487.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCACGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGACCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001350","ARO_id":"37750","ARO_name":"SHV-180","ARO_description":"From the Lahey list of beta-lactamases. Not yet released.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"294":{"model_id":"294","model_name":"CfxA4","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"1592":{"protein_sequence":{"accession":"AAV37205.1","sequence":"MEKNRKKQIVVLSIALVCIFILVFSLFHKSATKDSANPPLTNVLTDSISQIVSACPGEIGVAVIVNNRDTVKVNNKSVYPMMSVFKVHQALALCNDFDNKGISLDTLVNINRDKLDPKTWSPMLKDYSGPVISLTVRDLLRYTLTQSDNNASNLMFKDMVNVAQTDSFIATLIPRSSFQIAYTEEEMSADHNKAYSNYTSPLGAAMLMNRLFTEGLIDDEKQSFIKNTLKECKTGVDRIAAPLLDKEGVVIAHKTGSGNVNENGVLAAHNDVAYICLPNNISYTLAVFVKDFKGNESQASQYVAHISAVVYSLLMQTSVKS"},"dna_sequence":{"accession":"AY769933","fmin":"0","fmax":"966","strand":"+","sequence":"ATGGAAAAAAACAGAAAAAAACAAATCGTAGTTTTGAGTATAGCTTTAGTTTGCATTTTCATCTTGGTATTTTCATTGTTCCATAAATCAGCGACAAAAGATAGCGCAAATCCTCCTTTAACAAATGTTTTGACTGATAGCATTTCTCAAATTGTCTCAGCTTGTCCTGGCGAAATTGGTGTGGCGGTTATTGTTAATAACAGAGATACGGTTAAGGTCAATAATAAGAGTGTTTATCCTATGATGAGTGTGTTTAAGGTTCATCAGGCATTAGCTCTTTGTAATGACTTTGACAATAAAGGAATTTCACTTGATACCTTAGTAAATATAAATAGGGATAAACTTGACCCAAAGACTTGGAGTCCTATGCTGAAAGATTATTCAGGGCCAGTCATATCATTGACAGTGAGAGATTTGCTGCGTTATACTCTTACTCAGAGTGACAACAATGCAAGCAACCTTATGTTTAAGGATATGGTTAATGTCGCTCAAACAGATAGTTTTATAGCCACACTCATTCCTCGTTCAAGTTTTCAGATAGCTTATACGGAAGAGGAAATGTCGGCTGACCATAACAAGGCTTACTCTAACTATACATCTCCTCTTGGTGCTGCAATGTTGATGAATCGTTTGTTTACTGAAGGTCTTATCGATGATGAGAAACAAAGTTTCATTAAGAATACGTTAAAAGAATGCAAAACAGGTGTAGATAGGATAGCAGCTCCACTTCTTGATAAAGAAGGGGTTGTTATAGCGCATAAGACAGGTTCAGGTAATGTTAATGAAAATGGTGTTCTTGCAGCTCACAATGATGTTGCCTATATATGTCTGCCTAATAATATCAGTTATACCTTAGCGGTATTTGTTAAGGATTTCAAGGGAAATGAATCACAAGCGTCACAATATGTTGCGCATATATCAGCTGTAGTATATTCTTTATTAATGCAAACTTCAGTAAAATCTTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35916","NCBI_taxonomy_name":"Bacteroides fragilis","NCBI_taxonomy_id":"817"}}}},"ARO_accession":"3003005","ARO_id":"39439","ARO_name":"CfxA4","ARO_description":"cfxA4 beta-lactamase is a class A beta-lactamase found in Bacteroides fragilis","ARO_category":{"39434":{"category_aro_accession":"3003000","category_aro_cvterm_id":"39434","category_aro_name":"CfxA beta-lactamase","category_aro_description":"cfxA beta-lactamases are class A beta-lactamases","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"295":{"model_id":"295","model_name":"OXA-145","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1451":{"protein_sequence":{"accession":"ACN85419.1","sequence":"MKTFAAYVITACLSSTALASSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNNLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLSLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWEGQLRISAVNQVEFLESLFLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKGTEVYFFAFNMDIDNENKLPLRKSIPTKIMASEGIIGG"},"dna_sequence":{"accession":"FJ790516","fmin":"1287","fmax":"2085","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTACTGCGTGTCTTTCAAGTACGGCATTAGCTAGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTTTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATAACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAACAATGGGAAAGAGACTTGAGCTTAAGAGGGGCAATACAAGTTTCAGCGGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCATATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGGAGGGTCAGCTAAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATTTTTAAATAAATTGTCAGCATCAAAAGAAAATCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCTGCGCCTGAATATCTTGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGTTGGGTTGAGAAGGGAACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAATAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGCAAGTGAGGGCATCATTGGTGGCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001804","ARO_id":"38204","ARO_name":"OXA-145","ARO_description":"OXA-145 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"296":{"model_id":"296","model_name":"VIM-23","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1729":{"protein_sequence":{"accession":"ACT33323.1","sequence":"MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSSTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"GQ242167","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCAAGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAGC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3002293","ARO_id":"38693","ARO_name":"VIM-23","ARO_description":"VIM-23 is a beta-lactamase found in Enterobacter cloacae","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"297":{"model_id":"297","model_name":"CMY-98","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1778":{"protein_sequence":{"accession":"AGH70380.1","sequence":"MAAQSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYQGKPYYFTWGKADIANDRPVTRQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTQYWPELTGKQWQGISLLHLATYTAGGLPLQVPDDVTDKAALLRFYQNWQPQWAPGAKRLYANSSIGLFGALAVKPSGMGYEEAMTKRVLQPLKLAHTWITVPQSEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSLVDMTRWIQANMDASQVQEKTLRQGIEIAQARYWHIGDMYQGLGWEMLNWPVNADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRI"},"dna_sequence":{"accession":"KC603538","fmin":"0","fmax":"1131","strand":"+","sequence":"ATGGCTGCACAATCGTTATGCTGCGCGTTGCTGCTGACAGCCTCTTTCTCTACGTTTGCCGCCGCAAAAACAGAACAACAGATTGCCGATATCGTAAACCGTACCATCACACCGCTGATGCAAGAACAGGCTATTCCGGGTATGGCCGTAGCAATTATCTACCAGGGAAAACCCTATTACTTTACCTGGGGGAAAGCCGATATCGCCAATGACCGCCCCGTCACCCGGCAAACGCTGTTTGAGCTTGGATCGGTAAGTAAGACGTTTAACGGTGTGCTGGGCGGCGATGCTATCGCCCGTGGTGAAATTAAGCTCAGCGATCCGGTCACCCAATACTGGCCCGAATTAACTGGCAAACAATGGCAGGGTATCAGCCTGCTGCACCTGGCCACCTATACGGCGGGTGGTCTGCCGCTTCAGGTACCTGACGACGTTACAGATAAAGCGGCATTACTGCGCTTTTATCAAAACTGGCAGCCGCAATGGGCCCCGGGTGCTAAACGCCTGTATGCTAACTCCAGTATTGGTCTGTTTGGCGCACTGGCGGTGAAACCTTCAGGAATGGGCTATGAAGAGGCGATGACCAAACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCACAGAGCGAACAAAAGGATTATGCCTGGGGTTATCGCGAAGGGAAGCCCGTACACGTATCTCCGGGCCAGCTTGATGCCGAAGCCTACGGGGTGAAATCCAGCCTTGTCGATATGACTCGTTGGATTCAGGCCAACATGGACGCCAGCCAGGTGCAGGAGAAAACGCTCCGACAGGGAATTGAAATTGCGCAGGCTCGTTACTGGCATATTGGCGATATGTACCAGGGATTAGGTTGGGAGATGCTGAACTGGCCGGTGAATGCCGACTCGATAATCAACGGTAGCGACAGTAAAGTCGCACTAGCGGCGCTTCCCGCCGTTGAGGTCAATCCGCCCGCCCCTGCAGTGAAAGCCTCATGGGTGCACAAAACCGGCTCCACTGGCGGATTTGGCAGCTACGTTGCGTTCGTTCCGGAAAAAAATCTCGGCATCGTGATGCTGGCAAACAAAAGCTACCCAAACCCTGCTCGCGTCGAGGCCGCCTGGCGCATCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002111","ARO_id":"38511","ARO_name":"CMY-98","ARO_description":"CMY-98 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"298":{"model_id":"298","model_name":"vanYG1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"416":{"protein_sequence":{"accession":"ABA71729.1","sequence":"MNHMNMKHRRRKRRRNQSFLFTGILLLVVVSASSFLWYGFGNAAKKDSVIEEMPFTITQDGMQAKEEIKKTVLETSYGGKQQVAEENHGNTQNAGTDEAWNLMLVNRDNAIPDNYEVNLVEVEGGERVDERIYEPLMEMLNAAREENWGELPMVVSGYRTQEKQQSLYDEKIAKFKKEGYSDSEAVRQAEQWVAVPGHSEHQLGFAVDINGATYDVYLWLQENSYKYGFIFRYPGSKTDITGTAEEVWHYRYVGVEAATEMYENGLCLEEYLEKKQSEN"},"dna_sequence":{"accession":"DQ212986","fmin":"4222","fmax":"5062","strand":"+","sequence":"ATGAACCATATGAATATGAAACACAGACGCAGAAAACGCAGACGTAACCAATCTTTTTTGTTCACAGGAATTTTACTCTTAGTTGTAGTATCTGCAAGCAGTTTTTTATGGTACGGTTTTGGCAATGCGGCAAAAAAAGACAGTGTTATTGAAGAAATGCCATTTACCATTACACAGGACGGAATGCAGGCAAAGGAAGAAATAAAGAAAACGGTACTGGAAACTTCCTATGGCGGCAAACAGCAGGTAGCGGAAGAAAATCACGGCAATACACAAAATGCAGGGACAGACGAAGCGTGGAATTTAATGCTTGTCAACAGAGATAATGCGATTCCAGACAATTACGAAGTAAATCTGGTCGAAGTAGAGGGCGGGGAGCGTGTAGATGAGCGTATCTATGAACCTCTTATGGAAATGCTTAATGCGGCAAGGGAGGAAAACTGGGGCGAATTGCCGATGGTAGTATCTGGCTATCGGACGCAGGAAAAACAGCAGAGCCTTTATGATGAAAAGATTGCAAAGTTCAAAAAAGAGGGGTATTCAGACAGTGAAGCCGTAAGGCAGGCAGAACAATGGGTTGCAGTGCCAGGTCACAGTGAGCATCAGCTCGGTTTTGCAGTGGATATTAACGGGGCAACTTATGATGTTTATCTATGGTTGCAGGAAAACAGCTATAAATACGGCTTTATCTTCAGATATCCCGGCAGTAAAACGGATATTACCGGGACTGCTGAAGAAGTATGGCATTACCGTTATGTTGGAGTGGAAGCGGCAACTGAAATGTATGAAAATGGATTATGTCTTGAGGAATATCTTGAGAAAAAGCAATCAGAAAACTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3002959","ARO_id":"39393","ARO_name":"vanYG1","ARO_description":"vanYG1 is a vanY variant found in the vanG gene cluster","ARO_category":{"36216":{"category_aro_accession":"3000077","category_aro_cvterm_id":"36216","category_aro_name":"vanY","category_aro_description":"VanY is a D,D-carboxypeptidase that cleaves removes the terminal D-Ala from peptidoglycan for the addition of D-Lactate. The D-Ala-D-Lac peptidoglycan subunits have reduced binding affinity with vancomycin compared to D-Ala-D-Ala.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"299":{"model_id":"299","model_name":"CepS beta-lactamase","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"725"}},"model_sequences":{"sequence":{"3286":{"protein_sequence":{"accession":"CAA56561.1","sequence":"MKQTRALPLLALGTLLLAPLSLAAPVDPLKAVVDDAIRPVLKQHRIPGMAVAVLKGGQAHYFNYGLADVATGAKVNEQTLFEIGSVSKTYTATLGAYAVVKGGFKLDDQVSGHAPWLKGSAFDGITMAELATYSAGGLPLQFPDEVDSSDTMRAYYRHWTPPYQAGTQRQYSNPSIGLFGHLAASSLQQPFSTLMEQTLLPALGLEHTYLQVPEAAMARYAFGYSKEDKPIRVNPGMLADEAYGIKTGSADLLAFVKANISGVDDKALQQAIALTHTGFYRIGEMSQGLGWESYAYPVSEQTLLAGNSPAVSLKANPVTKFETPAAPGAMRLYNKTGSTGGFGAYVAFVPAKGIGIVMLANRNYPIEARVSAAHAILSQLAP"},"dna_sequence":{"accession":"X80277","fmin":"0","fmax":"1149","strand":"+","sequence":"ATGAAACAGACCAGAGCCCTGCCACTGCTGGCCCTCGGCACCCTGCTGCTTGCCCCGCTCTCCCTGGCGGCCCCCGTCGATCCGCTGAAGGCGGTGGTGGATGACGCCATCCGCCCCGTGCTCAAGCAGCACAGGATCCCGGGCATGGCGGTCGCCGTGCTGAAGGGGGGGCAGGCCCACTACTTCAACTACGGGCTGGCCGATGTGGCGACCGGGGCCAAGGTCAATGAGCAGACCCTGTTCGAGATTGGCTCGGTCAGCAAGACCTATACCGCCACCCTTGGCGCCTACGCCGTGGTCAAGGGGGGCTTCAAGCTCGATGACCAGGTGAGCGGGCACGCACCCTGGCTCAAGGGCTCCGCCTTCGATGGCATCACCATGGCGGAACTTGCCACCTACAGTGCCGGGGGGCTGCCGCTGCAATTCCCCGACGAGGTTGATTCGAGCGATACCATGCGGGCCTATTACCGGCACTGGACGCCGCCATATCAGGCGGGAACCCAGCGCCAATACTCCAATCCCAGCATCGGCCTGTTCGGCCATCTGGCGGCGAGCAGCCTGCAGCAGCCGTTTTCCACGTTGATGGAGCAGACCCTGCTGCCAGCACTCGGGTTGGAGCACACCTATCTGCAGGTGCCCGAGGCCGCCATGGCTCGCTACGCCTTCGGCTACTCGAAGGAGGACAAACCCATCAGGGTCAACCCTGGCATGCTGGCCGACGAGGCCTACGGCATCAAGACCGGCTCGGCGGATCTGCTCGCCTTCGTGAAGGCCAATATCAGCGGGGTTGATGACAAGGCGTTGCAACAGGCGATCGCCCTGACCCACACCGGTTTTTATCGGATAGGGGAGATGAGCCAGGGGCTGGGCTGGGAGAGCTACGCCTACCCGGTCAGCGAGCAGACGCTGCTGGCGGGCAACTCCCCGGCGGTGAGCCTCAAGGCCAATCCGGTCACTAAGTTCGAGACGCCAGCCGCGCCCGGGGCTATGCGCCTCTACAACAAGACCGGGTCGACCGGTGGCTTCGGCGCCTACGTGGCCTTCGTGCCCGCCAAAGGGATCGGCATCGTCATGCTGGCCAATCGCAATTATCCCATCGAGGCCAGAGTCAGCGCGGCCCATGCCATTTTGAGCCAGCTGGCACCCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36957","NCBI_taxonomy_name":"Aeromonas sobria","NCBI_taxonomy_id":"646"}}}},"ARO_accession":"3003553","ARO_id":"40156","ARO_name":"CepS","ARO_description":"CEPS is a typical class C cephalosporinase found in Aeromonas sobria, first isolated from strain 163a.","ARO_category":{"41363":{"category_aro_accession":"3004199","category_aro_cvterm_id":"41363","category_aro_name":"CepS beta-lactamase","category_aro_description":"CepS beta-lactamases are Class C beta-lactamases capable of hydrolyzing cephalosporin.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"300":{"model_id":"300","model_name":"AAC(6')-29a","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"4408":{"protein_sequence":{"accession":"AAK26252.2","sequence":"MSILPVKEQDAADWLALRNLLWLADDHASEIEQYFSGGLEGLVEVLIARDATGAAVGHVELSIRHDLEELQGIKTGYIEGLYVAPSHRSTDLVRRFLRESEKWALEQGCSAFASDRSDRVITHRKFAGSAV"},"dna_sequence":{"accession":"AF263519.1","fmin":"1402","fmax":"1798","strand":"+","sequence":"GTTTCGATCTTACCTGTGAAAGAACAAGACGCTGCCGACTGGCTAGCGCTGCGGAATCTTCTTTGGCTCGCGGATGATCACGCCTCGGAGATTGAGCAGTACTTCTCTGGTGGACTTGAGGGGCTTGTAGAAGTGCTCATCGCCCGTGATGCTACCGGCGCGGCTGTTGGGCATGTCGAACTCTCGATAAGACATGACTTGGAAGAACTCCAAGGAATCAAGACCGGCTACATCGAAGGCCTTTATGTGGCCCCAAGCCATCGATCAACAGACCTTGTGAGGCGTTTCTTGCGTGAGTCCGAGAAGTGGGCCCTAGAACAAGGGTGCAGCGCATTTGCCTCAGACAGAAGTGATCGGGTCATCACGCACCGCAAGTTCGCAGGCAGCGCCGTCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002583","ARO_id":"38983","ARO_name":"AAC(6')-29a","ARO_description":"AAC(6')-29a is an integron-encoded aminoglycoside acetyltransferase in P. aeruginosa","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"301":{"model_id":"301","model_name":"CMY-95","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1702":{"protein_sequence":{"accession":"AGC54799.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHASPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVASAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"JX514369","fmin":"296","fmax":"1442","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGCTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATCGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002108","ARO_id":"38508","ARO_name":"CMY-95","ARO_description":"CMY-95 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"302":{"model_id":"302","model_name":"TEM-207","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"848":{"protein_sequence":{"accession":"AGK40892.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGGRGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"KC818234","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGGGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001384","ARO_id":"37784","ARO_name":"TEM-207","ARO_description":"From the Lahey list of beta-lactamases. Not yet released.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"303":{"model_id":"303","model_name":"ErmQ","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"678":{"protein_sequence":{"accession":"AAC36915.1","sequence":"MKAKSNNYRGKVDISVSQNFITSKNTIYKLIKKTNISKNDFVIEIGPGKGHITEALCEKSYWVTAIELDRSLYGNLINKFKSKNNVTLINKDFLNWKLPKKREYKVFSNIPFYITTKIIKKLLLEELNSPTDMWLVMEKGSAKRFMGIPRESKLSLLLKTKFDIKIVHYFNREDFHPMPSVDCVLVYFKRKYKYDISKDEWNEYTSFISKSINNLRDVFTKNQIHAVIKYLGINLNNISEVSYNDWIQLFRYKQKID"},"dna_sequence":{"accession":"L22689","fmin":"261","fmax":"1035","strand":"+","sequence":"ATGAAAGCTAAAAGTAATAATTATAGAGGAAAAGTTGATATTAGTGTATCGCAAAATTTTATTACTAGTAAAAATACTATATATAAATTAATAAAAAAAACAAATATATCCAAAAATGATTTTGTTATTGAAATTGGACCAGGAAAAGGTCATATAACAGAAGCTTTATGTGAAAAAAGTTATTGGGTTACAGCTATAGAACTAGATAGAAGTTTATATGGAAATTTAATAAATAAATTTAAAAGTAAAAATAATGTTACTCTTATTAATAAAGATTTTTTAAATTGGAAATTACCTAAAAAAAGAGAATATAAGGTATTTTCTAATATTCCTTTTTATATAACAACAAAGATTATTAAGAAATTATTATTAGAAGAGTTAAATTCACCAACTGATATGTGGCTAGTTATGGAGAAAGGTTCCGCAAAAAGATTTATGGGAATACCTAGAGAGAGTAAATTATCATTACTTTTAAAAACTAAATTTGATATTAAGATAGTGCACTATTTTAATAGAGAAGACTTCCATCCCATGCCTAGTGTAGATTGCGTCTTAGTATATTTTAAAAGAAAATATAAATATGATATATCTAAAGATGAATGGAATGAATATACAAGTTTTATATCTAAGTCTATTAATAACTTAAGAGATGTATTTACAAAAAATCAAATTCATGCAGTAATTAAATACCTAGGTATAAATCTTAATAATATTAGTGAAGTTTCTTATAATGATTGGATACAGTTATTTAGATATAAACAAAAGATAGATTAGT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36812","NCBI_taxonomy_name":"Clostridium perfringens","NCBI_taxonomy_id":"1502"}}}},"ARO_accession":"3000593","ARO_id":"36732","ARO_name":"ErmQ","ARO_description":"ErmQ confers MLSb phenotype.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35946":{"category_aro_accession":"0000027","category_aro_cvterm_id":"35946","category_aro_name":"roxithromycin","category_aro_description":"Roxithromycin is a semi-synthetic, 14-carbon ring macrolide antibiotic derived from erythromycin. It is used to treat respiratory tract, urinary and soft tissue infections. Roxithromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35974":{"category_aro_accession":"0000057","category_aro_cvterm_id":"35974","category_aro_name":"telithromycin","category_aro_description":"Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36315":{"category_aro_accession":"3000176","category_aro_cvterm_id":"36315","category_aro_name":"dirithromycin","category_aro_description":"Dirithromycin is an oxazine derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome to inhibit bacterial protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin 1A is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"vernamycin B-gamma","category_aro_description":"Vernamycin B-gamma is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"304":{"model_id":"304","model_name":"IND-11","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1747":{"protein_sequence":{"accession":"ADK25050.1","sequence":"MKKSIQLLMMSMFLSPLINAQVKDFVIEPPVKPNLYLYKSFGVFGGKEYSANAVYLTTKKGVVLFDVPWQKEQYQTLMDTIQKRHHLPVIAVFATHSHDDRAGDLSFYNQKGIKTYATAKTNELLKKDGKATSTEIIKTGKPYKIGGEEFMVDFLGEGHTVDNVVVWFPKYKVLDGGCLVKSRTATDLGYTGEANVKQWPETMRKLKTKYAHATLVIPGHDEWKGGGHVQHTLDLLDKNKKPE"},"dna_sequence":{"accession":"HM245379","fmin":"56","fmax":"788","strand":"+","sequence":"ATGAAAAAAAGTATTCAGCTTTTGATGATGTCAATGTTTTTAAGCCCATTGATCAATGCCCAGGTTAAAGATTTTGTAATTGAGCCGCCTGTTAAACCCAACCTGTATCTTTATAAAAGTTTCGGAGTTTTCGGGGGTAAAGAATATTCTGCCAATGCTGTATATCTTACCACTAAGAAAGGAGTTGTCTTATTTGATGTCCCATGGCAAAAGGAACAATATCAAACCCTTATGGACACCATACAAAAGCGTCATCACCTTCCTGTAATTGCTGTATTTGCCACCCACTCTCATGATGACAGAGCGGGTGATCTAAGCTTTTACAATCAAAAAGGAATTAAAACATATGCGACCGCCAAGACCAATGAACTGTTGAAAAAAGACGGAAAAGCAACCTCAACCGAAATTATAAAAACAGGAAAACCTTACAAAATTGGTGGTGAAGAATTTATGGTAGACTTTCTTGGAGAAGGACATACAGTTGATAATGTTGTTGTATGGTTCCCCAAATATAAAGTACTGGACGGAGGATGTCTTGTAAAAAGCAGGACAGCCACTGACCTGGGATATACCGGTGAAGCAAATGTAAAACAATGGCCGGAAACCATGCGAAAACTAAAAACGAAATATGCTCATGCCACTCTGGTAATCCCGGGACACGACGAATGGAAAGGCGGTGGCCATGTACAGCATACTCTGGATCTTCTGGATAAGAATAAAAAGCCGGAATAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36916","NCBI_taxonomy_name":"Chryseobacterium indologenes","NCBI_taxonomy_id":"253"}}}},"ARO_accession":"3002267","ARO_id":"38667","ARO_name":"IND-11","ARO_description":"IND-11 is a beta-lactamase found in Escherichia coli","ARO_category":{"36199":{"category_aro_accession":"3000060","category_aro_cvterm_id":"36199","category_aro_name":"IND beta-lactamase","category_aro_description":"IND beta-lactamases are class B carbapenem-hydrolyzing beta-lactamases","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"305":{"model_id":"305","model_name":"chrB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4301":{"protein_sequence":{"accession":"AAS79458.1","sequence":"MLNRIVRYLACPHCGASLAQGDRALFCPAGHSFDIAKQGYVNLLPRATKLRADTKEMVEARDAFLSAGHYDPVMDALVDLARRTADPAVPGCVVDIGGGTGHYHAGVMEAFPDAQGLLLDISKYAVRRAAKAHPRIAAAVTDAWQTLPLRDAAAGMVINTFAPRNGPELHRVLHPRGVLLVVTPLPDHLREVIGALGLLQVDEGKESRLAEQLAPHFSAVATEELTRTMALDHQALAHLVGMGPNAWHRDAQRDLETIQRLPAPTRVTLSVRLSAYRLSA"},"dna_sequence":{"accession":"AY509120","fmin":"22652","fmax":"23495","strand":"-","sequence":"CTACGCCGACAACCGGTAGGCGGAGAGCCGCACGGAGAGCGTGACCCGAGTCGGCGCCGGCAGCCGCTGGATCGTCTCCAGATCCCGCTGCGCGTCACGGTGCCAGGCATTGGGCCCCATGCCGACCAGGTGCGCCAGAGCCTGGTGGTCGAGAGCCATGGTCCGGGTCAACTCCTCCGTGGCGACGGCCGAGAAGTGCGGAGCGAGCTGCTCCGCGAGACGCGACTCCTTGCCTTCGTCCACCTGCAGCAGGCCGAGGGCGCCGATCACCTCCCGCAGGTGATCGGGCAGAGGAGTGACAACCAGGAGAACGCCACGGGGATGGAGAACGCGATGCAGTTCAGGACCGTTGCGGGGAGCGAACGTGTTGATCACCATGCCGGCTGCGGCATCCCGCAGCGGAAGCGTCTGCCAGGCGTCGGTCACCGCGGCCGCGATCCGCGGATGCGCCTTCGCGGCACGCCGCACGGCGTACTTGGAGATGTCCAGCAGCAGGCCCTGGGCATCGGGGAACGCTTCCATGACCCCGGCGTGATAGTGGCCCGTCCCCCCACCGATGTCGACCACACAGCCGGGCACGGCCGGATCGGCCGTCCGCCGCGCCAGATCGACCAGCGCATCCATCACGGGGTCGTAGTGACCCGCCGACAGGAATGCGTCCCGGGCCTCCACCATTTCCTTGGTGTCGGCCCGCAGCTTCGTCGCCCTGGGAAGCAGATTCACATAACCCTGCTTCGCGATGTCGAAGGAGTGTCCGGCGGGGCAGAAAAGTGCGCGGTCGCCCTGAGCCAGCGAAGCACCGCAGTGCGGGCAGGCGAGGTAGCGCACGATCCTGTTGAGCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39573","NCBI_taxonomy_name":"Streptomyces bikiniensis","NCBI_taxonomy_id":"1896"}}}},"ARO_accession":"3001302","ARO_id":"37701","ARO_name":"chrB","ARO_description":"ChrB is a methyltransferase found in Streptomyces bikiniensis and confers resistance to chalcomycin, mycinamicin, tylosin and lincosamides. Specifically, this enzyme adds a methyl group to guanosine 748 (E. coli numbering). chrB is found in the chalcomycin biosynthetic cluster and is responsible for self-resistance in S. bikiniensis.","ARO_category":{"37697":{"category_aro_accession":"3001298","category_aro_cvterm_id":"37697","category_aro_name":"non-erm 23S ribosomal RNA methyltransferase (G748)","category_aro_description":"Non-erm 23S ribosomal RNA methyltransferases modify guanosine 748 (E. coli numbering) to confer resistance to some macrolides and lincosamides","category_aro_class_name":"AMR Gene Family"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"306":{"model_id":"306","model_name":"SHV-32","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1066":{"protein_sequence":{"accession":"AAK69828.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAVITMSDNSAANLLLATVGGPAGLTAFLRQIDDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AY037778","fmin":"91","fmax":"952","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGTCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGACGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001090","ARO_id":"37470","ARO_name":"SHV-32","ARO_description":"SHV-32 is a broad-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"307":{"model_id":"307","model_name":"CTX-M-101","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"865":{"protein_sequence":{"accession":"ADY02545.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELIAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"HQ398214","fmin":"249","fmax":"1125","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTATCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001960","ARO_id":"38360","ARO_name":"CTX-M-101","ARO_description":"CTX-M-101 is a beta-lactamase. From the Lahey list of CTX-M beta-lactamases.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"308":{"model_id":"308","model_name":"CMY-118","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1265":{"protein_sequence":{"accession":"AIT76091.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"KM087838","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCGCTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGCGGTGAAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGTTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACAGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATAGTGATGCTGGCAAACAAAAGCTATCCTAACCCGGCTCGCGTAGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002129","ARO_id":"38529","ARO_name":"CMY-118","ARO_description":"CMY-118 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"309":{"model_id":"309","model_name":"CMY-35","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"782":{"protein_sequence":{"accession":"ABN51007.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKAVHVSPGQLDAEAYGVKSSVIDMARWVQVNMDASRVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"EF394371","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACATGGATTACAGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGGCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGTGTTATTGATATGGCCCGCTGGGTTCAGGTCAACATGGACGCCAGCCGCGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCAATCATCAACGGTAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCTGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACTGGAGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002046","ARO_id":"38446","ARO_name":"CMY-35","ARO_description":"CMY-35 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"310":{"model_id":"310","model_name":"SHV-78","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"840":{"protein_sequence":{"accession":"CAJ47133.2","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASSRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM176553","fmin":"30","fmax":"891","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCAGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001132","ARO_id":"37512","ARO_name":"SHV-78","ARO_description":"SHV-78 is a broad-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"311":{"model_id":"311","model_name":"IND-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"774":{"protein_sequence":{"accession":"AAG29757.1","sequence":"MKKSIQLLMMSMFLSPLINAQVKDFVIEPPVKPNLYLYKSFGVFGGKEYSANAVYLTTKKGVVLFDVPWQKEQYQTLMDTIQKRHHLPVIAVFATHSHDDRAGDLSFYNQKGIKTYATAKTNELLKKDGKATSTEIIKTGKPYKIGGEEFMVDFLGEGHTVDNVVVWFPKYKVLDGGCLVKSRTATDLGYTGEANVKQWPETMRKLKTKYAQATLVIPGHDEWKGGGHVQHTLDLLDKNKKPE"},"dna_sequence":{"accession":"AF219127","fmin":"0","fmax":"732","strand":"+","sequence":"ATGAAAAAAAGTATTCAGCTTTTGATGATGTCAATGTTTTTAAGCCCATTGATCAATGCCCAGGTTAAAGATTTTGTAATTGAGCCGCCTGTTAAACCCAACCTGTATCTTTATAAAAGTTTCGGAGTTTTCGGGGGTAAAGAATATTCTGCCAATGCTGTATATCTTACCACTAAGAAAGGAGTTGTCTTATTTGATGTCCCATGGCAAAAGGAACAATATCAAACCCTTATGGACACCATACAAAAGCGTCATCACCTTCCTGTAATTGCTGTATTTGCCACCCACTCTCATGATGACAGAGCGGGCGATCTAAGCTTTTACAATCAAAAAGGAATTAAAACATATGCGACCGCCAAGACCAATGAACTGTTGAAAAAAGACGGAAAAGCAACCTCAACCGAAATTATAAAAACAGGAAAACCTTACAAAATTGGTGGTGAAGAATTTATGGTAGACTTTCTTGGAGAAGGACATACAGTTGATAATGTTGTTGTATGGTTCCCCAAATATAAAGTACTGGACGGAGGATGTCTTGTAAAAAGCAGGACAGCCACTGACCTGGGATATACAGGTGAAGCAAACGTAAAACAATGGCCGGAAACCATGCGAAAACTAAAAACGAAATATGCTCAGGCCACTCTGGTAATCCCGGGACACGACGAATGGAAAGGCGGTGGCCATGTACAGCATACTCTGGATCTTCTGGATAAGAATAAAAAGCCGGAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36916","NCBI_taxonomy_name":"Chryseobacterium indologenes","NCBI_taxonomy_id":"253"}}}},"ARO_accession":"3002257","ARO_id":"38657","ARO_name":"IND-2","ARO_description":"IND-2 is a beta-lactamase found in Chryseobacterium indologenes","ARO_category":{"36199":{"category_aro_accession":"3000060","category_aro_cvterm_id":"36199","category_aro_name":"IND beta-lactamase","category_aro_description":"IND beta-lactamases are class B carbapenem-hydrolyzing beta-lactamases","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"312":{"model_id":"312","model_name":"OXA-167","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1370":{"protein_sequence":{"accession":"ADK35871.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETPSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKPQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELMMKSLKQLNII"},"dna_sequence":{"accession":"HM488988","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGACCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCCCAATTAGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTAATGATGAAATCATTAAAACAGCTGAATATTATTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001467","ARO_id":"37867","ARO_name":"OXA-167","ARO_description":"OXA-167 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"313":{"model_id":"313","model_name":"OXA-143","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1291":{"protein_sequence":{"accession":"ACX70402.1","sequence":"MKKFILPILSISTLLSVSACSSIQTKFEDTFHTSNQQHEKAIKSYFDEAQTQGVIIIKKGKNISTYGNNLTRAHTEYVPASTFKMLNALIGLENHKATTTEIFKWDGKKRSYPMWEKDMTLGDAMALSAVPVYQELARRTGLDLMQKEVKRVGFGNMNIGTQVDNFWLVGPLKITPIQEVNFADDFANNRLPFKLETQEEVKKMLLIKEFNGSKIYAKSGWGMDVTPQVGWLTGWVEKSNGEKVAFSLNIEMKQGMPGSIRNEITYKSLENLGII"},"dna_sequence":{"accession":"GQ861437","fmin":"2913","fmax":"3741","strand":"+","sequence":"ATGAAAAAATTTATACTTCCTATTCTCAGCATTTCTACTCTACTTTCTGTCAGTGCATGCTCATCTATTCAAACTAAATTTGAAGACACTTTTCATACTTCTAATCAGCAACATGAAAAAGCCATTAAAAGCTATTTTGATGAAGCTCAAACACAGGGTGTAATCATTATTAAAAAGGGAAAAAATATTAGTACCTATGGTAATAACCTGACACGAGCACATACAGAATATGTCCCTGCATCAACATTTAAGATGCTAAATGCCTTAATTGGACTAGAAAATCATAAAGCTACAACAACTGAGATTTTCAAATGGGACGGTAAAAAGAGATCTTATCCCATGTGGGAAAAAGATATGACTTTAGGTGATGCCATGGCACTTTCAGCAGTTCCTGTATATCAAGAACTTGCAAGACGGACTGGCTTAGACCTAATGCAAAAAGAAGTTAAACGGGTTGGTTTTGGTAATATGAACATTGGAACACAAGTTGATAACTTCTGGTTGGTTGGCCCCCTCAAGATTACACCAATACAAGAGGTTAATTTTGCCGATGATTTTGCAAATAATCGATTACCCTTTAAATTAGAGACTCAAGAAGAAGTTAAAAAAATGCTTCTGATTAAAGAATTCAATGGTAGTAAAATTTATGCAAAAAGCGGCTGGGGAATGGATGTAACCCCTCAAGTAGGTTGGTTAACAGGTTGGGTAGAAAAATCTAATGGAGAAAAAGTTGCCTTTTCTCTAAACATAGAAATGAAGCAAGGAATGCCTGGTTCTATTCGTAATGAAATTACTTATAAATCATTAGAGAATTTAGGGATTATATAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001654","ARO_id":"38054","ARO_name":"OXA-143","ARO_description":"OXA-143 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"314":{"model_id":"314","model_name":"TEM-176","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1324":{"protein_sequence":{"accession":"ADB90239.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSVLPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"GU550123","fmin":"144","fmax":"1005","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGTCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001041","ARO_id":"37421","ARO_name":"TEM-176","ARO_description":"TEM-176 is a beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"315":{"model_id":"315","model_name":"DHA-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1337":{"protein_sequence":{"accession":"AAG36927.1","sequence":"MKKSLSATLISALLAFSAPGFSAADNVAAVVDSTIKPLMAQQDIPGMAVAVSVKGKPYYFNYGFADVQAKQPVTENTLFELGSVSKTFTGVLGAVSVAKKEMMLNDPAEKYQPELALPQWKGITLLDLATYTTGGLPLQVPDAVKNRAELLHFYQQWQPSRKPGDMRLYANSSIGLFGALTANAAGMPYEQLLTARILAPLGLSHTFITVPESAQSQYAYGYKNKKPVRVSPGQLDAESYGVKSASKDMLRWAEMNMEPSRAGNADLEMAMYLAQTRYYKTAAINQGLGWEMYDWPQQKDMIINGVTNEVALQPHPVTDNQVQPYNRASWVHKTGATTGFGAYVAFIPEKQVAIVILANKNYPNTERVKAAQAILSALE"},"dna_sequence":{"accession":"AF259520","fmin":"1512","fmax":"2652","strand":"+","sequence":"ATGAAAAAATCGTTATCTGCAACACTGATTTCCGCTCTGCTGGCGTTTTCCGCCCCGGGGTTTTCTGCCGCTGATAATGTCGCGGCGGTGGTGGACAGCACCATTAAACCGCTGATGGCACAGCAGGATATTCCCGGGATGGCGGTTGCCGTCTCTGTAAAGGGCAAGCCCTATTATTTCAATTATGGTTTTGCCGATGTTCAGGCAAAACAGCCGGTCACTGAAAATACACTATTTGAGCTGGGATCTGTAAGTAAAACTTTCACAGGTGTGCTGGGTGCGGTTTCTGTGGCGAAAAAAGAGATGATGTTGAATGACCCGGCAGAAAAATACCAGCCGGAGCTGGCTCTGCCGCAGTGGAAGGGGATCACACTGCTGGATCTGGCCACCTACACCACAGGCGGGCTGCCGTTACAGGTGCCGGATGCGGTGAAAAACCGTGCGGAACTGCTGCACTTCTATCAGCAGTGGCAGCCGTCCCGGAAACCGGGCGATATGCGTCTGTATGCAAACAGCAGTATCGGCCTGTTTGGTGCTCTGACCGCCAACGCAGCGGGGATGCCGTATGAGCAGTTGCTGACCGCGCGGATCCTGGCACCGCTGGGATTATCTCACACCTTTATTACCGTGCCGGAAAGCGCGCAAAGCCAGTATGCGTACGGCTATAAAAACAAAAAACCGGTCCGCGTGTCGCCGGGACAGCTTGATGCGGAGTCTTACGGCGTGAAATCCGCCTCAAAAGATATGCTGCGCTGGGCGGAAATGAATATGGAGCCGTCACGGGCCGGTAATGCGGATCTGGAAATGGCAATGTATCTTGCACAGACCCGCTACTATAAAACCGCCGCGATTAACCAGGGGCTGGGCTGGGAGATGTATGACTGGCCGCAGCAGAAAGATATGATCATTAACGGCGTGACCAACGAGGTCGCACTGCAGCCGCACCCGGTAACAGACAACCAGGTTCAGCCGTATAACCGTGCTTCCTGGGTGCATAAAACGGGGGCAACAACTGGTTTCGGCGCCTATGTGGCCTTTATTCCGGAAAAACAGGTGGCGATTGTGATTCTGGCGAATAAAAACTACCCGAATACCGAAAGAGTCAAAGCCGCACAGGCTATTTTGAGTGCGCTGGAATAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002133","ARO_id":"38533","ARO_name":"DHA-2","ARO_description":"DHA-2 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36207":{"category_aro_accession":"3000068","category_aro_cvterm_id":"36207","category_aro_name":"DHA beta-lactamase","category_aro_description":"DHA beta-lactamases are plasmid-mediated AmpC \u03b2-lactamases that confer resistance to cephamycins and oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"316":{"model_id":"316","model_name":"CTX-M-36","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1186":{"protein_sequence":{"accession":"BAD16611.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVDGTMSLAELSAAALQYSDNVAMNKLISHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTNGL"},"dna_sequence":{"accession":"AB177384","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGTCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGAAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACTTGGTTAACTATAATCCGATTGCGGAAAAGCACGTCGATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTTCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGTAATCTGACGCTGGGTAAAGCATTGGGTGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCAACGGTTTGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001898","ARO_id":"38298","ARO_name":"CTX-M-36","ARO_description":"CTX-M-36 is a beta-lactamase found in Escherichia coli","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"317":{"model_id":"317","model_name":"TEM-148","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1954":{"protein_sequence":{"accession":"CAJ32372.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMAKTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AM087454","fmin":"208","fmax":"1069","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAAAAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001015","ARO_id":"37395","ARO_name":"TEM-148","ARO_description":"TEM-148 is a TEM beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"318":{"model_id":"318","model_name":"OXA-358","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1688":{"protein_sequence":{"accession":"AGZ83154.1","sequence":"MYKKALIVATSILFLSACSSNTVKQHQIHSISANKNSEEIKSLFDQAQTTGVLVIKRGQTEEIYGNDLKRASTAYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSQEVKRVGFGNANIGSKVDNFWLVGPLKITPQQETQFAYQLAHKTLPFSQDVQEQVQSMVFIEEKNGSKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGIPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"KF421161","fmin":"0","fmax":"822","strand":"+","sequence":"ATGTATAAAAAAGCCCTTATCGTTGCAACAAGTATCCTATTTTTATCCGCCTGTTCTTCCAATACGGTAAAACAACATCAAATACACTCTATTTCTGCCAATAAAAATTCAGAAGAAATTAAATCACTGTTTGATCAGGCACAGACCACGGGTGTTTTGGTGATTAAGCGAGGGCAAACAGAAGAAATTTATGGCAATGATCTTAAAAGAGCATCAACCGCCTATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTAATTGGACTTGAACATCATAAGGCAACTACAACTGAAGTATTTAAATGGGATGGGCAAAAACGTTTATTTCCTGATTGGGAAAAGGACATGACACTGGGTGATGCCATGAAAGCTTCTGCGATTCCAGTTTACCAAGAATTAGCCCGACGAATTGGTCTAGATCTTATGTCCCAAGAGGTGAAACGAGTTGGTTTTGGTAATGCTAACATTGGTTCAAAAGTAGATAATTTTTGGCTCGTTGGCCCTCTAAAAATTACACCTCAACAAGAAACCCAATTTGCTTATCAATTAGCCCATAAAACGCTTCCATTTAGCCAAGATGTACAAGAACAAGTTCAATCAATGGTGTTCATAGAGGAAAAAAATGGAAGTAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTTGAACCACAAGTTGGTTGGCTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTGGCATTCTCACTAAATTTAGAAATGAAAAAAGGAATCCCTAGTTCTATCCGAAAAGAAATTGCTTATAAAGGATTAGAACAACTCGGTATTTTATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3001545","ARO_id":"37945","ARO_name":"OXA-358","ARO_description":"OXA-358 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"319":{"model_id":"319","model_name":"OXA-366","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2111":{"protein_sequence":{"accession":"AJO16038.1","sequence":"MNKYFTCYVVASLFLSGCTAQHNLINETPSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKPQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"KP050485","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGCTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGACCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCCCAATTAGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001553","ARO_id":"37953","ARO_name":"OXA-366","ARO_description":"OXA-366 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"321":{"model_id":"321","model_name":"CTX-M-35","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1106":{"protein_sequence":{"accession":"BAD83775.1","sequence":"MMTQSIRRSMLTVMATLPLLFSSATLHAQANSVQQQLEALEKSSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKQSESDKHLLNQRVEIKKSDLVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDRTESTLNTAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSASIRAGLPKSWVVGDKTGSGDYGTTNDIAVIWPENHAPLVLVTYFTQPEQKAESRRDILAAAAKIVTHGF"},"dna_sequence":{"accession":"AB176534","fmin":"0","fmax":"876","strand":"+","sequence":"ATGATGACTCAGAGCATTCGCCGCTCAATGTTAACGGTGATGGCGACGCTACCCCTGCTATTTAGCAGCGCAACGCTGCATGCGCAGGCGAACAGCGTGCAACAGCAGCTGGAAGCCCTGGAGAAAAGTTCGGGAGGTCGGCTTGGCGTTGCGCTGATTAACACCGCCGATAATTCGCAGATTCTCTACCGTGCCGATGAACGTTTTGCGATGTGCAGTACCAGTAAGGTGATGGCGGCCGCGGCGGTGCTTAAACAGAGCGAGAGCGATAAGCACCTGCTAAATCAGCGCGTTGAAATCAAGAAGAGCGACCTGGTTAACTACAATCCCATTGCGGAGAAACACGTTAACGGCACGATGACGCTGGCTGAGCTTGGCGCAGCGGCGCTGCAGTATAGCGACAATACTGCCATGAATAAGCTGATTGCCCATCTGGGTGGTCCCGATAAAGTGACGGCGTTTGCTCGCTCGTTGGGTGATGAGACCTTCCGTCTGGACAGAACCGAGTCCACGCTCAATACCGCCATTCCAGGCGACCCGCGTGATACCACCACGCCGCTCGCGATGGCGCAGACCCTGAAAAATCTGACGCTGGGTAAAGCGCTGGCGGAAACTCAGCGGGCACAGTTGGTGACGTGGCTTAAGGGCAATACTACCGGTAGCGCGAGCATTCGGGCGGGTCTGCCGAAATCATGGGTAGTGGGCGATAAAACCGGCAGCGGAGATTATGGCACCACCAACGATATCGCGGTTATCTGGCCGGAAAACCACGCACCGCTGGTTCTGGTGACCTACTTTACCCAACCGGAGCAGAAGGCGGAAAGCCGTCGGGATATTCTGGCTGCGGCGGCGAAAATCGTAACCCACGGTTTCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3001897","ARO_id":"38297","ARO_name":"CTX-M-35","ARO_description":"CTX-M-35 is a beta-lactamase found in Citrobacter koseri","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"322":{"model_id":"322","model_name":"FEZ-1 beta-lactamase","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"789":{"protein_sequence":{"accession":"CAB96921.1","sequence":"MKKVLSLTALMMVLNHSSFAYPMPNPFPPFRIAGNLYYVGTDDLASYLIVTPRGNILINSDLEANVPMIKASIKKLGFKFSDTKILLISHAHFDHAAGSELIKQQTKAKYMVMDEDVSVILSGGKSDFHYANDSSTYFTQSTVDKVLHDGERVELGGTVLTAHLTPGHTRGCTTWTMKLKDHGKQYQAVIIGSIGVNPGYKLVDNITYPKIAEDYKHSIKVLESMRCDIFLGSHAGMFDLKNKYVLLQKGQNNPFVDPTGCKNYIEQKANDFYTELKKQETA"},"dna_sequence":{"accession":"Y17896","fmin":"0","fmax":"849","strand":"+","sequence":"ATGAAAAAAGTATTAAGTTTAACCGCATTGATGATGGTATTGAACCATTCAAGCTTCGCATATCCAATGCCAAATCCTTTTCCCCCATTCCGTATTGCTGGAAACTTGTACTATGTAGGCACTGATGATCTCGCAAGCTACCTGATTGTCACACCGAGAGGGAACATTTTGATCAATAGTGATCTTGAGGCTAATGTTCCCATGATTAAAGCAAGTATAAAAAAACTAGGTTTTAAATTCAGTGATACTAAAATTTTGCTGATTAGCCATGCTCATTTTGATCATGCGGCCGGTAGCGAATTAATTAAGCAACAAACAAAAGCAAAATATATGGTTATGGACGAGGATGTTTCGGTGATCCTGTCTGGCGGTAAATCTGATTTTCATTATGCTAATGATTCCAGTACTTATTTTACTCAGAGTACTGTGGATAAGGTTCTTCACGACGGAGAACGGGTGGAATTAGGAGGGACCGTATTAACTGCTCATTTGACTCCTGGACACACTAGAGGCTGTACCACCTGGACAATGAAACTAAAAGATCACGGCAAGCAATATCAGGCCGTAATTATAGGAAGTATTGGCGTAAATCCTGGGTATAAATTGGTTGATAATATAACTTATCCAAAAATTGCCGAAGATTATAAGCACTCCATAAAGGTACTTGAGTCAATGCGTTGCGATATTTTTCTAGGATCGCATGCCGGAATGTTTGATCTGAAGAATAAATATGTACTATTACAAAAAGGTCAAAACAATCCCTTTGTTGATCCCACAGGCTGTAAAAATTATATTGAACAAAAGGCAAACGATTTTTACACAGAACTTAAGAAGCAAGAAACTGCCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36922","NCBI_taxonomy_name":"Fluoribacter gormanii","NCBI_taxonomy_id":"464"}}}},"ARO_accession":"3000606","ARO_id":"36745","ARO_name":"FEZ-1","ARO_description":"FEZ-1 is an Ambler class B MBL; subclass B3 first isolated from Legionella gormanii.  It has activity against a broad range of beta-lactams and is only active with two Zn(II) ions in the active site.","ARO_category":{"41375":{"category_aro_accession":"3004211","category_aro_cvterm_id":"41375","category_aro_name":"FEZ beta-lactamase","category_aro_description":"The FEZ family of beta-lactamases are subclass B3 beta-lactamases that hydrolyze penicillins, cephalosporins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"323":{"model_id":"323","model_name":"aadA9","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"4302":{"protein_sequence":{"accession":"ABG49324.1","sequence":"MLWSSNDVTQQGSRPKTKLDMMSNSIHTGISRQLSQARDVIKRHLASTLKAIHLYGSAIDGGLKPYSDIDLLVTVDARLDEATRRSLMLDFLNISAPPCESSILRPLEVTVVACNEVVPWRYPARRELQFGEWLREDILEGVFEPAALDADLAILITKARQHSIALVGPVAQKVFMPVPEHDFLQVLSDTLKLWNTHEDWENEERNIVLTLARIWYSTETGGIVPKDVAAEWVLERLPAEHKPILVEARQAYLGLCKDSLALRADETSAFIGYAKSAVADLLEKRKSQTSHICDGAKNV"},"dna_sequence":{"accession":"DQ390458","fmin":"3095","fmax":"3995","strand":"-","sequence":"TTAGACGTTCTTGGCGCCATCGCAAATATGCGAAGTTTGAGATTTTCGCTTTTCGAGCAAATCAGCGACCGCAGACTTTGCATAGCCAATGAACGCCGAAGTCTCATCTGCACGCAAAGCAAGACTATCCTTGCAAAGCCCAAGATAGGCTTGCCGCGCCTCAACCAGTATTGGCTTATGCTCAGCTGGCAAGCGCTCTAAAACCCATTCGGCGGCCACATCCTTGGGGACGATTCCTCCAGTTTCAGTGCTATACCAGATCCGAGCTAACGTGAGTACGATGTTCCGCTCCTCATTTTCCCAATCCTCATGAGTATTCCACAGCTTAAGGGTATCGGAAAGCACCTGGAGAAAGTCATGCTCTGGCACCGGCATGAAGACTTTTTGAGCCACTGGACCTACTAAAGCGATGCTGTGTTGCCTAGCTTTCGTTATTAGAATTGCAAGGTCGGCGTCCAAGGCGGCTGGCTCGAAGACACCTTCAAGAATATCCTCCCGCAGCCACTCCCCGAACTGCAGTTCTCGTCGTGCCGGATAACGCCAAGGCACTACTTCGTTGCATGCAACAACAGTTACCTCTAGCGGCCGGAGTATTGAGCTTTCGCATGGTGGTGCCGAGATATTCAAGAAATCGAGCATCAGGGAGCGTCTGGTAGCTTCATCCAAGCGTGCATCCACGGTAACCAGCAGATCAATGTCGCTATATGGTTTGAGGCCACCATCAATTGCAGAACCATACAAGTGTATGGCTTTCAGCGTTGATGCCAAATGGCGTTTAATTACATCGCGTGCCTGTGAAAGCTGTCTTGAGATTCCGGTGTGTATAGAGTTGCTCATCATGTCTAACTTTGTTTTAGGGCGACTGCCCTGCTGCGTAACATCGTTGCTGCTCCATAACAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39645","NCBI_taxonomy_name":"Corynebacterium sp. L2-79-05","NCBI_taxonomy_id":"373068"}}}},"ARO_accession":"3002609","ARO_id":"39009","ARO_name":"aadA9","ARO_description":"aadA9 is a plasmid-encoded aminoglycoside nucleotidyltransferase gene in C. glutamicum","ARO_category":{"41439":{"category_aro_accession":"3004275","category_aro_cvterm_id":"41439","category_aro_name":"ANT(3'')","category_aro_description":"Nucleotidylylation of streptomycin at the hydroxyl group at position 3''","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"324":{"model_id":"324","model_name":"QnrB54","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"350":{"protein_sequence":{"accession":"CCI51002.2","sequence":"MALALVSEKIDRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNASALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAIIG"},"dna_sequence":{"accession":"HE820727","fmin":"586","fmax":"1231","strand":"+","sequence":"ATGGCACTGGCACTCGTTAGCGAAAAAATTGACAGAAACCGCTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCGATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATGCCAGTGCGCTTGGCATTGAAATTCGCCACTGTCGTGCGCAAGGCGCAGATTTCCGCGGCGCAAGCTTTATGAATATGATCACTACTCGCACCTGGTTTTGTAGTGCATATATCACTAACACAAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGCTGGAAAAGTGTGAGCTGTGGGAAAACCGTTGGATGGGTACCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTGACTTAGATATTCGGGGCGTTGATTTACAAGGCGTTAAGTTGGACAACTACCAGGCATCGTTGCTCATGGAACGTCTTGGCATCGCGATTATTGGCTAGT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002767","ARO_id":"39201","ARO_name":"QnrB54","ARO_description":"QnrB54 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"325":{"model_id":"325","model_name":"LEN-23","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1898":{"protein_sequence":{"accession":"CAP12351.2","sequence":"MRYVRLCVISLLATLPLAVYAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGLEQLDRRIHYRQQDLVDYSPVSEKHLTDGMTIGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPPGWFIADKTGAGERGARGIVALLGPDGKPERIVVLYLRDTPASMAERNQHIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM850913","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCACCCTGCCACTGGCGGTATACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCGGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTAGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTACCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGCCGGGCTGGTTTATCGCCGACAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGCTCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002470","ARO_id":"38870","ARO_name":"LEN-23","ARO_description":"LEN-23 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"172":{"model_id":"172","model_name":"OprN","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"309":{"protein_sequence":{"accession":"NP_251185.1","sequence":"MIHAQSIRSGLASALGLFSLLALSACTVGPDYRTPDTAAAKIDATASKPYDRSRFESLWWKQFDDPTLNQLVEQSLSGNRDLRVAFARLRAARALRDDVANDRFPVVTSRASADIGKGQQPGVTEDRVNSERYDLGLDSAWELDLFGRIRRQLESSDALSEAAEADLQQLQVSLIAELVDAYGQLRGAQLREKIALSNLENQKESRQLTEQLRDAGVGAELDVLRADARLAATAASVPQLQAEAERARHRIATLLGQRPEELTVDLSPRDLPAITKALPIGDPGELLRRRPDIRAAERRLAASTADVGVATADLFPRVSLSGFLGFTAGRGSQIGSSAARAWSVGPSISWAAFDLGSVRARLRGAKADADAALASYEQQVLLALEESANAFSDYGKRQERLVSLVRQSEASRAAAQQAAIRYREGTTDFLVLLDAEREQLSAEDAQAQAEVELYRGIVAIYRSLGGGWQPSA"},"dna_sequence":{"accession":"NC_002516","fmin":"2813193","fmax":"2814612","strand":"+","sequence":"ATGATTCACGCGCAGTCGATCCGGAGCGGGCTCGCGTCCGCCCTGGGTCTGTTCAGTCTGCTGGCGCTCAGCGCCTGCACGGTGGGTCCGGACTACCGGACCCCCGACACCGCGGCGGCGAAGATCGACGCCACGGCGAGCAAGCCCTACGACCGCAGCCGCTTCGAAAGCCTGTGGTGGAAACAGTTCGACGATCCGACCCTGAACCAGTTGGTCGAACAGTCGCTGAGCGGCAACCGCGACCTGCGCGTGGCCTTCGCCCGCCTGCGCGCCGCCCGCGCCCTGCGCGACGACGTGGCCAACGATCGCTTCCCGGTGGTCACCAGCCGCGCCAGCGCCGACATCGGCAAGGGCCAGCAACCGGGAGTGACCGAGGACCGGGTCAACAGCGAGCGCTACGACCTTGGCCTGGATAGCGCCTGGGAGCTTGACCTGTTCGGGCGCATCCGCCGTCAGCTGGAGTCCAGCGACGCCCTCAGCGAAGCGGCCGAGGCCGACCTGCAGCAACTGCAGGTCAGCCTGATCGCCGAGCTGGTGGACGCCTACGGCCAACTGCGCGGCGCGCAACTGCGCGAGAAGATTGCCCTGAGCAACCTGGAGAACCAGAAGGAGTCGCGCCAGCTCACCGAGCAACTGCGCGACGCCGGGGTCGGTGCCGAACTCGACGTACTGCGCGCCGATGCGCGCCTGGCGGCCACCGCCGCCAGCGTGCCGCAACTGCAGGCGGAAGCCGAGCGCGCCAGGCACCGTATCGCCACCCTCCTCGGCCAACGGCCGGAAGAGTTGACAGTGGACCTTTCGCCGCGCGACCTGCCGGCGATCACCAAGGCCCTGCCGATCGGCGATCCCGGCGAACTGCTGCGCCGCCGGCCGGACATCCGCGCCGCCGAACGGCGCCTGGCCGCCAGCACCGCCGACGTCGGCGTGGCCACCGCCGACCTGTTCCCGCGGGTCAGCCTCAGCGGCTTCCTCGGCTTCACCGCCGGGCGGGGCTCGCAGATCGGCTCAAGCGCCGCCCGCGCCTGGAGCGTCGGCCCGAGCATCAGTTGGGCCGCCTTCGACCTCGGCAGCGTGCGTGCCCGCCTGCGCGGCGCCAAGGCCGACGCCGACGCCGCGCTGGCCAGCTACGAACAGCAGGTGCTGCTGGCCCTGGAAGAATCGGCGAATGCCTTCAGCGACTATGGCAAGCGCCAGGAGCGCCTGGTCTCGCTGGTCCGCCAGTCGGAAGCCAGCCGCGCCGCCGCGCAACAGGCGGCGATCCGCTACCGCGAAGGCACCACCGATTTCCTGGTGCTGCTGGACGCCGAACGCGAGCAACTCTCCGCCGAAGATGCCCAGGCCCAGGCCGAGGTCGAGCTGTACCGCGGCATCGTGGCGATCTACCGCTCCCTCGGCGGTGGCTGGCAACCCAGCGCCTGAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3000805","ARO_id":"37185","ARO_name":"OprN","ARO_description":"OprN is the outer membrane channel component of the MexEF-OprN multidrug efflux complex.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"250":{"model_id":"250","model_name":"Rhodococcus fascians cmr","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"663":{"protein_sequence":{"accession":"CAA78046.1","sequence":"MPFAIYVLGIAVFAQGTSEFMLSGLIPDMAQDLQVSVPTAGLLTSAFAIGMIIGAPLMAIVSMRWQRRRALLTFLITFMVVHVIGALTDSFGVLLVTRIVGALANAGFLAVALGAAMSMVPADMKGRATSVLLGGVTIACVVGVPGGALLGELWGWRASFWEVVLISAPAVAAIMASTPADSPTDSVPNATRELSSLRQRKLQLILVLGALINGATFCSFTYLAPTLTDVAGFDSRWIPLLLGLFGLGSFIGVSVGGRLADTRPFQLLVAGSAALLVGWIVFAITASHPVVTLVMLFVQGTLSFAVGSTLISRVLYVADGAPTLGGSFATAAFNVGAALGPALGGVAIGIGMGYRAPLWTSAALVALAIVIGAATWTRWREPRPALDTVPP"},"dna_sequence":{"accession":"Z12001","fmin":"992","fmax":"2168","strand":"+","sequence":"GTGCCATTCGCCATCTATGTCCTGGGTATTGCTGTATTCGCCCAGGGCACATCGGAATTCATGCTGTCCGGACTCATACCGGATATGGCTCAGGATCTACAGGTTTCGGTCCCCACTGCAGGACTTCTCACTTCGGCATTCGCAATCGGCATGATCATCGGTGCCCCGTTGATGGCAATTGTCAGTATGCGGTGGCAACGTCGACGAGCGCTCTTGACCTTCCTCATCACTTTTATGGTTGTGCATGTCATCGGCGCACTCACCGACAGTTTCGGCGTCTTGCTGGTCACCCGGATCGTAGGAGCACTGGCCAACGCCGGTTTCCTGGCTGTAGCGCTGGGCGCAGCCATGTCGATGGTTCCTGCCGACATGAAGGGACGAGCGACCTCAGTTCTACTGGGCGGAGTGACCATCGCCTGCGTAGTTGGAGTCCCGGGCGGAGCGCTATTGGGCGAACTGTGGGGATGGCGCGCCTCGTTCTGGGAGGTAGTGCTGATTTCCGCACCGGCAGTGGCAGCGATCATGGCATCGACCCCTGCTGATTCCCCTACAGATTCTGTTCCGAACGCGACCCGCGAACTGTCCTCGCTGCGTCAACGCAAACTTCAACTGATCTTGGTGCTGGGCGCGCTGATCAACGGTGCCACCTTCTGTTCCTTCACCTACCTGGCTCCGACGCTCACCGACGTCGCCGGGTTCGACTCTCGCTGGATCCCTTTGCTTCTCGGACTGTTCGGACTGGGGTCGTTCATCGGCGTCAGTGTCGGTGGCCGGCTCGCTGACACCCGTCCGTTTCAATTGCTGGTGGCGGGCTCGGCAGCTCTTCTGGTCGGGTGGATCGTGTTCGCTATCACTGCCTCTCACCCGGTAGTGACCCTGGTGATGCTGTTCGTGCAAGGAACGCTGTCGTTCGCTGTGGGGTCGACGTTGATCTCGCGAGTGCTCTACGTCGCCGACGGTGCTCCGACTTTGGGGGGATCCTTCGCTACGGCTGCCTTCAATGTCGGAGCCGCATTGGGGCCGGCCCTCGGCGGTGTGGCCATCGGTATCGGAATGGGCTATCGCGCTCCACTGTGGACCAGCGCGGCTCTGGTGGCACTTGCGATCGTGATCGGTGCCGCGACGTGGACGCGTTGGCGGGAACCACGTCCAGCGCTGGACACCGTTCCTCCGTGAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39552","NCBI_taxonomy_name":"Rhodococcus fascians","NCBI_taxonomy_id":"1828"}}}},"ARO_accession":"3002701","ARO_id":"39135","ARO_name":"Rhodococcus fascians cmr","ARO_description":"cmr is a plasmid-encoded chloramphenicol exporter that is found in Rhodococcus fascians and Corynebacterium glutamicum","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"326":{"model_id":"326","model_name":"OXA-225","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1837":{"protein_sequence":{"accession":"AEP43731.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETPSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKSQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"JN638887","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGACCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCCCAATTAGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAATCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001493","ARO_id":"37893","ARO_name":"OXA-225","ARO_description":"OXA-225 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"327":{"model_id":"327","model_name":"GES-17","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"911":{"protein_sequence":{"accession":"ADZ48685.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVKWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMGDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGARNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"HQ874631","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCAAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGGGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGCCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002346","ARO_id":"38746","ARO_name":"GES-17","ARO_description":"GES-17 is a beta-lactamase. From the Lahey list of GES beta-lactamases.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"329":{"model_id":"329","model_name":"CTX-M-159","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2120":{"protein_sequence":{"accession":"AJO16046.1","sequence":"MMRKSVRRAMLMTTACVSLLLASVPLCAQANDVQQKLAALEKSSGGRLGVALINTADNTQTLYRADERFAMCSTSKVMAVAAVLKQSETQKGLLSQRVEIKPSDLVNYNPIAEKHVNGTMTFGELSAAALQYSDNTAMNKLIAHLGGPDKVTAFARTIGDDTFRLDRTEPTLNTAIPGDPRDTTTPLAMAQALRNLTLGNALGDTQRAQLVMWLKGNTTGAASIQAGLPTSWVVGDKTGSGGYGTTNDIAVIWPEGRAPLVLVTYFTQSEPKAESRRDVLAAAARIVTDGY"},"dna_sequence":{"accession":"KP050493","fmin":"0","fmax":"876","strand":"+","sequence":"ATGATGAGAAAAAGCGTAAGGCGGGCGATGTTAATGACGACAGCCTGTGTTTCGCTGCTGTTGGCCAGTGTGCCGCTGTGTGCCCAGGCGAACGATGTTCAACAAAAGCTCGCGGCGCTGGAGAAAAGCAGCGGGGGACGACTGGGTGTGGCGTTGATTAACACCGCCGATAACACGCAGACGCTCTACCGCGCCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCGGTAGCGGCGGTGCTTAAGCAAAGTGAAACGCAAAAGGGCTTGTTGAGTCAGCGGGTTGAAATTAAGCCCTCAGACTTGGTTAACTACAACCCCATTGCGGAAAAACACGTCAATGGCACGATGACATTCGGGGAGTTGAGCGCGGCGGCGCTACAGTACAGCGATAATACTGCCATGAATAAGCTGATTGCCCATCTCGGGGGGCCGGATAAAGTGACGGCATTTGCCCGTACGATTGGCGATGACACGTTCCGGCTCGATCGTACCGAGCCGACGCTCAACACCGCGATCCCCGGCGACCCGCGCGATACCACCACGCCGTTAGCGATGGCGCAGGCTCTGCGCAATCTGACGTTGGGCAATGCCCTGGGTGACACTCAGCGTGCGCAGCTGGTGATGTGGCTGAAAGGCAACACCACCGGCGCTGCCAGCATTCAGGCAGGGCTACCCACATCGTGGGTTGTCGGGGATAAAACCGGCAGCGGCGGTTATGGTACGACGAATGATATCGCGGTTATTTGGCCGGAAGGTCGCGCGCCGCTCGTTCTGGTGACTTACTTCACCCAGTCGGAGCCGAAGGCAGAGAGCCGTCGTGACGTGCTCGCTGCTGCCGCCAGAATTGTCACCGACGGTTATTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3003167","ARO_id":"39744","ARO_name":"CTX-M-159","ARO_description":"From the Lahey list of beta-lactamases.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"330":{"model_id":"330","model_name":"IMP-26","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"773":{"protein_sequence":{"accession":"ACY01749.1","sequence":"MSKLSVFFIFLFCSIATAAEPLPDLKIEKLDEGVYVHTSFEEVNGWGVFPKHGLVVLVDAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKDGKVQAKNSFGGVNYWLVKNKIEVFYPGPGHTPDNLVVWLPERKILFGGCFIKPYGLGNLGDANLEAWPKSAKLLISKYGKAKLVVPSHSEAGDASLLKLTLEQAVKGLNESKKPSKLSN"},"dna_sequence":{"accession":"GU045307","fmin":"100","fmax":"841","strand":"+","sequence":"ATGAGCAAGTTATCTGTATTCTTTATATTTTTGTTTTGTAGCATTGCTACCGCAGCAGAGCCTTTGCCAGATTTAAAAATTGAAAAACTTGATGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGGTGGGGCGTTTTTCCTAAACATGGTTTGGTTGTTCTTGTAGATGCTGAAGCTTATCTAATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAACGTGGCTATAAAATAAAAGGCAGTATTTCCTCTCATTTTCATAGTGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCAATCCATCCCCACGTATGCGTCTGAATTAACTAATGAGCTGCTTAAAAAAGACGGTAAGGTTCAAGCTAAAAATTCATTTGGCGGGGTTAACTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCAGGACACACTCCAGATAACCTAGTAGTTTGGCTGCCTGAAAGGAAAATATTATTCGGTGGTTGTTTTATTAAACCGTACGGTCTAGGTAATTTGGGTGACGCAAATTTAGAAGCTTGGCCAAAGTCCGCTAAATTATTAATATCCAAATATGGTAAGGCAAAACTGGTTGTTCCAAGTCACAGTGAAGCTGGAGACGCATCACTCTTGAAACTTACATTAGAGCAGGCGGTTAAAGGGTTAAACGAAAGTAAAAAACCATCAAAACTAAGCAACTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002217","ARO_id":"38617","ARO_name":"IMP-26","ARO_description":"IMP-26 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"331":{"model_id":"331","model_name":"TEM-166","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"846":{"protein_sequence":{"accession":"ACI25375.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVGELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"FJ197316","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAGGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001032","ARO_id":"37412","ARO_name":"TEM-166","ARO_description":"TEM-166 is a beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"332":{"model_id":"332","model_name":"r39 beta-lactamase","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"3308":{"protein_sequence":{"accession":"CAA37699.1","sequence":"MLFPTARRTGFAALAALALVPAAACSGSAAPAEAEPASAEVTAEDLSGEFERLESEFDARLGVYAVDTGTGEEVFHRADERFGYASTHKAFTAALVLGQNTPEELEEVVTYTEEDLVDYSPITEQHVDTGMTLLEVADAAVRHSDNTAANLLFEELGGPEGFEEDMRELGDDVISADRIETELNEVPPGETRDTSTPRAMAGSLEAFVLGDVLEEGPRDVLTEMLLNNTTGDELIRAGVPEDWRVGDKTGGGSHGSRNDIAVVWPPEDDPIVIAVMSTREQEDAEFDNALVSGATEVVVEALAP"},"dna_sequence":{"accession":"X53650","fmin":"320","fmax":"1235","strand":"+","sequence":"ATGTTGTTCCCCACGGCCCGCAGGACCGGGTTCGCGGCCCTGGCCGCGCTCGCGCTCGTCCCCGCCGCGGCCTGCTCCGGCTCCGCCGCGCCCGCCGAGGCGGAGCCGGCGAGCGCGGAGGTGACGGCCGAGGACCTCTCCGGTGAGTTCGAGCGGCTGGAATCGGAGTTCGACGCCCGTCTCGGGGTCTACGCGGTGGACACCGGGACCGGGGAGGAGGTCTTCCACCGCGCCGACGAGCGGTTCGGCTACGCCTCCACCCACAAGGCGTTCACGGCGGCCCTGGTCCTGGGGCAGAACACCCCCGAGGAGCTGGAGGAGGTCGTCACCTACACCGAAGAGGACCTGGTCGACTACTCCCCCATCACCGAGCAGCACGTCGACACGGGGATGACCCTGCTGGAGGTGGCCGACGCCGCCGTCCGCCACAGCGACAACACCGCCGCGAACCTGCTGTTCGAGGAGCTGGGCGGACCCGAGGGGTTCGAGGAGGACATGCGGGAGCTCGGCGACGACGTGATCTCGGCGGACCGGATCGAGACCGAGCTCAACGAGGTGCCGCCCGGCGAGACCCGGGACACGAGCACGCCGCGCGCCATGGCCGGGAGCCTGGAGGCGTTCGTGCTCGGTGACGTCCTGGAGGAGGGCCCGCGCGACGTGCTCACCGAGATGCTCCTCAACAACACGACCGGTGACGAGCTGATCCGGGCGGGGGTCCCCGAGGACTGGCGTGTCGGTGACAAGACCGGCGGCGGCAGCCACGGTTCGCGCAACGACATCGCCGTCGTCTGGCCCCCCGAGGACGACCCCATCGTCATCGCGGTCATGTCCACCCGTGAGCAGGAGGACGCCGAATTCGACAACGCCCTGGTCTCGGGGGCGACCGAGGTCGTCGTGGAGGCACTGGCCCCGTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40175","NCBI_taxonomy_name":"Actinomadura sp. R39","NCBI_taxonomy_id":"72570"}}}},"ARO_accession":"3003565","ARO_id":"40174","ARO_name":"R39","ARO_description":"Class A beta-lactamase found in Actinomadura R39","ARO_category":{"41362":{"category_aro_accession":"3004198","category_aro_cvterm_id":"41362","category_aro_name":"R39 beta-lactamase","category_aro_description":"R39 beta-lactamases are Class A beta-lactamases encoded in Actinomadura R39 with the ability to hydrolyze penicillins.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"333":{"model_id":"333","model_name":"CARB-23","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1420":{"protein_sequence":{"accession":"AHJ02283.1","sequence":"MVRVFTRYSLLNIAKVRIKTKERRTPRMKKLFLLVGLMVCSTVSYASKLNLNEDISLIEKQTSGRIGVSVWDTQTDERWDYRGDERFPLMSTFKTLACATMLSDMDSGKLNKNATAKIDERNIVVWSPVMDKLAGQSTRIEHACEAAMLMSDNTAANLVLNEIGGPKAVTLFLRSIGDKATRLDRLEPRLNEAKPGDKRDTTTPNAMVNTLHTLMEDNALSYESRTQLKIWMQDNKVSDSLMRSVLPKGWSIADRSGAGNYGSRGISAMIWKDNYKPVYISIYVTDTDLSLQARDQLIAQISQLILEHYKES"},"dna_sequence":{"accession":"CP007005","fmin":"1250264","fmax":"1251203","strand":"+","sequence":"GTGGTTAGAGTATTCACTCGTTATAGTTTGCTTAACATCGCCAAAGTGCGAATCAAAACCAAAGAACGAAGAACACCACGCATGAAAAAGTTATTCCTGTTGGTTGGGCTGATGGTTTGCTCAACTGTTAGTTACGCCTCCAAATTAAATTTAAATGAAGACATCTCCCTCATCGAGAAACAAACATCTGGGCGAATTGGAGTGTCAGTCTGGGATACACAAACGGACGAGCGTTGGGATTATCGCGGAGACGAACGTTTCCCATTAATGAGCACATTTAAAACGTTAGCGTGTGCCACCATGCTAAGCGACATGGACAGCGGCAAACTCAACAAAAATGCCACAGCGAAAATCGATGAACGCAATATTGTGGTTTGGTCTCCGGTGATGGATAAACTGGCTGGACAAAGTACACGTATCGAACACGCTTGTGAGGCCGCCATGTTGATGAGCGACAACACCGCCGCGAACTTAGTGCTAAATGAAATTGGTGGTCCTAAAGCGGTCACACTGTTTTTGCGCTCTATTGGCGACAAAGCAACGCGACTTGACCGATTGGAGCCCCGTTTGAATGAAGCAAAACCGGGCGACAAGCGAGACACCACAACGCCTAACGCCATGGTAAACACCCTACACACCTTGATGGAAGATAACGCCCTATCTTACGAGTCACGCACACAGCTGAAAATCTGGATGCAAGACAACAAAGTATCGGATTCTCTCATGCGCTCTGTTCTGCCAAAAGGCTGGTCGATTGCAGACCGCTCTGGCGCAGGTAACTACGGTTCACGCGGCATTAGCGCGATGATTTGGAAAGACAACTACAAGCCGGTTTACATCAGTATTTACGTCACAGACACTGACCTTTCGCTTCAAGCTCGCGATCAACTGATCGCGCAAATCAGCCAACTGATTTTAGAGCACTACAAAGAAAGTTAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39777","NCBI_taxonomy_name":"Vibrio parahaemolyticus UCM-V493","NCBI_taxonomy_id":"1429044"}}}},"ARO_accession":"3003186","ARO_id":"39763","ARO_name":"CARB-23","ARO_description":"Present in Lahey's list of beta-lactamases, not yet released","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"334":{"model_id":"334","model_name":"mexX","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"730"}},"model_sequences":{"sequence":{"244":{"protein_sequence":{"accession":"BAA34299.1","sequence":"MDRLAARLLAALVALFLLGCEEAADAGKTAEAPAEVGVIVARPAPIGITSELPGRLEAYRQAEVRARVAGIVTRRLYEEGQDVRAGTVLFQIDPAPLKAALDISRGALPGRGQPRAAADKLKAYADLIKDRAISEREYTEAQTDARQALAQIASAKAELEQARLRLGYATVTAPIDGRARRALVTEGALVGEDSPTPLTRVEQIDPIYVNFSQPAAKSRHAAGDPRRPGEGCRRQGHRRAPGPGRRQRVPLAGELLFIDLAVDPGTDTIAMRALFRNPHRELLPGGYVQVRLQRAVNPQAITVPDALIRTAQSAVVKVVNPKGLVEDVEVRADTLQGRDWIISRGLKGGEWVIVENAAQHAAGSSVQAVVRQPASADAPSPLAASPAGQ"},"dna_sequence":{"accession":"AB015853","fmin":"145","fmax":"1315","strand":"+","sequence":"ATGGACCGGCTCGCTGCGCGGCTGCTGGCGGCCCTGGTCGCCCTATTCCTGCTGGGCTGCGAAGAAGCAGCGGACGCCGGGAAGACTGCGGAGGCCCCCGCCGAGGTCGGCGTGATCGTCGCCAGGCCGGCGCCTATCGGCATCACCAGCGAGCTGCCCGGACGCCTGGAAGCGTACCGCCAGGCTGAAGTGCGGGCGCGCGTCGCCGGCATCGTCACCCGTCGCCTGTACGAGGAAGGCCAGGACGTCCGCGCCGGCACCGTGCTGTTCCAGATCGACCCTGCGCCCTTGAAGGCGGCCCTGGACATCAGCCGCGGCGCCCTGCCCGGCCGAGGCCAGCCACGCGCGGCGGCCGACAAGCTCAAGGCGTACGCCGACCTGATCAAGGACCGCGCCATCAGCGAACGCGAGTACACCGAAGCGCAGACCGACGCGCGCCAGGCCCTGGCGCAGATCGCCTCGGCCAAGGCCGAACTGGAGCAGGCCCGCCTGCGCCTGGGCTACGCCACGGTCACCGCGCCGATCGACGGCCGCGCGCGGCGTGCGCTGGTCACCGAAGGCGCGCTGGTCGGCGAGGACTCGCCGACACCGCTGACCCGCGTCGAGCAGATCGATCCGATCTACGTGAACTTCTCCCAGCCGGCCGCGAAGTCGCGCCATGCAGCGGGCGATCCGCGAAGGCCAGGTGAAGGGTGTCGCCGACAAGGACATCGCCGTGCGCCTGGTCCTGGCCGACGGCAGCGAGTACCGCTGGCCGGCGAGCTGCTGTTCATCGACCTGGCGGTCGACCCCGGCACCGACACCATCGCCATGCGTGCCCTGTTCCGCAATCCGCATCGCGAATTGCTGCCCGGCGGCTACGTGCAGGTGCGCCTGCAGCGCGCGGTGAACCCGCAGGCGATCACCGTCCCGGACGCGCTGATCCGTACCGCCCAGTCCGCCGTGGTCAAGGTGGTCAACCCAAAGGGCTTGGTGGAAGACGTGGAGGTCCGCGCCGACACCCTGCAGGGCCGCGACTGGATCATCAGCCGCGGGCTCAAGGGCGGCGAGTGGGTGATCGTCGAGAACGCCGCCCAGCATGCCGCCGGCTCCAGCGTCCAGGCGGTGGTCCGCCAGCCGGCCAGCGCCGACGCCCCCTCACCGCTGGCCGCCTCGCCGGCGGGCCAGTGAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3003034","ARO_id":"39468","ARO_name":"mexX","ARO_description":"MexX is the membrane fusion protein of the MexXY-OprM multidrug efflux complex.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavin","category_aro_description":"Acriflavin is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36193":{"category_aro_accession":"3000054","category_aro_cvterm_id":"36193","category_aro_name":"acridine dye","category_aro_description":"Acridine dyes are cell permeable, basic molecules with an acridine chromophore. These compounds intercalate DNA. The image shown represents the core structure of the acridine family, with specific dyes containing varying substituents.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"337":{"model_id":"337","model_name":"adeC","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"850"}},"model_sequences":{"sequence":{"3839":{"protein_sequence":{"accession":"ALX99516.1","sequence":"MSKSTIVSRGLILSTLSIALVACVNMQAPQPAITSHIPQNFSQNHSGKMIAEKSYKEFISDPKLLQVIEISLNNNRDLRTATLNIERVQQEYQITKNSQLPTIGVTGNAVRQVSPSINPNNPVSTFQVGLGMTAYELDFWGRVQNLKDAALNNYLATQSAKEAVQIGLISNITQVWLNYAFAQANLNLAEQTLKAQVDAYNLNKKRFDVGIDSEVPLKQAQISVETARNDVATYKTQIQQAKNLLDLLAGHPVPQNLLPDHAIQNITFEKNFAAGLPSDLLNHRPDLKAAEYELRVAGANIGAAKARMFPTISLTGSTGYASSELKDLFKTGNFAWSIGPNIDLPIFDWGTRKTNIKIAETDQKIALAKYEKAIQSAFREVNDALATHAHIGERLDAQRRLVSATAATYKLSMARYKAGVDSYFTVLDAQRSAYAAQQGLLALEQIKLNNQIEIYKVLGGGISKV"},"dna_sequence":{"accession":"CP013924.1","fmin":"2063742","fmax":"2065140","strand":"+","sequence":"ATGTCTAAATCGACAATCGTATCTCGTGGACTCATTCTTTCTACACTCTCAATTGCACTCGTTGCATGTGTCAATATGCAAGCGCCACAGCCTGCAATTACATCTCATATTCCTCAAAATTTTAGTCAAAATCATTCTGGAAAAATGATTGCAGAAAAAAGTTATAAAGAATTTATTTCTGATCCGAAATTATTACAGGTCATTGAAATCAGTTTAAATAACAACCGTGATTTACGGACTGCTACGCTTAATATTGAACGTGTACAGCAAGAATACCAAATCACAAAAAATAGCCAGCTCCCAACCATTGGTGTAACGGGAAATGCAGTGCGGCAGGTTAGCCCATCGATTAACCCCAATAACCCAGTTTCTACATTTCAAGTTGGCTTGGGAATGACTGCCTATGAGCTAGATTTTTGGGGCCGTGTTCAAAATTTAAAAGATGCTGCATTAAATAACTATCTTGCAACTCAAAGTGCAAAAGAAGCTGTACAAATTGGTTTAATCAGTAATATTACACAGGTCTGGTTAAATTATGCTTTTGCACAAGCAAATTTAAACCTTGCCGAGCAAACCTTAAAAGCACAAGTCGATGCTTATAACCTTAACAAGAAGCGCTTTGATGTTGGTATTGATAGTGAAGTGCCATTAAAACAAGCACAAATTTCGGTAGAGACTGCTCGAAATGATGTTGCAACTTATAAAACTCAAATTCAACAGGCAAAAAATTTACTGGATTTGTTAGCAGGTCATCCTGTTCCGCAAAATTTACTTCCGGATCATGCTATTCAAAATATTACCTTTGAGAAAAACTTTGCAGCCGGTTTACCAAGTGATTTATTAAATCATCGTCCAGACCTTAAAGCTGCCGAATATGAGTTACGTGTTGCAGGAGCAAATATTGGTGCTGCTAAAGCACGGATGTTCCCAACCATAAGCTTGACAGGCTCGACGGGTTATGCATCATCTGAACTGAAAGATTTATTTAAAACAGGCAATTTTGCATGGTCGATTGGACCTAATATCGATCTACCAATTTTTGATTGGGGAACAAGAAAAACTAATATTAAAATTGCGGAAACTGACCAGAAAATTGCTTTAGCTAAATATGAAAAAGCCATTCAATCAGCTTTTCGTGAAGTTAATGATGCACTTGCTACACATGCACATATTGGTGAACGATTAGACGCTCAGCGTCGCTTAGTCTCTGCGACTGCTGCAACCTATAAACTCTCAATGGCACGTTACAAAGCTGGAGTGGATAGTTATTTTACGGTTTTAGATGCTCAGCGTTCTGCTTATGCTGCACAACAAGGCTTACTTGCACTTGAACAAATAAAATTAAATAACCAAATTGAAATTTATAAAGTTTTAGGAGGAGGAATATCAAAAGTCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003811","ARO_id":"40499","ARO_name":"adeC","ARO_description":"AdeC is the outer membrane factor of the AdeABC multidrug efflux complex. It can be replaced by other outer membrane channels, and is not essential for antibiotic resistance.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"338":{"model_id":"338","model_name":"OXY-1-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2016":{"protein_sequence":{"accession":"CAI43413.1","sequence":"MLKSSWRKTALMAAAAVPLLLASGSLWASADAIQQKLADLEKRSGGRLGVALINTADDSQTLYRGDERFAMCSTGKVMAAAAVLKQSESNPEVVNKRLEIKKSDLVVWSPITEKHLQSGMTLAELSAAALQYSDNTAMNKMISYLGGPEKVTAFAQSIGDVTFRLDRTEPALNSAIPGDKRDTTTPLAMAESLRKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPASWVVGDKTGGGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKSRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"AJ871865","fmin":"0","fmax":"876","strand":"+","sequence":"ATGTTGAAAAGTTCGTGGCGTAAAACCGCCCTGATGGCCGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGTTCATTATGGGCCAGTGCCGATGCTATCCAGCAAAAGCTGGCTGATTTAGAAAAACGTTCCGGCGGTCGGCTGGGCGTAGCGCTGATTAACACGGCAGATGATTCGCAAACCCTCTATCGCGGCGATGAACGTTTTGCCATGTGCAGCACCGGTAAAGTGATGGCCGCCGCCGCGGTGTTAAAACAGAGCGAAAGCAATCCAGAGGTGGTGAATAAAAGGCTGGAGATTAAAAAATCGGATTTAGTGGTCTGGAGCCCGATCACCGAAAAACATCTGCAAAGCGGAATGACCCTGGCGGAACTCAGCGCGGCGGCGCTGCAGTACAGCGACAATACCGCGATGAATAAGATGATTAGCTACCTTGGCGGACCGGAAAAGGTGACCGCATTCGCCCAGAGTATCGGGGATGTCACTTTTCGTCTCGATCGTACGGAGCCGGCGCTGAACAGCGCGATTCCCGGCGATAAGCGCGATACCACCACCCCGTTGGCGATGGCCGAAAGCCTGCGCAAGCTGACGCTGGGCAATGCGCTGGGCGAACAGCAGCGCGCCCAGTTAGTAACGTGGCTAAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCAGGCCTGCCCGCAAGCTGGGTGGTCGGGGATAAAACCGGCGGCGGAGATTACGGCACCACCAACGATATCGCGGTGATCTGGCCCGAAAATCATGCCCCGCTGGTGCTGGTGACCTATTTTACCCAGCCGCAGCAGGATGCGAAAAGCCGCAAAGAGGTGTTAGCCGCGGCGGCAAAAATCGTCACCGAAGGGCTTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002390","ARO_id":"38790","ARO_name":"OXY-1-2","ARO_description":"OXY-1-2 is a beta-lactamase found in Klebsiella oxytoca","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"340":{"model_id":"340","model_name":"CMY-51","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"904":{"protein_sequence":{"accession":"AFK73431.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLNDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVQPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"JQ733571","fmin":"1027","fmax":"2173","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCGCTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGCATGGCCGTGGCAATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGTTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAACGACCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTACACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGCGGTGCAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACAGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATAGTGATGCTGGCAAACAAAAGCTATCCTAACCCGGCTCGCGTAGAGGCGGCCTGGCGCATTCTTGAAAAACTGCAATAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002062","ARO_id":"38462","ARO_name":"CMY-51","ARO_description":"CMY-51 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"341":{"model_id":"341","model_name":"IMP-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1594":{"protein_sequence":{"accession":"CAA11471.1","sequence":"MSKLSVFFIFLFCSIATAAESLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNESKKPSKPSN"},"dna_sequence":{"accession":"AJ223604","fmin":"1484","fmax":"2225","strand":"+","sequence":"ATGAGCAAGTTATCTGTATTCTTTATATTTTTGTTTTGCAGCATTGCTACCGCAGCAGAGTCTTTGCCAGATTTAAAAATTGAAAAGCTTGATGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGGTGGGGCGTTGTTCCTAAACATGGTTTGGTGGTTCTTGTAAATGCTGAGGCTTACCTAATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAGCGTGGCTATAAAATAAAAGGCAGCATTTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCGATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTGCTTAAAAAAGACGGTAAGGTTCAAGCCACAAATTCATTTAGCGGAGTTAACTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCGGGACACACTCCAGATAACGTAGTGGTTTGGTTGCCTGAAAGGAAAATATTATTCGGTGGTTGTTTTATTAAACCGTACGGTTTAGGCAATTTGGGTGACGCAAATATAGAAGCTTGGCCAAAGTCCGCCAAATTATTAAAGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAAGTCACAGTGAAGTTGGAGACGCATCACTCTTGAAACTTACATTAGAGCAGGCGGTTAAAGGGTTAAACGAAAGTAAAAAACCATCAAAACCAAGCAACTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002192","ARO_id":"38592","ARO_name":"IMP-1","ARO_description":"IMP-1 is a beta-lactamase found in Serratia marcescens","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"342":{"model_id":"342","model_name":"smeS","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"910"}},"model_sequences":{"sequence":{"4303":{"protein_sequence":{"accession":"AAD51347.1","sequence":"MAFAMAKFQLKFGLTAKTFLAIFTACLLVLAVNGIASRVAFQTGFLDYLNDQGDLRMQRLMPHLQREYREHGGWEHLHGDGDRWARLLRPDLAHGHEGPVPSLSDQTGVPSRLGLFDAQHRFVAGNPDATSDDEPHAVQVDGQTVGWLGMVPFQTVIATNDLNFYNTQVRAWWVIGIALLLVTVLLAWLVSRALRQRLAKLAAATHRLAAGDYATRIERTSDDELDALVNDFNRMAQALDDTERNRRAFIADISHELRTPLAVVRAELEAIEDGIRPLDRANLVGLQGEIRQLGKLIDDLHDLSMTQSGGLAYRFAPLDLVALLRSELNGMRVRFANAGLALEEDLPATPLQVSGDERRLQQVLANLLENALRYTHAGGRVRVQAARVPAGVQLVVEDTAPGVPPDKCALVFERFYRVESSRNRASGGSGLGLAISHNIILAHHGVIHAAPSPLGGLRVVITLPEPA"},"dna_sequence":{"accession":"AF173226","fmin":"1037","fmax":"2441","strand":"-","sequence":"TCATGCAGGCTCCGGCAGGGTGATGACCACGCGCAGCCCGCCCAGCGGCGAGGGCGCGGCGTGGATGACGCCGTGGTGGGCGAGGATGATGTTGTGGCTGATGGCCAGGCCCAGCCCGCTGCCGCCACTGGCGCGGTTGCGCGAACTTTCCACGCGGTAGAAGCGTTCGAACACCAGTGCACACTTGTCGGGCGGAACGCCCGGCGCGGTGTCTTCCACGACCAGCTGCACGCCGGCAGGCACGCGCGCCGCCTGCACGCGTACGCGGCCACCGGCATGGGTGTAGCGCAGTGCGTTTTCCAGCAGGTTGGCCAGCACCTGCTGCAGGCGCCGCTCGTCACCGGACACCTGCAACGGCGTGGCGGGCAGGTCTTCTTCCAACGCCAGGCCTGCATTGGCGAAGCGCACGCGCATGCCATTGAGTTCGCTGCGCAGCAGCGCCACCAGGTCCAGTGGCGCGAAGCGGTACGCCAGGCCGCCGGACTGGGTCATCGACAGGTCGTGCAGGTCGTCGATCAGCTTGCCCAGCTGGCGGATCTCGCCCTGCAGGCCCACCAGGTTGGCCCGGTCCAGCGGACGGATGCCATCTTCGATCGCCTCCAGCTCGGCCCGCACCACGGCCAATGGCGTGCGCAGCTCATGCGAGATGTCGGCAATGAAGGCGCGGCGGTTGCGTTCGGTATCGTCCAGCGCCTGCGCCATCCGGTTGAAGTCGTTGACCAGCGCGTCCAGCTCATCGTCACTGGTGCGCTCGATGCGGGTGGCGTAGTCACCGGCGGCCAACCGGTGGGTGGCAGCGGCCAGCTTGGCAAGGCGCTGGCGCAGCGCACGCGATACCAGCCAGGCCAGCAGTACCGTCACCAGCAGTAGCGCGATGCCGATCACCCACCAGGCGCGCACCTGGGTGTTGTAGAAATTCAGGTCGTTGGTGGCGATGACGGTCTGGAACGGCACCATGCCCAGCCAACCGACGGTCTGCCCGTCCACCTGCACCGCATGCGGCTCGTCATCGCTGGTGGCGTCGGGGTTGCCGGCCACGAAACGGTGCTGCGCGTCGAACAGGCCCAGGCGCGACGGCACGCCGGTCTGGTCGGACAGCGACGGCACCGGTCCTTCGTGCCCATGGGCCAGGTCCGGGCGCAGCAGCCGCGCCCAGCGGTCGCCATCACCGTGCAGATGCTCCCAGCCACCGTGCTCGCGGTACTCGCGCTGCAGGTGTGGCATCAGCCGCTGCATGCGCAGGTCGCCCTGGTCGTTGAGGTAGTCCAGGAAGCCGGTCTGGAAGGCCACGCGGCTGGCAATACCGTTCACTGCCAGCACCAGCAGGCAGGCGGTGAAGATCGCGAGGAAGGTCTTCGCGGTCAGGCCGAATTTGAGTTGGAACTTCGCCATCGCGAAGGCCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37076","NCBI_taxonomy_name":"Stenotrophomonas maltophilia","NCBI_taxonomy_id":"40324"}}}},"ARO_accession":"3003067","ARO_id":"39501","ARO_name":"smeS","ARO_description":"smeS is the protein kinase sensor component of a two component signal transduction system that includes smeR","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"343":{"model_id":"343","model_name":"OXA-31","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1211":{"protein_sequence":{"accession":"AAK52604.1","sequence":"MKNTIHINFAIFLIIANIIYSSASASTDISTVASPLFEGTEGCFLLYDVSTNAEIAQFNKAKCATQMPPDSTFKIALSLMAFDAEIIDQKTIFKWDKTPKGMEIWNSNHTPKTWMQFSVVWVSQEITQKIGLNKIKNYLKDFDYGNQDFSGDKERNNGLTEAWLESSLKISPEEQIQFLRKIINHNLPVKNSAIENTIENMYLQDLENSTKLYGKTGAGFTANRTLQNGWFEGFIISKSGHKYVFVSALTGNLGSNLTSSIKAKKNAITILNTLNL"},"dna_sequence":{"accession":"AF294653","fmin":"753","fmax":"1584","strand":"+","sequence":"ATGAAAAACACAATACATATCAACTTCGCTATTTTTTTAATAATTGCAAATATTATCTACAGCAGCGCCAGTGCATCAACAGATATCTCTACTGTTGCATCTCCATTATTTGAAGGAACTGAAGGTTGTTTTTTACTTTACGATGTATCCACAAACGCTGAAATTGCTCAATTCAATAAAGCAAAGTGTGCAACGCAAATGCCACCAGATTCAACTTTCAAGATCGCATTATCACTTATGGCATTTGATGCGGAAATAATAGATCAGAAAACCATATTCAAATGGGATAAAACCCCCAAAGGAATGGAGATCTGGAACAGCAATCATACACCAAAGACGTGGATGCAATTTTCTGTTGTTTGGGTTTCGCAAGAAATAACCCAAAAAATTGGATTAAATAAAATCAAGAATTATCTCAAAGATTTTGATTATGGAAATCAAGACTTCTCTGGAGATAAAGAAAGAAACAACGGATTAACAGAAGCATGGCTCGAAAGTAGCTTAAAAATTTCACCAGAAGAACAAATTCAATTCCTGCGTAAAATTATTAATCACAATCTCCCAGTTAAAAACTCAGCCATAGAAAACACCATAGAGAACATGTATCTACAAGATCTGGAGAATAGTACAAAACTGTATGGGAAAACTGGTGCAGGATTCACAGCAAATAGAACCTTACAAAACGGATGGTTTGAAGGGTTTATTATAAGCAAATCAGGACATAAATATGTTTTTGTGTCCGCACTTACAGGAAACTTGGGGTCGAATTTAACATCAAGCATAAAAGCCAAGAAAAATGCGATCACCATTCTAAACACACTAAATTTATAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001425","ARO_id":"37825","ARO_name":"OXA-31","ARO_description":"OXA-31 is a beta-lactamase found in P. aeruginosa","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"344":{"model_id":"344","model_name":"SHV-188","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"989":{"protein_sequence":{"accession":"CEA29751.1","sequence":"MVKRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELKLNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"LN515534","fmin":"0","fmax":"873","strand":"+","sequence":"GTGGTTAAGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGGATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3003155","ARO_id":"39732","ARO_name":"SHV-188","ARO_description":"From the Lahey list of beta-lactamases.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"345":{"model_id":"345","model_name":"bcrA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"570"}},"model_sequences":{"sequence":{"745":{"protein_sequence":{"accession":"AAA99504.1","sequence":"MSTIIKTTDLTKMYGSQKSVDHLNINVKQGDIYGFLGRNGAGKTTTIRMLLGLIKPTSGQIEIFGENFFKNKKEILRRIGSIVEVPGFYANLTARENLLINAKIIGIHKKNAIDEVLEIVGLQHETKKLVGKFSLGMKQRLGIARALLHYPELLILDEPTNGLDPIGIKEMRRLIHSLAKERNITIFISSHILSEIEQLVDHVGIIHEGKLLEEIPFDHLKKRNRKYLEFQLSDQNKAVVLMEQHFDIHDYEVHQDGIIRVYSHLGQQGKLNKLFVENGIDVLKITMSEDSLEDYFVKLIGGGTIG"},"dna_sequence":{"accession":"L20573","fmin":"297","fmax":"1218","strand":"+","sequence":"TTGAGCACAATTATTAAAACGACGGATCTCACGAAAATGTACGGGTCGCAAAAGTCTGTAGACCATCTCAATATCAATGTAAAACAAGGAGATATATACGGCTTTTTGGGACGGAACGGCGCCGGCAAAACGACGACGATCAGAATGCTGCTGGGTCTGATCAAACCGACCAGTGGGCAGATAGAAATTTTCGGAGAAAATTTTTTCAAGAATAAAAAAGAAATTTTAAGAAGAATCGGATCTATCGTGGAAGTGCCCGGCTTTTACGCGAACTTGACGGCGAGGGAAAACCTGCTGATCAATGCGAAAATCATAGGTATCCATAAAAAAAATGCGATCGATGAAGTATTGGAGATCGTGGGCCTGCAGCATGAAACGAAAAAGCTCGTCGGCAAGTTTTCCTTGGGCATGAAACAAAGGCTGGGAATTGCAAGAGCCTTGCTTCACTATCCGGAGCTGTTGATACTGGACGAGCCGACAAACGGCTTGGACCCGATCGGGATCAAAGAAATGAGAAGACTCATTCATTCTCTCGCCAAAGAAAGAAACATCACCATCTTTATATCAAGCCACATTTTGTCTGAAATCGAACAGCTCGTCGATCATGTCGGGATCATTCATGAAGGAAAACTGCTTGAAGAAATTCCGTTTGACCATCTTAAAAAAAGAAACCGCAAATATCTGGAATTTCAATTATCCGATCAAAATAAAGCGGTCGTTCTGATGGAACAGCATTTTGATATTCATGACTACGAAGTTCACCAGGACGGGATCATCCGGGTATACTCCCATTTGGGCCAGCAGGGAAAGCTCAATAAATTGTTTGTCGAAAACGGAATAGACGTATTGAAGATTACGATGAGCGAAGACAGTCTTGAAGACTACTTCGTGAAGTTGATAGGGGGCGGGACGATTGGCTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36834","NCBI_taxonomy_name":"Bacillus licheniformis","NCBI_taxonomy_id":"1402"}}}},"ARO_accession":"3002987","ARO_id":"39421","ARO_name":"bcrA","ARO_description":"bcrA is an ABC transporter found in Bacillus licheniformis that confers bacitracin resistance","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"36973":{"category_aro_accession":"3000629","category_aro_cvterm_id":"36973","category_aro_name":"bacitracin A","category_aro_description":"Bacitracin A is the primary component of bacitracin. It contains many uncommon amino acids and interferes with bacterial cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36974":{"category_aro_accession":"3000630","category_aro_cvterm_id":"36974","category_aro_name":"bacitracin B","category_aro_description":"Bacitracin B is a component of bacitracin, an antibiotic mixture that interferes with bacterial cell wall synthesis. It differs from Bacitracin A with a valine instead of an isoleucine in its peptide.","category_aro_class_name":"Antibiotic"},"36975":{"category_aro_accession":"3000631","category_aro_cvterm_id":"36975","category_aro_name":"bacitracin F","category_aro_description":"Bacitracin F is a component of bacitracin, an antibiotic mixture that interferes with bacterial cell wall synthesis. It is formed when the thiazoline ring of bacitracin A is oxidatively deaminated.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"346":{"model_id":"346","model_name":"QnrB23","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"720":{"protein_sequence":{"accession":"ACS71747.1","sequence":"MTPLLYKKTGTNMALALVGEKIDRNRFTGEKIENSTFFYCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNASALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAIIG"},"dna_sequence":{"accession":"FJ981622","fmin":"0","fmax":"681","strand":"+","sequence":"ATGACGCCATTACTGTATAAAAAAACAGGTACAAATATGGCTCTGGCACTCGTTGGCGAAAAAATTGACAGAAACCGCTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTTACTGTGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCGATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATGCCAGTGCGCTTGGCATTGAAATTCGCCACTGTCGTGCGCAAGGCGCAGATTTCCGCGGCGCAAGCTTTATGAATATGATCACTACTCGCACCTGGTTTTGCAGCGCATATATCACTAACACAAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGCTGGAAAAGTGTGAGCTGTGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGGGACTTAGATATTCGGGGCGTTGATTTACAAGGCGTTAAGTTGGACAACTACCAGGCATCGTTGCTCATGGAACGTCTTGGCATCGCGATTATTGGCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002738","ARO_id":"39172","ARO_name":"QnrB23","ARO_description":"QnrB23 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"348":{"model_id":"348","model_name":"OXY-3-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1848":{"protein_sequence":{"accession":"AAN28732.1","sequence":"MIKTSWRKSALIAAALPLLLCSSSLWANAIQQKLADLEKSTGGRLGVALIDTTDNSQILYRGDERFAMCSTGKVMAAAAVLKQSESNKDVVNKRLEIKASDLVVWSPVTEKHLQSGMTLAELSAAALQYSDNTAMNKMIGYLGGPEKVTAFARSIGDVTFRLDRTEPALNTAIPGDERDTTTPLAMAESLHKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPASWVVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPLQDAKSRKDVLAAAAKIVTEGL"},"dna_sequence":{"accession":"AF491278","fmin":"183","fmax":"1050","strand":"+","sequence":"ATGATTAAAACTTCGTGGCGTAAAAGCGCCCTGATTGCCGCCGCCCTGCCTTTATTGCTCTGTAGCAGTTCATTATGGGCCAATGCTATTCAGCAGAAGCTGGCCGATTTGGAAAAAAGTACCGGCGGGCGACTGGGCGTCGCGCTGATTGACACCACAGATAACTCTCAAATTCTATATCGCGGTGACGAGCGTTTTGCTATGTGCAGTACCGGTAAAGTGATGGCTGCCGCCGCGGTGTTAAAACAGAGCGAAAGCAATAAAGATGTGGTGAATAAAAGGCTGGAGATTAAAGCATCGGATCTGGTGGTCTGGAGCCCGGTGACTGAAAAACATCTGCAGAGCGGAATGACGTTGGCGGAATTAAGCGCCGCCGCGCTGCAATATAGCGACAATACCGCGATGAATAAGATGATTGGTTATCTTGGCGGACCGGAAAAAGTGACCGCCTTCGCCCGCAGTATCGGCGATGTCACTTTTCGTCTCGATCGTACGGAGCCTGCACTAAACACCGCGATCCCGGGTGACGAACGCGATACCACCACGCCGCTGGCGATGGCCGAAAGCCTGCACAAGCTGACGCTGGGTAATGCGCTGGGTGAACAACAGCGCGCACAGTTAGTGACATGGTTGAAAGGCAACACCACCGGCGGGCAGAGTATTCGTGCGGGGCTGCCTGCAAGCTGGGTCGTGGGAGATAAAACCGGAGCTGGTGATTACGGCACCACCAATGATATCGCCGTTATCTGGCCGGAAAATCATGCTCCGCTGGTATTAGTCACTTATTTCACCCAACCGCTGCAGGATGCGAAAAGCCGCAAAGATGTGCTAGCCGCAGCGGCAAAAATCGTGACCGAAGGGCTTTAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002409","ARO_id":"38809","ARO_name":"OXY-3-1","ARO_description":"OXY-3-1 is a beta-lactamase found in Klebsiella oxytoca","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"349":{"model_id":"349","model_name":"vanL","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"650"}},"model_sequences":{"sequence":{"612":{"protein_sequence":{"accession":"ABX54687.1","sequence":"MMKLKKIAIIFGGQSSEYEVSLKSTVSVLETLSTCNFEIIKIGIDLGGKWYLTTSNNKDIEYDVWQTDPSLQEIIPCFNNRGFYNKTTNKYFRPDVLFPILHGGTGEDGTLQGVFELMNIPYVGCGVTPSAICMDKYLLHEFAQSVGVKSAPTLIIRTRNCKDEIDKFIEKNDFPIFVKPNEAGSSKGINKVNEPDKLEDALTEAFKYSKSVIIQKAIIGREIGCAVLGNEKLLVGECDEVSLNSDFFDYTEKYQMISAKVNIPASISVEFSNEMKKQAQLLYRLLGCSGLARIDFFLSDNNEILLNEINTLPGFTEHSRYPKMMEAVGVTYKEIITKLINLAEEKYYG"},"dna_sequence":{"accession":"EU250284","fmin":"954","fmax":"2004","strand":"+","sequence":"ATGATGAAATTGAAAAAGATAGCCATAATATTCGGAGGTCAATCTTCGGAATATGAAGTCTCACTTAAATCAACAGTAAGTGTACTAGAAACTCTATCAACTTGTAATTTTGAAATTATAAAAATAGGAATTGATTTAGGCGGAAAGTGGTATCTCACCACAAGCAACAACAAAGATATTGAATATGATGTTTGGCAAACTGATCCTTCATTACAAGAAATAATCCCATGTTTCAATAATCGAGGCTTTTATAACAAAACTACAAATAAATATTTCAGACCAGATGTACTCTTTCCAATTCTTCATGGGGGGACTGGAGAAGATGGAACCCTCCAAGGTGTATTTGAATTAATGAATATTCCTTACGTTGGATGTGGGGTGACGCCTTCGGCTATTTGTATGGACAAATACTTATTGCATGAGTTTGCTCAGAGTGTGGGTGTAAAAAGTGCCCCTACGCTCATAATTCGCACTAGAAACTGCAAAGATGAAATTGACAAGTTCATAGAAAAAAATGACTTCCCTATTTTTGTAAAGCCTAACGAAGCGGGCTCATCAAAAGGAATAAACAAAGTAAATGAGCCAGATAAGCTAGAGGATGCTTTAACAGAAGCGTTTAAGTATAGTAAAAGTGTTATCATTCAGAAAGCTATAATTGGAAGAGAAATTGGCTGTGCTGTCTTAGGTAATGAAAAACTCCTAGTAGGAGAATGTGATGAAGTTTCCCTTAATAGCGATTTTTTTGATTATACCGAGAAATACCAAATGATCTCAGCAAAGGTAAATATACCTGCTTCTATATCTGTAGAATTTTCTAATGAAATGAAGAAACAAGCTCAGCTGTTATATAGGTTACTAGGCTGTTCAGGACTAGCACGAATTGATTTCTTCTTATCAGATAATAACGAAATACTATTAAACGAAATTAATACTTTGCCTGGTTTTACTGAGCATTCCAGATATCCCAAAATGATGGAAGCTGTAGGTGTTACCTATAAAGAGATTATCACGAAGTTAATCAATTTAGCGGAGGAAAAATATTATGGATAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3002910","ARO_id":"39344","ARO_name":"vanL","ARO_description":"VanL is a D-Ala-D-Ala ligase homolog that can synthesize D-Ala-D-Ser, an alternative substrate for peptidoglycan synthesis that reduces vancomycin binding affinity in Enterococcus faecalis","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"39340":{"category_aro_accession":"3002906","category_aro_cvterm_id":"39340","category_aro_name":"van ligase","category_aro_description":"van ligases synthesize alternative substrates for peptidoglycan synthesis that reduce vancomycin binding affinity.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"350":{"model_id":"350","model_name":"ykkD","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"180"}},"model_sequences":{"sequence":{"536":{"protein_sequence":{"accession":"CAB13167.1","sequence":"MLHWISLLCAGCLEMAGVALMNQYAKEKSVKWVLLIIVGFAASFSLLSYAMETTPMGTAYAVWTGIGTAGGALIGILFYKEQKDAKRIFFIALILCSAVGLKILS"},"dna_sequence":{"accession":"AL009126","fmin":"1376854","fmax":"1377172","strand":"+","sequence":"ATGCTGCACTGGATCAGTTTATTGTGCGCGGGCTGTTTAGAAATGGCCGGCGTGGCCCTTATGAATCAATATGCGAAAGAAAAAAGCGTGAAATGGGTGCTGTTGATCATTGTTGGTTTTGCCGCTTCATTTTCCTTGCTGTCGTACGCAATGGAAACCACTCCGATGGGAACGGCTTACGCGGTCTGGACAGGAATTGGCACCGCCGGCGGGGCGCTTATCGGCATCCTCTTTTACAAGGAGCAGAAAGACGCCAAACGGATCTTCTTTATCGCGTTGATTTTATGCTCAGCAGTTGGTTTAAAAATTCTGTCATAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39579","NCBI_taxonomy_name":"Bacillus subtilis subsp. subtilis str. 168","NCBI_taxonomy_id":"224308"}}}},"ARO_accession":"3003064","ARO_id":"39498","ARO_name":"ykkD","ARO_description":"ykkD is an SMR-type protein that is a subunit of the ykkCD efflux pump","ARO_category":{"36004":{"category_aro_accession":"0010003","category_aro_cvterm_id":"36004","category_aro_name":"small multidrug resistance (SMR) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Small multidrug resistance (SMR) proteins are a relatively small family of transporters, restricted to prokaryotic cells. They are also the smallest multidrug transporters, with only four transmembrane alpha-helices and no significant extramembrane domain.","category_aro_class_name":"AMR Gene Family"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"351":{"model_id":"351","model_name":"SHV-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1875":{"protein_sequence":{"accession":"CAA71948.1","sequence":"MLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARATTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERN"},"dna_sequence":{"accession":"Y11069","fmin":"0","fmax":"780","strand":"+","sequence":"CTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGCCACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001065","ARO_id":"37445","ARO_name":"SHV-6","ARO_description":"SHV-6 is an extended-spectrum beta-lactamase that has been found in clinical isolates.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"352":{"model_id":"352","model_name":"PDC-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"1696":{"protein_sequence":{"accession":"ACQ82810.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"FJ666068","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTATGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002502","ARO_id":"38902","ARO_name":"PDC-5","ARO_description":"PDC-5 is a extended-spectrum beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"353":{"model_id":"353","model_name":"QnrB2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"531":{"protein_sequence":{"accession":"ABO93588.1","sequence":"MALALVGEKINRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNASALGIEISHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRRVDLQGVKLDNYQASLLMERLGIAIIG"},"dna_sequence":{"accession":"EF488762","fmin":"0","fmax":"645","strand":"+","sequence":"ATGGCTCTGGCACTCGTTGGCGAAAAAATTAACAGAAACCGCTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCGATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATGCCAGTGCGCTTGGCATTGAAATTAGCCACTGTCGTGCGCAAGGCGCAGATTTTCGCGGCGCAAGTTTTATGAATATGATCACTACTCGCACCTGGTTTTGCAGTGCATATATCACTAACACAAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAGCTGTGGGAAAACCGTTGGATGGGGGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTGACTTAGATATTCGGCGCGTTGATTTACAAGGCGTTAAGTTGGACAACTACCAGGCATCGTTGCTCATGGAACGTCTTGGCATCGCGATTATTGGCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3002715","ARO_id":"39149","ARO_name":"QnrB2","ARO_description":"QnrB2 is a plasmid-mediated quinolone resistance protein found in Citrobacter koseri","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"354":{"model_id":"354","model_name":"QnrB24","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"756":{"protein_sequence":{"accession":"ADI46626.1","sequence":"MTPLLYKKTGTNMALALVGEKIDRNRFTGEKIENSTFFNCDFSGADMSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMVDFRNASALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"HM192542","fmin":"0","fmax":"681","strand":"+","sequence":"ATGACGCCATTACTGTATAAAAAAACAGGTACAAATATGGCACTGGCACTCGTTGGCGAAAAAATTGACAGAAACCGCTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACATGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCGATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGTGGATTTTCGCAATGCCAGTGCGCTTGGCATTGAAATTCGCCACTGTCGTGCGCAAGGCGCAGATTTCCGCGGCGCAAGCTTTATGAATATGATCACTACTCGCACCTGGTTTTGCAGCGCATATATCACTAACACAAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGCTGGAAAAATGTGAGCTGTGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTTTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTGACTTAGATATTCGGGGCGTTGATTTACAAGGCGTTAAGTTGGACAACTACCAGGCATCGTTGCTCATGGAACGTCTTGGCATCGCGGTGATTGGCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002739","ARO_id":"39173","ARO_name":"QnrB24","ARO_description":"QnrB24 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"355":{"model_id":"355","model_name":"TEM-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1951":{"protein_sequence":{"accession":"CAD09800.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AL513383","fmin":"161910","fmax":"162771","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35776","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhi str. CT18","NCBI_taxonomy_id":"220341"}}}},"ARO_accession":"3000873","ARO_id":"37253","ARO_name":"TEM-1","ARO_description":"TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"356":{"model_id":"356","model_name":"ErmU","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"455":{"protein_sequence":{"accession":"CAA44667.1","sequence":"MPSRYGSRQDLGQNFLVDPDIIKLIRRAPNERKVPSLIWRRRGHVTLPLSRLGRPVTAVELDPRRVKRLSARAPENVKVVGEDILRFRLPTVPHTVVGNIPFHVTTATMRRILVAPAWVSAVLVVQWEVARRRAGIGGCSLVTAESWPWFDFSVLKRVPRFAFRPAPSVDGGILVIERRPEPLVRERREYQAFVRQVFTGRGHGLREILQRIGRVQDSDLSAWFRAHGVSPQALPKDLTAEQWASLWGMARGGRSVPRTRRPRGLPPRTSRGPRRNSG"},"dna_sequence":{"accession":"X62867","fmin":"360","fmax":"1197","strand":"+","sequence":"GTGCCCAGCCGGTACGGCAGCCGGCAGGACCTCGGTCAGAACTTCCTCGTCGACCCCGACATCATCAAGCTGATCCGCCGAGCGCCGAACGAGCGGAAGGTCCCATCGTTGATCTGGCGCCGGAGAGGGCACGTGACGCTGCCCTTGAGTCGCTTGGGCCGCCCGGTCACCGCGGTTGAGCTCGACCCCCGCCGGGTCAAACGGCTCTCGGCGCGTGCCCCGGAAAACGTCAAGGTCGTCGGCGAGGACATCCTGCGCTTCCGGCTCCCGACCGTTCCGCACACCGTCGTGGGGAACATCCCCTTCCATGTCACGACGGCCACGATGCGCCGGATCCTCGTGGCTCCCGCATGGGTGTCGGCCGTCCTCGTGGTGCAGTGGGAAGTGGCGCGCCGCCGGGCCGGCATCGGCGGCTGCTCGCTGGTCACGGCGGAGTCCTGGCCGTGGTTCGACTTCTCGGTGCTCAAGCGGGTGCCGAGGTTCGCCTTCCGGCCCGCGCCCTCCGTGGACGGCGGGATCCTCGTCATCGAGCGGCGGCCCGAGCCACTGGTGCGGGAGCGCAGGGAGTACCAGGCATTCGTCAGACAGGTCTTCACCGGGCGCGGTCACGGGCTGCGGGAGATCCTCCAACGCATCGGGCGGGTCCAGGACAGCGACCTGTCCGCGTGGTTCAGGGCACATGGAGTCTCGCCGCAGGCGCTGCCGAAGGACCTCACCGCCGAGCAGTGGGCGTCGCTCTGGGGCATGGCGCGTGGCGGCCGGTCCGTGCCGCGGACGCGGCGACCCCGGGGCCTGCCGCCCCGCACGTCCCGCGGGCCGCGGCGCAACAGCGGCTGAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36862","NCBI_taxonomy_name":"Streptomyces lincolnensis","NCBI_taxonomy_id":"1915"}}}},"ARO_accession":"3001305","ARO_id":"37704","ARO_name":"ErmU","ARO_description":"ErmU is a methyltransferase found in the lincomycin producer Streptomyces lincolnensis. Like other Erm enzymes, it catalyzes the methylation of A2058 of the 23S ribosomal RNA. Specifically, this enzyme transfers only one methyl group. The gene is found in the lincomycin biosynthetic cluster and is responsible for self-resistance.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"357":{"model_id":"357","model_name":"VIM-38","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1730":{"protein_sequence":{"accession":"AGE83081.2","sequence":"MLKVISSLLVYLTASVMAVASPLAHSGEPSGEYPTVNEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRKAGVATYASPSTRRLAEAEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSANVLYGGCAVLALSRTSAGNVADADLAEWPTSVERIQKHYPEAEVVIPGHGLPGGLDLLQHTANVVTAHKNRSVVE"},"dna_sequence":{"accession":"KC469971","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTATTTGACCGCGTCTGTCATGGCTGTAGCTAGTCCGTTAGCCCATTCCGGGGAGCCGAGTGGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGAGAGGTCCGGCTTTACCAGATTGCTGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCGGTCTACCCATCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCCCTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCCGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGAAGGCTGGAGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGCAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGCTCTTCTATCCCGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAACGTGCTATACGGTGGTTGTGCCGTTCTTGCGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCGTTGAGCGGATTCAAAAACACTACCCGGAAGCAGAGGTCGTCATTCCCGGGCACGGTCTACCGGGCGGTCTAGACTTGCTCCAGCACACAGCGAACGTTGTCACAGCACACAAAAATCGCTCAGTCGTTGAGTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002308","ARO_id":"38708","ARO_name":"VIM-38","ARO_description":"VIM-38 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"358":{"model_id":"358","model_name":"QnrB42","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"35":{"protein_sequence":{"accession":"AEQ94272.1","sequence":"MALVLVGEKIDRNCFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNSSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWIGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAIIG"},"dna_sequence":{"accession":"JN680743","fmin":"0","fmax":"645","strand":"+","sequence":"ATGGCTCTGGTATTAGTTGGCGAAAAAATTGACAGAAACTGTTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCGATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATTCCAGTGCGCTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGCGCAAGCTTTATGAATATGATCACCACGCGCACCTGGTTTTGTAGCGCATATATCACGAATACCAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAGCTGTGGGAAAACCGTTGGATAGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTGACTTAGATATTCGGGGCGTTGATTTACAAGGCGTTAAGTTGGACAACTACCAGGCATCGTTGCTCATGGAGCGACTTGGCATCGCTATTATTGGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002757","ARO_id":"39191","ARO_name":"QnrB42","ARO_description":"QnrB42 is a plasmid-mediated quinolone resistance protein found in Klebsiella pneumoniae","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"359":{"model_id":"359","model_name":"TEM-112","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1719":{"protein_sequence":{"accession":"AAS89982.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLRNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AY589493","fmin":"166","fmax":"1027","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCGCAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000975","ARO_id":"37355","ARO_name":"TEM-112","ARO_description":"TEM-112 is an extended-spectrum beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"360":{"model_id":"360","model_name":"AAC(6')-Iy","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"397":{"protein_sequence":{"accession":"AAF03531.1","sequence":"MDIRQMNKTHLEHWRGLRKQLWPGHPDDAHLADGEEILQADHLASFIAMADGVAIGFADASIRHDYVNGCDSSPVVFLEGIFVLPSFRQRGVAKQLIAAVQRWGTNKGCREMASDTSPENTISQKVHQALGFEETERVIFYRKRC"},"dna_sequence":{"accession":"AF144880","fmin":"3541","fmax":"3979","strand":"+","sequence":"ATGGACATCAGGCAAATGAACAAAACCCATCTGGAGCACTGGCGCGGATTGCGAAAACAGCTCTGGCCTGGTCACCCGGATGACGCCCATCTGGCGGACGGCGAAGAAATTCTGCAAGCCGATCATCTGGCATCATTTATTGCGATGGCAGACGGGGTGGCGATTGGCTTTGCGGATGCCTCAATCCGCCACGATTATGTCAATGGCTGTGACAGTTCGCCCGTGGTTTTCCTTGAAGGTATTTTTGTTCTCCCCTCATTCCGTCAACGCGGCGTAGCGAAACAATTGATTGCAGCGGTGCAACGATGGGGAACGAATAAAGGGTGTCGGGAAATGGCCTCCGATACCTCGCCGGAAAATACAATTTCCCAGAAAGTTCATCAGGCGTTAGGATTTGAGGAAACAGAGCGCGTCATTTTCTACCGAAAGCGTTGTTGAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35750","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Enteritidis","NCBI_taxonomy_id":"149539"}}}},"ARO_accession":"3002569","ARO_id":"38969","ARO_name":"AAC(6')-Iy","ARO_description":"AAC(6')-Iy is a chromosomal-encoded aminoglycoside acetyltransferase in S. enteritidis and S. enterica. Regulatory mutation required to increase expression of this chromosomally-encoded gene for resistance. In the specific system, aminoglycoside resistance was due to a transcriptional fusion secondary to a chromosomal deletion in which the downstream aac(6')-Iy gene was placed under the control of the upstream nmpC promoter.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"361":{"model_id":"361","model_name":"OXA-278","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"806":{"protein_sequence":{"accession":"AGI65307.1","sequence":"MKILILWPLLSYLSLTACSFPVSNSPSQITSTQSIQAIAKLFDQAQSSGVLVIQRGPHLQVYGNDLSRAHTEYVPASTFKIFNALIGLQHGKATTNEIFKWDGKKRSFAAWEKDMTLGQAMQASAVPVYQELARRIGLELMEQEVRRIQFGNQHIGQQVDNFWLVGPLKITPKQEVEFVSALAQEQLAFDPQVQQQVKAMLLLQEQQAYRLYAKSGWGMDVEPQVGWLTGWVETPQAEIVAFSLNMQMQSNMDPAIRLKILQQALAELGLYPKAEG"},"dna_sequence":{"accession":"KC771279","fmin":"0","fmax":"831","strand":"+","sequence":"ATGAAAATTCTTATTTTGTGGCCTTTACTCAGTTACTTGAGCCTGACAGCCTGTAGCTTCCCTGTTTCAAATTCGCCCTCTCAAATCACTTCAACTCAATCTATTCAAGCTATTGCAAAGTTATTTGATCAGGCACAAAGCTCTGGCGTTTTAGTAATTCAACGGGGTCCACATCTACAGGTCTATGGCAATGATTTGAGTCGTGCACATACCGAATATGTTCCTGCTTCAACCTTTAAAATATTTAATGCTCTGATTGGCCTGCAACATGGTAAAGCCACGACCAATGAAATCTTTAAATGGGATGGCAAGAAGCGCAGTTTTGCAGCCTGGGAAAAAGACATGACTCTCGGCCAAGCCATGCAAGCTTCTGCTGTACCCGTCTATCAGGAACTAGCACGTCGCATTGGCCTTGAATTGATGGAACAGGAAGTGAGACGTATTCAATTCGGCAATCAACATATTGGGCAGCAGGTCGATAACTTCTGGTTGGTAGGCCCTTTGAAAATCACTCCAAAACAGGAAGTCGAATTTGTCTCTGCGCTTGCTCAAGAGCAGCTTGCCTTTGATCCTCAAGTCCAGCAACAAGTCAAAGCCATGTTACTTTTACAGGAACAGCAAGCTTATCGCCTATATGCCAAATCCGGTTGGGGCATGGATGTGGAACCGCAAGTCGGCTGGCTCACCGGCTGGGTTGAAACACCGCAGGCTGAAATCGTGGCATTTTCACTGAATATGCAGATGCAAAGTAATATGGATCCGGCGATCCGTCTTAAAATTTTGCAGCAGGCCTTGGCCGAATTAGGGCTTTATCCGAAAGCTGAAGGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39096","NCBI_taxonomy_name":"Acinetobacter schindleri","NCBI_taxonomy_id":"108981"}}}},"ARO_accession":"3001681","ARO_id":"38081","ARO_name":"OXA-278","ARO_description":"OXA-278 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"362":{"model_id":"362","model_name":"CTX-M-151","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1511":{"protein_sequence":{"accession":"BAP34782.1","sequence":"MINKRLSIALALAAMIGTPVAMALESQKPGSDSANHIQHQMVQQLSALEKSANGRLGVAVIDTGSGAIAGWRMDEPFPMCSTSKVMAVAALLKQSEQTPELMSQPQPVASGDLVNYNPITERFVGKSMTFDELSAATLQYSDNAAMNLILAKLGGPQKVTAFARSIGDDKFRLDRNEPSLNTAIPGDLRDTSTPRAMALSLQKLALGDALGQVQREKLSHWLRGNTTGAASIRAGLPSGWSVGDKTGSGDYGTTNDIAVVWPTGRPPLVIVTYFTQPQQQAESQRPVLAKAAAIVASHYVLPKG"},"dna_sequence":{"accession":"AB916359","fmin":"793","fmax":"1708","strand":"+","sequence":"ATGATCAATAAACGGCTGAGTATTGCTCTGGCGCTGGCGGCCATGATAGGTACGCCTGTGGCGATGGCCCTCGAGAGCCAGAAGCCGGGGAGCGATTCTGCTAATCATATTCAGCACCAGATGGTGCAACAGCTGTCGGCGCTGGAGAAAAGCGCTAACGGGCGGCTTGGCGTAGCGGTTATCGATACCGGCAGCGGCGCAATTGCGGGCTGGCGGATGGATGAACCTTTCCCCATGTGCAGTACCAGTAAAGTGATGGCGGTAGCGGCGCTGCTGAAACAGAGCGAACAGACTCCTGAACTTATGAGTCAGCCTCAGCCGGTAGCGAGCGGAGATCTGGTGAACTACAACCCGATAACTGAACGTTTTGTGGGTAAGAGCATGACGTTTGATGAGCTAAGCGCCGCAACGCTGCAATATAGCGATAACGCCGCAATGAACCTGATTCTGGCCAAACTGGGTGGGCCGCAAAAAGTAACGGCGTTTGCCCGCAGTATTGGCGATGATAAATTCCGGCTCGACCGCAATGAACCTTCGCTAAATACCGCCATTCCCGGCGATCTTCGGGATACCAGCACTCCACGAGCTATGGCCTTAAGCCTGCAAAAGCTGGCGCTGGGGGATGCTTTAGGCCAGGTTCAGCGCGAGAAACTTAGCCACTGGTTGCGCGGCAATACCACCGGTGCGGCCAGCATTCGGGCCGGGCTGCCATCGGGATGGAGCGTTGGGGATAAGACCGGCAGCGGTGATTACGGCACAACCAACGATATTGCCGTGGTATGGCCGACCGGCAGACCGCCGCTGGTTATTGTGACTTACTTTACTCAGCCGCAGCAGCAGGCAGAAAGCCAGCGGCCGGTGCTGGCGAAAGCGGCTGCTATCGTTGCCAGCCATTATGTATTGCCTAAAGGCTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35672","NCBI_taxonomy_name":"Salmonella enterica","NCBI_taxonomy_id":"28901"}}}},"ARO_accession":"3002008","ARO_id":"38408","ARO_name":"CTX-M-151","ARO_description":"CTX-M-151 is a beta-lactamase. From the Lahey list of CTX-M beta-lactamases.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"363":{"model_id":"363","model_name":"TEM-155","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1323":{"protein_sequence":{"accession":"ABG77582.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGKRGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"DQ679961","fmin":"114","fmax":"975","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTAAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3001021","ARO_id":"37401","ARO_name":"TEM-155","ARO_description":"TEM-155 is an extended-spectrum beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"364":{"model_id":"364","model_name":"CMY-83","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"959":{"protein_sequence":{"accession":"AFU25638.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYQGKPYYFTWGKADIANNRPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTHYWPELTGKQWQGISLLHLATYTAGGLPLQVPDDVTDKAALLRFYQNWQPQWAPGAKRLYANSSIGLFGALAVNPSGMSYEEAMTKRVLRPLKLAHTWITVPQSEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMTRWVQANMDASQVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPVKADSIISGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"JX440351","fmin":"1026","fmax":"2172","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCGCTGCTGCTGACAGCTTCGTTCTCCACGTTTGCCGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCGCTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCGATTATCTATCAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCGTCCAGTCACTCAACAAACGCTGTTTGAACTCGGATCGGTCAGTAAAACGTTCAACGGCGTGCTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGCATTACTGGCCTGAACTGACTGGTAAGCAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTACACGGCAGGCGGCCTGCCGCTTCAGGTTCCGGACGACGTTACGGATAAAGCCGCGTTACTACGCTTTTATCAAAACTGGCAGCCGCAATGGGCCCCAGGCGCTAAACGTCTTTATGCTAACTCCAGCATTGGTCTGTTTGGCGCCCTGGCGGTGAACCCCTCAGGCATGAGCTACGAAGAGGCGATGACCAAACGCGTCCTGCGCCCCTTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAGCGAACAAAAAGATTATGCCTGGGGTTATCGCGAAGGAAAGCCAGTGCATGTATCCCCTGGGCAACTTGATGCCGAAGCCTACGGGGTGAAATCGAGCGTTATCGATATGACCCGTTGGGTTCAGGCCAACATGGACGCCAGCCAGGTTCAGGAGAAAACGCTCCAGCAGGGCATCGAGCTTGCGCAGTCACGTTACTGGCGTATTGGCGATATGTACCAGGGCCTGGGCTGGGAGATGCTGAACTGGCCGGTGAAGGCCGACTCGATAATTAGCGGTAGCGACAGCAAAGTGGCCCTGGCAGCGCTTCCTGCCGTTGAGGTAAACCCGCCCGCGCCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGCGGATTCGGCAGCTACGTTGCTTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAGAGCTACCCAAACCCTGTTCGCGTCGAAGCCGCCTGGCGCATTCTTGAAAAACTGCAGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39584","NCBI_taxonomy_name":"Citrobacter braakii","NCBI_taxonomy_id":"57706"}}}},"ARO_accession":"3002096","ARO_id":"38496","ARO_name":"CMY-83","ARO_description":"CMY-83 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"365":{"model_id":"365","model_name":"TEM-122","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1241":{"protein_sequence":{"accession":"AAQ98890.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDEQNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AY307100","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACAAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000984","ARO_id":"37364","ARO_name":"TEM-122","ARO_description":"TEM-122 is an inhibitor-resistant beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"367":{"model_id":"367","model_name":"CTX-M-25","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1551":{"protein_sequence":{"accession":"AAM70498.1","sequence":"MMRKSVRRAMLMTTACVSLLLASVPLCAQANDVQQKLAALEKSSGGRLGVALINTADNTQTLYRADERFAMCSTSKVMAVAAVLKQSETQKGLLSQRVEIKPSDLINYNPIAEKHVNGTMTFGELSAAALQYSDNTAMNKLIAHLGGPDKVTAFARTIGDDTFRLDRTEPTLNTAIPGDPRDTTTPLAMAQALRNLTLGNALGDTQRAQLVMWLKGNTTGAASIQAGLPTSWVVGDKTGSGGYGTTNDIAVIWPEGRAPLVLVTYFTQSEPKAESRRDVLAAAARIVTDGY"},"dna_sequence":{"accession":"AF518567","fmin":"2320","fmax":"3196","strand":"+","sequence":"ATGATGAGAAAAAGCGTAAGGCGGGCGATGTTAATGACGACAGCCTGTGTTTCGCTGCTGTTGGCCAGTGTGCCGCTGTGTGCCCAGGCGAACGATGTTCAACAAAAGCTCGCGGCGCTGGAGAAAAGCAGCGGGGGACGACTGGGTGTGGCGTTGATTAACACCGCCGATAACACGCAGACGCTCTACCGCGCCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCGGTAGCGGCGGTGCTTAAGCAAAGTGAAACGCAAAAGGGCTTGTTGAGTCAGCGGGTTGAAATTAAGCCCTCAGACTTGATTAACTACAACCCCATTGCGGAAAAACACGTCAATGGCACGATGACATTCGGGGAGTTGAGCGCGGCGGCGCTACAGTACAGCGATAATACTGCCATGAATAAGCTGATTGCCCATCTCGGGGGGCCGGATAAAGTGACGGCATTTGCCCGTACGATTGGCGATGACACGTTCCGGCTCGATCGTACCGAGCCGACGCTCAACACCGCGATCCCCGGCGACCCGCGCGATACCACCACGCCGTTAGCGATGGCGCAGGCTCTGCGCAATCTGACGTTGGGCAATGCCCTGGGTGACACTCAGCGTGCGCAGCTGGTGATGTGGCTGAAAGGCAACACCACCGGCGCTGCCAGCATTCAGGCAGGGCTACCCACATCGTGGGTTGTCGGGGATAAAACCGGCAGCGGCGGTTATGGTACGACGAATGATATCGCGGTTATTTGGCCGGAAGGTCGCGCGCCGCTCGTTCTGGTGACTTACTTCACCCAGTCGGAGCCGAAGGCAGAGAGCCGTCGTGACGTGCTCGCTGCTGCCGCCAGAATTGTCACCGACGGTTATTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001887","ARO_id":"38287","ARO_name":"CTX-M-25","ARO_description":"CTX-M-25 is a beta-lactamase found in Escherichia coli","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"368":{"model_id":"368","model_name":"CARB-14","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1991":{"protein_sequence":{"accession":"AFI72872.1","sequence":"MDVRKHKASFFSVVITFLCLTLSLNANATDSVLEAVTNAETELGARIGLAVHDLETGKRWEHKSNERFPLSSTFKTLACANVLQRVDLGKERIDRVVRFSESNLVTYSPVTEKHVGKKGMSLAELCQATLSTSDNSAANFILQAIGGPKALTKFLRSIGDDTTRLDRWETELNEAVPGDKRDTTTPIAMVTTLEKLLIDETLSIKSRQQLESWLKGNEVGDALFRKGVPSDWIVADRTGAGGYGSRAITAVMWPPNRKPIVAALYITETDASFEERNAVIAKIGEQIAKIVLMENSRN"},"dna_sequence":{"accession":"JQ364968","fmin":"3332","fmax":"4229","strand":"+","sequence":"ATGGACGTACGTAAACACAAGGCTAGTTTTTTTAGCGTAGTAATTACTTTTTTATGTCTCACGCTATCATTAAATGCTAATGCAACAGACTCAGTACTTGAAGCGGTTACCAATGCTGAAACTGAATTAGGCGCTAGAATTGGTCTAGCTGTGCATGATTTGGAAACGGGAAAACGTTGGGAACATAAATCTAATGAACGTTTTCCTCTAAGTAGTACCTTTAAAACACTTGCCTGTGCAAACGTTCTTCAAAGAGTTGATCTAGGTAAAGAAAGAATTGATAGAGTTGTGAGATTCTCTGAAAGCAATCTCGTTACATACTCACCTGTAACAGAAAAACATGTGGGTAAAAAAGGGATGTCGCTCGCAGAGCTGTGTCAGGCCACATTATCAACCAGTGATAATTCAGCTGCCAATTTTATTCTACAAGCGATTGGTGGACCTAAGGCTCTAACGAAATTTTTGCGTTCCATTGGCGACGATACTACGCGCCTTGATCGCTGGGAAACAGAACTTAACGAAGCGGTACCTGGAGATAAGCGAGACACGACAACACCAATTGCAATGGTAACGACACTTGAAAAGTTACTAATTGACGAAACACTATCTATCAAATCTCGTCAACAACTAGAATCTTGGCTTAAAGGTAATGAGGTTGGCGATGCATTGTTTCGTAAAGGCGTTCCAAGTGACTGGATAGTAGCAGATAGAACAGGCGCTGGTGGTTATGGGTCGCGTGCTATTACTGCGGTGATGTGGCCTCCAAATCGCAAGCCTATCGTAGCCGCTCTATACATTACAGAGACAGACGCCTCGTTTGAAGAAAGAAATGCTGTCATTGCAAAAATTGGTGAGCAAATAGCGAAGATAGTATTAATGGAGAATAGCCGTAACTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3002252","ARO_id":"38652","ARO_name":"CARB-14","ARO_description":"CARB-14 is a beta-lactamase found in Acinetobacter baumannii","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"369":{"model_id":"369","model_name":"SHV-15","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"987":{"protein_sequence":{"accession":"CAB37325.2","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAMLARVDAGDKQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASKRGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AJ011428","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAATGCTGGCGCGGGTGGATGCCGGTGACAAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCAAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001074","ARO_id":"37454","ARO_name":"SHV-15","ARO_description":"SHV-15 is an extended-spectrum beta-lactamase found in E. coli.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"370":{"model_id":"370","model_name":"SHV-112","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1310":{"protein_sequence":{"accession":"ACC99191.1","sequence":"WETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPDNKAERIVVIYLRDTP"},"dna_sequence":{"accession":"EU477409","fmin":"0","fmax":"308","strand":"+","sequence":"CTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGAATTGTCGCCCTGCTTGGCCCGGATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001161","ARO_id":"37541","ARO_name":"SHV-112","ARO_description":"SHV-112 is a beta-lactamase that has been found in clinical isolates.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"371":{"model_id":"371","model_name":"SHV-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"993":{"protein_sequence":{"accession":"AAB51384.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARNTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"U92041","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCAACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001067","ARO_id":"37447","ARO_name":"SHV-8","ARO_description":"SHV-8 is an extended-spectrum beta-lactamase found in E. coli.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"372":{"model_id":"372","model_name":"qacA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"990"}},"model_sequences":{"sequence":{"265":{"protein_sequence":{"accession":"BAJ09383.1","sequence":"MISFFTKTTDMMTSKKRWTALVVLAVSLFVVTMDMTILIMALPELVRELDPSGTQQLWIVDIYSLVLAGFIIPLSAFADKWGRKKALLTGFALFGLVSLAIFFAESAEFVIAIRFLLGIAGALIMPTTLSMIRVIFENPKERATALAVWSIASSIGAVFGPIIGGALLEQFSWHSAFLINVPFAIIAVVAGLFLLPESKLSKEKSHSWDIPSTILSIAGMIGLVWSIKEFSKEGLADIIPWVVIVLAITMIVIFVKRNLSSSDPMLDVRLFKKRSFSAGTIAAFMTMFAMASVLLLASQWLQVVEELSPFKAGLYLLPMAIGDMVFAPIAPGLAARFGPKIVLPSGIGIAAIGMFIMYFFGHPLSYSTMALALILVGAGMASLAVASALIMLETPTSKAGNAAAVEESMYDLGNVFGVAVLGSLSSMLYRVFLDISSFSSKGIVGDLAHVAEESVVGAVEVAKATGIKQLANEAVTSFNDAFVATALVGGIIMIIISIVVYLLIPKSLDITKQK"},"dna_sequence":{"accession":"AB566411","fmin":"0","fmax":"1545","strand":"+","sequence":"ATGATTTCATTTTTTACAAAAACTACTGATATGATGACATCAAAAAAAAGATGGACTGCACTAGTAGTATTAGCTGTTAGTTTGTTTGTTGTTACAATGGATATGACAATATTAATTATGGCTTTACCGGAATTAGTAAGAGAGTTAGACCCTTCTGGTACCCAACAGTTATGGATAGTTGATATATACTCTCTTGTTTTAGCTGGCTTTATAATTCCATTGAGTGCCTTTGCTGATAAATGGGGAAGAAAAAAAGCATTATTAACTGGATTTGCTTTATTTGGCCTCGTTTCATTAGCTATATTTTTCGCAGAAAGTGCAGAGTTCGTAATAGCTATTCGATTTTTACTTGGTATTGCAGGTGCTTTAATAATGCCAACTACTCTTTCAATGATAAGAGTAATTTTTGAAAACCCTAAAGAAAGGGCCACTGCATTAGCTGTATGGTCAATCGCTTCATCGATAGGTGCTGTTTTTGGACCAATTATCGGAGGAGCTTTACTTGAGCAATTTTCATGGCACTCGGCATTTTTAATTAATGTACCGTTTGCGATAATAGCAGTTGTAGCAGGTTTATTTTTATTACCAGAGTCTAAGTTATCAAAAGAAAAGTCTCACTCGTGGGATATTCCTTCTACAATTTTATCAATTGCAGGCATGATTGGACTGGTATGGAGTATCAAAGAATTTTCAAAAGAAGGACTAGCAGATATTATTCCATGGGTTGTAATAGTATTAGCAATTACCATGATAGTGATATTTGTTAAACGTAATTTATCAAGTTCTGATCCAATGTTAGACGTAAGACTTTTTAAAAAGAGATCATTTTCAGCTGGTACAATTGCTGCATTTATGACAATGTTTGCAATGGCATCTGTTTTGTTATTAGCTTCACAATGGTTACAGGTTGTGGAAGAACTTTCTCCTTTTAAAGCTGGCTTATACCTATTACCTATGGCAATAGGAGATATGGTGTTTGCACCAATTGCACCCGGATTAGCGGCGCGATTTGGACCGAAAATAGTGTTACCTTCCGGAATTGGAATTGCAGCCATTGGCATGTTTATTATGTATTTCTTTGGTCATCCATTATCATATTCTACAATGGCTTTAGCATTAATTTTAGTTGGAGCTGGTATGGCTTCACTAGCAGTTGCATCTGCTCTAATAATGTTAGAAACACCTACATCAAAAGCAGGTAATGCAGCTGCTGTTGAAGAGTCTATGTATGACCTTGGAAATGTTTTTGGTGTAGCAGTACTTGGTAGCCTATCTTCTATGCTTTATCGTGTATTTTTAGATATTTCATCTTTTTCATCAAAAGGTATAGTTGGAGATTTAGCTCATGTAGCTGAAGAATCTGTAGTGGGCGCTGTCGAAGTAGCTAAAGCTACGGGGATAAAACAGCTTGCAAACGAGGCTGTAACATCATTTAATGATGCTTTTGTAGCAACTGCTTTAGTAGGTGGGATTATCATGATTATCATTTCAATAGTTGTCTATTTGTTAATTCCCAAATCACTTGATATAACTAAACAAAAATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3003046","ARO_id":"39480","ARO_name":"qacA","ARO_description":"qacA is a subunit of the qac multidrug efflux pump","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"373":{"model_id":"373","model_name":"MIR-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"1810":{"protein_sequence":{"accession":"AAU95779.1","sequence":"MMTKSLSCALLLSVASAAFAAPMSEKQLAEVVERTVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEIALGDPVAKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDTASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEEAHYAWGYREGKAVHVSPGMLDAEAYGVKTNVKDMASWLIANMKPDSLHAPSLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"AY743435","fmin":"13","fmax":"1159","strand":"+","sequence":"ATGATGACAAAATCCCTAAGCTGTGCCCTGCTGCTCAGCGTCGCCAGCGCTGCATTCGCCGCACCGATGTCCGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTAATTTATCAGGGTCAGCCACACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGCGGCGATGCCATTGCCCGGGGTGAAATAGCGCTGGGCGATCCGGTAGCAAAATACTGGCCTGAGCTCACGGGCAAGCAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTATACCGCAGGCGGTCTGCCGTTACAGGTGCCGGATGAGGTCACGGATACCGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCTAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAACCCCTCAAGCTGGACCATACCTGGATTAACGTCCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGAGGGTAAAGCGGTCCACGTTTCGCCAGGGATGCTGGACGCGGAAGCCTATGGCGTAAAAACTAACGTGAAGGATATGGCGAGCTGGCTGATAGCCAACATGAAGCCGGATTCTCTTCACGCTCCCTCACTCAAGCAAGGCATTGCTCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCTATGTATCAGGGGTTAGGCTGGGAGATGCTCAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCATTGCCCGTGGCAGAAGTGAATCCACCCGCGCCGCCGGTCAAAGCCTCCTGGGTCCATAAAACAGGCTCGACGGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3002169","ARO_id":"38569","ARO_name":"MIR-3","ARO_description":"MIR-3 is a beta-lactamase. From the Lahey list of MIR beta-lactamases.","ARO_category":{"36197":{"category_aro_accession":"3000058","category_aro_cvterm_id":"36197","category_aro_name":"MIR beta-lactamase","category_aro_description":"MIR beta-lactamases are plasmid-mediated beta-lactamases that confer resistance to oxyimino- and alpha-methoxy beta-lactams","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"374":{"model_id":"374","model_name":"SHV-21","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1391":{"protein_sequence":{"accession":"AAF34335.1","sequence":"MLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGEFCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEAFPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASERGARGIVALLGPNNKAERIVVIYLRDTPASMAERN"},"dna_sequence":{"accession":"AF117745","fmin":"0","fmax":"780","strand":"+","sequence":"CTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAATTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGTTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001079","ARO_id":"37459","ARO_name":"SHV-21","ARO_description":"SHV-21 is a broad-spectrum beta-lactamase that has been found in clinical isolates.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"375":{"model_id":"375","model_name":"mdtH","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"4305":{"protein_sequence":{"accession":"AAC74149.2","sequence":"MSRVSQARNLGKYFLLIDNMLVVLGFFVVFPLISIRFVDQMGWAAVMVGIALGLRQFIQQGLGIFGGAIADRFGAKPMIVTGMLMRAAGFATMGIAHEPWLLWFSCLLSGLGGTLFDPPRSALVVKLIRPQQRGRFFSLLMMQDSAGAVIGALLGSWLLQYDFRLVCATGAVLFVLCAAFNAWLLPAWKLSTVRTPVREGMTRVMRDKRFVTYVLTLAGYYMLAVQVMLMLPIMVNDVAGAPSAVKWMYAIEACLSLTLLYPIARWSEKHFRLEHRLMAGLLIMSLSMMPVGMVSGLQQLFTLICLFYIGSIIAEPARETLSASLADARARGSYMGFSRLGLAIGGAIGYIGGGWLFDLGKSAHQPELPWMMLGIIGIFTFLALGWQFSQKRAARRLLERDA"},"dna_sequence":{"accession":"U00096","fmin":"1124117","fmax":"1125326","strand":"-","sequence":"TCAGGCGTCGCGTTCAAGCAAACGACGCGCGGCGCGTTTCTGGCTAAACTGCCAACCCAGCGCAAGGAAAGTGAAGATGCCAATAATGCCCAGCATCATCCACGGAAGCTCTGGCTGGTGCGCCGATTTGCCCAGGTCAAACAGCCAGCCGCCACCGATATAACCAATAGCGCCGCCAATCGCCAGACCCAGACGGCTAAACCCCATATAGCTGCCGCGAGCTCTTGCGTCCGCCAGCGAAGCACTTAAGGTTTCACGCGCAGGCTCGGCAATGATCGACCCGATATAAAACAGACAAATCAGGGTGAAAAGTTGTTGCAGGCCGCTGACCATGCCCACCGGCATCATGCTTAATGACATTATCAACAGCCCAGCCATCAACCGGTGTTCCAGACGAAAATGCTTTTCACTCCAGCGGGCGATAGGGTAGAGCAACGTTAACGACAGACACGCTTCAATGGCATACATCCATTTAACGGCAGAGGGCGCGCCAGCCACGTCGTTGACCATAATTGGCAGCATCAGCATCACTTGTACAGCCAGCATGTAGTAACCCGCCAGCGTCAGAACATAGGTGACAAAACGCTTGTCACGCATCACGCGGGTCATGCCTTCGCGAACGGGCGTGCGTACGGTGGAGAGTTTCCATGCTGGTAACAACCACGCATTGAACGCCGCACATAGCACAAATAGAACTGCCCCTGTGGCGCAGACCAGGCGAAAGTCGTATTGCAACAGCCAGCTCCCCAACAATGCGCCAATGACCGCACCGGCACTGTCCTGCATCATCAACAGCGAGAAAAAACGACCACGCTGCTGTGGACGGATTAATTTCACCACCAGCGCCGAACGCGGCGGATCAAACAACGTGCCACCGAGTCCCGAGAGCAGGCATGAAAACCACAATAGCCACGGTTCGTGGGCGATACCCATTGTGGCGAATCCGGCGGCGCGCATCAGCATACCGGTAACAATCATCGGTTTGGCACCAAAGCGGTCGGCAATTGCACCGCCGAAAATACCCAGACCTTGCTGAATAAATTGGCGTAGACCGAGAGCAATACCGACCATGACGGCGGCCCAGCCCATTTGATCAACGAAGCGGATAGAGATCAGCGGGAAGACAACAAAGAACCCCAGCACGACCAGCATATTATCGATGAGCAGGAAATATTTACCCAGGTTCCTCGCCTGCGACACGCGGGACAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3001216","ARO_id":"37615","ARO_name":"mdtH","ARO_description":"Multidrug resistance protein MdtH","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35942":{"category_aro_accession":"0000023","category_aro_cvterm_id":"35942","category_aro_name":"enoxacin","category_aro_description":"Enoxacin belongs to a group called fluoroquinolones. Its mode of action depends upon blocking bacterial DNA replication by binding itself to DNA gyrase and causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"376":{"model_id":"376","model_name":"lnuC","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"110":{"protein_sequence":{"accession":"AAY32951.1","sequence":"MVNITDVNQIFQFAIDAEIKVFLDGGWGVDALLGYQSRAHNDIDIFVEKNDYQNFIEIMKANGFYEIKMEYTTLNHTVWEDLKNRIIDLHCFEYTDEGEILYDGDCFPVETLSGKGRIEEIEVSCIEPYSQVMFHLGYEFDENDAHDVKLLCETLHIEIPNEYR"},"dna_sequence":{"accession":"AY928180","fmin":"0","fmax":"495","strand":"+","sequence":"ATGGTCAATATAACAGATGTAAACCAGATTTTCCAATTTGCAATAGATGCGGAGATTAAAGTCTTTCTTGATGGTGGCTGGGGTGTAGATGCTCTTCTTGGATATCAGTCAAGAGCCCATAATGATATTGACATTTTTGTAGAAAAGAACGATTATCAGAACTTTATAGAAATAATGAAAGCTAATGGCTTTTATGAGATTAAGATGGAATATACAACATTGAACCATACTGTATGGGAAGATTTGAAAAACAGAATTATTGATTTGCATTGTTTTGAATATACGGACGAAGGTGAAATTCTTTATGATGGGGATTGTTTTCCGGTAGAAACTCTTTCGGGTAAAGGAAGAATTGAGGAAATAGAGGTTTCCTGTATTGAACCATATAGTCAAGTAATGTTCCATCTGGGATACGAGTTTGATGAAAATGATGCACATGATGTGAAGTTATTGTGTGAGACACTTCATATCGAAATTCCAAATGAGTATAGATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36847","NCBI_taxonomy_name":"Streptococcus agalactiae","NCBI_taxonomy_id":"1311"}}}},"ARO_accession":"3002837","ARO_id":"39271","ARO_name":"lnuC","ARO_description":"lnuC is a transposon-mediated nucleotidyltransferase found in Streptococcus agalactiae","ARO_category":{"36360":{"category_aro_accession":"3000221","category_aro_cvterm_id":"36360","category_aro_name":"lincosamide nucleotidyltransferase (LNU)","category_aro_description":"Resistance to the lincosamide antibiotic by ATP-dependent modification of the 3' and\/or 4'-hydroxyl groups of the methylthiolincosamide sugar.","category_aro_class_name":"AMR Gene Family"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"377":{"model_id":"377","model_name":"mepA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"850"}},"model_sequences":{"sequence":{"3623":{"protein_sequence":{"accession":"AAU95768.1","sequence":"MKDEQLYYFEKSPVFKAMMHFSLPMMIGTLLSVIYGILNIYFIGFLEDSHMISAISLTLPVFAILMGLGNLFGVGAGTYISRLLGAKDYSKSKFVSSFSIYGGIALGLIVILVTLPFSDQIAAILGARGETLALTSNYLKVMFLSAPFVILFFILEQFARAIGAPMVSMIGMLASVGLNIILDPILIFGFDLNVVGAALGTAISNVAAALFFIIYFMKNSDVVSVNIKLAKPNKEMLSEIFKIGIPAFLMSILMGFTGLVLNLFLAHYGNFAIASYGISFRLVQFPELIIMGLCEGVVPLIAYNFMANKGRMKDVIKAVIMSIGVIFVVCMSAVFTIGHHMVGLFTTDQAIVEMATFILKVTMASLLLNGIGFLFTGMLQATGQGRGATIMAILQGAIIIPVLFIMNALFGLTGVIWSLLIAESLCALAAMLIVYLLRDRLTVDTSELIEG"},"dna_sequence":{"accession":"AY661734.1","fmin":"839","fmax":"2195","strand":"+","sequence":"ATGAAAGACGAACAATTATATTATTTTGAGAAATCGCCAGTATTTAAAGCGATGATGCATTTCTCATTGCCAATGATGATAGGGACTTTATTAAGCGTTATTTATGGCATATTAAATATTTACTTTATAGGATTTTTAGAAGATAGCCACATGATTTCTGCTATCTCTCTAACACTGCCAGTATTTGCTATCTTAATGGGGTTAGGTAATTTATTTGGCGTTGGTGCAGGAACTTATATTTCACGTTTATTAGGTGCGAAAGACTATAGTAAGAGTAAATTTGTAAGTAGTTTCTCTATTTATGGTGGTATTGCACTAGGACTTATCGTGATTTTAGTTACTTTACCATTCAGTGATCAAATCGCAGCAATTTTAGGGGCGAGAGGTGAAACGTTAGCTTTAACAAGTAATTATTTGAAAGTAATGTTTTTAAGTGCACCTTTTGTAATTTTGTTCTTCATATTAGAACAATTTGCACGTGCAATTGGGGCACCAATGGTTTCTATGATTGGTATGTTAGCTAGTGTAGGCTTAAATATTATTTTAGATCCAATTTTAATTTTTGGTTTTGATTTAAACGTTGTTGGTGCAGCTTTGGGTACTGCAATCAGTAATGTTGCTGCTGCTCTGTTCTTTATCATTTATTTTATGAAAAATAGTGACGTTGTGTCAGTTAATATTAAACTTGCGAAACCTAATAAAGAAATGCTTTCTGAAATCTTTAAAATCGGTATTCCTGCATTTTTAATGAGTATCTTAATGGGATTCACAGGATTAGTTTTAAATTTATTTTTAGCACATTATGGAAACTTCGCGATTGCAAGTTATGGTATCTCATTTAGACTTGTGCAATTTCCAGAACTTATTATCATGGGATTATGTGAAGGTGTTGTACCACTAATTGCATATAACTTTATGGCAAATAAAGGCCGTATGAAAGACGTTATCAAAGCAGTTATCATGTCTATCGGCGTTATCTTTGTTGTATGTATGAGTGCTGTATTTACAATTGGACATCATATGGTCGGACTATTTACTACTGATCAAGCCATTGTTGAGATGGCGACATTTATTTTGAAAGTAACAATGGCATCATTATTATTAAATGGTATAGGTTTCTTGTTTACTGGTATGCTTCAAGCGACTGGGCAAGGTCGTGGTGCTACAATTATGGCCATTTTACAAGGTGCAATTATCATTCCAGTATTATTTATTATGAATGCTTTGTTTGGACTAACAGGTGTCATTTGGTCATTATTAATTGCTGAGTCACTTTGTGCTTTAGCAGCAATGTTAATCGTCTATTTATTACGTGATCGTTTGACAGTTGATACATCTGAATTAATAGAAGGTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3000026","ARO_id":"36035","ARO_name":"mepA","ARO_description":"MepA is an efflux protein regulated by MepR and part of the MepRAB cluster. Its presence in Staphylococcus aureus led to multidrug resistance, while it has also been shown to decrease tigecycline susceptibility.","ARO_category":{"36251":{"category_aro_accession":"3000112","category_aro_cvterm_id":"36251","category_aro_name":"multidrug and toxic compound extrusion (MATE) transporter","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Multidrug and toxic compound extrusion (MATE) transporters utilize the cationic gradient across the membrane as an energy source. Although there is a diverse substrate specificity, almost all MATE transporters recognize fluoroquinolones. Arciflavine, ethidium and aminoglycosides are also good substrates.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"378":{"model_id":"378","model_name":"TEM-214","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2126":{"protein_sequence":{"accession":"AJO16044.1","sequence":"MSIQHFRVALFPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"KP050491","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTTTTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001391","ARO_id":"37791","ARO_name":"TEM-214","ARO_description":"From the Lahey list of beta-lactamases. Not yet released.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"379":{"model_id":"379","model_name":"OXA-148","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1679":{"protein_sequence":{"accession":"ACX31140.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDKKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKASTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVKSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"GQ853679","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATAAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAAGCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGAAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001453","ARO_id":"37853","ARO_name":"OXA-148","ARO_description":"OXA-148 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"380":{"model_id":"380","model_name":"CTX-M-147","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1272":{"protein_sequence":{"accession":"AHA80961.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAVAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTESTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"KF513180","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGTCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAATCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002005","ARO_id":"38405","ARO_name":"CTX-M-147","ARO_description":"CTX-M-147 is a beta-lactamase. From the Lahey list of CTX-M beta-lactamases.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"381":{"model_id":"381","model_name":"QnrS1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"87":{"protein_sequence":{"accession":"ABG56870.1","sequence":"METYNHTYRHHNFSHKDLSDLTFTACTFIRSDFRRANLRDTTFVNCKFIEQGDIEGCHFDVADLRDASFQQCQLAMANFSNANCYGIEFRACDLKGANFSRTNFAHQVSNRMYFCSAFISGCNLSYANMERVCLEKCELFENRWIGTNLAGASLKESDLSRGVFSEDVWGQFSLQGANLCHAELDGLDPRKVDTSGIKIAAWQQELILEALGIVVYPD"},"dna_sequence":{"accession":"DQ449578","fmin":"0","fmax":"657","strand":"+","sequence":"ATGGAAACCTACAATCATACATATCGGCACCACAACTTTTCACATAAAGACTTAAGTGATCTCACCTTCACCGCTTGCACATTCATTCGCAGCGACTTTCGACGTGCTAACTTGCGTGATACGACATTCGTCAACTGCAAGTTCATTGAACAGGGTGATATCGAAGGCTGCCACTTTGATGTCGCAGATCTTCGTGATGCAAGTTTCCAACAATGCCAACTTGCGATGGCAAACTTCAGTAATGCCAATTGCTACGGTATAGAGTTCCGTGCGTGTGATTTAAAAGGTGCCAACTTTTCCCGAACAAACTTTGCCCATCAAGTGAGTAATCGTATGTACTTTTGCTCAGCATTTATTTCTGGATGTAATCTTTCCTATGCCAATATGGAGAGGGTTTGTTTAGAAAAATGTGAGTTGTTTGAAAATCGCTGGATAGGAACGAACCTAGCGGGTGCATCACTGAAAGAGTCAGACTTAAGTCGAGGTGTTTTTTCCGAAGATGTCTGGGGGCAATTTAGCCTACAGGGTGCCAATTTATGCCACGCCGAACTCGACGGTTTAGATCCCCGCAAAGTCGATACATCAGGTATCAAAATTGCAGCCTGGCAGCAAGAACTGATTCTCGAAGCACTGGGTATTGTTGTTTATCCTGACTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002790","ARO_id":"39224","ARO_name":"QnrS1","ARO_description":"QnrS1 is a plasmid-mediated quinolone resistance protein found in Shigella flexneri","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"382":{"model_id":"382","model_name":"QnrB61","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"721":{"protein_sequence":{"accession":"BAN04737.1","sequence":"MTLALVGEKIDRNRFTSEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"AB734053","fmin":"2303","fmax":"2948","strand":"+","sequence":"ATGACTCTGGCATTAGTTGGCGAAAAAATTGACAGAAATCGCTTCACCAGTGAGAAAGTTGAAAATAGTACATTTTTTAACTGCGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGCCAGTTCTATGATCGCGAAAGTCAGAAAGGATGCAATTTTAGTCGCGCAATGCTGAAAGATGCCATTTTCAAAAGCTGTGATTTATCAATGGCAGATTTCCGCAACGTCAGCGCATTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGTGCAAGCTTTATGAATATGATCACCACGCGCACCTGGTTTTGCAGCGCATATATCACTAATACCAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAGCTATGGGAAAACCGCTGGATGGGGACTCAGGTACTGGGTGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTAGGTGACTTAGATATTCGGGGTGTTGATTTACAAGGCGTTAAGTTAGACAACTACCAGGCATCGTTGCTCATGGAGCGGCTTGGCATCGCTGTGATTGGTTAGC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39584","NCBI_taxonomy_name":"Citrobacter braakii","NCBI_taxonomy_id":"57706"}}}},"ARO_accession":"3002774","ARO_id":"39208","ARO_name":"QnrB61","ARO_description":"QnrB61 is a plasmid-mediated quinolone resistance protein found in Citrobacter braakii","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"384":{"model_id":"384","model_name":"APH(2'')-IVa","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"729":{"protein_sequence":{"accession":"AAC14693.1","sequence":"MRTYTFDQVEKAIEQLYPDFTINTIEISGEGNDCIAYEINRDFIFKFPKHSRGSTNLFNEVNILKRIHNKLPLPIPEVVFTGMPSETYQMSFAGFTKIKGVPLTPLLLNNLPKQSQNQAAKDLARFLSELHSINISGFKSNLVLDFREKINEDNKKIKKLLSRELKGPQMKKVDDFYRDILENEIYFKYYPCLIHNDFSSDHILFDTEKNTICGIIDFGDAAISDPDNDFISLMEDDEEYGMEFVSKILNHYKHKDIPTVLEKYRMKEKYWSFEKIIYGKEYGYMDWYEEGLNEIRSIKIK"},"dna_sequence":{"accession":"AF016483","fmin":"0","fmax":"906","strand":"+","sequence":"ATGAGAACTTATACTTTCGACCAGGTAGAAAAGGCAATAGAGCAGTTATATCCTGATTTTACTATCAATACAATAGAGATTTCAGGAGAAGGCAATGACTGTATTGCATATGAAATAAACAGGGATTTCATTTTTAAATTTCCAAAGCATTCAAGAGGATCTACTAATCTTTTTAATGAAGTAAATATACTCAAAAGAATCCACAATAAATTACCCCTCCCCATTCCGGAGGTGGTTTTTACAGGAATGCCATCAGAAACGTACCAAATGTCTTTCGCAGGTTTTACAAAAATTAAAGGAGTACCATTGACACCTCTTCTACTCAATAATCTGCCGAAGCAATCTCAAAATCAGGCAGCTAAGGACCTGGCCCGATTTCTAAGTGAACTTCACAGCATAAACATCTCTGGATTCAAAAGTAATCTGGTATTAGATTTTCGAGAGAAGATAAATGAAGATAATAAAAAAATCAAAAAGTTACTATCCAGGGAATTAAAGGGTCCCCAGATGAAGAAAGTGGATGATTTTTACAGGGATATTCTAGAGAACGAAATCTACTTCAAATACTATCCTTGTCTTATTCATAACGATTTTAGCAGTGATCATATTTTATTTGATACCGAAAAAAATACTATTTGTGGAATAATCGATTTTGGAGATGCAGCTATTTCTGATCCCGACAATGATTTTATAAGTTTGATGGAAGATGATGAAGAATACGGCATGGAATTTGTATCAAAAATATTGAACCATTACAAACATAAGGATATACCGACAGTTTTGGAAAAATATAGGATGAAAGAAAAATACTGGTCGTTCGAAAAGATTATCTATGGAAAGGAATATGGTTATATGGATTGGTATGAAGAGGGATTAAATGAAATCAGAAGCATTAAAATTAAATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36767","NCBI_taxonomy_name":"Enterococcus casseliflavus","NCBI_taxonomy_id":"37734"}}}},"ARO_accession":"3002637","ARO_id":"39037","ARO_name":"APH(2'')-IVa","ARO_description":"APH(2'')-IVa is a chromosomal-encoded aminoglycoside phosphotransferase in E. casseliflavus","ARO_category":{"36267":{"category_aro_accession":"3000128","category_aro_cvterm_id":"36267","category_aro_name":"APH(2'')","category_aro_description":"Phosphorylation of 2-deoxystreptamine aminoglycosides on the hydroxyl group at position 2''","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"385":{"model_id":"385","model_name":"OXA-46","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1536":{"protein_sequence":{"accession":"AFP97030.1","sequence":"MAIRFFTILLSTFFLTSFVYAQEHVVIRSDWKKFFSDLQAEGAIVIADERQAKHTLSVFDQERAAKRYSPASTFKIPHTLFALDADAVRDEFQVFRWDGVNRSFAGHNQDQDLRSAMRNSTVWVYELFAKDIGEDKARRYLKQIDYGNVDPSTIKGDYWIDGNLKISAHEQILFLRKLYRNQLPFKVEHQRLVKDLMITEAGRSWILRAKTGWEGRFGWWVGWIEWPTGPVFFALNIDTPNRTDDLFKREAIARAILRSIDALPPN"},"dna_sequence":{"accession":"JX131372","fmin":"1478","fmax":"2279","strand":"+","sequence":"ATGGCAATCCGATTCTTCACCATACTGCTATCCACCTTCTTTCTTACCTCATTCGTGTATGCGCAAGAACATGTGGTAATCCGTTCGGACTGGAAAAAGTTCTTCAGCGACCTCCAGGCCGAAGGTGCAATCGTTATTGCAGACGAACGTCAAGCGAAGCATACTTTATCGGTTTTTGATCAAGAGCGAGCGGCAAAGCGTTACTCGCCAGCTTCAACCTTCAAGATACCCCACACACTTTTTGCACTTGATGCAGACGCCGTTCGTGATGAGTTCCAGGTTTTTCGATGGGACGGCGTTAACCGAAGCTTTGCAGGTCACAATCAAGACCAAGATTTGCGATCAGCGATGCGAAATTCTACGGTTTGGGTTTATGAGCTGTTTGCAAAAGATATCGGAGAGGACAAAGCAAGACGTTATTTAAAGCAAATTGATTATGGCAACGTCGATCCTTCGACAATCAAGGGCGATTACTGGATAGATGGAAATCTTAAAATCTCAGCGCACGAACAGATTTTGTTTCTCAGAAAACTCTATCGAAATCAGTTACCATTTAAGGTGGAGCACCAGCGCTTGGTGAAAGATCTCATGATTACGGAAGCCGGGCGCAGTTGGATACTACGCGCAAAGACCGGCTGGGAAGGCAGGTTTGGCTGGTGGGTAGGGTGGATTGAATGGCCAACAGGCCCCGTATTCTTTGCGCTGAATATTGATACGCCAAACAGAACGGACGATCTTTTCAAAAGAGAGGCCATCGCACGGGCAATCCTTCGTTCTATTGACGCATTGCCACCCAACTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001797","ARO_id":"38197","ARO_name":"OXA-46","ARO_description":"OXA-46 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"386":{"model_id":"386","model_name":"LEN-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1118":{"protein_sequence":{"accession":"CAG25835.1","sequence":"ATLPLVVYAGPQPLEQIKQSESQLPGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGLEQLDRRIHYRQQDLVDYSPVSEKHLVDGMTIGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTHLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPPGWFIADKTGAGERGARGIVALLGPDGKPERIVVIYLRDTPASMAERNQHIAG"},"dna_sequence":{"accession":"AJ635424","fmin":"0","fmax":"789","strand":"+","sequence":"GCCACCCTGCCACTGGTGGTATACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGCCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGTCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCATCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGCCGGGCTGGTTTATCGCCGACAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGCAATCAACATATCGCCGGG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002458","ARO_id":"38858","ARO_name":"LEN-8","ARO_description":"LEN-8 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"387":{"model_id":"387","model_name":"mdtA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"725"}},"model_sequences":{"sequence":{"15":{"protein_sequence":{"accession":"AAC75135.2","sequence":"MKGSYKSRWVIVIVVVIAAIAAFWFWQGRNDSRSAAPGATKQAQQSPAGGRRGMRSGPLAPVQAATAVEQAVPRYLTGLGTITAANTVTVRSRVDGQLIALHFQEGQQVKAGDLLAEIDPSQFKVALAQAQGQLAKDKATLANARRDLARYQQLAKTNLVSRQELDAQQALVSETEGTIKADEASVASAQLQLDWSRITAPVDGRVGLKQVDVGNQISSGDTTGIVVITQTHPIDLVFTLPESDIATVVQAQKAGKPLVVEAWDRTNSKKLSEGTLLSLDNQIDATTGTIKVKARFNNQDDALFPNQFVNARMLVDTEQNAVVIPTAALQMGNEGHFVWVLNSENKVSKHLVTPGIQDSQKVVIRAGISAGDRVVTDGIDRLTEGAKVEVVEAQSATTPEEKATSREYAKKGARS"},"dna_sequence":{"accession":"U00096","fmin":"2154015","fmax":"2155263","strand":"+","sequence":"ATGAAAGGTAGTTATAAATCCCGTTGGGTAATCGTAATCGTGGTGGTTATCGCCGCCATCGCCGCATTCTGGTTCTGGCAAGGCCGCAATGACTCCCGGAGTGCAGCCCCAGGGGCGACGAAACAAGCGCAGCAATCGCCAGCGGGTGGTCGACGTGGTATGCGTTCCGGCCCATTAGCCCCGGTTCAGGCGGCGACCGCCGTAGAACAGGCAGTTCCGCGTTACCTCACCGGGCTTGGCACCATTACCGCCGCTAATACCGTTACGGTGCGCAGCCGCGTGGACGGCCAACTGATAGCGTTACATTTCCAGGAAGGCCAGCAGGTCAAAGCAGGCGATTTACTGGCAGAAATTGACCCCAGCCAGTTCAAAGTTGCATTAGCACAAGCCCAGGGCCAACTGGCAAAAGATAAAGCCACGCTTGCCAACGCCCGCCGTGACCTGGCGCGTTATCAACAACTGGCAAAAACCAATCTCGTTTCCCGCCAGGAGCTGGATGCCCAACAGGCGCTGGTCAGTGAAACCGAAGGCACCATTAAGGCTGATGAAGCAAGCGTTGCCAGCGCGCAGCTGCAACTCGACTGGAGCCGGATTACCGCACCAGTCGATGGTCGCGTTGGTCTCAAGCAGGTTGATGTTGGTAACCAAATCTCCAGTGGTGATACCACCGGGATCGTGGTGATCACCCAGACGCATCCTATCGATTTAGTCTTTACCCTGCCGGAAAGCGATATCGCTACCGTAGTGCAGGCGCAGAAAGCCGGAAAACCGCTGGTGGTAGAAGCCTGGGATCGCACCAACTCGAAGAAATTAAGTGAAGGCACGCTGTTAAGTCTAGATAACCAAATCGATGCCACTACCGGTACGATTAAAGTGAAAGCACGCTTTAATAATCAGGATGATGCGCTGTTTCCCAATCAGTTTGTTAACGCGCGCATGTTAGTCGACACCGAACAAAACGCCGTAGTGATCCCAACAGCCGCCCTGCAAATGGGCAATGAAGGCCATTTTGTCTGGGTGCTGAATAGCGAAAACAAGGTCAGCAAACATCTGGTGACGCCGGGCATTCAGGACAGTCAGAAAGTGGTGATCCGTGCAGGTATTTCTGCGGGCGATCGCGTGGTGACAGACGGCATTGATCGCCTGACCGAAGGGGCGAAAGTGGAAGTGGTGGAAGCCCAGAGCGCCACTACTCCGGAAGAGAAAGCCACCAGCCGCGAATACGCGAAAAAAGGAGCACGCTCCTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3000792","ARO_id":"37172","ARO_name":"mdtA","ARO_description":"MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"388":{"model_id":"388","model_name":"QnrB71","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"406":{"protein_sequence":{"accession":"AGL43632.1","sequence":"MTLALVGEKIGRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"KC580660","fmin":"0","fmax":"645","strand":"+","sequence":"ATGACTCTGGCATTAGTTGGCGAAAAAATTGGCAGAAATCGCTTCACCGGTGAGAAAGTTGAAAATAGTACATTTTTTAACTGCGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGCCAGTTCTATGATCGCGAAAGTCAGAAAGGATGCAATTTTAGTCGCGCAATGCTGAAAGATGCCATTTTCAAAAGCTGTGATTTATCAATGGCAGATTTCCGCAACGTCAGCGCATTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGTGCAAGCTTTATGAATATGATCACCACGCGCACCTGGTTTTGCAGCGCATATATCACTAATACCAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAGCTATGGGAAAACCGCTGGATGGGGACTCAGGTACTGGGTGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTAGGTGACTTAGATATTCGGGGTGTTGATTTACAAGGCGTTAAGTTAGACAACTACCAGGCATCGTTGCTCATGGAGCGGCTTGGCATCGCTGTGATTGGTTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39584","NCBI_taxonomy_name":"Citrobacter braakii","NCBI_taxonomy_id":"57706"}}}},"ARO_accession":"3002783","ARO_id":"39217","ARO_name":"QnrB71","ARO_description":"QnrB71 is a plasmid-mediated quinolone resistance protein found in Citrobacter braakii","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"389":{"model_id":"389","model_name":"tetW","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1200"}},"model_sequences":{"sequence":{"657":{"protein_sequence":{"accession":"ACA23185.1","sequence":"MKIINIGILAHVDAGKTTLTESLLYASGAISEPGSVEKGTTRTDTMFLERQRGITIQAAVTSFQWHRCKVNIVDTPGHMDFLAEVYRSLAVLDGAILVISAKDGVQAQTRILFHALRKMNIPTVIFINKIDQAGVDLQSVVQSVRDKLSADIIIKQTVSLSPEIVLEENTDIEAWDAVIENNDELLEKYIAGEPISREKLAREEQQRVQDASLFPVYHGSAKNGLGIQPLMDAVTGLFQPIGEQGGAALCGSVFKVEYTDCGQRRVYLRLYSGTLRLRDTVALGGREKLKITEMRIPSKGEIVRTDTAYQGEIVILPSDSVRLNDVLGDQTRLPRKRWREDPLPMLRTTIAPKTAAQRERLLDALTQLADTDPLLRCEVDSITHEIILSFLGRVQLEVVSALLSEKYKLETVVKEPSVIYMERPLKAASHTIHIEVPPNPFWASIGLSVTPLSLGSGVQYESRVSLGYLNQSFQNAVRDGIRYGLEQGLFGWNVTDCKICFEYGLYYSPVSTPADFRSLAPIVLEQALKESGTQLLEPYLSFILYAPQEYLSRAYHDAPKYCATIETAQVKKDEVVFTGEIPARCIQAYRTDLAFYTNGRSVCLTELKGYQAAVGQPVIQPRRPNSRLDKVRHMFQKVM"},"dna_sequence":{"accession":"EU434751","fmin":"658","fmax":"2578","strand":"+","sequence":"ATGAAAATAATCAATATTGGAATTCTTGCCCATGTAGACGCTGGAAAGACGACCTTGACGGAGAGCCTGCTATATGCCAGCGGAGCCATTTCAGAACCGGGGAGCGTCGAAAAAGGGACAACGAGGACGGACACCATGTTTTTGGAGCGGCAGCGTGGGATTACCATTCAAGCGGCAGTCACTTCCTTCCAGTGGCACAGATGTAAAGTTAACATTGTGGATACGCCCGGCCACATGGATTTTTTGGCGGAGGTGTACCGCTCTTTGGCTGTTTTAGATGGGGCCATCTTGGTGATCTCCGCTAAAGATGGCGTGCAGGCCCAGACCCGTATTCTGTTCCATGCCCTGCGGAAAATGAACATTCCCACCGTTATCTTTATCAACAAGATCGACCAGGCTGGCGTTGATTTGCAGAGCGTGGTTCAGTCTGTTCGGGATAAGCTCTCCGCCGATATTATCATCAAGCAGACGGTGTCGCTGTCCCCGGAAATAGTCCTGGAGGAAAATACCGACATAGAAGCATGGGATGCGGTCATCGAAAATAACGATGAATTATTGGAAAAGTATATCGCAGGAGAACCAATCAGCCGGGAAAAACTTGCGCGGGAGGAACAGCAGCGGGTTCAAGACGCCTCCCTGTTCCCAGTCTATCATGGCAGCGCCAAAAATGGCCTTGGCATTCAACCGTTGATGGATGCGGTGACAGGGCTGTTCCAACCGATTGGGGAACAGGGGGGCGCCGCCCTATGCGGCAGCGTTTTCAAGGTTGAGTACACCGATTGCGGCCAGCGGCGTGTCTATCTACGGTTATACAGCGGAACGCTGCGCCTGCGGGATACGGTGGCCCTGGGCGGGAGAGAAAAGCTGAAAATCACAGAGATGCGTATTCCATCCAAAGGGGAAATTGTTCGGACAGACACCGCTTATCAGGGTGAAATTGTTATCCTTCCCAGCGACAGCGTGAGGTTAAACGATGTATTAGGGGACCAAACCCGGCTCCCTCGTAAAAGGTGGCGCGAGGACCCCCTCCCCATGCTGCGGACGACGATTGCGCCGAAAACGGCAGCGCAAAGAGAACGGCTGCTGGACGCTCTTACGCAACTTGCGGATACTGACCCGCTTTTGCGTTGCGAAGTGGATTCCATCACCCATGAGATCATTCTTTCTTTTTTGGGCCGGGTGCAGTTGGAGGTTGTTTCCGCTTTGCTGTCGGAAAAATACAAGCTTGAAACAGTGGTAAAGGAACCCTCCGTCATTTATATGGAGCGGCCGCTCAAAGCAGCCAGCCACACCATCCATATCGAGGTGCCGCCCAACCCGTTTTGGGCATCCATAGGACTGTCTGTTACACCACTCTCGCTTGGCTCCGGTGTACAATACGAGAGCCGGGTTTCGCTGGGATACTTGAACCAGAGTTTTCAAAACGCTGTCAGGGATGGTATCCGTTACGGGCTGGAGCAGGGCTTGTTCGGCTGGAACGTAACGGACTGTAAGATTTGCTTTGAATACGGGCTTTATTACAGTCCGGTCAGCACGCCGGCGGACTTCCGCTCATTGGCCCCGATTGTATTGGAACAGGCATTGAAGGAATCGGGGACGCAGCTGCTGGAACCTTATCTCTCCTTCATCCTCTATGCGCCCCAGGAATACCTTTCCAGGGCTTATCATGATGCACCGAAATACTGTGCCACCATCGAAACGGCCCAGGTAAAAAAGGATGAAGTTGTCTTTACTGGCGAGATTCCCGCCCGCTGTATACAGGCATACCGTACTGATCTGGCCTTTTACACCAACGGGCGGAGCGTATGCCTTACAGAGCTGAAAGGATATCAGGCCGCTGTCGGTCAGCCGGTCATCCAGCCCCGCCGTCCAAACAGCCGCCTGGACAAGGTGCGCCATATGTTTCAGAAGGTAATGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39590","NCBI_taxonomy_name":"Bifidobacterium longum","NCBI_taxonomy_id":"216816"}}}},"ARO_accession":"3000194","ARO_id":"36333","ARO_name":"tetW","ARO_description":"TetW is a ribosomal protection protein. It is associated with both conjugative and non conjugative DNA and has been found strains of C. difficile.","ARO_category":{"35921":{"category_aro_accession":"0000002","category_aro_cvterm_id":"35921","category_aro_name":"tetracycline-resistant ribosomal protection protein","category_aro_description":"A family of proteins known to bind to the 30S ribosomal subunit. This interaction prevents tetracycline and tetracycline derivatives from inhibiting ribosomal function. Thus, these proteins confer elevated resistance to tetracycline derivatives as a ribosomal protection protein.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"390":{"model_id":"390","model_name":"vanSG","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"706":{"protein_sequence":{"accession":"ABA71728.1","sequence":"MDSDYTQLQTKILIRTAVVLFGAFALISASLSLLSGHFSRAVVGILEIFYKDYEKALVVYTYVFRDNKEWFVMIAAFVSFLIVLRLYLKGFTKYFNEINRGINALKEESSEDVVLSSELAATEKTINTIKHTLEQQKTAALVAEQRKNDLVVYLAHDLKTPLTSVIGYLTLLRDEKQISDELREKYICISLEKAERLENLINEFFEITRFNLSNIILEYSVVNLTRMLEQLVFEFNPMLAEKKLNCVLKTMPNKMIRCDANKMQRVFDNLLRNAVNYSFENTEISITVTQNENMVHIKFVNHGNTIPKEKLERIFEQFYRLDTSRSTGNGGAGLGLAIAREIVMLHGGTITARSEDEKIEFEVTILSS"},"dna_sequence":{"accession":"DQ212986","fmin":"2979","fmax":"4086","strand":"+","sequence":"ATGGACAGTGACTATACACAGCTCCAGACAAAAATATTAATAAGGACAGCGGTTGTGCTATTCGGGGCGTTTGCTCTGATTTCCGCATCTCTTAGTTTATTAAGCGGGCATTTTTCAAGGGCTGTTGTGGGGATTTTGGAAATATTCTATAAAGATTATGAAAAGGCTTTGGTGGTATACACCTATGTGTTTCGGGACAATAAAGAATGGTTTGTGATGATAGCTGCATTTGTGTCGTTTCTAATTGTATTACGATTGTATCTGAAAGGCTTCACAAAGTATTTTAATGAAATAAACAGAGGTATTAATGCCTTGAAAGAGGAAAGTTCAGAAGATGTTGTATTATCTTCTGAGCTTGCGGCGACTGAAAAAACAATCAATACAATTAAGCATACCCTTGAACAGCAGAAAACTGCGGCGCTGGTTGCAGAGCAAAGGAAGAACGACCTTGTAGTGTATCTTGCTCATGATTTAAAGACTCCGCTTACATCTGTGATTGGATATTTGACATTGCTTAGGGACGAGAAGCAAATTTCAGATGAATTAAGGGAAAAGTATATATGTATTTCACTGGAAAAAGCAGAACGATTGGAAAATCTGATCAATGAATTTTTTGAGATTACACGTTTTAATCTTTCCAACATAATACTTGAATATAGTGTGGTAAATTTAACTCGTATGTTGGAGCAGTTGGTTTTTGAATTCAATCCAATGCTTGCGGAAAAAAAATTAAATTGTGTTCTTAAGACGATGCCGAATAAAATGATACGCTGCGACGCCAATAAAATGCAGAGGGTATTCGATAATTTATTGAGAAATGCAGTGAATTATAGTTTTGAGAATACAGAGATTTCTATTACAGTCACACAAAATGAAAATATGGTTCATATTAAATTTGTAAATCATGGAAATACAATTCCAAAAGAGAAACTGGAACGTATTTTTGAACAGTTTTATCGTCTGGATACTTCCAGAAGCACAGGGAATGGCGGCGCAGGCTTAGGGCTTGCTATTGCAAGGGAAATCGTAATGCTGCATGGAGGGACAATAACCGCCCGCAGTGAAGATGAAAAGATTGAATTTGAAGTGACGATTCTTTCATCGTAGG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3002937","ARO_id":"39371","ARO_name":"vanSG","ARO_description":"vanSG is a vanS variant found in the vanG gene cluster","ARO_category":{"36210":{"category_aro_accession":"3000071","category_aro_cvterm_id":"36210","category_aro_name":"vanS","category_aro_description":"VanS is similar to histidine protein kinases like EnvZ and acts as a response regulator by activating VanR. VanS is required for high level transcription of other van glycopeptide resistance genes.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"391":{"model_id":"391","model_name":"VIM-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1577":{"protein_sequence":{"accession":"ABR10840.1","sequence":"MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"EF614235","fmin":"2948","fmax":"3749","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAGC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002272","ARO_id":"38672","ARO_name":"VIM-2","ARO_description":"VIM-2 is a beta-lactamase found in Pseudomonas spp.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"392":{"model_id":"392","model_name":"TUS-1 beta-lactamase","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"1163":{"protein_sequence":{"accession":"AAN63648.1","sequence":"MYHYFSSLFVLIFSTLVYPQSDKLKIEPLNDHMYVYTTYQVFQGVEYSSNALYVVTDEGVILIDTPWDKDQYAPLVEHIRREHNKEIKWVITTHFHEDRSGGLDYFNKAGAETYTYALTNEILKQRNEPQATFTFGSTKQFNLGKEKIEVYFLGEGHSKDNTVVWFPEEAILYGGCLIKSAEATTIGNIVDGNVEAWPTTIKAVKRKFKKAKVIIPGHDAWNQSGHLENTARILSAYQAQKLKNNKQL"},"dna_sequence":{"accession":"AF441287","fmin":"260","fmax":"1007","strand":"+","sequence":"ATGTACCACTACTTTAGCAGTTTATTTGTACTGATTTTTTCTACTTTGGTCTATCCTCAATCGGATAAATTAAAAATTGAGCCGTTGAACGATCATATGTATGTCTATACGACCTACCAAGTATTTCAAGGCGTCGAATATTCTTCCAATGCTTTATATGTAGTGACGGATGAAGGAGTAATTCTCATTGATACCCCTTGGGATAAAGATCAGTACGCCCCTTTAGTAGAACACATCAGACGTGAACATAACAAAGAAATAAAATGGGTCATTACCACTCACTTCCACGAAGATCGTTCGGGTGGACTTGATTACTTCAATAAAGCTGGAGCAGAAACCTATACTTATGCTTTGACCAACGAAATCTTAAAACAGCGCAATGAACCACAAGCGACTTTTACTTTTGGTTCAACAAAGCAGTTCAACTTGGGCAAAGAAAAAATAGAGGTCTATTTCTTAGGAGAAGGTCATAGTAAAGATAATACGGTGGTTTGGTTTCCAGAAGAAGCGATTTTATACGGTGGTTGTTTGATTAAAAGTGCAGAGGCAACGACTATCGGCAATATCGTCGATGGCAATGTAGAGGCTTGGCCTACGACAATCAAAGCCGTAAAGCGCAAATTCAAAAAGGCCAAAGTGATTATTCCAGGGCATGATGCCTGGAATCAATCCGGTCATCTTGAAAATACAGCCCGTATCTTATCGGCTTATCAGGCACAAAAATTAAAGAACAACAAGCAATTATAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39073","NCBI_taxonomy_name":"Myroides odoratus DSM 2801","NCBI_taxonomy_id":"929704"}}}},"ARO_accession":"3000844","ARO_id":"37224","ARO_name":"TUS-1","ARO_description":"TUS-1 is a chromosome-encoded beta-lactamase from Myroides odoratus and Myroides odoratimimus","ARO_category":{"41369":{"category_aro_accession":"3004205","category_aro_cvterm_id":"41369","category_aro_name":"TUS beta-lactamase","category_aro_description":"TUS beta-lactamases are Class B beta-lactamases that can hydrolyze a variety of beta-lactams, such as cephems and carbapenems","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"393":{"model_id":"393","model_name":"QnrS5","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"254":{"protein_sequence":{"accession":"AEG74319.1","sequence":"METYRHTYRHHNFSHKDLSALTFTACTFIRSDFRRANLRDTTFVNCKFIEQGDIEGCHFDVADLRDASFQQCQLAMANFSNANCYGIEFRACDLKGANFSRTNFAHQVSNRMYFCSAFITGCTLSYANMERVCLERCELFENRWIGTHLAGASLKESDLSRGVFSEDVWGQFSLQGANLCHAELDGLDPRKVDTSGIKIAAWQQEQLLEALGIVVFPD"},"dna_sequence":{"accession":"HQ631377","fmin":"0","fmax":"657","strand":"+","sequence":"ATGGAAACCTACCGTCACACATATCGGCACCACAACTTTTCACATAAAGACTTAAGTGCTCTCACCTTCACTGCTTGCACATTTATTCGCAGCGACTTTCGACGAGCTAACTTGCGCGATACGACATTCGTCAACTGCAAGTTCATTGAACAGGGTGATATCGAAGGCTGCCACTTTGATGTCGCAGATCTTCGTGATGCAAGTTTCCAACAATGCCAACTGGCGATGGCAAACTTCAGTAACGCCAATTGCTACGGTATTGAGTTCCGTGCGTGTGATTTAAAAGGTGCCAACTTTTCCCGAACAAACTTTGCCCATCAAGTGAGTAATCGTATGTACTTTTGCTCAGCCTTTATTACAGGATGTACTCTTTCCTATGCCAATATGGAGAGGGTTTGTTTAGAAAGATGTGAGTTGTTTGAAAATCGCTGGATAGGAACTCATCTAGCGGGTGCATCATTGAAAGAGTCAGACTTAAGTCGAGGTGTTTTTTCCGAAGATGTCTGGGGGCAATTTAGCCTACAGGGTGCCAATTTATGCCACGCCGAACTAGACGGTTTAGATCCCCGCAAAGTCGATACATCAGGTATCAAAATTGCAGCTTGGCAGCAAGAACAGCTTCTCGAAGCACTGGGTATTGTTGTTTTTCCTGACTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36957","NCBI_taxonomy_name":"Aeromonas sobria","NCBI_taxonomy_id":"646"}}}},"ARO_accession":"3002794","ARO_id":"39228","ARO_name":"QnrS5","ARO_description":"QnrS5 is a plasmid-mediated quinolone resistance protein found in Aeromonas sobria","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"394":{"model_id":"394","model_name":"OXA-130","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1601":{"protein_sequence":{"accession":"ACD84988.1","sequence":"MNIKALLLITSAIFISACSPYIVTTNPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNTDIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"EU547445","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTACTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATACAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001651","ARO_id":"38051","ARO_name":"OXA-130","ARO_description":"OXA-130 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"396":{"model_id":"396","model_name":"sul3","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4306":{"protein_sequence":{"accession":"ACJ63260.1","sequence":"MSKIFGIVNITTDSFSDGGLYLDTDKAIEHALHLVEDGADVIDLGAASSNPDTTEVGVVEEIKRLKPVIKALKEKGISISVDTFKPEVQSFCIEQKVDFINDIQGFPYPEIYSGLAKSDCKLVLMHSVQRIGAATKVETNPEEVFTSMMEFFKERIAALVEAGVKRERIILDPGMGFFLGSNPETSILVLKRFPEIQEAFNLQVMIAVSRKSFLGKITGTDVKSRLAPTLAAEMYAYKKGADYLRTHDVKSLSDALKISKALG"},"dna_sequence":{"accession":"FJ196385","fmin":"8531","fmax":"9323","strand":"-","sequence":"CTAACCTAGGGCTTTGGATATTTTCAAGGCATCTGATAAAGACTTAACATCATGGGTGCGGAGATAATCTGCACCTTTTTTGTATGCATACATTTCTGCTGCAAGAGTTGGTGCTAAACGAGATTTCACATCGGTTCCAGTTATTTTACCTAAGAATGATTTCCGTGACACTGCAATCATTACTTGCAAATTAAAAGCTTCTTGAATTTCAGGGAAACGCTTCAAAACAAGAATAGATGTTTCTGGATTAGAGCCTAAAAAGAAGCCCATACCCGGATCAAGAATAATTCGTTCACGCTTTACACCAGCCTCAACTAAAGCAGCAATTCTTTCTTTAAAAAATTCCATCATGGAAGTAAAAACCTCTTCCGGATTCGTTTCAACTTTAGTAGCTGCACCAATTCGCTGAACGGAGTGCATCAACACAAGTTTGCAATCTGACTTTGCCAAGCCTGAATAAATCTCAGGATAAGGAAAACCTTGAATATCATTAATAAAATCAACCTTTTGTTCTATGCAAAAACTCTGAACCTCAGGTTTAAATGTATCAACAGAAATAGAAATGCCTTTTTCTTTTAAAGCCTTAATGACAGGTTTGAGTCTTTTGATTTCTTCCACAACGCCCACTTCAGTTGTATCAGGATTACTGGAAGCGGCTCCCAAATCAATCACATCTGCTCCATCTTCAACCAAATGCAGAGCATGCTCAATTGCCTTATCTGTATCTAAATAAAGTCCTCCATCGGAAAAACTATCGGTGGTTATATTTACGATTCCAAAAATCTTGCTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000413","ARO_id":"36552","ARO_name":"sul3","ARO_description":"Sul3 is a sulfonamide resistant dihydropteroate synthase similar to Sul1 and Sul2. Its resistance gene was found encoded in E. coli plasmid DNA of sulfonamide resistant isolates.","ARO_category":{"41402":{"category_aro_accession":"3004238","category_aro_cvterm_id":"41402","category_aro_name":"sulfonamide resistant sul","category_aro_description":"The sul genes encode forms of dihydropteroate synthase that confer resistance to sulfonamide.","category_aro_class_name":"AMR Gene Family"},"36463":{"category_aro_accession":"3000324","category_aro_cvterm_id":"36463","category_aro_name":"sulfadiazine","category_aro_description":"Sulfadiazine is a potent inhibitor of dihydropteroate synthase, interfering with the tetrahydrofolic biosynthesis pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor to many nucleotides and amino acids.","category_aro_class_name":"Antibiotic"},"36464":{"category_aro_accession":"3000325","category_aro_cvterm_id":"36464","category_aro_name":"sulfadimidine","category_aro_description":"Sulfadimidine is an alkaline sulfonamide antibiotic that inhibits dihydropteroate synthase, and enzyme in the tetrahydrofolic acid biosynthesis pathway. This interferes with the production of folate, which is a precursor to many amino acids and nucleotides.","category_aro_class_name":"Antibiotic"},"36466":{"category_aro_accession":"3000327","category_aro_cvterm_id":"36466","category_aro_name":"sulfadoxine","category_aro_description":"Sulfadoxine is an inhibitor of dihydropteroate synthase, interfering with the tetrahydrofolic biosynthesis pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor to many nucleotides and amino acids.","category_aro_class_name":"Antibiotic"},"36468":{"category_aro_accession":"3000329","category_aro_cvterm_id":"36468","category_aro_name":"sulfamethoxazole","category_aro_description":"Sulfamethoxazole is a sulfonamide antibiotic usually taken with trimethoprim, a diaminopyrimidine antibiotic. Sulfamethoxazole inhibits dihydropteroate synthase, essential to tetrahydrofolic acid biosynthesis. This pathway generates compounds used in the synthesis of many amino acids and nucleotides.","category_aro_class_name":"Antibiotic"},"36469":{"category_aro_accession":"3000330","category_aro_cvterm_id":"36469","category_aro_name":"sulfisoxazole","category_aro_description":"Sulfisoxazole is an inhibitor of dihydropteroate synthase, interfering with the tetrahydrofolic biosynthesis pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor to many nucleotides and amino acids.","category_aro_class_name":"Antibiotic"},"37027":{"category_aro_accession":"3000683","category_aro_cvterm_id":"37027","category_aro_name":"sulfacetamide","category_aro_description":"Sulfacetamide is a very soluable sulfonamide antibiotic previously used to treat urinary tract infections. Its relatively low activity and toxicity to those with Stevens-Johnson syndrome have reduced its use and availability.","category_aro_class_name":"Antibiotic"},"37028":{"category_aro_accession":"3000684","category_aro_cvterm_id":"37028","category_aro_name":"mafenide","category_aro_description":"Mafenide is a sulfonamide used topically for treating burns.","category_aro_class_name":"Antibiotic"},"37042":{"category_aro_accession":"3000698","category_aro_cvterm_id":"37042","category_aro_name":"sulfasalazine","category_aro_description":"Sulfasalazine is a derivative of the early sulfonamide sulfapyridine (salicylazosulfapyridine). It was developed to increase water solubility and is taken orally for ulcerative colitis.","category_aro_class_name":"Antibiotic"},"37043":{"category_aro_accession":"3000699","category_aro_cvterm_id":"37043","category_aro_name":"sulfamethizole","category_aro_description":"Sulfamethizole is a short-acting sulfonamide that inhibits dihydropteroate synthetase.","category_aro_class_name":"Antibiotic"},"39996":{"category_aro_accession":"3003412","category_aro_cvterm_id":"39996","category_aro_name":"dapsone","category_aro_description":"Dapsone is a sulfone in which it inhibits folic acid synthesis, such as the dihydropteroate synthase.","category_aro_class_name":"Antibiotic"},"36421":{"category_aro_accession":"3000282","category_aro_cvterm_id":"36421","category_aro_name":"sulfonamide antibiotic","category_aro_description":"Sulfonamides are broad spectrum, synthetic antibiotics that contain the sulfonamide group. Sulfonamides inhibit dihydropteroate synthase, which catalyzes the conversion of p-aminobenzoic acid to dihydropteroic acid as part of the tetrahydrofolic acid biosynthetic pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor of many nucleotides and amino acids. Many sulfamides are taken with trimethoprim, an inhibitor of dihydrofolate reductase, also disturbing the trihydrofolic acid synthesis pathway.","category_aro_class_name":"Drug Class"},"39985":{"category_aro_accession":"3003401","category_aro_cvterm_id":"39985","category_aro_name":"sulfone antibiotic","category_aro_description":"A sulfone active against a wide range of bacteria but mainly employed for its actions against mycobacterium laprae. Its mechanism of action  involves inhibition of folic acid synthesis in susceptible organisms.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"397":{"model_id":"397","model_name":"OXA-357","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1611":{"protein_sequence":{"accession":"AGZ83153.1","sequence":"MYKKALIAATSILFLSSCSSNTVKQHQIHSISANKNSEEIKSLFDQAQTTGVLVIKRGQTEEIYGNDLKRASTDYVPASTFKMLNALIGLEHHKVTTTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVDNFWLVGPLKISPEQETQFAYKLANKTLPFSKNVQEQVQSMVFIEEKNGSKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGVL"},"dna_sequence":{"accession":"KF421160","fmin":"0","fmax":"822","strand":"+","sequence":"ATGTATAAAAAAGCCCTTATCGCTGCAACAAGTATCCTATTTTTATCCTCCTGTTCTTCCAATACGGTAAAACAACATCAAATACACTCTATTTCTGCCAATAAAAATTCAGAAGAAATTAAATCACTGTTTGATCAGGCACAGACCACGGGTGTTTTGGTGATTAAGCGAGGGCAAACAGAAGAAATTTATGGAAATGATCTTAAAAGAGCATCAACCGACTATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTAATTGGACTTGAACATCATAAGGTAACTACAACTGAAGTATTTAAATGGGATGGGCAGAAACGTTTATTTCCTGACTGGGAAAAGGACATGACACTGGGTGATGCCATGAAAGCTTCTGCGATTCCAGTTTATCAAGAACTAGCTCGTCGTATTGGACTTGATCTTATGTCTAAAGAGGTAAAACGTATTGGTTTCGGTAATGCGGACATTGGTTCAAAAGTAGATAATTTTTGGCTTGTAGGTCCACTTAAAATTTCACCTGAGCAAGAAACCCAATTTGCTTATAAATTAGCCAATAAAACTCTTCCATTTAGTAAAAATGTACAAGAACAAGTCCAATCAATGGTGTTCATAGAAGAAAAAAATGGAAGTAAGATTTATGCCAAAAGTGGGTGGGGATGGGATGTTGAACCACAAGTTGGTTGGTTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTCGCATTCTCACTTAATTTAGAAATGAAAAAAGGAACTCCCAGCTCTATTCGCAAAGAAATTGCTTATAAAGGCTTAGAACAACTCGGTGTTTTATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3001544","ARO_id":"37944","ARO_name":"OXA-357","ARO_description":"OXA-357 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"398":{"model_id":"398","model_name":"TEM-71","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1574":{"protein_sequence":{"accession":"AAL03985.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASKRGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AF203816","fmin":"210","fmax":"1071","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTAAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000937","ARO_id":"37317","ARO_name":"TEM-71","ARO_description":"TEM-71 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"399":{"model_id":"399","model_name":"MIR-16","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"1581":{"protein_sequence":{"accession":"AIT76114.1","sequence":"MMTKSLSCALLLSVASAAFAAPMSEKQLAEVVERTVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEIALGDPVAKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDTASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEEAHYAWGYREGKAVHVSPGMLDAEAYGVKTNVKDMASWVIANMKPDSLQAPSLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"KM087861","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGACAAAATCCCTAAGCTGTGCCCTGCTGCTCAGCGTCGCCAGCGCTGCATTCGCCGCACCGATGTCCGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTAATTTATCAGGGTCAGCCACACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGCGGCGATGCCATTGCCCGGGGTGAAATAGCGCTGGGCGATCCGGTAGCAAAATACTGGCCTGAGCTCACGGGCAAGCAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTATACCGCAGGCGGTCTGCCGTTACAGGTGCCGGATGAGGTCACGGATACCGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCTAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAACCCCTCAAGCTGGACCATACATGGATTAACGTCCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGAGGGTAAAGCGGTCCACGTTTCGCCAGGGATGCTGGACGCGGAAGCCTATGGCGTAAAAACTAACGTGAAGGATATGGCGAGCTGGGTGATAGCCAACATGAAGCCGGATTCTCTTCAGGCTCCCTCACTCAAGCAAGGCATTGCTCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCTATGTATCAGGGGTTAGGCTGGGAGATGCTCAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCATTGCCCGTGGCAGAAGTGAATCCACCCGCGCCTCCGGTCAAGGCCTCCTGGGTCCATAAAACAGGCTCGACGGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36926","NCBI_taxonomy_name":"Enterobacter asburiae","NCBI_taxonomy_id":"61645"}}}},"ARO_accession":"3002181","ARO_id":"38581","ARO_name":"MIR-16","ARO_description":"MIR-16 is a beta-lactamase. From the Lahey list of MIR beta-lactamases.","ARO_category":{"36197":{"category_aro_accession":"3000058","category_aro_cvterm_id":"36197","category_aro_name":"MIR beta-lactamase","category_aro_description":"MIR beta-lactamases are plasmid-mediated beta-lactamases that confer resistance to oxyimino- and alpha-methoxy beta-lactams","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"400":{"model_id":"400","model_name":"PDC-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"1308":{"protein_sequence":{"accession":"ACQ82807.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"FJ666065","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTATGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3002497","ARO_id":"38897","ARO_name":"PDC-1","ARO_description":"PDC-1 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"401":{"model_id":"401","model_name":"ACT-22","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1911":{"protein_sequence":{"accession":"AHM76774.1","sequence":"MMKKSLCCALLLSTSCAALAAPMSETQLAKVVARTVTPLMKAQSIPGMAVAVIYQGQPHYFTFGKADVAANTPVTAQTLFELGSISKTFTGVLGGDAIARGEISLSDPVTKYWPELTGKQWQGVRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQSWQPQWAPGTTRLYANASIGLFGALAVKPSGMRFEQAMTERVLKPLNLNHTWINVPKAEEQHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVKDMASWVVANMAPDGVQDASLKQGMALAQSRYWRTGSMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKKLGIVMLANKSYPNPARVEAAYRILSALQ"},"dna_sequence":{"accession":"KF992027","fmin":"700","fmax":"1846","strand":"+","sequence":"ATGATGAAAAAATCCCTGTGCTGCGCCCTGCTGCTCAGCACCTCCTGCGCTGCATTAGCCGCACCTATGTCAGAAACACAGCTGGCGAAGGTCGTGGCACGTACCGTTACGCCCCTGATGAAAGCGCAGTCTATTCCGGGTATGGCGGTCGCCGTGATCTATCAGGGCCAGCCGCACTACTTCACCTTCGGCAAGGCCGATGTCGCAGCGAACACACCCGTCACTGCACAAACGCTGTTTGAGCTGGGCTCAATCAGCAAAACCTTCACCGGCGTTCTGGGTGGCGATGCTATTGCTCGCGGTGAAATTTCGCTGAGCGATCCGGTGACCAAATACTGGCCTGAGCTGACCGGCAAACAGTGGCAGGGCGTTCGCATGCTGGACCTGGCAACCTATACTGCCGGTGGCCTGCCGTTACAGGTGCCCGATGAGGTTACCGATAATGCCTCGCTGCTGCGTTTTTACCAGTCCTGGCAACCACAGTGGGCGCCAGGCACCACGCGTCTTTATGCGAATGCCAGCATCGGTCTGTTTGGGGCTCTGGCGGTGAAACCTTCTGGCATGCGCTTTGAGCAGGCGATGACAGAGCGGGTCCTGAAGCCGCTTAACCTGAACCATACGTGGATTAACGTTCCGAAGGCAGAAGAACAGCATTACGCCTGGGGTTATCGTGACGGTAAAGCGGTTCACGTTTCGCCGGGCATGCTCGATGCCGAAGCGTATGGCGTGAAAACCAACGTGAAGGATATGGCGAGCTGGGTAGTGGCTAACATGGCCCCCGATGGCGTACAGGATGCCTCACTGAAGCAGGGCATGGCGCTTGCACAGTCTCGCTACTGGCGCACAGGCTCGATGTACCAGGGCCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTGGTGGAGGGCAGCGACAACAAAGTAGCGCTTGCGCCGTTGCCCGTGGCAGAAGTGAACCCTCCTGCTCCACCGGTAAAAGCGTCATGGGTACATAAAACAGGCTCGACGGGCGGATTTGGCAGCTACGTGGCATTTATCCCTGAGAAGAAACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCGCGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001843","ARO_id":"38243","ARO_name":"ACT-22","ARO_description":"ACT-22 is a beta-lactamase. From the Lahey list of ACT beta-lactamases.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"403":{"model_id":"403","model_name":"dfrA8","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"568":{"protein_sequence":{"accession":"AHV80711.1","sequence":"MIELHAILAATANGCIGKDNALPWPPLKGDLARFKKLTMGKVVIMGRKTYESLPVKLEGRTCIVMTRQALELPGVRDANGAIFVNNVSDAMRFAQEESVGDVAYVIGGAEIFKRLALMITQIELTFVKRLYEGDTYVDLAEMVKDYEQNGMEEHDLHTYFTYRKKELTE"},"dna_sequence":{"accession":"KJ174469","fmin":"710","fmax":"1220","strand":"+","sequence":"ATGATCGAGCTTCATGCCATTTTAGCTGCCACCGCCAATGGTTGCATTGGGAAGGACAACGCACTTCCCTGGCCACCACTAAAAGGCGATCTGGCCAGATTCAAAAAATTGACCATGGGGAAGGTGGTCATTATGGGGCGCAAGACCTATGAGAGCTTGCCCGTCAAATTAGAAGGTCGCACCTGCATCGTTATGACGCGCCAAGCGCTGGAGCTTCCGGGTGTTCGTGACGCTAACGGCGCTATCTTCGTGAACAACGTCAGCGACGCCATGCGGTTCGCTCAAGAAGAGAGCGTGGGCGATGTGGCCTACGTCATTGGTGGCGCTGAGATATTCAAGCGACTTGCCTTGATGATCACGCAGATTGAATTGACCTTTGTTAAGCGACTGTACGAAGGCGACACCTACGTTGATCTGGCCGAAATGGTCAAAGACTACGAGCAGAATGGCATGGAAGAACATGACCTTCACACTTACTTCACTTACCGTAAAAAGGAGCTTACAGAATGAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35732","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium","NCBI_taxonomy_id":"90371"}}}},"ARO_accession":"3002863","ARO_id":"39297","ARO_name":"dfrA8","ARO_description":"dfrA8 is a transposon-encoded dihydrofolate reductase found in Salmonella enterica","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36408":{"category_aro_accession":"3000269","category_aro_cvterm_id":"36408","category_aro_name":"brodimoprim","category_aro_description":"Brodimoprim is a structural derivative of trimethoprim and an inhibitor of bacterial dihydrofolate reductase. The 4-methoxy group of trimethoprim is replaced with a bromine atom.","category_aro_class_name":"Antibiotic"},"36423":{"category_aro_accession":"3000284","category_aro_cvterm_id":"36423","category_aro_name":"tetroxoprim","category_aro_description":"Tetroxoprim is a trimethoprim derivative that inhibits bacterial dihydrofolate reductase.","category_aro_class_name":"Antibiotic"},"36476":{"category_aro_accession":"3000337","category_aro_cvterm_id":"36476","category_aro_name":"iclaprim","category_aro_description":"Iclaprim is a bactericidal compound that inhibits dihydrofolate reductase. It is used against clinically important Gram-positive pathogens, including methicillin-sensitive Staphylococcus aureus and methicillin-resistant S. aureus.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"404":{"model_id":"404","model_name":"OXA-217","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1455":{"protein_sequence":{"accession":"AEO44980.1","sequence":"MNIKALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTAVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"JN603240","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGCAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTAGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001489","ARO_id":"37889","ARO_name":"OXA-217","ARO_description":"OXA-217 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"405":{"model_id":"405","model_name":"OXA-202","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1454":{"protein_sequence":{"accession":"ADX07747.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAMPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"HQ734813","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATGCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001667","ARO_id":"38067","ARO_name":"OXA-202","ARO_description":"OXA-202 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"406":{"model_id":"406","model_name":"ACC-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"4307":{"protein_sequence":{"accession":"ABP49606.1","sequence":"MQNTLKLLSVITCLAATVQGALAANIDESKIKDTVDDLIQPLMQKNNIPGMSVAVTVNGKNYIYNYGLAAKQPQQPVTENTLFEVGSLSKTFAATLASYAQVSGKLSLDQSVSHYVPELRGSSFDHVSVLNVGTHTSGLQLFMPEDIKNTTQLMAYLKAWKPADAAGTHRVYSNIGTGLLGMIAAKSLGVSYEDAIEKTLLPQLGMHHSYLKVPADQMENYAWGYNKKDEPVHGNMEILGNEAYGIKTTSSDLLRYVQANMGQLKLDANAKMQQALTATHTGYFKSGEITQDLMWEQLPYPVSLPNLLTGNDMAMTKSVATPIVPPLPPQENVWINKTGSTNGFGAYIAFVPAKKMGIVMLANKNYSIDQRVTVAYKILSSLEGNK"},"dna_sequence":{"accession":"EF504260","fmin":"1994","fmax":"3155","strand":"-","sequence":"CTACTTATTCCCTTCCAATGAGCTCAGGATTTTATACGCCACCGTCACTCGCTGATCGATTGAGTAGTTTTTGTTAGCCAGCATCACGATCCCCATCTTCTTAGCAGGAACAAACGCAATATAGGCACCGAAGCCGTTAGTTGATCCGGTCTTATTAATCCACACATTTTCCTGTGGCGGTAACGGCGGAACAATCGGCGTAGCCACGCTTTTCGTCATCGCCATATCGTTACCGGTGAGCAAATTCGGCAGAGAAACCGGATATGGCAGCTGCTCCCACATCAGATCCTGAGTAATCTCACCCGATTTGAAATAGCCGGTGTGGGTGGCTGTCAGAGCCTGTTGCATCTTGGCATTAGCATCAAGCTTTAACTGCCCCATATTGGCTTGCACGTAGCGTAACAAGTCGCTGGAGGTGGTTTTGATACCATAAGCTTCGTTACCCAAAATCTCCATATTCCCGTGCACTGGCTCATCTTTCTTGTTGTAGCCCCACGCATAGTTTTCCATCTGGTCAGCCGGAACCTTCAAGTAGCTGTGATGCATGCCTAACTGAGGAAGGAGGGTTTTCTCAATCGCATCTTCATAGCTCACACCCAGACTTTTCGCCGCAATCATCCCTAGCAAACCAGTACCGATATTGGAATAAACGCGATGGGTTCCAGCCGCATCGGCAGGTTTCCATGCTTTTAGATAAGCCATCAGCTGTGTGGTATTTTTAATATCTTCCGGCATAAATAGCTGTAGGCCTGAGGTATGCGTGCCCACATTGAGTACGCTAACGTGGTCAAAGCTGCTGCCACGCAACTCTGGAACGTAATGGCTAACGCTTTGATCCAAAGACAGCTTACCGCTCACCTGCGCATAGGACGCCAAGGTGGCAGCAAACGTTTTACTCAGCGAACCCACTTCAAATAACGTATTTTCCGTAACCGGCTGCTGAGGCTGTTTTGCCGCTAACCCATAGTTATAAATGTAGTTTTTACCGTTGACGGTCACTGCGACCGACATACCGGGAATATTATTCTTCTGCATCAGCGGCTGGATCAGGTCATCAACGGTGTCTTTAATTTTGCTCTCATCGATATTAGCAGCCAGAGCACCTTGGACAGTTGCTGCCAGACAGGTAATCACGGATAACAGCTTCAATGTGTTCTGCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001818","ARO_id":"38218","ARO_name":"ACC-4","ARO_description":"ACC-4 is a beta-lactamase found in Escherichia coli","ARO_category":{"36212":{"category_aro_accession":"3000073","category_aro_cvterm_id":"36212","category_aro_name":"ACC beta-lactamase","category_aro_description":"ACC beta-lactamases or Ambler class C beta-lactamases are AmpC beta-lactamases. They possess an interesting resistance phenotype due to their low activity against cephamycins.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"407":{"model_id":"407","model_name":"OXA-352","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1213":{"protein_sequence":{"accession":"AGW83450.1","sequence":"MYKKALIVATSILFLSACSSNTVKQHQIHSISANKNSEEIKSLFDQAQTTGVLVIKRGQTEEIYGNDLKRASTDYIPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNANIGSKVDDFWLVGPLKITPQQETQFAYQLAHKTLPFSKNVQEQVQSMVFIEEKNGRKIYAKSGWGWDIEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"KF297581","fmin":"0","fmax":"822","strand":"+","sequence":"ATGTATAAAAAAGCCCTTATCGTTGCAACAAGTATCCTATTTTTATCCGCCTGTTCTTCCAATACGGTAAAACAACATCAAATACATTCTATTTCTGCCAATAAAAATTCAGAAGAAATTAAATCACTATTTGATCAAGCACAGACCACGGGTGTTTTGGTGATTAAGCGAGGGCAAACAGAAGAAATTTATGGCAATGATCTTAAAAGAGCATCAACCGACTATATTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTAATTGGACTTGAACATCATAAGGCAACTACAACTGAAGTATTTAAATGGGATGGGCAAAAACGTTTATTTCCTGATTGGGAAAAGGACATGACACTGGGTGATGCCATGAAAGCTTCTGCAATCCCAGTTTACCAAGAATTAGCCCGACGTATTGGTCTGGATCTTATGTCCAAAGAGGTGAAACGAATTGGTTTCGGTAATGCTAACATTGGCTCAAAAGTAGATGATTTCTGGCTTGTTGGCCCTCTAAAAATTACACCTCAACAAGAAACCCAATTTGCTTATCAATTAGCCCATAAAACGCTTCCATTTAGCAAAAATGTACAAGAACAAGTTCAATCAATGGTGTTCATAGAAGAAAAAAATGGACGTAAAATTTATGCAAAAAGCGGTTGGGGATGGGATATTGAGCCACAAGTTGGTTGGTTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTGGCATTCTCACTTAATTTAGAAATGAAAAAAGGAACTCCTAGCTCTATTCGCAAAGAAATTGCTTATAAAGGCTTAGAACAACTGGGTATCTTATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3001539","ARO_id":"37939","ARO_name":"OXA-352","ARO_description":"OXA-352 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"408":{"model_id":"408","model_name":"OXA-380","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4308":{"protein_sequence":{"accession":"AHL30280.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEIFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSLKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KF986261","fmin":"44","fmax":"869","strand":"-","sequence":"CTATAAAATACCTAATTGTTCTAAACTTTTATAAGTAATCTCTTTTCGAACAGAGCTAGGTATTCCTTTTTTCATTTCTAAGTTAAGGGAGAACGCTACAATATTTCCTTGAGGCTGAACAACCCATCCAGTTAACCAGCCTACTTGTGGGTCTACATCCCATCCCCAACCACTTTTTGCGTATATTTTATTTCCATTCTTTTCTTCTATGAATAACATGGATTGCACTTCATCTTGGACTTTTAGGCTAAATGGAAGCGTTTTATTAGCTAGCTTGTAAGCAAACTGTGCCTCTTGCTGAGGAGTAATTTTTAAAGGACCCACCAGCCAAAAATTATCGACTTGGGTACCGATATCTGCATTGCCATAACCAACACGCTTCACTTCCTTAGACATGAGTTCAAGTCCAATACGACGAGCTAAATCTTGATAAACCGGAATAGCGGAAGCTTTCATAGCATCACCTAGGGTCATGTCCTTTTCCCATTCTGGGAACAGCCTTTTTTGCCCGTCCCACTTAAATATTTCTGTGGTGGTTGCCTTATGGTGCTCAAGGCCGATCAAAGCATTAAGCATTTTGAAGGTCGAAGCAGGTACATACTCGGTCGAAGCACGAGCAAGATCATTACCATAGCTTTGTTGAGTTTGACCTTGATGGATAACTAAAACACCCGTAGTGTGTGCTTCGTTAAATAAATTTTTAATTTTCTCTGCTTTGTCATCAGATTTTGAAGCACTGTGATTTGGATTAGCAGTCACTATATAAGGTGAGCAGGCTGAAATAAAAATAGCGCTTGTTATAAGTAAGAGTGCTTTAATGTTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001566","ARO_id":"37966","ARO_name":"OXA-380","ARO_description":"OXA-380 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"409":{"model_id":"409","model_name":"vanRL","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"287":{"protein_sequence":{"accession":"ABX54691.1","sequence":"MTDRIVVVDDEQEIANLITTFLENEGFQVTTFYKGEDFLTYIARESISLAILDVMLPDIDGFRILQEIRKNFYFPVLMLTAKEENMDKIMGLTLGADDYITKPFNPIEVVARVKTQLRRVQKYNRKVENESVIEFNKDGLTLKKDSHQVFLFDKEITVTPIEFNLLLYLFEHQGVVVSSEELFEAVWKEKYLENNNTIMAHIARLREKLDEQPRKPKFIKTVWGVGYIIEK"},"dna_sequence":{"accession":"EU250284","fmin":"4730","fmax":"5426","strand":"+","sequence":"ATGACGGATAGAATAGTTGTTGTGGATGATGAACAAGAGATAGCCAATTTGATTACAACTTTTTTAGAAAATGAAGGGTTTCAAGTAACAACCTTTTATAAAGGAGAAGATTTTTTGACTTATATAGCTAGAGAGTCAATTTCTTTAGCTATATTAGATGTCATGCTACCTGATATTGATGGGTTTCGAATCTTGCAAGAAATTAGAAAGAATTTTTATTTTCCGGTATTAATGCTTACAGCTAAGGAAGAAAATATGGACAAGATTATGGGACTAACCTTGGGAGCGGATGATTATATTACTAAACCATTTAACCCAATAGAAGTAGTTGCCCGGGTAAAAACACAACTAAGACGAGTCCAAAAGTATAACCGGAAAGTGGAAAATGAATCAGTCATAGAGTTTAACAAAGACGGACTAACGCTAAAAAAAGACAGTCATCAAGTATTTTTATTTGATAAAGAAATAACTGTAACACCTATTGAATTCAATTTGCTTTTATATTTATTTGAACACCAAGGAGTGGTTGTTAGTTCAGAAGAACTATTTGAAGCTGTTTGGAAAGAGAAATATTTAGAAAATAATAACACAATCATGGCACACATTGCTCGCTTAAGGGAAAAATTAGACGAACAGCCACGCAAACCTAAATTCATAAAAACCGTATGGGGGGTAGGATATATTATTGAAAAGTAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3002927","ARO_id":"39361","ARO_name":"vanRL","ARO_description":"vanRL is a vanR variant found in the vanL gene cluster","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36713":{"category_aro_accession":"3000574","category_aro_cvterm_id":"36713","category_aro_name":"vanR","category_aro_description":"VanR is a OmpR-family transcriptional activator in the VanSR regulatory system. When activated by VanS, it promotes cotranscription of VanA, VanH, and VanX.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"410":{"model_id":"410","model_name":"AAC(3)-IIIb","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"188":{"protein_sequence":{"accession":"AAA25682.1","sequence":"MVHAAVSRVGRLLDGPDTIIAALRDTVGPGGTVLAYADWEARYEDLVDDAGRVPPEWREHVPPFDPQRSRAIRDNGVLPEFLRTTPGTLRSGNPGASLVALGAKAEWFTADHPLDYGYGEGSPLAKLVEAGGKVLMLGAPLDTLTLLHHAEHLADIPGKRIKRIEVPFATPTGTQWRMIEEFDTGDPIVAGLAEDYFAGIVTEFLASGQGRQGLIGAAPSVLVDAAAITAFGVTWLEKRFGTPSP"},"dna_sequence":{"accession":"L06160","fmin":"983","fmax":"1721","strand":"+","sequence":"ATGGTCCATGCCGCCGTCAGCAGGGTCGGCCGCCTGCTCGATGGCCCCGACACCATCATCGCCGCCCTGCGCGATACCGTCGGCCCGGGCGGTACCGTTCTCGCCTATGCCGATTGGGAGGCACGATACGAGGACCTGGTCGACGACGCGGGCCGCGTGCCTCCGGAATGGCGCGAACATGTCCCACCCTTCGACCCGCAGCGCTCGCGTGCGATCCGCGACAATGGTGTGCTGCCGGAATTCCTGCGGACCACGCCCGGCACGCTCCGCAGCGGCAACCCCGGCGCCTCGCTCGTCGCGCTCGGGGCGAAGGCGGAGTGGTTCACTGCCGACCACCCGCTCGACTACGGCTATGGCGAGGGCTCGCCGCTGGCCAAGCTGGTCGAGGCCGGCGGCAAGGTGCTGATGCTTGGGGCGCCGCTCGACACGCTGACCCTGCTGCACCATGCCGAGCATCTGGCTGATATCCCCGGCAAGCGGATCAAGCGGATCGAGGTGCCGTTCGCGACACCTACAGGCACGCAATGGCGCATGATCGAGGAGTTCGACACCGGCGATCCGATCGTCGCAGGGCTGGCCGAGGACTATTTCGCGGGAATCGTGACCGAATTCCTCGCCAGCGGCCAGGGTCGGCAAGGGTTGATCGGCGCCGCTCCCTCGGTGCTGGTCGATGCCGCGGCGATCACCGCCTTCGGCGTCACCTGGCTCGAAAAACGGTTCGGTACGCCCTCGCCCTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002537","ARO_id":"38937","ARO_name":"AAC(3)-IIIb","ARO_description":"AAC(3)-IIIb is an aminoglycoside acetyltransferase in P. aeruginosa","ARO_category":{"36461":{"category_aro_accession":"3000322","category_aro_cvterm_id":"36461","category_aro_name":"AAC(3)","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 3.","category_aro_class_name":"AMR Gene Family"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"411":{"model_id":"411","model_name":"QnrB11","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"146":{"protein_sequence":{"accession":"ABS30107.1","sequence":"MMTLALVGEKIDRNRFTGAKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAILKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGSDFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFSSFDWRAANFTHCDLTNSELGDLDVRGVDLQGVKLDSYQASLILERLGIAVMG"},"dna_sequence":{"accession":"EF653270","fmin":"0","fmax":"648","strand":"+","sequence":"ATGATGACTCTGGCGTTAGTTGGCGAAAAAATTGACAGAAACAGATTCACTGGTGCGAAAGTTGAAAATAGCACATTTTTCAACTGTGATTTTTCGGGCGCCGACCTCAGCGGCACTGAGTTTATTGGCTGCCAGTTCTATGATCGAGAAAGCCAGAAAGGGTGTAATTTTAGTCGCGCTATCCTGAAAGATGCCATTTTCAAAAGTTGTGATCTCTCCATGGCGGATTTCAGGAATGTGAGCGCGCTGGGAATCGAAATTCGCCACTGCCGCGCACAAGGTTCAGATTTTCGCGGCGCAAGCTTTATGAATATGATTACCACACGCACCTGGTTTTGTAGCGCCTATATCACCAATACCAACTTAAGCTACGCCAACTTTTCAAAAGTCGTACTGGAAAAGTGCGAGCTGTGGGAAAACCGTTGGATGGGTACTCAGGTACTGGGGGCGACGTTCAGTGGTTCGGATCTTTCCGGCGGTGAGTTTTCGTCGTTCGACTGGCGGGCCGCAAACTTTACGCACTGTGATTTGACCAATTCAGAACTGGGCGATCTCGATGTCCGGGGTGTTGATTTGCAAGGCGTCAAACTGGACAGCTACCAGGCATCGTTGATCCTGGAACGTCTTGGTATCGCTGTCATGGGTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002725","ARO_id":"39159","ARO_name":"QnrB11","ARO_description":"QnrB11 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"412":{"model_id":"412","model_name":"OXA-117","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"879":{"protein_sequence":{"accession":"ABW95048.1","sequence":"LLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTEWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSL"},"dna_sequence":{"accession":"EU220745","fmin":"0","fmax":"786","strand":"+","sequence":"TTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTAGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGAATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001442","ARO_id":"37842","ARO_name":"OXA-117","ARO_description":"OXA-117 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"413":{"model_id":"413","model_name":"OXA-144","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1369":{"protein_sequence":{"accession":"ACY56711.1","sequence":"MNIKALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQEVQDEVQSILFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"FJ872530","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTAGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAGAAGTCCAAGATGAAGTGCAATCCATTCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3002480","ARO_id":"38880","ARO_name":"OXA-144","ARO_description":"OXA-144 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"414":{"model_id":"414","model_name":"OXA-377","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1612":{"protein_sequence":{"accession":"AHL30277.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTKGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KF986258","fmin":"14","fmax":"839","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTAAGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001563","ARO_id":"37963","ARO_name":"OXA-377","ARO_description":"OXA-377 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"415":{"model_id":"415","model_name":"TEM-33","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4309":{"protein_sequence":{"accession":"ADL13944.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMLSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"GU371926","fmin":"50304","fmax":"51165","strand":"-","sequence":"TTACCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCTGACTCCCCGTCGTGTAGATAACTACGATACGGGAGGGCTTACCATCTGGCCCCAGTGCTGCAATGATACCGCGAGACCCACGCTCACCGGCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGTTTGCGCAACGTTGTTGCCATTGCTGCAGGCATCGTGGTGTCACGCTCGTCGTTTGGTATGGCTTCATTCAGCTCCGGTTCCCAACGATCAAGGCGAGTTACATGATCCCCCATGTTGTGCAAAAAAGCGGTTAGCTCCTTCGGTCCTCCGATCGTTGTCAGAAGTAAGTTGGCAGCAGTGTTATCACTCATGGTTATGGCAGCACTGCATAATTCTCTTACTGTCATGCCATCCGTAAGATGCTTTTCTGTGACTGGTGAGTACTCAACCAAGTCATTCTGAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGCCCGGCGTCAACACGGGATAATACCGCACCACATAGCAGAACTTTAAAAGTGCTCAGCATTGGAAAACGTTCTTCGGGGCGAAAACTCTCAAGGATCTTACCGCTGTTGAGATCCAGTTCGATGTAACCCACTCGTGCACCCAACTGATCTTCAGCATCTTTTACTTTCACCAGCGTTTCTGGGTGAGCAAAAACAGGAAGGCAAAATGCCGCAAAAAAGGGAATAAGGGCGACACGAAAATGTTGAATACTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000903","ARO_id":"37283","ARO_name":"TEM-33","ARO_description":"TEM-33 is an inhibitor-resistant beta-lactamase that has been found in clinical isolates.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"416":{"model_id":"416","model_name":"OXA-204","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1605":{"protein_sequence":{"accession":"AFU91598.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGHRRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"JQ809466","fmin":"5374","fmax":"6172","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACATCGGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGACAGTTTCTGGCTCGATGGTGGTATTCGAATTTCGGCCACTGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATGCTGACCGAAGCCAATGGCGACTATATTATTCGGGCTAAAACGGGATACTCGACTAGAATCGAACCTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTGGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001788","ARO_id":"38188","ARO_name":"OXA-204","ARO_description":"OXA-204 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"417":{"model_id":"417","model_name":"QnrB6","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"610":{"protein_sequence":{"accession":"ABP87778.1","sequence":"MTPLLYKKTGTNMALALVGEKIDRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNASALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"EF520349","fmin":"0","fmax":"681","strand":"+","sequence":"ATGACGCCATTACTGTATAAAAAAACAGGTACAAATATGGCTCTGGCACTCGTTGGCGAAAAAATTGACAGAAACCGTTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCGATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATGCCAGTGCGCTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGCGCAAGCTTTATGAATATGATCACCACGCGCACCTGGTTTTGTAGCGCATATATCACGAATACCAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAGCTGTGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTGACTTAGATATTCGGGGCGTTGATTTACAAGGCGTTAAGCTGGACAACTACCAGGCGTCGTTGCTCATGGAGCGGCTTGGCATCGCGGTGATTGGTTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36950","NCBI_taxonomy_name":"Pantoea agglomerans","NCBI_taxonomy_id":"549"}}}},"ARO_accession":"3002720","ARO_id":"39154","ARO_name":"QnrB6","ARO_description":"QnrB6 is a plasmid-mediated quinolone resistance protein found in Pantoea agglomerans","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"418":{"model_id":"418","model_name":"OXA-325","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"888":{"protein_sequence":{"accession":"AGW16407.1","sequence":"MYKKALIVATSILFLSACSSNTVKQHQIHTISANKNSEEIKSLFDQAQTTGVLVIKRGQTEEIYGNDLKRASTDYIPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNANIGSKVDDFWLVGPLKITPQQETQFAYQLAHKTLPFSKNVQEQVQSMVFIEEKNGRKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"KF203099","fmin":"0","fmax":"822","strand":"+","sequence":"ATGTATAAAAAAGCCCTTATCGTTGCAACAAGTATTCTATTTTTATCCGCCTGTTCTTCCAATACGGTAAAACAACATCAAATACATACTATTTCTGCCAATAAAAATTCAGAAGAAATTAAATCACTTTTTGATCAAGCACAGACCACGGGAGTTTTGGTGATTAAGCGAGGGCAAACAGAAGAAATTTATGGCAATGATCTTAAAAGAGCATCAACCGACTATATTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTAATTGGACTTGAACATCATAAGGCAACTACAACTGAAGTATTTAAATGGGATGGGCAAAAACGTTTATTTCCTGATTGGGAAAAGGACATGACACTGGGTGATGCCATGAAAGCTTCTGCAATCCCAGTTTACCAAGAATTAGCCCGACGAATTGGTCTGGATCTTATGTCCAAAGAGGTGAAACGAATTGGTTTCGGTAATGCTAACATTGGCTCAAAAGTAGATGATTTCTGGCTTGTTGGCCCTCTAAAAATTACACCTCAACAAGAAACCCAATTTGCTTATCAATTAGCCCATAAAACTCTTCCATTTAGCAAAAATGTACAAGAACAAGTTCAATCAATGGTGTTCATAGAAGAAAAAAATGGACGTAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTGGAACCACAAGTTGGTTGGTTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTCGCATTCTCACTTAATTTAGAAATGAAAAAAGGAACTCCTAGCTCTATTCGCAAAGAAATTGCTTATAAAGGCTTAGAACAACTGGGTATCTTATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3001513","ARO_id":"37913","ARO_name":"OXA-325","ARO_description":"OXA-325 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"419":{"model_id":"419","model_name":"SLB-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"3312":{"protein_sequence":{"accession":"AAT90846.1","sequence":"MLSLPSYSHEVEPTSTTIQSVTSSLEGQLSISKLADGVYLHHSYKNVSNFGLVEANGLVVIKDKQAFIIDTPWTDNDTQKLVDWITQQGFIPVASISTHSHQDRAGGIGYLNRQGITTTVSETTQQILTENDKTTAKSTFTGMQYIMKTDLVEVYDLGAGHTKDNLVVWLPTQQILFGGCLIKSLNSSTLGYTGEADLQQWPLTIAKVQAQFPQVKIVVPGHGQVGDKALLEHTIELLIPKNETVNSSS"},"dna_sequence":{"accession":"AY590118","fmin":"0","fmax":"750","strand":"+","sequence":"ATGCTCAGCTTACCTAGCTATAGTCATGAAGTAGAGCCCACATCGACAACAATCCAATCAGTAACATCCAGCCTTGAAGGCCAATTAAGTATTTCCAAGCTTGCCGATGGCGTGTACTTACATCACTCCTATAAAAATGTCAGTAATTTCGGTTTAGTCGAAGCCAACGGCCTTGTAGTGATTAAGGATAAACAAGCATTTATTATTGATACCCCGTGGACCGACAACGATACCCAAAAATTAGTTGACTGGATAACTCAGCAAGGTTTTATCCCCGTCGCCAGTATTTCAACCCATTCACATCAAGATCGGGCTGGCGGTATCGGTTACCTTAATCGCCAAGGTATTACGACTACAGTGTCCGAAACGACTCAACAAATTTTAACCGAAAATGATAAAACTACCGCTAAAAGTACTTTTACAGGCATGCAATACATTATGAAAACGGATTTAGTCGAAGTGTATGACTTAGGTGCAGGGCATACCAAAGACAACCTAGTGGTATGGCTGCCGACACAGCAAATCTTATTTGGTGGGTGTTTAATAAAATCGCTTAACTCAAGCACATTAGGTTACACAGGTGAAGCGGACTTACAGCAGTGGCCCTTAACTATCGCCAAGGTACAAGCCCAATTTCCTCAAGTAAAAATAGTCGTACCCGGTCATGGACAGGTTGGCGATAAAGCGCTACTTGAGCATACTATCGAGTTACTAATACCAAAAAATGAAACAGTTAATAGCAGCAGTTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40161","NCBI_taxonomy_name":"Shewanella livingstonensis","NCBI_taxonomy_id":"150120"}}}},"ARO_accession":"3003556","ARO_id":"40159","ARO_name":"SLB-1","ARO_description":"This enzyme breaks the beta-lactam antibiotic ring open and deactivates the molecule's antibacterial properties.","ARO_category":{"40158":{"category_aro_accession":"3003555","category_aro_cvterm_id":"40158","category_aro_name":"SHW beta-lactamase","category_aro_description":"This family of sublcass B1 beta-lactamases were discovered in species of the Shewanella genus.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"420":{"model_id":"420","model_name":"CTX-M-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1916":{"protein_sequence":{"accession":"CAA63262.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAVAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVDGTMSLAELSAAALQYSDNVAMNKLISHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTNGL"},"dna_sequence":{"accession":"X92506","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGTCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGAAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGTGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACTTGGTTAACTATAATCCGATTGCGGAAAAGCACGTCGATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTTCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGTAATCTGACGCTGGGTAAAGCATTGGGTGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCAACGGTTTGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001864","ARO_id":"38264","ARO_name":"CTX-M-1","ARO_description":"CTX-M-1 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"421":{"model_id":"421","model_name":"TEM-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1724":{"protein_sequence":{"accession":"CAA38429.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"X54606","fmin":"214","fmax":"1075","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3000874","ARO_id":"37254","ARO_name":"TEM-2","ARO_description":"TEM-2 is a broad-spectrum beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"422":{"model_id":"422","model_name":"FOX-10","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"951":{"protein_sequence":{"accession":"AGE45503.1","sequence":"MQQRRAFALLTLGSLLLAPCTYASGEAPLTAAVDGIIQPMLKAYRIPGMAVAVLKDGKAHYFNYGVANRESGQRVSEQTLFEIGSVSKTLTATLGAYAAVKGGFELDDKVSQHAPWLKGSALDGVTMAELATYSAGGLPLQFPDEVDSNDKMRTYYRSWSPVYPAGTHRQYSNPSISLFGHLAANSLGQPFEQLMSQTLLPKLGLHHTYIQVPESAMVNYAYGYSKEDKPVRVTPGVLAAEAYGIKTGSADLLKFAEANMGYQGDAAVKSAIALTHTGFYSVGDMTQGLGWESYAYPVTEQTLLAGNAPAVSFQANPVTRFAVPKAMGEQRLYNKTGSTGGFGAYVAFVPARGIAIVMLANRNYPIEARVKAAHAILSQLAE"},"dna_sequence":{"accession":"JX049131","fmin":"0","fmax":"1149","strand":"+","sequence":"ATGCAACAACGGCGTGCGTTCGCGCTACTGACGCTGGGTAGCCTGCTGTTAGCCCCTTGTACTTATGCCAGCGGGGAGGCTCCGTTGACCGCCGCTGTGGACGGCATTATCCAGCCGATGCTCAAGGCGTATCGGATCCCGGGGATGGCGGTCGCCGTACTGAAAGATGGCAAAGCCCACTATTTCAACTATGGGGTTGCCAACCGGGAGAGTGGCCAGCGCGTCAGCGAGCAGACCCTGTTCGAGATTGGCTCGGTCAGCAAGACCCTGACTGCGACCCTCGGTGCCTATGCCGCGGTCAAGGGGGGCTTTGAGCTGGATGACAAGGTGAGCCAGCACGCCCCCTGGCTCAAAGGTTCCGCCTTGGATGGTGTGACCATGGCCGAGCTTGCCACCTACAGTGCGGGTGGTTTGCCGCTGCAGTTCCCCGATGAGGTGGATTCGAATGACAAGATGCGCACTTACTATCGGAGCTGGTCACCGGTTTATCCGGCGGGGACCCATCGCCAGTATTCCAACCCCAGCATCAGCCTGTTTGGTCACCTGGCCGCAAATAGTCTGGGCCAGCCATTTGAGCAACTGATGAGCCAGACCCTGCTGCCCAAGCTGGGTTTGCACCACACCTATATCCAGGTACCGGAGTCGGCTATGGTGAACTATGCCTACGGCTATTCGAAGGAAGATAAGCCCGTCCGGGTCACTCCGGGCGTGCTGGCAGCCGAGGCTTACGGGATCAAGACCGGCTCGGCGGATCTGCTGAAGTTTGCCGAGGCAAACATGGGGTATCAGGGAGATGCCGCGGTAAAAAGCGCGATCGCGCTGACCCACACCGGTTTCTACTCGGTGGGAGACATGACCCAGGGACTGGGCTGGGAGAGTTACGCCTATCCGGTGACCGAGCAGACATTGCTGGCGGGTAACGCACCGGCGGTGAGCTTCCAGGCCAATCCGGTTACGCGCTTTGCGGTGCCCAAGGCGATGGGCGAGCAGCGGCTCTATAACAAGACGGGCTCGACTGGCGGCTTTGGCGCCTATGTGGCGTTCGTGCCCGCCAGAGGGATCGCCATCGTCATGCTGGCCAATCGCAACTATCCCATCGAGGCCAGGGTGAAGGCGGCTCACGCCATCCTGAGTCAGTTGGCCGAGTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002162","ARO_id":"38562","ARO_name":"FOX-10","ARO_description":"FOX-10 is a beta-lactamase. From the Lahey list of FOX beta-lactamases.","ARO_category":{"36206":{"category_aro_accession":"3000067","category_aro_cvterm_id":"36206","category_aro_name":"FOX beta-lactamase","category_aro_description":"FOX beta-lactamases are plasmid-encoded AmpC-type beta-lactamase which conferred resistance to broad-spectrum cephalosporins and cephamycins","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"423":{"model_id":"423","model_name":"DHA-16","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1012":{"protein_sequence":{"accession":"AIT76105.1","sequence":"MKKSLSATLVSALLAFSAPGFSAADNVAAVVDSTIKPLMAQQDIPGMAVAVSVKGKPYYFNYGFADVQAKQPVTENTLFELGSVSKTFTGVLGAVSVAKKETSLNDPAVKYQPELTQPQWKGITLLDLATYTAGGLPLQVPEAVKSSEDLLHFYQQWQPSWQPGKMRLYANSSIGLFGALTATAAGMPYEQLLTARILAPLGLSHTFITVPESAQSQYAYGYKNNQPVRVTGGPLDAESYGVKSASKDMLRWAEINMSPSRAGNADLEMAMYLAQTRYYKTAAINQGLGWEMYDWPQQKDMIINGVTNEVALQPHPVTDNQVQPYNRASWVHKTGATTGFGAYVAFIPEKQVAIVILANKNYPNTERVKAAQAILSALE"},"dna_sequence":{"accession":"KM087852","fmin":"0","fmax":"1140","strand":"+","sequence":"ATGAAAAAATCGTTATCTGCAACACTGGTTTCCGCCCTGCTGGCCTTTTCTGCCCCGGGGTTCTCTGCCGCTGATAATGTCGCGGCAGTCGTCGACAGCACCATTAAACCGCTGATGGCACAGCAGGATATCCCCGGGATGGCGGTTGCTGTCTCCGTAAAGGGAAAACCGTATTACTTCAACTATGGTTTTGCGGATGTGCAGGCAAAACAGCCGGTCACTGAAAATACACTATTTGAACTCGGATCTGTAAGTAAAACTTTCACAGGTGTGCTGGGTGCGGTTTCCGTGGCGAAAAAAGAGACGTCGCTGAATGACCCGGCAGTCAAATACCAGCCTGAACTGACACAGCCGCAGTGGAAAGGGATCACATTACTGGATCTGGCCACCTATACCGCAGGCGGGCTGCCGTTACAGGTGCCGGAAGCGGTGAAAAGCAGTGAGGATCTGCTGCATTTCTATCAGCAGTGGCAGCCGTCATGGCAACCGGGAAAGATGCGTCTGTATGCGAACAGCAGTATCGGCCTGTTCGGTGCGCTGACCGCGACAGCGGCGGGAATGCCTTATGAGCAGCTGCTGACCGCACGTATCCTGGCGCCGCTGGGGTTATCACATACCTTTATTACTGTACCGGAAAGTGCGCAAAGTCAGTATGCATACGGTTATAAAAACAATCAGCCGGTACGGGTGACGGGGGGACCGCTCGATGCGGAATCTTACGGGGTAAAATCCGCCTCAAAAGATATGCTGCGCTGGGCAGAAATCAATATGTCGCCGTCACGGGCGGGCAATGCGGATCTGGAAATGGCGATGTATCTCGCACAGACCCGTTACTATAAAACGGCGGCAATCAACCAGGGACTGGGCTGGGAGATGTATGACTGGCCGCAGCAGAAAGATATGATCATTAACGGCGTGACCAATGAAGTGGCATTGCAGCCGCATCCGGTAACGGATAATCAGGTTCAGCCGTATAACCGCGCTTCCTGGGTACATAAAACAGGAGCAACAACCGGTTTCGGTGCTTATGTGGCCTTTATTCCGGAAAAACAGGTGGCGATTGTGATTCTGGCAAATAAAAACTACCCGAATACCGAAAGAGTCAAAGCCGCACAGGCTATTTTGAGTGCACTGGAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36917","NCBI_taxonomy_name":"Morganella morganii","NCBI_taxonomy_id":"582"}}}},"ARO_accession":"3002147","ARO_id":"38547","ARO_name":"DHA-16","ARO_description":"DHA-16 is a beta-lactamase. From the Lahey list of DHA beta-lactamases.","ARO_category":{"36207":{"category_aro_accession":"3000068","category_aro_cvterm_id":"36207","category_aro_name":"DHA beta-lactamase","category_aro_description":"DHA beta-lactamases are plasmid-mediated AmpC \u03b2-lactamases that confer resistance to cephamycins and oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"424":{"model_id":"424","model_name":"SHV-36","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1392":{"protein_sequence":{"accession":"AAL82592.1","sequence":"MRYVRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AF467947","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001094","ARO_id":"37474","ARO_name":"SHV-36","ARO_description":"SHV-36 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"425":{"model_id":"425","model_name":"TEM-182","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1570":{"protein_sequence":{"accession":"ADP20705.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMISTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRLEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDELNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"HQ317449","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATTAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTTGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACTAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36927","NCBI_taxonomy_name":"Haemophilus parainfluenzae","NCBI_taxonomy_id":"729"}}}},"ARO_accession":"3001373","ARO_id":"37773","ARO_name":"TEM-182","ARO_description":"TEM-182 is a beta-lactamase found in clinical isolates of H. parainfluenzae","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"426":{"model_id":"426","model_name":"aadK","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4310":{"protein_sequence":{"accession":"CAB14620.1","sequence":"MRSEQEMMDIFLDFALNDERIRLVTLEGSRTNRNIPPDNFQDYDISYFVTDVESFKENDQWLEIFGKRIMMQKPEDMELFPPELGNWFSYIILFEDGNKLDLTLIPIREAEDYFANNDGLVKVLLDKDSFINYKVTPNDRQYWIKRPTAREFDDCCNEFWMVSTYVVKGLARNEILFAIDHLNEIVRPNLLRMMAWHIASQKGYSFSMGKNYKFMKRYLSNKEWEELMSTYSVNGYQEMWKSLFTCYALFRKYSKAVSEGLAYKYPDYDEGITKYTEGIYCSVK"},"dna_sequence":{"accession":"AL009126","fmin":"2735681","fmax":"2736536","strand":"-","sequence":"TCACTTTACTGAGCAATAAATACCTTCCGTATACTTAGTAATACCTTCATCGTAATCAGGATACTTATATGCAAGACCTTCTGATACAGCTTTTGAATACTTTCTAAATAATGCATAGCAAGTAAATAAAGACTTCCACATTTCCTGATACCCATTCACAGAATATGTAGACATGAGTTCCTCCCATTCTTTATTTGAAAGGTACCGCTTCATAAATTTATAGTTCTTCCCCATACTAAATGAATACCCTTTCTGAGATGCGATATGCCAGGCCATCATTCTCAATAAATTAGGACGTACAATTTCATTTAAATGGTCAATGGCAAAAAGGATTTCATTTCTTGCTAGTCCTTTTACTACGTAAGTCGAAACCATCCAGAACTCATTACAGCAATCATCAAATTCCCTTGCAGTCGGCCTTTTTATCCAGTATTGGCGATCATTTGGGGTCACTTTATAGTTGATGAACGAATCCTTATCAAGCAATACCTTAACCAAACCATCGTTATTAGCAAAATAATCTTCTGCTTCACGAATTGGAATAAGGGTTAGATCTAATTTGTTGCCATCCTCAAAAAGAATAATGTATGAAAACCAATTACCTAATTCGGGAGGAAAAAGCTCCATATCTTCTGGTTTTTGCATCATAATGCGCTTCCCAAAGATTTCGAGCCACTGATCATTTTCTTTAAAAGATTCTACATCAGTTACAAAATACGAGATGTCATAATCTTGGAAGTTGTCAGGAGGGATATTTCTGTTTGTACGTGACCCTTCCAAAGTGACCAATCGGATTCTCTCATCGTTCAAAGCAAAGTCCAAAAAAATGTCCATCATTTCCTGCTCACTTCGCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39579","NCBI_taxonomy_name":"Bacillus subtilis subsp. subtilis str. 168","NCBI_taxonomy_id":"224308"}}}},"ARO_accession":"3002627","ARO_id":"39027","ARO_name":"aadK","ARO_description":"aadK is a chromosomal-encoded aminoglycoside nucleotidyltransferase gene in B. subtilis and Bacillus spp.","ARO_category":{"36364":{"category_aro_accession":"3000225","category_aro_cvterm_id":"36364","category_aro_name":"ANT(6)","category_aro_description":"Nucelotidylylation of streptomycin at the hydroxyl group at position 6","category_aro_class_name":"AMR Gene Family"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"427":{"model_id":"427","model_name":"OCH-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1900":{"protein_sequence":{"accession":"CAC17627.1","sequence":"MRKSTTLLIGFLTTAAIIPNSGALAASKVNDGDLRRIVDETVRPLMAEQKIPGMAVAITIDGKSHFFGYGVASKESGQKVTEDTIFEIGSVSKTFTAMLGGYGLATGAFSLSDPATKWAPELAGSSFDKITMRDLGTYTPGGLPLQFPDAVTDDSSMLAYFKKWKPDYPAGTQRRYSNPSIGLFGYLAARSMDKPFDVLMEQKLLPAFGLKNTFINVPASQMKNYAYGYSKANKPIRVSGGALDAQAYGIKTTALDLARFVELNIDSSSLEPDFQKAVAATHTGYYHVGANNQGLGWEFYNYPTALKTLLAGNSSDMALKSHKIEKFDTPRQPSADVWLNKTGSTNGFGAYAAFIPAKKTGIVLLANRNYPIDERVKAAYRILQALDNKQ"},"dna_sequence":{"accession":"AJ295345","fmin":"0","fmax":"1173","strand":"+","sequence":"ATGAGAAAATCTACGACACTTTTGATCGGTTTCCTCACCACTGCCGCTATTATCCCGAATAGCGGCGCGCTGGCTGCGAGCAAGGTGAATGATGGCGACTTGCGCCGTATTGTCGATGAAACGGTGCGCCCGCTCATGGCCGAGCAGAAAATCCCCGGCATGGCGGTTGCCATAACCATCGACGGCAAGAGCCACTTCTTCGGTTATGGTGTGGCATCGAAAGAAAGCGGGCAAAAAGTCACTGAAGACACGATTTTCGAGATCGGTTCGGTCAGCAAGACCTTCACTGCAATGCTTGGCGGTTACGGGCTGGCGACAGGCGCGTTCTCCCTGTCCGATCCCGCGACCAAATGGGCTCCTGAACTGGCAGGCAGCAGCTTCGACAAGATCACCATGCGTGATCTTGGGACCTACACGCCGGGCGGATTGCCCCTCCAGTTTCCCGATGCTGTCACCGATGACAGTTCGATGCTGGCATATTTCAAGAAATGGAAGCCGGACTATCCGGCAGGGACGCAGCGTCGCTATTCGAATCCCAGCATCGGCCTGTTCGGCTATCTGGCGGCACGAAGCATGGACAAGCCGTTCGACGTTTTGATGGAGCAAAAGCTTCTGCCTGCATTCGGCCTGAAGAACACCTTCATCAATGTGCCGGCAAGCCAGATGAAGAACTACGCCTACGGCTATTCCAAAGCCAACAAGCCGATCCGGGTATCGGGCGGGGCGCTGGATGCACAAGCCTATGGCATCAAGACCACCGCGCTTGATCTTGCCCGCTTCGTCGAACTGAACATCGACAGCTCATCTCTGGAGCCTGATTTCCAGAAAGCCGTCGCCGCAACGCATACCGGTTACTACCATGTCGGAGCGAACAATCAGGGACTTGGCTGGGAGTTCTACAACTATCCGACTGCGCTCAAGACACTTCTTGCCGGCAATTCGTCGGACATGGCGCTGAAGTCGCACAAAATCGAGAAATTCGATACACCTCGCCAACCGTCAGCTGATGTGTGGCTCAACAAGACAGGCTCAACCAACGGCTTTGGCGCTTATGCGGCCTTTATTCCTGCGAAGAAGACCGGAATTGTTCTGCTTGCCAACCGGAATTATCCGATCGATGAGCGCGTAAAGGCTGCCTATCGGATATTGCAGGCGCTCGACAACAAGCAATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37077","NCBI_taxonomy_name":"Ochrobactrum anthropi","NCBI_taxonomy_id":"529"}}}},"ARO_accession":"3002520","ARO_id":"38920","ARO_name":"OCH-7","ARO_description":"OCH-7 beta-lactamase is an Ambler class C chromosomal-encoded beta-lactamases in Ochrobactrum anthropi","ARO_category":{"36233":{"category_aro_accession":"3000094","category_aro_cvterm_id":"36233","category_aro_name":"OCH beta-lactamase","category_aro_description":"OCH beta-lactamases are Ambler class C chromosomal-encoded beta-lactamases in Ochrobactrum anthropi","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"428":{"model_id":"428","model_name":"OXY-2-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1618":{"protein_sequence":{"accession":"CAA88908.1","sequence":"MIKSSWRKIAMLAAAVPLLLASGALWASTDAIHQKLTDLEKRSGGRLGVALINTADNSQILYRGDERFAMCSTSKVMAAAAVLKQSESNKEVVNKRLEINAADLVVWSPITEKHLQSGMTLAELSAATLQYSDNTAMNLIIGYLGGPEKVTAFARSIGDATFRLDRTEPTLNTAIPGDERDTSTPLAMAESLRKLTLGDALGEQQRAQLVTWLKGNTTGGQSIRAGLPESWVVGDKTGAGDYGTTNDIAVIWPEDHAPLVLVTYFTQPQQDAKNRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"Z49084","fmin":"311","fmax":"1184","strand":"+","sequence":"ATGATAAAAAGTTCGTGGCGTAAAATTGCAATGCTAGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGCGCACTGTGGGCCAGTACCGATGCTATCCATCAGAAGCTGACAGATCTCGAGAAGCGTTCAGGCGGCAGGTTGGGCGTGGCGCTAATCAACACGGCAGATAATTCTCAAATCTTATATCGCGGCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCCGCCGCCGCGGTATTAAAACAGAGCGAAAGCAATAAAGAGGTGGTAAATAAAAGGCTGGAGATTAACGCAGCCGATTTGGTGGTCTGGAGTCCGATTACCGAAAAACATCTCCAGAGCGGAATGACGCTGGCTGAGCTAAGCGCGGCGACGCTGCAATATAGCGACAATACGGCGATGAATCTGATCATCGGCTACCTTGGCGGGCCGGAAAAAGTCACCGCCTTCGCCCGCAGTATCGGCGATGCCACCTTTCGTCTCGATCGTACGGAGCCCACGCTGAATACCGCCATCCCGGGCGATGAGCGTGATACCAGCACGCCGCTGGCGATGGCTGAAAGCCTACGCAAGCTGACGCTTGGCGATGCGCTGGGCGAACAGCAACGCGCCCAGTTAGTCACCTGGCTGAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCGGGCCTGCCTGAAAGCTGGGTGGTCGGCGATAAAACCGGCGCCGGAGATTACGGCACCACCAATGATATTGCGGTTATCTGGCCGGAAGATCACGCTCCGCTGGTATTAGTCACCTACTTTACCCAGCCGCAGCAGGATGCGAAAAACCGCAAAGAGGTGTTAGCCGCAGCGGCAAAAATCGTGACCGAAGGGCTTTAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002402","ARO_id":"38802","ARO_name":"OXY-2-7","ARO_description":"OXY-2-7 is a beta-lactamase found in Klebsiella oxytoca","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"429":{"model_id":"429","model_name":"mdsA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"770"}},"model_sequences":{"sequence":{"4324":{"protein_sequence":{"accession":"NP_459347.3","sequence":"MRRTFKIMLIAGVIAAIGGVIYMAGEALWDKDNAVGPPASAPPPPSVPVAKALSRTLAPTAEFTGFLAAPETVELRSRVGGTLDAISVPEGRLVSRGQLLFQIDPRPFEVALDTAVAQLRQAEVLARQAQADFDRIQRLVASGAVSRKNADDVTATRNARQAQMQSAKAAVAAARLELSWTRITAPIAGRVDRILVTRGNLVSGGVAGNATLLTTIVSHNPMYVYFDIDEATWLKALRHTRSDKNPPVVNMGLTTDNGLPYQGVLDFMGNQMNRSTGTIRARAVIPDPDGMLSPGLFARISLPIGEPRETVLIDDLAVSADQGKNYVLIVGKENQVEYRPVELGQMVDGFRVVTQGVLPGEKIILKGLVRPGMTVAPRLVPMRQNVTDKQTATLTKADGDSAPKAVRQ"},"dna_sequence":{"accession":"NC_003197.2","fmin":"397057","fmax":"398284","strand":"-","sequence":"TCATTGGCGCACCGCCTTCGGCGCACTGTCGCCGTCCGCTTTAGTCAATGTCGCGGTCTGTTTGTCGGTCACATTCTGCCGCATCGGCACCAGACGTGGCGCAACGGTCATGCCAGGACGCACCAGCCCCTTGAGGATGATTTTTTCTCCCGGCAGTACTCCCTGTGTAACGACGCGGAATCCATCGACCATTTGTCCCAACTCAACCGGACGATACTCCACCTGATTCTCCTTGCCGACGATCAGCACATAGTTTTTGCCCTGATCGGCGCTCACCGCCAGATCGTCAATCAGCACGGTTTCCCGCGGCTCGCCGATGGGCAAACTGATTCGGGCAAACAGGCCGGGAGAAAGCATTCCGTCGGGGTCAGGAATCACGGCGCGTGCCCGGATAGTGCCGGTGCTGCGGTTCATCTGATTGCCCATAAAGTCGAGTACGCCCTGATAAGGCAGCCCGTTATCGGTGGTTAACCCCATGTTGACTACCGGTGGATTTTTGTCGGAGCGGGTATGCCGTAACGCCTTCAGCCAGGTGGCTTCGTCAATATCGAAATACACATACATGGGATTGTGAGACACGATAGTCGTCAGAAGCGTGGCGTTACCCGCTACGCCGCCGCTGACCAGATTGCCCCGGGTCACCAGTATGCGGTCAACGCGTCCGGCAATGGGCGCGGTAATACGGGTCCAGGAGAGTTCAAGGCGCGCTGCGGCGACGGCGGCTTTGGCCGATTGCATCTGCGCCTGTCGCGCATTACGCGTGGCGGTGACATCGTCAGCGTTTTTACGTGATACGGCGCCGCTGGCGACCAGTCGTTGAATGCGATCGAAATCCGCCTGCGCCTGGCGGGCCAGTACTTCAGCCTGACGTAATTGCGCGACGGCGGTGTCGAGGGCGACCTCGAACGGGCGCGGATCGATCTGGAACAGCAGTTGTCCGCGGCTTACCAGACGTCCTTCCGGAACGCTGATGGCGTCAAGGGTTCCTCCCACGCGCGAACGCAGCTCCACGGTTTCCGGCGCGGCCAGAAAACCGGTGAATTCCGCCGTAGGCGCGAGTGTACGGCTAAGGGCTTTAGCAACCGGTACCGACGGTGGAGGCGGCGCGCTGGCCGGGGGGCCGACGGCGTTGTCTTTATCCCATAGTGCTTCGCCGGCCATGTAAATCACGCCCCCGATGGCGGCGATGACGCCGGCTATCAACATAATTTTGAATGTTCTACGCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35734","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium str. LT2","NCBI_taxonomy_id":"99287"}}}},"ARO_accession":"3000789","ARO_id":"37169","ARO_name":"mdsA","ARO_description":"MdsA is the membrane fusion protein of the multidrug and metal efflux complex MdsABC.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"430":{"model_id":"430","model_name":"OXA-87","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"981":{"protein_sequence":{"accession":"ABC84263.1","sequence":"MNIKTLLLITSTIFISACSPYIVTANPNHSTSKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASIEYVPASTFKMLNALIGLEHHKATTTEIFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSLKAQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"DQ348075","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCACTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCACTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGATCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAATATTTAAGTGGGACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGTGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCTAAAAGCCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001704","ARO_id":"38104","ARO_name":"OXA-87","ARO_description":"OXA-87 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"432":{"model_id":"432","model_name":"sav1866","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1120"}},"model_sequences":{"sequence":{"4311":{"protein_sequence":{"accession":"YP_186749.1","sequence":"MIKRYLQFVKPYKYRIFATIIVGIIKFGIPMLIPLLIKYAIDGVINNHALTTDEKVHHLTIAIGIALFIFVIVRPPIEFIRQYLAQWTSNKILYDIRKKLYNHLQALSARFYANNQVGQVISRVINDVEQTKDFILTGLMNIWLDCITIIIALSIMFFLDVKLTLAALFIFPFYILTVYVFFGRLRKLTRERSQALAEVQGFLHERVQGISVVKSFAIEDNEAKNFDKKNTNFLTRALKHTRWNAYSFAAINTVTDIGPIIVIGVGAYLAISGSITVGTLAAFVGYLELLFGPLRRLVASFTTLTQSFASMDRVFQLIDEDYDIKNGVGAQPIEIKQGRIDIDHVSFQYNDNEAPILKDINLSIEKGETVAFVGMSGGGKSTLINLIPRFYDVTSGQILIDGHNIKDFLTGSLRNQIGLVQQDNILFSDTVKENILLGRPTATDEEVVEAAKMANAHDFIMNLPQGYDTEVGERGVKLSGGQKQRLSIARIFLNNPPILILDEATSALDLESESIIQEALDVLSKDRTTLIVAHRLSTITHADKIVVIENGHIVETGTHRELIAKQGAYEHLYSIQNL"},"dna_sequence":{"accession":"NC_002951","fmin":"1987719","fmax":"1989456","strand":"-","sequence":"TTATAAGTTTTGAATGCTATATAAATGCTCGTAAGCACCTTGTTTTGCAATCAATTCACGATGCGTACCTGTTTCAACAATATGTCCATTTTCAATTACGACAATTTTGTCAGCATGTGTAATAGTGGACAAGCGATGCGCTACGATAAGTGTCGTTCGATCTTTACTCAACACATCTAATGCTTCTTGAATAATGGATTCACTTTCTAAATCAAGTGCACTTGTTGCTTCATCCAAGATAAGAATTGGCGGATTATTTAAAAATATTCTAGCAATCGATAATCTTTGTTTTTGACCACCTGATAATTTAACACCTCGTTCACCTACTTCAGTGTCATATCCCTGTGGCAAGTTCATAATAAAGTCATGTGCATTAGCCATTTTCGCCGCTTCAACTACTTCTTCATCTGTTGCTGTTGGACGACCAAGTAAAATATTTTCCTTAACTGTATCAGAGAATAAAATATTATCCTGTTGCACCAATCCTATTTGATTTCTTAAACTTCCCGTTAAAAAATCTTTAATGTTGTGACCATCTATTAAAATTTGCCCAGAAGTTACATCGTAAAATCTCGGTATTAAGTTAATTAATGTTGATTTACCACCACCACTCATACCTACGAAAGCAACTGTTTCTCCTTTTTCAATACTCAAATTAATATCTTTTAAAATTGGAGCTTCGTTATCGTTATATTGAAAACTAACATGATCAATATCAATACGACCTTGTTTAATTTCAATAGGTTGAGCACCAACACCATTTTTGATGTCATAATCTTCATCAATTAATTGGAATACACGGTCCATTGAAGCAAAACTTTGCGTTAAAGTTGTAAATGATGCGACTAAACGACGTAAAGGCCCGAACAATAACTCTAAGTATCCAACAAATGCTGCAAGTGTACCTACTGTGATTGATCCAGAAATAGCAAGATATGCACCAACACCGATGACAATAATTGGTCCAATATCTGTAACTGTATTAATTGCGGCAAAGGAATAGGCATTCCATCTTGTATGTTTCAACGCACGTGTTAGGAAATTAGTATTCTTTTTATCAAAGTTTTTCGCTTCATTGTCTTCAATCGCAAAACTTTTAACGACTGAAATACCTTGAACACGTTCATGCAAGAATCCTTGAACCTCAGCTAATGCTTGAGATCTTTCACGTGTCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATACAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTAAATGGTTGTATAACTTTTTACGTATATCATACAATATTTTATTACTTGTCCATTGCGCCAAATATTGACGTATAAATTCAATTGGTGGTCTCACTATTACAAAAATAAATAATGCGATACCAATGGCAATAGTTAAATGATGAACTTTTTCATCAGTCGTTAGTGCGTGGTTATTAATCACGCCATCTATTGCATATTTAATTAATAGTGGTATAAGCATTGGTATACCAAACTTAATTATCCCAACAATAATCGTTGCAAAAATACGATATTTGTATGGCTTAACAAATTGCAAATATCGTTTAATCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35512","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus COL","NCBI_taxonomy_id":"93062"}}}},"ARO_accession":"3000489","ARO_id":"36628","ARO_name":"sav1866","ARO_description":"Sav1866 is a multidrug efflux pump in the Gram-positive Staphylococcus aureus. It is a homolog of the human ABC transporter Mdr1 and pumps out toxic compounds including verapamil, tetraphenylphosphorchloride, and Hoechst 33342.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"433":{"model_id":"433","model_name":"ACT-25","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"861":{"protein_sequence":{"accession":"AHL39338.1","sequence":"MMKKSLCCALLLGLSCSALAAPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKSHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPEKVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYHILKALQ"},"dna_sequence":{"accession":"KJ207208","fmin":"539","fmax":"1685","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTGGGCCTCTCTTGCTCTGCTCTCGCCGCGCCAGTATCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAATCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACAGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAAGGTTGCCGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAAGGCAGCGACAGTAAGGTAGCGCTGGCGCCATTACCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGTTCTACTGGCGGATTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCAAGGCGCTTCAGTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001845","ARO_id":"38245","ARO_name":"ACT-25","ARO_description":"ACT-25 is a beta-lactamase. From the Lahey list of ACT beta-lactamases.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"434":{"model_id":"434","model_name":"LEN-16","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1347":{"protein_sequence":{"accession":"AAU89706.1","sequence":"MRYVRLCVISLLATLPLAVYAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGLEQLDRRIHYRQQDLVDYSPVSEKHLTDGMTIGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPPGWFIADKTGAGERGARGIVALLGPDGKPERIVVIYLRDTPASMAERNQHIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AY743416","fmin":"67","fmax":"928","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCACCCTGCCACTGGCGGTATACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCGGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTACCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGCCGGGCTGGTTTATCGCCGACAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCAACGCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002464","ARO_id":"38864","ARO_name":"LEN-16","ARO_description":"LEN-16 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"435":{"model_id":"435","model_name":"OKP-A-9","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1919":{"protein_sequence":{"accession":"CAJ19607.1","sequence":"MRYVRLCLISLIAALPLAVFASPPPLEQITRSESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKALLCGAVLARVDAGDEQLDRRIRYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKSVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMAATLRKLLTSHALSDRSQQQLLQWMVDDQVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPNGKAERIVVIYLRDTPATMAERNQQIAKIGAALIEHWQR"},"dna_sequence":{"accession":"AM051148","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCCGCCGCTTGAGCAAATTACACGCAGCGAAAGTCAGCTGGCGGGCCGCGTGGGCTATGTTGAAATGGATCTGGCGAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGCGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGAGACGAACAGCTGGATCGGCGGATCCGCTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGAGCGTTGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAGCTCAATGAAGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCAGCCAGCATGGCCGCCACCCTGCGCAAGCTGCTAACCAGCCACGCGCTGAGCGACCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGACCAGGTGGCCGGTCCGCTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGCGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGAACGGCAAAGCGGAGCGCATCGTGGTGATCTATCTGCGGGATACGCCGGCGACCATGGCCGAGCGTAACCAGCAGATCGCCAAAATAGGCGCGGCGCTGATCGAGCACTGGCAGCGCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002426","ARO_id":"38826","ARO_name":"OKP-A-9","ARO_description":"OKP-A-9 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"436":{"model_id":"436","model_name":"OXY-4-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1939":{"protein_sequence":{"accession":"AAL78161.1","sequence":"MLKSSWRKSALMAAAVPLLLASGSLWASADTLQQKLADLEKRSGGRLGVALINTADDSQTLYRGDERFAMCSTGKVMAAAAVLKQSESHPDVVNKRLEIKKSDLVVWSPITEKHLQSGMTLAELSAAALQYSDNTAMNKIIGYLGGPEKVTAFAQSIGDVTFRLDRMEPALNSAIPGDKRDTTTPLAMAESLRKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPASWAVGDKTGGGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKSRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"AY077481","fmin":"185","fmax":"1058","strand":"+","sequence":"ATGTTGAAAAGTTCGTGGCGTAAAAGCGCCCTGATGGCCGCCGCCGTTCCGCTACTGCTGGCGAGCGGTTCATTATGGGCCAGTGCCGATACTCTCCAGCAGAAGCTGGCTGATTTAGAAAAACGTTCCGGCGGTCGGCTGGGCGTGGCGCTGATTAACACGGCAGATGATTCGCAGACCCTCTATCGCGGCGACGAACGTTTTGCCATGTGCAGCACCGGTAAAGTGATGGCCGCCGCCGCGGTGTTAAAACAGAGCGAAAGCCATCCCGATGTGGTGAATAAAAGGCTGGAGATTAAAAAATCGGATTTAGTGGTCTGGAGCCCGATTACCGAAAAACATCTGCAAAGCGGAATGACCCTGGCGGAACTCAGCGCTGCGGCGCTGCAGTATAGCGACAATACCGCGATGAATAAGATTATCGGTTACCTTGGCGGGCCGGAAAAAGTCACCGCATTCGCCCAGAGCATCGGTGACGTTACTTTTCGTCTCGATCGGATGGAGCCGGCGCTGAACAGCGCGATTCCCGGTGATAAGCGCGATACCACCACCCCATTGGCGATGGCCGAAAGTCTGCGTAAGCTGACGCTGGGCAATGCGCTGGGCGAACAGCAGCGCGCCCAGTTAGTGACATGGCTGAAAGGCAATACCACCGGCGGGCAAAGCATTCGTGCAGGCCTGCCCGCAAGCTGGGCGGTCGGGGATAAAACCGGCGGCGGAGATTACGGCACCACCAACGATATCGCGGTGATCTGGCCGGAAAATCATGCTCCGCTGGTGCTAGTGACCTATTTTACCCAACCGCAGCAGGATGCGAAAAGCCGCAAAGAGGTGCTAGCCGCGGCGGCGAAAATCGTGACCGAAGGGCTTTAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002410","ARO_id":"38810","ARO_name":"OXY-4-1","ARO_description":"OXY-4-1 is a beta-lactamase found in Klebsiella oxytoca","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"437":{"model_id":"437","model_name":"SHV-69","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1317":{"protein_sequence":{"accession":"ABA06590.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLTDGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"DQ174308","fmin":"4","fmax":"865","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTACCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGGATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001123","ARO_id":"37503","ARO_name":"SHV-69","ARO_description":"SHV-69 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"438":{"model_id":"438","model_name":"VIM-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"936":{"protein_sequence":{"accession":"AAN84550.1","sequence":"MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATRSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGSEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"AY165025","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCGGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAGCGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAGC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36803","NCBI_taxonomy_name":"Pseudomonas putida","NCBI_taxonomy_id":"303"}}}},"ARO_accession":"3002276","ARO_id":"38676","ARO_name":"VIM-6","ARO_description":"VIM-6 is a beta-lactamase found in Pseudomonas spp.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"439":{"model_id":"439","model_name":"SHV-83","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1318":{"protein_sequence":{"accession":"CAJ47138.2","sequence":"KRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM176558","fmin":"0","fmax":"861","strand":"+","sequence":"AAGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGGATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001137","ARO_id":"37517","ARO_name":"SHV-83","ARO_description":"SHV-83 is a broad-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"441":{"model_id":"441","model_name":"OXA-54","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"893":{"protein_sequence":{"accession":"AAR89917.1","sequence":"MRVLALSAVLVVASIVGMPAMANEWQEKPSWNTHFSEHKAQGVIVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIAAWNRDHDLITAMKYSVVPVYQEFARQIGQARMSKMLHAFDYGNEDISGNLDSFWLDGGIRISATEQVAFLRKLYHNKLHVSERSQRIVKQAMLTEANSDYIIRAKTGYSTRIEPQIGWWVGWVELDDNVWFFAMNMDMPTADGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"AY500137","fmin":"0","fmax":"798","strand":"+","sequence":"ATGCGTGTGTTAGCCTTATCGGCTGTATTAGTGGTGGCATCGATTGTTGGCATGCCGGCGATGGCAAACGAATGGCAGGAAAAACCGAGTTGGAATACTCATTTTTCGGAACATAAAGCGCAGGGTGTGATAGTGCTTTGGAACGAGAACAAACAGCAAGGATTTACCAATAATCTTAAGCGGGCAAACCAAGCATTTTTACCCGCATCGACCTTTAAAATCCCCAATAGCTTGATTGCCTTGGATTTAGGTGTCGTGAAGGATGAGCATCAAGTCTTTAAATGGGATGGACAGACTCGGGATATCGCGGCGTGGAATCGCGACCATGACTTAATCACTGCGATGAAATACTCGGTCGTGCCCGTGTATCAAGAGTTTGCGCGCCAAATTGGGCAGGCGCGCATGAGTAAAATGTTGCACGCATTTGATTATGGCAATGAAGATATTTCGGGCAATCTAGACAGCTTTTGGCTCGATGGCGGCATTCGGATTTCGGCAACGGAGCAAGTCGCATTTCTACGAAAGCTGTATCATAACAAGTTGCATGTATCAGAACGCAGTCAGCGTATCGTCAAGCAAGCCATGCTTACCGAGGCTAATAGTGACTACATAATCCGCGCTAAAACCGGATACTCGACCAGAATTGAGCCTCAGATCGGTTGGTGGGTCGGTTGGGTTGAACTCGATGATAATGTGTGGTTCTTCGCGATGAATATGGATATGCCTACGGCTGATGGTTTAGGGCTACGTCAAGCCATCACTAAAGAAGTGCTTAAACAGGAAAAGATAATTCCATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36933","NCBI_taxonomy_name":"Shewanella oneidensis","NCBI_taxonomy_id":"70863"}}}},"ARO_accession":"3001812","ARO_id":"38212","ARO_name":"OXA-54","ARO_description":"OXA-54 is a beta-lactamase found in Shewanella spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"442":{"model_id":"442","model_name":"opmD","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"920"}},"model_sequences":{"sequence":{"548":{"protein_sequence":{"accession":"NP_252897.1","sequence":"MKRSYPNLSRLALALAVGTGLAACSVGPDYQRPQSPPPRVASEHLGEFSGERREAPWWSFFDDPQLVRLVDQALARNHDIREARANLRSARALFDDRWLDQLPQVTSQAGYSRSIEQQLDYDGEPRRRLAESYRAGFDAQWEIDLFGRLGRLSDAALARAEAADADLRLVRLSIAADTARAYFEIQGYQRRLDVARAQVRSWRDTLELTRSSLQLGSGLPEDVENAQANLLRSEAAIPPLTTALESARYRLDVLRGEAPGSGAPILDGGAAAPLAKNLPLGDVDRLILQRPDVVSAERQLAASTEDVGAATAELYPRLDLGGFIGFFALRSGDLGSASRAFELAPSVSWPAFRLGNVRARLRAVEAQSDAALARYQRSLLLAQEDVGNALNQLAEHQRRLVALFQSATHGANALEIANERYRAGAGSYLAVLENQRALYQIREELAQAETASFVNVIALYKALGWGSGDLAPGAGQLAAGETAGANR"},"dna_sequence":{"accession":"NC_002516","fmin":"4710620","fmax":"4712084","strand":"+","sequence":"ATGAAGCGCTCCTACCCGAACCTTTCGCGCCTGGCGCTGGCCCTGGCGGTCGGCACCGGCCTGGCCGCCTGCAGCGTCGGCCCCGACTACCAGCGTCCGCAGTCGCCGCCGCCACGCGTCGCCAGCGAGCACCTCGGCGAGTTCTCCGGCGAGCGGCGGGAAGCGCCCTGGTGGAGTTTCTTCGACGATCCGCAACTGGTGCGCCTGGTCGACCAGGCGCTGGCGCGCAACCACGACATCCGCGAGGCCCGCGCCAACCTGCGCAGCGCCCGCGCGCTGTTCGACGACCGCTGGCTCGACCAGTTGCCGCAGGTCACCAGCCAGGCCGGCTACAGCCGCAGCATCGAACAACAGCTGGACTACGACGGCGAGCCGCGCCGGCGCCTGGCGGAGAGCTACCGCGCCGGCTTCGACGCGCAGTGGGAAATCGACCTGTTCGGCCGCCTCGGCCGACTTTCCGACGCCGCCTTGGCCCGCGCCGAAGCGGCCGACGCCGACCTCCGGCTGGTACGCCTGAGCATCGCCGCCGACACCGCCCGCGCCTACTTCGAGATCCAGGGCTACCAGCGCCGGCTGGACGTGGCGCGCGCCCAGGTGCGCAGTTGGCGCGACACCCTGGAGCTGACCCGCAGCAGCCTGCAACTGGGCAGCGGCCTGCCGGAGGACGTGGAGAACGCCCAGGCCAACCTGCTGCGCAGCGAAGCGGCGATTCCGCCACTGACGACCGCGCTGGAGAGCGCCCGCTATCGCCTCGACGTGCTGCGCGGCGAGGCACCCGGCAGCGGCGCGCCGATCCTCGACGGCGGCGCCGCCGCGCCATTGGCGAAGAACCTGCCGCTGGGCGACGTCGACCGCCTGATCCTCCAGCGCCCCGACGTAGTCAGCGCCGAGCGGCAACTGGCAGCGAGCACCGAAGACGTCGGCGCGGCCACCGCCGAACTCTATCCGCGCCTCGACCTGGGCGGCTTCATCGGTTTCTTCGCCCTGCGCAGCGGCGACCTCGGCAGCGCCTCGCGCGCCTTCGAACTGGCGCCCAGCGTCAGTTGGCCGGCGTTCCGCCTGGGCAACGTGCGGGCCCGCCTGCGCGCCGTCGAGGCGCAGTCCGACGCCGCGCTGGCGCGCTACCAGCGCTCCCTGCTGCTGGCCCAGGAGGACGTCGGCAACGCGCTCAACCAACTGGCCGAACACCAGCGTCGGCTGGTCGCCCTGTTCCAGTCCGCGACCCATGGCGCGAACGCCCTGGAGATCGCCAACGAACGCTACCGCGCCGGCGCCGGCAGCTACCTGGCGGTGCTGGAGAACCAGCGCGCGCTGTACCAGATCCGCGAGGAACTGGCGCAGGCGGAGACCGCCTCGTTCGTCAACGTCATCGCGCTCTACAAGGCGCTCGGCTGGGGCAGCGGCGACCTGGCGCCGGGCGCCGGCCAACTGGCCGCCGGCGAAACCGCCGGGGCCAACCGTTGAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3000809","ARO_id":"37189","ARO_name":"OpmD","ARO_description":"OpmD is the outer membrane channel protein of the efflux complex MexGHI-OpmD.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavin","category_aro_description":"Acriflavin is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36193":{"category_aro_accession":"3000054","category_aro_cvterm_id":"36193","category_aro_name":"acridine dye","category_aro_description":"Acridine dyes are cell permeable, basic molecules with an acridine chromophore. These compounds intercalate DNA. The image shown represents the core structure of the acridine family, with specific dyes containing varying substituents.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"443":{"model_id":"443","model_name":"OKP-B-10","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"795":{"protein_sequence":{"accession":"CAJ19619.1","sequence":"MRYVRLCLISLIAALPLAVFASPQPLEQIKISESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNTAGNLLLKIVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPANMATTLRKLLTTPSLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPDGKAERIVVIYLRDTAATMAERNQQIAVIGAALIEHWQR"},"dna_sequence":{"accession":"AM051160","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCAGCCGCTTGAGCAGATTAAAATCAGCGAAAGTCAGCTGGCGGGCCGGGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGCGACGAACAGCTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACACCGCCGGCAATCTGCTGTTGAAGATCGTCGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGAACTCAATGAGGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCGGCCAACATGGCCACCACCCTGCGCAAGCTGCTAACCACCCCCTCTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTTGACGACCGGGTGGCCGGCCCGTTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGTGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAAGCGGAGCGTATCGTGGTGATCTATCTGCGGGATACCGCAGCGACCATGGCCGAACGTAACCAGCAGATCGCCGTGATAGGCGCGGCGCTGATCGAGCACTGGCAGCGCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002443","ARO_id":"38843","ARO_name":"OKP-B-10","ARO_description":"OKP-B-10 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"444":{"model_id":"444","model_name":"AAC(6')-Ib-Suzhou","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"83":{"protein_sequence":{"accession":"ABU55430.1","sequence":"MTEHDLAMLYEWLNRSHIVEWWGGEEARPTLADVQEQYLPSVLAQESVTPYIAMLNGEPIGYAQSYVALGSGDGWWEEETDPGVRGIDQLLANASQLGKGLGTKLVRALVELLFNDPEVTKIQTDPSPSNLRAIRCYEKAGFERQGTVTTPDGPAVYMVQTRQAFERTRMDA"},"dna_sequence":{"accession":"EU085533","fmin":"0","fmax":"519","strand":"+","sequence":"ATGACTGAGCATGACCTTGCGATGCTCTATGAGTGGCTAAATCGATCTCATATCGTCGAGTGGTGGGGCGGAGAAGAAGCACGCCCGACACTTGCTGACGTACAGGAACAGTACTTGCCAAGCGTTTTAGCGCAAGAGTCCGTCACTCCATACATTGCAATGCTGAATGGAGAGCCGATTGGGTATGCCCAGTCGTACGTTGCTCTTGGAAGCGGGGACGGATGGTGGGAAGAAGAAACCGATCCAGGAGTACGCGGAATAGACCAGTTACTGGCGAATGCATCACAACTGGGCAAAGGCTTGGGAACCAAGCTGGTTCGAGCTCTGGTTGAGTTGCTGTTCAATGATCCCGAGGTCACCAAGATCCAAACGGACCCGTCGCCGAGCAACTTGCGAGCGATCCGATGCTACGAGAAAGCGGGGTTTGAGAGGCAAGGTACCGTAACCACCCCAGATGGTCCAGCCGTGTACATGGTTCAAACACGCCAGGCATTCGAGCGAACACGCATGGATGCCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3002591","ARO_id":"38991","ARO_name":"AAC(6')-Ib-Suzhou","ARO_description":"AAC(6')-Ib-Suzhou is an aminoglycoside acetyltransferase in E. cloacae and K. pneumoniae","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"445":{"model_id":"445","model_name":"TEM-22","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1725":{"protein_sequence":{"accession":"CAA76795.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGGSERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"Y17583","fmin":"213","fmax":"1071","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGGCAGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000893","ARO_id":"37273","ARO_name":"TEM-22","ARO_description":"TEM-22 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"446":{"model_id":"446","model_name":"catB8","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"3700":{"protein_sequence":{"accession":"YP_009077553.1","sequence":"MKNYFNSPFKGELLSEQVKNPNIRVGRYSYYSGYYHGHSFDECARYLLPDRDDVDKLIIGSFCSIGSGASFIMAGNQGHRHDWASSFPFFYMQEEPAFSRALDAFQRAGDTVIGNDVWIGSEAMIMPGIKIGDGAVIGSRSLVTKDVEPYAIIGGNPAKQIKKRFSDEEISLLMEMEWWNWPLDKIKTAMPLLCSSNIFGLHKYWREFAV"},"dna_sequence":{"accession":"NG_035647.1","fmin":"811","fmax":"1444","strand":"+","sequence":"ATGAAAAACTACTTTAACAGCCCTTTCAAAGGGGAACTTCTTTCTGAGCAAGTGAAAAATCCAAATATCAGAGTAGGCCGGTATAGCTATTACTCTGGCTACTATCACGGGCACTCATTTGATGAATGCGCGCGATACTTGCTTCCAGATCGTGATGACGTTGATAAATTGATCATTGGCAGCTTTTGTTCTATAGGAAGCGGGGCTTCCTTCATCATGGCTGGCAATCAGGGGCATCGGCATGACTGGGCATCATCCTTCCCCTTCTTCTATATGCAAGAGGAGCCTGCTTTCTCAAGAGCACTCGACGCCTTCCAAAGAGCAGGTGATACCGTCATTGGCAATGATGTCTGGATAGGCTCGGAGGCAATGATTATGCCTGGCATCAAAATTGGAGACGGTGCCGTGATAGGTAGTCGCTCGTTGGTGACAAAAGATGTAGAGCCTTATGCCATCATCGGGGGAAATCCCGCAAAGCAAATTAAGAAGCGCTTCTCCGATGAGGAAATCTCATTGCTCATGGAGATGGAGTGGTGGAACTGGCCACTAGATAAAATTAAGACAGCAATGCCTCTGCTGTGCTCGTCAAATATTTTTGGTCTGCATAAGTATTGGCGCGAGTTTGCCGTCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35731","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhi","NCBI_taxonomy_id":"90370"}}}},"ARO_accession":"3002680","ARO_id":"39114","ARO_name":"catB8","ARO_description":"catB8 is a plasmid or integron-encoded variant of the cat gene found in Klebsiella pneumoniae, Salmonella typhi and Pseudomonas aeruginosa","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. cat is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Bacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini","category_aro_class_name":"AMR Gene Family"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"447":{"model_id":"447","model_name":"SHV-67","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1237":{"protein_sequence":{"accession":"ABA06589.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWCADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"DQ174307","fmin":"4","fmax":"865","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGTGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001122","ARO_id":"37502","ARO_name":"SHV-67","ARO_description":"SHV-67 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"448":{"model_id":"448","model_name":"dfrG","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"750":{"protein_sequence":{"accession":"BAE15963.1","sequence":"MKVSLIAAMDKNRVIGKENDIPWRIPKDWEYVKNTTKGHPIILGRKNLESIGRALPDRRNIILTRDKGFTFNGCEIVHSIEDVFELCKNEEEIFIFGGEQIYNLFFPYVEKMYITKIHHEFEGDTFFPEVNYEEWNEVFAQKGIKNDKNPYNYYFHVYERKNLLS"},"dna_sequence":{"accession":"AB205645","fmin":"1012","fmax":"1510","strand":"+","sequence":"ATGAAAGTTTCTTTGATTGCTGCGATGGATAAGAATAGAGTGATTGGCAAAGAGAATGACATTCCTTGGAGGATTCCCAAGGACTGGGAATATGTTAAAAATACTACAAAGGGACATCCGATAATATTAGGTAGGAAGAACCTTGAATCAATCGGAAGAGCCTTACCTGACAGAAGAAATATTATTCTGACGAGAGATAAGGGGTTTACCTTTAATGGTTGTGAAATTGTTCATTCAATAGAAGATGTTTTTGAGTTATGTAAAAACGAAGAAGAAATTTTTATTTTCGGAGGAGAACAGATTTATAATTTGTTTTTCCCTTATGTTGAGAAAATGTACATCACAAAAATACATCATGAATTCGAAGGAGATACTTTTTTTCCAGAAGTGAATTATGAGGAATGGAATGAGGTATTTGCCCAAAAAGGGATAAAGAATGATAAAAATCCGTATAACTACTATTTTCATGTATATGAAAGAAAAAACTTATTGAGTTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3002868","ARO_id":"39302","ARO_name":"dfrG","ARO_description":"dfrG is a plasmid-encoded dihydrofolate reductase found in Staphylococcus aureus","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36408":{"category_aro_accession":"3000269","category_aro_cvterm_id":"36408","category_aro_name":"brodimoprim","category_aro_description":"Brodimoprim is a structural derivative of trimethoprim and an inhibitor of bacterial dihydrofolate reductase. The 4-methoxy group of trimethoprim is replaced with a bromine atom.","category_aro_class_name":"Antibiotic"},"36423":{"category_aro_accession":"3000284","category_aro_cvterm_id":"36423","category_aro_name":"tetroxoprim","category_aro_description":"Tetroxoprim is a trimethoprim derivative that inhibits bacterial dihydrofolate reductase.","category_aro_class_name":"Antibiotic"},"36476":{"category_aro_accession":"3000337","category_aro_cvterm_id":"36476","category_aro_name":"iclaprim","category_aro_description":"Iclaprim is a bactericidal compound that inhibits dihydrofolate reductase. It is used against clinically important Gram-positive pathogens, including methicillin-sensitive Staphylococcus aureus and methicillin-resistant S. aureus.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"449":{"model_id":"449","model_name":"SHV-133","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1144":{"protein_sequence":{"accession":"BAI94487.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDGVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AB551737","fmin":"14","fmax":"875","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATGGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATATATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001177","ARO_id":"37557","ARO_name":"SHV-133","ARO_description":"SHV-133 is a beta-lactamase.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"450":{"model_id":"450","model_name":"OXA-51","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2013":{"protein_sequence":{"accession":"CAC83905.2","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"AJ309734","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001612","ARO_id":"38012","ARO_name":"OXA-51","ARO_description":"OXA-51 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"40512":{"category_aro_accession":"3003821","category_aro_cvterm_id":"40512","category_aro_name":"BAL30072","category_aro_description":"BAL30072 is a monocyclic beta-lactam antibiotic belonging to the sulfactams. BAL30072 was found to trigger the spheroplasting and lysis of Escherichia coli rather than the formation of extensive filaments.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"451":{"model_id":"451","model_name":"LRA-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"4313":{"protein_sequence":{"accession":"ACH59002.1","sequence":"MKTIFGKRRQSAVVLITLIAILLASGQPYQSSQVRGAACLPDIIFDEPSQGPEKNEAISMLTERLSSIINAAGGDIGIAVIHVETGHTTAIQGTTQLPLYSVFKLPLAIAVLKEIEENRLQLDRKVRVTPADVAPGWTANAAMWRRPIDRTVAQLIEVSIIRSDNTSSDKLLQLVGGPAAVTHRMRALGFPNIEIVSTVREFSENRTRPNTGSAEDLARLLVQLQKGELLQPQHSALLLGFMHRATTGTERLRGSLPVGTPVADKTGTGDAGVVTNDVGIITLPKGQGHLAIAVLISGSKLSPAAQEKLIAEIARAAYDAHVSRAE"},"dna_sequence":{"accession":"EU408358","fmin":"27458","fmax":"28439","strand":"-","sequence":"TCACTCCGCACGAGAAACGTGAGCGTCATAAGCGGCTCGTGCAATTTCGGCAATGAGCTTTTCTTGTGCCGCGGGTGACAGTTTTGATCCACTTATAAGCACCGCGATAGCCAGATGCCCTTGTCCTTTTGGTAGTGTGATGATTCCCACATCGTTTGTAACGACTCCCGCATCGCCGGTGCCCGTCTTGTCAGCTACAGGAGTGCCGACCGGCAGACTGCCTCGCAAGCGCTCTGTTCCCGTCGTCGCTCGGTGCATAAAACCCAAAAGCAAAGCGGAATGTTGTGGCTGTAGCAGTTCGCCTTTTTGCAGCTGAACCAGCAAGCGCGCAAGGTCCTCCGCCGACCCAGTATTTGGTCTGGTCCGATTCTCGGAGAACTCGCGTACCGTCGACACGATCTCGATGTTGGGAAAACCCAGAGCGCGCATGCGGTGCGTCACTGCAGCCGGCCCACCGACTAGTTGAAGCAGCTTATCGCTCGATGTGTTGTCGCTTCGTATGATTGACACTTCTATTAGTTGAGCGACAGTTCGGTCGATGGGCCGGCGCCACATAGCAGCATTCGCTGTCCAGCCCGGCGCAACATCCGCGGGCGTGACACGGACTTTCCTGTCGAGCTGAAGTCGGTTTTCTTCGATCTCCTTGAGCACCGCAATCGCAAGTGGCAGTTTGAAGACACTGTAGAGAGGTAACTGCGTTGTTCCTTGAATTGCGGTGGTATGGCCCGTCTCGACGTGGATGACGGCTATTCCGATATCACCGCCTGCCGCATTGATGATTGAACTCAGCCGTTCAGTCAGCATGGAGATGGCTTCGTTCTTTTCCGGGCCTTGAGATGGCTCGTCAAAAATGATGTCTGGAAGGCACGCGGCCCCCCTCACCTGAGAGCTTTGGTAGGGCTGGCCCGAAGCAAGGAGAATTGCAATTAAAGTGATGAGCACTACGGCTGATTGCCTACGCTTACCAAAGATAGTTTTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39088","NCBI_taxonomy_name":"uncultured bacterium BLR5","NCBI_taxonomy_id":"506522"}}}},"ARO_accession":"3002483","ARO_id":"38883","ARO_name":"LRA-5","ARO_description":"LRA-5 is a beta-lactamase isolated from soil samples in Alaska","ARO_category":{"41392":{"category_aro_accession":"3004228","category_aro_cvterm_id":"41392","category_aro_name":"class A LRA beta-lactamase","category_aro_description":"Beta-lactamases that are part of the LRA gene family and are classified as Class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"452":{"model_id":"452","model_name":"QnrVC4","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"530":{"protein_sequence":{"accession":"ADI55014.1","sequence":"MDKTDQLYVQADFSHQDMSGQYFKNCKFFCCSFKRANLRDTQFVDCSFIERGELEGCDFSYSDLRDASFKNCSLSMSYFKGANCFGIEFRECDLKGANFAQASFMNQVSNRMYFCSAYITGCNLSYANFERQCIEKCDLFENRWIGANLSGASFKESDLSRGVFSEGCWSQCRLQGCDLSHSELYGLDPRKVDLTGVKICSWQQEQLLEQLGLIVVPD"},"dna_sequence":{"accession":"GQ891757","fmin":"2004","fmax":"2661","strand":"+","sequence":"ATGGATAAAACAGACCAGTTATATGTACAAGCAGACTTTTCACATCAAGACATGAGTGGTCAGTATTTTAAAAATTGCAAATTTTTCTGCTGTTCCTTTAAACGAGCGAACCTCCGCGATACACAATTTGTAGATTGTTCTTTCATTGAACGAGGTGAATTAGAGGGGTGTGATTTTTCTTACTCGGATCTTAGAGATGCATCTTTTAAAAACTGCAGTCTTTCAATGTCGTATTTCAAAGGTGCAAATTGTTTTGGTATCGAGTTCAGAGAATGCGATTTAAAGGGTGCCAATTTTGCTCAAGCTAGCTTCATGAATCAGGTATCGAACAGAATGTATTTTTGTTCAGCTTATATAACAGGTTGTAATCTTTCATACGCCAACTTTGAAAGGCAGTGTATCGAAAAGTGTGATTTGTTTGAGAATAGATGGATTGGCGCAAATCTGAGTGGTGCATCATTTAAAGAGTCTGATTTAAGTCGGGGAGTATTTTCTGAAGGGTGTTGGAGCCAGTGTAGGTTGCAAGGTTGTGATTTGAGCCACTCGGAGTTGTATGGTTTAGACCCTCGGAAAGTTGACCTTACAGGTGTAAAAATCTGTTCGTGGCAGCAAGAACAACTTTTAGAGCAATTAGGTTTAATAGTAGTTCCTGACTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36936","NCBI_taxonomy_name":"Aeromonas caviae","NCBI_taxonomy_id":"648"}}}},"ARO_accession":"3002801","ARO_id":"39235","ARO_name":"QnrVC4","ARO_description":"QnrVC4 is an integron-mediated quinolone resistance protein found in Aeromonas punctata","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"453":{"model_id":"453","model_name":"mtrE","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"910"}},"model_sequences":{"sequence":{"400":{"protein_sequence":{"accession":"CAA64891.1","sequence":"MNTTLKTTLTSVAAAFALSACTMIPQYEQPKVEVAETFQNDTSVSSIRAVDLGWHDYFADPRLQKLIDIALERNTSLRTAVLNSEIYRKQYMIERNNLLPTLAANANGSRQGSLSGGNVSSSYNVGLGAASYELDLFGRVRSSSEAALQGYFASVANRDAAHLSLIATVAKAYFNERYAEEAMSLAQRVLKTREETYNAVRIAVQGRRDFRRRPAPAEALIESAKADYAHAARSREQARNALATLINRPIPEDLPAGLPLDKQFFVEKLPAGLSSEVLLDRPDIRAAEHALKQANANIGAARAAFFPSIRLTGSVGTGSVELGGLFKSGTGVWAFAPSITLPIFTWGTNKANLDVAKLRQQAQIVAYESAVQSAFQDVANALAAREQLDKAYDALSKQSRASKEALRLVGLRYKHGVSGALDLLDAERSSYSAEGAALSAQLTRAENLADLYKALGGGLKRDTQTGK"},"dna_sequence":{"accession":"X95635","fmin":"259","fmax":"1663","strand":"+","sequence":"ATGAATACTACATTGAAAACTACCTTGACCTCTGTTGCAGCAGCCTTTGCATTGTCTGCCTGCACCATGATTCCTCAATACGAGCAGCCCAAAGTCGAAGTTGCGGAAACCTTCCAAAACGACACATCGGTTTCTTCCATCCGCGCGGTTGATTTGGGTTGGCATGACTATTTTGCCGACCCGCGCCTGCAAAAGCTGATCGACATCGCACTCGAGCGCAATACCAGTTTGCGTACAGCCGTATTGAACAGCGAAATCTACCGCAAACAATACATGATCGAGCGCAACAACCTCCTGCCCACGCTTGCCGCCAATGCGAACGGCTCGCGCCAAGGCAGCTTGAGCGGCGGCAATGTCAGCAGCAGCTACAATGTCGGACTGGGTGCGGCATCTTACGAACTCGATCTGTTCGGGCGCGTGCGCAGCAGCAGCGAAGCAGCACTGCAAGGCTATTTTGCCAGCGTTGCCAACCGCGATGCGGCACATTTGAGTCTGATTGCCACCGTTGCCAAAGCCTATTTCAACGAGCGTTATGCCGAAGAAGCGATGTCTTTGGCGCAGCGTGTCTTGAAAACGCGCGAGGAAACCTACAATGCTGTCCGAATTGCGGTACAAGGCAGGCGTGATTTCCGCCGTCGCCCTGCGCCAGCAGAAGCCTTGATTGAATCTGCCAAAGCCGATTATGCCCATGCCGCGCGCAGCCGCGAACAGGCGCGCAATGCCTTGGCAACCTTGATTAACCGTCCGATACCCGAAGACCTGCCCGCCGGTTTGCCGTTGGACAAGCAGTTTTTTGTTGAAAAACTGCCTGCCGGTTTGAGTTCCGAAGTATTGCTCGACCGTCCCGACATCCGCGCCGCCGAACACGCGCTCAAACAGGCAAACGCCAATATCGGTGCGGCGCGCGCCGCCTTTTTCCCGTCCATCCGCCTGACCGGAAGCGTCGGTACGGGTTCTGTCGAATTGGGCGGGCTGTTCAAAAGCGGCACGGGCGTTTGGGCGTTCGCGCCGTCTATTACCCTGCCGATTTTTACTTGGGGAACGAACAAGGCGAACCTTGATGTGGCAAAACTGCGCCAACAGGCACAAATTGTTGCCTATGAATCCGCCGTCCAATCCGCCTTTCAAGACGTGGCAAACGCATTGGCGGCGCGCGAGCAGCTGGATAAAGCCTATGACGCTTTAAGCAAACAAAGCCGCGCCTCTAAAGAAGCGTTGCGCTTGGTCGGACTGCGTTACAAACACGGCGTATCCGGCGCGCTCGATTTGCTCGATGCGGAACGCAGCAGCTATTCGGCGGAAGGTGCGGCTTTGTCGGCACAACTGACCCGCGCCGAAAACCTTGCCGATTTGTACAAGGCGCTCGGCGGCGGATTGAAACGGGATACCCAAACCGGCAAATAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36806","NCBI_taxonomy_name":"Neisseria gonorrhoeae","NCBI_taxonomy_id":"485"}}}},"ARO_accession":"3000812","ARO_id":"37192","ARO_name":"mtrE","ARO_description":"MtrE is an outer membrane exporter protein that is part of the MtrCDE multidrug efflux complex.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35971":{"category_aro_accession":"0000054","category_aro_cvterm_id":"35971","category_aro_name":"penicillin","category_aro_description":"Penicillin (sometimes abbreviated PCN) is a beta-lactam antibiotic used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms. It works by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"454":{"model_id":"454","model_name":"KPC-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1279":{"protein_sequence":{"accession":"AAU06362.1","sequence":"SLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVRWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGGYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"AY700571","fmin":"0","fmax":"879","strand":"+","sequence":"TGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCGGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGGGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39663","NCBI_taxonomy_name":"Enterobacter sp. E624","NCBI_taxonomy_id":"291398"}}}},"ARO_accession":"3002314","ARO_id":"38714","ARO_name":"KPC-4","ARO_description":"KPC-4 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"455":{"model_id":"455","model_name":"vanC","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"650"}},"model_sequences":{"sequence":{"150":{"protein_sequence":{"accession":"AAA24786.1","sequence":"MKKIAVLFGGNSPEYSVSLTSAASVIQAIDPLKYEVMTIGIAPTMDWYWYQGNLANVRNDTWLEDHKNCHQLTFSSQGFILGEKRIVPDVLFPVLHGKYGEDGCIQGLLELMNLPYVGCHVAASALCMNKWLLHQLADTMGIASAPTLLLSRYENDPATIDRFIQDHGFPIFIKPNEAGSSKGITKVTDKTALQSALTTAFAYGSTVLIQKAIAGIEIGCGILGNEQLTIGACDAISLVDGFFDFEEKYQLISATITVPAPLPLALESQIKEQAQLLYRNLGLTGLARIDFFVTNQGAIYLNEINTMPGFTGHSRYPAMMAEVGLSYEILVEQLIALAEEDKR"},"dna_sequence":{"accession":"AF162694","fmin":"1410","fmax":"2442","strand":"+","sequence":"ATGAAAAAAATTGCCGTTTTATTTGGAGGGAATTCTCCAGAATACTCAGTGTCACTAACCTCAGCAGCAAGTGTGATCCAAGCTATTGACCCGCTGAAATATGAAGTAATGACCATTGGCATCGCACCAACAATGGATTGGTATTGGTATCAAGGAAACCTCGCGAATGTTCGCAATGATACTTGGCTAGAAGATCACAAAAACTGTCACCAGCTGACTTTTTCTAGCCAAGGATTTATATTAGGAGAAAAACGAATCGTCCCTGATGTCCTCTTTCCAGTCTTGCATGGGAAGTATGGCGAGGATGGCTGTATCCAAGGACTGCTTGAACTAATGAACCTGCCTTATGTTGGTTGCCATGTCGCTGCCTCCGCATTATGTATGAACAAATGGCTCTTGCATCAACTTGCTGATACCATGGGAATCGCTAGTGCTCCCACTTTGCTTTTATCCCGCTATGAAAACGATCCTGCCACAATCGATCGTTTTATTCAAGACCATGGATTCCCGATCTTTATCAAGCCGAATGAAGCCGGTTCTTCAAAAGGGATCACAAAAGTAACTGACAAAACAGCGCTCCAATCTGCATTAACGACTGCTTTTGCTTACGGTTCTACTGTGTTGATCCAAAAGGCGATAGCGGGTATTGAAATTGGCTGCGGCATCTTAGGAAATGAGCAATTGACGATTGGTGCTTGTGATGCGATTTCTCTTGTCGACGGTTTTTTTGATTTTGAAGAGAAATACCAATTAATCAGCGCCACGATCACTGTCCCAGCACCATTGCCTCTCGCGCTTGAATCACAGATCAAGGAGCAGGCACAGCTGCTTTATCGAAACTTGGGATTGACGGGTCTGGCTCGAATCGATTTTTTCGTCACCAATCAAGGAGCGATTTATTTAAACGAAATCAACACCATGCCGGGATTTACTGGGCACTCCCGCTACCCAGCTATGATGGCGGAAGTCGGGTTATCCTACGAAATATTAGTAGAGCAATTGATTGCACTGGCAGAGGAGGACAAACGATGAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36781","NCBI_taxonomy_name":"Enterococcus gallinarum","NCBI_taxonomy_id":"1353"}}}},"ARO_accession":"3000368","ARO_id":"36507","ARO_name":"vanC","ARO_description":"VanC is a D-Ala-D-Ala ligase homolog that synthesizes D-Ala-D-Ser, an alternative substrate for peptidoglycan synthesis that reduces vancomycin binding affinity. It is specific to Enterococcus gallinarum and E. casseliflavus, providing intrinsic resistance.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"39340":{"category_aro_accession":"3002906","category_aro_cvterm_id":"39340","category_aro_name":"van ligase","category_aro_description":"van ligases synthesize alternative substrates for peptidoglycan synthesis that reduce vancomycin binding affinity.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"456":{"model_id":"456","model_name":"adeR","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"480"}},"model_sequences":{"sequence":{"711":{"protein_sequence":{"accession":"ADM92605.1","sequence":"MFDHSFSFDCQDKVILVVEDDYDIGDIIENYLKREGMSVIRAMNGKQAIELHASQPIDLILLDIKLPELNGWEVLNKIRQKAQTPVIMLTALDQDIDKVMALRIGADDFVVKPFNPNEVVARVQAVLRRTQFANKATNKNKLYKNIEIDTDTHSVYIHSENKKILLNLTLTEYKIISFMIDQPHKVFTRGELMNHCMNDSDALERTVDSHVSKLRKKLEEQGIFQMLINVRGVGYRLDNPLAVKDDA"},"dna_sequence":{"accession":"HM440348","fmin":"0","fmax":"744","strand":"+","sequence":"ATGTTTGATCATTCTTTTTCTTTTGATTGCCAAGATAAAGTTATTCTTGTGGTAGAAGATGACTACGATATTGGCGACATTATTGAAAATTATTTAAAACGTGAAGGCATGAGTGTTATTCGGGCCATGAATGGAAAGCAAGCGATTGAATTGCACGCTAGCCAACCCATCGATTTAATCTTACTTGATATTAAATTACCCGAATTAAACGGTTGGGAAGTATTAAATAAAATACGCCAAAAAGCTCAGACTCCCGTGATCATGTTGACGGCGCTAGATCAAGATATTGATAAAGTTATGGCATTACGCATAGGTGCAGATGACTTTGTGGTGAAGCCTTTTAACCCAAATGAAGTCGTCGCTAGAGTTCAGGCAGTCCTAAGACGTACTCAGTTTGCAAACAAAGCAACTAATAAAAATAAACTCTATAAAAATATTGAAATTGATACCGACACTCATAGCGTTTATATACACTCTGAGAATAAGAAGATCTTGCTTAATCTGACGCTGACTGAATATAAAATTATTTCATTCATGATTGATCAGCCTCATAAAGTTTTTACGCGCGGAGAGCTTATGAATCACTGCATGAATGATAGCGATGCACTAGAGCGAACCGTAGATAGCCATGTGAGTAAGCTGAGAAAAAAACTAGAAGAACAAGGCATATTTCAAATGTTAATTAATGTGCGTGGCGTGGGATATAGACTAGATAATCCCCTAGCTGTAAAAGATGATGCCTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3000553","ARO_id":"36692","ARO_name":"adeR","ARO_description":"AdeR is a positive regulator of AdeABC efflux system. AdeR inactivation leads to susceptibility to aminoglycoside antibiotics.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"457":{"model_id":"457","model_name":"OXA-93","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1428":{"protein_sequence":{"accession":"ABF47916.1","sequence":"MNIKALLLITSTIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALISLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"DQ519087","fmin":"38","fmax":"863","strand":"+","sequence":"ATGAACATTAAAGCCCTCTTACTTATAACAAGCACTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTCTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCAGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001628","ARO_id":"38028","ARO_name":"OXA-93","ARO_description":"OXA-93 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"459":{"model_id":"459","model_name":"CTX-M-94","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"788":{"protein_sequence":{"accession":"ADK11041.1","sequence":"MMRKSVRRAMLMTTACVSLLLASVPLCAQANDVQQKLAALEKSSGGRLGVALINTADNTQTLYRADERFAMCSTSKVMAAAAVLKQSETQKGLLSQRVEIKPSDLINYNPIAEKHVNGTMTLGELSAAALQYSDNTAMNKLIAHLGGPDKVTAFARTIGDDTFRLDRTEPTLNTAIPGDPRDTTTPLAMAQALRNLTLGNALGDTQRAQLVMWLKGNTTGAASIQAGLPTSWVVGDKTGSGGYGTTNDIAVIWPEGRAPLVLVTYFTQSEPKAESRRDVLAAAARIVTDGY"},"dna_sequence":{"accession":"HM167760","fmin":"0","fmax":"876","strand":"+","sequence":"ATGATGAGAAAAAGCGTAAGGCGGGCGATGTTAATGACGACAGCCTGTGTTTCGCTGCTGTTGGCCAGTGTGCCGCTGTGTGCCCAGGCGAACGATGTTCAACAAAAGCTCGCGGCGCTGGAGAAAAGCAGCGGGGGACGACTGGGTGTGGCGTTGATTAACACCGCCGATAACACGCAGACGCTCTACCGCGCCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCGGCAGCGGCGGTGCTTAAGCAAAGTGAAACGCAAAAGGGCTTGTTGAGTCAGCGGGTTGAAATTAAGCCCTCAGACTTGATTAACTACAACCCCATTGCGGAAAAACACGTCAATGGCACGATGACATTAGGGGAGTTGAGCGCGGCGGCGCTACAGTACAGCGATAATACTGCCATGAATAAGCTGATTGCCCATCTCGGGGGGCCGGATAAAGTGACGGCATTTGCCCGTACGATTGGCGATGACACGTTCCGGCTCGATCGTACCGAGCCGACGCTCAACACCGCGATCCCCGGCGACCCGCGCGATACCACCACGCCGTTAGCGATGGCGCAGGCTCTGCGCAATCTGACGTTGGGCAATGCCCTGGGTGACACTCAGCGTGCGCAGCTGGTGATGTGGCTGAAAGGCAACACCACCGGCGCTGCCAGCATTCAGGCAGGGCTACCCACATCGTGGGTTGTCGGGGATAAAACCGGCAGCGGCGGTTATGGTACGACGAATGATATCGCGGTTATTTGGCCGGAAGGTCGCGCGCCGCTCGTTCTGGTGACTTACTTCACCCAGTCGGAGCCGAAGGCAGAGAGCCGTCGTGACGTGCTCGCTGCTGCCGCCAGAATTGTCACCGACGGTTATTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001954","ARO_id":"38354","ARO_name":"CTX-M-94","ARO_description":"CTX-M-94 is a beta-lactamase found in Escherichia coli","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"460":{"model_id":"460","model_name":"CMY-29","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1624":{"protein_sequence":{"accession":"ABS12248.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQFPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGELAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"EF685371","fmin":"0","fmax":"1143","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGTTCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGAGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002040","ARO_id":"38440","ARO_name":"CMY-29","ARO_description":"CMY-29 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"461":{"model_id":"461","model_name":"OXA-13","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1523":{"protein_sequence":{"accession":"AAC46344.1","sequence":"MKTFAAYVITACLSSTALASSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNNLARASKEYLPASTFKIPSAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLSLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLFLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKGTEVYFFAFNMDIDNENKLPLRKSIPTKIMASEGIIGG"},"dna_sequence":{"accession":"U59183","fmin":"939","fmax":"1740","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTACTGCGTGTCTTTCAAGTACGGCATTAGCTAGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTTTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATAACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAGCGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAACAATGGGAAAGAGACTTGAGCTTAAGAGGGGCAATACAAGTTTCAGCGGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCATATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAGGGTCAGCTAAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATTTTTAAATAAATTGTCAGCATCAAAAGAAAATCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCTGCGCCTGAATATCTTGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGTTGGGTTGAGAAGGGAACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAATAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGCAAGTGAGGGCATCATTGGTGGCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001408","ARO_id":"37808","ARO_name":"OXA-13","ARO_description":"OXA-13 is a beta-lactamase found in P. aeruginosa.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"463":{"model_id":"463","model_name":"CTX-M-30","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2043":{"protein_sequence":{"accession":"AAP43508.1","sequence":"MVKKSLRQFTLMATAAVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVDGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"AY292654","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTCATGGCGACGGCAGCCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGGGTGGCATTGATTAACACTGCGGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTGGTTAACTATAATCCGATTGCGGAAAAGCACGTCGATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGCAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCAGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATTTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGTGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3001892","ARO_id":"38292","ARO_name":"CTX-M-30","ARO_description":"CTX-M-30 is a beta-lactamase found in Citrobacter freundii","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"464":{"model_id":"464","model_name":"NDM-13","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1918":{"protein_sequence":{"accession":"BAQ02518.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTNDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGLVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"LC012596","fmin":"3585","fmax":"4398","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCAATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGCTGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3003182","ARO_id":"39759","ARO_name":"NDM-13","ARO_description":"Beta-lactamase found in Escherichia coli clinical isolates in Nepal.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"465":{"model_id":"465","model_name":"vanSO","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"4314":{"protein_sequence":{"accession":"AHA41504.1","sequence":"MLAGVLLLAAVWVFLLRGRSTNFQFPALADFARVFDPSNFGPVVFVPAAILALGFLLVFGLVGGWILAGRMLAPLARITRAAREAGSGSLSYRIELEGRNDEFRELADAFDAMLARLEARDAAQQRFAANASHELRTPLAITQTLLDVARNDPNRDGGELDERLRAVNARAIELTEALLLLSRTDQRSFSREDVDLSLIAEEAAETLLPFAEKHGVSIETSGDIAPVIGSHALLLQLTTNLLHNAIVHNVPEHGSVQISTAIGSESVMLTVENTGDKLSPQLVSTLTEPFQRGTARTRGDDARVGLGLAIVKSITQAHDGSLTLSPRAAGGLSVAVRLPAAQRRP"},"dna_sequence":{"accession":"KF478993","fmin":"4909","fmax":"5947","strand":"-","sequence":"TTACGGTCGTCGCTGAGCGGCGGGCAGTCGCACTGCTACGGAGAGCCCGCCGGCAGCTCGGGGGCTGAGCGTGAGGGATCCGTCGTGTGCCTGCGTGATGCTCTTGACGATCGCCAGGCCAAGGCCCACCCTCGCATCGTCCCCGCGGGTGCGAGCAGTGCCGCGCTGAAACGGCTCGGTGAGTGTCGAGACCAACTGTGGACTGAGCTTGTCGCCGGTGTTCTCGACCGTGAGCATGACGGACTCGGAGCCGATGGCGGTGCTGATCTGCACGCTGCCGTGCTCGGGGACATTGTGGACGATCGCATTGTGCAGAAGGTTCGTAGTCAACTGCAGCAAGAGTGCGTGTGAGCCGATGACCGGCGCGATGTCCCCGGAGGTCTCGATGCTGACGCCGTGCTTCTCCGCGAACGGGAGGAGTGTCTCGGCGGCTTCTTCCGCGATGAGCGACAGATCGACGTCTTCTCGGCTGAAGGACCGTTGGTCGGTACGGCTGAGCAGGAGCAATGCCTCGGTGAGCTCGATCGCCCGTGCGTTGACAGCGCGGAGGCGTTCGTCGAGCTCGCCGCCGTCGCGGTTCGGATCGTTGCGGGCGACATCGAGAAGGGTTTGTGTGATCGCCAGCGGGGTGCGCAACTCGTGGGAGGCGTTGGCGGCGAATCGCTGCTGCGCGGCGTCTCGTGCTTCGAGCCGTGCGAGCATGGCGTCGAAGGCATCGGCAAGTTCACGGAACTCGTCGTTGCGTCCCTCCAGTTCGATCCGGTACGACAGCGAGCCACTCCCCGCCTCCCGCGCGGCGCGCGTAATGCGCGCCAACGGGGCAAGCATTCGGCCCGCGAGAATCCAACCACCCACAAGGCCGAACACCAGCAAGAACCCGAGCGCCAAGATCGCTGCCGGGACAAACACCACGGGACCGAAGTTGCTCGGGTCGAAGACCCGGGCAAAGTCGGCCAGAGCAGGGAATTGGAAATTCGTGGACCGCCCTCTCAGCAGGAAAACCCAAACCGCCGCAAGGAGCAAGACACCAGCGAGCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36897","NCBI_taxonomy_name":"Rhodococcus equi","NCBI_taxonomy_id":"43767"}}}},"ARO_accession":"3002941","ARO_id":"39375","ARO_name":"vanSO","ARO_description":"vanSO is a vanS variant found in the vanO gene cluster","ARO_category":{"36210":{"category_aro_accession":"3000071","category_aro_cvterm_id":"36210","category_aro_name":"vanS","category_aro_description":"VanS is similar to histidine protein kinases like EnvZ and acts as a response regulator by activating VanR. VanS is required for high level transcription of other van glycopeptide resistance genes.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"466":{"model_id":"466","model_name":"CTX-M-76","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1821":{"protein_sequence":{"accession":"CAQ42486.1","sequence":"MMTQSIRRSMLTVMATLPLLFSSATLHAQTNSVQQQLEALEKSSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKQSESDKHLLNQRVEIKKSDLVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSASIRAGLPKSWGVGDKTGSGDYGTTNDIAVIWPENHAPLVLVTYFTQPEQKAESRRDVLAAAAKIVTHGF"},"dna_sequence":{"accession":"AM982520","fmin":"5548","fmax":"6424","strand":"+","sequence":"ATGATGACTCAGAGCATTCGCCGCTCAATGTTAACGGTGATGGCGACGCTACCCCTGCTATTTAGCAGCGCAACGCTGCACGCGCAGACGAACAGCGTGCAACAGCAGCTGGAAGCCCTGGAGAAAAGTTCGGGAGGTCGGCTTGGCGTTGCGCTGATTAACACCGCCGATAATTCGCAGATTCTCTACCGTGCCGATGAACGTTTTGCGATGTGCAGTACCAGTAAGGTGATGGCGGCCGCGGCGGTGCTTAAACAGAGCGAGAGCGATAAGCACCTGTTAAATCAGCGCGTTGAAATCAAGAAGAGCGACCTGGTTAACTACAATCCCATTGCGGAGAAACACGTTAACGGCACGATGACGCTGGCTGAGCTTGGCGCAGCGGCGCTGCAGTATAGCGACAATACTGCCATGAATAAGCTGATTGCCCATCTGGGTGGGCCCGATAAAGTGACGGCGTTTGCTCGCTCGTTGGGTGATGAGACCTTCCGTCTGGACAGAACCGAGCCCACGCTCAATACCGCCATTCCAGGCGACCCGCGTGATACCACCACGCCGCTCGCGATGGCGCAGACCCTGAAAAATCTGACGCTGGGTAAAGCGCTGGCGGAAACTCAGCGGGCACAGTTGGTGACGTGGCTTAAGGGCAATACTACCGGTAGCGCGAGCATTCGGGCGGGTCTGCCGAAATCATGGGGAGTGGGCGATAAAACCGGCAGCGGAGATTATGGCACCACCAACGATATCGCGGTTATCTGGCCGGAAAACCACGCACCGCTGGTTCTGGTGACCTACTTTACCCAACCGGAGCAGAAGGCGGAAAGCCGTCGGGATGTTCTGGCTGCGGCGGCGAAAATCGTAACCCACGGTTTCTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36928","NCBI_taxonomy_name":"Kluyvera ascorbata","NCBI_taxonomy_id":"51288"}}}},"ARO_accession":"3001937","ARO_id":"38337","ARO_name":"CTX-M-76","ARO_description":"CTX-M-76 is a beta-lactamase found in Kluyvera spp.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"467":{"model_id":"467","model_name":"CARB-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1506":{"protein_sequence":{"accession":"AAB19430.2","sequence":"MLLYKMCDNQNYGVTYMKFLLAFSLLIPSVVFASSSKFQQVEQDVKAIEVSLSARIGVSVLDTQNGEYWDYNGNQRFPLTSTFKTIACAKLLYDAEQGKVNPNSTVEIKKADLVTYSPVIEKQVGQAITLDDACFATMTTSDNTAANIILSAVGGPKGVTDFLRQIGDKETRLDRIEPDLNEGKLGDLRDTTTPKAIASTLNKLLFGSALSEMNQKKLESWMVNNQVTGNLLRSVLPAGWNIADRSGAGGFGARSITAVVWSEHQAPIIVSIYLAQTQASMAERNDAIVKIGHSIFDVYTSQSR"},"dna_sequence":{"accession":"S46063","fmin":"121","fmax":"1036","strand":"+","sequence":"ATGCTTTTATATAAAATGTGTGACAATCAAAATTATGGGGTTACTTACATGAAGTTTTTATTGGCATTTTCGCTTTTAATACCATCCGTGGTTTTTGCAAGTAGTTCAAAGTTTCAGCAAGTTGAACAAGACGTTAAGGCAATTGAAGTTTCTCTTTCTGCTCGTATAGGTGTTTCCGTTCTTGATACTCAAAATGGAGAATATTGGGATTACAATGGCAATCAGCGCTTCCCGTTAACAAGTACTTTTAAAACAATAGCTTGCGCTAAATTACTATATGATGCTGAGCAAGGAAAAGTTAATCCCAATAGTACAGTCGAGATTAAGAAAGCAGATCTTGTGACCTATTCCCCTGTAATAGAAAAGCAAGTAGGGCAGGCAATCACACTCGATGATGCGTGCTTCGCAACTATGACTACAAGTGATAATACTGCGGCAAATATCATCCTAAGTGCTGTAGGTGGCCCCAAAGGCGTTACTGATTTTTTAAGACAAATTGGGGACAAAGAGACTCGTCTAGACCGTATTGAGCCTGATTTAAATGAAGGTAAGCTCGGTGATTTGAGGGATACGACAACTCCTAAGGCAATAGCCAGTACTTTGAATAAACTTTTATTTGGTTCCGCGCTATCTGAAATGAACCAGAAAAAATTAGAGTCTTGGATGGTGAACAATCAAGTCACTGGTAATTTACTACGTTCAGTATTGCCGGCGGGATGGAACATTGCGGATCGCTCAGGTGCTGGCGGATTTGGTGCTCGGAGTATTACAGCAGTTGTGTGGAGTGAGCATCAAGCCCCAATTATTGTGAGCATCTATCTAGCTCAAACACAGGCTTCAATGGCAGAGCGAAATGATGCGATTGTTAAAATTGGTCATTCAATTTTTGACGTTTATACATCACAGTCGCGCTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002242","ARO_id":"38642","ARO_name":"CARB-3","ARO_description":"CARB-3 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"468":{"model_id":"468","model_name":"Erm(37)","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"582":{"protein_sequence":{"accession":"CCP44758.1","sequence":"MSALGRSRRAWGWHRLHDEWAARVVSAAAVRPGELVFDIGAGEGALTAHLVRAGARVVAVELHPRRVGVLRERFPGITVVHADAASIRLPGRPFRVVANPPYGISSRLLRTLLAPNSGLVAADLVLQRALVCKFASRNARRFTLTVGLMLPRRAFLPPPHVDSAVLVVRRRKCGDWQGR"},"dna_sequence":{"accession":"AL123456","fmin":"2231679","fmax":"2232219","strand":"+","sequence":"GTGTCCGCCCTCGGACGGTCGCGACGGGCATGGGGCTGGCACCGGCTCCATGACGAATGGGCAGCGCGGGTAGTCAGCGCGGCCGCAGTGCGGCCCGGTGAGCTCGTGTTTGACATCGGCGCCGGCGAAGGGGCACTGACGGCGCATCTAGTGCGAGCGGGGGCGCGGGTGGTCGCCGTGGAGTTGCACCCGCGACGAGTCGGTGTCCTCCGCGAGCGATTCCCTGGCATTACCGTGGTGCACGCGGACGCCGCCTCGATCCGGTTGCCCGGCCGGCCGTTCCGGGTTGTGGCGAACCCGCCGTACGGGATTTCGTCCCGCCTGCTGCGGACGCTGCTGGCACCCAACAGCGGGCTTGTCGCGGCCGATCTCGTGCTGCAGCGAGCCCTCGTATGTAAATTCGCTTCTCGCAACGCGCGAAGGTTCACCCTGACCGTCGGCCTCATGCTGCCACGGCGCGCGTTCCTGCCACCGCCGCATGTGGATTCCGCGGTGCTCGTCGTCCGCCGCCGGAAGTGCGGTGACTGGCAGGGGCGGTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3000392","ARO_id":"36531","ARO_name":"Erm(37)","ARO_description":"Erm(37) is found in Mycobacterium species and confers the MLSb phenotype. In addition to methylation of A2058 this Erm methylates adjacent adenosines (A2057 and A2059) as well.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35946":{"category_aro_accession":"0000027","category_aro_cvterm_id":"35946","category_aro_name":"roxithromycin","category_aro_description":"Roxithromycin is a semi-synthetic, 14-carbon ring macrolide antibiotic derived from erythromycin. It is used to treat respiratory tract, urinary and soft tissue infections. Roxithromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35974":{"category_aro_accession":"0000057","category_aro_cvterm_id":"35974","category_aro_name":"telithromycin","category_aro_description":"Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36315":{"category_aro_accession":"3000176","category_aro_cvterm_id":"36315","category_aro_name":"dirithromycin","category_aro_description":"Dirithromycin is an oxazine derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome to inhibit bacterial protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin 1A is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"vernamycin B-gamma","category_aro_description":"Vernamycin B-gamma is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"469":{"model_id":"469","model_name":"SHV-49","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1067":{"protein_sequence":{"accession":"AAS98184.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMISTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AY528718","fmin":"413","fmax":"1274","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATAAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001106","ARO_id":"37486","ARO_name":"SHV-49","ARO_description":"SHV-49 is an inhibitor-resistant beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"470":{"model_id":"470","model_name":"OXA-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1690":{"protein_sequence":{"accession":"AET05998.1","sequence":"MKNTIHINFAIFLIIANIIYSSASASTDISTVASPLFEGTEGCFLLYDVSTNAEIAQFNKAKCATQMAPDSTFKIALSLMAFDAEIIDQKTIFKWDKTPKGMEIWNSNHTPKTWMQFSVVWVSQEITQKIGLNKIKNYLKDFDYGNQDFSGDKERNNGLTEAWLESSLKISPEEQIQFLRKIINHNLPVKNSAIENTIENMYLQDLENSTKLYGKTGAGFTANRTLQNGWFEGFIISKSGHKYVFVSALTGNLGSNLTSSIKAKKNAITILNTLNL"},"dna_sequence":{"accession":"JN129451","fmin":"1036","fmax":"1867","strand":"+","sequence":"ATGAAAAACACAATACATATCAACTTCGCTATTTTTTTAATAATTGCAAATATTATCTACAGCAGCGCCAGTGCATCAACAGATATCTCTACTGTTGCATCTCCATTATTTGAAGGAACTGAAGGTTGTTTTTTACTTTACGATGTATCCACAAACGCTGAAATTGCTCAATTCAATAAAGCAAAGTGTGCAACGCAAATGGCACCAGATTCAACTTTCAAGATCGCATTATCACTTATGGCATTTGATGCGGAAATAATAGATCAGAAAACCATATTCAAATGGGATAAAACCCCCAAAGGAATGGAGATCTGGAACAGCAATCATACACCAAAGACGTGGATGCAATTTTCTGTTGTTTGGGTTTCGCAAGAAATAACCCAAAAAATTGGATTAAATAAAATCAAGAATTATCTCAAAGATTTTGATTATGGAAATCAAGACTTCTCTGGAGATAAAGAAAGAAACAACGGATTAACAGAAGCATGGCTCGAAAGTAGCTTAAAAATTTCACCAGAAGAACAAATTCAATTCCTGCGTAAAATTATTAATCACAATCTCCCAGTTAAAAACTCAGCCATAGAAAACACCATAGAGAACATGTATCTACAAGATCTGGAGAATAGTACAAAACTGTATGGGAAAACTGGTGCAGGATTCACAGCAAATAGAACCTTACAAAACGGATGGTTTGAAGGGTTTATTATAAGCAAATCAGGACATAAATATGTTTTTGTGTCCGCACTTACAGGAAACTTGGGGTCGAATTTAACATCAAGCATAAAAGCCAAGAAAAATGCGATCACCATTCTAAACACACTAAATTTATAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001399","ARO_id":"37799","ARO_name":"OXA-4","ARO_description":"OXA-4 is a beta-lactamase found in Enterobacteriaceae and P. aeruginosa","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"471":{"model_id":"471","model_name":"TEM-151","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"998":{"protein_sequence":{"accession":"ABI74448.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMVSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDHWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERDRQIAEIGGSLIKHW"},"dna_sequence":{"accession":"DQ834729","fmin":"205","fmax":"1066","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGGTGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCATTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAGATAGACAGATCGCTGAGATAGGTGGCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001018","ARO_id":"37398","ARO_name":"TEM-151","ARO_description":"TEM-151 is a CMT-type, inhibitor-resistant, extended-spectrum beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"472":{"model_id":"472","model_name":"TEM-128","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1720":{"protein_sequence":{"accession":"AAR89359.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGEHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AY368237","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGAGCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000990","ARO_id":"37370","ARO_name":"TEM-128","ARO_description":"TEM-128 is a broad-spectrum beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"473":{"model_id":"473","model_name":"mphE","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"602":{"protein_sequence":{"accession":"WP_010550189.1","sequence":"MRGTGQTAGMTETSPSSPSSATADAGTPPPADLEQLLALAADHGLDLLGDSLRTEEIGLDFRVAFARSRDWQDWVLRIPRRAEVLARAAVEGRLLAHLAPHLDIAIPDWRISTERLIAYPLLPGTPGLTVSADGTVEWHVDMASTEYARALGTFLAQLHTVDPEEAAATGIPSRTPSEVRGVWREDLTRVAEAFPIAPALRERWEAWLAEDSYWPDRSVLTHGEVYPGHTLVEGERLSAVLDWTTASVGDPARDLMFHRSSAPPEAFAATLAAYVAGGGTLHPRLGEHAEEMFSASPLAYGLYALETGEEEHRAAAAAALDPPDAD"},"dna_sequence":{"accession":"NZ_AGSO01000004","fmin":"76451","fmax":"77432","strand":"+","sequence":"GTGCGCGGGACCGGGCAGACTGCCGGCATGACCGAGACCTCTCCCTCGAGCCCGTCGTCGGCCACGGCCGATGCCGGGACTCCCCCGCCCGCCGACCTCGAGCAGCTCCTCGCCCTCGCCGCCGATCACGGGCTCGACCTCCTCGGCGACTCGCTGCGCACCGAGGAGATCGGCCTCGACTTCCGCGTCGCCTTCGCCCGGTCGCGGGACTGGCAGGACTGGGTGCTGCGCATCCCCCGCCGCGCCGAGGTGCTGGCCCGCGCCGCGGTCGAGGGCCGGCTGCTCGCCCACCTCGCCCCGCACCTGGACATCGCGATCCCCGACTGGCGGATCAGCACGGAGCGCCTGATCGCCTATCCCCTCCTGCCCGGCACCCCGGGACTGACCGTCAGCGCCGACGGCACGGTCGAGTGGCACGTGGACATGGCCTCGACCGAGTACGCCCGCGCCCTCGGCACCTTCCTCGCCCAGCTCCACACCGTGGACCCCGAGGAGGCCGCCGCCACCGGGATCCCGTCCCGCACCCCGTCGGAGGTGCGCGGTGTATGGCGCGAGGACCTCACCCGGGTCGCGGAGGCCTTCCCCATCGCGCCGGCGCTGCGGGAGCGGTGGGAGGCGTGGCTGGCGGAGGACTCCTACTGGCCGGACCGCAGCGTGCTCACCCACGGTGAGGTGTACCCCGGCCACACCCTCGTCGAGGGCGAGCGGCTCAGCGCGGTGCTCGACTGGACCACGGCGTCCGTCGGCGATCCGGCGCGGGACCTCATGTTCCACCGCTCGAGCGCACCCCCGGAAGCCTTCGCGGCGACGCTCGCCGCCTACGTGGCCGGCGGCGGCACCCTCCACCCGCGGCTCGGCGAGCACGCCGAGGAGATGTTCTCCGCCTCCCCGCTCGCCTACGGGCTCTACGCGCTGGAGACCGGCGAGGAGGAGCACCGCGCCGCGGCGGCGGCCGCGCTCGACCCGCCGGACGCCGACTGAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39642","NCBI_taxonomy_name":"Brachybacterium paraconglomeratum LC44","NCBI_taxonomy_id":"1064537"}}}},"ARO_accession":"3003071","ARO_id":"39606","ARO_name":"mphE","ARO_description":"mphE is a macrolide phosphotransferase that phosphorylates macrolides in GTP- dependent manner at 2'-OH hydroxyl of desosamine sugar of macrolides.","ARO_category":{"36472":{"category_aro_accession":"3000333","category_aro_cvterm_id":"36472","category_aro_name":"macrolide phosphotransferase (MPH)","category_aro_description":"Macrolide phosphotransferases (MPH) are enzymes encoded by macrolide phosphotransferase genes (mph genes). These enzymes phosphorylate macrolides in GTP dependent manner at 2'-OH of desosamine sugar thereby inactivating them. Characterized MPH's are differentiated based on their substrate specificity.","category_aro_class_name":"AMR Gene Family"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"474":{"model_id":"474","model_name":"dfrD","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"683":{"protein_sequence":{"accession":"AAA85213.1","sequence":"MKISLIVAMDKKRVIGKDNDIPWRISSDWEYVKNTTKGHAIILGRKNLQSIGRALPDRRNIILTRDKNFNFKDCEIAHSIEAAFKLCENEEEVFIFGGEQIYVMFLPYVEKMYVTKIHHEFEGDTFFPVVNFDDWKEVSVEKGIKDEKNPYDYYFHIYERIR"},"dna_sequence":{"accession":"U43152","fmin":"93","fmax":"582","strand":"+","sequence":"TTGAAAATTTCTTTAATTGTTGCGATGGATAAGAAAAGAGTAATCGGCAAGGATAACGACATTCCATGGAGAATTTCTAGTGATTGGGAATATGTAAAAAACACTACAAAAGGACATGCAATCATATTAGGTAGAAAGAACCTTCAATCAATCGGAAGGGCTTTACCTGACAGAAGAAATATTATTTTGACTAGAGATAAAAACTTTAACTTTAAGGATTGTGAAATTGCCCATTCAATAGAAGCTGCATTTAAGTTATGCGAAAATGAAGAAGAGGTTTTCATTTTCGGGGGAGAACAGATATATGTTATGTTCTTGCCTTATGTCGAGAAAATGTACGTTACAAAAATTCATCATGAATTCGAAGGAGATACATTTTTTCCAGTAGTTAATTTTGACGATTGGAAAGAAGTATCTGTTGAAAAAGGAATAAAAGATGAAAAGAATCCTTACGATTATTATTTTCATATATATGAGAGAATTCGTTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36757","NCBI_taxonomy_name":"Listeria monocytogenes","NCBI_taxonomy_id":"1639"}}}},"ARO_accession":"3002866","ARO_id":"39300","ARO_name":"dfrD","ARO_description":"dfrD is a plasmid-encoded dihydrofolate reductase found in Listeria monocytogenes","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36408":{"category_aro_accession":"3000269","category_aro_cvterm_id":"36408","category_aro_name":"brodimoprim","category_aro_description":"Brodimoprim is a structural derivative of trimethoprim and an inhibitor of bacterial dihydrofolate reductase. The 4-methoxy group of trimethoprim is replaced with a bromine atom.","category_aro_class_name":"Antibiotic"},"36423":{"category_aro_accession":"3000284","category_aro_cvterm_id":"36423","category_aro_name":"tetroxoprim","category_aro_description":"Tetroxoprim is a trimethoprim derivative that inhibits bacterial dihydrofolate reductase.","category_aro_class_name":"Antibiotic"},"36476":{"category_aro_accession":"3000337","category_aro_cvterm_id":"36476","category_aro_name":"iclaprim","category_aro_description":"Iclaprim is a bactericidal compound that inhibits dihydrofolate reductase. It is used against clinically important Gram-positive pathogens, including methicillin-sensitive Staphylococcus aureus and methicillin-resistant S. aureus.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"475":{"model_id":"475","model_name":"OXA-106","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1202":{"protein_sequence":{"accession":"ABV31686.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDKKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"EF650032","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATAAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001637","ARO_id":"38037","ARO_name":"OXA-106","ARO_description":"OXA-106 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"476":{"model_id":"476","model_name":"amrB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1750"}},"model_sequences":{"sequence":{"4079":{"protein_sequence":{"accession":"YP_108402.1","sequence":"MARFFIDRPVFAWVISLFIMLGGIFAIRALPVAQYPDIAPPVVSLYATYPGASAQVVEESVTAVIEREMNGVPGLLYTSATSSAGQASLSLTFKQGVSADLAAVDVQNRLKIVEARLPEPVRRDGISIEKAADNAQIIVSLTSEDGRLSGVELGEYASANVLQALRRVEGVGKVQFWGAEYAMRIWPDPVKMAALGLTASDIASAVRAHNARVTIGDVGRSAVPDSAPIAATVLADAPLTTPDAFGAIALRARADGSTLYLRDVARIEFGGNDYNYPSFVNGKTATGMGIKLAPGSNAVATEKRVRATMEELAKFFPPGVKYQIPYETASFVRVSMSKVVTTLVEAGVLVFAVMFLFMQNFRATLIPTLVVPVALLGTFGAMLAAGFSINVLTMFGMVLAIGILVDDAIVVVENVERLMVEEKLPPYEATVKAMKQISGAIVGITVVLTSVFVPMAFFGGAVGNIYRQFAFALAVSIGFSAFLALSLTPALCATLLKPVADDHHEKDGFFGWFNRFVARSTHRYTRRVGRVLERPLRWLVVYGALTAAAALLITKLPAAFLPDEDQGNFMVMVIRPQGTPLAETMQSVRRVEEYVRTHSPSAYTFALGGYNLYGEGPNGGMIFVTMKDWKERKRARDQVQAIIAEINAHFAGTPNTMVFAINMPALPDLGLTGGFDFRLQDRGGLGYGAFVAAREKLLAEGRKDPVLTDLMFAGTQDAPQLKLDIDRAKASALGVSMEEINATLAVMFGSDYIGDFMHGSQVRRVIVQADGRHRLDAADVTKLRVRNAKGEMVPLAAFATLHWTMGPPQLTRYNGFPSFTINGAASAGHSSGEAMAAIERIASTLPAGTGYAWSGQSYEERLSGAQAPMLFALSVLVVFLALAALYESWSIPFAVMLVVPLGVIGAVAGVTLRGMPNDIYFKVGLIATIGLSAKNAILIVEVAKDLVAQRMSLADAALEAARLRLRPIVMTSLAFGVGVLPLAFATGAASGAQIAIGTGVLGGVISATLFAIFLVPLFFVCVGRVFDVVPRRRGGAQAALEAK"},"dna_sequence":{"accession":"NC_006350.1","fmin":"2147817","fmax":"2150949","strand":"-","sequence":"TCACTTGGCCTCCAGTGCCGCTTGCGCGCCGCCTCGGCGGCGCGGAACGACGTCGAACACGCGCCCGACGCAGACGAAAAAGAGCGGGACGAGGAAGATCGCGAACAGCGTCGCGCTGATCACGCCGCCGAGCACCCCCGTGCCGATCGCGATCTGCGCGCCGGATGCGGCGCCCGTCGCGAACGCGAGCGGCAGCACGCCGACGCCGAACGCGAGCGAGGTCATCACGATCGGCCGCAGCCGCAGCCGCGCGGCCTCGAGCGCCGCGTCGGCGAGCGACATGCGCTGCGCGACCAGATCCTTCGCGACCTCGACGATCAGGATCGCGTTCTTCGCGGACAAACCGATCGTCGCGATCAGCCCCACCTTGAAATAGATGTCGTTCGGCATCCCGCGCAGCGTGACGCCCGCGACCGCGCCGATCACGCCGAGCGGCACGACGAGCATCACCGCGAACGGAATCGACCAGCTCTCGTACAGCGCCGCGAGCGCGAGGAACACGACGAGCACCGACAGCGCGAACAGCATCGGCGCCTGCGCGCCCGACAGCCGCTCCTCGTACGACTGGCCGGACCACGCGTAGCCGGTGCCGGCGGGCAGCGTCGACGCGATCCGCTCGATCGCCGCCATCGCCTCGCCGCTGCTGTGCCCGGCCGACGCCGCGCCGTTGATCGTAAACGACGGAAAGCCGTTGTAGCGCGTCAACTGCGGCGGGCCCATCGTCCAGTGCAGCGTCGCGAACGCCGCGAGCGGCACCATCTCGCCCTTCGCGTTGCGCACGCGCAGCTTCGTCACGTCGGCGGCGTCGAGCCGGTGCCGCCCGTCCGCCTGCACGATCACGCGGCGCACCTGCGAGCCGTGCATGAAATCGCCGATGTAGTCCGAGCCGAACATCACAGCGAGCGTCGCGTTGATTTCCTCCATCGATACGCCGAGCGCCGACGCCTTCGCGCGATCGATGTCGAGCTTCAGCTGCGGCGCGTCCTGCGTGCCGGCGAACATCAAATCGGTCAGGACGGGGTCCTTGCGCCCCTCGGCGAGCAGCTTCTCGCGCGCGGCGACGAACGCGCCGTAGCCGAGCCCGCCGCGGTCCTGCAGCCGGAAGTCGAAGCCGCCCGTCAGGCCGAGGTCCGGCAGCGCCGGCATGTTGATCGCGAACACCATCGTGTTCGGCGTGCCGGCGAAATGCGCGTTGATCTCCGCGATGATCGCCTGCACCTGGTCCCGCGCCCGCTTGCGCTCCTTCCAGTCCTTCATCGTGACGAAGATCATCCCGCCGTTCGGCCCTTCGCCGTACAGGTTGTAGCCGCCGAGCGCGAACGTGTACGCGCTCGGCGAATGCGTGCGCACGTATTCCTCGACGCGCCGCACGCTCTGCATCGTCTCGGCGAGCGGCGTGCCCTGCGGGCGAATCACCATCACCATGAAGTTGCCCTGATCCTCGTCGGGCAGGAACGCGGCCGGCAGCTTCGTGATCAGCAGCGCGGCGGCGGCCGTCAGCGCGCCGTAGACGACGAGCCAGCGCAGCGGGCGCTCGAGCACCCGCCCGACGCGCCGCGTGTAGCGGTGCGTCGAGCGCGCGACGAAACGGTTGAACCAGCCGAAGAAGCCGTCCTTCTCGTGATGGTCGTCGGCGACGGGCTTGAGCAGCGTCGCGCAGAGCGCCGGCGTGAGCGACAGCGCGAGAAACGCCGAGAAGCCGATCGACACCGCCAGCGCGAACGCGAACTGCCGGTAGATGTTGCCGACCGCGCCGCCGAAGAACGCCATCGGCACGAACACCGACGTGAGCACGACGGTGATCCCGACGATCGCGCCGCTGATCTGCTTCATCGCCTTCACGGTGGCCTCGTACGGCGGCAGCTTCTCCTCGACCATCAGCCGCTCGACGTTCTCGACGACGACGATCGCGTCGTCGACGAGGATGCCGATCGCGAGCACCATCCCGAACATCGTCAGCACGTTGATCGAGAAGCCCGCGGCGAGCATCGCGCCGAACGTGCCGAGCAGCGCGACGGGCACGACGAGCGTCGGAATCAGCGTCGCGCGGAAGTTCTGCATGAAGAGGAACATCACCGCGAACACGAGCACGCCCGCCTCGACGAGCGTCGTGACGACCTTGCTCATCGACACGCGCACGAACGACGCCGTCTCGTACGGAATCTGGTACTTGACGCCCGGCGGAAAGAACTTCGCGAGCTCCTCCATCGTCGCGCGCACGCGCTTTTCGGTGGCGACCGCATTCGAACCGGGCGCGAGCTTGATGCCCATGCCCGTCGCCGTCTTGCCGTTCACGAACGACGGGTAGTTGTAATCGTTGCCGCCGAACTCGATTCTCGCGACGTCGCGCAGGTACAGCGTCGAGCCGTCGGCGCGCGCGCGCAGCGCGATCGCGCCGAACGCGTCGGGCGTCGTGAGCGGCGCGTCGGCGAGCACGGTCGCCGCGATCGGCGCGCTGTCGGGCACCGCGCTGCGGCCGACGTCGCCGATCGTCACGCGCGCGTTGTGCGCGCGCACGGCCGACGCGATATCGGACGCCGTCAGGCCGAGCGCCGCCATCTTCACGGGGTCCGGCCAGATCCGCATCGCATACTCGGCGCCCCAGAACTGCACCTTGCCGACGCCCTCGACGCGCCGCAGCGCCTGCAACACGTTCGCCGACGCGTATTCGCCGAGCTCCACGCCCGATAACCGTCCGTCCTCCGACGTGAGCGACACGATGATCTGCGCGTTGTCGGCCGCCTTCTCGATCGAGATGCCGTCGCGCCGCACGGGCTCGGGCAGCCGCGCCTCGACGATTTTCAGGCGGTTCTGCACGTCGACGGCCGCGAGATCGGCGCTCACGCCCTGCTTGAACGTGAGCGACAGCGACGCCTGGCCGGCGCTGCTCGTCGCCGACGTGTACAGCAGGCCGGGCACGCCGTTCATCTCGCGCTCGATCACGGCGGTGACCGATTCCTCGACGACCTGCGCGGACGCGCCCGGATACGTCGCATAGAGGCTGACGACGGGCGGCGCGATGTCCGGATACTGCGCGACGGGCAGCGCGCGGATCGCGAAGATGCCGCCCAGCATGATGAACAAGGAGATCACCCATGCGAACACCGGGCGATCGATGAAGAAACGAGCCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41211","NCBI_taxonomy_name":"Burkholderia pseudomallei K96243","NCBI_taxonomy_id":"272560"}}}},"ARO_accession":"3002983","ARO_id":"39417","ARO_name":"amrB","ARO_description":"amrB is the membrane fusion protein of the AmrAB-OprM multidrug efflux complex.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"477":{"model_id":"477","model_name":"catP","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"571":{"protein_sequence":{"accession":"AAB51421.1","sequence":"MVFEKIDKNSWNRKEYFDHYFASVPCTYSMTVKVDITQIKEKGMKLYPAMLYYIAMIVNRHSEFRTAINQDGELGIYDEMIPSYTIFHNDTETFSSLWTECKSDFKSFLADYESDTQRYGNNHRMEGKPNAPENIFNVSMIPWSTFDGFNLNLQKGYDYLIPIFTMGKYYKEDNKIILPLAIQVHHAVCDGFHICRFVNELQELINS"},"dna_sequence":{"accession":"U15027","fmin":"0","fmax":"624","strand":"+","sequence":"ATGGTATTTGAAAAAATTGATAAAAATAGTTGGAACAGAAAAGAGTATTTTGACCACTACTTTGCAAGTGTACCTTGTACATACAGCATGACCGTTAAAGTGGATATCACACAAATAAAGGAAAAGGGAATGAAACTATATCCTGCAATGCTTTATTATATTGCAATGATTGTAAACCGCCATTCAGAGTTTAGGACGGCAATCAATCAAGATGGTGAATTGGGGATATATGATGAGATGATACCAAGCTATACAATATTTCACAATGATACTGAAACATTTTCCAGCCTTTGGACTGAGTGTAAGTCTGACTTTAAATCATTTTTAGCAGATTATGAAAGTGATACGCAACGGTATGGAAACAATCATAGAATGGAAGGAAAGCCAAATGCTCCGGAAAACATTTTTAATGTATCTATGATACCGTGGTCAACCTTCGATGGCTTTAATCTGAATTTGCAGAAAGGATATGATTATTTGATTCCTATTTTTACTATGGGGAAATATTATAAAGAAGATAACAAAATTATACTTCCTTTGGCAATTCAAGTTCATCACGCAGTATGTGACGGATTTCACATTTGCCGTTTTGTAAACGAATTGCAGGAATTGATAAATAGTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36812","NCBI_taxonomy_name":"Clostridium perfringens","NCBI_taxonomy_id":"1502"}}}},"ARO_accession":"3002686","ARO_id":"39120","ARO_name":"catP","ARO_description":"catP is a transposon and chromosome-encoded variant of the cat gene found in Clostridium perfringens and Neisseria meningitidis","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. cat is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Bacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini","category_aro_class_name":"AMR Gene Family"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"478":{"model_id":"478","model_name":"AAC(3)-IIa","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"560"}},"model_sequences":{"sequence":{"4266":{"protein_sequence":{"accession":"CAA31895.1","sequence":"MHTQKAITEALQKLGVQSGDLLMVHASLKSIGPVEGGAETVVAALRSAVGPTGTVMGYASWDRSPYEETLNGARLDDNARRTWPPFDPATAGTYRGFGLLNQFLVQAPGARRSAHPDASMVAVGPLAETLTEPHELGHALGEGSPNERFVRLGGKALLLGAPLNSVTALHYAEAVADIPNKRWVTYEMPMPGRDGEVAWKTASDYDSNGILDCFAIEGKQDAVETIANAYVKLGRHREGVVGFAQCYLFDAQDIVTFGVTYLEKHFGTTPIVPAHEAIERSCEPSG"},"dna_sequence":{"accession":"X13543.1","fmin":"185","fmax":"1046","strand":"+","sequence":"ATGCATACGCAGAAGGCAATAACGGAGGCGCTTCAAAAACTCGGAGTCCAATCCGGTGACCTGTTGATGGTGCATGCCTCACTTAAATCGATTGGTCCGGTCGAAGGAGGAGCGGAGACGGTCGTCGCCGCGTTACGCTCCGCGGTTGGGCCGACTGGCACTGTGATGGGATACGCATCGTGGGACCGATCACCCTACGAGGAGACTCTGAATGGCGCTCGGTTGGATGACAATGCCCGCCGTACCTGGCCGCCGTTCGATCCCGCAACGGCCGGGACTTACCGTGGGTTCGGCCTGCTGAATCAGTTTCTGGTTCAAGCCCCCGGCGCGCGGCGCAGCGCGCACCCCGATGCATCGATGGTCGCGGTTGGTCCGCTGGCTGAAACGCTGACGGAGCCTCACGAACTCGGTCACGCCTTGGGGGAAGGGTCGCCCAACGAGCGGTTCGTCCGCCTTGGCGGGAAGGCCCTGCTGTTGGGTGCGCCGCTAAACTCCGTTACCGCATTGCACTACGCCGAGGCGGTTGCCGATATACCCAATAAACGGTGGGTGACGTATGAGATGCCGATGCCTGGAAGAGACGGTGAAGTCGCCTGGAAAACGGCATCGGATTACGATTCAAACGGCATTCTCGATTGCTTTGCTATCGAAGGAAAGCAGGATGCGGTCGAAACTATAGCAAATGCTTACGTGAAGCTCGGTCGCCATCGAGAAGGTGTCGTGGGCTTTGCCCAGTGCTACCTGTTCGACGCGCAGGACATCGTGACGTTCGGCGTCACCTATCTTGAGAAGCATTTCGGAACCACTCCGATCGTGCCTGCGCACGAAGCCATCGAGCGCTCTTGCGAGCCTTCAGGTTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39505","NCBI_taxonomy_name":"Plasmid pWP113a","NCBI_taxonomy_id":"28425"}}}},"ARO_accession":"3002533","ARO_id":"38933","ARO_name":"AAC(3)-IIa","ARO_description":"AAC(3)-IIa is a plasmid-encoded aminoglycoside acetyltransferase in K. pneumoniae, E. cloacae, Actinobacillus pleuropneumoniae, S. typhimurium, Citrobacter freundii, and P. aeruginosa.","ARO_category":{"36461":{"category_aro_accession":"3000322","category_aro_cvterm_id":"36461","category_aro_name":"AAC(3)","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 3.","category_aro_class_name":"AMR Gene Family"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"479":{"model_id":"479","model_name":"IMP-29","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1015":{"protein_sequence":{"accession":"AFG25462.1","sequence":"MSKLFVFLIFLFCSITAAAESLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNTEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKGGKVQAKNSFSGVSYWLVKKKIEVFYPGPGHTPDNVVVWLPENRVLFGGCFVKPYGLGNLDDANVEAWPHSAEILMSRYGNAKLVVPSHSDIGNASLLKLTWEQAVKGLKESKKPSQPSN"},"dna_sequence":{"accession":"JQ041634","fmin":"1122","fmax":"1863","strand":"+","sequence":"ATGAGCAAGTTATTTGTATTCCTTATTTTTTTGTTTTGTAGCATTACTGCCGCAGCAGAGTCTTTGCCAGATTTAAAAATTGAGAAGCTCGACGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGTTGGGGTGTTGTTCCTAAACATGGCTTGGTGGTTCTTGTAAATACTGAGGCCTATCTGATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAACGCGGCTATAAAATAAAAGGCAGTATTTCCTCTCATTTTCATAGCGACAGCACAGGCGGAATAGAGTGGCTTAATTCTCAATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTTCTTAAAAAAGGCGGTAAAGTACAAGCTAAAAATTCATTTAGCGGAGTTAGCTATTGGCTAGTTAAGAAAAAGATTGAAGTTTTTTATCCTGGTCCAGGGCACACTCCAGATAACGTAGTGGTTTGGCTACCTGAAAATAGAGTTTTGTTCGGTGGTTGTTTTGTTAAACCGTACGGTCTTGGAAATCTCGATGACGCAAATGTTGAAGCATGGCCACATTCTGCTGAAATATTAATGTCTAGGTATGGTAATGCAAAACTGGTTGTTCCAAGCCATAGTGACATCGGAAATGCGTCGCTCTTGAAGCTTACATGGGAGCAGGCTGTTAAAGGGCTAAAAGAAAGTAAAAAACCATCACAGCCAAGTAACTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002220","ARO_id":"38620","ARO_name":"IMP-29","ARO_description":"IMP-29 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"480":{"model_id":"480","model_name":"GES-9","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"871":{"protein_sequence":{"accession":"AAY43207.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMGDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGSRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"AY920928","fmin":"2689","fmax":"3553","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGGGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCCAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGAGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAGT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002338","ARO_id":"38738","ARO_name":"GES-9","ARO_description":"GES-9 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"481":{"model_id":"481","model_name":"VIM-30","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1083":{"protein_sequence":{"accession":"AET05999.1","sequence":"MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVNEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"JN129451","fmin":"87","fmax":"888","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAGC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002300","ARO_id":"38700","ARO_name":"VIM-30","ARO_description":"VIM-30 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"482":{"model_id":"482","model_name":"LEN-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"776":{"protein_sequence":{"accession":"CAA28198.1","sequence":"MRYVRLCVISLLATLPLVVYAGPQPLEQIKQSESQLSGRVGMVEMDLANGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGLEQLDRRIHYRQQDLVDYSPVSEKHLVDGMTIGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPPGWFIADKTGAGERGARGIVALLGPDGKPERIVVIYLRDTPASMAERNQHIAGIGQR"},"dna_sequence":{"accession":"X04515","fmin":"285","fmax":"1125","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCACCCTGCCACTGGTGGTATACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAACGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGTCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGCCGGGCTGGTTTATCGCCGACAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCCAGCGCTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002454","ARO_id":"38854","ARO_name":"LEN-1","ARO_description":"LEN-1 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"483":{"model_id":"483","model_name":"GES-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"2047":{"protein_sequence":{"accession":"AAP22974.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVKWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMGDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"AY260546","fmin":"4477","fmax":"5341","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCATCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCAAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGGGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAGT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002336","ARO_id":"38736","ARO_name":"GES-7","ARO_description":"GES-7 is a beta-lactamase found in Enterobacter cloacae","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"484":{"model_id":"484","model_name":"QnrB49","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"214":{"protein_sequence":{"accession":"AFD54601.1","sequence":"MTPLLYKKTGTNMALALVGEKIDRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNASALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRRVDLQGVKLDNYQASLLMERLGIAIIG"},"dna_sequence":{"accession":"JQ582718","fmin":"0","fmax":"681","strand":"+","sequence":"ATGACGCCATTACTGTATAAAAAAACAGGTACAAATATGGCACTGGCACTCGTTGGCGAAAAAATTGACAGAAACCGCTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCGATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATGCCAGTGCGCTTGGCATTGAAATTCGCCACTGTCGTGCGCAAGGCGCAGATTTTCGCGGCGCAAGTTTTATGAATATGATCACTACTCGCACCTGGTTTTGCAGTGCATATATCACTAACACAAATCTAAGCTACGCCAATTTTTCGAAAGTAGTGTTGGAAAAGTGTGAGCTGTGGGAAAACCGTTGGATGGGGACCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTGACTTAGATATTCGGCGCGTTGATTTACAAGGCGTTAAGTTGGACAACTACCAGGCATCGTTGCTCATGGAACGTCTTGGCATCGCGATTATTGGCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002764","ARO_id":"39198","ARO_name":"QnrB49","ARO_description":"QnrB49 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"485":{"model_id":"485","model_name":"TEM-191","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1076":{"protein_sequence":{"accession":"AEQ59621.1","sequence":"MPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGKRGSRGIIAALGPDGKPSRIVVIYTT"},"dna_sequence":{"accession":"JF949916","fmin":"0","fmax":"757","strand":"+","sequence":"ATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTAAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001051","ARO_id":"37431","ARO_name":"TEM-191","ARO_description":"TEM-191 is a beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"440":{"model_id":"440","model_name":"MexA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"650"}},"model_sequences":{"sequence":{"68":{"protein_sequence":{"accession":"NP_249116.1","sequence":"MQRTPAMRVLVPALLVAISALSGCGKSEAPPPAQTPEVGIVTLEAQTVTLNTELPGRTNAFRIAEVRPQVNGIILKRLFKEGSDVKAGQQLYQIDPATYEADYQSAQANLASTQEQAQRYKLLVADQAVSKQQYADANAAYLQSKAAVEQARINLRYTKVLSPISGRIGRSAVTEGALVTNGQANAMATVQQLDPIYVDVTQPSTALLRLRRELASGQLERAGDNAAKVSLKLEDGSQYPLEGRLEFSEVSVDEGTGSVTIRAVFPNPNNELLPGMFVHAQLQEGVKQKAILAPQQGVTRDLKGQATALVVNAQNKVELRVIKADRVIGDKWLVTEGLNAGDKIITEGLQFVQPGVEVKTVPAKNVASAQKADAAPAKTDSKG"},"dna_sequence":{"accession":"NC_002516","fmin":"472023","fmax":"473175","strand":"+","sequence":"ATGCAACGAACGCCAGCCATGCGTGTACTGGTTCCGGCCCTGCTGGTCGCGATTTCGGCCCTTTCCGGGTGCGGAAAAAGCGAGGCGCCGCCGCCGGCGCAAACGCCGGAGGTCGGGATCGTGACCCTGGAAGCGCAGACGGTGACCCTGAATACCGAGCTGCCGGGCCGGACCAATGCGTTCCGCATCGCCGAGGTGCGTCCCCAGGTGAACGGCATCATCCTCAAGCGCCTGTTCAAGGAAGGCAGCGACGTCAAGGCCGGGCAGCAGCTCTACCAGATCGACCCCGCCACCTACGAGGCCGACTACCAGAGCGCCCAGGCCAACCTGGCTTCGACCCAGGAACAGGCCCAGCGCTACAAGCTGCTGGTCGCCGACCAGGCCGTGAGCAAGCAGCAGTACGCCGACGCCAATGCCGCCTACCTGCAGTCCAAGGCGGCGGTGGAGCAGGCGCGGATCAACCTGCGCTACACCAAGGTGCTGTCGCCGATCTCCGGCCGCATCGGCCGTTCCGCGGTGACCGAAGGCGCCCTGGTGACCAACGGCCAGGCCAACGCGATGGCCACCGTGCAACAGCTCGACCCGATCTACGTCGACGTCACCCAGCCGTCCACCGCCCTGCTGCGCCTGCGCCGCGAACTGGCCAGCGGCCAGTTGGAGCGCGCCGGCGACAACGCGGCGAAGGTCTCCCTGAAGCTGGAGGACGGTAGCCAATACCCGCTGGAAGGTCGCCTCGAATTCTCCGAGGTTTCCGTCGACGAAGGCACCGGCTCGGTCACCATCCGCGCCGTGTTCCCCAACCCGAACAACGAGCTGCTGCCCGGCATGTTCGTTCACGCGCAGTTGCAGGAAGGCGTCAAGCAGAAGGCCATCCTCGCTCCGCAGCAAGGCGTGACCCGCGACCTCAAGGGCCAGGCTACCGCGCTGGTGGTGAACGCGCAGAACAAGGTCGAGCTGCGGGTGATCAAGGCCGACCGGGTGATCGGCGACAAGTGGCTGGTTACCGAAGGCCTGAACGCCGGCGACAAGATCATTACCGAAGGCCTGCAGTTCGTGCAGCCGGGTGTCGAGGTGAAGACCGTGCCGGCGAAGAATGTCGCGTCCGCGCAGAAGGCCGACGCCGCTCCGGCGAAAACCGACAGCAAGGGCTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3000377","ARO_id":"36516","ARO_name":"MexA","ARO_description":"MexA is the membrane fusion protein of the MexAB-OprM multidrug efflux complex.","ARO_category":{"35996":{"category_aro_accession":"0000079","category_aro_cvterm_id":"35996","category_aro_name":"clavulanate","category_aro_description":"Clavulanic acid is a beta-lactamase inhibitor (marketed by GlaxoSmithKline, formerly Beecham) combined with penicillin group antibiotics to overcome certain types of antibiotic resistance. It is used to overcome resistance in bacteria that secrete beta-lactamase, which otherwise inactivates most penicillins.","category_aro_class_name":"Adjuvant"},"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35979":{"category_aro_accession":"0000062","category_aro_cvterm_id":"35979","category_aro_name":"ceftriaxone","category_aro_description":"Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36468":{"category_aro_accession":"3000329","category_aro_cvterm_id":"36468","category_aro_name":"sulfamethoxazole","category_aro_description":"Sulfamethoxazole is a sulfonamide antibiotic usually taken with trimethoprim, a diaminopyrimidine antibiotic. Sulfamethoxazole inhibits dihydropteroate synthase, essential to tetrahydrofolic acid biosynthesis. This pathway generates compounds used in the synthesis of many amino acids and nucleotides.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36689":{"category_aro_accession":"3000550","category_aro_cvterm_id":"36689","category_aro_name":"aztreonam","category_aro_description":"Aztreonam was the first monobactam discovered, and is greatly effective against Gram-negative bacteria while inactive against Gram-positive bacteria. Artreonam is a poor substrate for beta-lactamases, and may even act as an inhibitor. In Gram-negative bacteria, Aztreonam interferes with filamentation, inhibiting cell division and leading to cell death.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"40362":{"category_aro_accession":"3003708","category_aro_cvterm_id":"40362","category_aro_name":"panipenem","category_aro_description":"Panipenem is a carbapenem antibacterial agent with a broad spectrum of in vitro activity covering a wide range of Gram-negative and Gram-positive aerobic and anaerobic bacterial.  It is used in combination with betamipron to inhibit panipenem uptake into the renal tubule and prevent nephrotoxicity.","category_aro_class_name":"Antibiotic"},"40523":{"category_aro_accession":"3003832","category_aro_cvterm_id":"40523","category_aro_name":"ticarcillin","category_aro_description":"Ticarcillin is a carboxypenicillin used for the treatment of Gram-negative bacteria, particularly P. aeruginosa. Ticarcillin's antibiotic properties arise from its ability to prevent cross-linking of peptidoglycan during cell wall synthesis, when the bacteria try to divide, causing cell death.","category_aro_class_name":"Antibiotic"},"40957":{"category_aro_accession":"3004024","category_aro_cvterm_id":"40957","category_aro_name":"trimethoprim-sulfamethoxazole","category_aro_description":"An antibiotic cocktail containing the diaminopyrimidine antibiotic Trimethoprim and the sulfonamide antibiotic sulfamethoxazole (1 TMP:5 SMX).","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36421":{"category_aro_accession":"3000282","category_aro_cvterm_id":"36421","category_aro_name":"sulfonamide antibiotic","category_aro_description":"Sulfonamides are broad spectrum, synthetic antibiotics that contain the sulfonamide group. Sulfonamides inhibit dihydropteroate synthase, which catalyzes the conversion of p-aminobenzoic acid to dihydropteroic acid as part of the tetrahydrofolic acid biosynthetic pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor of many nucleotides and amino acids. Many sulfamides are taken with trimethoprim, an inhibitor of dihydrofolate reductase, also disturbing the trihydrofolic acid synthesis pathway.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"458":{"model_id":"458","model_name":"tet(B)","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"325":{"protein_sequence":{"accession":"BAC67143.1","sequence":"MNSSTKIALAITLLDAMGIGLIMPVLPTLLREFIASEDIANHFGVLLALYALMQVIFAPWLGKMSDRFGRRPVLLLSLIGASLDYLLLAFSSALWMLYLGRLLSGITGATGAVAASVIADTTSASQRVKWFGWLGASFGLGLIAGPIIGGFAGEISPHSPFFIAALLNIVTFLVVMFWFRETKNTRDNTDTEVGVETQSNSVYITLFKTMPILLIIYFSAQLIGQIPATVWVLFTENRFGWNSMMVGFSLAGLGLLHSVFQAFVAGRIATKWGEKTAVLLGFIADSSAFAFLAFISEGWLVFPVLILLAGGGIALPALQGVMSIQTKSHQQGALQGLLVSLNNATGVIGPLLFAVIYNHSLPIWDGWIWIIGLAFYCIIILLSMTFMLTPQAQGSKQETSA"},"dna_sequence":{"accession":"AB089595","fmin":"0","fmax":"1206","strand":"+","sequence":"ATGAATAGTTCGACAAAGATCGCATTGGCAATTACGTTACTCGATGCCATGGGGATTGGCCTTATCATGCCAGTCTTGCCAACGTTATTACGTGAATTTATTGCTTCGGAAGATATCGCTAACCACTTTGGCGTATTGCTTGCACTTTATGCGTTAATGCAGGTTATCTTTGCTCCTTGGCTTGGAAAAATGTCTGACCGATTTGGTCGGCGCCCAGTGCTGTTGTTGTCATTAATAGGCGCATCGCTGGATTACTTATTGCTGGCTTTTTCAAGTGCGCTTTGGATGCTGTATTTAGGCCGTTTGCTTTCAGGGATCACAGGAGCTACTGGGGCTGTCGCGGCATCGGTCATTGCCGATACCACCTCAGCTTCTCAACGCGTGAAGTGGTTCGGTTGGTTAGGGGCAAGTTTTGGGCTTGGTTTAATAGCGGGGCCTATTATTGGTGGTTTTGCAGGAGAGATTTCACCGCATAGTCCCTTTTTTATCGCTGCGTTGCTAAATATTGTCACTTTCCTTGTGGTTATGTTTTGGTTCCGTGAAACCAAAAATACACGTGATAATACAGATACCGAAGTAGGGGTTGAGACGCAATCGAATTCGGTATACATCACTTTATTTAAAACGATGCCCATTTTGTTGATTATTTATTTTTCAGCGCAATTGATAGGCCAAATTCCCGCAACGGTGTGGGTGCTATTTACCGAAAATCGTTTTGGATGGAATAGCATGATGGTTGGCTTTTCATTAGCGGGTCTTGGTCTTTTACACTCAGTATTCCAAGCCTTTGTGGCAGGAAGAATAGCCACTAAATGGGGCGAAAAAACGGCAGTACTGCTCGGATTTATTGCAGATAGTAGTGCATTTGCCTTTTTAGCGTTTATATCTGAAGGTTGGTTAGTTTTCCCTGTTTTAATTTTATTGGCTGGTGGTGGGATCGCTTTACCTGCATTACAGGGAGTGATGTCTATCCAAACAAAGAGTCATCAGCAAGGTGCTTTACAGGGATTATTGGTGAGCCTTAACAATGCAACCGGTGTTATTGGCCCATTACTGTTTGCTGTTATTTATAATCATTCACTACCAATTTGGGATGGCTGGATTTGGATTATTGGTTTAGCGTTTTACTGTATTATTATCCTGCTATCGATGACCTTCATGTTAACCCCTCAAGCTCAGGGGAGTAAACAGGAGACAAGTGCTTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39591","NCBI_taxonomy_name":"Gram-negative bacterium TC71","NCBI_taxonomy_id":"203855"}}}},"ARO_accession":"3000166","ARO_id":"36305","ARO_name":"tet(B)","ARO_description":"Tet(B) is a tetracycline efflux protein expressed in many Gram-negative bacteria. It confers resistance to tetracycline, doxycycline, and minocycline, but not tigecycline.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"402":{"model_id":"402","model_name":"tet(Y)","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"3343":{"protein_sequence":{"accession":"AAC72341.1","sequence":"MSKSLITALIVVALDAIGLGLIMPVVPALLNEFVPAEQTAFHYGVFLSLYAFMQVFCAPVLGRLSDRYGRRIILLVSFLGATIDYSIMAAAPVLWVLYIGRIISGVTGATGAIAASIIADTTKQEERARWFGFMGACFGAGMIAGPAIGGVLGDISVHAPFVAGALLNAIAFCLVAFLLPKTPSQPPEGQPAKINLFEGFRFNFAVQGLASFFALFFLMQLIGQAPAALWVIYGEQRLNWDIGTAGVSLAVFGAAHTFVQAVLTGTLSKRLGDRGVLLLGMGADMCGFLLLAFITQSWMVLPAIFMLATGGIGMPALQAIISGLVCDEKQGALQGTLTGLTNITSIIGPVGFTTLYGLTAGQWDGWVWLVAASLYLIAIPLLRQSASLLRS"},"dna_sequence":{"accession":"AF070999","fmin":"1679","fmax":"2855","strand":"+","sequence":"ATGTCAAAATCACTTATAACCGCACTCATTGTTGTCGCGCTTGATGCGATTGGTTTGGGATTAATCATGCCGGTGGTTCCGGCTTTATTAAATGAATTTGTACCGGCAGAGCAAACAGCATTTCACTATGGTGTTTTTTTATCGCTTTATGCGTTTATGCAGGTCTTTTGCGCGCCCGTTTTAGGGCGGTTATCTGACCGCTATGGACGGCGGATTATTTTGCTGGTTTCATTTTTAGGTGCCACGATTGATTATAGCATAATGGCGGCAGCGCCTGTTTTATGGGTGCTTTATATCGGCCGGATTATCTCAGGTGTTACCGGAGCAACTGGTGCAATCGCGGCATCAATTATCGCTGATACAACTAAACAGGAAGAACGTGCGCGTTGGTTTGGTTTTATGGGGGCGTGTTTTGGTGCAGGTATGATTGCAGGGCCTGCTATTGGCGGTGTTCTTGGTGATATATCTGTGCATGCGCCCTTTGTGGCAGGGGCTCTTCTCAATGCAATTGCCTTTTGTTTGGTGGCTTTCTTGTTGCCCAAAACGCCGTCACAACCGCCTGAAGGACAGCCAGCCAAAATCAATTTGTTTGAAGGCTTTCGCTTCAATTTTGCAGTTCAGGGACTTGCCAGCTTTTTTGCGTTGTTTTTTCTTATGCAGCTGATTGGGCAGGCGCCCGCCGCTTTGTGGGTGATTTATGGCGAACAGCGCTTGAATTGGGATATTGGCACAGCAGGTGTGTCGCTGGCCGTTTTTGGTGCAGCACATACATTCGTACAAGCTGTTTTAACCGGCACTCTTTCAAAGCGACTGGGTGACCGCGGTGTGTTGCTGCTTGGAATGGGCGCTGATATGTGCGGGTTTTTATTGCTGGCTTTTATCACGCAAAGCTGGATGGTTCTGCCGGCAATTTTTATGCTGGCCACAGGCGGCATTGGTATGCCTGCTTTGCAGGCCATTATTTCAGGTCTTGTTTGCGATGAAAAACAAGGTGCTTTACAGGGAACTTTAACGGGGTTGACGAATATAACCTCGATTATCGGGCCGGTCGGATTTACGACGCTTTATGGCTTAACCGCGGGGCAGTGGGATGGTTGGGTTTGGCTCGTCGCAGCAAGCCTTTATCTTATTGCTATACCATTATTGCGCCAGTCAGCCAGTTTATTGCGATCTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36774","NCBI_taxonomy_name":"IncQ plasmid pIE1120","NCBI_taxonomy_id":"77644"}}}},"ARO_accession":"3000182","ARO_id":"36321","ARO_name":"tet(Y)","ARO_description":"TetY is a tetracycline efflux pump found in Gram-negative bacteria (Aeromonas and Escherichia). It is associated with plasmid DNA.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"336":{"model_id":"336","model_name":"tlrB conferring tylosin resistance","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"546":{"protein_sequence":{"accession":"AAD12162.1","sequence":"MRKNVVRYLRCPHCAAPLRSSDRTLRCENGHTFDVARQGYVNLLRRPTKLAADTTDMVAARAALLDSGHYAPLTERLAGTAGRAAGAGAPDCVVDIGGGTGHHLARVLEEFEDAEGLLLDMSKPAVRRAARAHPRASSAVADVWDTLPLRDGAAAMALNVFAPRNPPEIRRILRPGGTLLVVTPQQDHLAELVDALGLLRVRDHKEGRLAEQLAPHFEAVGQERLRTTLRLDHDALGRVVAMGPSSWHQDPDELARRIAELPGIHEVTLSVTFTVCRPLP"},"dna_sequence":{"accession":"AF055922","fmin":"1787","fmax":"2630","strand":"+","sequence":"ATGCGGAAGAACGTCGTGCGATATCTGCGCTGTCCGCACTGCGCAGCCCCTCTGCGGTCATCCGACCGCACCCTCCGCTGCGAAAACGGGCACACCTTCGACGTCGCCCGGCAGGGCTATGTGAATCTGCTCAGACGCCCGACGAAGCTCGCCGCCGACACCACCGACATGGTCGCCGCCCGGGCCGCGCTGCTGGACAGCGGGCATTACGCGCCGCTGACCGAGCGGCTGGCCGGGACGGCCGGGCGCGCGGCGGGCGCCGGGGCACCGGACTGCGTCGTGGACATCGGCGGGGGCACCGGTCACCATCTCGCCCGTGTCCTGGAGGAGTTCGAGGACGCCGAGGGACTCCTGCTGGACATGTCCAAGCCGGCCGTGCGCAGGGCCGCCCGCGCCCATCCCCGGGCCAGCTCCGCCGTCGCCGACGTATGGGACACACTTCCGCTGCGGGACGGGGCCGCCGCGATGGCCCTCAACGTCTTCGCCCCGCGCAACCCGCCGGAGATCCGCAGGATCCTCCGCCCCGGCGGCACCCTGCTGGTCGTCACGCCCCAGCAGGACCACCTCGCCGAACTCGTGGACGCGCTGGGGCTGTTGCGCGTACGGGACCACAAGGAGGGCCGGCTGGCCGAACAGCTCGCGCCGCACTTCGAGGCCGTCGGGCAGGAGCGGCTGCGGACCACTCTCCGCCTCGATCACGACGCGCTCGGCCGGGTGGTCGCCATGGGGCCCAGTTCCTGGCACCAGGACCCGGATGAACTGGCGCGGCGGATCGCGGAGTTGCCCGGCATCCACGAGGTCACGCTCTCGGTCACCTTCACCGTCTGCCGCCCTCTGCCCTGAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36838","NCBI_taxonomy_name":"Streptomyces fradiae","NCBI_taxonomy_id":"1906"}}}},"ARO_accession":"3001299","ARO_id":"37698","ARO_name":"tlrB conferring tylosin resistance","ARO_description":"TlrB is a methyltransferase found in Streptomyces fradiae and confers resistance to mycinamicin, tylosin and lincosamides. Specifically, this enzyme adds a methyl group to guanosine 748 (E. coli numbering). TlrB is found in the tylosin biosynthetic cluster and is one mechanism by which S. fradiae protects itself from self-destruction when producing this macrolide.","ARO_category":{"37697":{"category_aro_accession":"3001298","category_aro_cvterm_id":"37697","category_aro_name":"non-erm 23S ribosomal RNA methyltransferase (G748)","category_aro_description":"Non-erm 23S ribosomal RNA methyltransferases modify guanosine 748 (E. coli numbering) to confer resistance to some macrolides and lincosamides","category_aro_class_name":"AMR Gene Family"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"276":{"model_id":"276","model_name":"tetR","model_type":"protein overexpression model","model_type_id":"41091","model_description":"This model detects protein overexpression based on the presence of mutations.The detection of the protein without an associated mutation indicates that the protein is likely to be expressed at low or basal levels. The detection of the protein with the mutation indicates that the protein is likely overexpressed. This model reflects how certain proteins are functional with and without mutations. For example, efflux pump subunits and regulators are functional with mutations and without mutations. Without mutations, efflux pump subunits and regulators are usually expressed at a low level. When an efflux pump regulator has a mutation, it can cause the overexpression of the efflux pump it is responsible for regulating, leading to resistance to specific drugs. Protein overexpression models have two parameters: a curated BLASTP cutoff, and a curated set of mutations (single resistance variants, frameshift mutations, indels, etc.) shown clinically to confer resistance. This model type is a combination of the protein homolog and protein variant model. A detected hit can be categorized as Perfect, Strict, or Loose with no mutation(s) or as Strict or Loose with mutation(s).","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2710":"H64Y","2711":"N82H","2712":"T103I"},"clinical":{"2710":"H64Y","2711":"N82H","2712":"T103I"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"2090":{"protein_sequence":{"accession":"CAD09823.1","sequence":"MMSRLDKSKVINSALELLNEVGIEGLTTRKLAQKLGVEQPTLYWHVKNKRALLDALAIEMLDRHHTHFCPLEGESWQDFLRNNAKSFRCALLSHRDGAKVHLGTRPTEKQYETLENQLAFLCQQGFSLENALYALSAVGHFTLGCVLEDQEHQVAKEERETPTTDSMPPLLRQAIELFDHQGAEPAFLFGLELIICGLEKQLKCESGS"},"dna_sequence":{"accession":"AL513383","fmin":"179218","fmax":"179845","strand":"+","sequence":"ATGATGTCTAGATTAGATAAAAGTAAAGTGATTAACAGCGCATTAGAGCTGCTTAATGAGGTCGGAATCGAAGGTTTAACAACCCGTAAACTCGCCCAGAAGCTAGGTGTAGAGCAGCCTACATTGTATTGGCATGTAAAAAATAAGCGGGCTTTGCTCGACGCCTTAGCCATTGAGATGTTAGATAGGCACCATACTCACTTTTGCCCTTTAGAAGGGGAAAGCTGGCAAGATTTTTTACGTAATAACGCTAAAAGTTTTAGATGTGCTTTACTAAGTCATCGCGATGGAGCAAAAGTACATTTAGGTACACGGCCTACAGAAAAACAGTATGAAACTCTCGAAAATCAATTAGCCTTTTTATGCCAACAAGGTTTTTCACTAGAGAATGCATTATATGCACTCAGCGCTGTGGGGCATTTTACTTTAGGTTGCGTATTGGAAGATCAAGAGCATCAAGTCGCTAAAGAAGAAAGGGAAACACCTACTACTGATAGTATGCCGCCATTATTACGACAAGCTATCGAATTATTTGATCACCAAGGTGCAGAGCCAGCCTTCTTATTCGGCCTTGAATTGATCATATGCGGATTAGAAAAACAACTTAAATGTGAAAGTGGGTCTTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35776","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhi str. CT18","NCBI_taxonomy_id":"220341"}}}},"ARO_accession":"3003479","ARO_id":"40072","ARO_name":"tetR","ARO_description":"TetR is the repressor of the tetracycline resistance element; its N-terminal region forms a helix-turn-helix structure and binds DNA. Binding of tetracycline to TetR reduces the repressor affinity for the tetracycline resistance gene (tetA) promoter operator sites. Mutations arise within tetR results in lower affinity for tetracyclin","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"395":{"model_id":"395","model_name":"blaF","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"3317":{"protein_sequence":{"accession":"AAA19882.1","sequence":"MTGLSRRNVLIGSLVAAAAVGAGVGGAAPAFAAPIDDQLAELERRDNVLIGLYAANLQSGRRITHRLDEMFAMCSTFKGYAAARVLQMAEHGEISLDNRVFVDADALVPNSPVTEARAGAEMTLAELCQAALQRSDNTAANLLLKTIGGPAAVTAFARSVGDERTRLDRWEVELNSAIPGDPRDTSTAAALAVGYRAILAGDALSPPQRGLLEDWMRANQTSSMRAGLPEGWTTADKTGSGDYGSTNDAGIAFGPDGQRLLLVMMTRSQAHDPKAENLRPLIGELTALVLPSLL"},"dna_sequence":{"accession":"L25634","fmin":"1273","fmax":"2158","strand":"+","sequence":"ATGACCGGACTATCGCGACGCAACGTTCTGATCGGTTCGCTCGTGGCGGCAGCTGCCGTCGGTGCCGGCGTCGGTGGCGCCGCACCGGCATTCGCGGCACCGATCGATGACCAGCTGGCGGAACTGGAGCGTCGGGACAACGTCCTGATCGGCTTGTACGCAGCCAATCTGCAGTCTGGGCGGAGGATCACGCACCGTCTCGACGAGATGTTCGCGATGTGCTCGACGTTCAAGGGCTACGCCGCTGCGCGGGTGCTGCAGATGGCCGAGCACGGCGAGATCTCACTGGACAACCGGGTCTTCGTCGATGCGGATGCGCTCGTGCCGAACTCACCCGTCACCGAGGCACGTGCCGGTGCCGAGATGACGTTGGCCGAGCTGTGCCAGGCGGCGCTGCAGCGCAGTGACAACACCGCGGCGAACCTGCTGCTGAAGACCATTGGCGGGCCTGCGGCTGTCACCGCCTTCGCCCGCAGCGTCGGCGATGAGCGCACCCGCCTGGACCGCTGGGAGGTAGAGCTGAACTCCGCGATACCCGGGGACCCGAGGGACACCAGCACCGCTGCGGCGCTGGCGGTCGGATACCGCGCGATTCTGGCCGGTGACGCACTGAGCCCGCCGCAGCGCGGCCTGTTGGAAGACTGGATGCGGGCCAATCAGACCTCGAGCATGCGTGCCGGGCTTCCGGAGGGCTGGACCACCGCGGACAAAACCGGCAGCGGCGATTACGGCAGCACCAACGACGCCGGAATCGCTTTCGGACCCGACGGACAACGGTTGCTGTTGGTGATGATGACGCGATCGCAGGCCCATGACCCCAAGGCCGAGAACCTGCGACCGCTCATCGGTGAGCTGACGGCGCTGGTGCTGCCGTCCTTACTCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36886","NCBI_taxonomy_name":"Mycobacterium fortuitum","NCBI_taxonomy_id":"1766"}}}},"ARO_accession":"3003562","ARO_id":"40169","ARO_name":"blaF","ARO_description":"Class A beta-lactamase found in Mycobacterium fortuitum","ARO_category":{"41397":{"category_aro_accession":"3004233","category_aro_cvterm_id":"41397","category_aro_name":"blaF family beta-lactamase","category_aro_description":"Class A Beta-lactamases first isolated from Mycobacterium fortuitum.","category_aro_class_name":"AMR Gene Family"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"486":{"model_id":"486","model_name":"cmlB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"17":{"protein_sequence":{"accession":"AAD22144.1","sequence":"MRSKNCNWRYSLAVTVLLLSPFDLLASLGMDMYLPAVPFMPHALGTTAGTIQLTLTTYLVMIGAGQLLFGPLSDRLGRRPVLLAGGAAYVAASIGLVVTSSAGVFLGFRILQACGASACLVATFATVRDIYAGRKESNVIYGLLGSMLAMVPAIGPLLGAVIDTWFGWRAIFAFLGLGMIAALTAAWRLWPETRVQRPAALQWSQLLLPIKHLNFWLYTVCYAAGMGSFFVFFSIAPGLMMGRQGMSQFGFSLLFATVAIAMMLAARFMGRVIAKWGSLSALRMGMGCLIAGAVLLVITELWIPQSVLGFIAPMWLVGVGVATAVSVAPNGALRGFDHIAGAVTAVYFCLGGLLLGSVGTLIISLLPRDTAWPVIAYCLVLATIVLGLSCVSRARDLRGHGEYDAVART"},"dna_sequence":{"accession":"AF034958","fmin":"0","fmax":"1230","strand":"+","sequence":"GTGCGCTCAAAGAACTGTAATTGGCGGTATTCCCTTGCCGTCACTGTGTTGTTGTTATCACCTTTCGATTTACTGGCATCACTCGGCATGGACATGTACTTGCCAGCGGTGCCTTTCATGCCACATGCTCTTGGTACGACAGCGGGCACAATTCAGCTTACGCTGACAACGTATTTGGTCATGATAGGGGCCGGTCAGCTTTTGTTTGGGCCACTGTCGGACCGGCTGGGACGTCGTCCCGTGCTACTGGCGGGCGGTGCCGCCTACGTTGCGGCCTCAATCGGCCTCGTCGTCACGTCATCGGCTGGAGTATTTCTGGGTTTTCGGATTCTCCAAGCTTGTGGTGCCTCGGCATGCCTTGTTGCCACATTTGCAACAGTGCGTGATATCTACGCAGGTCGCAAGGAAAGTAACGTCATCTACGGCTTGCTTGGCTCTATGCTTGCTATGGTTCCGGCGATAGGCCCATTGCTGGGAGCGGTCATAGACACCTGGTTCGGGTGGCGGGCGATCTTTGCGTTCTTGGGATTGGGAATGATCGCTGCATTGACAGCAGCGTGGCGGCTCTGGCCTGAGACCCGGGTGCAGCGACCAGCAGCTTTGCAATGGTCACAACTTCTGCTTCCCATCAAGCACCTTAACTTCTGGTTGTACACAGTGTGTTATGCCGCAGGAATGGGCAGCTTCTTCGTCTTCTTCTCCATAGCGCCCGGATTGATGATGGGTAGGCAAGGCATGTCCCAGTTTGGCTTCAGTCTGTTGTTCGCAACAGTGGCAATTGCGATGATGCTTGCGGCCCGCTTCATGGGGCGCGTAATCGCCAAGTGGGGCAGCCTGAGTGCCTTGCGAATGGGGATGGGCTGCCTGATAGCAGGCGCAGTCTTGCTTGTCATCACCGAGCTATGGATTCCGCAGTCCGTGTTGGGCTTTATTGCCCCAATGTGGCTAGTGGGCGTCGGCGTCGCGACAGCGGTATCCGTTGCACCCAATGGTGCGCTTCGAGGGTTCGACCATATTGCAGGAGCCGTTACGGCAGTCTACTTCTGCTTGGGGGGGCTGCTGCTGGGGAGTGTTGGAACGCTCATCATTTCGCTGTTGCCGCGCGACACGGCCTGGCCAGTTATCGCGTATTGTTTGGTTCTTGCAACAATCGTGCTTGGACTGTCGTGTGTTTCCCGAGCGAGAGACCTTCGCGGTCACGGGGAGTATGATGCGGTTGCACGCACATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36770","NCBI_taxonomy_name":"Enterobacter aerogenes","NCBI_taxonomy_id":"548"}}}},"ARO_accession":"3002698","ARO_id":"39132","ARO_name":"cmlB","ARO_description":"cmlB is a plasmid-encoded chloramphenicol exporter that is found in Enterobacter aerogenes","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"487":{"model_id":"487","model_name":"macB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1280"}},"model_sequences":{"sequence":{"539":{"protein_sequence":{"accession":"AAV85982.1","sequence":"MSLIECKNINRYFGSGENRVHILKDISLSIEKGDFVAIIGQSGSGKSTLMNILGCLDTAGSGSYRIDGIETAKMQPDELAALRRERFGFIFQRYNLLSSLTARDNVALPAVYMGMGGKERSARADKLLQDLGLASKEGNKPGELSGGQQQRVSIARALMNGGEIIFADEPTGALDTASGKNVMEIIRRLHEAGHTVIMVTHDPGIAANANRVIEIRDGEIISDTSKNPEIPASNVGRIQEKASWSFYYDQFVEAFRMSVQAVLAHKMRSLLTMLGIIIGIASVVSVVALGNGSQKKILEDISSMGTNTISIFPGRGFGDRRSGKIKTLTIDDAKIIAKQSYVASATPMTSSGGTLTYRNTDLTASLYGVGEQYFDVRGLKLETGRLFDENDVKEDAQVVVIDQNVKDKLFADSDPLGKTILFRKRPLTVIGVMKKDENAFGNSDVLMLWSPYTTVMHQITGESHTNSITVKIKDNANTRVAEKGLAELLKARHGTEDFFMNNSDSIRQMVESTTGTMKLLISSIALISLVVGGIGVMNIMLVSVTERTKEIGIRMAIGARRGNILQQFLIEAVLICIIGGLVGVGLSAAVSLVFNHFVTDFPMDISAASVIGAVACSTGIGIAFGFMPANKAAKLNPIDALAQD"},"dna_sequence":{"accession":"AY768532","fmin":"0","fmax":"1935","strand":"+","sequence":"ATGAGCTTGATCGAATGTAAAAACATCAACCGCTATTTCGGCAGCGGCGAGAACCGCGTCCATATTTTGAAAGACATCAGCCTGTCGATAGAGAAGGGTGATTTTGTCGCCATCATCGGGCAGTCCGGTTCGGGCAAGTCCACGCTGATGAACATACTCGGTTGTTTGGATACCGCCGGTTCCGGTTCGTACCGAATCGACGGCATCGAAACTGCCAAAATGCAGCCTGACGAACTGGCGGCATTGCGGCGCGAACGCTTCGGTTTCATCTTCCAACGCTACAACCTCTTAAGCTCGCTGACCGCAAGGGACAACGTCGCGCTGCCAGCCGTGTATATGGGTATGGGAGGCAAAGAGCGTTCCGCGCGGGCGGACAAACTCTTGCAGGATTTGGGTTTGGCAAGTAAAGAGGGCAACAAGCCCGGCGAACTCTCGGGCGGACAGCAGCAGCGCGTCTCCATCGCCCGCGCCCTGATGAACGGCGGAGAAATCATCTTCGCCGACGAGCCGACCGGCGCACTCGATACCGCCAGCGGCAAAAATGTGATGGAAATCATCCGCAGGCTGCACGAAGCCGGGCATACCGTCATTATGGTCACGCACGACCCCGGCATTGCCGCCAATGCCAACCGCGTCATCGAAATCCGGGACGGCGAAATCATTTCCGACACCTCGAAAAATCCCGAAATCCCCGCAAGCAATGTCGGGAGGATTCAGGAAAAAGCCTCGTGGTCGTTTTATTACGACCAGTTTGTCGAAGCCTTCAGAATGTCGGTGCAAGCAGTATTGGCGCACAAAATGCGTTCGCTTCTGACCATGCTCGGCATCATCATCGGTATCGCTTCGGTTGTCTCCGTCGTCGCGCTGGGCAACGGGTCGCAGAAAAAAATCCTCGAAGACATCAGTTCGATGGGGACGAACACCATCAGCATCTTCCCCGGGCGCGGCTTCGGCGACAGGCGCAGCGGCAAAATCAAAACCCTGACCATAGACGACGCAAAAATCATCGCCAAACAAAGCTATGTTGCTTCCGCCACGCCCATGACTTCGAGCGGCGGCACGCTGACCTACCGCAATACCGACCTGACCGCTTCTTTGTACGGCGTGGGCGAACAATATTTCGACGTGCGCGGGCTGAAGCTGGAAACGGGGCGGCTGTTTGATGAGAACGATGTGAAAGAAGACGCGCAAGTCGTCGTCATCGACCAAAATGTCAAAGACAAACTCTTTGCGGACTCGGATCCGTTGGGTAAAACCATTTTGTTCAGGAAACGCCCCTTGACCGTCATCGGCGTGATGAAAAAAGACGAAAACGCTTTCGGCAATTCCGACGTGCTGATGCTTTGGTCGCCCTATACGACGGTGATGCACCAAATCACAGGCGAGAGCCACACCAACTCCATCACCGTCAAAATCAAAGACAATGCCAATACCCGGGTTGCCGAAAAAGGGCTGGCCGAGCTGCTCAAAGCACGGCACGGCACGGAAGACTTCTTTATGAACAACAGCGACAGCATCAGGCAGATGGTCGAAAGCACCACCGGTACGATGAAGCTGCTGATTTCCTCCATCGCCCTGATTTCATTGGTAGTCGGCGGCATCGGCGTGATGAACATTATGCTGGTGTCCGTTACCGAGCGCACCAAAGAAATCGGCATACGGATGGCAATCGGCGCGCGGCGCGGCAATATTTTGCAGCAGTTTTTGATTGAGGCGGTGTTAATCTGCATCATCGGAGGCTTGGTCGGCGTAGGTTTGTCCGCCGCCGTCAGCCTCGTGTTCAATCATTTTGTAACCGATTTCCCGATGGACATTTCGGCGGCATCCGTTATCGGGGCGGTCGCCTGTTCGACCGGAATCGGCATCGCGTTCGGCTTTATGCCTGCCAATAAGGCAGCCAAACTCAATCCGATAGACGCATTGGCGCAGGATTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36806","NCBI_taxonomy_name":"Neisseria gonorrhoeae","NCBI_taxonomy_id":"485"}}}},"ARO_accession":"3000535","ARO_id":"36674","ARO_name":"macB","ARO_description":"MacB is an ATP-binding cassette (ABC) transporter that exports macrolides with 14- or 15- membered lactones. It forms an antibiotic efflux complex with MacA and TolC. macB corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"488":{"model_id":"488","model_name":"SHV-156","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1558":{"protein_sequence":{"accession":"AFQ23962.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQPERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTTFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"JX121123","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCCGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTACCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001195","ARO_id":"37575","ARO_name":"SHV-156","ARO_description":"SHV-156 is a beta-lactamase.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"490":{"model_id":"490","model_name":"TEM-188","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2034":{"protein_sequence":{"accession":"AEL17198.1","sequence":"MSIQHFRVALIPFFAAFCFPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASKRGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"JN211012","fmin":"213","fmax":"1074","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCTTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTAAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35672","NCBI_taxonomy_name":"Salmonella enterica","NCBI_taxonomy_id":"28901"}}}},"ARO_accession":"3001048","ARO_id":"37428","ARO_name":"TEM-188","ARO_description":"TEM-188 is an extended-spectrum beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"491":{"model_id":"491","model_name":"PER-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"898":{"protein_sequence":{"accession":"CAA63714.1","sequence":"MNVITKCVFTASALLMLGLSSFVVSAQSPLLKEQIETIVTGKKATVGVAVWGPDDLEPLLLNPFEKFPMQSVFKLHLAMLVLHQVDQGKLDLNQSVTVNRAAVLQNTWSPMMKDHQGDEFTVAVQQLLQYSVSHSDNVACDLLFELVGGPQALHAYIQSLGVKEAAVVANEAQMHADDQVQYQNWTSMKAAAQVLQKFEQKKQLSETSQALLWKWMVETTTGPQRLKGLLPAGTIVAHKTGTSGVRAGKTAATNDAGVIMLPDGRPLLVAVFVKDSAESERTNEAIIAQVAQAAYQFELKKLSAVSPD"},"dna_sequence":{"accession":"X93314","fmin":"0","fmax":"927","strand":"+","sequence":"ATGAATGTCATCACAAAATGTGTTTTCACCGCTTCTGCTCTGCTGATGCTTGGCTTAAGTTCATTTGTAGTATCAGCCCAATCCCCTTTGTTAAAAGAGCAGATTGAAACCATAGTGACGGGTAAAAAGGCCACTGTAGGTGTAGCAGTGTGGGGGCCTGACGATCTGGAACCTTTGTTGCTGAATCCATTTGAAAAGTTTCCGATGCAAAGTGTGTTTAAACTGCATTTAGCTATGTTAGTTCTGCATCAGGTCGATCAGGGGAAACTGGATTTAAATCAGTCTGTTACTGTTAATCGTGCTGCAGTATTACAAAATACCTGGTCGCCAATGATGAAAGATCATCAGGGCGATGAATTTACTGTTGCAGTACAGCAGTTACTGCAGTATTCGGTGTCACACAGCGACAATGTGGCCTGCGATTTGTTATTTGAACTGGTGGGCGGGCCGCAAGCTTTGCATGCTTATATCCAGTCTTTAGGCGTTAAAGAAGCTGCCGTGGTAGCAAATGAAGCGCAAATGCATGCGGATGATCAGGTGCAATATCAAAACTGGACGTCGATGAAAGCCGCAGCACAAGTTCTGCAAAAGTTTGAACAGAAAAAGCAGTTGTCTGAAACCTCTCAGGCCTTGTTATGGAAATGGATGGTTGAAACCACCACAGGACCACAGCGGTTAAAAGGCTTGTTACCTGCTGGTACTATAGTGGCGCATAAAACCGGTACTTCGGGCGTCAGAGCAGGAAAAACTGCGGCGACTAATGATGCGGGCGTCATTATGTTGCCTGATGGACGGCCTTTATTGGTGGCGGTATTTGTCAAGGATTCGGCTGAATCAGAACGAACCAATGAAGCTATTATTGCGCAGGTTGCGCAAGCGGCTTATCAGTTTGAGCTGAAAAAACTCTCTGCAGTGAGTCCGGATTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35732","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium","NCBI_taxonomy_id":"90371"}}}},"ARO_accession":"3002364","ARO_id":"38764","ARO_name":"PER-2","ARO_description":"PER-2 is a beta-lactamase found in Salmonella typhimurium","ARO_category":{"36195":{"category_aro_accession":"3000056","category_aro_cvterm_id":"36195","category_aro_name":"PER beta-lactamase","category_aro_description":"PER beta-lactamases are plasmid-mediated extended spectrum beta-lactamases found in the Enterobacteriaceae family.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"493":{"model_id":"493","model_name":"TEM-84","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1328":{"protein_sequence":{"accession":"AAL29436.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERDRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AF427130","fmin":"208","fmax":"1069","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAGATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000951","ARO_id":"37331","ARO_name":"TEM-84","ARO_description":"TEM-84 is an inhibitor-resistant beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"494":{"model_id":"494","model_name":"KPC-14","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1971":{"protein_sequence":{"accession":"AFV48348.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"JX524191","fmin":"395","fmax":"1271","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002324","ARO_id":"38724","ARO_name":"KPC-14","ARO_description":"KPC-14 is a beta-lactamase. From the Lahey list of KPC beta-lactamases.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"495":{"model_id":"495","model_name":"CMY-28","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1547":{"protein_sequence":{"accession":"ABQ51091.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGELAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDNKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"EF561644","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGAGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAACAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002039","ARO_id":"38439","ARO_name":"CMY-28","ARO_description":"CMY-28 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"496":{"model_id":"496","model_name":"KPC-16","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"792":{"protein_sequence":{"accession":"AGJ01153.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAASQRQQLVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"KC465199","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGTTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGTCGCAGCGGCAGCAGCTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002326","ARO_id":"38726","ARO_name":"KPC-16","ARO_description":"KPC-16 is a beta-lactamase. From the Lahey list of KPC beta-lactamases.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"497":{"model_id":"497","model_name":"OXA-79","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1693":{"protein_sequence":{"accession":"ABV71246.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGGDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"EU019534","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGAGGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001633","ARO_id":"38033","ARO_name":"OXA-79","ARO_description":"OXA-79 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"498":{"model_id":"498","model_name":"QnrB17","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"388":{"protein_sequence":{"accession":"CAP45902.1","sequence":"MTPLLYKKTGTNMALALVGEKIDRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNSSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"AM919398","fmin":"0","fmax":"681","strand":"+","sequence":"ATGACGCCATTACTGTATAAAAAAACAGGTACAAATATGGCTCTGGCACTCGTTGGCGAAAAAATTGACAGAAACCGTTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCGATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATTCCAGTGCGCTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGCGCAAGCTTTATGAATATGATCACCACGCGCACCTGGTTTTGTAGCGCATATATCACGAATACCAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAGCTGTGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCGAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTGACTTAGATATTCGGGGCGTTGATTTACAAGGCGTTAAGCTGGACAACTACCAGGCGTCGTTGCTCATGGAGCGGCTTGGCATCGCGGTGATTGGTTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002732","ARO_id":"39166","ARO_name":"QnrB17","ARO_description":"QnrB17 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"499":{"model_id":"499","model_name":"vanSB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3454":{"protein_sequence":{"accession":"AAB05623.1","sequence":"MERKGIFIKVFSYTIIVLLLLVGVTATLFAQQFVSYFRAMEAQQTVKSYQPLVELIQNSDRLDMQEVAGLFHYNNQSFEFYIEDKEGSVLYATPNADTSNSVRPDFLYVVHRDDNISIVAQSKAGVGLLYQGLTIRGIVMIAIMVVFSLLCAYIFARQMTTPIKALADSANKMANLKEVPPPLERKDELGALAHDMHSMYIRLKETIARLEDEIAREHELEETQRYFFAAASHELKTPIAAVSVLLEGMLENIGDYKDHSKYLRECIKMMDRQGKTISEILELVSLNDGRIVPIAEPLDIGRTVAELLPDFQTLAEANNQRFVTDIPAGQIVLSDPKLIQKALSNVILNAVQNTPQGGEVRIWSEPGAEKYRLSVLNMGVHIDDTALSKLFIPFYRIDQARSRKSGRSGLGLAIVQKTLDAMSLQYALENTSDGVLFWLDLPPTSTL"},"dna_sequence":{"accession":"U35369","fmin":"839","fmax":"2183","strand":"+","sequence":"ATGGAAAGAAAAGGGATTTTCATTAAGGTTTTTTCCTATACGATCATTGTCCTGTTACTGCTTGTCGGTGTAACGGCAACACTGTTTGCACAGCAATTTGTGTCTTATTTCAGAGCGATGGAAGCACAGCAAACAGTAAAATCCTATCAGCCATTGGTGGAACTGATTCAGAATAGCGATAGGCTTGATATGCAAGAGGTGGCAGGGCTGTTTCACTACAATAACCAATCCTTTGAGTTTTATATTGAAGATAAAGAGGGAAGCGTACTCTATGCCACACCGAATGCCGATACATCAAATAGTGTTAGGCCCGACTTTCTTTATGTGGTACATAGAGATGATAATATTTCGATTGTTGCTCAAAGCAAGGCAGGTGTGGGATTGCTTTATCAAGGGCTGACAATTCGGGGAATTGTTATGATTGCGATAATGGTTGTATTCAGCCTTTTATGCGCGTATATCTTTGCGCGGCAAATGACAACGCCGATCAAAGCCTTAGCGGACAGTGCGAATAAAATGGCAAACCTGAAAGAAGTACCGCCGCCGCTGGAGCGAAAGGATGAGCTTGGCGCACTGGCTCACGACATGCATTCCATGTATATCAGGCTGAAAGAAACCATCGCAAGGCTGGAGGATGAAATCGCAAGGGAACATGAGTTGGAGGAAACACAGCGATATTTCTTTGCGGCAGCCTCTCATGAGTTAAAAACGCCCATCGCGGCTGTAAGCGTTCTGTTGGAGGGAATGCTTGAAAATATCGGTGACTACAAAGACCATTCTAAGTATCTGCGCGAATGCATCAAAATGATGGACAGGCAGGGCAAAACCATTTCCGAAATACTGGAGCTTGTCAGCCTGAACGATGGGAGAATCGTACCCATAGCCGAACCGCTGGACATAGGGCGCACGGTTGCCGAGCTGCTACCCGATTTTCAAACCTTGGCAGAGGCAAACAACCAGCGGTTCGTCACAGATATTCCAGCCGGACAAATTGTCCTGTCCGATCCGAAGCTGATCCAAAAGGCGCTATCCAATGTCATATTGAATGCGGTTCAGAACACGCCCCAGGGAGGTGAGGTACGGATATGGAGTGAGCCTGGGGCTGAAAAATACCGTCTTTCCGTTTTGAACATGGGCGTTCACATTGATGATACTGCACTTTCAAAGCTGTTCATCCCATTCTATCGCATTGATCAGGCGCGAAGCAGAAAAAGTGGGCGAAGCGGTTTGGGGCTTGCCATCGTACAAAAAACGCTGGATGCCATGAGCCTCCAATATGCGCTGGAAAACACCTCAGATGGCGTTTTGTTCTGGCTGGATTTACCGCCCACATCAACACTATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3002932","ARO_id":"39366","ARO_name":"vanSB","ARO_description":"vanSB is a vanS variant found in the vanB gene cluster","ARO_category":{"36210":{"category_aro_accession":"3000071","category_aro_cvterm_id":"36210","category_aro_name":"vanS","category_aro_description":"VanS is similar to histidine protein kinases like EnvZ and acts as a response regulator by activating VanR. VanS is required for high level transcription of other van glycopeptide resistance genes.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"500":{"model_id":"500","model_name":"OXA-164","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1125":{"protein_sequence":{"accession":"ADK34116.1","sequence":"MKLLKILSLVCLSISIGACAEHSMSRAKTSTIPQVNNSIIDQNVQALFNEISADAVFVTYDGQNIKKYGTHLDRAKTAYIPASTFKIANALIGLENHKATSTEIFKWDGKPRFLKAWDKDFTLGEAMQASTVPVYQELARRIGPSLMQSELQRIGYGNMQIGTEVDQFWLKGPLTITPIQEVKFVYDLAQGQLPFKPEVQQQVKEMLYVERRGENRLYAKSGWGMAVDPQVGWYVGFVEKADGQVVAFALNMQMKAGDDIALRKQLSLDVLDKLGVFHYL"},"dna_sequence":{"accession":"GU831575","fmin":"0","fmax":"843","strand":"+","sequence":"ATGAAATTATTAAAAATATTGAGTTTAGTTTGCTTAAGCATAAGTATTGGGGCTTGTGCTGAGCATAGTATGAGTCGAGCAAAAACAAGTACAATTCCACAAGTGAATAACTCAATCATCGATCAGAATGTTCAAGCGCTTTTTAATGAAATCTCAGCTGATGCTGTGTTTGTCACATATGATGGTCAAAATATTAAAAAATATGGCACGCATTTAGACCGAGCAAAAACAGCTTATATTCCTGCATCTACATTTAAAATTGCCAATGCACTAATTGGTTTAGAAAATCATAAAGCAACATCTACAGAAATATTTAAGTGGGATGGAAAGCCACGTTTTTTAAAAGCATGGGACAAAGATTTTACTTTGGGCGAAGCCATGCAAGCATCTACAGTGCCTGTATATCAAGAATTGGCACGTCGTATTGGTCCAAGCTTAATGCAAAGTGAATTGCAACGTATTGGTTATGGCAATATGCAAATAGGCACGGAAGTTGATCAATTTTGGTTGAAAGGGCCTTTGACAATTACACCTATACAAGAAGTAAAGTTTGTGTATGATTTAGCCCAAGGGCAATTGCCTTTTAAACCTGAAGTTCAGCAACAAGTGAAAGAGATGTTGTATGTAGAGCGCAGAGGGGAGAATCGTCTATATGCTAAAAGTGGCTGGGGAATGGCTGTAGACCCGCAAGTGGGTTGGTATGTGGGTTTTGTTGAAAAGGCAGATGGGCAAGTGGTGGCATTTGCTTTAAATATGCAAATGAAAGCTGGTGATGATATTGCTCTACGTAAACAATTGTCTTTAGATGTGCTAGATAAGTTGGGTGTTTTTCATTATTTATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001662","ARO_id":"38062","ARO_name":"OXA-164","ARO_description":"OXA-164 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"501":{"model_id":"501","model_name":"AAC(3)-VIIIa","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"12":{"protein_sequence":{"accession":"AAA26685.1","sequence":"MDEKELIERAGGPVTRGRLVRDLEALGVGAGDTVMVHTRMSAIGYVVGGPQTVIDAVRDAVGADGTLMAYCGWNDAPPYDLAEWPPAWREAARAEWPAYDPLLSEADRGNGRVPEALRHQPGAVRSRHPDASFVAVGPAAHPLMDDHPWDDPHGPDSPLARLAGAGGRVLLLGAPLDTLTLLHHAEARAEAPGKRFVAYEQPVTVGGRRVWRRFRDVDTSRGVPYGRVVPEGVVPFTVIAQDMLAAGIGRTGRVAAAPVHLFEAADVVRFGVEWIESRMGGAAGGA"},"dna_sequence":{"accession":"M55426","fmin":"465","fmax":"1326","strand":"+","sequence":"GTGGACGAGAAGGAACTGATCGAGCGCGCCGGCGGCCCCGTCACCCGCGGCCGGCTCGTGCGCGACCTCGAGGCACTCGGCGTCGGCGCCGGCGACACCGTCATGGTGCACACCCGCATGTCGGCGATCGGCTACGTCGTGGGCGGCCCGCAGACCGTGATCGACGCCGTCCGCGACGCCGTCGGCGCCGACGGCACCCTCATGGCCTACTGCGGCTGGAACGACGCCCCGCCCTACGACCTCGCCGAGTGGCCCCCCGCGTGGCGGGAGGCCGCACGAGCCGAGTGGCCCGCCTACGACCCGCTGCTCAGCGAGGCCGACCGGGGCAACGGCCGGGTCCCCGAGGCCCTGCGCCACCAGCCCGGCGCGGTCCGCAGCCGGCACCCCGACGCGAGCTTCGTCGCGGTCGGGCCGGCCGCCCACCCGCTCATGGACGACCACCCCTGGGACGACCCGCACGGACCGGACAGCCCGCTCGCCCGGCTCGCCGGGGCCGGCGGACGGGTACTGCTGCTCGGCGCCCCGCTGGACACCCTGACGCTGCTGCACCACGCGGAGGCACGGGCCGAGGCCCCCGGCAAGCGGTTCGTCGCGTACGAGCAGCCCGTGACCGTCGGCGGGCGACGGGTCTGGCGGCGCTTCCGCGACGTCGACACCAGCCGAGGCGTTCCCTACGGGCGGGTGGTGCCCGAGGGGGTCGTGCCGTTCACCGTCATCGCCCAGGACATGCTCGCAGCCGGGATCGGCCGGACCGGCCGGGTCGCCGCCGCCCCCGTCCACCTCTTCGAGGCCGCCGACGTGGTCCGCTTCGGCGTCGAGTGGATCGAGAGCCGGATGGGGGGCGCGGCCGGCGGGGCGTGAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36838","NCBI_taxonomy_name":"Streptomyces fradiae","NCBI_taxonomy_id":"1906"}}}},"ARO_accession":"3002542","ARO_id":"38942","ARO_name":"AAC(3)-VIIIa","ARO_description":"AAC(3)-VIIIa is a chromosomal-encoded aminoglycoside acetyltransferase in Streptomyces fradiae","ARO_category":{"36461":{"category_aro_accession":"3000322","category_aro_cvterm_id":"36461","category_aro_name":"AAC(3)","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 3.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"502":{"model_id":"502","model_name":"aadA17","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"160":{"protein_sequence":{"accession":"ACK43806.1","sequence":"MRVAVTIEISNQLSEVLSVIERHLEPTLLAVHLYGSAVDGGLKPHSDIDLLVTVTVRLDETTRRALINDLLETSASPGESEILRAVEVTIVVHDDIIPWRYPAKRELQFGEWQRNDILAGIFEPATIDIDLAILLTKAREHSVALVGPAAEEFFDPVPEQDLFEALRETLKLWNSQPDWAGDERNVVLTLSRIWYSAITGKIAPKDVAADWAIKRLPAQYQPVLLEAKQAYLGQKEDHLASRADHLEEFIRFVKGEIIKSVGK"},"dna_sequence":{"accession":"FJ460181","fmin":"1790","fmax":"2582","strand":"+","sequence":"ATGAGGGTAGCGGTGACCATCGAAATTTCGAACCAACTATCAGAGGTGCTAAGCGTCATCGAGCGCCATCTCGAACCGACGTTGCTGGCCGTACATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCACACAGTGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCGAGCTTTGATCAACGACCTTTTGGAAACTTCGGCTTCCCCTGGAGAGAGCGAGATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGATCTAGCTATCCTGCTTACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCGGCAGCGGAGGAATTCTTTGACCCGGTTCCTGAACAGGATCTATTCGAGGCGCTGAGGGAAACCTTGAAGCTATGGAACTCGCAGCCCGACTGGGCCGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAATAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATAAAACGCCTACCTGCCCAGTATCAGCCCGTCTTACTTGAAGCTAAGCAAGCTTATCTGGGACAAAAAGAAGATCACTTGGCCTCACGCGCAGATCACTTGGAAGAATTTATTCGCTTTGTGAAAGGCGAGATCATCAAGTCAGTTGGTAAATGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39526","NCBI_taxonomy_name":"Aeromonas media","NCBI_taxonomy_id":"651"}}}},"ARO_accession":"3002617","ARO_id":"39017","ARO_name":"aadA17","ARO_description":"aadA17 is an integron-encoded aminoglycoside nucleotidyltransferase gene in Aeromonas media","ARO_category":{"41439":{"category_aro_accession":"3004275","category_aro_cvterm_id":"41439","category_aro_name":"ANT(3'')","category_aro_description":"Nucleotidylylation of streptomycin at the hydroxyl group at position 3''","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"503":{"model_id":"503","model_name":"CTX-M-69","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1353":{"protein_sequence":{"accession":"ABY91281.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAVAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPNAESRRDVLASAAKIVTNGL"},"dna_sequence":{"accession":"EU402393","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGTGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAACGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCAACGGTTTGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001930","ARO_id":"38330","ARO_name":"CTX-M-69","ARO_description":"CTX-M-69 is a beta-lactamase found in Escherichia coli","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"504":{"model_id":"504","model_name":"TEM-52","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1802":{"protein_sequence":{"accession":"CAA73933.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTTPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"Y13612","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000921","ARO_id":"37301","ARO_name":"TEM-52","ARO_description":"TEM-52 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae and Salmonella enterica.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"506":{"model_id":"506","model_name":"IMP-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1191":{"protein_sequence":{"accession":"AAK27847.1","sequence":"MSKLFVFFMFLFCSITAAAESLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNTEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKDGKVQAKNSFSGASYWLVKKKIEVFYPGPGHTPDNVVVWLPENRVLFGGCFVKPYGLGNLGDANVEAWPKSAKLLMSKYGKAKLVVPSHSEVGDASLLKRTLEQAVKGLNESKKPSKPSN"},"dna_sequence":{"accession":"AF290912","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAGCAAGTTATTTGTATTCTTTATGTTTTTGTTTTGTAGCATTACTGCCGCAGCAGAGTCTTTGCCAGATTTAAAAATTGAGAAGCTTGACGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGTTGGGGTGTTGTTCCTAAACACGGCTTGGTGGTTCTTGTAAATACTGAGGCCTATCTGATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAACGCGGCTATAAAATAAAAGGCAGTATTTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCAATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTTCTTAAAAAAGACGGTAAAGTACAAGCTAAAAATTCATTTAGCGGAGCTAGCTATTGGCTAGTTAAGAAAAAGATTGAAGTTTTTTATCCTGGTCCAGGGCACACTCCAGATAACGTAGTGGTTTGGCTACCTGAAAATAGAGTTTTGTTCGGTGGTTGTTTTGTTAAACCGTACGGTCTAGGTAATTTGGGTGACGCAAATGTAGAAGCTTGGCCAAAGTCCGCCAAATTATTAATGTCCAAATATGGTAAGGCAAAACTGGTAGTTCCAAGTCACAGTGAAGTTGGAGACGCATCACTCTTGAAACGTACGTTAGAACAGGCGGTTAAAGGGTTAAACGAAAGTAAAAAACCATCAAAACCAAGTAACTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3002196","ARO_id":"38596","ARO_name":"IMP-5","ARO_description":"IMP-5 is a beta-lactamase found in Acinetobacter baumannii","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"507":{"model_id":"507","model_name":"rosB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1080"}},"model_sequences":{"sequence":{"4317":{"protein_sequence":{"accession":"AAC60780.1","sequence":"MHHSTPLITTIVGGLVLAFLLGSLAHRLRSSPLVGYLAAGVLAGPFTPGFVADTSLAPELAEIGVILLMFGVGLHFSLKDLLAVKAIAIPGAVAQIAVATLLGMGLSHLLGWDLMTGFVFGLCLSTASTVVLLRALEERQLIDSQRGQIAIGRSIVEDLAMVLTLVLLPAFAGVMGNETTSLSQLFTELAITIGKVIAFITLMIVVGRRLVPWILAKTASTGSRELFTLAVLVLALGIAYGAVGLFDVSFALGAFFAGMVLNESELSHRAAQDTLPLRDAFAVLFFVSVGMLFDPMILLREPLAVLASLAIIIFGKSAAAFILVRMFGHSNVYSTHHFCPWRKSVNLPFILAGLGISLGLMSEHGRNLVLAGAILSIMLNPLLFTLLDRYLAKNETMEDLILEEAVEEEKQIPGRFVQSCTVSRLWSGGSLLGAKLHAEGIPLVVIENSRPRVEALREQGINAVLGNAASADIMSLARLDCALVIILTIPNGYEAGEIVASARIKRPDLEIIARAHYDDEVVYISVRGANQVVMGEREIANSMLNMLKIETLTEEDKRPLCPI"},"dna_sequence":{"accession":"U46859","fmin":"22365","fmax":"24057","strand":"-","sequence":"TTAAATTGGGCAAAGCGGGCGTTTGTCTTCTTCGGTCAGCGTTTCTATCTTCAACATATTAAGCATACTGTTGGCAATTTCACGTTCGCCCATCACAACCTGGTTCGCGCCACGTACCGAGATATAAACCACTTCGTCGTCATAATGCGCGCGAGCAATTATCTCAAGGTCTGGCCGTTTAATTCTGGCGGAGGCGACAATTTCCCCAGCTTCGTAGCCATTCGGTATGGTCAGTATAATAACCAGGGCACAATCCAAACGAGCCAGCGACATAATATCTGCACTTGCAGCATTGCCTAATACCGCATTAATGCCTTGTTCACGTAGCGCCTCAACTCTTGGTCGAGAGTTCTCAATGACCACTAATGGAATACCTTCCGCGTGCAGTTTTGCACCTAATAAACTCCCACCCGACCATAACCGACTAACAGTGCATGATTGCACAAATCTACCGGGTATCTGCTTTTCCTCTTCGACTGCCTCTTCCAGAATCAGATCTTCCATCGTCTCGTTTTTAGCCAAATAGCGATCTAATAATGTAAACAGTAGCGGGTTGAGCATAATTGATAAAATTGCGCCCGCCAGCACCAGATTACGGCCATGCTCAGACATTAAACCGAGAGAAATTCCAAGCCCGGCGAGAATAAAGGGCAAATTCACCGATTTGCGCCAGGGACAGAAATGGTGAGTGCTGTACACGTTTGAGTGACCAAACATCCGCACTAATATAAACGCTGCTGCTGATTTGCCGAAGATAATGATAGCTAGTGAAGCCAGTACAGCTAATGGTTCACGTAGCAAAATCATTGGGTCGAACAACATCCCAACTGAAACGAAGAACAGTACGGCAAATGCATCACGTAGCGGTAAGGTATCTTGCGCCGCACGGTGGCTGAGCTCTGATTCATTCAATACCATTCCTGCGAAGAATGCACCGAGAGCAAAGGATACGTCGAACAGCCCTACAGCGCCGTAAGCAATACCAAGCGCTAATACCAGCACTGCCAAGGTAAATAGCTCACGGGAACCGGTACTGGCGGTTTTAGCCAGTATCCAGGGGACCAAACGACGACCGACAACAATCATCAGCGTAATGAAGGCAATGACTTTACCGATGGTTATTGCTAGTTCAGTGAATAACTGGCTGAGACTGGTGGTTTCGTTACCCATCACGCCGGCAAAGGCTGGTAATAGCACCAATGTGAGTACCATCGCCAAATCTTCGACAATCGACCGACCGATAGCAATTTGCCCCCGCTGGCTATCTATGAGTTGCCGTTCTTCTAGAGCTCGTAGTAATACCACGGTACTTGCTGTTGATAGACAAAGACCGAAGACAAAACCTGTCATCAAATCCCAGCCTAATAAATGAGACAGTCCCATTCCGAGTAAGGTGGCAACGGCAATTTGTGCCACAGCACCGGGTATGGCGATGGCTTTTACTGCGAGGAGGTCTTTAAGTGAGAAGTGAAGTCCGACACCAAACATCAACAAGATAACACCAATTTCAGCCAGTTCTGGTGCTAATGAGGTATCAGCAACGAAACCTGGCGTAAATGGCCCGGCCAGCACCCCTGCGGCAAGGTACCCCACCAGTGGTGATGAGCGCAGGCGGTGAGCCAAGGAGCCCAAGAGGAAGGCGAGAACAAGGCCTCCGACGATCGTGGTAATTAAGGGTGTTGAGTGGTGCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39589","NCBI_taxonomy_name":"Yersinia enterocolitica (type O:8)","NCBI_taxonomy_id":"34054"}}}},"ARO_accession":"3003049","ARO_id":"39483","ARO_name":"rosB","ARO_description":"rosB is part of an efflux pump\/potassium antiporter system (RosAB) in Yersinia that confers resistance to cationic antimicrobial peptides such as polymyxin B.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"508":{"model_id":"508","model_name":"tetA(P)","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"30":{"protein_sequence":{"accession":"AAA20116.1","sequence":"MVNKLSAYKTYLLFSAITAMCFSLVATVMMVYHIEIVHLNPLQLILVGTTLELACFIFEIPTAIVADVYSRKLSIVIGGVLTGVGFILEGSISSFVFVLVAQIVWGLGSTFISGSLEAWIAEEEKNKDLDEIYIKGAQAGQIGAFIGIVLSTVIANFSVRLPIIVSGVLFIILALFLWLYMPENNFKPSAPGDLNTFKKMVYTFKSGLKFVKSKSIIMILLAVTLFYGLSSEGYDRLSNAHFLQDTTLPKLGNLSSVTWFGIFGILGMILSFIVMHFMAKNLKNEDNRKNGKLLLCINILYISSMLIFALTRNFSLMLIAYLATNTFRIINKPIFSAWLNGHIDDNSRATVLSINGQMNSLGQILGGPIIGIIATNISVSIGIVCTSLLVTPVLVLYIVAMIIDKKVDDRVGGIDYEENN"},"dna_sequence":{"accession":"L20800","fmin":"1062","fmax":"2325","strand":"+","sequence":"ATGGTTAATAAACTTTCAGCATATAAAACTTATTTATTATTTTCAGCTATTACAGCAATGTGTTTTTCGTTAGTAGCTACAGTTATGATGGTGTATCACATTGAAATAGTTCATTTAAATCCACTTCAGCTTATACTTGTTGGAACTACTTTGGAATTAGCATGCTTTATATTTGAAATTCCTACAGCTATAGTTGCAGATGTGTATAGTCGTAAACTATCTATTGTTATTGGGGGAGTTTTAACAGGAGTGGGATTTATTTTAGAAGGTTCTATTTCTAGTTTTGTTTTCGTACTTGTAGCACAGATTGTATGGGGATTAGGGTCTACTTTTATCAGTGGCTCGCTTGAAGCTTGGATTGCGGAAGAAGAGAAGAATAAAGATTTAGATGAAATTTATATAAAGGGAGCACAAGCAGGGCAGATAGGAGCATTTATTGGAATAGTACTAAGCACTGTAATAGCTAATTTCTCTGTAAGGCTTCCTATTATAGTTAGTGGAGTTTTATTTATAATTCTTGCATTATTTTTATGGTTATATATGCCAGAAAATAATTTTAAACCATCTGCTCCTGGGGATTTAAATACATTCAAAAAGATGGTATATACATTTAAATCTGGTCTTAAATTTGTAAAAAGTAAATCTATAATTATGATTTTACTTGCAGTAACTTTATTTTATGGATTATCAAGTGAAGGTTATGATAGACTTTCTAATGCGCATTTTTTACAAGATACTACACTTCCTAAACTTGGAAACCTTAGTTCAGTGACTTGGTTTGGAATTTTTGGAATTTTAGGAATGATATTGAGCTTCATAGTAATGCATTTTATGGCAAAGAATCTTAAGAATGAGGATAATAGGAAAAATGGAAAACTATTATTATGCATAAATATACTTTATATATCGTCTATGTTGATATTTGCTCTTACAAGAAACTTTAGTTTAATGTTAATAGCTTATTTGGCAACAAATACCTTTAGAATTATAAATAAACCTATATTCAGTGCGTGGTTAAATGGGCATATAGATGATAATTCTAGAGCTACTGTGCTTTCTATAAATGGACAAATGAATTCCTTAGGTCAAATTTTAGGTGGACCGATTATAGGAATCATAGCTACAAATATTTCAGTAAGTATTGGTATAGTATGTACTTCGTTATTAGTAACACCGGTATTAGTGTTATATATTGTTGCTATGATAATTGATAAAAAGGTGGATGATAGAGTTGGAGGTATTGATTATGAAGAAAATAATTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36812","NCBI_taxonomy_name":"Clostridium perfringens","NCBI_taxonomy_id":"1502"}}}},"ARO_accession":"3000180","ARO_id":"36319","ARO_name":"tetA(P)","ARO_description":"TetA(P) is a inner membrane tetracycline efflux protein found on the same operon as the ribosomal protection protein TetB(P). It is found in Clostridium, a Gram-positive bacterium.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"509":{"model_id":"509","model_name":"FOX-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"870":{"protein_sequence":{"accession":"CAA54602.1","sequence":"MQQRRAFALLTLGSLLLAPCTYARGEAPLTAAVDGIIQPMLKEYRIPGMAVAVLKDGKAHYFNYGVANRESGQRVSEQTLFEIGSVSKTLTATLGAYAAVKGGFELDDKVSQHAPWLKGSAFDGVTMAELATYSAGGLPLQFPDEVDSNDKMRTYYRHWSPVYPAGTHRQYSNPSIGLFGHLAANSLGQPFEQLMSQTLLPKLGLHHTYIQVPESAIANYAYGYSKEDKPVRVTPGVLAAEAYGIKTGSADLLKFTEANMGYQGDAALKTRIALTHTGFYSVGDMTQGLGWESYAYPLTEQALLAGNSPAVSFQANPVTRFAVPKAMGEQRLYNKTGSTGGFGAYVAFVPARGIAIVMLANRNYPIEARVKAAHAILSQLAE"},"dna_sequence":{"accession":"X77455","fmin":"700","fmax":"1849","strand":"+","sequence":"ATGCAACAACGACGTGCGTTCGCGCTACTGACGCTGGGTAGCCTGCTGCTAGCCCCTTGTACTTATGCCCGCGGGGAGGCTCCGCTGACCGCCGCTGTGGACGGCATTATCCAGCCGATGCTCAAGGAGTATCGGATCCCGGGGATGGCGGTCGCCGTGCTGAAAGATGGCAAGGCCCACTATTTCAACTATGGGGTTGCCAACCGCGAGAGTGGTCAGCGCGTCAGCGAGCAGACCCTGTTCGAGATTGGCTCGGTCAGCAAGACCCTGACCGCGACCCTCGGTGCCTATGCTGCGGTCAAGGGGGGCTTTGAGCTGGATGACAAGGTGAGCCAGCACGCCCCCTGGCTCAAAGGTTCCGCCTTTGATGGTGTGACCATGGCCGAGCTTGCCACCTACAGTGCGGGTGGTTTGCCGCTGCAGTTCCCCGATGAGGTGGATTCGAATGACAAGATGCGCACTTACTATCGGCACTGGTCACCGGTTTATCCGGCGGGGACCCATCGCCAGTATTCCAACCCCAGCATAGGCCTGTTTGGTCACCTGGCCGCAAATAGTCTGGGCCAGCCATTTGAGCAACTGATGAGCCAGACCCTGCTGCCCAAGCTGGGTTTGCACCACACCTATATTCAGGTGCCGGAGTCGGCCATAGCGAACTATGCCTACGGCTATTCGAAGGAAGATAAGCCCGTCCGGGTCACTCCGGGCGTGCTGGCGGCCGAGGCTTACGGGATCAAGACCGGCTCGGCGGATCTGCTGAAGTTTACCGAGGCCAACATGGGGTATCAGGGAGATGCCGCGCTAAAAACGCGGATCGCGCTGACCCATACCGGTTTCTACTCGGTGGGAGACATGACTCAGGGGCTGGGTTGGGAGAGCTACGCCTATCCGTTGACCGAGCAGGCGCTGCTGGCGGGCAACTCCCCGGCGGTGAGCTTCCAGGCCAATCCGGTTACGCGCTTTGCGGTGCCCAAAGCGATGGGCGAGCAGCGGCTCTATAACAAGACGGGCTCGACTGGCGGCTTTGGCGCCTATGTGGCGTTCGTGCCCGCCAGAGGGATCGCCATCGTCATGCTGGCCAATCGCAACTATCCCATCGAGGCCAGGGTGAAGGCGGCTCACGCCATCCTGAGTCAGTTGGCCGAGTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002155","ARO_id":"38555","ARO_name":"FOX-1","ARO_description":"FOX-1 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36206":{"category_aro_accession":"3000067","category_aro_cvterm_id":"36206","category_aro_name":"FOX beta-lactamase","category_aro_description":"FOX beta-lactamases are plasmid-encoded AmpC-type beta-lactamase which conferred resistance to broad-spectrum cephalosporins and cephamycins","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"510":{"model_id":"510","model_name":"CTX-M-9","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1706":{"protein_sequence":{"accession":"AAF05311.2","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTAGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"AF174129","fmin":"6335","fmax":"7211","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAGCTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCACAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGCAGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001872","ARO_id":"38272","ARO_name":"CTX-M-9","ARO_description":"CTX-M-9 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"511":{"model_id":"511","model_name":"dfrA3","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"69":{"protein_sequence":{"accession":"AAA25550.1","sequence":"MLISLIAALAHNNLIGKDNLIPWHLPADLRHFKAVTLGKPVVMGRRTFESIGRPLPGRRNVVVSRNPQWQAEGVEVAPSLDAALALLTDCEEAMIIGGGQLYAEALPRADRLYLTYIDAQLNGDTHFPDYLSLGWQELERSTHPADDKNSYACEFVTLSRQR"},"dna_sequence":{"accession":"J03306","fmin":"0","fmax":"489","strand":"+","sequence":"ATGTTGATTTCTTTGATTGCAGCTTTGGCTCATAACAACTTGATTGGCAAAGATAATCTTATTCCATGGCATCTACCTGCCGATCTGCGTCATTTCAAAGCTGTCACCCTGGGGAAACCTGTGGTGATGGGACGTCGCACCTTTGAGTCGATCGGGCGGCCATTGCCAGGACGGCGCAATGTTGTCGTTAGTCGCAATCCCCAATGGCAGGCCGAAGGGGTGGAGGTGGCTCCCTCGCTGGATGCGGCTCTGGCGCTATTAACCGACTGTGAGGAAGCGATGATCATCGGTGGCGGGCAACTCTATGCCGAGGCTCTGCCCCGAGCGGATCGCTTGTATCTAACCTACATTGACGCTCAGTTGAACGGTGATACCCATTTCCCGGATTACCTATCGCTTGGGTGGCAGGAGTTGGAGCGGTCAACGCATCCTGCTGACGATAAGAACAGCTATGCCTGCGAATTTGTTACCTTGAGTCGTCAGCGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36820","NCBI_taxonomy_name":"Plasmid pAZ1","NCBI_taxonomy_id":"2525"}}}},"ARO_accession":"3003105","ARO_id":"39679","ARO_name":"dfrA3","ARO_description":"dfrA3 is an integron-encoded dihydrofolate reductase found in Escherichia coli","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36408":{"category_aro_accession":"3000269","category_aro_cvterm_id":"36408","category_aro_name":"brodimoprim","category_aro_description":"Brodimoprim is a structural derivative of trimethoprim and an inhibitor of bacterial dihydrofolate reductase. The 4-methoxy group of trimethoprim is replaced with a bromine atom.","category_aro_class_name":"Antibiotic"},"36423":{"category_aro_accession":"3000284","category_aro_cvterm_id":"36423","category_aro_name":"tetroxoprim","category_aro_description":"Tetroxoprim is a trimethoprim derivative that inhibits bacterial dihydrofolate reductase.","category_aro_class_name":"Antibiotic"},"36476":{"category_aro_accession":"3000337","category_aro_cvterm_id":"36476","category_aro_name":"iclaprim","category_aro_description":"Iclaprim is a bactericidal compound that inhibits dihydrofolate reductase. It is used against clinically important Gram-positive pathogens, including methicillin-sensitive Staphylococcus aureus and methicillin-resistant S. aureus.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"512":{"model_id":"512","model_name":"CTX-M-82","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1088":{"protein_sequence":{"accession":"ABB59946.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFPMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"DQ256091","fmin":"98","fmax":"974","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTCCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001943","ARO_id":"38343","ARO_name":"CTX-M-82","ARO_description":"CTX-M-82 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"513":{"model_id":"513","model_name":"CARB-19","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1019":{"protein_sequence":{"accession":"AIL92328.1","sequence":"MKKLFLLAGLMVCSTVSYASKLNEDISLIEKQTSGRIGVSVWDTQTDERWDYRGDERFPLMSTFKTLACATMLSDMDSGKLNKNATAKIDERNIVVWSPVMDKLAGQSTRIEHACEAAMLMSDNTAANLVLNEIGGPKAVTLFLRSIGDKATRLDRLEPRLNEAKPGDKRDTTTPNAMVNTLHTLMEDNALSYESRTQLKIWMQDNKVSDSLMRSVLPKGWSIADRSGAGNYGSRGISAMIWKDNYKPVYISIYVTDTDLSLQARDQLIAQISQLILEHYKES"},"dna_sequence":{"accession":"KJ934267","fmin":"0","fmax":"852","strand":"+","sequence":"ATGAAAAAGTTATTCCTGTTGGCTGGGCTGATGGTTTGCTCAACTGTTAGTTACGCCTCCAAATTAAACGAAGACATATCCCTCATCGAGAAACAAACATCTGGGCGAATTGGAGTGTCAGTCTGGGATACACAAACGGACGAGCGTTGGGATTATCGCGGAGACGAACGTTTCCCATTAATGAGCACATTCAAAACGTTAGCGTGTGCCACCATGCTAAGCGATATGGACAGCGGCAAACTCAACAAAAATGCTACAGCGAAAATCGATGAACGCAATATTGTGGTTTGGTCTCCGGTGATGGATAAACTGGCTGGACAAAGCACACGTATCGAACACGCTTGTGAGGCCGCCATGTTGATGAGCGACAACACCGCCGCGAACTTAGTGCTAAATGAAATTGGTGGTCCTAAAGCGGTCACGCTGTTTTTGCGATCTATTGGCGACAAAGCAACGCGACTTGACCGATTGGAACCCCGTTTGAATGAAGCAAAACCGGGCGATAAGCGAGACACCACAACGCCTAACGCCATGGTAAACACCCTACATACCTTGATGGAAGATAACGCCCTATCTTACGAGTCACGCACACAGCTGAAAATCTGGATGCAAGATAACAAAGTATCGGATTCTCTCATGCGCTCCGTTCTACCAAAAGGCTGGTCGATTGCAGACCGCTCTGGCGCAGGTAACTACGGTTCACGCGGCATTAGCGCGATGATCTGGAAAGACAACTACAAGCCGGTTTACATCAGTATTTACGTCACAGACACCGACCTTTCGCTTCAAGCTCGCGATCAACTGATCGCGCAAATCAGCCAACTGATTTTAGAGCACTACAAAGAAAGTTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39615","NCBI_taxonomy_name":"Vibrio parahaemolyticus","NCBI_taxonomy_id":"670"}}}},"ARO_accession":"3003175","ARO_id":"39752","ARO_name":"CARB-19","ARO_description":"From the Lahey list of beta-lactamases.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"514":{"model_id":"514","model_name":"LEN-10","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"857":{"protein_sequence":{"accession":"CAG25830.1","sequence":"ATLPLAVDAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGLEQLDRRIHYRQQDLVDYSPVSEKHLTDGMTIGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPPGWFIADKTGAGERGARGIVALLGPDGKPERIVVLYLRDTPASMAERNQHIAG"},"dna_sequence":{"accession":"AJ635419","fmin":"0","fmax":"789","strand":"+","sequence":"GCCACCCTGCCACTGGCGGTAGACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCGGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTACCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGCCGGGCTGGTTTATCGCCGACAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGCTCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002460","ARO_id":"38860","ARO_name":"LEN-10","ARO_description":"LEN-10 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"517":{"model_id":"517","model_name":"QnrD2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"33":{"protein_sequence":{"accession":"AHY03238.1","sequence":"MEKHFINEKFSRDQFTGNRVKNIAFSNCDFSGVDLTDTEFVDCSFYDRNSLEGCDFNRAKLKNASFKSCDLSMSNFKNISALGLEISECLAQGADFRGANFMNMITTRSWFCSAYITKTNLSYANFSRVILEKCELWENRWNGTVITGAVFRGSDLSCGEFSSFDWSLADFTGCDLTGGALGELDARRTNLDGVKLDGEQAFQLVESLGVIVHR"},"dna_sequence":{"accession":"KJ158441","fmin":"2732","fmax":"3377","strand":"+","sequence":"ATGGAAAAGCACTTTATCAATGAAAAGTTTTCACGAGATCAATTTACGGGGAATAGAGTTAAAAATATTGCCTTTTCAAATTGTGATTTTTCAGGGGTTGATTTAACTGATACTGAATTTGTTGATTGTAGTTTTTACGACAGGAATAGCTTGGAAGGGTGTGATTTTAATAGAGCCAAACTAAAAAACGCTAGCTTTAAAAGCTGCGATTTATCAATGAGTAATTTTAAAAACATTAGCGCCTTAGGTCTTGAGATTAGTGAGTGTTTAGCTCAAGGAGCTGATTTTCGAGGGGCTAATTTTATGAATATGATAACTACAAGGTCATGGTTTTGTAGTGCTTATATAACCAAGACAAATCTTAGTTACGCTAATTTTTCTAGAGTCATATTAGAAAAGTGCGAACTGTGGGAAAATCGCTGGAATGGCACTGTGATAACTGGCGCCGTGTTTCGTGGCTCCGATCTTTCTTGTGGGGAGTTTTCATCGTTTGATTGGTCTTTGGCTGATTTTACTGGTTGTGATTTAACGGGTGGGGCGCTTGGCGAGCTTGATGCAAGACGAACTAATTTAGATGGCGTGAAGTTGGATGGAGAACAGGCGTTTCAGCTTGTTGAGAGTTTAGGTGTTATTGTTCACCGATAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35743","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Hadar","NCBI_taxonomy_id":"149385"}}}},"ARO_accession":"3002789","ARO_id":"39223","ARO_name":"QnrD2","ARO_description":"QnrD2 is a plasmid-mediated quinolone resistance protein found in Salmonella enterica","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"518":{"model_id":"518","model_name":"vanXYN","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"203":{"protein_sequence":{"accession":"AEP40501.1","sequence":"MHNFYLQLVNQQHPWKSFNHSPQLVQATYAEEKILIDSKVNHQFNQLLETLQLTDRIMIVDGHRTVAEQKHLWNYSLNAHGVNYTKSYVASPGCSEHHTGLAIDLGLRKTEHDLIAPRFEGPEAELFLQHMKDYGFILRYPKNKQKITGIAYEPWHFRYVGTPHSQIIMDHGWTLEEYIEFLKHQIEAVS"},"dna_sequence":{"accession":"JF802084","fmin":"1592","fmax":"2165","strand":"+","sequence":"ATGCATAATTTTTATTTACAGCTTGTAAACCAACAACACCCTTGGAAATCATTTAATCATTCGCCACAGCTTGTTCAAGCGACCTATGCGGAAGAAAAGATTTTAATAGATTCCAAGGTTAACCATCAATTCAATCAGTTACTTGAAACACTACAATTAACTGATCGCATCATGATCGTTGATGGTCATCGAACGGTTGCTGAGCAAAAACATTTGTGGAACTATTCTTTAAACGCACATGGGGTGAATTATACAAAAAGTTATGTAGCATCTCCTGGCTGTAGTGAACATCATACGGGACTAGCAATTGATCTCGGTCTACGAAAGACAGAACATGATCTCATTGCGCCACGCTTCGAGGGACCAGAAGCCGAACTGTTTTTACAACATATGAAAGATTATGGATTTATTTTACGCTATCCTAAAAATAAGCAAAAAATTACAGGAATTGCTTATGAGCCTTGGCATTTTCGCTATGTAGGTACCCCTCATAGTCAAATCATCATGGACCACGGATGGACCTTAGAAGAGTATATTGAATTTTTAAAACATCAAATTGAGGCGGTCTCATGAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002969","ARO_id":"39403","ARO_name":"vanXYN","ARO_description":"vanXYN is a vanXY variant found in the vanN gene cluster","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36635":{"category_aro_accession":"3000496","category_aro_cvterm_id":"36635","category_aro_name":"vanXY","category_aro_description":"VanXY is a protein with both D,D-carboxypeptidase and D,D-dipeptidase activity, found in Enterococcus gallinarum. It cleaves and removes the terminal D-Ala of peptidoglycan subunits for the incorporation of D-Ser by VanC. D-Ala-D-Ser has low binding affinity with vancomycin.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"519":{"model_id":"519","model_name":"VIM-26","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1963":{"protein_sequence":{"accession":"CBY80143.1","sequence":"MLKVISSLLVYMTASVMAVASPLAHSGEPSGEYPTVNEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEAEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSANVLYGGCAVLELSSTSAGNVADADLAEWPTSVERIQKHYPEAEVVIPGHGLPGGLDLLQHTANVVKAHKNRSVAE"},"dna_sequence":{"accession":"FR748153","fmin":"259","fmax":"1060","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTACATGACCGCGTCTGTCATGGCTGTCGCAAGTCCGTTAGCCCATTCCGGGGAGCCGAGTGGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGAGAGGTCCGACTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCGGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAAAAGCAAATTGGACTTCCCGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGCAGAGGGGAACGAGATTCCCACGCATTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGCTCTTCTATCCTGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAACGTGCTATACGGTGGTTGTGCCGTTCTTGAGTTGTCAAGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCGTTGAGCGGATTCAAAAACACTACCCGGAAGCAGAGGTCGTCATTCCCGGGCACGGTCTACCGGGCGGTCTAGACTTGCTCCAGCACACAGCGAACGTTGTCAAAGCACACAAAAATCGCTCAGTCGCCGAGTAGC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002296","ARO_id":"38696","ARO_name":"VIM-26","ARO_description":"VIM-26 is a beta-lactamase. From the Lahey list of VIM beta-lactamases.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"520":{"model_id":"520","model_name":"acrS","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"380"}},"model_sequences":{"sequence":{"4320":{"protein_sequence":{"accession":"AAC76296.1","sequence":"MAKRTKAEALKTRQELIETAIAQFAQHGVSKTTLNDIADAANVTRGAIYWHFENKTQLFNEMWLQQPSLRELIQEHLTAGLEHDPFQQLREKLIVGLQYIAKIPRQQALLKILYHKCEFNDEMLAEGVIREKMGFNPQTLREVLQACQQQGCVANNLDLDVVMIIIDGAFSGIVQNWLMNMAGYDLYKQAPALVDNVLRMFMPDENITKLIHQTNELSVM"},"dna_sequence":{"accession":"U00096","fmin":"3412802","fmax":"3413465","strand":"-","sequence":"TTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCTTGTTGCTGACACGCCTGCAATACTTCGCGGAGAGTCTGCGGATTAAAGCCCATCTTTTCGCGTATCACTCCCTCGGCCAGCATCTCATCATTAAATTCACATTTGTGATATAAGATTTTCAGCAACGCCTGCTGGCGGGGAATTTTGGCAATATATTGCAAGCCGACAATCAATTTTTCACGCAATTGTTGAAACGGGTCATGCTCTAATCCAGCCGTCAAGTGTTCCTGGATTAACTCCCGCAATGAAGGCTGTTGCAACCACATCTCATTAAACAGTTGAGTCTTGTTTTCGAAGTGCCAGTAGATAGCGCCACGCGTAACGTTAGCGGCGTCGGCAATGTCGTTGAGCGTCGTCTTGCTTACGCCATGCTGCGCAAACTGGGCGATGGCAGTTTCAATCAGTTCTTGCCGGGTCTTCAGAGCTTCGGCTTTGGTTCTTTTTGCCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3000656","ARO_id":"37000","ARO_name":"AcrS","ARO_description":"AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"521":{"model_id":"521","model_name":"OXA-386","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4321":{"protein_sequence":{"accession":"AHL30273.1","sequence":"MKIKALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KF986254","fmin":"34","fmax":"859","strand":"-","sequence":"CTATAAAATACCTAATTGTTCTAAGCTTTTATAAGTAATCTCTTTTCGAACAGAGCTAGGTATTCCTTTTTTCATTTCTAAGTTAAGGGAGAACGCTACAATATTCCCTTGAGGCTGAACAACCCATCCAGTTAACCAGCCTACTTGTGGGTTTACATCCCATCCCCAACCACTTTTTGCGTATATTTTATTTCCATTCTTTTCTTCTATGAATAGCATGGATTGCACTTCATCTTGGACTTTTTGGCTAAATGGAAGCGTTTTATTAGCTAGCTTGTAAGCAAATTGTGCCTCTTGCTGAGGAGTAATTTTTAAAGGACCCACTAGCCAAAAATTATCGACTTGGGTACCGATATCTGCATTGCCATAACCAACACGCTTCACTTCATTAGACATGAGTTCAAGTCCAATACGACGAGCTAAATCTTGATAAACCGGAATAGCGGAAGCTTTCATAGCATCGCCTAGGGTCATGTTCTTTTCCCATTCTGGGAATAGCCTTTTTTGCCCGTCCCACTTAAATACTTCTGTAGTGGTTGCCTTATGGTGCTCAAGGCCGATCAAAGCATTAAGCATTTTGAAGGTCGAAGCAGGTACATACTCGGTCGAAGCACGAGCAAGATCATTACCATAGCTTTGTTGAGTTTGGCCTTGTTGGATAACTAAAACACCCGTAGTGTGTGCTTCGTTAAATAAATTTTTAATTTTCTCTGCTTTTTCATCAGATTTTGAAGCACTGTGATTTGGATTAGCAGACACTATATAAGGTGAGCAGGCTGAAATAAAAATAGCGCTTGTTATAAGTAAGAGTGCTTTAATCTTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001572","ARO_id":"37972","ARO_name":"OXA-386","ARO_description":"OXA-386 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"523":{"model_id":"523","model_name":"OXA-75","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1382":{"protein_sequence":{"accession":"YP_001707429.1","sequence":"MNIQALLLITSAIFISACSPYIVTANPNYSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRIGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGISSSVRKEITYRGLEQLGIL"},"dna_sequence":{"accession":"NC_010400","fmin":"1959577","fmax":"1960402","strand":"+","sequence":"ATGAACATTCAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATTACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATAGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTATTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAACAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATATCTAGCTCTGTTCGAAAAGAGATTACTTATAGAGGTTTAGAACAATTAGGTATTTTATAGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35534","NCBI_taxonomy_name":"Acinetobacter baumannii SDF","NCBI_taxonomy_id":"509170"}}}},"ARO_accession":"3001620","ARO_id":"38020","ARO_name":"OXA-75","ARO_description":"OXA-75 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"524":{"model_id":"524","model_name":"dfrA25","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"49":{"protein_sequence":{"accession":"ABB71176.1","sequence":"MAARAKNGVIGCGPDIPWSAKGEQLLFKALTYNQWLLVGRKTFESMGPLPNRKYAVVTRSNWTAANENVVVFPSIDEAMGRLGEITDHVIVAGGGEIYHETIPMASTLHVSTIDVEPEGDVFFPNIPGKFDVVFEQQFTSNINYCYQIWQKG"},"dna_sequence":{"accession":"DQ267940","fmin":"53","fmax":"512","strand":"+","sequence":"ATGGCTGCAAGAGCGAAAAATGGCGTAATCGGTTGCGGTCCTGACATTCCTTGGTCTGCCAAAGGGGAACAGCTTCTTTTCAAAGCACTGACCTATAACCAATGGCTTTTGGTAGGGCGCAAAACATTTGAGTCTATGGGGCCGCTGCCCAATAGGAAATACGCGGTTGTTACCCGCTCAAACTGGACAGCGGCTAATGAAAACGTAGTGGTTTTCCCGTCGATTGACGAAGCGATGGGTAGATTAGGCGAGATCACTGACCATGTCATCGTCGCCGGTGGTGGAGAAATCTACCATGAAACGATACCCATGGCCTCTACTCTGCATGTGTCGACAATCGACGTTGAGCCAGAGGGAGACGTTTTCTTTCCGAACATTCCTGGGAAGTTTGATGTCGTTTTTGAGCAACAATTTACATCAAACATTAACTATTGCTATCAAATCTGGCAAAAGGGTTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35709","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Agona","NCBI_taxonomy_id":"58095"}}}},"ARO_accession":"3003020","ARO_id":"39454","ARO_name":"dfrA25","ARO_description":"dfrA25 is an integron-encoded dihydrofolate reductase found in Salmonella agona","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36408":{"category_aro_accession":"3000269","category_aro_cvterm_id":"36408","category_aro_name":"brodimoprim","category_aro_description":"Brodimoprim is a structural derivative of trimethoprim and an inhibitor of bacterial dihydrofolate reductase. The 4-methoxy group of trimethoprim is replaced with a bromine atom.","category_aro_class_name":"Antibiotic"},"36423":{"category_aro_accession":"3000284","category_aro_cvterm_id":"36423","category_aro_name":"tetroxoprim","category_aro_description":"Tetroxoprim is a trimethoprim derivative that inhibits bacterial dihydrofolate reductase.","category_aro_class_name":"Antibiotic"},"36476":{"category_aro_accession":"3000337","category_aro_cvterm_id":"36476","category_aro_name":"iclaprim","category_aro_description":"Iclaprim is a bactericidal compound that inhibits dihydrofolate reductase. It is used against clinically important Gram-positive pathogens, including methicillin-sensitive Staphylococcus aureus and methicillin-resistant S. aureus.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"525":{"model_id":"525","model_name":"CMY-13","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"4323":{"protein_sequence":{"accession":"AAQ16660.2","sequence":"MMKKSLCCALLLTASFSTFASAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWAPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSNVTDMARWVQVNMDASRVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"AY339625","fmin":"3640","fmax":"4786","strand":"-","sequence":"TTATTGCAGCTTTTCAAGAATGCGCCAGGCCGCCTCGACACGGACAGGGTTAGGATAGCTTTTGTTTGCCAGCATCACGATGCCAAGGTTTTTTTCTGGAACGAAGGCTACGTAGCTGCCAAATCCTCCAGTGGATCCCGTTTTATGCACCCATGAGGCTTTCACTGCCGGGGCGGGCGGGTTTACCTCAACGGCGGGAAGCGCTGCCAATGCCACTTTGCTGTCGCTACCGTTGATGATCGAATCAGCTTTCAGCGGCCAGTTCAGCATCTCCCAGCCTAATCCCTGGTACATATCGCCAATACGCCAGTAGCGAGACTGCGCAAGCGCAATGCCCTGCTGGAGCGTTTTCTCCTGAACGCGGCTGGCGTCCATGTTGACCTGAACCCAGCGTGCCATATCGGTAACGTTGGATTTCACGCCATAGGCTTCGGCGTCAAGTTGTCCCGGAGAAACGTGTACAGGTTTCCCTTCGCGATAGCCCCAGGCATAATCTTTTTGTTCGTTCTGCGGAACTGTAATCCAGGTATGCGCCAGTTTTAATGGTTGCAGGACGCGTCTGGTCATTGCCTCTTCGTAACTCATTCCTGAGGGTTTCACCGCCAGCGCGCCAAACAGACCAATGCTGGAGTTAGCGTAAAGACGCTTAGCGCCCGGGGCCCATTGCGGCTGCCAGTTTTGATAAAAACGCAGTAATGCGGCTTTATCAGTAACGTCATCGGGGATCTGCAGCGGTAGGCCGCCTGCCGTATAGGTGGCTAAGTGCAGCAGGCTGATACCCTGCCACTGTTTGCCTGTCAGTTCTGGCCAGTATTTCGTGACCGGATCGCTGAGCTTAATTTCGCCGCGGGCGATAGCATCGCCGCCCAACACGCCGTTAAACGTCTTACTGACCGACCCTAGCTCAAACAGCGTTTGCTGCGTGACTGGGTGGTTATTGGCGATATCGGCTTTACCCCAGGTGAAATAATAGGGTTTTCCCTGGTAGATAATGGCAACGGCCATACCCGGAATAGCCTGCTCCTGCATCAACGGGGTGATGGTGCGATTAACGATATCGGCAATCTGTTGTTCTGTTTTGGCGGAGGCAAACGTGGAGAAAGAGGCTGTCAGCAGCAGAGCGCAGCATAACGATTTTTTCATCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002024","ARO_id":"38424","ARO_name":"CMY-13","ARO_description":"CMY-13 is a beta-lactamase found in Escherichia coli","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"526":{"model_id":"526","model_name":"ACT-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1812":{"protein_sequence":{"accession":"CAJ28994.1","sequence":"MMMTKSLCCALLLSTSCSVLATPMSEKQLAEVVERTVTPLMKAQAIPGMAVAVIYEGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAITTRVFKPLKLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMVNMKPDSLQDNSLRKGLTLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVEGSDNKVALAPLPAREVNPPAPPVNASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILSAL"},"dna_sequence":{"accession":"AM076977","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGATGACTAAATCCCTTTGCTGCGCCCTGCTGCTCAGCACCTCCTGCTCGGTATTGGCTACCCCGATGTCAGAAAAACAGCTGGCTGAGGTGGTGGAACGGACCGTTACGCCGCTGATGAAAGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTGATTTATGAGGGTCAGCCGCACTACTTCACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCTGTCACTCCACAAACCTTGTTCGAACTGGGTTCTATAAGTAAAACCTTCACCGGCGTACTCGGTGGCGATGCCATTGCTCGCGGTGAAATATCGCTGGGCGATCCGGTGACAAAATACTGGCCTGAGCTGACAGGCAAGCAGTGGCAGGGGATCCGCATGCTGGATCTGGCAACCTATACCGCAGGAGGTTTGCCGTTACAGGTACCGGATGAGGTCACGGATAACGCCTCTCTGTTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCCAATGCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATAACGACGCGGGTCTTTAAGCCGCTCAAGCTGGACCATACGTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGCGACGGTAAAGCGGTACACGTTTCGCCAGGAATGCTGGACGCTGAAGCCTATGGCGTAAAAACCAACGTGCAGGATATGGCAAGCTGGGTGATGGTCAACATGAAGCCGGACTCCCTTCAGGATAATTCACTCAGGAAAGGCCTTACCCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCCATGTATCAGGGGTTAGGCTGGGAAATGCTTAACTGGCCGGTCGATGCCAAAACCGTGGTTGAAGGTAGCGACAATAAGGTGGCACTGGCACCGCTGCCTGCGAGAGAAGTGAATCCACCGGCGCCCCCGGTCAACGCATCCTGGGTCCATAAAACAGGCTCTACCGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGTATTGTGATGCTGGCAAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATTTTGAGCGCGCTGTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36926","NCBI_taxonomy_name":"Enterobacter asburiae","NCBI_taxonomy_id":"61645"}}}},"ARO_accession":"3001822","ARO_id":"38222","ARO_name":"ACT-2","ARO_description":"ACT-2 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"527":{"model_id":"527","model_name":"SHV-38","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1561":{"protein_sequence":{"accession":"AAL79576.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPVGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AY079099","fmin":"148","fmax":"1009","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGTAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGGATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001096","ARO_id":"37476","ARO_name":"SHV-38","ARO_description":"SHV-38 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"528":{"model_id":"528","model_name":"OCH-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1979":{"protein_sequence":{"accession":"ABF50909.1","sequence":"MRKSTTLLIGFLTTAAIIPNNGALATSKANDGDLRRIVDETVRPLMAEQKIPGMAVAITIDGKSHFFGYGVASKESGQKVTEDTIFEIGSVSKTFTAMLGGYGLATGAFSLSDPATKWAPELAGSSFDKITMLDLGTYTPGGLPLQFPDAVTDDSSMLAYFKKWKPDYPAGTQRRYSNPSIGLFGYLAARSMDKPFDVLMEQKLLPAFGLKNTFINVPESQMKNYAYGYSKANKPIRVSGGALDAQAYGIKTTALDLARFVELNIDSSSLEPDFQKAVAATHTGYYHVGANNQGLGWEFYNYPTALKTLLAGNSSDMALKSHKIEKFDTPRQPSADVLINKTGSTNGFGAYAAFIPAKKIGIVLLANRNYPIDERVKAAYRILQALDNKQ"},"dna_sequence":{"accession":"DQ489307","fmin":"1070","fmax":"2243","strand":"+","sequence":"ATGAGAAAATCTACGACACTTTTGATCGGTTTCCTCACCACTGCCGCTATTATCCCGAATAATGGCGCGCTGGCTACGAGCAAGGCGAATGATGGCGACTTGCGCCGTATTGTCGATGAAACGGTGCGCCCGCTCATGGCCGAGCAGAAAATCCCCGGCATGGCGGTTGCCATAACCATCGACGGCAAGAGCCACTTCTTCGGTTATGGTGTGGCATCGAAAGAAAGCGGGCAAAAAGTCACTGAAGACACGATTTTCGAGATCGGTTCGGTCAGCAAGACCTTCACTGCAATGCTTGGCGGTTACGGGCTGGCGACAGGCGCGTTCTCCCTGTCCGATCCCGCGACCAAATGGGCTCCTGAACTGGCAGGCAGCAGCTTCGACAAGATCACCATGCTTGATCTTGGGACCTACACGCCGGGCGGATTGCCCCTCCAGTTTCCCGATGCTGTCACCGATGACAGTTCGATGCTGGCATATTTCAAGAAATGGAAACCCGATTATCCGGCAGGGACGCAGCGTCGTTATTCGAATCCCAGCATCGGCCTGTTCGGCTATCTGGCGGCACGAAGCATGGACAAGCCGTTCGACGTTTTGATGGAGCAAAAGCTTCTGCCTGCATTCGGCCTGAAGAACACCTTCATCAATGTGCCGGAAAGCCAGATGAAGAACTACGCCTACGGCTATTCCAAAGCCAACAAGCCGATCCGGGTATCGGGCGGGGCGCTGGATGCACAAGCCTATGGCATCAAGACCACCGCGCTTGATCTTGCCCGCTTCGTCGAACTGAACATCGACAGCTCATCTCTGGAGCCTGATTTCCAGAAAGCCGTCGCCGCAACGCATACCGGTTACTACCATGTCGGAGCGAACAATCAGGGACTTGGCTGGGAGTTCTACAACTATCCGACTGCGCTCAAGACACTTCTTGCCGGCAATTCGTCGGACATGGCGCTGAAGTCGCACAAAATCGAGAAATTCGATACACCTCGCCAACCGTCAGCTGATGTGCTGATCAATAAGACAGGCTCAACCAACGGCTTTGGCGCTTATGCGGCCTTTATTCCTGCGAAGAAGATCGGAATTGTTCTGCTTGCCAACCGGAATTATCCGATCGATGAGCGCGTAAAGGCTGCCTATCGGATATTGCAGGCGCTCGACAACAAGCAATAGG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37077","NCBI_taxonomy_name":"Ochrobactrum anthropi","NCBI_taxonomy_id":"529"}}}},"ARO_accession":"3002521","ARO_id":"38921","ARO_name":"OCH-8","ARO_description":"OCH-8 beta-lactamase is an Ambler class C chromosomal-encoded beta-lactamases in Ochrobactrum anthropi","ARO_category":{"36233":{"category_aro_accession":"3000094","category_aro_cvterm_id":"36233","category_aro_name":"OCH beta-lactamase","category_aro_description":"OCH beta-lactamases are Ambler class C chromosomal-encoded beta-lactamases in Ochrobactrum anthropi","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"529":{"model_id":"529","model_name":"SHV-185","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"2023":{"protein_sequence":{"accession":"AIS67768.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVMIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"KM233164","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGATGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3003152","ARO_id":"39729","ARO_name":"SHV-185","ARO_description":"From the Lahey list of beta-lactamases.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"530":{"model_id":"530","model_name":"VIM-11","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"853":{"protein_sequence":{"accession":"AAT36613.1","sequence":"MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGSEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"AY605049","fmin":"127","fmax":"928","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAGCGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAGC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002281","ARO_id":"38681","ARO_name":"VIM-11","ARO_description":"VIM-11 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"532":{"model_id":"532","model_name":"CTX-M-47","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"825":{"protein_sequence":{"accession":"AAV97952.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGRRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"AY847143","fmin":"82","fmax":"958","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAAGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001909","ARO_id":"38309","ARO_name":"CTX-M-47","ARO_description":"CTX-M-47 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"533":{"model_id":"533","model_name":"CARB-16","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4325":{"protein_sequence":{"accession":"CCW43444.1","sequence":"MDVRKHKASFFSVVITFLCLTLSLNANATDSVLEAVTNAETELGARIGLAVHDLETGKRWEHKSNERFPLSSTFKTLACANVLQRVDLGKERIDRVVRFSESNLVTYSPVTEKHVGKKGMSLAELCQATLSTSDNSAANFILQAIGGPKALTKFLRSIGDDTTRLDRWETELNEAVPGDKRDTTTPIAMVTTLEKLLIDETLSIKSRQQLESWLKGNEVGDALFRKGVPSDWIVADRTGAGGYGSRAITAVMWPPNRKPIVAALYITETDASFEERNAVIAKIGEQIAKTVLMENSRN"},"dna_sequence":{"accession":"HF953351","fmin":"2461","fmax":"3358","strand":"-","sequence":"TCAGTTACGGCTATTCTCCATTAATACTGTCTTCGCTATTTGCTCACCAATTTTTGCAATGACAGCATTTCTTTCTTCAAACGAGGCGTCTGTCTCTGTAATGTATAGAGCGGCTACGATAGGCTTGCGATTTGGAGGCCACATCACCGCAGTAATAGCACGCGACCCATAACCACCAGCGCCTGTTCTATCTGCTACTATCCAGTCACTTGGAACGCCTTTACGAAACAATGCATCGCCAACCTCATTACCTTTAAGCCAAGATTCTAGTTGTTGACGAGATTTGATAGATAGTGTTTCGTCAATTAGTAACTTTTCAAGTGTCGTTACCATTGCAATTGGTGTTGTCGTGTCTCGCTTATCTCCAGGCACCGCTTCGTTAAGTTCTGTTTCCCAGCGATCAAGGCGCGTAGTATCGTCGCCAATGGAACGCAAAAATTTCGTTAGAGCCTTAGGTCCACCAATCGCTTGTAGAATAAAATTGGCAGCTGAATTATCACTGGTTGATAATGTGGCCTGACACAGCTCTGCGAGCGACATCCCTTTTTTACCCACATGTTTTTCTGTTACAGGTGAGTATGTAACGAGATTGCTTTCAGAGAATCTCACAACTCTATCAATTCTTTCTTTACCTAGATCAACTCTTTGAAGAACGTTTGCACAGGCAAGTGTTTTAAAGGTGCTACTTAGAGGAAAACGTTCATTAGATTTATGTTCCCAACGTTTTCCCGTTTCCAAATCATGCACAGCTAGACCAATTCTAGCGCCTAATTCAGTTTCAGCATTGGTAACCGCTTCAAGTACTGAGTCTGTTGCATTAGCATTTAATGATAGCGTGAGACATAAAAAAGTAATTACTACGCTAAAAAAACTAGCCTTGTGTTTACGTACGTCCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39652","NCBI_taxonomy_name":"Psychrobacter maritimus","NCBI_taxonomy_id":"256325"}}}},"ARO_accession":"3002255","ARO_id":"38655","ARO_name":"CARB-16","ARO_description":"CARB-16 is a beta-lactamase. From the Lahey list of IMP beta-lactamases.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"536":{"model_id":"536","model_name":"TEM-95","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"933":{"protein_sequence":{"accession":"CAC67290.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGAKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AJ308558","fmin":"181","fmax":"1042","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGAGCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000962","ARO_id":"37342","ARO_name":"TEM-95","ARO_description":"TEM-93 is a broad-spectrum beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"537":{"model_id":"537","model_name":"OXA-120","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1203":{"protein_sequence":{"accession":"CCJ32595.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEIFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"HE963768","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAATATTTAAGTGGGACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGTGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001672","ARO_id":"38072","ARO_name":"OXA-120","ARO_description":"OXA-120 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"539":{"model_id":"539","model_name":"QnrB59","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"574":{"protein_sequence":{"accession":"AFR46590.1","sequence":"MLSLLYKNTGIDMTLALVGEKIDRNRFTSEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAIIG"},"dna_sequence":{"accession":"JX259320","fmin":"0","fmax":"681","strand":"+","sequence":"ATGTTGTCATTACTGTATAAAAACACAGGCATAGATATGACTCTGGCATTAGTTGGCGAAAAAATTGACAGAAATCGCTTCACCAGTGAGAAAGTTGAAAATAGTACATTTTTTAACTGCGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGCCAGTTCTATGATCGCGAAAGTCAGAAAGGATGCAATTTTAGTCGCGCAATGCTGAAAGATGCCATTTTCAAAAGCTGTGATTTATCAATGGCAGATTTCCGCAACGTCAGCGCATTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGTGCAAGCTTTATGAATATGATCACCACACGCACCTGGTTTTGCAGCGCATATATCACTAATACCAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAGCTATGGGAAAACCGCTGGATGGGGACTCAGGTACTGGGTGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTAGGTGACTTAGATATTCGGGGTGTTGATTTACAAGGCGTTAAGTTAGACAACTACCAGGCATCGTTGCTCATGGAGCGGCTTGGCATCGCGATTATTGGCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002772","ARO_id":"39206","ARO_name":"QnrB59","ARO_description":"QnrB59 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"540":{"model_id":"540","model_name":"emrY","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"900"}},"model_sequences":{"sequence":{"65":{"protein_sequence":{"accession":"BAA11237.1","sequence":"MAITKSTPAPLTGGTLWCVTIALSLATFMQMLDSTISNVAIPTISGFLGASTDEGTWVITSFGVANAIAIPVTGRLAQRIGELRLFLLSVTFFSLSSLMCSLSTNLDVLIFFRVVQGLMAGPLIPLSQSLLLRNYPPEKRTFALALWSMTVIIAPICGPILGGYICDNFSWGWIFLINVPMGIIVLTLCLTLLKGRETETSPVKMNLPGLTLLVLGVGGLQIMLDKGRDLDWFNSSTIIILTVVSVISLISLVIWESTSENPILDLSLFKSRNFTIGIVSITCAYLFYSGAIVLMPQLLQETMGYNAIWAGLAYAPIGIMPLLISPLIGRYGNKIDMRLLVTFSFLMYAVCYYWRSVTFMPTIDFTGIILPQFFQGFAVACFFLPLTTISFSGLPDNKFANASSMSNFFRTLSGSVGTSLTMTLWGRRESLHHSQLTATIDQFNPVFNSSSQIMDKYYGSLSGVLNEINNEITQQSLSISANEIFRMAAIAFILLTVLVWFAKPPFTAKGVG"},"dna_sequence":{"accession":"D78168","fmin":"1591","fmax":"3130","strand":"+","sequence":"ATGGCAATCACTAAATCAACTCCGGCACCATTAACCGGTGGGACGTTATGGTGCGTCACTATTGCATTGTCATTAGCGACATTTATGCAAATGTTGGATTCCACTATTTCTAACGTCGCAATACCGACAATATCTGGCTTTCTGGGAGCATCAACAGACGAAGGCACCTGGGTTATCACCTCGTTTGGTGTAGCAAATGCCATTGCGATCCCTGTTACTGGCAGGTTGGCACAAAGAATAGGCGAATTAAGATTATTTTTACTTTCAGTCACTTTTTTTTCGCTGTCTTCATTAATGTGTAGCCTATCGACCAATCTTGATGTGCTGATATTTTTTAGAGTCGTTCAGGGGTTAATGGCGGGGCCGTTAATTCCACTGTCACAGAGTTTATTATTAAGGAATTATCCGCCAGAAAAAAGAACATTTGCTCTGGCATTATGGTCAATGACCGTGATTATCGCTCCGATATGTGGACCGATATTGGGCGGTTATATTTGTGATAACTTTAGCTGGGGTTGGATATTTTTAATCAATGTCCCTATGGGGATTATCGTCCTGACATTATGCTTAACCTTACTTAAAGGAAGAGAAACTGAGACTTCACCGGTCAAAATGAATCTACCAGGACTGACCCTGTTAGTGCTCGGTGTTGGTGGCTTGCAAATTATGCTTGATAAAGGGCGCGATCTGGATTGGTTCAACTCGAGTACAATAATAATATTAACAGTAGTATCAGTTATTTCTCTGATCTCTTTAGTCATTTGGGAGTCGACCTCAGAGAACCCGATTCTTGATCTCAGTTTGTTTAAGTCCCGTAACTTCACCATTGGTATTGTGAGTATCACATGCGCGTATTTATTTTACTCTGGAGCGATCGTCCTTATGCCGCAGTTACTCCAGGAAACGATGGGGTATAATGCGATATGGGCCGGACTTGCTTATGCGCCCATCGGCATCATGCCACTATTAATTTCACCTTTGATAGGACGTTATGGCAACAAAATAGACATGCGGTTGTTAGTGACATTTAGTTTTTTGATGTATGCGGTTTGCTATTACTGGCGTTCTGTGACATTTATGCCAACGATTGATTTTACAGGCATCATTTTGCCGCAGTTTTTTCAGGGATTCGCCGTTGCCTGTTTCTTTTTACCCTTAACAACGATTTCGTTTTCAGGCTTGCCAGATAATAAATTTGCCAATGCCTCGAGTATGAGTAATTTTTTTCGTACCTTGTCAGGATCAGTTGGTACGTCGTTGACAATGACGCTGTGGGGACGACGCGAATCGTTACACCATAGTCAGTTGACAGCAACCATCGATCAATTTAACCCCGTGTTTAATTCATCGTCACAAATTATGGATAAATATTATGGTTCGCTTTCAGGAGTTCTTAATGAAATTAATAATGAAATAACCCAGCAGTCACTTTCTATTTCTGCAAATGAGATTTTCCGTATGGCGGCTATTGCTTTTATCTTACTTACGGTTTTGGTTTGGTTTGCGAAACCGCCGTTTACAGCGAAAGGCGTTGGGTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000254","ARO_id":"36393","ARO_name":"emrY","ARO_description":"emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"541":{"model_id":"541","model_name":"TEM-133","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"844":{"protein_sequence":{"accession":"AAS19171.1","sequence":"MSIQHFRVALIPFFAAFCFPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AY528425","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCTTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000997","ARO_id":"37377","ARO_name":"TEM-133","ARO_description":"TEM-133 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"542":{"model_id":"542","model_name":"adeH","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"900"}},"model_sequences":{"sequence":{"4253":{"protein_sequence":{"accession":"CAJ77855.1","sequence":"MVITSKQNWLLSSLMGSLLLAGCSLAPEYQPAKVIVPVKFKESDPKLEDNNWKIAQPADQQTRGEWWRIYNDAQLNELEQQAIAGNQNLKAVAANIQASRALRSAAQAERLPSIDAGFGPTRQKPSPASLGLDDNAHTSAQTLWRAQANVSYELDLFGRVASSVNAATADLQQQEALYQSALLALQADVAQGYFLIRQLDTEQAIYNRTIKLLGETRDLMQLRFKNGLVSELDVSRAQTELATAQTTALNIARNRASAEHALAVLLGKPPADFNLAVQPLTANSIRLPAGLPSTLLERRPDIAAAERAMAADNARIGIARAAFFPKLSLTGALGYESSSLSELGKWSSRTFLLGPVAGTILSLPLFDGGQRKAGVAQARAAYEESVANYRQTVLNAFREVENGLSDQRILDQQIQAQNQALSSSRHANQLSHLRYREGAISYLDVIDSDRTILQQEQLAAQLKGSQIIASINLIRALGGGWSS"},"dna_sequence":{"accession":"CT025802.2","fmin":"0","fmax":"1452","strand":"+","sequence":"TTGGTGATTACATCAAAACAAAACTGGTTGTTGTCCTCACTCATGGGAAGCCTGCTCCTTGCAGGCTGCTCATTGGCCCCAGAATATCAACCTGCAAAAGTTATAGTGCCAGTCAAATTCAAAGAATCTGACCCCAAACTTGAAGATAATAACTGGAAGATTGCCCAACCTGCTGATCAGCAAACTCGTGGTGAATGGTGGCGCATTTACAATGATGCTCAACTGAATGAACTTGAACAGCAAGCTATCGCGGGCAACCAGAACCTAAAAGCGGTGGCAGCAAATATTCAGGCTTCACGTGCATTACGTTCGGCAGCTCAAGCTGAACGCTTACCAAGTATTGATGCCGGATTTGGGCCAACCCGCCAAAAGCCGTCTCCGGCTTCACTCGGTTTAGATGACAATGCACATACTTCGGCTCAAACCTTATGGCGAGCTCAAGCCAATGTTTCATATGAGCTCGATTTATTTGGTCGTGTAGCAAGTAGTGTCAACGCAGCAACAGCGGATCTACAGCAACAAGAGGCACTATATCAGTCGGCACTTTTAGCTCTACAAGCGGATGTAGCTCAAGGTTATTTTCTGATACGTCAACTTGATACCGAACAGGCAATTTATAACCGTACAATCAAATTATTAGGTGAAACACGAGATTTAATGCAGCTTCGTTTTAAAAACGGACTGGTCAGTGAATTAGATGTTTCTCGTGCACAAACCGAACTTGCTACCGCACAAACCACTGCCCTAAATATTGCTCGTAACAGAGCCAGTGCAGAACATGCGCTTGCAGTCTTATTAGGAAAACCACCAGCAGACTTTAACTTGGCAGTTCAACCTTTAACTGCAAATAGTATCCGTCTCCCTGCCGGTTTGCCGTCAACTTTACTTGAAAGACGACCCGATATTGCGGCTGCAGAGCGTGCAATGGCAGCAGATAATGCGCGTATTGGAATTGCTCGTGCAGCATTTTTCCCAAAACTCAGTCTTACAGGAGCTTTAGGTTATGAATCTTCAAGTTTAAGCGAGTTGGGTAAATGGTCGAGTCGGACTTTTTTACTAGGACCTGTCGCTGGTACTATTTTGTCGTTACCTTTATTTGATGGTGGACAACGTAAAGCAGGCGTTGCTCAAGCAAGAGCGGCTTATGAGGAAAGCGTCGCCAACTATAGACAAACTGTACTGAATGCATTTCGCGAAGTTGAAAATGGTTTATCTGATCAAAGAATTCTCGATCAGCAAATTCAGGCTCAAAACCAAGCACTCTCCTCTTCTCGTCATGCCAATCAACTTTCTCATTTACGTTATCGAGAAGGTGCTATTAGCTATCTTGATGTCATTGATTCTGACCGCACTATTTTGCAACAAGAACAATTAGCAGCTCAGCTGAAAGGCAGCCAAATCATTGCAAGCATCAATTTAATCCGTGCTTTAGGGGGCGGTTGGAGTAGTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35535","NCBI_taxonomy_name":"Acinetobacter baumannii AYE","NCBI_taxonomy_id":"509173"}}}},"ARO_accession":"3000779","ARO_id":"37159","ARO_name":"adeH","ARO_description":"AdeH is the outer membrane channel protein of the AdeFGH multidrug efflux complex.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"543":{"model_id":"543","model_name":"TEM-106","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1153":{"protein_sequence":{"accession":"AAM52207.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTTPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AY101578","fmin":"214","fmax":"1075","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000969","ARO_id":"37349","ARO_name":"TEM-106","ARO_description":"TEM-106 is an extended-spectrum beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"544":{"model_id":"544","model_name":"AAC(6')-Is","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"669":{"protein_sequence":{"accession":"AAD03491.1","sequence":"MNIMPISESQLSDWLALRSLLWPDHEDAHLLEMRHVLKQTDTLQLLVYSETQLAIAMLEASIRHEYVNGTQTSPVAFLEGIYVLPEYRRSGIATQLVQCVEEWAKQFACTEFASDAALENTISHAMHRALGFHETERVVYFKKNIG"},"dna_sequence":{"accession":"AF031327","fmin":"0","fmax":"441","strand":"+","sequence":"ATGAATATTATGCCGATATCTGAATCACAATTATCAGATTGGCTAGCATTAAGAAGCTTACTCTGGCCTGATCATGAAGATGCGCATTTATTGGAAATGCGCCACGTACTTAAACAAACCGATACTTTACAGTTATTGGTGTATTCGGAAACGCAACTTGCGATAGCAATGTTGGAAGCATCGATCCGACATGAATATGTGAATGGTACACAAACCTCACCCGTGGCTTTTCTTGAAGGGATTTATGTATTGCCTGAATATCGACGTTCAGGCATTGCGACCCAGTTGGTTCAGTGCGTAGAGGAATGGGCGAAACAATTTGCATGTACAGAGTTCGCTTCAGATGCAGCGCTTGAAAATACGATCAGTCATGCAATGCATCGGGCTTTGGGTTTTCATGAAACTGAACGCGTGGTGTACTTTAAGAAAAATATCGGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39513","NCBI_taxonomy_name":"Acinetobacter genomosp. 15","NCBI_taxonomy_id":"70346"}}}},"ARO_accession":"3002562","ARO_id":"38962","ARO_name":"AAC(6')-Is","ARO_description":"AAC(6')-Is is a chromosomal-encoded aminoglycoside acetyltransferase in Acinetobacter genomosp. 15","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"545":{"model_id":"545","model_name":"GES-22","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1415":{"protein_sequence":{"accession":"AFU25739.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPELGDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGARNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"JX023441","fmin":"37","fmax":"901","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGCTGGGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGCCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAGT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3002351","ARO_id":"38751","ARO_name":"GES-22","ARO_description":"GES-22 is a beta-lactamase. From the Lahey list of GES beta-lactamases.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"546":{"model_id":"546","model_name":"TLA-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"3315":{"protein_sequence":{"accession":"AAD37403.1","sequence":"MTVPISIIFWGNIMKKHLVVIAFCVLFASASAFAAKGTDSLKSSIEKYLKDKKAKVGVAVLGIEDNFKLNVNEKHHYPMQSTYKFHLALAVLDKLDKENISIDKKLFVKKSELLPNTWSPLRDKYPDGNVDLSISEILKATVSRSDNNGCDILFRFVGGTNKVHNFISKLGVKNISIKATEEEMHKAWNVQYTNWTTPDATVQLLKKFYKNEILSKNSYDYLLNTMIETTTGPKRLKGLLPDGTVVAHKTGSSDTNDKGITAATNDIGIITLPNGKHFAIAVYVSDSSEKSDVNEKIIAEICKSVWDYLVKDGK"},"dna_sequence":{"accession":"AF148067","fmin":"213","fmax":"1158","strand":"+","sequence":"ATGACAGTTCCTATCAGTATTATTTTTTGGGGGAATATAATGAAAAAACATCTTGTTGTAATTGCATTTTGTGTGCTTTTTGCTTCTGCTTCTGCTTTTGCGGCTAAAGGTACGGATTCGCTTAAAAGCAGTATTGAAAAATATCTTAAAGATAAAAAAGCTAAAGTGGGTGTTGCCGTTTTGGGAATTGAAGATAATTTTAAATTGAACGTTAACGAAAAGCATCACTATCCTATGCAGAGCACTTATAAGTTCCATCTTGCATTGGCTGTGCTCGATAAACTTGATAAGGAGAATATTTCCATTGACAAGAAGCTTTTTGTAAAAAAATCGGAGCTTCTGCCGAATACTTGGAGTCCGCTAAGAGATAAATATCCCGATGGAAATGTGGATTTATCCATAAGCGAAATTCTGAAAGCTACCGTTTCGCGTAGCGATAATAACGGTTGTGATATTCTCTTCAGATTTGTTGGTGGAACAAATAAAGTCCACAATTTTATTAGCAAGCTTGGCGTTAAGAATATTTCTATCAAAGCTACAGAAGAAGAAATGCACAAGGCATGGAATGTACAATATACCAATTGGACAACTCCCGACGCTACCGTTCAGCTCTTAAAGAAGTTCTACAAAAATGAAATACTCTCAAAAAATAGTTACGACTATTTGCTTAATACTATGATTGAAACTACTACCGGACCGAAACGACTCAAAGGACTTTTGCCCGATGGAACTGTTGTTGCTCATAAAACCGGAAGCTCCGATACTAACGATAAAGGCATTACTGCTGCCACAAATGATATCGGTATTATTACTCTGCCGAACGGTAAACACTTTGCCATTGCTGTTTATGTGTCGGATTCAAGCGAAAAGAGCGATGTTAACGAAAAGATTATTGCCGAAATTTGCAAAAGCGTTTGGGATTATCTAGTTAAGGATGGGAAATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3003202","ARO_id":"39786","ARO_name":"TLA-1","ARO_description":"TLA-1 is a beta-lactamase found in plasmids of clinical isolates of Escherichia coli strain R170 in Latin America. It preferentially hydrolyzed cephaloridine, cefotaxime, cephalothin, benzylpenicillin, and ceftazidime. The enzyme was markedly inhibited by sulbactam, tazobactam, and clavulanic acid.","ARO_category":{"39785":{"category_aro_accession":"3003201","category_aro_cvterm_id":"39785","category_aro_name":"TLA beta-lactamase","category_aro_description":"The TLA beta-lactamases are resistant to expanded-spectrum cephalosporins, aztreonam, ciprofloxacin, and ofloxacin but was susceptible to amikacin, cefotetan, and imipenem.","category_aro_class_name":"AMR Gene Family"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"547":{"model_id":"547","model_name":"arr-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"250"}},"model_sequences":{"sequence":{"567":{"protein_sequence":{"accession":"ABV26707.1","sequence":"MTVDWIPISHDNYHQVRGPFYHGTKAELAIGDLISTGFISHFERDRALKHVYFSALMEPAIWGAELAVALSGSDGPGHIYIIEPTGPFEDDPNLTNKRFPGNPTQSYRTCHPLKIVGILREWERHSPEALKTMLDSLADLKRRGLAIIEE"},"dna_sequence":{"accession":"EF660563","fmin":"392","fmax":"845","strand":"+","sequence":"ATGACGGTAGACTGGATCCCCATTTCGCACGACAACTACCATCAAGTGCGTGGCCCGTTTTATCACGGAACAAAAGCCGAACTCGCCATTGGCGACTTAATTTCAACCGGATTTATTTCTCACTTTGAGCGGGACAGAGCACTAAAGCATGTGTACTTTTCCGCGCTGATGGAGCCAGCAATCTGGGGGGCCGAGCTCGCTGTAGCACTCTCTGGCTCTGACGGGCCAGGCCATATTTACATCATTGAGCCAACCGGCCCGTTTGAAGACGACCCCAATCTCACAAACAAACGATTCCCTGGCAATCCAACACAGTCCTATCGCACATGCCACCCACTTAAAATTGTTGGCATACTGCGGGAGTGGGAGCGCCATTCTCCTGAAGCATTGAAGACCATGCTAGATTCTCTGGCAGACCTCAAGCGACGCGGCTTGGCCATCATTGAAGAATGAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002850","ARO_id":"39284","ARO_name":"arr-5","ARO_description":"arr-5 is an integron-encoded ribosyltransferase found in Pseudomonas aeruginosa","ARO_category":{"36529":{"category_aro_accession":"3000390","category_aro_cvterm_id":"36529","category_aro_name":"rifampin ADP-ribosyltransferase (Arr)","category_aro_description":"Enzyme responsible for the ADP-ribosylative inactivation of rifampin at the 23-OH position using NAD+.","category_aro_class_name":"AMR Gene Family"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36656":{"category_aro_accession":"3000517","category_aro_cvterm_id":"36656","category_aro_name":"rifaximin","category_aro_description":"Rifaximin is a semi-synthetic rifamycin used to treat traveller's diarrhea. Rifaximin inhibits RNA synthesis by binding to the beta subunit of bacterial RNA polymerase.","category_aro_class_name":"Antibiotic"},"36669":{"category_aro_accession":"3000530","category_aro_cvterm_id":"36669","category_aro_name":"rifabutin","category_aro_description":"Rifabutin is a semisynthetic rifamycin used in tuberculosis therapy. It inhibits DNA-dependent RNA synthesis.","category_aro_class_name":"Antibiotic"},"36673":{"category_aro_accession":"3000534","category_aro_cvterm_id":"36673","category_aro_name":"rifapentine","category_aro_description":"Rifapentine is a semisynthetic rifamycin that inhibits DNA-dependent RNA synthesis. It is often used in the treatment of tuberculosis and leprosy.","category_aro_class_name":"Antibiotic"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"548":{"model_id":"548","model_name":"QnrB3","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"277":{"protein_sequence":{"accession":"ABC17629.1","sequence":"MTPLLYKKTGTNMALALVGEKIDRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCKFSRAMLKDAIFKSCDLSMADFRNSSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"DQ303920","fmin":"0","fmax":"681","strand":"+","sequence":"ATGACGCCATTACTGTATAAAAAAACAGGTACAAATATGGCTCTGGCACTCGTTGGCGAAAAAATTGACAGAAACCGTTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAAATTTAGTCGTGCGATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATTCCAGTGCGCTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGCGCAAGCTTTATGAATATGATCACCACGCGCACCTGGTTTTGTAGCGCATATATCACGAATACCAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAGCTGTGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCGGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTGACTTAGATATTCGGGGCGTTGATTTACAAGGCGTTAAGCTGGACAACTACCAGGCGTCGTTGCTCATGGAGCGGCTTGGCATCGCGGTGATTGGTTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002716","ARO_id":"39150","ARO_name":"QnrB3","ARO_description":"QnrB3 is a plasmid-mediated quinolone resistance protein found in Escherichia coli","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"549":{"model_id":"549","model_name":"TEM-107","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1240":{"protein_sequence":{"accession":"AAM52215.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDHWEPELNEAIPNDERDTTTPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AY101764","fmin":"206","fmax":"1067","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCATTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000970","ARO_id":"37350","ARO_name":"TEM-107","ARO_description":"TEM-107 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"550":{"model_id":"550","model_name":"CMY-71","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1267":{"protein_sequence":{"accession":"AFK08538.1","sequence":"MMKKSLCCALLLTAPFSTFAAAKTEQQIADTVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADITNNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWAPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKAVHVSPGQLDAEAYGVKSSVIDMARWVQVNMDASRVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKKLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"JQ711184","fmin":"1026","fmax":"2172","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCCCTTTCTCCACGTTTGCCGCAGCCAAAACAGAACAACAGATTGCCGATACCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCACCAATAACCACCCAGTCACGCAGCAAACTCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTACACGGCAGGCGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCGTTTTTATCAAAACTGGCAGCCGCAATGGGCCCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACAGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGGCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGTCAACATGGACGCCAGCCGCGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGGTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGTAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACTGGAGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAAACTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002084","ARO_id":"38484","ARO_name":"CMY-71","ARO_description":"CMY-71 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"551":{"model_id":"551","model_name":"CTX-M-117","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"906":{"protein_sequence":{"accession":"AET99223.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIQGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"JN227085","fmin":"351","fmax":"1227","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCAGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001977","ARO_id":"38377","ARO_name":"CTX-M-117","ARO_description":"CTX-M-117 is a beta-lactamase found in Escherichia coli","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"552":{"model_id":"552","model_name":"QnrB28","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"191":{"protein_sequence":{"accession":"ADM52188.1","sequence":"MTLALVSEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGSDFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVAGATFSGSDLSGGEFSAFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDSYQAALLMERLGIAVIG"},"dna_sequence":{"accession":"HM439643","fmin":"0","fmax":"645","strand":"+","sequence":"ATGACTCTGGCATTAGTTAGCGAAAAAATTGACAGAAACCGCTTCACCGGGGAAAAAGTTGAAAACAGTACTTTTTTTAACTGTGATTTTTCAGGGGCCGATCTTAGCGGCACTGAATTTATCGGCTGTCAGTTTTATGATCGCGAAAGCCAGAAAGGGTGTAATTTTAGTCGCGCAATGCTGAAAGATGCCATTTTTAAAAGTTGCGATTTATCCATGGCGGATTTTCGCAACGTCAGTGCCCTGGGAATTGAAATTCGCCACTGCCGCGCGCAGGGTTCAGATTTTCGCGGCGCGAGTTTTATGAACATGATCACCACGCGGACCTGGTTTTGCAGCGCATACATCACGAATACCAATCTAAGCTACGCCAACTTTTCGAAGGTTGTCCTGGAAAAGTGCGAGCTGTGGGAAAACCGCTGGATGGGAACTCAGGTAGCGGGTGCAACGTTCAGTGGATCAGATCTCTCGGGAGGTGAATTTTCAGCGTTCGACTGGCGGGCCGCAAATTTCACGCACTGTGATTTGACCAATTCAGAACTGGGTGATTTAGATATTCGGGGTGTAGATTTACAAGGCGTCAAATTGGATAGCTATCAGGCAGCGTTGCTGATGGAGCGGCTTGGCATCGCGGTGATTGGTTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002743","ARO_id":"39177","ARO_name":"QnrB28","ARO_description":"QnrB28 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"553":{"model_id":"553","model_name":"VIM-35","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1500":{"protein_sequence":{"accession":"AGC50805.1","sequence":"MLKVISSLLVYMTASVMAVASPLAHSGEPSGEYPTVNEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEAEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSANVLYGGCAVHELSSTSAGNVTDADLAEWPTSVERIQKHYPEAEVVIPGHGLPGGLDLLQHTANVVKAHKNRSVAE"},"dna_sequence":{"accession":"JX982634","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTACATGACCGCGTCTGTCATGGCTGTCGCAAGTCCGTTAGCCCATTCCGGGGAGCCGAGTGGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGAGAGGTCCGACTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCGGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAAAAGCAAATTGGACTTCCCGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGCAGAGGGGAACGAGATTCCCACGCATTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGCTCTTCTATCCTGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAACGTGCTATACGGTGGTTGTGCCGTTCATGAGTTGTCAAGCACGTCTGCGGGGAACGTGACCGATGCCGATCTGGCTGAATGGCCCACCTCCGTTGAGCGGATTCAAAAACACTACCCGGAAGCAGAGGTCGTCATTCCCGGGCACGGTCTACCGGGCGGTCTAGACTTGCTCCAGCACACAGCGAACGTTGTCAAAGCACACAAAAATCGCTCAGTCGCCGAGTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002305","ARO_id":"38705","ARO_name":"VIM-35","ARO_description":"VIM-35 is a beta-lactamase. From the Lahey list of VIM beta-lactamases.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"554":{"model_id":"554","model_name":"OXA-163","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1045":{"protein_sequence":{"accession":"ADY06444.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYDTKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"HQ700343","fmin":"0","fmax":"786","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGACAGTTTCTGGCTCGACGGTGGTATTCGAATTTCGGCCACGGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATGCTGACCGAAGCCAATGGCGACTATATTATTCGGGCTAAAACTGGATACGATACTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001783","ARO_id":"38183","ARO_name":"OXA-163","ARO_description":"OXA-163 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"555":{"model_id":"555","model_name":"OXA-133","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1833":{"protein_sequence":{"accession":"ACE63186.1","sequence":"MNKYFTCYVVASLFFSGCTVQHNLINETQSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTTWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVERIDFGNAEIGQQVDNFWLIGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEENNGYKIFGKTGWAMDIKPQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"EU571228","fmin":"822","fmax":"1644","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTTTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCAGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATTTGTATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCACTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCAAGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAGAACGTATTGATTTCGGTAATGCTGAAATTGGACAGCAGGTTGACAATTTCTGGTTGATAGGCCCATTAAAGGTCACGCCTATTCAAGAGGTAGAGTTTGTTTCTCAATTGGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTACTTCTAGAAGAGAATAATGGCTACAAGATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCTGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39672","NCBI_taxonomy_name":"Acinetobacter radioresistens","NCBI_taxonomy_id":"40216"}}}},"ARO_accession":"3001702","ARO_id":"38102","ARO_name":"OXA-133","ARO_description":"OXA-133 is a beta-lactamase found in A. radioresistens","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"556":{"model_id":"556","model_name":"vanYB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"3457":{"protein_sequence":{"accession":"AAB05624.1","sequence":"MEKSNYHSNVNHHKRHMKQSGEKRAFLWAFIISFTVCTLFLGWRLVSVLEATQLPPIPATHTGSGTGVAENPEENTLATAKEQGDEQEWSLILVNRQNPIPAQYDVELEQLSNGERIDIRISPYLQDLFDAARADGVYPIVASGYRTTEKQQEIMDEKVAEYKAKGYTSAQAKAEAETWVAVPGTSEHQLGLAVDINADGIHSTGNEVYRWLDENSYRFGFIRRYPPDKTEITGVSNEPWHYRYVGIEAATKIYHQGLCLEEYLNTEK"},"dna_sequence":{"accession":"U35369","fmin":"2358","fmax":"3165","strand":"+","sequence":"ATGGAAAAAAGCAACTATCATTCCAATGTGAATCATCACAAACGGCATATGAAACAATCTGGGGAAAAACGGGCTTTTCTATGGGCGTTCATTATCTCGTTCACAGTCTGCACGCTGTTTTTGGGGTGGAGATTGGTTTCCGTATTGGAGGCAACACAGCTACCGCCCATCCCTGCAACTCATACAGGCAGCGGGACTGGTGTAGCGGAGAATCCAGAGGAAAACACTCTTGCCACCGCCAAAGAACAGGGAGATGAACAGGAATGGAGCCTGATTTTAGTGAACAGGCAGAACCCCATCCCCGCCCAGTACGATGTGGAACTTGAGCAGCTGTCAAATGGTGAGCGGATAGACATTCGGATTTCTCCCTACCTCCAGGATTTGTTTGATGCCGCAAGAGCTGATGGAGTTTACCCGATTGTCGCATCCGGATACCGGACAACAGAAAAACAGCAAGAAATCATGGATGAAAAAGTCGCCGAATACAAGGCGAAAGGCTACACCTCTGCACAGGCTAAAGCGGAAGCAGAAACTTGGGTGGCCGTGCCGGGAACAAGCGAGCATCAGCTTGGTCTTGCTGTGGATATCAATGCGGATGGAATTCATTCAACCGGCAACGAGGTTTACAGATGGCTGGATGAAAACAGCTATCGCTTTGGTTTTATTCGCCGCTACCCGCCAGACAAGACAGAGATAACCGGTGTGAGCAACGAGCCGTGGCATTACCGATATGTCGGCATCGAAGCTGCCACAAAGATATACCACCAAGGGCTTTGCCTTGAGGAATATTTAAACACAGAAAAATGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3002956","ARO_id":"39390","ARO_name":"vanYB","ARO_description":"vanYB is a vanY variant found in the vanB gene cluster","ARO_category":{"36216":{"category_aro_accession":"3000077","category_aro_cvterm_id":"36216","category_aro_name":"vanY","category_aro_description":"VanY is a D,D-carboxypeptidase that cleaves removes the terminal D-Ala from peptidoglycan for the addition of D-Lactate. The D-Ala-D-Lac peptidoglycan subunits have reduced binding affinity with vancomycin compared to D-Ala-D-Ala.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"557":{"model_id":"557","model_name":"SHV-9","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1717":{"protein_sequence":{"accession":"AAB37395.2","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLRTVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRNVLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASKRGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"S82452","fmin":"120","fmax":"978","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTCCGGACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAACGTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCAAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001068","ARO_id":"37448","ARO_name":"SHV-9","ARO_description":"SHV-9 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"558":{"model_id":"558","model_name":"qacB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"990"}},"model_sequences":{"sequence":{"307":{"protein_sequence":{"accession":"AAQ10694.1","sequence":"MISFFTKTTDMMTSKKRWAALVVLAVSLFVVTMDMTILIMALPELVRELEPSGTQQLWIVDIYSLVLAGFIIPLSAFADKWGRKKALLTGFALFGLVSLAIFFAESAEFVIAIRFLLGIAGALIMPTTLSMIRVIFENPKERATALAVWSIVSSIGAVFGPIIGGALLEQFSWHSAFLINVPFAIIAVVAGLFLLPESKLSKEKSHSWDIPSTILSIAGMIGLVWSIKEFSKEGLADIIPWVVIVLAITMIVIFVKRNLSSSDPMLDVRLFKKRSFSAGTIAAFMTMFAMTSVLLLASQWLQVVEELSPFKAGLYLLPMAIGAMVFAPIAPGLAARFGPKIVLPSGIGIAAIGMFIMYFFGHPLSYSTMALALILVEAGTASLAVASALIMLETPTSKAGNAAAVEESMYDLGNVFGVAVLGSLSSMLYRVFLDISSFSSKGIVGDLAHVAEESVVGAVEVAKATGIKQLANEAVTSFNDAFVATALVGGIIMIIISIVVYLLIPKSLDITKQK"},"dna_sequence":{"accession":"AF535087","fmin":"28","fmax":"1573","strand":"+","sequence":"ATGATTTCATTTTTTACAAAAACTACTGATATGATGACATCAAAAAAAAGATGGGCTGCACTAGTAGTATTAGCTGTTAGTTTGTTTGTTGTTACAATGGATATGACAATATTAATTATGGCTTTACCGGAATTAGTAAGAGAGTTAGAGCCTTCTGGTACCCAACAGTTATGGATAGTTGATATATACTCTCTTGTTTTAGCTGGCTTTATAATTCCATTGAGTGCCTTTGCTGATAAATGGGGAAGAAAAAAAGCATTATTAACTGGATTTGCTTTATTTGGCCTCGTTTCATTAGCTATATTTTTCGCAGAAAGTGCAGAGTTCGTAATAGCTATTCGATTTTTACTTGGTATTGCAGGTGCTTTAATAATGCCAACTACCCTTTCAATGATAAGAGTAATTTTTGAAAACCCTAAAGAAAGGGCCACTGCATTAGCTGTATGGTCAATCGTTTCATCGATAGGTGCTGTTTTTGGACCAATTATCGGAGGAGCTTTACTTGAGCAATTTTCATGGCACTCGGCATTTTTAATTAATGTACCGTTTGCGATAATAGCAGTTGTAGCAGGTTTATTTTTATTACCAGAGTCTAAGTTATCAAAAGAAAAGTCTCACTCGTGGGATATTCCTTCTACAATTTTATCAATTGCAGGCATGATTGGACTGGTATGGAGTATCAAAGAATTTTCAAAAGAAGGACTAGCAGATATTATTCCATGGGTTGTAATAGTATTAGCAATTACCATGATAGTGATATTTGTTAAACGTAATTTATCAAGTTCTGATCCAATGTTAGACGTAAGACTTTTTAAAAAGAGATCATTTTCAGCTGGTACAATTGCTGCATTTATGACAATGTTTGCAATGACATCTGTTTTGTTATTAGCTTCACAATGGTTACAGGTTGTGGAAGAACTTTCTCCTTTTAAAGCTGGCTTATACCTATTACCTATGGCAATAGGAGCTATGGTGTTTGCACCAATTGCACCCGGATTAGCGGCGCGATTTGGACCGAAAATAGTGTTACCTTCCGGAATTGGAATTGCAGCCATTGGCATGTTTATTATGTATTTCTTTGGTCATCCATTATCATATTCTACAATGGCTTTAGCATTAATTTTAGTTGAAGCTGGTACGGCTTCACTAGCAGTTGCATCTGCTCTAATAATGTTAGAAACACCTACATCAAAAGCAGGTAATGCAGCTGCTGTTGAAGAGTCTATGTATGACCTTGGAAATGTTTTTGGTGTAGCAGTACTTGGTAGCCTATCTTCTATGCTTTATCGTGTATTTTTAGATATTTCATCTTTTTCATCAAAAGGTATAGTTGGAGATTTAGCTCATGTAGCTGAAGAATCTGTAGTGGGCGCTGTCGAAGTAGCTAAAGCTACGGGGATAAAACAGCTTGCAAACGAGGCTGTAACATCATTTAATGATGCTTTTGTAGCAACTGCTTTAGTAGGTGGGATTATCATGATTATCATTTCAATAGTTGTCTATTTGTTAATTCCCAAATCACTTGATATAACTAAACAAAAATAGT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3003047","ARO_id":"39481","ARO_name":"qacB","ARO_description":"qacB is a subunit of the qac multidrug efflux pump","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"559":{"model_id":"559","model_name":"vanXYE","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"106":{"protein_sequence":{"accession":"AAL27443.1","sequence":"MKKNYLRLINENNEIKDSERPSHLVQAPFAQTNILVDPMVAIQLEKLIKTTGLDSQIITIDGYRSKETQQALWDETIQEKGLEFAHKYVAKPGCSEHEIGLAVDLGLATKENDFIRPSFTDSPIVDKFLKHMTDFGFILRYQKGKESITNINYEPWHFRYVGTPHSSIMVQQNWVLEEYIEFIESIRGTAYEA"},"dna_sequence":{"accession":"FJ872411","fmin":"40765","fmax":"41347","strand":"+","sequence":"ATGAAAAAAAATTATCTACGATTGATTAATGAAAACAATGAAATAAAAGACTCTGAGAGACCAAGTCACCTTGTTCAGGCTCCGTTTGCACAAACAAATATACTAGTTGATCCTATGGTAGCGATACAGCTAGAAAAACTAATAAAGACAACAGGTCTTGATAGCCAAATTATTACCATTGATGGCTATCGTTCAAAGGAGACACAGCAAGCACTTTGGGATGAGACGATTCAAGAAAAAGGGCTTGAATTTGCGCACAAATATGTGGCAAAGCCTGGATGTAGTGAACATGAAATTGGTTTAGCAGTGGATTTGGGGTTAGCTACGAAAGAAAATGATTTTATTCGCCCAAGTTTCACTGATAGTCCGATTGTTGATAAATTTTTAAAGCATATGACAGATTTCGGCTTTATCTTAAGATATCAAAAAGGAAAAGAATCTATTACCAATATAAACTATGAACCATGGCATTTCAGGTATGTAGGGACACCCCATAGTTCGATTATGGTACAGCAAAACTGGGTATTAGAAGAATACATTGAATTCATTGAGTCAATAAGAGGAACTGCTTATGAAGCATAGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3002967","ARO_id":"39401","ARO_name":"vanXYE","ARO_description":"vanXYE is a vanXY variant found in the vanE gene cluster","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36635":{"category_aro_accession":"3000496","category_aro_cvterm_id":"36635","category_aro_name":"vanXY","category_aro_description":"VanXY is a protein with both D,D-carboxypeptidase and D,D-dipeptidase activity, found in Enterococcus gallinarum. It cleaves and removes the terminal D-Ala of peptidoglycan subunits for the incorporation of D-Ser by VanC. D-Ala-D-Ser has low binding affinity with vancomycin.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"560":{"model_id":"560","model_name":"OXA-77","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1538":{"protein_sequence":{"accession":"AAX51233.1","sequence":"MNIKALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLPRRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"AY949202","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATCACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTACCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001622","ARO_id":"38022","ARO_name":"OXA-77","ARO_description":"OXA-77 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"561":{"model_id":"561","model_name":"OKP-B-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1920":{"protein_sequence":{"accession":"CAJ19616.1","sequence":"MRYVRLCLISLIAALPLAVFASPQPLEQIKISESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNTAGNLLLKIVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMATTLRKLLTTPSLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPDGKAERIVVIYLRDTAATMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM051157","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGTCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCAGCCGCTTGAGCAGATTAAAATCAGCGAAAGTCAGCTGGCGGGCCGGGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGCGACGAACAGCTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACACCGCCGGCAATCTGCTGTTGAAGATCGTCGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTCAATGAGGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCGGCCAGCATGGCCACCACCCTGCGCAAGTTGCTAACCACCCCCTCTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGACCGGGTGGCCGGCCCGTTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGTGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAAGCGGAGCGTATCGTGGTGATCTATCTGCGGGATACCGCGGCGACCATGGCCGAACGTAACCAGCAGATCGCCGGGATAGGCGCGGCGCTGATCGAGCACTGGCAGCGCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002441","ARO_id":"38841","ARO_name":"OKP-B-8","ARO_description":"OKP-B-8 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"562":{"model_id":"562","model_name":"TEM-187","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1956":{"protein_sequence":{"accession":"ADM61585.1","sequence":"MSIQHFRVALIPFFAAFCFPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDHWEPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYMTGSQATMDERNRQIAEIGASLIKH"},"dna_sequence":{"accession":"HM246246","fmin":"211","fmax":"1069","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCTTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCATTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACATGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3001047","ARO_id":"37427","ARO_name":"TEM-187","ARO_description":"TEM-187 is an extended-spectrum beta-lactamase found in P. mirabilis","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"563":{"model_id":"563","model_name":"OKP-B-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1751":{"protein_sequence":{"accession":"CAP12355.2","sequence":"MRYVRLCLISLIAALPLAVFASPQPLEQIKISESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKSVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMATTLRKLLTTPSLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPDGKAERIVVIYLRDTAATMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM850917","fmin":"17","fmax":"878","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCAGCCGCTTGAGCAGATTAAAATCAGCGAAAGTCAGCTGGCGGGCCGGGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGCGACGAACAGCTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGAGCGTCGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTCAATGAGGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCGGCCAGCATGGCCACCACCCTGCGCAAGTTGCTAACCACCCCCTCTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGACCGGGTGGCCGGCCCGTTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGTGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAAGCGGAGCGTATCGTGGTGATCTATCTGCGGGATACCGCAGCGACCATGGCCGAACGTAACCAGCAGATCGCCGGGATAGGCGCGGCGCTGATCGAGCACTGGCAGCGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002439","ARO_id":"38839","ARO_name":"OKP-B-6","ARO_description":"OKP-B-6 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"564":{"model_id":"564","model_name":"IMP-22","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1825":{"protein_sequence":{"accession":"ABC88434.1","sequence":"MKKLFVLCVFLFCSITAAGESLPDLKIEKLEEGVYVHTSFEEVNGWGVVSKHGLVILVNTDAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSQSIPTYASELTNDLLKQNGKVQAKNSFSGVSYWLVKNKIEVFYPGPGHTQDNVVVWLPEKKILFGGCFVKPYGLGNLDDANVVAWPHSAEILMSRYGNAKLVVPSHSDIGDASLLKLTWEQAVKGLKESKKPSEPSN"},"dna_sequence":{"accession":"DQ361087","fmin":"356","fmax":"1097","strand":"+","sequence":"ATGAAGAAATTATTTGTTTTATGTGTGTTTTTGTTTTGTAGCATTACTGCCGCAGGAGAGTCTTTGCCCGATTTAAAAATTGAAAAGCTTGAAGAAGGTGTTTATGTTCATACATCGTTTGAAGAAGTTAATGGTTGGGGCGTTGTTTCTAAACACGGTTTGGTTATTCTTGTGAATACTGACGCCTATCTGATTGACACTCCATTCACGGCTAAAGATACTGAAAAGTTAGTCACCTGGTTTGTGGAGCGCGGCTATAAAATCAAAGGTAGCATTTCCTCACATTTCCATAGCGACAGCACGGGTGGAATAGAGTGGCTTAATTCTCAATCAATTCCCACGTATGCATCTGAATTAACAAATGACCTTCTTAAACAAAACGGTAAGGTACAAGCTAAAAACTCATTTAGCGGAGTTAGTTATTGGTTAGTTAAAAATAAAATTGAAGTTTTCTATCCCGGCCCCGGGCACACTCAAGATAACGTAGTGGTTTGGTTGCCTGAAAAGAAAATTTTATTTGGTGGGTGCTTTGTTAAACCGTACGGTCTTGGAAATCTCGATGACGCAAATGTTGTAGCATGGCCACATTCTGCTGAAATATTAATGTCTAGGTATGGTAATGCAAAACTGGTTGTTCCAAGCCATAGTGACATCGGAGATGCGTCGCTCTTGAAGCTTACATGGGAGCAGGCTGTTAAAGGGCTAAAAGAAAGTAAAAAACCATCAGAGCCAAGTAACTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36937","NCBI_taxonomy_name":"Pseudomonas fluorescens","NCBI_taxonomy_id":"294"}}}},"ARO_accession":"3002213","ARO_id":"38613","ARO_name":"IMP-22","ARO_description":"IMP-22 is a beta-lactamase found in Pseudomonas spp.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"565":{"model_id":"565","model_name":"SHV-82","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1238":{"protein_sequence":{"accession":"CAJ47137.2","sequence":"MRYVRLCIISLLATLPLAVHTSPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM176557","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACACCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001136","ARO_id":"37516","ARO_name":"SHV-82","ARO_description":"SHV-82 is a broad-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"566":{"model_id":"566","model_name":"OXA-32","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1761":{"protein_sequence":{"accession":"AAK58418.1","sequence":"MAIRIFAILFSIFSLATFAHAQEGTLERSDWRKFFSEFQAKGTIVVADERQADRAMLVFDPVRSKKRYSPASTFKIPHTLFALDAGAVRDEFQIFRWDGVNRGFAGHNQDQDLRSAMRNSTVWVYELFAKEIGDDKARRYLKKIDYGNADPSTSNGDYWIEGSIAISAQEQIAFLRKLYRNELPFRVEHQRLVKDLMIVEAGRNWILRAKTGWEGRMGWWVGWVEWPTGSVFFALNIDTPNRMDDLFKREAIVRAILRSIEALPPNPAVNSDAAR"},"dna_sequence":{"accession":"AF315351","fmin":"672","fmax":"1500","strand":"+","sequence":"ATGGCAATCCGAATCTTCGCGATACTTTTCTCCATTTTTTCTCTTGCCACTTTCGCGCATGCGCAAGAAGGCACGCTAGAACGTTCTGACTGGAGGAAGTTTTTCAGCGAATTTCAAGCCAAAGGCACGATAGTTGTGGCAGACGAACGCCAAGCGGATCGTGCCATGTTGGTTTTTGATCCTGTGCGATCGAAGAAACGCTACTCGCCTGCATCGACATTCAAGATACCTCATACACTTTTTGCACTTGATGCAGGCGCTGTTCGTGATGAGTTCCAGATTTTTCGATGGGACGGCGTTAACAGGGGCTTTGCAGGCCACAATCAAGACCAAGATTTGCGATCAGCAATGCGGAATTCTACTGTTTGGGTGTATGAGCTATTTGCAAAGGAAATTGGTGATGACAAAGCTCGGCGCTATTTGAAGAAAATCGACTATGGCAACGCCGATCCTTCGACAAGTAATGGCGATTACTGGATAGAAGGCAGCATTGCAATCTCGGCGCAGGAGCAAATTGCATTTCTCAGGAAGCTCTATCGTAACGAGCTGCCCTTTCGGGTAGAACATCAGCGCTTGGTCAAGGATCTCATGATTGTGGAAGCCGGTCGCAACTGGATACTGCGTGCAAAGACGGGCTGGGAAGGCCGTATGGGTTGGTGGGTAGGATGGGTTGAGTGGCCGACTGGCTCCGTATTCTTCGCACTGAATATTGATACGCCAAACAGAATGGATGATCTTTTCAAGAGGGAGGCAATCGTGCGGGCAATCCTTCGCTCTATTGAAGCGTTACCGCCCAACCCGGCAGTCAACTCGGACGCAGCGCGATAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001426","ARO_id":"37826","ARO_name":"OXA-32","ARO_description":"OXA-32 is a beta-lactamase found in P. aeruginosa","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"567":{"model_id":"567","model_name":"CTX-M-41","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1667":{"protein_sequence":{"accession":"AAY43008.1","sequence":"MMRKSVRRAMLMTTACVSLLLASVPLCAQANDVQQKLAALEKSSGGRLGVALINTADNTQTLYRADERFAMCSTSKVMAAAAVLKQSETQKGLLSQRVEIKPSDLVNYNPIAEKHVNGTMTFGELIAAALQYSDNTAMNKLIAHLGGPDKVTAFARTIGDDTFRLDRTEPTLNTAIPGDPRDTTTPLAMAQALRNLTLGNALGDTQRAQLVMWLKGNTTGAASIQAGLPTSWVVGDKTGSGGYGTTNDIAVIWPEGRAPLVLVTYFTQSEPKAESRRDVLAAAARIVTDGY"},"dna_sequence":{"accession":"DQ023162","fmin":"0","fmax":"876","strand":"+","sequence":"ATGATGAGAAAAAGCGTAAGGCGGGCGATGTTAATGACGACAGCCTGTGTTTCGCTGCTGTTGGCCAGTGTGCCGCTGTGTGCCCAGGCGAACGATGTTCAACAAAAGCTCGCGGCGCTGGAGAAAAGCAGCGGGGGACGACTGGGTGTGGCGTTGATTAACACCGCCGATAACACGCAGACGCTCTACCGCGCCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCGGCAGCGGCGGTGCTTAAGCAAAGTGAAACGCAAAAGGGCTTGTTGAGTCAGCGGGTTGAAATTAAGCCCTCAGACTTGGTTAACTACAACCCCATTGCGGAAAAACACGTCAATGGCACGATGACATTCGGGGAGTTGATCGCGGCGGCGCTACAGTACAGCGATAATACTGCCATGAATAAGCTGATTGCCCATCTCGGGGGGCCGGATAAAGTGACGGCATTTGCCCGTACGATTGGCGATGACACGTTCCGGCTCGATCGTACCGAGCCGACGCTCAACACCGCGATCCCCGGCGACCCGCGCGATACCACCACGCCGTTAGCGATGGCGCAGGCTCTGCGCAATCTGACGTTGGGCAATGCCCTGGGTGACACTCAGCGTGCGCAGCTGGTGATGTGGCTGAAAGGCAACACCACCGGCGCTGCCAGCATTCAGGCAGGGCTACCCACATCGTGGGTTGTCGGGGATAAAACCGGCAGCGGCGGTTATGGTACGACGAATGATATCGCGGTTATTTGGCCGGAAGGTCGCGCGCCGCTCGTTCTGGTGACTTACTTCACCCAGTCGGAGCCGAAGGCAGAGAGCCGTCGTGACGTGCTCGCTGCTGCCGCCAGAATTGTCACCGACGGTTATTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3001903","ARO_id":"38303","ARO_name":"CTX-M-41","ARO_description":"CTX-M-41 is a beta-lactamase found in Proteus mirabilis","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"568":{"model_id":"568","model_name":"CTX-M-20","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1168":{"protein_sequence":{"accession":"CAC95175.1","sequence":"MMTQSIRRSMLTVMATLPLLFSSATLHAQANSVQQQLEALEKSSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKQSESDKHLLNQRVEIKKSDLVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSASIRAGLPKSWVVGDKTGSGDYGTTNDIAVIWPENHAPLVLVTYFTQPEQKAESRRDFLAAAAKIVTHGF"},"dna_sequence":{"accession":"AJ416344","fmin":"303","fmax":"1179","strand":"+","sequence":"ATGATGACTCAGAGCATTCGCCGCTCAATGTTAACGGTGATGGCGACGCTACCCCTGCTATTTAGCAGCGCAACGCTGCATGCGCAGGCGAACAGCGTGCAACAGCAGCTGGAAGCCCTGGAGAAAAGTTCGGGAGGTCGGCTTGGCGTTGCGCTGATTAACACCGCCGATAATTCGCAGATTCTCTACCGTGCCGATGAACGTTTTGCGATGTGCAGTACCAGTAAGGTGATGGCGGCCGCGGCGGTGCTTAAACAGAGCGAGAGCGATAAGCACCTGCTAAATCAGCGCGTTGAAATCAAGAAGAGCGACCTGGTTAACTACAATCCCATTGCGGAGAAACACGTTAACGGCACGATGACGCTGGCTGAGCTTGGCGCAGCGGCGCTGCAGTATAGCGACAATACTGCCATGAATAAGCTGATTGCCCATCTGGGTGGTCCCGATAAAGTGACGGCGTTTGCTCGCTCGTTGGGTGATGAGACCTTCCGTCTGGACAGAACCGAGCCCACGCTCAATACCGCCATTCCAGGCGACCCGCGTGATACCACCACGCCGCTCGCGATGGCGCAGACCCTGAAAAATCTGACGCTGGGTAAAGCGCTGGCGGAAACTCAGCGGGCACAGTTGGTGACGTGGCTTAAGGGCAATACTACCGGTAGCGCGAGCATTCGGGCGGGTCTGCCGAAATCATGGGTAGTGGGCGATAAAACCGGCAGCGGAGATTATGGCACCACCAACGATATCGCGGTTATCTGGCCGGAAAACCACGCACCGCTGGTTCTGGTGACCTACTTTACCCAACCGGAGCAGAAGGCGGAAAGCCGTCGGGATTTTCTGGCTGCGGCGGCGAAAATCGTAACCCACGGTTTCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3001882","ARO_id":"38282","ARO_name":"CTX-M-20","ARO_description":"CTX-M-20 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"569":{"model_id":"569","model_name":"OXA-228","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2005":{"protein_sequence":{"accession":"AFM55001.1","sequence":"MKFKMKGLFCVILSSLAFSGCVYDSKLQRPVISERVTEIPLLFNQAQTQAVFVTYDGIHLKSYGNDLSRAKTEYIPASTFKMLNALIGLQNAKATNTEVFHWNGEKRAFSAWEKDMTLAEAMQASAVPVYQELARRIGLELMREEVKRVGFGNAEIGQQVDNFWLVGPLKISPEQEVQFAYQLAMKQLPFDSNVQQQVKDMLYIERRGDSKLYAKSGWGMDVEPQVGWYTGWVEQPNGKVTAFALNMNMQAGNDPAERKQLTLSILDKLGLFFYLR"},"dna_sequence":{"accession":"JQ422053","fmin":"99","fmax":"930","strand":"+","sequence":"ATGAAGTTTAAAATGAAAGGTTTATTTTGTGTCATCCTCAGTAGTTTGGCATTTTCAGGTTGTGTTTATGATTCAAAATTACAACGCCCAGTCATATCAGAGCGAGTAACTGAGATTCCTTTATTATTTAATCAAGCACAGACTCAAGCTGTGTTTGTTACTTATGATGGGATTCATCTAAAAAGTTATGGTAATGATCTAAGCCGAGCAAAGACTGAATATATTCCTGCATCTACATTTAAGATGTTGAATGCTTTAATTGGCTTGCAAAATGCAAAAGCAACCAATACTGAAGTATTTCATTGGAATGGTGAAAAGCGCGCTTTTTCAGCATGGGAAAAAGATATGACTTTGGCAGAAGCGATGCAGGCTTCAGCTGTTCCTGTATATCAAGAGCTTGCTCGACGTATTGGCTTGGAATTGATGCGTGAAGAAGTGAAGCGTGTAGGTTTTGGCAATGCGGAGATTGGTCAGCAAGTCGATAATTTTTGGTTGGTGGGTCCTTTAAAAATCTCCCCTGAACAAGAAGTTCAATTTGCCTATCAACTGGCAATGAAGCAATTGCCTTTTGATTCAAATGTACAGCAACAAGTCAAAGATATGCTTTATATCGAGAGACGTGGTGACAGTAAACTGTATGCTAAAAGTGGTTGGGGAATGGATGTTGAACCTCAAGTGGGTTGGTATACGGGATGGGTTGAACAACCCAATGGCAAGGTGACTGCATTTGCGTTAAATATGAACATGCAAGCAGGTAATGATCCAGCTGAACGTAAACAATTAACCTTAAGTATTTTGGACAAATTGGGTCTATTTTTTTATTTAAGATAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39090","NCBI_taxonomy_name":"Acinetobacter bereziniae","NCBI_taxonomy_id":"106648"}}}},"ARO_accession":"3001691","ARO_id":"38091","ARO_name":"OXA-228","ARO_description":"OXA-228 is a beta-lactamase found in A. bereziniae","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"571":{"model_id":"571","model_name":"clbA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"4248":{"protein_sequence":{"accession":"AGZ55247.1","sequence":"MQQKNKYIRIQEFLKQNKFPDFRMNQIKNAVFQGRINHFNEITVLPKSLRKLLIEEFGESILNIAPLKVQHSEQVTKVLFEISGDEKIETVNMKYKAGWESFCISSQCGCHFGCKFCATGDIGLKRNLTSDEMTDQILYFHLKGHSIDSISFMGMGEALANVQVFDALHVLTNPELFALSPRRLSISTIGIIPGIKKITQDYPQVNLTFSLHSPFNEQRSKLMPINERYPLLEVMDTLDEHIRVTSRKVYIAYIMLPGVNDSIDHANEVVNLLRSRYKRGNLFHVNIIRYNPTVSSPMRFEEVNEKQVVNFYKKLKSAGINVTVRSQFGIDIDAACGQLYGNYQKNKNQ"},"dna_sequence":{"accession":"CP006845.1","fmin":"539695","fmax":"540745","strand":"+","sequence":"ATGCAACAAAAAAACAAGTATATAAGAATCCAAGAGTTCCTGAAGCAAAATAAATTTCCTGATTTTAGAATGAATCAAATCAAAAATGCTGTATTCCAAGGGAGAATAAATCATTTCAATGAAATAACGGTTCTTCCTAAATCCCTGAGAAAATTGTTAATAGAGGAGTTCGGAGAGTCGATTTTAAATATTGCTCCTTTAAAAGTGCAGCATTCTGAGCAAGTAACAAAAGTCTTATTTGAAATTTCCGGAGACGAAAAAATAGAAACGGTTAATATGAAATATAAAGCCGGTTGGGAGTCATTTTGTATATCCTCGCAGTGCGGCTGTCATTTCGGCTGTAAATTTTGTGCAACAGGAGATATTGGTTTAAAACGCAATTTAACGTCAGATGAAATGACTGACCAAATTTTGTACTTTCACTTAAAAGGACATTCAATTGACAGTATTTCTTTTATGGGAATGGGAGAAGCATTAGCGAATGTACAAGTTTTTGATGCTTTACATGTGCTTACAAATCCGGAGTTGTTTGCTTTAAGCCCTCGCAGGTTATCTATTTCGACTATAGGTATTATTCCGGGCATTAAAAAAATCACTCAGGATTATCCGCAGGTCAACCTGACGTTTTCATTACATTCTCCTTTTAATGAACAGCGAAGCAAGTTAATGCCGATTAATGAACGCTACCCGTTATTGGAGGTAATGGACACATTAGATGAGCATATACGTGTGACCTCAAGAAAAGTTTATATTGCTTATATTATGCTGCCGGGAGTTAATGATTCTATTGATCATGCGAATGAAGTAGTAAATCTTTTAAGAAGCAGATATAAGAGAGGGAACTTGTTCCATGTAAACATCATTAGATATAACCCGACTGTTAGTTCACCTATGAGATTTGAAGAAGTAAATGAGAAACAAGTTGTAAACTTCTATAAAAAATTAAAGTCAGCAGGAATTAACGTGACCGTCAGAAGTCAATTTGGTATTGATATAGATGCTGCTTGCGGACAATTATATGGAAATTATCAAAAAAATAAGAACCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41528","NCBI_taxonomy_name":"Bacillus amyloliquefaciens CC178","NCBI_taxonomy_id":"1412898"}}}},"ARO_accession":"3002814","ARO_id":"39248","ARO_name":"clbA","ARO_description":"clbA is a plasmid-encoded cfr gene found in Bacillus velezensis (Bacillus amyloliquefaciens subsp. plantarum).","ARO_category":{"36341":{"category_aro_accession":"3000202","category_aro_cvterm_id":"36341","category_aro_name":"Cfr 23S ribosomal RNA methyltransferase","category_aro_description":"Cfr genes produce enzymes which catalyze the methylation of the 23S rRNA subunit at position 8 of adenine-2503. Methylation of 23S rRNA at this site confers resistance to some classes of antibiotics, including streptogramins, chloramphenicols, florfenicols, linezolids and clindamycin.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"35989":{"category_aro_accession":"0000072","category_aro_cvterm_id":"35989","category_aro_name":"linezolid","category_aro_description":"Linezolid is a synthetic antibiotic used for the treatment of serious infections caused by Gram-positive bacteria that are resistant to several other antibiotics. It inhibits protein synthesis by binding to domain V of the 23S rRNA of the 50S subunit of bacterial ribosomes.","category_aro_class_name":"Antibiotic"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37015":{"category_aro_accession":"3000671","category_aro_cvterm_id":"37015","category_aro_name":"tiamulin","category_aro_description":"Tiamulin is a pleuromutilin derivative currently used in veterinary medicine. It binds to the 23 rRNA of the 50S ribosomal subunit to inhibit protein translation.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"36218":{"category_aro_accession":"3000079","category_aro_cvterm_id":"36218","category_aro_name":"oxazolidinone antibiotic","category_aro_description":"Oxazolidinones are a class of synthetic antibiotics discovered the the 1980's.  They inhibit protein synthesis by binding to domain V of the 23S rRNA of the 50S subunit of bacterial ribosomes.  Linezolid is the only member of this class currently in clinical use.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"572":{"model_id":"572","model_name":"OXA-137","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"799":{"protein_sequence":{"accession":"ABW76138.1","sequence":"MSKKNFILIFIFVILTSCKNTEKISNETTLIDNIFTNSNAEGTLVIYNLNDDKYIIHNKERAEQRFYPASTFKIYNSLIGLNEKAVKDVDEVFYKYNGEKVFLESWAKDSNLRYAIKNSQVPAYKELARRIGLKKMKENIEKLDFGNKSIGDSVDTFWLEGPLEISAMEQIKLLTKLAQNELPYPIEIQKAVSDITILEQTYNYTLHGKTGLADSKNMTTEPIGWFVGWLEENDNIYVFALNIDNINSDDLAKRINIVKESLKALNLLK"},"dna_sequence":{"accession":"EU086834","fmin":"88","fmax":"898","strand":"+","sequence":"ATGTCTAAAAAAAATTTTATATTAATATTTATTTTTGTTATTTTAACATCTTGTAAAAATACAGAAAAAATATCAAATGAAACTACATTAATAGATAATATATTTACTAATAGCAATGCTGAAGGAACATTAGTTATATATAATTTAAATGATGATAAATATATAATTCATAATAAAGAAAGAGCTGAACAAAGATTTTATCCAGCATCAACATTTAAAATATATAATAGTTTAATAGGCTTAAATGAAAAAGCAGTTAAAGATGTAGATGAAGTATTTTATAAATATAATGGCGAAAAAGTTTTTCTTGAATCTTGGGCTAAGGACTCTAATTTAAGATATGCAATTAAAAATTCGCAAGTACCGGCATATAAAGAATTAGCAAGAAGAATAGGTCTTAAAAAGATGAAAGAGAATATAGAAAAACTAGATTTTGGTAATAAAAGTATAGGTGATAGTGTAGATACTTTTTGGCTTGAAGGACCTTTGGAAATAAGTGCGATGGAGCAAATTAAATTATTAACTAAATTAGCTCAAAATGAATTACCGTATCCTATAGAAATACAAAAAGCTGTTTCTGATATTACTATACTAGAGCAAACTTACAATTATACGCTTCATGGAAAAACTGGATTAGCTGATTCTAAAAACATGACAACTGAGCCTATTGGTTGGTTCGTAGGCTGGCTTGAAGAAAATGATAATATATATGTCTTTGCTTTAAATATTGATAATATAAATTCAGATGACCTTGCAAAAAGGATAAATATAGTAAAAGAAAGTTTAAAAGCATTAAATTTATTAAAATAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36935","NCBI_taxonomy_name":"Brachyspira pilosicoli","NCBI_taxonomy_id":"52584"}}}},"ARO_accession":"3001767","ARO_id":"38167","ARO_name":"OXA-137","ARO_description":"OXA-137 is a beta-lactamase found in Brachyspira spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"573":{"model_id":"573","model_name":"OXA-136","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2000":{"protein_sequence":{"accession":"ABW76134.1","sequence":"MSKKNFILIFIFVILISCKNTEKISNETTLIDNIFTNSNAEGTLVIYNLNDDKYIIHNKERAEQRFYPASTFKIYNSLIGLNEKAVKDVDEVFYKYNGEKVFLESWAKDSNLRYAIKNSQVPAYKELARRIGLKKMKENIEKLDFGNKSIGDSVDTFWLEGPLEISAMEQVKLLTKLAQNELPYPIEIQKAVSDITILEQTYNYTLHGKTGLADSKNMTTEPIGWFVGWLEENDNIYVFALNIDNINSDDLAKRINIVKESLKALNLLK"},"dna_sequence":{"accession":"EU086830","fmin":"88","fmax":"898","strand":"+","sequence":"ATGTCTAAAAAAAATTTTATATTAATATTTATTTTTGTTATTTTAATATCTTGTAAAAATACAGAAAAAATATCAAATGAAACTACATTAATAGATAATATATTTACTAATAGCAATGCTGAAGGAACATTAGTTATATATAATTTAAATGATGATAAATATATAATTCATAATAAAGAAAGAGCTGAACAAAGATTTTATCCAGCATCAACATTTAAAATATATAATAGTTTAATAGGCTTAAATGAAAAAGCAGTTAAAGATGTAGATGAAGTATTTTATAAATATAATGGCGAAAAAGTTTTTCTTGAATCTTGGGCTAAGGACTCTAATTTAAGATATGCAATTAAAAATTCGCAAGTACCGGCATATAAAGAATTAGCAAGAAGAATAGGTCTTAAAAAGATGAAAGAGAATATAGAAAAACTAGATTTTGGTAATAAAAGTATAGGTGATAGTGTAGATACTTTTTGGCTTGAAGGACCTTTGGAAATAAGTGCGATGGAGCAAGTTAAATTATTAACTAAATTAGCTCAAAATGAATTACCGTATCCTATAGAAATACAAAAAGCTGTTTCTGATATTACTATACTAGAGCAAACTTACAATTATACGCTTCATGGAAAAACTGGATTAGCTGATTCTAAAAACATGACAACTGAGCCTATTGGTTGGTTCGTAGGCTGGCTTGAAGAAAATGATAATATATATGTCTTTGCTTTAAATATTGATAATATCAATTCAGATGACCTTGCAAAAAGGATAAATATAGTAAAAGAAAGTTTAAAAGCATTAAATTTATTAAAATAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36935","NCBI_taxonomy_name":"Brachyspira pilosicoli","NCBI_taxonomy_id":"52584"}}}},"ARO_accession":"3001765","ARO_id":"38165","ARO_name":"OXA-136","ARO_description":"OXA-136 is a beta-lactamase found in Brachyspira spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"574":{"model_id":"574","model_name":"AAC(6')-Ia","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"547":{"protein_sequence":{"accession":"AAA98298.1","sequence":"MNYQIVNIAECSNYQLEAANILTEAFNDLGNNSWPDMTSATKEVKECIESPNLCFGLLINNSLVGWIGLRPMYKETWELHPLVVRPDYQNKGIGKILLKELENRAREQGIIGIALGTDDEYYRTSLSLITITEDNIFDSIKNIKNINKHPYEFYQKNGYYIVGIIPNANGKNKPDIWMWKSLIKE"},"dna_sequence":{"accession":"M18967","fmin":"756","fmax":"1314","strand":"+","sequence":"ATGAATTATCAAATTGTGAATATTGCGGAATGCAGCAATTATCAGTTAGAAGCAGCAAATATACTAACAGAAGCGTTCAATGATCTTGGTAACAATTCATGGCCAGATATGACGAGTGCAACAAAAGAAGTAAAAGAATGTATTGAGAGTCCAAACCTTTGTTTCGGTCTGCTAATAAATAACTCCTTAGTTGGCTGGATAGGCTTAAGGCCAATGTACAAGGAAACCTGGGAATTGCATCCATTGGTTGTCAGACCAGATTATCAAAATAAAGGTATTGGCAAGATCCTGCTTAAGGAATTAGAAAACAGAGCTAGAGAGCAAGGTATTATTGGAATCGCTTTAGGAACAGATGATGAATACTATAGAACAAGTCTCTCTTTAATAACTATAACAGAAGATAATATATTTGATTCAATAAAAAATATTAAAAATATTAATAAACATCCATATGAGTTTTATCAGAAGAATGGTTATTATATTGTTGGAATAATTCCAAATGCCAATGGTAAAAACAAACCAGATATTTGGATGTGGAAAAGTTTAATCAAAGAGTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39508","NCBI_taxonomy_name":"Plasmid R","NCBI_taxonomy_id":"2508"}}}},"ARO_accession":"3002545","ARO_id":"38945","ARO_name":"AAC(6')-Ia","ARO_description":"AAC(6')-Ia is an aminoglycoside acetyltransferase encoded by plasmids, transposons, integrons in Citrobacter diversus, E. coli, K. pneumoniae, Shigella sonnei, and P. aeruginosa.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"575":{"model_id":"575","model_name":"AAC(3)-Ib","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"224":{"protein_sequence":{"accession":"AAA88422.1","sequence":"MLWSSNDVTQQGSRPKTKLGGSMSIIATVKIGPDEISAMRAVLDLFGKEFEDIPTYSDRQPTNEYLANLLHSETFIALAAFDRGTAIGGLAAYVLPKFEQARSEIYIYDLAVASSHRRLGVATALISHLKRVAVELGAYVIYVQADYGDDPAVALYTKLGVREDVMHFDIDPRTAT"},"dna_sequence":{"accession":"L06157","fmin":"554","fmax":"1085","strand":"+","sequence":"ATGTTATGGAGCAGCAACGATGTTACGCAGCAGGGCAGTCGCCCTAAAACAAAGTTAGGTGGCTCAATGAGCATCATTGCAACCGTCAAGATCGGCCCTGACGAAATTTCAGCCATGAGGGCTGTGCTCGATCTCTTCGGCAAAGAGTTTGAGGACATTCCAACCTACTCTGATCGCCAGCCGACCAATGAGTATCTTGCCAATCTTCTGCACAGCGAGACGTTCATCGCGCTCGCTGCTTTTGACCGCGGAACAGCAATAGGTGGGCTCGCCGCCTACGTTCTACCCAAGTTCGAGCAAGCGCGAAGCGAGATCTACATTTATGACTTGGCAGTCGCTTCCAGCCATCGAAGGCTAGGAGTCGCAACTGCCCTGATTAGCCACCTGAAGCGTGTGGCGGTTGAACTTGGCGCGTATGTAATCTATGTGCAAGCAGACTACGGTGACGATCCGGCAGTCGCTCTCTACACAAAGCTTGGAGTTCGGGAAGACGTCATGCACTTCGACATTGATCCAAGAACCGCCACCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002530","ARO_id":"38930","ARO_name":"AAC(3)-Ib","ARO_description":"AAC(3)-Ib is an integron-encoded aminoglycoside acetyltransferase in P. aeruginosa","ARO_category":{"36461":{"category_aro_accession":"3000322","category_aro_cvterm_id":"36461","category_aro_name":"AAC(3)","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 3.","category_aro_class_name":"AMR Gene Family"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"576":{"model_id":"576","model_name":"MIR-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"1978":{"protein_sequence":{"accession":"AJO16037.1","sequence":"MMTKSLSCALLLSVASSAFAAPMSEKQLAEVVERTVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEIALGDPVAKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDTASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEEAHYAWGYREGKAVHVSPGMLDAEAYGVKTNVKDMASWLIANMKPDSLQAPSLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"KP050484","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGACAAAATCCCTAAGCTGTGCCCTGCTGCTCAGCGTCGCCAGTTCTGCATTCGCCGCACCGATGTCCGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTAATTTATCAGGGTCAGCCACACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGCGGCGATGCCATTGCCCGGGGTGAAATAGCGCTGGGCGATCCGGTAGCAAAATACTGGCCTGAGCTCACGGGCAAGCAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTATACCGCAGGCGGTCTGCCGTTACAGGTGCCGGATGAGGTCACGGATACCGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCTAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTTAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAACCCCTCAAGCTGGACCATACCTGGATTAACGTCCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGAGGGTAAAGCGGTCCACGTTTCGCCAGGGATGCTGGACGCGGAAGCCTATGGCGTAAAAACTAACGTGAAGGATATGGCGAGCTGGCTGATAGCCAACATGAAGCCGGATTCTCTTCAGGCTCCCTCACTCAAGCAAGGCATTGCTCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCTATGTATCAGGGGTTAGGCTGGGAGATGCTCAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCATTGCCCGTGGCAGAAGTGAATCCACCCGCGCCGCCGGTCAAGGCCTCCTGGGTCCATAAAACAGGCTCGACGGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36926","NCBI_taxonomy_name":"Enterobacter asburiae","NCBI_taxonomy_id":"61645"}}}},"ARO_accession":"3002170","ARO_id":"38570","ARO_name":"MIR-5","ARO_description":"MIR-5 is a beta-lactamase. From the Lahey list of MIR beta-lactamases.","ARO_category":{"36197":{"category_aro_accession":"3000058","category_aro_cvterm_id":"36197","category_aro_name":"MIR beta-lactamase","category_aro_description":"MIR beta-lactamases are plasmid-mediated beta-lactamases that confer resistance to oxyimino- and alpha-methoxy beta-lactams","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"577":{"model_id":"577","model_name":"QnrB65","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"115":{"protein_sequence":{"accession":"AGL43626.1","sequence":"MTLALVGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRANLKDAIFKSCDLSMADFRNINALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFSSFDWRAANVTHCDLTNSELGDLDIRGVDLQGVKLDSYQASLLLERLGIAVMG"},"dna_sequence":{"accession":"KC580654","fmin":"0","fmax":"645","strand":"+","sequence":"ATGACTCTGGCGTTAGTTGGCGAAAAAATTGACAGAAACAGGTTCACCGGTGAGAAAGTCGAAAATAGCACATTTTTCAACTGTGATTTTTCGGGTGCCGACCTTAGCGGTACTGAATTTATTGGCTGCCAGTTTTATGATCGAGAAAGCCAGAAAGGGTGTAATTTTAGTCGCGCTAACCTGAAGGATGCCATTTTCAAAAGTTGTGATCTCTCCATGGCGGATTTCAGAAATATCAATGCGCTGGGAATCGAAATTCGCCACTGCCGGGCACAAGGGGCAGATTTTCGCGGCGCAAGCTTTATGAATATGATCACCACCCGCACCTGGTTTTGTAGCGCCTATATCACCAATACCAACTTAAGCTACGCCAACTTTTCTAAAGTCGTACTGGAAAAGTGCGAGCTGTGGGAAAACCGCTGGATGGGTACTCAGGTGCTGGGCGCAACGTTCAGTGGATCAGACCTCTCTGGCGGCGAGTTTTCATCCTTCGACTGGCGAGCAGCAAACGTTACGCACTGTGATTTGACCAATTCGGAACTGGGCGATTTAGATATCCGTGGGGTTGATTTGCAAGGCGTCAAACTGGACAGCTACCAGGCATCGTTGCTCCTGGAACGTCTTGGCATCGCTGTCATGGGTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002777","ARO_id":"39211","ARO_name":"QnrB65","ARO_description":"QnrB65 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"578":{"model_id":"578","model_name":"SHV-11","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1062":{"protein_sequence":{"accession":"CAA66729.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"X98101","fmin":"73","fmax":"934","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001070","ARO_id":"37450","ARO_name":"SHV-11","ARO_description":"SHV-11 is a broad-spectrum beta-lactamase found in E. coli, Klebsiella pneumoniae, Proteus mirabilis, and Shigella dysenteriae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"579":{"model_id":"579","model_name":"vgaA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"376":{"protein_sequence":{"accession":"AGN33258.1","sequence":"MKIMLEGLHIKHYVQDRLLLNINRLKIYQNDRIGLVGKNGNGKTTLLHILYKKIVPEEGIVKQFSHCELIPQLKLIESTKSGGEVTRNYIRQALDKNPELLLADEPTTNLDNDYIEKLEQDLKNWHGAFIIVSHDRAFLDNLCTTIWEIEEGRITEYKGNYSNYVEQKELERHREELEYEKYEKEKKRLEKAINIKEQKAQRATKKPKNLSSSESRIKGTKPYFAGKQKKLRKTIKSLETRLEKLESVEKRNELPPLKMDLVNLESVKNRTIIRGEDVSGTIEGRVLWKAKSFSIRGGDKMAIIGSNGTGKTTFIKKIVHGNHGISLSPSVKIGYFSQKIDTLELDKSILENVQSSSQQNETLIRTILARMHFFRDDVYKPINVLSGGERVKVALTKVFLSEVNTLVLDEPTNFLDMEAIEAFESLLKEYNGSIIFVSHDRKFIEKVATRIMTIDNKEIKIFDGTYEQFKQAEKPTRNIKEDKKLLLETKITEVLSRLSIEPSEELEQEFQNLINEKRNLDK"},"dna_sequence":{"accession":"KC539823","fmin":"1017","fmax":"2586","strand":"+","sequence":"ATGAAAATAATGTTAGAGGGACTTCATATAAAACATTATGTTCAAGATCGTTTATTGTTGAACATAAATCGCCTAAAGATTTATCAGAATGATCGTATTGGTTTAGTTGGTAAAAATGGAAATGGAAAAACAACGTTACTTCACATATTATATAAAAAAATTGTGCCTGAAGAAGGTATTGTAAAACAATTTTCACATTGTGAACTTATTCCTCAATTGAAGCTCATAGAATCAACTAAAAGTGGTGGTGAAGTAACACGAAACTATATTCGGCAAGCGCTTGATAAAAATCCAGAACTGCTATTAGCAGATGAACCAACAACTAACTTAGATAATGACTATATAGAAAAATTAGAACAGGATTTAAAAAATTGGCATGGAGCATTTATTATAGTTTCACATGATCGCGCTTTTTTAGATAACTTGTGTACTACTATATGGGAAATTGAAGAAGGAAGAATAACTGAATATAAGGGGAATTATAGTAACTATGTTGAACAAAAAGAATTAGAAAGACATCGAGAAGAATTAGAATATGAAAAATATGAAAAAGAAAAGAAGCGATTGGAAAAAGCTATAAATATAAAAGAACAGAAAGCTCAACGAGCAACTAAAAAACCGAAAAACTTAAGTTCATCTGAAAGCAGAATAAAAGGAACAAAGCCATACTTTGCAGGTAAGCAGAAGAAGTTACGAAAAACTATAAAATCTCTAGAAACCAGACTAGAAAAACTTGAAAGCGTCGAAAAGAGAAACGAACTTCCTCCACTTAAAATGGATTTAGTGAATTTAGAAAGTGTAAAAAATAGAACTATAATACGTGGTGAAGATGTCTCGGGCACAATTGAAGGACGGGTATTGTGGAAAGCAAAAAGTTTTAGTATTCGTGGAGGAGACAAGATGGCAATTATCGGATCTAATGGTACAGGAAAGACAACGTTTATTAAAAAAATTGTTCATGGGAATCATGGTATTTCATTATCGCCATCTGTCAAAATCGGTTATTTTAGCCAAAAAATAGATACATTAGAATTAGATAAGAGTATTTTAGAAAATGTTCAATCTTCTTCACAACAAAATGAAACTCTTATTCGAACTATTCTAGCTAGAATGCATTTTTTTAGAGATGATGTTTATAAACCAATAAATGTCTTAAGTGGTGGAGAGCGAGTTAAAGTAGCACTAACTAAAGTATTCTTAAGTGAAGTTAACACGTTAGTACTAGATGAACCAACAAACTTTCTTGATATGGAAGCTATAGAGGCGTTTGAATCTTTGTTAAAGGAATATAATGGCAGTATAATCTTTGTATCTCACGATCGTAAATTTATCGAAAAAGTAGCCACTCGAATAATGACAATTGATAATAAAGAAATAAAAATATTTGATGGTACATATGAACAATTTAAACAAGCTGAAAAGCCAACAAGGAATATTAAAGAAGATAAAAAACTTTTACTTGAGACAAAAATTACAGAAGTACTCAGTCGATTGAGTATTGAACCTTCGGAAGAATTAGAACAAGAGTTTCAAAACTTAATAAATGAAAAAAGAAATTTAGATAAATAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36868","NCBI_taxonomy_name":"Staphylococcus epidermidis","NCBI_taxonomy_id":"1282"}}}},"ARO_accession":"3002829","ARO_id":"39263","ARO_name":"vgaA","ARO_description":"vgaA is an efflux protein expressed in staphylococci that confers resistance to streptogramin A antibiotics and related compounds. It is associated with plasmid DNA.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37716":{"category_aro_accession":"3001317","category_aro_cvterm_id":"37716","category_aro_name":"pleuromutilin","category_aro_description":"Pleuromutilin is a natural product antibiotic produced by Clitopilus passeckerianus. Related antibiotics of clinical significance, such as tiamulin and retapamulin, are semi-synthetic derivatives of this compound.","category_aro_class_name":"Antibiotic"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"580":{"model_id":"580","model_name":"TEM-110","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1566":{"protein_sequence":{"accession":"AAL68923.1","sequence":"MSIQHFRVALIPFFAAFCFPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYMTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AY072920","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCTTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACATGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000973","ARO_id":"37353","ARO_name":"TEM-110","ARO_description":"TEM-110 is a broad-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"581":{"model_id":"581","model_name":"QnrB19","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"484":{"protein_sequence":{"accession":"AGK90303.1","sequence":"MTLALVGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDSYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"JX298080","fmin":"433","fmax":"1078","strand":"+","sequence":"ATGACTCTGGCATTAGTTGGCGAAAAAATTGACAGAAATCGCTTCACCGGTGAGAAAGTTGAAAATAGTACATTTTTTAACTGCGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGCCAGTTCTATGATCGCGAAAGTCAGAAAGGGTGCAATTTTAGTCGCGCAATGCTGAAAGATGCCATTTTCAAAAGCTGTGATTTATCAATGGCAGATTTCCGCAACGTCAGTGCCTTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGTGCAAGCTTTATGAATATGATCACCACGCGCACCTGGTTTTGCAGCGCATATATCACTAATACTAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAGCTGTGGGAAAACCGCTGGATGGGGACTCAGGTACTGGGTGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTAGGTGACTTAGATATTCGGGGTGTTGATTTACAAGGCGTTAAGTTAGACAGCTACCAGGCATCGTTGCTCATGGAGCGGCTTGGCATCGCTGTGATTGGTTAGT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002734","ARO_id":"39168","ARO_name":"QnrB19","ARO_description":"QnrB19 is a plasmid-mediated quinolone resistance protein found in Escherichia coli","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"582":{"model_id":"582","model_name":"FOX-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1355":{"protein_sequence":{"accession":"CAG28256.1","sequence":"MQQRRAFALLTLGSLLLAPCTYARGEAPLTAAVDGIIQPMLKEYRIPGMAVAVLKDGKAHYFNYGVANRESGQRVSEQTLFEIGSVSKTLTATLGAYAAVKGGFELDDKVSQHAPWLKGSAFDGVTMAELATYSAGGLPLQFPDEVDSNDKMRTYYRHWSPVYPAGTHRQYSNPSIGLFGHLAANSLGQPFEQLMSQTLLPKLGLHHTYIQVPESAIANYAYGYSKEDKPVRATPGVLAAEAYGIKTGSADLLKFTEANMGYQGDAALKSAIALTHTGFYSVGDMTQGLGWESYAYPLTEQALLAGNSPAVSFQANPVTRFAVPKAMGEQRLYNKTGSTGGFGAYVAFVPARGIAIVMLANRNYPIEARVKAAHAILSQLAE"},"dna_sequence":{"accession":"AJ703795","fmin":"0","fmax":"1149","strand":"+","sequence":"ATGCAACAACGACGTGCGTTCGCGCTACTGACGCTGGGTAGCCTGCTGCTAGCCCCTTGTACTTATGCCCGCGGGGAGGCTCCGCTGACCGCCGCTGTGGACGGCATTATCCAGCCGATGCTCAAGGAGTATCGGATCCCGGGGATGGCGGTCGCCGTGCTGAAAGATGGCAAGGCCCACTATTTCAACTATGGGGTTGCCAACCGCGAGAGTGGTCAGCGCGTCAGCGAGCAGACCCTGTTCGAGATTGGCTCGGTCAGCAAGACCCTGACCGCGACCCTCGGTGCCTATGCTGCGGTCAAGGGGGGCTTTGAGCTGGATGACAAGGTGAGCCAGCACGCCCCCTGGCTCAAAGGTTCCGCCTTTGATGGTGTGACCATGGCCGAGCTTGCCACCTACAGTGCGGGTGGTTTGCCGCTGCAGTTCCCCGATGAGGTGGATTCGAATGACAAGATGCGCACTTACTATCGGCACTGGTCACCGGTTTATCCGGCGGGGACCCATCGCCAGTATTCCAACCCCAGCATAGGCCTGTTTGGTCACCTGGCCGCAAATAGTCTGGGCCAGCCATTTGAGCAACTGATGAGCCAGACCCTGCTGCCCAAGCTGGGTTTGCACCACACCTATATTCAGGTGCCGGAGTCGGCCATAGCGAACTATGCCTACGGCTATTCGAAGGAAGATAAGCCCGTCCGGGCCACTCCGGGCGTGCTGGCGGCCGAGGCTTACGGGATCAAGACCGGCTCGGCGGATCTGCTGAAGTTTACCGAGGCCAACATGGGGTATCAGGGAGATGCCGCGCTAAAAAGCGCGATCGCGCTGACCCATACCGGTTTCTACTCGGTGGGAGACATGACTCAGGGGCTGGGTTGGGAGAGCTACGCCTATCCGTTGACCGAGCAGGCGCTGCTGGCGGGCAACTCCCCGGCGGTGAGCTTCCAGGCCAATCCGGTTACGCGCTTTGCGGTGCCCAAAGCGATGGGCGAGCAGCGGCTCTATAACAAGACGGGCTCGACTGGCGGCTTTGGCGCCTATGTGGCGTTCGTGCCCGCCAGAGGGATCGCCATCGTCATGCTGGCCAATCGCAACTATCCCATCGAGGCCAGGGTGAAGGCGGCTCACGCCATCCTGAGTCAGTTGGCCGAGTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002160","ARO_id":"38560","ARO_name":"FOX-7","ARO_description":"FOX-7 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36206":{"category_aro_accession":"3000067","category_aro_cvterm_id":"36206","category_aro_name":"FOX beta-lactamase","category_aro_description":"FOX beta-lactamases are plasmid-encoded AmpC-type beta-lactamase which conferred resistance to broad-spectrum cephalosporins and cephamycins","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"583":{"model_id":"583","model_name":"SHV-100","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1542":{"protein_sequence":{"accession":"CAQ03505.1","sequence":"MRFIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIESESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM941846","fmin":"0","fmax":"900","strand":"+","sequence":"ATGCGTTTTATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGAGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATCGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001338","ARO_id":"37738","ARO_name":"SHV-100","ARO_description":"SHV-100 is a beta-lactamase found in Klebsiella pneumoniae. It differs from SHV-1 by a 35SESQLSGRVGMIE36 insertion.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"584":{"model_id":"584","model_name":"aadA21","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"195":{"protein_sequence":{"accession":"AAN87151.1","sequence":"MRVAVTIEISNQLSEVLSVIERHLESTLLAVHLYGSAVDGGLKPYSDIDLLVTVTVRLDETTRRALINDLLETSASPGESEILRAVEVTIVVHDDIIPWRYPAKRELQFGEWQRNDILAGIFEPATIDIDLAILLTKAREHSVALVGPAAEELFDPVPEQDLFEALNETLTLWNSPPDWAGDERNVVLTLSRIWYSAVTGKIAPKDVARDWAMERLPAQYQPVILEARQAYLGQEEDRLASRADQLEEFVHYVKGEITKVVGK"},"dna_sequence":{"accession":"AY171244","fmin":"46","fmax":"838","strand":"+","sequence":"ATGAGGGTAGCGGTGACCATCGAAATTTCGAACCAACTATCAGAGGTGCTAAGCGTCATTGAGCGCCATCTGGAATCAACGTTGCTGGCCGTGCATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCATACAGCGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCGAGCTTTGATCAACGACCTTTTGGAAACTTCGGCTTCCCCTGGAGAGAGCGAGATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCTGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAGTAACCGGCAAAATCGCGCCGAAGGATGTCGCTCGCGACTGGGCAATGGAGCGCCTGCCGGCCCAGTATCAGCCCGTCATACTTGAAGCTAGACAGGCTTATCTTGGACAAGAAGAAGATCGCTTGGCCTCGCGCGCAGATCAGTTGGAAGAATTTGTCCACTACGTGAAAGGCGAGATCACCAAGGTAGTCGGCAAATAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35732","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium","NCBI_taxonomy_id":"90371"}}}},"ARO_accession":"3002618","ARO_id":"39018","ARO_name":"aadA21","ARO_description":"aadA21 is an integron-encoded aminoglycoside nucleotidyltransferase gene in Salmonella spp.","ARO_category":{"41439":{"category_aro_accession":"3004275","category_aro_cvterm_id":"41439","category_aro_name":"ANT(3'')","category_aro_description":"Nucleotidylylation of streptomycin at the hydroxyl group at position 3''","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"585":{"model_id":"585","model_name":"NDM-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1183":{"protein_sequence":{"accession":"AFQ31613.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMNALHAAGIATYANALSNQLAPQEGLVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"JX262694","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGAACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGCTGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002357","ARO_id":"38757","ARO_name":"NDM-7","ARO_description":"NDM-7 is a beta-lactamase found in Escherichia coli","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"586":{"model_id":"586","model_name":"VIM-20","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1654":{"protein_sequence":{"accession":"ACV13198.1","sequence":"MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQRYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"GQ414736","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACGCTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002290","ARO_id":"38690","ARO_name":"VIM-20","ARO_description":"VIM-20 is a beta-lactamase. From the Lahey list of VIM beta-lactamases.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"587":{"model_id":"587","model_name":"TEM-73","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"3324":{"protein_sequence":{"accession":"CAB65358.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMLSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSSGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AJ012256","fmin":"208","fmax":"1069","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGCTGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTAGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3000939","ARO_id":"37319","ARO_name":"TEM-73","ARO_description":"TEM-73 is an inhibitor-resistant beta-lactamase that has been found in clinical isolates.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"588":{"model_id":"588","model_name":"OKP-A-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1750":{"protein_sequence":{"accession":"CAJ19605.1","sequence":"MRCVRLCLISLIAALPLAVFASPQPLEQITLSESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDERLDRRIRYPQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKSVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMAATLRKLLTSHALSDRSQQQLLQWMVDDQVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPNGKAERIVVIYLRDTPAAMAERNQQIAKIGAALIEHWQR"},"dna_sequence":{"accession":"AM051146","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTGTGTTCGCCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCAGCCGCTCGAACAAATTACACTCAGCGAAAGTCAGCTGGCGGGCCGCGTGGGCTATGTTGAAATGGATCTGGCGAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGAGACGAACGGCTGGATCGGCGGATCCGCTACCCCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGAGCGTTGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGATAACGTCACCCGCCTTGACCGCTGGGAAACGGAGCTCAATGAGGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCAGCCAGCATGGCCGCCACCCTGCGCAAGCTGCTAACCAGCCACGCGCTGAGCGACCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGACCAGGTGGCCGGTCCGCTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGCGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGAACGGCAAAGCGGAGCGCATCGTGGTGATCTATCTGCGGGATACGCCGGCGGCCATGGCCGAGCGTAACCAGCAGATCGCCAAAATAGGCGCGGCGCTGATCGAGCACTGGCAGCGCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002424","ARO_id":"38824","ARO_name":"OKP-A-7","ARO_description":"OKP-A-7 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"589":{"model_id":"589","model_name":"TEM-145","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1721":{"protein_sequence":{"accession":"AAZ14083.2","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLMRSALPAGWFIADKSGAGERGSHGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"DQ105528","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCAGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTATGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCACGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAAGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001012","ARO_id":"37392","ARO_name":"TEM-145","ARO_description":"TEM-145 is an inhibitor-resistant beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"590":{"model_id":"590","model_name":"IND-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1175":{"protein_sequence":{"accession":"CAJ32373.2","sequence":"MKRRIQFFMVSMMLTPLFSAQVKDFVIEPPIKKNLYIYKTFGVFGGKEYSANSVYLVTKTGVVLFDVPWEKAQYQSLMDTIKKRHNLPVVAVFATHSHDDRAGDLSFFNNKGIKTYATPKTNQFLKRDGKATSTELIKPGKPYRFGGEEFVVDFLGEGHTADNVVVWFPKYKVLDGGCLVKSNSATDLGYIKEANLEQWPKTMHKLKTKYSEAVLIIPGHDEWKGGGHVEHTLELLDKK"},"dna_sequence":{"accession":"AM087455","fmin":"291","fmax":"1011","strand":"+","sequence":"ATGAAAAGAAGAATTCAGTTCTTTATGGTTTCAATGATGCTTACCCCATTATTCAGTGCCCAGGTAAAAGATTTTGTAATTGAACCGCCAATAAAAAAGAACTTATATATTTATAAAACTTTCGGAGTGTTCGGGGGAAAAGAATATTCTGCCAATTCAGTGTATCTTGTCACCAAAACCGGGGTTGTTTTATTTGATGTTCCCTGGGAAAAAGCGCAATACCAAAGCCTGATGGATACCATCAAAAAACGTCATAATTTACCTGTTGTTGCGGTATTTGCGACACATTCCCATGATGACCGGGCAGGAGATTTAAGCTTTTTCAATAATAAAGGAATTAAAACCTATGCTACTCCTAAAACCAATCAATTTCTGAAAAGAGACGGAAAGGCTACTTCTACAGAGCTCATTAAGCCCGGAAAACCTTACCGCTTTGGCGGAGAGGAATTTGTAGTGGATTTTCTTGGTGAAGGGCATACTGCCGATAATGTAGTGGTATGGTTTCCAAAATATAAAGTGCTGGATGGCGGCTGCCTTGTAAAAAGCAATTCAGCTACCGATTTAGGGTATATCAAAGAAGCTAATCTAGAGCAATGGCCTAAAACCATGCATAAACTGAAAACAAAATATTCAGAAGCAGTATTAATTATTCCCGGACATGATGAATGGAAAGGCGGCGGGCACGTTGAACATACTTTGGAGCTGCTGGATAAGAAATAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36916","NCBI_taxonomy_name":"Chryseobacterium indologenes","NCBI_taxonomy_id":"253"}}}},"ARO_accession":"3002262","ARO_id":"38662","ARO_name":"IND-6","ARO_description":"IND-6 is a beta-lactamase found in Chryseobacterium indologenes","ARO_category":{"36199":{"category_aro_accession":"3000060","category_aro_cvterm_id":"36199","category_aro_name":"IND beta-lactamase","category_aro_description":"IND beta-lactamases are class B carbapenem-hydrolyzing beta-lactamases","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"591":{"model_id":"591","model_name":"CTX-M-122","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1167":{"protein_sequence":{"accession":"AFA51700.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARSIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAERRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"JN790863","fmin":"232","fmax":"1108","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCTCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGCGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001981","ARO_id":"38381","ARO_name":"CTX-M-122","ARO_description":"CTX-M-122 is a beta-lactamase. From the Lahey list of CTX-M beta-lactamases.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"592":{"model_id":"592","model_name":"lmrB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"900"}},"model_sequences":{"sequence":{"3625":{"protein_sequence":{"accession":"KIX81495.1","sequence":"METTAKASQQYKVMPIMISLLLAGFIGMFSETALNIALTDLMKELNITAATVQWLTTGYLLVLGILVPVSGLLLQWFTTRQLFTVSLIFSILGTFIAALAPSFSFLLAARIVQALGTGLLLPLMFNTILVIFPPHKRGAAMGTIGLVIMFAPAIGPTFSGLVLEHLNWHWIFWISLPFLVLALVFGIAYMQNVSETTKPKIDVLSIILSTIGFGGIVFGFSNAGEGSGGWSSPTVIVSLIVGVVGLILFSIRQLTMKQPMMNLRAFKYPMFILGVIMVFICMMVILSSMLLLPMYLQGGLVLTAFASGLVLLPGGILNGFMSPVTGRLFDKYGPKWLVIPGFVIVTVVLWFFSNVTTTSTAVLIIILHTCLMIGISMIMMPAQTNGLNQLPREFYPDGTAIMNTLQQMAGAIGTAVAVSIMAAGQHDYMSTVKNPADPAVIPQALTAGVQHAFVFAMIVAIIGLIGAFFMKRVKVDH"},"dna_sequence":{"accession":"JYFL01000006.1","fmin":"112069","fmax":"113503","strand":"-","sequence":"TTAATGATCTACTTTAACGCGTTTCATAAAGAAAGCGCCAATTAAACCGATAATGGCAACAATCATTGCAAACACAAATGCGTGCTGTACGCCTGCTGTCAAAGCTTGCGGGATGACTGCCGGATCGGCAGGGTTTTTAACTGTACTCATATAATCATGCTGGCCTGCAGCCATAATGCTGACCGCAACCGCTGTTCCGATAGCGCCGGCCATTTGCTGCAGCGTGTTCATAATGGCGGTGCCGTCTGGATAAAATTCACGCGGCAGTTGGTTTAAACCGTTTGTCTGTGCAGGCATCATGATCATAGAAATCCCGATCATCAAGCAGGTGTGCAGGATGATAATCAGCACAGCTGTTGAAGTGGTCGTGACATTTGAGAAGAACCATAGTACAACGGTGACAATCACAAATCCCGGAATGACAAGCCATTTCGGCCCGTATTTATCGAACAAGCGGCCTGTAACAGGGGACATAAATCCATTTAAAATACCGCCCGGCAAGAGAACAAGACCAGATGCAAATGCAGTGAGGACTAAGCCGCCTTGCAGATACATCGGCAGAAGCAGCATAGATGACAGAATGACCATCATACAAATGAACACCATGATCACACCCAAAATAAACATCGGGTATTTGAACGCACGGAGGTTCATCATAGGCTGCTTCATTGTCAGCTGGCGGATTGAAAATAAGATAAGGCCGACAACGCCGACAATCAGCGACACGATAACAGTCGGGCTGGACCATCCCCCGGAGCCTTCACCCGCGTTGCTGAATCCGAATACAATGCCGCCGAAGCCAATCGTCGACAGGATGATAGACAATACATCGATTTTCGGCTTTGTCGTTTCAGATACATTTTGCATATATGCGATACCGAAAACAAGCGCCAGCACAAGGAATGGAAGAGAGATCCAGAAAATCCAGTGCCAGTTGAGATGCTCCAGAACCAATCCTGAGAAAGTTGGGCCGATGGCGGGCGCGAACATAATGACAAGCCCGATCGTTCCCATTGCGGCACCCCGTTTATGAGGCGGGAAAATCACCAAGATTGTGTTAAACATCAGCGGCAGTAAAAGACCGGTTCCAAGTGCCTGAACGATCCTTGCCGCTAATAAAAACGAGAAGCTCGGCGCAAGCGCCGCAATGAATGTACCTAAAATTGAAAAGATAAGTGACACGGTAAAAAGCTGTCTTGTTGTGAACCACTGCAACAGCAGTCCTGAAACAGGAACAAGGATACCGAGTACAAGCAGGTAGCCCGTCGTTAACCATTGGACGGTTGCCGCTGTAATGTTCAATTCCTTCATAAGGTCGGTTAACGCAATATTCAGCGCTGTTTCACTGAACATGCCGATAAAACCGGCCAACAGCAAGGAAATCATAATCGGCATCACTTTGTATTGCTGAGATGCTTTAGCTGTTGTTTCCAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36833","NCBI_taxonomy_name":"Bacillus subtilis","NCBI_taxonomy_id":"1423"}}}},"ARO_accession":"3002813","ARO_id":"39247","ARO_name":"lmrB","ARO_description":"lmrB is a chromosomally-encoded efflux pump that confers resistance to lincosamides in Bacillus subtilis","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"593":{"model_id":"593","model_name":"abeS","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"175"}},"model_sequences":{"sequence":{"4255":{"protein_sequence":{"accession":"ACJ59254.1","sequence":"MSYLYLAIAIACEVIATSALKASQGFTVPIPSIITVVGYAVAFYLLSLTLKTIPIGIAYAIWSGAGIILISAIGWIFYKQHLDLAACIGLALMIAGIVIINVFSKNTHL"},"dna_sequence":{"accession":"CP001172.1","fmin":"1249018","fmax":"1249348","strand":"-","sequence":"TTATAGATGGGTGTTTTTAGAAAACACATTAATAATCACAATGCCTGCGATCATTAAAGCTAAACCAATGCAGGCAGCTAAGTCTAAATGTTGTTTGTAAAATATCCAGCCAATTGCAGAAATTAAAATAATACCTGCGCCTGACCAAATGGCATAGGCAATCCCGATTGGAATTGTTTTGAGCGTAAGAGATAATAAATAAAAAGCAACTGCATAACCCACAACTGTAATAATAGACGGAATTGGAACAGTAAAACCTTGAGATGCTTTTAATGCTGAAGTTGCAATAACTTCACAAGCAATCGCAATTGCTAAATAAAGATAAGACAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35595","NCBI_taxonomy_name":"Acinetobacter baumannii AB307-0294","NCBI_taxonomy_id":"557600"}}}},"ARO_accession":"3000768","ARO_id":"37148","ARO_name":"abeS","ARO_description":"AbeS in an efflux pump of the SMR family of transporters found in Acinetobacter baumannii.","ARO_category":{"36004":{"category_aro_accession":"0010003","category_aro_cvterm_id":"36004","category_aro_name":"small multidrug resistance (SMR) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Small multidrug resistance (SMR) proteins are a relatively small family of transporters, restricted to prokaryotic cells. They are also the smallest multidrug transporters, with only four transmembrane alpha-helices and no significant extramembrane domain.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"594":{"model_id":"594","model_name":"QnrB41","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"645":{"protein_sequence":{"accession":"AEL31272.1","sequence":"MTPLLYKKTGTNMALALVGDKIDRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNSSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIGS"},"dna_sequence":{"accession":"JN166690","fmin":"0","fmax":"681","strand":"+","sequence":"ATGACGCCATTACTGTATAAAAAAACAGGTACAAATATGGCTCTGGCACTCGTTGGCGATAAAATTGACAGAAACCGTTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCGATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATTCCAGTGCGCTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGCGCAAGCTTTATGAATATGATCACTACTCGCACCTGGTTTTGCAGCGCATATATCACTAACACAAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGCTGGAAAAATGTGAGCTGTGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTTTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTGACTTAGATATTCGGGGCGTTGATTTACAAGGCGTTAAGCTGGACAACTACCAGGCGTCGTTGCTCATGGAGCGACTTGGCATCGCGGTGATTGGTAGC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002756","ARO_id":"39190","ARO_name":"QnrB41","ARO_description":"QnrB41 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"595":{"model_id":"595","model_name":"SHV-75","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1876":{"protein_sequence":{"accession":"CAJ47130.2","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPHNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM176550","fmin":"30","fmax":"891","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGCATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001129","ARO_id":"37509","ARO_name":"SHV-75","ARO_description":"SHV-75 is a broad-spectrum beta-lactamase that is found in clinical isolates.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"596":{"model_id":"596","model_name":"ROB-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"1386":{"protein_sequence":{"accession":"CAA37052.1","sequence":"MLNKLKIGTLLLLTLTACSPNSVHSVTSNPQPASAPVQQSATQATFQQTLANLEQQYQARIGVYVWDTETGHSLSYRADERFAYASTFKALLAGAVLQSLPEKDLNRTISYSQKDLVSYSPETQKYVGKGMTIAQLCEAAVRFSDNSATNLLLKELGGVEQYQRILRQLGDNVTHTNRLEPDLNQAKPNDIRDTSTPKQMAMNLNAYLLGNTLTESQKTILWNWLDNNATGNPLIRAATPTSWKVYDKSGAGKYGVRNDIAVVRIPNRKPIVMAIMSTQFTEEAKFNNKLVEDAAKQVFHTLQLN"},"dna_sequence":{"accession":"X52872","fmin":"220","fmax":"1138","strand":"+","sequence":"ATGTTAAATAAGTTAAAAATCGGCACATTATTATTGCTGACATTAACGGCTTGTTCGCCCAATTCTGTTCATTCGGTAACGTCTAATCCGCAGCCTGCTAGTGCGCCTGTGCAACAATCAGCCACACAAGCCACCTTTCAACAGACTTTGGCGAATTTGGAACAGCAGTATCAAGCCCGAATTGGCGTTTATGTATGGGATACAGAAACGGGACATTCTTTGTCTTATCGTGCAGATGAACGCTTTGCTTATGCGTCCACTTTCAAGGCGTTGTTGGCTGGGGCGGTGTTGCAATCGCTGCCTGAAAAAGATTTAAATCGTACCATTTCATATAGCCAAAAAGATTTGGTTAGTTATTCTCCCGAAACCCAAAAATACGTTGGCAAAGGCATGACGATTGCCCAATTATGTGAAGCAGCCGTGCGGTTTAGCGACAACAGCGCGACCAATTTGCTGCTCAAAGAATTGGGTGGCGTGGAACAATATCAACGTATTTTGCGACAATTAGGCGATAACGTAACCCATACCAATCGGCTAGAACCCGATTTAAATCAAGCCAAACCCAACGATATTCGTGATACGAGTACACCCAAACAAATGGCGATGAATTTAAATGCGTATTTATTGGGCAACACATTAACCGAATCGCAAAAAACGATTTTGTGGAATTGGTTGGACAATAACGCAACAGGCAATCCATTGATTCGCGCTGCTACGCCAACATCGTGGAAAGTGTACGATAAAAGCGGGGCGGGTAAATATGGTGTACGCAATGATATTGCGGTGGTTCGCATACCAAATCGCAAACCGATTGTGATGGCAATCATGAGTACGCAATTTACCGAAGAAGCCAAATTCAACAATAAATTAGTAGAAGATGCAGCAAAGCAAGTATTTCATACTTTACAGCTCAACTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39540","NCBI_taxonomy_name":"Mannheimia haemolytica","NCBI_taxonomy_id":"75985"}}}},"ARO_accession":"3002995","ARO_id":"39429","ARO_name":"ROB-1","ARO_description":"ROB-1 is a beta-lactamase found in Pasteurella and Haemophilus","ARO_category":{"39428":{"category_aro_accession":"3002994","category_aro_cvterm_id":"39428","category_aro_name":"ROB beta-lactamase","category_aro_description":"ROB beta-lactamases are a class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"598":{"model_id":"598","model_name":"dfrA16","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"2103":{"protein_sequence":{"accession":"AAK60186.1","sequence":"MKLSLMAAKSKNGIIGNGPDIPWSAKGEQLLFKAITYNQWLLVGRKTFESMGALPNRKYAVVTRSNFSTNDEGVMVFSSIQDALINLEEITDHVIVSGGGEIYKSLISKVDTLHISTVDIERDGDIVFPEIPDTFKLVFEQDFESNINYCYQIWQKS"},"dna_sequence":{"accession":"AF174129","fmin":"1351","fmax":"1825","strand":"+","sequence":"GTGAAGTTATCACTAATGGCTGCCAAGTCGAAGAACGGTATTATCGGTAATGGACCAGATATTCCATGGAGCGCCAAAGGCGAGCAACTTCTATTTAAGGCAATTACATATAATCAATGGCTTTTAGTTGGACGCAAAACTTTTGAGTCAATGGGCGCTCTCCCAAATCGAAAGTATGCAGTTGTAACTCGCTCTAATTTTTCTACGAATGATGAGGGTGTAATGGTTTTCTCCTCAATTCAGGATGCCTTAATAAATTTAGAGGAAATCACGGATCATGTTATCGTTTCTGGTGGTGGTGAAATATACAAAAGCTTGATTTCCAAAGTAGATACTTTGCATATTTCAACAGTCGACATCGAGCGAGATGGAGACATAGTTTTTCCTGAAATCCCAGATACATTCAAGTTGGTATTTGAGCAAGATTTCGAGTCTAACATTAACTATTGTTATCAAATCTGGCAAAAGAGTTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3003014","ARO_id":"39448","ARO_name":"dfrA16","ARO_description":"dfrA16 is an integron-encoded dihydrofolate reductase found in Salmonella enterica","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36408":{"category_aro_accession":"3000269","category_aro_cvterm_id":"36408","category_aro_name":"brodimoprim","category_aro_description":"Brodimoprim is a structural derivative of trimethoprim and an inhibitor of bacterial dihydrofolate reductase. The 4-methoxy group of trimethoprim is replaced with a bromine atom.","category_aro_class_name":"Antibiotic"},"36423":{"category_aro_accession":"3000284","category_aro_cvterm_id":"36423","category_aro_name":"tetroxoprim","category_aro_description":"Tetroxoprim is a trimethoprim derivative that inhibits bacterial dihydrofolate reductase.","category_aro_class_name":"Antibiotic"},"36476":{"category_aro_accession":"3000337","category_aro_cvterm_id":"36476","category_aro_name":"iclaprim","category_aro_description":"Iclaprim is a bactericidal compound that inhibits dihydrofolate reductase. It is used against clinically important Gram-positive pathogens, including methicillin-sensitive Staphylococcus aureus and methicillin-resistant S. aureus.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"599":{"model_id":"599","model_name":"OKP-A-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1447":{"protein_sequence":{"accession":"CAJ19599.1","sequence":"MRYVRLCLISLIAALPLAVFASPPPLEQITRSESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIRYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKSVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMAATLRKLLTSHALSDRSQQQLLQWMVDDQVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPNGKAERIVVIYLRDTPATMAERNQQIAKIGAALIEHWQR"},"dna_sequence":{"accession":"AM051140","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCCGCCGCTTGAGCAAATTACACGCAGCGAAAGTCAGCTGGCGGGCCGCGTGGGCTATGTTGAAATGGATCTGGCGAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGAGACGAACAGCTGGATCGGCGGATCCGCTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGAGCGTTGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAGCTCAATGAAGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCAGCCAGCATGGCCGCCACCCTGCGCAAGCTGCTAACCAGCCACGCGCTGAGCGACCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGACCAGGTGGCCGGTCCGCTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGCGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGAACGGCAAAGCGGAGCGCATCGTGGTGATCTATCTGCGGGATACGCCGGCGACCATGGCCGAGCGTAACCAGCAGATCGCCAAAATAGGCGCGGCGCTGATCGAGCACTGGCAGCGCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002420","ARO_id":"38820","ARO_name":"OKP-A-3","ARO_description":"OKP-A-3 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"600":{"model_id":"600","model_name":"CMY-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"821":{"protein_sequence":{"accession":"CAA62957.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"X91840","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002013","ARO_id":"38413","ARO_name":"CMY-2","ARO_description":"CMY-2 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35927":{"category_aro_accession":"0000008","category_aro_cvterm_id":"35927","category_aro_name":"cefoxitin","category_aro_description":"Cefoxitin is a cephamycin antibiotic often grouped with the second generation cephalosporins. Cefoxitin is bactericidal and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. Cefoxitin's 7-alpha-methoxy group and 3' leaving group make it a poor substrate for most beta-lactamases.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"601":{"model_id":"601","model_name":"dfrA20","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"342":{"protein_sequence":{"accession":"CAE53424.1","sequence":"MGIKYSLIVAIGKHREMGADNDLLWHLPRDMQFFKETTTGHAVVMGRKSWESIPQKYRPLPNRLNFVLTRDKNYSAEGATVIYDLKEVAQHLEGKNLTCFIIGGAQIYQLALETGLLNEMYVTQVHNTFEEADTFFPFVNWGEWEEEDILEQDKDEKHLYSFNIKKFTR"},"dna_sequence":{"accession":"AJ605332","fmin":"1303","fmax":"1813","strand":"+","sequence":"ATGGGTATTAAATATAGCTTAATTGTTGCAATTGGGAAACACCGAGAAATGGGTGCTGACAATGATTTGCTTTGGCACTTACCAAGAGATATGCAATTTTTTAAGGAAACGACAACGGGTCACGCTGTTGTAATGGGAAGAAAAAGTTGGGAATCTATTCCTCAGAAGTACAGACCGCTTCCAAATCGTTTAAACTTCGTTTTAACACGAGATAAAAACTATAGTGCAGAAGGTGCAACAGTGATTTATGATTTAAAAGAAGTCGCACAACATCTTGAAGGAAAAAACTTAACATGCTTCATTATTGGTGGTGCTCAAATCTACCAACTGGCCTTAGAAACAGGACTTTTAAATGAAATGTATGTCACACAAGTACATAACACATTTGAAGAAGCTGACACCTTTTTCCCTTTTGTAAATTGGGGAGAATGGGAAGAAGAAGATATTTTAGAACAAGATAAAGATGAAAAACATCTTTATTCATTTAATATAAAGAAATTTACGCGTTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36867","NCBI_taxonomy_name":"Pasteurella multocida","NCBI_taxonomy_id":"747"}}}},"ARO_accession":"3003016","ARO_id":"39450","ARO_name":"dfrA20","ARO_description":"dfrA20 is a plasmid-encoded dihydrofolate reductase found in Pasteurella multocida","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36408":{"category_aro_accession":"3000269","category_aro_cvterm_id":"36408","category_aro_name":"brodimoprim","category_aro_description":"Brodimoprim is a structural derivative of trimethoprim and an inhibitor of bacterial dihydrofolate reductase. The 4-methoxy group of trimethoprim is replaced with a bromine atom.","category_aro_class_name":"Antibiotic"},"36423":{"category_aro_accession":"3000284","category_aro_cvterm_id":"36423","category_aro_name":"tetroxoprim","category_aro_description":"Tetroxoprim is a trimethoprim derivative that inhibits bacterial dihydrofolate reductase.","category_aro_class_name":"Antibiotic"},"36476":{"category_aro_accession":"3000337","category_aro_cvterm_id":"36476","category_aro_name":"iclaprim","category_aro_description":"Iclaprim is a bactericidal compound that inhibits dihydrofolate reductase. It is used against clinically important Gram-positive pathogens, including methicillin-sensitive Staphylococcus aureus and methicillin-resistant S. aureus.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"602":{"model_id":"602","model_name":"VIM-16","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1251":{"protein_sequence":{"accession":"ACB54703.1","sequence":"MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWLHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"EU419746","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTTGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002286","ARO_id":"38686","ARO_name":"VIM-16","ARO_description":"VIM-16 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"603":{"model_id":"603","model_name":"mdtG","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"4258":{"protein_sequence":{"accession":"ABV18113.1","sequence":"MSPCENDTPINWKRNLIVAWLGCFLTGAAFSLVMPFLPLYVEQLGVTGHSALNMWSGIVFSITFLFSAIASPFWGGLADRKGRKLMLLRSALGMGIVMVLMGLAQNIWQFLILRALLGLLGGFVPNANALIATQVPRNKSGWALGTLSTGGVSGALLGPMAGGLLADSYGLRPVFFITASVLILCFFVTLFCIREKFQPVSKKEMLHMREVVTSLKNPKLVLSLFVTTLIIQVATGSIAPILTLYVRELAGNVSNVAFISGMIASVPGVAALLSAPRLGKLGDRIGPEKILITALIFSVLLLIPMSYVQTPLQLGILRFLLGAADGALLPAVQTLLVYNSSNQIAGRIFSYNQSFRDIGNVTGPLMGAAISANYGFRAVFLVTAGVVLFNAVYSWNSLRRRRIPQVSN"},"dna_sequence":{"accession":"CP000800.1","fmin":"1191727","fmax":"1192954","strand":"-","sequence":"TCAGTTCGATACCTGGGGTATTCGACGACGACGTAGACTGTTCCATGAATAGACTGCGTTGAATAACACTACGCCAGCGGTGACGAGAAATACCGCTCTGAAACCGTAGTTCGCTGAAATCGCTGCTCCCATCAATGGTCCGGTAACGTTGCCAATATCACGAAACGATTGGTTATAGCTGAAGATACGCCCGGCGATCTGGTTGCTCGAGTTGTAAACCAACAGTGTCTGTACGGCGGGGAGTAGTGCACCATCGGCGGCACCGAGCAAAAAACGTAAAATCCCAAGTTGCAATGGCGTCTGAACGTAAGACATTGGGATCAACAGCAGTACAGAAAAGATCAGCGCTGTAATCAGGATCTTTTCGGGTCCGATTCGATCGCCAAGTTTGCCGAGTCGTGGTGCACTTAGCAGAGCCGCCACGCCTGGCACCGAGGCGATCATGCCACTGATAAAGGCGACGTTACTGACGTTACCCGCCAGTTCGCGGACATACAGCGTCAGAATGGGGGCAATTGAGCCCGTCGCCACCTGGATGATTAACGTAGTGACAAACAGGCTGAGTACCAGTTTCGGGTTTTTAAGTGATGTCACCACTTCCCGCATGTGCAGCATCTCTTTTTTGCTGACCGGCTGGAATTTTTCTCTGATGCAAAACAGGGTGACGAAAAAGCAGAGTATGAGCACACTGGCGGTAATAAAGAATACCGGACGTAAGCCGTAGCTATCGGCGAGCAGGCCGCCAGCCATTGGGCCGAGCAACGCACCACTAACGCCGCCTGTGGAGAGCGTACCCAGCGCCCAGCCGCTTTTATTACGCGGTACTTGTGTGGCGATAAGAGCATTAGCGTTGGGGACAAATCCGCCAAGTAACCCAAGAAGCGCCCGTAGGATCAAAAACTGCCAGATATTTTGTGCCAGTCCCATCAACACCATCACGATGCCCATGCCGAGAGCAGAGCGTAATAGCATGAGTTTTCGACCTTTACGGTCGGCGAGTCCACCCCAAAACGGTGAGGCGATGGCCGAAAATAAAAATGTAATGCTGAAGACAATACCGGACCACATATTCAGGGCGGAGTGGCCGGTAACACCAAGCTGCTCAACGTAGAGGGGTAAGAAGGGCATTACCAGACTGAAGGCGGCCCCGGTAAGAAAACAGCCTAGCCAGGCGACGATCAGGTTTCGTTTCCAGTTTATAGGGGTGTCATTTTCACAGGGTGACAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41529","NCBI_taxonomy_name":"Escherichia coli O139:H28 str. E24377A","NCBI_taxonomy_id":"331111"}}}},"ARO_accession":"3001329","ARO_id":"37728","ARO_name":"mdtG","ARO_description":"The MdtG protein, also named YceE, appears to be a member of the major facilitator superfamily of transporters, and it has been reported, when overexpressed, to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"604":{"model_id":"604","model_name":"OXA-385","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4333":{"protein_sequence":{"accession":"AHL30272.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALISLEHHKATATEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KF986253","fmin":"15","fmax":"840","strand":"-","sequence":"CTATAAAATACCTAATTGTTCTAAACTTTTATAAGTAATCTCTTTTCGAACAGAGCTAGGTATTCCTTTTTTCATTTCTAAGTTAAGGGAGAACGCTACAATATTCCCTTGAGGCTGAACAACCCATCCAGTTAACCAGCCTACTTGTGGGTCTACATCCCATCCCCAACCACTTTTTGCGTATATTTTATTTCCATTCTTTTCTTCTATGAATAGCATGGATTGCACTTCATCTTGGACTTTTTGGCTAAATGGAAGCGTTTTATTAGCTAGCTTGTAAGCAAATTGTGCCTCTTGCTGAGGAGTAATTTTTAAAGGGCCCACCAGCCAAAAATTATCGACTTGGGTACCGATATCTGCATTGCCATAACCAACACGCTTCACTTCCTTAGACATGAGTTCAAGTCCAATACGACGAGCTAAATCTTGATAAACCGGAATAGCGGAAGCTTTCATAGCGTCGCCTAGGGTCATGTCCTTTTCCCATTCTGGGAATAGCCTTTTTTGCCCGTCCCACTTAAATACTTCTGTGGCGGTTGCCTTATGGTGCTCAAGGCTGATCAAAGCATTAAGCATTTTGAAGGTCGAAGCAGGTACATACTCGGTCGAAGCACGAGCAAGATCATTACCATAGCTTTGTTGAGTTTGGCCTTGTTGGATAACTAAGACACCCGTAGTGTGTGCTTCGTTAAATAAATTTTTAATTTTCTCTGCTTTTTCATCAGATTTTGAAGCGCTGTGATTTGGATTAGCAGTCACTATATAAGGTGAGCAGGCTGAAATAAAAATAGCGCTTGTTATAAGTAAGAGGGCTTTAATGTTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001571","ARO_id":"37971","ARO_name":"OXA-385","ARO_description":"OXA-385 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"605":{"model_id":"605","model_name":"OXA-96","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1617":{"protein_sequence":{"accession":"ABF47919.1","sequence":"MKLLKILSLVCLSISIGACAEHSMSRAKTSTIPQVNNSIIDQNVQALFNEISADAVFVTYDGQNIKKYGTHLDRAKTAYIPASTFKIANALIGLENHKATSTEIFKWDGKPRFFKAWDKDFTLGEAMQASTVPVYQELARRIGPSLMQSELQRIGYGNMQMGTEVDQFWLKGPLTITPIQEVKFVYDLAQGQLPFKPEVQQQVKEMLYVERRGENRLYAKSGWGMAVDPQVGWYVGFVEKADGQVVAFALNMQMKAGDDIALRKQLSLDVLDKLGVFHYL"},"dna_sequence":{"accession":"DQ519090","fmin":"62","fmax":"905","strand":"+","sequence":"ATGAAATTATTAAAAATATTGAGTTTAGTTTGCTTAAGCATAAGTATTGGGGCTTGTGCTGAGCATAGTATGAGTCGAGCAAAAACAAGTACAATTCCACAAGTGAATAACTCAATCATCGATCAGAATGTTCAAGCGCTTTTTAATGAAATCTCAGCTGATGCTGTGTTTGTCACATATGATGGTCAAAATATTAAAAAATATGGCACGCATTTAGACCGAGCAAAAACAGCTTATATTCCTGCATCTACATTTAAAATTGCCAATGCACTAATTGGTTTAGAAAATCATAAAGCAACATCTACAGAAATATTTAAGTGGGATGGAAAGCCACGTTTTTTTAAAGCATGGGACAAAGATTTTACTTTGGGCGAAGCCATGCAAGCATCTACAGTGCCTGTATATCAAGAATTGGCACGTCGTATTGGTCCAAGCTTAATGCAAAGTGAATTGCAACGTATTGGTTATGGCAATATGCAAATGGGCACGGAAGTTGATCAATTTTGGTTGAAAGGGCCTTTGACAATTACACCTATACAAGAAGTAAAGTTTGTGTATGATTTAGCCCAAGGGCAATTGCCTTTTAAACCTGAAGTTCAGCAACAAGTGAAAGAGATGTTGTATGTAGAGCGCAGAGGGGAGAATCGTCTATATGCTAAAAGTGGCTGGGGAATGGCTGTAGACCCGCAAGTGGGTTGGTATGTGGGTTTTGTTGAAAAGGCAGATGGGCAAGTGGTGGCATTTGCTTTAAATATGCAAATGAAAGCTGGTGATGATATTGCTCTACGTAAACAATTGTCTTTAGATGTGCTAGATAAGTTGGGTGTTTTTCATTATTTATAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001631","ARO_id":"38031","ARO_name":"OXA-96","ARO_description":"OXA-96 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"606":{"model_id":"606","model_name":"IMI-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1277":{"protein_sequence":{"accession":"ABA00479.1","sequence":"MSLNVKPSRIAILFSSCLVSISFFSQANTKGIDEIKNLETDFNGRIGVYALDTGSGKSFSYKANERFPLCSSFKGFLAAAVLKGSQDNQLNLNQIVNYNTRSLEFYSPITTKYKDNGMSLGDMAAAALQYSDNGATNIILERYIGGPEGMTKFMRSIGDKDFRLDRWELDLNTAIPGDERDTSTPAAVAKSLKTLALGNILNEREKETYQTWLKGNTTGAARIRASVPSDWVVGDKTGSCGAYGTANDYAVVWPKNRAPLIISVYTTKNEKEAKHEDKVIAEASRIAIDNLK"},"dna_sequence":{"accession":"DQ173429","fmin":"0","fmax":"879","strand":"+","sequence":"ATGTCACTTAATGTAAAACCAAGTAGAATAGCCATCTTGTTTAGCTCTTGTTTAGTTTCAATATCATTTTTCTCACAGGCCAATACAAAGGGAATCGATGAGATTAAAAACCTTGAAACAGATTTCAATGGTAGAATTGGTGTCTACGCTTTAGACACTGGCTCAGGTAAATCATTTTCGTACAAAGCAAATGAACGATTTCCATTATGTAGTTCTTTCAAAGGTTTTTTAGCTGCTGCTGTATTAAAAGGCTCTCAAGATAATCAACTAAATCTTAATCAGATCGTGAATTATAATACAAGAAGTTTAGAGTTCTATTCACCCATCACAACTAAATATAAAGATAATGGAATGTCATTAGGTGATATGGCTGCTGCCGCTTTACAATATAGCGACAATGGTGCTACTAATATTATTCTTGAACGATATATCGGTGGTCCTGAGGGTATGACTAAATTCATGCGGTCGATTGGAGATAAAGATTTTAGACTCGATCGTTGGGAGTTAGATCTAAACACAGCAATTCCTGGCGATGAACGTGACACATCTACACCTGCAGCAGTAGCTAAGAGCCTGAAAACCCTTGCTCTGGGTAACATACTTAATGAGCGTGAAAAGGAAACCTATCAGACATGGTTAAAGGGTAACACAACCGGTGCAGCGCGTATTCGTGCTAGCGTACCAAGCGATTGGGTAGTTGGCGATAAAACTGGTAGTTGCGGAGCATACGGTACGGCAAATGATTATGCGGTAGTCTGGCCAAAGAACCGAGCTCCTCTTATAATTTCTGTATACACTACAAAAAACGAAAAAGAAGCCAAGCATGAGGATAAAGTAATCGCAGAAGCTTCAAGAATCGCAATTGATAACCTTAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36926","NCBI_taxonomy_name":"Enterobacter asburiae","NCBI_taxonomy_id":"61645"}}}},"ARO_accession":"3001859","ARO_id":"38259","ARO_name":"IMI-2","ARO_description":"IMI-2 is a beta-lactamase found in Enterobacteriaceae","ARO_category":{"36027":{"category_aro_accession":"3000018","category_aro_cvterm_id":"36027","category_aro_name":"IMI beta-lactamase","category_aro_description":"IMI beta-lactamases are a group of TEM-1-like beta-lactamase that are known to hydrolyze imipenem. IMI beta-lactamases are inhibited by clavulanic acid and tazobactam.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"607":{"model_id":"607","model_name":"TEM-201","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1884":{"protein_sequence":{"accession":"AFS44742.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETVVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGGQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"JX310327","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGGTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGGGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001378","ARO_id":"37778","ARO_name":"TEM-201","ARO_description":"TEM-201 is a beta-lactamase found in Enterobacteriaceae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"608":{"model_id":"608","model_name":"OXA-361","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2010":{"protein_sequence":{"accession":"AHA11124.1","sequence":"MKILILLPLFSCLGLTACSLPVSSSPSQITSIQSTQAIAQLFDQAQSAGVLVIQRGQQIQVYGNDLSRANTEYVPASTFKMLNALIGLQHGKATTNEIFKWDGKKRSFSAWEKDMTLGQAMQASAVPVYQELARRIGLELMQQEVQCIQFGNQQIGQQVDNFWLVGPLKVTPKQEVQFVSALAREQLAFDPQVQQQVKVMLLLQEQQAYRLYAKSGWGMDVEPQVGWLTGWVKTPQAEIVAFSLNMQMRNGMDPAIRLEILQQALAELGLYPKAEG"},"dna_sequence":{"accession":"KF460531","fmin":"0","fmax":"831","strand":"+","sequence":"ATGAAAATTCTGATTTTGCTGCCTTTATTTAGTTGCTTGGGACTGACGGCGTGTAGTCTGCCCGTTTCATCCTCCCCCTCTCAGATCACTTCAATTCAATCGACTCAAGCCATTGCCCAATTATTTGATCAGGCGCAAAGCGCTGGCGTTTTAGTGATTCAGCGTGGTCAACAGATACAGGTTTATGGTAATGATTTAAGTCGTGCAAATACCGAATATGTTCCAGCCTCTACTTTCAAAATGCTCAATGCCCTGATTGGTCTACAACATGGTAAAGCCACAACCAATGAAATTTTTAAATGGGATGGCAAGAAACGCAGTTTTTCAGCTTGGGAAAAAGACATGACTCTCGGCCAAGCCATGCAAGCGTCTGCTGTACCCGTTTATCAGGAACTGGCACGTCGTATTGGCCTTGAACTGATGCAACAGGAAGTACAATGCATCCAATTTGGTAATCAGCAGATTGGTCAACAGGTCGATAACTTCTGGCTGGTAGGCCCTTTGAAAGTTACTCCAAAACAGGAAGTCCAATTTGTTTCTGCGTTGGCCCGAGAGCAACTGGCCTTTGATCCTCAAGTCCAGCAGCAAGTCAAAGTCATGTTACTGCTACAGGAGCAGCAAGCTTATCGACTATATGCCAAATCTGGTTGGGGCATGGATGTGGAACCGCAAGTCGGCTGGCTCACCGGCTGGGTTAAAACACCGCAAGCCGAGATCGTGGCATTTTCACTGAATATGCAGATGCGAAATGGTATGGATCCGGCGATCCGCCTTGAAATTTTGCAGCAGGCTTTGGCCGAATTAGGGCTTTATCCAAAAGCAGAAGGATGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36948","NCBI_taxonomy_name":"Acinetobacter lwoffii","NCBI_taxonomy_id":"28090"}}}},"ARO_accession":"3001548","ARO_id":"37948","ARO_name":"OXA-361","ARO_description":"OXA-361 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"609":{"model_id":"609","model_name":"emrK","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"173":{"protein_sequence":{"accession":"BAA11236.1","sequence":"MELEDMISTDDAYVTGNADPISAQVSGSVTVVNHKDTNYVRQGDILVSLDKTDATIALNKAKNNLANIVRQTNKLYLQDKQYSAEVASARIQYQQSLEDYNRRVPLAKQGVISKETLEHTKDTLISSKAALNAAIQAYKANKALVMNTPLNRQPQVVEAADATKEAWLALKRTDIKSPVTGYIAQRSVQVGETVSPGQSLMAVVPARQMWVNANFKETQLTDVRIGQSVNIISDLYGENVVFHGRVTGINMGTGNAFSLLPAQNATGNWIKIVQRVPVEVSLDPKELMEHPLRIGLSMTATIDTKNEDIAEMPELASTVTSMPAYTSKALVIDTSPIEKEISNIISHNGQL"},"dna_sequence":{"accession":"D78168","fmin":"536","fmax":"1592","strand":"+","sequence":"ATGGAATTAGAAGACATGATTAGTACAGATGACGCCTATGTCACGGGGAATGCAGATCCAATTTCTGCACAAGTCTCAGGTAGTGTCACTGTCGTTAATCATAAAGATACGAACTACGTTCGACAAGGTGACATTTTAGTTTCACTGGATAAAACTGATGCCACTATCGCACTCAATAAAGCTAAAAATAATCTGGCAAATATTGTTCGGCAAACGAATAAACTATACTTACAGGATAAACAATACAGTGCCGAAGTCGCTTCAGCACGTATTCAGTATCAACAATCTTTAGAAGATTATAACCGTCGAGTGCCGTTAGCGAAGCAGGGGGTTATTTCAAAAGAAACGCTGGAGCATACCAAAGATACGTTAATAAGTAGCAAAGCGGCATTGAATGCCGCTATCCAGGCTTATAAAGCGAATAAAGCTTTAGTAATGAACACACCATTAAACCGTCAGCCACAAGTCGTTGAAGCGGCGGATGCAACTAAAGAAGCCTGGTTGGCGCTTAAACGTACGGATATTAAGAGTCCGGTTACCGGCTATATTGCCCAGAGAAGTGTTCAGGTCGGCGAAACAGTGAGCCCCGGACAATCGTTAATGGCTGTCGTACCGGCACGTCAAATGTGGGTTAATGCCAACTTTAAAGAAACACAACTCACGGATGTACGGATTGGTCAATCGGTCAATATTATCAGCGATCTTTATGGTGAAAATGTTGTGTTTCATGGTCGGGTGACAGGGATCAATATGGGAACCGGCAATGCGTTCTCCTTATTACCTGCACAAAATGCGACAGGGAACTGGATCAAAATCGTTCAGCGTGTACCGGTTGAAGTTTCTCTTGATCCAAAAGAACTCATGGAACACCCCTTGCGTATTGGTTTATCGATGACAGCAACTATTGATACGAAGAACGAAGACATTGCCGAGATGCCTGAGCTGGCTTCAACCGTGACCTCCATGCCGGCTTATACCAGTAAGGCTTTAGTTATCGATACCAGTCCGATAGAAAAAGAAATTAGCAACATTATTTCGCATAATGGACAACTTTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000206","ARO_id":"36345","ARO_name":"emrK","ARO_description":"emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC, it mediates multidrug efflux.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"610":{"model_id":"610","model_name":"SHV-153","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1312":{"protein_sequence":{"accession":"AFQ23959.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASERGARGIVALLGPNNKAERIVVIYLRDTPASMVERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"JX121120","fmin":"0","fmax":"858","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGTCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001192","ARO_id":"37572","ARO_name":"SHV-153","ARO_description":"SHV-153 is a beta-lactamase.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"611":{"model_id":"611","model_name":"OXA-328","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1132":{"protein_sequence":{"accession":"AGW16410.1","sequence":"MYKKALIVATSLLFLSACSSNTVTQHQIHSISANKNSEEIKSLFDQAQTTGVLVIKRGKTEEIYGNDLKRASTAYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPDWEKDMTLGNAMKASAIPVYQELAQRIGLDLMSKEVKRIGFGNANIGSKVDNFWLVGPLKITPQQETQFAYQLAHKTLPFSKNVQEQVQSMVFIEEKNGSKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"KF203102","fmin":"0","fmax":"822","strand":"+","sequence":"ATGTATAAAAAAGCCCTTATCGTTGCAACAAGCCTCCTATTTTTATCCGCCTGTTCTTCCAATACAGTAACACAACATCAAATACACTCTATCTCTGCCAATAAAAATTCAGAAGAAATTAAATCACTGTTTGATCAAGCACAGACCACGGGAGTCTTGGTAATTAAGCGAGGGAAAACAGAAGAAATTTATGGCAATGATCTTAAAAGAGCATCAACCGCCTATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTAATTGGACTTGAACATCATAAGGCAACTACAACTGAAGTATTTAAATGGGATGGGCAAAAACGTTTATTTCCTGATTGGGAAAAGGACATGACACTGGGTAATGCCATGAAAGCTTCTGCAATTCCAGTTTACCAAGAATTAGCCCAACGAATTGGACTTGACCTTATGTCTAAAGAGGTAAAAAGAATTGGTTTCGGTAATGCTAACATTGGTTCAAAAGTAGATAATTTTTGGCTTGTTGGCCCTCTAAAAATTACGCCTCAACAAGAAACCCAATTTGCTTATCAATTAGCCCATAAAACGCTTCCATTTAGCAAAAATGTACAAGAACAAGTTCAATCAATGGTGTTCATAGAGGAAAAAAATGGAAGTAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTTGAACCACAAGTTGGTTGGTTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTCGCATTCTCACTTAATTTAGAAATGAAAAAAGGAACTCCTAGCTCTATTCGCAAAGAAATTGCTTATAAAGGCTTAGAACAACTGGGTATCTTATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3001516","ARO_id":"37916","ARO_name":"OXA-328","ARO_description":"OXA-328 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"612":{"model_id":"612","model_name":"PDC-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"1849":{"protein_sequence":{"accession":"ACQ82812.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"FJ666070","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGACGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTATGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002506","ARO_id":"38906","ARO_name":"PDC-7","ARO_description":"PDC-7 is a extended-spectrum beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"613":{"model_id":"613","model_name":"VEB-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1498":{"protein_sequence":{"accession":"ABM54868.1","sequence":"MKIVKRILLVLLSLFFTIVYSNAQADNLTLKIENVLKAKNARIGVAIFNSNEKDTLKINNDFHFPMQSVMKFPIALAVLSEIDKGNLSFEQKIEITPQDLLPKMWSPIKEEFPNGTTLTIEQILNYTVSESDNIGCDILLKLIGGTDSVQKFLNANHFTDISIKANEEQMHKDWNTQYQNWATPTAMNKLLIDTYNNKNQLLSKKSYDFIWKIMRETTTGSNRLKGQLPKNTIVAHKTGTSGINNGIAAATNDVGVITLPNGQLIFISVFVAESKETSEINEKIISDIAKITWNYYLNK"},"dna_sequence":{"accession":"EF136375","fmin":"0","fmax":"900","strand":"+","sequence":"ATGAAAATCGTAAAAAGGATATTATTAGTATTGTTAAGTTTATTTTTTACAATTGTGTATTCAAATGCTCAAGCTGACAACTTAACTTTGAAAATTGAGAATGTTTTAAAGGCAAAAAATGCCAGAATAGGAGTAGCAATATTCAACAGCAATGAGAAGGATACTTTGAAGATTAATAACGACTTCCATTTCCCGATGCAAAGCGTTATGAAATTTCCGATTGCTTTAGCCGTTTTGTCTGAGATAGATAAAGGGAATCTTTCTTTTGAACAAAAAATAGAGATTACCCCTCAAGACCTTTTGCCTAAAATGTGGAGTCCGATTAAAGAGGAATTCCCTAATGGAACAACTTTGACGATTGAACAAATACTAAATTATACAGTATCAGAGAGCGACAATATTGGTTGTGATATTTTGCTAAAATTAATCGGAGGAACTGATTCTGTTCAAAAATTCTTGAATGCTAATCATTTCACTGATATTTCAATCAAAGCAAACGAAGAACAAATGCACAAGGATTGGAATACCCAATATCAAAATTGGGCAACCCCAACAGCGATGAACAAACTGTTAATAGATACTTATAATAATAAGAACCAATTACTTTCTAAAAAAAGTTATGATTTTATTTGGAAAATTATGAGAGAAACAACAACAGGAAGTAACCGATTAAAAGGACAATTACCAAAGAATACAATTGTTGCTCATAAAACAGGGACTTCCGGAATAAATAATGGAATTGCAGCAGCCACTAATGATGTTGGGGTAATTACTTTACCGAATGGACAATTAATTTTTATAAGCGTATTTGTTGCAGAGTCCAAAGAAACTTCGGAAATTAATGAAAAGATTATTTCAGACATTGCAAAAATAACGTGGAATTACTATTTGAATAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3002373","ARO_id":"38773","ARO_name":"VEB-4","ARO_description":"VEB-4 is a beta-lactamase found in Proteus mirabilis","ARO_category":{"36182":{"category_aro_accession":"3000043","category_aro_cvterm_id":"36182","category_aro_name":"VEB beta-lactamase","category_aro_description":"VEB beta-lactamases or Vietnamese extended-spectrum beta-lactamases are class A beta-lactamases that confer high-level resistance to oxyimino cephalosporins and to aztreonam","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"614":{"model_id":"614","model_name":"SFB-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"3311":{"protein_sequence":{"accession":"AAT90847.1","sequence":"MISAPSFAHENEQQTDQSNTDAVKKPQQQPTELFLSPLVPDVYLHQSYKQVSGFGLVESNGLVVVQNKQAFIIDTPWTDSDTAKLVDWITQQGLTVTASISTHSHQDRAGGIGYLNSQGIATWVSDKTQRLLTANKLSTASHTFRTKQHTLQQQLIEVYDLGAGHTVDNLLVWLPKQQILFGGCLIKSLSSRTLGYTGEADLEQWPLTVAKVQAQFIQAKIVVPGHGKIGDTSLLSHTIDLLTQ"},"dna_sequence":{"accession":"AY590119","fmin":"0","fmax":"735","strand":"+","sequence":"ATGATAAGTGCACCTTCATTTGCCCATGAAAACGAACAACAAACAGATCAAAGCAACACCGATGCAGTAAAAAAGCCACAGCAGCAACCCACTGAACTCTTCCTATCGCCTCTCGTGCCAGATGTGTATTTACACCAGTCATATAAACAGGTCAGCGGCTTTGGATTAGTTGAGTCTAATGGCTTAGTGGTGGTGCAAAACAAGCAGGCGTTTATTATTGATACTCCCTGGACAGATAGCGATACCGCCAAGCTTGTGGATTGGATTACCCAGCAAGGTTTAACCGTTACAGCCAGTATATCGACTCATTCACATCAAGACCGCGCAGGTGGAATTGGCTACCTTAACAGCCAAGGCATCGCCACTTGGGTGTCAGATAAAACCCAACGCCTATTAACCGCCAACAAACTCAGCACTGCAAGCCACACATTTAGAACTAAGCAACACACACTTCAGCAGCAACTCATTGAAGTGTATGATCTGGGCGCTGGCCACACGGTCGATAACCTGTTGGTGTGGCTGCCTAAGCAACAGATTTTATTCGGCGGCTGTTTAATAAAATCACTGAGTTCACGCACTCTTGGTTATACCGGTGAAGCAGACCTAGAGCAATGGCCGCTGACGGTGGCAAAAGTACAAGCACAATTTATTCAGGCAAAAATAGTCGTACCTGGGCATGGCAAAATAGGTGATACTTCACTGCTAAGCCATACCATAGACTTGTTAACACAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40162","NCBI_taxonomy_name":"Shewanella frigidimarina","NCBI_taxonomy_id":"56812"}}}},"ARO_accession":"3003557","ARO_id":"40160","ARO_name":"SFB-1","ARO_description":"This enzyme breaks the beta-lactam antibiotic ring open and deactivates the molecule's antibacterial properties.","ARO_category":{"40158":{"category_aro_accession":"3003555","category_aro_cvterm_id":"40158","category_aro_name":"SHW beta-lactamase","category_aro_description":"This family of sublcass B1 beta-lactamases were discovered in species of the Shewanella genus.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"615":{"model_id":"615","model_name":"OXA-211","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"970":{"protein_sequence":{"accession":"AEV91550.1","sequence":"MKTLQLALIALITTFGSACTTIPPSVETAKNHQQQSAQQQIQQAFDQLQTTGVIVIKDKHGLHSYGNDLSRAQTPYVPASTFKMLNALIGLEHGKATSTEVFKWDGQKRSFPAWEKDMTLGQAMQASAVPVYQELARRIGLDLMKKEVQRIGYGNQQIGTVVDNFWLVGPLQITPVQEVLFVEKLANTQLAFKPDVQHTVQDMLLIEQKPNYKLYAKSGWGMDLEPQVGWWTGWVETATSEKVYFALNMHMKTGISASVREQLVKQSLTALGII"},"dna_sequence":{"accession":"JN861779","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAAAACTTTACAGTTGGCTCTCATCGCCCTCATTACAACCTTCGGTTCCGCATGTACCACAATACCCCCCTCCGTAGAAACAGCTAAAAATCACCAGCAACAAAGTGCTCAGCAGCAGATCCAACAGGCCTTCGATCAACTCCAAACCACGGGGGTGATTGTCATTAAGGATAAGCATGGCTTACACAGCTACGGCAATGACTTGAGCCGTGCTCAGACACCCTATGTACCCGCCTCTACCTTTAAAATGCTGAATGCCTTAATCGGACTAGAACATGGTAAAGCAACCAGCACCGAGGTATTTAAATGGGATGGTCAAAAGCGCAGCTTCCCTGCTTGGGAAAAAGACATGACTTTAGGGCAAGCCATGCAAGCATCTGCCGTTCCCGTTTATCAGGAGCTAGCACGGCGCATTGGCCTAGACCTGATGAAAAAAGAAGTGCAACGCATTGGATATGGCAATCAACAGATTGGCACCGTTGTCGATAATTTTTGGTTAGTCGGTCCACTGCAAATTACGCCTGTTCAAGAAGTCCTTTTTGTAGAGAAGCTGGCCAATACACAACTCGCTTTTAAGCCAGATGTGCAACATACCGTACAAGACATGCTGCTGATTGAACAAAAACCGAATTATAAACTCTACGCCAAATCTGGTTGGGGCATGGACCTAGAACCGCAAGTGGGCTGGTGGACAGGCTGGGTCGAAACAGCAACAAGTGAAAAAGTGTATTTTGCTTTGAATATGCATATGAAAACGGGAATTTCAGCCAGCGTACGTGAGCAACTGGTCAAACAAAGTCTGACAGCACTGGGGATAATTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39092","NCBI_taxonomy_name":"Acinetobacter johnsonii","NCBI_taxonomy_id":"40214"}}}},"ARO_accession":"3001710","ARO_id":"38110","ARO_name":"OXA-211","ARO_description":"OXA-211 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"616":{"model_id":"616","model_name":"NDM-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1270":{"protein_sequence":{"accession":"BAM84089.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMGALHAAGIATYANALSNQLAPQEGLVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"AB744718","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGGCGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGCTGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002358","ARO_id":"38758","ARO_name":"NDM-8","ARO_description":"NDM-8 is a beta-lactamase found in Escherichia coli","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"617":{"model_id":"617","model_name":"OXA-147","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1602":{"protein_sequence":{"accession":"ACO72579.1","sequence":"MKTFAAYVITACLSSTALASSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNNLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLSLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFLLEGQLRISAVNQVEFLESLFLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKGTEVYFFAFNMDIDNENKLPLRKSIPTKIMASEGIIGG"},"dna_sequence":{"accession":"FJ848783","fmin":"1270","fmax":"2071","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTACTGCGTGTCTTTCAAGTACGGCATTAGCTAGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTTTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATAACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAACAATGGGAAAGAGACTTGAGCTTAAGAGGGGCAATACAAGTTTCAGCGGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCATATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCTTGTTGGAGGGTCAGCTAAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATTTTTAAATAAATTGTCAGCATCAAAAGAAAATCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCTGCGCCTGAATATCTTGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGTTGGGTTGAGAAGGGAACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAATAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGCAAGTGAGGGCATCATTGGTGGCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001801","ARO_id":"38201","ARO_name":"OXA-147","ARO_description":"OXA-147 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"618":{"model_id":"618","model_name":"emeA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"720"}},"model_sequences":{"sequence":{"3290":{"protein_sequence":{"accession":"BAC11911.1","sequence":"MTKKNSMMYLAISNLFLVFLGVGLVIPVIPQLKEEMHFSGTTMGMMISIFAIAQLITSPIAGVLSDKIGRKKMIATGMLVFSISELLFGLAQAKSGFYISRGLGGIAAALLMPSVTAFVADMTTISERPKAMGLVSAAISGGFIIGPGVGGFIIGPGVGGFIAYLGIRAPFFAAAFLAFIGFILTLTVLKEPEKRILAAVEAKKGSFMDILRNPMFTSLFVIILISSFGLQAFESIYSIMATINFGFTTSEIAIVITVSGILALICQLFFFDAIVQKIGEMGLIQLTFFASAIFIAVIAFTKNNLVVVFSTFIVFLAFDLFRPAVTTYLSKHAGDQQGTINGLNSTFTSFGNILGPMAAGALFDINHFFPYYVSAVILLGTGFLSLFLNRNKM"},"dna_sequence":{"accession":"AB091338","fmin":"173","fmax":"1355","strand":"+","sequence":"ATGACGAAAAAAAATAGTATGATGTACTTAGCAATTTCTAACTTATTTCTTGTTTTTCTAGGCGTAGGCCTAGTCATTCCCGTAATTCCCCAATTAAAAGAAGAAATGCATTTTTCTGGTACCACAATGGGAATGATGATTTCTATTTTTGCGATTGCCCAATTAATCACATCGCCAATCGCAGGTGTCCTTTCGGATAAAATTGGTCGGAAAAAAATGATTGCGACGGGCATGTTGGTGTTTTCAATTTCTGAGTTATTATTTGGTTTAGCCCAAGCGAAAAGCGGTTTTTATATTTCTCGTGGTTTAGGTGGGATTGCCGCCGCGTTATTAATGCCGTCAGTGACAGCCTTTGTGGCAGATATGACCACGATTTCTGAACGTCCGAAAGCGATGGGGCTTGTGTCAGCTGCAATTAGTGGTGGTTTTATTATCGGACCAGGAGTTGGTGGTTTTATTATCGGACCAGGAGTTGGTGGTTTTATTGCTTATTTAGGAATTCGCGCTCCATTTTTTGCGGCCGCATTTTTAGCGTTTATTGGTTTTATTTTGACATTAACTGTTTTGAAGGAGCCAGAGAAACGAATTTTAGCCGCTGTTGAAGCGAAAAAAGGTTCATTTATGGATATTTTAAGAAATCCAATGTTTACCTCATTATTTGTGATTATCTTAATTTCCTCTTTTGGCCTGCAAGCGTTCGAATCTATTTATAGTATTATGGCGACCATTAATTTTGGCTTTACCACAAGTGAAATAGCAATCGTGATTACGGTTAGTGGTATTTTAGCGTTGATTTGTCAGCTGTTTTTCTTTGATGCAATCGTCCAAAAAATAGGTGAAATGGGTTTAATCCAATTAACCTTTTTTGCAAGTGCCATTTTTATTGCCGTGATTGCCTTTACAAAAAATAATTTAGTTGTTGTATTTTCAACGTTTATTGTCTTTTTAGCGTTTGACTTGTTTAGACCAGCAGTAACTACTTATTTATCCAAACATGCTGGAGATCAACAAGGAACCATCAACGGACTAAATTCGACATTTACAAGTTTTGGTAATATTTTAGGACCAATGGCAGCAGGAGCTTTATTTGATATCAATCACTTTTTCCCTTATTATGTTTCAGCAGTAATTCTGTTAGGAACGGGCTTTTTATCGTTATTTTTAAATCGAAATAAGATGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40154","NCBI_taxonomy_name":"Enterococcus faecalis ATCC 29212","NCBI_taxonomy_id":"1201292"}}}},"ARO_accession":"3003551","ARO_id":"40153","ARO_name":"emeA","ARO_description":"A multidrug efflux pump from Enterococcus faecalis. There exist efflux activity of several antimicrobial agents such as DAPI, Hoechst 33342 and acriflavine. Efflux of DAPI via EmeA was strongly inhibited by reserpine.","ARO_category":{"36251":{"category_aro_accession":"3000112","category_aro_cvterm_id":"36251","category_aro_name":"multidrug and toxic compound extrusion (MATE) transporter","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Multidrug and toxic compound extrusion (MATE) transporters utilize the cationic gradient across the membrane as an energy source. Although there is a diverse substrate specificity, almost all MATE transporters recognize fluoroquinolones. Arciflavine, ethidium and aminoglycosides are also good substrates.","category_aro_class_name":"AMR Gene Family"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavin","category_aro_description":"Acriflavin is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"36193":{"category_aro_accession":"3000054","category_aro_cvterm_id":"36193","category_aro_name":"acridine dye","category_aro_description":"Acridine dyes are cell permeable, basic molecules with an acridine chromophore. These compounds intercalate DNA. The image shown represents the core structure of the acridine family, with specific dyes containing varying substituents.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"619":{"model_id":"619","model_name":"SHV-30","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"918":{"protein_sequence":{"accession":"AAT75225.1","sequence":"MRYFRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGSVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AY661885","fmin":"48","fmax":"909","strand":"+","sequence":"ATGCGTTATTTTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCAGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGGATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001088","ARO_id":"37468","ARO_name":"SHV-30","ARO_description":"SHV-30 is an extended-spectrum beta-lactamase found in Enterobacter cloacae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"620":{"model_id":"620","model_name":"OXA-320","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1840":{"protein_sequence":{"accession":"AGR55864.1","sequence":"MKNTIHINFAIFLIIANIIYSSASASTDISTVASPLFEGTEGCFLLYDASTNAEIAQFNKAKCATQMAPDSTFKIALSLMAFDAEIIDQKTIFKWDKTPKGMEIWNSNHTPKTWMQFSVVWVSQEITQKIGLNKIKNYLKDFDYGNQDFSGDKERNNGLTEAWLESSLKISPEEQIQFLRKIINHNLPVKNSAIENTIENMYLQDLDNSTKLYGKTGAGFTANRTLQNGWFEGFIISKSGHKYVFVSALTGNLGSNLTSSIKAKKIAITILNTLNL"},"dna_sequence":{"accession":"KF151169","fmin":"0","fmax":"831","strand":"+","sequence":"ATGAAAAACACAATACATATCAACTTCGCTATTTTTTTAATAATTGCAAATATTATCTACAGCAGCGCCAGTGCATCAACAGATATCTCTACTGTTGCATCTCCATTATTTGAAGGAACTGAAGGTTGTTTTTTACTTTACGATGCATCCACAAACGCTGAAATTGCTCAATTCAATAAAGCAAAGTGTGCAACGCAAATGGCACCAGATTCAACTTTCAAGATCGCATTATCACTTATGGCATTTGATGCGGAAATAATAGATCAGAAAACCATATTCAAATGGGATAAAACCCCCAAAGGAATGGAGATCTGGAACAGCAATCATACACCAAAGACGTGGATGCAATTTTCTGTTGTTTGGGTTTCGCAAGAAATAACCCAAAAAATTGGATTAAATAAAATCAAGAATTATCTCAAAGATTTTGATTATGGAAATCAAGACTTCTCTGGAGATAAAGAAAGAAACAACGGATTAACAGAAGCATGGCTCGAAAGTAGCTTAAAAATTTCACCAGAAGAACAAATTCAATTCCTGCGTAAAATTATTAATCACAATCTCCCAGTTAAAAACTCAGCCATAGAAAACACCATAGAGAACATGTATCTACAAGATCTGGATAATAGTACAAAACTGTATGGGAAAACTGGTGCAGGATTCACAGCAAATAGAACCTTACAAAACGGATGGTTTGAAGGGTTTATTATAAGCAAATCAGGACATAAATATGTTTTTGTGTCCGCACTTACAGGAAACTTGGGGTCGAATTTAACATCAAGCATAAAAGCCAAGAAAATTGCGATCACCATTCTAAACACACTAAATTTATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3001793","ARO_id":"38193","ARO_name":"OXA-320","ARO_description":"OXA-320 is a beta-lactamase found in Proteus mirabilis","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"621":{"model_id":"621","model_name":"ErmF","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"593":{"protein_sequence":{"accession":"AAA88675.1","sequence":"MTKKKLPVRFTGQHFTIDKVLIKDAIRQANISNQDTVLDIGAGKGFLTVHLLKIANNVVAIENDTALVEHLRKLFSDARNVQVVGCDFRNFAVPKFPFKVVSNIPYGITSDIFKILMFESLGNFLGGSIVLQLEPTQKLFSRKLYNPYTVFYHTFFDLKLVYEVGPESFLPPPTVKSALLNIKRKHLFFDFKFKAKYLAFISYLLEKPDLSVKTALKSIFRKSQVRSISEKFGLNLNAQIVCLSPSQWLNCFLEMLEVVPEKFHPS"},"dna_sequence":{"accession":"M17124","fmin":"1181","fmax":"1982","strand":"+","sequence":"ATGACAAAAAAGAAATTGCCCGTTCGTTTTACGGGTCAGCACTTTACTATTGATAAAGTGCTAATAAAAGATGCAATAAGACAAGCAAATATAAGTAATCAGGATACGGTTTTAGATATTGGGGCAGGCAAGGGGTTTCTTACTGTTCATTTATTAAAAATCGCCAACAATGTTGTTGCTATTGAAAACGACACAGCTTTGGTTGAACATTTACGAAAATTATTTTCTGATGCCCGAAATGTTCAAGTTGTCGGTTGTGATTTTAGGAATTTTGCAGTTCCGAAATTTCCTTTCAAAGTGGTGTCAAATATTCCTTATGGCATTACTTCCGATATTTTCAAAATCCTGATGTTTGAGAGTCTTGGAAATTTTCTGGGAGGTTCCATTGTCCTTCAATTAGAACCTACACAAAAGTTATTTTCGAGGAAGCTTTACAATCCATATACCGTTTTCTATCATACTTTTTTTGATTTGAAACTTGTCTATGAGGTAGGTCCTGAAAGTTTCTTGCCACCGCCAACTGTCAAATCAGCCCTGTTAAACATTAAAAGAAAACACTTATTTTTTGATTTTAAGTTTAAAGCCAAATACTTAGCATTTATTTCCTATCTGTTAGAGAAACCTGATTTATCTGTAAAAACAGCTTTAAAGTCGATTTTCAGGAAAAGTCAGGTCAGGTCAATTTCGGAAAAATTCGGTTTAAACCTTAATGCTCAAATTGTTTGTTTGTCTCCAAGTCAATGGTTAAACTGTTTTTTGGAAATGCTGGAAGTTGTCCCTGAAAAATTTCATCCTTCGTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35916","NCBI_taxonomy_name":"Bacteroides fragilis","NCBI_taxonomy_id":"817"}}}},"ARO_accession":"3000498","ARO_id":"36637","ARO_name":"ErmF","ARO_description":"ErmF confers the MLSb phenotype.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35946":{"category_aro_accession":"0000027","category_aro_cvterm_id":"35946","category_aro_name":"roxithromycin","category_aro_description":"Roxithromycin is a semi-synthetic, 14-carbon ring macrolide antibiotic derived from erythromycin. It is used to treat respiratory tract, urinary and soft tissue infections. Roxithromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35974":{"category_aro_accession":"0000057","category_aro_cvterm_id":"35974","category_aro_name":"telithromycin","category_aro_description":"Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36315":{"category_aro_accession":"3000176","category_aro_cvterm_id":"36315","category_aro_name":"dirithromycin","category_aro_description":"Dirithromycin is an oxazine derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome to inhibit bacterial protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin 1A is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"vernamycin B-gamma","category_aro_description":"Vernamycin B-gamma is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"622":{"model_id":"622","model_name":"DHA-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1865":{"protein_sequence":{"accession":"ADQ00385.1","sequence":"MKKSLSATLISALLAFSAPGFSAADNVAAVVDSTIKPLMAQQDIPGMAVAVSVKGKPYYFNYGFADIQAKQPVTENTLFELGSVSKTFTGVLGAVSVAKKEMALNDPAAKYQPELALPQWKGITLLDLATYTAGGLPLQVPDAVKSRADLLNFYQQWQPSRKPGDMRLYANSSIGLFGALTANAAGMPYEQLLTARILAPLGLSHTFITVPESAQSQYAYGYKNKKPVRVSPGQLDAESYGVKSASKDMLRWAEMNMEPSRAGNADLEMAMYLAQTRYYKTAAINQGLGWEMYDWPQQKDMIINGVTNEVALQPHPVTDNQVQPYNRASWVHKTGATTGSGAYVAFIPEKQVAIVILANKNYPNTERVKAAQAILSALE"},"dna_sequence":{"accession":"HQ456945","fmin":"0","fmax":"1140","strand":"+","sequence":"ATGAAAAAATCGTTATCTGCAACACTGATTTCCGCTCTGCTGGCGTTTTCCGCCCCGGGGTTTTCTGCCGCTGATAATGTCGCGGCGGTGGTGGACAGCACCATTAAACCGCTGATGGCACAGCAGGATATTCCCGGGATGGCGGTTGCCGTCTCCGTAAAGGGTAAGCCCTATTATTTCAATTATGGTTTTGCCGATATTCAGGCAAAACAGCCGGTCACTGAAAATACACTATTTGAGCTCGGATCTGTAAGTAAAACTTTCACAGGTGTGCTGGGTGCGGTTTCTGTGGCGAAAAAAGAGATGGCGCTGAATGATCCGGCGGCAAAATACCAGCCGGAGCTGGCTCTGCCGCAGTGGAAGGGGATCACATTGCTGGATCTGGCTACCTATACCGCAGGCGGACTGCCGTTACAGGTGCCGGATGCGGTAAAAAGCCGTGCGGATCTGCTGAATTTCTATCAGCAGTGGCAGCCGTCCCGGAAACCGGGCGATATGCGTCTGTATGCAAACAGCAGTATCGGCCTGTTTGGTGCTCTGACCGCAAACGCGGCGGGGATGCCGTATGAGCAGTTGCTGACTGCACGGATCCTGGCACCGCTGGGGTTATCTCACACCTTTATTACTGTGCCGGAAAGTGCGCAAAGCCAGTATGCGTACGGTTATAAAAACAAAAAACCGGTCCGCGTGTCGCCGGGACAGCTTGATGCGGAATCTTACGGCGTGAAATCCGCCTCAAAAGATATGCTGCGCTGGGCGGAAATGAATATGGAGCCGTCACGGGCCGGTAATGCGGATCTGGAAATGGCAATGTATCTCGCCCAGACCCGCTACTATAAAACCGCCGCGATTAACCAGGGGCTGGGCTGGGAAATGTATGACTGGCCGCAGCAGAAAGATATGATCATTAACGGTGTGACCAACGAGGTCGCATTGCAGCCGCATCCGGTAACAGACAACCAGGTTCAGCCGTATAACCGTGCTTCCTGGGTGCATAAAACGGGCGCAACAACTGGTTCCGGCGCCTATGTCGCCTTTATTCCGGAAAAACAGGTGGCGATTGTGATTCTGGCGAATAAAAACTACCCGAATACCGAAAGAGTCAAAGCTGCACAGGCTATTTTGAGTGCACTGGAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3002136","ARO_id":"38536","ARO_name":"DHA-7","ARO_description":"DHA-7 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36207":{"category_aro_accession":"3000068","category_aro_cvterm_id":"36207","category_aro_name":"DHA beta-lactamase","category_aro_description":"DHA beta-lactamases are plasmid-mediated AmpC \u03b2-lactamases that confer resistance to cephamycins and oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"623":{"model_id":"623","model_name":"OXA-68","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2014":{"protein_sequence":{"accession":"AAW81339.1","sequence":"MNIKALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQEVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"AY750910","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTAGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAGAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001616","ARO_id":"38016","ARO_name":"OXA-68","ARO_description":"OXA-68 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"625":{"model_id":"625","model_name":"QnrB46","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"89":{"protein_sequence":{"accession":"ADW54092.1","sequence":"MTPLLYKKTGTNMALALVGEKIDRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNASALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKAVLEKCELWENRWMGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRRVDLQGVKLDNYQASLLMERLGIAIIG"},"dna_sequence":{"accession":"HQ704413","fmin":"0","fmax":"681","strand":"+","sequence":"ATGACGCCATTACTGTATAAGAAAACAGGAACAAATATGGCTCTAGCGCTCGTGGGCGAAAAAATTGACAGAAACCGTTTCACCGGTGAAAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGAGCGGACCTGAGCGGCACTGAGTTTATCGGCTGCCAATTTTATGATCGTGAAAGCCAGAAAGGCTGTAATTTTAGCCGTGCGATGTTAAAGGATGCTATTTTTAAAAGCTGCGATTTATCCATGGCCGATTTTCGCAATGCAAGCGCCCTGGGTATTGAGATTCGTCATTGTAGGGCTCAGGGTGCAGATTTTCGCGGCGCAAGCTTTATGAACATGATTACCACGCGAACTTGGTTCTGCAGCGCGTATATCACGAATACGAATCTGTCTTATGCCAATTTTTCGAAAGCAGTGTTGGAGAAGTGTGAATTATGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCAACTTTCGACTGGCGAGCAGCAAACTTTACACATTGCGATCTCACAAATTCGGAGTTGGGTGACTTAGATATTCGTCGGGTTGATTTACAAGGCGTTAAGTTGGACAACTACCAGGCTTCGTTGCTCATGGAGCGACTTGGCATCGCGATAATTGGATGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002761","ARO_id":"39195","ARO_name":"QnrB46","ARO_description":"QnrB46 is a plasmid-mediated quinolone resistance protein found in Escherichia coli","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"626":{"model_id":"626","model_name":"vanHB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"3452":{"protein_sequence":{"accession":"AAB05626.1","sequence":"MRKSMGITVFGCEQDEANAFRTLSPDFHIIPTLISDAISADNAKLAAGNQCISVGHKSEVSEATILALRKVGVKYISTRSIGCNHIDTTAAERMGISVGTVAYSPDSVADYALMLMLMAIRGAKSTIHAVAQQNFRLDCVRGKELRDMTVGVIGTGHIGQAVVKRLRGFGCRVLAYDNSRKIEADYVQLDELLKNSDIVTLHVPLCADTRHLIGQSEIGEMKQGAFLINTGRGALVDTGSLVEALGSGKLGGAALDVLEGEDQFVYTDCSQKVLDHPFLSQLLRMPNVIITPHTAYYTERVLRDTTEKTIRNCLNFERSLQHE"},"dna_sequence":{"accession":"U35369","fmin":"4006","fmax":"4978","strand":"+","sequence":"ATGAGAAAAAGTATGGGCATTACTGTTTTTGGATGCGAGCAGGATGAGGCAAATGCTTTCCGCACCTTATCACCAGATTTTCATATTATCCCTACGCTGATCAGTGATGCGATATCGGCAGACAACGCAAAATTGGCCGCTGGCAATCAATGCATTAGCGTAGGCCATAAGTCCGAGGTTTCCGAGGCGACAATTCTTGCGCTGAGAAAGGTCGGGGTAAAATACATTTCTACCCGCAGCATCGGCTGCAATCACATTGATACGACTGCCGCCGAGAGAATGGGGATCTCGGTTGGCACAGTTGCGTATTCGCCGGACAGCGTTGCGGATTATGCTTTGATGCTGATGCTGATGGCCATACGGGGTGCAAAGTCCACCATACACGCCGTGGCGCAACAAAATTTCAGACTGGATTGTGTCCGGGGGAAAGAGCTGCGGGATATGACTGTGGGAGTTATTGGAACCGGCCATATAGGGCAAGCGGTCGTCAAAAGGCTGCGGGGATTTGGATGCCGTGTGCTAGCCTATGATAACAGCCGAAAAATTGAGGCAGATTATGTCCAGCTTGATGAGCTTCTAAAAAACAGCGATATTGTTACGCTCCATGTGCCGCTTTGTGCGGATACCCGCCATCTGATCGGCCAGAGCGAAATCGGAGAGATGAAGCAAGGCGCATTTTTAATCAACACTGGGCGCGGGGCGCTTGTCGATACCGGGTCGCTGGTGGAGGCACTGGGAAGCGGAAAGCTGGGCGGTGCGGCACTGGATGTGTTGGAGGGCGAGGATCAGTTTGTTTATACCGACTGCTCGCAGAAAGTGCTTGACCATCCCTTTTTGTCGCAGCTCCTAAGGATGCCAAATGTGATCATCACACCCCATACGGCGTACTACACCGAGCGTGTGCTGCGAGATACCACAGAAAAAACAATCAGGAATTGTCTTAACTTTGAAAGGAGTTTACAGCATGAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3002943","ARO_id":"39377","ARO_name":"vanHB","ARO_description":"vanHB is a vanH variant in the vanB gene cluster","ARO_category":{"36015":{"category_aro_accession":"3000006","category_aro_cvterm_id":"36015","category_aro_name":"vanH","category_aro_description":"VanH is a D-specific alpha-ketoacid dehydrogenase that synthesizes D-lactate. D-lactate is incorporated into the end of the peptidoglycan subunits, decreasing vancomycin binding affinity.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"628":{"model_id":"628","model_name":"catB10","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"70":{"protein_sequence":{"accession":"CAI47810.1","sequence":"MTNYFESPFKGKLLADQVKNPNIKVGRYSYYSGYYHGHSFDECARFLLPDRDDIDQLIVGSFCSIGTGASFIMAGNQGHRYDWASSFPFFYMKEEPAFSGALDAFQKAGDTVIGSDVWIGSEAMIMPGINVGHGAVIGSRALVTKDVEPYTIVGGNPAKPIKKRFSDEEIAMLLKMNWWDWPTEKIEEAMPLLCSSNIVGLHRYWQGFAV"},"dna_sequence":{"accession":"AJ878850","fmin":"1196","fmax":"1829","strand":"+","sequence":"ATGACCAACTATTTTGAAAGTCCATTTAAAGGCAAACTGCTGGCCGACCAGGTAAAGAACCCGAACATCAAAGTCGGACGGTATAGCTATTATTCCGGCTATTACCATGGCCATTCGTTTGACGAGTGCGCTCGCTTTCTCTTGCCAGATCGCGATGACATCGACCAACTGATCGTTGGTAGCTTCTGTTCCATCGGCACGGGCGCCTCCTTCATCATGGCCGGAAATCAGGGGCACCGTTATGACTGGGCGTCTTCTTTTCCCTTCTTCTACATGAAAGAGGAGCCAGCATTCTCGGGCGCACTTGATGCATTCCAAAAAGCCGGTGACACAGTCATCGGAAGTGATGTCTGGATAGGCTCTGAGGCCATGATCATGCCCGGCATCAACGTCGGTCATGGCGCTGTGATTGGAAGCCGCGCTTTGGTCACGAAAGATGTGGAGCCGTACACTATCGTTGGCGGAAATCCCGCCAAACCGATCAAGAAACGCTTCTCCGACGAGGAGATCGCCATGCTTTTGAAAATGAATTGGTGGGATTGGCCAACTGAAAAAATTGAGGAAGCAATGCCTTTGCTATGCTCATCCAACATCGTTGGGCTGCATCGATACTGGCAAGGCTTTGCCGTCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3003110","ARO_id":"39686","ARO_name":"catB10","ARO_description":"catB10 is an integron-encoded variant of the cat gene found in P. aeruginosa","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. cat is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Bacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini","category_aro_class_name":"AMR Gene Family"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"629":{"model_id":"629","model_name":"VIM-28","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"854":{"protein_sequence":{"accession":"AEI25539.1","sequence":"MLKVISSLLVYMTASVMAVASPLAHSGEPSGEYPTVNEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEAEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSANVLYGGCAVLELSRTSAGNVADADLAEWPTSVERIQKHYPEAEVVIPGHGLPGGLDLLQHTANVVKAHKNRSVAE"},"dna_sequence":{"accession":"JF900599","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTACATGACCGCGTCTGTCATGGCTGTCGCAAGTCCGTTAGCCCATTCCGGGGAGCCGAGTGGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGAGAGGTCCGACTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCGGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAAAAGCAAATTGGACTTCCCGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGCAGAGGGGAACGAGATTCCCACGCATTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGCTCTTCTATCCTGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAACGTGCTATACGGTGGTTGTGCCGTTCTTGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCGTTGAGCGGATTCAAAAACACTACCCGGAAGCAGAGGTCGTCATTCCCGGGCACGGTCTACCGGGCGGTCTAGACTTGCTCCAGCACACAGCGAACGTTGTCAAAGCACACAAAAATCGCTCAGTCGCCGAGTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002298","ARO_id":"38698","ARO_name":"VIM-28","ARO_description":"VIM-28 is a beta-lactamase. From the Lahey list of VIM beta-lactamases.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"630":{"model_id":"630","model_name":"adeJ","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"2100"}},"model_sequences":{"sequence":{"1":{"protein_sequence":{"accession":"AAX14802.1","sequence":"MAQFFIHRPIFAWVIALVIMLAGILTLTKMPIAQYPTIAPPTVTIAATYPGASAETVENTVTQIIEQQMNGLDGLRYISSNSAGNGQASIQLNFEQGVDPDIAQVQVQNKLQSATALLPEDVQRQGVTVTKSGASFLQVIAFYSPDNNLSDSDIKDYVNSSIKEPLSRVAGVGEVQVFGGSYAMRIWLDPAKLTSYQLTPSDIATALQAQNSQVAVGQLGGAPAVQGQVLNATVNAQSLLQTPEQFKNIFLKNTASGAEVRLKDVARVELGSDNYQFDSKFNGKPAAGLAIKIATGANALDTAEAVEQRLSELRKNYPTGLADKLAYDTTPFIRLSIESVVHTLIEAVILVFIVMFLFLQNWRATIIPTLAVPVVVLGTFAVINIFGFSINTLTMFAMVLAIGLLVDDAIVVVENVERVMSEDHTDPVTATSRSMQQISGALVGITSVLTAVFVPMAFFGGTTGVIYRQFSITLVTAMVLSLIVALTFTPALCATILKQHDPNKEPSNNIFARFFRSFNNGFDRMSHSYQNGVSRMLKGKIFSGVLYAVVVALLVFLFQKLPSSFLPEEDQGVVMTLVQLPPNATLDRTGKVIDTMTNFFMNEKDTVESIFTVSGFSFTGVGQNAGIGFVKLKDWSKRTTPETQIGSLIQRGMALNMIIKDASYVMPLQLPAMPELGVTAGFNLQLKDSSGQGHEKLIAARNTILGLASQDKRLVGVRPNGQEDTPQYQINVDQAQAGAMGVSIAEINNTMRIAWGGSYINDFVDRGRVKKVYVQGDAGSRMMPEDLNKWYVRNNKGEMVPFSAFATGEWTYGSPRLERYNGVSSVNIQGTPAPGVSSGDAMKAMEEIIGKLPSMGLQGFDYEWTGLSLEERESGAQAPFLYALSLLIVFLCLAALYESWSIPFSVLLVVPLGVIGAIVLTYLGMIIKGDPNLSNNIYFQVAIIAVIGLSAKNAILIVEFAKELQEKGEDLLDATLHAAKMRLRPIIMTTLAFGFGVLPLALSTGAGAGSQHSVGFGVLGGVLSATFLGIFFIPVFYVWIRSMFKYKPKTINTQEHKS"},"dna_sequence":{"accession":"AY769962","fmin":"2434","fmax":"5611","strand":"+","sequence":"ATGGCACAATTTTTTATTCATCGCCCCATATTTGCGTGGGTGATTGCATTAGTCATTATGTTGGCGGGTATTCTTACGCTAACAAAAATGCCTATTGCACAATATCCAACGATTGCACCACCAACCGTAACGATTGCTGCGACTTATCCTGGTGCATCGGCTGAAACAGTTGAAAATACTGTAACCCAGATCATTGAACAACAAATGAATGGTCTTGATGGCTTACGTTATATTTCATCTAACAGTGCTGGTAATGGTCAGGCATCTATTCAATTAAACTTTGAACAAGGTGTTGACCCTGATATTGCACAGGTTCAAGTTCAAAACAAATTGCAATCTGCAACTGCGCTTTTACCTGAAGATGTACAACGTCAAGGTGTAACAGTTACTAAATCTGGTGCGAGCTTCTTGCAAGTTATTGCATTCTATTCACCAGATAACAACCTGTCAGACTCTGACATTAAAGACTACGTAAACTCGTCAATTAAAGAACCGCTTAGCCGTGTTGCCGGTGTTGGTGAGGTACAGGTCTTCGGTGGCTCATACGCAATGCGTATCTGGCTTGATCCAGCTAAATTAACAAGCTATCAACTTACTCCTAGTGATATTGCAACTGCCTTACAAGCGCAGAACTCGCAAGTTGCCGTAGGTCAGTTAGGTGGTGCTCCGGCTGTACAAGGTCAAGTTCTTAACGCAACAGTAAATGCACAAAGCTTATTGCAGACTCCTGAACAGTTTAAAAATATCTTCTTAAAGAACACAGCATCAGGTGCTGAGGTTCGATTAAAAGATGTTGCTCGCGTAGAATTAGGTTCGGATAACTATCAATTCGACTCGAAGTTTAACGGTAAACCGGCAGCTGGTCTTGCAATTAAAATTGCAACAGGTGCTAACGCACTCGACACAGCCGAAGCAGTTGAACAACGTTTATCTGAACTACGTAAGAACTATCCAACAGGTCTTGCAGATAAACTGGCTTATGACACGACTCCATTTATCCGTCTTTCAATTGAAAGTGTAGTACACACATTAATTGAAGCCGTGATTTTGGTATTCATTGTCATGTTCCTATTCTTACAAAACTGGCGTGCAACGATTATTCCAACGCTTGCAGTTCCAGTAGTTGTATTAGGTACATTTGCGGTCATTAATATCTTTGGCTTCTCAATTAACACCTTAACCATGTTCGCTATGGTATTGGCAATCGGTCTTCTGGTCGACGACGCCATTGTTGTAGTCGAAAACGTTGAACGTGTGATGAGTGAAGACCATACCGATCCGGTTACGGCCACTTCTCGCTCAATGCAGCAGATTTCTGGTGCGTTAGTAGGTATTACCAGCGTATTGACAGCGGTATTCGTACCAATGGCTTTCTTTGGTGGTACAACAGGTGTAATTTACCGCCAGTTCTCGATTACCCTTGTAACTGCAATGGTTCTGTCGTTAATTGTAGCGTTGACGTTCACACCGGCACTTTGTGCAACTATCTTGAAACAGCATGATCCTAATAAAGAACCAAGCAATAATATCTTTGCGCGTTTCTTTAGAAGCTTTAACAATGGTTTTGACCGCATGTCGCATAGCTACCAAAATGGTGTTAGCCGCATGCTTAAAGGCAAAATCTTCTCTGGCGTGCTCTATGCTGTTGTAGTTGCCCTTTTAGTCTTCTTGTTCCAAAAACTCCCGTCTTCATTCTTACCAGAAGAAGATCAGGGTGTGGTCATGACACTTGTACAATTACCACCAAATGCAACGCTTGACCGTACCGGTAAAGTGATTGATACCATGACTAACTTCTTTATGAATGAAAAAGATACCGTGGAATCTATTTTCACTGTTTCTGGTTTCTCATTCACAGGTGTTGGTCAAAACGCGGGTATTGGCTTCGTTAAGTTGAAAGACTGGAGCAAACGTACGACACCAGAAACTCAAATTGGTTCATTGATTCAGCGTGGTATGGCATTAAATATGATCATTAAAGATGCATCATACGTTATGCCGTTACAGCTTCCAGCAATGCCTGAACTTGGTGTAACTGCCGGATTTAACTTGCAGCTTAAAGATTCAAGTGGTCAAGGCCATGAGAAACTGATTGCAGCTCGTAACACGATTTTAGGTTTGGCATCACAAGATAAACGTCTTGTAGGTGTGCGTCCAAATGGTCAGGAAGATACTCCTCAGTATCAAATTAATGTAGATCAGGCTCAAGCTGGTGCTATGGGCGTTAGTATTGCCGAAATCAACAATACAATGCGTATTGCATGGGGTGGCTCATACATTAACGATTTCGTTGACCGTGGTCGTGTGAAAAAAGTTTATGTTCAAGGTGATGCGGGCAGCCGTATGATGCCTGAAGACTTAAACAAATGGTATGTACGTAATAACAAAGGTGAGATGGTTCCATTCTCGGCATTTGCTACAGGCGAATGGACGTATGGTTCTCCACGTCTCGAACGTTATAACGGCGTGTCATCGGTTAACATTCAAGGTACACCTGCACCTGGCGTGAGCTCTGGTGATGCCATGAAAGCAATGGAAGAAATTATTGGTAAGTTACCATCTATGGGCTTACAAGGTTTCGACTATGAGTGGACAGGCTTATCACTTGAAGAACGTGAGTCTGGTGCTCAAGCGCCGTTCTTATACGCACTTTCATTGTTAATCGTATTCCTTTGCTTGGCTGCACTATATGAAAGCTGGTCAATTCCGTTCTCGGTTTTACTTGTGGTACCACTTGGTGTCATTGGTGCAATCGTATTGACCTACTTGGGCATGATTATTAAAGGAGATCCAAATCTCTCAAATAACATTTACTTCCAGGTAGCGATTATTGCGGTTATCGGTCTTTCTGCAAAAAATGCGATCTTGATTGTTGAATTCGCAAAAGAATTGCAGGAAAAAGGTGAAGATCTACTTGATGCAACCTTACATGCTGCAAAAATGCGTTTACGTCCAATTATCATGACCACCCTTGCCTTCGGTTTCGGTGTACTTCCACTTGCACTTTCAACAGGTGCCGGTGCAGGAAGTCAGCACTCTGTAGGCTTTGGTGTACTTGGTGGCGTACTCAGCGCGACGTTCTTAGGAATCTTCTTTATCCCTGTATTCTATGTGTGGATTCGTAGTATGTTTAAGTACAAACCAAAAACCATAAACACTCAGGAGCATAAATCGTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3000781","ARO_id":"37161","ARO_name":"adeJ","ARO_description":"AdeJ is a RND efflux protein that acts as the inner membrane transporter of the AdeIJK efflux complex. It has 57% identity with E. coli AcrB.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36309":{"category_aro_accession":"3000170","category_aro_cvterm_id":"36309","category_aro_name":"imipenem","category_aro_description":"Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"40523":{"category_aro_accession":"3003832","category_aro_cvterm_id":"40523","category_aro_name":"ticarcillin","category_aro_description":"Ticarcillin is a carboxypenicillin used for the treatment of Gram-negative bacteria, particularly P. aeruginosa. Ticarcillin's antibiotic properties arise from its ability to prevent cross-linking of peptidoglycan during cell wall synthesis, when the bacteria try to divide, causing cell death.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"631":{"model_id":"631","model_name":"TEM-21","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1077":{"protein_sequence":{"accession":"CAA76794.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLRNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"Y17582","fmin":"0","fmax":"858","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCGCAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000892","ARO_id":"37272","ARO_name":"TEM-21","ARO_description":"TEM-21 is an extended-spectrum beta-lactamase found in many species of Gram-negative bacteria.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"633":{"model_id":"633","model_name":"OXA-355","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1460":{"protein_sequence":{"accession":"AGW83453.1","sequence":"MKFKMKGLFCVILSSLAFSGCVYDSKLQRPVISERETEIPLLFNQAQTQAVFVTYDGIHLKSYGNDLSRAKTEYIPASTFKMLNALIGLQNAKATNTEVFHWNGEKRAFSAWEKDMTLAEAMQASAVPVYQELARRIGLELMREEVKRVGFGNAEIGQQVDNFWLVGPLKISPEQEVQFAYQLAMKQLPFDRNVQQQVKDMLYIERRGDSKLYAKSGWGMDVEPQVGWYTGWVEQPNGKVTAFALNMNMQAGDDPAERKQLTLSILDKLGLFFYLR"},"dna_sequence":{"accession":"KF297584","fmin":"0","fmax":"831","strand":"+","sequence":"ATGAAGTTTAAAATGAAAGGTTTATTTTGTGTCATCCTCAGTAGTTTGGCATTTTCAGGTTGTGTTTATGATTCAAAACTACAACGCCCAGTCATATCAGAGCGAGAAACTGAGATTCCTTTATTATTTAATCAAGCACAGACTCAAGCTGTGTTTGTTACTTATGATGGGATTCATCTAAAAAGTTATGGTAATGATCTAAGCCGAGCAAAGACTGAATATATTCCTGCATCTACATTTAAGATGTTGAATGCTTTAATTGGCTTGCAAAATGCAAAAGCAACCAATACTGAAGTATTTCATTGGAATGGTGAAAAGCGCGCTTTTTCAGCATGGGAAAAAGATATGACTTTGGCAGAAGCGATGCAGGCTTCAGCTGTTCCCGTATATCAGGAGCTTGCTCGACGTATTGGCTTGGAATTGATGCGTGAAGAAGTGAAGCGTGTAGGTTTTGGTAATGCAGAGATTGGTCAGCAAGTCGATAATTTTTGGTTGGTGGGTCCTTTAAAAATCTCCCCTGAACAAGAAGTTCAATTTGCCTATCAACTGGCGATGAAGCAATTACCTTTTGATCGAAATGTACAGCAACAAGTCAAAGATATGCTTTATATCGAGAGACGTGGTGACAGTAAACTGTATGCTAAAAGTGGTTGGGGAATGGATGTTGAACCTCAAGTGGGTTGGTATACGGGATGGGTTGAACAACCCAATGGCAAGGTGACTGCATTTGCGTTAAATATGAACATGCAAGCAGGTGATGATCCAGCTGAACGTAAACAATTAACCTTAAGTATTTTGGACAAATTGGGTCTATTTTTTTATTTAAGATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39090","NCBI_taxonomy_name":"Acinetobacter bereziniae","NCBI_taxonomy_id":"106648"}}}},"ARO_accession":"3001542","ARO_id":"37942","ARO_name":"OXA-355","ARO_description":"OXA-355 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"634":{"model_id":"634","model_name":"smeF","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"890"}},"model_sequences":{"sequence":{"509":{"protein_sequence":{"accession":"CAC14596.1","sequence":"MEVIPMKSASLFLSIAATLALAGCSTLAPKNTAVAPAIPAQWPAEAAQGEVADVAAVGWRDFFTDARLQQVIEQSLQNNRDLRVAVLNVERARGQYRVQRADRVPGVAVTGQMDRRGTDAGVTEQFSAGVGVAEFELDLFGRVRNLSEAALQQYFAVAANRRNAQLSLVAETATAWLTYGADAQRLKIADATLKTYEDSLRLAEARHERGGSSALELTQTRTLVETARTDAARLRGQLAQDRNALALLAGGQLDPALLPDSIEPQLLALAPPPAGLPSDVLLQRPDIMAAEHQLLAANANIGAARAAFFPSISLTGSIGSGSSELSNLFDSGTRVWSFLPKITLPIFQGGKLRANLAIANADRDIALAQYEKSIQVGFRETADALALNVSLDEQVSSQQRLVEAAEQANRLSQARYDAGLDSFVTLLDARRTAYNAQQTQLQAQLAQQANRITLYKVLGGGWHERG"},"dna_sequence":{"accession":"AJ252200","fmin":"4493","fmax":"5894","strand":"+","sequence":"ATGGAAGTGATCCCCATGAAAAGTGCATCCCTGTTCCTCTCCATTGCCGCCACGCTCGCGCTGGCCGGCTGCTCCACCCTGGCGCCGAAGAACACCGCCGTCGCTCCGGCGATTCCTGCGCAGTGGCCGGCCGAGGCCGCGCAGGGCGAGGTGGCCGATGTCGCCGCCGTCGGCTGGCGCGATTTCTTCACCGATGCGCGCCTGCAGCAGGTGATCGAGCAGTCGCTGCAGAACAACCGCGACCTGCGCGTGGCCGTGCTCAATGTCGAGCGCGCGCGTGGCCAGTACCGCGTGCAGCGCGCCGATCGCGTGCCCGGCGTGGCCGTGACCGGCCAGATGGACCGCCGTGGTACCGATGCCGGTGTCACCGAGCAGTTCAGCGCGGGCGTGGGTGTGGCCGAGTTCGAGCTGGACCTGTTCGGTCGCGTGCGCAACCTCAGCGAGGCGGCGCTGCAGCAGTACTTCGCCGTGGCTGCCAACCGCCGCAACGCGCAGCTGAGCCTGGTGGCCGAGACCGCCACCGCGTGGCTGACCTATGGGGCTGATGCGCAGCGGCTGAAGATCGCCGATGCCACGCTGAAGACCTACGAGGATTCGCTGCGCTTGGCCGAGGCCCGCCACGAACGCGGCGGCAGTTCGGCGCTGGAGCTGACCCAGACCCGTACCTTGGTCGAGACCGCACGCACCGATGCCGCGCGCCTGCGCGGCCAGCTGGCCCAGGACCGCAACGCACTGGCGCTGCTGGCCGGTGGCCAGCTCGATCCGGCACTGCTGCCGGACAGCATCGAACCGCAGCTGCTGGCGCTGGCCCCGCCGCCGGCCGGCCTGCCCAGCGACGTGCTGCTGCAGCGCCCGGACATCATGGCCGCCGAACACCAGCTGCTGGCCGCCAATGCCAACATCGGTGCGGCACGCGCAGCGTTCTTCCCGAGCATCTCGCTGACCGGCAGCATCGGCAGCGGCTCCAGCGAACTGTCCAACCTGTTCGACAGCGGCACCCGTGTGTGGAGCTTCCTGCCGAAGATCACCCTGCCGATCTTCCAGGGCGGCAAGCTGCGCGCCAACCTGGCCATCGCCAACGCGGATCGTGATATCGCACTGGCGCAGTACGAGAAGTCGATCCAGGTGGGATTCCGCGAAACGGCCGATGCGCTGGCGTTGAATGTCAGCCTGGATGAGCAGGTGAGTTCACAGCAGCGCCTGGTGGAAGCGGCCGAACAGGCCAATCGCCTGTCGCAGGCACGCTACGACGCGGGGCTGGACAGCTTTGTCACCCTGCTTGACGCGCGGCGTACCGCCTACAACGCGCAGCAGACCCAGCTGCAGGCGCAGTTGGCGCAGCAGGCCAACCGCATCACCCTGTACAAGGTGCTGGGCGGCGGCTGGCACGAGCGCGGGTAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37076","NCBI_taxonomy_name":"Stenotrophomonas maltophilia","NCBI_taxonomy_id":"40324"}}}},"ARO_accession":"3003057","ARO_id":"39491","ARO_name":"smeF","ARO_description":"smeF is an outer membrane multidrug efflux protein of the smeDEF complex in Stenotrophomonas maltophilia","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"635":{"model_id":"635","model_name":"OXA-332","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1532":{"protein_sequence":{"accession":"AGW16414.1","sequence":"MYKKALIVATSILFLSACSSNTVKQHQIHSISANKNSEEIKSLFDQAQTTGVLVIKRGQTEEIYGNDLKRASTAYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNANIGSKVDNFWLVGPLKITPQQETQFAYQLAHKTLPFSKDVQEQVQSMVFIEEKNGSKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"KF203106","fmin":"0","fmax":"822","strand":"+","sequence":"ATGTATAAAAAAGCCCTTATCGTTGCAACAAGTATTCTATTTTTATCCGCCTGTTCTTCCAATACGGTAAAACAACATCAAATACACTCTATTTCTGCCAATAAAAATTCAGAAGAAATTAAATCACTATTTGATCAGGCACAAACCACGGGTGTTTTGGTGATTAAGCGAGGACAAACAGAAGAAATTTATGGCAATGATCTTAAAAGAGCATCAACCGCCTATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTAATTGGACTTGAACATCATAAGGCAACTACAACTGAAGTATTTAAATGGGATGGGCAAAAACGTTTATTTCCTGATTGGGAAAAGGACATGACACTGGGTGATGCCATGAAAGCTTCTGCGATTCCAGTTTACCAAGAATTAGCCCGACGAATTGGCCTTGACCTTATGTCCAAAGAGGTGAAAAGAATTGGTTTCGGTAATGCTAACATTGGTTCAAAAGTAGATAATTTTTGGCTCGTTGGCCCTCTAAAAATTACACCTCAACAAGAAACCCAATTTGCTTATCAATTAGCCCATAAAACGCTTCCATTTAGCAAAGATGTACAAGAACAAGTTCAATCAATGGTGTTCATAGAGGAAAAAAATGGAAGTAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTTGAACCACAAGTTGGTTGGCTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTGGCATTCTCACTTAATTTAGAAATGAAAAAAGGAACTCCTAGCTCTATTCGCAAAGAAATTGCTTATAAAGGCTTAGAACAACTGGGTATCTTATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3001520","ARO_id":"37920","ARO_name":"OXA-332","ARO_description":"OXA-332 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"636":{"model_id":"636","model_name":"CFE-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"902":{"protein_sequence":{"accession":"BAC76072.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYQGKPYYFTWGKADIANNRPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTQYWPELTGKQWQGISLLHLATYTAGGLPLQVPDDVTDKAALLRFYQNWQPQWAPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTTRVLQPLKLAHTWITVPQSEQKDYALGYREGKPVHVSPGQLDAEAYGVKSSVVDMTRWVQANMDASQVQEKTLQQGIKLAQSRYWRIGDMYQGLGWEMLNWPVKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"AB107899","fmin":"1007","fmax":"2153","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCGCTGCTGCTGACAGCCTCTTTTTCCACCTTTGCCGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCGCTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCGATTATCTACCAGGGAAAACCTTATTACTTTACCTGGGGTAAAGCTGATATCGCCAATAACCGTCCAGTCACTCAGCAAACGCTGTTTGAACTCGGCTCGGTCAGTAAAACGTTCAACGGCGTGCTGGGCGGCGATGCTATCGCTCGCGGCGAAATCAAGCTCAGCGATCCGGTCACGCAATACTGGCCTGAGCTGACGGGTAAGCAGTGGCAGGGTATCAGCCTGCTGCACTTAGCGACCTACACGGCAGGCGGCCTGCCGCTTCAGGTTCCCGACGACGTCACGGATAAAGCCGCCTTACTGCGTTTTTATCAAAACTGGCAGCCACAATGGGCACCGGGCGCTAAACGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCACTGGCGGTGAAACCTTCAGGCATGAGCTACGAAGAGGCGATGACCACCCGCGTCCTGCAGCCCTTAAAACTGGCGCATACATGGATTACGGTTCCACAGAGCGAACAAAAAGATTATGCATTGGGCTATCGCGAAGGAAAGCCTGTGCATGTATCCCCTGGCCAACTTGATGCCGAAGCCTATGGGGTAAAATCAAGCGTTGTCGATATGACCCGCTGGGTCCAGGCCAACATGGATGCCAGCCAGGTTCAGGAGAAAACGCTCCAGCAGGGAATCAAGCTTGCGCAGTCACGTTACTGGCGTATTGGCGATATGTACCAGGGTCTGGGCTGGGAGATGCTGAACTGGCCGGTGAAAGCCGACTCAATAATTAACGGTAGCGACAGCAAAGTGGCGCTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCGCCTGCTGTGAAAGCATCATGGGTGCATAAAACGGGCTCCACTGGCGGATTCGGCAGCTACGTTGCTTTCGTTCCAGAAAAAAACCTTGGCATTGTGATGCTGGCAAACAAGAGCTATCCAAACCCTGCTCGCGTCGAGGCCGCCTGGCGCATTCTTGAAAAACTGCAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001856","ARO_id":"38256","ARO_name":"CFE-1","ARO_description":"CFE-1 is a beta-lactamase found in Escherichia coli","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"637":{"model_id":"637","model_name":"OXY-6-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"983":{"protein_sequence":{"accession":"CAI43423.1","sequence":"MLKSSWRKSALMAAAVPLLLASGSLWASADAIQQKLADLEKRSGGRLGVALINTADDSQTLYRGDERFAMCSTGKVMAAAAVLKQSESHPDVVNKRLEIKKSDLVVWSPITEKHLQSGMTLAELSAAALQYSDNTAMNKMISYLGGPEKVTAFAQSIGDVTFRLDRTEPALNSAIPGDKRDTTTPLAMAESLRKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPASWAVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKSRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"AJ871875","fmin":"0","fmax":"873","strand":"+","sequence":"ATGTTGAAAAGTTCGTGGCGTAAAAGCGCCCTGATGGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGTTCATTATGGGCCAGTGCCGATGCTATCCAGCAAAAGCTGGCTGATTTAGAAAAACGGTCCGGTGGCCGGCTGGGCGTGGCGCTGATTAACACGGCGGATGATTCGCAAACCCTTTATCGCGGCGACGAACGTTTTGCCATGTGCAGCACCGGTAAAGTGATGGCCGCCGCCGCGGTGTTAAAGCAGAGCGAAAGCCATCCCGATGTGGTGAATAAAAGGCTGGAGATTAAAAAATCGGATTTAGTGGTCTGGAGCCCGATTACCGAAAAACATCTGCAAAGCGGAATGACCCTGGCGGAACTCAGCGCGGCGGCGCTGCAGTACAGCGACAATACCGCGATGAATAAGATGATTAGCTACCTTGGCGGACCGGAAAAGGTGACCGCATTCGCCCAGAGCATCGGGGACGTTACTTTTCGTCTCGATCGTACGGAGCCGGCGCTGAACAGCGCGATACCCGGCGATAAGCGCGATACCACCACCCCGTTGGCGATGGCCGAAAGCCTGCGCAAGCTGACGCTGGGCAATGCGCTGGGCGAACAGCAGCGCGCCCAGTTAGTGACGTGGCTAAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCAGGCCTGCCCGCAAGCTGGGCGGTCGGGGATAAAACCGGCGCCGGAGATTACGGCACCACCAACGATATCGCGGTGATCTGGCCGGAAAATCATGCCCCGCTGGTGTTAGTGACCTATTTTACCCAGCCGCAGCAGGATGCGAAAAGCCGCAAAGAGGTGTTAGCCGCGGCGGCGAAAATCGTGACCGAAGGGCTGTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002414","ARO_id":"38814","ARO_name":"OXY-6-2","ARO_description":"OXY-6-2 is a beta-lactamase found in Klebsiella oxytoca","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"638":{"model_id":"638","model_name":"ACT-16","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1341":{"protein_sequence":{"accession":"BAM34463.1","sequence":"MMKKSLCCALLLGLSCSALAAPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKSHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPEKVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYHILEAL"},"dna_sequence":{"accession":"AB737978","fmin":"0","fmax":"1140","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTGGGCCTCTCTTGCTCTGCTCTCGCCGCGCCAGTATCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAATCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAAGGTTGCCGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAAGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTACCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGTTCTACCGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001827","ARO_id":"38227","ARO_name":"ACT-16","ARO_description":"ACT-16 is a beta-lactamase found in Enterobacteriaceae","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"641":{"model_id":"641","model_name":"CARB-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1736":{"protein_sequence":{"accession":"AAD19217.1","sequence":"MKFLLAFSLLIPSVVFASSSKFQQVEQDVKAIEVSLSARIGVSVLDTQNGEYWDYNGNQRFPLTSTFKTIACAKLLYDAEQGKVNPNSTVEIKKADLVTYSPVIEKQVGQAITLDDACFATMTTSDNTAANIILSAVGGPKGVTDFLRQIGDKETRLDRIEPDLNEGKLGDLRDTTTPKAIASTLNQLLFGSTLSEASQKKLESWMVNNQVTGNLLRSVLPVKWSIADRSGAGGFGARSITAIVWSEEKKTIIVSIYLAQTEASMAERNDAIVKIGRSIFEVYTSQSR"},"dna_sequence":{"accession":"AF030945","fmin":"95","fmax":"962","strand":"+","sequence":"ATGAAGTTTTTATTGGCATTTTCGCTTTTAATACCATCCGTGGTTTTTGCAAGTAGTTCAAAGTTTCAGCAAGTTGAACAAGACGTTAAGGCAATTGAAGTTTCTCTTTCTGCTCGTATAGGTGTTTCCGTTCTTGATACTCAAAATGGAGAATATTGGGATTACAATGGCAATCAGCGCTTCCCGTTAACAAGTACTTTTAAAACAATAGCTTGCGCTAAATTACTATATGATGCTGAGCAAGGAAAAGTTAATCCCAATAGTACAGTCGAGATTAAGAAAGCAGATCTTGTGACCTATTCCCCTGTAATAGAAAAGCAAGTAGGGCAGGCAATCACACTCGATGATGCGTGCTTCGCAACTATGACTACAAGTGATAATACTGCGGCAAATATCATCCTAAGTGCTGTAGGTGGCCCCAAAGGCGTTACTGATTTTTTAAGACAAATTGGGGACAAAGAGACTCGTCTAGACCGTATTGAGCCTGATTTAAATGAAGGTAAGCTCGGTGATTTGAGGGATACGACAACTCCTAAGGCAATAGCCAGCACGTTAAATCAATTATTATTTGGTTCCACATTATCTGAAGCTAGTCAGAAAAAATTAGAGTCTTGGATGGTGAACAATCAAGTTACGGGTAATTTATTGAGGTCAGTATTGCCAGTGAAGTGGAGTATTGCTGATCGCTCAGGAGCAGGTGGATTTGGTGCTAGGAGTATTACAGCGATTGTGTGGAGTGAAGAAAAAAAAACGATTATCGTAAGTATTTATCTAGCTCAAACCGAGGCTTCAATGGCAGAACGAAATGATGCGATAGTTAAAATTGGTCGTTCAATTTTTGAAGTTTATACATCACAGTCGCGCTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36789","NCBI_taxonomy_name":"Vibrio cholerae","NCBI_taxonomy_id":"666"}}}},"ARO_accession":"3002245","ARO_id":"38645","ARO_name":"CARB-6","ARO_description":"CARB-6 is a beta-lactamase found in Vibrio cholerae","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"642":{"model_id":"642","model_name":"aadA25","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"3329":{"protein_sequence":{"accession":"AET15272.1","sequence":"MREAVTIEISNQLSEVLSVIERHLESTLLAVHLYGSAVDGGLKPYSDIDLLVTVAVKLDETTRRALLNDLMEASAFPGESETLRAIEVTLVVHDDIIPWRYPAKRELQFGEWQRNDILAGIFEPAMIDIDLAILLTKAREHSVALVGPAAEELFDPVPEQDLFEALNETLTLWNSPPDWAGDERNVVLTLSRIWYSAITGKIAPKDVAADWAIKRLPAQYQPVLLEARQAYLGQEEDRLASRADQLEEFVHYVKGEITKVVGK"},"dna_sequence":{"accession":"CP003022","fmin":"336788","fmax":"337580","strand":"+","sequence":"ATGAGGGAAGCGGTGACCATCGAAATTTCGAACCAACTATCAGAGGTGCTAAGCGTCATTGAGCGCCATCTGGAATCAACGTTGCTGGCCGTGCATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCATACAGCGATATTGATTTGTTGGTTACTGTGGCCGTAAAGCTTGATGAAACGACGCGGCGAGCATTGCTCAATGATCTTATGGAGGCTTCGGCTTTCCCTGGCGAGAGCGAGACGCTCCGCGCTATAGAAGTCACCCTTGTCGTGCATGACGACATCATCCCGTGGCGTTATCCGGCTAAGCGCGAGCTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCGGGTATCTTCGAGCCAGCCATGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCTGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAATAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATAAAACGCCTACCTGCCCAGTATCAGCCCGTCTTACTTGAAGCTAGACAGGCTTATCTTGGACAAGAAGAAGATCGCTTGGCCTCGCGCGCAGATCAGTTGGAAGAATTTGTTCACTACGTGAAAGGCGAGATCACCAAGGTAGTCGGCAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39783","NCBI_taxonomy_name":"Pasteurella multocida 36950","NCBI_taxonomy_id":"1075089"}}}},"ARO_accession":"3003197","ARO_id":"39780","ARO_name":"aadA25","ARO_description":"streptomycin\/spectinomycin resistance gene found in Pasteurella multocida isolated from bovine respiratory tract","ARO_category":{"41439":{"category_aro_accession":"3004275","category_aro_cvterm_id":"41439","category_aro_name":"ANT(3'')","category_aro_description":"Nucleotidylylation of streptomycin at the hydroxyl group at position 3''","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"643":{"model_id":"643","model_name":"OXY-2-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1467":{"protein_sequence":{"accession":"CAG34107.1","sequence":"MIKSSWRKIAMLAAAVPLLLASGALWASTDAIHQKLTDLEKRSGGRLGVALINTADNSQILYRGDERFAMCSTSKVMAAAAVLKQSESNKEVVNKRLEINAADLVVWSPITEKHLQSGMTLAELSAATLQYSDNTAMNLIIGYLGGPEKVTAFARSIGDATFRLDRTESTLNTAIPGDERDTSTPLAMAESLRKLTLGDALGEQQRAQLVTWLKGNTTGGQSIRAGLPESWVVGDKTGSGDYGTTNDIAVIWPEDHAPLVLVTYFTQPQQDAKNRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"AJ746227","fmin":"94","fmax":"967","strand":"+","sequence":"ATGATAAAAAGTTCGTGGCGTAAAATTGCAATGCTAGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGCGCACTGTGGGCCAGTACCGATGCTATCCATCAGAAGCTGACAGATCTCGAGAAGCGTTCAGGCGGCAGGTTGGGCGTGGCGCTAATCAACACGGCAGATAATTCTCAAATCTTATATCGCGGCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCCGCCGCCGCGGTATTAAAACAGAGCGAAAGCAATAAAGAGGTGGTAAATAAAAGGCTGGAGATTAACGCAGCCGATTTGGTGGTCTGGAGCCCGATTACCGAAAAACATCTCCAGAGCGGAATGACGCTGGCTGAGCTAAGCGCGGCGACGCTGCAATATAGCGACAATACGGCGATGAATCTGATCATCGGCTACCTTGGCGGGCCGGAAAAAGTCACCGCCTTCGCCCGCAGTATCGGCGATGCCACCTTTCGTCTCGATCGTACGGAGTCCACGCTGAATACCGCCATCCCGGGCGATGAGCGTGATACCAGCACGCCGCTGGCGATGGCTGAAAGCCTGCGCAAGCTGACGCTTGGCGATGCGCTGGGCGAACAGCAACGCGCCCAGTTAGTCACCTGGCTGAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCGGGCCTGCCTGAAAGCTGGGTGGTCGGCGATAAAACCGGCTCCGGAGATTACGGCACCACCAATGATATTGCGGTTATCTGGCCGGAAGATCACGCTCCGCTGGTATTAGTCACCTACTTTACCCAGCCGCAGCAGGATGCGAAAAACCGCAAAGAGGTGTTAGCCGCAGCGGCAAAAATCGTGACCGAAGGGCTTTAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002400","ARO_id":"38800","ARO_name":"OXY-2-5","ARO_description":"OXY-2-5 is a beta-lactamase found in Klebsiella oxytoca","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"644":{"model_id":"644","model_name":"OXY-2-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1059":{"protein_sequence":{"accession":"CAI43414.1","sequence":"MIKSSWRKIAMLAAAVPLLLASGALWASTDAIHQKLTDLEKRSGGRLGVALINTADNSQILYRGDERFAMCSTSKVMAAAAVLKQSESNKEVVNKRLEINAADLVVWSPITEKHLQSGMTLAELSAATLQYSDNTAMNLIIGYLGGPEKVTAFAHSIGDATFRLDRTEPTLNTAIPGDERDTSTPLAMAESLRKLTLGDALGEQQRAQLVTWLKGNTTGGQSIRAGLPESWVVGDKTGAGDYGTTNDIAVIWPEDHAPLVLVTYFTQPQQDAKNRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"AJ871866","fmin":"0","fmax":"873","strand":"+","sequence":"ATGATAAAAAGTTCGTGGCGTAAAATTGCAATGCTAGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGCGCACTGTGGGCCAGTACCGATGCTATCCATCAGAAGCTGACAGATCTCGAGAAGCGTTCAGGCGGCAGGTTGGGCGTGGCGCTAATCAACACGGCAGATAATTCTCAAATCTTATATCGCGGCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCCGCCGCCGCGGTATTAAAACAGAGCGAAAGCAATAAAGAGGTGGTAAATAAAAGGCTGGAGATTAACGCAGCCGATTTGGTGGTCTGGAGTCCGATTACCGAAAAACATCTCCAGAGCGGAATGACGCTGGCTGAGCTAAGCGCGGCGACGCTGCAATATAGCGACAATACGGCGATGAATCTGATCATCGGCTACCTTGGCGGGCCGGAAAAAGTCACCGCCTTCGCCCACAGTATCGGCGATGCCACCTTTCGTCTCGATCGTACGGAGCCCACGCTGAATACCGCCATCCCGGGCGATGAGCGTGATACCAGCACGCCGCTGGCGATGGCTGAAAGCCTACGCAAGCTGACGCTTGGCGATGCGCTGGGCGAACAGCAACGCGCCCAGTTAGTCACCTGGCTGAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCGGGCCTGCCTGAAAGCTGGGTGGTCGGCGATAAAACCGGCGCCGGAGATTACGGCACCACCAATGATATTGCGGTTATCTGGCCGGAAGATCACGCTCCGCTGGTATTAGTCACCTACTTTACCCAGCCGCAGCAGGATGCGAAAAACCGCAAAGAGGTGTTAGCCGCAGCGGCAAAAATCGTGACCGAAGGGCTTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002396","ARO_id":"38796","ARO_name":"OXY-2-1","ARO_description":"OXY-2-1 is a beta-lactamase found in Klebsiella oxytoca","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"645":{"model_id":"645","model_name":"mecR1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1100"}},"model_sequences":{"sequence":{"351":{"protein_sequence":{"accession":"YP_001245420.1","sequence":"MLSSFLMLSIISSLLTICVIFLVRMLYIKYTQNIMSHKIWLLVLVSTLIPLIPFYKISNFTFSKDMMNRNVSDTTSSVSHMLDGQQSSVTKDLAINVNQFETSNITYMILLIWVFGSLLCLFYMIKAFRQIDVIKSSSLESSYLNERLKVCQSKMQFYKKHITISYSSNIDNPMVFGLVKSQIVLPTVVVETMNDKEIEYIILHELSHVKSHDLIFNQLYVVFKMIFWFNPALYISKTMMDNDCEKVCDRNVLKILNRHEHIRYGESILKCSILKSQHINNVAAQYLLGFNSNIKERVKYIALYDSMPKPNRNKRIVAYIVCSISLLIQAPLLSAHVQQDKYETNVSYKKLNQLAPYFKGFDGSFVLYNEREQAYSIYNEPESKQRYSPNSTYKIYLALMAFDQNLLSLNHTEQQWDKHQYPFKEWNQDQNLNSSMKYSVNWYYENLNKHLRQDEVKSYLDLIEYGNEEISGNENYWNESSLKISAIEQVNLLKNMKQHNMHFDNKAIEKVENSMTLKQKDTYKYVGKTGTGIVNHKEANGWFVGYVETKDNTYYFATHLKGEDNANGEKAQQISERILKEMELI"},"dna_sequence":{"accession":"NC_009487","fmin":"40848","fmax":"42606","strand":"+","sequence":"GTGTTATCATCTTTTTTAATGTTAAGTATAATCAGTTCATTGCTCACGATATGTGTAATTTTTTTAGTGAGAATGCTCTATATAAAATATACTCAAAATATTATGTCACATAAGATTTGGTTATTAGTGCTCGTCTCCACGTTAATTCCATTAATACCATTTTACAAAATATCGAATTTTACATTTTCAAAAGATATGATGAATCGAAATGTATCTGACACGACTTCTTCGGTTAGTCATATGTTAGATGGTCAACAATCATCTGTTACGAAAGACTTAGCAATTAATGTTAATCAGTTTGAGACCTCAAATATAACGTATATGATTCTTTTGATATGGGTATTTGGTAGTTTGTTGTGCTTATTTTATATGATTAAGGCATTCCGACAAATTGATGTTATTAAAAGTTCGTCATTGGAATCGTCATATCTTAATGAACGACTTAAAGTATGTCAAAGTAAGATGCAGTTCTACAAAAAGCATATAACAATTAGTTATAGTTCAAACATTGATAATCCGATGGTATTTGGTTTAGTGAAATCCCAAATTGTACTACCAACTGTCGTAGTCGAAACCATGAATGACAAAGAAATTGAATATATTATTCTACATGAACTATCACATGTGAAAAGTCATGACTTAATATTCAACCAGCTTTATGTTGTTTTTAAAATGATATTCTGGTTTAATCCTGCACTATATATAAGTAAAACAATGATGGACAATGACTGTGAAAAAGTATGTGATAGAAACGTTTTAAAAATTTTGAATCGCCATGAACATATACGTTATGGTGAATCGATATTAAAATGCTCTATTTTAAAATCTCAGCACATAAATAATGTGGCAGCACAATATTTACTAGGTTTTAATTCAAATATTAAAGAACGTGTTAAGTATATTGCACTTTATGATTCAATGCCTAAACCTAATCGAAACAAGCGTATTGTTGCGTATATTGTATGTAGTATATCGCTTTTAATACAAGCACCGTTACTATCTGCACATGTTCAACAAGACAAATATGAAACAAATGTATCATATAAAAAATTAAATCAACTAGCTCCGTATTTCAAAGGATTTGATGGAAGTTTTGTGCTTTATAATGAACGGGAGCAAGCTTATTCTATTTATAATGAACCAGAAAGTAAACAACGATATTCACCTAATTCTACTTACAAAATTTATTTAGCGTTAATGGCATTCGACCAAAATTTACTCTCATTAAATCATACTGAACAACAATGGGATAAACATCAATATCCATTTAAAGAATGGAACCAAGATCAAAATTTAAATTCTTCAATGAAATATTCAGTAAATTGGTATTACGAAAATTTAAACAAACATTTAAGACAAGATGAGGTTAAATCTTATTTAGATCTAATTGAATATGGTAATGAAGAAATATCAGGGAATGAAAATTATTGGAATGAATCTTCATTAAAAATTTCTGCAATAGAACAGGTTAATTTGTTGAAAAATATGAAACAACATAACATGCATTTTGATAATAAGGCTATTGAAAAAGTTGAAAATAGTATGACTTTGAAACAAAAAGATACTTATAAATATGTAGGTAAAACTGGAACAGGAATCGTGAATCACAAAGAAGCAAATGGATGGTTCGTAGGTTATGTTGAAACGAAAGATAATACGTATTATTTTGCTACACATTTAAAAGGCGAAGACAATGCGAATGGCGAAAAAGCACAACAAATTTCTGAGCGTATTTTAAAAGAAATGGAATTAATATAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35519","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus JH9","NCBI_taxonomy_id":"359786"}}}},"ARO_accession":"3000215","ARO_id":"36354","ARO_name":"mecR1","ARO_description":"mecR1 is a transmembrane spanning and signal transducing protein which in response to interaction with beta-lactam antibiotics results in upregulation of the mecA\/mecR1\/mecI operon.","ARO_category":{"37589":{"category_aro_accession":"3001208","category_aro_cvterm_id":"37589","category_aro_name":"methicillin resistant PBP2","category_aro_description":"In methicillin sensitive S. aureus (MSSA), beta-lactams bind to native penicillin-binding proteins (PBPs) and disrupt synthesis of the cell membrane's peptidoglycan layer. In methicillin resistant S. aureus (MRSA), foreign PBP2a acquired by lateral gene transfer is able to perform peptidoglycan synthesis in the presence of beta-lactams.","category_aro_class_name":"AMR Gene Family"},"35927":{"category_aro_accession":"0000008","category_aro_cvterm_id":"35927","category_aro_name":"cefoxitin","category_aro_description":"Cefoxitin is a cephamycin antibiotic often grouped with the second generation cephalosporins. Cefoxitin is bactericidal and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. Cefoxitin's 7-alpha-methoxy group and 3' leaving group make it a poor substrate for most beta-lactamases.","category_aro_class_name":"Antibiotic"},"35930":{"category_aro_accession":"0000011","category_aro_cvterm_id":"35930","category_aro_name":"cloxacillin","category_aro_description":"Cloxacillin is a semisynthetic, isoxazolyl penicillin derivative in the beta-lactam class of antibiotics. It interferes with peptidogylcan synthesis and is commonly used for treating penicillin-resistant Staphylococcus aureus infections.","category_aro_class_name":"Antibiotic"},"35934":{"category_aro_accession":"0000015","category_aro_cvterm_id":"35934","category_aro_name":"methicillin","category_aro_description":"Derived from penicillin to combat penicillin-resistance, methicillin is insensitive to beta-lactamases (also known as penicillinases) secreted by many penicillin-resistant bacteria. Methicillin is bactericidal, and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Antibiotic"},"35961":{"category_aro_accession":"0000043","category_aro_cvterm_id":"35961","category_aro_name":"carbenicillin","category_aro_description":"Carbenicillin is a semi-synthetic antibiotic belonging to the carboxypenicillin subgroup of the penicillins. It has gram-negative coverage which includes Pseudomonas aeruginosa but limited gram-positive coverage. The carboxypenicillins are susceptible to degradation by beta-lactamase enzymes. Carbenicillin antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Antibiotic"},"35971":{"category_aro_accession":"0000054","category_aro_cvterm_id":"35971","category_aro_name":"penicillin","category_aro_description":"Penicillin (sometimes abbreviated PCN) is a beta-lactam antibiotic used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms. It works by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Antibiotic"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35975":{"category_aro_accession":"0000058","category_aro_cvterm_id":"35975","category_aro_name":"cefazolin","category_aro_description":"Cefazolin (INN), also known as cefazoline or cephazolin, is a first generation cephalosporin antibiotic. It is administered parenterally, and is active against a broad spectrum of bacteria.","category_aro_class_name":"Antibiotic"},"35976":{"category_aro_accession":"0000059","category_aro_cvterm_id":"35976","category_aro_name":"cefepime","category_aro_description":"Cefepime (INN) is a fourth-generation cephalosporin antibiotic developed in 1994. It contains an aminothiazolyl group that decreases its affinity with beta-lactamases. Cefepime shows high binding affinity with penicillin-binding proteins and has an extended spectrum of activity against Gram-positive and Gram-negative bacteria, with greater activity against both Gram-negative and Gram-positive organisms than third-generation agents.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35978":{"category_aro_accession":"0000061","category_aro_cvterm_id":"35978","category_aro_name":"ceftobiprole","category_aro_description":"Ceftobiprole (Zeftera\/Zevtera) is a next generation (5th generation) cephalosporin antibiotic with activity against methicillin-resistant Staphylococcus aureus, penicillin-resistant Streptococcus pneumoniae, Pseudomonas aeruginosa, and Enterococci. Ceftobiprole inhibits transpeptidases essential to building cell walls, and is a poor substrate for most beta-lactamases.","category_aro_class_name":"Antibiotic"},"35979":{"category_aro_accession":"0000062","category_aro_cvterm_id":"35979","category_aro_name":"ceftriaxone","category_aro_description":"Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"35980":{"category_aro_accession":"0000063","category_aro_cvterm_id":"35980","category_aro_name":"cefuroxime","category_aro_description":"Cefuroxime is a second-generation cephalosporin antibiotic with increased stability with beta-lactamases than first-generation cephalosporins. Cefuroxime is active against Gram-positive organisms but less active against methicillin-resistant strains.","category_aro_class_name":"Antibiotic"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"35987":{"category_aro_accession":"0000070","category_aro_cvterm_id":"35987","category_aro_name":"ertapenem","category_aro_description":"Ertapenem is a carbapenem antibiotic and is highly resistant to beta-lactamases like other carbapenems. It inhibits bacterial cell wall synthesis.","category_aro_class_name":"Antibiotic"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"35995":{"category_aro_accession":"0000078","category_aro_cvterm_id":"35995","category_aro_name":"piperacillin","category_aro_description":"Piperacillin is an acetylureidopenicillin and has an extended spectrum of targets relative to other beta-lactam antibiotics. It inhibits cell wall synthesis in bacteria, and is usually taken with the beta-lactamase inhibitor tazobactam to overcome penicillin-resistant bacteria.","category_aro_class_name":"Antibiotic"},"36309":{"category_aro_accession":"3000170","category_aro_cvterm_id":"36309","category_aro_name":"imipenem","category_aro_description":"Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.","category_aro_class_name":"Antibiotic"},"36689":{"category_aro_accession":"3000550","category_aro_cvterm_id":"36689","category_aro_name":"aztreonam","category_aro_description":"Aztreonam was the first monobactam discovered, and is greatly effective against Gram-negative bacteria while inactive against Gram-positive bacteria. Artreonam is a poor substrate for beta-lactamases, and may even act as an inhibitor. In Gram-negative bacteria, Aztreonam interferes with filamentation, inhibiting cell division and leading to cell death.","category_aro_class_name":"Antibiotic"},"36976":{"category_aro_accession":"3000632","category_aro_cvterm_id":"36976","category_aro_name":"benzylpenicillin","category_aro_description":"Benzylpenicillin, commonly referred to as penicillin G, is effective against both Gram-positive and Gram-negative bacteria. It is unstable in acid.","category_aro_class_name":"Antibiotic"},"36977":{"category_aro_accession":"3000633","category_aro_cvterm_id":"36977","category_aro_name":"phenoxymethylpenicillin","category_aro_description":"Phenoxymethylpenicillin, or penicillin V, is a penicillin derivative that is acid stable but less active than benzylpenicillin (penicillin G).","category_aro_class_name":"Antibiotic"},"36978":{"category_aro_accession":"3000634","category_aro_cvterm_id":"36978","category_aro_name":"propicillin","category_aro_description":"Propicillin is an orally taken penicillin derivative that has high absorption but poor activity.","category_aro_class_name":"Antibiotic"},"36979":{"category_aro_accession":"3000635","category_aro_cvterm_id":"36979","category_aro_name":"dicloxacillin","category_aro_description":"Dicloxacillin is a penicillin derivative that has an extra chlorine atom in comparison to cloxacillin. While more active than cloxacillin, its high affinity for serum protein reduces its activity in human serum in vitro.","category_aro_class_name":"Antibiotic"},"36980":{"category_aro_accession":"3000636","category_aro_cvterm_id":"36980","category_aro_name":"flucloxacillin","category_aro_description":"Flucloxacillin is similar to cloxacillin, with an extra additional fluorine atom.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"36982":{"category_aro_accession":"3000638","category_aro_cvterm_id":"36982","category_aro_name":"azlocillin","category_aro_description":"Azlocillin is a semisynthetic derivative of penicillin that is notably active against Ps. aeruginosa and other Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36983":{"category_aro_accession":"3000639","category_aro_cvterm_id":"36983","category_aro_name":"mezlocillin","category_aro_description":"Mezlocillin is a penicillin derivative taken parenterally.","category_aro_class_name":"Antibiotic"},"36984":{"category_aro_accession":"3000640","category_aro_cvterm_id":"36984","category_aro_name":"doripenem","category_aro_description":"Doripenem is a carbapenem with a broad range of activity against Gram-positive and Gram-negative bacteria, and along with meropenem, it is the most active beta-lactam antibiotic against Pseudomonas aeruginosa. It inhibits bacterial cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36985":{"category_aro_accession":"3000641","category_aro_cvterm_id":"36985","category_aro_name":"cefalexin","category_aro_description":"Cefalexin is a cephalosporin antibiotic that causes filamentation. It is resistant to staphylococcal beta-lactamase, but degraded by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"36986":{"category_aro_accession":"3000642","category_aro_cvterm_id":"36986","category_aro_name":"cefadroxil","category_aro_description":"Cefadroxil, or p-hydroxycephalexin, is an cephalosporin antibiotic similar to cefalexin.","category_aro_class_name":"Antibiotic"},"36987":{"category_aro_accession":"3000643","category_aro_cvterm_id":"36987","category_aro_name":"cefotiam","category_aro_description":"Cefotiam is a cephalosporin antibiotic with similar activity to cefuroxime but more active against enterobacteria. It is consumed orally as the prodrug cefotiam hexetil.","category_aro_class_name":"Antibiotic"},"36988":{"category_aro_accession":"3000644","category_aro_cvterm_id":"36988","category_aro_name":"cefaclor","category_aro_description":"Cefaclor is a semisynthetic cephalosporin derived from cephalexin. It has broad-spectrum antibiotic activity.","category_aro_class_name":"Antibiotic"},"36989":{"category_aro_accession":"3000645","category_aro_cvterm_id":"36989","category_aro_name":"cefotaxime","category_aro_description":"Cefotaxime is a semisynthetic cephalosporin taken parenterally. It is resistant to most beta-lactamases and active against Gram-negative rods and cocci due to its aminothiazoyl and methoximino functional groups.","category_aro_class_name":"Antibiotic"},"36990":{"category_aro_accession":"3000646","category_aro_cvterm_id":"36990","category_aro_name":"cefixime","category_aro_description":"Cefixime is a cephalosporin resistant to most beta-lactamases. It is active against many enterobacteria, but activity against staphylococci is poor.","category_aro_class_name":"Antibiotic"},"36991":{"category_aro_accession":"3000647","category_aro_cvterm_id":"36991","category_aro_name":"cefpodoxime","category_aro_description":"Cefpodoxime is a semisynthetic cephalosporin that acts similarly to cefotaxime with broad-spectrum activity. It is stable to many plasmid-mediated beta-lactamses. Cefpodoxime is consumed as the prodrug cefpodoxime proxetil.","category_aro_class_name":"Antibiotic"},"36992":{"category_aro_accession":"3000648","category_aro_cvterm_id":"36992","category_aro_name":"ceftibuten","category_aro_description":"Ceftibuten is a semisynthetic cephalosporin active against Gram-negative bacilli. It is resistant against many plasmid-mediated beta-lactamases.","category_aro_class_name":"Antibiotic"},"36993":{"category_aro_accession":"3000649","category_aro_cvterm_id":"36993","category_aro_name":"cefditoren","category_aro_description":"Cefditoren is a semisynthetic cephalosporin active against staphylococci, streptococci, and and most enterobacteria. It is resistant to staphylococcal and most enterobacterial beta-lactamases, and is usually taken as the prodrug cefditoren pivoxil.","category_aro_class_name":"Antibiotic"},"36994":{"category_aro_accession":"3000650","category_aro_cvterm_id":"36994","category_aro_name":"cefdinir","category_aro_description":"Cefdinir is similar to cefixime with a modified side-chain at its 7-amino position. It also shares similar activity with cefixime but is more active against staphylococci. It has also be shown to enhance phagocytosis.","category_aro_class_name":"Antibiotic"},"36995":{"category_aro_accession":"3000651","category_aro_cvterm_id":"36995","category_aro_name":"ceftaroline","category_aro_description":"Ceftaroline is a novel cephalosporin active against methicillin resistant Staphylococcus aureus. Like other cephalosporins it binds penicillin-binding proteins to inhibit cell wall synthesis. It strongly binds with PBP2a, associated with methicillin resistance. It is taken orally as the prodrug ceftaroline fosamil.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"37085":{"category_aro_accession":"3000705","category_aro_cvterm_id":"37085","category_aro_name":"isopenicillin N","category_aro_description":"Isopenicillin N is a natural penicillin derivative produced by Penicillium chrysogenum with activity similar to penicillin N.","category_aro_class_name":"Antibiotic"},"37086":{"category_aro_accession":"3000706","category_aro_cvterm_id":"37086","category_aro_name":"penicillin N","category_aro_description":"Penicillin N is a penicillin derivative produced by Cephalosporium acremonium.","category_aro_class_name":"Antibiotic"},"37141":{"category_aro_accession":"3000761","category_aro_cvterm_id":"37141","category_aro_name":"mecillinam","category_aro_description":"Mecillinam is a broad-spectrum beta-lactam antibiotic that was semi-synthetically derived to have a different drug centre, being a 6-alpha-amidinopenicillanate instead of a 6-alpha-acylaminopenicillanate. Contrasting most beta-lactam drugs, mecillinam is most active against Gram-negative bacteria. It binds specifically to penicillin binding protein 2 (PBP2).","category_aro_class_name":"Antibiotic"},"40928":{"category_aro_accession":"3004001","category_aro_cvterm_id":"40928","category_aro_name":"cefmetazole","category_aro_description":"Cefmetazole is a semi-synthetic cephamycin antibiotic with broad spectrum antibiotic activity against both gram-positive and gram-negative bacteria, that disrupt cell wall synthesis through binding to PBPs causing cell lysis.","category_aro_class_name":"Antibiotic"},"40929":{"category_aro_accession":"3004002","category_aro_cvterm_id":"40929","category_aro_name":"cefonicid","category_aro_description":"Cefonicid is a second-generation cephalosporin-class beta-lactam antibiotic with broad spectrum activity. Particularly used against urinary tract infections and lower respiratory infections. Causes cell lysis by inactivation of PBPs through binding, inhibiting peptidoglycan synthesis.","category_aro_class_name":"Antibiotic"},"40932":{"category_aro_accession":"3004005","category_aro_cvterm_id":"40932","category_aro_name":"cefprozil","category_aro_description":"Cefprozil is a cephalosporin and beta-lactam antibiotic with bactericidal activity. It selectively binds to PBPs and inhibits peptidoglycan synthesis, a major cell wall component, resulting in cell lysis.","category_aro_class_name":"Antibiotic"},"40933":{"category_aro_accession":"3004006","category_aro_cvterm_id":"40933","category_aro_name":"ceftiofur","category_aro_description":"Ceftiofur is a third-generation broad spectrum cephalosporin and beta-lactam antibiotic. It causes cell lysis by disrupting peptidoglycan cross-linkage and cell wall formation by binding to PBPs.","category_aro_class_name":"Antibiotic"},"40934":{"category_aro_accession":"3004007","category_aro_cvterm_id":"40934","category_aro_name":"ceftizoxime","category_aro_description":"Ceftizoxime is a third-generation cephalosporin and broad spectrum beta-lactam antibiotic. Ceftizoxime causes bacterial cell lysis through peptidoglycan cross-linking inhibition by binding to PBPs.","category_aro_class_name":"Antibiotic"},"40935":{"category_aro_accession":"3004008","category_aro_cvterm_id":"40935","category_aro_name":"cephapirin","category_aro_description":"Cephapirin is a first-generation cephalosporin and broad spectrum beta-lactam antibiotic. Inactivation of penicillin-binding proteins through cephapirin binding disrupts peptidoglycan cross-linking, resulting in cell lysis.","category_aro_class_name":"Antibiotic"},"40936":{"category_aro_accession":"3004009","category_aro_cvterm_id":"40936","category_aro_name":"cefradine","category_aro_description":"Cefradine is a first-generation cephalosporin and broad spectrum beta-lactam antibiotic. Cefradine binding to penicillin-binding proteins disrupts cell wall peptidoglycan cross-linkage, resulting in cell lysis.","category_aro_class_name":"Antibiotic"},"40943":{"category_aro_accession":"3004016","category_aro_cvterm_id":"40943","category_aro_name":"loracarbef","category_aro_description":"Loracarbef is a second-generation cephalosporin (carbacephem) and broad spectrum beta-lactam antibiotic. Loracarbef inhibits PBPs through binding, disrupting peptidoglycan cell wall cross-linkage and resulting in cell death.","category_aro_class_name":"Antibiotic"},"40944":{"category_aro_accession":"3004017","category_aro_cvterm_id":"40944","category_aro_name":"moxalactam","category_aro_description":"Moxalactam (Latamoxef) is a broad spectrum cephalosporin (oxacephem) and beta-lactam antibiotic. Moxalactam binding to PBPs inhibits peptidoglycan cross-linkage in the cell wall, resulting in cell death. Moxalactam is proposed to be effective against meningitides as it passes the blood-brain barrier.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"646":{"model_id":"646","model_name":"OXA-349","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"889":{"protein_sequence":{"accession":"AGW83447.1","sequence":"MYKKALIAATSILFLSSCSSNTVKQHQIHSISANKNSEEIKSLFDQAQTTGVLVIKRGQTEEIYGNDLKRAPTAYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRVGFGNASIGSKVDNFWLVGPLKITPQQETQFAYQLALKTLPFSQDVQEQVQSMVFIEEKNGSKIYAKSGWGWDVEPQVGWLTGWIVQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"KF297578","fmin":"0","fmax":"822","strand":"+","sequence":"ATGTATAAAAAAGCCCTTATCGCTGCAACAAGTATCCTATTTTTATCCTCCTGTTCTTCCAATACGGTAAAACAACATCAAATACACTCTATTTCTGCCAATAAAAATTCAGAAGAAATTAAATCACTGTTTGATCAGGCACAGACCACGGGTGTTTTGGTGATTAAGCGAGGGCAAACAGAAGAAATTTATGGCAATGATCTTAAAAGAGCACCAACCGCCTATGTTCCCGCCTCAACCTTTAAAATGTTAAATGCTTTAATTGGACTTGAACATCATAAGGCAACTACAACTGAAGTATTTAAATGGGATGGGCAAAAACGTTTATTTCCTGATTGGGAAAAGGACATGACACTGGGTGATGCCATGAAAGCTTCTGCGATTCCAGTTTACCAAGAATTAGCCCGACGAATTGGTCTAGATCTTATGTCTAAAGAGGTGAAACGAGTTGGTTTTGGTAATGCTAGCATTGGTTCAAAAGTAGATAATTTTTGGCTTGTTGGCCCTCTAAAAATTACACCTCAACAAGAAACCCAATTTGCTTATCAATTAGCCCTTAAAACGCTTCCATTTAGCCAAGATGTACAAGAACAAGTTCAATCAATGGTGTTCATAGAGGAAAAAAATGGAAGTAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTTGAACCACAAGTTGGTTGGTTAACAGGCTGGATCGTTCAACCACAAGGAGAAATTGTCGCATTCTCACTTAATTTAGAAATGAAAAAAGGAACTCCTAGCTCTATTCGCAAAGAAATTGCTTATAAAGGCTTAGAACAACTGGGTATTTTATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3001536","ARO_id":"37936","ARO_name":"OXA-349","ARO_description":"OXA-349 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"647":{"model_id":"647","model_name":"TEM-89","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1727":{"protein_sequence":{"accession":"AAK71474.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMGDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEI"},"dna_sequence":{"accession":"AY039040","fmin":"188","fmax":"1022","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGGGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3000956","ARO_id":"37336","ARO_name":"TEM-89","ARO_description":"TEM-89 is an inhibitor-resistant, extended-spectrum beta-lactamase that has been found in clinical isolates.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"648":{"model_id":"648","model_name":"GES-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1784":{"protein_sequence":{"accession":"BAD08689.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRTAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVKWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMSDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"AB116260","fmin":"1329","fmax":"2193","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAACGGCGCAGCGCTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCAAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGAGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAGT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002333","ARO_id":"38733","ARO_name":"GES-4","ARO_description":"GES-4 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"649":{"model_id":"649","model_name":"OXA-115","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1999":{"protein_sequence":{"accession":"ABS71123.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAILVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWVVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"EU029998","fmin":"575","fmax":"1400","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCTAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGGTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001440","ARO_id":"37840","ARO_name":"OXA-115","ARO_description":"OXA-115 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"650":{"model_id":"650","model_name":"aadA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"4279":{"protein_sequence":{"accession":"YP_001715321.1","sequence":"MREAVIAEVSTQLSEVVGVIERHLEPTLLAVHLYGSAVDGGLKPHSDIDLLVTVTVRLDETTRRALINDLLETSASPGESEILRAVEVTIVVHDDIIPWRYPAKRELQFGEWQRNDILAGIFEPATIDIDLAILLTKAREHSVALVGPAAEELFDPVPEQDLFEALNETLTLWNSPPDWAGDERNVVLTLSRIWYSAVTGKIAPKDVAADWAMERLPAQYQPVILEARQAYLGQEEDRLASRADQLEEFVHYVKGEITKVVGK"},"dna_sequence":{"accession":"NC_010410","fmin":"3621491","fmax":"3622283","strand":"-","sequence":"TTATTTGCCGACTACCTTGGTGATCTCGCCTTTCACGTAGTGGACAAATTCTTCCAACTGATCTGCGCGCGAGGCCAAGCGATCTTCTTCTTGTCCAAGATAAGCCTGTCTAGCTTCAAGTATGACGGGCTGATACTGGGCCGGCAGGCGCTCCATTGCCCAGTCGGCAGCGACATCCTTCGGCGCGATTTTGCCGGTTACTGCGCTGTACCAAATGCGGGACAACGTAAGCACTACATTTCGCTCATCGCCAGCCCAGTCGGGCGGCGAGTTCCATAGCGTTAAGGTTTCATTTAGCGCCTCAAATAGATCCTGTTCAGGAACCGGATCAAAGAGTTCCTCCGCCGCTGGACCTACCAAGGCAACGCTATGTTCTCTTGCTTTTGTCAGCAAGATAGCCAGATCAATGTCGATCGTGGCTGGCTCGAAGATACCTGCAAGAATGTCATTGCGCTGCCATTCTCCAAATTGCAGTTCGCGCTTAGCTGGATAACGCCACGGAATGATGTCGTCGTGCACAACAATGGTGACTTCTACAGCGCGGAGAATCTCGCTCTCTCCAGGGGAAGCCGAAGTTTCCAAAAGGTCGTTGATCAAAGCTCGCCGCGTTGTTTCATCAAGCCTTACGGTCACCGTAACCAGCAAATCAATATCACTGTGTGGCTTCAGGCCGCCATCCACTGCGGAGCCGTACAAATGTACGGCCAGCAACGTCGGTTCGAGATGGCGCTCGATGACGCCAACTACCTCTGATAGTTGAGTCGATACTTCGGCGATCACCGCTTCCCTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35535","NCBI_taxonomy_name":"Acinetobacter baumannii AYE","NCBI_taxonomy_id":"509173"}}}},"ARO_accession":"3002601","ARO_id":"39001","ARO_name":"aadA","ARO_description":"ANT(3'')-Ia is an aminoglycoside nucleotidyltransferase gene encoded by plasmids, transposons, integrons in Enterobacteriaceae, A. baumannii, P. aeruginosa and Vibrio cholerae","ARO_category":{"41439":{"category_aro_accession":"3004275","category_aro_cvterm_id":"41439","category_aro_name":"ANT(3'')","category_aro_description":"Nucleotidylylation of streptomycin at the hydroxyl group at position 3''","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"652":{"model_id":"652","model_name":"tcr3","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"950"}},"model_sequences":{"sequence":{"332":{"protein_sequence":{"accession":"BAA07390.1","sequence":"MGMANATSQTGEAVADEAGGPAGFTHRQIITALSGLLLAVLLAALDQTIVSTALRTIGDQLHGQTVQAWVITGYLVSSTIAMPFYGKLSDIYGRKPLYLAAIAVFIVGSAACAMANSMETLAIARVLQGFGGAGLMSLPTAVIADLAPVRERGRYFSYLMMAWVAASVLGPLVGGLFAGAGEILGVTGWRWAFLINVPLGLVALLSVRKALNLPHRRVDHPIDFRGALTLALCLVPLLIVAEEGLDWGWGSARSLTLFAVSLIGLVLFVLAERARGLEAMVPLRLFRRGGITMATAVNFTIGVGIFGTVSTLPLFLQLVQGRSATVAGLVIIPVMTGAIVSQTICAKIIKKWNRYKKPAIVGLGSMAGALLSLSAAGADTPLAVIVVIAAWLGFGIGLSQTVITLAIQSSAPKSELGVANAASGLFRQLGGTSGAAVFMSVLFGVAAGRLDGADPDEAVRRALSDPGSTGGLSASAVDAFTSGFDTMFLVGGLILAVGFLLTFPLRELRDEE"},"dna_sequence":{"accession":"D38215","fmin":"0","fmax":"1539","strand":"+","sequence":"ATGGGAATGGCGAACGCCACCTCGCAGACCGGCGAGGCCGTCGCGGACGAGGCCGGCGGCCCCGCCGGCTTCACTCACCGCCAGATCATCACCGCGCTGTCCGGGCTCCTGTTGGCCGTGCTGCTCGCCGCACTCGACCAGACGATCGTCTCCACCGCGCTGCGTACGATCGGCGACCAACTGCACGGCCAGACCGTCCAGGCCTGGGTGATCACCGGCTACCTGGTCAGCTCCACGATCGCGATGCCGTTCTACGGCAAGCTGTCCGACATCTACGGCCGCAAGCCGCTCTATCTGGCGGCGATCGCGGTCTTCATCGTCGGCTCGGCGGCCTGCGCGATGGCGAACTCGATGGAGACGCTGGCGATCGCCCGCGTCCTCCAGGGCTTCGGCGGCGCCGGGCTGATGTCGCTGCCGACGGCCGTCATCGCCGACCTCGCCCCGGTGCGCGAGCGCGGGCGCTACTTCTCGTACCTGATGATGGCCTGGGTGGCGGCCAGTGTGCTCGGCCCGCTCGTCGGGGGCCTGTTCGCGGGCGCCGGCGAGATCCTCGGGGTGACCGGCTGGCGCTGGGCCTTCCTGATCAACGTGCCGCTCGGTCTCGTGGCGCTGCTCAGCGTGCGCAAGGCGCTCAACCTGCCGCACCGCAGGGTGGACCACCCGATCGACTTCCGGGGGGCGCTCACCCTGGCGCTCTGCCTGGTGCCGCTGCTGATCGTGGCGGAGGAGGGCCTCGACTGGGGCTGGGGATCGGCGCGTTCGCTGACGCTGTTCGCCGTCTCGCTGATCGGCCTGGTGCTGTTCGTGCTCGCCGAGCGGGCCCGCGGGCTGGAGGCGATGGTCCCGCTGCGGCTGTTCCGGCGCGGTGGCATCACGATGGCCACGGCCGTCAACTTCACCATCGGCGTCGGCATCTTCGGTACGGTCTCCACCCTGCCGCTGTTCCTGCAGCTGGTGCAGGGGCGCAGTGCCACCGTCGCCGGACTGGTGATCATCCCGGTGATGACCGGGGCGATCGTCTCCCAGACGATCTGCGCCAAGATCATCAAGAAGTGGAACCGCTACAAGAAGCCCGCGATCGTGGGCCTCGGCTCGATGGCCGGAGCACTGCTGTCGCTCTCCGCCGCGGGCGCGGACACCCCGCTCGCGGTGATCGTGGTGATCGCGGCCTGGCTGGGCTTCGGCATCGGGCTCTCCCAGACCGTCATCACCCTGGCGATCCAGAGCTCGGCGCCCAAGTCCGAGCTGGGCGTGGCCAACGCCGCCTCCGGGCTGTTCCGCCAGCTCGGCGGCACGAGCGGCGCCGCCGTCTTCATGTCGGTGCTGTTCGGCGTCGCCGCCGGCAGGCTCGACGGGGCCGACCCGGACGAGGCCGTGCGCCGTGCGCTCTCCGACCCGGGCTCCACCGGCGGCCTGAGCGCCTCGGCGGTCGACGCCTTCACCTCGGGCTTCGACACGATGTTCCTGGTCGGCGGCCTGATCCTTGCGGTGGGCTTCCTGCTCACCTTCCCGCTGCGGGAACTGCGCGACGAGGAGTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36813","NCBI_taxonomy_name":"Streptomyces aureofaciens","NCBI_taxonomy_id":"1894"}}}},"ARO_accession":"3002893","ARO_id":"39327","ARO_name":"tcr3","ARO_description":"tcr3 is a tetracycline efflux pump that confers self-resistance to Streptomyces aureofaciens","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"531":{"model_id":"531","model_name":"SAT-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"673":{"protein_sequence":{"accession":"CAA88265.1","sequence":"MTPQSMRELVICRASDADVLQLARCDFSFEVTAELEEPFDDMRSVPVKPPYLKNYGFDADELVEHMNNSAGALFVARADNCLVGYLAVSQSWNEYAVIDDIAVDVPYRGSGVSRLLMDAAVDWARNVPSAGVRLETQSVNLAACRFYRRYGFRLGGYDRYLYRGLHPGSREVALFWYLSF"},"dna_sequence":{"accession":"Z48231","fmin":"220","fmax":"763","strand":"+","sequence":"ATGACGCCACAGTCAATGCGTGAATTGGTCATCTGTCGTGCAAGCGATGCCGACGTTCTTCAGCTTGCGCGGTGCGATTTCTCTTTCGAGGTCACAGCTGAGCTCGAAGAGCCGTTCGATGACATGCGGTCCGTTCCAGTCAAGCCGCCCTACCTCAAGAACTATGGCTTTGATGCCGATGAGTTGGTCGAGCATATGAACAACTCTGCTGGGGCGTTGTTTGTGGCTCGGGCGGACAATTGCCTTGTTGGCTACTTGGCCGTGTCTCAAAGCTGGAACGAATATGCCGTCATCGATGATATCGCGGTCGATGTGCCCTATCGGGGGAGTGGCGTTTCGCGCTTGCTGATGGATGCAGCTGTGGACTGGGCACGAAATGTGCCGTCGGCAGGCGTACGTCTGGAGACGCAGTCCGTTAATCTCGCCGCATGTCGCTTTTACCGACGATACGGTTTCCGGTTAGGTGGTTATGATCGCTACCTGTATCGTGGCCTGCATCCGGGCAGCCGAGAGGTAGCTCTGTTCTGGTATTTGAGTTTTTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002898","ARO_id":"39332","ARO_name":"SAT-3","ARO_description":"SAT-3 is a plasmid-mediated streptothricin acetyltransferase and streptothricin resistance determinant. Originally described from an E. coli plasmid gene by Tietze and Brevet, 1995.","ARO_category":{"37249":{"category_aro_accession":"3000869","category_aro_cvterm_id":"37249","category_aro_name":"streptothricin acetyltransferase (SAT)","category_aro_description":"AcetylCoA dependent acetyltransferase that acetylate streptothricins such as nourseothricin at position 16 (beta position of beta-lysine).","category_aro_class_name":"AMR Gene Family"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"640":{"model_id":"640","model_name":"tet(31)","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"3344":{"protein_sequence":{"accession":"CAC80727.1","sequence":"MIGKLIMMNRYITIALLITFLDATGMGLIMPVLPTLLEEFSVKESIATHYGFILAIYALMQVIFAPILGQLSDKFGRKPVLILSLIGAVCDYTLLSFSSALWMLYLGRMIAGISAATGAVAASMVADHTKKAERTKWFGKLGAAFGAGLIAGPAIGGFIGQYSAHFPFIIAAILNAIALIMVIILFPKEQSRPKEIEQDQSKIHEKTTINAPLIHILKPVLLLLMLFFTVQLIGQIPASTWVLFTEYRFEWNTFNIGLSLAGLGLMHIIFQAFVAGYIASRWKNETVFILGFILDASAFLLLAFISQVWLVIPTLILLAGGGIALPALQGLISIKTADEHQGKIQGIMVSLTNITGIIGPPIFAFSFAKTVTNWDGTLWLIGAVLYSILLGLYFLYQKIRAYKQLKSQTA"},"dna_sequence":{"accession":"AJ250203","fmin":"1650","fmax":"2883","strand":"+","sequence":"ATGATAGGGAAGCTTATAATGATGAATCGCTATATCACAATCGCCCTCTTAATTACCTTCCTAGATGCAACAGGAATGGGCTTAATCATGCCTGTATTACCAACACTTTTAGAAGAGTTCTCTGTCAAAGAGTCTATCGCCACTCATTATGGTTTTATCCTCGCAATCTATGCGCTGATGCAAGTTATTTTTGCACCAATATTAGGACAACTCTCGGATAAATTTGGCAGAAAACCGGTCTTGATTCTCTCATTAATAGGCGCTGTTTGTGATTACACCCTACTCTCATTTTCTAGCGCCTTATGGATGCTCTATCTAGGGAGAATGATTGCCGGCATTTCTGCTGCAACAGGAGCCGTAGCAGCATCAATGGTCGCAGATCACACAAAAAAAGCAGAGAGAACTAAATGGTTTGGAAAGTTAGGCGCAGCTTTTGGGGCGGGACTCATTGCCGGACCCGCTATTGGTGGATTTATCGGACAATATTCTGCACATTTCCCCTTTATCATTGCCGCAATTTTAAATGCCATTGCTCTTATCATGGTCATTATCCTCTTCCCTAAAGAGCAATCACGCCCAAAAGAAATCGAGCAAGATCAATCTAAAATTCATGAAAAAACCACCATCAATGCCCCGCTAATTCATATTCTCAAACCCGTTTTGCTACTTCTCATGCTGTTTTTTACAGTACAACTCATCGGACAAATCCCTGCATCAACTTGGGTTCTATTTACTGAGTACCGTTTTGAGTGGAATACCTTTAACATTGGTTTATCCCTTGCAGGGCTAGGGTTAATGCATATTATCTTTCAGGCTTTTGTCGCAGGATATATCGCATCTCGCTGGAAAAATGAAACCGTATTTATTCTCGGATTTATACTAGATGCGAGCGCATTCTTATTACTGGCCTTTATCTCTCAAGTTTGGCTGGTAATTCCTACATTGATCTTATTAGCAGGAGGAGGCATCGCCTTACCGGCATTACAAGGATTAATCTCTATAAAGACAGCAGATGAACATCAAGGAAAGATACAAGGTATCATGGTTAGCCTCACTAATATTACCGGAATAATTGGACCGCCCATTTTTGCATTTTCCTTTGCAAAAACGGTTACAAACTGGGATGGCACACTTTGGCTAATCGGTGCTGTACTCTATAGCATTTTATTAGGTCTCTATTTTCTCTATCAAAAGATACGCGCCTATAAACAACTTAAGTCTCAAACTGCTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40299","NCBI_taxonomy_name":"Aeromonas salmonicida subsp. salmonicida","NCBI_taxonomy_id":"29491"}}}},"ARO_accession":"3000476","ARO_id":"36615","ARO_name":"tet(31)","ARO_description":"Tet31 is a tetracycline efflux pump found in Aeromonas salmonicida, a Gram-negative bacteria. It has also been shown to be expressed in Gallibacterium anatis.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"534":{"model_id":"534","model_name":"vanVB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"4327":{"protein_sequence":{"accession":"AAO82019.1","sequence":"MFTEKFCADGICFIMRAKNEIDHIFSELYSVPNCLQKPYFKLKVQELLLFLCMPLVICTPILIGFAILIPYLCFKNLEKRSIVNRLRAEQKENQQKQVVLALLIHSELFDSGFR"},"dna_sequence":{"accession":"AE016830","fmin":"2211932","fmax":"2212277","strand":"-","sequence":"TCAACGAAAACCCGAATCAAACAGTTCCGAGTGAATCAGCAGAGCAAGAACGACTTGTTTCTGCTGGTTCTCTTTTTGCTCTGCCCGCAGCCGATTCACAATGCTTCGTTTTTCCAAATTCTTAAAGCAGAGATACGGAATGAGAATTGCAAAGCCAATTAAGATAGGTGTACAAATCACGAGGGGCATACACAAAAACAAAAGCAATTCCTGAACTTTCAGCTTAAAATAAGGCTTTTGCAGGCAATTCGGTACAGAGTAAAGTTCTGAAAAAATATGGTCAATTTCATTTTTCGCCCGCATAATAAAGCAGATTCCATCAGCGCAGAATTTTTCTGTAAACAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37592","NCBI_taxonomy_name":"Enterococcus faecalis V583","NCBI_taxonomy_id":"226185"}}}},"ARO_accession":"3004254","ARO_id":"41418","ARO_name":"vanVB","ARO_description":"vanVB is a vanV variant found in the vanB gene cluster. It is found in some but not all vanB operons in E. faecalis, suggesting the existence of varied gene compositions in vanB operons.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"39350":{"category_aro_accession":"3002916","category_aro_cvterm_id":"39350","category_aro_name":"vanV","category_aro_description":"vanV is an accessory protein of van operons, first identified in the vanB operon. It is not required for vancomycin resistance.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"516":{"model_id":"516","model_name":"eptA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"4319":{"protein_sequence":{"accession":"BAE78116.1","sequence":"MLKRLLKRPSLNLLAWLLLAAFYISICLNIAFFKQVLQALPLDSLHNVLVFLSMPVVAFSVINIVLTLSSFLWLNRPLACLFILVGAAAQYFIMTYGIVIDRSMIANIIDTTPAESYALMTPQMLLTLGFSGVLAALIACWIKIKPATSRLRSVLFRGANILVSVLLILLVAALFYKDYASLFRNNKELVKSLSPSNSIVASWSWYSHQRLANLPLVRIGEDAHRNPLMQNEKRKNLTILIVGETSRAENFSLNGYPRETNPRLAKDNVVYFPNTASCGTATAVSVPCMFSDMPREHYKEELAQHQEGVLDIIQRAGINVLWNDNDGGCKGACDRVPHQNVTALNLPDQCINGECYDEVLFHGLEEYINNLQGDGVIVLHTIGSHGPTYYNRYPPQFRKFTPTCDTNEIQTCTKEQLVNTYDNTLVYVDYIVDKAINLLKEHQDKFTTSLVYLSDHGESLGENGIYLHGLPYAIAPDSQKQVPMLLWLSEDYQKRYQVDQNCLQKQAQTQHYSQDNLFSTLLGLTGVETKYYQAADDILQTCRRVSE"},"dna_sequence":{"accession":"AP009048","fmin":"4338624","fmax":"4340268","strand":"-","sequence":"TCATTCACTCACTCTCCTGCAAGTTTGCAGAATATCATCCGCAGCCTGGTAATACTTCGTCTCAACGCCAGTTAATCCCAATAGCGTGGAGAATAAATTGTCTTGTGAATAGTGTTGCGTTTGCGCCTGTTTTTGCAGGCAGTTCTGGTCAACCTGATACCGTTTTTGATAATCCTCCGACAGCCACAGCAGCATCGGCACCTGTTTTTGGCTATCCGGGGCGATGGCATAAGGCAGACCGTGCAGATAGATGCCATTTTCACCTAACGATTCACCGTGGTCAGAAAGATAAACCAGGCTGGTGGTAAATTTATCCTGATGTTCTTTCAGCAGATTAATCGCTTTATCAACAATATAGTCGACGTAAACCAGCGTGTTGTCGTAAGTGTTCACCAGTTGCTCTTTGGTACAGGTCTGGATCTCATTGGTGTCGCAGGTTGGGGTAAATTTCCTGAACTGAGGCGGATAGCGGTTGTAATAGGTCGGACCGTGGCTGCCGATGGTGTGTAAGACAATCACGCCATCACCTTGCAGGTTATTGATGTACTCTTCAAGCCCGTGGAACAGCACTTCGTCATAGCATTCGCCGTTGATGCACTGATCAGGTAGATTCAGCGCGGTGACGTTCTGGTGAGGCACGCGGTCGCAGGCACCTTTACAGCCGCCATCGTTGTCATTCCACAGCACGTTGATGCCCGCTCGCTGAATGATATCCAGCACGCCTTCCTGGTGCTGTGCCAGCTCTTCTTTGTAGTGCTCACGCGGCATATCCGAGAACATGCACGGTACTGAAACTGCCGTTGCCGTGCCGCAAGATGCGGTATTAGGGAAATAGACCACGTTATCTTTCGCCAGCCGCGGGTTAGTTTCACGCGGGTAGCCGTTGAGGGAGAAGTTCTCCGCCCGCGAGGTTTCGCCGACAATCAGGATGGTCAAATTTTTACGTTTTTCGTTCTGCATTAACGGGTTGCGGTGCGCGTCTTCACCAATTCGCACCAGCGGCAGATTTGCCAGTCGCTGATGGGAGTACCATGACCAGCTGGCAACAATGCTGTTAGAGGGGCTTAAGGATTTCACCAGCTCTTTGTTATTGCGGAACAACGAGGCGTAGTCTTTATAAAACAGTGCGGCGACCAGCAAAATCAGTAGTACAGAAACCAGAATATTGGCTCCACGGAAAAGAACACTGCGCAGACGCGAGGTGGCAGGTTTGATTTTTATCCAGCAGGCAATCAGCGCAGCAAGCACGCCGCTGAATCCCAGCGTTAATAACATTTGCGGTGTCATCAGCGCATAACTTTCTGCCGGAGTGGTATCAATAATATTGGCAATCATCGAGCGGTCGATGACGATGCCGTAAGTCATTATGAAATATTGTGCAGCCGCGCCAACCAGAATAAACAGGCAGGCCAGTGGTCGATTAAGCCATAAGAAAGAGCTTAGTGTCAGGACAATATTAATCACGCTGAAAGCGACGACCGGCATCGACAAGAAAACCAGTACGTTATGCAGCGAATCCAGCGGCAGCGCCTGCAACACCTGTTTAAAAAAGGCAATATTCAGGCAGATAGAGATATAAAAAGCGGCCAACAATAGCCAGGCGAGTAAATTCAAAGAGGGTCTTTTTAGTAGGCGCTTCAACAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36839","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. W3110","NCBI_taxonomy_id":"316407"}}}},"ARO_accession":"3003576","ARO_id":"40186","ARO_name":"eptA","ARO_description":"PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine, resulting in a less negative cell membrane and decreased binding of polymyxin B.","ARO_category":{"41433":{"category_aro_accession":"3004269","category_aro_cvterm_id":"41433","category_aro_name":"pmr phosphoethanolamine transferase","category_aro_description":"This family of phosphoethanolamine transferase catalyze the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine to lipid A, which impedes the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"492":{"model_id":"492","model_name":"Clostridium butyricum catB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"174":{"protein_sequence":{"accession":"AAA73865.1","sequence":"MNFNLIDINHWSRKPYFEHYLNNVKCTYSMTANIEITDLLYEIKLKNIKFYPTLIYMIATVVNNHKEFRICFDHKGSLGYWDSMNPSYTIFHKENETFSSIWTEYNKSFLRFYSDYLDDIKNYGNIMKFTPKSNEPDNTFSVSSIPWVSFTGFNLNVYNEGTYLIPIFTAGKYFKQENKIFIPISIQVHHAICDGYHASRFINEMQELAFSFQEWLENK"},"dna_sequence":{"accession":"M93113","fmin":"0","fmax":"660","strand":"+","sequence":"ATGAATTTTAATTTAATAGATATTAATCATTGGAGTAGAAAGCCATACTTTGAACATTATTTAAACAATGTGAAATGTACTTACAGTATGACTGCCAATATAGAAATAACTGATTTATTGTATGAAATTAAACTTAAAAATATTAAATTTTATCCTACACTTATTTATATGATTGCAACTGTGGTTAATAATCATAAAGAATTCCGTATTTGTTTTGATCATAAAGGTAGTTTAGGATATTGGGATAGCATGAATCCAAGCTATACTATTTTTCATAAAGAAAACGAAACATTTTCAAGTATTTGGACGGAATATAACAAAAGTTTTTTACGTTTTTATAGTGATTATCTTGACGATATAAAAAACTATGGAAATATCATGAAGTTTACTCCGAAATCAAATGAACCTGACAATACATTTTCTGTATCAAGTATTCCTTGGGTGAGTTTTACAGGATTTAACTTGAATGTTTATAATGAAGGAACATATTTAATTCCTATTTTTACTGCAGGAAAGTATTTCAAACAAGAAAATAAAATATTTATTCCTATATCAATACAAGTACATCATGCTATCTGTGACGGTTATCATGCTAGTAGATTTATTAATGAAATGCAAGAATTAGCATTTAGTTTTCAAGAATGGTTAGAAAATAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36845","NCBI_taxonomy_name":"Clostridium butyricum","NCBI_taxonomy_id":"1492"}}}},"ARO_accession":"3002674","ARO_id":"39108","ARO_name":"Clostridium butyricum catB","ARO_description":"catB is a chromosome-encoded variant of the cat gene found in Clostridium butyricum","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. cat is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Bacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini","category_aro_class_name":"AMR Gene Family"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"653":{"model_id":"653","model_name":"AAC(3)-VIIa","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"694":{"protein_sequence":{"accession":"AAA88552.1","sequence":"MDELALLKRSDGPVTRTRLARDLTALGLGDGDTVMFHTRMSAVGYVAGGPETVIGALRDVVGERGTLMVTCGWNDAPPYDFTDWPQTWQDARRAEHPAYDPVLSEADHNNGRLPEALRRRPGAVRSRHPDASFAALGAAATALTADHPWDDPHGPDSPLARLVAMGGRVLLLGAPLEALTLLHHAEALADAPGKRFVDYEQPILVDGERVWRRFHDIDSEDGAFDYSALVPEGTEAFEIIGRDMRAAGIGRRGTVGAADSHLFEARDVVDFGVAWMEEKLGRERGPGG"},"dna_sequence":{"accession":"M22999","fmin":"492","fmax":"1359","strand":"+","sequence":"ATGGACGAACTCGCCTTGCTCAAGCGCTCCGACGGCCCGGTCACCCGGACCCGCCTCGCCCGGGACCTGACCGCGCTCGGCCTCGGCGACGGGGACACCGTGATGTTCCATACGCGGATGTCCGCCGTCGGCTACGTGGCAGGCGGCCCGGAGACGGTCATCGGAGCCCTCCGCGACGTCGTGGGAGAGCGGGGAACCCTGATGGTGACCTGCGGCTGGAACGACGCCCCGCCGTACGACTTCACCGACTGGCCGCAGACCTGGCAGGACGCCCGTCGGGCGGAGCACCCGGCGTACGACCCCGTGCTGAGCGAGGCTGACCACAACAACGGGCGCCTCCCGGAAGCGCTGCGCCGCCGGCCCGGAGCCGTCCGCAGCCGTCACCCCGACGCGAGCTTCGCGGCGCTCGGCGCGGCGGCCACCGCGTTGACGGCCGACCATCCGTGGGACGACCCGCACGGCCCTGACAGCCCGCTGGCGCGGCTGGTCGCGATGGGCGGCCGGGTGCTGCTGCTGGGCGCCCCGCTGGAGGCGCTCACGCTCCTGCACCACGCCGAGGCGCTGGCCGACGCGCCCGGTAAGCGGTTCGTGGACTACGAGCAGCCGATCCTCGTCGACGGGGAGCGGGTCTGGCGGCGGTTCCACGACATCGACTCGGAGGACGGGGCGTTCGACTACTCCGCCCTCGTGCCCGAGGGAACGGAAGCGTTCGAGATCATCGGACGGGACATGCGTGCCGCGGGCATCGGCCGCAGGGGAACGGTCGGGGCGGCCGACAGCCATCTCTTCGAAGCCCGTGACGTGGTCGACTTCGGTGTGGCCTGGATGGAGGAGAAGCTGGGCCGGGAAAGGGGGCCCGGCGGATGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36773","NCBI_taxonomy_name":"Streptomyces rimosus","NCBI_taxonomy_id":"1927"}}}},"ARO_accession":"3002541","ARO_id":"38941","ARO_name":"AAC(3)-VIIa","ARO_description":"AAC(3)-VIIa is a chromosomal-encoded aminoglycoside acetyltransferase in Streptomyces rimosus","ARO_category":{"36461":{"category_aro_accession":"3000322","category_aro_cvterm_id":"36461","category_aro_name":"AAC(3)","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 3.","category_aro_class_name":"AMR Gene Family"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"654":{"model_id":"654","model_name":"dfrA26","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"111":{"protein_sequence":{"accession":"CAL48457.1","sequence":"MADEEYDPLLDDDMEDAKVAVIAARAQNGCIGRHGKLPWKLPGDLKYFRERTWGKPIIMGRKTWESLNGALPGRTNIVVTRQQGYEAEGARVVDSIEEAISLAQSIALIEAVDEIMVLGGGEIYTQALPQADILYLTEVHASVDGDAFFPDVDLSQYQETQRQDFEPSGGNPYPFSFVVYQRT"},"dna_sequence":{"accession":"AM403715","fmin":"302","fmax":"854","strand":"+","sequence":"ATGGCTGATGAAGAATACGACCCGCTACTCGATGACGACATGGAAGATGCCAAAGTCGCCGTCATTGCTGCCCGTGCGCAAAACGGTTGCATTGGTCGCCACGGCAAGCTGCCGTGGAAGCTGCCCGGTGACCTGAAATACTTCCGTGAGCGCACCTGGGGCAAGCCCATCATCATGGGGCGCAAAACCTGGGAATCACTCAATGGTGCCTTGCCGGGGCGCACCAACATCGTGGTAACGCGTCAACAAGGTTATGAAGCCGAAGGTGCTCGCGTGGTCGATAGCATCGAAGAAGCCATTAGCTTGGCACAGTCTATCGCCTTAATCGAAGCCGTTGATGAAATCATGGTGCTGGGCGGCGGCGAAATCTATACCCAAGCCTTACCGCAAGCCGACATTCTCTATCTCACCGAAGTACACGCCTCGGTCGACGGCGATGCCTTCTTCCCCGACGTGGACCTCAGCCAATATCAAGAAACCCAACGCCAGGACTTCGAGCCATCGGGCGGCAACCCTTACCCGTTTAGCTTTGTGGTCTATCAGCGGACGTAGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002857","ARO_id":"39291","ARO_name":"dfrA26","ARO_description":"dfrA26 is an integron-encoded dihydrofolate reductase found in Escherichia coli","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36408":{"category_aro_accession":"3000269","category_aro_cvterm_id":"36408","category_aro_name":"brodimoprim","category_aro_description":"Brodimoprim is a structural derivative of trimethoprim and an inhibitor of bacterial dihydrofolate reductase. The 4-methoxy group of trimethoprim is replaced with a bromine atom.","category_aro_class_name":"Antibiotic"},"36423":{"category_aro_accession":"3000284","category_aro_cvterm_id":"36423","category_aro_name":"tetroxoprim","category_aro_description":"Tetroxoprim is a trimethoprim derivative that inhibits bacterial dihydrofolate reductase.","category_aro_class_name":"Antibiotic"},"36476":{"category_aro_accession":"3000337","category_aro_cvterm_id":"36476","category_aro_name":"iclaprim","category_aro_description":"Iclaprim is a bactericidal compound that inhibits dihydrofolate reductase. It is used against clinically important Gram-positive pathogens, including methicillin-sensitive Staphylococcus aureus and methicillin-resistant S. aureus.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"655":{"model_id":"655","model_name":"OXA-243","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1928":{"protein_sequence":{"accession":"AFQ90085.1","sequence":"MTVRLSSTALGAALSLSALAGAPAQAAVLCTVVADAADGRIVYQQGTQQACAARYTPASTFKLPIALMGADAGILTGPHAPVWNYQPGYPDWGGDAWRQPTDPARWIKYSVVWYSQLTARALGQERFQRYASAFHYGNEDVSGEPGKHNGLDGAWINSSLRISPLEQLAFLRKLVNRQLPLKAAAYDLAENLFEVGEAGGWHLYGKTGTGSPGSNGVYTAANAYGWFVGWARKDGRQLVFARLVQDEQATKPNAGLRARDDLMRDWPAMADAPRK"},"dna_sequence":{"accession":"JX206446","fmin":"0","fmax":"828","strand":"+","sequence":"ATGACCGTTCGCCTCTCTTCGACCGCTCTCGGCGCGGCCCTTTCCCTGTCCGCGCTGGCCGGCGCCCCCGCCCAGGCGGCCGTCCTGTGCACCGTGGTGGCCGACGCCGCCGACGGCCGCATCGTGTACCAGCAGGGCACGCAGCAGGCCTGCGCCGCGCGCTACACGCCGGCCTCGACCTTCAAGCTGCCCATCGCCCTGATGGGCGCGGACGCCGGCATCCTGACGGGCCCGCACGCGCCGGTCTGGAACTACCAGCCCGGCTACCCCGACTGGGGCGGCGACGCCTGGCGCCAGCCCACGGATCCGGCGCGCTGGATCAAGTATTCGGTGGTCTGGTATTCGCAGCTGACCGCCCGGGCGCTGGGGCAGGAACGCTTCCAGCGCTATGCCTCGGCCTTCCATTACGGCAACGAGGACGTCTCGGGCGAACCCGGCAAACACAACGGCCTGGACGGCGCATGGATCAACTCGTCGCTGCGGATTTCTCCGTTGGAACAACTGGCGTTCTTGCGCAAGCTGGTCAACCGGCAATTGCCGCTCAAGGCGGCGGCCTACGACCTGGCCGAGAACCTGTTCGAGGTCGGCGAAGCCGGCGGCTGGCACCTGTATGGCAAGACCGGCACCGGCTCGCCTGGCAGCAACGGCGTCTACACGGCGGCCAACGCCTACGGCTGGTTCGTCGGCTGGGCACGCAAGGACGGCCGCCAGCTGGTGTTCGCCCGCCTGGTGCAGGACGAGCAGGCCACCAAGCCCAACGCCGGCCTGCGCGCCCGCGACGACCTGATGCGCGACTGGCCCGCCATGGCCGACGCGCCGCGCAAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36941","NCBI_taxonomy_name":"Achromobacter xylosoxidans","NCBI_taxonomy_id":"85698"}}}},"ARO_accession":"3001610","ARO_id":"38010","ARO_name":"OXA-243","ARO_description":"OXA-243 is a beta-lactamase found in Achromobacter xylosoxidans.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"656":{"model_id":"656","model_name":"OXA-219","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1528":{"protein_sequence":{"accession":"AEL17179.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWVVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"JN215211","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGGTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001668","ARO_id":"38068","ARO_name":"OXA-219","ARO_description":"OXA-219 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"657":{"model_id":"657","model_name":"SHV-142","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1711":{"protein_sequence":{"accession":"AEX99752.1","sequence":"MRYIRLCIISLLAALPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"JQ029959","fmin":"28","fmax":"889","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCGCCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATATATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001184","ARO_id":"37564","ARO_name":"SHV-142","ARO_description":"SHV-142 is a beta-lactamase.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"658":{"model_id":"658","model_name":"CMY-104","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1546":{"protein_sequence":{"accession":"AGR82311.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNHTITPLMQKQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWTPSTKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASQVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVDAAWRILEKLQ"},"dna_sequence":{"accession":"KF150216","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACGTTTGCCGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCACACCATCACCCCGTTGATGCAGAAGCAGGCTATTCCGGGGATGGCCGTTGCAGTTATCTACCAGGGTAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGTGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTATACGGCAGGTGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCGCTTTTATCAAAACTGGCAGCCACAATGGACTCCGAGCACTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGTATGAGCTACGAAGAGGCGATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCAGGTTCAGGAAAAAACACTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGTTGAAAGCTGATTCGATCATCAACGGTAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTACATAAAACGGGATCCACTGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGCCCGCGTCGATGCAGCCTGGCGTATTCTTGAAAAACTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39654","NCBI_taxonomy_name":"Citrobacter sp. OTESBL0707","NCBI_taxonomy_id":"1367686"}}}},"ARO_accession":"3002116","ARO_id":"38516","ARO_name":"CMY-104","ARO_description":"CMY-104 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"659":{"model_id":"659","model_name":"AAC(6')-29b","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"4433":{"protein_sequence":{"accession":"ACI31326.1","sequence":"MSILPVKEQDAADWLALRNLLWLADDHASEIEQYFSGGFEEPAEVLIARDATGAAVGHVELSIRHDLEELQGIKTGYIEGLYVAPSHRSTDLVRRFLRESEKWALEQGCSAFASDRSDRVITHRKFAGSAV"},"dna_sequence":{"accession":"EU118148","fmin":"2006","fmax":"2402","strand":"+","sequence":"GTTTCGATCTTACCTGTGAAAGAACAAGACGCTGCCGACTGGCTAGCGCTGCGGAATCTTCTTTGGCTCGCGGATGATCACGCCTCGGAGATTGAGCAGTACTTCTCTGGTGGATTTGAGGAGCCTGCAGAAGTGCTCATCGCCCGTGATGCTACCGGCGCGGCTGTTGGGCATGTCGAACTCTCGATAAGACATGACTTGGAAGAACTCCAAGGAATCAAGACCGGCTACATCGAAGGCCTTTATGTGGCCCCAAGCCATCGATCAACAGACCTTGTGAGGCGTTTCTTGCGTGAGTCCGAGAAGTGGGCCCTAGAACAAGGGTGCAGCGCATTTGCCTCAGACAGAAGTGATCGGGTCATCACGCACCGCAAGTTCGCAGGCAGCGCCGTCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002584","ARO_id":"38984","ARO_name":"AAC(6')-29b","ARO_description":"AAC(6')-29b is an integron-encoded aminoglycoside acetyltransferase in P. aeruginosa","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"661":{"model_id":"661","model_name":"VIM-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"855":{"protein_sequence":{"accession":"AAN52134.1","sequence":"MLKVISSLLVYMTASVMAVASPLAHSGEPSGEYPTVNEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRKAGVATYASPSTRRLAEAEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSANVLYGGCAVLALSRTSAGNVADADLAEWPTSVERIQKHYPEAEVVIPGHGLPGGLDLLQHTANVVTAHKNRSVAE"},"dna_sequence":{"accession":"AY144612","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTACATGACCGCGTCTGTCATGGCTGTAGCTAGTCCGTTAGCCCATTCCGGGGAGCCGAGTGGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGAGAGGTCCGGCTTTACCAGATTGCTGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCGGTCTACCCATCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCCCTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCCGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGAAGGCTGGAGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGCAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGCTCTTCTATCCCGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAACGTGCTATACGGTGGTTGTGCCGTTCTTGCGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCGTTGAGCGGATTCAAAAACACTACCCGGAAGCAGAGGTCGTCATTCCCGGGCACGGTCTACCGGGCGGTCTAGACTTGCTCCAGCACACAGCGAACGTTGTCACAGCACACAAAAATCGCTCAGTCGCCGAGTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002275","ARO_id":"38675","ARO_name":"VIM-5","ARO_description":"VIM-5 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"662":{"model_id":"662","model_name":"TEM-162","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1882":{"protein_sequence":{"accession":"ABO64442.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPKTLVKVKDAENQLGARVGYIELDLNSGKILESFRPEKRFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQSDVVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"EF468463","fmin":"66","fmax":"927","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCTTTTTGCCTTCCTGTTTTTGCTCACCCAAAAACGCTGGTGAAAGTAAAAGATGCTGAAAATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAAAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTATTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAGTGACGTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36938","NCBI_taxonomy_name":"Acinetobacter haemolyticus","NCBI_taxonomy_id":"29430"}}}},"ARO_accession":"3001028","ARO_id":"37408","ARO_name":"TEM-162","ARO_description":"TEM-162 is a beta-lactamase found in Acinetobacter haemolyticus.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"663":{"model_id":"663","model_name":"ACT-36","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1660":{"protein_sequence":{"accession":"AJG06170.1","sequence":"MMKKSLCCALLLGISCSALAAPVSEKQLAEVVANTITPLMKAQSIPGMAVAVIYQGKPHYYTFGKADIAASKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNAALLRFYQNWQPQWKPGTTRLYANASIGLFGALTVKPSGMGYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGISLAQSRYWRIGSMYQGLGWEMLNWPVEANTVIEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYHILDALQ"},"dna_sequence":{"accession":"KM926621","fmin":"751","fmax":"1897","strand":"+","sequence":"ATGATGAAAAAATCTCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCGCGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGATTACCCCGCTGATGAAAGCCCAGTCGATTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGTAAACCGCACTATTACACGTTTGGCAAAGCCGATATCGCGGCCAGCAAACCCGTTACGCCTCAGACTCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGGGTTTTAGGAGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGGATTCGTATGCTGGATCTCGCAACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAATGCCGCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGTATCGGTCTTTTTGGCGCGCTGACGGTCAAACCTTCCGGCATGGGCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAACGTTGCTGATGCCTCACTTAAGCAGGGCATCTCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCTGTGGAGGCCAACACGGTGATCGAGGGCAGCGACAGTAAGGTGGCGCTGGCACCGCTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGACGCGCTACAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3003171","ARO_id":"39748","ARO_name":"ACT-36","ARO_description":"From the Lahey list of beta-lactamases.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"664":{"model_id":"664","model_name":"CMY-43","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1508":{"protein_sequence":{"accession":"ACJ05361.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFAALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"FJ360626","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGCCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002054","ARO_id":"38454","ARO_name":"CMY-43","ARO_description":"CMY-43 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"665":{"model_id":"665","model_name":"TEM-10","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2029":{"protein_sequence":{"accession":"AAC72362.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGKRGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AF093512","fmin":"197","fmax":"1058","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTAAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36917","NCBI_taxonomy_name":"Morganella morganii","NCBI_taxonomy_id":"582"}}}},"ARO_accession":"3000882","ARO_id":"37262","ARO_name":"TEM-10","ARO_description":"TEM-10 is an extended-spectrum beta-lactamase round in Morganella morganii.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"666":{"model_id":"666","model_name":"CTX-M-34","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1028":{"protein_sequence":{"accession":"AAR99493.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTVDVQQKLAELEQQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSCDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"AY515297","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGTGGACGTACAGCAAAAACTTGCCGAATTAGAGCAGCAGTCGGGAGGAAGGCTGGGTGTGGCATTGATTAACACGGCGGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTCGAGATCAAAAAATCTGACCTGGTTAACTATAATCCGATTGCGGAAAAACACGTCAATGGGACGATGTCACTGGCTGAGCTCAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTTACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCTGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACGCTGCGTAATCTGACGCTGGGTAAAGCATTGGGTGACAGCCAACGGGCGCAGCTGGTGACGTGGATGAAAGGCAATACTACCGGTGCAGCGAGTATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCTGTGACTATGGTACCACCAACGATATCGCGGTGATTTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCCCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001896","ARO_id":"38296","ARO_name":"CTX-M-34","ARO_description":"CTX-M-34 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"667":{"model_id":"667","model_name":"ACT-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"860":{"protein_sequence":{"accession":"AAC45086.2","sequence":"MMMTKSLCCALLLSTSCSVLATPMSEKQLAEVVERTVTPLMKAQAIPGMAVAVIYEGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVKDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAITTRVFKPLKLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMVNMKPDSLQDNSLRKGLTLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVEGSDNKVALAPLPAREVNPPAPPVNASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILSAL"},"dna_sequence":{"accession":"U58495","fmin":"27","fmax":"1173","strand":"+","sequence":"ATGATGATGACTAAATCCCTTTGCTGCGCCCTGCTGCTCAGCACCTCCTGCTCGGTATTGGCTACCCCGATGTCAGAAAAACAGCTGGCTGAGGTGGTGGAACGGACCGTTACGCCGCTGATGAAAGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTGATTTATGAGGGTCAGCCGCACTACTTCACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCTGTCACTCCACAAACCTTGTTCGAACTGGGTTCTATAAGTAAAACCTTCACCGGCGTACTCGGTGGCGATGCCATTGCTCGCGGTGAAATATCGCTGGGCGATCCGGTGACAAAATACTGGCCTGAGCTGACAGGCAAGCAGTGGCAGGGGATCCGCATGCTGGATCTGGCAACCTATACCGCAGGAGGTTTGCCGTTACAGGTACCGGATGAGGTCAAGGATAACGCCTCTCTGTTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCCAATGCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATAACGACGCGGGTCTTTAAGCCGCTCAAGCTGGACCATACGTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGCGACGGTAAAGCAGTACACGTTTCGCCAGGAATGCTGGACGCTGAAGCCTATGGCGTAAAAACCAACGTGCAGGATATGGCAAGCTGGGTGATGGTCAACATGAAGCCGGACTCCCTTCAGGATAATTCACTCAGGAAAGGCCTTACCCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCCATGTATCAGGGGTTAGGCTGGGAAATGCTTAACTGGCCGGTCGATGCCAAAACCGTGGTTGAAGGTAGCGACAATAAGGTTGCACTGGCACCGCTGCCTGCGAGAGAAGTGAATCCACCAGCGCCCCCGGTCAACGCATCCTGGGTCCATAAAACAGGCTCTACCGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGTATTGTGATGCTGGCAAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATTTTGAGCGCGCTGTAGT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001821","ARO_id":"38221","ARO_name":"ACT-1","ARO_description":"ACT-1 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"668":{"model_id":"668","model_name":"CTX-M-65","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1029":{"protein_sequence":{"accession":"ABN69105.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAVAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAERRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"EF418608","fmin":"9","fmax":"885","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGTCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGCGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001926","ARO_id":"38326","ARO_name":"CTX-M-65","ARO_description":"CTX-M-65 is a beta-lactamase found in Escherichia coli","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"669":{"model_id":"669","model_name":"MIR-12","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"1269":{"protein_sequence":{"accession":"AIT76116.1","sequence":"MMTKSLSCALLLSVTSSAFAAPMSEKQLAEVVERTVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEVALGDPVAKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDTASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEEAHYAWGYREGKAVHVSPGMLDAEAYGVKTNVKDMASWLIANMKPDSLQAPSLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"KM087863","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGACAAAATCCCTAAGCTGTGCCCTGCTGCTCAGCGTCACCAGCTCTGCATTCGCCGCACCGATGTCCGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTAATTTATCAGGGTCAGCCACACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGCGGCGATGCCATTGCCCGGGGTGAAGTAGCGCTGGGCGATCCGGTAGCAAAATACTGGCCTGAGCTCACGGGCAAGCAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTATACCGCAGGCGGTCTGCCGTTACAGGTGCCGGATGAGGTCACGGATACCGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCTAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAACCCCTCAAGCTGGACCATACATGGATTAACGTCCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGAGGGTAAAGCGGTCCACGTTTCGCCAGGGATGCTGGACGCGGAAGCCTATGGCGTAAAAACTAACGTGAAGGATATGGCGAGCTGGCTGATAGCCAACATGAAGCCGGATTCTCTTCAGGCTCCCTCACTCAAGCAAGGCATTGCTCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCTATGTATCAGGGGTTGGGCTGGGAGATGCTCAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCATTGCCCGTGGCAGAAGTGAATCCACCCGCGCCGCCGGTCAAGGCCTCCTGGGTCCATAAAACAGGCTCGACGGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3002177","ARO_id":"38577","ARO_name":"MIR-12","ARO_description":"MIR-12 is a beta-lactamase. From the Lahey list of MIR beta-lactamases.","ARO_category":{"36197":{"category_aro_accession":"3000058","category_aro_cvterm_id":"36197","category_aro_name":"MIR beta-lactamase","category_aro_description":"MIR beta-lactamases are plasmid-mediated beta-lactamases that confer resistance to oxyimino- and alpha-methoxy beta-lactams","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"670":{"model_id":"670","model_name":"IND-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"914":{"protein_sequence":{"accession":"AAG29761.2","sequence":"MKKRIQFFMVSMMLSSLFSAQVKDFVIEPPIKKNLHIYKTFGVFGGKEYSANSVYLVTQKGVVLFDVPWEKVQYQSLMDTIQKRHNLPVIAVFATHSHDDRAGDLSFFNNKGIKTYATSKTNEFLKKDGKATSTEIIKTGKPYRIGGEEFVVDFLGEGHTADNVVVWFPKYNVLDGGCLVKSKAATDLGYIKEANVEQWPKTINKLKSKYSKASLVIPGHDEWKGGGHVKHTLELLNKK"},"dna_sequence":{"accession":"AF219131","fmin":"0","fmax":"720","strand":"+","sequence":"ATGAAAAAAAGAATTCAGTTCTTTATGGTTTCAATGATGCTAAGTTCATTATTCAGTGCCCAGGTAAAAGATTTTGTCATCGAACCACCGATTAAAAAGAATTTACATATTTACAAAACTTTTGGTGTATTCGGAGGTAAAGAATATTCTGCCAATTCAGTATATCTTGTTACCCAAAAAGGAGTTGTCTTATTTGACGTCCCGTGGGAAAAGGTACAGTACCAAAGCCTGATGGATACCATCCAAAAACGCCACAATTTACCCGTAATAGCTGTGTTTGCCACTCACTCCCATGATGACCGTGCCGGAGATCTGAGCTTTTTTAACAACAAAGGAATTAAAACCTACGCTACTTCCAAAACCAATGAATTCCTGAAAAAAGACGGAAAAGCAACATCCACAGAGATCATTAAGACCGGAAAGCCATATCGCATAGGAGGTGAGGAATTTGTGGTTGATTTTCTTGGAGAAGGGCATACTGCTGATAATGTAGTGGTATGGTTTCCCAAATACAACGTCCTGGATGGCGGATGCCTTGTAAAAAGTAAAGCTGCAACCGATCTTGGATATATTAAGGAAGCCAATGTAGAGCAATGGCCCAAGACCATCAATAAACTGAAATCCAAATATTCAAAAGCAAGCCTGGTTATTCCCGGACATGATGAATGGAAAGGTGGAGGCCATGTAAAACATACTCTTGAACTTCTTAACAAAAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36916","NCBI_taxonomy_name":"Chryseobacterium indologenes","NCBI_taxonomy_id":"253"}}}},"ARO_accession":"3002259","ARO_id":"38659","ARO_name":"IND-3","ARO_description":"IND-3 is a beta-lactamase found in Chryseobacterium indologenes","ARO_category":{"36199":{"category_aro_accession":"3000060","category_aro_cvterm_id":"36199","category_aro_name":"IND beta-lactamase","category_aro_description":"IND beta-lactamases are class B carbapenem-hydrolyzing beta-lactamases","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"671":{"model_id":"671","model_name":"CTX-M-137","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"785":{"protein_sequence":{"accession":"BAO37256.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"AB900900","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATTGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001994","ARO_id":"38394","ARO_name":"CTX-M-137","ARO_description":"CTX-M-137 is a beta-lactamase found in Escherichia coli","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"672":{"model_id":"672","model_name":"CMY-27","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1442":{"protein_sequence":{"accession":"ACA30421.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYACGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"EU515250","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGTGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002038","ARO_id":"38438","ARO_name":"CMY-27","ARO_description":"CMY-27 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"673":{"model_id":"673","model_name":"IMP-48","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1111":{"protein_sequence":{"accession":"AIT76110.1","sequence":"MKKLFVLCVFFFCNIAVAEESLPDLKIEKLEEGVYVHTSFEEVKGWSVVTKHGLVVLVKNDAYLIDTPTTAKDTEKLVNWFVERGYKIKGSISTHFHGDSTAGIEWLNSQSIPTYASELTNELLKKDNKVQAKHSFNGVSYSLIKNKIEVFYPGPGHTQDNVVVWLPEKKILFGGCFVKPDGLGYLGDANLEAWPKSAKILMSKYGKAKLVVSSHSDIGDVSLLKRTWEQAVKGLNESKKSSQPSD"},"dna_sequence":{"accession":"KM087857","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAAAAAATTATTTGTTTTATGTGTATTCTTCTTCTGCAACATTGCAGTTGCAGAAGAATCTTTGCCTGATTTAAAAATTGAGAAGCTTGAAGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAAAGGTTGGAGTGTGGTCACTAAACACGGTTTGGTGGTTCTTGTGAAAAATGACGCCTATCTGATTGATACTCCAACTACTGCTAAAGATACTGAAAAATTAGTCAATTGGTTTGTTGAGCGGGGCTATAAAATCAAAGGCAGTATTTCCACACATTTCCATGGTGACAGTACGGCTGGAATAGAGTGGCTTAATTCTCAATCTATCCCCACATATGCTTCTGAATTAACAAATGAACTTCTTAAAAAAGACAATAAGGTACAAGCTAAACACTCTTTTAATGGGGTTAGTTATTCACTAATTAAAAACAAAATTGAAGTTTTTTATCCAGGCCCAGGGCACACTCAAGATAACGTAGTGGTTTGGTTACCTGAAAAGAAAATTTTATTCGGTGGTTGCTTTGTTAAACCGGACGGTCTTGGCTATTTGGGGGACGCAAATTTAGAAGCTTGGCCAAAGTCCGCTAAAATATTAATGTCTAAATATGGTAAAGCAAAACTAGTTGTGTCGAGTCATAGTGATATTGGAGATGTATCACTCTTGAAACGTACATGGGAGCAGGCTGTTAAAGGGCTGAATGAAAGTAAAAAATCATCACAGCCAAGCGACTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002239","ARO_id":"38639","ARO_name":"IMP-48","ARO_description":"IMP-48 is a beta-lactamase. From the Lahey list of IMP beta-lactamases.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"674":{"model_id":"674","model_name":"OXA-15","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1834":{"protein_sequence":{"accession":"AAB05874.1","sequence":"MAIRIFAILFSIFSLATFAHAQEGTLERSDWRKFFSEFQAKGTIVVADERQADRAMLVFDPVRSKKRYSPASTFKIPHTLFALDAGAVRDEFQIFRWDGVNRGFAGHNQDQDLRSAMRNSTVWVYELFAKEIGDDKARRYLKKIDYGNAGPSTSNGDYWIEGSLAISAQEQIAFLRKLYRNELPFRVEHQRLVKDLMIVEAGRNWILRAKTGWEGRMGWWVGWVEWPTGSVFFALNIDTPNRMDDLFKREAIVRAILRSIEALPPNPAVNSDAAR"},"dna_sequence":{"accession":"U63835","fmin":"127","fmax":"955","strand":"+","sequence":"ATGGCAATCCGAATCTTCGCGATACTTTTCTCCATTTTTTCTCTTGCCACTTTCGCGCATGCGCAAGAAGGCACGCTAGAACGTTCTGACTGGAGGAAGTTTTTCAGCGAATTTCAAGCCAAAGGCACGATAGTTGTGGCAGACGAACGCCAAGCGGATCGTGCCATGTTGGTTTTTGATCCTGTGCGATCGAAGAAACGCTACTCGCCTGCATCGACATTCAAGATACCTCATACACTTTTTGCACTTGATGCAGGCGCTGTTCGTGATGAGTTCCAGATTTTTCGATGGGACGGCGTTAACAGGGGCTTTGCAGGCCACAATCAAGACCAAGATTTGCGATCAGCAATGCGGAATTCTACTGTTTGGGTGTATGAGCTATTTGCAAAGGAAATTGGTGATGACAAAGCTCGGCGCTATTTGAAGAAAATCGACTATGGCAACGCCGGTCCTTCGACAAGTAATGGCGATTACTGGATAGAAGGCAGCCTTGCAATCTCGGCGCAGGAGCAAATTGCATTTCTCAGGAAGCTCTATCGTAACGAGCTGCCCTTTCGGGTAGAACATCAGCGCTTGGTCAAGGATCTCATGATTGTGGAAGCCGGTCGCAACTGGATACTGCGTGCAAAGACGGGCTGGGAAGGCCGTATGGGTTGGTGGGTAGGATGGGTTGAGTGGCCGACTGGCTCCGTATTCTTCGCACTGAATATTGATACGCCAAACAGAATGGATGATCTTTTCAAGAGGGAGGCAATCGTGCGGGCAATCCTTCGCTCTATTGAAGCGTTACCGCCCAACCCGGCAGTCAACTCGGACGCTGCGCGATAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001410","ARO_id":"37810","ARO_name":"OXA-15","ARO_description":"OXA-15 is a beta-lactamase found in P. aeruginosa.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"675":{"model_id":"675","model_name":"OXA-25","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1210":{"protein_sequence":{"accession":"AAG35607.1","sequence":"MKKFILPIFSISILVSLSACSSIKTKSEDNFHISSQQHEKAIKSYFDEAQTQGVIIIKEGKNLSTYGNALARANKEYVPASTFKMLNALIGLENHKATTNEIFKWDGKKRTYPMWEKDMTLGEAMALSAVPVYQELARRTGLELMQKEVKRVNFGNTNIGTQVDNFWLVGPLKITPVQEVNFADDLAHNRLPFKLETQEEVEKMLLIKEVNGSKIYAKSGWGMGVTPQVGWLTGWVEQANGKKIPFSLNLEMKEGMSGSIRNEITYKLLENLGII"},"dna_sequence":{"accession":"AF201826","fmin":"21","fmax":"849","strand":"+","sequence":"ATGAAAAAATTTATACTTCCTATATTCAGCATTTCTATTCTAGTTTCTCTCAGTGCATGTTCATCTATTAAAACTAAATCTGAAGATAATTTTCATATTTCTTCTCAGCAACATGAAAAAGCTATTAAAAGCTATTTTGATGAAGCTCAAACACAGGGTGTAATTATTATTAAAGAGGGTAAAAATCTTAGCACCTATGGTAATGCTCTTGCACGAGCAAATAAAGAATATGTCCCTGCATCAACATTTAAGATGCTAAATGCTTTAATCGGGCTAGAAAATCATAAAGCAACAACAAATGAGATTTTCAAATGGGATGGTAAAAAAAGAACTTATCCTATGTGGGAGAAAGATATGACTTTAGGTGAGGCAATGGCATTGTCAGCAGTTCCAGTATATCAAGAGCTTGCAAGACGGACTGGCCTAGAGCTAATGCAGAAAGAAGTAAAGCGGGTTAATTTTGGAAATACAAATATTGGAACACAGGTCGATAATTTTTGGTTAGTTGGCCCCCTTAAAATTACACCAGTACAAGAAGTTAATTTTGCCGATGACCTTGCACATAACCGATTACCTTTTAAATTAGAAACTCAAGAAGAAGTTGAAAAAATGCTTCTAATTAAAGAAGTAAATGGTAGTAAGATTTATGCAAAAAGTGGATGGGGAATGGGTGTTACTCCACAGGTAGGTTGGTTGACTGGTTGGGTGGAGCAAGCTAATGGAAAAAAAATCCCCTTTTCGCTCAACTTAGAAATGAAAGAAGGAATGTCTGGTTCTATTCGTAATGAAATTACTTATAAGTTGCTAGAAAATCTTGGAATCATTTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001420","ARO_id":"37820","ARO_name":"OXA-25","ARO_description":"OXA-25 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"676":{"model_id":"676","model_name":"AAC(6')-Ih","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"456":{"protein_sequence":{"accession":"AAC41391.1","sequence":"MNIMPISESQLSDWLALRCLLWPDHEDVHLQEMRQLITQAHRLQLLAYTDTQQAIAMLEASIRYEYVNGTQTSPVAFLEGIFVLPEYRRSGIATGLVQQVEIWAKQFACTEFASDAALDNQISHAMHQALGFHETERVVYFKKNIG"},"dna_sequence":{"accession":"L29044","fmin":"351","fmax":"792","strand":"+","sequence":"ATGAATATTATGCCGATATCTGAATCACAATTATCAGATTGGTTAGCATTAAGATGCTTACTTTGGCCTGATCATGAAGATGTGCATTTACAGGAAATGCGCCAACTGATCACACAGGCACATCGTTTACAATTATTGGCTTATACCGACACCCAACAAGCAATTGCCATGTTGGAAGCTTCAATTCGGTATGAATATGTGAATGGCACACAAACATCGCCTGTGGCTTTTTTGGAAGGGATTTTTGTATTGCCTGAATATCGTCGTTCAGGTATCGCAACGGGGTTGGTTCAACAAGTGGAAATTTGGGCGAAACAGTTTGCATGTACAGAGTTTGCTTCGGATGCAGCGTTGGATAATCAGATCAGCCACGCCATGCATCAAGCACTCGGTTTTCATGAAACTGAACGTGTGGTGTATTTTAAGAAAAATATCGGCTAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3002555","ARO_id":"38955","ARO_name":"AAC(6')-Ih","ARO_description":"AAC(6')-Ih is a plasmid-encoded aminoglycoside acetyltransferase in A. baumannii","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"677":{"model_id":"677","model_name":"OXA-171","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1755":{"protein_sequence":{"accession":"ADK35875.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETPSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKPQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASTRNELLMKSLKQLNII"},"dna_sequence":{"accession":"HM488992","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGACCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCCCAATTAGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTACACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001471","ARO_id":"37871","ARO_name":"OXA-171","ARO_description":"OXA-171 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"678":{"model_id":"678","model_name":"PDC-10","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"1385":{"protein_sequence":{"accession":"ACQ82815.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"FJ666073","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTATGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002509","ARO_id":"38909","ARO_name":"PDC-10","ARO_description":"PDC-10 is a extended-spectrum beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"679":{"model_id":"679","model_name":"SHV-108","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"899":{"protein_sequence":{"accession":"ADR80606.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLAIVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"HM751100","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCATCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTAGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001157","ARO_id":"37537","ARO_name":"SHV-108","ARO_description":"SHV-108 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"680":{"model_id":"680","model_name":"CMY-54","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1036":{"protein_sequence":{"accession":"ADK55604.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLELDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"HM544039","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002065","ARO_id":"38465","ARO_name":"CMY-54","ARO_description":"CMY-54 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"681":{"model_id":"681","model_name":"TEM-120","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1072":{"protein_sequence":{"accession":"AAO85882.1","sequence":"MSIQHFRVALIPFFAAFCFPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AY243512","fmin":"208","fmax":"1069","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCTTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3000982","ARO_id":"37362","ARO_name":"TEM-120","ARO_description":"TEM-120 is an extended-spectrum beta-lactamase found in Klebsiella oxytoca.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"682":{"model_id":"682","model_name":"QnrS4","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"212":{"protein_sequence":{"accession":"ACJ24509.1","sequence":"METYNHTYRHHNFSHKDLSDLTFTACTFIRSDFRRANLRDTTFVNCKFIEQGDIEGCHFDAADLRDASFQQCQLAMANFSNANCYGIEFRACDLKGANFSRTNFAHQVSNRMYFCSAFISGCNLSYANMERVCLEKCELFENRWIGTNLAGASLKESDLSRGVFSEDVWGQFSLQGANLCHAELDGLDPRKVDTSGIKIAAWQQELILEALGIVVYPD"},"dna_sequence":{"accession":"FJ418153","fmin":"0","fmax":"657","strand":"+","sequence":"ATGGAAACCTACAATCATACATATCGGCACCACAACTTTTCACATAAAGACTTAAGTGATCTCACCTTCACCGCTTGCACATTCATTCGCAGCGACTTTCGACGTGCTAACTTGCGTGATACGACATTCGTCAACTGCAAGTTCATTGAACAGGGTGATATCGAAGGCTGCCACTTTGATGCCGCAGATCTTCGTGATGCAAGTTTCCAACAATGCCAACTTGCGATGGCAAACTTCAGTAATGCCAATTGCTACGGTATAGAGTTCCGTGCGTGTGATTTAAAAGGTGCCAACTTTTCCCGAACAAACTTTGCCCATCAAGTGAGTAATCGTATGTACTTTTGCTCAGCATTTATTTCTGGATGTAATCTTTCCTATGCCAATATGGAGAGGGTTTGTTTAGAAAAATGTGAGTTGTTTGAAAATCGCTGGATAGGAACGAACCTAGCGGGTGCATCACTGAAAGAGTCAGACTTAAGTCGAGGTGTTTTTTCCGAAGATGTCTGGGGGCAATTTAGCCTACAGGGTGCCAATTTATGCCACGCCGAACTCGACGGTTTAGATCCCCGCAAAGTCGATACATCAGGTATCAAAATTGCAGCCTGGCAGCAAGAACTGATTCTCGAAGCACTGGGTATTGTTGTTTATCCTGACTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35767","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Stanley","NCBI_taxonomy_id":"192953"}}}},"ARO_accession":"3002793","ARO_id":"39227","ARO_name":"QnrS4","ARO_description":"QnrS4 is a plasmid-mediated quinolone resistance protein found in Salmonella enterica","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"683":{"model_id":"683","model_name":"CMY-75","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1587":{"protein_sequence":{"accession":"AFK73434.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDDVTDKAELLRFYQNWQPQWTPGAKRLYANSSIGLFGALVVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"JQ733572","fmin":"1027","fmax":"2173","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCGCTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGCATGGCCGTGGCAATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAATTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGAATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTATGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGTGGTAAAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACAGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATAGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGCGTCGAGGCGGCCTGGCGCATTCTTGAAAAACTGCAATAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002088","ARO_id":"38488","ARO_name":"CMY-75","ARO_description":"CMY-75 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"684":{"model_id":"684","model_name":"SHV-37","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1475":{"protein_sequence":{"accession":"AAL82593.1","sequence":"MRYIRLCIISLLAALPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITVSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQHIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AF467948","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCGCCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCGTGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGGGACAATGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCATATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001095","ARO_id":"37475","ARO_name":"SHV-37","ARO_description":"SHV-37 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"685":{"model_id":"685","model_name":"OXA-239","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1529":{"protein_sequence":{"accession":"AFN65709.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETPSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRLFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMNIKSQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"JQ837239","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTTATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGACCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCCCAATTAGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGAATATAAAATCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39095","NCBI_taxonomy_name":"Acinetobacter sp. enrichment culture clone 8407","NCBI_taxonomy_id":"1182652"}}}},"ARO_accession":"3001498","ARO_id":"37898","ARO_name":"OXA-239","ARO_description":"OXA-239 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"686":{"model_id":"686","model_name":"OXA-162","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"967":{"protein_sequence":{"accession":"ADG27454.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSARIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"HM015773","fmin":"2126","fmax":"2924","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGACAGTTTCTGGCTCGACGGTGGTATTCGAATTTCGGCCACGGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATGCTGACCGAAGCCAATGGTGACTATATTATTCGGGCTAAAACTGGATACTCGGCTAGAATCGAACCTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001776","ARO_id":"38176","ARO_name":"OXA-162","ARO_description":"OXA-162 is a beta-lactamase found in Enterobacteriaceae","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"687":{"model_id":"687","model_name":"APH(3')-Vc","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"470":{"protein_sequence":{"accession":"AAB21326.1","sequence":"MYAMLRRKYQHYEWTSVNEGDSGASVYRLAGQQPELYVKFAPREPENSAFDLAGEADRLTWLTRHGIPVPCIVECGGDDTSVFLVTEAVTGVSAAEEWPEHQRFAVVEAMADLARTLHELPVGGCPFDRSLAVTVAEARHNLREGLVDLDDLQEEHANWSGDQLLAELDRTRPEKEDLVLCHGDLCPNNVLLDPETCRVTGMIDVGRLGRADRHADLALAARELEIDEDPWFGPEYAQRFLERYGAHHVDENKMAFYQLLDEFF"},"dna_sequence":{"accession":"S81599","fmin":"281","fmax":"1076","strand":"+","sequence":"ATGTACGCCATGTTGCGCCGGAAATACCAGCACTACGAATGGACCTCCGTGAACGAAGGAGATTCGGGCGCCTCCGTTTACCGCCTCGCCGGACAGCAGCCCGAGCTCTATGTGAAATTCGCTCCGCGCGAACCGGAAAATTCCGCGTTCGACCTGGCGGGCGAGGCCGACCGGCTCACCTGGCTCACCCGCCACGGCATCCCGGTTCCGTGCATTGTCGAGTGCGGCGGCGACGACACCTCGGTTTTCCTCGTCACCGAGGCCGTCACCGGCGTATCGGCCGCCGAGGAGTGGCCGGAGCACCAGCGCTTCGCCGTCGTCGAGGCGATGGCCGACCTCGCCCGCACCCTGCACGAACTGCCCGTTGGTGGCTGCCCCTTCGATCGCAGCCTGGCGGTGACGGTTGCCGAAGCCCGCCACAACCTACGCGAGGGCCTCGTGGACCTGGACGACCTCCAAGAGGAGCACGCCAACTGGTCCGGTGACCAGCTTCTCGCCGAGCTCGACCGAACGCGGCCCGAGAAAGAGGATCTGGTCCTCTGCCACGGGGACCTGTGCCCCAACAACGTGCTGCTCGATCCCGAGACATGCCGAGTCACCGGAATGATCGATGTGGGCCGCCTCGGCCGCGCCGATCGCCACGCCGACCTGGCCCTCGCCGCCCGCGAGCTGGAGATCGACGAGGATCCCTGGTTTGGCCCCGAGTACGCCCAGCGGTTCCTCGAACGCTACGGCGCGCACCACGTCGACGAGAACAAGATGGCCTTTTACCAGCTGCTCGACGAGTTTTTCTAGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39506","NCBI_taxonomy_name":"Micromonospora chalcea","NCBI_taxonomy_id":"1874"}}}},"ARO_accession":"3002651","ARO_id":"39051","ARO_name":"APH(3')-Vc","ARO_description":"APH(3')-Vc is a chromosomal-encoded aminoglycoside phosphotransferase in M. chalcea","ARO_category":{"36265":{"category_aro_accession":"3000126","category_aro_cvterm_id":"36265","category_aro_name":"APH(3')","category_aro_description":"Phosphorylation of 2-deoxystreptamine aminoglycosides on the hydroxyl group at position 3'","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"688":{"model_id":"688","model_name":"MOX-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1039":{"protein_sequence":{"accession":"CAB82578.1","sequence":"MQQRQSILWGALATLMWAGLAHAGETSPVDPLRPVVDASIRPLLKEHRIPGMAVAVLKDGKAHYFNYGVADRERAVGVSEQTLFEIGSVSKPLTATLGAYAVVKGAMQLDDKASRHAPWLKGSAFDSITMGELATYSAGGLPLQFPEEVDSLEKMQAYYRQWTPAYSPGSHRQYSNPSIGLFGHLAASSMKQPFAQLMEQTLLPGLGLHHTYVNVPKQAMASYAYGYSKEDKPIRVSPGMLADEAYGIKTSSADLLRFVKANISGVHDKALQQAISLTHKGHYSVGGMTQGLGWESYAYPVSEQTLLAGNSAKVILEANPTAAPRESGSQMLFNKTGSTSGFGAYVAFVPAKGIGIVMLANRNYPIPARVKAAHAILTQLAR"},"dna_sequence":{"accession":"AJ276453","fmin":"4619","fmax":"5768","strand":"+","sequence":"ATGCAACAACGACAATCCATCCTGTGGGGCGCTCTGGCCACCCTGATGTGGGCCGGTCTGGCCCATGCAGGTGAGACTTCACCGGTCGATCCCCTGCGCCCCGTGGTGGATGCCAGCATCCGGCCGCTGCTCAAGGAGCACAGGATCCCGGGCATGGCGGTGGCCGTGCTCAAGGATGGCAAGGCCCACTATTTCAACTACGGTGTGGCCGATCGGGAGCGCGCAGTCGGTGTCAGCGAGCAGACCCTGTTCGAGATAGGCTCCGTGAGCAAGCCCCTGACCGCGACCCTAGGAGCCTATGCGGTGGTCAAGGGAGCGATGCAACTGGATGACAAGGCGAGCCGGCACGCCCCCTGGCTCAAGGGATCCGCCTTTGACAGCATCACCATGGGGGAGCTGGCTACCTACAGCGCGGGCGGCTTGCCGCTGCAATTCCCCGAGGAGGTGGATTCGCTCGAGAAGATGCAGGCCTACTACCGCCAGTGGACCCCAGCCTACTCGCCGGGTTCCCATCGCCAGTACTCTAACCCCAGCATAGGGCTGTTCGGCCACCTGGCGGCGAGCAGCATGAAGCAGCCGTTTGCCCAGTTGATGGAGCAGACGCTCCTGCCGGGGCTTGGCCTGCACCACACCTATGTCAATGTGCCGAAGCAGGCCATGGCGAGTTATGCCTATGGCTATTCGAAAGAGGACAAGCCCATCAGGGTCAGCCCCGGCATGCTGGCGGACGAGGCCTACGGCATCAAGACCAGCTCGGCGGATCTGCTGCGCTTTGTGAAGGCCAACATCAGCGGGGTTCATGACAAGGCGTTGCAGCAGGCCATCTCCCTGACCCACAAAGGGCACTACTCGGTAGGCGGGATGACCCAGGGACTGGGTTGGGAGAGTTACGCCTATCCCGTCAGCGAGCAGACATTGCTGGCGGGCAATTCGGCCAAGGTGATCCTCGAAGCCAATCCGACGGCGGCGCCCCGGGAGTCGGGGAGCCAGATGCTCTTCAACAAGACCGGCTCGACCAGCGGCTTCGGCGCCTATGTGGCCTTCGTGCCGGCCAAAGGGATCGGCATCGTCATGCTGGCCAACCGCAACTATCCTATCCCGGCCAGGGTGAAAGCGGCCCACGCCATCCTGACGCAACTGGCCAGGTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002183","ARO_id":"38583","ARO_name":"MOX-2","ARO_description":"MOX-2 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36222":{"category_aro_accession":"3000083","category_aro_cvterm_id":"36222","category_aro_name":"MOX beta-lactamase","category_aro_description":"MOX beta-lactamases are plasmid-mediated AmpC-type beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"689":{"model_id":"689","model_name":"CTX-M-123","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1254":{"protein_sequence":{"accession":"AFA51701.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"JN790864","fmin":"238","fmax":"1114","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001982","ARO_id":"38382","ARO_name":"CTX-M-123","ARO_description":"CTX-M-123 is a beta-lactamase found in Escherichia coli","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"690":{"model_id":"690","model_name":"OXA-347","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4335":{"protein_sequence":{"accession":"AET35493.1","sequence":"MKNILFVVFISMIFLFVCCNTTTNKNIIETEISDFDKILDSFQVNGSILIYDNDKNTFYSNDFDWAKNGKLPASTFKIPNSIIAVELGIIENDTTILKWNGEQRKMDIWEKDLSFKDAFRISCVPCYQEIARKIGTIKMKEYLEKFEYKNMIFDSLTIDNFWLEGNSKISQKQQIDFLRKFYFSKFPISDRTIKIVKNIMEIERTENYILSGKTGLSSIEEKYNGWFVGYVETKSNVYFFATNVIPTDGLNVDDFISSRINVTKNALKQMNIMK"},"dna_sequence":{"accession":"JN086160","fmin":"1582","fmax":"2407","strand":"-","sequence":"TCATTTCATTATATTCATTTGCTTTAACGCATTTTTTGTTACATTAATTCTCGATGAAATAAAATCATCAACATTCAATCCGTCTGTCGGAATTACATTTGTTGCAAAAAAATAAACATTAGATTTTGTTTCAACATAACCAACAAACCAACCATTATATTTTTCTTCTATCGAACTTAATCCAGTCTTACCGCTTAAAATGTAATTTTCAGTTCGCTCAATTTCCATAATATTTTTGACAATCTTTATTGTCCTATCAGAAATTGGAAATTTTGAAAAATAGAATTTCCTTAAAAAGTCGATTTGTTGTTTTTGAGATATTTTTGAATTTCCTTCAAGCCAAAAATTGTCAATCGTTAAACTGTCAAAAATCATATTTTTATACTCAAATTTTTCTAAATATTCTTTCATTTTAATTGTTCCGATTTTCCTTGCAATTTCCTGATAGCAAGGAACACAGGAAATTCTAAAAGCATCTTTAAATGATAAATCTTTTTCCCAAATATCCATTTTTCTCTGCTCGCCATTCCATTTTAAAATAGTTGTATCATTTTCAATAATGCCTAATTCAACAGCAATTATAGAATTTGGAATTTTGAATGTTGATGCAGGTAATTTTCCGTTTTTAGCCCAATCAAAGTCATTTGAGTAAAAAGTATTCTTGTCGTTATCATAAATTAGAATTGAACCATTTACTTGAAAACTATCTAAAATTTTGTCAAAATCAGAAATTTCTGTTTCAATTATGTTTTTATTCGTTGTTGTGTTACAGCAAACAAATAAAAATATCATTGAAATAAAAACTACAAATAAAATATTTTTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3001777","ARO_id":"38177","ARO_name":"OXA-347","ARO_description":"OXA-347 is a beta-lactamase found in Enterobacteriaceae","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"691":{"model_id":"691","model_name":"vanRE","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"167":{"protein_sequence":{"accession":"AAL27445.1","sequence":"MAKILILDDEKEIVSLLSTLLSNEGYEVYEAMSGKESLEIIENNKIDLAILDVMLPDISGFDVLQSIREKQFFPVLMLTARGQDMDKITGLSMGADDYIVKPFNPFEVLARVKTQLRRYQTYNSQSIDETNEYAKNGLNISVNSRKVFLYDEEIKLTPIEFDILWYLCRNEGRVISSEELFEKVWKEDYLENNNTVMAHIAKIREKMHEKPRQPNIIKTVWGVGYTIEK"},"dna_sequence":{"accession":"FJ872411","fmin":"43513","fmax":"44203","strand":"+","sequence":"ATGGCTAAAATACTAATTTTAGATGATGAAAAAGAGATTGTAAGTCTTCTAAGTACGCTACTTTCTAACGAAGGATATGAGGTTTATGAGGCTATGTCAGGAAAAGAAAGCTTGGAGATTATAGAAAATAACAAGATCGATTTAGCCATACTAGATGTCATGCTTCCCGATATTTCCGGTTTTGATGTATTGCAAAGCATTAGAGAAAAACAATTTTTTCCTGTGTTGATGCTAACTGCTCGAGGTCAGGATATGGATAAAATTACTGGACTGTCTATGGGGGCAGATGACTATATTGTTAAGCCGTTCAATCCTTTTGAAGTGTTGGCTAGAGTGAAAACACAGCTACGTAGATATCAAACGTATAATTCTCAAAGTATAGATGAAACAAATGAATATGCAAAAAATGGATTAAATATATCTGTCAACAGTCGAAAAGTATTCTTATATGATGAAGAAATTAAATTAACGCCTATTGAATTTGATATCTTGTGGTATTTGTGTAGAAATGAAGGTCGCGTAATATCGTCAGAAGAGTTATTTGAAAAAGTCTGGAAAGAAGACTATCTAGAGAATAATAATACTGTTATGGCGCATATTGCTAAAATTAGAGAAAAGATGCATGAAAAGCCGAGACAGCCAAATATTATAAAAACGGTATGGGGAGTAGGTTATACAATTGAAAAATAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3002924","ARO_id":"39358","ARO_name":"vanRE","ARO_description":"vanRE is a vanR variant found in the vanE gene cluster","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36713":{"category_aro_accession":"3000574","category_aro_cvterm_id":"36713","category_aro_name":"vanR","category_aro_description":"VanR is a OmpR-family transcriptional activator in the VanSR regulatory system. When activated by VanS, it promotes cotranscription of VanA, VanH, and VanX.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"692":{"model_id":"692","model_name":"TEM-159","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1646":{"protein_sequence":{"accession":"ABM54869.1","sequence":"MSIQHFRVALIPFFAAFCFPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMISTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTTPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"EF136376","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCTTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATTAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3001025","ARO_id":"37405","ARO_name":"TEM-159","ARO_description":"TEM-159 is an inhibitor-resistant beta-lactamase found in Proteus mirabilis.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"693":{"model_id":"693","model_name":"OXA-22","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1606":{"protein_sequence":{"accession":"AAD12233.1","sequence":"MKRRHAAIGALLAALATFAHAEHPICTIVADAATGKAVLHEGKCDERVTPASTFKLALAVMGFDHGFLKDEHTPVEHFRHGDPDWGGEAWHQPIDPALWLKYSVVWYSQRITHAMGAQTFQAYVRKLGYGNMDVSGDPGKNNGMDRSWITSSLKISPEEQVGLMRRIVNRQLPVSAHTYEMLDRTVQTWQVPGGWAVQGKTGTAGPAPGNTSPDGTWDQAHAYGWFVGWARKGDKTYVFANLIQDDKVEPTSGGIRSRDALFARLSEVLAFAGH"},"dna_sequence":{"accession":"AF064820","fmin":"951","fmax":"1776","strand":"+","sequence":"ATGAAACGCCGCCACGCCGCCATCGGCGCCCTGCTTGCCGCGCTTGCCACCTTTGCCCACGCCGAGCACCCGATCTGCACGATCGTGGCCGATGCCGCCACGGGCAAGGCCGTCTTGCATGAAGGCAAGTGCGACGAGCGCGTGACGCCCGCTTCCACCTTCAAGCTGGCGCTGGCCGTCATGGGCTTCGACCACGGCTTCCTCAAAGATGAGCACACCCCGGTTGAGCACTTCAGGCACGGTGACCCCGACTGGGGCGGCGAAGCCTGGCACCAGCCGATCGACCCGGCGCTGTGGCTCAAGTATTCGGTGGTCTGGTATTCGCAGCGCATTACGCATGCGATGGGCGCGCAGACCTTCCAGGCCTACGTGCGCAAGCTTGGCTACGGCAACATGGATGTGAGCGGCGATCCGGGCAAGAACAACGGCATGGACCGCTCGTGGATCACCTCGTCGCTGAAGATTTCGCCGGAAGAGCAAGTCGGCTTGATGCGCCGGATCGTCAACCGGCAGTTGCCGGTGTCGGCGCACACCTACGAGATGCTCGACCGTACCGTGCAGACCTGGCAGGTGCCCGGCGGCTGGGCGGTGCAGGGCAAGACGGGCACTGCCGGTCCGGCGCCGGGCAACACGTCGCCCGATGGCACGTGGGATCAGGCACACGCTTACGGCTGGTTTGTCGGCTGGGCCAGGAAGGGCGACAAGACCTACGTATTCGCCAACCTGATCCAGGACGACAAGGTTGAGCCGACGTCGGGCGGTATCCGCTCGCGCGATGCGCTGTTTGCTCGCCTGTCGGAAGTGCTGGCCTTTGCTGGGCACTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36921","NCBI_taxonomy_name":"Ralstonia pickettii","NCBI_taxonomy_id":"329"}}}},"ARO_accession":"3001417","ARO_id":"37817","ARO_name":"OXA-22","ARO_description":"OXA-22 is a beta-lactamase found in Ralstonia pickettii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"694":{"model_id":"694","model_name":"CTX-M-40","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4239":{"protein_sequence":{"accession":"AAV28215.2","sequence":"MRHRVKRMMLMTTACISLLLGSAPLYAQANDVQQKLAALEKSSGGRLGVALIDTADNAQTLYRADERFAMCSTSKVMAAAAVLKQSETQKNVLSQKVEIKSSDLINYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAHLGGPDKVTAFARAIGDDTFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLRHLTLGSALGETQRAQLVTWLKGNTTGAASIQAGLPTSWVVGDKTGSGDYGTTNDIAVIWPEGRAPLILVTYFTQPEQKAESRRDVLAAAAKIVTDGY"},"dna_sequence":{"accession":"AY750914.2","fmin":"206","fmax":"1079","strand":"+","sequence":"ATGAGACATCGCGTTAAGCGGATGATGCTAATGACAACGGCCTGTATTTCGCTGTTGCTGGGGAGTGCGCCGCTGTATGCGCAGGCGAACGACGTTCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGGGGGCGGTTGGGAGTGGCGCTGATTGACACCGCCGATAACGCACAGACGCTCTACCGCGCCGACGAGCGCTTTGCCATGTGCAGCACCAGTAAGGTGATGGCAGCCGCGGCGGTGCTCAAGCAAAGTGAAACGCAAAAGAACGTGTTGAGTCAGAAGGTTGAGATTAAATCCTCGGACCTGATTAACTACAATCCCATCGCTGAAAAACACGTCAACGGCACGATGACGCTGGCGGAATTGAGCGCCGCGGCGTTGCAGTACAGCGATAATACGGCCATGAACAAGCTGATTGCCCATCTTGGGGGGCCGGATAAAGTGACGGCGTTTGCCCGTGCGATTGGGGATGACACCTTCCGGCTCGATCGTACTGAGCCGACGCTCAACACCGCGATCCCCGGCGACCCGCGCGATACCACCACGCCATTAGCGATGGCGCAGACGCTTCGCCATCTGACGTTGGGCAGTGCCTTAGGTGAAACTCAGCGTGCGCAACTGGTAACGTGGCTGAAAGGCAACACCACCGGTGCTGCCAGCATTCAGGCTGGGCTACCCACATCGTGGGTTGTCGGGGATAAAACCGGCAGCGGTGATTATGGTACGACGAATGACATCGCCGTCATCTGGCCGGAAGGGCGTGCGCCGCTTATTCTGGTCACTTACTTCACCCAACCGGAGCAGAAGGCAGAAAGTCGTCGTGACGTGCTCGCGGCTGCCGCGAAAATCGTCACCGACGGTTATTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001902","ARO_id":"38302","ARO_name":"CTX-M-40","ARO_description":"CTX-M-40 is a beta-lactamase found in Escherichia coli","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"695":{"model_id":"695","model_name":"CMY-66","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"783":{"protein_sequence":{"accession":"AEZ49849.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDDITDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALVVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASLVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"JN714478","fmin":"1034","fmax":"2180","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCACTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGACATTACGGATAAAGCCGCATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGTGGTAAAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGGCAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCTCGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACAGGATCCACAGGCGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTAATGTTGGCAAACAAAAGCTACCCCAACCCGGCTCGCGTCGAGGCGGCCTGGCGCATTCTTGAAAAACTGCAATAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002079","ARO_id":"38479","ARO_name":"CMY-66","ARO_description":"CMY-66 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"696":{"model_id":"696","model_name":"cfrA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"3289":{"protein_sequence":{"accession":"CAL64019.1","sequence":"MNFNNKTKYGKIQEFLRSNNEPDYRIKQITNAIFKQRISRFEDMKVLPKLLREDLINNFGETVLNIKLLAEQNSEQVTKVLFEVSKNERVETVNMKYKAGWESFCISSQCGCNFGCKFCATGDIGLKKNLTVDEITDQVLYFHLLGHQIDSISFMGMGEALANRQVFDALDSFTDPNLFALSPRRLSISTIGIIPSIKKITQEYPQVNLTFSLHSPYSEERSKLMPINDRYPIDEVMNILDEHIRLTSRKVYIAYIMLPGVNDSLEHANEVVSLLKSRYKSGKLYHVNLIRYNPTISAPEMYGEANEGQVEAFYKVLKSAGIHVTIRSQFGIDIDAACGQLYGNYQNSQ"},"dna_sequence":{"accession":"AM408573","fmin":"10027","fmax":"11077","strand":"-","sequence":"CTATTGGCTATTTTGATAATTACCATATAATTGACCACAAGCAGCGTCAATATCAATCCCAAATTGACTTCTAATTGTGACATGGATACCAGCAGACTTCAAAACTTTGTAAAAGGCTTCTACCTGCCCTTCGTTTGCTTCTCCATACATCTCAGGTGCACTTATTGTAGGATTGTATCGTATCAAATTTACATGATATAACTTCCCTGATTTATAGCGACTTTTAAGAAGGCTAACAACTTCGTTTGCATGCTCAAGAGAATCATTTACACCAGGCAACATGATATAAGCTATATATACTTTCCTTGAAGTTAATCTTATATGTTCATCGAGTATATTCATTACCTCATCTATTGGGTATCTATCATTTATTGGCATCAATTTGCTGCGTTCCTCACTATAAGGTGAGTGTAATGAAAATGTAAGATTTACTTGAGGATATTCCTGGGTTATTTTTTTGATACTAGGTATAATACCAATCGTTGATATAGAAAGTCTACGAGGACTTAATGCAAATAAATTAGGATCCGTAAACGAATCAAGAGCATCAAATACTTGACGGTTGGCTAGAGCTTCACCCATTCCCATAAAAGAAATGCTATCAATTTGATGACCTAATAAATGGAAGTATAAAACTTGATCTGTTATCTCATCTACAGTTAGGTTTTTTTTCAATCCAATGTCGCCTGTAGCACAAAATTTACACCCAAAATTACATCCGCATTGTGATGATATACAAAATGACTCCCAACCTGCTTTATACTTCATGTTTACCGTTTCTACTCTCTCATTCTTTGATACTTCAAAAAGCACTTTCGTAACTTGCTCTGAATTTTGCTCTGCTAAGAGCTTGATATTCAAAACTGTTTCTCCAAAATTATTTATTAAATCCTCCCTAAGTAATTTTGGAAGAACCTTCATATCCTCAAATCGACTAATTCTTTGTTTAAAAATCGCATTGGTTATTTGTTTTATTCTATAATCAGGCTCATTATTACTTCTTAAAAATTCCTGTATTTTACCATACTTTGTTTTATTATTAAAATTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40034","NCBI_taxonomy_name":"Staphylococcus warneri","NCBI_taxonomy_id":"1292"}}}},"ARO_accession":"3003441","ARO_id":"40028","ARO_name":"cfrA","ARO_description":"CfrA is a chloramphenicol-florfenicol resistance gene and methyltransferase enzyme. Methylation of position 8 of A2503 in 23S rRNA confers resistance to chloramphenicol antibiotics. Additional Oxazolidinone resistance mediated by the cfr gene in a human isolated was first reported from Colombia in linezolid- and methicillin-resistant staphylocci. Described by Arias et al. 2008.","ARO_category":{"36341":{"category_aro_accession":"3000202","category_aro_cvterm_id":"36341","category_aro_name":"Cfr 23S ribosomal RNA methyltransferase","category_aro_description":"Cfr genes produce enzymes which catalyze the methylation of the 23S rRNA subunit at position 8 of adenine-2503. Methylation of 23S rRNA at this site confers resistance to some classes of antibiotics, including streptogramins, chloramphenicols, florfenicols, linezolids and clindamycin.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"35989":{"category_aro_accession":"0000072","category_aro_cvterm_id":"35989","category_aro_name":"linezolid","category_aro_description":"Linezolid is a synthetic antibiotic used for the treatment of serious infections caused by Gram-positive bacteria that are resistant to several other antibiotics. It inhibits protein synthesis by binding to domain V of the 23S rRNA of the 50S subunit of bacterial ribosomes.","category_aro_class_name":"Antibiotic"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37015":{"category_aro_accession":"3000671","category_aro_cvterm_id":"37015","category_aro_name":"tiamulin","category_aro_description":"Tiamulin is a pleuromutilin derivative currently used in veterinary medicine. It binds to the 23 rRNA of the 50S ribosomal subunit to inhibit protein translation.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"36218":{"category_aro_accession":"3000079","category_aro_cvterm_id":"36218","category_aro_name":"oxazolidinone antibiotic","category_aro_description":"Oxazolidinones are a class of synthetic antibiotics discovered the the 1980's.  They inhibit protein synthesis by binding to domain V of the 23S rRNA of the 50S subunit of bacterial ribosomes.  Linezolid is the only member of this class currently in clinical use.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"697":{"model_id":"697","model_name":"Erm(42)","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"11":{"protein_sequence":{"accession":"CBY77552.1","sequence":"MNKNTKIKNKNFNIKDSQNFLHNTKLVEDLLFKSNITKEDFVVEIGPGKGIITKALSKICKAVNAIEFDSVLADKLSHEFKSSNVSIIEADFLKYNLPDHNYKVFSNIPFNITASILNKLLDSENPPLDTFLIMQYEPFLKYAGAPSYKESYKSLLYKPFFKTNILHSFSKFDFKPAPNANIILGQFSYKDFTDINLEDRHAWKDFLAFVFLEKGVTFKEKTKRIFSYKQQKIILKESRINDDSNISNWSYEFWLKMFKLYNSNMVSKDKKVLVNNSYKRMLEHESSLEKIHRNRKQNNRK"},"dna_sequence":{"accession":"FR734406","fmin":"0","fmax":"906","strand":"+","sequence":"ATGAATAAAAACACTAAAATAAAAAACAAAAATTTCAACATTAAAGACTCACAGAATTTTTTGCATAATACTAAATTAGTCGAAGATTTGCTTTTTAAAAGCAATATAACTAAGGAGGATTTTGTTGTTGAGATTGGGCCTGGAAAAGGCATAATAACCAAGGCATTAAGCAAAATCTGCAAAGCCGTTAATGCTATTGAGTTCGATAGTGTATTGGCTGATAAGTTGAGCCATGAATTTAAAAGTTCAAATGTGTCTATTATTGAAGCCGATTTTTTAAAATACAATTTACCAGACCATAATTATAAAGTTTTTTCAAACATTCCATTTAACATAACGGCAAGTATTTTAAATAAATTGTTAGATAGTGAGAACCCACCCTTAGATACTTTTTTAATTATGCAATATGAACCTTTTTTAAAGTATGCGGGTGCACCATCTTACAAGGAGTCTTATAAATCTTTATTATATAAACCATTTTTCAAAACTAACATATTGCATAGCTTTAGCAAATTTGATTTTAAGCCAGCTCCAAACGCAAACATTATTTTGGGCCAATTTTCTTATAAAGACTTTACAGATATAAACCTTGAAGACAGGCATGCTTGGAAAGATTTTTTAGCCTTTGTCTTTTTAGAAAAGGGAGTTACATTTAAAGAAAAAACAAAACGAATTTTTAGTTATAAGCAACAAAAAATAATTTTAAAAGAAAGCCGAATTAATGATGATTCAAATATAAGTAATTGGAGTTATGAATTTTGGCTAAAAATGTTTAAACTCTATAATTCGAACATGGTAAGCAAGGATAAAAAAGTTTTAGTTAACAATTCGTATAAAAGAATGTTAGAACATGAGTCTAGTTTAGAAAAGATTCATAGAAATAGAAAGCAAAATAACAGAAAATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36867","NCBI_taxonomy_name":"Pasteurella multocida","NCBI_taxonomy_id":"747"}}}},"ARO_accession":"3003106","ARO_id":"39680","ARO_name":"Erm(42)","ARO_description":"Erm42 confers MLSb phenotype in Pasteurella multocida","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"698":{"model_id":"698","model_name":"TEM-205","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1957":{"protein_sequence":{"accession":"AGZ20205.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTTPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"KC900516","fmin":"0","fmax":"858","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTATTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACGCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001382","ARO_id":"37782","ARO_name":"TEM-205","ARO_description":"From the Lahey list of beta-lactamases. Not yet released.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"699":{"model_id":"699","model_name":"QnrS9","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"632":{"protein_sequence":{"accession":"AHF20043.1","sequence":"METYNHTYRHHNFSHKDLSDLTFTACTFIRSDFRRANLRDTTFVNCKFIEQGDIEGCHFDVADLRDASFQQCQLAMANFSNANCYGIEFRACDLKGANFFRTNFAHQVSNRMYFCSAFISGCNLSYANMERVCLEKCELFENRWIGTNLAGASLKESDLSRGVFSEDVWGQFSLQGANLCHAELDGLDPRKVDTSGIKIAAWQQELILEALGIVVYPD"},"dna_sequence":{"accession":"KF732714","fmin":"0","fmax":"657","strand":"+","sequence":"ATGGAAACCTACAATCATACATATCGGCACCACAACTTTTCACATAAAGACTTAAGTGATCTCACCTTCACCGCTTGCACATTCATTCGCAGCGACTTTCGACGTGCTAACTTGCGTGATACGACATTCGTCAACTGCAAGTTCATTGAACAGGGTGATATCGAAGGCTGCCACTTTGATGTCGCAGATCTTCGTGATGCAAGTTTCCAACAATGCCAACTTGCGATGGCAAACTTCAGTAATGCCAATTGCTACGGTATAGAGTTCCGTGCGTGTGATTTAAAAGGTGCCAACTTTTTCCGAACAAACTTTGCCCATCAAGTGAGTAATCGTATGTACTTTTGCTCAGCATTTATTTCTGGATGTAATCTTTCCTATGCCAATATGGAGAGGGTTTGTTTAGAAAAATGTGAGTTGTTTGAAAATCGCTGGATAGGAACGAACCTAGCGGGTGCATCACTGAAAGAGTCAGACTTAAGTCGAGGTGTTTTTTCCGAAGATGTCTGGGGGCAATTTAGCCTACAGGGTGCCAATTTATGCCACGCCGAACTCGACGGTTTAGATCCCCGCAAAGTCGATACATCAGGTATCAAAATTGCAGCCTGGCAGCAAGAACTGATTCTCGAAGCACTGGGTATTGTTGTTTATCCTGACTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002798","ARO_id":"39232","ARO_name":"QnrS9","ARO_description":"QnrS9 is a plasmid-mediated quinolone resistance protein found in Klebsiella pneumoniae","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"700":{"model_id":"700","model_name":"ACT-31","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1342":{"protein_sequence":{"accession":"AIT76096.1","sequence":"MMKKSLCCALLLGLSCSALAAPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKSHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPEKVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYHILDALQ"},"dna_sequence":{"accession":"KM087843","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCTCTTTGCTGCGCCCTGCTGCTGGGCCTCTCTTGCTCTGCTCTCGCCGCGCCAGTATCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAATCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACAGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTTCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAAGGTTGCCGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAAGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTACCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGTTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTACCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGACGCGCTACAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001851","ARO_id":"38251","ARO_name":"ACT-31","ARO_description":"ACT-31 is a beta-lactamase. From the Lahey list of ACT beta-lactamases.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"701":{"model_id":"701","model_name":"SHV-129","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"986":{"protein_sequence":{"accession":"ADE08533.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASKRGARGIVALLGPNNKAERIVVIYLRDTPASMAELDQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"GU827715","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCAAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCTCGATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001176","ARO_id":"37556","ARO_name":"SHV-129","ARO_description":"SHV-129 is an extended-spectrum beta-lactamase that has been found in clinical isolates.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"702":{"model_id":"702","model_name":"CTX-M-98","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1030":{"protein_sequence":{"accession":"ADO17948.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAVAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGGYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"HM755448","fmin":"244","fmax":"1120","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGTCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGGCTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001957","ARO_id":"38357","ARO_name":"CTX-M-98","ARO_description":"CTX-M-98 is a beta-lactamase found in Escherichia coli","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"703":{"model_id":"703","model_name":"cmlv","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"82":{"protein_sequence":{"accession":"AAB36568.1","sequence":"MPSPSAEPTTSTPTPDAGPAASPRMPLAVYILGLSAFALGTSEFMLSGLVPPIAEDMNVSIPRAGLLISAFAIGMVVGAPLLAVATLRLPRKTTLIALITVFGLRQMAGALAPNYAVLFASRVISALPCAGFWAVGAAVAIAMVPVGSRARALAVMIGGLSIANVLRVPAGAFLGEHLGWASAFWAVGLASAIALVGVVTRIPRIPLPETRPRPLKNEVAIYRDRQVLLSIAVTALAAGGVFCAFSYLAPLLTDVSGLDEAWVSGVLGLFGIGAVVGTTIGGRVADAHLFGVLLTGISASTVFLVALALFASNPAATIVLTFLLGVSAFYTAPALNARMFNVAGAAPTLAGATTTAAFNLGNTGGPWLGGTVIDANLGFASTAWAGAAMTVLGLGTAALALRLTKRPAPGHVVARSRGAGGTTPSEPARGKATSSC"},"dna_sequence":{"accession":"U09991","fmin":"27","fmax":"1338","strand":"+","sequence":"ATGCCGTCTCCCTCCGCCGAGCCCACGACATCCACCCCGACCCCCGACGCCGGGCCCGCCGCATCCCCCCGGATGCCCCTGGCCGTCTACATCCTCGGACTGTCCGCGTTCGCGCTCGGGACGAGCGAATTCATGCTCTCCGGCCTCGTGCCGCCCATCGCGGAGGACATGAACGTCTCCATCCCCCGCGCCGGACTCCTCATCTCGGCGTTCGCGATCGGCATGGTCGTCGGCGCACCGCTCCTCGCCGTCGCCACCCTCCGGCTCCCCCGCAAGACCACCCTCATCGCCCTCATCACCGTCTTCGGCCTGCGCCAGATGGCCGGCGCCCTCGCCCCCAACTACGCGGTCCTCTTCGCCTCCCGCGTGATCAGCGCCCTGCCCTGCGCGGGCTTCTGGGCGGTCGGCGCGGCGGTGGCCATCGCGATGGTCCCGGTCGGCTCACGGGCCCGGGCGCTGGCGGTCATGATCGGCGGCCTCTCCATCGCCAACGTCCTGCGCGTCCCCGCCGGCGCCTTCCTCGGCGAGCACCTCGGCTGGGCCTCCGCCTTCTGGGCCGTCGGCCTCGCCTCCGCCATCGCGCTCGTCGGCGTCGTCACCCGCATCCCCCGCATCCCGCTCCCCGAGACCAGGCCCCGCCCTCTCAAGAACGAGGTCGCCATCTACCGCGACCGCCAGGTCCTCCTGTCGATCGCGGTCACGGCCCTCGCGGCGGGCGGCGTCTTCTGCGCCTTCTCGTACCTCGCGCCGCTGCTCACCGACGTCTCCGGCCTCGACGAGGCCTGGGTCTCCGGCGTCCTCGGCCTCTTCGGCATCGGCGCCGTCGTCGGTACGACGATCGGCGGCCGGGTCGCCGACGCGCACCTCTTCGGCGTGCTGCTCACCGGCATCTCCGCCTCCACCGTCTTCCTCGTGGCCCTGGCCCTGTTCGCCTCGAACCCGGCCGCCACGATCGTGCTGACCTTCCTCCTCGGCGTCTCGGCCTTCTACACGGCCCCGGCCCTCAACGCCCGCATGTTCAACGTCGCCGGCGCCGCCCCCACCCTCGCGGGCGCCACCACCACCGCCGCCTTCAACCTCGGCAACACGGGCGGCCCCTGGCTCGGCGGCACGGTCATCGACGCGAACCTCGGCTTCGCCTCGACGGCCTGGGCGGGCGCGGCGATGACGGTCCTGGGCCTGGGAACGGCGGCCCTGGCCCTCCGCCTGACCAAGCGCCCGGCCCCCGGCCACGTGGTCGCCCGGAGCAGAGGGGCGGGCGGGACCACCCCGTCCGAACCGGCCAGGGGGAAGGCCACGTCGAGCTGCTGAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36896","NCBI_taxonomy_name":"Streptomyces venezuelae ATCC 10712","NCBI_taxonomy_id":"953739"}}}},"ARO_accession":"3002700","ARO_id":"39134","ARO_name":"cmlv","ARO_description":"cmlv is a chromosome-encoded chloramphenicol phoshotransferase that is found in Streptomyces venezuelae","ARO_category":{"36388":{"category_aro_accession":"3000249","category_aro_cvterm_id":"36388","category_aro_name":"chloramphenicol phosphotransferase","category_aro_description":"ATP-dependent kinase modifies the C-3 hydroxyl group of chloramphenicol.  Source is the chloramphenicol producer Streptomyces venezuelae.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"705":{"model_id":"705","model_name":"CMY-116","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1098":{"protein_sequence":{"accession":"AIT76093.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDDITDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPVPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"KM087840","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCACTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGACATTACGGATAAAGCCGCATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTAGCGGTGAAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAACTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTGCACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGTACCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACAGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATAGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGCGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002127","ARO_id":"38527","ARO_name":"CMY-116","ARO_description":"CMY-116 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"706":{"model_id":"706","model_name":"APH(7'')-Ia","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"600":{"protein_sequence":{"accession":"CAA27276.1","sequence":"MTQESLLLLDRIDSDDSYASLRNDQEFWEPLARRALEELGLPVPPVLRVPGESTNPVLVGEPDPVIKLFGEHWCGPESLASESEAYAVLADAPVPVPRLLGRGELRPGTGAWPWPYLVMSRMTGTTWRSAMDGTTDRNALLALARELGRVLGRLHRVPLTGNTVLTPHSEVFPELLRERRAATVEDHRGWGYLSPRLLDRLEDWLPDVDTLLAGREPRFVHGDLHGTNIFVDLAATEVTGIVDFTDVYAGDSRYSLVQLHLNAFRGDREILAALLDGAQWKRTEDFARELLAFTFLHDFEVFEETPLDLSGFTDPEELAQFLWGPPDTAPGA"},"dna_sequence":{"accession":"X03615","fmin":"231","fmax":"1230","strand":"+","sequence":"GTGACACAAGAATCCCTGTTACTTCTCGACCGTATTGATTCGGATGATTCCTACGCGAGCCTGCGGAACGACCAGGAATTCTGGGAGCCGCTGGCCCGCCGAGCCCTGGAGGAGCTCGGGCTGCCGGTGCCGCCGGTGCTGCGGGTGCCCGGCGAGAGCACCAACCCCGTACTGGTCGGCGAGCCCGACCCGGTGATCAAGCTGTTCGGCGAGCACTGGTGCGGTCCGGAGAGCCTCGCGTCGGAGTCGGAGGCGTACGCGGTCCTGGCGGACGCCCCGGTGCCGGTGCCCCGCCTCCTCGGCCGCGGCGAGCTGCGGCCCGGCACCGGAGCCTGGCCGTGGCCCTACCTGGTGATGAGCCGGATGACCGGCACCACCTGGCGGTCCGCGATGGACGGCACGACCGACCGGAACGCGCTGCTCGCCCTGGCCCGCGAACTCGGCCGGGTGCTCGGCCGGCTGCACAGGGTGCCGCTGACCGGGAACACCGTGCTCACCCCCCATTCCGAGGTCTTCCCGGAACTGCTGCGGGAACGCCGCGCGGCGACCGTCGAGGACCACCGCGGGTGGGGCTACCTCTCGCCCCGGCTGCTGGACCGCCTGGAGGACTGGCTGCCGGACGTGGACACGCTGCTGGCCGGCCGCGAACCCCGGTTCGTCCACGGCGACCTGCACGGGACCAACATCTTCGTGGACCTGGCCGCGACCGAGGTCACCGGGATCGTCGACTTCACCGACGTCTATGCGGGAGACTCCCGCTACAGCCTGGTGCAACTGCATCTCAACGCCTTCCGGGGCGACCGCGAGATCCTGGCCGCGCTGCTCGACGGGGCGCAGTGGAAGCGGACCGAGGACTTCGCCCGCGAACTGCTCGCCTTCACCTTCCTGCACGACTTCGAGGTGTTCGAGGAGACCCCGCTGGATCTCTCCGGCTTCACCGATCCGGAGGAACTGGCGCAGTTCCTCTGGGGGCCGCCGGACACCGCCCCCGGCGCCTGAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36900","NCBI_taxonomy_name":"Streptomyces hygroscopicus","NCBI_taxonomy_id":"1912"}}}},"ARO_accession":"3002661","ARO_id":"39061","ARO_name":"APH(7'')-Ia","ARO_description":"APH(7'')-Ia is a chromosomal-encoded aminoglycoside phosphotransferase in S. hygroscopicus","ARO_category":{"36293":{"category_aro_accession":"3000154","category_aro_cvterm_id":"36293","category_aro_name":"APH(7'')","category_aro_description":"Phosphorylation of hygromycin on the hydroxyl group at position 7''","category_aro_class_name":"AMR Gene Family"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"707":{"model_id":"707","model_name":"AIM-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1033":{"protein_sequence":{"accession":"CAQ53840.1","sequence":"MKRRFTLLGSVVALALSSTALASDAPASRGCADDAGWNDPAMPLKVYGNTWYVGTCGISALLVTSDAGHILVDAATPQAGPQILANIRALGFRPEDVRAIVFSHEHFDHAGSLAELQKATGAPVYARAPAIDTLKRGLPDRTDPQFEVAEPVAPVANIVTLADDGVVSVGPLALTAVASPGHTPGGTSWTWRSCEGDDCRQMVYADSLTAISDDVFRYSDDAAHPGYLAAFRNTLARVAALDCDILVTPHPSASGLWNRIGPRAAAPLMDTTACRRYAQGARQRLEKRLAEEAATSPSSGARP"},"dna_sequence":{"accession":"AM998375","fmin":"1172","fmax":"2084","strand":"+","sequence":"ATGAAACGTCGCTTCACCCTGCTGGGCAGCGTAGTCGCCCTCGCCCTCTCATCCACAGCCCTCGCCTCCGATGCGCCCGCCTCCAGGGGCTGCGCCGACGATGCCGGCTGGAACGATCCGGCAATGCCCCTGAAGGTGTACGGAAACACCTGGTACGTTGGCACCTGCGGCATCAGTGCGCTGCTGGTCACTTCCGACGCGGGCCATATCCTGGTCGATGCCGCCACGCCGCAGGCGGGCCCACAGATCCTGGCCAACATCCGCGCACTCGGTTTCAGGCCGGAGGACGTGCGCGCCATCGTGTTCTCGCACGAGCATTTCGACCATGCCGGCAGCCTCGCCGAACTGCAGAAGGCCACGGGTGCACCGGTGTACGCGCGCGCGCCCGCGATCGACACGCTGAAGCGCGGCCTGCCGGACCGCACCGACCCGCAATTCGAGGTGGCCGAACCCGTTGCGCCGGTCGCCAACATCGTCACCCTGGCCGACGACGGCGTGGTGAGCGTCGGCCCGCTGGCCCTGACGGCGGTCGCCTCGCCTGGCCACACCCCGGGTGGCACCAGTTGGACCTGGCGCTCCTGCGAAGGCGACGACTGTCGCCAGATGGTCTACGCCGACAGCCTGACGGCGATCTCGGACGACGTCTTCCGCTACAGCGACGACGCCGCGCATCCCGGCTACCTGGCGGCATTCCGCAACACCCTCGCACGGGTCGCAGCGCTCGACTGCGACATCCTGGTCACCCCGCACCCCTCGGCCAGCGGCCTGTGGAACCGGATCGGCCCGAGGGCCGCCGCACCGCTGATGGACACCACCGCCTGCCGCCGCTACGCGCAGGGCGCGAGGCAGCGGCTGGAGAAGCGCCTGGCCGAGGAAGCCGCCACCTCCCCCTCCAGCGGCGCGCGGCCTTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3000853","ARO_id":"37233","ARO_name":"AIM-1","ARO_description":"AIM-1 is an Ambler class B beta-lactamase that hydrolyzes most beta-lactams except aztreonam and ceftazidime. It was isolated from Pseudomonas aeruginosa and was the first subclass B3 mobile-elements encoded beta-lactamase discovered.","ARO_category":{"41380":{"category_aro_accession":"3004216","category_aro_cvterm_id":"41380","category_aro_name":"AIM beta-lactamase","category_aro_description":"A subclass B3 family of beta-lactamases that confer resistance to a range of beta-lactam antibiotics including penams, cephamycins, and cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"708":{"model_id":"708","model_name":"CTX-M-49","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1010":{"protein_sequence":{"accession":"AAV97954.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGRRLGVPLIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"AY847145","fmin":"81","fmax":"957","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAAGGCGGCTGGGCGTCCCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001911","ARO_id":"38311","ARO_name":"CTX-M-49","ARO_description":"CTX-M-49 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"709":{"model_id":"709","model_name":"TEM-213","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1246":{"protein_sequence":{"accession":"AHA58207.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEFSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"KF663615","fmin":"0","fmax":"858","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTTCTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACGCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001390","ARO_id":"37790","ARO_name":"TEM-213","ARO_description":"From the Lahey list of beta-lactamases. Not yet released.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"710":{"model_id":"710","model_name":"dfrB6","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"430":{"protein_sequence":{"accession":"ADO00942.1","sequence":"MDQGSNEVINPVAGQFASPSNATFGMGDRVRKKSGAAWQGQIVGWYSTKLTPEGYAVESEAHPGSVQIYPVAALERVN"},"dna_sequence":{"accession":"GU060319","fmin":"624","fmax":"861","strand":"+","sequence":"ATGGACCAAGGTAGCAATGAAGTCATTAATCCAGTCGCTGGCCAGTTTGCGTCCCCATCGAACGCCACGTTTGGTATGGGAGATCGCGTGCGCAAGAAATCTGGCGCCGCCTGGCAAGGTCAGATTGTCGGGTGGTACAGCACAAAGTTGACCCCTGAAGGCTACGCTGTCGAGTCTGAGGCTCACCCTGGCTCGGTGCAGATTTATCCTGTTGCCGCGCTTGAACGCGTCAACTGAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3003023","ARO_id":"39457","ARO_name":"dfrB6","ARO_description":"dfrB6 is an integron-encoded dihydrofolate reductase found in Salmonella enterica","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36408":{"category_aro_accession":"3000269","category_aro_cvterm_id":"36408","category_aro_name":"brodimoprim","category_aro_description":"Brodimoprim is a structural derivative of trimethoprim and an inhibitor of bacterial dihydrofolate reductase. The 4-methoxy group of trimethoprim is replaced with a bromine atom.","category_aro_class_name":"Antibiotic"},"36423":{"category_aro_accession":"3000284","category_aro_cvterm_id":"36423","category_aro_name":"tetroxoprim","category_aro_description":"Tetroxoprim is a trimethoprim derivative that inhibits bacterial dihydrofolate reductase.","category_aro_class_name":"Antibiotic"},"36476":{"category_aro_accession":"3000337","category_aro_cvterm_id":"36476","category_aro_name":"iclaprim","category_aro_description":"Iclaprim is a bactericidal compound that inhibits dihydrofolate reductase. It is used against clinically important Gram-positive pathogens, including methicillin-sensitive Staphylococcus aureus and methicillin-resistant S. aureus.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"711":{"model_id":"711","model_name":"SHV-62","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"839":{"protein_sequence":{"accession":"CAI30651.2","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKYLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AJ866285","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAATACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCAGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001117","ARO_id":"37497","ARO_name":"SHV-62","ARO_description":"SHV-62 is a broad-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"712":{"model_id":"712","model_name":"catB2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"4336":{"protein_sequence":{"accession":"NP_848167.1","sequence":"MTNYFESPFKGKLLTEQVKNPNIKVGRYSYYSGYYHGHSFDDCARYLLPDRDDVDQLIIGSFCSIGSGAAFIMAGNQGHRYDWVSSFPFFYMNEEPAFAKSVDAFQRAGDTVIGSDVWIGSEAMIMPGIKIGHGAVIGSRALVTKDVEPYTIVGGNPAKSIRKRFSEEEISMLLDMAWWDWPLEQIKEAMPFLCSSGIASLYRRWQGTSA"},"dna_sequence":{"accession":"NC_004771","fmin":"3524","fmax":"4157","strand":"-","sequence":"TTAGGCGCTTGTGCCTTGCCAGCGACGATACAGGCTGGCAATGCCAGACGAACAAAGAAAAGGCATTGCTTCCTTGATTTGTTCCAGCGGCCAATCCCACCAAGCCATATCTAAAAGCATAGAAATTTCTTCTTCAGAAAAGCGCTTCCTAATCGACTTTGCAGGGTTTCCCCCCACTATGGTGTAGGGTTCCACGTCTTTGGTAACCAAAGCGCGGCTACCTATCACCGCTCCATGCCCGATCTTGATCCCGGGCATGATCATGGCCTCCGAACCGATCCACACATCACTTCCTATAACTGTGTCGCCAGCCCGCTGGAATGCATCGACTGATTTTGCAAACGCGGGCTCCTCGTTCATGTAGAAGAAAGGGAAAGAAGAGACCCAATCATATCGGTGGCCTTGATTCCCAGCCATAATAAAAGCTGCGCCTGATCCGATGGAGCAGAAGCTGCCGATAATCAGCTGATCAACGTCATCACGGTCTGGTAGAAGGTAGCGAGCACAATCATCAAACGAGTGCCCATGGTAATAGCCGGAATAGTAGCTATACCGCCCTACCTTGATGTTCGGATTCTTCACCTGCTCAGTCAGAAGCTTCCCTTTGAAGGGACTCTCAAAATAATTCGTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36867","NCBI_taxonomy_name":"Pasteurella multocida","NCBI_taxonomy_id":"747"}}}},"ARO_accession":"3002675","ARO_id":"39109","ARO_name":"catB2","ARO_description":"catB2 is a plasmid-encoded variant of the cat gene found in Escherichia coli, Salmonella enteritidis and Pasteurella multocida","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. cat is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Bacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini","category_aro_class_name":"AMR Gene Family"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"713":{"model_id":"713","model_name":"CTX-M-81","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1011":{"protein_sequence":{"accession":"ABV57756.3","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLEQSETQKQLLNQPVEIQPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDHTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"EU136031","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTGAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCCAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACCATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACCATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001942","ARO_id":"38342","ARO_name":"CTX-M-81","ARO_description":"CTX-M-81 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"714":{"model_id":"714","model_name":"dfrB1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"538":{"protein_sequence":{"accession":"AAN41433.1","sequence":"MQRVVGPHRTPRSSQERSEMERSSNEVSNPVAGNFVFPSNATFGMGDRVRKKSGAAWQGQIVGWYCTNLTPEGYAVESEAHPGSVQIYPVAALERIN"},"dna_sequence":{"accession":"AY139601","fmin":"110","fmax":"404","strand":"+","sequence":"ATGCAGCGTGTCGTCGGGCCACATAGAACACCTAGAAGTTCACAAGAAAGGTCGGAAATGGAACGAAGTAGCAATGAAGTCAGTAATCCAGTTGCTGGCAATTTTGTATTCCCATCGAACGCCACGTTTGGTATGGGAGATCGCGTGCGCAAGAAATCCGGCGCCGCCTGGCAAGGTCAGATTGTCGGGTGGTACTGCACAAATTTGACCCCCGAAGGCTACGCCGTCGAGTCTGAGGCTCACCCAGGCTCAGTACAGATTTATCCTGTTGCGGCGCTTGAACGCATCAACTGAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3002864","ARO_id":"39298","ARO_name":"dfrB1","ARO_description":"dfrB1 is an integron-encoded dihydrofolate reductase found in Pseudomonas aeruginosa","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36408":{"category_aro_accession":"3000269","category_aro_cvterm_id":"36408","category_aro_name":"brodimoprim","category_aro_description":"Brodimoprim is a structural derivative of trimethoprim and an inhibitor of bacterial dihydrofolate reductase. The 4-methoxy group of trimethoprim is replaced with a bromine atom.","category_aro_class_name":"Antibiotic"},"36423":{"category_aro_accession":"3000284","category_aro_cvterm_id":"36423","category_aro_name":"tetroxoprim","category_aro_description":"Tetroxoprim is a trimethoprim derivative that inhibits bacterial dihydrofolate reductase.","category_aro_class_name":"Antibiotic"},"36476":{"category_aro_accession":"3000337","category_aro_cvterm_id":"36476","category_aro_name":"iclaprim","category_aro_description":"Iclaprim is a bactericidal compound that inhibits dihydrofolate reductase. It is used against clinically important Gram-positive pathogens, including methicillin-sensitive Staphylococcus aureus and methicillin-resistant S. aureus.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"715":{"model_id":"715","model_name":"PDC-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"1541":{"protein_sequence":{"accession":"ACQ82808.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"FJ666066","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTATGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002500","ARO_id":"38900","ARO_name":"PDC-3","ARO_description":"PDC-3 is a extended-spectrum beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"716":{"model_id":"716","model_name":"QnrB32","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"405":{"protein_sequence":{"accession":"AEL00450.1","sequence":"MALALVGEKIDRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNASALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNSNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAIIG"},"dna_sequence":{"accession":"JN173054","fmin":"36","fmax":"681","strand":"+","sequence":"ATGGCTCTGGCACTCGTTGGCGAAAAAATTGACAGAAACCGTTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTAAGTGGTACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCAATGCTAAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATGCCAGTGCGCTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGCGCAAGCTTTATGAATATGATCACTACACGCACCTGGTTTTGCAGCGCATATATCACTAACTCAAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGCTGGAAAAGTGTGAGCTGTGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTGACTTAGATATTCGGGGCGTTGATTTACAAGGCGTTAAGTTGGACAACTACCAGGCATCGTTGCTCATGGAACGTCTTGGCATCGCGATTATTGGCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002747","ARO_id":"39181","ARO_name":"QnrB32","ARO_description":"QnrB32 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"717":{"model_id":"717","model_name":"CTX-M-100","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"784":{"protein_sequence":{"accession":"CBW46935.1","sequence":"MMRKSVRRAMLMTTACVSLLLASVPLCAQANDVQQKLAALEKSSGGRLGVALINTADNTQTLYRADERFAMCSTSKVMAAAAVLKQSETQKGLLSQRVEIKPSDLINYNPIAEKHVNGTMTFGELSAAALQYSDNTAMNKLIAHLGGPDKVTAFARTIGDDTFRLDRTEPTLNTAIPGDPRDTTTPLAMAQALRNLTLGNALGDTQRAQLVMWLKGNTTGAASIQAGLPTSWVVGDKTGSGGYGTTNDIAVIWPEGRAPLVLVTYFTQSEPKAESRRDVLAAAARIVTDGY"},"dna_sequence":{"accession":"FR682582","fmin":"0","fmax":"876","strand":"+","sequence":"ATGATGAGAAAAAGCGTAAGGCGGGCGATGTTAATGACGACAGCCTGTGTTTCGCTGCTGTTGGCCAGTGTGCCGCTGTGTGCCCAGGCGAACGATGTTCAACAAAAGCTCGCGGCGCTGGAGAAAAGCAGCGGGGGACGACTGGGTGTGGCGTTGATTAACACCGCCGATAACACGCAGACGCTCTACCGCGCCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCGGCAGCGGCGGTGCTTAAGCAAAGTGAAACGCAAAAGGGCTTGTTGAGTCAGCGGGTTGAAATTAAGCCCTCAGACTTGATTAACTACAACCCCATTGCGGAAAAACACGTCAATGGCACGATGACATTCGGGGAGTTGAGCGCGGCGGCGCTACAGTACAGCGATAATACTGCCATGAATAAGCTGATTGCCCATCTCGGGGGGCCGGATAAAGTGACGGCATTTGCCCGTACGATTGGCGATGACACGTTCCGGCTCGATCGTACCGAGCCGACGCTCAACACCGCGATCCCCGGCGACCCGCGCGATACCACCACGCCGTTAGCGATGGCGCAGGCTCTGCGCAATCTGACGTTGGGCAATGCCCTGGGTGACACTCAGCGTGCGCAGCTGGTGATGTGGCTGAAAGGCAACACCACCGGCGCTGCCAGCATTCAGGCAGGGCTACCCACATCGTGGGTTGTCGGGGATAAAACCGGCAGCGGCGGTTATGGTACGACGAATGATATCGCGGTTATTTGGCCGGAAGGTCGCGCGCCGCTCGTTCTGGTGACTTACTTCACCCAGTCGGAGCCGAAGGCAGAGAGCCGTCGTGACGTGCTCGCTGCTGCCGCCAGAATTGTCACCGACGGTTATTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001959","ARO_id":"38359","ARO_name":"CTX-M-100","ARO_description":"CTX-M-100 is a beta-lactamase found in Escherichia coli","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"718":{"model_id":"718","model_name":"LRA-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"858":{"protein_sequence":{"accession":"ACH58988.1","sequence":"MSKSSLKGLVLLALVAAIAAPSWAARKEKPAAKAPPCEQCAVWNADQEPFKIWGNTYYVGVKGLSSVLVTSDWGHVLLDGGLPESAPKIAANIEKLGFKVTDVKAILSSHVHADHAGGIAELQRRSGAKVYQRRPSDQVLRTGKPDPGDPQLARAGPIPPVENVWVVHDEELLGLGPTRFTVVATPGHTPGGTSWAWESCEGAQCLKIVYADSLNAVSAEGFRFTASTTYPNVLQDLEQSFKRVESLPCDVIVSVHPEQSDFFPRMAKRVDGKPESIKDPEGCKRYVAGARERLALRVASEKQGS"},"dna_sequence":{"accession":"EU408349","fmin":"107","fmax":"1025","strand":"+","sequence":"ATGTCGAAATCTTCCCTGAAGGGTCTGGTTCTTCTGGCTCTGGTGGCAGCCATCGCGGCCCCGTCGTGGGCGGCGCGCAAGGAAAAACCGGCCGCAAAGGCGCCGCCGTGCGAGCAGTGCGCGGTGTGGAACGCGGACCAGGAGCCGTTCAAGATCTGGGGCAACACGTACTACGTGGGCGTGAAGGGCCTGTCGTCCGTGCTCGTGACCTCCGACTGGGGCCACGTGCTCCTCGACGGCGGACTGCCCGAGTCCGCGCCGAAGATCGCCGCGAACATCGAGAAGCTCGGCTTCAAGGTCACGGACGTGAAGGCGATCCTGAGCTCGCACGTCCACGCGGATCACGCCGGCGGCATCGCCGAGCTGCAGCGGCGCAGCGGCGCCAAGGTGTACCAGCGCCGCCCGAGCGACCAGGTGCTGCGCACGGGCAAGCCCGATCCCGGCGATCCGCAGCTCGCGCGCGCCGGTCCGATCCCGCCGGTGGAGAACGTGTGGGTCGTGCACGACGAGGAGCTCCTCGGGCTCGGCCCCACGCGCTTCACGGTGGTGGCCACGCCGGGCCACACGCCCGGCGGCACCAGCTGGGCCTGGGAGTCCTGCGAAGGGGCGCAGTGCCTGAAGATCGTGTACGCCGACAGCCTCAACGCGGTGTCCGCCGAGGGGTTCCGCTTCACCGCGAGCACTACCTATCCGAACGTGCTGCAGGACTTGGAGCAGAGCTTCAAGCGCGTCGAGTCGTTGCCGTGCGACGTGATCGTGTCCGTGCATCCCGAGCAGTCCGACTTTTTCCCGCGCATGGCGAAGCGTGTGGACGGCAAGCCCGAGTCGATCAAGGACCCGGAAGGCTGCAAGCGCTATGTGGCCGGCGCACGCGAGCGTCTCGCGCTGCGCGTCGCCAGCGAGAAGCAAGGCTCCTGAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39082","NCBI_taxonomy_name":"uncultured bacterium BLR8","NCBI_taxonomy_id":"506524"}}}},"ARO_accession":"3002487","ARO_id":"38887","ARO_name":"LRA-8","ARO_description":"LRA-8 is a beta-lactamase isolated from soil samples in Alaska","ARO_category":{"41390":{"category_aro_accession":"3004226","category_aro_cvterm_id":"41390","category_aro_name":"subclass B3 LRA beta-lactamase","category_aro_description":"Beta-lactamases that are part of the LRA gene family and are classified as B3 (metallo-) beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"719":{"model_id":"719","model_name":"CMY-33","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1914":{"protein_sequence":{"accession":"ACA97847.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"EU496816","fmin":"0","fmax":"1140","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002044","ARO_id":"38444","ARO_name":"CMY-33","ARO_description":"CMY-33 is a beta-lactamase found in Escherichia coli","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"720":{"model_id":"720","model_name":"BcI","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"1622":{"protein_sequence":{"accession":"CAA29819.1","sequence":"MKNKRMLKIGICVGILGLSITSLEAFTGESLQVEAKEKTGQVKHKNQATHKEFSQLEKKFDARLGVYAIDTGTNQTISYRPNERFAFASTYKALAAGVLLQQNSIDSLNEVITYTKEDLVDYSPVTEKHVDTGMKLGEIAEAAVRSSDNTAGNILFNKIGGPKGYEKALRHMGDRITMSNRFETELNEAIPGDIRDTSTAKAIATNLKAFTVGNALPAEKRKILTEWMKGNATGDKLIRAGIPTDWVVGDKSGAGSYGTRNDIAVVWPPNRAPIIIAILSSKDEKEAIYDNQLIAEATKVIVKALR"},"dna_sequence":{"accession":"X06599","fmin":"272","fmax":"1193","strand":"+","sequence":"TTGAAAAATAAGAGGATGCTAAAAATAGGAATATGCGTTGGTATATTAGGTTTAAGTATTACAAGCCTAGAAGCTTTTACAGGAGAGTCACTGCAAGTTGAAGCGAAAGAAAAGACTGGACAAGTGAAACACAAAAATCAGGCAACGCATAAAGAGTTCTCTCAACTTGAGAAAAAATTTGATGCTCGATTAGGTGTATATGCGATTGATACTGGTACAAATCAAACAATCTCTTATCGACCTAACGAAAGATTTGCCTTCGCATCAACATACAAGGCTTTAGCCGCGGGAGTATTACTACAGCAAAACTCAATTGATTCATTAAATGAAGTAATCACATATACGAAAGAAGACTTAGTGGATTATTCACCTGTTACAGAGAAACATGTAGATACTGGAATGAAACTAGGAGAAATTGCAGAGGCAGCTGTTCGTTCAAGTGATAATACTGCAGGGAACATTTTATTTAATAAAATAGGAGGACCGAAAGGATATGAAAAAGCGCTTAGGCATATGGGGGATCGGATTACTATGTCTAATCGCTTTGAAACAGAATTAAACGAAGCTATTCCAGGAGACATTCGTGACACTAGTACAGCGAAAGCTATTGCTACGAATCTTAAAGCTTTTACGGTCGGAAATGCACTTCCAGCTGAAAAACGTAAAATTCTTACAGAGTGGATGAAAGGAAATGCTACAGGGGACAAACTTATTCGTGCAGGCATACCAACTGACTGGGTAGTTGGAGATAAATCAGGTGCTGGTAGTTACGGGACAAGAAATGATATTGCTGTCGTTTGGCCTCCAAATAGAGCACCAATTATCATCGCAATTTTATCTAGTAAAGATGAGAAAGAGGCAATCTATGATAATCAACTCATTGCAGAGGCAACTAAAGTTATAGTTAAGGCTCTTAGGTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36751","NCBI_taxonomy_name":"Bacillus cereus","NCBI_taxonomy_id":"1396"}}}},"ARO_accession":"3002877","ARO_id":"39311","ARO_name":"BcI","ARO_description":"Bacillus cereus beta-lactamase I is a zinc metallo-beta-lactamase that hydrolyzes a large number of penicillins and cephalosporins in the Bacillus cereus strain 569\/H\/9","ARO_category":{"36716":{"category_aro_accession":"3000577","category_aro_cvterm_id":"36716","category_aro_name":"Bc beta-lactamase","category_aro_description":"Bacillus cereus beta-lactamases are zinc metallo-beta-lactamases that hydrolyze a large number of penicillins and cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"721":{"model_id":"721","model_name":"OXA-28","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"887":{"protein_sequence":{"accession":"AAF72942.1","sequence":"MKTFAAYVITACLSSTALASSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNNLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLSLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFGLEGQLRISAVNQVEFLESLFLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKGTEVYFFAFNMDIDNENKLPLRKSIPTKIMASEGIIGG"},"dna_sequence":{"accession":"AF231133","fmin":"1345","fmax":"2146","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTACTGCGTGTCTTTCAAGTACGGCATTAGCTAGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTTTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATAACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAACAATGGGAAAGAGACTTGAGCTTAAGAGGGGCAATACAAGTTTCAGCGGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCATATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCGGGTTGGAGGGTCAGCTAAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATTTTTAAATAAATTGTCAGCATCAAAAGAAAATCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCTGCGCCTGAATATCTTGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGTTGGGTTGAGAAGGGAACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAATAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGCAAGTGAGGGCATCATTGGTGGCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001423","ARO_id":"37823","ARO_name":"OXA-28","ARO_description":"OXA-28 is a beta-lactamase found in P. aeruginosa","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"722":{"model_id":"722","model_name":"vanRA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"3275":{"protein_sequence":{"accession":"AAA65953.1","sequence":"MSDKILIVDDEHEIADLVELYLKNENYTVFKYYTAKEALECIDKSEIDLAILDIMLPGTSGLTICQKIRDKHTYPIIMLTGKDTEVDKITGLTIGADDYITKPFRPLELIARVKAQLRRYKKFSGVKEQNENVIVHSGLVINVNTHECYLNEKQLSLTPTEFSILRILCENKGNVVSSELLFHEIWGDEYFSKSNNTITVHIRHLREKMNDTIDNPKYIKTVWGVGYKIEK"},"dna_sequence":{"accession":"M97297","fmin":"3976","fmax":"4671","strand":"+","sequence":"ATGAGCGATAAAATACTTATTGTGGATGATGAACATGAAATTGCCGATTTGGTTGAATTATACTTAAAAAACGAGAATTATACGGTTTTCAAATACTATACCGCCAAAGAAGCATTGGAATGTATAGACAAGTCTGAGATTGACCTTGCCATATTGGACATCATGCTTCCCGGCACAAGCGGCCTTACTATCTGTCAAAAAATAAGGGACAAGCACACCTATCCGATTATCATGCTGACCGGGAAAGATACAGAGGTAGATAAAATTACAGGGTTAACAATCGGCGCGGATGATTATATAACGAAGCCCTTTCGCCCACTGGAGTTAATTGCTCGGGTAAAGGCCCAGTTGCGCCGATACAAAAAATTCAGTGGAGTAAAGGAGCAGAACGAAAATGTTATCGTCCACTCCGGCCTTGTCATTAATGTTAACACCCATGAGTGTTATCTGAACGAGAAGCAGTTATCCCTTACTCCCACCGAGTTTTCAATACTGCGAATCCTCTGTGAAAACAAGGGGAATGTGGTTAGCTCCGAGCTGCTATTTCATGAGATATGGGGCGACGAATATTTCAGCAAGAGCAACAACACCATCACCGTGCATATCCGGCATTTGCGCGAAAAAATGAACGACACCATTGATAATCCGAAATATATAAAAACGGTATGGGGGGTTGGTTATAAAATTGAAAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002919","ARO_id":"39353","ARO_name":"vanRA","ARO_description":"vanRA, also known as vanR, is a vanR variant found in the vanA gene cluster","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36713":{"category_aro_accession":"3000574","category_aro_cvterm_id":"36713","category_aro_name":"vanR","category_aro_description":"VanR is a OmpR-family transcriptional activator in the VanSR regulatory system. When activated by VanS, it promotes cotranscription of VanA, VanH, and VanX.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"35948":{"category_aro_accession":"0000029","category_aro_cvterm_id":"35948","category_aro_name":"teicoplanin","category_aro_description":"Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation  and transpeptidation.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"723":{"model_id":"723","model_name":"SHV-72","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1640":{"protein_sequence":{"accession":"CAJ47127.2","sequence":"MRYFRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPVGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADRTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM176547","fmin":"30","fmax":"891","strand":"+","sequence":"ATGCGTTATTTTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGTAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAGGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGGATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001126","ARO_id":"37506","ARO_name":"SHV-72","ARO_description":"SHV-72 is an inhibitor-resistant beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"724":{"model_id":"724","model_name":"AAC(6')-Ij","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"494":{"protein_sequence":{"accession":"AAC41392.1","sequence":"MNIMPVSESLMADWLGLRKLLWPDHDEAHLQEMQRLLQQTQSLQLLAYSDTQQAIAMLEASIRYEYVNGTQTSPVAFLEGIYVLPDYRRSGIATHLVQQVEAWAKPFGCIEFASDAALDNRISHAMHQALGFHETERVVYFKKHIG"},"dna_sequence":{"accession":"L29045","fmin":"259","fmax":"700","strand":"+","sequence":"ATGAATATTATGCCTGTATCTGAATCCCTGATGGCAGATTGGTTAGGATTGAGAAAACTGCTCTGGCCTGATCATGACGAGGCACATTTACAGGAAATGCAGCGGCTACTTCAACAGACACAAAGCTTACAGCTACTCGCATATTCAGATACTCAACAAGCGATTGCCATGCTAGAAGCATCGATTCGATATGAATATGTAAATGGCACGCAAACTTCACCAGTTGCATTTCTTGAAGGGATTTATGTCCTTCCTGATTATCGGCGTTCAGGCATCGCAACACATCTGGTTCAACAAGTAGAAGCGTGGGCAAAACCGTTTGGATGTATTGAATTTGCCTCGGATGCAGCCCTCGATAATCGTATTAGCCATGCGATGCATCAGGCGCTTGGTTTTCATGAAACTGAACGTGTGGTTTATTTCAAGAAACACATTGGCTGAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39510","NCBI_taxonomy_name":"Acinetobacter genomosp. 13","NCBI_taxonomy_id":"72607"}}}},"ARO_accession":"3002557","ARO_id":"38957","ARO_name":"AAC(6')-Ij","ARO_description":"AAC(6')-Ij is a chromosomal-encoded aminoglycoside acetyltransferase in Acinetobacter genomosp. 13","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"725":{"model_id":"725","model_name":"GES-11","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1745":{"protein_sequence":{"accession":"ACS44714.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMGDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGARNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"FJ854362","fmin":"701","fmax":"1565","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGGGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGCCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAGT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3002340","ARO_id":"38740","ARO_name":"GES-11","ARO_description":"GES-11 is a beta-lactamase found in Acinetobacter baumannii","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"726":{"model_id":"726","model_name":"PC1 beta-lactamase (blaZ)","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4250":{"protein_sequence":{"accession":"ABX30738.1","sequence":"MKKLIFLIVIALVLSACNSNSSHAKELNDLEKKYNAHIGVYALDTKSGKEVKFNSDKRFAYASTSKAINSAILLEQVPYNKLNKKVHINKDDIVAYSPILEKYVGKDIALKELIEASMKYSDNTANNKIINEIGGIKKIKKRLKKLGDKVTNPVRYEIELNYYSPKSKKDTSTPAAFGKTLNKLIANGKLSKKNKNFLLDLMLNNKNGDTLIKDGIPKDYKVADKSGQAITYASRNDVAFVYPKGQSEPIVLVIFTNKDNKSDKPNDKLISETAKSVMKEF"},"dna_sequence":{"accession":"CP000732.1","fmin":"9682","fmax":"10528","strand":"-","sequence":"TTAAAATTCCTTCATTACACTCTTGGCGGTTTCACTTATCAACTTATCATTTGGCTTATCACTTTTATTGTCTTTATTCGTAAAAATGACTAAAACAATAGGTTCAGATTGGCCCTTAGGATAAACAAAAGCAACATCATTTCTAGAAGCATATGTTATTGCTTGACCACTTTTATCAGCAACTTTATAGTCTTTTGGAATACCATCTTTAATTAAAGTGTCTCCGTTTTTATTATTTAACATTAAATCAAGTAAGAAATTTTTATTTTTTTTGCTTAATTTTCCATTTGCGATAAGTTTATTTAAAGTCTTGCCGAAAGCAGCAGGCGTTGAAGTATCTTTTTTGCTCTTTGGTGAATAGTAATTTAATTCTATTTCATATCTAACTGGATTTGTTACTTTATCTCCCAATTTTTTTAAACGTTTTTTAATTTTTTTGATTCCACCGATTTCGTTTATAATTTTATTGTTTGCTGTATTATCACTGTACTTCATTGAAGCCTCAATAAGTTCTTTTAAAGCGATATCTTTTCCTACATATTTTTCTAAAATAGGAGAATAAGCAACTATATCATCTTTGTTAATATGTACTTTTTTATTTAACTTATTATAAGGTACTTGTTCTAACAAAATAGCACTATTTATCGCTTTTGAAGTCGAAGCATAGGCAAATCTCTTATCTGAATTAAATTTTACTTCCTTACCACTTTTAGTATCTAAAGCATAAACACCAATATGAGCATTATATTTTTTTTCTAAATCATTTAACTCTTTGGCATGTGAACTGTTTGAATTACATGCACTTAAAACTAAAGCAATTACAATTAAAAATATTAACTTTTTCAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35526","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus USA300_TCH959","NCBI_taxonomy_id":"450394"}}}},"ARO_accession":"3000621","ARO_id":"36963","ARO_name":"PC1 beta-lactamase (blaZ)","ARO_description":"The blaZ beta-lactamase is found in Bacillus subtilis and Staphylococcus aureus.","ARO_category":{"41361":{"category_aro_accession":"3004197","category_aro_cvterm_id":"41361","category_aro_name":"blaZ beta-lactamase","category_aro_description":"blaZ beta-lactamases are Class A beta-lactamases. These beta-lactamases are responsible for penicillin resistance in Staphylococcus aures.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"727":{"model_id":"727","model_name":"ErmS","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"290":{"protein_sequence":{"accession":"AAA26742.1","sequence":"MARAPRSPHPARSRETSRAHPPYGTRADRAPGRGRDRDRSPDSPGNTSSRDGGRSPDRARRELSQNFLARRAVAERVARLVRPAPGGLLLEVGAGRGVLTEALAPYCGRLVAHEIDPRLLPALRDRFGGPHHAHVRISGGDFLAAPVPREPFALAGNIPYSRTAGIVDWALRARTLTSATFVTQLEYARKRTGDYGRWSLLTVRTWPRHEWRLLGRVSRREFRPVPRVDSGILRIERRERPLLPSAALGDYHRMVELGFSGVGGSLYASLRRAHRAGPLDAAFRAARLDRSVVVAYVTPEQWLTVFRTLRPVRSRPAGR"},"dna_sequence":{"accession":"M19269","fmin":"459","fmax":"1419","strand":"+","sequence":"GTGGCCCGTGCACCCCGATCGCCCCACCCTGCCCGCTCGCGGGAGACCTCCCGCGCCCACCCGCCGTACGGCACCCGTGCGGATCGCGCCCCCGGCCGTGGCCGTGACCGTGACCGCAGCCCCGACAGCCCCGGCAACACCAGCAGCCGCGACGGCGGCCGCAGCCCCGACCGCGCGCGGCGCGAGCTCTCGCAGAACTTCCTCGCCCGCCGGGCCGTCGCCGAGCGCGTCGCGCGCCTGGTCCGGCCGGCCCCCGGCGGTCTGTTGCTGGAGGTCGGCGCCGGGCGCGGCGTCCTGACCGAGGCGCTGGCCCCGTACTGCGGGCGGCTGGTCGCCCACGAGATCGACCCCCGTCTGCTGCCGGCGCTGCGCGACCGGTTCGGCGGCCCGCACCATGCCCATGTGCGGATCAGCGGCGGCGACTTCCTGGCAGCCCCCGTCCCCCGTGAGCCGTTCGCCCTCGCGGGGAACATCCCCTACTCCCGGACCGCGGGAATCGTGGACTGGGCGCTGCGGGCGCGCACGCTCACCTCGGCGACCTTCGTCACCCAGCTCGAGTACGCCCGCAAGCGGACCGGCGACTATGGACGCTGGAGCCTGCTGACGGTGCGGACCTGGCCCCGCCACGAGTGGCGGCTGCTCGGCAGGGTCTCCCGCCGGGAGTTCCGGCCGGTGCCCCGCGTGGACTCGGGCATCCTCCGGATCGAGCGGCGCGAGCGGCCCCTGCTGCCGTCCGCCGCCCTCGGCGACTACCACCGCATGGTGGAGCTGGGTTTCTCCGGCGTGGGCGGATCGCTGTACGCATCGCTGCGCCGGGCCCACCGGGCGGGGCCGCTCGACGCCGCGTTCCGTGCCGCGCGGCTGGACCGCTCCGTCGTCGTCGCGTATGTCACACCGGAGCAGTGGCTCACGGTCTTCCGCACGTTGCGGCCCGTCCGCAGCCGACCGGCCGGACGGTGAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36838","NCBI_taxonomy_name":"Streptomyces fradiae","NCBI_taxonomy_id":"1906"}}}},"ARO_accession":"3001304","ARO_id":"37703","ARO_name":"ErmS","ARO_description":"ErmS is a methyltransferase found in the tylosin producer Streptomyces fradiae. Like other Erm enzymes, it catalyzes the methylation of A2058 of the 23S ribosomal RNA. Specifically, this enzyme transfers two methyl groups. The gene is found within the tylosin biosynthetic cluster and is responsible for self-resistance","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"728":{"model_id":"728","model_name":"TEM-192","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1158":{"protein_sequence":{"accession":"AEQ59620.1","sequence":"MPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPIMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYT"},"dna_sequence":{"accession":"JF949915","fmin":"0","fmax":"754","strand":"+","sequence":"ATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATAATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001052","ARO_id":"37432","ARO_name":"TEM-192","ARO_description":"TEM-192 is a beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"729":{"model_id":"729","model_name":"CTX-M-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"826":{"protein_sequence":{"accession":"AAF04388.1","sequence":"MMRHRVKRMMLMTTACISLLLGSAPLYAQANDVQQKLAALEKSSGGRLGVALIDTADNAQTLYRADERFAMCSTSKVMAAAAVLKQSETQKKVLSQKVEIKSSDLINYNPITEKHVNGTMTLAELSAAALQYSDNTAMNKLIAHLGGPDKVTAFARAIGDNTFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLRNLTLGSALGETQRAQLVTWLKGNTTGAASIQAGLPTSWVVGDKTGSGDYGTTNDIAVIWPEGRAPLILVTYFTQPEQKAESRRDVLAAAAKIVTDGY"},"dna_sequence":{"accession":"AF189721","fmin":"273","fmax":"1149","strand":"+","sequence":"ATGATGAGACATCGCGTTAAGCGGATGATGCTAATGACAACGGCCTGTATTTCGCTGTTGCTGGGGAGTGCGCCGCTGTATGCGCAGGCGAACGACGTTCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGGGGGCGGTTGGGAGTGGCGCTGATTGACACCGCCGATAACGCACAGACGCTCTACCGCGCCGATGAGCGCTTTGCCATGTGCAGCACCAGTAAGGTGATGGCGGCAGCGGCTGTGCTCAAGCAAAGTGAAACGCAAAAGAAGGTGTTGAGTCAGAAGGTTGAGATTAAATCTTCAGACCTGATTAACTACAATCCCATTACTGAAAAACACGTCAACGGCACGATGACGCTGGCGGAATTGAGCGCCGCGGCGTTGCAGTACAGCGACAATACGGCCATGAACAAGCTGATTGCCCATCTTGGGGGGCCGGATAAAGTGACGGCGTTTGCCCGTGCGATTGGGGATAACACCTTCCGGCTCGATCGTACTGAGCCGACGCTCAACACCGCGATCCCCGGCGACCCGCGCGATACCACCACGCCATTAGCGATGGCGCAGACGCTTCGCAATCTGACGTTGGGCAGTGCCTTAGGTGAAACTCAGCGTGCGCAACTGGTAACGTGGCTGAAAGGCAATACCACCGGCGCTGCCAGCATTCAGGCTGGGCTACCCACATCGTGGGTTGTCGGGGATAAAACCGGCAGCGGTGATTATGGTACGACGAATGACATCGCCGTTATCTGGCCGGAAGGGCGTGCGCCGCTTATTCTGGTCACTTACTTCACCCAGCCAGAGCAGAAGGCAGAAAGTCGTCGTGACGTACTCGCGGCTGCCGCGAAAATCGTCACCGACGGTTATTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36919","NCBI_taxonomy_name":"Citrobacter amalonaticus","NCBI_taxonomy_id":"35703"}}}},"ARO_accession":"3001871","ARO_id":"38271","ARO_name":"CTX-M-8","ARO_description":"CTX-M-8 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"730":{"model_id":"730","model_name":"AAC(6')-IIc","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"313":{"protein_sequence":{"accession":"AAD46626.1","sequence":"MSANNAAIVLRVMAENDLPMLHAWLNRPHIVEWWGGEDERPTLDEVLEHYSPEVLAKQAVVPYIAMLDDEPIGYAQSYIALGSGDGWWEDETDPGVRGIDQSLANPSQLNKGLGTKLVRSLVELLFSDPAVTKIQTDPSPSNHRAIRCYEKAGFVQEKNILTPDGPAVYMVQTRQAFESLRTVQSFKIKGKWS"},"dna_sequence":{"accession":"AF162771","fmin":"61","fmax":"643","strand":"+","sequence":"ATGTCCGCCAACAATGCCGCAATAGTTCTACGAGTCATGGCCGAGAACGATCTGCCAATGCTCCATGCTTGGCTGAACCGCCCCCACATAGTCGAGTGGTGGGGCGGCGAGGATGAACGCCCAACTCTTGACGAAGTCTTAGAACACTATTCGCCCGAAGTTCTGGCAAAGCAAGCTGTAGTGCCTTACATCGCAATGCTAGATGACGAACCCATCGGCTACGCCCAATCCTACATCGCACTTGGAAGTGGCGATGGATGGTGGGAAGACGAAACTGATCCAGGGGTCCGCGGGATTGACCAGTCTTTGGCTAATCCATCACAGTTAAACAAGGGGTTGGGTACAAAGCTCGTACGCTCGCTCGTTGAACTCCTGTTTAGCGACCCGGCCGTAACGAAAATCCAAACCGATCCATCTCCTAGCAACCATCGCGCCATTCGCTGCTACGAGAAGGCCGGGTTCGTTCAAGAAAAAAACATCCTCACACCTGACGGCCCTGCGGTGTACATGGTCCAAACACGCCAGGCGTTCGAAAGCCTGCGCACTGTTCAAAGCTTCAAAATCAAGGGGAAGTGGTCATGAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002596","ARO_id":"38996","ARO_name":"AAC(6')-IIc","ARO_description":"AAC(6')-IIc is an aminoglycoside acetyltransferase encoded by plasmids and integrons in E. cloacae","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"731":{"model_id":"731","model_name":"IMP-11","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1746":{"protein_sequence":{"accession":"BAB72072.1","sequence":"MKKLFVLCIFLFCSITAAGASLPDLKIEKLEEGVYVHTSFEEVNGWGVVSKHGLVVLVNTDAYLIDTPFTAKDTEKLVNWFVERGYKIKGSISSHFHSDSTGGIEWLNSQSIPTYASVLTNELLKKDGKVQAKNSFSGVSYWLVKNKIEVFYPGPGHTQDNVVVWLPKNKILFGGCFVKPYGLGNLDDANVEAWPHSAEKLISKYGNAKLVVPSHSDIGDASLLKLTWEQAVKGLNESKKSNTVH"},"dna_sequence":{"accession":"AB074436","fmin":"16","fmax":"754","strand":"+","sequence":"ATGAAAAAACTATTTGTTTTATGTATATTTTTGTTTTGTAGCATTACTGCCGCAGGAGCGTCTTTGCCTGATTTAAAAATTGAGAAGCTTGAAGAGGGTGTTTATGTTCATACATCGTTTGAAGAAGTTAACGGCTGGGGTGTTGTTTCTAAACACGGTTTGGTGGTTCTTGTAAATACTGACGCCTATCTGATTGACACTCCATTTACTGCTAAAGATACTGAAAAGTTAGTCAATTGGTTTGTGGAGCGCGGCTATAAAATCAAAGGCAGTATTTCCTCACATTTCCATAGCGACAGCACGGGTGGAATAGAGTGGCTTAATTCTCAATCTATTCCCACGTATGCATCTGTATTAACAAATGAACTTCTCAAAAAAGACGGTAAGGTGCAAGCTAAAAACTCATTTAGCGGAGTTAGCTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCAGGGCACACTCAAGATAACGTAGTGGTTTGGCTACCTAAAAATAAAATCTTATTTGGTGGTTGTTTTGTTAAACCATATGGTCTTGGTAATCTAGATGACGCAAATGTTGAAGCATGGCCACATTCGGCTGAAAAATTAATATCTAAGTATGGTAATGCAAAACTGGTTGTTCCAAGCCATAGTGACATAGGAGATGCGTCGCTCTTGAAGCTTACGTGGGAACAGGCGGTAAAAGGGCTTAATGAAAGCAAAAAAAGTAACACTGTTCATTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3002202","ARO_id":"38602","ARO_name":"IMP-11","ARO_description":"IMP-11 is a beta-lactamase found in Pseudomonas and Acinetobacter spp.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"732":{"model_id":"732","model_name":"OXA-237","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1456":{"protein_sequence":{"accession":"AFH36331.1","sequence":"MKTLILLPLLSCLSLTACSLPVSNSSSQITSTQSIQTIAKLFDQAQSSGVLVIQRGPHLQVYGNDLSRAHTEYIPASTFKILNALIGLQHGKATTNEIFKWDGKKRSFAAWEKDMTLGQAMQASAVPVYQELARRIGLELMQQEVQRIRFGNQQIGQHIDNFWLVGPLKITPEQEVEFASALAQEQLAFDPQVQQQVKAMLLLQERQGYRLYAKSGWGMDVEPQVGWLTGWIETPQDEIVAFSLNMQMQSNMDPAIRLKILQQALAELALYPKAEG"},"dna_sequence":{"accession":"JQ820241","fmin":"0","fmax":"831","strand":"+","sequence":"ATGAAAACTCTTATTTTGTTGCCTTTACTTAGTTGCTTGAGCCTGACAGCCTGTAGCTTGCCTGTTTCAAATTCGTCCTCTCAAATCACTTCAACTCAATCTATTCAAACCATTGCCAAATTATTTGATCAGGCACAAAGCTCTGGCGTTTTAGTAATTCAACGGGGCCCACATCTACAGGTCTATGGCAATGATTTGAGTCGTGCACATACCGAATATATTCCTGCTTCAACCTTTAAAATACTCAATGCCCTGATTGGCCTGCAACATGGTAAAGCCACGACCAATGAAATCTTTAAATGGGATGGCAAGAAGCGCAGTTTTGCAGCCTGGGAAAAAGACATGACTCTCGGCCAAGCCATGCAAGCTTCTGCTGTACCCGTCTATCAGGAACTGGCACGTCGCATTGGTCTGGAACTAATGCAACAGGAAGTGCAACGCATTCGATTTGGTAATCAGCAGATTGGTCAGCATATCGACAACTTCTGGTTAGTCGGACCTTTGAAAATCACCCCGGAACAAGAAGTCGAATTTGCCTCTGCGCTTGCTCAAGAGCAACTTGCCTTTGATCCTCAAGTCCAGCAACAAGTCAAAGCCATGTTACTGTTACAGGAGCGACAAGGTTATCGACTATATGCCAAATCTGGTTGGGGTATGGATGTGGAGCCGCAAGTCGGCTGGCTCACCGGCTGGATCGAAACACCTCAGGACGAAATCGTGGCATTTTCACTGAATATGCAGATGCAAAGTAATATGGATCCGGCGATCCGTCTTAAAATTTTGCAGCAGGCCTTGGCCGAATTAGCGCTTTATCCGAAAGCTGAAGGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001678","ARO_id":"38078","ARO_name":"OXA-237","ARO_description":"OXA-237 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"734":{"model_id":"734","model_name":"vanTC","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1300"}},"model_sequences":{"sequence":{"151":{"protein_sequence":{"accession":"AAD22403.1","sequence":"MKNKGIDQFRVIAAMMVVAIHCLPLHYLWPEGDILITLTIFRVAVPFFFMISGYYVFAELAVANSYPSRQRVFNFIKKQLKVYLLATLMFLPLALYSQTIGFDLPVGTLVQVLLVNGILYHLWYFPALITGSLLLTSLLIHVSFKKVFWLAAGLYLIGLGGDSWFGLIQQTPIEPFYTAVFHLLDGTRNGIFFTPLFLCLGVLVRKQSEKRSLSKTALFFLISLIGLLIESAYLHGFSIPKHDSMYLFLPVVLFFLFPLILRWHPHRTWKHPGQLSLWLYLLHPYTIAGTHFLSQKISILQNNLINYLVVLILTIGFICLFLRQKHSWFRHKQTTPVKRAVKEFSKTALLHNLQEIQRIISPKTKVMAVVKADAYGCGAKEVAPVLEQAGIDFFAVATIDEGIRLRKNAVKSPILVLGYTSPKRIKELRRYSLTQSIISEGHAVALSQRKVAIDCHLAIDTGMHRLGVTPTIDSILSIFDLPFLTISGVYSHLGSADRLNPDSMIRTQKQIACFDQILLELDQRQISYGITHLQSSYGILNYPDLNYDYVRPGILLTGSLSDTNEPTKQRVSLQPILTLKAQLITKRVVAKGEAIGYGQTAVANQETTVGVVSIGYCDGLPRSLSNQEFCLSYRGQSLPQIGLICMDMLLIDLSHCPTIPIESEIEILTDWSDTAEQVQTITNELICRIGPRVSARIK"},"dna_sequence":{"accession":"AF162694","fmin":"3007","fmax":"5104","strand":"+","sequence":"ATGAAAAATAAAGGAATCGATCAATTTCGTGTGATTGCAGCCATGATGGTGGTTGCGATCCATTGTCTTCCCCTTCACTATTTATGGCCAGAAGGCGATATCCTAATCACATTGACGATTTTTCGAGTAGCTGTTCCTTTCTTTTTTATGATCAGTGGTTACTATGTGTTTGCAGAACTTGCTGTGGCCAATAGTTATCCTTCGCGACAACGAGTATTCAACTTTATCAAAAAACAGCTAAAAGTCTATCTATTAGCCACACTAATGTTTTTACCATTAGCACTCTATAGTCAAACGATCGGCTTCGATCTACCAGTTGGAACATTAGTACAAGTACTTTTGGTCAATGGCATTCTTTATCATCTTTGGTACTTTCCGGCTTTGATTACTGGGAGCCTGCTCCTAACAAGTTTGCTGATACATGTCTCCTTCAAAAAAGTGTTCTGGCTTGCGGCTGGATTGTACCTGATTGGATTAGGTGGTGATAGTTGGTTTGGACTGATCCAACAGACACCAATCGAACCATTCTATACTGCTGTGTTCCACCTATTAGATGGTACCCGCAACGGTATTTTCTTTACACCATTGTTTTTGTGCTTAGGTGTGCTGGTCAGAAAACAATCAGAGAAAAGAAGTTTATCCAAAACAGCTCTCTTCTTTTTGATCAGTCTTATCGGATTGCTTATTGAGAGTGCGTACTTGCATGGGTTTTCTATACCTAAACATGACAGTATGTATCTCTTCTTGCCTGTTGTACTCTTTTTCTTATTTCCGCTGATCTTGCGCTGGCATCCCCACAGGACTTGGAAGCATCCAGGACAGCTATCTTTGTGGCTTTACCTTTTACATCCTTATACAATTGCCGGCACACACTTTTTGAGCCAAAAAATCAGCATTCTGCAAAACAATCTAATCAACTATTTGGTTGTTTTGATCTTGACGATTGGATTCATTTGCCTCTTTTTAAGACAAAAACACTCATGGTTTAGACACAAACAAACAACGCCCGTTAAAAGGGCCGTAAAAGAATTCTCAAAGACAGCCCTTTTGCATAATCTACAGGAGATCCAGCGGATCATCTCACCGAAAACAAAAGTGATGGCAGTCGTTAAAGCCGATGCCTACGGCTGTGGTGCCAAGGAAGTTGCTCCTGTTTTAGAACAAGCCGGAATTGATTTTTTTGCGGTGGCTACGATTGATGAAGGTATTCGATTGCGGAAAAATGCTGTCAAAAGCCCCATCTTGGTCTTGGGATATACCTCTCCAAAACGCATAAAAGAACTTCGTCGCTACTCATTGACCCAATCGATCATCAGCGAAGGTCATGCTGTAGCATTGTCACAAAGAAAAGTAGCGATTGACTGTCATTTAGCCATCGATACTGGGATGCATCGGTTAGGTGTAACACCGACTATCGATTCGATTCTTTCGATTTTCGATTTGCCCTTCTTGACGATCAGTGGTGTTTATTCTCATCTTGGTTCGGCAGATCGCTTAAATCCTGATAGTATGATTCGCACTCAGAAGCAGATTGCCTGCTTCGATCAGATTCTCCTAGAGTTGGATCAGAGACAGATTTCTTATGGTATCACACACTTACAAAGCAGTTATGGTATTTTGAATTATCCAGACTTAAACTATGATTATGTGCGTCCGGGGATTTTATTGACAGGATCCCTCAGTGATACGAACGAGCCTACAAAACAACGAGTAAGCTTACAGCCTATTCTGACCCTCAAAGCACAGTTGATCACTAAGCGAGTCGTTGCCAAAGGGGAAGCGATCGGTTATGGGCAAACCGCCGTCGCGAATCAAGAAACAACTGTTGGTGTTGTGAGCATCGGCTATTGTGACGGACTGCCCCGTTCTCTATCAAATCAAGAGTTTTGTCTTTCCTATCGCGGTCAGTCCTTGCCGCAGATCGGCTTGATCTGCATGGACATGCTTTTGATAGACTTGAGCCATTGTCCTACGATCCCAATTGAAAGTGAAATTGAAATTCTGACAGATTGGAGCGATACTGCCGAGCAAGTACAAACTATAACCAATGAGTTGATTTGTCGGATCGGTCCACGAGTCAGTGCTAGGATCAAATAGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36781","NCBI_taxonomy_name":"Enterococcus gallinarum","NCBI_taxonomy_id":"1353"}}}},"ARO_accession":"3002970","ARO_id":"39404","ARO_name":"vanTC","ARO_description":"vanTC is a vanT variant found in the vanC gene cluster","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36511":{"category_aro_accession":"3000372","category_aro_cvterm_id":"36511","category_aro_name":"vanT","category_aro_description":"VanT is a membrane bound serine racemase, converting L-serine to D-serine. It is associated with VanC, which incorporated D-serine into D-Ala-D-Ser terminal end of peptidoglycan subunits that have a decreased binding affinity with vancomycin. It was isolated from Enterococcus gallinarum.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"735":{"model_id":"735","model_name":"TEM-30","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"930":{"protein_sequence":{"accession":"CAD24670.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSSGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AJ437107","fmin":"208","fmax":"1069","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTAGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000900","ARO_id":"37280","ARO_name":"TEM-30","ARO_description":"TEM-30 is an inhibitor-resistant beta-lactamase found in E. coli. Confers resistance to amoxycilllin-clavulanic acid, ticarcillin-clavulanic acid, kanamycin, neomycin, and intermediate resistance to mezlocillin and piperacillin.","ARO_category":{"35996":{"category_aro_accession":"0000079","category_aro_cvterm_id":"35996","category_aro_name":"clavulanate","category_aro_description":"Clavulanic acid is a beta-lactamase inhibitor (marketed by GlaxoSmithKline, formerly Beecham) combined with penicillin group antibiotics to overcome certain types of antibiotic resistance. It is used to overcome resistance in bacteria that secrete beta-lactamase, which otherwise inactivates most penicillins.","category_aro_class_name":"Adjuvant"},"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"736":{"model_id":"736","model_name":"arr-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"250"}},"model_sequences":{"sequence":{"603":{"protein_sequence":{"accession":"CAZ48628.1","sequence":"MPNDWIPTSHENCSLVPGPFYHGTKAKLAIGDLLSPGHPSHFEQGRRLKHIYFAALMEPAIWGAELAMSLSRQEGRGYIYIVEPLGPFEDDPNLTNKKFPGNPTKSYRTSESLRIVEVVEDWQGHSPDVLQGMLASLEDLQRRGLAIIED"},"dna_sequence":{"accession":"FN397623","fmin":"1188","fmax":"1641","strand":"+","sequence":"ATGCCGAATGACTGGATTCCCACCTCGCACGAAAACTGCTCGCTCGTGCCGGGGCCGTTCTACCACGGCACCAAAGCAAAACTCGCAATAGGTGACTTGCTTTCGCCTGGACACCCGTCTCACTTTGAGCAAGGCCGTAGGCTCAAACACATCTATTTTGCCGCACTGATGGAGCCAGCCATCTGGGGTGCTGAGCTTGCAATGTCATTGTCACGCCAAGAGGGGCGCGGTTACATTTACATTGTTGAACCGCTCGGGCCGTTTGAGGACGACCCAAACCTTACAAACAAAAAATTTCCGGGCAATCCAACCAAGTCCTACCGCACCAGTGAGTCGCTACGGATTGTGGAGGTAGTAGAGGACTGGCAAGGCCACTCACCGGATGTGCTGCAGGGCATGTTGGCATCACTGGAGGATCTTCAGCGTCGCGGCCTCGCAATCATTGAGGACTAGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002852","ARO_id":"39286","ARO_name":"arr-7","ARO_description":"arr-7 is an integron-encoded ribosyltransferase found in Pseudomonas aeruginosa","ARO_category":{"36529":{"category_aro_accession":"3000390","category_aro_cvterm_id":"36529","category_aro_name":"rifampin ADP-ribosyltransferase (Arr)","category_aro_description":"Enzyme responsible for the ADP-ribosylative inactivation of rifampin at the 23-OH position using NAD+.","category_aro_class_name":"AMR Gene Family"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36656":{"category_aro_accession":"3000517","category_aro_cvterm_id":"36656","category_aro_name":"rifaximin","category_aro_description":"Rifaximin is a semi-synthetic rifamycin used to treat traveller's diarrhea. Rifaximin inhibits RNA synthesis by binding to the beta subunit of bacterial RNA polymerase.","category_aro_class_name":"Antibiotic"},"36669":{"category_aro_accession":"3000530","category_aro_cvterm_id":"36669","category_aro_name":"rifabutin","category_aro_description":"Rifabutin is a semisynthetic rifamycin used in tuberculosis therapy. It inhibits DNA-dependent RNA synthesis.","category_aro_class_name":"Antibiotic"},"36673":{"category_aro_accession":"3000534","category_aro_cvterm_id":"36673","category_aro_name":"rifapentine","category_aro_description":"Rifapentine is a semisynthetic rifamycin that inhibits DNA-dependent RNA synthesis. It is often used in the treatment of tuberculosis and leprosy.","category_aro_class_name":"Antibiotic"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"737":{"model_id":"737","model_name":"MIR-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"3325":{"protein_sequence":{"accession":"ACJ05687.1","sequence":"MMTKSLSCALLLSVASSAFAAPMSEKQLAEVVERTVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEIALGDPVAKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDTASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEEAHYAWGYREGKAVHVSPGMLDAEAYGVKTNVKDMASWLIANMKPDSLQAPSLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"FJ237367","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGACAAAATCCCTAAGCTGTGCCCTGCTGCTCAGCGTCGCCAGCTCTGCATTCGCCGCACCGATGTCCGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTAATTTATCAGGGTCAGCCACACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGCGGCGATGCCATTGCCCGGGGTGAAATAGCGCTGGGCGATCCGGTAGCAAAATACTGGCCTGAGCTCACGGGCAAGCAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTACACCGCAGGCGGTCTGCCGTTACAGGTGCCGGATGAGGTCACGGATACCGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGTACCACGCGTCTTTACGCTAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTTAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAACCCCTCAAGCTGGACCATACCTGGATTAACGTCCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGAGGGTAAAGCGGTCCACGTTTCGCCAGGGATGCTGGACGCGGAAGCCTATGGCGTAAAAACTAACGTGAAGGATATGGCGAGCTGGCTGATAGCCAACATGAAGCCGGATTCTCTTCAGGCTCCCTCACTCAAGCAAGGCATTGCTCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCCATGTATCAGGGGTTGGGCTGGGAGATGCTCAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCATTGCCCGTGGCAGAAGTGAATCCACCCGCGCCGCCGGTTAAGGCCTCCTGGGTCCATAAAACAGGCTCGACGGGTGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002173","ARO_id":"38573","ARO_name":"MIR-8","ARO_description":"MIR-8 is a beta-lactamase. From the Lahey list of MIR beta-lactamases.","ARO_category":{"36197":{"category_aro_accession":"3000058","category_aro_cvterm_id":"36197","category_aro_name":"MIR beta-lactamase","category_aro_description":"MIR beta-lactamases are plasmid-mediated beta-lactamases that confer resistance to oxyimino- and alpha-methoxy beta-lactams","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"738":{"model_id":"738","model_name":"AAC(6')-Iae","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"583":{"protein_sequence":{"accession":"BAD14386.1","sequence":"MKYNIVNIKDSEKYITQAAEILFDVFSHINFDSWPSLQKATETVIECISAENICIGILINDELCGWVGLREMYKKTWELHPMVIKKKHQNKGFGKILIFETEKKAKERNLEGIVLGTDDETFRTTLSMSELNNENIFHEIKNIKNLKNHPFEFYEKCGYSIIGVIPNANGKNKPDILMWKNIM"},"dna_sequence":{"accession":"AB104852","fmin":"1934","fmax":"2486","strand":"+","sequence":"ATGAAATACAACATTGTTAATATTAAAGATTCTGAAAAGTATATAACGCAAGCTGCAGAAATTCTATTTGATGTATTTTCACACATAAATTTCGATTCTTGGCCGTCACTCCAAAAGGCTACAGAAACTGTAATAGAATGTATTAGCGCCGAAAACATTTGTATTGGCATTTTAATAAACGATGAATTGTGTGGTTGGGTTGGATTAAGAGAAATGTATAAAAAAACTTGGGAACTACATCCAATGGTTATTAAGAAAAAACATCAAAATAAGGGATTTGGTAAAATACTAATTTTTGAAACAGAAAAGAAAGCGAAAGAAAGAAATTTAGAAGGAATTGTACTTGGAACAGACGATGAAACATTTAGAACTACATTATCAATGTCAGAATTAAATAATGAAAATATATTCCATGAAATTAAAAATATAAAAAATCTAAAAAATCATCCATTTGAATTTTATGAAAAATGTGGTTACAGTATTATTGGTGTGATTCCTAATGCAAATGGGAAAAATAAACCTGATATATTAATGTGGAAAAATATAATGTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002573","ARO_id":"38973","ARO_name":"AAC(6')-Iae","ARO_description":"AAC(6')-Iae is an integron-encoded aminoglycoside acetyltransferase in P. aeruginosa and S. enterica","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"739":{"model_id":"739","model_name":"LRA-18","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"1673":{"protein_sequence":{"accession":"ACH58997.1","sequence":"MLKRIRLPQLALALAALFPLAAYAAPDAAALRQAVDAAVGPVMAQFDVPGMAVAVTVDGQPHFFNYGVAARDSKQPVTEATIFELGSNSKTFTATLAAYAQAQGKLALDDHPGKYVPQLQGSALDGATLLHLGTYTAGGFPLQIPDNLKTREQLFSYFQHWKPDAAPGKQRNYSNPSIGLFGHIAGLALGGGFADAAERDLFPQLGLQHTYIRVPQSAMAHYAWGYSKDQAVRVQPDLFDSEAYGVKSTAADMIRYVQLQIDPSRLAAPMRRAVQATHTGYFKAGPMTQGLGWESYPYPVSLEQLLQGNSTDMAWKPQPVQAIQPVQTAAPALYNKTGSTRGFGSYVAFVPSQKIGIVLLANRAYPNDARIKLAYAILNQLAPAAN"},"dna_sequence":{"accession":"EU408355","fmin":"24321","fmax":"25482","strand":"+","sequence":"ATGTTGAAACGTATCCGCTTGCCCCAACTGGCGCTGGCCCTTGCGGCGCTGTTCCCCTTGGCCGCCTACGCGGCGCCGGACGCCGCCGCGCTGCGCCAGGCCGTCGACGCGGCAGTCGGCCCCGTCATGGCGCAGTTCGATGTGCCGGGCATGGCGGTCGCCGTCACGGTCGATGGCCAGCCGCACTTTTTCAATTACGGCGTCGCCGCGCGCGACAGCAAGCAACCCGTGACGGAAGCGACCATCTTTGAGTTGGGTTCGAACAGCAAGACTTTTACGGCCACCCTGGCGGCCTATGCCCAGGCGCAAGGCAAACTGGCGCTGGACGATCACCCCGGCAAGTATGTGCCGCAATTGCAGGGCAGTGCGCTCGATGGCGCCACCTTGCTGCACCTCGGCACCTACACGGCGGGCGGCTTTCCGTTGCAAATTCCGGACAACCTGAAAACCCGGGAGCAGTTGTTCAGTTACTTTCAGCACTGGAAACCGGACGCGGCGCCGGGCAAGCAGCGTAACTATTCCAATCCCAGCATCGGCCTATTCGGCCATATTGCCGGCCTGGCGCTCGGTGGCGGCTTTGCCGACGCGGCGGAGCGCGACTTGTTCCCGCAACTGGGTTTGCAACACACTTACATCCGCGTGCCGCAGTCAGCCATGGCCCATTACGCGTGGGGCTATTCGAAAGACCAGGCGGTCCGTGTCCAGCCTGATTTGTTCGATAGTGAAGCCTATGGCGTGAAATCCACGGCGGCCGACATGATCCGCTACGTGCAACTGCAAATCGACCCGTCGCGCCTGGCCGCACCGATGCGGCGCGCGGTGCAAGCGACCCATACCGGCTACTTCAAGGCCGGCCCGATGACGCAGGGACTGGGATGGGAATCGTACCCGTATCCCGTCAGCCTGGAGCAACTGTTGCAGGGCAATTCCACCGACATGGCGTGGAAGCCGCAGCCAGTCCAGGCAATACAACCAGTGCAGACCGCGGCCCCGGCCCTGTACAACAAGACCGGTTCCACGCGGGGCTTCGGCAGCTATGTCGCCTTTGTCCCGTCGCAAAAAATTGGTATCGTGCTGCTGGCCAACCGGGCTTATCCGAACGATGCGCGGATCAAGCTGGCGTATGCGATCTTGAATCAGCTGGCCCCGGCGGCAAATTGAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39683","NCBI_taxonomy_name":"uncultured bacterium BLR18","NCBI_taxonomy_id":"506518"}}}},"ARO_accession":"3002492","ARO_id":"38892","ARO_name":"LRA-18","ARO_description":"LRA-18 is a beta-lactamase isolated from soil samples in Alaska","ARO_category":{"41395":{"category_aro_accession":"3004231","category_aro_cvterm_id":"41395","category_aro_name":"class C LRA beta-lactamase","category_aro_description":"Beta-lactamases that are part of the LRA gene family and are classified as Class C beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"740":{"model_id":"740","model_name":"QnrB21","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"609":{"protein_sequence":{"accession":"ACM50952.1","sequence":"MTLALVGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAILKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKAVLEKCELWENRWMGTQVLGATLSGSDLSGGEFSSFDWRTANFTHCDLTNSELGDLDIRGVDLQGVKLDSYQAALLMERLGIAVIG"},"dna_sequence":{"accession":"FJ611948","fmin":"0","fmax":"645","strand":"+","sequence":"ATGACTCTGGCATTAGTTGGCGAAAAAATTGACAGAAACCGCTTCACCGGTGAAAAAGTTGAAAATAGCACTTTTTTTAACTGTGATTTTTCGGGTGCCGACCTTAGCGGTACTGAATTTATCGGCTGTCAGTTCTATGATCGAGAAAGCCAGAAAGGGTGCAATTTCAGTCGCGCAATACTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAACGTCAGTGCGTTGGGCATAGAAATTCGCCACTGCCGCGCACAGGGTGCAGATTTTCGCGGCGCAAGTTTCATGAATATGATCACCACGCGCACCTGGTTTTGCAGCGCATATATCACTAATACCAATCTAAGCTACGCCAACTTTTCGAAGGCCGTGCTTGAAAAGTGCGAATTGTGGGAAAATCGCTGGATGGGAACTCAGGTACTGGGTGCGACGTTGAGTGGTTCCGATCTCTCCGGTGGCGAGTTTTCGTCGTTCGACTGGCGGACGGCAAATTTCACGCACTGTGATTTGACCAATTCAGAACTGGGTGATTTAGATATTCGGGGCGTCGATTTACAAGGTGTCAAATTGGACAGCTATCAGGCCGCATTGCTCATGGAACGTCTTGGCATCGCTGTGATTGGCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002736","ARO_id":"39170","ARO_name":"QnrB21","ARO_description":"QnrB21 is a plasmid-mediated quinolone resistance protein found in Escherichia coli","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"741":{"model_id":"741","model_name":"CfxA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"1354":{"protein_sequence":{"accession":"AAB17891.1","sequence":"MEKNRKKQIVVLSIALVCIFILVFSLFHKSATKDSANPPLTNVLTDSISQIVSACPGEIGVAVIVNNRDTVKVNNKSVYPMMSVFKVHQALALCNDFDNKGISLDTLVNINRDKLDPKTWSPMLKDYSGPVISLTVRDLLRYTLTQSDNNASNLMFKDMVNVAQTDSFIATLIPRSSFQIAYTEEEMSADHNKAYSNYTSPLGAAMLMNRLFTEGLIDDEKQSFIKNTLKECKTGVDRIAAPLLDKEGVVIAHKTGSGYVNENGVLAAHNDVAYICLPNNISYTLAVFVKDFKGNKSQASQYVAHISAVVYSLLMQTSVKS"},"dna_sequence":{"accession":"U38243","fmin":"149","fmax":"1115","strand":"+","sequence":"ATGGAAAAAAACAGAAAAAAACAAATCGTAGTTTTGAGTATAGCTTTAGTTTGCATTTTCATCTTGGTATTTTCATTGTTCCATAAATCAGCGACAAAAGATAGCGCAAATCCTCCTTTAACAAATGTTTTGACTGATAGCATTTCTCAAATTGTCTCAGCTTGTCCTGGCGAAATTGGTGTGGCGGTTATTGTTAATAACAGAGATACGGTTAAGGTCAATAATAAGAGTGTTTATCCTATGATGAGTGTGTTTAAGGTTCATCAGGCATTAGCTCTTTGTAATGACTTTGACAATAAAGGAATTTCACTTGATACCTTAGTAAATATAAATAGGGATAAACTTGACCCAAAGACTTGGAGTCCTATGCTGAAAGATTATTCAGGGCCAGTCATATCATTGACAGTGAGAGATTTGCTGCGTTATACTCTTACTCAGAGTGACAACAATGCAAGCAACCTTATGTTTAAGGATATGGTTAATGTCGCTCAAACAGATAGTTTTATAGCCACACTCATTCCTCGTTCAAGTTTTCAGATAGCTTATACGGAAGAGGAAATGTCGGCTGACCATAACAAGGCTTACTCTAACTATACATCTCCTCTTGGTGCTGCAATGTTGATGAATCGTTTGTTTACTGAAGGTCTTATCGATGATGAGAAACAAAGTTTCATTAAGAATACGTTAAAAGAATGCAAAACAGGTGTAGATAGGATAGCAGCTCCACTTCTTGATAAAGAAGGGGTTGTTATAGCGCATAAGACAGGTTCAGGTTATGTTAATGAAAATGGTGTTCTTGCAGCTCACAATGATGTTGCCTATATATGTCTGCCTAATAATATCAGTTATACCTTAGCGGTATTTGTTAAGGATTTCAAGGGAAATAAATCACAAGCGTCACAATATGTTGCGCATATATCAGCTGTAGTATATTCTTTATTAATGCAAACTTCAGTAAAATCTTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39546","NCBI_taxonomy_name":"Bacteroides vulgatus","NCBI_taxonomy_id":"821"}}}},"ARO_accession":"3003001","ARO_id":"39435","ARO_name":"CfxA","ARO_description":"cfxA beta-lactamase is a class A beta-lactamase found in Bacteroides vulgatus","ARO_category":{"39434":{"category_aro_accession":"3003000","category_aro_cvterm_id":"39434","category_aro_name":"CfxA beta-lactamase","category_aro_description":"cfxA beta-lactamases are class A beta-lactamases","category_aro_class_name":"AMR Gene Family"},"35927":{"category_aro_accession":"0000008","category_aro_cvterm_id":"35927","category_aro_name":"cefoxitin","category_aro_description":"Cefoxitin is a cephamycin antibiotic often grouped with the second generation cephalosporins. Cefoxitin is bactericidal and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. Cefoxitin's 7-alpha-methoxy group and 3' leaving group make it a poor substrate for most beta-lactamases.","category_aro_class_name":"Antibiotic"},"40928":{"category_aro_accession":"3004001","category_aro_cvterm_id":"40928","category_aro_name":"cefmetazole","category_aro_description":"Cefmetazole is a semi-synthetic cephamycin antibiotic with broad spectrum antibiotic activity against both gram-positive and gram-negative bacteria, that disrupt cell wall synthesis through binding to PBPs causing cell lysis.","category_aro_class_name":"Antibiotic"},"40931":{"category_aro_accession":"3004004","category_aro_cvterm_id":"40931","category_aro_name":"cefotetan","category_aro_description":"Cefotetan is a cephamycin-class beta-lactam antibiotic that is highly resistant to beta-lactamases and effective against a wide range of gram-negative and gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"40941":{"category_aro_accession":"3004014","category_aro_cvterm_id":"40941","category_aro_name":"flomoxef","category_aro_description":"Flomoxef is a second-generation cephamycin (oxacephem) and beta-lactam antibiotic.","category_aro_class_name":"Antibiotic"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"742":{"model_id":"742","model_name":"AAC(3)-Id","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"223":{"protein_sequence":{"accession":"AAR21614.1","sequence":"MSVEIIHLTGNDVALLQSINAMFGEAFNDQDSYARNKPSSSYLQKLLSTSSFIALAAVDEQKVIGAIAAYELQKFEQQRSEIYIYDLAVAATRRREGIATALIKKLKAIGAARGAYVIYVQADKGVEDQPAIELYKKLGTIEDVFHFDIAVEQSKNHA"},"dna_sequence":{"accession":"AY458224","fmin":"706","fmax":"1183","strand":"+","sequence":"GTGTCAGTCGAAATCATCCATCTCACTGGAAACGATGTTGCGTTGTTGCAGTCAATAAATGCCATGTTCGGCGAGGCATTCAACGACCAAGATAGTTATGCCCGCAACAAGCCGTCATCAAGCTATCTTCAAAAACTGCTTAGCACTTCTAGTTTTATTGCGTTGGCTGCGGTTGACGAGCAAAAAGTCATTGGCGCTATCGCCGCGTATGAGTTGCAAAAATTCGAGCAGCAAAGAAGCGAGATTTATATCTACGATCTCGCTGTAGCGGCAACCCGCCGCAGAGAAGGCATAGCTACAGCTCTAATTAAAAAACTCAAGGCTATAGGCGCAGCGCGTGGAGCTTATGTGATTTACGTCCAAGCTGATAAAGGCGTAGAAGACCAACCAGCCATAGAGCTCTATAAAAAACTAGGAACCATCGAAGACGTATTTCATTTCGACATTGCGGTTGAGCAGAGTAAAAATCATGCCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35735","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Newport","NCBI_taxonomy_id":"108619"}}}},"ARO_accession":"3002529","ARO_id":"38929","ARO_name":"AAC(3)-Id","ARO_description":"AAC(3)-Id is an aminoglycoside acetyltransferase encoded by genomic islands and integrons in S. enterica, P. mirabilis and Vibrio fluvialis","ARO_category":{"36461":{"category_aro_accession":"3000322","category_aro_cvterm_id":"36461","category_aro_name":"AAC(3)","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 3.","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"743":{"model_id":"743","model_name":"arr-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"250"}},"model_sequences":{"sequence":{"707":{"protein_sequence":{"accession":"ACD56151.1","sequence":"MVKDWIPISHDNYKQVQGPFYHGTKANLAIGDLLTTGFISHFEDGRILKHIYFSALMEPAVWGAELAMSLSGLEGRGYIYIVEPTGPFEDDPNLTNKRFPGNPTQSYRTCEPLRIVGVVEDWEGHPVELIRGMLDSLEDLKRRGLHVIED"},"dna_sequence":{"accession":"EU675686","fmin":"1956","fmax":"2409","strand":"+","sequence":"ATGGTAAAAGATTGGATTCCCATCTCTCATGATAATTACAAGCAGGTGCAAGGACCGTTCTATCATGGAACCAAAGCCAATTTGGCGATTGGTGACTTGCTAACCACAGGGTTCATCTCTCATTTCGAGGACGGTCGTATTCTTAAGCACATCTACTTTTCAGCCTTGATGGAGCCAGCAGTTTGGGGAGCTGAACTTGCTATGTCACTGTCTGGCCTCGAGGGTCGCGGCTACATATACATAGTTGAGCCAACAGGACCGTTCGAAGACGATCCGAATCTTACGAACAAAAGATTTCCCGGTAATCCAACACAGTCCTATAGAACCTGCGAACCCTTGAGAATTGTTGGCGTTGTTGAAGACTGGGAGGGGCATCCTGTTGAATTAATAAGGGGAATGTTGGATTCGTTGGAGGACTTAAAGCGCCGTGGTTTACACGTCATTGAAGACTAGT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002848","ARO_id":"39282","ARO_name":"arr-3","ARO_description":"arr-3 is a plasmid-encoded ribosyltransferase found in Vibrio fluvialis","ARO_category":{"36529":{"category_aro_accession":"3000390","category_aro_cvterm_id":"36529","category_aro_name":"rifampin ADP-ribosyltransferase (Arr)","category_aro_description":"Enzyme responsible for the ADP-ribosylative inactivation of rifampin at the 23-OH position using NAD+.","category_aro_class_name":"AMR Gene Family"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36656":{"category_aro_accession":"3000517","category_aro_cvterm_id":"36656","category_aro_name":"rifaximin","category_aro_description":"Rifaximin is a semi-synthetic rifamycin used to treat traveller's diarrhea. Rifaximin inhibits RNA synthesis by binding to the beta subunit of bacterial RNA polymerase.","category_aro_class_name":"Antibiotic"},"36669":{"category_aro_accession":"3000530","category_aro_cvterm_id":"36669","category_aro_name":"rifabutin","category_aro_description":"Rifabutin is a semisynthetic rifamycin used in tuberculosis therapy. It inhibits DNA-dependent RNA synthesis.","category_aro_class_name":"Antibiotic"},"36673":{"category_aro_accession":"3000534","category_aro_cvterm_id":"36673","category_aro_name":"rifapentine","category_aro_description":"Rifapentine is a semisynthetic rifamycin that inhibits DNA-dependent RNA synthesis. It is often used in the treatment of tuberculosis and leprosy.","category_aro_class_name":"Antibiotic"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"744":{"model_id":"744","model_name":"vanSL","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"744":{"protein_sequence":{"accession":"ABX54692.1","sequence":"MKSKAETTTIKQILIKYLVTIGLSMLAYLVFLLTILIIMRNFVWDGTEPIYRVLHFFYRLFNFEGILIIGVILILFVVTLFFVMKIIGYLKQIIEATKQLLEKPEQRVKLSSGLFELQEEMNQLREKNNADNRAAKEAEKRKNDLIVYLAHDLRTPLTSVIGYLTLLKEEPEISVQTRAKYTNIALSKAFRLEELLSEFFDVTRFNLTNLTINEELVDLSVMLEQISYEFLPILEEKKLSWNLHVESNIKSLLDPGKMERVFDNLMRNAINYSFEDTIIDLSLEKKESQAIFKITNRTYTIPKEKLEKIFEPFYRMDTSRSSSTGGTGLGLPIVREIIEASKGTINVSSSNNEMTFIIYLPYID"},"dna_sequence":{"accession":"EU250284","fmin":"5415","fmax":"6510","strand":"+","sequence":"TTGAAAAGTAAGGCGGAAACTACAACTATAAAACAGATACTAATAAAATATTTAGTAACTATAGGTTTATCGATGCTTGCCTATTTAGTATTTCTTCTAACAATACTTATTATAATGAGAAATTTTGTATGGGACGGCACGGAGCCTATCTATCGTGTCTTGCACTTTTTTTATCGTCTTTTTAATTTTGAAGGGATATTGATTATCGGTGTGATACTTATCCTATTCGTTGTTACATTGTTTTTTGTTATGAAGATAATTGGCTATTTAAAACAAATCATCGAGGCGACGAAACAATTGCTTGAAAAACCAGAACAGCGTGTTAAGCTATCAAGTGGCCTGTTCGAATTACAAGAAGAAATGAACCAACTACGTGAAAAAAATAATGCTGACAATCGCGCAGCTAAAGAAGCGGAAAAGAGAAAAAACGATTTGATTGTTTATTTAGCTCATGATTTACGTACGCCATTAACTAGCGTAATTGGGTATTTAACGCTGTTAAAAGAAGAACCGGAAATATCGGTTCAAACTAGAGCTAAGTATACGAACATCGCTTTGAGTAAAGCTTTTCGCCTTGAAGAATTATTGAGTGAATTTTTTGATGTGACGAGATTTAATTTGACTAACTTAACAATAAATGAAGAACTAGTAGATTTAAGTGTGATGTTAGAGCAAATCAGCTACGAATTTTTACCTATTTTGGAAGAAAAAAAACTTTCTTGGAATCTACACGTCGAGAGTAATATAAAATCTCTTTTAGATCCAGGAAAAATGGAACGTGTTTTTGATAACTTGATGCGAAATGCTATTAATTATAGCTTTGAAGATACAATAATTGATTTAAGTTTAGAAAAAAAAGAATCTCAAGCTATTTTTAAAATTACAAATAGGACCTATACAATCCCAAAAGAAAAATTAGAAAAAATATTCGAACCGTTTTACCGAATGGACACATCTAGAAGTAGCAGTACAGGTGGAACTGGGCTTGGTCTACCGATTGTAAGGGAAATTATTGAAGCTTCCAAAGGAACTATAAACGTTAGTAGTAGCAATAATGAAATGACTTTTATAATCTATTTACCATACATAGATTAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3002938","ARO_id":"39372","ARO_name":"vanSL","ARO_description":"vanSL is a vanS variant found in the vanL gene cluster","ARO_category":{"36210":{"category_aro_accession":"3000071","category_aro_cvterm_id":"36210","category_aro_name":"vanS","category_aro_description":"VanS is similar to histidine protein kinases like EnvZ and acts as a response regulator by activating VanR. VanS is required for high level transcription of other van glycopeptide resistance genes.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"745":{"model_id":"745","model_name":"CMY-40","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1266":{"protein_sequence":{"accession":"ACA30422.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGTLAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMAHWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGYTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"EU515251","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAACCGCACCATCACACCGCTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCGGTTATCTACCAGGGAAAACCCTATTATTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCAGTCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGCACGCTGGCGGTGAAACCCTCCGGTATGAGCTACGAAGAGGCGATGACCAGACGCGTTCTGCAGCCATTAAAGCTGGCGCATACCTGGATTACGGTTCCACAGAGCGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAACCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCACTGGGTACAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAACAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCCGATTCGATCATCAACGGCAGCGACAGCAAAGTAGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTACACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002051","ARO_id":"38451","ARO_name":"CMY-40","ARO_description":"CMY-40 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"746":{"model_id":"746","model_name":"AAC(2')-Ib","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"85":{"protein_sequence":{"accession":"AAC44793.1","sequence":"MPFQDVSAPVRGGILHTARLVHTSDLDQETREGARRMVIEAFEGDFSDADWEHALGGMHAFICHHGALIAHAAVVQRRLLYRDTALRCGYVEAVAVREDWRGQGLATAVMDAVEQVLRGAYQLGALSASDTARGMYLSRGWLPWQGPTSVLQPAGVTRTPEDDEGLFVLPVGLPAGMELDTTAEITCDWRDGDVW"},"dna_sequence":{"accession":"U41471","fmin":"264","fmax":"852","strand":"+","sequence":"GTGCCTTTCCAGGATGTCAGCGCGCCCGTTCGAGGCGGGATCCTGCACACCGCTCGACTCGTCCACACCTCCGATCTCGATCAGGAGACTCGAGAGGGCGCCCGCCGCATGGTCATCGAGGCGTTCGAGGGTGATTTCAGCGACGCCGACTGGGAGCACGCGCTCGGTGGCATGCACGCCTTCATCTGTCACCACGGCGCTCTGATCGCGCATGCCGCGGTGGTCCAGCGCCGGCTGCTCTACCGCGACACCGCGCTGCGCTGCGGGTACGTGGAAGCCGTGGCGGTGCGCGAAGATTGGCGCGGCCAAGGCCTGGCCACCGCCGTCATGGACGCGGTCGAACAGGTGCTGCGCGGCGCCTACCAGCTCGGCGCCCTCAGTGCGTCCGACACAGCCAGAGGCATGTACCTCTCTCGCGGGTGGCTGCCGTGGCAGGGGCCGACCTCGGTGCTGCAGCCGGCCGGCGTGACGCGTACACCCGAGGACGACGAGGGACTGTTCGTGCTGCCCGTCGGTCTCCCGGCGGGAATGGAACTCGACACCACAGCCGAGATCACCTGCGACTGGCGCGACGGGGACGTCTGGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36886","NCBI_taxonomy_name":"Mycobacterium fortuitum","NCBI_taxonomy_id":"1766"}}}},"ARO_accession":"3002524","ARO_id":"38924","ARO_name":"AAC(2')-Ib","ARO_description":"AAC(2')-Ib is a chromosomal-encoded aminoglycoside acetyltransferase in M. fortuitum and A. baumannii","ARO_category":{"36480":{"category_aro_accession":"3000341","category_aro_cvterm_id":"36480","category_aro_name":"AAC(2')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 2'.","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"747":{"model_id":"747","model_name":"QnrA4","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"553":{"protein_sequence":{"accession":"AAZ04783.1","sequence":"MDIIDKVFQQEDFSRQDLSDSRFRRCRFYQCDFSHCQLRDASFEDCSFIESGAVEGCHFSYADLRDASFKACRLSLANFSGANCFGIEFRECDLKGANFSRARFYNQISHKMYFCSAYISGCNLAYANLNGQCLEKCELFENNWSNANLSGASLMGSDLSRGTFSRDCWQQVNLRGCDLTFADLDGLDPRRVNLEGVKICAWQQEQLLEPLGVIVLPD"},"dna_sequence":{"accession":"DQ058662","fmin":"0","fmax":"657","strand":"+","sequence":"ATGGATATTATTGATAAAGTTTTTCAGCAAGAGGATTTCTCACGCCAGGATTTGAGTGACAGCCGTTTTCGCCGCTGCCGCTTTTATCAGTGTGACTTCAGCCATTGCCAGCTAAGGGATGCCAGTTTCGAGGATTGCAGTTTCATTGAAAGCGGCGCCGTCGAAGGGTGCCACTTCAGCTATGCCGATCTGCGCGATGCCAGTTTCAAGGCCTGCCGCCTGTCTTTGGCCAATTTCAGCGGCGCCAACTGCTTTGGCATAGAGTTCAGGGAGTGCGATCTCAAGGGCGCCAATTTTTCCCGGGCCCGTTTTTACAATCAAATCAGCCATAAGATGTACTTCTGCTCGGCTTATATCTCAGGCTGCAACCTGGCCTATGCCAATTTGAACGGCCAATGCCTGGAAAAGTGCGAGCTGTTTGAAAACAACTGGAGCAATGCCAACCTCAGCGGCGCTTCCTTGATGGGCTCCGACCTCAGCCGCGGCACCTTCTCCCGCGACTGCTGGCAGCAGGTAAACCTGCGGGGCTGTGACCTGACCTTTGCCGATCTGGATGGGCTCGATCCCAGACGGGTCAACCTCGAAGGGGTCAAGATCTGTGCCTGGCAGCAGGAGCAACTGCTGGAACCCTTGGGAGTCATAGTGCTGCCGGATTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36891","NCBI_taxonomy_name":"Shewanella algae","NCBI_taxonomy_id":"38313"}}}},"ARO_accession":"3002710","ARO_id":"39144","ARO_name":"QnrA4","ARO_description":"QnrA4 is a plasmid-mediated quinolone resistance protein found in Shewanella algae","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"748":{"model_id":"748","model_name":"cmeB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"2090"}},"model_sequences":{"sequence":{"166":{"protein_sequence":{"accession":"ABS43151.1","sequence":"MFSKFFIERPVFASVVAIIISLAGVIGLTNLPIEQYPSLTPPTVKVSATYTGADAQTIASTVASPIEDAINGADNMIYMDSTSSSSGTMSLTVYFDIGTDPDQATIDVNNRISAATAKMPDAVKKLGVTVRKTSSATLAAISMYSSDGSMSAVDVYNYIALNVLDELKRVPGVGDANAIGNRNYSLRIWLKPDLLNKFKITATDVISAVNDQNAQYATGKIGEEPVTQKSPYVYSITMQGRLQNPSEFENIILRTNDDGSFLRLKDIADVEIGSQQYSSQGRLNGNDAVPIIINLQSGANALHTAELVQAKMQELSKNFPKGLTYKIPYDTTKFVIESIKEVIKTFIEALILVIIVMYMFLKNFRATLIPMIAVPVSLLGTFAGLYVLGFSINLLTLFALILAIGIVVDDAIIVVENIDRILHENEQISVKDAAIQAMQEVSSPVISIVLVLCAVFIPVSFISGFVGEIQRQFALTLAISVTISGFVALTLTPSLCALFLRRNEGEPFKFVRKFNDFFDWSTSVFSAGVAYILKRTIRFVLIFCIMLGTIFYLNKAVPNSLVPEEDQGLMIGIINLPSASALHRTISEVDHISQEVLKTNGIKDAMAMIGFDLFTSSLKENAAAMFIGLQDWKDRNVSADKIAMELNKKFAFDRNASSIFIGLPPIPGLSITGGFEMYVQNKSGKSYDQIQKDVNKLVAAANQRKELSRVRTTLDTTFPQYKLIIDRDKLKHYNLNMQDVFNTMNATIGTYYVNDFSMLGKNFQVNIRAKGDFRNTQDALKNIFVRSNDGKMIPLDSFLTLQRSSGPDDVKRFNLFPAAQVQGQPAPGYTSGQAIEAIAQVAKETLGDDYSIAWSGSAYQEVSSKGTASYAFALGMIFVFLILAAQYERWLIPLAVVTAVPFAVFGSFLLVYLRGFSNDIYFQTGLLLLIGLSAKNAILIVEFAMEERFKKGKGVFEAAVAAAKLRFRPIIMTSLAFTFGVLPMIFATGAGSASRHSLGTGLIGGMIAASTLAIFFVPLFFYLLENFNEWLDKKRGKIHE"},"dna_sequence":{"accession":"CP000768","fmin":"1406494","fmax":"1409617","strand":"+","sequence":"ATGTTTTCTAAATTTTTTATCGAAAGACCTGTTTTTGCCTCAGTTGTTGCAATTATCATTTCTTTAGCTGGAGTCATAGGTCTTACAAATTTACCTATAGAACAATACCCTTCTTTAACCCCTCCTACAGTTAAGGTAAGTGCAACTTACACAGGAGCTGATGCACAAACCATTGCTTCAACAGTTGCAAGTCCTATCGAAGATGCAATCAATGGTGCAGATAATATGATTTATATGGATTCGACTTCAAGTTCTTCAGGAACTATGAGTTTGACCGTTTATTTTGATATTGGCACAGATCCTGATCAAGCCACCATAGATGTTAATAATAGAATTTCAGCTGCAACTGCAAAAATGCCAGATGCAGTTAAAAAACTTGGAGTAACTGTTAGAAAAACTTCTTCGGCAACCCTAGCTGCAATTTCTATGTATTCAAGTGATGGCTCAATGAGTGCAGTGGATGTATACAATTACATCGCCTTAAATGTTTTAGATGAGTTAAAAAGGGTTCCAGGAGTTGGAGATGCAAACGCTATAGGAAATCGTAATTATTCTTTAAGAATTTGGCTAAAACCTGATTTGTTAAATAAATTTAAAATCACAGCTACTGATGTAATTTCTGCGGTTAACGATCAAAATGCCCAATACGCAACTGGTAAAATTGGCGAAGAACCTGTAACTCAAAAATCTCCTTATGTTTATTCAATCACCATGCAAGGAAGATTGCAAAATCCTAGCGAATTTGAAAACATTATTTTAAGAACAAATGATGATGGATCATTTTTAAGACTTAAAGATATAGCTGATGTGGAAATAGGATCACAACAATACAGCTCACAAGGACGATTAAATGGTAATGATGCGGTTCCGATTATAATCAATCTTCAATCAGGAGCAAATGCATTACATACAGCAGAACTTGTCCAGGCTAAAATGCAAGAACTTTCAAAAAATTTCCCAAAAGGTTTAACATATAAAATTCCTTACGACACAACAAAATTTGTGATAGAATCAATCAAAGAAGTAATTAAAACTTTTATTGAAGCTCTAATTTTAGTTATCATTGTTATGTATATGTTCTTAAAAAATTTCCGCGCAACACTTATTCCTATGATAGCTGTACCTGTTTCATTGTTAGGAACTTTTGCTGGACTTTATGTTTTAGGCTTTAGTATTAACCTACTTACGCTTTTTGCCTTAATTTTAGCCATAGGGATTGTTGTAGATGATGCGATTATAGTTGTGGAAAATATCGACAGGATTTTACACGAGAATGAACAAATAAGCGTAAAAGATGCTGCTATCCAAGCGATGCAAGAAGTTAGCTCTCCAGTCATTTCAATTGTTCTTGTGCTTTGTGCTGTTTTTATACCGGTTTCTTTTATATCAGGCTTTGTTGGAGAAATTCAAAGACAATTTGCTCTTACCTTAGCTATATCTGTAACCATATCAGGTTTTGTTGCTCTTACCTTAACACCTTCTTTATGCGCACTCTTTTTGCGACGTAATGAAGGAGAGCCATTTAAATTTGTAAGGAAATTCAATGATTTTTTTGATTGGAGCACTTCTGTATTTAGCGCAGGAGTAGCATATATTTTAAAAAGAACCATTCGTTTTGTTTTAATTTTTTGTATCATGCTTGGGACAATTTTTTATCTTAATAAAGCTGTGCCAAATTCTTTAGTTCCTGAAGAAGATCAAGGTTTGATGATTGGCATTATTAACCTTCCTTCAGCTTCAGCACTCCATAGAACAATCTCAGAAGTTGATCACATAAGTCAAGAAGTTTTAAAAACTAATGGAATTAAAGATGCAATGGCTATGATAGGATTTGATCTTTTTACAAGTTCACTCAAAGAAAACGCTGCTGCAATGTTTATAGGCTTGCAAGATTGGAAAGATAGAAATGTGAGTGCTGATAAAATCGCCATGGAGCTTAATAAAAAATTTGCCTTTGATCGCAATGCTTCAAGTATATTTATAGGCTTACCTCCTATACCTGGATTAAGTATCACAGGTGGTTTTGAAATGTATGTTCAAAACAAAAGTGGAAAAAGCTATGATCAAATTCAAAAAGATGTAAATAAACTTGTTGCTGCAGCCAACCAAAGAAAAGAACTATCAAGAGTAAGAACAACCCTTGATACAACTTTCCCTCAATACAAGCTTATAATTGATAGAGATAAATTAAAACACTACAATCTTAACATGCAAGATGTTTTTAACACGATGAATGCAACTATAGGCACTTATTATGTTAATGATTTTTCTATGCTAGGTAAAAACTTCCAAGTAAATATCCGCGCAAAAGGTGATTTTAGAAATACACAAGATGCATTAAAAAATATTTTTGTAAGATCAAATGATGGAAAAATGATACCACTTGATTCTTTCTTAACTTTACAAAGAAGTTCAGGGCCTGATGATGTAAAACGATTCAACCTTTTCCCAGCAGCACAAGTTCAAGGTCAACCCGCACCAGGTTATACTTCAGGTCAAGCTATAGAAGCGATTGCTCAAGTAGCAAAAGAAACTTTAGGGGATGATTATTCCATAGCTTGGAGTGGATCAGCTTATCAAGAAGTTTCTAGTAAAGGAACAGCAAGTTATGCTTTTGCTTTAGGTATGATATTTGTATTTTTAATTCTAGCTGCTCAATATGAAAGGTGGCTTATACCTTTAGCAGTTGTAACAGCTGTGCCTTTTGCAGTATTTGGATCATTTTTATTGGTATATTTAAGAGGGTTTAGTAATGATATATATTTTCAAACAGGACTTTTGCTCTTGATTGGACTTTCAGCTAAAAATGCTATCTTGATCGTAGAATTTGCAATGGAAGAGCGCTTTAAAAAAGGCAAAGGAGTTTTTGAAGCAGCTGTTGCAGCAGCAAAACTTCGTTTTCGTCCTATCATAATGACTTCTTTGGCGTTTACTTTTGGGGTCTTACCAATGATTTTTGCAACAGGAGCAGGAAGTGCTTCAAGACACTCTTTAGGAACAGGGCTTATTGGTGGAATGATCGCAGCATCAACTTTAGCGATATTCTTTGTGCCTTTATTTTTCTATCTTTTAGAAAATTTTAATGAATGGCTAGATAAAAAAAGAGGTAAGATTCATGAATAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37595","NCBI_taxonomy_name":"Campylobacter jejuni subsp. doylei 269.97","NCBI_taxonomy_id":"360109"}}}},"ARO_accession":"3000784","ARO_id":"37164","ARO_name":"cmeB","ARO_description":"CmeB is the inner membrane transporter the CmeABC multidrug efflux complex.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"36989":{"category_aro_accession":"3000645","category_aro_cvterm_id":"36989","category_aro_name":"cefotaxime","category_aro_description":"Cefotaxime is a semisynthetic cephalosporin taken parenterally. It is resistant to most beta-lactamases and active against Gram-negative rods and cocci due to its aminothiazoyl and methoximino functional groups.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"37139":{"category_aro_accession":"3000759","category_aro_cvterm_id":"37139","category_aro_name":"fusidic acid","category_aro_description":"Fusidic acid is the only commercially available fusidane, a group of steroid-like antibiotics. It is most active against Gram-positive bacteria, and acts by inhibiting elongation factor G to  block protein synthesis.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"749":{"model_id":"749","model_name":"SHV-97","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"922":{"protein_sequence":{"accession":"ABN49114.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGKRGARGIVALLGPNNKAERIVVIYLRDSPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"EF373973","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGATGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCAAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATTCGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3001149","ARO_id":"37529","ARO_name":"SHV-97","ARO_description":"SHV-97 is a beta-lactamase found in Enterococcus faecalis.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"750":{"model_id":"750","model_name":"SHV-172","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1313":{"protein_sequence":{"accession":"AHA80958.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKADRIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"KF513177","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGATCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001356","ARO_id":"37756","ARO_name":"SHV-172","ARO_description":"From the Lahey list of beta-lactamases.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"751":{"model_id":"751","model_name":"TEM-217","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1572":{"protein_sequence":{"accession":"CDN33426.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVMYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"HG934763","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATGTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001394","ARO_id":"37794","ARO_name":"TEM-217","ARO_description":"From the Lahey list of beta-lactamases. Not yet released.Isolated from Enterobacter cloacae","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"752":{"model_id":"752","model_name":"vanRM","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"337":{"protein_sequence":{"accession":"ACL82957.1","sequence":"MRRISILIAEDEEEIADLLAIHLEKEGYDVIKVHDGQEALHVIQAQSIDLIILDIMMPKMDGYEVTRQVRAQYNMPIIFLSAKTSDFDKVHGLVIGGDDYITKPFTPIELVARVNAQLRRSMKLNHPQADDKKSILEFGEIVISPDQRTVFLYGENIGLTPKEFDILYLLASHPKKVYSVENIFQQVWNDAYFGGGNTVMVHIRTLRKKLGEDKRKNKLIKTVWGVGYTFNG"},"dna_sequence":{"accession":"FJ349556","fmin":"981","fmax":"1680","strand":"+","sequence":"ATGAGACGTATATCGATTTTAATTGCTGAAGATGAAGAAGAAATTGCTGATTTGCTTGCCATTCACCTGGAAAAAGAAGGATATGACGTTATTAAAGTACATGACGGACAAGAAGCCCTCCATGTAATCCAGGCTCAATCAATTGATTTGATAATTTTAGATATTATGATGCCGAAAATGGATGGATATGAAGTAACCCGTCAAGTCCGTGCACAGTATAATATGCCAATCATTTTTTTAAGTGCGAAAACTTCTGATTTCGATAAGGTGCATGGTCTAGTGATTGGAGGGGATGATTATATAACAAAGCCATTTACCCCGATTGAATTGGTTGCTCGTGTGAACGCTCAATTGCGGCGCTCTATGAAGTTGAATCACCCCCAAGCAGATGATAAAAAATCTATCTTGGAGTTCGGTGAGATCGTGATTTCTCCTGATCAACGTACAGTTTTTCTTTATGGTGAAAACATCGGGTTAACGCCGAAAGAGTTTGATATTTTGTATTTATTAGCCAGTCATCCAAAGAAAGTTTATAGTGTCGAAAATATTTTCCAGCAAGTTTGGAATGATGCATACTTTGGAGGCGGTAATACGGTAATGGTGCATATTCGCACCTTGCGGAAAAAACTTGGAGAAGATAAGCGAAAAAATAAGTTAATCAAAACTGTGTGGGGAGTGGGGTATACGTTCAATGGCTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002928","ARO_id":"39362","ARO_name":"vanRM","ARO_description":"vanRM is a vanR variant found in the vanM gene cluster","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36713":{"category_aro_accession":"3000574","category_aro_cvterm_id":"36713","category_aro_name":"vanR","category_aro_description":"VanR is a OmpR-family transcriptional activator in the VanSR regulatory system. When activated by VanS, it promotes cotranscription of VanA, VanH, and VanX.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"753":{"model_id":"753","model_name":"SMB-1 beta-lactamase","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1239":{"protein_sequence":{"accession":"BAL14456.1","sequence":"MKIIASLILAAFASVAQAQDRDWSSPQQPFTIYGNTHYVGTGGISAVLLSSPQGHILVDGTTEKGAQVVAANIRAMGFKLSDVKYILSTHSHEDHAGGISAMQKLTGATVLAGAANVDTLRTGVSPKSDPQFGSLSNFPGSAKVRAVADGELVKLGPLAVKAHATPGHTEGGITWTWQSCEQGKCKDVVFADSLTAVSADSYRFSDHPEVVASLRGSFEAVEKLSCDIAIAAHPEVNDMWTRQQRAAKEGNSAYVDNGACRAIAAAGRKRLETRLASEKR"},"dna_sequence":{"accession":"AB636283","fmin":"0","fmax":"843","strand":"+","sequence":"ATGAAAATCATCGCTTCCCTGATCCTGGCGGCGTTTGCGTCTGTTGCGCAGGCGCAGGATCGTGATTGGAGCTCGCCGCAGCAGCCATTCACCATCTACGGCAATACCCATTACGTCGGCACCGGCGGCATCAGTGCGGTGCTGCTGTCCTCACCGCAAGGCCATATCCTGGTCGATGGCACCACCGAGAAGGGCGCGCAGGTTGTGGCTGCCAATATCCGTGCCATGGGCTTCAAGCTGTCGGACGTGAAGTACATCCTCAGCACCCATTCGCATGAGGACCATGCGGGCGGCATCTCGGCCATGCAGAAGCTGACCGGCGCTACGGTGCTGGCGGGGGCTGCGAATGTGGATACCTTGCGCACCGGTGTCTCGCCCAAGAGCGATCCGCAATTCGGCTCGCTGTCGAACTTCCCCGGCTCGGCAAAAGTGCGCGCGGTGGCTGATGGGGAGCTGGTGAAACTGGGGCCGCTGGCTGTCAAGGCCCATGCCACGCCGGGGCATACCGAGGGCGGCATCACCTGGACCTGGCAGTCCTGCGAACAGGGCAAGTGCAAGGACGTGGTCTTCGCGGACAGCCTGACTGCAGTTTCCGCCGACAGCTATCGTTTCTCCGATCATCCGGAAGTGGTGGCGTCGCTGCGCGGCAGCTTTGAGGCGGTGGAGAAGCTGTCCTGCGATATCGCGATTGCCGCCCATCCGGAAGTGAACGATATGTGGACGCGCCAGCAGCGCGCGGCAAAAGAGGGGAATTCGGCTTACGTGGATAACGGCGCTTGCCGCGCCATCGCGGCAGCCGGCCGCAAACGGCTTGAAACCCGCCTGGCCAGCGAGAAACGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36783","NCBI_taxonomy_name":"Serratia marcescens","NCBI_taxonomy_id":"615"}}}},"ARO_accession":"3000854","ARO_id":"37234","ARO_name":"SMB-1","ARO_description":"SMB-1 can hydrolyze a variety of beta-lactams, including penicillins, cephalosporins, and carbapenems. It was identified in Serratia marcescens.","ARO_category":{"41381":{"category_aro_accession":"3004217","category_aro_cvterm_id":"41381","category_aro_name":"SMB beta-lactamase","category_aro_description":"SMB beta-lactamases are a subclass B3 beta-lactamases that hydrolyze a variety of beta-lactams, including penicillins, cephalosporins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"754":{"model_id":"754","model_name":"CTX-M-48","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"908":{"protein_sequence":{"accession":"AAV97953.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTNAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"AY847144","fmin":"81","fmax":"957","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAATGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001910","ARO_id":"38310","ARO_name":"CTX-M-48","ARO_description":"CTX-M-48 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"755":{"model_id":"755","model_name":"KPC-9","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1827":{"protein_sequence":{"accession":"ACM91559.1","sequence":"RLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGAYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLG"},"dna_sequence":{"accession":"FJ624872","fmin":"0","fmax":"851","strand":"+","sequence":"GCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGCGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002319","ARO_id":"38719","ARO_name":"KPC-9","ARO_description":"KPC-9 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"757":{"model_id":"757","model_name":"CMY-80","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"762":{"protein_sequence":{"accession":"AFK73449.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEPQIADIVNRTITPLMQEQAIPGMAVAVIYQGKSYYFTWGKADITNNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWAPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWIKVPQSEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQVNMDASRVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"JQ733577","fmin":"1026","fmax":"2172","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCATTCTCCACGTTTGCCGCCGCCAAAACAGAACCACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAATCCTATTATTTCACCTGGGGTAAAGCCGATATCACCAATAACCACCCAGTCACGCAGCAAACTCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTACACGGCAGGCGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCGTTTTTATCAAAACTGGCAGCCGCAATGGGCCCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTAAAGTTCCGCAAAGCGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGTCAACATGGACGCCAGCCGCGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGTAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACTGGAGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGTATTCTTGAAAAGCTGCAATAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002093","ARO_id":"38493","ARO_name":"CMY-80","ARO_description":"CMY-80 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"758":{"model_id":"758","model_name":"OXA-198","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"969":{"protein_sequence":{"accession":"ADT70779.1","sequence":"MHKHMSKLFIAFLAFLLSVPAAAEDQTLAELFAQQGIDGTIVISSLHNGKTFIHNDPRAKQRFSTASTFKILNTLISLEEKAISGKDDVLKWDGHIYDFPDWNRDQTLESAFKVSCVWCYQALARQVGAEKYRNYLRKSVYGELREPFEETTFWLDGSLQISAIEQVNFLKKVHLRTLPFSASSYETLRQIMLIEQTPAFTLRAKTGWATRVKPQVGWYVGHVETPTDVWFFATNIEVRDEKDLPLRQKLTRKALQAKGIIE"},"dna_sequence":{"accession":"HQ634775","fmin":"3012","fmax":"3801","strand":"+","sequence":"ATGCATAAACACATGAGTAAGCTCTTCATCGCTTTTTTAGCCTTTCTGCTGTCGGTGCCAGCAGCCGCTGAAGACCAGACACTTGCCGAGCTCTTTGCCCAACAAGGCATTGACGGGACTATAGTGATTTCGTCGCTACACAACGGAAAGACATTTATCCACAACGATCCCCGCGCAAAACAGAGATTCTCGACAGCATCCACGTTCAAGATACTGAACACGCTGATCTCGCTCGAAGAAAAAGCCATCTCTGGAAAAGACGATGTGCTGAAATGGGACGGGCATATTTACGATTTTCCAGATTGGAATCGTGACCAGACGCTAGAAAGTGCGTTCAAGGTTTCCTGTGTCTGGTGTTATCAGGCGCTTGCACGCCAGGTCGGCGCGGAGAAGTATCGAAATTATTTACGCAAGTCAGTTTACGGAGAATTACGCGAGCCTTTTGAGGAAACAACATTCTGGCTTGATGGTTCACTTCAAATCAGCGCAATTGAACAAGTGAATTTCCTCAAGAAAGTTCATCTGCGCACTCTCCCATTCAGTGCATCGTCCTACGAAACGCTACGACAAATCATGCTTATCGAGCAAACGCCGGCTTTTACGCTGCGGGCCAAGACAGGCTGGGCAACAAGAGTAAAGCCGCAAGTTGGCTGGTATGTGGGCCATGTCGAAACTCCAACGGATGTATGGTTCTTTGCCACGAATATTGAAGTCCGTGACGAAAAAGACTTGCCCTTACGTCAGAAGCTAACGCGAAAAGCATTACAAGCAAAGGGGATCATCGAATAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001805","ARO_id":"38205","ARO_name":"OXA-198","ARO_description":"OXA-198 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"759":{"model_id":"759","model_name":"OCH-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1504":{"protein_sequence":{"accession":"CAC17622.1","sequence":"MRTSTTLLIGFLTTAAVIPNNGALAASKVNDGDLRRIVDETVRPLMAEQKIPGMAVAITIDGKSHFFGYGVASKESGQKVTEDTIFEIGSVSKTFTAMLGGYGLATGAFSLSDPATKWAPELAGSSFDKITMLDLGTYTPGGLPLQFPDAVTDDSSMLAYFKNWKPDYPAGTQRRYSNPSIGLFGYLAARSMDKPFDVLMEQKLLPAFGLKNTFINVPESQMKNYAYGYSKANKPIRVSGGALDAQAYGIKTTALDLARFVELNIDSSSLELDFQKAVAATHTGYYHVGANNQGLGWEFYNYPTALKTLLAGNSSDMALKSHKIEKFDTPRQPSADVWLNKTGSTNGFGAYAAFIPAKKTGIVLLANRNYPIDERIKAAYRILQALDNKQ"},"dna_sequence":{"accession":"AJ295340","fmin":"0","fmax":"1173","strand":"+","sequence":"ATGAGAACATCTACGACACTTTTGATCGGTTTCCTCACCACTGCCGCTGTTATCCCGAATAACGGCGCGCTGGCTGCGAGCAAGGTGAATGATGGCGACTTGCGCCGTATTGTCGATGAAACGGTGCGCCCGCTCATGGCCGAGCAGAAAATCCCCGGCATGGCCGTCGCTATAACCATCGACGGCAAGAGCCACTTCTTCGGTTATGGTGTGGCATCGAAGGAAAGCGGGCAAAAAGTCACCGAAGACACGATTTTCGAGATCGGCTCGGTCAGCAAGACCTTCACTGCAATGCTCGGCGGCTACGGGCTTGCGACCGGCGCGTTCTCCCTGTCCGATCCCGCGACCAAATGGGCTCCCGAACTGGCAGGCAGCAGCTTCGACAAGATCACCATGCTTGATCTTGGGACCTACACGCCGGGCGGATTGCCCCTCCAGTTTCCCGATGCTGTCACCGATGACAGTTCGATGCTGGCATATTTCAAGAACTGGAAACCCGATTACCCGGCAGGGACGCAGCGTCGCTATTCGAATCCCAGCATCGGCCTGTTCGGCTATCTGGCGGCACGAAGCATGGACAAGCCGTTCGACGTTTTGATGGAGCAAAAGCTTCTGCCTGCATTCGGCCTGAAGAACACCTTCATCAATGTGCCGGAAAGCCAGATGAAGAACTACGCCTACGGCTATTCCAAAGCCAACAAGCCGATCCGGGTATCGGGCGGGGCGCTGGATGCACAAGCCTATGGCATCAAGACCACCGCGCTTGATCTTGCCCGCTTCGTCGAACTGAACATCGACAGCTCATCTCTGGAGCTTGATTTCCAGAAAGCCGTCGCCGCAACGCATACCGGTTACTACCATGTCGGAGCGAACAATCAGGGACTTGGCTGGGAGTTCTACAACTATCCGACTGCGCTCAAGACACTTCTTGCCGGCAATTCGTCGGACATGGCGCTGAAGTCGCACAAAATCGAGAAATTCGATACACCTCGCCAACCGTCAGCTGATGTGTGGCTCAACAAGACAGGCTCAACCAACGGCTTTGGCGCTTATGCGGCCTTTATTCCTGCGAAGAAGACCGGAATTGTTCTGCTTGCCAACCGGAATTATCCGATCGATGAGCGCATAAAGGCTGCCTATCGGATATTGCAGGCGCTCGACAACAAGCAATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37077","NCBI_taxonomy_name":"Ochrobactrum anthropi","NCBI_taxonomy_id":"529"}}}},"ARO_accession":"3002515","ARO_id":"38915","ARO_name":"OCH-2","ARO_description":"OCH-2 beta-lactamase is an Ambler class C chromosomal-encoded beta-lactamases in Ochrobactrum anthropi","ARO_category":{"36233":{"category_aro_accession":"3000094","category_aro_cvterm_id":"36233","category_aro_name":"OCH beta-lactamase","category_aro_description":"OCH beta-lactamases are Ambler class C chromosomal-encoded beta-lactamases in Ochrobactrum anthropi","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"760":{"model_id":"760","model_name":"TEM-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1002":{"protein_sequence":{"accession":"CAA41038.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDHWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"X57972","fmin":"339","fmax":"1200","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCATTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000878","ARO_id":"37258","ARO_name":"TEM-6","ARO_description":"TEM-6 is an extended-spectrum beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"761":{"model_id":"761","model_name":"GES-13","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1905":{"protein_sequence":{"accession":"ACZ54536.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVKWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMNDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"GU169702","fmin":"608","fmax":"1472","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCAAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGAACGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAGT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002342","ARO_id":"38742","ARO_name":"GES-13","ARO_description":"GES-13 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"762":{"model_id":"762","model_name":"CTX-M-55","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1552":{"protein_sequence":{"accession":"ABI34705.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAVAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"DQ885477","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGTGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001917","ARO_id":"38317","ARO_name":"CTX-M-55","ARO_description":"CTX-M-55 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35979":{"category_aro_accession":"0000062","category_aro_cvterm_id":"35979","category_aro_name":"ceftriaxone","category_aro_description":"Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"763":{"model_id":"763","model_name":"catI","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"482":{"protein_sequence":{"accession":"CAA23899.1","sequence":"MEKKITGYTTVDISQWHRKEHFEAFQSVAQCTYNQTVQLDITAFLKTVKKNKHKFYPAFIHILARLMNAHPEFRMAMKDGELVIWDSVHPCYTVFHEQTETFSSLWSEYHDDFRQFLHIYSQDVACYGENLAYFPKGFIENMFFVSANPWVSFTSFDLNVANMDNFFAPVFTMGKYYTQGDKVLMPLAIQVHHAVCDGFHVGRMLNELQQYCDEWQGGA"},"dna_sequence":{"accession":"V00622","fmin":"243","fmax":"903","strand":"+","sequence":"ATGGAGAAAAAAATCACTGGATATACCACCGTTGATATATCCCAATGGCATCGTAAAGAACATTTTGAGGCATTTCAGTCAGTTGCTCAATGTACCTATAACCAGACCGTTCAGCTGGATATTACGGCCTTTTTAAAGACCGTAAAGAAAAATAAGCACAAGTTTTATCCGGCCTTTATTCACATTCTTGCCCGCCTGATGAATGCTCATCCGGAATTCCGTATGGCAATGAAAGACGGTGAGCTGGTGATATGGGATAGTGTTCACCCTTGTTACACCGTTTTCCATGAGCAAACTGAAACGTTTTCATCGCTCTGGAGTGAATACCACGACGATTTCCGGCAGTTTCTACACATATATTCGCAAGATGTGGCGTGTTACGGTGAAAACCTGGCCTATTTCCCTAAAGGGTTTATTGAGAATATGTTTTTCGTCTCAGCCAATCCCTGGGTGAGTTTCACCAGTTTTGATTTAAACGTGGCCAATATGGACAACTTCTTCGCCCCCGTTTTCACCATGGGCAAATATTATACGCAAGGCGACAAGGTGCTGATGCCGCTGGCGATTCAGGTTCATCATGCCGTCTGTGATGGCTTCCATGTCGGCAGAATGCTTAATGAATTACAACAGTACTGCGATGAGTGGCAGGGCGGGGCGTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002683","ARO_id":"39117","ARO_name":"catI","ARO_description":"catI is a chromosome and transposon-encoded variant of the cat gene found in Escherichia coli and Acinetobacter baumannii","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. cat is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Bacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini","category_aro_class_name":"AMR Gene Family"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"764":{"model_id":"764","model_name":"FOX-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1031":{"protein_sequence":{"accession":"CAA71325.1","sequence":"MQQRRALALLTLGSLLLAPCTYASGEAPLTAAVDGIIQPMLKEYRIPGMAVAVLKDGKAHYFNYGVANRESGQRVSEQTLFEIGSVSKTLTATLGAYAAVKGGFELDDKVSHHAPWLKGSAFDGVTMAELATYSAGGLPLQFPDEVDSNDKMQTYYRSWSPVYPAGTHRQYSNPSIGLFGHLAANSLGQPFEKLMSQTLLPKLGLHHTYIQVPESAMANYAYGYSKEDKPIRVTPGVLAAEAYGIKTGSADLLKFVEANMGYQGDAALKSAIALTHTGFYSVGDMTQGLGWESYAYPVTEQALLAGNSPAVSFQANPVTRFAVPKAMGEQRLYNKTGSTGGFGAYVAFVPARGIAIVMLANRNYPIEARVKAAHAILSQLAE"},"dna_sequence":{"accession":"Y10282","fmin":"0","fmax":"1149","strand":"+","sequence":"ATGCAACAACGACGTGCGCTCGCGCTACTGACGCTGGGTAGCCTGCTGCTAGCCCCTTGTACTTATGCCAGCGGGGAGGCTCCGCTGACCGCCGCTGTGGACGGCATTATCCAGCCGATGCTCAAGGAGTATCGGATCCCGGGGATGGCGGTCGCCGTGCTGAAAGATGGCAAGGCCCACTATTTCAACTATGGGGTTGCCAACCGCGAGAGTGGCCAGCGCGTCAGCGAGCAGACGCTGTTCGAGATTGGCTCGGTCAGCAAGACCCTGACCGCGACCCTCGGTGCCTATGCTGCGGTCAAGGGGGGCTTTGAGCTGGATGACAAGGTGAGCCACCACGCCCCTTGGCTCAAAGGTTCCGCTTTCGATGGTGTGACTATGGCCGAGCTTGCCACCTACAGTGCGGGTGGTTTGCCGCTGCAGTTCCCTGATGAGGTGGATTCGAATGACAAGATGCAAACTTACTATCGGAGCTGGTCACCGGTTTATCCGGCGGGGACCCATCGCCAGTATTCCAACCCCAGCATAGGCCTGTTTGGTCACCTGGCCGCAAATAGTCTGGGCCAGCCATTTGAGAAACTGATGAGCCAGACCCTGCTGCCCAAGCTTGGTTTGCACCACACCTATATCCAGGTGCCGGAGTCGGCCATGGCGAACTATGCCTACGGCTATTCGAAGGAAGATAAGCCCATCCGGGTCACTCCGGGCGTACTGGCGGCCGAGGCTTACGGGATCAAAACCGGCTCGGCGGATCTGCTGAAGTTTGTCGAGGCAAACATGGGGTATCAGGGAGATGCCGCGCTAAAAAGCGCGATCGCGCTGACCCACACCGGTTTCTACTCGGTGGGAGACATGACCCAGGGACTGGGCTGGGAGAGCTACGCCTATCCGGTGACCGAGCAGGCGTTGCTGGCGGGCAACTCCCCGGCGGTGAGCTTCCAGGCCAATCCGGTTACGCGCTTTGCGGTGCCCAAAGCGATGGGCGAGCAGCGGCTCTATAACAAGACGGGCTCGACCGGCGGCTTTGGCGCCTATGTGGCGTTCGTGCCCGCCAGAGGGATCGCCATCGTCATGCTGGCCAATCGCAACTATCCCATCGAGGCCAGGGTGAAGGCGGCTCACGCCATCCTGAGTCAGTTGGCCGAGTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002156","ARO_id":"38556","ARO_name":"FOX-2","ARO_description":"FOX-2 is a beta-lactamase found in Escherichia coli","ARO_category":{"36206":{"category_aro_accession":"3000067","category_aro_cvterm_id":"36206","category_aro_name":"FOX beta-lactamase","category_aro_description":"FOX beta-lactamases are plasmid-encoded AmpC-type beta-lactamase which conferred resistance to broad-spectrum cephalosporins and cephamycins","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"765":{"model_id":"765","model_name":"QnrB7","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"328":{"protein_sequence":{"accession":"ABW03156.3","sequence":"MALALVGEKIDRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNASALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFTTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAIIG"},"dna_sequence":{"accession":"EU043311","fmin":"0","fmax":"645","strand":"+","sequence":"ATGGCTCTGGCACTCGTTGGCGAAAAAATTGACAGAAACCGTTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTAAGTGGTACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCAATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATGCCAGTGCGCTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGCGCAAGCTTTATGAATATGATCACTACACGCACCTGGTTTTGCAGCGCATATATCACTAACACAAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGCTGGAAAAGTGTGAGCTGTGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTACGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTGACTTAGATATTCGGGGCGTTGATTTACAAGGCGTTAAGTTGGACAACTACCAGGCATCGTTGCTCATGGAACGTCTTGGCATCGCGATTATTGGCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3002721","ARO_id":"39155","ARO_name":"QnrB7","ARO_description":"QnrB7 is a plasmid-mediated quinolone resistance protein found in Enterobacter cloacae","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"766":{"model_id":"766","model_name":"SHV-102","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1697":{"protein_sequence":{"accession":"ABS72342.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAAERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"EU024485","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGCCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCAGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001151","ARO_id":"37531","ARO_name":"SHV-102","ARO_description":"SHV-102 is an extended spectrum beta-lactamase found in E. coli.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"767":{"model_id":"767","model_name":"OXA-207","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1836":{"protein_sequence":{"accession":"AFK28473.1","sequence":"MKKFILPIFSISILVSLSACSSIKTKSEDNFHISSQQHEKAIKSYFDEAQTQGVIIIKEGKNLSTYGNALARANKEYVPASTFKMLNALIGLENHKATTNEIFKWDGKKRTYPMWEKDMTLGEAMALSAVPVYQELARRTGLELMQKEVKRVNFGNTNIGTQVDNFWLVGPLKITPVQEVNFADDLAHNRLPFKLETQEEVKKMLLIKEVNGSKIYAKSGWVMGVTPQVGWLTGWVEQANGKKIPFSLNLEMKEGMSGSIRNEITYKSLENLGII"},"dna_sequence":{"accession":"JQ838185","fmin":"0","fmax":"828","strand":"+","sequence":"ATGAAAAAATTTATACTTCCTATATTCAGCATTTCTATTCTAGTTTCTCTCAGTGCATGTTCATCTATTAAAACTAAATCTGAAGATAATTTTCATATTTCTTCTCAGCAACATGAAAAAGCTATTAAAAGCTATTTTGATGAAGCTCAAACACAGGGTGTAATTATTATTAAAGAGGGTAAAAATCTTAGCACCTATGGTAATGCTCTTGCACGAGCAAATAAAGAATATGTCCCTGCATCAACATTTAAGATGCTAAATGCTTTAATCGGGCTAGAAAATCATAAAGCAACAACAAATGAGATTTTCAAATGGGATGGTAAAAAAAGAACTTATCCTATGTGGGAGAAAGATATGACTTTAGGTGAGGCAATGGCATTGTCAGCAGTTCCAGTATATCAAGAGCTTGCAAGACGGACTGGCCTAGAGCTAATGCAGAAAGAAGTAAAGCGGGTTAATTTTGGAAATACAAATATTGGAACACAGGTCGATAATTTTTGGTTAGTTGGCCCCCTTAAAATTACACCAGTACAAGAAGTTAATTTTGCCGATGACCTTGCACATAACCGATTACCTTTTAAATTAGAAACTCAAGAAGAAGTTAAAAAAATGCTTCTAATTAAAGAAGTAAATGGTAGTAAGATTTATGCAAAAAGTGGATGGGTAATGGGTGTTACTCCACAGGTAGGTTGGTTGACTGGTTGGGTGGAGCAAGCTAATGGAAAAAAAATCCCCTTTTCGCTCAACTTAGAAATGAAAGAAGGAATGTCTGGTTCTATTCGTAATGAAATTACTTATAAGTCGCTAGAAAATCTTGGAATCATTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3001485","ARO_id":"37885","ARO_name":"OXA-207","ARO_description":"OXA-207 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"768":{"model_id":"768","model_name":"SHV-43","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1947":{"protein_sequence":{"accession":"AAL40899.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHFADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLSAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AY065991","fmin":"6","fmax":"867","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATTTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGTCTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACACCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGAGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATCGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001101","ARO_id":"37481","ARO_name":"SHV-43","ARO_description":"SHV-43 is a broad-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"769":{"model_id":"769","model_name":"KPC-11","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1710":{"protein_sequence":{"accession":"ADH95186.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVLWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"HM066995","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCTGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002321","ARO_id":"38721","ARO_name":"KPC-11","ARO_description":"KPC-11 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"770":{"model_id":"770","model_name":"SHV-57","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1715":{"protein_sequence":{"accession":"AAO66446.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETERNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AY223863","fmin":"170","fmax":"1031","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACGGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001113","ARO_id":"37493","ARO_name":"SHV-57","ARO_description":"SHV-57 is an extended-spectrum beta-lactamase found in E. coli.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"771":{"model_id":"771","model_name":"CMY-24","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1195":{"protein_sequence":{"accession":"ABN69070.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVYVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"EF415650","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTATACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002035","ARO_id":"38435","ARO_name":"CMY-24","ARO_description":"CMY-24 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"772":{"model_id":"772","model_name":"LEN-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"960":{"protein_sequence":{"accession":"AAP93848.1","sequence":"MISLLATLPLAVDAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGLEQLDRRIHYRQQDLVDYSPVSEKHLVDGMTIGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETE"},"dna_sequence":{"accession":"AY265890","fmin":"0","fmax":"472","strand":"+","sequence":"ATTATCTCCCTGTTAGCCACCCTGCCACTGGCGGTAGACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGTCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002476","ARO_id":"38876","ARO_name":"LEN-6","ARO_description":"LEN-6 is a beta-lactamase. From the Pasteur Institute list of LEN beta-lactamases.","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"773":{"model_id":"773","model_name":"OCH-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1659":{"protein_sequence":{"accession":"CAC17624.1","sequence":"MRKSTTLLIGFLTTAAIIPNNGALATSKANDGDLRRIVDETVRPLMAEQKIPGMAVAITIDGKSHFFGYGVASKESGQKVTEDTIFEIGSVSKTFTAMLGGYGLATGAFSLSDPATKWAPELAGSSFDKITMRDLGTYTPGGLPLQFPDAVTDDSSMLAYFKKWKPDYPAGTQRRYSNPSIGLFGYLAARSMDKPFDVLMEQKLLPAFGLKNTFINVPASQMKNYAYGYSKANKPIRVSGGALDAQAYGIKTTALDLARFVELNIDSSSLEPDFQKAVAATHTGYYHVGANNQGLGWEFYNYPTALKTLLAGNSSDMALKSHKIEKFDTPRQPSADVLINKTGSTNGFGAYAAFIPAKKIGIVLLANRNYPIDERVKAAYRILQALDNKQ"},"dna_sequence":{"accession":"AJ295342","fmin":"0","fmax":"1173","strand":"+","sequence":"ATGAGAAAATCTACGACACTTTTGATCGGTTTCCTCACCACTGCCGCTATTATCCCGAATAATGGCGCGCTGGCTACGAGCAAGGCGAATGATGGCGACTTGCGCCGTATTGTCGATGAAACGGTGCGCCCGCTCATGGCCGAGCAGAAAATCCCCGGCATGGCCGTCGCTATAACCATCGACGGCAAGAGCCACTTCTTCGGTTATGGTGTGGCATCGAAAGAAAGCGGGCAAAAAGTCACTGAAGACACGATTTTCGAGATCGGTTCGGTCAGCAAGACCTTCACTGCAATGCTTGGCGGTTACGGGCTGGCGACAGGCGCGTTCTCCCTGTCCGATCCCGCGACCAAATGGGCTCCTGAACTGGCAGGCAGCAGCTTCGACAAGATCACCATGCGTGATCTTGGGACCTACACGCCGGGCGGATTGCCCCTCCAGTTTCCCGATGCTGTCACCGATGACAGTTCGATGCTGGCATATTTCAAGAAATGGAAGCCGGACTATCCGGCAGGCACGCAGCGTCGCTATTCGAATCCCAGCATCGGCCTGTTCGGCTATCTGGCGGCACGAAGCATGGACAAGCCGTTCGACGTTTTGATGGAGCAAAAGCTTCTGCCTGCATTCGGCCTGAAGAACACCTTCATCAATGTGCCGGCAAGCCAGATGAAGAACTACGCCTACGGATATTCCAAAGCCAACAAGCCGATCCGGGTATCGGGCGGGGCGCTGGATGCACAAGCCTATGGCATCAAGACCACCGCGCTTGATCTTGCCCGCTTCGTCGAACTGAACATCGACAGCTCATCTCTGGAGCCTGATTTCCAGAAAGCCGTCGCCGCAACGCATACCGGTTACTACCATGTCGGAGCGAACAATCAGGGACTTGGCTGGGAGTTCTACAACTATCCGACTGCGCTCAAGACACTTCTTGCCGGCAATTCGTCGGACATGGCGCTGAAGTCGCACAAAATCGAGAAATTCGATACACCTCGCCAACCGTCAGCTGATGTGCTGATCAATAAGACAGGCTCAACCAACGGCTTTGGCGCTTATGCGGCCTTTATTCCTGCGAAGAAGATCGGAATTGTTCTGCTTGCCAACCGGAATTATCCGATCGATGAGCGCGTAAAGGCTGCCTATCGGATATTGCAGGCGCTCGACAACAAGCAATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37077","NCBI_taxonomy_name":"Ochrobactrum anthropi","NCBI_taxonomy_id":"529"}}}},"ARO_accession":"3002517","ARO_id":"38917","ARO_name":"OCH-4","ARO_description":"OCH-4 beta-lactamase is an Ambler class C chromosomal-encoded beta-lactamases in Ochrobactrum anthropi","ARO_category":{"36233":{"category_aro_accession":"3000094","category_aro_cvterm_id":"36233","category_aro_name":"OCH beta-lactamase","category_aro_description":"OCH beta-lactamases are Ambler class C chromosomal-encoded beta-lactamases in Ochrobactrum anthropi","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"774":{"model_id":"774","model_name":"tet37","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"24":{"protein_sequence":{"accession":"AAN28721.1","sequence":"MVRYYSNIVGKYGIPVQNALKKLAGIHIDYICSTHGPVWHENVEKVVNLYDRMSKYETDPGLVICYGTMYGNTEDRTPSMYEYIWIKENREAKVVSSFAANIYLGWGR"},"dna_sequence":{"accession":"AF540889","fmin":"0","fmax":"327","strand":"+","sequence":"ATGGTTCGCTATTACTCTAACATTGTAGGTAAATACGGTATTCCAGTTCAGAATGCACTGAAGAAACTTGCAGGTATTCACATTGATTATATCTGTTCAACACATGGTCCTGTATGGCATGAGAACGTTGAAAAGGTGGTGAACCTGTATGATCGTATGTCGAAATATGAGACTGATCCAGGCTTGGTTATCTGCTACGGAACGATGTATGGGAACACAGAGGATCGCACACCGTCGATGTATGAATATATATGGATAAAAGAGAATCGAGAAGCTAAGGTTGTTTCATCATTTGCAGCTAATATTTATTTAGGATGGGGGCGGTGAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3002871","ARO_id":"39305","ARO_name":"tet37","ARO_description":"tet37 is a chromosome-encoded oxidoreductase isolated from an uncultured bacterium that confers resistance to tetracycline","ARO_category":{"36176":{"category_aro_accession":"3000036","category_aro_cvterm_id":"36176","category_aro_name":"tetracycline inactivation enzyme","category_aro_description":"Enzymes or other gene products which hydroxylate tetracycline and other tetracycline derivatives. Hydroxylation inactivates tetracycline-like antibiotics, thus conferring resistance to these compounds.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"775":{"model_id":"775","model_name":"CMY-113","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"863":{"protein_sequence":{"accession":"AIT76089.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDDVTDKAELLRFYQNWQPQWTPGAKRLYANSSIGLFGALVVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASLVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"KM087836","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCACTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGAATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGTGGTAAAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGGCAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCTCGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACAGGATCCACAGGCGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTAATGTTGGCAAACAAAAGCTACCCCAACCCGGCTCGCGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002124","ARO_id":"38524","ARO_name":"CMY-113","ARO_description":"CMY-113 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"776":{"model_id":"776","model_name":"tetX","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"79":{"protein_sequence":{"accession":"AAA27471.1","sequence":"MTMRIDTDKQMNLLSDKNVAIIGGGPVGLTMAKLLQQNGIDVSVYERDNDREARIFGGTLDLHKGSGQEAMKKAGLLQTYYDLALPMGVNIADKKGNILSTKNVKPENRFDNPEINRNDLRAILLNSLENDTVIWDRKLVMLEPGKKKWTLTFENKPSETADLVILANGGMSKVRKFVTDTEVEETGTFNIQADIHQPEINCPGFFQLCNGNRLMASHQGNLLFANPNNNGALHFGISFKTPDEWKNQTQVDFQNRNSVVDFLLKEFSDWDERYKELIHTTLSFVGLATRIFPLEKPWKSKRPLPITMIGDAAHLMPPFAGQGVNSGLVDALILSDNLADGKFNSIEEAVKNYEQQMFMYGKEAQEESTQNEIEMFKPDFTFQQLLNV"},"dna_sequence":{"accession":"M37699","fmin":"585","fmax":"1752","strand":"+","sequence":"ATGACAATGCGAATAGATACAGACAAACAAATGAATTTACTTAGTGATAAGAACGTTGCAATAATTGGTGGTGGACCCGTTGGACTGACTATGGCAAAATTATTACAGCAAAACGGCATAGACGTTTCAGTTTACGAAAGAGACAACGACCGAGAGGCAAGAATTTTTGGTGGAACCCTTGACCTACACAAAGGTTCAGGTCAGGAAGCAATGAAAAAAGCGGGATTGTTACAAACTTATTATGACTTAGCCTTACCAATGGGTGTAAATATTGCTGATAAAAAAGGCAATATTTTATCCACAAAAAATGTAAAGCCCGAAAATCGATTTGACAATCCTGAAATAAACAGAAATGACTTAAGGGCTATCTTGTTGAATAGTTTAGAAAACGACACGGTTATTTGGGATAGAAAACTTGTTATGCTTGAACCTGGTAAGAAGAAGTGGACACTAACTTTTGAGAATAAACCGAGTGAAACAGCAGATTTGGTTATTCTTGCCAATGGCGGGATGTCCAAGGTAAGAAAATTTGTTACCGACACGGAAGTTGAAGAAACAGGTACTTTCAATATACAAGCCGATATTCATCAACCAGAGATAAACTGTCCTGGATTTTTTCAGCTATGCAATGGAAACCGGCTAATGGCATCTCACCAAGGTAATTTATTATTTGCTAACCCCAATAATAATGGTGCATTGCATTTTGGAATAAGTTTTAAAACACCTGATGAATGGAAAAACCAAACGCAGGTAGATTTTCAAAACAGAAATAGTGTCGTTGATTTTCTTCTGAAAGAATTTTCCGATTGGGACGAACGCTACAAAGAATTGATTCATACGACGTTGTCATTTGTAGGATTGGCTACACGGATATTTCCTTTAGAAAAGCCTTGGAAAAGCAAGCGCCCATTACCCATAACAATGATTGGGGATGCCGCACATTTGATGCCGCCTTTTGCAGGGCAGGGAGTAAATAGTGGGTTGGTGGATGCCTTGATATTGTCTGATAATCTAGCCGATGGAAAATTTAATAGCATTGAAGAGGCTGTTAAAAATTATGAACAGCAAATGTTTATGTATGGCAAAGAAGCACAAGAAGAATCAACTCAAAACGAAATTGAAATGTTTAAACCCGACTTTACGTTTCAGCAATTGTTAAATGTATAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35916","NCBI_taxonomy_name":"Bacteroides fragilis","NCBI_taxonomy_id":"817"}}}},"ARO_accession":"3000205","ARO_id":"36344","ARO_name":"tetX","ARO_description":"TetX is a flavin-dependent monooxygenase conferring resistance to tetracycline antibiotics. TetX hydroxylates position 11a of the tetraketide group thus inactivating the antibiotic.","ARO_category":{"36176":{"category_aro_accession":"3000036","category_aro_cvterm_id":"36176","category_aro_name":"tetracycline inactivation enzyme","category_aro_description":"Enzymes or other gene products which hydroxylate tetracycline and other tetracycline derivatives. Hydroxylation inactivates tetracycline-like antibiotics, thus conferring resistance to these compounds.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"778":{"model_id":"778","model_name":"IMP-25","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1986":{"protein_sequence":{"accession":"ACB41775.1","sequence":"MSKLSVFFIFLFCSIATAAESLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLSDANIEAWPKSAKLLKSKYGKAKLVVPGHSEVGDASLLKLTLEQAVKGLNESKKPSKPSN"},"dna_sequence":{"accession":"EU541448","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAGCAAGTTATCTGTATTCTTTATATTTTTGTTTTGCAGCATTGCTACCGCAGCAGAGTCTTTGCCAGATTTAAAAATTGAAAAGCTTGATGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGGTGGGGCGTTGTTCCTAAACATGGTTTGGTGGTTCTTGTAAATGCTGAGGCTTACCTAATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAGCGTGGCTATAAAATAAAAGGCAGCATTTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCGATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTGCTTAAAAAAGACGGTAAGGTTCAAGCCACAAATTCATTTAGCGGAGTTAACTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCGGGACACACTCCAGATAACGTAGTGGTTTGGTTGCCTGAAAGGAAAATATTATTCGGTGGTTGTTTTATTAAACCGTACGGTTTAGGCAATTTGAGTGACGCAAATATAGAAGCTTGGCCAAAGTCCGCCAAATTATTAAAGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAGGTCACAGTGAAGTTGGAGACGCATCACTCTTGAAACTTACATTAGAGCAGGCGGTTAAAGGGTTAAACGAAAGTAAAAAACCATCAAAACCAAGCAACTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002216","ARO_id":"38616","ARO_name":"IMP-25","ARO_description":"IMP-25 is a beta-lactamase found in Serratia marcescens","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"779":{"model_id":"779","model_name":"OXA-350","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1053":{"protein_sequence":{"accession":"AGW83448.1","sequence":"MYKKALIVTTSILFLSACSSNSVKQNQIHSISANKNSEEIKSLFDQAQTTGVLVIKRGQTEEIYGNDLKRASTAYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNANIGSKVDDFWLVGPLKITPQQETQFAYQLAHKTLPFSKNVQEQVQSMVFIEEKNGSKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMNKGTPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"KF297579","fmin":"0","fmax":"822","strand":"+","sequence":"ATGTATAAAAAAGCCCTTATCGTTACAACAAGTATCCTATTTTTATCCGCCTGTTCTTCTAATTCAGTAAAACAAAATCAAATACATTCTATTTCTGCCAATAAAAATTCAGAAGAAATTAAATCACTGTTTGATCAGGCACAGACCACGGGTGTTTTGGTTATTAAGCGAGGGCAAACAGAAGAAATTTATGGAAATGATCTTAAAAGAGCATCAACCGCCTATGTTCCCGCTTCTACCTTTAAAATGTTAAATGCTTTAATTGGACTTGAACATCATAAGGCAACTACAACTGAAGTATTTAAATGGGATGGGCAAAAGCGTTTATTTCCTGATTGGGAAAAGGACATGACACTGGGTGATGCCATGAAAGCTTCTGCAATTCCAGTTTACCAAGAATTAGCCCGACGTATTGGTCTGGATCTTATGTCCAAAGAGGTGAAACGAATTGGTTTCGGTAATGCTAACATTGGCTCAAAAGTAGATGATTTCTGGCTTGTTGGGCCTCTAAAAATTACACCTCAACAAGAAACCCAATTTGCTTATCAATTAGCCCATAAAACTCTTCCATTTAGCAAAAATGTACAAGAACAAGTTCAATCAATGGTGTTCATAGAAGAAAAAAATGGAAGTAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTTGAACCACAAGTTGGTTGGTTAACAGGTTGGGTCGTTCAACCACAAGGAGAAATTGTCGCATTCTCACTTAATTTAGAAATGAACAAAGGAACTCCTAGCTCTATTCGCAAAGAAATTGCTTATAAAGGCTTAGAACAACTGGGTATCTTATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3001537","ARO_id":"37937","ARO_name":"OXA-350","ARO_description":"OXA-350 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"780":{"model_id":"780","model_name":"CARB-9","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1973":{"protein_sequence":{"accession":"AAP22374.1","sequence":"MKSLLVFALLMPSVVFASSSKFQSVEQEIKGIESSLSARIGVAILDTQNGESWDYNGDQRFPLTSTFKTIACAKLLYDAEHGKVNLNSTVEVKKADLVTYSPVLEKQVGKPITLSDACFATMTTSDNTAANIVINAVGDPKSITDFLRQIGDKETRLDRVEPELNEGKLGDLRDTTTPNAITSTLNQLLFGSTLSEASQKKLESWMVNNQVTGNLLRSVLPVTWSIADRSGAGGFGARSITAIVWSEEKKPIIVSIYLAQTEASMAERNDAIVKIGRSIFEVYTSQSR"},"dna_sequence":{"accession":"AY248038","fmin":"2072","fmax":"2939","strand":"+","sequence":"ATGAAGTCTTTGTTGGTATTTGCGCTTTTAATGCCATCTGTAGTTTTTGCAAGCAGTTCAAAATTTCAATCAGTTGAACAAGAAATTAAGGGAATTGAGTCTTCACTCTCTGCTCGTATAGGAGTTGCCATTTTGGATACTCAAAATGGCGAAAGCTGGGATTATAATGGTGATCAACGATTTCCATTAACAAGTACTTTCAAAACAATAGCTTGTGCTAAGTTGCTGTATGATGCAGAGCATGGGAAAGTTAATCTCAATAGTACAGTTGAGGTTAAGAAAGCAGATCTTGTTACGTATTCGCCTGTATTAGAAAAGCAAGTAGGTAAACCAATAACGCTCTCTGATGCATGCTTTGCTACTATGACAACAAGCGACAATACAGCAGCCAATATTGTTATAAATGCTGTGGGTGATCCTAAAAGCATTACTGATTTTCTGAGACAAATTGGTGACAAAGAAACTCGTCTAGATCGTGTCGAGCCTGAGCTCAATGAAGGTAAACTCGGTGATTTGAGGGATACGACAACGCCTAATGCAATAACCAGCACGTTAAATCAATTATTATTTGGTTCCACATTATCTGAAGCTAGTCAGAAAAAATTAGAGTCTTGGATGGTGAACAATCAAGTTACGGGTAATTTATTGAGGTCAGTATTGCCAGTGACGTGGAGTATTGCTGATCGCTCAGGGGCAGGTGGATTTGGTGCTAGGAGTATTACAGCGATTGTGTGGAGTGAAGAAAAAAAACCGATTATCGTAAGTATTTATCTAGCTCAAACCGAGGCTTCAATGGCAGAACGAAATGATGCGATAGTTAAGATTGGTCGTTCAATTTTTGAAGTTTATACATCACAGTCGCGTTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36920","NCBI_taxonomy_name":"Vibrio cholerae non-O1\/non-O139","NCBI_taxonomy_id":"156539"}}}},"ARO_accession":"3002248","ARO_id":"38648","ARO_name":"CARB-9","ARO_description":"CARB-9 is a beta-lactamase found in Vibrio cholerae","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"781":{"model_id":"781","model_name":"QnrB25","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"73":{"protein_sequence":{"accession":"ADN94685.1","sequence":"MALALVGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAILKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITSTNLSYANFSKAVLEKCELWENRWMGTQVLGATLSGSDLSGGEFSSFDWRTANFTHCDLTNSELGDLDIRGVDLQGVKLDSYQAALLMERLGIAIIG"},"dna_sequence":{"accession":"HQ172108","fmin":"0","fmax":"645","strand":"+","sequence":"ATGGCTCTGGCGTTAGTTGGCGAAAAAATTGACAGAAACCGCTTCACCGGTGAAAAAGTTGAAAATAGCACTTTTTTTAACTGTGATTTTTCGGGTGCCGACCTTAGCGGTACTGAATTTATCGGCTGTCAGTTCTATGATCGAGAAAGCCAGAAAGGGTGCAATTTCAGTCGCGCAATACTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATGTCAGTGCGTTGGGCATAGAAATTCGCCACTGCCGCGCACAGGGTGCAGATTTTCGCGGCGCAAGTTTCATGAATATGATCACCACGCGCACCTGGTTTTGCAGCGCATATATCACTAGTACCAATCTAAGCTACGCCAACTTTTCGAAGGCCGTGCTTGAAAAGTGCGAATTGTGGGAAAATCGCTGGATGGGAACTCAGGTGCTGGGTGCGACGTTGAGTGGTTCCGATCTCTCCGGTGGCGAGTTTTCGTCGTTCGACTGGCGGACGGCAAATTTCACGCACTGTGATTTGACCAATTCAGAACTGGGTGATTTAGATATTCGGGGCGTCGATTTACAAGGTGTCAAATTGGACAGCTATCAGGCCGCATTGCTCATGGAACGTCTTGGCATCGCTATCATTGGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002740","ARO_id":"39174","ARO_name":"QnrB25","ARO_description":"QnrB25 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"782":{"model_id":"782","model_name":"OXA-63","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1615":{"protein_sequence":{"accession":"AAU88145.1","sequence":"MSKKNFILIFIFVILISCKNTEKISNETTLIDNIFTNSNAEGTLVIYNLNDDKYIIHNKERAEQRFYPASTFKIYNSLIGLNEKAVKDVDEVFYKLMAKSFLESWAKDSNLRYAIKNSQVPAYKELARRIGIKKMKENIEKLDFGNKSIGDSVDTFWLEGPLEISAMEQVKLLTKLAQNELQYPIEIQKAISDITITRANLHITLHGKTGLADSKNMTTEPIGWFVGWLEENDNIYVFALNIDNINSDDLAKRINIVKESLKALNLLK"},"dna_sequence":{"accession":"AY619003","fmin":"703","fmax":"1510","strand":"+","sequence":"ATGTCTAAAAAAAATTTTATATTAATATTTATTTTTGTTATTTTAATATCTTGTAAAAATACAGAAAAAATATCAAATGAAACTACATTAATAGATAATATATTTACTAATAGCAATGCTGAAGGAACATTAGTTATATATAATTTAAATGATGATAAATATATAATTCATAATAAAGAAAGAGCTGAACAAAGATTTTATCCAGCATCAACATTTAAAATATATAATAGTTTAATAGGCTTAAATGAAAAAGCAGTTAAAGATGTAGATGAAGTATTTTATAAATTAATGGCGAAAAGTTTTCTCGAATCTTGGGCTAAAGACTCTAATTTAAGATATGCAATTAAAAATTCGCAAGTACCGGCATATAAAGAATTAGCAAGAAGAATAGGTATTAAAAAGATGAAAGAGAATATAGAAAAACTAGATTTTGGTAATAAAAGTATAGGTGATAGTGTAGATACTTTTTGGCTTGAAGGACCTTTGGAAATAAGTGCGATGGAGCAAGTTAAATTATTAACTAAATTAGCTCAAAATGAATTACAGTATCCTATAGAAATACAAAAAGCTATTTCTGATATTACTATTACTAGAGCAAACTTACATATTACGCTTCATGGAAAAACTGGATTAGCTGATTCTAAAAACATGACAACTGAGCCTATTGGTTGGTTCGTAGGCTGGCTTGAAGAAAATGATAATATATACGTCTTTGCTTTAAATATTGATAATATCAATTCAGATGACCTTGCAAAAAGGATAAATATAGTAAAAGAAAGTTTAAAAGCATTAAATTTATTAAAATAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36935","NCBI_taxonomy_name":"Brachyspira pilosicoli","NCBI_taxonomy_id":"52584"}}}},"ARO_accession":"3001764","ARO_id":"38164","ARO_name":"OXA-63","ARO_description":"OXA-63 is a beta-lactamase found in Brachyspira spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"783":{"model_id":"783","model_name":"NDM-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"3746":{"protein_sequence":{"accession":"CAZ39946.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"FN396876","fmin":"2406","fmax":"3219","strand":"-","sequence":"TCAGCGCAGCTTGTCGGCCATGCGGGCCGTATGAGTGATTGCGGCGCGGCTATCGGGGGCGGAATGGCTCATCACGATCATGCTGGCCTTGGGGAACGCCGCACCAAACGCGCGCGCTGACGCGGCGTAGTGCTCAGTGTCGGCATCACCGAGATTGCCGAGCGACTTGGCCTTGCTGTCCTTGATCAGGCAGCCACCAAAAGCGATGTCGGTGCCGTCGATCCCAACGGTGATATTGTCACTGGTGTGGCCGGGGCCGGGGTAAAATACCTTGAGCGGGCCAAAGTTGGGCGCGGTTGCTGGTTCGACCCAGCCATTGGCGGCGAAAGTCAGGCTGTGTTGCGCCGCAACCATCCCCTCTTGCGGGGCAAGCTGGTTCGACAACGCATTGGCATAAGTCGCAATCCCCGCCGCATGCAGCGCGTCCATACCGCCCATCTTGTCCTGATGCGCGTGAGTCACCACCGCCAGCGCGACCGGCAGGTTGATCTCCTGCTTGATCCAGTTGAGGATCTGGGCGGTCTGGTCATCGGTCCAGGCGGTATCGACCACCAGCACGCGGCCGCCATCCCTGACGATCAAACCGTTGGAAGCGACTGCCCCGAAACCCGGCATGTCGAGATAGGAAGTGTGCTGCCAGACATTCGGTGCGAGCTGGCGGAAAACCAGATCGCCAAACCGTTGGTCGCCAGTTTCCATTTGCTGGCCAATCGTCGGGCGGATTTCACCGGGCATGCACCCGCTCAGCATCAATGCAGCGGCTAATGCGGTGCTCAGCTTCGCGACCGGGTGCATAATATTGGGCAATTCCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000589","ARO_id":"36728","ARO_name":"NDM-1","ARO_description":"NDM-1 is a metallo-beta-lactamase isolated from Klebsiella pneumoniae with nearly complete resistance to all beta-lactam antibiotics.","ARO_category":{"35996":{"category_aro_accession":"0000079","category_aro_cvterm_id":"35996","category_aro_name":"clavulanate","category_aro_description":"Clavulanic acid is a beta-lactamase inhibitor (marketed by GlaxoSmithKline, formerly Beecham) combined with penicillin group antibiotics to overcome certain types of antibiotic resistance. It is used to overcome resistance in bacteria that secrete beta-lactamase, which otherwise inactivates most penicillins.","category_aro_class_name":"Adjuvant"},"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"35987":{"category_aro_accession":"0000070","category_aro_cvterm_id":"35987","category_aro_name":"ertapenem","category_aro_description":"Ertapenem is a carbapenem antibiotic and is highly resistant to beta-lactamases like other carbapenems. It inhibits bacterial cell wall synthesis.","category_aro_class_name":"Antibiotic"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"36309":{"category_aro_accession":"3000170","category_aro_cvterm_id":"36309","category_aro_name":"imipenem","category_aro_description":"Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"784":{"model_id":"784","model_name":"AAC(6')-Iv","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"81":{"protein_sequence":{"accession":"AAD03494.1","sequence":"MKIMPISESQLSDWLVLRCLLWPDHEEQHLQEMRQLITQAHCLQLLAYTDTQQAIAMLEASIRYEYVNGTQTSPVAFLEGIYVLPEYRRSGIATGLVQHVEIWAKQFSCTEFASDAALDNQITHAMHQALGFQETERVVYFKKNIG"},"dna_sequence":{"accession":"AF031330","fmin":"0","fmax":"441","strand":"+","sequence":"ATGAAGATTATGCCGATATCTGAATCACAATTATCAGATTGGCTAGTATTGAGATGCTTACTCTGGCCTGATCATGAGGAACAGCATTTACAGGAAATGCGTCAACTGATCACACAGGCACATTGCTTACAATTATTGGCTTATACCGACACCCAACAAGCAATTGCCATGCTGGAAGCTTCAATTCGATATGAATATGTGAATGGCACACAGACATCACCTGTGGCTTTTCTTGAAGGGATTTATGTATTGCCTGAATATCGCCGTTCAGGTATCGCAACGGGTTTGGTTCAGCATGTCGAAATCTGGGCCAAACAGTTTTCATGCACAGAGTTTGCCTCAGATGCAGCGCTGGATAATCAGATCACCCATGCAATGCATCAAGCACTCGGTTTTCAAGAAACTGAACGTGTGGTGTATTTTAAGAAAAATATTGGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39517","NCBI_taxonomy_name":"Acinetobacter sp. 631","NCBI_taxonomy_id":"70349"}}}},"ARO_accession":"3002566","ARO_id":"38966","ARO_name":"AAC(6')-Iv","ARO_description":"AAC(6')-Iv is a chromosomal-encoded aminoglycoside acetyltransferase in Acinetobacter sp.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"785":{"model_id":"785","model_name":"OXY-2-9","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1770":{"protein_sequence":{"accession":"ACV44455.1","sequence":"MIKSSWRKIAMLAAVPLLLASGALWASTDAIHQKLTDLEKRSGGRLGVALINTADNSQILYRGDERFAMCSTSKVMAAAAVLKQSESNKEVVNKRLEINAADLVVWSPITEKHLQSGMTLAELSAATLQYSDNTAMNLIIGYLGGPEKVTAFARSIGDATFRLDRTEPTLNTAIPGDERDTSTPLAMAESLRKLTLGDALGEQQRAQLVTWLKGNTTGGQSIRAGLPESWVVGDKTGTGDYGTTNDIAVIWPEDHAPLVLVTYFTQPQQDAKNRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"FJ785625","fmin":"131","fmax":"1001","strand":"+","sequence":"ATGATAAAAAGTTCGTGGCGTAAAATTGCAATGCTAGCCGCCGTTCCGCTGCTGCTGGCGAGCGGCGCACTGTGGGCCAGTACCGATGCTATCCATCAGAAGCTGACAGATCTCGAGAAGCGTTCAGGCGGCAGGTTGGGCGTGGCGCTAATCAACACGGCAGATAATTCTCAAATCTTATATCGCGGCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCCGCCGCCGCGGTATTAAAACAGAGCGAAAGCAATAAAGAGGTGGTAAATAAAAGGCTGGAGATTAACGCAGCCGATTTGGTGGTCTGGAGTCCGATTACCGAAAAACATCTCCAGAGCGGAATGACGCTGGCTGAGCTAAGCGCGGCGACGCTGCAATATAGCGACAATACGGCGATGAATCTGATCATCGGCTACCTTGGCGGGCCGGAAAAAGTCACCGCCTTCGCCCGCAGTATCGGCGATGCCACCTTTCGTCTCGATCGTACGGAGCCCACGCTGAATACCGCCATCCCGGGCGATGAGCGTGATACCAGCACGCCGCTGGCGATGGCTGAAAGCCTACGCAAGCTGACGCTTGGCGATGCGCTGGGCGAACAGCAACGCGCCCAGTTAGTCACCTGGCTGAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCGGGCCTGCCTGAAAGCTGGGTGGTCGGCGATAAAACCGGCACCGGAGATTACGGCACCACCAATGATATTGCGGTTATCTGGCCGGAAGATCACGCTCCGCTGGTATTAGTCACCTACTTTACCCAGCCGCAGCAGGATGCGAAAAACCGCAAAGAGGTGTTAGCCGCAGCGGCAAAAATCGTGACCGAAGGGCTTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002404","ARO_id":"38804","ARO_name":"OXY-2-9","ARO_description":"OXY-2-9 is a beta-lactamase found in Klebsiella oxytoca","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"786":{"model_id":"786","model_name":"vanHO","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"576":{"protein_sequence":{"accession":"AHA41499.1","sequence":"MSYRDLGLIDSEVIAERRVRALDDSSPSAVPTTGVRVFGCGHDEAVLFREMGTRLGITPSITEEAISETNAELARGNRCISVSHKTQIDNSTLLALSRVGVEYISTRSVGYNHIDVEFAASIGISVGNVDYSPDSVGDYTLMLMLMTVRHAKSIVRRADTHDYRLNDTRGRELRDLTVGVIGTGRIGTAVIDRLQGFGCRVLAHDSGPHASADYVPLDELLRQSDIVTLHTPLTADTHHLLDRQRIDQMKHGAYIVNTGRGPLLDTEALLSALESGRLGGAALDVVEGEEGIFYADCRNRLIENKALVRLQRLPNVLISPHSAYYTDHALNDTVENSLVNCLNFESGRTA"},"dna_sequence":{"accession":"KF478993","fmin":"490","fmax":"1543","strand":"+","sequence":"ATGTCCTACAGAGACCTGGGTTTGATCGACAGCGAAGTGATCGCGGAGCGACGCGTCCGAGCGCTCGACGATTCGTCACCCTCGGCCGTCCCGACCACTGGGGTCAGAGTTTTCGGATGCGGTCACGACGAAGCCGTTTTGTTCCGCGAGATGGGAACCCGCCTCGGGATAACGCCAAGCATCACCGAGGAAGCGATCAGTGAAACCAACGCTGAACTGGCGCGTGGCAACCGATGCATCAGCGTGAGCCACAAGACGCAGATCGACAATTCCACGCTGCTGGCGCTGAGCCGAGTCGGAGTGGAGTACATCTCCACCAGAAGCGTCGGGTACAACCACATCGACGTGGAATTCGCGGCGAGCATCGGCATCTCGGTCGGCAACGTCGACTACTCGCCCGACAGCGTGGGCGACTACACACTGATGTTGATGCTGATGACCGTACGCCACGCGAAATCAATTGTCCGCCGCGCCGATACGCATGATTACCGGCTGAATGACACGCGCGGCAGGGAGCTGCGCGACTTGACCGTCGGGGTGATCGGAACAGGGCGCATCGGCACAGCAGTCATCGACCGGCTGCAGGGATTTGGCTGCCGCGTGCTGGCACATGACAGCGGGCCTCACGCCTCCGCCGACTACGTTCCGCTCGATGAACTGCTGCGGCAGAGCGACATTGTCACGCTCCACACTCCACTCACCGCGGACACACACCATCTCCTCGATCGCCAACGCATCGACCAGATGAAGCACGGCGCGTACATCGTCAACACGGGTCGCGGACCGCTGCTCGATACCGAGGCCCTCCTCTCCGCATTGGAGAGCGGCCGGTTGGGCGGCGCGGCGCTCGATGTCGTCGAAGGAGAGGAAGGGATCTTCTACGCCGACTGCAGGAACAGGCTCATCGAGAACAAGGCCCTGGTGCGGCTACAGCGCCTGCCGAATGTGCTGATCAGTCCGCACTCCGCCTACTACACAGACCACGCCCTGAACGACACCGTCGAAAACAGCCTCGTCAACTGCCTGAACTTTGAAAGTGGGAGAACAGCATGAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36897","NCBI_taxonomy_name":"Rhodococcus equi","NCBI_taxonomy_id":"43767"}}}},"ARO_accession":"3002948","ARO_id":"39382","ARO_name":"vanHO","ARO_description":"vanHO is a vanH variant in the vanO gene cluster","ARO_category":{"36015":{"category_aro_accession":"3000006","category_aro_cvterm_id":"36015","category_aro_name":"vanH","category_aro_description":"VanH is a D-specific alpha-ketoacid dehydrogenase that synthesizes D-lactate. D-lactate is incorporated into the end of the peptidoglycan subunits, decreasing vancomycin binding affinity.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"787":{"model_id":"787","model_name":"dfrA23","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"4338":{"protein_sequence":{"accession":"CAG34233.2","sequence":"MPTVEIIVAVDPVGGFGRNGQIPWTCKEDMKRFTTISKEIRVCVMGKNTYKDMLDMQMKKEGAEERIKEKGILPERESYVVSSTLKPEDVIGATVVPDLRAVLNQYHDSDQRIAVIGGEKLYVQALASATKVHMTVMHKPYNCDRTLPMSYIDKKFVAGQGSITIQTAVDGETHPVKFITYERARP"},"dna_sequence":{"accession":"AJ746361","fmin":"6742","fmax":"7303","strand":"-","sequence":"TTACGGCCGAGCGCGCTCATATGTGATGAACTTCACGGGATGGGTCTCACCATCTACCGCAGTTTGAATGGTGATAGACCCTTGACCTGCAACAAACTTTTTGTCGATGTATGACATCGGCAACGTCCGATCGCAGTTATATGGCTTGTGCATTACCGTCATGTGGACTTTTGTGGCAGATGCGAGGGCTTGCACGTACAGCTTTTCTCCACCAATGACAGCTATTCGTTGATCGCTGTCGTGATATTGATTGAGCACCGCACGTAGGTCCGGAACTACCGTGGCTCCAATGACGTCCTCGGGCTTCAAAGTCGAGGACACGACGTAAGATTCGCGCTCCGGAAGAATTCCCTTCTCTTTGATTCGTTCTTCAGCGCCTTCCTTCTTCATTTGCATATCGAGCATGTCTTTGTATGTGTTCTTCCCCATCACACACACTCGAATCTCTTTGGATATGGTGGTGAAGCGCTTCATGTCTTCCTTGCACGTCCAAGGGATTTGGCCATTCCGGCCAAATCCCCCAACAGGATCAACTGCAACAATAATCTCAACTGTTGGCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35732","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium","NCBI_taxonomy_id":"90371"}}}},"ARO_accession":"3003019","ARO_id":"39453","ARO_name":"dfrA23","ARO_description":"dfrA23 is an integron-encoded dihydrofolate reductase found in Salmonella enterica","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36408":{"category_aro_accession":"3000269","category_aro_cvterm_id":"36408","category_aro_name":"brodimoprim","category_aro_description":"Brodimoprim is a structural derivative of trimethoprim and an inhibitor of bacterial dihydrofolate reductase. The 4-methoxy group of trimethoprim is replaced with a bromine atom.","category_aro_class_name":"Antibiotic"},"36423":{"category_aro_accession":"3000284","category_aro_cvterm_id":"36423","category_aro_name":"tetroxoprim","category_aro_description":"Tetroxoprim is a trimethoprim derivative that inhibits bacterial dihydrofolate reductase.","category_aro_class_name":"Antibiotic"},"36476":{"category_aro_accession":"3000337","category_aro_cvterm_id":"36476","category_aro_name":"iclaprim","category_aro_description":"Iclaprim is a bactericidal compound that inhibits dihydrofolate reductase. It is used against clinically important Gram-positive pathogens, including methicillin-sensitive Staphylococcus aureus and methicillin-resistant S. aureus.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"788":{"model_id":"788","model_name":"SHV-46","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"919":{"protein_sequence":{"accession":"AAO53445.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLNSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASKRGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AY210887","fmin":"111","fmax":"972","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGAACAGCCAACGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCAAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAACAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3001104","ARO_id":"37484","ARO_name":"SHV-46","ARO_description":"SHV-46 is an extended-spectrum beta-lactamase found in Klebsiella oxytoca.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"789":{"model_id":"789","model_name":"IMP-43","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"791":{"protein_sequence":{"accession":"BAM98935.1","sequence":"MKKLSVFFMFLFCSIAASGEALPDLKIEKLDEGVYVHTSFEEVNGWGVFPKHGLVVLVNTDAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKDGKVQAKNSFSGASYWLVKKKIEIFYPGPGHTPDNVVVWLPEHRVLFGGCFVKPYGLGNLGDANLEAWPKSAKLLVSKYGKAKLVVPSHSEVGDASLLKRTLEQAVKGLNESKKLSKPSN"},"dna_sequence":{"accession":"AB777500","fmin":"2034","fmax":"2775","strand":"+","sequence":"ATGAAAAAGTTATCAGTATTCTTTATGTTTTTGTTTTGTAGCATTGCTGCCTCAGGAGAGGCTTTGCCAGATTTAAAAATTGAGAAGCTTGACGAAGGCGTTTATGTTCATACTTCGTTTGAGGAAGTTAACGGCTGGGGCGTGTTTCCTAAACACGGCTTGGTGGTTCTTGTAAATACTGACGCTTATTTGATTGACACTCCATTTACAGCTAAAGATACTGAAAAGTTAGTTACTTGGTTTGTAGAGCGCGGCTATAAAATAAAAGGCAGTATCTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCAATCTATTCCAACATATGCATCTGAATTAACAAATGAACTTCTTAAAAAAGACGGTAAGGTACAAGCTAAAAATTCATTTAGCGGAGCCAGCTATTGGTTAGTTAAGAAAAAGATTGAAATTTTTTATCCTGGCCCAGGGCACACTCCAGATAACGTAGTGGTTTGGCTACCTGAACATAGAGTTTTGTTTGGTGGTTGTTTTGTTAAACCGTATGGTCTAGGTAATTTGGGTGACGCAAATTTAGAAGCTTGGCCAAAGTCTGCCAAATTATTAGTGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAAGTCACAGTGAAGTTGGAGATGCATCACTCTTGAAACGTACATTAGAACAGGCTGTTAAAGGATTAAACGAAAGTAAAAAGCTATCAAAACCAAGTAACTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002234","ARO_id":"38634","ARO_name":"IMP-43","ARO_description":"IMP-43 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"790":{"model_id":"790","model_name":"CMY-32","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1858":{"protein_sequence":{"accession":"ACA97846.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPEQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"EU496815","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGAACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002043","ARO_id":"38443","ARO_name":"CMY-32","ARO_description":"CMY-32 is a beta-lactamase found in Escherichia coli","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"791":{"model_id":"791","model_name":"SHV-14","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1471":{"protein_sequence":{"accession":"AAG17550.1","sequence":"MRYFRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGSVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AF226622","fmin":"54","fmax":"915","strand":"+","sequence":"ATGCGTTATTTTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCAGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001073","ARO_id":"37453","ARO_name":"SHV-14","ARO_description":"SHV-14 is an broad-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"792":{"model_id":"792","model_name":"OXY-1-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1938":{"protein_sequence":{"accession":"CAA82916.1","sequence":"MLKSSWRKTALMAAAAVPLLLASGSLWASADAIQQKLADLEKRSGGRLGVALINTADDSQTLYRGDERFAMCSTGKVMAAAAVLKQSESNPEVVNKRLEIKKSDLVVWSPITEKHLQSGMTLAELSAAALQYSDNTAMNKMISYLGGPEKVTAFAQSIGDVTFRLDRTEPALNSAIPGDKRDTTTPLAMAESLRKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPASWAVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKSRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"Z30177","fmin":"348","fmax":"1224","strand":"+","sequence":"ATGTTGAAAAGTTCGTGGCGTAAAACCGCCCTGATGGCCGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGTTCATTATGGGCCAGTGCCGATGCTATCCAGCAAAAGCTGGCTGATTTAGAAAAACGTTCCGGCGGTCGGCTGGGCGTAGCGCTGATTAACACGGCAGATGATTCGCAAACCCTCTATCGCGGCGATGAACGTTTTGCCATGTGCAGCACCGGTAAAGTGATGGCCGCCGCCGCGGTGTTAAAACAGAGCGAAAGCAATCCAGAGGTGGTGAATAAAAGGCTGGAGATTAAAAAATCGGATTTAGTGGTCTGGAGCCCGATCACCGAAAAACATCTGCAAAGCGGAATGACCCTGGCGGAACTCAGCGCGGCGGCGCTGCAGTACAGCGACAATACCGCGATGAATAAGATGATTAGCTACCTTGGCGGACCGGAAAAGGTGACCGCATTCGCCCAGAGTATCGGGGATGTCACTTTTCGTCTCGATCGTACGGAGCCGGCGCTGAACAGCGCGATTCCCGGCGATAAGCGCGATACCACCACCCCGTTGGCGATGGCCGAAAGCCTGCGCAAGCTGACGCTGGGCAATGCGCTGGGCGAACAGCAGCGCGCCCAGTTAGTGACGTGGCTAAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCAGGCCTGCCCGCAAGCTGGGCGGTCGGGGATAAAACCGGCGCCGGAGATTACGGCACCACCAACGATATCGCGGTGATCTGGCCGGAAAATCATGCCCCGCTGGTGCTGGTGACCTATTTTACCCAGCCGCAGCAGGATGCGAAAAGCCGCAAAGAGGTGTTAGCCGCGGCGGCAAAAATCGTCACCGAAGGGCTTTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002389","ARO_id":"38789","ARO_name":"OXY-1-1","ARO_description":"OXY-1-1 is a beta-lactamase found in Klebsiella oxytoca","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"793":{"model_id":"793","model_name":"IMP-34","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1482":{"protein_sequence":{"accession":"BAM38093.1","sequence":"MSKLSVFFIFLFCSIATAAESLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIGWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNESKKPSKPSN"},"dna_sequence":{"accession":"AB715422","fmin":"1695","fmax":"2436","strand":"+","sequence":"ATGAGCAAGTTATCTGTATTCTTTATATTTTTGTTTTGCAGCATTGCTACCGCAGCAGAGTCTTTGCCAGATTTAAAAATTGAAAAGCTTGATGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGGTGGGGCGTTGTTCCTAAACATGGTTTGGTGGTTCTTGTAAATGCTGAGGCTTATTTAATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAGCGTGGCTATAAAATAAAAGGCAGTATTTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGGGTGGCTTAATTCTCGATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTGCTTAAAAAAGACGGTAAGGTTCAAGCCACAAATTCATTTAGCGGAGTTAACTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCGGGACACACTCCAGATAACGTAGTGGTTTGGCTGCCTGAAAGGAAAATATTATTCGGTGGTTGTTTTATTAAACCGTACGGTTTAGGCAATTTGGGTGACGCAAATATAGAAGCTTGGCCAAAGTCCGCCAAATTATTAAAGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAAGTCACAGTGAAGTTGGAGACGCATCACTCTTGAAACTTACATTAGAGCAGGCGGTTAAAGGATTAAACGAAAGTAAAAAACCATCAAAACCAAGCAACTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002225","ARO_id":"38625","ARO_name":"IMP-34","ARO_description":"IMP-34 is a beta-lactamase found in Klebsiella spp.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"795":{"model_id":"795","model_name":"OXA-324","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"807":{"protein_sequence":{"accession":"AGW16406.1","sequence":"MYKKTLIVTTSILFLSACSSNSVKQHQIHSMSANKNSEEIKSLFDQAQTTGVLVIKRGKTEEIYGNDLKRASTAYVPASTFKMLNALIGLEHHKATATEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNANIGSKVDNFWLVGPLKITPQQETQFAYQLAHKTLPFSKDVQEQVQSMVFIEEKNGSKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLAIL"},"dna_sequence":{"accession":"KF203098","fmin":"0","fmax":"822","strand":"+","sequence":"ATGTATAAAAAAACCCTTATCGTTACAACAAGTATCCTATTTTTATCCGCCTGTTCTTCTAATTCAGTAAAACAACATCAAATACACTCTATGTCTGCCAATAAAAATTCAGAAGAAATTAAATCACTGTTTGATCAAGCACAAACCACGGGTGTTTTGGTAATTAAGCGAGGGAAAACAGAAGAAATTTATGGCAATGATCTTAAAAGAGCATCAACCGCCTATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTAATTGGACTTGAACACCATAAGGCAACTGCAACTGAAGTGTTTAAATGGGATGGGCAAAAACGTTTATTTCCTGATTGGGAAAAAGACATGACGCTGGGCGATGCCATGAAAGCTTCTGCTATTCCAGTTTATCAAGAATTAGCCCGACGAATTGGACTTGACCTTATGTCTAAAGAGGTAAAAAGAATTGGTTTCGGTAATGCTAACATTGGTTCAAAAGTAGATAATTTTTGGCTTGTTGGCCCTCTAAAAATTACGCCTCAACAAGAAACCCAATTTGCTTATCAATTAGCCCATAAAACGCTTCCATTTAGCAAAGATGTACAAGAACAAGTTCAATCAATGGTGTTCATAGAGGAAAAAAATGGAAGTAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTTGAACCACAAGTTGGTTGGTTAACAGGTTGGGTCGTTCAACCACAAGGAGAAATTGTGGCATTCTCACTTAATTTAGAAATGAAAAAAGGAACTCCTAGCTCTATTCGCAAAGAAATTGCTTATAAAGGCTTAGAACAACTGGCTATCCTATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3001512","ARO_id":"37912","ARO_name":"OXA-324","ARO_description":"OXA-324 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"796":{"model_id":"796","model_name":"iri","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"900"}},"model_sequences":{"sequence":{"474":{"protein_sequence":{"accession":"AAB41059.1","sequence":"MSDVIIVGAGPTGLMLAGELRLQGVDVVVVDKDEEPTQFVRALGIHVRSIEIMEQRGLLDKFLAHGRKYPLGGFFAGISKPAPAHLDTAHGYVLGIPQPEIDRILAEHATEVGADIQRGKRVVAIRQDTDNVAAELSDGTTLHARYLVGCDGGRSTVRKLRSTSVFPASRTSADTLIGEMDVTMPADELAAVVAEIRETHKRFGVGPAGNGAFRVVVPAAEVADGRATPTTLDDIKQQLLAIAGTDFGVHSPRWLSRFGDATRLADDYRRDRVFLAGDAAHIHPPMGGQGLNLGVQDAFNLGWKLAAEINGWAPVGLLDTYESERRPVAADVLDNTRAQAELISTAAGPQAVRRLISELMEFEDVKRYLTEKITAISIRYDFGEGDDLLGRRLRNIALTRGNLYDLMRSGRGLLLDQGGQLSVDGWSDRADHIVDTSTELEAPAVLLRPDGHVAWIGDAQAELDTQLSTWFGRSARDRA"},"dna_sequence":{"accession":"U56415","fmin":"279","fmax":"1719","strand":"+","sequence":"ATGAGTGACGTCATCATTGTCGGTGCTGGACCAACTGGATTGATGCTGGCAGGTGAGCTCCGGCTACAGGGCGTCGATGTCGTCGTCGTGGACAAGGACGAGGAGCCGACTCAGTTCGTCCGTGCCCTCGGCATCCATGTGCGCAGCATCGAAATCATGGAGCAGCGCGGGTTGCTGGACAAGTTCCTCGCGCACGGCCGCAAGTATCCGCTCGGTGGATTCTTCGCGGGGATCAGCAAACCGGCACCCGCGCACCTCGATACTGCGCACGGGTACGTCCTGGGCATACCTCAGCCCGAGATCGACAGGATTCTTGCCGAACATGCCACCGAAGTCGGCGCGGACATTCAGCGAGGGAAGCGCGTCGTCGCGATCCGTCAAGATACCGACAACGTCGCAGCGGAATTGTCCGACGGCACAACACTTCACGCGCGGTACCTTGTAGGCTGCGACGGCGGCCGCAGCACTGTTCGGAAGCTGAGATCGACGTCGGTATTCCCGGCGAGCCGTACGAGCGCCGACACGTTGATCGGCGAAATGGACGTGACCATGCCTGCTGATGAACTGGCCGCCGTTGTCGCCGAAATCCGGGAAACGCACAAACGATTCGGAGTCGGTCCCGCCGGCAACGGTGCTTTTCGTGTCGTGGTCCCTGCGGCCGAAGTTGCCGACGGTCGCGCAACACCGACCACCCTCGACGACATCAAACAACAGCTACTGGCCATTGCCGGTACCGACTTCGGTGTGCACTCGCCGCGGTGGCTCTCGCGCTTCGGCGACGCCACTCGTCTGGCGGACGACTACCGGCGCGACCGGGTGTTTCTCGCCGGCGACGCCGCACACATCCACCCACCGATGGGCGGTCAAGGTCTCAATCTCGGTGTGCAGGACGCCTTCAACCTCGGCTGGAAGCTCGCCGCCGAGATCAACGGCTGGGCACCGGTGGGCCTGCTCGACACGTACGAATCGGAACGGCGTCCGGTGGCTGCCGACGTGCTGGACAACACGCGCGCCCAGGCCGAGTTGATCTCCACCGCTGCCGGACCACAAGCGGTGCGGCGCTTGATCTCCGAGCTGATGGAATTCGAAGACGTCAAGCGCTATTTGACCGAGAAGATCACTGCGATCTCGATTCGCTACGATTTCGGCGAAGGCGACGACCTACTCGGTCGGAGGCTGCGGAACATCGCGTTGACGCGCGGCAACCTGTACGACCTGATGCGATCCGGCCGCGGACTTCTTCTCGACCAGGGTGGCCAACTGTCCGTCGATGGTTGGAGCGATCGCGCCGACCATATCGTTGACACAAGCACTGAATTGGAAGCTCCGGCTGTCCTGCTTCGGCCGGACGGTCATGTGGCATGGATCGGGGATGCGCAGGCGGAGTTGGATACTCAGCTGTCCACATGGTTCGGCCGGTCGGCGAGGGACCGCGCGTGAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36897","NCBI_taxonomy_name":"Rhodococcus equi","NCBI_taxonomy_id":"43767"}}}},"ARO_accession":"3002884","ARO_id":"39318","ARO_name":"iri","ARO_description":"iri is a monooxygenase that confers resistance to rifampin found in Rhodococcus equi","ARO_category":{"36584":{"category_aro_accession":"3000445","category_aro_cvterm_id":"36584","category_aro_name":"rifampin monooxygenase","category_aro_description":"Enzyme responsible for the decolorization of rifampin by monoxygenation.","category_aro_class_name":"AMR Gene Family"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36656":{"category_aro_accession":"3000517","category_aro_cvterm_id":"36656","category_aro_name":"rifaximin","category_aro_description":"Rifaximin is a semi-synthetic rifamycin used to treat traveller's diarrhea. Rifaximin inhibits RNA synthesis by binding to the beta subunit of bacterial RNA polymerase.","category_aro_class_name":"Antibiotic"},"36669":{"category_aro_accession":"3000530","category_aro_cvterm_id":"36669","category_aro_name":"rifabutin","category_aro_description":"Rifabutin is a semisynthetic rifamycin used in tuberculosis therapy. It inhibits DNA-dependent RNA synthesis.","category_aro_class_name":"Antibiotic"},"36673":{"category_aro_accession":"3000534","category_aro_cvterm_id":"36673","category_aro_name":"rifapentine","category_aro_description":"Rifapentine is a semisynthetic rifamycin that inhibits DNA-dependent RNA synthesis. It is often used in the treatment of tuberculosis and leprosy.","category_aro_class_name":"Antibiotic"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"797":{"model_id":"797","model_name":"TEM-55","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2037":{"protein_sequence":{"accession":"ABB97007.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAEPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"DQ286729","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGAACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000924","ARO_id":"37304","ARO_name":"TEM-55","ARO_description":"TEM-55 is a broad-spectrum beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"798":{"model_id":"798","model_name":"cmeC","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"960"}},"model_sequences":{"sequence":{"492":{"protein_sequence":{"accession":"BAO79432.1","sequence":"MNKIISISAIASFTLLISACSLSPNLNIPEANYSIDNKLGALSWEKENNSSITKNWWKDFDDENLNKVVDLALKNNNDLKLAFIHMEQAAAQLGIDFSSLLPKFDGSASGSRAKTAINAPSNRTGEVSYGNDFKMGLNLSYEIDLWGKYRDTYRASKSSFKASEYDYEAARLSVISNTVQTYFNLVNAYENENALKEAYESAKEIYRINDEKFQVGAVGEYELAQARANLESMALQYNEAKLNKENYLKALKILTSNDLNDILYKNQSYQVFNLKEFDIPTGISSTILLQRPDIGSSLEKLTQQNYLVGVARTAFLPSLSLTGLLGFESGDLDTLVKGGSKTWNIGGNFTLPIFHWGEIYQNVNLAKLNKDEAFVNYQNTLITAFGEIRYALVARKTIRLQYDNAQASEQSYKRIYEIAKERYDIGEMSLQDYLEARQNWLNAAVAFNNTKYSYANSIIDVIKAFGGGFEQSEDTSKNIKEESKNLDMSFRE"},"dna_sequence":{"accession":"AB894099","fmin":"4218","fmax":"5697","strand":"+","sequence":"ATGAATAAAATAATTTCAATTAGTGCTATAGCAAGTTTTACTCTTTTGATTTCAGCTTGCTCTTTAAGTCCAAATTTAAATATTCCCGAAGCAAACTATAGCATTGATAATAAGCTTGGAGCCTTATCTTGGGAAAAAGAAAACAATAGCTCTATCACAAAAAATTGGTGGAAAGATTTTGATGATGAAAATTTAAATAAAGTGGTTGATTTAGCACTTAAAAATAATAATGATTTAAAACTTGCCTTCATACACATGGAACAAGCTGCTGCTCAATTAGGTATAGATTTTAGCAGTTTGTTGCCAAAATTTGATGGTAGCGCAAGCGGTAGTCGTGCAAAAACAGCTATAAATGCTCCAAGCAATCGAACTGGGGAAGTAAGTTACGGTAATGATTTTAAAATGGGGCTTAATTTAAGCTATGAAATCGATCTTTGGGGAAAATATCGCGATACATATCGTGCCTCAAAATCAAGCTTTAAAGCAAGTGAGTATGATTATGAAGCTGCAAGACTTTCTGTTATTTCAAATACGGTTCAAACTTATTTTAATCTTGTAAATGCTTATGAAAATGAAAATGCTCTTAAAGAAGCCTATGAATCTGCAAAAGAAATTTATAGGATTAATGATGAAAAATTTCAAGTTGGTGCTGTAGGTGAATATGAACTTGCTCAAGCAAGAGCCAACTTAGAAAGTATGGCTTTGCAATATAATGAAGCAAAATTAAATAAAGAAAATTACCTTAAAGCTTTAAAAATTTTAACTTCAAATGATTTAAATGACATACTTTACAAAAATCAAAGCTATCAAGTTTTTAATCTTAAAGAATTTGACATTCCAACTGGAATTTCAAGCACCATCTTGCTTCAACGTCCAGATATTGGCTCTTCTTTAGAAAAATTAACTCAGCAAAATTATCTTGTTGGAGTAGCTCGCACGGCTTTCTTACCTAGCCTTTCTTTAACAGGATTATTGGGATTTGAAAGTGGGGATTTAGATACCTTGGTTAAAGGAGGTTCTAAGACTTGGAATATAGGTGGAAACTTTACTCTGCCTATTTTTCATTGGGGTGAAATTTACCAAAATGTAAATTTAGCTAAGCTTAATAAAGATGAAGCTTTTGTAAATTATCAAAATACTTTGATTACTGCTTTTGGAGAAATTCGCTATGCTTTAGTAGCTAGAAAAACTATACGCTTACAATACGATAATGCACAAGCAAGCGAACAATCTTACAAAAGAATCTATGAAATTGCTAAAGAACGCTATGATATAGGAGAAATGTCTTTGCAAGATTATTTAGAAGCACGTCAAAATTGGCTTAATGCTGCCGTTGCTTTTAATAATACTAAATATTCTTATGCCAATTCCATAATAGATGTAATCAAAGCATTTGGTGGAGGATTTGAGCAAAGTGAAGATACGAGTAAAAATATAAAAGAAGAATCAAAAAATTTAGATATGTCTTTTAGAGAATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39578","NCBI_taxonomy_name":"Campylobacter jejuni subsp. jejuni","NCBI_taxonomy_id":"32022"}}}},"ARO_accession":"3000785","ARO_id":"37165","ARO_name":"cmeC","ARO_description":"CmeC is the outer membrane channel protein of the CmeABC multidrug efflux complex.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"36989":{"category_aro_accession":"3000645","category_aro_cvterm_id":"36989","category_aro_name":"cefotaxime","category_aro_description":"Cefotaxime is a semisynthetic cephalosporin taken parenterally. It is resistant to most beta-lactamases and active against Gram-negative rods and cocci due to its aminothiazoyl and methoximino functional groups.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"37139":{"category_aro_accession":"3000759","category_aro_cvterm_id":"37139","category_aro_name":"fusidic acid","category_aro_description":"Fusidic acid is the only commercially available fusidane, a group of steroid-like antibiotics. It is most active against Gram-positive bacteria, and acts by inhibiting elongation factor G to  block protein synthesis.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"799":{"model_id":"799","model_name":"CTX-M-31","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"786":{"protein_sequence":{"accession":"CAD99181.1","sequence":"MMTQSIRRSMLTVMATLPLLFSSATLHAQANSVQQQLEALEKSSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKQSESDKHLLNQRVEIKKSDLVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDESFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSASIRAGLPKSWVVGDKTGSGDYGTTNDIAVIWPENHAPLVLVTYFTQPEQKAESRRDILAAAAKIVTHGF"},"dna_sequence":{"accession":"AJ567481","fmin":"0","fmax":"876","strand":"+","sequence":"ATGATGACTCAGAGCATTCGCCGCTCAATGTTAACGGTGATGGCGACGCTACCCCTGCTATTTAGCAGCGCAACGCTGCATGCGCAGGCGAACAGCGTGCAACAGCAGCTGGAAGCCCTGGAGAAAAGTTCGGGAGGTCGGCTTGGCGTTGCGCTGATTAACACCGCCGATAATTCGCAGATTCTCTACCGTGCCGATGAACGTTTTGCGATGTGCAGTACCAGTAAGGTGATGGCGGCCGCGGCGGTGCTTAAACAGAGCGAGAGCGATAAGCACCTGCTAAATCAGCGCGTTGAAATCAAGAAGAGCGACCTGGTTAACTACAATCCCATTGCGGAGAAACACGTTAACGGCACGATGACGCTGGCTGAGCTTGGCGCAGCGGCGCTGCAGTATAGCGACAATACTGCCATGAATAAGCTGATTGCCCATCTGGGTGGTCCCGATAAAGTGACGGCGTTTGCTCGCTCGTTGGGTGATGAGTCCTTCCGTCTGGACAGAACCGAGCCCACGCTCAATACCGCCATTCCAGGCGACCCGCGTGATACCACCACGCCGCTCGCGATGGCGCAGACCCTGAAAAATCTGACGCTGGGTAAAGCGCTGGCGGAAACTCAGCGGGCACAGTTGGTGACGTGGCTTAAGGGCAATACTACCGGTAGCGCGAGCATTCGGGCGGGTCTGCCGAAATCATGGGTAGTGGGCGATAAAACCGGCAGCGGAGATTATGGCACCACCAACGATATCGCGGTTATCTGGCCGGAAAACCACGCACCGCTGGTTCTGGTGACCTACTTTACCCAACCGGAGCAGAAGGCGGAAAGCCGTCGGGATATTCTGGCTGCGGCGGCGAAAATCGTAACCCACGGTTTCTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36924","NCBI_taxonomy_name":"Providencia sp. 4440","NCBI_taxonomy_id":"235468"}}}},"ARO_accession":"3001893","ARO_id":"38293","ARO_name":"CTX-M-31","ARO_description":"CTX-M-31 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"800":{"model_id":"800","model_name":"CTX-M-87","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1479":{"protein_sequence":{"accession":"ACB41777.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAVAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTELTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"EU545409","fmin":"80","fmax":"956","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGTCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACTTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001947","ARO_id":"38347","ARO_name":"CTX-M-87","ARO_description":"CTX-M-87 is a beta-lactamase found in Escherichia coli","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"801":{"model_id":"801","model_name":"mfpA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"4339":{"protein_sequence":{"accession":"CCP46182.1","sequence":"MQQWVDCEFTGRDFRDEDLSRLHTERAMFSECDFSGVNLAESQHRGSAFRNCTFERTTLWHSTFAQCSMLGSVFVACRLRPLTLDDVDFTLAVLGGNDLRGLNLTGCRLRETSLVDTDLRKCVLRGADLSGARTTGARLDDADLRGATVDPVLWRTASLVGARVDVDQAVAFAAAHGLCLAGG"},"dna_sequence":{"accession":"AL123456","fmin":"3773015","fmax":"3773567","strand":"-","sequence":"CTAGCCCCCTGCCAAGCACAGCCCGTGCGCCGCCGCAAAGGCCACGGCTTGGTCGACGTCGACACGCGCACCCACCAACGACGCGGTCCGCCACAATACCGGGTCCACGGTCGCGCCCCGCAAGTCGGCGTCATCCAGCCGGGCGCCCGTGGTACGGGCACCACTGAGGTCGGCGCCGCGCAGCACGCACTTGCGCAAGTCGGTATCCACCAGGCTGGTCTCTCGCAACCGGCAGCCGGTCAAGTTGAGACCACGCAGATCATTTCCGCCGAGCACGGCGAGCGTGAAATCCACGTCGTCCAACGTCAGCGGCCGCAGCCGGCAAGCCACGAAGACCGAGCCCAACATGCTGCACTGGGCAAATGTGCTGTGCCACAGTGTCGTCCGTTCGAAGGTGCAATTACGAAACGCCGACCCTCGGTGTTGTGACTCGGCCAGATTCACGCCGCTGAAATCGCATTCGCTGAACATCGCCCGTTCGGTGTGCAGGCGGCTAAGGTCCTCGTCGCGGAAGTCTCGACCGGTGAATTCGCAATCAACCCACTGCTGCAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3003035","ARO_id":"39469","ARO_name":"mfpA","ARO_description":"mfpA is a qnr homolog and a pentapeptide repeat protein that confers resistance to fluoroquinolones in Mycobacterium smegmatis","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"802":{"model_id":"802","model_name":"QnrA3","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"510":{"protein_sequence":{"accession":"AAZ04782.1","sequence":"MDIIDKVFQQEDFSRQDLSDSRFRRCRFYQCDFSHCQLRDASFEDCSFIESGAVEGCHFSYADLRDASFKACRLSLANFSGANCFGIEFRECDLKGANFSRARFYNQISHKMYFCSAYISGCNLAYANLSGQCLEKCELFENNWSNANLSGASLMGSDLSRGTFSRDCWQQVNLRGCDLTFADLDGLDPRRVNLEGVKICAWQQEQLLEPLGVIVLPD"},"dna_sequence":{"accession":"DQ058661","fmin":"0","fmax":"657","strand":"+","sequence":"ATGGATATTATTGATAAAGTTTTTCAGCAAGAGGATTTCTCACGCCAGGATTTGAGTGACAGTCGTTTTCGCCGCTGCCGCTTTTATCAGTGTGACTTCAGCCATTGCCAGCTAAGGGATGCCAGTTTCGAGGATTGCAGTTTCATTGAAAGCGGCGCCGTCGAAGGGTGCCACTTCAGCTATGCCGATCTGCGCGATGCCAGTTTCAAGGCCTGCCGCCTGTCTTTGGCCAATTTCAGCGGTGCCAACTGCTTTGGCATAGAGTTCAGGGAGTGCGATCTCAAGGGCGCCAATTTTTCCCGGGCCCGTTTTTACAATCAAATCAGCCATAAGATGTACTTCTGCTCGGCTTATATCTCAGGCTGCAACCTGGCCTATGCCAATTTGAGCGGCCAATGCCTGGAAAAGTGCGAGCTGTTTGAAAACAACTGGAGCAATGCCAACCTCAGCGGCGCTTCCTTGATGGGCTCCGACCTCAGCCGCGGCACCTTCTCCCGCGACTGCTGGCAACAGGTAAACCTGCGGGGCTGTGACCTGACCTTTGCCGATCTGGATGGGCTCGATCCCAGACGGGTCAACCTCGAAGGGGTCAAGATCTGTGCCTGGCAGCAGGAGCAACTGCTGGAACCCTTGGGAGTCATAGTGCTGCCGGATTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36891","NCBI_taxonomy_name":"Shewanella algae","NCBI_taxonomy_id":"38313"}}}},"ARO_accession":"3002709","ARO_id":"39143","ARO_name":"QnrA3","ARO_description":"QnrA3 is a plasmid-mediated quinolone resistance protein found in Shewanella algae","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"803":{"model_id":"803","model_name":"cphA4","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"1409":{"protein_sequence":{"accession":"AAP69912.1","sequence":"MMKGWMKCTLAGAVVLMASFWGGSVRAAGISLKQVSGPVYVVEDNYYVKENSVVYFGAKGVTVVGATWTPDTARELHKLIKRVSSKPVLEVINTNYHTDRVGGNAYWKSIGAKVVATRQTRDLMKSDWAEIVAFTRKGLPEYPDLPLVLPNVVHDGDFTLQEGKVRAFYAGPAHTPDGIFVYFPDEQVLYGNCILKEKLGNLSFANVKAYPQTIERLKAMKLPIKTVIGGHDSPLHGPELIDHYEELIKAAAAV"},"dna_sequence":{"accession":"AY227050","fmin":"130","fmax":"895","strand":"+","sequence":"ATGATGAAAGGTTGGATGAAGTGCACATTAGCCGGGGCCGTGGTGCTGATGGCGAGTTTCTGGGGTGGCAGCGTGCGGGCGGCGGGGATCTCCCTTAAGCAGGTGAGTGGCCCTGTGTATGTGGTTGAAGATAACTACTACGTAAAGGAAAACTCCGTGGTCTATTTCGGGGCCAAGGGGGTGACGGTGGTGGGGGCGACCTGGACGCCGGATACCGCCCGCGAGCTGCACAAGCTGATCAAACGGGTCAGCAGCAAGCCGGTGCTGGAGGTGATCAACACCAACTACCACACCGATCGGGTGGGCGGTAATGCCTACTGGAAGTCCATCGGGGCCAAGGTGGTGGCGACGCGCCAGACCCGGGATCTGATGAAGAGCGACTGGGCCGAGATTGTCGCCTTTACCCGCAAGGGGCTGCCGGAGTATCCGGATCTGCCGCTGGTGCTGCCCAACGTGGTGCACGATGGCGACTTCACCCTGCAAGAGGGCAAGGTGCGCGCTTTCTACGCGGGCCCGGCCCATACGCCGGACGGCATCTTTGTCTACTTCCCTGACGAGCAGGTGCTTTATGGCAACTGCATCCTCAAGGAGAAGCTGGGCAACCTGAGCTTTGCCAATGTGAAGGCCTATCCGCAGACCATCGAGCGGCTTAAAGCGATGAAGTTGCCGATCAAGACGGTGATTGGNGGTCACGACTCGCCGCTGCATGGCCCCGAGCTGATTGATCACTACGAGGAGCTGATCAAGGCGGCCGCCGCAGTCTAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36947","NCBI_taxonomy_name":"Aeromonas allosaccharophila","NCBI_taxonomy_id":"656"}}}},"ARO_accession":"3003100","ARO_id":"39666","ARO_name":"cphA4","ARO_description":"CphA4 is an Ambler Class B MBL; subclass B2 originally isolated from Aeromonas allosaccharophila. This enzyme has specific activity against carbapenems and is active as a mono-zinc protein.","ARO_category":{"36720":{"category_aro_accession":"3000581","category_aro_cvterm_id":"36720","category_aro_name":"CphA beta-lactamase","category_aro_description":"CphA is an Ambler Class B MBL; subclass B2 originally isolated from Aeromonas hydrophilia.  This enzyme has specific activity against carbapenems and is active as a mono-zinc protein.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"804":{"model_id":"804","model_name":"tetB(P)","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1200"}},"model_sequences":{"sequence":{"473":{"protein_sequence":{"accession":"AAA20117.1","sequence":"MKKIINIGIVAHVDAGKTTITENLLYYSGAIKSVGRVDLGNTQTDSMELERKRGITIKSSTISFNWNNVKVNIIDTPGHVDFISEVERSLNSLDGAILVISGVEGIQSQTRILFDTLKELNIPTIIFVNKLDRIGANFNKVFEEIKKNMSNKVVRLQEVYDVGSKAVYIKKLFDTCIINDDAINVLSDLDEAFLERYIGGIEPDKEEIQEKLSLYAREGSLYPVFCGAAAIGLGIEDLLDGICSYFPFASNDCESDLSGVVFKIERTSKNEKKVYVRLFGGKISVRDKIQVPNKEIAEKVKKINRLENGGVVEAQRIEAGDIGILYGLTSFQVGDVIGISNDKIKNISIAKPALKTTISAIDKEKNPELFKALTLLAEEDPLLAFAMNDIDKEIYVNLFGEVQMEILSSMLDDLYGIKVEFSNIETIYKETPKGFGASIMHMQEDLNPFWATVGLEIEPAGRGEGLRYISNVSVGSLPKSFQNAIEEAVIKTSKQGLFGWEVTDVKVTLSCGEFFSPASTPADFRNVTPMVFMEALYKAQTVLLEPLHEFELKIPQNALSKAVWDLETMRATFDNPIVIGDEFSIKGLIPVENSKEYKMKIASYTEGRGMFVTKFYGYKEASAEFSKARKKTTYDPLNKKEYLLHKLNAIRD"},"dna_sequence":{"accession":"L20800","fmin":"2308","fmax":"4267","strand":"+","sequence":"ATGAAGAAAATAATTAATATAGGAATCGTAGCACACGTGGATGCAGGAAAAACAACTATAACAGAAAACTTATTATATTATAGTGGAGCTATAAAATCAGTTGGAAGAGTTGATTTAGGCAATACACAGACGGATTCTATGGAGCTTGAGCGTAAGAGAGGAATTACCATTAAATCGTCAACCATATCTTTTAATTGGAATAATGTTAAGGTGAATATTATTGATACTCCAGGACATGTGGATTTTATTTCGGAAGTTGAACGTTCATTAAATAGCTTAGATGGAGCAATACTAGTTATATCAGGAGTAGAGGGGATTCAGTCACAAACAAGAATATTATTTGACACATTAAAGGAGTTAAATATTCCAACAATAATTTTTGTAAATAAGCTAGATAGAATTGGGGCAAATTTCAACAAAGTATTTGAAGAAATAAAGAAGAATATGTCCAATAAAGTAGTTAGATTACAAGAAGTATATGATGTAGGAAGCAAAGCTGTTTATATAAAAAAACTATTTGATACATGCATAATAAATGATGATGCTATTAATGTTTTATCAGACTTAGACGAAGCATTTTTAGAAAGATATATTGGTGGAATAGAACCTGATAAAGAAGAAATACAAGAAAAGCTTTCATTATATGCAAGAGAAGGAAGTCTATATCCAGTATTTTGTGGTGCTGCAGCAATTGGACTTGGAATTGAAGATTTATTAGATGGAATTTGTAGTTATTTTCCATTTGCAAGTAATGATTGTGAAAGTGATTTATCTGGGGTAGTATTTAAAATCGAAAGAACAAGTAAAAATGAAAAGAAGGTTTATGTAAGATTATTTGGAGGAAAAATATCTGTAAGAGATAAAATTCAAGTACCTAATAAGGAGATAGCAGAAAAAGTAAAGAAAATTAATAGGTTAGAAAATGGGGGAGTTGTTGAAGCACAGAGGATAGAAGCAGGGGATATAGGTATTTTATATGGACTTACAAGTTTCCAAGTGGGAGATGTTATTGGAATTTCAAATGATAAAATTAAAAATATATCTATAGCTAAACCAGCATTAAAAACAACAATTTCTGCAATTGATAAAGAAAAAAATCCAGAGCTATTTAAAGCATTAACATTACTTGCAGAGGAAGATCCACTACTCGCCTTCGCGATGAATGACATAGATAAAGAAATTTATGTCAACTTATTCGGTGAAGTTCAAATGGAAATACTAAGTTCCATGTTAGATGATTTATATGGAATAAAAGTAGAGTTTTCGAATATTGAGACTATCTATAAGGAAACACCTAAAGGTTTTGGAGCGTCAATAATGCATATGCAGGAAGACTTAAATCCATTTTGGGCGACAGTAGGCTTAGAAATAGAACCAGCAGGGAGAGGCGAAGGTCTTAGGTATATTTCTAATGTTTCAGTAGGGTCATTGCCAAAATCTTTTCAAAATGCAATTGAAGAAGCAGTTATTAAGACAAGTAAACAAGGATTATTTGGATGGGAGGTTACAGATGTAAAAGTCACTCTTAGCTGTGGTGAATTTTTTAGTCCAGCCAGCACTCCAGCAGATTTTAGAAATGTGACACCTATGGTATTCATGGAAGCATTATATAAAGCACAAACTGTTTTATTAGAGCCATTACATGAGTTTGAGTTAAAGATTCCTCAAAATGCTTTAAGCAAAGCGGTATGGGATTTAGAAACTATGAGGGCAACCTTTGATAATCCTATTGTTATAGGGGATGAATTCTCAATAAAGGGATTAATTCCAGTAGAAAATTCAAAAGAATATAAAATGAAAATAGCTTCATATACAGAAGGTAGAGGAATGTTTGTGACAAAATTTTATGGGTATAAGGAAGCTTCAGCTGAATTTTCAAAAGCACGCAAAAAAACAACGTATGATCCATTGAATAAAAAAGAGTATTTGCTTCATAAACTAAACGCAATTAGAGATTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36812","NCBI_taxonomy_name":"Clostridium perfringens","NCBI_taxonomy_id":"1502"}}}},"ARO_accession":"3000195","ARO_id":"36334","ARO_name":"tetB(P)","ARO_description":"TetB(P) is a tetracycline ribosomal protection protein found on the same operon as tetA(P), a tetracycline efflux protein.","ARO_category":{"35921":{"category_aro_accession":"0000002","category_aro_cvterm_id":"35921","category_aro_name":"tetracycline-resistant ribosomal protection protein","category_aro_description":"A family of proteins known to bind to the 30S ribosomal subunit. This interaction prevents tetracycline and tetracycline derivatives from inhibiting ribosomal function. Thus, these proteins confer elevated resistance to tetracycline derivatives as a ribosomal protection protein.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"806":{"model_id":"806","model_name":"SHV-150","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1064":{"protein_sequence":{"accession":"AFQ23956.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVVLLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"JX121117","fmin":"0","fmax":"858","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGTCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001189","ARO_id":"37569","ARO_name":"SHV-150","ARO_description":"SHV-150 is a beta-lactamase.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"807":{"model_id":"807","model_name":"OKP-B-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1997":{"protein_sequence":{"accession":"CAG25813.2","sequence":"MRYVRLCLISLIAALPLAVFASPQPLEQIKISEGQLAGRVGYVEMDLASGRMLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKSVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMATTLRKLLTTPSLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPDGKAERIVVIYLRDTAATMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AJ635402","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCAGCCGCTTGAGCAGATTAAAATCAGCGAAGGTCAGCTGGCGGGCCGGGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCATGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGCGACGAACAGCTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCCGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGAGCGTCGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTCAATGAGGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCGGCCAGCATGGCCACCACCCTGCGCAAGTTGCTAACCACCCCCTCTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGACCGGGTGGCCGGCCCGTTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGTGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAAGCGGAGCGTATCGTGGTGATCTATCTGCGGGATACCGCGGCGACCATGGCCGAACGTAACCAGCAGATCGCCGGGATAGGCGCGGCGCTGATCGAGCACTGGCAGCGCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002434","ARO_id":"38834","ARO_name":"OKP-B-1","ARO_description":"OKP-B-1 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"808":{"model_id":"808","model_name":"TEM-171","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1244":{"protein_sequence":{"accession":"ADA79630.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"GQ149347","fmin":"5269","fmax":"6130","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTATTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001037","ARO_id":"37417","ARO_name":"TEM-171","ARO_description":"TEM-171 is a beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"809":{"model_id":"809","model_name":"lnuB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"726":{"protein_sequence":{"accession":"AGI42804.1","sequence":"MLKQKELIANVKNLTESDERITACMMYGSFTKGEGDQYSDIEFYIFLKDSITSNFDSSNWLFDVAPYLMLYKNEYGTEVVIFDNLIRGEFHFLSEKDMNIIPSFKDSGYIPDTKAMLIYDETGQLENYLSEISGARPNRLTEENANFLLCNFSNLWLMGINVLKRGEYARSLELLSQLQKNTLQLIRMAEKNADNWLNMSKNLEKEISLENYKKFAKTTARLDKVELFEAYKNSLLLVMDLQSHLIEQYNLKVTHDILERLLNYISE"},"dna_sequence":{"accession":"KC688833","fmin":"0","fmax":"804","strand":"+","sequence":"ATGTTAAAACAAAAAGAATTAATTGCAAACGTTAAGAATCTTACTGAGTCAGATGAACGAATTACAGCTTGTATGATGTATGGATCGTTTACCAAAGGAGAAGGTGACCAATACTCTGATATAGAGTTCTATATATTTTTGAAAGATAGTATAACCTCGAACTTTGATTCATCCAACTGGTTGTTTGACGTAGCTCCGTACTTGATGCTTTATAAAAATGAGTACGGAACAGAGGTAGTTATTTTTGATAATCTTATACGTGGGGAATTTCATTTCCTTTCTGAAAAAGATATGAACATAATCCCCTCGTTTAAAGATTCAGGTTATATTCCTGATACGAAGGCTATGCTTATTTACGATGAAACAGGGCAATTAGAAAATTATTTATCAGAGATAAGTGGTGCAAGACCAAATAGACTTACTGAAGAAAATGCTAATTTTTTGTTGTGTAATTTCTCTAATCTATGGTTGATGGGAATCAACGTTCTAAAAAGAGGAGAATATGCTCGTTCATTAGAACTCTTATCACAACTTCAAAAAAATACACTACAACTTATACGTATGGCAGAAAAAAATGCTGATAATTGGCTAAACATGAGTAAAAACCTTGAAAAAGAAATTAGCCTTGAAAATTATAAAAAATTTGCAAAGACCACTGCTCGATTAGATAAGGTAGAATTATTTGAAGCCTATAAAAATTCTTTGCTATTAGTTATGGATTTGCAAAGTCACCTTATTGAACAATACAACTTAAAAGTTACACATGACATTTTAGAAAGATTGTTGAATTACATTAGTGAATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39575","NCBI_taxonomy_name":"Streptococcus lutetiensis","NCBI_taxonomy_id":"150055"}}}},"ARO_accession":"3002836","ARO_id":"39270","ARO_name":"lnuB","ARO_description":"lnuB is a plasmid-mediated nucleotidyltransferase found in Streptococcus lutetiensis","ARO_category":{"36360":{"category_aro_accession":"3000221","category_aro_cvterm_id":"36360","category_aro_name":"lincosamide nucleotidyltransferase (LNU)","category_aro_description":"Resistance to the lincosamide antibiotic by ATP-dependent modification of the 3' and\/or 4'-hydroxyl groups of the methylthiolincosamide sugar.","category_aro_class_name":"AMR Gene Family"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"810":{"model_id":"810","model_name":"mecC","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1250"}},"model_sequences":{"sequence":{"3735":{"protein_sequence":{"accession":"WP_000725529.1","sequence":"MKKIYISVLVLLLIMIIITWLFKDDDIEKTISSIEKGNYNEVYKNSSEKSKLAYGEEEIVDRNKKIYKDLSVNNLKITNHEIKKTGKDKKQVDVKYNIYTKYGTIRRNTQLNFIYEDKHWKLDWRPDVIVPGLKNGQKINIETLKSERGKIKDRNGIELAKTGNTYEIGIVPNKTPKEKYDDIARDLQIDTKAITNKVNQKWVQPDSFVPIKKINKQDEYIDKLIKSYNLQINTIKSRVYPLNEATVHLLGYVGPINSDELKSKQFRNYSKNTVIGKKGLERLYDKQLQNTDGFKVSIANTYDNKPLDTLLEKKAENGKDLHLTIDARVQESIYKHMKNDDGSGTALQPKTGEILALVSTPSYDVYPFMNGLSNNDYRKLTNNKKEPLLNKFQITTSPGSTQKILTSIIALKENKLDKNTNFDIYGKGWQKDASWGNYNITRFKVVDGNIDLKQAIESSDNIFFARIALALGAKKFEQGMQDLGIGENIPSDYPFYKAQISNSNLKNEILLADSGYGQGEILVNPIQILSIYSALENNGNIQNPHVLRKTKSQIWKKDIIPKKDIDILTNGMERVVNKTHRDDIYKNYARIIGKSGTAELKMNQGETGRQIGWFVSYNKNNPNMLMAINVKDVQNKGMASYNATISGKVYDDLYDNGKTQFDIDQ"},"dna_sequence":{"accession":"NC_017349.1","fmin":"35680","fmax":"37678","strand":"-","sequence":"TTACTGATCTATATCAAATTGAGTTTTTCCATTATCATACAAATCATCATAAACTTTTCCAGATATAGTAGCATTATAGCTGGCCATCCCTTTATTTTGAACGTCTTTAACATTAATCGCCATTAACATATTAGGATTATTTTTATTATATGAAACAAACCAACCTATTTGTCTTCCAGTTTCCCCTTGATTCATTTTTAATTCTGCTGTGCCAGATTTACCAATAATTCGGGCATAATTTTTGTATATATCATCCCTATGTGTTTTATTAACTACACGTTCCATACCATTAGTTAATATATCTATGTCTTTTTTAGGTATAATATCTTTTTTCCATATTTGAGATTTTGTTTTACGTAAAACATGAGGATTTTGTATATTTCCGTTATTTTCTAAAGCACTGTATATTGATAAAATTTGTATAGGGTTTACTAGTATCTCGCCTTGGCCATATCCTGAATCTGCTAATAATATTTCATTTTTTAAATTACTATTTGAGATTTGTGCTTTATAAAAGGGATAATCACTCGGGATATTTTCACCGATTCCCAAATCTTGCATACCTTGCTCAAATTTTTTGGCTCCTAATGCTAATGCAATGCGGGCAAAAAATATGTTGTCTGATGATTCTATTGCTTGCTTTAAATCGATATTGCCGTCTACTACTTTAAATCTTGTGATATTATAATTCCCCCATGATGCATCTTTTTGCCAACCCTTACCATAAATATCAAAATTAGTATTTTTGTCTAGTTTATTTTCTTTTAAGGCTATAATAGATGTTAATATTTTTTGGGTTGAACCTGGTGATGTAGTGATTTGAAATTTGTTGAGCAAAGGCTCTTTTTTATTGTTAGTTAATTTACGGTAGTCATTATTGCTTAATCCATTCATGAATGGATAAACATCGTACGATGGGGTACTTACCAAAGCTAAAATTTCTCCAGTTTTTGGTTGTAATGCTGTACCAGATCCATCGTCATTTTTCATATGTTTATAAATACTTTCTTGTACTCTAGCATCTATAGTTAAATGAAGATCTTTTCCGTTTTCAGCCTTTTTCTCCAATAATGTGTCTAAAGGTTTATTGTCATAAGTATTTGCAATGGATACCTTAAAACCATCAGTGTTTTGCAATTGTTTATCATAGAGGCGTTCTAAGCCTTTTTTTCCAATAACAGTATTTTTGCTATAGTTTCTAAATTGCTTACTTTTTAACTCGTCAGAATTAATTGGACCCACATAACCTAAAAGGTGTACTGTTGCTTCGTTCAATGGATAAACACGGCTTTTTATAGTGTTTATTTGTAAATTGTATGATTTAATTAATTTGTCTATATATTCATCTTGTTTATTTATCTTTTTAATTGGTACAAATGAATCTGGCTGAACCCATTTTTGATTAACTTTATTGGTTATAGCTTTTGTATCAATTTGTAAGTCACGAGCAATATCATCATATTTTTCTTTGGGTGTTTTGTTAGGGACAATACCGATTTCATATGTATTTCCAGTTTTAGCTAATTCTATACCATTTCTATCTTTTATTTTGCCTCGCTCTGATTTTAATGTTTCTATATTAATTTTCTGTCCATTTTTCAAACCAGGTACTATTACGTCTGGTCTCCAATCTAATTTCCAATGCTTATCTTCATAAATAAAGTTTAATTGTGTATTACGTCGTATAGTTCCATATTTTGTATATATGTTATATTTAACATCAACTTGCTTTTTATCTTTTCCAGTTTTTTTAATTTCATGATTAGTAATTTTTAAGTTATTGACACTTAAATCTTTGTAAATTTTTTTATTCCTATCTACAATTTCTTCTTCTCCATATGCCAGTTTAGATTTTTCTGAACTATTTTTATATACTTCGTTATAGTTTCCTTTTTCAATAGAACTAATTGTTTTCTCAATATCGTCATCTTTGAATAACCAAGTTATTATAATCATAATTAGTAAAAGAACTAGCACACTAATATAAATTTTTTTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37074","NCBI_taxonomy_name":"Staphylococcus","NCBI_taxonomy_id":"1279"}}}},"ARO_accession":"3001209","ARO_id":"37590","ARO_name":"mecC","ARO_description":"A foreign PBP2a acquired by lateral gene transfer that able to perform peptidoglycan synthesis in the presence of beta-lactams.","ARO_category":{"37589":{"category_aro_accession":"3001208","category_aro_cvterm_id":"37589","category_aro_name":"methicillin resistant PBP2","category_aro_description":"In methicillin sensitive S. aureus (MSSA), beta-lactams bind to native penicillin-binding proteins (PBPs) and disrupt synthesis of the cell membrane's peptidoglycan layer. In methicillin resistant S. aureus (MRSA), foreign PBP2a acquired by lateral gene transfer is able to perform peptidoglycan synthesis in the presence of beta-lactams.","category_aro_class_name":"AMR Gene Family"},"35927":{"category_aro_accession":"0000008","category_aro_cvterm_id":"35927","category_aro_name":"cefoxitin","category_aro_description":"Cefoxitin is a cephamycin antibiotic often grouped with the second generation cephalosporins. Cefoxitin is bactericidal and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. Cefoxitin's 7-alpha-methoxy group and 3' leaving group make it a poor substrate for most beta-lactamases.","category_aro_class_name":"Antibiotic"},"35930":{"category_aro_accession":"0000011","category_aro_cvterm_id":"35930","category_aro_name":"cloxacillin","category_aro_description":"Cloxacillin is a semisynthetic, isoxazolyl penicillin derivative in the beta-lactam class of antibiotics. It interferes with peptidogylcan synthesis and is commonly used for treating penicillin-resistant Staphylococcus aureus infections.","category_aro_class_name":"Antibiotic"},"35934":{"category_aro_accession":"0000015","category_aro_cvterm_id":"35934","category_aro_name":"methicillin","category_aro_description":"Derived from penicillin to combat penicillin-resistance, methicillin is insensitive to beta-lactamases (also known as penicillinases) secreted by many penicillin-resistant bacteria. Methicillin is bactericidal, and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Antibiotic"},"35961":{"category_aro_accession":"0000043","category_aro_cvterm_id":"35961","category_aro_name":"carbenicillin","category_aro_description":"Carbenicillin is a semi-synthetic antibiotic belonging to the carboxypenicillin subgroup of the penicillins. It has gram-negative coverage which includes Pseudomonas aeruginosa but limited gram-positive coverage. The carboxypenicillins are susceptible to degradation by beta-lactamase enzymes. Carbenicillin antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Antibiotic"},"35971":{"category_aro_accession":"0000054","category_aro_cvterm_id":"35971","category_aro_name":"penicillin","category_aro_description":"Penicillin (sometimes abbreviated PCN) is a beta-lactam antibiotic used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms. It works by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Antibiotic"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35975":{"category_aro_accession":"0000058","category_aro_cvterm_id":"35975","category_aro_name":"cefazolin","category_aro_description":"Cefazolin (INN), also known as cefazoline or cephazolin, is a first generation cephalosporin antibiotic. It is administered parenterally, and is active against a broad spectrum of bacteria.","category_aro_class_name":"Antibiotic"},"35976":{"category_aro_accession":"0000059","category_aro_cvterm_id":"35976","category_aro_name":"cefepime","category_aro_description":"Cefepime (INN) is a fourth-generation cephalosporin antibiotic developed in 1994. It contains an aminothiazolyl group that decreases its affinity with beta-lactamases. Cefepime shows high binding affinity with penicillin-binding proteins and has an extended spectrum of activity against Gram-positive and Gram-negative bacteria, with greater activity against both Gram-negative and Gram-positive organisms than third-generation agents.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35978":{"category_aro_accession":"0000061","category_aro_cvterm_id":"35978","category_aro_name":"ceftobiprole","category_aro_description":"Ceftobiprole (Zeftera\/Zevtera) is a next generation (5th generation) cephalosporin antibiotic with activity against methicillin-resistant Staphylococcus aureus, penicillin-resistant Streptococcus pneumoniae, Pseudomonas aeruginosa, and Enterococci. Ceftobiprole inhibits transpeptidases essential to building cell walls, and is a poor substrate for most beta-lactamases.","category_aro_class_name":"Antibiotic"},"35979":{"category_aro_accession":"0000062","category_aro_cvterm_id":"35979","category_aro_name":"ceftriaxone","category_aro_description":"Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"35980":{"category_aro_accession":"0000063","category_aro_cvterm_id":"35980","category_aro_name":"cefuroxime","category_aro_description":"Cefuroxime is a second-generation cephalosporin antibiotic with increased stability with beta-lactamases than first-generation cephalosporins. Cefuroxime is active against Gram-positive organisms but less active against methicillin-resistant strains.","category_aro_class_name":"Antibiotic"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"35987":{"category_aro_accession":"0000070","category_aro_cvterm_id":"35987","category_aro_name":"ertapenem","category_aro_description":"Ertapenem is a carbapenem antibiotic and is highly resistant to beta-lactamases like other carbapenems. It inhibits bacterial cell wall synthesis.","category_aro_class_name":"Antibiotic"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"35995":{"category_aro_accession":"0000078","category_aro_cvterm_id":"35995","category_aro_name":"piperacillin","category_aro_description":"Piperacillin is an acetylureidopenicillin and has an extended spectrum of targets relative to other beta-lactam antibiotics. It inhibits cell wall synthesis in bacteria, and is usually taken with the beta-lactamase inhibitor tazobactam to overcome penicillin-resistant bacteria.","category_aro_class_name":"Antibiotic"},"36309":{"category_aro_accession":"3000170","category_aro_cvterm_id":"36309","category_aro_name":"imipenem","category_aro_description":"Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.","category_aro_class_name":"Antibiotic"},"36689":{"category_aro_accession":"3000550","category_aro_cvterm_id":"36689","category_aro_name":"aztreonam","category_aro_description":"Aztreonam was the first monobactam discovered, and is greatly effective against Gram-negative bacteria while inactive against Gram-positive bacteria. Artreonam is a poor substrate for beta-lactamases, and may even act as an inhibitor. In Gram-negative bacteria, Aztreonam interferes with filamentation, inhibiting cell division and leading to cell death.","category_aro_class_name":"Antibiotic"},"36976":{"category_aro_accession":"3000632","category_aro_cvterm_id":"36976","category_aro_name":"benzylpenicillin","category_aro_description":"Benzylpenicillin, commonly referred to as penicillin G, is effective against both Gram-positive and Gram-negative bacteria. It is unstable in acid.","category_aro_class_name":"Antibiotic"},"36977":{"category_aro_accession":"3000633","category_aro_cvterm_id":"36977","category_aro_name":"phenoxymethylpenicillin","category_aro_description":"Phenoxymethylpenicillin, or penicillin V, is a penicillin derivative that is acid stable but less active than benzylpenicillin (penicillin G).","category_aro_class_name":"Antibiotic"},"36978":{"category_aro_accession":"3000634","category_aro_cvterm_id":"36978","category_aro_name":"propicillin","category_aro_description":"Propicillin is an orally taken penicillin derivative that has high absorption but poor activity.","category_aro_class_name":"Antibiotic"},"36979":{"category_aro_accession":"3000635","category_aro_cvterm_id":"36979","category_aro_name":"dicloxacillin","category_aro_description":"Dicloxacillin is a penicillin derivative that has an extra chlorine atom in comparison to cloxacillin. While more active than cloxacillin, its high affinity for serum protein reduces its activity in human serum in vitro.","category_aro_class_name":"Antibiotic"},"36980":{"category_aro_accession":"3000636","category_aro_cvterm_id":"36980","category_aro_name":"flucloxacillin","category_aro_description":"Flucloxacillin is similar to cloxacillin, with an extra additional fluorine atom.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"36982":{"category_aro_accession":"3000638","category_aro_cvterm_id":"36982","category_aro_name":"azlocillin","category_aro_description":"Azlocillin is a semisynthetic derivative of penicillin that is notably active against Ps. aeruginosa and other Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36983":{"category_aro_accession":"3000639","category_aro_cvterm_id":"36983","category_aro_name":"mezlocillin","category_aro_description":"Mezlocillin is a penicillin derivative taken parenterally.","category_aro_class_name":"Antibiotic"},"36984":{"category_aro_accession":"3000640","category_aro_cvterm_id":"36984","category_aro_name":"doripenem","category_aro_description":"Doripenem is a carbapenem with a broad range of activity against Gram-positive and Gram-negative bacteria, and along with meropenem, it is the most active beta-lactam antibiotic against Pseudomonas aeruginosa. It inhibits bacterial cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36985":{"category_aro_accession":"3000641","category_aro_cvterm_id":"36985","category_aro_name":"cefalexin","category_aro_description":"Cefalexin is a cephalosporin antibiotic that causes filamentation. It is resistant to staphylococcal beta-lactamase, but degraded by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"36986":{"category_aro_accession":"3000642","category_aro_cvterm_id":"36986","category_aro_name":"cefadroxil","category_aro_description":"Cefadroxil, or p-hydroxycephalexin, is an cephalosporin antibiotic similar to cefalexin.","category_aro_class_name":"Antibiotic"},"36987":{"category_aro_accession":"3000643","category_aro_cvterm_id":"36987","category_aro_name":"cefotiam","category_aro_description":"Cefotiam is a cephalosporin antibiotic with similar activity to cefuroxime but more active against enterobacteria. It is consumed orally as the prodrug cefotiam hexetil.","category_aro_class_name":"Antibiotic"},"36988":{"category_aro_accession":"3000644","category_aro_cvterm_id":"36988","category_aro_name":"cefaclor","category_aro_description":"Cefaclor is a semisynthetic cephalosporin derived from cephalexin. It has broad-spectrum antibiotic activity.","category_aro_class_name":"Antibiotic"},"36989":{"category_aro_accession":"3000645","category_aro_cvterm_id":"36989","category_aro_name":"cefotaxime","category_aro_description":"Cefotaxime is a semisynthetic cephalosporin taken parenterally. It is resistant to most beta-lactamases and active against Gram-negative rods and cocci due to its aminothiazoyl and methoximino functional groups.","category_aro_class_name":"Antibiotic"},"36990":{"category_aro_accession":"3000646","category_aro_cvterm_id":"36990","category_aro_name":"cefixime","category_aro_description":"Cefixime is a cephalosporin resistant to most beta-lactamases. It is active against many enterobacteria, but activity against staphylococci is poor.","category_aro_class_name":"Antibiotic"},"36991":{"category_aro_accession":"3000647","category_aro_cvterm_id":"36991","category_aro_name":"cefpodoxime","category_aro_description":"Cefpodoxime is a semisynthetic cephalosporin that acts similarly to cefotaxime with broad-spectrum activity. It is stable to many plasmid-mediated beta-lactamses. Cefpodoxime is consumed as the prodrug cefpodoxime proxetil.","category_aro_class_name":"Antibiotic"},"36992":{"category_aro_accession":"3000648","category_aro_cvterm_id":"36992","category_aro_name":"ceftibuten","category_aro_description":"Ceftibuten is a semisynthetic cephalosporin active against Gram-negative bacilli. It is resistant against many plasmid-mediated beta-lactamases.","category_aro_class_name":"Antibiotic"},"36993":{"category_aro_accession":"3000649","category_aro_cvterm_id":"36993","category_aro_name":"cefditoren","category_aro_description":"Cefditoren is a semisynthetic cephalosporin active against staphylococci, streptococci, and and most enterobacteria. It is resistant to staphylococcal and most enterobacterial beta-lactamases, and is usually taken as the prodrug cefditoren pivoxil.","category_aro_class_name":"Antibiotic"},"36994":{"category_aro_accession":"3000650","category_aro_cvterm_id":"36994","category_aro_name":"cefdinir","category_aro_description":"Cefdinir is similar to cefixime with a modified side-chain at its 7-amino position. It also shares similar activity with cefixime but is more active against staphylococci. It has also be shown to enhance phagocytosis.","category_aro_class_name":"Antibiotic"},"36995":{"category_aro_accession":"3000651","category_aro_cvterm_id":"36995","category_aro_name":"ceftaroline","category_aro_description":"Ceftaroline is a novel cephalosporin active against methicillin resistant Staphylococcus aureus. Like other cephalosporins it binds penicillin-binding proteins to inhibit cell wall synthesis. It strongly binds with PBP2a, associated with methicillin resistance. It is taken orally as the prodrug ceftaroline fosamil.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"37085":{"category_aro_accession":"3000705","category_aro_cvterm_id":"37085","category_aro_name":"isopenicillin N","category_aro_description":"Isopenicillin N is a natural penicillin derivative produced by Penicillium chrysogenum with activity similar to penicillin N.","category_aro_class_name":"Antibiotic"},"37086":{"category_aro_accession":"3000706","category_aro_cvterm_id":"37086","category_aro_name":"penicillin N","category_aro_description":"Penicillin N is a penicillin derivative produced by Cephalosporium acremonium.","category_aro_class_name":"Antibiotic"},"37141":{"category_aro_accession":"3000761","category_aro_cvterm_id":"37141","category_aro_name":"mecillinam","category_aro_description":"Mecillinam is a broad-spectrum beta-lactam antibiotic that was semi-synthetically derived to have a different drug centre, being a 6-alpha-amidinopenicillanate instead of a 6-alpha-acylaminopenicillanate. Contrasting most beta-lactam drugs, mecillinam is most active against Gram-negative bacteria. It binds specifically to penicillin binding protein 2 (PBP2).","category_aro_class_name":"Antibiotic"},"40928":{"category_aro_accession":"3004001","category_aro_cvterm_id":"40928","category_aro_name":"cefmetazole","category_aro_description":"Cefmetazole is a semi-synthetic cephamycin antibiotic with broad spectrum antibiotic activity against both gram-positive and gram-negative bacteria, that disrupt cell wall synthesis through binding to PBPs causing cell lysis.","category_aro_class_name":"Antibiotic"},"40929":{"category_aro_accession":"3004002","category_aro_cvterm_id":"40929","category_aro_name":"cefonicid","category_aro_description":"Cefonicid is a second-generation cephalosporin-class beta-lactam antibiotic with broad spectrum activity. Particularly used against urinary tract infections and lower respiratory infections. Causes cell lysis by inactivation of PBPs through binding, inhibiting peptidoglycan synthesis.","category_aro_class_name":"Antibiotic"},"40932":{"category_aro_accession":"3004005","category_aro_cvterm_id":"40932","category_aro_name":"cefprozil","category_aro_description":"Cefprozil is a cephalosporin and beta-lactam antibiotic with bactericidal activity. It selectively binds to PBPs and inhibits peptidoglycan synthesis, a major cell wall component, resulting in cell lysis.","category_aro_class_name":"Antibiotic"},"40933":{"category_aro_accession":"3004006","category_aro_cvterm_id":"40933","category_aro_name":"ceftiofur","category_aro_description":"Ceftiofur is a third-generation broad spectrum cephalosporin and beta-lactam antibiotic. It causes cell lysis by disrupting peptidoglycan cross-linkage and cell wall formation by binding to PBPs.","category_aro_class_name":"Antibiotic"},"40934":{"category_aro_accession":"3004007","category_aro_cvterm_id":"40934","category_aro_name":"ceftizoxime","category_aro_description":"Ceftizoxime is a third-generation cephalosporin and broad spectrum beta-lactam antibiotic. Ceftizoxime causes bacterial cell lysis through peptidoglycan cross-linking inhibition by binding to PBPs.","category_aro_class_name":"Antibiotic"},"40935":{"category_aro_accession":"3004008","category_aro_cvterm_id":"40935","category_aro_name":"cephapirin","category_aro_description":"Cephapirin is a first-generation cephalosporin and broad spectrum beta-lactam antibiotic. Inactivation of penicillin-binding proteins through cephapirin binding disrupts peptidoglycan cross-linking, resulting in cell lysis.","category_aro_class_name":"Antibiotic"},"40936":{"category_aro_accession":"3004009","category_aro_cvterm_id":"40936","category_aro_name":"cefradine","category_aro_description":"Cefradine is a first-generation cephalosporin and broad spectrum beta-lactam antibiotic. Cefradine binding to penicillin-binding proteins disrupts cell wall peptidoglycan cross-linkage, resulting in cell lysis.","category_aro_class_name":"Antibiotic"},"40943":{"category_aro_accession":"3004016","category_aro_cvterm_id":"40943","category_aro_name":"loracarbef","category_aro_description":"Loracarbef is a second-generation cephalosporin (carbacephem) and broad spectrum beta-lactam antibiotic. Loracarbef inhibits PBPs through binding, disrupting peptidoglycan cell wall cross-linkage and resulting in cell death.","category_aro_class_name":"Antibiotic"},"40944":{"category_aro_accession":"3004017","category_aro_cvterm_id":"40944","category_aro_name":"moxalactam","category_aro_description":"Moxalactam (Latamoxef) is a broad spectrum cephalosporin (oxacephem) and beta-lactam antibiotic. Moxalactam binding to PBPs inhibits peptidoglycan cross-linkage in the cell wall, resulting in cell death. Moxalactam is proposed to be effective against meningitides as it passes the blood-brain barrier.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"632":{"model_id":"632","model_name":"basR","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"4374":"L157Q","4375":"L71R"},"clinical":{"4374":"L157Q","4375":"L71R"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"375"}},"model_sequences":{"sequence":{"3673":{"protein_sequence":{"accession":"NP_253464.1","sequence":"MRILLAEDDLLLGDGIRAGLRLEGDTVEWVTDGVAAENALVTDEFDLLVLDIGLPRRSGLDILRNLRHQGLLTPVLLLTARDKVADRVAGLDSGADDYLTKPFDLDELQARVRALTRRTTGRALPQLVHGELRLDPATHQVTLSGQAVELAPREYALLRLLLENSGKVLSRNQLEQSLYGWSGDVESNAIEVHVHHLRRKLGNQLIRTVRGIGYGIDQPAP"},"dna_sequence":{"accession":"NC_002516.2","fmin":"5364070","fmax":"5364736","strand":"+","sequence":"ATGAGAATACTGCTGGCCGAGGACGACCTGCTGCTCGGCGACGGCATCCGCGCCGGGCTGCGCCTGGAAGGCGATACCGTGGAATGGGTGACCGACGGCGTGGCCGCGGAGAACGCGCTGGTCACCGACGAGTTCGACCTGCTGGTGCTCGACATCGGACTGCCGCGCCGCAGCGGCCTGGACATCCTGCGCAACCTGCGTCACCAGGGCCTGCTCACCCCGGTGCTGCTGCTCACCGCGCGGGACAAGGTGGCCGACCGGGTCGCCGGGCTCGACAGCGGTGCCGACGACTACCTGACCAAGCCCTTCGATCTCGACGAACTGCAGGCACGGGTGCGCGCCCTGACCCGCCGCACCACCGGTCGCGCCCTGCCGCAACTGGTGCACGGCGAGCTGCGCCTGGACCCGGCGACCCACCAGGTGACCCTGTCCGGGCAGGCGGTGGAACTGGCGCCGCGCGAATACGCACTGCTGCGCCTGCTGCTGGAGAACAGCGGCAAGGTGCTCTCGCGCAACCAACTGGAGCAGAGCCTCTACGGCTGGAGCGGCGACGTCGAGAGCAACGCCATCGAAGTCCACGTCCACCACCTGCGGCGCAAGCTCGGCAACCAGTTGATCCGCACCGTCCGCGGCATCGGCTACGGCATCGACCAGCCGGCGCCCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3003582","ARO_id":"40192","ARO_name":"basR","ARO_description":"Response regulator for Lipid A modification genes; two-component system involved in polymyxin resistance that senses high extracellular Fe(2+)","ARO_category":{"41433":{"category_aro_accession":"3004269","category_aro_cvterm_id":"41433","category_aro_name":"pmr phosphoethanolamine transferase","category_aro_description":"This family of phosphoethanolamine transferase catalyze the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine to lipid A, which impedes the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"805":{"model_id":"805","model_name":"MexC","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"52":{"protein_sequence":{"accession":"AAB41956.1","sequence":"MADLRAIGRIGALAMAIALAGCGPAEERQEAAEMVLPVEVLTVQAEPLALSSELPGRIEPVRVAEVRARVAGIVVRKRFEEGADVKAGDLLFQIDPAPLKAAVSRAEGELARNRAVLFEAQARVRRYEPLVKIQAVSQQDFDTATADLRSAEAATRSAQADLETARLNLGYASVTAPISGRIGRALVTEGALVGQGEATLMARIQQLDPIYADFTQTAAEALRLRDALKKGTLAAGDSQALTLRVEGTPYERQGALQFADVAVDRGTGQIALRGKFANPDGVLLPGMYVRVRTPQGIDNQAILVPQRAVHRSSDGSAQVMVVGADERAESRSVGTGVMQGSRWQITEGLEPGDRVIVGGLAAVQPGVKIVPKPDGAQAQAQSPAPQQ"},"dna_sequence":{"accession":"U57969","fmin":"294","fmax":"1458","strand":"+","sequence":"ATGGCTGATTTGCGTGCAATAGGAAGGATCGGGGCGTTGGCTATGGCCATCGCGTTGGCGGGTTGTGGGCCGGCGGAAGAGCGACAGGAGGCCGCCGAAATGGTGTTGCCGGTGGAGGTCCTGACGGTGCAGGCCGAGCCCCTGGCGCTGAGTTCGGAACTGCCTGGGCGGATCGAACCGGTGCGGGTCGCCGAGGTGCGCGCGCGGGTGGCCGGCATCGTCGTGCGGAAGCGCTTCGAGGAGGGCGCCGACGTCAAGGCTGGCGACCTGCTGTTCCAGATCGATCCGGCACCGCTGAAGGCTGCGGTGTCGCGCGCCGAGGGTGAGCTGGCGCGGAACCGCGCGGTGCTGTTCGAGGCGCAGGCGCGGGTGCGTCGCTACGAGCCGCTGGTGAAGATCCAGGCGGTCAGCCAGCAGGACTTCGATACCGCCACCGCCGACCTGCGCAGCGCCGAGGCGGCGACCCGCTCGGCCCAGGCCGACCTGGAGACCGCGCGCCTGAACCTCGGCTACGCCTCGGTCACTGCGCCGATCTCCGGGCGCATCGGCCGCGCGCTGGTGACCGAGGGCGCGCTGGTCGGGCAGGGCGAGGCGACGCTGATGGCGCGCATCCAGCAGCTCGATCCGATCTATGCGGATTTCACCCAGACCGCGGCCGAGGCCCTGCGCCTGCGCGACGCCCTGAAGAAAGGCACCTTGGCCGCCGGCGACAGCCAGGCGCTGACCCTGCGCGTCGAAGGGACGCCCTACGAGCGCCAGGGCGCGTTGCAGTTCGCCGACGTGGCGGTGGATCGCGGCACCGGCCAGATCGCCCTGCGCGGCAAGTTCGCCAACCCCGACGGGGTCCTGCTGCCGGGCATGTACGTGCGCGTACGTACGCCCCAGGGCATCGACAACCAGGCGATCCTGGTGCCGCAACGGGCCGTGCACCGCTCCAGCGACGGCAGCGCCCAGGTGATGGTGGTGGGCGCCGACGAGCGCGCCGAGTCGCGCAGCGTCGGTACCGGCGTCATGCAGGGTTCGCGCTGGCAGATCACCGAGGGCCTGGAGCCGGGTGACCGGGTCATAGTCGGCGGCCTGGCTGCGGTGCAGCCGGGGGTGAAGATCGTGCCGAAGCCGGATGGTGCCCAGGCGCAAGCCCAGTCACCTGCGCCGCAACAGTAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3000800","ARO_id":"37180","ARO_name":"MexC","ARO_description":"MexC is the membrane fusion protein of the MexCD-OprJ multidrug efflux complex.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"704":{"model_id":"704","model_name":"OprJ","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"850"}},"model_sequences":{"sequence":{"385":{"protein_sequence":{"accession":"AAB41958.1","sequence":"MRKPAFGVSALLIALTLGACSMAPTYERPAAPVADSWSGAAAQRQGAAIDTLDWKSFIVDAELRRLVDMALDNIRSLRQTLLDIEAARAQYRIQRADRVPGLNAAATGNRQRQPADLSAGNRSEVASSYQVGLALPEYELDLFGRVKSLTDAALQQYLASEEAARAARIALVAEVSQAYLSYDGALRRLALTRQTLVSREYSFALIDQRRAAGAATALDYQEALGLVEQARAEQERNLRQKQQAFNALVLLLGSDDAAQAIPRSPGQRPKLLQDIAPGTPSELIERRPDILAAEHRLRARNADIGAARAAFFPRISLTGSFGTSSAEMSGLFDGGSRSCSFLPTLTLPIFDGGRNRANLSLAEARKDSAVAAYEGTIQTAFREVADALAASDTLRREEKALRALANSSNEALKLAKARYESGVDNHLRYLDAQRSSFLNEIAFIDGSTQRQIALVDLFRALGGGWDEGRSLVVHRGGRS"},"dna_sequence":{"accession":"U57969","fmin":"4622","fmax":"6062","strand":"+","sequence":"ATGCGCAAACCTGCTTTCGGCGTATCGGCGCTGCTGATCGCCCTGACCCTCGGCGCCTGCTCCATGGCGCCGACCTACGAACGTCCCGCCGCGCCGGTGGCCGACAGCTGGAGCGGCGCCGCCGCCCAGCGCCAGGGCGCGGCGATCGACACGCTGGATTGGAAGAGTTTCATCGTCGATGCCGAACTACGCCGCCTGGTGGACATGGCCCTGGATAACATCCGCTCGCTGCGCCAGACCCTCCTGGATATCGAGGCGGCCCGCGCGCAGTACCGAATCCAGCGCGCCGACCGGGTTCCGGGCCTGAATGCCGCTGCCACCGGCAACCGCCAGCGGCAGCCGGCCGACCTGTCCGCCGGCAATCGCTCGGAAGTGGCCAGCAGCTACCAGGTCGGGCTGGCCCTGCCGGAGTACGAACTGGACCTCTTCGGTCGGGTCAAGAGCCTGACCGACGCAGCCCTGCAACAGTACCTGGCCAGCGAGGAGGCAGCGCGCGCGGCACGGATCGCCCTGGTCGCCGAGGTCAGCCAGGCCTACCTGAGCTACGACGGCGCCCTGCGGCGCCTGGCGCTGACCCGTCAGACCCTGGTCAGCCGCGAGTATTCCTTCGCCCTGATCGACCAGCGCCGCGCGGCCGGCGCCGCCACCGCGCTGGACTACCAGGAAGCCCTTGGCCTGGTGGAGCAGGCGCGCGCCGAGCAGGAGCGCAACCTGCGGCAGAAACAGCAGGCATTCAACGCGCTGGTGTTGCTGCTGGGTAGCGACGATGCCGCGCAGGCGATTCCGCGGAGTCCGGGGCAGCGGCCGAAGCTGCTGCAGGACATCGCTCCCGGCACGCCGTCCGAGCTGATCGAGCGACGTCCGGACATCCTTGCCGCCGAACATCGTTTGCGGGCGCGCAACGCGGATATCGGCGCGGCGCGCGCGGCGTTCTTCCCGCGCATCAGCCTGACCGGCAGCTTCGGCACCTCCAGCGCGGAAATGTCCGGCCTGTTCGATGGCGGCTCGCGCTCCTGTAGCTTCCTGCCGACGTTGACGCTGCCGATCTTCGATGGCGGGCGCAACCGTGCCAACCTGAGCCTGGCCGAGGCGCGCAAGGATTCGGCGGTGGCCGCCTACGAGGGGACCATCCAGACCGCTTTCCGCGAGGTCGCCGACGCCCTGGCGGCCAGCGATACCCTGCGTCGCGAAGAGAAGGCCCTGCGCGCCCTGGCGAACAGCAGCAACGAAGCCCTGAAGCTGGCCAAGGCACGCTACGAGAGTGGCGTCGACAACCACCTGCGCTACCTCGATGCGCAGCGCAGCAGCTTCCTCAACGAGATCGCCTTCATCGACGGCAGCACCCAGCGGCAGATCGCCCTGGTCGACCTGTTCCGCGCGCTCGGCGGAGGCTGGGACGAGGGACGGAGCCTGGTGGTACATCGAGGCGGCAGGAGTTGAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3000802","ARO_id":"37182","ARO_name":"OprJ","ARO_description":"OprJ is the outer membrane channel component of the MexCD-OprJ multidrug efflux complex.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"811":{"model_id":"811","model_name":"TEM-26","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1885":{"protein_sequence":{"accession":"AAC36883.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMD"},"dna_sequence":{"accession":"L19940","fmin":"197","fmax":"1006","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000896","ARO_id":"37276","ARO_name":"TEM-26","ARO_description":"TEM-26 is an extended-spectrum beta-lactamase that has been found in clinical isolates.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"812":{"model_id":"812","model_name":"CMY-10","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1114":{"protein_sequence":{"accession":"AAK31368.1","sequence":"MQQRQSILWGAVATLMWAGLAHAGEASPVDPLRPVVDASIQPLLKEHRIPGMAVAVLKDGKAHYFNYGVANRESGAGVSEQTLFEIGSVSKTLTATLGAYAVVKGAMQLDDKASRHAPWLKGSAFDSITMGELATYSAGGLPLQFPEEVDSSEKMRAYYRQWAPVYSPGSHRQYSNPSIGLFGHLAASSLKQPFAPLMEQTLLPGLGMHHTYVNVPKQAMASYAYGYSKEDKPIRVNPGMLADEAYGIKTSSADLLRFVKANIGGVDDKALQQAISLTHQGHYSVGGMTQGLGWESYAYPVTEQTLLAGNSAKVILEANPTAAPRESGSQVLFNKTGSTNGFGAYVAFVPARGIGIVMLANRNYPIEARIKAAHAILAQLAG"},"dna_sequence":{"accession":"AF357597","fmin":"250","fmax":"1399","strand":"+","sequence":"ATGCAACAACGACAATCCATCCTGTGGGGGGCCGTGGCCACCCTGATGTGGGCCGGTCTGGCCCATGCAGGTGAGGCTTCACCGGTCGATCCCCTGCGCCCCGTGGTGGATGCCAGCATCCAGCCGCTGCTCAAGGAGCACAGGATCCCGGGCATGGCGGTGGCCGTGCTCAAGGATGGCAAGGCCCACTACTTCAATTACGGGGTGGCCAACCGGGAGAGCGGGGCCGGCGTCAGCGAGCAGACCCTGTTCGAGATAGGATCCGTGAGCAAGACCCTGACTGCGACCCTGGGGGCCTATGCGGTGGTCAAGGGAGCGATGCAGCTGGATGACAAGGCGAGCCGGCACGCGCCCTGGCTCAAGGGATCCGCCTTTGACAGCATCACCATGGGGGAGCTTGCCACCTACAGCGCCGGAGGCCTGCCACTGCAATTCCCCGAGGAGGTGGATTCATCCGAGAAGATGCGCGCCTACTACCGCCAGTGGGCCCCTGTCTATTCGCCGGGCTCCCATCGCCAGTACTCCAACCCCAGCATAGGGCTGTTCGGCCACCTGGCGGCGAGCAGCCTGAAGCAGCCGTTTGCCCCCTTGATGGAGCAGACCCTGCTGCCCGGGCTCGGCATGCACCACACCTATGTCAATGTGCCGAAGCAGGCCATGGCGAGTTATGCCTATGGCTATTCGAAAGAGGACAAGCCCATCCGTGTCAACCCTGGCATGCTGGCGGACGAGGCCTATGGCATCAAGACCAGCTCGGCGGATCTGCTGCGTTTTGTGAAGGCCAACATCGGCGGGGTTGATGACAAGGCGTTGCAGCAGGCCATCTCCCTGACCCACCAAGGGCATTACTCGGTAGGCGGGATGACCCAGGGGCTGGGTTGGGAGAGTTACGCCTATCCCGTCACCGAGCAGACATTGCTGGCGGGCAATTCGGCCAAGGTGATCCTCGAAGCCAATCCGACGGCGGCGCCCCGGGAGTCGGGGAGCCAGGTGCTCTTCAACAAGACCGGCTCGACCAATGGCTTTGGCGCCTATGTGGCCTTCGTGCCGGCCAGGGGGATCGGCATCGTCATGCTGGCCAATCGCAACTACCCCATCGAGGCGCGCATCAAGGCGGCCCACGCCATCCTGGCGCAGTTGGCCGGTTGAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36770","NCBI_taxonomy_name":"Enterobacter aerogenes","NCBI_taxonomy_id":"548"}}}},"ARO_accession":"3002021","ARO_id":"38421","ARO_name":"CMY-10","ARO_description":"CMY-10 is a beta-lactamase found in Enterobacter aerogenes","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"813":{"model_id":"813","model_name":"OXA-216","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1373":{"protein_sequence":{"accession":"CCA94649.1","sequence":"MNIKALLLITSAISISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAIKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"FR865168","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTCTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATAAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001488","ARO_id":"37888","ARO_name":"OXA-216","ARO_description":"OXA-216 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"814":{"model_id":"814","model_name":"TEM-113","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1795":{"protein_sequence":{"accession":"AAS89983.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTTPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AY589494","fmin":"193","fmax":"1054","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACGATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3000976","ARO_id":"37356","ARO_name":"TEM-113","ARO_description":"TEM-113 is an extended-spectrum beta-lactamase found in Proteus mirabilis.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"815":{"model_id":"815","model_name":"GOB-1 beta-lactamase","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1110":{"protein_sequence":{"accession":"AAF04458.1","sequence":"MRNFATLFFMFICLGLNAQVVKEPENMPKEWNQAYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGTAESLPIIKANIQKLGFNYKDIKILLLTQAHYDHTGALQDFKTETAAKFYADKADVDVLRTGGKSDYEMGKYGVTFKPVTPDKTLKDQDKIKLGNITLTLLHHPGHTKGSCSFIFETKDEKRKYRVLIANMPSVIVDKKFSEVTAYPNIQSDYAYTFGVMKKLDFDIWVASHASQFDLHEKRKEGDPYNPQLFMDKQSYFQNLNDLEKSYLDKIKKDSQDK"},"dna_sequence":{"accession":"AF090141","fmin":"242","fmax":"1115","strand":"+","sequence":"ATGAGAAATTTTGCTACACTGTTTTTCATGTTCATTTGCTTGGGCTTGAATGCTCAGGTAGTAAAAGAACCTGAAAATATGCCCAAAGAATGGAACCAGGCTTATGAACCATTCAGAATTGCAGGTAATTTATATTACGTAGGAACCTATGATTTGGCTTCTTACCTTATTGTGACAGACAAAGGCAATATTCTCATTAATACAGGAACGGCAGAATCGCTTCCAATAATAAAAGCAAATATCCAAAAGCTCGGGTTTAATTATAAAGACATTAAGATCTTGCTGCTTACTCAGGCTCACTACGACCATACAGGTGCATTACAGGATTTTAAAACAGAAACCGCTGCAAAATTCTATGCCGATAAAGCAGATGTTGATGTCCTGAGAACAGGGGGGAAGTCCGATTATGAAATGGGAAAATATGGTGTGACATTTAAACCTGTTACTCCGGATAAAACATTGAAAGATCAGGATAAAATAAAACTGGGAAATATAACCCTGACTTTGCTTCATCATCCGGGACATACAAAAGGTTCCTGTAGTTTTATTTTTGAAACAAAAGACGAGAAGAGAAAATATAGAGTTTTGATAGCTAATATGCCCTCCGTTATTGTTGATAAGAAATTTTCTGAAGTTACCGCATATCCAAATATTCAGTCCGATTATGCTTATACCTTTGGTGTTATGAAAAAGCTGGATTTTGATATTTGGGTGGCCTCCCATGCAAGTCAGTTCGATCTCCATGAAAAACGTAAAGAAGGAGATCCGTACAATCCGCAATTGTTTATGGATAAGCAAAGCTATTTCCAAAACCTTAATGATTTGGAAAAAAGCTATCTCGACAAAATAAAAAAAGATTCCCAAGATAAATAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36960","NCBI_taxonomy_name":"Elizabethkingia meningoseptica","NCBI_taxonomy_id":"238"}}}},"ARO_accession":"3000850","ARO_id":"37230","ARO_name":"GOB-1","ARO_description":"GOB-1 confers resistance to cephalosporins in Elizabethkingia (Chryseobacterium) meningoseptica.","ARO_category":{"41376":{"category_aro_accession":"3004212","category_aro_cvterm_id":"41376","category_aro_name":"GOB beta-lactamase","category_aro_description":"The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"816":{"model_id":"816","model_name":"OXA-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1051":{"protein_sequence":{"accession":"AAC41449.1","sequence":"MAIRIFAILFSTFVFGTFAHAQEGMRERSDWRKFFSEFQAKGTIVVADERQTDRVILVFDQVRSEKRYSPASTFKIPHTLFALDAGAARDEFQVFRWDGIKRSFAAHNQDQDLRSAMRNSTVWIYELFAKEIGEDKARRYLKQIDYGNADPSTSNGDYWIDGNLAIAAQEQIAFLRKLYHNELPFRVEHQRLVKDLMIVEAGRNWILRAKTGWEGRIGWWVGWVEWPTGPVFFALNIDTPNRMDDLFKREAIVRAILRSIEALPPNPAVNSDAAR"},"dna_sequence":{"accession":"L07945","fmin":"60","fmax":"888","strand":"+","sequence":"ATGGCAATCCGAATCTTTGCAATACTTTTCTCCACTTTTGTTTTTGGCACGTTCGCGCATGCACAAGAAGGCATGCGCGAACGTTCTGACTGGCGGAAGTTTTTCAGCGAATTTCAAGCCAAAGGCACGATAGTTGTGGCAGACGAACGCCAAACAGATCGTGTCATATTGGTTTTTGATCAGGTGCGGTCAGAGAAACGCTACTCGCCGGCCTCGACATTCAAGATTCCACATACACTTTTTGCACTTGACGCAGGCGCTGCACGTGATGAGTTTCAAGTTTTCCGATGGGACGGCATCAAAAGAAGCTTTGCAGCTCACAACCAAGACCAAGACTTGCGATCAGCAATGCGGAATTCTACTGTCTGGATTTATGAGCTATTTGCAAAAGAGATCGGTGAAGACAAGGCTCGACGCTATTTGAAGCAAATCGACTATGGCAACGCCGATCCTTCGACAAGTAATGGCGATTACTGGATAGATGGCAATCTTGCTATCGCGGCACAAGAACAGATTGCATTTCTCAGGAAGCTCTATCATAACGAGTTGCCCTTTCGGGTAGAACATCAGCGCTTGGTCAAGGACCTCATGATTGTGGAAGCCGGTCGCAACTGGATACTGCGCGCAAAGACGGGCTGGGAAGGCCGCATTGGTTGGTGGGTAGGATGGGTTGAGTGGCCGACTGGCCCCGTATTCTTCGCACTGAATATTGATACGCCAAACAGGATGGATGACCTTTTCAAAAGGGAGGCAATAGTGCGGGCAATCCTTCGCTCTATCGAAGCGTTGCCGCCCAACCCGGCAGTCAACTCGGACGCAGCGCGATAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001398","ARO_id":"37798","ARO_name":"OXA-3","ARO_description":"OXA-3 is a beta-lactamase found in P. aeruginosa","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"817":{"model_id":"817","model_name":"CTX-M-158","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1902":{"protein_sequence":{"accession":"AIT97310.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAVAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVDGTMSLAELSVAALQYSDNVAMNKLISHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTNGL"},"dna_sequence":{"accession":"KM211691","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGTCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGAAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGTGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACTTGGTTAACTATAATCCGATTGCGGAAAAGCACGTCGATGGGACGATGTCACTGGCTGAGCTTAGCGTGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTTCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGTAATCTGACGCTGGGTAAAGCATTGGGTGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCAACGGTTTGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3003166","ARO_id":"39743","ARO_name":"CTX-M-158","ARO_description":"From the Lahey list of beta-lactamases.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"818":{"model_id":"818","model_name":"SHV-141","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1634":{"protein_sequence":{"accession":"AFC60795.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGSVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"JQ388884","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCAGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGGATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001183","ARO_id":"37563","ARO_name":"SHV-141","ARO_description":"SHV-141 is a broad-spectrum beta-lactamase.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"819":{"model_id":"819","model_name":"CTX-M-68","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1274":{"protein_sequence":{"accession":"ABV81082.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLHAQTVDVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDDTFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"EU177100","fmin":"4","fmax":"880","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTATTAGGAAGTGTGCCGCTGCATGCGCAAACGGTGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGAAGGCTGGGTGTGGCATTGATTAACACGGCGGATAATTCGCAAATACTTTATCGTGCTGATGAGCGTTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTAAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTCGAGATCAAAAAATCTGACCTGGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTCAGCGCGGCCGCGCTACAGTACAGCGATAATGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGATGACACGTTCCGTCTCGACCGCACCGAGCCGACGTTAAACACCGCCATTCCTGGCGATCCGCGTGATACCACTTCACCTCGGGCGATGGCGCAAACGCTGCGTAATCTGACGCTGGGTAAAGCGTTGGGCGACAGCCAACGGGCGCAGCTGGTGACGTGGATGAAAGGCAATACTACCGGTGCCGCGAGTATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGTACCACCAACGATATCGCGGTGATTTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36940","NCBI_taxonomy_name":"Klebsiella sp. ARS06-441","NCBI_taxonomy_id":"474576"}}}},"ARO_accession":"3001929","ARO_id":"38329","ARO_name":"CTX-M-68","ARO_description":"CTX-M-68 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"820":{"model_id":"820","model_name":"mdtB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1800"}},"model_sequences":{"sequence":{"215":{"protein_sequence":{"accession":"AAC75136.1","sequence":"MQVLPPSSTGGPSRLFIMRPVATTLLMVAILLAGIIGYRALPVSALPEVDYPTIQVVTLYPGASPDVMTSAVTAPLERQFGQMSGLKQMSSQSSGGASVITLQFQLTLPLDVAEQEVQAAINAATNLLPSDLPNPPVYSKVNPADPPIMTLAVTSTAMPMTQVEDMVETRVAQKISQISGVGLVTLSGGQRPAVRVKLNAQAIAALGLTSETVRTAITGANVNSAKGSLDGPSRAVTLSANDQMQSAEEYRQLIIAYQNGAPIRLGDVATVEQGAENSWLGAWANKEQAIVMNVQRQPGANIISTADSIRQMLPQLTESLPKSVKVTVLSDRTTNIRASVDDTQFELMMAIALVVMIIYLFLRNIPATIIPGVAVPLSLIGTFAVMVFLDFSINNLTLMALTIATGFVVDDAIVVIENISRYIEKGEKPLAAALKGAGEIGFTIISLTFSLIAVLIPLLFMGDIVGRLFREFAITLAVAILISAVVSLTLTPMMCARMLSQESLRKQNRFSRASEKMFDRIIAAYGRGLAKVLNHPWLTLSVALSTLLLSVLLWVFIPKGFFPVQDNGIIQGTLQAPQSSSFANMAQRQRQVADVILQDPAVQSLTSFVGVDGTNPSLNSARLQINLKPLDERDDRVQKVIARLQTAVDKVPGVDLFLQPTQDLTIDTQVSRTQYQFTLQATSLDALSTWVPQLMEKLQQLPQLSDVSSDWQDKGLVAYVNVDRDSASRLGISMADVDNALYNAFGQRLISTIYTQANQYRVVLEHNTENTPGLAALDTIRLTSSDGGVVPLSSIAKIEQRFAPLSINHLDQFPVTTISFNVPDNYSLGDAVQAIMDTEKTLNLPVDITTQFQGSTLAFQSALGSTVWLIVAAVVAMYIVLGILYESFIHPITILSTLPTAGVGALLALLIAGSELDVIAIIGIILLIGIVKKNAIMMIDFALAAEREQGMSPREAIYQACLLRFRPILMTTLAALLGALPLMLSTGVGAELRRPLGIGMVGGLIVSQVLTLFTTPVIYLLFDRLALWTKSRFARHEEEA"},"dna_sequence":{"accession":"U00096","fmin":"2155262","fmax":"2158385","strand":"+","sequence":"ATGCAGGTGTTACCCCCGAGCAGCACAGGCGGCCCGTCGCGCCTGTTTATTATGCGTCCTGTGGCCACCACGCTGCTGATGGTGGCGATCTTACTCGCCGGGATTATCGGTTATCGCGCCCTGCCCGTTTCGGCGCTGCCGGAAGTGGACTATCCGACCATTCAGGTGGTCACGCTCTACCCAGGTGCCAGCCCGGATGTCATGACCTCTGCCGTTACCGCGCCGCTAGAACGCCAGTTCGGGCAGATGTCTGGCCTGAAACAGATGTCGTCGCAAAGTTCCGGCGGTGCGTCAGTTATCACTTTGCAGTTCCAGCTAACATTACCGCTCGATGTCGCCGAGCAGGAAGTGCAGGCCGCGATTAACGCTGCGACCAACTTGTTGCCGAGCGATCTGCCTAACCCGCCGGTTTACAGCAAAGTGAACCCGGCAGATCCGCCGATCATGACGCTCGCCGTCACCTCAACCGCCATGCCGATGACGCAAGTGGAAGATATGGTGGAAACCCGCGTCGCGCAGAAAATCTCGCAGATTTCCGGCGTCGGCCTGGTGACGCTTTCCGGCGGTCAGCGTCCGGCTGTTCGCGTCAAACTTAACGCTCAGGCGATTGCCGCCCTCGGCCTGACCAGCGAAACCGTGCGCACCGCCATTACCGGCGCTAACGTTAACTCGGCAAAAGGTAGCCTCGACGGCCCTTCCCGTGCGGTCACGCTTTCCGCGAACGACCAGATGCAATCCGCCGAAGAGTATCGCCAGCTAATCATCGCCTACCAGAACGGCGCGCCAATTCGTCTGGGCGATGTCGCAACTGTAGAGCAAGGTGCAGAAAACAGCTGGCTCGGCGCGTGGGCGAACAAAGAACAGGCCATTGTGATGAATGTTCAGCGCCAGCCCGGTGCTAACATTATCTCCACCGCCGACAGCATTCGGCAGATGCTGCCACAGCTCACTGAGAGTCTGCCGAAATCGGTGAAGGTGACAGTGCTTTCCGATCGCACCACCAATATCCGCGCATCCGTCGATGATACTCAGTTTGAATTGATGATGGCTATCGCGCTGGTAGTCATGATTATCTACCTGTTTTTGCGCAATATTCCGGCGACCATCATTCCCGGTGTTGCTGTACCGCTGTCGTTAATCGGCACTTTCGCGGTTATGGTGTTTCTCGATTTTTCAATCAATAACCTGACACTGATGGCGTTAACTATCGCCACCGGATTCGTGGTCGATGACGCCATCGTGGTGATCGAAAACATTTCCCGCTATATCGAAAAAGGCGAAAAACCGTTGGCGGCGGCGCTCAAGGGCGCAGGTGAAATCGGCTTTACCATTATCTCGCTGACCTTCTCACTGATTGCGGTGTTGATCCCACTGCTGTTTATGGGCGATATCGTCGGGCGACTGTTCCGCGAATTTGCTATTACCCTGGCGGTAGCGATTTTGATCTCAGCGGTGGTGTCGCTGACCCTGACACCGATGATGTGCGCGCGGATGCTCAGCCAGGAGTCGTTGCGTAAACAGAACCGCTTCTCCCGTGCCTCGGAAAAAATGTTCGACAGGATAATCGCCGCCTATGGTCGTGGACTGGCGAAAGTGCTGAATCATCCGTGGCTGACCTTAAGCGTGGCACTCAGCACGCTGCTGCTTAGCGTGCTGCTGTGGGTGTTCATTCCGAAAGGTTTCTTCCCGGTACAGGACAATGGCATTATTCAGGGCACTTTGCAGGCACCGCAATCCAGCTCCTTTGCCAATATGGCCCAGCGACAACGCCAGGTCGCGGACGTGATTTTGCAGGATCCGGCAGTGCAAAGCCTGACCTCATTTGTTGGCGTTGATGGCACTAACCCGTCGCTGAACAGTGCACGTTTACAAATCAACCTCAAACCGTTGGATGAACGTGATGATCGGGTGCAAAAAGTCATCGCCCGTCTGCAAACGGCGGTAGATAAAGTGCCGGGCGTCGATCTCTTCCTGCAACCAACGCAGGATCTGACTATTGATACTCAGGTCAGCCGCACCCAGTACCAGTTTACCTTGCAGGCCACGTCACTGGATGCGCTCAGTACCTGGGTGCCACAGTTGATGGAAAAACTCCAGCAACTGCCACAGCTTTCTGATGTCTCCAGCGACTGGCAGGACAAAGGGCTGGTGGCGTATGTCAATGTTGATCGCGACAGCGCCAGCCGTCTGGGGATCAGCATGGCGGATGTCGATAACGCCCTGTACAACGCGTTTGGTCAGCGGCTGATTTCCACTATTTATACTCAGGCCAACCAGTATCGCGTGGTGCTGGAGCACAACACCGAAAATACCCCAGGCCTCGCGGCGCTGGATACCATTCGCCTGACCAGCAGCGACGGCGGCGTGGTGCCGCTAAGCTCAATTGCCAAAATTGAGCAGCGTTTTGCGCCGCTCTCCATCAACCATCTGGATCAGTTCCCGGTAACGACCATCTCCTTTAACGTGCCGGATAACTATTCGCTGGGCGATGCGGTGCAGGCGATTATGGACACCGAAAAGACGCTGAATCTGCCGGTGGATATCACCACGCAGTTCCAGGGCAGCACCCTCGCCTTCCAGTCGGCGCTGGGCAGCACTGTCTGGCTGATTGTCGCGGCGGTGGTGGCGATGTATATCGTGCTCGGCATTCTGTACGAGAGCTTTATTCACCCGATCACCATTCTCTCGACGCTACCCACCGCAGGGGTTGGCGCACTGCTGGCGTTGCTGATTGCTGGTAGCGAACTGGATGTGATTGCGATTATCGGCATTATTTTGCTGATCGGTATCGTGAAGAAGAACGCCATCATGATGATCGACTTCGCGCTGGCTGCTGAGCGCGAGCAAGGCATGTCGCCGCGCGAGGCAATCTACCAGGCTTGTCTGTTGCGTTTTCGTCCGATCCTGATGACCACTCTGGCGGCTCTGCTTGGCGCGCTGCCGCTGATGTTGAGTACCGGGGTCGGCGCGGAACTGCGTCGTCCGTTAGGTATCGGCATGGTCGGCGGTCTGATTGTCAGCCAGGTGCTGACGCTGTTTACCACGCCGGTGATTTATTTGCTGTTCGACCGCCTGGCATTGTGGACCAAAAGCCGCTTTGCCCGTCATGAAGAGGAGGCGTAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3000793","ARO_id":"37173","ARO_name":"mdtB","ARO_description":"MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"822":{"model_id":"822","model_name":"QnrD1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"746":{"protein_sequence":{"accession":"ACG70184.1","sequence":"MEKHFINEKFSRDQFTGNRVKNIAFSNCDFSGVDLTDTEFVDCSFYDRNSLEGCDFNRAKLKNASFKSCDLSMSNFKNISALGLEISECLAQGADFRGANFMNMITTRSWFCSAYITKTNLSYANFSRVILEKCELWENRWNGTVITGAVFRGSDLSCGEFSSFDWSLADFTGCDLTGGALGELDARRINLDGVKLDGEQALQLVESLGVIVHR"},"dna_sequence":{"accession":"FJ228229","fmin":"553","fmax":"1198","strand":"+","sequence":"ATGGAAAAGCACTTTATCAATGAAAAGTTTTCACGAGATCAATTTACGGGGAATAGAGTTAAAAATATTGCCTTTTCAAATTGTGATTTTTCAGGGGTTGATTTAACTGATACTGAATTTGTTGATTGTAGTTTTTACGACAGGAATAGCTTGGAAGGGTGTGATTTTAATAGAGCCAAACTAAAAAACGCTAGCTTTAAAAGCTGCGATTTATCAATGAGTAATTTTAAAAACATTAGCGCCTTAGGTCTTGAAATTAGTGAGTGTTTAGCTCAAGGAGCTGATTTTCGAGGGGCTAATTTTATGAATATGATAACTACAAGGTCATGGTTTTGTAGTGCTTATATAACCAAGACAAATCTTAGTTACGCTAATTTTTCTAGAGTCATATTAGAAAAGTGCGAACTGTGGGAAAATCGCTGGAATGGCACTGTGATAACTGGCGCCGTGTTTCGTGGCTCCGATCTTTCTTGTGGGGAGTTTTCATCGTTTGATTGGTCTTTGGCTGATTTTACTGGTTGTGATTTAACGGGTGGGGCGCTTGGCGAGCTTGATGCAAGGCGAATTAATTTAGATGGAGTGAAGTTGGATGGAGAGCAGGCGCTTCAGCTTGTTGAGAGTTTAGGTGTTATTGTTCACCGATAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35711","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Bovismorbificans","NCBI_taxonomy_id":"58097"}}}},"ARO_accession":"3002788","ARO_id":"39222","ARO_name":"QnrD1","ARO_description":"QnrD1 is a plasmid-mediated quinolone resistance protein found in Salmonella enterica","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"824":{"model_id":"824","model_name":"vanD","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"650"}},"model_sequences":{"sequence":{"179":{"protein_sequence":{"accession":"AAM09849.1","sequence":"MYKLKIAVLFGGCSEEHDVSVKSAMEVAANINKEKYQPFYIGITKSGAWKLCDKPCRDWENYAGYPAVISPDRRIHGLLIQKDGGYESQPVDVVLPMIHGKFGEDGTIQGLLELSGIPYVGCDIQSSVICMDKSLAYMVVKNAGIEVPGFRVLQKGDSLEAETLSYPVFVKPARSGSSFGVNKVCRAEELQAAVTEAGKYDSKILVEEAVSGSEVGCAILGNGNDLITGEVDQIELKHGFFKIHQEAQPEKGSENAVIRVPAALPDEVREQIQETAKKIYRVLGCRGLARIDLFLREDGSIVLNEVNTMPGFTSYSRYPRMMTAAGFTLSEILDRLIGLSLRR"},"dna_sequence":{"accession":"AY082011","fmin":"5900","fmax":"6932","strand":"+","sequence":"ATGTATAAGCTTAAAATTGCAGTCCTGTTTGGAGGCTGCTCAGAGGAACATGATGTTTCAGTGAAATCTGCGATGGAGGTTGCAGCAAATATAAACAAGGAAAAATACCAGCCGTTTTATATTGGAATCACAAAATCCGGCGCATGGAAACTATGCGATAAGCCCTGCCGGGACTGGGAGAACTATGCGGGATACCCGGCTGTGATTTCTCCGGACAGAAGGATCCATGGCCTGCTGATACAAAAGGACGGCGGATATGAGAGCCAGCCTGTAGACGTGGTGCTTCCGATGATTCATGGAAAATTTGGCGAGGACGGAACCATACAGGGTCTGCTTGAGCTGTCCGGCATTCCTTATGTGGGATGCGACATTCAAAGTTCTGTAATCTGTATGGATAAGTCGCTCGCTTATATGGTTGTGAAAAATGCGGGAATTGAGGTACCTGGGTTTCGAGTTCTACAAAAGGGGGACAGCCTGGAAGCAGAGACGCTCTCGTATCCGGTCTTTGTAAAGCCTGCCCGTTCCGGCTCCTCTTTTGGCGTGAATAAGGTATGCCGGGCAGAGGAACTGCAGGCAGCGGTCACAGAGGCGGGTAAGTATGACAGCAAAATATTGGTTGAGGAGGCCGTTTCCGGGAGTGAGGTAGGATGTGCCATACTGGGAAACGGAAACGATCTCATCACCGGCGAGGTCGATCAGATTGAATTGAAACACGGGTTTTTTAAGATCCATCAGGAAGCACAGCCGGAAAAGGGGTCTGAAAATGCTGTGATTAGAGTTCCAGCCGCCCTGCCGGATGAAGTTAGGGAGCAGATTCAGGAAACGGCGAAGAAGATTTACCGGGTACTTGGCTGCAGAGGTCTGGCCCGCATTGATTTGTTTTTACGGGAGGATGGAAGCATTGTCCTGAATGAAGTGAACACCATGCCCGGATTTACTTCCTATAGCCGTTATCCACGCATGATGACAGCAGCAGGGTTTACGCTTTCTGAAATATTGGACCGCTTGATTGGACTTTCACTTAGGAGGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3000005","ARO_id":"36014","ARO_name":"vanD","ARO_description":"VanD is a D-Ala-D-Ala ligase homolog similar to VanA, and can synthesize D-Ala-D-Lac, an alternative substrate for peptidoglycan synthesis that reduces vancomycin binding affinity. It is associated with both vancomycin and teicoplanin resistance.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"39340":{"category_aro_accession":"3002906","category_aro_cvterm_id":"39340","category_aro_name":"van ligase","category_aro_description":"van ligases synthesize alternative substrates for peptidoglycan synthesis that reduce vancomycin binding affinity.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"825":{"model_id":"825","model_name":"SHV-20","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1314":{"protein_sequence":{"accession":"AAF34334.1","sequence":"MLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEAFPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASERGARGIVALLGPNNKAERIVVIYLRDTPASMAERN"},"dna_sequence":{"accession":"AF117744","fmin":"0","fmax":"780","strand":"+","sequence":"CTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGTTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001078","ARO_id":"37458","ARO_name":"SHV-20","ARO_description":"SHV-20 is a broad-spectrum beta-lactamase that has been found in clinical isolates.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"826":{"model_id":"826","model_name":"tolC","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"900"}},"model_sequences":{"sequence":{"563":{"protein_sequence":{"accession":"ACN32294.1","sequence":"MQMKKLLPILIGLSLSGFSSLSQAENLMQVYQQARLSNPELRKSAADRDAAFEKINEARSPLLPQLGLGADYTYSNGYRDANGINSNATSASLQLTQSIFDMSKWRALTLQEKAAGIQDVTYQTDQQTLILNTATAYFNVLNAIDVLSYTQAQKEAIYRQLDQTTQRFNVGLVAITDVQNARAQYDTVLANEVTARNNLDNAVEQLRQITGNYYPELAALNVENFKTDKPQPVNALLKEAEKRNLSLLQARLSQDLAREQIRQAQDGHLPTLDLTASTGISDTSYSGSKTRGAAGTQYDDSNMGQNKVGLSFSLPIYQGGMVNSQVKQAQYNFVGASEQLESAHRSVVQTVRSSFNNINASISSINAYKQAVVSAQSSLDAMEAGYSVGTRTIVDVLDATTTLYNAKQELANARYNYLINQLNIKSALGTLNEQDLLALNNALSKPVSTNPENVAPQTPEQNAIADGYAPDSPAPVVQQTSARTTTSNGHNPFRN"},"dna_sequence":{"accession":"FJ768952","fmin":"0","fmax":"1488","strand":"+","sequence":"ATGCAAATGAAGAAATTGCTCCCCATTCTTATCGGCCTGAGCCTTTCTGGGTTCAGTTCGTTGAGCCAGGCCGAGAACCTGATGCAAGTTTATCAGCAAGCACGCCTTAGTAACCCGGAATTGCGTAAGTCTGCCGCCGATCGTGATGCTGCCTTTGAAAAAATTAATGAAGCGCGCAGTCCATTACTGCCACAGCTAGGTTTAGGTGCAGATTACACCTATAGCAACGGCTACCGCGACGCGAACGGCATCAACTCTAACGCGACCAGTGCGTCCTTGCAGTTAACTCAATCCATTTTTGATATGTCGAAATGGCGTGCGTTAACGCTGCAGGAAAAAGCAGCAGGGATTCAGGACGTCACGTATCAGACCGATCAGCAAACCTTGATCCTCAACACCGCGACCGCTTATTTCAACGTGTTGAATGCTATTGACGTTCTTTCCTATACACAGGCACAAAAAGAAGCGATCTACCGTCAATTAGATCAAACCACCCAACGTTTTAACGTGGGCCTGGTAGCGATCACCGACGTGCAGAACGCCCGCGCACAGTACGATACCGTGCTGGCGAACGAAGTGACCGCACGTAATAACCTTGATAACGCGGTAGAGCAGCTGCGCCAGATCACCGGTAACTACTATCCGGAACTGGCTGCGCTGAATGTCGAAAACTTTAAAACCGACAAACCACAGCCGGTTAACGCGCTGCTGAAAGAAGCCGAAAAACGCAACCTGTCGCTGTTACAGGCACGCTTGAGCCAGGACCTGGCGCGCGAGCAAATTCGCCAGGCGCAGGATGGTCACTTACCGACTCTGGATTTAACGGCTTCTACCGGGATTTCTGACACCTCTTATAGCGGTTCGAAAACCCGTGGTGCCGCTGGTACCCAGTATGACGATAGCAATATGGGCCAGAACAAAGTTGGCCTGAGCTTCTCGCTGCCGATTTATCAGGGCGGAATGGTTAACTCGCAGGTGAAACAGGCACAGTACAACTTTGTCGGTGCCAGCGAGCAACTGGAAAGTGCCCATCGTAGCGTCGTGCAGACCGTGCGTTCCTCCTTCAACAACATTAATGCATCTATCAGTAGCATTAACGCCTACAAACAAGCCGTAGTTTCCGCTCAAAGCTCATTAGACGCGATGGAAGCGGGCTACTCGGTCGGTACGCGTACCATTGTTGATGTGTTGGATGCGACCACCACGTTGTACAACGCCAAGCAAGAGCTGGCGAATGCGCGTTATAACTACCTGATTAATCAGCTGAATATTAAGTCAGCTCTGGGTACGTTGAACGAGCAGGATCTGCTGGCACTGAACAATGCGCTGAGCAAACCGGTTTCCACTAATCCGGAAAACGTTGCACCGCAAACGCCGGAACAGAATGCTATTGCTGATGGTTATGCGCCTGATAGCCCGGCACCAGTCGTTCAGCAAACATCCGCACGCACTACCACCAGTAACGGTCATAACCCTTTCCGTAACTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000237","ARO_id":"36376","ARO_name":"TolC","ARO_description":"TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35930":{"category_aro_accession":"0000011","category_aro_cvterm_id":"35930","category_aro_name":"cloxacillin","category_aro_description":"Cloxacillin is a semisynthetic, isoxazolyl penicillin derivative in the beta-lactam class of antibiotics. It interferes with peptidogylcan synthesis and is commonly used for treating penicillin-resistant Staphylococcus aureus infections.","category_aro_class_name":"Antibiotic"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"827":{"model_id":"827","model_name":"QnrB55","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"389":{"protein_sequence":{"accession":"AHE41343.1","sequence":"MTLALVGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQLYDRESQKGCNFSRANLKDAIFKSCDLSMADFRNINALGIEIRHCRAQGSDFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFSSFDWRAANVTHCDLTNSELGDLDIRGVDLQGVKLDSYQASLLLERLGIAVMG"},"dna_sequence":{"accession":"KF730650","fmin":"0","fmax":"645","strand":"+","sequence":"ATGACTCTGGCGTTAGTTGGCGAAAAAATTGACAGAAACAGGTTCACCGGTGAAAAAGTTGAAAATAGCACATTTTTCAACTGTGATTTTTCGGGTGCCGACCTGAGCGGCACTGAATTTATTGGCTGCCAGTTATATGATCGAGAAAGTCAGAAAGGATGTAATTTTAGTCGCGCTAACCTGAAAGATGCCATTTTCAAAAGTTGTGATCTCTCCATGGCTGATTTCAGGAATATCAATGCGCTGGGAATCGAAATTCGCCACTGCCGGGCACAAGGGTCAGATTTTCGCGGCGCAAGTTTTATGAATATGATCACCACCCGCACCTGGTTTTGTAGCGCCTATATCACCAATACCAACTTAAGCTACGCCAACTTTTCAAAAGTCGTACTGGAAAAGTGCGAGCTGTGGGAAAACCGCTGGATGGGTACTCAGGTGCTGGGCGCAACGTTCAGTGGATCAGACCTCTCTGGCGGCGAGTTTTCATCCTTCGACTGGCGAGCAGCAAACGTTACGCACTGTGATTTGACCAATTCGGAACTGGGCGATTTAGATATCCGCGGGGTTGATTTGCAAGGCGTCAAACTGGACAGCTACCAGGCATCGTTGCTCCTGGAACGTCTTGGTATCGCTGTCATGGGTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39585","NCBI_taxonomy_name":"Raoultella terrigena","NCBI_taxonomy_id":"577"}}}},"ARO_accession":"3002768","ARO_id":"39202","ARO_name":"QnrB55","ARO_description":"QnrB55 is a plasmid-mediated quinolone resistance protein found in Raoultella terrigena","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"828":{"model_id":"828","model_name":"TEM-83","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1249":{"protein_sequence":{"accession":"AAL29435.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMLSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRCEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDEQNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AF427129","fmin":"208","fmax":"1069","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGTTGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGTGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACAAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000950","ARO_id":"37330","ARO_name":"TEM-83","ARO_description":"TEM-83 is an inhibitor-resistant beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"829":{"model_id":"829","model_name":"DHA-17","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1089":{"protein_sequence":{"accession":"AIT76103.1","sequence":"MKKSLSATLISALLAFSAPGFSAADNVAVVVDSTIKPLMAQQDIPGMAVAVSVKGKPYYFNYGFADIQAKQPVTENTLFELGSVSKTFTGVLGAVSVAKKEMALNDPAAKYQPELALPQWKGITLLDLATYTAGGLPLQVPDAVKSRADLLNFYQQWQPSRKPGDMRLYANSSIGLFGALTANAAGMPYEQLLTARILAPLGLSHTFITVPESAQSQYAYGYKNKKPVRVSPGQLDAESYGVKSASKDMLRWAEMNMEPSRAGNADLEMAMYLAQTRYYKTAAINQGLGWEMYDWPQQKDMIINGVTNEVALQPHPVTDNQVQPYNRASWVHKTGATTGFGAYVAFIPEKQVAIVILANKNYPNTERVKAAQAILSALE"},"dna_sequence":{"accession":"KM087850","fmin":"0","fmax":"1140","strand":"+","sequence":"ATGAAAAAATCGTTATCTGCAACACTGATTTCCGCTCTGCTGGCGTTTTCCGCCCCGGGGTTTTCTGCCGCTGATAATGTCGCGGTGGTGGTGGACAGCACCATTAAACCGCTGATGGCACAGCAGGATATTCCCGGGATGGCGGTTGCCGTCTCCGTAAAGGGTAAGCCCTATTATTTCAATTATGGTTTTGCCGATATTCAGGCAAAACAGCCGGTCACTGAAAATACACTATTTGAGCTCGGATCTGTAAGTAAAACTTTCACAGGTGTGCTGGGTGCGGTTTCTGTGGCGAAAAAAGAGATGGCGCTGAATGATCCGGCGGCAAAATACCAGCCGGAGCTGGCTCTGCCGCAGTGGAAGGGGATCACATTGCTGGATCTGGCTACCTATACCGCAGGCGGACTGCCGTTACAGGTGCCGGATGCGGTAAAAAGCCGTGCGGATCTGCTGAATTTCTATCAGCAGTGGCAGCCGTCCCGGAAACCGGGCGATATGCGTCTGTATGCAAACAGCAGTATCGGCCTGTTTGGTGCTCTGACCGCAAACGCGGCGGGGATGCCGTATGAGCAGTTGCTGACTGCACGGATCCTGGCACCGCTGGGGTTATCTCACACCTTTATTACTGTGCCGGAAAGTGCGCAAAGCCAGTATGCGTACGGTTATAAAAACAAAAAACCGGTCCGCGTGTCGCCGGGACAGCTTGATGCGGAATCTTACGGCGTGAAATCCGCCTCAAAAGATATGCTGCGCTGGGCGGAAATGAATATGGAGCCGTCACGGGCCGGTAATGCGGATCTGGAAATGGCAATGTATCTTGCACAGACCCGCTACTATAAAACCGCCGCGATTAACCAGGGGCTGGGCTGGGAAATGTATGACTGGCCGCAGCAGAAAGATATGATCATTAACGGCGTGACCAACGAGGTCGCATTGCAGCCGCACCCGGTAACAGACAACCAGGTTCAGCCGTATAACCGTGCTTCCTGGGTGCATAAAACGGGGGCAACAACTGGTTTCGGCGCCTATGTGGCCTTTATTCCGGAAAAACAGGTGGCGATTGTGATTCTGGCGAATAAAAACTACCCGAATACCGAAAGAGTCAAAGCCGCACAGGCTATTTTGAGTGCACTGGAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36917","NCBI_taxonomy_name":"Morganella morganii","NCBI_taxonomy_id":"582"}}}},"ARO_accession":"3002148","ARO_id":"38548","ARO_name":"DHA-17","ARO_description":"DHA-17 is a beta-lactamase. From the Lahey list of DHA beta-lactamases.","ARO_category":{"36207":{"category_aro_accession":"3000068","category_aro_cvterm_id":"36207","category_aro_name":"DHA beta-lactamase","category_aro_description":"DHA beta-lactamases are plasmid-mediated AmpC \u03b2-lactamases that confer resistance to cephamycins and oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"830":{"model_id":"830","model_name":"SHV-157","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1635":{"protein_sequence":{"accession":"AFQ23963.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVMLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"JX121124","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAATGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCAGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001196","ARO_id":"37576","ARO_name":"SHV-157","ARO_description":"SHV-157 is a beta-lactamase.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"831":{"model_id":"831","model_name":"OKP-B-13","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1041":{"protein_sequence":{"accession":"AAV80715.1","sequence":"MRYIRLCLISLIAALPLAVFASPQPLEQIKISESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNTAGNLLLKIVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMATTLRKLLTTPSLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPDGKAERIVVIYLRDTAATMAERNQQIAVIGAALIEHWQR"},"dna_sequence":{"accession":"AY825330","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCAGCCGCTTGAGCAGATTAAAATCAGCGAAAGTCAGCTGGCGGGCCGGGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGCGACGAACAGCTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACACCGCCGGCAATCTGCTGTTGAAGATCGTCGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGAACTCAATGAGGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCGGCCAGCATGGCCACCACCCTGCGCAAGCTGCTAACCACCCCCTCTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTTGACGACCGGGTGGCCGGCCCGTTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGTGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAAGCGGAGCGTATCGTGGTGATCTATCTGCGGGATACCGCAGCGACCATGGCCGAACGTAACCAGCAGATCGCCGTGATAGGCGCGGCGCTGATCGAGCACTGGCAACGCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002446","ARO_id":"38846","ARO_name":"OKP-B-13","ARO_description":"OKP-B-13 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"832":{"model_id":"832","model_name":"SHV-161","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"2022":{"protein_sequence":{"accession":"AFQ23967.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGSVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"JX121128","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCAGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001200","ARO_id":"37580","ARO_name":"SHV-161","ARO_description":"SHV-161 is a beta-lactamase.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"833":{"model_id":"833","model_name":"CfxA5","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"1669":{"protein_sequence":{"accession":"AAV37206.1","sequence":"MEKNRKKQIVVLSIALVCIFILVFSLFHKSATKDSANPPLTNVLTDSISQIVSACPGEIGVAVIVNNRDTVKVNNKSVYPMMSVFKVHQALALCNDFDNKGISLDTLVNINRDKLDPKTWSPMLKDYSGPVISLTVRDLLRYTLTQSDNNASNLMFKDMVNVAQTDSFIATLIPRSSFQIAYTEEEMSADHNKAYSNYTSPLGAAMLMNRLFTEGLIDDEKQSFIKNTLKECKTGVDRIAAPLLDKEGVVIAHKTGSGCVNENGVLAAHNDVAYICLPNNISYTLAVFVKDFKGNESQASQYVAHISAVVYSLLMQTSVKS"},"dna_sequence":{"accession":"AY769934","fmin":"27","fmax":"993","strand":"+","sequence":"ATGGAAAAAAACAGAAAAAAACAAATCGTAGTTTTGAGTATAGCTTTAGTTTGCATTTTCATCTTGGTATTTTCATTGTTCCATAAATCAGCGACAAAAGATAGCGCAAATCCTCCTTTAACAAATGTTTTGACTGATAGCATTTCTCAAATTGTCTCAGCTTGTCCTGGCGAAATTGGTGTGGCGGTTATTGTTAATAACAGAGATACGGTTAAGGTCAATAATAAGAGTGTTTATCCTATGATGAGTGTGTTTAAGGTTCATCAGGCATTAGCTCTTTGTAATGACTTTGACAATAAAGGAATTTCACTTGATACCTTAGTAAATATAAATAGGGATAAACTTGACCCAAAGACTTGGAGTCCTATGCTGAAAGATTATTCAGGGCCAGTCATATCATTGACAGTGAGAGATTTGCTGCGTTATACTCTTACTCAGAGTGACAACAATGCAAGCAACCTTATGTTTAAGGATATGGTTAATGTCGCTCAAACAGATAGTTTTATAGCCACACTCATTCCTCGTTCAAGTTTTCAGATAGCTTATACGGAAGAGGAAATGTCGGCTGACCATAACAAGGCTTACTCTAACTATACATCTCCTCTTGGTGCTGCAATGTTGATGAATCGTTTGTTTACTGAAGGTCTTATCGATGATGAGAAACAAAGTTTCATTAAGAATACGTTAAAAGAATGCAAAACAGGTGTAGATAGGATAGCAGCTCCACTTCTTGATAAAGAAGGGGTTGTTATAGCGCATAAGACAGGTTCAGGTTGTGTTAATGAAAATGGTGTTCTTGCAGCTCACAATGATGTTGCCTATATATGTCTGCCTAATAATATCAGTTATACCTTAGCGGTATTTGTTAAGGATTTCAAGGGAAATGAATCACAAGCGTCACAATATGTTGCGCATATATCAGCTGTAGTATATTCTTTATTAATGCAAACTTCAGTAAAATCTTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39660","NCBI_taxonomy_name":"Parabacteroides distasonis","NCBI_taxonomy_id":"823"}}}},"ARO_accession":"3003096","ARO_id":"39649","ARO_name":"CfxA5","ARO_description":"cfxA5 beta-lactamase is a class A beta-lactamase found in Bacteroides distasonis","ARO_category":{"39434":{"category_aro_accession":"3003000","category_aro_cvterm_id":"39434","category_aro_name":"CfxA beta-lactamase","category_aro_description":"cfxA beta-lactamases are class A beta-lactamases","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"834":{"model_id":"834","model_name":"FosA3","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"540":{"protein_sequence":{"accession":"AEG78825.1","sequence":"MLQGLNHLTLAVSDLASSLAFYQQLPGMRLHASWDSGAYLSCGALWLCLSLDEQRRKTPPQESDYTHYAFSVAEEEFAGVVALLAQAGAEVWKDNRSEGASYYFLDPDGHKLELHVGNLAQRLAACRERPYKGMVFFD"},"dna_sequence":{"accession":"JF411006","fmin":"951","fmax":"1368","strand":"+","sequence":"ATGCTGCAGGGATTGAATCATCTGACGCTGGCGGTCAGCGATCTGGCGTCAAGCCTGGCATTTTATCAGCAGTTACCTGGAATGCGCCTGCACGCCAGCTGGGATAGCGGAGCCTATCTCTCCTGTGGGGCGCTGTGGCTGTGCTTGTCGCTGGATGAGCAGCGGCGTAAAACGCCCCCTCAGGAAAGCGACTATACCCACTACGCCTTCAGCGTGGCGGAAGAAGAGTTTGCCGGGGTGGTGGCTCTGCTGGCGCAGGCGGGGGCTGAGGTATGGAAAGATAACCGCAGTGAAGGGGCGTCTTACTATTTTCTCGACCCTGACGGCCATAAGCTGGAGCTGCATGTGGGGAATCTGGCGCAGCGGCTGGCCGCCTGTCGCGAACGCCCCTACAAGGGGATGGTCTTTTTTGATTGAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002872","ARO_id":"39306","ARO_name":"FosA3","ARO_description":"An enzyme that confers resistance to fosfomycin in Escherichia coli by breaking the epoxide ring of the molecule. It depends on the cofactors Manganese (II) and Potassium and uses Glutathione (GSH) as the nucleophilic molecule.","ARO_category":{"36272":{"category_aro_accession":"3000133","category_aro_cvterm_id":"36272","category_aro_name":"fosfomycin thiol transferase","category_aro_description":"Catalyzes the addition of a thiol group from a nucleophilic molecule to fosfomycin.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"835":{"model_id":"835","model_name":"APH(3')-Ib","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"329":{"protein_sequence":{"accession":"AAA26412.1","sequence":"MNDIDREEPCAAAAVPESMAAHVMGYKWARDKVGQSGCAVYRLHSKSGGSDLFLKHGKDAFADDVTDEMVRLRWLAGHISVPSVVSFVRTPNQAWLLTTAIHGKTAYQVLKSDFGARLVVVDALAAFMRRLHAIPVSECSVQQWTTHAGLPERGSIEAGVVDVDDFDKEREGWTAEQVWEAMHRLLPLAPDPVVTHGDFSLDNLLIVEGKVVGCIDVGRAGIADRYQDLAVLWNCLEEFEPSLQERLVAQYGIADPDRRKLQFHLLLDELF"},"dna_sequence":{"accession":"M20305","fmin":"778","fmax":"1594","strand":"+","sequence":"GTGAACGATATTGATCGAGAAGAGCCCTGCGCAGCCGCTGCCGTGCCCGAGAGCATGGCGGCTCACGTGATGGGATACAAATGGGCGCGTGATAAGGTTGGTCAGTCCGGCTGCGCGGTCTATCGGCTGCATAGCAAGTCAGGCGGCTCCGACTTGTTTCTGAAGCACGGCAAAGATGCTTTTGCCGACGACGTGACTGATGAAATGGTGAGATTGCGTTGGCTGGCGGGGCACATTTCTGTGCCCTCCGTTGTAAGCTTCGTTCGCACGCCCAATCAGGCATGGCTCCTGACAACAGCAATACATGGAAAAACGGCATATCAAGTGCTGAAATCGGATTTCGGAGCCCGTCTCGTTGTTGTTGACGCATTGGCGGCGTTCATGCGCCGACTGCATGCGATCCCAGTGAGCGAATGCTCCGTTCAACAGTGGACCACGCATGCAGGCTTGCCCGAGCGCGGGAGTATCGAGGCGGGGGTTGTTGATGTCGATGACTTCGATAAGGAGCGCGAAGGGTGGACGGCCGAACAGGTTTGGGAGGCGATGCATCGCCTCCTACCGCTCGCGCCGGACCCAGTCGTGACGCACGGCGATTTTTCACTCGATAATCTACTTATCGTCGAAGGTAAGGTAGTCGGCTGCATCGACGTTGGGCGGGCTGGTATTGCTGATCGATACCAAGACCTTGCCGTGTTATGGAACTGTCTTGAGGAGTTCGAACCTTCGCTTCAGGAGAGGCTTGTTGCGCAATATGGCATTGCCGATCCGGATAGGCGCAAGCTGCAATTTCATCTCCTGCTGGACGAACTTTTCTAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39529","NCBI_taxonomy_name":"Plasmid RP4","NCBI_taxonomy_id":"2503"}}}},"ARO_accession":"3002642","ARO_id":"39042","ARO_name":"APH(3')-Ib","ARO_description":"APH(3')-Ib is a plasmid-encoded aminoglycoside phosphotransferase in E. coli","ARO_category":{"36265":{"category_aro_accession":"3000126","category_aro_cvterm_id":"36265","category_aro_name":"APH(3')","category_aro_description":"Phosphorylation of 2-deoxystreptamine aminoglycosides on the hydroxyl group at position 3'","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37044":{"category_aro_accession":"3000700","category_aro_cvterm_id":"37044","category_aro_name":"lividomycin A","category_aro_description":"Lividomycin A is a pentasaccharide antibiotic which interferes with bacterial protein synthesis.","category_aro_class_name":"Antibiotic"},"37045":{"category_aro_accession":"3000701","category_aro_cvterm_id":"37045","category_aro_name":"lividomycin B","category_aro_description":"Lividomycin B is a derivative of lividomycin A with a removed mannose group (demannosyllividomycin A). Livodomycins interfere with bacterial protein synthesis.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"836":{"model_id":"836","model_name":"TEM-68","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1327":{"protein_sequence":{"accession":"CAB92324.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASKRGSRGIIAALGPDGKPSRIVVIYMTGSQATMDELNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AJ239002","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTAAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACATGACGGGGAGTCAGGCAACTATGGATGAACTAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000935","ARO_id":"37315","ARO_name":"TEM-68","ARO_description":"TEM-68 is an inhibitor resistant, extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"837":{"model_id":"837","model_name":"vatH","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"253":{"protein_sequence":{"accession":"ACX92987.1","sequence":"MAEKLKGPNSNEMYPIAGNKSVQFVKPSLTRPNIIVGEFTYYDSKNGELFEDQVLYHYEIIGDRLIIGKFCSIGPGVTFIMNGANHRMDGSTYPFNIFGHGWEKHTPTLDMLPLKGDTIVGNDVWIGLDATIMPGVKIGDGAIIAAKSVVTKDVDPSTIVGGNPAKQIKKRFSESKIQELLKIKWWDFEDQVISDNIDAILSLDVEALNNISKEND"},"dna_sequence":{"accession":"GQ205627","fmin":"3036","fmax":"3687","strand":"+","sequence":"ATGGCAGAAAAATTAAAAGGACCCAACTCAAATGAAATGTATCCGATTGCCGGAAATAAAAGTGTTCAATTTGTTAAACCGTCATTAACAAGGCCCAATATTATAGTTGGTGAGTTCACTTATTATGATAGCAAGAACGGAGAGCTTTTTGAGGATCAAGTTCTGTATCATTATGAAATTATAGGGGATCGACTGATCATCGGGAAATTTTGTTCAATCGGTCCTGGAGTCACTTTTATTATGAATGGAGCTAATCATCGCATGGATGGCTCCACTTATCCATTTAATATCTTTGGGCATGGGTGGGAAAAGCATACACCTACACTAGATATGCTGCCTTTAAAGGGGGATACTATTGTTGGTAATGACGTATGGATTGGACTAGATGCTACAATTATGCCAGGCGTAAAAATAGGAGACGGCGCGATTATTGCAGCCAAATCTGTAGTAACAAAAGACGTTGACCCCTCCACAATTGTTGGTGGTAATCCTGCAAAACAAATAAAGAAACGATTTTCGGAGTCAAAAATTCAAGAACTATTAAAGATAAAATGGTGGGATTTTGAAGACCAGGTTATTAGCGATAATATTGATGCTATTCTAAGTTTGGATGTTGAAGCGCTTAATAATATTTCTAAAGAAAATGATTAGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002845","ARO_id":"39279","ARO_name":"vatH","ARO_description":"vatH is a plasmid-mediated acetyltransferase found in Enterococcus faecium","ARO_category":{"36592":{"category_aro_accession":"3000453","category_aro_cvterm_id":"36592","category_aro_name":"streptogramin vat acetyltransferase","category_aro_description":"vat (Virginiamycin acetyltransferases) enzymes catalyze the transfer of an acetyl group from acetyl-CoA to the secondary alcohol of streptogramin A compounds, thus inactivating virginiamycin-like antibiotics and conferring resistance to these compounds.","category_aro_class_name":"AMR Gene Family"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"838":{"model_id":"838","model_name":"CTX-M-102","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"946":{"protein_sequence":{"accession":"ADY02546.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQREQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGGYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"HQ398215","fmin":"244","fmax":"1120","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGAGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGGCTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001961","ARO_id":"38361","ARO_name":"CTX-M-102","ARO_description":"CTX-M-102 is a beta-lactamase found in Escherichia coli","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"839":{"model_id":"839","model_name":"CMY-44","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1586":{"protein_sequence":{"accession":"ACJ65711.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVAPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"FJ437066","fmin":"0","fmax":"1134","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCACCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002055","ARO_id":"38455","ARO_name":"CMY-44","ARO_description":"CMY-44 is a beta-lactamase found in Escherichia coli","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"840":{"model_id":"840","model_name":"CMY-20","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"903":{"protein_sequence":{"accession":"AAX58682.2","sequence":"MKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGISLLHLATYTAGGLPLQIPDDVTDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDNKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"AY960293","fmin":"0","fmax":"1143","strand":"+","sequence":"ATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCCGAACTGACAGGCAAACAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGTTTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAACAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTCCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002031","ARO_id":"38431","ARO_name":"CMY-20","ARO_description":"CMY-20 is a beta-lactamase found in Escherichia coli","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"841":{"model_id":"841","model_name":"CTX-M-14","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"947":{"protein_sequence":{"accession":"AAF72530.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"AF252622","fmin":"1740","fmax":"2616","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001877","ARO_id":"38277","ARO_name":"CTX-M-14","ARO_description":"CTX-M-14 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"843":{"model_id":"843","model_name":"QnrB14","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"255":{"protein_sequence":{"accession":"ABX72044.1","sequence":"MTPLLYKKTGTNMALALVGEKIDRNRFTGEKIDNSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNASALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLTERLGIAIIG"},"dna_sequence":{"accession":"EU273757","fmin":"0","fmax":"681","strand":"+","sequence":"ATGACGCCATTACTGTATAAAAAAACAGGTACAAATATGGCTCTGGCACTCGTCGGCGAAAAAATTGACAGAAACCGTTTCACCGGTGAGAAAATTGATAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCGATGCTGAAAGATGCCATTTTTAAAAGCTGTGATCTATCCATGGCGGATTTTCGCAATGCCAGTGCGCTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGCGCAAGTTTTATGAATATGATCACTACTCGCACCTGGTTTTGTAGTGCATATATCACTAACACAAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGCTGGAAAAGTGTGAGCTGTGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGGGACTTAGATATTCGGGGCGTTGATTTACAGGGCGTTAAGTTGGACAACTACCAGGCATCGTTGCTCACGGAACGTCTTGGCATCGCGATTATTGGCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002728","ARO_id":"39163","ARO_name":"QnrB14","ARO_description":"QnrB14 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"844":{"model_id":"844","model_name":"CMY-117","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1178":{"protein_sequence":{"accession":"AIT76097.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDDITDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHAQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPVPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"KM087844","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCACTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGACATTACGGATAAAGCCGCATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGCGGTGAAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAACTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTGCACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGCTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGTACCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACAGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATAGTGATGCTGGCAAACAAAAGCTATCCTAACCCGGCTCGCGTAGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002128","ARO_id":"38528","ARO_name":"CMY-117","ARO_description":"CMY-117 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"845":{"model_id":"845","model_name":"TEM-163","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1955":{"protein_sequence":{"accession":"ACF32746.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDEQNRQIAEIGASLIKLW"},"dna_sequence":{"accession":"EU815939","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACAAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCTTTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001029","ARO_id":"37409","ARO_name":"TEM-163","ARO_description":"TEM-163 is an inhibitor resistant beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"846":{"model_id":"846","model_name":"DHA-12","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1983":{"protein_sequence":{"accession":"CDL68900.1","sequence":"MKKSLSATLISALLAFSAPGFSAADNVAAVVDSTIKPLMAQQDIPGMAVAVSVKGKPYYFNYGFADVEAKQPVTENTLFELGSVSKTFTGVLGAVSVAKKEMSLNDPAAKYRPELTQPQWKGITLLDLATYTAGGLPLQVPDAVKSRADLLHFYQQWQPSWKPGDMRLYANSSIGLFGALTANAAGMPYEQLLTTRILSPLGLSHTFITVPESAQSQYAYGYKNKKPVRVSPGQLDAESYGVKSASKDMLRWAEMNMEPSRAGNADLEMAMYLAQTRYYKTAAINQGLGWEMYDWPQQKDMIVNGVTNEVALQPHPVTDNQVQPYNRASWVHKTGATTGFGAYVAFIPEKQVAIVILANKNYPNTERVKAAQAILSALE"},"dna_sequence":{"accession":"HG798963","fmin":"0","fmax":"1140","strand":"+","sequence":"ATGAAAAAATCGTTATCTGCAACACTGATTTCTGCCCTGCTGGCGTTTTCCGCCCCGGGGTTTTCCGCCGCTGACAATGTCGCGGCGGTGGTGGACAGCACCATTAAACCGCTGATGGCACAGCAGGATATTCCCGGGATGGCAGTTGCTGTTTCCGTAAAGGGCAAGCCCTATTATTTCAACTATGGTTTTGCCGATGTTGAGGCAAAACAGCCGGTCACTGAAAATACACTATTTGAGCTCGGATCTGTAAGTAAAACTTTCACAGGTGTGCTGGGTGCAGTTTCCGTGGCGAAAAAAGAGATGTCCCTGAATGACCCGGCGGCAAAATACCGGCCTGAACTGACACAACCGCAGTGGAAGGGGATCACATTGCTCGATCTGGCTACTTATACCGCAGGCGGGCTGCCGTTACAGGTGCCGGACGCGGTGAAAAGCCGTGCGGATCTGTTGCATTTCTATCAGCAGTGGCAGCCGTCATGGAAACCGGGCGATATGCGTCTGTATGCAAACAGCAGTATCGGCCTGTTTGGTGCTCTGACCGCCAACGCCGCAGGAATGCCGTATGAGCAGTTGCTGACCACGCGTATCCTGTCTCCGCTGGGGTTATCACACACCTTTATTACCGTGCCGGAAAGCGCGCAAAGCCAGTATGCGTACGGCTATAAAAACAAAAAACCGGTCCGCGTGTCGCCGGGACAGCTTGATGCAGAATCTTACGGGGTGAAATCCGCCTCAAAAGATATGCTGCGCTGGGCGGAAATGAATATGGAACCGTCACGGGCCGGTAATGCGGATCTGGAAATGGCAATGTATCTTGCACAGACCCGCTACTATAAAACCGCCGCGATTAACCAGGGGCTGGGCTGGGAAATGTATGATTGGCCGCAGCAGAAGGACATGATCGTGAACGGCGTGACCAATGAAGTCGCATTGCAGCCGCATCCGGTAACCGACAATCAGGTGCAGCCGTACAACCGCGCTTCCTGGGTGCATAAAACGGGGGCGACAACCGGTTTCGGCGCCTATGTGGCCTTTATTCCGGAAAAACAGGTGGCGATTGTGATCCTGGCGAATAAAAACTACCCGAATACCGAAAGAGTCAAAGCTGCACAGGCTATTTTGAGTGCACTGGAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3002143","ARO_id":"38543","ARO_name":"DHA-12","ARO_description":"DHA-12 is a beta-lactamase. From the Lahey list of DHA beta-lactamases.","ARO_category":{"36207":{"category_aro_accession":"3000068","category_aro_cvterm_id":"36207","category_aro_name":"DHA beta-lactamase","category_aro_description":"DHA beta-lactamases are plasmid-mediated AmpC \u03b2-lactamases that confer resistance to cephamycins and oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"847":{"model_id":"847","model_name":"CTX-M-108","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1429":{"protein_sequence":{"accession":"AEM44651.1","sequence":"VKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRAEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVT"},"dna_sequence":{"accession":"JF274245","fmin":"0","fmax":"863","strand":"+","sequence":"GGTTAAAAAATCACTGCGTCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGCTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39657","NCBI_taxonomy_name":"Shigella sp. SH223","NCBI_taxonomy_id":"1074434"}}}},"ARO_accession":"3001968","ARO_id":"38368","ARO_name":"CTX-M-108","ARO_description":"CTX-M-108 is a beta-lactamase found in Shigella spp.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"848":{"model_id":"848","model_name":"OKP-A-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1365":{"protein_sequence":{"accession":"CAG25815.2","sequence":"MRYVRLCLFSLIAALPLAVFASPQPLEQVTRSESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIRYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKSVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMAATLRKLLTSHTLSARSQQQLLQWMVDDQVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPNGKAERIVVIYLRDTPATMAERNQQIARIGAALIEHWQR"},"dna_sequence":{"accession":"AJ635404","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTTTCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCAGCCGCTCGAGCAAGTTACACGCAGCGAAAGTCAGCTGGCGGGCCGCGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGAGACGAACAGCTGGATCGGCGGATCCGCTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGAGCGTTGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAGCTCAATGAAGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCAGCCAGCATGGCCGCCACCCTGCGCAAGCTGCTAACCAGCCACACTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGACCAGGTAGCCGGTCCGCTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGCGAGCGGGGCTCACGTGGCATTGTCGCCCTGCTCGGCCCGAACGGCAAAGCGGAGCGCATCGTGGTGATCTATCTGCGGGATACGCCGGCGACCATGGCCGAGCGTAACCAGCAGATCGCCAGAATAGGCGCGGCGCTGATCGAGCACTGGCAGCGCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002419","ARO_id":"38819","ARO_name":"OKP-A-2","ARO_description":"OKP-A-2 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"849":{"model_id":"849","model_name":"OXA-138","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"880":{"protein_sequence":{"accession":"ACD45467.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWVVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"EU670845","fmin":"1594","fmax":"2419","strand":"+","sequence":"ATGAACATTAAAACCCTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGGTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36949","NCBI_taxonomy_name":"Acinetobacter nosocomialis","NCBI_taxonomy_id":"106654"}}}},"ARO_accession":"3001655","ARO_id":"38055","ARO_name":"OXA-138","ARO_description":"OXA-138 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"850":{"model_id":"850","model_name":"OXA-26","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1929":{"protein_sequence":{"accession":"AAG35608.1","sequence":"MKKFILPIFSISILVSLSACSSIKTKSEDNFHISSQQHEKAIKSYFDEAQTQGVIIIKEGKNLSTYGNALARANKEYVPASTFKMLNALIGLENHKATTNEIFKWDGKKRTYPMWEKDMTLGEAMALSAVPVYQELARRTGLELMQKEVKRVNFGNTNIGTQVDNFWLVGPLKITPVQEVNFADDLAHNRLPFKLETQEEVKKMLLIKEVNGSKIYAKSGWGMGVTPQVGWLTGWVEQANGKKIPFSLNLEMKEGMTGSIRNEITYKSLENLGII"},"dna_sequence":{"accession":"AF201827","fmin":"21","fmax":"849","strand":"+","sequence":"ATGAAAAAATTTATACTTCCTATATTCAGCATTTCTATTCTAGTTTCTCTCAGTGCATGTTCATCTATTAAAACTAAATCTGAAGATAATTTTCATATTTCTTCTCAGCAACATGAAAAAGCTATTAAAAGCTATTTTGATGAAGCTCAAACACAGGGTGTAATTATTATTAAAGAGGGTAAAAATCTTAGCACCTATGGTAATGCTCTTGCACGAGCAAATAAAGAATATGTCCCTGCATCAACATTTAAGATGCTAAATGCTTTAATCGGGCTAGAAAATCATAAAGCAACAACAAATGAGATTTTCAAATGGGATGGTAAAAAAAGAACTTATCCTATGTGGGAGAAAGATATGACTTTAGGTGAGGCAATGGCATTGTCAGCAGTTCCAGTATATCAAGAGCTTGCAAGACGGACTGGCCTAGAGCTAATGCAGAAAGAAGTAAAGCGGGTTAATTTTGGAAATACAAATATTGGAACACAGGTCGATAATTTTTGGTTAGTTGGCCCCCTTAAAATTACACCAGTACAAGAAGTTAATTTTGCCGATGACCTTGCACATAACCGATTACCTTTTAAATTAGAAACTCAAGAAGAAGTTAAAAAAATGCTTCTAATTAAAGAAGTAAATGGTAGTAAGATTTATGCAAAAAGTGGATGGGGAATGGGTGTTACTCCACAGGTAGGTTGGTTGACTGGTTGGGTGGAGCAAGCTAATGGAAAAAAAATCCCCTTTTCGCTCAACTTAGAAATGAAAGAAGGAATGACTGGTTCTATTCGTAATGAAATTACTTATAAGTCGCTAGAAAATCTTGGAATCATTTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001421","ARO_id":"37821","ARO_name":"OXA-26","ARO_description":"OXA-26 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"852":{"model_id":"852","model_name":"QnrB62","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"757":{"protein_sequence":{"accession":"AFY16910.1","sequence":"MTPLLYKNTGIDMTLALVGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAIIG"},"dna_sequence":{"accession":"JX987101","fmin":"0","fmax":"681","strand":"+","sequence":"ATGACGCCATTACTGTATAAAAACACAGGCATAGATATGACTCTGGCATTAGTTGGCGAAAAAATTGACAGAAATCGCTTCACCGGTGAGAAAGTTGAAAATAGTACATTTTTTAACTGCGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGCCAGTTCTATGATCGCGAAAGTCAAAAAGGATGCAATTTTAGTCGCGCAATGCTGAAAGATGCCATTTTCAAAAGCTGTGATTTATCAATGGCAGATTTCCGCAACGTCAGCGCATTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGTGCAAGCTTTATGAATATGATCACCACGCGCACCTGGTTTTGCAGCGCATATATCACTAATACCAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAGCTATGGGAAAACCGCTGGATGGGGACTCAGGTACTGGGTGCGACGTTTAGTGGTTCAGATCTCTCCGGTGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTAGGTGACTTAGATATTCGGGGTGTTGATTTACAAGGCGTTAAGTTAGACAACTACCAGGCATCGTTGCTCATGGAGCGACTTGGCATCGCGATTATTGGCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002775","ARO_id":"39209","ARO_name":"QnrB62","ARO_description":"QnrB62 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"853":{"model_id":"853","model_name":"OXA-160","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"800":{"protein_sequence":{"accession":"ADB28891.1","sequence":"MKKFILPIFSISILVSLSACSSIKTKSEDNFHISSQQHEKAIKSYFDEAQTQGVIIIKEGKNLSTYGNALARANKEYVPASTFKMLNALIGLENHKATTNEIFKWDGKKRTYPMWEKDMTLGEAMALSAVPVYQELARRTGLELMQKEVKRVNFGNTNIGTQVDNFWLVGPLKITPVQEVNFADDLAHNRLPFKLETQEEVKKMLLIKEVNGSKIYAKSGWGMGVTSQVGWLTGWVEQANGKKIPFSLNLEMKEGMSGSIRNEITYKSLENLGII"},"dna_sequence":{"accession":"GU199038","fmin":"1195","fmax":"2023","strand":"+","sequence":"ATGAAAAAATTTATACTTCCTATATTCAGCATTTCTATTCTAGTTTCTCTCAGTGCATGTTCATCTATTAAAACTAAATCTGAAGATAATTTTCATATTTCTTCTCAGCAACATGAAAAAGCTATTAAAAGCTATTTTGATGAAGCTCAAACACAGGGTGTAATTATTATTAAAGAGGGTAAAAATCTTAGCACCTATGGTAATGCTCTTGCACGAGCAAATAAAGAATATGTCCCTGCATCAACATTTAAGATGCTAAATGCTTTAATCGGGCTAGAAAATCATAAAGCAACAACAAATGAGATTTTCAAATGGGATGGTAAAAAAAGAACTTATCCTATGTGGGAGAAAGATATGACTTTAGGTGAGGCAATGGCATTGTCAGCAGTTCCAGTATATCAAGAGCTTGCAAGACGGACTGGCCTAGAGCTAATGCAGAAAGAAGTAAAGCGGGTTAATTTTGGAAATACAAATATTGGAACACAGGTCGATAATTTTTGGTTAGTTGGCCCCCTTAAAATTACACCAGTACAAGAAGTTAATTTTGCCGATGACCTTGCACATAACCGATTACCTTTTAAATTAGAAACTCAAGAAGAAGTTAAAAAAATGCTTCTAATTAAAGAAGTAAATGGTAGTAAGATTTATGCAAAAAGTGGATGGGGAATGGGTGTTACTTCACAGGTAGGTTGGTTGACTGGTTGGGTGGAGCAAGCTAATGGAAAAAAAATCCCCTTTTCGCTCAACTTAGAAATGAAAGAAGGAATGTCTGGTTCTATTCGTAATGAAATTACTTATAAGTCGCTAGAAAATCTTGGAATCATTTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001663","ARO_id":"38063","ARO_name":"OXA-160","ARO_description":"OXA-160 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"854":{"model_id":"854","model_name":"CMY-58","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1362":{"protein_sequence":{"accession":"ADY19254.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYCVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"HQ185697","fmin":"1267","fmax":"2413","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATTGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002072","ARO_id":"38472","ARO_name":"CMY-58","ARO_description":"CMY-58 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"855":{"model_id":"855","model_name":"TEM-142","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1490":{"protein_sequence":{"accession":"ABD60314.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGANERGSRGIIAALGPDGKPSRIVVIYMTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"DQ388882","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAATGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACATGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001005","ARO_id":"37385","ARO_name":"TEM-142","ARO_description":"TEM-142 is an beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"856":{"model_id":"856","model_name":"mepR","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"250"}},"model_sequences":{"sequence":{"80":{"protein_sequence":{"accession":"YP_001440920.1","sequence":"MEFTYSYLFRMISHEMKQKADQKLEQFDITNEQGHTLGYLYAHQQDGLTQNDIAKALQRTGPTVSNLLRNLERKKLIYRYVDAQDTRRKNIGLTTSGIKLVEAFTSIFDEMEQTLVSQLSEEENEQMKANLTKMLSSLQ"},"dna_sequence":{"accession":"NC_009782","fmin":"379934","fmax":"380354","strand":"+","sequence":"ATGGAATTCACTTATTCGTATTTATTTAGAATGATTAGTCATGAGATGAAACAAAAGGCTGATCAAAAGTTAGAGCAATTTGATATTACAAATGAGCAAGGTCATACGTTAGGTTATCTTTATGCACATCAACAAGATGGACTGACACAAAATGATATTGCTAAAGCATTACAACGAACAGGTCCAACTGTCAGTAATTTATTAAGGAACCTTGAACGTAAAAAGCTGATCTATCGCTATGTCGATGCACAAGATACGAGAAGAAAGAATATAGGACTGACTACCTCTGGGATTAAACTTGTAGAAGCATTCACTTCGATATTTGATGAAATGGAGCAAACACTCGTATCGCAGTTATCTGAAGAAGAAAATGAACAAATGAAAGCAAACTTAACTAAAATGTTATCTAGTTTACAATAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35524","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus Mu3","NCBI_taxonomy_id":"418127"}}}},"ARO_accession":"3000746","ARO_id":"37126","ARO_name":"mepR","ARO_description":"MepR is an upstream repressor of MepA in Staphylococcus aureus. It is part of the mepRAB operon.","ARO_category":{"36251":{"category_aro_accession":"3000112","category_aro_cvterm_id":"36251","category_aro_name":"multidrug and toxic compound extrusion (MATE) transporter","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Multidrug and toxic compound extrusion (MATE) transporters utilize the cationic gradient across the membrane as an energy source. Although there is a diverse substrate specificity, almost all MATE transporters recognize fluoroquinolones. Arciflavine, ethidium and aminoglycosides are also good substrates.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"858":{"model_id":"858","model_name":"IND-14","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1908":{"protein_sequence":{"accession":"ADK38716.1","sequence":"MKKRIQFFMVSMMLSPLFSAQVKDFVIEPPIKKNLHIYKTFGVFGGKEYSANSVYLVTQKGVVLFDVPWEKVQYQSLMDTIQKRHNLPVIAVFATHSHDDRAGDLSFFNNKGIKTYATAKTNEFLKKDGKATSTEIIKTGKPYRIGGEEFVVDFLGEGHTADNVVVWFPKYNVLDGGCLVKSKAATDLGYIKEANVEQWPKTINKLKSKYSKASLVIPGHDEWKGGGHIEHTLELLNKK"},"dna_sequence":{"accession":"HM367709","fmin":"7","fmax":"727","strand":"+","sequence":"ATGAAAAAAAGAATTCAGTTCTTTATGGTTTCAATGATGCTAAGTCCATTATTCAGTGCCCAGGTAAAAGATTTTGTCATCGAACCACCGATTAAAAAGAATTTACATATTTACAAAACTTTTGGTGTATTCGGAGGTAAAGAATATTCTGCCAATTCAGTATATCTTGTTACCCAAAAAGGAGTTGTCTTATTTGATGTTCCGTGGGAAAAGGTACAGTACCAAAGCCTGATGGATACCATCCAAAAACGCCACAATTTACCCGTAATAGCGGTGTTTGCCACTCACTCCCATGATGACCGTGCCGGAGATCTGAGCTTTTTTAACAACAAAGGAATTAAAACCTACGCTACTGCCAAAACCAATGAGTTCCTGAAAAAAGACGGAAAAGCAACATCCACAGAGATCATTAAGACCGGAAAACCTTATCGCATAGGAGGTGAGGAATTTGTGGTTGATTTTCTTGGAGAAGGGCATACTGCTGATAATGTAGTGGTATGGTTTCCCAAATATAACGTCCTGGATGGCGGATGCCTTGTAAAAAGTAAAGCTGCAACCGATCTTGGATATATTAAGGAAGCCAATGTAGAGCAATGGCCCAAGACCATCAATAAACTGAAATCCAAATATTCAAAAGCAAGCCTGGTTATTCCCGGACATGATGAATGGAAAGGTGGAGGCCATATAGAGCATACTCTTGAACTTCTTAACAAAAAATAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36916","NCBI_taxonomy_name":"Chryseobacterium indologenes","NCBI_taxonomy_id":"253"}}}},"ARO_accession":"3002269","ARO_id":"38669","ARO_name":"IND-14","ARO_description":"IND-14 is a beta-lactamase found in Escherichia coli","ARO_category":{"36199":{"category_aro_accession":"3000060","category_aro_cvterm_id":"36199","category_aro_name":"IND beta-lactamase","category_aro_description":"IND beta-lactamases are class B carbapenem-hydrolyzing beta-lactamases","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"860":{"model_id":"860","model_name":"TEM-42","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1326":{"protein_sequence":{"accession":"CAA66659.1","sequence":"QHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGVRVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASKRGSRGIIAALGPDGKPSRIVVIYMTGSQATMDERNRQIAEIGASLIK"},"dna_sequence":{"accession":"X98047","fmin":"0","fmax":"844","strand":"+","sequence":"CAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGTACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTAAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACATGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3000911","ARO_id":"37291","ARO_name":"TEM-42","ARO_description":"TEM-42 is an extended-spectrum beta-lactamase that has been found in clinical isolates.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"861":{"model_id":"861","model_name":"OXA-215","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1295":{"protein_sequence":{"accession":"AEV91554.1","sequence":"MKLSKLYTLTVLIGFGLSGVACQHIHTPVSFNQIENDQTKQIASLFENVQTTGVLITFDGQAYKAYGNDLNRAKTAYIPASTFKILNALIGIEHDKTSPNEVFKWDGQKRAFESWEKDLTLAEAMQASAVPVYQALAQRIGLDLMAKEVKRVGFGNTRIGTQVDNFWLIGPLKITPIEEAQFAYRLAKQELPFTPKTQQQVIDMLLVDEIRGTKVYAKSGWGMDITPQVGWWTGWIEDPNGKVIAFSLNMEMNQPTHAAARKEIVYQALTQLKLL"},"dna_sequence":{"accession":"JN861783","fmin":"0","fmax":"828","strand":"+","sequence":"ATGAAGCTATCAAAATTATACACCCTCACTGTGCTCATAGGATTTGGATTAAGCGGTGTCGCCTGCCAGCATATCCATACTCCAGTCTCGTTCAATCAAATTGAAAACGATCAAACAAAGCAGATCGCTTCCTTGTTTGAGAATGTTCAAACAACAGGTGTTCTAATTACCTTTGATGGACAGGCGTATAAAGCATACGGTAATGATCTGAATCGTGCCAAAACTGCGTATATCCCAGCATCTACTTTCAAAATATTAAATGCTTTGATTGGCATTGAACATGATAAAACTTCACCAAATGAAGTATTTAAGTGGGATGGTCAGAAGCGTGCTTTTGAAAGTTGGGAAAAAGATCTGACTTTAGCTGAAGCCATGCAAGCTTCTGCTGTACCTGTTTATCAAGCGCTTGCCCAGAGAATCGGATTGGATTTGATGGCAAAGGAAGTCAAAAGAGTCGGCTTCGGTAATACACGCATCGGAACACAAGTTGATAACTTCTGGCTCATTGGACCTTTAAAGATCACGCCAATCGAAGAAGCTCAATTTGCTTACAGGCTTGCGAAACAGGAGTTACCGTTTACCCCAAAAACACAACAGCAAGTGATTGATATGCTGCTGGTGGATGAAATACGGGGAACTAAAGTTTACGCCAAAAGTGGTTGGGGAATGGATATTACTCCGCAAGTAGGATGGTGGACTGGATGGATTGAAGATCCGAACGGAAAAGTGATCGCTTTTTCTCTCAATATGGAAATGAATCAACCTACACATGCAGCTGCACGTAAAGAAATTGTTTATCAGGCACTTACGCAATTGAAATTATTGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36938","NCBI_taxonomy_name":"Acinetobacter haemolyticus","NCBI_taxonomy_id":"29430"}}}},"ARO_accession":"3001714","ARO_id":"38114","ARO_name":"OXA-215","ARO_description":"OXA-215 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"862":{"model_id":"862","model_name":"IMP-16","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"836":{"protein_sequence":{"accession":"CAE48334.1","sequence":"MKKLFVLCIFLFCSITAAGESLPDLKIEKLEDGVYVHTSFEEVNGWGVVTKHGLVFLVNTDAYLIDTPFAAKDTEKLVNWFVERGYKIKGSISSHFHSDSSGGIEWLNSQSIPTYASELTNELLKKNGKVQAKNSFSGVSYWLLKNKIEIFYPGPGHTQDNVVVWLPEKKILFGGCFVKPYGLGNLDDANVEAWPHSAEILMSRYGNAKLVVPSHSDVGDASLLKLTWEQAVKGLKESKKPSQPSN"},"dna_sequence":{"accession":"AJ584652","fmin":"1043","fmax":"1784","strand":"+","sequence":"ATGAAAAAATTATTTGTTTTATGTATCTTTTTGTTTTGTAGCATTACTGCCGCAGGAGAGTCTTTGCCTGATTTAAAAATTGAGAAGCTTGAAGACGGTGTTTATGTTCATACATCGTTTGAAGAAGTTAACGGTTGGGGTGTTGTTACTAAACACGGTTTGGTGTTTCTTGTAAACACAGACGCCTATCTGATTGACACTCCATTTGCTGCTAAAGACACTGAAAAGTTAGTAAATTGGTTTGTGGAGCGCGGTTATAAAATAAAAGGCAGTATTTCCTCACATTTTCATAGCGACAGCTCGGGTGGAATAGAATGGCTTAACTCTCAATCTATTCCCACGTATGCATCTGAATTAACAAACGAACTTCTTAAAAAGAACGGTAAGGTGCAAGCTAAAAACTCATTTAGCGGAGTTAGTTATTGGCTACTTAAAAATAAAATTGAAATTTTTTATCCGGGCCCTGGGCACACTCAAGATAACGTAGTGGTTTGGTTGCCTGAAAAGAAAATTTTATTTGGTGGGTGTTTTGTTAAACCGTACGGTCTTGGAAATCTCGATGATGCAAATGTTGAAGCGTGGCCACATTCTGCTGAAATATTAATGTCTAGGTATGGTAATGCAAAACTGGTTGTTCCAAGCCATAGTGACGTCGGAGATGCGTCGCTCTTGAAGCTTACATGGGAGCAGGCTGTTAAAGGGCTAAAAGAAAGTAAAAAACCATCACAGCCAAGTAACTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002207","ARO_id":"38607","ARO_name":"IMP-16","ARO_description":"IMP-16 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"863":{"model_id":"863","model_name":"PER-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1309":{"protein_sequence":{"accession":"AEI54993.1","sequence":"MNVIIKAVVTASTLLMVSFSSFETSAQSPLLKEQIESIVIGKKATVGVAVWGPDDLEPLLINPFEKFPMQSVFKLHLAMLVLHQVDQGKLDLNQTVIVNRAKVLQNTWAPIMKAYQGDQFSVPVQQLLQYSVSHSDNVACDLLFELVGGPAALHDYIQSMGIKETAVVANEAQMHADDQVQYQNWTSMKGAAEILKKFEQKTQLSETSQALLWKWMVETTTGPERLKGLLPAGTVVAHKTGTSGVRAGKTAATNDLGIILLPDGRPLLVAVFVKDSAESSRTNEAIIAQVAQAAYQFELKKLSALSPN"},"dna_sequence":{"accession":"HQ713678","fmin":"5756","fmax":"6683","strand":"+","sequence":"ATGAATGTCATTATAAAAGCTGTAGTTACTGCCTCGACGCTACTGATGGTATCTTTTAGTTCATTCGAAACCTCAGCGCAATCCCCACTGTTAAAAGAGCAAATTGAATCCATAGTCATTGGAAAAAAAGCCACTGTAGGCGTTGCAGTGTGGGGGCCTGACGATCTGGAACCTTTACTGATTAATCCTTTTGAAAAATTCCCAATGCAAAGTGTATTTAAATTGCATTTAGCTATGTTGGTACTGCATCAGGTTGATCAGGGAAAGTTGGATTTAAATCAGACCGTTATCGTAAACAGGGCTAAGGTTTTACAGAATACCTGGGCTCCGATAATGAAAGCGTATCAGGGAGACCAGTTTAGTGTTCCAGTGCAGCAACTGCTGCAATACTCGGTCTCGCACAGCGATAACGTGGCCTGTGATTTGTTATTTGAACTGGTTGGTGGACCAGCTGCTTTGCATGACTATATCCAGTCTATGGGTATAAAGGAGACCGCTGTGGTCGCAAATGAAGCGCAGATGCACGCCGATGATCAGGTGCAGTATCAAAACTGGACCTCGATGAAGGGGGCCGCAGAGATCCTGAAAAAGTTTGAGCAAAAAACACAGCTGTCTGAAACCTCGCAGGCTTTGTTATGGAAGTGGATGGTCGAAACCACCACAGGACCAGAGCGGTTAAAAGGTTTGTTACCAGCTGGTACTGTGGTCGCACATAAAACTGGTACTTCGGGTGTCAGAGCCGGGAAAACTGCGGCCACTAATGATTTAGGTATCATTCTGTTGCCTGATGGACGGCCCTTGCTGGTTGCTGTTTTTGTGAAAGACTCAGCCGAGTCAAGCCGAACCAATGAAGCTATCATTGCGCAGGTTGCTCAGGCTGCGTATCAATTTGAATTGAAAAAGCTTTCTGCCCTAAGCCCAAATTAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3002369","ARO_id":"38769","ARO_name":"PER-7","ARO_description":"PER-7 is a beta-lactamase found in Acinetobacter baumannii","ARO_category":{"36195":{"category_aro_accession":"3000056","category_aro_cvterm_id":"36195","category_aro_name":"PER beta-lactamase","category_aro_description":"PER beta-lactamases are plasmid-mediated extended spectrum beta-lactamases found in the Enterobacteriaceae family.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"864":{"model_id":"864","model_name":"CMY-61","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1701":{"protein_sequence":{"accession":"AEM97673.1","sequence":"MMNRYAAALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"JF460795","fmin":"0","fmax":"1143","strand":"+","sequence":"ATGATGAATCGTTATGCTGCAGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002074","ARO_id":"38474","ARO_name":"CMY-61","ARO_description":"CMY-61 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"865":{"model_id":"865","model_name":"OXA-244","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2006":{"protein_sequence":{"accession":"AGC60012.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTGIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"JX438000","fmin":"0","fmax":"798","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGACAGTTTCTGGCTCGACGGTGGTATTCGAATTTCGGCCACGGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATGCTGACCGAAGCCAATGGTGACTATATTATTCGGGCTAAAACTGGATACTCGACTGGAATCGAACCTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001786","ARO_id":"38186","ARO_name":"OXA-244","ARO_description":"OXA-244 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"866":{"model_id":"866","model_name":"adeB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"2060"}},"model_sequences":{"sequence":{"4257":{"protein_sequence":{"accession":"AAL14440.1","sequence":"MSQFFIRRPVFAWVIAIFIIIFGLLSIPKLPIARFPSVAPPQVNISATYPGATAKTINDSVVTLIERELSGVKNLLYYSATTDTSGTAEITATFKPGTDVEMAQVDVQNKIKAVEARLPQVVRQQGLQVEASSSGFLMLVGINSPNNQYSEVDLSDYLVRNVVEELKRVEGVGKVQSFGAEKAMRIWVDPNKLVSYGLSISDVNNAIRENNVEIAPGRLGDLPAEKGQLITIPLSAQGQLSSLEQFKNISLKSKTNGSVIKLSDVANVEIGSQAYNFAILENGKPATAAAIQLSPGANAVKTAEVVRAKIEELKLNLPEGMEFSIPYDTAPFVKISIEKVIHTLLEAMVLVFIVMYLFLHNVRYTLIPAIVAPIALLGTFTVMLLAGFSINVLTMFGMVLAIGIIVDDAIVVVENVERIMATEGLSPKDATSKAMKEITSPIIGITLVLAAVFLPMAFASGSVGVIYKQFTLTMSVSILFSALLALILTPALCATILKPIDGHHQKKGFFAWFDRSFDKVTKKYELMLLKIIKHTVPMMVIFLVITGITFTGMKYWPTAFMPEEDQGWFMTSFQLPSDATAERTRNVVNQFENNLKDNPDVKSNTTILGWGFSGAGQNVAVAFTTLKDFKERTSSASKMTSDVNSSMANSTEGETMAVLPPAIDELGTFSGFSLRLQDRANLGMPALLAAQDELMAMAAKNKKFYMVWNEGLPQGDNISLKIDREKLSAFGVKFSDVSDIISTSMGSMYINDFPNQGRMQQVIVQVEAKSRMQLKDILNLKVMGSSGQLVSLSEVVTPQWNKAPQQYNRYNGRPSLSIAGIPNFDTSSGEAMREMEQLIAKLPKGIGYEWTGISLQEKQSESQMAFLLGLSMLVVFLVLAALYESWAIPLSVMLVVPLGIFGAIIAIMSRGLMNDVFFKIGLITIIGLSAKNAILIVEFAKMLKEEGMSLIEATVAAAKLRLRPILMTSLAFTCGVIPLVIASGASSETQHALGTGVFGGMISATILAIFFVPVFFIFILGAVEKLFSSKKKISS"},"dna_sequence":{"accession":"AF370885.1","fmin":"4628","fmax":"7736","strand":"+","sequence":"ATGTCACAATTTTTTATTCGTCGTCCCGTTTTTGCTTGGGTTATTGCGATCTTCATTATTATATTTGGATTGCTGAGCATTCCTAAACTGCCAATTGCACGTTTTCCAAGTGTGGCCCCGCCACAGGTGAATATTAGTGCGACTTATCCTGGTGCTACAGCTAAAACCATTAACGATAGCGTTGTAACCTTAATTGAGCGCGAATTATCGGGTGTAAAAAATCTACTCTACTATAGTGCGACAACAGATACCTCCGGTACAGCAGAGATTACGGCTACGTTTAAACCAGGCACAGATGTGGAAATGGCTCAGGTTGACGTTCAAAATAAAATCAAGGCTGTAGAAGCTCGCTTACCGCAAGTTGTACGTCAGCAAGGTTTACAGGTTGAGGCTTCATCGTCCGGATTTTTAATGCTGGTCGGGATTAACTCTCCAAATAATCAATATTCCGAAGTTGATTTGAGTGATTATTTGGTTCGAAATGTTGTAGAAGAGCTAAAACGTGTCGAAGGTGTAGGGAAGGTTCAATCTTTCGGTGCCGAGAAAGCTATGCGTATTTGGGTCGACCCGAATAAGCTTGTTTCTTACGGTTTATCGATTAGTGATGTGAATAATGCCATTCGTGAAAATAATGTCGAAATTGCACCCGGCCGACTTGGTGATTTACCAGCTGAAAAAGGCCAGCTCATTACTATTCCATTGTCTGCTCAAGGGCAATTGTCTAGTCTCGAGCAATTTAAAAATATTAGCTTAAAAAGTAAAACTAACGGTAGCGTAATTAAGTTATCTGATGTTGCCAATGTAGAAATAGGCTCACAGGCATATAACTTTGCCATTTTGGAAAATGGTAAGCCTGCTACCGCGGCAGCAATTCAATTAAGCCCGGGTGCTAACGCCGTGAAAACTGCCGAAGTTGTTCGAGCAAAAATTGAAGAGTTGAAGCTAAATTTACCGGAAGGCATGGAGTTTAGTATTCCTTACGACACCGCGCCGTTTGTCAAAATTTCAATTGAAAAGGTAATTCATACATTACTTGAAGCCATGGTTCTGGTTTTCATTGTGATGTATCTATTTTTACATAATGTCCGCTATACGCTTATTCCAGCGATTGTGGCGCCTATTGCCTTACTCGGTACTTTTACCGTGATGTTGCTTGCCGGCTTTTCAATTAACGTACTCACCATGTTCGGTATGGTGCTTGCCATCGGGATTATTGTCGACGATGCCATTGTCGTGGTTGAAAACGTCGAAAGGATTATGGCGACAGAAGGATTATCGCCTAAAGATGCAACCTCTAAAGCAATGAAAGAGATTACCAGCCCGATTATTGGTATTACGCTGGTATTGGCGGCAGTATTTTTACCTATGGCATTTGCGAGTGGTTCTGTAGGGGTAATCTATAAACAGTTTACCTTGACCATGTCGGTATCTATTTTATTTTCAGCGCTATTGGCACTTATTTTAACACCGGCACTTTGTGCCACGATTTTAAAACCAATCGATGGGCATCACCAGAAGAAGGGCTTCTTTGCATGGTTTGACCGTAGTTTCGATAAAGTCACTAAAAAGTATGAATTGATGCTGCTTAAAATCATCAAACATACAGTTCCAATGATGGTGATCTTTTTAGTAATTACCGGTATTACCTTTACCGGAATGAAATATTGGCCAACAGCATTTATGCCAGAGGAAGATCAAGGTTGGTTCATGACTTCGTTCCAGCTACCTTCAGATGCAACCGCTGAGCGTACTCGGAATGTAGTCAATCAATTTGAAAATAATTTGAAAGACAATCCCGATGTAAAAAGTAATACCACCATTTTGGGATGGGGTTTTAGTGGCGCAGGACAAAATGTAGCTGTGGCTTTTACGACACTTAAAGACTTCAAAGAGCGGACTAGCTCTGCATCTAAGATGACAAGCGACGTTAATTCTTCTATGGCGAACAGTACGGAAGGCGAGACTATGGCCGTGTTACCACCCGCTATTGATGAGTTAGGTACTTTTTCAGGTTTCAGTTTACGTTTACAAGACCGCGCTAACTTAGGTATGCCTGCTTTACTGGCTGCTCAAGATGAACTTATGGCAATGGCAGCCAAGAATAAAAAGTTCTATATGGTTTGGAATGAAGGGTTGCCACAAGGTGACAATATTTCTTTAAAAATTGACCGTGAAAAGCTTAGTGCATTTGGTGTTAAGTTTTCTGATGTTTCAGACATCATTTCTACATCAATGGGTTCAATGTATATCAATGACTTCCCTAATCAAGGACGTATGCAACAAGTCATTGTACAGGTTGAGGCTAAATCACGTATGCAATTGAAAGATATCTTGAATCTGAAAGTCATGGGTTCAAGCGGTCAATTAGTCTCGTTATCAGAAGTTGTAACGCCACAATGGAATAAGGCACCACAACAATATAATCGTTATAACGGACGACCATCTTTGAGTATTGCTGGTATTCCTAACTTCGATACGTCATCGGGTGAAGCAATGCGTGAAATGGAACAACTGATTGCGAAATTACCGAAAGGTATTGGCTACGAGTGGACAGGTATTTCCTTACAGGAAAAGCAGTCTGAATCACAAATGGCCTTTTTACTTGGTTTATCCATGTTAGTTGTCTTCCTTGTCTTGGCTGCACTCTATGAAAGCTGGGCAATTCCACTTTCTGTGATGCTAGTTGTGCCACTCGGTATTTTTGGAGCAATCATTGCCATTATGTCTAGGGGGTTAATGAATGATGTGTTCTTCAAAATCGGGCTAATTACCATTATTGGTCTATCGGCAAAGAATGCGATTTTGATTGTTGAATTTGCGAAAATGCTGAAAGAAGAAGGCATGAGTTTGATTGAAGCCACTGTTGCCGCAGCCAAACTTCGCTTACGGCCAATTCTGATGACATCACTTGCATTTACGTGTGGTGTAATTCCTTTGGTGATTGCCTCAGGTGCAAGTTCAGAAACTCAACATGCTTTAGGCACAGGGGTTTTTGGCGGCATGATTTCAGCCACCATTCTGGCTATTTTCTTTGTTCCCGTGTTTTTTATCTTCATTTTGGGTGCAGTAGAAAAGCTATTTTCCTCTAAGAAAAAAATCTCATCTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3000775","ARO_id":"37155","ARO_name":"adeB","ARO_description":"AdeB is the multidrug transporter of the adeABC efflux system.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"867":{"model_id":"867","model_name":"OXA-175","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"801":{"protein_sequence":{"accession":"ADI58619.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIRNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWVVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"HM113561","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAGAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGGTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001659","ARO_id":"38059","ARO_name":"OXA-175","ARO_description":"OXA-175 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"868":{"model_id":"868","model_name":"DHA-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1822":{"protein_sequence":{"accession":"CAA76196.1","sequence":"MKKSLSATLISALLAFSAPGFSAADNVAAVVDSTIKPLMAQQDIPGMAVAVSVKGKPYYFNYGFADIQAKQPVTENTLFELGSVSKTFTGVLGAVSVAKKEMALNDPAAKYQPELALPQWKGITLLDLATYTAGGLPLQVPDAVKSRADLLNFYQQWQPSRKPGDMRLYANSSIGLFGALTANAAGMPYEQLLTARILAPLGLSHTFITVPESAQSQYAYGYKNKKPVRVSPGQLDAESYGVKSASKDMLRWAEMNMEPSRAGNADLEMAMYLAQTRYYKTAAINQGLGWEMYDWPQQKDMIINGVTNEVALQPHPVTDNQVQPYNRASWVHKTGATTGFGAYVAFIPEKQVAIVILANKNYPNTERVKAAQAILSALE"},"dna_sequence":{"accession":"Y16410","fmin":"986","fmax":"2126","strand":"+","sequence":"ATGAAAAAATCGTTATCTGCAACACTGATTTCCGCTCTGCTGGCGTTTTCCGCCCCGGGGTTTTCTGCCGCTGATAATGTCGCGGCGGTGGTGGACAGCACCATTAAACCGCTGATGGCACAGCAGGATATTCCCGGGATGGCGGTTGCCGTCTCCGTAAAGGGTAAGCCCTATTATTTCAATTATGGTTTTGCCGATATTCAGGCAAAACAGCCGGTCACTGAAAATACACTATTTGAGCTCGGATCTGTAAGTAAAACTTTCACAGGTGTGCTGGGTGCGGTTTCTGTGGCGAAAAAAGAGATGGCGCTGAATGATCCGGCGGCAAAATACCAGCCGGAGCTGGCTCTGCCGCAGTGGAAGGGGATCACATTGCTGGATCTGGCTACCTATACCGCAGGCGGACTGCCGTTACAGGTGCCGGATGCGGTAAAAAGCCGTGCGGATCTGCTGAATTTCTATCAGCAGTGGCAGCCGTCCCGGAAACCGGGCGATATGCGTCTGTATGCAAACAGCAGTATCGGCCTGTTTGGTGCTCTGACCGCAAACGCGGCGGGGATGCCGTATGAGCAGTTGCTGACTGCACGGATCCTGGCACCGCTGGGGTTATCTCACACCTTTATTACTGTGCCGGAAAGTGCGCAAAGCCAGTATGCGTACGGTTATAAAAACAAAAAACCGGTCCGCGTGTCGCCGGGACAGCTTGATGCGGAATCTTACGGCGTGAAATCCGCCTCAAAAGATATGCTGCGCTGGGCGGAAATGAATATGGAGCCGTCACGGGCCGGTAATGCGGATCTGGAAATGGCAATGTATCTCGCCCAGACCCGCTACTATAAAACCGCCGCGATTAACCAGGGGCTGGGCTGGGAAATGTATGACTGGCCGCAGCAGAAAGATATGATCATTAACGGTGTGACCAACGAGGTCGCATTGCAGCCGCATCCGGTAACAGACAACCAGGTTCAGCCGTATAACCGTGCTTCCTGGGTGCATAAAACGGGCGCAACAACTGGTTTCGGCGCCTATGTCGCCTTTATTCCGGAAAAACAGGTGGCGATTGTGATTCTGGCGAATAAAAACTACCCGAATACCGAAAGAGTCAAAGCTGCACAGGCTATTTTGAGTGCACTGGAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35750","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Enteritidis","NCBI_taxonomy_id":"149539"}}}},"ARO_accession":"3002132","ARO_id":"38532","ARO_name":"DHA-1","ARO_description":"DHA-1 is a class C beta-lactamase found in Morganella morganii and Salmonella enterica","ARO_category":{"36207":{"category_aro_accession":"3000068","category_aro_cvterm_id":"36207","category_aro_name":"DHA beta-lactamase","category_aro_description":"DHA beta-lactamases are plasmid-mediated AmpC \u03b2-lactamases that confer resistance to cephamycins and oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"869":{"model_id":"869","model_name":"CRP","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"4350":{"protein_sequence":{"accession":"BAE77933.1","sequence":"MVLGKPQTDPTLEWFLSHCHIHKYPSKSKLIHQGEKAETLYYIVKGSVAVLIKDEEGKEMILSYLNQGDFIGELGLFEEGQERSAWVRAKTACEVAEISYKKFRQLIQVNPDILMRLSAQMARRLQVTSEKVGNLAFLDVTGRIAQTLLNLAKQPDAMTHPDGMQIKITRQEIGQIVGCSRETVGRILKMLEDQNLISAHGKTIVVYGTR"},"dna_sequence":{"accession":"AP009048","fmin":"4153663","fmax":"4154296","strand":"-","sequence":"TTAACGAGTGCCGTAAACGACGATGGTTTTACCGTGTGCGGAGATCAGGTTCTGATCTTCCAGCATCTTCAGAATGCGTCCCACGGTTTCACGAGAACAGCCGACAATCTGACCAATTTCCTGACGGGTAATTTTGATTTGCATACCGTCCGGGTGAGTCATAGCGTCTGGTTGTTTTGCCAGATTCAGCAGAGTCTGTGCAATGCGGCCCGTCACGTCGAGGAACGCCAGGTTGCCCACTTTCTCTGAAGTGACTTGCAGACGACGCGCCATCTGTGCAGACAAACGCATCAGAATGTCCGGGTTTACCTGAATCAATTGGCGAAATTTTTTGTACGAAATTTCAGCCACTTCACAGGCGGTTTTCGCACGTACCCATGCGCTACGTTCCTGGCCCTCTTCAAACAGGCCCAGTTCGCCAATAAAATCACCCTGATTCAGATAGGAGAGGATCATTTCTTTACCCTCTTCGTCTTTGATCAGCACTGCCACAGAGCCTTTAACGATGTAGTACAGCGTTTCCGCTTTTTCACCCTGGTGAATAAGCTTGCTCTTGGATGGGTACTTATGAATGTGGCAATGAGACAAGAACCATTCGAGAGTCGGGTCTGTTTGCGGTTTGCCAAGCACCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36839","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. W3110","NCBI_taxonomy_id":"316407"}}}},"ARO_accession":"3000518","ARO_id":"36657","ARO_name":"CRP","ARO_description":"CRP is a global regulator that represses MdtEF multidrug efflux pump expression.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35930":{"category_aro_accession":"0000011","category_aro_cvterm_id":"35930","category_aro_name":"cloxacillin","category_aro_description":"Cloxacillin is a semisynthetic, isoxazolyl penicillin derivative in the beta-lactam class of antibiotics. It interferes with peptidogylcan synthesis and is commonly used for treating penicillin-resistant Staphylococcus aureus infections.","category_aro_class_name":"Antibiotic"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"871":{"model_id":"871","model_name":"CGB-1 beta-lactamase","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"956":{"protein_sequence":{"accession":"ABS29619.1","sequence":"MKKSIPFFIISMLLSPLANAQDTQVRDFVIEPQIQPNFYIYKTFGVFGGKEYSTNAVYLVTKKGVVLFDVPWQKTQYQSLMDTIQKRHHLPVIAVFATHSHEDRAGDLSFYNKKGIKTYATAKTNEILKKEGKATSTEIIKTGKPYRIGGEEFVVDFLGEGHTADNVVVWFPKYKILDGGCLVKSKAAADLGYTGEANVAQWPKTMEKLKSKYAQATLIIPGHDEWKGGGHVEHTLDLLNKK"},"dna_sequence":{"accession":"EF672680","fmin":"0","fmax":"729","strand":"+","sequence":"ATGAAAAAAAGCATTCCGTTTTTTATTATTTCGATGTTGCTAAGCCCATTGGCAAACGCCCAGGACACACAGGTAAGAGATTTTGTAATTGAGCCTCAAATTCAACCTAACTTTTATATTTACAAAACTTTCGGAGTATTCGGAGGGAAAGAATATTCTACCAATGCCGTGTATCTGGTAACTAAAAAAGGAGTTGTCCTGTTTGATGTTCCATGGCAGAAAACCCAATACCAAAGTCTGATGGATACCATTCAAAAACGTCATCATCTGCCGGTTATTGCGGTATTTGCCACCCATTCTCATGAAGACAGAGCGGGAGATTTAAGCTTTTATAATAAGAAAGGAATCAAAACCTACGCTACAGCAAAAACCAATGAAATTTTAAAGAAAGAAGGAAAAGCAACTTCTACAGAAATTATAAAAACCGGTAAACCTTACCGTATTGGCGGTGAAGAATTTGTAGTAGACTTTCTTGGTGAAGGTCATACGGCGGATAATGTAGTGGTTTGGTTTCCCAAATATAAGATACTGGACGGAGGCTGCCTTGTAAAAAGTAAAGCAGCAGCCGATCTTGGCTACACCGGCGAAGCCAACGTTGCACAATGGCCAAAAACAATGGAAAAGTTAAAATCCAAATACGCTCAGGCAACCCTGATCATTCCCGGACATGATGAATGGAAAGGCGGCGGCCATGTAGAGCACACACTTGATCTTTTAAATAAAAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39078","NCBI_taxonomy_name":"Chryseobacterium gleum","NCBI_taxonomy_id":"250"}}}},"ARO_accession":"3000841","ARO_id":"37221","ARO_name":"CGB-1","ARO_description":"CGB-1 is an Ambler class B beta-lactamase that mediates resistance for carbapenems in Chryseobacterium gleum","ARO_category":{"41367":{"category_aro_accession":"3004203","category_aro_cvterm_id":"41367","category_aro_name":"CGB beta-lactamase","category_aro_description":"CGB beta-lactamases are Class B beta-lactamases found in Chryseobacterium gleu that can hydrolyze penicillins; narrow- and expanded-spectrum cephalosporins; and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"872":{"model_id":"872","model_name":"vatC","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"211":{"protein_sequence":{"accession":"AAC61671.1","sequence":"MKWQNQQGPNPEEIYPIEGNKHVQFIKPSITKPNILVGEYSYYDSKDGESFESQVLYHYELIGDKLILGKFCSIGPGTTFIMNGANHRMDGSTFPFNLFGNGWEKHTPTLEDLPYKGNTEIGNDVWIGRDVTIMPGVKIGNGAIIAAKSVVTKNVDPYSVVGGNPSRLIKIRFSKEKIAALLKVRWWDLEIETINENIDCILNGDIKKVKRS"},"dna_sequence":{"accession":"AF015628","fmin":"1306","fmax":"1945","strand":"+","sequence":"ATGAAATGGCAAAATCAGCAAGGCCCCAATCCAGAAGAAATATACCCTATAGAAGGTAATAAACATGTTCAATTTATTAAACCATCTATAACAAAGCCCAATATTTTAGTTGGGGAATATTCATATTACGATAGTAAAGATGGTGAATCTTTTGAAAGCCAAGTTCTTTATCACTATGAATTGATTGGGGATAAACTAATATTAGGGAAGTTTTGTTCTATTGGACCCGGAACGACATTTATAATGAATGGGGCTAATCATCGTATGGATGGTTCAACATTTCCATTCAATCTTTTCGGAAATGGTTGGGAGAAGCATACCCCTACATTGGAAGACCTTCCTTATAAGGGTAACACGGAAATTGGGAACGATGTTTGGATTGGACGAGATGTGACAATTATGCCCGGTGTAAAAATAGGAAACGGGGCTATTATTGCAGCAAAATCGGTTGTGACAAAGAACGTTGATCCTTATTCAGTTGTTGGCGGTAATCCTTCACGATTAATTAAGATAAGGTTTTCCAAGGAAAAAATCGCAGCATTACTAAAAGTAAGGTGGTGGGACCTAGAGATAGAGACGATAAATGAAAATATTGATTGCATCCTGAATGGTGATATAAAAAAGGTTAAAAGAAGTTAGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36766","NCBI_taxonomy_name":"Staphylococcus cohnii","NCBI_taxonomy_id":"29382"}}}},"ARO_accession":"3002842","ARO_id":"39276","ARO_name":"vatC","ARO_description":"vatC is a plasmid-mediated acetyltransferase found in Staphylococcus cohnii","ARO_category":{"36592":{"category_aro_accession":"3000453","category_aro_cvterm_id":"36592","category_aro_name":"streptogramin vat acetyltransferase","category_aro_description":"vat (Virginiamycin acetyltransferases) enzymes catalyze the transfer of an acetyl group from acetyl-CoA to the secondary alcohol of streptogramin A compounds, thus inactivating virginiamycin-like antibiotics and conferring resistance to these compounds.","category_aro_class_name":"AMR Gene Family"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"873":{"model_id":"873","model_name":"KPC-19","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"954":{"protein_sequence":{"accession":"AIH07017.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVTGQ"},"dna_sequence":{"accession":"KJ775801","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCACGGGGCAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39097","NCBI_taxonomy_name":"Klebsiella pneumoniae subsp. pneumoniae","NCBI_taxonomy_id":"72407"}}}},"ARO_accession":"3002329","ARO_id":"38729","ARO_name":"KPC-19","ARO_description":"KPC-19 is a beta-lactamase. From the Lahey list of KPC beta-lactamases.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"875":{"model_id":"875","model_name":"dfrA19","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"716":{"protein_sequence":{"accession":"CAC81324.1","sequence":"MSHPQLELIVAVDSKLGFGKGGKIPWKCKEDMARFTRISKEIRVCVIGKHTYTDMRDMQLEKDGAEERIKEKGILPERESFVISSTLKQEDVIGATVVPDLRAVINLYENTDQRIAVIGGEKLYIQALSSATKLHMTIIPREFDCDRFIPVDPIQNNFHIDSSASETVEATVDETQERIHFATYVRNNQ"},"dna_sequence":{"accession":"AJ310778","fmin":"7003","fmax":"7573","strand":"+","sequence":"ATGAGTCACCCACAACTTGAGCTAATAGTCGCTGTGGATTCTAAGTTGGGATTCGGGAAAGGCGGCAAGATTCCATGGAAATGCAAAGAAGACATGGCGCGATTTACGCGGATTTCTAAAGAGATCCGCGTGTGCGTTATAGGGAAACACACGTATACTGACATGCGTGACATGCAGTTAGAAAAGGATGGCGCCGAGGAGCGAATCAAGGAGAAAGGAATTCTCCCCGAACGCGAATCGTTCGTGATCTCCTCGACGTTAAAACAAGAAGATGTCATAGGCGCTACTGTCGTTCCTGATCTTCGTGCTGTGATCAACCTGTATGAGAATACCGATCAACGCATTGCTGTCATTGGTGGGGAGAAGTTGTACATTCAAGCTCTTTCATCAGCAACGAAACTGCACATGACCATAATTCCAAGAGAGTTCGACTGTGATCGATTTATTCCTGTTGATCCGATCCAGAACAATTTTCACATTGATTCCAGTGCCAGCGAGACTGTGGAGGCAACCGTTGATGAGACTCAAGAGCGCATTCACTTTGCTACTTACGTGCGTAACAATCAGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35732","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium","NCBI_taxonomy_id":"90371"}}}},"ARO_accession":"3003015","ARO_id":"39449","ARO_name":"dfrA19","ARO_description":"dfrA19 is an integron-encoded dihydrofolate reductase found in Klebsiella pneumoniae","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36408":{"category_aro_accession":"3000269","category_aro_cvterm_id":"36408","category_aro_name":"brodimoprim","category_aro_description":"Brodimoprim is a structural derivative of trimethoprim and an inhibitor of bacterial dihydrofolate reductase. The 4-methoxy group of trimethoprim is replaced with a bromine atom.","category_aro_class_name":"Antibiotic"},"36423":{"category_aro_accession":"3000284","category_aro_cvterm_id":"36423","category_aro_name":"tetroxoprim","category_aro_description":"Tetroxoprim is a trimethoprim derivative that inhibits bacterial dihydrofolate reductase.","category_aro_class_name":"Antibiotic"},"36476":{"category_aro_accession":"3000337","category_aro_cvterm_id":"36476","category_aro_name":"iclaprim","category_aro_description":"Iclaprim is a bactericidal compound that inhibits dihydrofolate reductase. It is used against clinically important Gram-positive pathogens, including methicillin-sensitive Staphylococcus aureus and methicillin-resistant S. aureus.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"876":{"model_id":"876","model_name":"smeE","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"2070"}},"model_sequences":{"sequence":{"564":{"protein_sequence":{"accession":"CAC14595.1","sequence":"MARFFIDRPIFAWVIAIIIMLAGGLALFKLPVSMYPNVAPPAVEISATYPGASAKVVEDSVTQIIEQNMKGLDGLIYFSSNSSSNGQATITLTFESGTNPDIAQVQVQNKLQLAMPLLPQEVQRQGINVAKSSSGFLNAIAFVSENGSMDANDIADYVGSNVVDRLSRVPGVGNIQVFGGKYAMRIWLDPNKLHTYGLSVPEVTAAIKAQNAQVAIGQLGGAPSVKGQQLNATINAQSRLQTPEQFRNIIVRGAQDGAELRLGDVARVELGAESYDFVTRYNGQPASGLAVTLATGANALDTAAGVDAALEDMKGFFPAGLKAEIPYDTTPFVRVSIKGVVQTLIEAIVLVFVVMYLFLQNFRATLIPTIAVPVVLLGTFGVLAMLGFSVNMLTMFAMVLAIGLLVDDAIVVVENVERIMSEEGLSPLEATRKSMGQITGALVGIGLVLSAVFVPMAFMSGSTGVIYRQFSATIVSAMALSVLVAIVLTPALCATMLKPLKKGEHHVAHRGLAGRFFNGFNRGFDRTSESYQRGVRGIIHRPWRFMGIVAALFVLMGVLFVRLPSSFLPNEDQGVLMALVQAPVGATQERTLESIAALENHFLQNEKDAVDSVFSVQGFSFAGMGQNAGMAFVKLKDWSERDADNGVMPITGRAMAALGQIKDAFIFAFPPPAIPELGTASGYTFFLKDNSGQGHEALVAARNQLLGLAAGSKKLANVRPNGQEDTPQFRIDIDAAKATSLGLSIDQINGTLAAAWGSSYIDDFVDRGRVKRVFVQADQAFRMVPEDFDLWSVKNDKGEMVPFSAFATKHWDYGSPRLERYNGVSAMEIQGEPAPGVASGDAMAEIEQLAKQLPAGFGIEWTAMSYQERQAGSQTPLLYTLSLMIVFLCLAAMYESWSVPTAVLLAAPLGILGAVLANTFKGLERDIYFQVAMLTTVGLTSKNAILIVEFAKENLEKGASLIESIMHAVRDRLRPIVMTSLAFGMGVVPLAISTGAGSGAKQAIGTGVLGGMIVGTVLGVFFVPLFFVVVQRVFKRRSTT"},"dna_sequence":{"accession":"AJ252200","fmin":"1278","fmax":"4401","strand":"+","sequence":"ATGGCACGCTTTTTCATCGATCGACCCATCTTTGCGTGGGTGATCGCCATCATCATCATGCTCGCCGGCGGCCTGGCGCTGTTCAAGCTGCCGGTCTCGATGTACCCCAACGTCGCACCGCCGGCGGTGGAAATCAGCGCCACCTACCCGGGTGCATCGGCCAAGGTGGTCGAGGACTCGGTGACGCAGATCATCGAGCAGAACATGAAGGGCCTTGATGGCCTGATCTACTTCTCCTCCAACAGCTCGTCCAACGGCCAGGCCACCATCACCCTGACCTTCGAGAGCGGCACCAACCCGGATATCGCCCAGGTGCAGGTGCAGAACAAGCTGCAGCTGGCCATGCCGCTGCTGCCGCAGGAAGTGCAGCGGCAGGGCATCAACGTGGCCAAGTCCAGCTCGGGCTTCCTGAACGCCATCGCGTTCGTGTCCGAGAACGGCAGCATGGACGCCAACGACATCGCCGACTACGTCGGTTCCAATGTCGTCGACCGCCTGAGCCGCGTGCCGGGCGTGGGCAACATCCAGGTGTTCGGTGGCAAGTACGCCATGCGCATCTGGCTGGACCCGAACAAGCTGCATACCTATGGCCTGTCGGTGCCGGAAGTGACCGCCGCGATCAAGGCGCAGAACGCCCAGGTGGCGATCGGCCAGCTCGGCGGTGCGCCGTCGGTGAAGGGCCAGCAGCTCAACGCCACCATCAACGCGCAGTCGCGCCTGCAGACCCCGGAACAGTTCCGAAACATCATCGTGCGCGGTGCGCAGGACGGTGCCGAGCTGCGCCTGGGTGATGTCGCCCGCGTCGAGCTGGGTGCCGAGTCCTACGACTTCGTCACCCGCTACAACGGCCAGCCGGCCAGTGGCCTGGCGGTCACCCTGGCCACCGGCGCCAACGCGCTGGATACCGCGGCCGGTGTGGATGCCGCGCTGGAAGACATGAAGGGCTTCTTCCCGGCCGGCCTGAAGGCCGAGATCCCGTACGACACCACCCCGTTCGTGCGCGTGTCGATCAAGGGCGTGGTGCAGACCCTGATCGAAGCGATCGTGCTGGTGTTCGTGGTGATGTACCTGTTCCTGCAGAACTTCCGCGCCACGCTGATCCCGACCATCGCCGTGCCGGTGGTGCTGCTGGGTACCTTCGGCGTGCTGGCGATGCTGGGCTTCTCGGTGAACATGCTGACCATGTTCGCGATGGTGCTGGCGATCGGCCTGCTGGTGGACGATGCCATCGTGGTGGTGGAGAACGTCGAGCGCATCATGTCCGAGGAAGGGCTGTCGCCGCTCGAAGCGACCCGCAAGTCGATGGGCCAGATCACCGGTGCGCTGGTGGGTATCGGCCTGGTGCTGTCGGCGGTGTTCGTGCCGATGGCCTTCATGAGCGGCTCCACCGGCGTGATCTATCGCCAGTTCTCGGCCACGATTGTCTCTGCGATGGCGTTGTCGGTGCTGGTGGCGATCGTGCTGACCCCGGCACTGTGCGCGACCATGCTCAAGCCGCTGAAGAAGGGTGAGCACCACGTCGCCCACCGTGGCCTGGCCGGTCGCTTCTTCAATGGCTTCAACCGTGGCTTCGATCGCACCAGCGAAAGCTACCAGCGCGGCGTGCGCGGCATCATCCACCGTCCGTGGCGCTTCATGGGCATCGTGGCGGCCTTGTTCGTGCTGATGGGCGTGCTGTTCGTGCGCCTGCCCAGCTCGTTCCTGCCCAACGAAGACCAGGGTGTGCTGATGGCGCTGGTGCAGGCGCCGGTCGGTGCCACCCAGGAACGCACGCTGGAATCGATCGCGGCACTGGAAAACCACTTCCTGCAGAACGAGAAGGATGCGGTGGACTCGGTGTTCTCCGTGCAGGGCTTCAGCTTCGCCGGCATGGGCCAGAACGCGGGCATGGCGTTCGTCAAGCTGAAGGACTGGAGCGAGCGTGACGCCGACAATGGCGTGATGCCGATCACCGGACGTGCGATGGCGGCCCTGGGCCAGATCAAGGATGCCTTCATCTTCGCCTTCCCGCCGCCGGCCATTCCGGAGCTGGGGACCGCCTCGGGCTACACCTTCTTCCTGAAGGACAACAGCGGCCAGGGCCACGAGGCACTGGTGGCCGCGCGCAACCAGCTGCTCGGCCTGGCCGCAGGCAGCAAGAAGCTGGCCAACGTACGCCCGAACGGCCAGGAAGACACGCCGCAGTTCCGCATCGACATCGACGCGGCCAAGGCGACCTCGCTGGGACTGTCGATCGACCAGATCAACGGCACGCTGGCGGCCGCGTGGGGCAGCTCGTACATCGATGACTTCGTCGATCGTGGCCGCGTCAAGCGCGTGTTCGTGCAGGCCGACCAGGCGTTCCGCATGGTGCCGGAGGACTTCGATCTCTGGTCCGTGAAGAACGACAAGGGTGAGATGGTGCCGTTCAGCGCCTTCGCTACCAAGCACTGGGACTACGGTTCGCCGCGCCTGGAACGCTACAACGGTGTGTCGGCAATGGAAATCCAGGGCGAACCGGCCCCGGGTGTCGCCTCCGGTGATGCCATGGCCGAGATCGAACAGCTGGCCAAGCAGCTGCCGGCGGGTTTCGGCATCGAATGGACGGCGATGTCCTACCAGGAACGCCAGGCCGGCTCGCAGACGCCGCTGCTGTACACGCTGTCGCTGATGATCGTGTTCCTGTGCCTGGCCGCGATGTATGAAAGCTGGAGCGTACCGACCGCGGTGCTGCTGGCGGCCCCGCTGGGTATCCTCGGCGCGGTGCTGGCCAACACCTTCAAGGGCCTGGAGCGCGACATCTACTTCCAGGTGGCGATGCTGACCACGGTGGGCCTGACCAGCAAGAACGCGATCCTGATCGTCGAGTTCGCCAAGGAAAACCTGGAAAAGGGCGCCAGCCTGATCGAGTCGATCATGCACGCCGTGCGCGACCGCCTGCGCCCGATCGTGATGACCTCGCTCGCCTTCGGCATGGGCGTGGTACCGCTGGCGATCTCCACCGGTGCCGGCTCCGGCGCCAAGCAGGCGATCGGCACCGGCGTGCTCGGCGGCATGATCGTCGGCACCGTGCTCGGCGTGTTCTTCGTGCCGCTGTTCTTCGTGGTGGTGCAGCGCGTGTTCAAGCGCAGATCCACGACGTGAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37076","NCBI_taxonomy_name":"Stenotrophomonas maltophilia","NCBI_taxonomy_id":"40324"}}}},"ARO_accession":"3003056","ARO_id":"39490","ARO_name":"smeE","ARO_description":"smeE is the RND protein of the efflux complex smeDEF in Stenotrophomonas maltophilia","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"877":{"model_id":"877","model_name":"SHV-124","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1851":{"protein_sequence":{"accession":"ACV32634.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLDQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASKRGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQ"},"dna_sequence":{"accession":"GQ390806","fmin":"0","fmax":"813","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGATCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCAAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001171","ARO_id":"37551","ARO_name":"SHV-124","ARO_description":"SHV-124 is a beta-lactamase that has been found in clinical isolates.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"878":{"model_id":"878","model_name":"CTX-M-142","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1105":{"protein_sequence":{"accession":"AGW25368.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTANVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"KF240809","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGAACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002000","ARO_id":"38400","ARO_name":"CTX-M-142","ARO_description":"CTX-M-142 is a beta-lactamase. From the Lahey list of CTX-M beta-lactamases.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"879":{"model_id":"879","model_name":"TEM-185","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1799":{"protein_sequence":{"accession":"AEG64812.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMLSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRREPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"JF795538","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGCTGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTCGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001374","ARO_id":"37774","ARO_name":"TEM-185","ARO_description":"TEM-185 is a beta-lactamase found in E. coli","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"880":{"model_id":"880","model_name":"APH(6)-Ib","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"118":{"protein_sequence":{"accession":"CAA29136.1","sequence":"MSTSKLVEIPEPLAASYARAFGEEGQAWIAALPALVEELLDRWELTADGASASGEASLVLPVLRTDGTRAVLKLQLPREETSAAITGLRTWNGHGVVRLLDHDPRSSTMLLERLDASRTLASVEDDDAAMGVLAGLLARLVSVPAPRGLRGLGDIAGAMLEEVPRAVAALADPADRRLLNDWASAVAELVGEPGDRMLHWDLHYGNVLAAEREPWLAIDPEPLAGDPGFDLWPALDSRWDDIVAQRDVVRVVRRRFDLLTEVLGLDRARAAGWTYGRLLQNALWDIEDGSAALDPAAVTLAQALRGH"},"dna_sequence":{"accession":"X05648","fmin":"381","fmax":"1305","strand":"+","sequence":"ATGAGCACGTCAAAACTGGTGGAGATCCCGGAACCCCTGGCGGCGTCGTACGCCCGCGCCTTCGGCGAGGAGGGACAGGCATGGATCGCCGCCCTGCCCGCGCTGGTCGAGGAATTACTGGACCGCTGGGAGCTGACGGCGGACGGCGCCTCCGCGTCGGGCGAGGCCTCCCTCGTGCTGCCGGTGCTGCGCACCGACGGCACCCGCGCCGTCCTCAAGCTCCAGCTGCCCAGGGAGGAGACCTCCGCCGCCATCACCGGACTGCGCACCTGGAACGGGCACGGCGTCGTGCGGCTGCTCGACCACGACCCGCGCAGCAGCACCATGCTCCTGGAGCGGCTGGACGCGTCCCGCACGCTGGCCTCGGTCGAGGACGACGACGCCGCCATGGGCGTACTCGCCGGGCTGCTGGCCCGGCTGGTGTCCGTCCCCGCGCCGCGGGGGCTGCGCGGCCTCGGCGACATCGCCGGCGCCATGCTGGAGGAGGTGCCGCGGGCGGTCGCGGCGCTGGCCGACCCGGCCGACCGGCGGCTGCTGAACGACTGGGCGTCGGCGGTGGCCGAACTGGTCGGCGAACCCGGCGACCGGATGCTGCACTGGGACCTGCACTACGGCAACGTCCTCGCCGCCGAGCGCGAACCCTGGCTCGCCATCGACCCCGAACCGCTCGCCGGTGACCCCGGCTTCGACCTGTGGCCCGCCCTGGACAGCCGGTGGGACGACATCGTCGCACAGCGGGACGTCGTACGCGTCGTGCGACGCCGCTTCGACCTGCTGACCGAGGTCCTCGGCCTGGACCGGGCACGGGCGGCCGGCTGGACGTACGGCAGGCTGCTGCAGAACGCCCTGTGGGACATCGAGGACGGCAGTGCCGCCCTCGACCCCGCCGCCGTCACGCTCGCACAGGCGCTGCGGGGCCACTGAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36901","NCBI_taxonomy_name":"Streptomyces glaucescens","NCBI_taxonomy_id":"1907"}}}},"ARO_accession":"3002658","ARO_id":"39058","ARO_name":"APH(6)-Ib","ARO_description":"APH(6)-Ib is a chromosomal-encoded aminoglycoside phosphotransferase in S. glaucescens","ARO_category":{"36290":{"category_aro_accession":"3000151","category_aro_cvterm_id":"36290","category_aro_name":"APH(6)","category_aro_description":"Phosphorylation of streptomycin on the hydroxyl group at position 6","category_aro_class_name":"AMR Gene Family"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"881":{"model_id":"881","model_name":"ErmC","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"501":{"protein_sequence":{"accession":"AAA98296.1","sequence":"MNEKNIKHSQNFITSKHNIDKIMTNIRLNEHDNIFEIGSGKGHFTLELVQRCNFVTAIEIDHKLCKTTENKLVDHDNFQVLNKDILQFKFPKNQSYKIFGNIPYNISTDIIRKIVFDSIADEIYLIVEYGFAKRLLNTKRSFALFLMAEVDISILSMVPREYFHPKPKVNSSLIRLNRKKSRISHKDKQKYNYFVMKWVNKEYKKIFTKNQFNNSLKHAGIDDLNNISFEQFLSLFNSYKLFNK"},"dna_sequence":{"accession":"M12730","fmin":"779","fmax":"1514","strand":"+","sequence":"ATGAACGAGAAAAATATAAAACACAGTCAAAACTTTATTACTTCAAAACATAATATAGATAAAATAATGACAAATATAAGATTAAATGAACATGATAATATCTTTGAAATCGGCTCAGGAAAAGGGCATTTTACCCTTGAATTAGTACAGAGGTGTAATTTCGTAACTGCCATTGAAATAGACCATAAATTATGCAAAACTACAGAAAATAAACTTGTTGATCACGATAATTTCCAAGTTTTAAACAAGGATATATTGCAGTTTAAATTTCCTAAAAACCAATCCTATAAAATATTTGGTAATATACCTTATAACATAAGTACGGATATAATACGCAAAATTGTTTTTGATAGTATAGCTGATGAGATTTATTTAATCGTGGAATACGGGTTTGCTAAAAGATTATTAAATACAAAACGCTCATTCGCATTATTTTTAATGGCAGAAGTTGATATTTCTATATTAAGTATGGTTCCAAGAGAATATTTTCATCCTAAACCTAAAGTGAATAGCTCACTTATCAGATTAAATAGAAAAAAATCAAGAATATCACACAAAGATAAACAGAAGTATAATTATTTCGTTATGAAATGGGTTAACAAAGAATACAAGAAAATATTTACAAAAAATCAATTTAACAATTCCTTAAAACATGCAGGAATTGACGATTTAAACAATATTAGCTTTGAACAATTCTTATCTCTTTTCAATAGCTATAAATTATTTAATAAGTAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36868","NCBI_taxonomy_name":"Staphylococcus epidermidis","NCBI_taxonomy_id":"1282"}}}},"ARO_accession":"3000250","ARO_id":"36389","ARO_name":"ErmC","ARO_description":"ErmC is a methyltransferase that catalyzes the methylation of A2058 of the 23S ribosomal RNA in two steps. Expression of ErmC is inducible by erythromycin. The leader peptide causes attenuation of the mRNA and stabilizes the structure preventing further translation. When erythromycin is present, it binds the leader peptide causing a change in conformation allowing for the expression of ErmC.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35946":{"category_aro_accession":"0000027","category_aro_cvterm_id":"35946","category_aro_name":"roxithromycin","category_aro_description":"Roxithromycin is a semi-synthetic, 14-carbon ring macrolide antibiotic derived from erythromycin. It is used to treat respiratory tract, urinary and soft tissue infections. Roxithromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35974":{"category_aro_accession":"0000057","category_aro_cvterm_id":"35974","category_aro_name":"telithromycin","category_aro_description":"Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36315":{"category_aro_accession":"3000176","category_aro_cvterm_id":"36315","category_aro_name":"dirithromycin","category_aro_description":"Dirithromycin is an oxazine derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome to inhibit bacterial protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin 1A is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"vernamycin B-gamma","category_aro_description":"Vernamycin B-gamma is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"883":{"model_id":"883","model_name":"LRA-17","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"4352":{"protein_sequence":{"accession":"ACH58994.1","sequence":"MSIFRTILFVSILLLTSLANSPHATAQVTNTDRPEWSKPYKPFRIAGNIYYVGTYDLACYLITTPQGHILINAALAGTVDQVKANVEALGFKFSDIKILLISQAHFDHVGGLAAIQKMTGAKVMIDDQDAPVVEDGGNSDYIYGGKGVGSLFAPVHVDRKLHDHDNITLGGTQLEMLHHPGHTKGSCSYLLTVKDEHRSYRVLIANIPYMLSEVTLPGMPTYPNVGKDFMYTYGAMRKLQFDIWVAAHSSQFGLQDVRKETDGYNPGAFGDKKKYLTTIDKTEDIYKEHFKGGK"},"dna_sequence":{"accession":"EU408354","fmin":"3570","fmax":"4455","strand":"-","sequence":"CTATTTCCCTCCCTTAAAGTGCTCCTTATATATATCCTCCGTCTTGTCGATGGTGGTTAAGTATTTCTTTTTGTCGCCAAATGCACCGGGGTTGTAGCCGTCGGTCTCTTTGCGCACGTCTTGCAGGCCAAACTGGCTGGAGTGCGCAGCTACCCATATATCAAACTGCAGCTTCCTCATAGCGCCATAGGTATACATAAAGTCTTTACCGACATTGGGATATGTGGGCATGCCCGGCAACGTAACCTCAGACAGCATGTAAGGTATATTCGCTATCAGCACACGATAGCTGCGGTGCTCATCCTTTACGGTGAGCAGGTAGCTGCATGAACCTTTGGTATGGCCGGGATGATGCAGCATTTCCAACTGCGTACCGCCGAGGGTTATGTTATCATGGTCGTGCAGCTTGCGGTCTACATGCACGGGCGCGAACAGGCTGCCTACACCCTTGCCGCCATAGATATAGTCTGAATTGCCGCCATCTTCCACCACCGGCGCATCCTGATCGTCTATCATCACTTTGGCGCCTGTCATCTTCTGTATGGCTGCAAGGCCGCCCACATGATCAAAGTGCGCCTGCGAGATGAGCAGTATCTTGATATCGCTGAACTTAAATCCCAGCGCTTCCACATTAGCCTTGACCTGGTCTACCGTGCCGGCCAGCGCAGCATTAATGAGTATATGCCCCTGCGGCGTGGTGATGAGGTAGCAGGCCAGGTCATAAGTGCCTACGTAGTATATATTGCCTGCGATGCGGAATGGCTTGTAGGGTTTAGACCATTCGGGCCTGTCTGTGTTGGTTACCTGTGCTGTGGCATGCGGGCTATTTGCGAGTGAGGTCAGTAATAGTATGGATACAAAAAGTATGGTTCTGAATATCGACAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39086","NCBI_taxonomy_name":"uncultured bacterium BLR17","NCBI_taxonomy_id":"506517"}}}},"ARO_accession":"3002512","ARO_id":"38912","ARO_name":"LRA-17","ARO_description":"LRA-17 is a beta-lactamase isolated from soil samples in Alaska","ARO_category":{"41390":{"category_aro_accession":"3004226","category_aro_cvterm_id":"41390","category_aro_name":"subclass B3 LRA beta-lactamase","category_aro_description":"Beta-lactamases that are part of the LRA gene family and are classified as B3 (metallo-) beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"884":{"model_id":"884","model_name":"CTX-M-99","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1108":{"protein_sequence":{"accession":"ADL27532.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTESTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAERRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"HM803271","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAATCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGCGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001958","ARO_id":"38358","ARO_name":"CTX-M-99","ARO_description":"CTX-M-99 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"885":{"model_id":"885","model_name":"TEM-63","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1161":{"protein_sequence":{"accession":"AAK17194.1","sequence":"MSIQHFRVALIPFFAAFCFPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTTPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AF332513","fmin":"103","fmax":"964","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCTTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGGCCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000931","ARO_id":"37311","ARO_name":"TEM-63","ARO_description":"TEM-63 is an extended-spectrum beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"886":{"model_id":"886","model_name":"IND-10","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1672":{"protein_sequence":{"accession":"ADA13241.1","sequence":"MKKSIQFFIVSMLLSPFANAQVKDFVIEPPIKSNLYIYKTFGVFGGKEYSANAAYLKTKKGVILFDVPWEKVQYQSLMDTIKKRHNLPVIAVFATHSHDDRAGDLSFFNNKGIKKYATLKTNEFLKKDGKATSTEIIQTGKPYHIGGEEFVVDFLGEGHTADNVVVWFPKYNVLDGGCLVKSNSATDLGYIKEANVEQWPKTMNKLKTKYSKATLIIPGHDEWKGGGHVEHTLELLNKK"},"dna_sequence":{"accession":"GU206353","fmin":"18","fmax":"738","strand":"+","sequence":"ATGAAAAAAAGCATTCAATTTTTTATTGTTTCCATGTTGTTGAGCCCTTTTGCCAATGCACAGGTAAAAGATTTTGTAATTGAGCCACCTATTAAATCCAATCTATATATTTACAAGACTTTTGGAGTATTCGGAGGTAAAGAATATTCTGCCAATGCAGCCTATCTTAAGACTAAAAAAGGTGTAATTCTGTTTGATGTACCCTGGGAAAAAGTACAGTATCAAAGCCTGATGGATACCATCAAAAAACGTCATAACTTACCGGTAATTGCCGTATTTGCTACGCATTCCCATGATGACCGTGCAGGAGACTTAAGCTTTTTCAATAATAAAGGCATTAAGAAGTATGCTACCCTGAAAACCAATGAGTTTCTGAAGAAAGATGGAAAAGCAACATCCACAGAGATCATCCAAACCGGAAAACCTTATCACATTGGCGGAGAAGAATTTGTGGTCGATTTTCTTGGTGAAGGACATACTGCTGATAATGTAGTGGTATGGTTTCCAAAATATAATGTTTTGGATGGCGGATGTCTTGTAAAAAGTAATTCTGCTACTGACTTAGGATACATTAAAGAAGCCAATGTAGAACAATGGCCCAAGACGATGAATAAATTAAAAACCAAATATTCAAAAGCCACATTAATTATTCCCGGGCATGATGAATGGAAAGGGGGTGGACATGTTGAACACACTTTAGAGCTTTTGAACAAAAAATAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36916","NCBI_taxonomy_name":"Chryseobacterium indologenes","NCBI_taxonomy_id":"253"}}}},"ARO_accession":"3002266","ARO_id":"38666","ARO_name":"IND-10","ARO_description":"IND-10 is a beta-lactamase found in Escherichia coli","ARO_category":{"36199":{"category_aro_accession":"3000060","category_aro_cvterm_id":"36199","category_aro_name":"IND beta-lactamase","category_aro_description":"IND beta-lactamases are class B carbapenem-hydrolyzing beta-lactamases","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"887":{"model_id":"887","model_name":"SHV-33","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1148":{"protein_sequence":{"accession":"AFN82060.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLSAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"JX268631","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGTCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001091","ARO_id":"37471","ARO_name":"SHV-33","ARO_description":"SHV-33 is an broad-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"888":{"model_id":"888","model_name":"Erm(36)","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"197":{"protein_sequence":{"accession":"AAL68827.1","sequence":"MPTYRGGRHEHGQNFLTDHTTIDRLSRLVGDSTGPIVEIGPGQGRLTRELQKLGRSLTAVEIDSRLADRLASASQFREQKHVTVVNADFLHWPLPTTPYVVVGNVPFHLTTAILRRLLHDGAWTQVVLLVQWEVARRRAGIGGSSMMTAQWWPWIDFSLHGRVPRSAFKPAPSVDGGLLEMTRRPDPLLSPDARESYRQFVHDVFTSRGRGIGEILANVSSSLGKRGALQLLKSEGIRSSSLPKDLSAEQWARLFTSASPTKSAKTGRNAHPAHSARRQGR"},"dna_sequence":{"accession":"AF462611","fmin":"0","fmax":"846","strand":"+","sequence":"ATGCCCACTTACCGTGGCGGCCGACATGAGCACGGCCAGAACTTCCTCACTGACCACACCACGATCGACCGGCTCTCACGGCTGGTAGGCGACTCGACCGGTCCGATCGTCGAGATCGGCCCGGGCCAGGGCAGGCTCACAAGAGAGCTGCAGAAGCTCGGCCGGTCCCTGACTGCTGTCGAGATCGACAGCCGGCTGGCGGACCGACTTGCATCGGCCAGTCAGTTCCGCGAGCAGAAACACGTAACCGTCGTCAACGCAGACTTCCTTCACTGGCCGCTACCGACCACTCCGTATGTGGTGGTCGGCAACGTTCCGTTCCACCTGACCACAGCCATCCTGCGCAGACTGCTGCACGATGGAGCATGGACCCAGGTGGTCCTGCTCGTGCAGTGGGAAGTGGCCCGCCGGCGTGCCGGCATCGGTGGTAGCAGCATGATGACCGCGCAGTGGTGGCCTTGGATCGACTTCAGCTTGCACGGGCGCGTGCCCCGGTCGGCGTTCAAGCCAGCCCCGAGCGTGGACGGTGGCCTCTTGGAGATGACTCGTCGTCCGGACCCATTGCTCAGCCCAGACGCGAGAGAGTCCTACCGACAGTTCGTCCATGACGTTTTCACCAGTAGGGGCAGGGGTATCGGCGAGATCCTGGCTAACGTATCCAGCTCACTCGGAAAGCGGGGAGCGCTCCAGTTGTTGAAGAGCGAGGGGATTCGCTCCTCGTCCCTGCCCAAAGATCTCTCAGCGGAGCAGTGGGCTCGCCTCTTTACCAGCGCGTCGCCTACGAAGAGTGCCAAAACCGGAAGGAACGCACACCCCGCCCACTCCGCACGGCGGCAAGGTCGATGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36878","NCBI_taxonomy_name":"Micrococcus luteus","NCBI_taxonomy_id":"1270"}}}},"ARO_accession":"3000605","ARO_id":"36744","ARO_name":"Erm(36)","ARO_description":"ErmD confers MLSb phenotype.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35946":{"category_aro_accession":"0000027","category_aro_cvterm_id":"35946","category_aro_name":"roxithromycin","category_aro_description":"Roxithromycin is a semi-synthetic, 14-carbon ring macrolide antibiotic derived from erythromycin. It is used to treat respiratory tract, urinary and soft tissue infections. Roxithromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35974":{"category_aro_accession":"0000057","category_aro_cvterm_id":"35974","category_aro_name":"telithromycin","category_aro_description":"Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36315":{"category_aro_accession":"3000176","category_aro_cvterm_id":"36315","category_aro_name":"dirithromycin","category_aro_description":"Dirithromycin is an oxazine derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome to inhibit bacterial protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin 1A is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"vernamycin B-gamma","category_aro_description":"Vernamycin B-gamma is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"889":{"model_id":"889","model_name":"CMY-74","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1509":{"protein_sequence":{"accession":"AFU25632.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYQGKPYYFTWGKADIANNRPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTHYWPELTGKQWQGISLLHLATYTAGGLPLQVPDDVTDKAALLRFYQNWQPQWAPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTKRVLHPLKLAHTWITVPQSEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMTRWVQANMDASQVQEKTLQQGIELAQSRYWRVGDMYQGLGWEMLNWPVKADSIISGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"JX440349","fmin":"1026","fmax":"2172","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCGCTGCTGCTGACAGCTTCTTTCTCCACGTTTGCCGCCGCCAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCGCTGATGCAGGAGCAGGCAATTCCGGGCATGGCCGTTGCGATTATCTATCAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCGTCCAGTCACTCAACAAACGCTGTTTGAACTCGGATCGGTCAGTAAAACGTTCAACGGCGTGCTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGCATTACTGGCCTGAACTGACTGGTAAGCAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTACACGGCAGGCGGCCTGCCGCTTCAGGTTCCGGACGACGTTACGGATAAAGCCGCGTTACTACGCTTTTATCAAAACTGGCAGCCGCAATGGGCCCCAGGCGCTAAACGTCTTTATGCTAACTCCAGCATTGGTCTGTTTGGCGCCCTGGCGGTGAAACCCTCAGGCATGAGCTACGAAGAGGCGATGACCAAACGCGTCCTGCACCCCTTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAGCGAACAAAAAGATTATGCCTGGGGTTATCGCGAAGGAAAGCCAGTGCATGTATCCCCTGGCCAACTTGATGCCGAAGCCTACGGGGTGAAATCGAGCGTTATCGATATGACCCGTTGGGTTCAGGCCAACATGGACGCCAGCCAGGTTCAGGAGAAAACGCTCCAGCAGGGCATCGAGCTTGCGCAGTCACGTTACTGGCGTGTTGGCGATATGTACCAGGGCCTGGGCTGGGAGATGCTGAACTGGCCGGTGAAAGCCGACTCGATAATTAGCGGTAGCGACAGCAAAGTGGCACTGGCAGCGCTTCCTGCCGTTGAGGTAAACCCGCCCGCGCCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGCGGATTCGGCAGCTACGTTGCTTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAATAAGAGCTACCCAAACCCTGTTCGCGTCGAGGCCGCCTGGCGCATTCTTGAAAAACTGCAGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39584","NCBI_taxonomy_name":"Citrobacter braakii","NCBI_taxonomy_id":"57706"}}}},"ARO_accession":"3002087","ARO_id":"38487","ARO_name":"CMY-74","ARO_description":"CMY-74 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"890":{"model_id":"890","model_name":"SHV-53","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1484":{"protein_sequence":{"accession":"AAT01223.1","sequence":"IISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLISQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNN"},"dna_sequence":{"accession":"AY590467","fmin":"0","fmax":"729","strand":"+","sequence":"TATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGATCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001110","ARO_id":"37490","ARO_name":"SHV-53","ARO_description":"SHV-53 is a beta-lactamase that has been found in clinical isolates.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"891":{"model_id":"891","model_name":"QnrB37","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"679":{"protein_sequence":{"accession":"AEL00459.1","sequence":"MTLALVGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAILKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGSDFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFSSFDWRAANVTHCDLTNSELGDLDVRGVDLQGVKLDSYQASLILERLGIAVIG"},"dna_sequence":{"accession":"JN173059","fmin":"35","fmax":"680","strand":"+","sequence":"ATGACTCTTGCGTTAGTTGGCGAAAAAATTGACAGAAACAGGTTCACCGGTGAGAAAGTCGAAAATAGCACATTTTTCAACTGTGATTTTTCGGGTGCCGACCTTAGCGGTACTGAGTTTATTGGCTGCCAATTTTATGATCGAGAGAGCCAGAAAGGGTGTAATTTTAGCCGCGCTATCCTGAAAGATGCCATTTTCAAAAGTTGCGATCTCTCCATGGCGGATTTCAGGAATGTGAGTGCGCTGGGAATCGAAATTCGCCACTGCCGCGCACAAGGTTCAGATTTTCGCGGCGCAAGCTTTATGAATATGATTACCACACGCACCTGGTTTTGTAGCGCCTATATCACCAATACCAACTTAAGCTACGCCAACTTTTCAAAAGTCGTACTGGAAAAGTGCGAGCTGTGGGAAAACCGCTGGATGGGAACTCAGGTACTGGGGGCGACGTTCAGTGGTTCAGATCTTTCCGGCGGTGAGTTTTCGTCGTTCGACTGGCGAGCCGCAAACGTTACGCACTGTGATTTGACCAATTCAGAACTGGGCGATCTCGATGTCCGGGGTGTTGATTTGCAAGGAGTCAAACTGGACAGCTACCAGGCATCGTTGATCCTGGAACGTCTTGGCATCGCTGTCATTGGTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002752","ARO_id":"39186","ARO_name":"QnrB37","ARO_description":"QnrB37 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"892":{"model_id":"892","model_name":"APH(6)-Ic","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"404":{"protein_sequence":{"accession":"CAA25854.1","sequence":"MERWRLLRDGELLTTHSSWILPVRQGDMPAMLKVARIPDEEAGYRLLTWWDGQGAARVFASAAGALLMERASGAGDLAQIAWSGQDDEACRILCDTAARLHAPRSGPPPDLHPLQEWFQPLFRLAAEHAALAPAASVARQLLAAPREVCPLHGDLHHENVLDFGDRGWLAIDPHGLLGERTFDYANIFTNPDLSDPGRPLAILPGRLEARLSIVVATTGFEPERLLRWIIAWTGLSAAWFIGDGDGEGEGAAIDLAVNAMARRLLD"},"dna_sequence":{"accession":"X01702","fmin":"484","fmax":"1285","strand":"+","sequence":"ATGGAGCGCTGGCGCCTGCTGCGCGACGGCGAGCTGCTCACCACCCACTCGAGCTGGATACTTCCCGTCCGCCAGGGGGACATGCCGGCGATGCTGAAGGTCGCGCGCATTCCCGATGAAGAGGCCGGTTACCGCCTGTTGACCTGGTGGGACGGGCAGGGCGCCGCCCGAGTCTTCGCCTCGGCGGCGGGCGCTCTGCTCATGGAGCGCGCGTCCGGGGCCGGGGACCTTGCACAGATAGCGTGGTCCGGCCAGGACGACGAGGCTTGCAGGATCCTCTGCGACACCGCCGCTCGTCTGCACGCGCCGCGGTCCGGACCGCCGCCCGATCTCCATCCGCTACAGGAATGGTTCCAGCCGCTTTTCCGGTTGGCCGCTGAGCACGCGGCACTTGCGCCCGCCGCCAGCGTAGCGCGCCAACTTCTGGCGGCGCCGCGCGAGGTGTGCCCGCTCCACGGCGACCTGCACCACGAGAACGTGCTCGACTTCGGCGACCGCGGCTGGCTGGCCATCGACCCGCACGGACTGCTCGGCGAGCGCACCTTCGACTATGCCAACATCTTCACGAATCCCGATCTCAGCGACCCCGGTCGCCCGCTTGCGATCCTGCCGGGCAGGCTGGAGGCTCGACTCAGCATTGTGGTCGCGACGACCGGGTTTGAGCCCGAACGGCTTCTTCGCTGGATCATTGCATGGACGGGCTTGTCGGCAGCCTGGTTCATCGGCGACGGCGACGGCGAGGGCGAGGGCGCTGCGATTGATCTGGCCGTAAACGCCATGGCACGCCGGTTGCTTGACTAGC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002659","ARO_id":"39059","ARO_name":"APH(6)-Ic","ARO_description":"APH(6)-Ic is a transposon-encoded aminoglycoside phosphotransferase in S. enterica, P. aeruginosa and E. coli","ARO_category":{"36290":{"category_aro_accession":"3000151","category_aro_cvterm_id":"36290","category_aro_name":"APH(6)","category_aro_description":"Phosphorylation of streptomycin on the hydroxyl group at position 6","category_aro_class_name":"AMR Gene Family"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"894":{"model_id":"894","model_name":"CMY-90","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1444":{"protein_sequence":{"accession":"CCK86743.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPGDVTDKAELLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVKSSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYLEGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"HE819404","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCGCTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGGTGACGTTACGGATAAAGCCGAATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGCGGTGAAATCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAACTATGCCTGGGGCTATCTCGAAGGGAAGCCTGTGCACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACAGGATCCACAGGCGGATTTGGCAGCTACGTTGCTTTCGTTCCAGAAAAAAACCTTGGCATCGTAATGTTGGCAAACAAAAGCTACCCCAACCCGGCTCGCGTCGAGGCGGCCTGGCGCATTCTTGAAAAACTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002103","ARO_id":"38503","ARO_name":"CMY-90","ARO_description":"CMY-90 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"895":{"model_id":"895","model_name":"SHV-122","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"4356":{"protein_sequence":{"accession":"ADR80609.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDPPGGTELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"HM751103.1","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCCGCCTGGGGGAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATCGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001169","ARO_id":"37549","ARO_name":"SHV-122","ARO_description":"SHV-122 is a beta-lactamase that has been found in clinical isolates.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"896":{"model_id":"896","model_name":"CTX-M-131","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4241":{"protein_sequence":{"accession":"AEW46676.3","sequence":"MMTQSIRRSMLTVMATLPLLFSSATLHAQANSVQQQLEALEKSSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKQSESDKHLLNQRVEIKKSDLVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSASIRAGLPKSWVVGDKTGSGGYGTTNDIAVIWPENHAPLVLVTYFTQPEQKAESRRDILAAAAKIVTHGF"},"dna_sequence":{"accession":"JN969893.3","fmin":"2530","fmax":"3406","strand":"+","sequence":"ATGATGACTCAGAGCATTCGCCGCTCAATGTTAACGGTGATGGCGACGCTACCCCTGCTATTTAGCAGCGCAACGCTGCATGCGCAGGCGAACAGCGTGCAACAGCAGCTGGAAGCCCTGGAGAAAAGTTCGGGAGGTCGGCTTGGCGTTGCGCTGATTAACACCGCCGATAATTCGCAGATTCTCTACCGTGCCGATGAACGTTTTGCGATGTGCAGTACCAGTAAGGTGATGGCGGCCGCGGCGGTGCTTAAACAGAGCGAGAGCGATAAGCACCTGCTAAATCAGCGCGTTGAAATCAAGAAGAGCGACCTGGTTAACTACAATCCCATTGCGGAGAAACACGTTAACGGCACGATGACGCTGGCTGAGCTTGGCGCAGCGGCGCTGCAGTATAGCGACAATACTGCCATGAATAAGCTGATTGCCCATCTGGGTGGTCCCGATAAAGTGACGGCGTTTGCTCGCTCGTTGGGTGATGAGACCTTCCGTCTGGACAGAACCGAGCCCACGCTCAATACCGCCATTCCAGGCGACCCGCGTGATACCACCACGCCGCTCGCGATGGCGCAGACCCTGAAAAATCTGACGCTGGGTAAAGCGCTGGCGGAAACTCAGCGGGCACAGTTGGTGACGTGGCTTAAGGGCAATACTACCGGTAGCGCGAGCATTCGGGCGGGTCTGCCGAAATCATGGGTAGTGGGCGATAAAACCGGCAGCGGAGGTTATGGCACCACCAACGATATCGCGGTTATCTGGCCGGAAAACCACGCACCGCTGGTTCTGGTGACCTACTTTACCCAACCGGAGCAGAAGGCGGAAAGCCGTCGGGATATTCTGGCTGCGGCGGCGAAAATCGTAACCCACGGTTTCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36944","NCBI_taxonomy_name":"Providencia rettgeri","NCBI_taxonomy_id":"587"}}}},"ARO_accession":"3001990","ARO_id":"38390","ARO_name":"CTX-M-131","ARO_description":"CTX-M-131 is a beta-lactamase. From the Lahey list of CTX-M beta-lactamases.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"897":{"model_id":"897","model_name":"OXA-383","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4358":{"protein_sequence":{"accession":"AHL30281.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KF986262","fmin":"27","fmax":"852","strand":"-","sequence":"CTATAAAATACCTAATTGTTCTAAGCTTTTATAAGTAATCTCTTTTCGAACAGAGCTAGGTATTCCTTTTTTCATTTCTAAGTTAAGGGAGAACGCTACAATATTCCCTTGAGGCTGAACAACCCATCCAGTTAACCAGCCTACTTGTGGGTTTACATCCCATCCCCAACCACTTTTTGCGTATATTTTATTTCCATTCTTTTCTTCTATGAATAGCATGGATTGCACTTCATCTTGGACTTTTTGGCTAAATGGAAGCGTTTTATTAGCTAGCTTGTAAGCAAATTGTGCCTCTTGCTGAGGAGTAATTTTTAAAGGACCCACCAGCCAAAAATTATCGACTTGGGTACCGATATCTGCATTGCCATAACCAACACGCTTCACTTCATTAGACATGAGTTCAAGTCCAATACGACGAGCTAAATCTTGATAAACCGGAATAGCGGAAGCTTTCATAGCATCGCCTAGGGTCATGTTCTTTTCCCATTCTGGGAATAGCCTTTTTTGCCCGTCCCACTTAAATACTTCTGTGGTGGTTGCCTTATGGTGCTCAAGGCCGATCAAAGCATTAAGCATTTTGAAGGTCGAAGCAGGTACATACTCGGTCGAAGCACGAGCAAGATCATTACCATAGCTTTGTTGAGTTTGGCCTTGTTGGATAACTAAAACACCCGTAGTGTGTACTTCGTTAAATAAATTTTTAATTTTCTCTGCTTTTTCATCAGATTTTGAAGCGCTGTGATTTGGATTAGCAGTCACTATATAAGGTGAGCAGGCTGAAATAAAAATAGCGCTTGTTATAAGTAAGAGTGTTTTAATGTTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001569","ARO_id":"37969","ARO_name":"OXA-383","ARO_description":"OXA-383 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"898":{"model_id":"898","model_name":"VEB-9","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"3589":{"protein_sequence":{"accession":"AAK14293.1","sequence":"MKIVKRILLVLLSLFFTVVYSNAQTDNLTLKIENVLKAKNARIGVAIFNSNEKDTLKINNDFHFPMQSVMKFPIALAVLSEIDKGNLSFEQKIEITPQDLLPKTWSPIKEEFPNGTTLTIEQILNYTVSESDNIGCDILLKLIGGTDSVQKFLNANHFTDISIKANEEQMHKDWNTQYQNWATPTAMNKLLIDTYNNKNQLLSKKSYDFIWKIMRETTTGSNRLKGQLPKNTIVAHKTGTSGINNGIAAATNDVGVITLPNGQLIFISVFVAESKETSEINEKIISDIAKITWNYYLNK"},"dna_sequence":{"accession":"AF324833.1","fmin":"0","fmax":"900","strand":"+","sequence":"ATGAAAATCGTAAAAAGGATATTATTAGTATTGTTAAGTTTATTTTTTACAGTTGTGTATTCAAATGCTCAAACTGACAACTTAACTTTGAAAATTGAGAATGTTTTAAAGGCAAAAAATGCCAGAATAGGAGTAGCAATATTCAACAGCAATGAGAAGGATACTTTGAAGATTAATAACGACTTCCATTTCCCGATGCAAAGCGTTATGAAATTTCCGATTGCTTTAGCCGTTTTGTCTGAGATAGATAAAGGGAATCTTTCTTTTGAACAAAAAATAGAGATTACCCCTCAAGACCTTTTGCCTAAAACGTGGAGTCCGATTAAAGAGGAATTCCCTAATGGAACAACTTTGACGATTGAACAAATACTAAATTATACAGTATCAGAGAGCGACAATATTGGTTGTGATATTTTGCTAAAATTAATCGGAGGAACTGATTCTGTTCAAAAATTCTTGAATGCTAATCATTTCACTGATATTTCAATCAAAGCAAACGAAGAACAAATGCACAAGGATTGGAATACCCAATATCAAAATTGGGCAACCCCAACAGCGATGAACAAACTGTTAATAGATACTTATAATAATAAGAACCAATTACTTTCTAAAAAAAGTTATGATTTTATTTGGAAAATTATGAGAGAAACAACAACAGGAAGTAACCGATTAAAAGGACAATTACCAAAGAATACAATTGTTGCTCATAAAACAGGGACTTCCGGAATAAATAATGGAATTGCAGCAGCCACTAATGATGTTGGGGTAATTACTTTACCGAATGGACAATTAATTTTTATAAGCGTATTTGTTGCAGAGTCCAAAGAAACTTCGGAAATTAATGAAAAGATTATTTCAGACATTGCAAAAATAACGTGGAATTACTATTTGAATAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002378","ARO_id":"38778","ARO_name":"VEB-9","ARO_description":"VEB-9 is a beta-lactamase. From the Lahey list of VEB beta-lactamases.","ARO_category":{"36182":{"category_aro_accession":"3000043","category_aro_cvterm_id":"36182","category_aro_name":"VEB beta-lactamase","category_aro_description":"VEB beta-lactamases or Vietnamese extended-spectrum beta-lactamases are class A beta-lactamases that confer high-level resistance to oxyimino cephalosporins and to aztreonam","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"899":{"model_id":"899","model_name":"OXA-94","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1466":{"protein_sequence":{"accession":"ABF47917.1","sequence":"MNIQALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPHGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"DQ519088","fmin":"8","fmax":"833","strand":"+","sequence":"ATGAACATTCAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCATGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001629","ARO_id":"38029","ARO_name":"OXA-94","ARO_description":"OXA-94 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"901":{"model_id":"901","model_name":"LCR-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"775":{"protein_sequence":{"accession":"CAA40146.1","sequence":"MLKSTLLAFGLFIALSARAENQAIAKLFLRAGVDGTIVIESLTTGQRLVHNDPRAQQRYPAASTFKVLNTLIALEEGAISGENQIFHWNGTQYSIANWNQDQTLDSAFKVSCVWCYQQIALRVGALKYPAYIQQTNYGHLLEPFNGTEFWLDGSLTISAEEQVAFLRQVVERKLPFKASSYDSLKKVMFADENAQYRLYAKTGWATRMTPSVGWYVGYVEAKDDVWLFALNLATRDANDLPLRTQIAKDALKAIGAFPTK"},"dna_sequence":{"accession":"X56809","fmin":"111","fmax":"894","strand":"+","sequence":"ATGCTAAAGAGCACCCTTCTGGCCTTTGGTCTCTTTATTGCGCTCTCAGCGCGTGCAGAGAACCAGGCAATCGCCAAGCTTTTCCTGAGGGCAGGGGTCGATGGGACCATCGTCATCGAGTCTCTAACCACCGGACAGCGCTTGGTTCACAACGATCCTCGTGCGCAACAACGATACCCGGCAGCTTCCACGTTCAAGGTACTCAATACCTTGATTGCTCTCGAAGAGGGCGCCATTTCAGGTGAGAACCAGATCTTTCACTGGAACGGTACCCAGTATTCGATTGCGAATTGGAACCAGGACCAGACTCTAGACAGTGCGTTTAAAGTGAGTTGTGTCTGGTGCTACCAGCAGATTGCCCTTCGAGTGGGGGCACTCAAGTACCCAGCCTATATTCAACAGACAAACTATGGTCATTTACTGGAACCCTTCAATGGAACGGAGTTTTGGCTGGATGGCTCTTTGACGATCAGCGCGGAAGAACAGGTTGCCTTTCTCCGACAGGTTGTTGAGCGAAAACTACCGTTCAAGGCGAGCAGCTATGATTCCCTGAAGAAAGTCATGTTCGCCGATGAGAATGCCCAGTATCGCCTTTATGCAAAAACAGGTTGGGCGACCCGCATGACTCCCTCGGTGGGTTGGTATGTTGGCTATGTTGAAGCAAAGGACGATGTTTGGCTGTTTGCCCTGAATCTTGCTACCCGCGACGCGAATGACCTGCCCCTACGAACGCAGATAGCCAAAGACGCGCTGAAGGCGATAGGTGCGTTTCCTACGAAGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002997","ARO_id":"39431","ARO_name":"LCR-1","ARO_description":"LCR-1 is a class D beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"39430":{"category_aro_accession":"3002996","category_aro_cvterm_id":"39430","category_aro_name":"LCR beta-lactamase","category_aro_description":"LCR beta-lactamases are a class D beta-lactamase that hydrolyze a variety of penams and some cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"902":{"model_id":"902","model_name":"OXA-92","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1427":{"protein_sequence":{"accession":"ABC61637.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGEKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGSVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"DQ335566","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAATGGGATGGGGAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTCTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATCGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001632","ARO_id":"38032","ARO_name":"OXA-92","ARO_description":"OXA-92 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"903":{"model_id":"903","model_name":"APH(2'')-Ig","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"4361":{"protein_sequence":{"accession":"AGV10818.1","sequence":"MCEFSSPQIPITDIENAMERIGSPVRELRRLDAGDDSEVLLCNGLFVIKIPKRPSVRVTQQREFAVYSFLKQYDLPALIPEVIFQCSEFNVMSFIPGENFGFQEYALLSEKEKEALASDMAIFLRRLHGISVPLSEKPFCEIFEDKRKRYLEDQEQLLEVLENRKLLNAPLQKNIQTIYEHIGQNQELFNYAACLVHNDFSSSNMVFRHNRLYGVIDFGDVIVGDPDNDFLCLLDCSMDDFGKDFGRKVLRHYGHRNPQLAERKAEINDAYWPIQQVLLGVQREDRSLFCKGYRELLAIDPDAFIL"},"dna_sequence":{"accession":"CP004067","fmin":"43007","fmax":"43928","strand":"-","sequence":"TTATAAAATGAAAGCATCTGGGTCTATGGCTAGAAGTTCACGGTATCCCTTACAGAAAAGCGACCGATCTTCTCTCTGAACACCAAGCAGGACTTGCTGTATCGGCCAGTAAGCATCATTGATTTCTGCTTTTCTTTCTGCTAATTGTGGATTCCGATGGCCATAATGCCTTAAAACCTTTCGCCCGAAATCTTTCCCAAAGTCATCCATGCTGCAATCCAGAAGGCATAAAAAATCATTGTCCGGATCGCCGACAATTACATCTCCAAAATCGATCACGCCATACAGACGATTATGTCTGAACACCATATTGGAAGAGCTAAAATCATTGTGAACTAAACAGGCCGCATAGTTAAACAGTTCCTGATTCTGACCGATATGCTCGTATATCGTCTGGATATTTTTCTGGAGTGGTGCATTCAAGAGTTTTCGGTTTTCGAGCACTTCAAGCAGCTGTTCTTGGTCTTCCAAATATCTTTTGCGTTTATCTTCGAAGATTTCACAGAACGGTTTCTCTGAAAGCGGCACCGATATACCATGCAATCTCCGCAAAAATATCGCCATATCTGAAGCAAGCGCTTCTTTTTCCTTTTCTGAAAGCAAAGCATATTCTTGAAAGCCAAAGTTTTCTCCGGGGATAAACGACATAACATTAAATTCGCTGCATTGAAAAATCACTTCCGGAATCAAGGCAGGTAAATCATACTGTTTGAGAAAGGAGTATACTGCAAATTCTCTTTGCTGTGTCACGCGCACAGATGGCCGTTTGGGGATTTTGATGACAAACAGCCCATTGCAAAGCAGCACTTCGCTGTCATCCCCCGCATCCAAGCGGCGGAGTTCTCTCACCGGACTTCCGATCCGTTCCATGGCATTCTCAATATCCGTTATTGGAATTTGCGGACTACTAAATTCACACAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39528","NCBI_taxonomy_name":"Campylobacter coli CVM N29710","NCBI_taxonomy_id":"1273173"}}}},"ARO_accession":"3002669","ARO_id":"39069","ARO_name":"APH(2'')-Ig","ARO_description":"APH('')-Ig is a plasmid-encoded aminoglycoside phosphotransferase in Campylobacter coli","ARO_category":{"36267":{"category_aro_accession":"3000128","category_aro_cvterm_id":"36267","category_aro_name":"APH(2'')","category_aro_description":"Phosphorylation of 2-deoxystreptamine aminoglycosides on the hydroxyl group at position 2''","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"904":{"model_id":"904","model_name":"rmtB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"575":{"protein_sequence":{"accession":"YP_001816610.1","sequence":"MNINDALTSILASKKYRALCPDTVRRILTEEWGRHKSPKQTVEAARTRLHGICGAYVTPESLKAAAAALSAGDVKKALSLHASTKERLAELDTLYDFIFSAETPRRVLDIACGLNPLALYERGIASVWGCDIHQGLGDVITPFAREKDWDFTFALQDVLCAPPAEAGDLALIFKLLPLLEREQAGSAMALLQSLNTPRMAVSFPTRSLGGRGKGMEANYAAWFEGGLPAEFEIEDKKTIGTELIYLIKKNG"},"dna_sequence":{"accession":"NC_010558","fmin":"116479","fmax":"117235","strand":"+","sequence":"ATGAACATCAACGATGCCCTCACCTCCATCCTGGCCTCAAAAAAATACCGCGCCCTTTGCCCGGATACCGTGCGGCGCATCCTGACTGAGGAATGGGGGCGGCATAAATCCCCCAAACAGACCGTAGAGGCTGCACGCACCCGGCTGCATGGAATTTGCGGGGCATATGTCACCCCGGAATCGCTCAAGGCTGCTGCCGCCGCGCTTTCTGCGGGCGATGTAAAAAAGGCATTGTCGCTGCATGCCTCCACCAAGGAGCGACTGGCCGAGCTGGATACCCTGTACGATTTTATCTTTTCAGCCGAAACTCCCCGCCGCGTGCTGGATATCGCCTGCGGTCTTAACCCCTTGGCGCTATACGAGCGCGGCATTGCATCCGTGTGGGGCTGTGATATCCACCAGGGATTGGGGGATGTCATCACCCCCTTTGCTAGGGAAAAAGATTGGGATTTTACCTTTGCCCTGCAGGATGTGCTGTGTGCGCCGCCCGCCGAAGCCGGCGACCTGGCGCTGATTTTTAAGCTTTTGCCCCTGCTGGAGCGGGAGCAGGCCGGTTCTGCCATGGCACTTTTACAATCCCTCAATACCCCGCGCATGGCTGTCAGCTTTCCCACGCGTAGTTTAGGCGGGCGTGGAAAAGGCATGGAGGCGAACTACGCCGCATGGTTCGAGGGCGGCTTGCCCGCCGAGTTTGAGATTGAGGATAAAAAGACCATCGGAACAGAACTTATATACTTGATAAAAAAGAATGGATAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000860","ARO_id":"37240","ARO_name":"rmtB","ARO_description":"RmtB is a 16S rRNA methyltransferase that targets mature or nearly mature 30S subunits. It transfers a methyl group from S-adenosyl-L-methionine to N7-G1405 of the 16S rRNA, an aminoglycoside binding site.","ARO_category":{"41435":{"category_aro_accession":"3004271","category_aro_cvterm_id":"41435","category_aro_name":"16S rRNA methyltransferase (G1405)","category_aro_description":"Methyltransferases that methylate the G1405 position of 16S rRNA, which is part of an aminoglycoside binding site.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"905":{"model_id":"905","model_name":"CTX-M-93","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2045":{"protein_sequence":{"accession":"ADN26580.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTQNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGGYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"HQ166709","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCAGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGGCTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001953","ARO_id":"38353","ARO_name":"CTX-M-93","ARO_description":"CTX-M-93 is a beta-lactamase found in Escherichia coli","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"906":{"model_id":"906","model_name":"CARB-21","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1264":{"protein_sequence":{"accession":"AGQ93789.1","sequence":"MVRVFTRYSLLNIAKVRIKTKRTKNTRMKKLFLLVGLMVCSTVSYASKLNEDISLIEKQTSGRIGVSVWDTQMDERWDYRGDERFPLMSTFKTLACATMLSDMDSGKLNKNATARIDERNIVVWSPVMDKLAGQSTRIEHACEAAMLMSDNTAANLVLNEIGGPKAVTLFLRSIGDKATRLDRLEPRLNEAKPGDKRDTTTPNAMVNTLHTLMEDNALSYESRTQLKIWMQDNKVSDSLMRSVLPKGWSIADRSGAGNYGSRGISAMIWKDNYKPVYISIYVTDTDLSLQARDQLIAQISQLILEHYKES"},"dna_sequence":{"accession":"CP006005","fmin":"1728735","fmax":"1729668","strand":"+","sequence":"GTGGTTAGAGTATTCACTCGTTATAGTTTGCTTAACATCGCCAAAGTGCGAATCAAAACCAAAAGAACGAAGAACACACGCATGAAAAAGTTATTCCTGTTGGTTGGGCTGATGGTTTGCTCAACTGTTAGTTACGCTTCCAAATTAAACGAAGACATCTCCCTCATCGAGAAACAAACATCTGGGCGAATTGGAGTGTCAGTCTGGGATACACAAATGGACGAGCGTTGGGATTATCGCGGAGACGAACGTTTCCCATTAATGAGCACATTCAAAACGTTAGCGTGTGCCACCATGCTAAGCGACATGGACAGCGGCAAACTCAACAAAAATGCCACAGCGAGAATCGATGAACGCAATATTGTGGTTTGGTCTCCGGTGATGGATAAACTGGCTGGACAAAGCACGCGTATCGAACACGCTTGTGAAGCCGCCATGTTGATGAGCGACAACACCGCCGCAAACTTAGTGCTAAATGAAATTGGTGGTCCTAAAGCGGTCACGCTGTTTTTGCGCTCTATTGGCGACAAAGCAACGCGACTTGACCGATTGGAGCCCCGTTTGAACGAAGCAAAACCGGGCGACAAGCGAGACACCACAACGCCTAACGCCATGGTAAACACCCTACACACCTTGATGGAAGATAACGCCCTATCTTACGAGTCACGCACACAGCTGAAAATCTGGATGCAAGACAACAAAGTATCGGATTCTCTCATGCGCTCTGTTCTACCAAAAGGCTGGTCGATTGCAGACCGCTCTGGCGCAGGTAACTACGGTTCACGCGGCATTAGCGCGATGATTTGGAAAGACAACTACAAGCCGGTTTACATCAGTATTTACGTCACAGATACTGACCTTTCGCTTCAAGCTCGCGATCAACTGATCGCGCAAATCAGCCAACTGATTTTAGAGCACTACAAAGAAAGTTAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39775","NCBI_taxonomy_name":"Vibrio parahaemolyticus O1:Kuk str. FDA_R31","NCBI_taxonomy_id":"1338034"}}}},"ARO_accession":"3003176","ARO_id":"39753","ARO_name":"CARB-21","ARO_description":"From the Lahey list of beta-lactamases.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"907":{"model_id":"907","model_name":"fexA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"490":{"protein_sequence":{"accession":"CAD70268.1","sequence":"MKKDSKSKEMIQSEKRGSTRLLMMVLSLSVLVGAITADLVNPVLPLISKDLEASKSQVSWIVSGIALVLAIGVPIYGRISDFFELRKLYIFAIMILASGSLLCAIAPNLPLLVLGRMVQGAGMSAIPVLSIIAISKVFPQGKRGGALGIIAGSIGVGTAAGPIFGGVVGQYLGWNALFWFTFLLAIMIVIGAYYALPTIKPAESVGSNKNFDFIGGLFLGLTVGLLLFGITQGETSGFSSFSSLTSLIGSVVALVGFIWRIVTAENPFVPPVLFNNKDYVNTVIIAFFSMFAYFAVLVFVPLLVVEVNGLSSGQAGMILLPGGVAVAILSPFVGRLSDRFGDKRLIITGMTLMGLSTLFLSTYASGASPLLVSVGVLGVGIAFAFTNSPANNAAVSALDADKVGVGMGIFQGALYLGAGTGAGMIGALLSARRDATEPINPLYILDAMSYSDAFLAATGAILIALIAGLGLKKRG"},"dna_sequence":{"accession":"AJ549214","fmin":"176","fmax":"1604","strand":"+","sequence":"ATGAAAAAGGATAGTAAATCTAAAGAAATGATTCAATCTGAAAAAAGGGGTTCTACTAGGCTTTTAATGATGGTACTCTCCCTATCTGTACTTGTAGGTGCAATTACGGCTGATTTAGTCAATCCCGTACTTCCACTAATAAGCAAAGATTTAGAAGCTTCGAAATCTCAAGTGAGTTGGATAGTTAGTGGTATTGCACTTGTTCTTGCGATTGGAGTTCCGATTTATGGTCGAATCTCAGACTTTTTTGAGTTACGAAAGCTATATATCTTTGCCATTATGATTCTGGCAAGTGGTAGTCTTTTATGTGCAATTGCCCCGAACCTCCCATTGTTGGTTTTGGGAAGAATGGTTCAGGGTGCTGGGATGTCCGCAATTCCAGTTCTATCAATCATTGCAATTTCGAAGGTTTTCCCACAAGGAAAACGTGGGGGAGCTTTGGGAATTATCGCAGGAAGTATTGGTGTTGGAACTGCTGCTGGTCCAATATTTGGTGGAGTAGTTGGTCAATATTTAGGGTGGAATGCCTTGTTTTGGTTCACATTTTTGTTAGCCATTATGATTGTTATTGGTGCCTACTACGCGTTACCGACAATTAAACCGGCAGAATCCGTAGGAAGCAATAAGAACTTTGATTTCATTGGTGGTTTATTCCTCGGCCTCACAGTAGGATTACTCCTTTTTGGCATCACTCAAGGAGAAACTTCTGGTTTTTCTTCGTTCTCATCGTTAACTAGCCTAATTGGTTCTGTTGTAGCTTTGGTGGGATTTATTTGGAGAATTGTTACCGCAGAAAATCCATTTGTACCACCTGTCCTGTTCAATAACAAGGATTATGTCAATACGGTCATAATTGCATTTTTTTCGATGTTTGCTTATTTCGCTGTTCTTGTGTTCGTCCCATTACTAGTCGTTGAGGTGAATGGACTCTCTTCTGGACAGGCTGGAATGATATTGTTGCCAGGTGGTGTGGCTGTTGCAATCTTATCTCCCTTCGTTGGCCGTCTTTCTGATCGATTTGGGGATAAACGTCTGATAATTACTGGGATGACTCTGATGGGGCTGTCTACCTTATTCTTGTCCACCTATGCATCTGGTGCTTCACCTCTGTTAGTTTCCGTGGGGGTCCTCGGAGTAGGGATTGCTTTTGCATTCACGAATTCTCCCGCAAATAACGCCGCAGTAAGTGCACTCGATGCAGACAAGGTTGGTGTCGGAATGGGGATTTTCCAAGGTGCTTTGTACCTTGGAGCAGGAACTGGAGCAGGTATGATTGGAGCATTATTATCCGCTCGACGTGATGCTACTGAGCCGATAAATCCATTATATATATTGGACGCTATGTCCTACTCAGATGCGTTCCTTGCAGCTACAGGGGCAATACTCATTGCCTTAATAGCTGGATTAGGTTTAAAAAAGCGTGGGTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39555","NCBI_taxonomy_name":"Staphylococcus lentus","NCBI_taxonomy_id":"42858"}}}},"ARO_accession":"3002704","ARO_id":"39138","ARO_name":"fexA","ARO_description":"fexA is a plasmid-encoded chloramphenicol exporter that is found in Staphylococcus lentus","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36600":{"category_aro_accession":"3000461","category_aro_cvterm_id":"36600","category_aro_name":"florfenicol","category_aro_description":"Florfenicol is a fluorine derivative of chloramphenicol, where the nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3) and the hydroxyl group (-OH), by a fluorine group (-F). The action mechanism is the same as chloramphenicol's, where the antibiotic binds to the 23S RNA of the 50S subunit of bacterial ribosomes to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"908":{"model_id":"908","model_name":"CTX-M-139","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"866":{"protein_sequence":{"accession":"AFY98865.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLFAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"KC107824","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTTTGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001997","ARO_id":"38397","ARO_name":"CTX-M-139","ARO_description":"CTX-M-139 is a beta-lactamase. From the Lahey list of CTX-M beta-lactamases.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"909":{"model_id":"909","model_name":"OXA-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1844":{"protein_sequence":{"accession":"CAA41211.1","sequence":"MKTIAAYLVLVFYASTALSESISENLAWNKEFSSESVHGVFVLCKSSSNSCTTNNAARASTAYIPASTFKIPNALIGLETGAIKDERQVFKWDGKPRAMKQWEKDLKLRGAIQVSAVPVFQQIAREVGEIRMQKYLNLFSYGNANIGGGIDKFWLEGQLRISAFNQVKFLESLYLNNLPASKANQLIVKEAIVTEATPEYIVHSKTGYSGVGTESSPGVAWWVGWVEKGTEVYFFAFNMDIDNESKLPSRKSISTKIMASEGIIIGG"},"dna_sequence":{"accession":"X58272","fmin":"79","fmax":"883","strand":"+","sequence":"ATGAAAACCATAGCCGCATATTTAGTTCTAGTTTTTTATGCAAGCACCGCGCTCTCAGAGTCTATTTCTGAAAATTTGGCGTGGAATAAAGAATTTTCTAGTGAATCCGTACATGGCGTTTTTGTACTTTGTAAAAGTAGTAGCAATTCCTGTACTACAAATAATGCGGCACGTGCATCTACAGCCTATATTCCAGCATCAACATTCAAAATTCCTAATGCTCTAATAGGTCTTGAAACCGGCGCCATAAAAGATGAACGGCAGGTTTTCAAATGGGACGGCAAGCCCAGAGCCATGAAGCAATGGGAAAAAGACTTAAAGCTAAGGGGCGCTATACAGGTTTCTGCTGTTCCGGTATTTCAACAAATTGCCAGAGAAGTTGGCGAAATAAGAATGCAAAAATACCTTAACCTGTTTTCATACGGCAACGCCAATATAGGGGGAGGCATTGACAAATTCTGGCTAGAAGGTCAGCTTAGAATCTCAGCATTCAATCAAGTTAAATTTTTAGAGTCGCTCTACCTGAATAATTTGCCAGCATCAAAAGCAAACCAACTAATAGTAAAAGAGGCAATAGTTACAGAAGCAACTCCAGAATATATAGTTCATTCAAAAACTGGGTATTCCGGTGTTGGCACAGAATCAAGTCCTGGTGTCGCTTGGTGGGTTGGTTGGGTAGAGAAAGGAACTGAGGTTTACTTTTTTGCTTTTAACATGGACATAGACAATGAGAGTAAATTGCCGTCAAGAAAATCCATTTCAACGAAAATCATGGCAAGTGAAGGCATCATCATTGGTGGCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001400","ARO_id":"37800","ARO_name":"OXA-5","ARO_description":"OXA-5 is a beta-lactamase found in P. aeruginosa and Enterobacteriaceae.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"911":{"model_id":"911","model_name":"CMY-50","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"822":{"protein_sequence":{"accession":"CBI75447.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDEVTDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVQPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWCIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"FN645444","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCGCTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGTTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGACCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTACACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGAAGTTACGGATAAAGCCGCATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGCGGTGCAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGTGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACAGGATCCACAGGCGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTAATGTTGGCAAACAAAAGCTACCCTAACCCGGTCCGCGTAGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002061","ARO_id":"38461","ARO_name":"CMY-50","ARO_description":"CMY-50 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"912":{"model_id":"912","model_name":"LEN-13","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1101":{"protein_sequence":{"accession":"CAG25814.1","sequence":"ATLPLAVDAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGLEQLDRRIHYRQQDLVDYSPVSEKHLVDGMTIGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPPGWFIADKTGAGERGARGIVALLGPDGKPERIVVLYLRDTPASMAERNQHIAG"},"dna_sequence":{"accession":"AJ635403","fmin":"0","fmax":"789","strand":"+","sequence":"GCCACCCTGCCACTGGCGGTAGACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGTCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGCCGGGCTGGTTTATCGCCGACAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGCTCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002463","ARO_id":"38863","ARO_name":"LEN-13","ARO_description":"LEN-13 is a beta-lactamase found in Klebsiella pneumoniae and Klebsiella variicola.","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"913":{"model_id":"913","model_name":"OXY-6-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1141":{"protein_sequence":{"accession":"CAI43425.1","sequence":"MLKSSWRKSALMAAAAVPLLLASGSLWASADAIQQKLANLEKRSGGRLGVALINTADDSQTLYRGDERFAMCSTGKVMAAAAVLKQSESHPDVVNKRLEIKKSDLVVWSPITEKHLQSGMTLAELSAAALQYSDNTAMNKMISYLGGPEKVTAFAQSIGDVTFRLDRTEPALNSAIPGDKRDTTTPLAMAESLRKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPASWAVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKSRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"AJ871877","fmin":"0","fmax":"876","strand":"+","sequence":"ATGTTGAAAAGTTCGTGGCGTAAAAGCGCCCTGATGGCCGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGTTCATTATGGGCCAGTGCCGATGCTATCCAGCAAAAGCTGGCTAATTTAGAAAAACGGTCCGGTGGCCGGCTGGGCGTGGCGCTGATTAACACGGCGGATGATTCGCAAACCCTTTATCGCGGCGACGAACGTTTTGCCATGTGCAGCACCGGTAAAGTGATGGCCGCCGCCGCGGTGTTAAAGCAGAGCGAAAGCCATCCCGATGTGGTGAATAAAAGGCTGGAGATTAAAAAATCGGATTTAGTGGTCTGGAGCCCGATTACCGAAAAACATCTGCAAAGCGGAATGACCCTGGCGGAACTCAGCGCGGCGGCGCTGCAGTACAGCGACAATACCGCGATGAATAAGATGATTAGCTACCTTGGCGGACCGGAAAAGGTGACCGCATTCGCCCAGAGCATCGGGGACGTTACTTTTCGTCTCGATCGTACGGAGCCGGCGCTGAACAGCGCGATACCCGGCGATAAGCGCGATACCACCACCCCGTTGGCGATGGCCGAAAGCCTGCGCAAGCTGACGCTGGGCAATGCGCTGGGCGAACAGCAGCGCGCCCAGTTAGTGACGTGGCTAAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCAGGCCTGCCCGCAAGCTGGGCGGTCGGGGATAAAACCGGCGCCGGAGATTACGGCACCACCAACGATATCGCGGTGATCTGGCCGGAAAATCATGCCCCGCTGGTGTTAGTGACCTATTTTACCCAGCCGCAGCAGGATGCGAAAAGCCGCAAAGAGGTGTTAGCCGCGGCGGCGAAAATCGTGACCGAAGGGCTGTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002416","ARO_id":"38816","ARO_name":"OXY-6-4","ARO_description":"OXY-6-4 is a beta-lactamase found in Klebsiella oxytoca","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"914":{"model_id":"914","model_name":"ANT(6)-Ia","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"3403":{"protein_sequence":{"accession":"YP_008997281.1","sequence":"MRSEKEMMDLVLSLAEQDERIRIVTLEGSRANINIPKDEFQDYDITYFVSDIEPFISNDDWLNQFGNIIMMQKPEDMELFPPEEKGFSYLMLFDDYNKIDLTLLPLEELDNYLKGDKLIKVLIDKDCRIKRDIVPTDIDYHVRKPSAREYDDCCNEFWNVTPYVIKGLCRKEILFAIDHLNQILRFELLRMMSWKVGIKTEFSLSVGKNYKYINKYIDEDLWNRLLSTYRMDSYENIWKSLFICHQLFREVSKEVAELLGFDYPEYGKNITRYTEDMYKKYVENDYF"},"dna_sequence":{"accession":"NC_023287","fmin":"60996","fmax":"61860","strand":"-","sequence":"TTAAAAATAGTCATTTTCAACATATTTTTTATACATGTCCTCGGTATATCTTGTTATGTTCTTACCATACTCTGGATAATCAAACCCCAGTAGTTCTGCTACCTCTTTGGACACTTCCCTGAACAATTGGTGGCATATAAATAATGACTTCCAAATATTTTCATAGGAATCCATGCGATATGTAGATAATAATCTATTCCATAGATCTTCATCAATGTATTTGTTAATATACTTATAATTTTTCCCAACACTTAATGAAAATTCTGTCTTTATCCCAACCTTCCACGACATCATCCTAAGTAGTTCAAACCGTAGAATCTGGTTCAGATGATCGATTGCAAACAGTATCTCTTTGCGGCACAATCCTTTAATAACATAAGGTGTTACATTCCAAAATTCATTGCAGCAATCATCATACTCCCTTGCGCTTGGCTTTCTTACATGATAATCTATATCAGTCGGAACTATGTCCCTTTTAATTCTACAATCTTTATCAATTAGAACCTTTATTAATTTATCGCCCTTTAGGTAATTATCTAACTCTTCCAAGGGCAATAAGGTAAGATCAATTTTATTGTAATCATCAAATAGCATAAGATAGGAAAATCCCTTTTCTTCAGGTGGGAATAATTCCATATCCTCCGGCTTTTGCATCATTATTATATTCCCAAATTGATTAAGCCAGTCATCATTAGATATAAACGGTTCTATATCACTTACAAAATATGTAATATCATAATCCTGAAATTCATCTTTAGGTATATTAATATTTGCGCGTGACCCCTCAAGGGTCACAATTCGAATACGTTCATCCTGTTCTGCTAAAGAAAGTACTAAATCCATCATTTCTTTTTCTGATCTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39580","NCBI_taxonomy_name":"Exiguobacterium sp. S3-2","NCBI_taxonomy_id":"1389960"}}}},"ARO_accession":"3002626","ARO_id":"39026","ARO_name":"ANT(6)-Ia","ARO_description":"ANT(6)-Ia is an aminoglycoside nucleotidyltransferase gene encoded by plasmids and chromosomes in Staphylococcus epidermidis, E. faecium, Streptococcus suis, S. aureus, E. faecalis and Streptococcus mitis","ARO_category":{"36364":{"category_aro_accession":"3000225","category_aro_cvterm_id":"36364","category_aro_name":"ANT(6)","category_aro_description":"Nucelotidylylation of streptomycin at the hydroxyl group at position 6","category_aro_class_name":"AMR Gene Family"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"915":{"model_id":"915","model_name":"SHV-106","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"2019":{"protein_sequence":{"accession":"CAQ03506.1","sequence":"MRFIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM941847","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTTTATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGAGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATCGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001155","ARO_id":"37535","ARO_name":"SHV-106","ARO_description":"SHV-106 is an extended-spectrum beta-lactamase that has been found in clinical isolates.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"916":{"model_id":"916","model_name":"OXA-36","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1842":{"protein_sequence":{"accession":"AAG24866.1","sequence":"MFSLATFAHAQEGTLERSDWRKFFSEFQAKGTIVVADERQADRAMLVFDPVRSKKRYSPASTFKIPHTLFALDAGAVRDEFQIFRWDGVNRGFAGHNQDQDLRSAMRNSTVWVYELFAKEIGDDKARRYLKKIDYGNAYPSTSNGDYWIEGSLAISAQEQIAFLRKLYRNELPFRVEHQRLVKDLMIVEAGRNWILRAKTGWEGRMGWWVGWVEWPTGSVFFALNIDTPNRMDDLFKREAIVRAIL"},"dna_sequence":{"accession":"AF300985","fmin":"0","fmax":"739","strand":"+","sequence":"ATTTTTTCTCTTGCCACTTTCGCGCATGCGCAAGAAGGCACGCTAGAACGTTCTGACTGGAGGAAGTTTTTCAGCGAATTTCAAGCCAAAGGCACGATAGTTGTGGCAGACGAACGCCAAGCGGATCGTGCCATGTTGGTTTTTGATCCTGTGCGATCGAAGAAACGCTACTCGCCTGCATCGACATTCAAGATACCTCATACACTTTTTGCACTTGATGCAGGCGCTGTTCGTGATGAGTTCCAGATTTTTCGATGGGACGGCGTTAACAGGGGCTTTGCAGGCCACAATCAAGACCAAGATTTGCGATCAGCAATGCGGAATTCTACTGTTTGGGTGTATGAGCTATTTGCAAAGGAAATTGGTGATGACAAAGCTCGGCGCTATTTGAAGAAAATCGACTATGGCAACGCCTATCCTTCGACAAGTAATGGCGATTACTGGATAGAAGGCAGCCTTGCAATCTCGGCGCAGGAGCAAATTGCATTTCTCAGGAAGCTCTATCGTAACGAGCTGCCCTTTCGGGTAGAACATCAGCGCTTGGTCAAGGATCTCATGATTGTGGAAGCCGGTCGCAACTGGATACTGCGTGCAAAGACGGGCTGGGAAGGCCGTATGGGTTGGTGGGTAGGATGGGTTGAGTGGCCGACTGGCTCCGTATTCTTCGCACTGAATATTGATACGCCAAACAGAATGGATGATCTTTTCAAGAGGGAGGCAATCGTGCGGGCAATCCTTC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001430","ARO_id":"37830","ARO_name":"OXA-36","ARO_description":"OXA-36 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"917":{"model_id":"917","model_name":"SHV-186","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"832":{"protein_sequence":{"accession":"AIS67769.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMTATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERCARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"KM233165","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGACCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGTGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3003153","ARO_id":"39730","ARO_name":"SHV-186","ARO_description":"From the Lahey list of beta-lactamases.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"918":{"model_id":"918","model_name":"TEM-49","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1726":{"protein_sequence":{"accession":"CAA71324.1","sequence":"MSIQHFRVALIPFFAAFCFPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASKRGSRGIIAALGPDGKPSRIVVIYMTGGQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"Y10281","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCTTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTAAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACATGACGGGGGGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000918","ARO_id":"37298","ARO_name":"TEM-49","ARO_description":"TEM-49 extended-spectrum beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"919":{"model_id":"919","model_name":"PER-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"3414":{"protein_sequence":{"accession":"CAA79968.1","sequence":"MNVIIKAVVTASTLLMVSFSSFETSAQSPLLKEQIESIVIGKKATVGVAVWGPDDLEPLLINPFEKFPMQSVFKLHLAMLVLHQVDQGKLDLNQTVIVNRAKVLQNTWAPIMKAYQGDEFSVPVQQLLQYSVSHSDNVACDLLFELVGGPAALHDYIQSMGIKETAVVANEAQMHADDQVQYQNWTSMKGAAEILKKFEQKTQLSETSQALLWKWMVETTTGPERLKGLLPAGTVVAHKTGTSGIKAGKTAATNDLGIILLPDGRPLLVAVFVKDSAESSRTNEAIIAQVAQTAYQFELKKLSALSPN"},"dna_sequence":{"accession":"Z21957.1","fmin":"284","fmax":"1211","strand":"-","sequence":"TTAATTTGGGCTTAGGGCAGAAAGCTTTTTCAATTCAAATTGATACGCAGTCTGAGCAACCTGCGCAATGATAGCTTCATTGGTTCGGCTTGACTCGGCTGAGTCTTTCACAAAAACAGCAACCAGCAAGGGCCGTCCATCAGGCAACAGAATGATACCTAAATCATTAGTGGCCGCAGTTTTTCCGGCTTTGATACCCGAAGTACCAGTTTTATGTGCGACCACAGTACCAGCTGGTAACAAACCTTTTAACCGCTCTGGTCCTGTGGTGGTTTCGACCATCCACTTCCATAACAAAGCCTGCGAGGTTTCAGACAGCTGTGTTTTTTGCTCAAACTTTTTCAGGATCTCTGCAGCACCTTTCATCGAGGTCCAGTTTTGATACTGCACCTGATCATCGGCGTGCATCTGCGCTTCATTTGCGACCACAGCGGTCTCCTTTATACCCATAGACTGGATATAGTCATGCAAAGCAGCTGGTCCACCAACCAGTTCAAATAACAAATCACAGGCCACGTTATCGCTGTGCGAGACCGAGTATTGCAGCAGTTGCTGCACTGGAACACTAAACTCGTCTCCCTGATACGCTTTCATTATCGGAGCCCAGGTATTCTGTAAAACCTTAGCCCTGTTTACGATAACGGTCTGATTTAAATCCAACTTTCCCTGATCAACCTGATGCAGTACCAACATAGCTAAATGCAATTTAAATACACTTTGCATTGGGAATTTTTCAAAAGGATTAATCAGTAAAGGTTCCAGATCGTCAGGCCCCCACACTGCAACGCCTACAGTGGCTTTTTTTCCAATGACTATGGATTCAATTTGCTCTTTTAACAGTGGGGATTGCGCTGAGGTTTCGAATGAACTAAAAGATACCATCAGTAGCGTCGAGGCAGTAACTACAGCTTTTATAATGACATTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002363","ARO_id":"38763","ARO_name":"PER-1","ARO_description":"PER-1 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36195":{"category_aro_accession":"3000056","category_aro_cvterm_id":"36195","category_aro_name":"PER beta-lactamase","category_aro_description":"PER beta-lactamases are plasmid-mediated extended spectrum beta-lactamases found in the Enterobacteriaceae family.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"920":{"model_id":"920","model_name":"TEM-152","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1074":{"protein_sequence":{"accession":"ABI74447.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMVSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDHWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGKRGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERDRQIAEIGASLIKHW"},"dna_sequence":{"accession":"DQ834728","fmin":"205","fmax":"1066","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGGTGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCATTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTAAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAGATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001019","ARO_id":"37399","ARO_name":"TEM-152","ARO_description":"TEM-152 is a CMT-type, inhibitor-resistant, extended-spectrum beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"921":{"model_id":"921","model_name":"OKP-A-11","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"876":{"protein_sequence":{"accession":"CAP12353.2","sequence":"MRYVRLCLISLIAALPLAAFASPPPLEQVTRSESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIRYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKSVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMAATLRKLLTSHALSARSQQQLLQWMVDDQVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPNGKAERIVVIYLRDTPATMAERNQQIARIGAALIEHWQR"},"dna_sequence":{"accession":"AM850915","fmin":"19","fmax":"880","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGCATTCGCCAGCCCTCCGCCGCTCGAGCAAGTTACACGCAGCGAAAGTCAGCTGGCGGGCCGCGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGAGACGAACAGCTGGATCGGCGGATCCGCTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGAGCGTTGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAGCTCAATGAGGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCAGCCAGCATGGCCGCCACCCTGCGCAAGCTGCTAACCAGCCACGCGCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGACCAGGTGGCCGGTCCGCTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGCGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGAACGGCAAAGCGGAGCGCATCGTGGTGATCTATCTGCGGGATACGCCGGCGACCATGGCCGAGCGTAACCAGCAGATCGCCAGAATAGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002428","ARO_id":"38828","ARO_name":"OKP-A-11","ARO_description":"OKP-A-11 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"922":{"model_id":"922","model_name":"AAC(6')-30\/AAC(6')-Ib' fusion protein","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"186":{"protein_sequence":{"accession":"CAE48335.2","sequence":"MTFLIRPVEQSDAESWERLRNLLWEGDDHKSEITQFFNGEVEEPNEVLLAVTEENDAIAHIELSLRYDIDGLTGIKTGYIEGLFVEERHRAAGVVLKLLRAAEFWARDQGCLAFASDRDDRVIIYARYTGAPPNNSLGITKYSIVTNSNDSVTLRLMTEHDLAMLYEWLNRSHIVEWWGGEEARPTLADVQEQYLPSVLAQESVTPYIAMLNGEPIGYAQSYVALGSGDGWWEEETDPGVRGIDQSLANASQLGKGLGTKLVRALVELLFNDPEVTKIQTDPSPSNLRAIRCYEKAGFERQGTVTTPDGPAVYMVQTRQAFERTRSVA"},"dna_sequence":{"accession":"AJ584652","fmin":"1926","fmax":"2913","strand":"+","sequence":"ATGACATTCCTGATCCGACCCGTAGAACAAAGTGACGCTGAATCTTGGGAGCGCTTACGCAACCTTTTGTGGGAGGGCGACGACCACAAAAGCGAGATCACACAATTCTTCAACGGCGAAGTAGAAGAACCCAATGAAGTGTTGCTTGCCGTAACCGAAGAAAATGATGCAATAGCGCACATCGAGCTATCGTTGAGGTATGACATTGATGGCTTGACGGGCATCAAGACCGGTTACATCGAAGGCCTTTTTGTAGAGGAGCGGCACCGTGCCGCAGGTGTAGTCCTCAAGCTATTGCGAGCCGCAGAGTTCTGGGCAAGAGATCAAGGATGTCTGGCGTTTGCCTCAGACAGGGATGATCGTGTCATCATCTATGCTCGCTACACGGGAGCGCCACCTAACAATTCATTAGGCATCACAAAGTACAGCATCGTGACCAACAGCAACGATTCCGTCACACTGCGCCTCATGACTGAGCATGACCTTGCGATGCTCTATGAGTGGCTAAATCGATCTCATATCGTCGAGTGGTGGGGCGGAGAAGAAGCACGCCCGACACTTGCTGACGTACAGGAACAGTACTTGCCAAGCGTTTTAGCGCAAGAGTCCGTCACTCCATACATTGCAATGCTGAATGGAGAGCCGATTGGGTATGCCCAGTCGTACGTTGCTCTTGGAAGCGGGGACGGATGGTGGGAAGAAGAAACCGATCCAGGAGTACGCGGAATAGACCAGTCACTGGCGAATGCATCACAACTGGGCAAAGGCTTGGGAACCAAGCTGGTTCGAGCTCTGGTTGAGTTGCTGTTCAATGATCCCGAGGTCACCAAGATCCAAACGGACCCGTCGCCGAGCAACTTGCGAGCGATCCGATGCTACGAGAAAGCGGGGTTTGAGAGGCAAGGTACCGTAACCACCCCAGATGGTCCAGCCGTGTACATGGTTCAAACACGCCAGGCATTCGAGCGAACACGCAGTGTTGCCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002599","ARO_id":"38999","ARO_name":"AAC(6')-30\/AAC(6')-Ib' fusion protein","ARO_description":"AAC(6')-30\/AAC(6')-Ib' is an integron-encoded aminoglycoside acetyltransferase in P. aeruginosa","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"923":{"model_id":"923","model_name":"VIM-25","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1890":{"protein_sequence":{"accession":"ADO50679.1","sequence":"MLKVISSLLVYMTASVMAVASPLAHSGEPSGEYPTVNEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRKAGVATYASPSTRRLAEAEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSANVLYGGCAVLALSRTSAGNVADADLAEWPTSVERIQKHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"HM750249","fmin":"90","fmax":"891","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTACATGACCGCGTCTGTCATGGCTGTAGCTAGTCCGTTAGCCCATTCCGGGGAGCCGAGTGGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGAGAGGTCCGGCTTTACCAGATTGCTGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCGGTCTACCCATCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCCCTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCCGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGAAGGCTGGAGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGCAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGCTCTTCTATCCCGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAACGTGCTATACGGTGGTTGTGCCGTTCTTGCGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCGTTGAGCGGATTCAAAAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAGC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3002295","ARO_id":"38695","ARO_name":"VIM-25","ARO_description":"VIM-25 is a beta-lactamase. From the Lahey list of VIM beta-lactamases.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"924":{"model_id":"924","model_name":"AAC(6')-33","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"362":{"protein_sequence":{"accession":"AEZ05106.1","sequence":"MAYEFCEIGESNEYIILAARILTKSFLDIGNNSWPDMKSATKEVEECIEKPNICLGIHENEKLLGWIGLRPMYKLTWELHPLVISTQYQNKGIGRLLINELEKKAKQIGIIGIVLGTDDEYFKTSLSAVDLYGENILDEIRTIKNIKNHPYEFYQKCGYSIVGVIPDANGKRKPDIWMWKKIND"},"dna_sequence":{"accession":"JN596280","fmin":"1202","fmax":"1757","strand":"+","sequence":"ATGGCGTATGAGTTCTGCGAAATAGGTGAATCAAACGAATATATTATTCTGGCGGCTAGAATCTTAACGAAATCATTCCTAGATATCGGTAATAATTCCTGGCCTGACATGAAAAGTGCTACTAAAGAAGTTGAAGAATGCATTGAGAAGCCAAACATATGTCTTGGAATACATGAAAATGAAAAATTGCTTGGATGGATTGGCCTTAGGCCCATGTACAAATTAACATGGGAATTACATCCCTTGGTAATAAGTACTCAATATCAGAATAAAGGTATTGGAAGACTTTTAATAAATGAATTAGAAAAAAAAGCAAAGCAAATTGGAATAATTGGAATAGTATTGGGAACTGACGATGAATACTTTAAAACTTCATTATCAGCTGTTGATCTTTACGGCGAAAATATTCTTGATGAGATAAGGACTATTAAAAACATAAAAAATCATCCGTACGAATTCTATCAAAAATGTGGGTATTCCATTGTCGGAGTAATACCCGATGCAAATGGAAAAAGGAAGCCAGATATTTGGATGTGGAAGAAGATAAATGATTAGG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002587","ARO_id":"38987","ARO_name":"AAC(6')-33","ARO_description":"AAC(6')-33 is an integron-encoded aminoglycoside acetyltransferase in P. aeruginosa","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"925":{"model_id":"925","model_name":"AAC(3)-IIb","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"10":{"protein_sequence":{"accession":"AAA26548.1","sequence":"MNTIESITADLHGLGVRPGDLIMVHASLKAVGPVEGGAASVVSALRAAVGSAGTLMGYASWDRSPYEETLNGARMDEELRRRWPPFDLATSGTYPGFGLLNRFLLEAPDARRSAHPDASMVAVGPLAATLTEPHRLGQALGEGSPLERFVGHGGKVLLLGAPLDSVTVLHYAEAIAPIPNKRRVTYEMPMLGPDGRVRWELAEDFDSNGILDCFAVDGKPDAVETIAKAYVELGRHREGIVGRAPSYLFEAQDIVSFGVTYLEQHFGAP"},"dna_sequence":{"accession":"M97172","fmin":"655","fmax":"1465","strand":"+","sequence":"ATGAACACGATCGAATCGATCACGGCGGACCTGCACGGACTGGGCGTCCGGCCCGGCGACCTGATCATGGTCCATGCATCGCTGAAAGCCGTCGGCCCGGTCGAGGGAGGTGCGGCCTCGGTGGTGTCGGCCCTTCGCGCCGCGGTCGGGTCCGCAGGGACCCTGATGGGTTATGCCTCATGGGACCGCTCGCCCTATGAGGAGACGCTGAACGGCGCGCGGATGGACGAAGAACTGCGCCGCCGGTGGCCACCCTTCGATCTGGCCACATCCGGTACCTATCCCGGCTTCGGCCTGCTCAACCGGTTTCTGCTTGAGGCGCCCGACGCACGGCGCAGCGCGCATCCCGACGCCTCCATGGTCGCGGTCGGCCCCCTTGCCGCCACGCTGACAGAGCCGCACCGGCTTGGGCAGGCGCTGGGCGAAGGCTCGCCGCTGGAGCGCTTCGTCGGGCATGGCGGAAAGGTCCTGCTTCTGGGAGCGCCGCTCGACTCCGTCACCGTGCTGCATTACGCCGAGGCCATCGCCCCCATCCCGAACAAACGCCGCGTGACCTATGAAATGCCGATGCTCGGCCCGGATGGCAGGGTCCGATGGGAGCTGGCCGAGGATTTCGACAGCAACGGCATTCTCGATTGCTTCGCGGTCGATGGGAAGCCGGATGCCGTCGAGACGATCGCCAAGGCTTATGTCGAACTGGGCCGGCATCGGGAAGGCATCGTCGGTCGCGCACCCTCCTATCTGTTTGAAGCGCAGGATATCGTCTCGTTCGGCGTCACCTATCTCGAACAGCATTTCGGCGCGCCCTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36783","NCBI_taxonomy_name":"Serratia marcescens","NCBI_taxonomy_id":"615"}}}},"ARO_accession":"3002534","ARO_id":"38934","ARO_name":"AAC(3)-IIb","ARO_description":"AAC(3)-IIb is an aminoglycoside acetyltransferase in E. coli, A. faecalis and S. marcescens","ARO_category":{"36461":{"category_aro_accession":"3000322","category_aro_cvterm_id":"36461","category_aro_name":"AAC(3)","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 3.","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"926":{"model_id":"926","model_name":"KPC-15","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"2049":{"protein_sequence":{"accession":"AGF70638.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVRWSPISEKYLTTGMTVLELSAAAVQYSDNAAANLLLKELGGPAKLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGGYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"KC433553","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCGGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTTTTGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCAAACTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGGGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002325","ARO_id":"38725","ARO_name":"KPC-15","ARO_description":"KPC-15 is a beta-lactamase. From the Lahey list of KPC beta-lactamases.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"927":{"model_id":"927","model_name":"OXA-381","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1933":{"protein_sequence":{"accession":"AHL30285.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDKKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGFEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKVSAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KJ135344","fmin":"14","fmax":"839","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATAAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATAGGCTTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGTTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001567","ARO_id":"37967","ARO_name":"OXA-381","ARO_description":"OXA-381 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"928":{"model_id":"928","model_name":"carA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1050"}},"model_sequences":{"sequence":{"90":{"protein_sequence":{"accession":"AAC32027.1","sequence":"MSTAQLALHDITKRYQDHVVLDRIGFTIKPGEKVGVIGDNGSGKSTLIKLIAGREQPDNGAVTVVAPGGVGYLAQTLELPLEATVQDAVDLALADLRELEEGMRRTEAELAERPYQTGQDPELAGLLESYAALVDRYQARGGYEADSRVEIALHGLGLPGLERGRRLGTLSGGERSRLALAATLASEPELLLLDEPTNDLDDRAVDWLEEHLRKHKGTVVAVTHDRLFLDRLTTTILEIDSGKVMRYGNGYEGYLAAKAAERQRRLLEYEQWRAELDRSRDLIASNVARLDAIPRKLPFAVFGAGQFRMRGRGHGAMVRIRNAKERVARLTENPVAPPPEPLTFTAEITTEAAQSRETVAELTGVRVGDRLSVDSLHLGPGERLLVTGPNGAGKTTLLRVLSGELEPDSGSLLVSGRVGHLRQEQTPWRPGMTVLQAFSSGRAGDIDEHTEALLSLGLFSPDDLRQRVQDLSYGQRRRIELARLVTEPVDLLLLDEPTNHLSPALVEELEEALTGYQGTVVVVTHDRRMRSRFNGAHLTLQDGRVAEFTAA"},"dna_sequence":{"accession":"M80346","fmin":"0","fmax":"1656","strand":"+","sequence":"GTGTCGACAGCGCAACTAGCTCTGCATGACATCACCAAGCGTTACCAGGACCACGTCGTACTCGACCGGATCGGCTTCACCATCAAGCCGGGCGAGAAGGTCGGTGTCATCGGGGACAACGGATCCGGCAAGTCCACGCTGATCAAGCTCATCGCCGGGCGGGAACAGCCGGACAACGGTGCGGTGACGGTGGTCGCGCCCGGTGGCGTCGGCTATCTGGCCCAGACACTGGAGCTGCCGCTGGAGGCCACGGTCCAGGACGCCGTCGATCTGGCCCTGGCCGACCTGCGGGAGCTGGAGGAGGGCATGCGCCGGACCGAGGCCGAGCTGGCCGAACGGCCCTACCAAACGGGCCAAGACCCCGAACTCGCCGGCCTCCTGGAGAGTTACGCCGCGCTGGTGGACCGGTATCAGGCCCGCGGCGGCTACGAGGCCGACTCCCGCGTGGAGATCGCGCTGCACGGGCTCGGGCTGCCCGGGCTGGAACGCGGCCGGCGGCTGGGCACCCTGTCCGGCGGCGAGCGCTCGCGCCTCGCCCTGGCGGCGACGCTGGCCTCGGAACCCGAACTGCTGCTGTTGGACGAGCCGACCAACGACCTGGACGACCGGGCCGTGGACTGGCTGGAGGAACACCTGCGCAAGCACAAAGGCACCGTTGTCGCCGTTACCCACGACCGGCTCTTCCTCGACCGGCTCACCACCACGATCCTGGAGATCGACTCCGGCAAGGTGATGCGCTACGGCAACGGCTACGAGGGCTACCTGGCAGCCAAGGCGGCGGAACGGCAGCGCAGGCTGCTTGAGTACGAGCAGTGGCGCGCCGAGCTGGACCGCAGCCGCGACCTGATCGCGTCCAACGTGGCGCGTCTGGACGCCATCCCACGCAAGCTGCCCTTCGCCGTCTTCGGCGCCGGCCAGTTCCGGATGCGCGGGCGGGGCCATGGTGCGATGGTGCGGATCCGCAACGCCAAGGAACGCGTCGCGCGGCTGACCGAAAACCCGGTCGCGCCGCCGCCCGAGCCGCTCACCTTCACCGCGGAGATCACCACCGAGGCCGCGCAGTCCCGGGAGACGGTGGCCGAACTCACCGGCGTCCGGGTCGGCGACCGGCTCAGCGTCGACTCCCTGCACCTCGGGCCCGGTGAACGGCTGCTGGTCACCGGCCCCAACGGGGCGGGCAAGACGACGCTGCTGCGGGTGCTCTCCGGGGAGCTGGAACCCGACAGCGGATCCCTGCTGGTGTCGGGCCGGGTGGGACACCTGAGGCAGGAACAGACACCATGGCGGCCGGGTATGACGGTGCTTCAGGCGTTCAGCAGCGGACGGGCCGGTGACATCGACGAGCACACCGAGGCGCTGCTCTCCCTCGGGCTGTTCAGCCCGGACGACCTCCGCCAGCGTGTGCAGGACCTGTCGTACGGGCAGCGGCGCCGCATCGAGCTTGCCCGGCTGGTGACGGAGCCGGTCGACCTGCTGCTGCTGGACGAACCCACCAACCACCTCTCGCCCGCGCTCGTCGAGGAACTGGAGGAGGCGCTGACCGGTTATCAGGGCACGGTCGTCGTCGTCACCCACGACCGGCGCATGCGGTCCCGCTTCAACGGCGCCCATCTGACGCTGCAGGACGGGCGCGTCGCCGAGTTCACCGCCGCCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36843","NCBI_taxonomy_name":"Streptomyces thermotolerans","NCBI_taxonomy_id":"80858"}}}},"ARO_accession":"3002817","ARO_id":"39251","ARO_name":"carA","ARO_description":"carA is an ABC transporter involved in macrolide resistance. It is found in Streptomyces thermotolerans","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"929":{"model_id":"929","model_name":"GES-10","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1670":{"protein_sequence":{"accession":"ACS73598.1","sequence":"MRFIHALLLAGTAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRTAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLCDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMGDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"FJ820124","fmin":"1123","fmax":"1987","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGACCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAACGGCGCAGCGCTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTTGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGGGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAGT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3002339","ARO_id":"38739","ARO_name":"GES-10","ARO_description":"GES-10 is a beta-lactamase. From the Lahey list of GES beta-lactamases.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"931":{"model_id":"931","model_name":"OXA-316","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1609":{"protein_sequence":{"accession":"AGU69254.1","sequence":"MNIQALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMEASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPHGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KF057033","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTCAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGGAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCATGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001687","ARO_id":"38087","ARO_name":"OXA-316","ARO_description":"OXA-316 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"932":{"model_id":"932","model_name":"GES-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"790":{"protein_sequence":{"accession":"AAK18183.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQLAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMGDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"AF329699","fmin":"372","fmax":"1236","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCATCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAACTGGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGGGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAGT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002337","ARO_id":"38737","ARO_name":"GES-8","ARO_description":"GES-8 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"933":{"model_id":"933","model_name":"OKP-A-14","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1120":{"protein_sequence":{"accession":"ACL68095.1","sequence":"MRYIRLCLFSLIAALPLAVFASPPPLEQITRSESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIRYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKSVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMATTLRKLLTSHTLSARSQQQLLQWMVDDQVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPNGKAERIVVIYLRDTPATIAERNQQIARIGAALIEHWQR"},"dna_sequence":{"accession":"FJ534512","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGCCTTTTCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCCGCCGCTTGAGCAAATTACACGCAGCGAAAGTCAGCTGGCGGGCCGCGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGAGACGAACAGCTGGATCGGCGGATCCGCTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGAGCGTTGGCGGCCCCGCGGGATTGACCGCTTTTTTGCGCCAGATCGGTGACAACGTCACCCGCCTCGACCGCTGGGAAACGGAGCTCAATGAAGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCAGCCAGCATGGCCACCACCCTGCGCAAGCTGCTAACCAGCCACACTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGACCAGGTAGCCGGTCCGCTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGCGAGCGGGGCTCACGTGGCATTGTCGCCCTGCTCGGCCCGAACGGCAAAGCGGAGCGCATCGTGGTGATCTATCTGCGGGATACGCCGGCGACCATAGCCGAGCGTAACCAGCAGATCGCCAGAATAGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002431","ARO_id":"38831","ARO_name":"OKP-A-14","ARO_description":"OKP-A-14 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"934":{"model_id":"934","model_name":"IMP-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1436":{"protein_sequence":{"accession":"AAK13430.1","sequence":"MKKLFVLCVCFLCSITAAGAALPDLKIEKLEEGVYVHTSFEEVNGWGVVSKHGLVVLVNTDAYLIDTPFTATDTEKLVNWFVERGYKIKGTISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKDGKVQAKNSFSGVSYWLVKNKIEVFYPGPGHTQDNVVVWLPEKKILFGGCFVKPDGLGNLGDANLEAWPKSAKILMSKYGKAKLVVSSHSEIGDASLLKRTWEQAVKGLNESKKPSQPSN"},"dna_sequence":{"accession":"AF322577","fmin":"2081","fmax":"2822","strand":"+","sequence":"ATGAAGAAATTATTTGTTTTATGTGTATGCTTCCTTTGTAGCATTACTGCCGCAGGAGCGGCTTTGCCTGATTTAAAAATCGAGAAGCTTGAAGAAGGTGTTTATGTTCATACATCGTTCGAAGAAGTTAACGGTTGGGGTGTTGTTTCTAAACACGGTTTGGTGGTTCTTGTAAACACTGACGCCTATCTGATTGACACTCCATTTACTGCTACAGATACTGAAAAGTTAGTCAATTGGTTTGTGGAGCGCGGCTATAAAATCAAAGGCACTATTTCCTCACATTTCCATAGCGACAGCACAGGGGGAATAGAGTGGCTTAATTCTCAATCTATTCCCACGTATGCATCTGAATTAACAAATGAACTTCTTAAAAAAGACGGTAAGGTGCAAGCTAAAAACTCATTTAGCGGAGTTAGTTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCCGGCCCGGGGCACACTCAAGATAACGTAGTGGTTTGGTTACCTGAAAAGAAAATTTTATTCGGTGGTTGTTTTGTTAAACCGGACGGTCTTGGTAATTTGGGTGACGCAAATTTAGAAGCTTGGCCAAAGTCCGCCAAAATATTAATGTCTAAATATGGTAAAGCAAAACTGGTTGTTTCAAGTCATAGTGAAATTGGGGACGCATCACTCTTGAAACGTACATGGGAACAGGCTGTTAAAGGGCTAAATGAAAGTAAAAAACCATCACAGCCAAGTAACTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002199","ARO_id":"38599","ARO_name":"IMP-8","ARO_description":"IMP-8 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"935":{"model_id":"935","model_name":"OXA-314","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1458":{"protein_sequence":{"accession":"AGU69252.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KF057031","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCATTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001685","ARO_id":"38085","ARO_name":"OXA-314","ARO_description":"OXA-314 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"936":{"model_id":"936","model_name":"OKP-A-13","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1040":{"protein_sequence":{"accession":"ACL68096.1","sequence":"MRYIRLCLFSLIAALPLAVFASPPPLEQITRSESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIRYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKSVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMAATLRKLLTSHTLSARSQQQLLQWMVDDQVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPNGKAERIVVIYLRDTPATMAERNQQIARIGAALIEHWQR"},"dna_sequence":{"accession":"FJ534513","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGCCTTTTCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCCGCCGCTTGAGCAAATTACACGCAGCGAAAGTCAGCTGGCGGGCCGCGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGAGACGAACAGCTGGATCGGCGGATCCGCTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGAGCGTTGGCGGCCCCGCGGGATTGACCGCTTTTTTGCGCCAGATCGGTGACAACGTCACCCGCCTCGACCGCTGGGAAACGGAGCTCAATGAAGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCAGCCAGCATGGCCGCCACCCTGCGCAAGCTGCTAACCAGCCACACTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGACCAGGTAGCCGGTCCGCTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGCGAGCGGGGCTCACGTGGCATTGTCGCCCTGCTCGGCCCGAACGGCAAAGCGGAGCGCATCGTGGTGATCTATCTGCGGGATACGCCGGCGACCATGGCCGAGCGTAACCAGCAGATCGCCAGAATAGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002430","ARO_id":"38830","ARO_name":"OKP-A-13","ARO_description":"OKP-A-13 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"937":{"model_id":"937","model_name":"OXA-242","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1838":{"protein_sequence":{"accession":"AFO55202.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQRNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"JX025022","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACGCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCCTTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAAGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001680","ARO_id":"38080","ARO_name":"OXA-242","ARO_description":"OXA-242 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"938":{"model_id":"938","model_name":"QnrB70","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"370":{"protein_sequence":{"accession":"AGL43631.1","sequence":"MTLVLVGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"KC580659","fmin":"0","fmax":"645","strand":"+","sequence":"ATGACTCTGGTATTAGTAGGCGAAAAAATTGACAGAAATCGCTTCACCGGTGAGAAAGTTGAAAATAGTACATTTTTTAACTGCGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGCCAGTTCTATGATCGCGAAAGTCAGAAAGGATGCAATTTTAGTCGCGCAATGCTGAAAGATGCCATTTTCAAAAGCTGTGATTTATCAATGGCAGATTTCCGCAACGTCAGCGCATTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGTGCAAGCTTTATGAATATGATCACCACGCGCACCTGGTTTTGCAGCGCATATATCACTAATACCAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAGCTATGGGAAAACCGCTGGATGGGGACTCAGGTACTGGGTGCGACGTTTAGTGGTTCAGATCTCTCCGGTGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTAGGTGACTTAGATATTCGGGGTGTTGATTTACAAGGCGTTAAGTTAGACAACTACCAGGCATCGTTGCTCATGGAGCGGCTTGGCATCGCTGTGATTGGTTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39584","NCBI_taxonomy_name":"Citrobacter braakii","NCBI_taxonomy_id":"57706"}}}},"ARO_accession":"3002782","ARO_id":"39216","ARO_name":"QnrB70","ARO_description":"QnrB70 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"939":{"model_id":"939","model_name":"CTX-M-113","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1901":{"protein_sequence":{"accession":"AEM44653.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKRSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"JF274247","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCGGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36955","NCBI_taxonomy_name":"Shigella sp. SH284","NCBI_taxonomy_id":"1074436"}}}},"ARO_accession":"3001973","ARO_id":"38373","ARO_name":"CTX-M-113","ARO_description":"CTX-M-113 is a beta-lactamase found in Shigella spp.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"940":{"model_id":"940","model_name":"TEM-125","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1489":{"protein_sequence":{"accession":"AAT46414.1","sequence":"MSIQHFRVALIPFLAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMLSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSREPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERDRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AY628176","fmin":"75","fmax":"936","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTCTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGCTAAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAACAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATAGTCGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAGATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000987","ARO_id":"37367","ARO_name":"TEM-125","ARO_description":"TEM-125 is a CMT-type, inhibitor-resistant, extended-spectrum beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"941":{"model_id":"941","model_name":"GES-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1593":{"protein_sequence":{"accession":"AAF27723.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMGDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"AF156486","fmin":"1331","fmax":"2195","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGGGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACTTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAGT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002330","ARO_id":"38730","ARO_name":"GES-1","ARO_description":"GES-1 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"942":{"model_id":"942","model_name":"OXA-104","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1122":{"protein_sequence":{"accession":"ABQ52429.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"EF581285","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAACATTAAAGCGCTGCTGCTGATTACCAGCGCGATTTTTATTAGCGCGTGCAGCCCGTATATTGTGACCGCGAACCCGAACCATAGCGCGAGCAAAAGCGATGAAAAAGCGGAAAAAATTAAAAACCTGTTTAACGAAGCGCATACCACCGGCGTGCTGGTGATTCAGCAGGGCCAGACCCAGCAGAGCTATGGCAACGATCTGGCGCGCGCGAGCACCGAATATGTGCCGGCGAGCACCTTTAAAATGCTGAACGCGCTGATTGGCCTGGAACATCATAAAGCGACCACCACCGAAGTGTTTAAATGGGATGGCAAAAAACGCCTGTTTCCGGAATGGGAAAAAAACATGACCCTGGGCGATGCGATGAAAGCGAGCGCGATTCCGGTGTATCAGGATCTGGCGCGCCGCATTGGCCTGGAACTGATGAGCAACGAAGTGAAACGCGTGGGCTATGGCAACGCGGATATTGGCACCCAGGTGGATAACTTTTGGCTGGTGGGCCCGCTGAAAATTACCCCGCAGCAGGAAGCGCAGTTTGCGTATAAACTGGCGAACAAAACCCTGCCGTTTAGCCAGAAAGTGCAGGATGAAGTGCAGAGCATGCTGTTTATTGAAGAAAAAAACGGCAACAAAATTTATGCGAAAAGCGGCTGGGGCTGGGATGTGGATCCGCAGGTGGGCTGGCTGACCGGCTGGGTGGTGCAGCCGCAGGGCAACATTGTGGCGTTTAGCCTGAACCTGGAAATGAAAAAAGGCATTCCGAGCAGCGTGCGCAAAGAAATTACCTATAAAAGCCTGGAACAGCTGGGCATTCTG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001636","ARO_id":"38036","ARO_name":"OXA-104","ARO_description":"OXA-104 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"944":{"model_id":"944","model_name":"bcrB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"370"}},"model_sequences":{"sequence":{"585":{"protein_sequence":{"accession":"AAA99505.1","sequence":"MAKKAKYPDVPIRFSETFSDTNLYIVLLIGVPLYGVITSYLFNREYAESTLKNLLTIPVSRISLIVSKLVLLLIWIMMLTLIAWVLTLLFGLIGQFEGLSSAVLIEGFKQFMIGGALLFFLVSPIIFVTLLFKNYVPTIIFTIIISMVSIMVYGTEYSALFPWSAVWVIASGTFFPEYPPEYSFISVAATTVLGLAATIVYFKKIDIH"},"dna_sequence":{"accession":"L20573","fmin":"1317","fmax":"1944","strand":"+","sequence":"TTGGCTAAAAAAGCCAAGTACCCTGATGTACCGATTCGCTTCAGTGAGACCTTTTCCGATACCAACCTGTATATTGTGCTTTTGATCGGAGTCCCGTTGTATGGTGTGATTACATCATATTTATTCAATCGGGAATACGCTGAAAGCACGCTAAAGAATCTATTGACGATTCCTGTTTCAAGAATCAGCCTGATTGTCAGCAAATTGGTTCTGCTTCTCATTTGGATCATGATGCTGACGTTAATCGCCTGGGTGCTGACGCTGCTGTTCGGGCTGATCGGTCAGTTTGAAGGGCTCAGTTCGGCGGTTTTAATTGAAGGGTTTAAACAATTTATGATAGGCGGGGCACTTCTTTTCTTCCTGGTCAGTCCGATTATATTTGTGACACTGCTGTTTAAAAACTACGTGCCCACCATTATCTTTACGATCATTATATCAATGGTCAGCATTATGGTATACGGCACGGAATACAGCGCTTTATTCCCTTGGTCAGCGGTATGGGTGATCGCTTCGGGTACGTTCTTTCCGGAATATCCGCCCGAATATTCTTTTATCAGTGTTGCCGCCACAACCGTTCTTGGATTAGCCGCGACAATCGTTTACTTTAAAAAAATCGATATTCATTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36834","NCBI_taxonomy_name":"Bacillus licheniformis","NCBI_taxonomy_id":"1402"}}}},"ARO_accession":"3002988","ARO_id":"39422","ARO_name":"bcrB","ARO_description":"bcrB is an ABC transporter found in Bacillus licheniformis that confers bacitracin resistance","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"36973":{"category_aro_accession":"3000629","category_aro_cvterm_id":"36973","category_aro_name":"bacitracin A","category_aro_description":"Bacitracin A is the primary component of bacitracin. It contains many uncommon amino acids and interferes with bacterial cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36974":{"category_aro_accession":"3000630","category_aro_cvterm_id":"36974","category_aro_name":"bacitracin B","category_aro_description":"Bacitracin B is a component of bacitracin, an antibiotic mixture that interferes with bacterial cell wall synthesis. It differs from Bacitracin A with a valine instead of an isoleucine in its peptide.","category_aro_class_name":"Antibiotic"},"36975":{"category_aro_accession":"3000631","category_aro_cvterm_id":"36975","category_aro_name":"bacitracin F","category_aro_description":"Bacitracin F is a component of bacitracin, an antibiotic mixture that interferes with bacterial cell wall synthesis. It is formed when the thiazoline ring of bacitracin A is oxidatively deaminated.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"946":{"model_id":"946","model_name":"QnrB48","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"177":{"protein_sequence":{"accession":"AFH88686.1","sequence":"MALALVGEKIDRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNASALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGGLDIRGVDLQGVKLDNYQASLLMERLGIAIIG"},"dna_sequence":{"accession":"JQ762640","fmin":"36","fmax":"681","strand":"+","sequence":"ATGGCTCTGGCACTCGTTGGCGAAAAAATTGACAGGAACCGCTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCGATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATGCCAGTGCGCTTGGCATTGAAATTCGCCACTGTCGTGCGCAAGGCGCAGATTTTCGCGGCGCAAGCTTTATGAATATGATCACCACACGCACCTGGTTTTGCAGCGCATATATAACTAACACAAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGCTGGAAAAATGTGAGCTGTGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTTTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTGGCTTAGATATTCGGGGCGTTGATTTACAAGGCGTTAAGTTGGACAACTACCAGGCATCGTTGCTCATGGAACGTCTTGGCATCGCGATTATTGGCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002763","ARO_id":"39197","ARO_name":"QnrB48","ARO_description":"QnrB48 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"947":{"model_id":"947","model_name":"OXA-100","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"964":{"protein_sequence":{"accession":"CAJ77817.2","sequence":"MNIKALLLITSTIFISACSPYIVTANPNHSTSKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEIFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"AM231720","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCACTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCACTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAATATTTAAGTGGGACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGTGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACGCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001438","ARO_id":"37838","ARO_name":"OXA-100","ARO_description":"OXA-100 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"948":{"model_id":"948","model_name":"mecI","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"4247":{"protein_sequence":{"accession":"BAB41258.1","sequence":"MDNKTYEISSAEWEVMNIIWMKKYASANNIIEEIQMQKDWSPKTIRTLITRLYKKGFIDRKKDNKIFQYYSLVEESDIKYKTSKNFINKVYKGGFNSLVLNFVEKEDLSQDEIEELRNILNKK"},"dna_sequence":{"accession":"BA000018.3","fmin":"48893","fmax":"49265","strand":"+","sequence":"ATGGATAATAAAACGTATGAAATATCATCTGCAGAATGGGAAGTTATGAATATCATTTGGATGAAAAAATATGCAAGTGCGAATAATATAATAGAAGAAATACAAATGCAAAAGGACTGGAGTCCAAAAACCATTCGTACACTTATAACGAGATTGTATAAAAAGGGATTTATAGATCGTAAAAAAGACAATAAAATTTTTCAATATTACTCTCTTGTAGAAGAAAGTGATATAAAATATAAAACATCTAAAAACTTTATCAATAAAGTATACAAAGGCGGTTTCAATTCACTTGTCTTAAACTTTGTAGAAAAAGAAGATCTATCACAAGATGAAATAGAAGAATTGAGAAATATATTGAATAAAAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35514","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus N315","NCBI_taxonomy_id":"158879"}}}},"ARO_accession":"3000124","ARO_id":"36263","ARO_name":"mecI","ARO_description":"mecI acts as a repressor of transcription of the mecA\/mecR1\/mecI operon.","ARO_category":{"37589":{"category_aro_accession":"3001208","category_aro_cvterm_id":"37589","category_aro_name":"methicillin resistant PBP2","category_aro_description":"In methicillin sensitive S. aureus (MSSA), beta-lactams bind to native penicillin-binding proteins (PBPs) and disrupt synthesis of the cell membrane's peptidoglycan layer. In methicillin resistant S. aureus (MRSA), foreign PBP2a acquired by lateral gene transfer is able to perform peptidoglycan synthesis in the presence of beta-lactams.","category_aro_class_name":"AMR Gene Family"},"35927":{"category_aro_accession":"0000008","category_aro_cvterm_id":"35927","category_aro_name":"cefoxitin","category_aro_description":"Cefoxitin is a cephamycin antibiotic often grouped with the second generation cephalosporins. Cefoxitin is bactericidal and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. Cefoxitin's 7-alpha-methoxy group and 3' leaving group make it a poor substrate for most beta-lactamases.","category_aro_class_name":"Antibiotic"},"35930":{"category_aro_accession":"0000011","category_aro_cvterm_id":"35930","category_aro_name":"cloxacillin","category_aro_description":"Cloxacillin is a semisynthetic, isoxazolyl penicillin derivative in the beta-lactam class of antibiotics. It interferes with peptidogylcan synthesis and is commonly used for treating penicillin-resistant Staphylococcus aureus infections.","category_aro_class_name":"Antibiotic"},"35934":{"category_aro_accession":"0000015","category_aro_cvterm_id":"35934","category_aro_name":"methicillin","category_aro_description":"Derived from penicillin to combat penicillin-resistance, methicillin is insensitive to beta-lactamases (also known as penicillinases) secreted by many penicillin-resistant bacteria. Methicillin is bactericidal, and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Antibiotic"},"35961":{"category_aro_accession":"0000043","category_aro_cvterm_id":"35961","category_aro_name":"carbenicillin","category_aro_description":"Carbenicillin is a semi-synthetic antibiotic belonging to the carboxypenicillin subgroup of the penicillins. It has gram-negative coverage which includes Pseudomonas aeruginosa but limited gram-positive coverage. The carboxypenicillins are susceptible to degradation by beta-lactamase enzymes. Carbenicillin antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Antibiotic"},"35971":{"category_aro_accession":"0000054","category_aro_cvterm_id":"35971","category_aro_name":"penicillin","category_aro_description":"Penicillin (sometimes abbreviated PCN) is a beta-lactam antibiotic used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms. It works by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Antibiotic"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35975":{"category_aro_accession":"0000058","category_aro_cvterm_id":"35975","category_aro_name":"cefazolin","category_aro_description":"Cefazolin (INN), also known as cefazoline or cephazolin, is a first generation cephalosporin antibiotic. It is administered parenterally, and is active against a broad spectrum of bacteria.","category_aro_class_name":"Antibiotic"},"35976":{"category_aro_accession":"0000059","category_aro_cvterm_id":"35976","category_aro_name":"cefepime","category_aro_description":"Cefepime (INN) is a fourth-generation cephalosporin antibiotic developed in 1994. It contains an aminothiazolyl group that decreases its affinity with beta-lactamases. Cefepime shows high binding affinity with penicillin-binding proteins and has an extended spectrum of activity against Gram-positive and Gram-negative bacteria, with greater activity against both Gram-negative and Gram-positive organisms than third-generation agents.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35978":{"category_aro_accession":"0000061","category_aro_cvterm_id":"35978","category_aro_name":"ceftobiprole","category_aro_description":"Ceftobiprole (Zeftera\/Zevtera) is a next generation (5th generation) cephalosporin antibiotic with activity against methicillin-resistant Staphylococcus aureus, penicillin-resistant Streptococcus pneumoniae, Pseudomonas aeruginosa, and Enterococci. Ceftobiprole inhibits transpeptidases essential to building cell walls, and is a poor substrate for most beta-lactamases.","category_aro_class_name":"Antibiotic"},"35979":{"category_aro_accession":"0000062","category_aro_cvterm_id":"35979","category_aro_name":"ceftriaxone","category_aro_description":"Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"35980":{"category_aro_accession":"0000063","category_aro_cvterm_id":"35980","category_aro_name":"cefuroxime","category_aro_description":"Cefuroxime is a second-generation cephalosporin antibiotic with increased stability with beta-lactamases than first-generation cephalosporins. Cefuroxime is active against Gram-positive organisms but less active against methicillin-resistant strains.","category_aro_class_name":"Antibiotic"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"35987":{"category_aro_accession":"0000070","category_aro_cvterm_id":"35987","category_aro_name":"ertapenem","category_aro_description":"Ertapenem is a carbapenem antibiotic and is highly resistant to beta-lactamases like other carbapenems. It inhibits bacterial cell wall synthesis.","category_aro_class_name":"Antibiotic"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"35995":{"category_aro_accession":"0000078","category_aro_cvterm_id":"35995","category_aro_name":"piperacillin","category_aro_description":"Piperacillin is an acetylureidopenicillin and has an extended spectrum of targets relative to other beta-lactam antibiotics. It inhibits cell wall synthesis in bacteria, and is usually taken with the beta-lactamase inhibitor tazobactam to overcome penicillin-resistant bacteria.","category_aro_class_name":"Antibiotic"},"36309":{"category_aro_accession":"3000170","category_aro_cvterm_id":"36309","category_aro_name":"imipenem","category_aro_description":"Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.","category_aro_class_name":"Antibiotic"},"36689":{"category_aro_accession":"3000550","category_aro_cvterm_id":"36689","category_aro_name":"aztreonam","category_aro_description":"Aztreonam was the first monobactam discovered, and is greatly effective against Gram-negative bacteria while inactive against Gram-positive bacteria. Artreonam is a poor substrate for beta-lactamases, and may even act as an inhibitor. In Gram-negative bacteria, Aztreonam interferes with filamentation, inhibiting cell division and leading to cell death.","category_aro_class_name":"Antibiotic"},"36976":{"category_aro_accession":"3000632","category_aro_cvterm_id":"36976","category_aro_name":"benzylpenicillin","category_aro_description":"Benzylpenicillin, commonly referred to as penicillin G, is effective against both Gram-positive and Gram-negative bacteria. It is unstable in acid.","category_aro_class_name":"Antibiotic"},"36977":{"category_aro_accession":"3000633","category_aro_cvterm_id":"36977","category_aro_name":"phenoxymethylpenicillin","category_aro_description":"Phenoxymethylpenicillin, or penicillin V, is a penicillin derivative that is acid stable but less active than benzylpenicillin (penicillin G).","category_aro_class_name":"Antibiotic"},"36978":{"category_aro_accession":"3000634","category_aro_cvterm_id":"36978","category_aro_name":"propicillin","category_aro_description":"Propicillin is an orally taken penicillin derivative that has high absorption but poor activity.","category_aro_class_name":"Antibiotic"},"36979":{"category_aro_accession":"3000635","category_aro_cvterm_id":"36979","category_aro_name":"dicloxacillin","category_aro_description":"Dicloxacillin is a penicillin derivative that has an extra chlorine atom in comparison to cloxacillin. While more active than cloxacillin, its high affinity for serum protein reduces its activity in human serum in vitro.","category_aro_class_name":"Antibiotic"},"36980":{"category_aro_accession":"3000636","category_aro_cvterm_id":"36980","category_aro_name":"flucloxacillin","category_aro_description":"Flucloxacillin is similar to cloxacillin, with an extra additional fluorine atom.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"36982":{"category_aro_accession":"3000638","category_aro_cvterm_id":"36982","category_aro_name":"azlocillin","category_aro_description":"Azlocillin is a semisynthetic derivative of penicillin that is notably active against Ps. aeruginosa and other Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36983":{"category_aro_accession":"3000639","category_aro_cvterm_id":"36983","category_aro_name":"mezlocillin","category_aro_description":"Mezlocillin is a penicillin derivative taken parenterally.","category_aro_class_name":"Antibiotic"},"36984":{"category_aro_accession":"3000640","category_aro_cvterm_id":"36984","category_aro_name":"doripenem","category_aro_description":"Doripenem is a carbapenem with a broad range of activity against Gram-positive and Gram-negative bacteria, and along with meropenem, it is the most active beta-lactam antibiotic against Pseudomonas aeruginosa. It inhibits bacterial cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36985":{"category_aro_accession":"3000641","category_aro_cvterm_id":"36985","category_aro_name":"cefalexin","category_aro_description":"Cefalexin is a cephalosporin antibiotic that causes filamentation. It is resistant to staphylococcal beta-lactamase, but degraded by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"36986":{"category_aro_accession":"3000642","category_aro_cvterm_id":"36986","category_aro_name":"cefadroxil","category_aro_description":"Cefadroxil, or p-hydroxycephalexin, is an cephalosporin antibiotic similar to cefalexin.","category_aro_class_name":"Antibiotic"},"36987":{"category_aro_accession":"3000643","category_aro_cvterm_id":"36987","category_aro_name":"cefotiam","category_aro_description":"Cefotiam is a cephalosporin antibiotic with similar activity to cefuroxime but more active against enterobacteria. It is consumed orally as the prodrug cefotiam hexetil.","category_aro_class_name":"Antibiotic"},"36988":{"category_aro_accession":"3000644","category_aro_cvterm_id":"36988","category_aro_name":"cefaclor","category_aro_description":"Cefaclor is a semisynthetic cephalosporin derived from cephalexin. It has broad-spectrum antibiotic activity.","category_aro_class_name":"Antibiotic"},"36989":{"category_aro_accession":"3000645","category_aro_cvterm_id":"36989","category_aro_name":"cefotaxime","category_aro_description":"Cefotaxime is a semisynthetic cephalosporin taken parenterally. It is resistant to most beta-lactamases and active against Gram-negative rods and cocci due to its aminothiazoyl and methoximino functional groups.","category_aro_class_name":"Antibiotic"},"36990":{"category_aro_accession":"3000646","category_aro_cvterm_id":"36990","category_aro_name":"cefixime","category_aro_description":"Cefixime is a cephalosporin resistant to most beta-lactamases. It is active against many enterobacteria, but activity against staphylococci is poor.","category_aro_class_name":"Antibiotic"},"36991":{"category_aro_accession":"3000647","category_aro_cvterm_id":"36991","category_aro_name":"cefpodoxime","category_aro_description":"Cefpodoxime is a semisynthetic cephalosporin that acts similarly to cefotaxime with broad-spectrum activity. It is stable to many plasmid-mediated beta-lactamses. Cefpodoxime is consumed as the prodrug cefpodoxime proxetil.","category_aro_class_name":"Antibiotic"},"36992":{"category_aro_accession":"3000648","category_aro_cvterm_id":"36992","category_aro_name":"ceftibuten","category_aro_description":"Ceftibuten is a semisynthetic cephalosporin active against Gram-negative bacilli. It is resistant against many plasmid-mediated beta-lactamases.","category_aro_class_name":"Antibiotic"},"36993":{"category_aro_accession":"3000649","category_aro_cvterm_id":"36993","category_aro_name":"cefditoren","category_aro_description":"Cefditoren is a semisynthetic cephalosporin active against staphylococci, streptococci, and and most enterobacteria. It is resistant to staphylococcal and most enterobacterial beta-lactamases, and is usually taken as the prodrug cefditoren pivoxil.","category_aro_class_name":"Antibiotic"},"36994":{"category_aro_accession":"3000650","category_aro_cvterm_id":"36994","category_aro_name":"cefdinir","category_aro_description":"Cefdinir is similar to cefixime with a modified side-chain at its 7-amino position. It also shares similar activity with cefixime but is more active against staphylococci. It has also be shown to enhance phagocytosis.","category_aro_class_name":"Antibiotic"},"36995":{"category_aro_accession":"3000651","category_aro_cvterm_id":"36995","category_aro_name":"ceftaroline","category_aro_description":"Ceftaroline is a novel cephalosporin active against methicillin resistant Staphylococcus aureus. Like other cephalosporins it binds penicillin-binding proteins to inhibit cell wall synthesis. It strongly binds with PBP2a, associated with methicillin resistance. It is taken orally as the prodrug ceftaroline fosamil.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"37085":{"category_aro_accession":"3000705","category_aro_cvterm_id":"37085","category_aro_name":"isopenicillin N","category_aro_description":"Isopenicillin N is a natural penicillin derivative produced by Penicillium chrysogenum with activity similar to penicillin N.","category_aro_class_name":"Antibiotic"},"37086":{"category_aro_accession":"3000706","category_aro_cvterm_id":"37086","category_aro_name":"penicillin N","category_aro_description":"Penicillin N is a penicillin derivative produced by Cephalosporium acremonium.","category_aro_class_name":"Antibiotic"},"37141":{"category_aro_accession":"3000761","category_aro_cvterm_id":"37141","category_aro_name":"mecillinam","category_aro_description":"Mecillinam is a broad-spectrum beta-lactam antibiotic that was semi-synthetically derived to have a different drug centre, being a 6-alpha-amidinopenicillanate instead of a 6-alpha-acylaminopenicillanate. Contrasting most beta-lactam drugs, mecillinam is most active against Gram-negative bacteria. It binds specifically to penicillin binding protein 2 (PBP2).","category_aro_class_name":"Antibiotic"},"40928":{"category_aro_accession":"3004001","category_aro_cvterm_id":"40928","category_aro_name":"cefmetazole","category_aro_description":"Cefmetazole is a semi-synthetic cephamycin antibiotic with broad spectrum antibiotic activity against both gram-positive and gram-negative bacteria, that disrupt cell wall synthesis through binding to PBPs causing cell lysis.","category_aro_class_name":"Antibiotic"},"40929":{"category_aro_accession":"3004002","category_aro_cvterm_id":"40929","category_aro_name":"cefonicid","category_aro_description":"Cefonicid is a second-generation cephalosporin-class beta-lactam antibiotic with broad spectrum activity. Particularly used against urinary tract infections and lower respiratory infections. Causes cell lysis by inactivation of PBPs through binding, inhibiting peptidoglycan synthesis.","category_aro_class_name":"Antibiotic"},"40932":{"category_aro_accession":"3004005","category_aro_cvterm_id":"40932","category_aro_name":"cefprozil","category_aro_description":"Cefprozil is a cephalosporin and beta-lactam antibiotic with bactericidal activity. It selectively binds to PBPs and inhibits peptidoglycan synthesis, a major cell wall component, resulting in cell lysis.","category_aro_class_name":"Antibiotic"},"40933":{"category_aro_accession":"3004006","category_aro_cvterm_id":"40933","category_aro_name":"ceftiofur","category_aro_description":"Ceftiofur is a third-generation broad spectrum cephalosporin and beta-lactam antibiotic. It causes cell lysis by disrupting peptidoglycan cross-linkage and cell wall formation by binding to PBPs.","category_aro_class_name":"Antibiotic"},"40934":{"category_aro_accession":"3004007","category_aro_cvterm_id":"40934","category_aro_name":"ceftizoxime","category_aro_description":"Ceftizoxime is a third-generation cephalosporin and broad spectrum beta-lactam antibiotic. Ceftizoxime causes bacterial cell lysis through peptidoglycan cross-linking inhibition by binding to PBPs.","category_aro_class_name":"Antibiotic"},"40935":{"category_aro_accession":"3004008","category_aro_cvterm_id":"40935","category_aro_name":"cephapirin","category_aro_description":"Cephapirin is a first-generation cephalosporin and broad spectrum beta-lactam antibiotic. Inactivation of penicillin-binding proteins through cephapirin binding disrupts peptidoglycan cross-linking, resulting in cell lysis.","category_aro_class_name":"Antibiotic"},"40936":{"category_aro_accession":"3004009","category_aro_cvterm_id":"40936","category_aro_name":"cefradine","category_aro_description":"Cefradine is a first-generation cephalosporin and broad spectrum beta-lactam antibiotic. Cefradine binding to penicillin-binding proteins disrupts cell wall peptidoglycan cross-linkage, resulting in cell lysis.","category_aro_class_name":"Antibiotic"},"40943":{"category_aro_accession":"3004016","category_aro_cvterm_id":"40943","category_aro_name":"loracarbef","category_aro_description":"Loracarbef is a second-generation cephalosporin (carbacephem) and broad spectrum beta-lactam antibiotic. Loracarbef inhibits PBPs through binding, disrupting peptidoglycan cell wall cross-linkage and resulting in cell death.","category_aro_class_name":"Antibiotic"},"40944":{"category_aro_accession":"3004017","category_aro_cvterm_id":"40944","category_aro_name":"moxalactam","category_aro_description":"Moxalactam (Latamoxef) is a broad spectrum cephalosporin (oxacephem) and beta-lactam antibiotic. Moxalactam binding to PBPs inhibits peptidoglycan cross-linkage in the cell wall, resulting in cell death. Moxalactam is proposed to be effective against meningitides as it passes the blood-brain barrier.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"949":{"model_id":"949","model_name":"CTX-M-77","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1904":{"protein_sequence":{"accession":"CAQ42480.1","sequence":"MMTQSIRRSMLTVMATLPLLFSSATLHAQTNSVQQQLKALEKSSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKQSESDKHLLNQRVEIKKSDLVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSASIQAGLPKSWVVGDKTGSGDYGTTNDIAIIWPENHAPLVLVTYFTQPEQKAESRRDVLAAAAKIVTRGF"},"dna_sequence":{"accession":"AM982521","fmin":"1911","fmax":"2787","strand":"+","sequence":"ATGATGACTCAGAGCATTCGCCGCTCAATGTTAACGGTGATGGCGACGCTACCCCTGCTATTTAGCAGCGCAACGCTGCATGCGCAGACGAACAGCGTGCAACAGCAGCTGAAAGCCCTGGAGAAAAGTTCGGGAGGTCGGCTTGGCGTTGCGCTGATTAACACCGCCGATAATTCGCAGATTCTCTACCGTGCCGATGAACGTTTTGCGATGTGCAGTACCAGTAAGGTGATGGCGGCCGCGGCGGTGCTTAAACAGAGCGAGAGCGATAAGCACCTGCTAAATCAGCGCGTTGAAATCAAGAAGAGCGACCTGGTTAACTACAATCCCATTGCGGAGAAACACGTTAACGGCACGATGACGCTGGCTGAGCTTGGCGCAGCGGCGCTGCAGTATAGCGACAATACTGCCATGAATAAGCTGATTGCCCATCTGGGTGGGCCCGATAAAGTGACGGCGTTTGCTCGCTCGTTGGGTGATGAGACCTTCCGTCTGGACAGAACCGAGCCCACGCTCAATACCGCCATTCCAGGCGACCCGCGTGATACCACCACGCCGCTCGCGATGGCGCAGACCCTGAAAAATCTGACGCTGGGTAAAGCGCTGGCGGAAACCCAGCGGGCACAGTTGGTGACGTGGCTTAAGGGCAATACTACCGGTAGCGCGAGCATTCAGGCGGGTCTGCCGAAATCATGGGTAGTGGGCGATAAAACCGGCAGCGGAGATTATGGCACCACCAACGATATCGCGATTATCTGGCCGGAAAACCACGCACCGCTGGTTCTGGTGACCTACTTTACCCAACCGGAGCAGAAGGCGGAAAGCCGTCGGGATGTTCTGGCTGCGGCGGCGAAAATCGTAACCCGCGGTTTCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36928","NCBI_taxonomy_name":"Kluyvera ascorbata","NCBI_taxonomy_id":"51288"}}}},"ARO_accession":"3001938","ARO_id":"38338","ARO_name":"CTX-M-77","ARO_description":"CTX-M-77 is a beta-lactamase found in Kluyvera spp.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"950":{"model_id":"950","model_name":"ErmX","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"4366":{"protein_sequence":{"accession":"AAG03357.1","sequence":"MSAYGHGRHEHGQNFLTNHKIINSIIDLVKQTSGPIIEIGPGSGALTHPMAHLGRAITAVEVDAKLAAKITQETSSAAVEVVHDDFLNFRLPATPCVIVGNIPFHLTTAILRKLLHAPAWTDAVLLMQWEVARRRAGVGASTMMTAQWSPWFTFHLGSRVPRPAFRPQPNVDGGILVIRRVGDPKIPIEQRKAFQAMVHTVFTARGRGIGEILRRQGCFHHVQKHNHGCAREESTPRPYLPDCTPTTGSISSR"},"dna_sequence":{"accession":"AF024666","fmin":"2207","fmax":"2969","strand":"-","sequence":"TCACCTGGAAGAGATCGATCCAGTCGTTGGTGTGCAATCTGGGAGGTAGGGTCGCGGGGTCGATTCCTCGCGAGCGCAACCATGATTGTGTTTCTGAACGTGATGAAAACAACCCTGCCTTCGGAGAATTTCCCCTATCCCGCGTCCCCGGGCAGTGAAAACGGTGTGCACCATCGCCTGAAAGGCTTTGCGCTGCTCTATCGGAATCTTCGGGTCACCCACCCGGCGGATCACTAAGATCCCCCCGTCAACGTTTGGCTGTGGCCGGAAAGCAGGCCTTGGTACCCGAGAACCCAGGTGAAATGTGAACCATGGGGACCACTGAGCCGTCATCATCGTGCTTGCGCCTACCCCGGCCCGGCGGCGAGCGACTTCCCACTGCATGAGGAGTACAGCGTCAGTCCATGCTGGCGCATGCAGCAACTTTCGAAGAATGGCAGTGGTGAGGTGAAAGGGAATGTTTCCCACAATGACGCAGGGAGTGGCGGGTAACCGGAAGTTAAGGAAATCATCATGGACCACTTCGACCGCCGCCGAGGAGGTTTCTTGTGTGATTTTGGCAGCTAGTTTTGCGTCCACTTCAACTGCCGTTATCGCCCTCCCCAAGTGGGCCATCGGGTGAGTGAGGGCACCGCTTCCTGGTCCGATCTCAATGATGGGGCCGGAGGTTTGTTTCACAAGGTCGATGATGGAGTTGATGATCTTGTGGTTGGTGAGAAAATTTTGGCCATGCTCGTGACGGCCGTGTCCGTATGCAGACAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39554","NCBI_taxonomy_name":"Corynebacterium striatum","NCBI_taxonomy_id":"43770"}}}},"ARO_accession":"3000596","ARO_id":"36735","ARO_name":"ErmX","ARO_description":"ErmX is a rRNA methyltransferase that protects the ribosome from inactivation due to antibiotic binding.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35946":{"category_aro_accession":"0000027","category_aro_cvterm_id":"35946","category_aro_name":"roxithromycin","category_aro_description":"Roxithromycin is a semi-synthetic, 14-carbon ring macrolide antibiotic derived from erythromycin. It is used to treat respiratory tract, urinary and soft tissue infections. Roxithromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35974":{"category_aro_accession":"0000057","category_aro_cvterm_id":"35974","category_aro_name":"telithromycin","category_aro_description":"Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36315":{"category_aro_accession":"3000176","category_aro_cvterm_id":"36315","category_aro_name":"dirithromycin","category_aro_description":"Dirithromycin is an oxazine derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome to inhibit bacterial protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin 1A is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"vernamycin B-gamma","category_aro_description":"Vernamycin B-gamma is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"951":{"model_id":"951","model_name":"ACT-15","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1262":{"protein_sequence":{"accession":"AFU25653.1","sequence":"MMKKSLCCALLLGISCSALATPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKSGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVVEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEALQ"},"dna_sequence":{"accession":"JX440356","fmin":"754","fmax":"1900","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATTTCTTGCTCTGCTCTCGCCACGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGTCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAACGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAGGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTGCCCGTGGTAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGTGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001837","ARO_id":"38237","ARO_name":"ACT-15","ARO_description":"ACT-15 is a beta-lactamase. From the Lahey list of ACT beta-lactamases.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"952":{"model_id":"952","model_name":"sul2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4371":{"protein_sequence":{"accession":"AAL59753.1","sequence":"MNKSLIIFGIVNITSDSFSDGGRYLAPDAAIAQARKLMAEGADVIDLGPASSNPDAAPVSSDTEIARIAPVLDALKADGIPVSLDSYQPATQAYALSRGVAYLNDIRGFPDAAFYPQLAKSSAKLVVMHSVQDGQADRREAPAGDIMDHIAAFFDARIAALTGAGIKRNRLVLDPGMGFFLGAAPETSLSVLARFDELRLRFDLPVLLSVSRKSFLRALTGRGPGDVGAATLAAELAAAAGGADFIRTHEPRPLRDGLAVLAALKETARIR"},"dna_sequence":{"accession":"AY055428","fmin":"20268","fmax":"21084","strand":"-","sequence":"TTAACGAATTCTTGCGGTTTCTTTCAGCGCCGCCAATACCGCCAGCCCGTCGCGCAAGGGGCGCGGCTCGTGTGTGCGGATGAAGTCAGCTCCACCTGCGGCGGCGGCAAGCTCTGCAGCGAGTGTCGCGGCCCCGACATCCCCCGGACCACGGCCTGTGAGCGCGCGCAGAAAGGATTTGCGCGAAACAGACAGAAGCACCGGCAAATCGAAGCGCAGCCGCAATTCATCGAACCGCGCCAGCACCGAGAGCGAGGTTTCGGGAGCAGCCCCCAGAAAAAACCCCATGCCGGGATCAAGGACAAGGCGGTTGCGTTTGATACCGGCACCCGTCAGCGCCGCGATGCGCGCGTCAAAGAACGCCGCAATGTGATCCATGATGTCGCCAGCGGGTGCCTCGCGCCGATCTGCCTGCCCGTCTTGCACCGAATGCATAACGACGAGTTTGGCAGATGATTTCGCCAATTGCGGATAGAACGCAGCGTCTGGAAAACCGCGAATATCATTGAGATAGGCCACACCACGCGACAAGGCATAGGCTTGCGTCGCGGGTTGATAACTGTCGAGCGAGACGGGAATGCCATCTGCCTTGAGCGCGTCCAGCACCGGCGCGATACGCGCGATTTCTGTGTCGGACGAAACAGGCGCGGCGTCGGGATTGCTGGATGCCGGACCGAGGTCGATCACATCTGCCCCCTCGGCCATCAGCTTACGCGCCTGCGCAATGGCTGCGTCTGGCGCCAGATACCGGCCTCCATCGGAGAAACTGTCCGAGGTTATGTTGACGATGCCGAAAATGATGAGCGATTTATTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36789","NCBI_taxonomy_name":"Vibrio cholerae","NCBI_taxonomy_id":"666"}}}},"ARO_accession":"3000412","ARO_id":"36551","ARO_name":"sul2","ARO_description":"Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria, usually found on small plasmids.","ARO_category":{"41402":{"category_aro_accession":"3004238","category_aro_cvterm_id":"41402","category_aro_name":"sulfonamide resistant sul","category_aro_description":"The sul genes encode forms of dihydropteroate synthase that confer resistance to sulfonamide.","category_aro_class_name":"AMR Gene Family"},"36463":{"category_aro_accession":"3000324","category_aro_cvterm_id":"36463","category_aro_name":"sulfadiazine","category_aro_description":"Sulfadiazine is a potent inhibitor of dihydropteroate synthase, interfering with the tetrahydrofolic biosynthesis pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor to many nucleotides and amino acids.","category_aro_class_name":"Antibiotic"},"36464":{"category_aro_accession":"3000325","category_aro_cvterm_id":"36464","category_aro_name":"sulfadimidine","category_aro_description":"Sulfadimidine is an alkaline sulfonamide antibiotic that inhibits dihydropteroate synthase, and enzyme in the tetrahydrofolic acid biosynthesis pathway. This interferes with the production of folate, which is a precursor to many amino acids and nucleotides.","category_aro_class_name":"Antibiotic"},"36466":{"category_aro_accession":"3000327","category_aro_cvterm_id":"36466","category_aro_name":"sulfadoxine","category_aro_description":"Sulfadoxine is an inhibitor of dihydropteroate synthase, interfering with the tetrahydrofolic biosynthesis pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor to many nucleotides and amino acids.","category_aro_class_name":"Antibiotic"},"36468":{"category_aro_accession":"3000329","category_aro_cvterm_id":"36468","category_aro_name":"sulfamethoxazole","category_aro_description":"Sulfamethoxazole is a sulfonamide antibiotic usually taken with trimethoprim, a diaminopyrimidine antibiotic. Sulfamethoxazole inhibits dihydropteroate synthase, essential to tetrahydrofolic acid biosynthesis. This pathway generates compounds used in the synthesis of many amino acids and nucleotides.","category_aro_class_name":"Antibiotic"},"36469":{"category_aro_accession":"3000330","category_aro_cvterm_id":"36469","category_aro_name":"sulfisoxazole","category_aro_description":"Sulfisoxazole is an inhibitor of dihydropteroate synthase, interfering with the tetrahydrofolic biosynthesis pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor to many nucleotides and amino acids.","category_aro_class_name":"Antibiotic"},"37027":{"category_aro_accession":"3000683","category_aro_cvterm_id":"37027","category_aro_name":"sulfacetamide","category_aro_description":"Sulfacetamide is a very soluable sulfonamide antibiotic previously used to treat urinary tract infections. Its relatively low activity and toxicity to those with Stevens-Johnson syndrome have reduced its use and availability.","category_aro_class_name":"Antibiotic"},"37028":{"category_aro_accession":"3000684","category_aro_cvterm_id":"37028","category_aro_name":"mafenide","category_aro_description":"Mafenide is a sulfonamide used topically for treating burns.","category_aro_class_name":"Antibiotic"},"37042":{"category_aro_accession":"3000698","category_aro_cvterm_id":"37042","category_aro_name":"sulfasalazine","category_aro_description":"Sulfasalazine is a derivative of the early sulfonamide sulfapyridine (salicylazosulfapyridine). It was developed to increase water solubility and is taken orally for ulcerative colitis.","category_aro_class_name":"Antibiotic"},"37043":{"category_aro_accession":"3000699","category_aro_cvterm_id":"37043","category_aro_name":"sulfamethizole","category_aro_description":"Sulfamethizole is a short-acting sulfonamide that inhibits dihydropteroate synthetase.","category_aro_class_name":"Antibiotic"},"39996":{"category_aro_accession":"3003412","category_aro_cvterm_id":"39996","category_aro_name":"dapsone","category_aro_description":"Dapsone is a sulfone in which it inhibits folic acid synthesis, such as the dihydropteroate synthase.","category_aro_class_name":"Antibiotic"},"36421":{"category_aro_accession":"3000282","category_aro_cvterm_id":"36421","category_aro_name":"sulfonamide antibiotic","category_aro_description":"Sulfonamides are broad spectrum, synthetic antibiotics that contain the sulfonamide group. Sulfonamides inhibit dihydropteroate synthase, which catalyzes the conversion of p-aminobenzoic acid to dihydropteroic acid as part of the tetrahydrofolic acid biosynthetic pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor of many nucleotides and amino acids. Many sulfamides are taken with trimethoprim, an inhibitor of dihydrofolate reductase, also disturbing the trihydrofolic acid synthesis pathway.","category_aro_class_name":"Drug Class"},"39985":{"category_aro_accession":"3003401","category_aro_cvterm_id":"39985","category_aro_name":"sulfone antibiotic","category_aro_description":"A sulfone active against a wide range of bacteria but mainly employed for its actions against mycobacterium laprae. Its mechanism of action  involves inhibition of folic acid synthesis in susceptible organisms.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"954":{"model_id":"954","model_name":"APH(3')-IIb","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"159":{"protein_sequence":{"accession":"CAA62365.1","sequence":"MHDAATSMPPQAPSTWADYLAGYRWRGQGEGCSAATVHRLEAARRPTLFVKQEVLSAHAELPAEIARLRWLHGAGIDCPQVLNETQSDGRQWLLMSAMPGDTLSALAQRDELEPERLVRLVAAALRRLHDLDPAACPFDHRLERRLDTVRQRVEAGLVDEADFDDDHRGRSATELYRLLLDRRPAVEDLVVAHGDACLPNLLAEGRRFSGFIDCGRLGVADRHQDLALAARDIEAELGAAWAEAFLVEYGGDIDGERLAYFRLLDEFF"},"dna_sequence":{"accession":"X90856","fmin":"387","fmax":"1194","strand":"+","sequence":"ATGCATGATGCAGCCACCTCCATGCCGCCGCAGGCTCCCTCAACCTGGGCCGACTACCTTGCCGGCTACCGCTGGCGAGGGCAGGGCGAAGGATGTTCCGCGGCCACGGTCCACCGCCTGGAGGCTGCGCGGCGGCCGACCCTGTTCGTCAAGCAGGAAGTGCTGTCCGCACATGCCGAGCTGCCCGCCGAAATCGCCCGCCTGCGCTGGCTGCACGGTGCCGGCATCGACTGCCCGCAGGTGCTGAACGAAACCCAGAGCGACGGCCGGCAATGGCTGCTGATGAGCGCAATGCCGGGGGACACGCTGTCCGCGCTGGCGCAGCGCGACGAGCTGGAGCCCGAGCGCCTGGTGCGCCTGGTGGCCGCCGCCCTGCGCCGGCTGCACGATCTCGATCCGGCCGCCTGTCCCTTCGATCATCGCCTGGAACGGCGTCTGGACACCGTGCGCCAGCGGGTCGAGGCCGGGCTGGTGGACGAGGCGGACTTCGACGACGACCATCGCGGTCGCAGCGCCACGGAGCTGTACCGCCTGCTGCTCGACCGGCGTCCGGCGGTCGAAGACCTGGTGGTCGCCCACGGCGACGCCTGCCTGCCCAACCTCTTGGCGGAGGGCCGGCGCTTCAGCGGCTTCATCGATTGCGGGCGGCTCGGCGTCGCCGACCGGCACCAGGACCTGGCCCTGGCCGCGCGGGACATCGAGGCCGAACTCGGCGCGGCCTGGGCCGAGGCCTTCCTCGTCGAATACGGCGGCGATATCGACGGCGAACGGCTGGCGTACTTCAGGCTATTGGACGAGTTCTTCTAGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002645","ARO_id":"39045","ARO_name":"APH(3')-IIb","ARO_description":"APH(3')-IIb is a chromosomal-encoded aminoglycoside phosphotransferase in P. aeruginosa","ARO_category":{"36265":{"category_aro_accession":"3000126","category_aro_cvterm_id":"36265","category_aro_name":"APH(3')","category_aro_description":"Phosphorylation of 2-deoxystreptamine aminoglycosides on the hydroxyl group at position 3'","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"955":{"model_id":"955","model_name":"SHV-96","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"841":{"protein_sequence":{"accession":"ABN49112.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDARVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"EF373971","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGATGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGCTCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001148","ARO_id":"37528","ARO_name":"SHV-96","ARO_description":"SHV-96 is a beta-lactamase found in Acinetobacter baumannii.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"956":{"model_id":"956","model_name":"TEM-88","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1652":{"protein_sequence":{"accession":"AAK14792.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTTPAAMATTLRKLLTDELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AY027590","fmin":"112","fmax":"973","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGACGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000955","ARO_id":"37335","ARO_name":"TEM-88","ARO_description":"TEM-88 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"958":{"model_id":"958","model_name":"OXA-418","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2112":{"protein_sequence":{"accession":"AIN56719.1","sequence":"MKFKMKGLFCVILSSLAFSGCVYDSKLQRPVISERETEIPLLFNQAQTQAVFVTYDGIHLKSYGNDLSRAKTEYIPASTFKMLNALIGLQNAKATNTEVFHWNGEKRAFSAWEKDMTLAEAMQASAVPVYQELARRIGLELMREEVKRVGFGNAEIGQQVDNFWLVGPLKISPEQEVQFAYQLAMKQLPFDRNVQQQVKNMLYIERRGDSKLYAKSGWGMDVKPQVGWYTGWVEQPNGKVTAFALNMNMQAGDDPAERKQLTLSILDKLGLFFYLR"},"dna_sequence":{"accession":"KJ997966","fmin":"0","fmax":"831","strand":"+","sequence":"ATGAAGTTTAAAATGAAAGGTTTATTTTGTGTCATCCTCAGTAGTTTGGCATTTTCAGGTTGTGTTTATGATTCAAAACTACAACGCCCAGTCATATCAGAGCGAGAAACTGAGATTCCTTTATTATTTAATCAAGCACAGACTCAAGCTGTGTTTGTTACTTATGATGGGATTCATCTAAAAAGTTATGGTAATGATCTAAGCCGAGCAAAGACTGAATATATTCCTGCATCTACATTTAAGATGTTGAATGCTTTAATTGGATTGCAAAATGCAAAAGCAACCAATACTGAAGTATTTCATTGGAATGGTGAAAAGCGCGCTTTTTCAGCATGGGAAAAAGATATGACTTTGGCAGAAGCGATGCAGGCTTCAGCTGTTCCCGTATATCAGGAGCTTGCTCGACGTATTGGCTTGGAGTTGATGCGTGAAGAAGTGAAGCGTGTAGGTTTTGGCAATGCGGAGATTGGTCAGCAAGTCGATAATTTTTGGTTGGTGGGTCCTTTAAAAATCTCCCCTGAACAAGAAGTTCAATTTGCCTATCAACTGGCGATGAAGCAATTACCTTTTGATCGAAATGTACAGCAACAAGTCAAAAATATGCTTTATATCGAGAGACGTGGTGACAGTAAACTGTATGCTAAAAGTGGTTGGGGAATGGATGTTAAACCTCAAGTGGGTTGGTATACGGGATGGGTTGAACAACCCAATGGCAAGGTGACTGCATTTGCGTTAAATATGAACATGCAAGCAGGTGATGATCCAGCTGAACGTAAACAATTAACCTTAAGTATTTTGGACAAATTGGGTCTATTTTTTTATTTAAGATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39090","NCBI_taxonomy_name":"Acinetobacter bereziniae","NCBI_taxonomy_id":"106648"}}}},"ARO_accession":"3002496","ARO_id":"38896","ARO_name":"OXA-418","ARO_description":"OXA-418 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"959":{"model_id":"959","model_name":"OXA-64","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1692":{"protein_sequence":{"accession":"AAW81336.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKGEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"AY750907","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGGAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001613","ARO_id":"38013","ARO_name":"OXA-64","ARO_description":"OXA-64 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"960":{"model_id":"960","model_name":"TEM-137","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1155":{"protein_sequence":{"accession":"CAL08007.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGRRGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AM286274","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTAGGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36790","NCBI_taxonomy_name":"Shigella sonnei","NCBI_taxonomy_id":"624"}}}},"ARO_accession":"3001001","ARO_id":"37381","ARO_name":"TEM-137","ARO_description":"TEM-137 is an extended-spectrum beta-lactamase found in Shigella sonnei.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"961":{"model_id":"961","model_name":"SHV-93","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1877":{"protein_sequence":{"accession":"ABN49110.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGTVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIDDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"EF373969","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCACAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGACGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGATGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001145","ARO_id":"37525","ARO_name":"SHV-93","ARO_description":"SHV-93 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"962":{"model_id":"962","model_name":"OXA-356","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1533":{"protein_sequence":{"accession":"AGW83454.1","sequence":"MKFKMKGLFCVILSSLAFSGCVYDSKLQRPVISERETEIPLLFNQAQTQAVFVTYDGIHLKSYGNDLSRAKTEYIPASTFKMLNALIGLQNAKATNTEIFHWNGEKRAFSAWEKDMTLAEAMQASAVPVYQELARRIGLELMREEVKRVGFGNAEIGQQVDNFWLVGPLKISPEQEVQFAYQLAMKQLPFDRNVQQQVKDMLYIERRGDSKLYAKSGWGMDVEPQVGWYTGWVEQPNGKVTAFALNMNMQAGDDPAERKQLTLSILDKLGLFFYLR"},"dna_sequence":{"accession":"KF297585","fmin":"0","fmax":"831","strand":"+","sequence":"ATGAAGTTTAAAATGAAAGGTTTATTTTGTGTCATCCTCAGTAGTTTGGCATTTTCAGGTTGTGTTTATGATTCAAAACTACAACGCCCAGTCATATCAGAGCGAGAAACTGAGATTCCTTTATTATTTAATCAAGCACAGACTCAAGCTGTGTTTGTTACTTATGATGGGATTCATCTAAAAAGTTATGGTAATGATCTAAGCCGAGCAAAGACTGAATATATTCCTGCATCTACATTTAAGATGTTGAATGCTTTAATTGGCTTGCAAAATGCAAAAGCAACCAATACTGAAATATTTCATTGGAATGGTGAAAAGCGCGCTTTTTCAGCATGGGAAAAAGATATGACTTTGGCAGAAGCGATGCAGGCTTCAGCTGTTCCCGTATATCAGGAGCTTGCTCGACGTATTGGCTTGGAATTGATGCGTGAAGAAGTGAAGCGTGTAGGTTTCGGCAATGCGGAGATTGGTCAGCAAGTCGATAATTTTTGGTTGGTGGGTCCTTTAAAAATCTCCCCTGAACAAGAAGTTCAATTTGCCTATCAACTGGCAATGAAGCAATTACCTTTTGATCGAAATGTACAGCAACAAGTCAAAGATATGCTTTATATCGAGAGACGTGGTGACAGTAAACTGTATGCTAAAAGTGGTTGGGGAATGGATGTTGAACCTCAAGTGGGTTGGTATACGGGATGGGTTGAACAACCCAATGGCAAGGTGACTGCATTTGCGTTAAATATGAACATGCAAGCAGGTGATGATCCAGCTGAACGTAAACAATTAACCTTAAGTATTTTGGACAAATTGGGTCTATTTTTTTATTTAAGATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39090","NCBI_taxonomy_name":"Acinetobacter bereziniae","NCBI_taxonomy_id":"106648"}}}},"ARO_accession":"3001543","ARO_id":"37943","ARO_name":"OXA-356","ARO_description":"OXA-356 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"963":{"model_id":"963","model_name":"CMY-69","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1022":{"protein_sequence":{"accession":"AGE45504.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALPALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"JX049132","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGCCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002082","ARO_id":"38482","ARO_name":"CMY-69","ARO_description":"CMY-69 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"964":{"model_id":"964","model_name":"OXA-129","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1450":{"protein_sequence":{"accession":"CAP69660.1","sequence":"MKTIAAYLVLVFFAGTALSESISENLAWNKEFSSESVHGVFVLCKSSSNSCTTNNATRASTAYIPASTFKIPNALIGLETGAIKDARQVFKWDGKPRAMKQWEKDLTLRGAIQVSAVPVFQQIARDIGKKRMQKYLNLFSYGNANIGGGIDKFWLEGQLRISAVNQVKFLESLYLNNLPASKANQLIVKEAIVTEATPEYIVHSKTGYSGVGTESNPGVAWWVGWVEKGTEVYFFAFNMDIDNESKLPSRKSIPTKIMASEGIIIGG"},"dna_sequence":{"accession":"AM932669","fmin":"698","fmax":"1502","strand":"+","sequence":"ATGAAAACCATAGCCGCATATTTAGTTCTAGTATTTTTTGCAGGCACTGCACTTTCAGAGTCTATTTCTGAAAATTTAGCTTGGAATAAAGAATTTTCCAGTGAATCAGTGCATGGTGTTTTTGTACTTTGTAAAAGCAGTAGTAATTCCTGTACAACAAATAATGCAACACGTGCATCTACGGCCTATATTCCAGCATCAACATTCAAAATTCCCAATGCTCTCATAGGCCTTGAAACCGGCGCCATAAAAGATGCGCGGCAGGTTTTCAAATGGGACGGCAAGCCCAGAGCCATGAAGCAATGGGAAAAAGACTTAACGCTAAGGGGCGCTATACAAGTTTCTGCTGTTCCGGTATTTCAACAAATTGCCAGAGACATTGGCAAAAAAAGAATGCAAAAATACCTTAACCTTTTTTCATATGGCAACGCCAATATAGGCGGAGGCATTGACAAATTTTGGCTAGAAGGTCAGCTTAGAATCTCAGCAGTCAATCAAGTTAAATTTTTAGAGTCGCTTTACCTAAATAATTTGCCAGCATCTAAAGCAAACCAACTTATAGTAAAAGAGGCAATAGTTACAGAAGCAACTCCAGAATATATAGTGCATTCAAAAACCGGGTATTCCGGTGTGGGCACAGAATCAAATCCTGGTGTCGCTTGGTGGGTTGGTTGGGTAGAAAAAGGAACTGAGGTTTACTTTTTTGCATTTAACATGGACATAGACAATGAGAGTAAGTTGCCGTCAAGAAAATCCATTCCAACGAAAATCATGGCAAGTGAAGGTATCATCATTGGTGGCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35739","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Bredeney","NCBI_taxonomy_id":"134047"}}}},"ARO_accession":"3001811","ARO_id":"38211","ARO_name":"OXA-129","ARO_description":"OXA-129 is a beta-lactamase found in Salmonella enterica","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"965":{"model_id":"965","model_name":"OXA-333","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1610":{"protein_sequence":{"accession":"AGW16415.1","sequence":"MKNLQLGLIVLITTFGSACTTISPSVETAKNQHQQSAQQQIQQAFNQLQTTGVIVIKDKHGLHSYGNDLSRAQTPYVPASTFKILNALIGLEHGKATSTEVFKWDGQKRSFPTWEKDMTLGQAIQASAVPVYQELARRIGLDLMQKEVQRIGYGNQQIGTVVDNFWLVGPLQITPVQEVLFVEKLANIQLAFKPDVQHTVQDMLLIEQKANYELYAKSGWGMDLEPQVGWWTGWVETATGEKVYFALNMHMKTGISASVREQLVKQSLTALGII"},"dna_sequence":{"accession":"KF203107","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAAAAATTTACAGTTGGGACTCATCGTCCTCATTACAACCTTCGGTTCCGCGTGTACCACAATAAGCCCCTCCGTAGAAACAGCTAAAAACCAACATCAGCAAAGCGCGCAGCAGCAGATCCAACAGGCCTTCAATCAACTCCAAACCACTGGGGTGATTGTCATTAAGGATAAGCACGGTTTACACAGCTACGGCAATGACTTGAGCCGTGCTCAGACACCCTATGTACCCGCCTCTACCTTTAAAATATTAAATGCCTTAATCGGACTAGAACATGGTAAGGCAACCAGCACCGAGGTATTTAAATGGGATGGTCAAAAGCGTAGTTTCCCTACTTGGGAAAAAGACATGACTTTAGGGCAAGCCATACAAGCATCTGCCGTTCCCGTTTATCAGGAGCTTGCACGGCGCATTGGTCTAGACCTAATGCAAAAAGAAGTGCAGCGCATTGGATATGGCAATCAACAGATTGGCACCGTTGTCGATAATTTTTGGTTAGTCGGTCCACTGCAAATTACGCCTGTTCAAGAAGTCCTTTTTGTAGAGAAGCTGGCCAATATACAACTCGCTTTTAAGCCAGATGTGCAACATACCGTACAAGACATGCTGCTGATTGAACAAAAAGCGAATTATGAACTCTACGCCAAATCTGGTTGGGGCATGGACCTAGAACCGCAAGTGGGCTGGTGGACAGGCTGGGTCGAAACAGCAACAGGTGAAAAAGTGTATTTTGCTTTGAATATGCATATGAAAACGGGAATTTCAGCCAGCGTACGTGAGCAACTGGTCAAACAAAGTCTGACAGCACTGGGGATAATTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39092","NCBI_taxonomy_name":"Acinetobacter johnsonii","NCBI_taxonomy_id":"40214"}}}},"ARO_accession":"3001521","ARO_id":"37921","ARO_name":"OXA-333","ARO_description":"OXA-333 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"966":{"model_id":"966","model_name":"vanSC","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"565":{"protein_sequence":{"accession":"AAF86642.1","sequence":"MKNRNPLIRKLLTQYFVTTGILLAFLVMIPLVIRFIAGTRTWYGTEPIYYILRFFADRWLFCVAIGALLIWFGTTIYYMTKAIGYLNETIQATTQLIEEPSKRITLSSHLIDVQEEMNQLREKSLQDQRAAKEAEQRKNDLIVYLAHDLRTPLTSVIGYLTLLKEEPQLSNAMRNRYTEIALQKAQRLELLISEFFEITRFNLTTIVLQTETTDLSLMLEQLTFEFLPLLEEKNLNWQLNLQKNVLATVDTEKIARVFDNLIRNAINYSYPDSPLLLELVESDSIHIRLTNRGKTIPEEMIGRLFEPFYRMDSSRATATSGTGLGLPIAKEILLASGGDISAESKDETIIFNVRLPKPANN"},"dna_sequence":{"accession":"AF162694","fmin":"5877","fmax":"6963","strand":"+","sequence":"TTGAAAAATAGAAATCCTTTGATCCGAAAGCTCTTGACCCAATACTTCGTCACCACTGGAATCTTGCTGGCATTCCTTGTAATGATTCCATTAGTCATTCGCTTTATTGCCGGAACCCGGACTTGGTATGGAACGGAACCTATCTACTATATCTTACGTTTTTTTGCGGATCGCTGGTTGTTTTGTGTTGCGATTGGCGCTTTACTGATATGGTTTGGTACCACCATTTACTATATGACCAAAGCCATCGGTTATTTGAATGAAACGATCCAAGCCACGACTCAACTGATAGAAGAACCATCCAAACGCATCACTTTATCGAGCCATCTGATTGATGTTCAAGAGGAAATGAATCAACTGCGGGAGAAAAGTCTGCAAGATCAACGTGCCGCTAAAGAAGCGGAACAGCGGAAAAATGATTTGATCGTTTATCTCGCCCACGATTTGCGGACGCCTCTGACAAGTGTCATAGGTTATCTGACTCTTCTAAAAGAAGAACCACAATTATCCAATGCGATGCGGAATCGTTACACGGAGATTGCTTTACAAAAAGCCCAACGGCTGGAACTATTGATCAGTGAATTCTTCGAGATCACACGCTTCAATTTGACCACGATCGTTTTGCAGACAGAAACGACTGATTTAAGTTTAATGCTTGAACAGCTGACCTTTGAGTTTTTACCTCTCTTGGAAGAAAAGAATCTAAATTGGCAACTCAACTTACAAAAAAATGTTCTTGCAACAGTAGACACCGAAAAAATAGCTCGTGTCTTTGATAATCTCATTCGCAATGCCATCAACTACAGCTATCCAGATTCGCCTTTACTTCTTGAATTGGTCGAATCAGACAGTATTCACATTCGTCTGACGAATCGTGGAAAAACAATTCCAGAAGAGATGATCGGACGTCTCTTTGAACCTTTCTATCGCATGGATTCTTCCCGAGCTACAGCCACAAGCGGAACTGGTCTTGGTCTTCCGATTGCAAAAGAGATTCTGTTAGCATCTGGCGGGGATATCTCGGCAGAAAGCAAAGACGAAACCATCATTTTCAACGTTCGCTTGCCAAAACCTGCCAACAACTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36781","NCBI_taxonomy_name":"Enterococcus gallinarum","NCBI_taxonomy_id":"1353"}}}},"ARO_accession":"3002933","ARO_id":"39367","ARO_name":"vanSC","ARO_description":"vanSC is a vanS variant found in the vanC gene cluster","ARO_category":{"36210":{"category_aro_accession":"3000071","category_aro_cvterm_id":"36210","category_aro_name":"vanS","category_aro_description":"VanS is similar to histidine protein kinases like EnvZ and acts as a response regulator by activating VanR. VanS is required for high level transcription of other van glycopeptide resistance genes.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"967":{"model_id":"967","model_name":"AAC(6')-Isa","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"705":{"protein_sequence":{"accession":"BAD10948.2","sequence":"MELRGDDVVLRPVADGEGEVLDRIVREPEVAAWWSPPEDFAGMLAIVFEGEVVGAIQFYEETDPEFHHAGIDVFLTARHQGKGLGTDAVRTLARWLVAERGHHRLTIDPAAANTAAIRSYRKVGFRPVGIMRAYGRDHRTGRWQDALLMDLLADELT"},"dna_sequence":{"accession":"AB116646","fmin":"429","fmax":"903","strand":"+","sequence":"ATGGAGCTGCGCGGGGACGACGTCGTACTGCGACCGGTGGCCGACGGCGAGGGCGAGGTGCTCGACCGGATCGTGCGGGAGCCGGAGGTGGCGGCGTGGTGGTCGCCCCCGGAGGACTTCGCGGGCATGCTCGCCATCGTCTTCGAGGGCGAGGTCGTCGGAGCGATCCAGTTCTACGAGGAGACCGACCCCGAATTCCACCACGCCGGCATCGACGTCTTCCTGACGGCACGCCACCAGGGGAAGGGGCTGGGCACCGACGCGGTGCGCACGCTGGCCCGGTGGCTGGTGGCGGAACGCGGCCACCACCGGCTGACCATCGACCCCGCCGCCGCCAACACCGCGGCGATCCGCAGCTACCGCAAGGTCGGGTTCCGGCCGGTGGGCATCATGCGGGCGTACGGGCGCGACCACCGGACGGGACGCTGGCAGGACGCGCTGCTCATGGACCTGCTCGCCGACGAACTGACCTGAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39514","NCBI_taxonomy_name":"Streptomyces albulus","NCBI_taxonomy_id":"68570"}}}},"ARO_accession":"3002563","ARO_id":"38963","ARO_name":"AAC(6')-Isa","ARO_description":"AAC(6')-Isa is a plasmid-encoded aminoglycoside acetyltransferase in Streptomyces albulus","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"968":{"model_id":"968","model_name":"MIR-15","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"1503":{"protein_sequence":{"accession":"AIT76104.1","sequence":"MMTKSLSCALLLSVASAAFAAPMSEKQLAEVVERTVTPLINAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEIALGDPVAKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDTASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEEAHYAWGYREGKAVHVSPGMLDAEAYGVKTNVKDMASWVIANMKPDSLQAPSLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"KM087851","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGACAAAATCCCTAAGCTGTGCCCTGCTGCTCAGCGTCGCCAGCGCTGCATTCGCCGCACCGATGTCCGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATAAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTAATTTATCAGGGTCAGCCACACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGCGGCGATGCCATTGCCCGGGGTGAAATAGCGCTGGGCGATCCGGTAGCAAAATACTGGCCTGAGCTCACGGGCAAGCAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTACACCGCAGGCGGTCTGCCGTTACAGGTGCCGGATGAGGTCACGGATACCGCTTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCTAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTTAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAACCCCTCAAGCTGGACCATACCTGGATTAACGTCCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGAGGGTAAAGCGGTCCACGTTTCGCCAGGGATGCTGGACGCGGAAGCCTATGGCGTAAAAACTAACGTGAAGGATATGGCGAGCTGGGTGATAGCCAACATGAAGCCGGATTCTCTTCAGGCTCCCTCACTCAAGCAAGGCATTGCTCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCTATGTATCAGGGGTTGGGCTGGGAGATGCTCAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCATTGCCCGTGGCAGAAGTGAATCCACCCGCGCCGCCGGTTAAGGCCTCCTGGGTCCATAAAACAGGCTCGACGGGTGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39773","NCBI_taxonomy_name":"Enterobacter kobei","NCBI_taxonomy_id":"208224"}}}},"ARO_accession":"3002180","ARO_id":"38580","ARO_name":"MIR-15","ARO_description":"MIR-15 is a beta-lactamase. From the Lahey list of MIR beta-lactamases.","ARO_category":{"36197":{"category_aro_accession":"3000058","category_aro_cvterm_id":"36197","category_aro_name":"MIR beta-lactamase","category_aro_description":"MIR beta-lactamases are plasmid-mediated beta-lactamases that confer resistance to oxyimino- and alpha-methoxy beta-lactams","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"969":{"model_id":"969","model_name":"VEB-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1805":{"protein_sequence":{"accession":"AGH33739.1","sequence":"MKIVKRILLVLLSLFFTVEYSNAQTDNLTLKIENVLKAKNARIGVAIFNSNEKDTLKINNDFHFPMQSVMKFPIALAVLSEIDKGNLSFEQKIEITPQDLLPKMWSPIKEEFPNGTTLTIEQILNYTVSESDNIGCDILLKLIGGTDSVQKFLNANHFTDISIKANEEQMHKDWNTQYQNWATPTAMNKLLIDTYNNKNQLLSKKSYDFIWKIMRETTAGSNRLKGQLPKNTIVAHKTGTSGINNGIAAATNDVGVITLPNGQLIFISVFVAESKETSEINEKIISDIAKITWNYYLNK"},"dna_sequence":{"accession":"JX679208","fmin":"0","fmax":"900","strand":"+","sequence":"ATGAAAATCGTAAAAAGGATATTATTAGTATTGTTAAGTTTATTTTTTACAGTTGAGTATTCAAATGCTCAAACTGACAACTTAACTTTGAAAATTGAGAATGTTTTAAAGGCAAAAAATGCCAGAATAGGAGTAGCAATATTCAACAGCAATGAGAAGGATACTTTGAAGATTAATAACGACTTCCATTTCCCGATGCAAAGCGTTATGAAATTTCCGATTGCTTTAGCCGTTTTGTCTGAGATAGATAAAGGGAATCTTTCTTTTGAACAAAAAATAGAGATTACCCCTCAAGACCTTTTGCCTAAAATGTGGAGTCCGATTAAAGAGGAATTCCCTAATGGAACAACTTTGACGATTGAACAAATACTAAATTATACAGTATCAGAGAGCGACAATATTGGTTGTGATATTTTGCTAAAATTAATCGGAGGAACTGATTCTGTTCAAAAATTCTTGAATGCTAATCATTTCACTGATATTTCAATCAAAGCAAACGAAGAACAAATGCACAAGGATTGGAATACCCAATATCAAAATTGGGCAACCCCAACAGCGATGAACAAACTGTTAATAGATACTTATAATAATAAGAACCAATTACTTTCTAAAAAAAGTTATGATTTTATTTGGAAAATTATGAGAGAAACAACAGCAGGAAGTAACCGATTAAAAGGACAATTACCAAAGAATACAATTGTTGCTCATAAAACAGGGACTTCCGGAATAAATAATGGAATTGCAGCAGCCACTAATGATGTTGGGGTAATTACTTTACCGAATGGACAATTAATTTTTATAAGCGTATTTGTTGCAGAGTCCAAAGAAACTTCGGAAATTAATGAAAAGATTATTTCAGACATTGCAAAAATAACGTGGAATTACTATTTGAATAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002377","ARO_id":"38777","ARO_name":"VEB-8","ARO_description":"VEB-8 is a beta-lactamase. From the Lahey list of VEB beta-lactamases.","ARO_category":{"36182":{"category_aro_accession":"3000043","category_aro_cvterm_id":"36182","category_aro_name":"VEB beta-lactamase","category_aro_description":"VEB beta-lactamases or Vietnamese extended-spectrum beta-lactamases are class A beta-lactamases that confer high-level resistance to oxyimino cephalosporins and to aztreonam","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"870":{"model_id":"870","model_name":"otr(B)","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1100"}},"model_sequences":{"sequence":{"697":{"protein_sequence":{"accession":"AAD04032.1","sequence":"MSSANPGPAGTADQAGGAFTHRQILTAMSGLLLAVFLAALDQTVIATAMRTIADDLHGQTEQAWATTGYLIASVLAMPFYGKLSDIYGRKPMYLISIVVFIGGSVLCGTAGSMWELALFRAVQGLGGGGLMSLPTAVVADLAPVRERGRYFAFLQMAWVVASVAGPLAGGFFAEAGQVFGIDGWRWVFLLNVPLGLLALVTVRKALNLPHERREHRMDVLGAAALALFLVPLLIVAEQGRTWGWGSPAALALFALGAAGLAVFIPVELRRGDEAILPLGLFRRGSIALCSAVNFTIGVGIFGTVTTLPLFLQMVQGRTPTQAGLVVIPFMLGTIASQMVSGKLIASSGRFKKLAIVGLGSMAGALLAMATTGATTPMWGIVLIVLWLGVGIGLSQTVITSPMQNSAPKSQLGVANGASGLCRQIGGSTGIAVLFSVMFAVALGRLADLLHTPRYERLLTDPAITGDPANHRFLDMAESGQGAGINLDDTSLLNGIDARLMQPVTDSFAHGFHIMFLAGGVVLLAGFVMTWFLRELQEETAPEEERPAESGAGAKNGPLPASDA"},"dna_sequence":{"accession":"AF079900","fmin":"39","fmax":"1731","strand":"+","sequence":"GTGTCATCCGCAAATCCGGGCCCGGCGGGCACGGCGGACCAGGCAGGCGGGGCGTTCACGCATCGGCAGATCCTGACGGCCATGTCGGGACTGCTGCTGGCCGTGTTCCTCGCGGCCCTGGACCAGACGGTCATCGCCACCGCGATGCGCACCATCGCGGACGACCTCCACGGCCAGACCGAGCAGGCATGGGCGACGACGGGCTACCTCATCGCCTCCGTCCTGGCGATGCCGTTCTACGGCAAGCTGTCCGACATCTACGGGCGCAAGCCCATGTACCTGATCTCCATCGTGGTGTTCATCGGCGGCTCGGTGCTGTGCGGCACGGCCGGCTCGATGTGGGAGCTGGCCCTCTTCCGGGCCGTCCAGGGACTGGGCGGCGGCGGGCTGATGTCCCTGCCCACCGCGGTGGTCGCCGACCTCGCCCCGGTGCGCGAGCGCGGCCGCTACTTCGCCTTCCTCCAGATGGCGTGGGTGGTCGCCAGCGTCGCGGGCCCGCTGGCGGGCGGCTTCTTCGCGGAGGCGGGCCAGGTCTTCGGCATCGACGGCTGGCGCTGGGTGTTCCTGCTCAACGTACCGCTGGGCCTGCTGGCCCTGGTCACCGTGCGCAAGGCCCTGAACCTGCCGCACGAACGGCGCGAGCACCGCATGGACGTACTGGGCGCGGCGGCGCTGGCGCTGTTCCTGGTGCCCCTGCTGATCGTCGCCGAACAGGGCCGGACCTGGGGCTGGGGCTCGCCGGCCGCCCTCGCCCTCTTCGCGCTCGGCGCGGCCGGGCTGGCGGTCTTCATCCCCGTCGAGCTGCGGCGCGGCGACGAGGCCATCCTGCCGCTGGGGCTCTTCCGGCGCGGCAGCATCGCGCTGTGCTCCGCGGTCAACTTCACCATCGGCGTCGGCATCTTCGGCACGGTCACCACCCTGCCGCTGTTCCTCCAGATGGTGCAGGGGCGGACCCCGACCCAGGCCGGACTGGTGGTCATCCCGTTCATGCTGGGCACCATCGCCTCGCAGATGGTCTCCGGCAAGCTCATCGCGTCCTCGGGCCGGTTCAAGAAACTGGCGATCGTGGGCCTGGGCTCGATGGCCGGGGCGCTGCTGGCCATGGCCACCACCGGCGCGACGACCCCGATGTGGGGCATCGTCCTGATCGTCCTCTGGCTCGGCGTCGGCATCGGCCTGTCCCAGACCGTCATCACCTCGCCCATGCAGAACTCGGCCCCCAAGAGCCAGCTCGGCGTGGCGAACGGCGCCTCCGGCCTGTGCCGGCAGATCGGCGGCTCCACCGGCATCGCGGTTCTGTTCTCCGTGATGTTCGCGGTGGCGCTCGGCCGCCTCGCCGACCTGCTGCACACCCCGCGCTACGAGCGCCTCCTGACGGACCCGGCGATCACCGGCGACCCCGCCAACCACCGCTTCCTTGACATGGCCGAGTCCGGGCAGGGCGCGGGGATCAACCTTGACGACACGTCCCTGCTGAACGGCATCGACGCCCGGCTGATGCAGCCGGTGACGGATTCCTTCGCCCACGGCTTCCACATCATGTTCCTCGCCGGCGGCGTGGTGCTGCTGGCCGGGTTCGTCATGACCTGGTTCCTGCGCGAACTCCAGGAGGAGACCGCGCCGGAGGAGGAGCGGCCGGCCGAGAGCGGCGCCGGGGCGAAGAACGGGCCGCTGCCCGCGTCGGACGCCTGAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36773","NCBI_taxonomy_name":"Streptomyces rimosus","NCBI_taxonomy_id":"1927"}}}},"ARO_accession":"3002892","ARO_id":"39326","ARO_name":"otr(B)","ARO_description":"otr(B) is a tetracycline resistance efflux pump found in Streptomyces rimosus","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"910":{"model_id":"910","model_name":"rphA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1500"}},"model_sequences":{"sequence":{"7":{"protein_sequence":{"accession":"AIA08936.1","sequence":"MSGRLVVDLQDVDAAGLAEVGGKGAHLGELSRIDGVRVPSGFCVTTHAFRRIMAEAPESGELLDRLSRVDEGDQEAVRSLAARLRQVVGATPLPDEVAAAVTGALARHGERSAYAVRSSATAEDLPTASFAGQQDTYLNVVGTEEILRHVSRCWASLFTERAVTYRGRQGVDHRTVHMGVVVQRMVVPRASGILFTADPVTGDRRTATVDAGFGLGEALVSGLVDPDVLTVRHGEVVARTIAAKRRALHAVQGGGTRETPIEERRQREPVLTDDQAVELVALGRRIEAHFGSPQDIEWCLDDDGFHIVQSRPITTLFPVPERDDDVFRVYLSVGHQQMMTDAMKPLGLSMWRLTALAPMYEAGGRLFVDATARLAVPGSRATLLDVVGRGDPLTRDALETVLENGEFEPTPAETDGGAPPAGDGAEPDEADPSIVTELIERSRRSLAELEREIGTKSGPALFAFLREAFEEHKRVVGDPLNIRAIMAGMEATWWLNDRLEEWLGEKNAADTLTLSAPDNVTSEMGLELLDVADVVRTHPEVVAFLEGVEDDGFLDELPKVPGGAEARDAFEAYLDRYGMRCVGEIDITXPPVRERPSALVPVVLDHVRAFGPGAAARRFEDGRRRALAKEREVLERLRDLPDGERRADAARRMIRQVRAFAGYREYPKYAIVSRSFVYRQALLREADELVRAGVLADREDVHYLTFDEFEEAVRVRRVDERLVRRRKDAFRSYQALTPPRVLTSEGVALSGAYRRDDVPEGALAGLAVSAGTVEGRARVVLDMAEADLEAGDILVTRFTDPSWSPLFVGIAGLVTEVGGLMTHGAVIAREYGLAAVVGVERATRLIRDGQRIRVHGTEGYIELLS"},"dna_sequence":{"accession":"KJ151292","fmin":"294","fmax":"2892","strand":"+","sequence":"ATGAGCGGGCGTCTGGTCGTGGATCTTCAGGACGTCGACGCGGCGGGGCTCGCCGAGGTCGGCGGCAAGGGCGCCCACCTGGGCGAGCTGTCCCGGATCGACGGGGTCCGGGTGCCGTCCGGGTTCTGTGTGACGACGCACGCCTTCCGGCGGATCATGGCGGAGGCACCCGAGAGCGGGGAACTCCTCGACCGGCTGTCCCGCGTGGACGAGGGCGACCAGGAGGCGGTCCGATCCCTCGCCGCCCGTCTACGGCAGGTCGTCGGGGCGACGCCCCTCCCGGACGAGGTGGCGGCGGCCGTCACCGGGGCGCTCGCCCGGCACGGTGAGCGGTCCGCGTACGCCGTACGGTCCAGCGCGACGGCCGAGGACCTGCCGACCGCGTCGTTCGCCGGCCAGCAGGACACGTACCTGAACGTCGTCGGCACCGAGGAGATCCTCCGGCACGTCAGCCGGTGCTGGGCCTCCCTGTTCACCGAGCGGGCGGTGACCTACCGCGGGCGTCAGGGCGTCGACCACCGTACGGTCCACATGGGCGTGGTCGTGCAGCGGATGGTCGTGCCGCGGGCGTCCGGCATCCTGTTCACCGCCGACCCGGTGACGGGAGACCGCCGCACGGCGACCGTGGACGCCGGTTTCGGTCTCGGCGAGGCCCTGGTGTCGGGGCTGGTCGACCCGGACGTCCTCACGGTGCGGCACGGCGAGGTCGTCGCGCGGACGATCGCCGCGAAGCGGCGCGCCCTGCACGCCGTGCAGGGCGGTGGGACGCGCGAGACCCCGATCGAGGAACGGCGGCAGCGCGAACCGGTACTGACGGACGATCAGGCCGTGGAGCTGGTCGCGCTCGGGCGGCGGATCGAGGCGCACTTCGGCAGCCCGCAGGACATCGAGTGGTGCCTGGACGACGACGGCTTCCACATCGTGCAGAGCCGGCCGATCACCACGCTGTTCCCCGTGCCCGAGCGGGACGACGACGTCTTCCGCGTCTATCTCTCGGTCGGCCACCAGCAGATGATGACCGACGCCATGAAGCCCCTGGGCCTCTCGATGTGGCGGCTGACGGCCCTGGCACCGATGTACGAGGCCGGCGGGCGGCTGTTCGTCGACGCCACCGCCCGGCTGGCGGTGCCCGGGAGCCGTGCCACTCTCCTGGACGTCGTCGGCCGTGGCGACCCGCTGACCCGGGACGCGCTCGAAACGGTCCTGGAGAACGGCGAGTTCGAGCCGACGCCGGCGGAGACGGACGGAGGCGCGCCGCCCGCCGGTGACGGGGCCGAACCGGACGAGGCCGATCCTTCCATCGTCACCGAGCTGATCGAGCGCAGCCGGCGCTCCCTCGCCGAGCTGGAGCGGGAGATCGGCACGAAGAGCGGTCCCGCCCTGTTCGCGTTCCTGCGGGAGGCGTTCGAGGAGCACAAGCGGGTGGTCGGCGATCCGCTGAACATCCGCGCGATCATGGCGGGCATGGAGGCCACCTGGTGGCTGAACGACCGGCTGGAGGAGTGGCTCGGCGAGAAGAACGCCGCCGACACGCTCACGCTGTCCGCCCCCGACAACGTGACCTCGGAGATGGGGCTGGAGCTGCTCGACGTCGCCGACGTGGTCCGCACGCACCCGGAGGTGGTGGCCTTCCTGGAGGGCGTCGAGGACGACGGCTTCCTGGACGAGCTGCCCAAGGTCCCCGGTGGCGCCGAGGCCCGGGACGCCTTCGAGGCATACCTGGACCGGTACGGCATGCGCTGCGTCGGCGAGATCGACATCACGNGGCCCCCGGTGCGGGAACGGCCCAGCGCGCTCGTGCCGGTCGTCCTCGACCACGTGCGCGCCTTCGGGCCCGGCGCCGCCGCGCGCCGCTTCGAGGACGGCCGGCGCAGGGCGCTCGCGAAGGAGCGTGAGGTGCTGGAGCGGCTGCGGGACCTGCCGGACGGGGAGCGCAGGGCCGACGCGGCGCGCCGGATGATCCGGCAGGTCCGCGCGTTCGCCGGCTACCGGGAGTACCCGAAGTACGCGATCGTCAGCCGCTCCTTCGTCTACCGTCAGGCCCTGCTGCGGGAGGCCGACGAGCTGGTGCGGGCCGGCGTCCTCGCCGACCGGGAGGACGTCCACTACCTGACGTTCGACGAGTTCGAGGAGGCCGTCCGCGTGCGCCGGGTGGACGAGCGGCTGGTGCGGCGCCGCAAGGACGCCTTCCGTTCGTACCAGGCGCTGACCCCGCCCCGCGTCCTCACCTCGGAGGGTGTGGCCCTCTCCGGGGCGTACCGGCGCGACGACGTGCCGGAAGGGGCGCTGGCGGGTCTCGCGGTGTCCGCGGGGACCGTGGAGGGCCGGGCCCGGGTGGTCCTCGACATGGCGGAGGCCGATCTGGAGGCGGGCGACATCCTGGTCACGCGGTTCACGGACCCCAGCTGGTCACCGCTGTTCGTCGGGATCGCGGGCCTGGTGACGGAGGTGGGCGGTCTGATGACCCATGGCGCGGTGATCGCCCGCGAGTACGGTCTGGCGGCCGTGGTCGGGGTGGAGCGGGCCACCCGGCTGATCCGGGACGGGCAGCGCATCCGGGTGCACGGGACGGAGGGCTATATCGAGCTTCTGTCCTGAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39689","NCBI_taxonomy_name":"Streptomyces sp. WAC4747","NCBI_taxonomy_id":"1501383"}}}},"ARO_accession":"3000444","ARO_id":"36583","ARO_name":"rphA","ARO_description":"The enzymatic inactivation of rifampin by phosphorylation at the 21-OH position.","ARO_category":{"41087":{"category_aro_accession":"3004040","category_aro_cvterm_id":"41087","category_aro_name":"rifampin phosphotransferase","category_aro_description":"Enzymes, protein or other gene products that inactivate rifampin (rifamycin) antibiotics through phosphorylation of the antibiotic at the 21-OH position.","category_aro_class_name":"AMR Gene Family"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36656":{"category_aro_accession":"3000517","category_aro_cvterm_id":"36656","category_aro_name":"rifaximin","category_aro_description":"Rifaximin is a semi-synthetic rifamycin used to treat traveller's diarrhea. Rifaximin inhibits RNA synthesis by binding to the beta subunit of bacterial RNA polymerase.","category_aro_class_name":"Antibiotic"},"36669":{"category_aro_accession":"3000530","category_aro_cvterm_id":"36669","category_aro_name":"rifabutin","category_aro_description":"Rifabutin is a semisynthetic rifamycin used in tuberculosis therapy. It inhibits DNA-dependent RNA synthesis.","category_aro_class_name":"Antibiotic"},"36673":{"category_aro_accession":"3000534","category_aro_cvterm_id":"36673","category_aro_name":"rifapentine","category_aro_description":"Rifapentine is a semisynthetic rifamycin that inhibits DNA-dependent RNA synthesis. It is often used in the treatment of tuberculosis and leprosy.","category_aro_class_name":"Antibiotic"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"945":{"model_id":"945","model_name":"tet(40)","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"790"}},"model_sequences":{"sequence":{"741":{"protein_sequence":{"accession":"AFK31666.1","sequence":"MFAKNSKAYSVYLLFRFVCSLAVSMSTVLSIVYHLEVVQLDAFQLVLVGTVLETSCFLFEIPTGVVADLYSRRRSVLIGMFLYGLGFLMEGALPWFAPVLLAQVVWGCGDTFITGALEAWIASEEEDKPIDKVFLRGSQMGQIGGVLGVVLGTLLGNINLQMPVILGGSLCLLLGLVLVRIMPETNFSPAIEERQGLLKDFVCLFKLNLGFVKGAPVLLALLAITLCGGLASEGFDRLSTAHFLDDTVIPVIGPLNSVTWFGVISLIGSGLGILASQLLIARMEKKGTVSRTSVVMSTSAGYILCLVLFAVGRSFWFMLLVFLLAGLMRTIKEPVLAAWMNDHVDEKMRATVFSTSGQLDSFGQIIGGPIVGLVAQQVSIPWGLVCTAFLLLPALFLVPVAGKKRD"},"dna_sequence":{"accession":"JQ740052","fmin":"2108","fmax":"3329","strand":"+","sequence":"ATGTTTGCTAAAAATTCAAAGGCATATTCTGTCTACCTGCTGTTCCGATTTGTCTGTTCCCTGGCGGTTTCTATGTCCACAGTGCTTTCCATCGTGTACCACCTGGAGGTGGTGCAGCTGGATGCTTTCCAGCTTGTCCTGGTAGGGACGGTTCTGGAGACCTCCTGCTTTCTGTTCGAGATACCCACCGGTGTGGTGGCGGATTTGTATAGCCGTCGGCGCTCGGTGCTGATTGGAATGTTCCTCTACGGCCTGGGCTTTCTGATGGAGGGTGCGCTACCGTGGTTCGCGCCGGTTCTGCTGGCCCAGGTTGTCTGGGGTTGCGGTGATACCTTCATCACCGGCGCTCTGGAGGCGTGGATTGCCTCGGAGGAAGAGGACAAACCCATAGACAAGGTGTTCCTGCGGGGCAGTCAAATGGGGCAAATCGGCGGCGTTCTGGGCGTGGTGCTGGGCACACTGCTGGGAAACATAAACCTGCAAATGCCTGTCATCTTGGGGGGCAGTTTGTGCTTGTTGTTGGGGCTGGTGTTGGTTCGCATCATGCCAGAAACCAACTTCTCCCCTGCTATTGAGGAACGGCAGGGCTTGCTTAAAGACTTTGTCTGCCTGTTCAAGCTCAACCTGGGCTTTGTGAAAGGCGCACCTGTGTTGCTGGCGCTCTTAGCAATCACACTATGCGGGGGACTTGCCAGTGAAGGCTTTGACCGGCTCTCCACCGCTCATTTTCTGGATGACACGGTAATACCCGTTATCGGGCCGCTGAACAGCGTCACTTGGTTCGGTGTTATCAGTCTTATCGGCAGCGGCTTAGGTATTCTGGCTTCTCAGTTGCTCATCGCCCGCATGGAGAAAAAAGGGACTGTCAGCCGAACCAGTGTGGTCATGTCCACCAGCGCCGGGTATATCCTGTGCCTGGTTCTCTTCGCGGTGGGGCGGAGCTTTTGGTTCATGTTGTTGGTGTTCCTGCTGGCGGGGCTTATGCGCACCATCAAGGAGCCTGTGCTGGCCGCCTGGATGAACGACCATGTGGATGAGAAAATGCGCGCCACAGTCTTTTCCACCAGCGGACAGCTGGACTCTTTCGGGCAGATCATCGGCGGGCCTATTGTGGGGCTGGTAGCCCAGCAGGTGTCCATACCCTGGGGGCTGGTCTGTACCGCTTTCCTGCTGTTGCCCGCGCTGTTCTTAGTGCCGGTGGCGGGAAAGAAGCGGGATTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39534","NCBI_taxonomy_name":"Streptococcus suis","NCBI_taxonomy_id":"1307"}}}},"ARO_accession":"3000567","ARO_id":"36706","ARO_name":"tet(40)","ARO_description":"Tet40 is a tetracycline efflux pump found in the Gram-positive Clostridium. It is similar to tetA(P).","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"900":{"model_id":"900","model_name":"tet(C)","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4420":{"protein_sequence":{"accession":"AAK97755.1","sequence":"MKSNNALIVILGTVTLDAVGIGLVMPVLPGLLRDIVHSDSIASHYGVLLALYALMQFLCAPVLGALSDRFGRRPVLLASLLGATIDYAIMATTPVLWILYAGRIVAGITGATGAVAGAYIADITDGEDRARHFGLMSACFGVGMVAGPVAGGLLGAISLHAPFLAAAVLNGLNLLLGCFLMQESHKGERRPMPLRAFNPVSSFRWARGMTIVAALMTVFFIMQLVGQVPAALWVIFGEDRFRWSATMIGLSLAVFGILHALAQAFVTGPATKRFGEKQAIIAGMAADALGYVLLAFATRGWMAFPIMILLASGGIGMPALQAMLSRQVDDDHQGQLQGSLAALTSLTSIIGPLIVTAIYAASASTWNGLAWIVGAALYLVCLPALRRGAWSRATST"},"dna_sequence":{"accession":"AY043299.1","fmin":"3984","fmax":"5175","strand":"-","sequence":"TCAGGTCGAGGTGGCCCGGCTCCATGCACCGCGACGCAACGCGGGGAGGCAGACAAGGTATAGGGCGGCGCCTACAATCCATGCCAACCCGTTCCATGTGCTCGCCGAGGCGGCATAAATCGCCGTGACGATCAGCGGTCCAATGATCGAAGTTAGGCTGGTAAGAGCCGCGAGCGATCCTTGAAGCTGTCCCTGATGGTCGTCATCTACCTGCCTGGACAGCATGGCCTGCAACGCGGGCATCCCGATGCCGCCGGAAGCGAGAAGAATCATAATGGGGAAGGCCATCCAGCCTCGCGTCGCGAACGCCAGCAAGACGTAGCCCAGCGCGTCGGCCGCCATGCCGGCGATAATGGCCTGCTTCTCGCCGAAACGTTTGGTGGCGGGACCAGTGACGAAGGCTTGAGCGAGGGCGTGCAAGATTCCGAATACCGCAAGCGACAGGCCGATCATCGTCGCGCTCCAGCGAAAGCGGTCCTCGCCGAAAATGACCCAGAGCGCTGCCGGCACCTGTCCTACGAGTTGCATGATAAAGAAGACAGTCATAAGTGCGGCGACGATAGTCATGCCCCGCGCCCACCGGAAGGAGCTGACTGGGTTGAAGGCTCTCAAGGGCATCGGTCGACGCTCTCCCTTATGCGACTCCTGCATTAGGAAGCAGCCCAGTAGTAGGTTGAGGCCGTTGAGCACCGCCGCCGCAAGGAATGGTGCATGCAAGGAGATGGCGCCCAACAGTCCCCCGGCCACGGGGCCTGCCACCATACCCACGCCGAAACAAGCGCTCATGAGCCCGAAGTGGCGAGCCCGATCTTCCCCATCGGTGATGTCGGCGATATAGGCGCCAGCAACCGCACCTGTGGCGCCGGTGATGCCGGCCACGATGCGTCCGGCGTAGAGGATCCACAGGACGGGTGTGGTCGCCATGATCGCGTAGTCGATAGTGGCTCCAAGTAGCGAAGCGAGCAGGACTGGGCGGCGGCCAAAGCGGTCGGACAGTGCTCCGAGAACGGGTGCGCATAGAAATTGCATCAACGCATATAGCGCTAGCAGCACGCCATAGTGACTGGCGATGCTGTCGGAATGGACGATATCCCGCAAGAGGCCCGGCAGTACCGGCATAACCAAGCCTATGCCTACAGCATCCAGGGTGACGGTGCCGAGGATGACGATGAGCGCATTGTTAGATTTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36795","NCBI_taxonomy_name":"Aeromonas salmonicida","NCBI_taxonomy_id":"645"}}}},"ARO_accession":"3000167","ARO_id":"36306","ARO_name":"tet(C)","ARO_description":"Tet(C) is a tetracycline efflux pump found in many species of Gram-negative bacteria. It is typically found in plasmid DNA.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"957":{"model_id":"957","model_name":"tet(G)","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"730"}},"model_sequences":{"sequence":{"239":{"protein_sequence":{"accession":"AAD25538.1","sequence":"MRSSAIIALLIVGLDAIGLGLIMPVLPTLLRELVPAEQVAGHYGALLSLYALMQVVCAPLLGQFSDGYGRRPVLLASLAGAAVDYTIMASAPVLWVLYIGRLISGITGATGAVAASTIADSTGEGSRARWFGYMGACYGTGMIAGPALGGMLGGISAHAPFIAAALLNGFAFLLACIFLKETNRSHGETGKLVRIEPFVLFRLDDALRGLTALFAVFFTIQLIGQVPAALWVIYGEDRFQWDTTTVGLSLAAFGATHAIFQAFVTGPLSSRLGERRTLLFGMAADATGFILLAFATQGWMVFPILLLLAAGGVGMPALQAMLSNNVSSNKQGALQGTLTSLTNLSSIAGPLGFTALYSATIGAWTGWVWIVGAILYLICLPILRRPFATSL"},"dna_sequence":{"accession":"AF133139","fmin":"0","fmax":"1176","strand":"+","sequence":"GTGCGCAGCTCTGCCATCATTGCCCTGCTGATCGTCGGTCTCGACGCCATAGGACTCGGCCTCATAATGCCGGTCCTTCCGACGCTTCTGCGCGAGCTTGTGCCGGCAGAGCAGGTCGCTGGTCACTATGGTGCTTTGCTGTCGCTCTATGCGTTGATGCAGGTCGTCTGCGCCCCTCTACTTGGGCAATTTTCAGATGGTTACGGTCGGCGTCCGGTGCTTCTGGCTTCTCTTGCGGGGGCCGCAGTCGATTACACGATTATGGCATCAGCGCCGGTCTTATGGGTGCTGTATATTGGCCGGCTCATTTCTGGCATCACGGGAGCAACCGGAGCTGTAGCTGCCTCAACCATTGCCGATTCGACAGGGGAAGGGTCTCGCGCACGCTGGTTCGGCTACATGGGAGCCTGTTATGGGACAGGCATGATTGCCGGGCCAGCACTTGGTGGCATGCTCGGTGGTATTTCTGCTCATGCTCCGTTTATCGCCGCTGCCCTTCTAAACGGCTTCGCGTTCCTGCTTGCCTGCATTTTTCTCAAGGAGACTAATCGCAGCCATGGCGAGACCGGAAAACTGGTCCGCATCGAACCATTCGTTCTGTTCCGGCTGGATGATGCATTGCGTGGACTAACCGCGCTTTTCGCAGTTTTCTTCACTATTCAACTGATCGGCCAAGTGCCTGCGGCCCTATGGGTCATATATGGCGAGGACCGTTTTCAGTGGGACACCACGACCGTTGGTTTGTCGCTCGCGGCGTTTGGAGCAACACATGCGATCTTCCAAGCGTTTGTTACCGGCCCTCTTTCAAGCCGGCTTGGAGAGCGGCGCACATTACTGTTTGGCATGGCTGCGGATGCGACTGGCTTCATTCTTCTAGCTTTTGCCACGCAGGGATGGATGGTGTTCCCGATTCTGCTGCTGCTTGCCGCCGGGGGCGTTGGCATGCCGGCCTTGCAGGCAATGCTCTCAAACAATGTCAGCAGTAACAAGCAAGGAGCTCTACAGGGAACGCTTACAAGCCTCACCAATCTAAGCTCTATCGCGGGACCGCTTGGCTTCACGGCACTCTATTCTGCCACCATAGGAGCATGGACCGGTTGGGTTTGGATTGTCGGCGCGATCCTCTATTTAATATGTCTGCCAATACTACGCAGACCTTTCGCAACTTCATTGTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36778","NCBI_taxonomy_name":"Pseudomonas sp.","NCBI_taxonomy_id":"306"}}}},"ARO_accession":"3000174","ARO_id":"36313","ARO_name":"tet(G)","ARO_description":"TetG is a tetracycline efflux protein found in Gram-negative bacteria. It is found in both chromosomal and plasmid DNA, and is linked to floR, sul1, and cmlA9 (florfenicol\/chloramphenicol, sulfamethoxazole, and chloramphenicol resistance genes, respectively).","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"943":{"model_id":"943","model_name":"vanUG","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"125"}},"model_sequences":{"sequence":{"339":{"protein_sequence":{"accession":"ABA71726.1","sequence":"MRVSYNKLWKLLIDRDMKKGELREAVGVSKSTFAKLGKNENVSLTVLLAICEYLNCDFGDIIEALPETPDKERDS"},"dna_sequence":{"accession":"DQ212986","fmin":"2029","fmax":"2257","strand":"+","sequence":"ATGCGTGTTAGTTATAATAAGCTCTGGAAGCTTTTAATTGATAGGGACATGAAAAAAGGCGAGCTTCGTGAGGCTGTTGGAGTAAGTAAAAGCACATTTGCGAAATTGGGCAAGAATGAGAATGTTTCTTTGACTGTTTTGTTAGCAATATGTGAGTATTTGAATTGTGATTTTGGCGATATTATAGAAGCGTTGCCAGAAACCCCCGATAAGGAGCGTGACAGTTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3004253","ARO_id":"41417","ARO_name":"vanUG","ARO_description":"vanUG is a vanG variant found in the vanG gene cluster.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36714":{"category_aro_accession":"3000575","category_aro_cvterm_id":"36714","category_aro_name":"vanU","category_aro_description":"VanU is a transcriptional activator of vancomycin resistance genes.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"842":{"model_id":"842","model_name":"ugd","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"4341":{"protein_sequence":{"accession":"AAC75089.1","sequence":"MKITISGTGYVGLSNGLLIAQNHEVVALDILPSRVAMLNDRISPIVDKEIQQFLQSDKIHFNATLDKNEAYRDADYVIIATPTDYDPKTNYFNTSSVESVIKDVVEINPYAVMVIKSTVPVGFTAAMHKKYRTENIIFSPEFLREGKALYDNLHPSRIVIGERSERAERFAALLQEGAIKQNIPMLFTDSTEAEAIKLFANTYLAMRVAYFNELDSYAESLGLNSRQIIEGVCLDPRIGNHYNNPSFGYGGYCLPKDTKQLLANYQSVPNNLISAIVDANRTRKDFIADAILSRKPQVVGIYRLIMKSGSDNFRASSIQGIMKRIKAKGVEVIIYEPVMKEDSFFNSRLERDLATFKQQADVIISNRMAEELKDVADKVYTRDLFGSD"},"dna_sequence":{"accession":"U00096","fmin":"2098446","fmax":"2099613","strand":"-","sequence":"TTAGTCGCTGCCAAAGAGATCGCGGGTGTATACCTTATCTGCCACATCCTTAAGCTCTTCTGCCATTCGGTTAGAGATAATGACGTCGGCTTGTTGTTTGAAGGTGGCGAGATCACGTTCCAGGCGAGAGTTGAAGAATGAGTCTTCTTTCATCACTGGCTCGTAGATGATCACTTCAACACCTTTCGCCTTGATACGTTTCATAATCCCCTGAATAGAAGACGCACGGAAGTTATCTGAACCGCTCTTCATAATCAGACGATAAATACCCACCACTTGCGGCTTGCGTGACAAAATGGCATCGGCAATAAAATCTTTACGCGTGCGGTTAGCATCGACAATTGCCGAGATCAGGTTATTCGGCACAGACTGGTAGTTCGCCAGTAACTGCTTGGTATCTTTCGGCAGACAATAACCACCATAACCAAACGACGGATTGTTGTAATGGTTGCCAATACGTGGGTCGAGACAAACGCCTTCGATTATTTGACGGGAATTCAGACCTAAACTTTCTGCATAGCTATCCAGTTCGTTAAAGTACGCCACGCGCATCGCCAGGTAGGTGTTTGCAAAAAGTTTAATCGCTTCTGCTTCAGTGGAGTCGGTAAACAGCATCGGGATATTTTGCTTAATCGCGCCTTCCTGTAACAGAGCAGCGAAACGTTCTGCGCGTTCTGAACGCTCACCGATGACAATACGTGAAGGATGGAGATTATCGTAAAGGGCTTTACCCTCACGGAGAAATTCCGGGGAGAATATAATATTTTCAGTGCGATATTTCTTATGCATCGCTGCGGTAAAACCAACGGGAACCGTTGATTTGATGACCATAACCGCATAAGGATTTATCTCAACTACGTCTTTAATTACTGATTCTACACTGGATGTATTGAAATAATTAGTTTTAGGATCATAGTCGGTTGGAGTGGCGATGATGACATAATCAGCATCCCGGTAGGCTTCATTTTTATCTAATGTGGCATTAAAGTGTATTTTATCTGATTGCAAAAACTGCTGAATTTCCTTATCAACAATAGGAGATATCCGATCATTCAGCATAGCAACGCGTGACGGTAAAATATCTAATGCCACAACCTCATGATTTTGTGCGATTAGAAGCCCGTTTGACAAGCCTACATAGCCAGTACCGGAAATGGTGATTTTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3003577","ARO_id":"40187","ARO_name":"ugd","ARO_description":"PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A, which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin","ARO_category":{"41433":{"category_aro_accession":"3004269","category_aro_cvterm_id":"41433","category_aro_name":"pmr phosphoethanolamine transferase","category_aro_description":"This family of phosphoethanolamine transferase catalyze the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine to lipid A, which impedes the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"882":{"model_id":"882","model_name":"RCP-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"3306":{"protein_sequence":{"accession":"CAA33795.1","sequence":"MRFTATVLSRVATGLALGLSMATASLAETPVEALSETVARIEEQLGARVGLSLMETGTGWSWSHREDELFLMNSTVKVPVCGAILARWDAGRLSLSDALPVRKADLVPYAPVTETRVGGNMTLDELCLAAIDMSDNVAANILIGHLGGPEAVTQFFRSVGDPTSRLDRIEPKLNDFASGDERDTTSPAAMSETLRALLLGDVLSPEARGKLAEWMRHGGVTGALLRAEAEDAWLILDKSGSGSHTRNLVAVIQPEGGAPWIATMFISDTDAEFEVRNEALKDLGRAVVAVVRE"},"dna_sequence":{"accession":"X15791","fmin":"1375","fmax":"2257","strand":"+","sequence":"ATGCGGTTCACCGCTACCGTCCTGTCGCGTGTCGCGACAGGGCTCGCTCTCGGCCTGTCCATGGCCACGGCCTCCCTCGCCGAAACGCCTGTCGAGGCGCTCTCCGAAACCGTCGCCCGGATCGAGGAACAGCTCGGCGCCCGCGTCGGCCTCTCGCTCATGGAGACCGGCACGGGTTGGTCCTGGTCTCACCGCGAGGACGAGCTTTTCCTCATGAACAGCACGGTCAAGGTGCCGGTCTGCGGCGCCATCCTCGCGCGTTGGGACGCGGGCAGGCTGTCGCTCTCCGATGCGCTGCCGGTGCGCAAGGCCGACCTCGTGCCCTACGCGCCCGTCACGGAGACGCGGGTCGGCGGCAACATGACCCTCGACGAGCTCTGCCTCGCGGCGATCGACATGAGCGACAATGTGGCGGCGAACATCCTGATCGGGCATCTCGGGGGGCCGGAGGCGGTGACGCAGTTCTTCCGCAGCGTCGGCGACCCGACGAGCCGTCTCGACCGCATCGAGCCCAAGCTGAACGACTTCGCTTCTGGAGACGAGCGGGACACCACGAGCCCGGCCGCCATGTCCGAGACGCTGCGAGCGCTGCTGCTGGGCGACGTGCTGTCTCCGGAGGCCCGCGGGAAGCTGGCGGAGTGGATGCGCCACGGCGGCGTGACCGGCGCATTGCTGCGCGCCGAGGCCGAGGACGCCTGGCTGATCCTCGACAAGTCGGGCAGCGGAAGCCACACGCGCAACCTCGTCGCGGTGATCCAGCCTGAAGGCGGAGCGCCCTGGATCGCGACCATGTTCATCTCGGATACGGACGCGGAGTTCGAGGTTCGCAACGAGGCGCTCAAAGATCTGGGTAGGGCGGTGGTCGCGGTTGTTCGCGAATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40171","NCBI_taxonomy_name":"Rhodobacter capsulatus","NCBI_taxonomy_id":"1061"}}}},"ARO_accession":"3003563","ARO_id":"40170","ARO_name":"RCP-1","ARO_description":"RCP is a class A beta-lactamase found in Rhodopseudomonas capsulata.","ARO_category":{"41399":{"category_aro_accession":"3004235","category_aro_cvterm_id":"41399","category_aro_name":"RCP beta-lactamase","category_aro_description":"A family of class A beta-lactamases that have been discovered in the Rhodobacter genus.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"970":{"model_id":"970","model_name":"OKP-B-18","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1201":{"protein_sequence":{"accession":"CAP12358.1","sequence":"MRYVRLCLISLIAALPLAVFASPQPLEQIKISEGQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKIVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMATTLRKLLTTPSLSARSQQQLLQWMVDDQVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPDGKAERIVVIYLRDTAATMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM850920","fmin":"40","fmax":"901","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCAGCCGCTTGAGCAGATTAAAATCAGCGAAGGTCAGCTGGCGGGCCGGGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGCGACGAACAGCTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGATCGTCGGCGGCCCTGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGAACTCAATGAGGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCGGCCAGCATGGCCACCACCCTGCGCAAGCTGCTAACCACCCCCTCTCTGAGCGCCCGCTCGCAGCAGCAGCTGCTGCAGTGGATGGTTGACGACCAGGTGGCCGGCCCGTTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGTGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAAGCGGAGCGTATCGTGGTGATCTATCTGCGGGATACCGCAGCGACCATGGCCGAACGTAACCAGCAGATCGCCGGGATAGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002451","ARO_id":"38851","ARO_name":"OKP-B-18","ARO_description":"OKP-B-18 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"971":{"model_id":"971","model_name":"cmlA4","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"656":{"protein_sequence":{"accession":"AAF27726.1","sequence":"MRSKNFSWRYSLAATVLLLSPFDLLASLGMDMYLPAVPFMPNALGTTASTVQLTLATYLVMIGAGQLLFGPLSDRLGRRPVLLGGGLAYVVASMGLAFTSLAEVFLGLRILQACGASACLVSTFATVRDIYAGREESNVIYGILGSMLAMVPAVGPLLGALVDMWLGWRAIFAFLGLGMIAASAAAWRFWPETRVQRVTGLQWSQLLLPVKCLNFWLYTLCYAAGMGSFFVFFFIAPGLIMGRQGVSQLGFSLLFATVAIAMVFTARFMGRVIPKWGSPSVLRMGMGCLIAGAVLLAITEIWASQSVLGFIAPMWLVGIGVATAVSVAPNGALQGFDHVAGTVTAVYFCLGGVLLGSIGTLIISLLPRNTAWPVVVYCLTLATVVLGLSCVSRAKGSRGQGEHDVVALQSAESTSNPNR"},"dna_sequence":{"accession":"AF156486","fmin":"3648","fmax":"4908","strand":"+","sequence":"GTGCGCTCAAAAAACTTTAGTTGGCGGTACTCCCTTGCCGCCACGGTGTTGTTGTTATCACCGTTCGATTTGCTGGCATCACTCGGCATGGACATGTACTTGCCGGCAGTGCCTTTTATGCCAAACGCGCTTGGCACGACAGCGAGCACAGTTCAGCTTACGCTGGCAACGTACTTGGTCATGATCGGTGCCGGTCAGCTCTTGTTTGGACCGCTATCGGACCGACTGGGGCGCCGCCCCGTTCTACTGGGAGGTGGCCTCGCCTACGTTGTGGCGTCAATGGGCCTCGCTTTTACGTCATTGGCTGAAGTCTTTCTGGGGCTTCGGATTCTTCAGGCTTGTGGTGCCTCGGCGTGCCTTGTTTCCACGTTTGCAACAGTACGTGACATTTACGCAGGTCGCGAGGAAAGTAACGTCATTTACGGCATACTCGGATCCATGCTGGCCATGGTCCCGGCGGTAGGCCCATTGCTCGGAGCGCTCGTCGACATGTGGCTTGGGTGGCGGGCTATCTTTGCGTTTCTAGGTTTGGGCATGATCGCTGCATCTGCAGCAGCGTGGCGATTCTGGCCAGAAACCCGGGTGCAACGAGTTACGGGCTTGCAATGGTCGCAGCTGCTACTCCCCGTTAAGTGCCTGAACTTCTGGTTGTACACGTTGTGTTACGCCGCTGGAATGGGTAGCTTCTTCGTCTTTTTCTTCATTGCGCCCGGACTAATAATGGGCAGGCAAGGTGTGTCTCAGCTTGGCTTCAGCCTGCTGTTTGCCACAGTGGCAATTGCCATGGTGTTTACGGCTCGTTTTATGGGGCGTGTGATACCCAAGTGGGGCAGCCCAAGTGTCTTGCGAATGGGAATGGGATGCCTGATAGCTGGAGCAGTATTGCTTGCCATCACCGAAATATGGGCTTCGCAGTCCGTGTTAGGCTTTATTGCTCCGATGTGGCTAGTGGGTATTGGTGTCGCCACAGCGGTATCTGTGGCACCCAATGGCGCTCTTCAAGGATTCGACCATGTTGCTGGAACGGTCACGGCAGTTTACTTCTGCTTGGGCGGTGTACTGCTAGGAAGCATCGGAACGTTGATCATTTCGCTGTTGCCGCGCAACACGGCTTGGCCGGTTGTCGTGTACTGTTTGACCCTTGCAACAGTCGTGCTCGGTCTGTCTTGTGTTTCCCGAGCGAAGGGCTCTCGCGGCCAGGGGGAGCATGATGTGGTCGCGCTACAAAGTGCGGAAAGTACGTCAAATCCCAATCGTTGAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002694","ARO_id":"39128","ARO_name":"cmlA4","ARO_description":"cmlA4 is a plasmid-encoded chloramphenicol exporter that is found in Klebsiella pneumoniae","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"972":{"model_id":"972","model_name":"CMY-23","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1115":{"protein_sequence":{"accession":"ABF06441.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAGAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"DQ463751","fmin":"75","fmax":"1221","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGGAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35671","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Senftenberg","NCBI_taxonomy_id":"28150"}}}},"ARO_accession":"3002034","ARO_id":"38434","ARO_name":"CMY-23","ARO_description":"CMY-23 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"973":{"model_id":"973","model_name":"OXA-378","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4373":{"protein_sequence":{"accession":"AHL30278.1","sequence":"MNIQALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQIQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRIGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KF986259","fmin":"16","fmax":"841","strand":"-","sequence":"CTATAAAATACCTAATTGTTCTAAGCTTTTATAAGTAATCTCTTTTCGAACAGAGCTAGGTATTCCTTTTTTCATTTCTAAGTTAAGGGAGAACGCTACAATATTTCCTTGAGGCTGAACAACCCATCCAGTTAACCAGCCTACTTGTGGGTCTACATCCCATCCCCAACCACTTTTTGCGTATATTTTATTTCCATTCTTTTCTTCTATGAATAACATGGATTGCACTTCATCTTGGACTTTTTGGCTAAATGGAAGCGTTTTATTAGCTAGCTTGTAAGCAAACTGTGCCTCTTGCTGAGGAGTAATTTTTAAAGGACCCACCAGCCAAAAATTATCGACTTGGGTACCGATATCTGCATTGCCATAACCAATACGCTTCACTTCATTAGACATGAGTTCAAGTCCAATACGACGAGCTAAATCTTGATAAACCGGAATAGCGGAAGCTTTCATAGCATCGCCTAGGGTCATGTTCTTTTCCCATTCTGGGAATAGCCTTTTTTGCCCGTCCCACTTAAATACTTCTGTAGTGGTTGCCTTATGGTGCTCAAGGCCGATCAAAGCATTAAGCATTTTGAAGGTCGAAGCAGGTACATACTCGGTCGAAGCACGAGCAAGATCATTACCATAGCTTTGTTGAATTTGGCCTTGTTGAATAACTAAAACACCCGTAGTGTGTGCTTCGTTAAATAAATTTTTAATTTTCTCTGCTTTTTCATCAGATTTTGAAGCACTGTGATTTGGATTAGCAGTCACTATATAAGGTGAGCAGGCTGAAATAAAAATAGCGCTTGTTATAAGTAAGAGTGCTTGAATGTTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001564","ARO_id":"37964","ARO_name":"OXA-378","ARO_description":"OXA-378 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"974":{"model_id":"974","model_name":"lmrC","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1050"}},"model_sequences":{"sequence":{"245":{"protein_sequence":{"accession":"ABF66011.1","sequence":"KHKWVALFSIVSTFIYAGVQLYQPQIMKRIMTVMSSTTYSRHQMADKVSGYGVELLVVAGIGIIFAIFSTLSAARIAQEIGADVREATYKKINTFSYENVEKFNAGNLVVRMTNDVTQVQNLMMMVFQILMRIPVLLIGAVVLSITTLPRLWWITVLLIVLIVLVTAVLMGRMGPHFMAFQKLMDRINAIAKQNLRGSRVVKSFVQEKNQIKDFDETSDELYDHNWAVGKLFSAMIPLFTVIAQGAIWLAIYFVSTFVTESTTVAQDSIGGIATFMTYMGMIMFAIIMGGMISMFASRGMVSIGRINEVLNTDPAMKFDENAKDEVLSGSVKFDHVSFSYPNDEEPTLKDISFEVEPGQMVGIVGATGAGKSTLAQLIPRLFDPTEGTVSVGGKDLKTVSRGTLKKNISIVLQKAILFSGTIAGNIKQGKADATDEEMTRAARIAQAAEFITTKDGQYDSEVEERGNNFSGGQKQRLSITRGVVKNPNVLILDDSTSALDAKSEKLVQEALNKDLKDTTTIIIAQKISSVVHADNILVLDQGKLVGQGTHQELVAENKIYQEIYDTQKAQED"},"dna_sequence":{"accession":"DQ516954","fmin":"0","fmax":"1716","strand":"+","sequence":"GAAGCATAAATGGGTTGCCTTATTCTCAATCGTTTCAACCTTTATTTATGCAGGAGTACAGCTTTACCAACCCCAAATCATGAAACGAATTATGACCGTAATGTCATCAACAACTTATAGCCGTCATCAAATGGCTGACAAGGTTTCAGGATATGGAGTTGAGCTTTTGGTTGTTGCTGGGATAGGGATAATTTTTGCTATCTTTAGTACACTTTCAGCGGCACGTATTGCCCAAGAAATTGGAGCAGACGTTCGTGAAGCGACTTACAAAAAAATCAATACATTTTCTTATGAAAATGTTGAAAAGTTCAATGCCGGAAACCTTGTTGTTCGGATGACAAATGACGTCACACAAGTTCAAAACTTGATGATGATGGTTTTCCAAATTTTGATGCGGATTCCAGTCCTTTTGATTGGTGCGGTTGTTCTTTCTATCACAACTCTTCCAAGATTATGGTGGATTACAGTCCTTTTAATTGTTTTAATCGTATTAGTCACAGCCGTTTTAATGGGACGCATGGGCCCTCACTTTATGGCTTTCCAAAAATTGATGGACCGTATTAACGCCATTGCTAAACAAAACTTGCGTGGTTCACGTGTCGTTAAATCATTCGTTCAAGAAAAAAATCAAATCAAAGATTTTGATGAAACTTCTGATGAACTTTACGATCATAACTGGGCAGTAGGAAAACTCTTCTCAGCAATGATTCCACTCTTTACTGTGATTGCTCAAGGAGCAATTTGGCTTGCTATTTACTTTGTTTCAACTTTTGTAACAGAGTCAACAACAGTTGCCCAAGATAGTATTGGTGGGATTGCTACATTCATGACTTATATGGGAATGATTATGTTTGCCATTATCATGGGTGGTATGATTTCAATGTTTGCTTCACGTGGTATGGTATCAATTGGTCGTATTAATGAAGTGTTAAATACTGATCCAGCCATGAAATTTGATGAAAATGCTAAAGATGAAGTTCTTTCAGGTTCTGTCAAATTTGACCATGTGTCATTCTCTTATCCAAATGATGAAGAACCAACACTTAAAGATATTAGCTTTGAAGTAGAACCTGGTCAAATGGTTGGGATTGTCGGAGCGACTGGTGCTGGTAAATCTACATTGGCACAATTGATTCCAAGACTCTTTGACCCAACAGAAGGTACCGTTTCAGTTGGTGGAAAAGATCTTAAAACAGTTAGCCGTGGAACATTGAAGAAAAATATTTCTATTGTTCTTCAAAAAGCCATTCTCTTCTCAGGAACAATTGCTGGAAATATTAAACAGGGGAAAGCCGATGCAACTGATGAAGAAATGACTCGTGCTGCACGCATTGCCCAAGCCGCAGAATTTATTACAACTAAAGATGGTCAATATGATTCTGAAGTTGAAGAACGCGGAAATAACTTCTCAGGTGGTCAAAAGCAAAGACTTTCAATCACACGTGGAGTTGTTAAAAATCCAAATGTCTTAATTTTAGATGACTCAACATCAGCCCTTGATGCTAAATCTGAAAAACTTGTTCAAGAAGCTTTGAATAAAGACCTTAAAGACACAACCACAATTATTATTGCTCAAAAGATTTCATCAGTGGTTCATGCAGATAATATTTTGGTTCTTGACCAAGGAAAACTTGTTGGTCAAGGAACTCACCAAGAATTAGTTGCTGAGAATAAAATTTACCAAGAAATCTACGACACACAGAAAGCACAGGAGGAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39574","NCBI_taxonomy_name":"Lactococcus lactis subsp. lactis","NCBI_taxonomy_id":"1360"}}}},"ARO_accession":"3002881","ARO_id":"39315","ARO_name":"lmrC","ARO_description":"lmrC is a chromosomally-encoded efflux pump that confers resistance to lincosamides in Streptomyces lincolnensis and Lactococcus lactis. It can dimerize with lmrD","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"975":{"model_id":"975","model_name":"QnrB1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"34":{"protein_sequence":{"accession":"ABC86904.1","sequence":"MTPLLYKKTGTNMALALVGEKIDRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNSSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWIGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"DQ351241","fmin":"0","fmax":"681","strand":"+","sequence":"ATGACGCCATTACTGTATAAAAAAACAGGTACAAATATGGCTCTGGCACTCGTTGGCGAAAAAATTGACAGAAACCGTTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCGATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATTCCAGTGCGCTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGCGCAAGCTTTATGAATATGATCACCACGCGCACCTGGTTTTGTAGCGCATATATCACGAATACCAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAGCTGTGGGAAAACCGTTGGATAGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTGACTTAGATATTCGGGGCGTTGATTTACAAGGCGTTAAGTTGGACAACTACCAGGCATCGTTGCTCATGGAGCGACTTGGCATCGCGGTGATTGGTTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002714","ARO_id":"39148","ARO_name":"QnrB1","ARO_description":"QnrB1 is a plasmid-mediated quinolone resistance protein found in Klebsiella pneumoniae","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"976":{"model_id":"976","model_name":"CTX-M-61","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2044":{"protein_sequence":{"accession":"ABN09669.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAVAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVDGTMSLAELSAAALQYSDNVAMNKLISHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"EF219142","fmin":"10","fmax":"886","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGTCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGAAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGTGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACTTGGTTAACTATAATCCGATTGCGGAAAAGCACGTCGATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTTCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGTAATCTGACGCTGGGTAAAGCATTGGGTGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35732","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium","NCBI_taxonomy_id":"90371"}}}},"ARO_accession":"3001922","ARO_id":"38322","ARO_name":"CTX-M-61","ARO_description":"CTX-M-61 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"977":{"model_id":"977","model_name":"OXA-112","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1752":{"protein_sequence":{"accession":"ABV31692.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGEKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFPLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"EF650038","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAATGGGATGGGGAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTCTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCCCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001643","ARO_id":"38043","ARO_name":"OXA-112","ARO_description":"OXA-112 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"978":{"model_id":"978","model_name":"OXA-134","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1922":{"protein_sequence":{"accession":"ADM47435.1","sequence":"MKILIFLPLLSCLGLTACSLPVSSLPSQSISTQAIASLFDQAQSSGVLVIQRDQQVQVYGNDLNRANTEYVPASTFKMLNALIGLQHGKATTNEIFKWDGKKRSFTAWEKDMTLGQAMQASAVPVYQELARRIGLELMQQEVQRIQFGNQQIGQQVDNFWLVGPLKVTPKQEVQFVSALAREQLAFDPQVQQQVKAMLFLQERKAYRLYVKSGWGMDVEPQVGWLTGWVETPQAEIVAFSLNMQMQNGIDPAIRLEILQQALAELGLYPKAEG"},"dna_sequence":{"accession":"HQ122933","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAAAATTTTGATTTTTCTGCCTTTACTGAGTTGCTTGGGCCTGACAGCATGTAGCCTACCCGTTTCATCTCTCCCATCTCAAAGCATTTCGACTCAAGCGATTGCCAGCTTATTTGATCAGGCGCAAAGCTCTGGTGTTTTAGTGATTCAGCGTGATCAACAAGTACAGGTCTATGGCAATGATTTAAATCGTGCAAATACCGAATATGTTCCCGCCTCTACTTTTAAAATGCTCAATGCTCTGATTGGCCTGCAACATGGCAAAGCCACAACCAATGAAATTTTTAAATGGGATGGCAAGAAACGCAGCTTTACCGCCTGGGAAAAAGACATGACGCTCGGCCAAGCCATGCAAGCTTCTGCGGTACCGGTCTATCAAGAGCTGGCGCGTCGTATTGGTCTGGAATTAATGCAACAGGAAGTACAACGCATCCAATTTGGTAATCAGCAGATTGGTCAACAGGTCGATAACTTCTGGTTGGTAGGCCCTTTGAAAGTTACTCCAAAACAGGAAGTCCAATTTGTTTCTGCGTTGGCCCGAGAGCAACTGGCCTTTGATCCTCAAGTCCAGCAACAAGTCAAAGCCATGTTATTTTTACAGGAGCGGAAAGCTTATCGACTATATGTCAAATCCGGTTGGGGCATGGATGTGGAACCGCAAGTCGGCTGGCTCACCGGCTGGGTTGAAACACCGCAGGCTGAAATCGTGGCATTTTCACTCAATATGCAGATGCAAAATGGTATAGATCCGGCGATCCGCCTTGAAATTTTGCAGCAGGCTTTGGCCGAATTAGGGCTTTATCCAAAAGCTGAAGGATGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36948","NCBI_taxonomy_name":"Acinetobacter lwoffii","NCBI_taxonomy_id":"28090"}}}},"ARO_accession":"3001695","ARO_id":"38095","ARO_name":"OXA-134","ARO_description":"OXA-134 is a beta-lactamase found in A. lwoffii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"979":{"model_id":"979","model_name":"TEM-96","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1004":{"protein_sequence":{"accession":"AAM22276.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLGRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AY092401","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGGTCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGGGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000963","ARO_id":"37343","ARO_name":"TEM-96","ARO_description":"TEM-96 is a beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"980":{"model_id":"980","model_name":"y56 beta-lactamase","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"3318":{"protein_sequence":{"accession":"AAX55643.1","sequence":"MKHSSLRRALLLAGITLPLVNFSLPTWAAAIPGSLDKQLAALEHSANGRLGIAMINTGNGTKILYRGARRFPFCSTFKFMLAAAVLGQSQSQPNLLNKHINYHESDLLSYAPITRKNLAHGMTVSELCAATIQYSDNTAANLLLKELGGLAAVNQFARSIGDQMFRLDRWEPDLNTALPNDPRDTTTPAAMAASINKLVLGDALHPAQRSQLTAWLKGNTTGDATIRAGAPTDWIVGDKTGSGDYGTTNDIAVLWPTKGAPIVLVVYFTQREKDAKPRRDVLASATKIILSQIS"},"dna_sequence":{"accession":"AY954728","fmin":"11","fmax":"896","strand":"+","sequence":"ATGAAGCACTCTTCGCTACGGCGTGCGCTATTATTAGCCGGTATTACCCTGCCCTTAGTCAATTTTTCGCTGCCAACCTGGGCCGCTGCGATTCCGGGGTCATTAGACAAGCAATTGGCAGCACTTGAGCACAGTGCTAACGGTCGTTTAGGCATTGCGATGATTAATACCGGCAATGGCACCAAAATTCTGTATCGCGGAGCTCGACGTTTCCCATTCTGTAGTACTTTTAAGTTTATGTTAGCCGCTGCTGTATTGGGTCAAAGCCAATCTCAGCCGAATTTGCTCAATAAGCATATCAATTACCATGAGAGTGATTTGTTATCTTATGCCCCCATCACGCGTAAAAATCTGGCGCATGGTATGACAGTTTCTGAATTATGTGCGGCTACCATTCAATATAGCGATAACACGGCCGCGAATTTATTACTTAAAGAGTTGGGTGGTTTAGCGGCTGTTAATCAGTTTGCTCGCAGTATTGGCGATCAGATGTTCAGGTTAGACCGCTGGGAACCGGATTTAAACACCGCACTACCTAATGACCCACGTGATACCACCACTCCTGCGGCTATGGCAGCTAGTATAAATAAATTGGTATTGGGTGATGCATTGCACCCTGCCCAACGAAGCCAACTCACGGCATGGCTGAAAGGAAACACCACCGGGGATGCCACGATTCGCGCGGGTGCCCCTACTGACTGGATTGTGGGTGACAAAACAGGTAGTGGCGATTACGGAACCACCAATGATATTGCGGTACTTTGGCCGACGAAAGGTGCACCGATTGTTTTAGTGGTGTATTTCACGCAACGTGAAAAAGATGCGAAGCCACGTCGCGATGTATTGGCCTCTGCGACCAAAATAATTTTGTCGCAAATATCCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40164","NCBI_taxonomy_name":"Yersinia enterocolitica","NCBI_taxonomy_id":"630"}}}},"ARO_accession":"3003558","ARO_id":"40163","ARO_name":"y56 beta-lactamase","ARO_description":"Class A beta-lactamase found in Yersinia enterocolitica biovar 1A","ARO_category":{"41354":{"category_aro_accession":"3004190","category_aro_cvterm_id":"41354","category_aro_name":"BlaA beta-lactamase","category_aro_description":"BlaA beta-lactamases are Class A beta-lactamases first identified in Yersinia enterocolitica and have the ability to hydrolize penicilins and cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"981":{"model_id":"981","model_name":"OXA-86","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"895":{"protein_sequence":{"accession":"AAZ78361.1","sequence":"MNIKTLLLITSTIFISACSPYIVTANPNHSTSKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASIEYVPASTFKMLNALIGLEHHKATTTEIFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSLKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"DQ149247","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCACTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCACTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGATCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAATATTTAAGTGGGACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGTGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCTAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001703","ARO_id":"38103","ARO_name":"OXA-86","ARO_description":"OXA-86 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"982":{"model_id":"982","model_name":"TEM-153","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1156":{"protein_sequence":{"accession":"AGA83484.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTTPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTVSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"KC149518","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGTGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001369","ARO_id":"37769","ARO_name":"TEM-153","ARO_description":"TEM-153 is a beta-lactamase found in Enterobacteriaceae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"983":{"model_id":"983","model_name":"GES-20","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1259":{"protein_sequence":{"accession":"AEZ05108.1","sequence":"MRFIHALLLAAIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMSDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"JN596280","fmin":"2847","fmax":"3711","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGCGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGAGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAGT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002349","ARO_id":"38749","ARO_name":"GES-20","ARO_description":"GES-20 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"985":{"model_id":"985","model_name":"ErmA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"554":{"protein_sequence":{"accession":"YP_001315192.1","sequence":"MNQKNPKDTQNFITSKKHVKEILNHTNISKQDNVIEIGSGKGHFTKELVKMSRSVTAIEIDGGLCQVTKEAVNPSENIKVIQTDILKFSFPKHINYKIYGNIPYNISTDIVKRITFESQAKYSYLIVEKGFAKRLQNLQRALGLLLMVEMDIKMLKKVPPLYFHPKPSVDSVLIVLERHQPLISKKDYKKYRSFVYKWVNREYRVLFTKNQFRQALKHANVTNINKLSKEQFLSIFNSYKLFH"},"dna_sequence":{"accession":"NC_009632","fmin":"49744","fmax":"50476","strand":"+","sequence":"ATGAACCAGAAAAACCCTAAAGACACGCAAAATTTTATTACTTCTAAAAAGCATGTAAAAGAAATATTGAATCACACGAATATCAGTAAACAAGACAACGTAATAGAAATCGGATCAGGAAAAGGACATTTTACCAAAGAGCTAGTCAAAATGAGTCGATCAGTTACTGCTATAGAAATTGATGGAGGCTTATGTCAAGTGACTAAAGAAGCGGTAAACCCCTCTGAGAATATAAAAGTGATTCAAACGGATATTCTAAAATTTTCCTTCCCAAAACATATAAACTATAAGATATATGGTAATATTCCTTATAACATCAGTACGGATATTGTCAAAAGAATTACCTTTGAAAGTCAGGCTAAATATAGCTATCTTATCGTTGAGAAGGGATTTGCGAAAAGATTGCAAAATCTGCAACGAGCTTTGGGTTTACTATTAATGGTGGAGATGGATATAAAAATGCTCAAAAAAGTACCACCACTATATTTTCATCCTAAGCCAAGTGTAGACTCTGTATTGATTGTTCTTGAACGACATCAACCATTGATTTCAAAGAAGGACTACAAAAAGTATCGATCTTTTGTTTATAAGTGGGTAAACCGTGAATATCGTGTTCTTTTCACTAAAAACCAATTCCGACAGGCTTTGAAGCATGCAAATGTCACTAATATTAATAAACTATCGAAGGAACAATTTCTTTCTATTTTCAATAGTTACAAATTGTTTCACTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35520","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus JH1","NCBI_taxonomy_id":"359787"}}}},"ARO_accession":"3000347","ARO_id":"36486","ARO_name":"ErmA","ARO_description":"ErmA confers the MLSb phenotype. Similar to ErmC, Expression of ErmA is inducible by erythromycin. The leader peptide causes attenuation of the mRNA and stabilizes the structure preventing further translation. When erythromycin is present, it binds the leader peptide causing a change in conformation allowing for the expression of ErmA.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35946":{"category_aro_accession":"0000027","category_aro_cvterm_id":"35946","category_aro_name":"roxithromycin","category_aro_description":"Roxithromycin is a semi-synthetic, 14-carbon ring macrolide antibiotic derived from erythromycin. It is used to treat respiratory tract, urinary and soft tissue infections. Roxithromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35974":{"category_aro_accession":"0000057","category_aro_cvterm_id":"35974","category_aro_name":"telithromycin","category_aro_description":"Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36315":{"category_aro_accession":"3000176","category_aro_cvterm_id":"36315","category_aro_name":"dirithromycin","category_aro_description":"Dirithromycin is an oxazine derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome to inhibit bacterial protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin 1A is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"vernamycin B-gamma","category_aro_description":"Vernamycin B-gamma is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"986":{"model_id":"986","model_name":"baeS","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"850"}},"model_sequences":{"sequence":{"608":{"protein_sequence":{"accession":"BAA15934.1","sequence":"MKFWRPGITGKLFLAIFATCIVLLISMHWAVRISFERGFIDYIKHGNEQRLQLLSDALGEQYAQHGNWRFLRNNDRFVFQILRSFEHDNSEDKPGPGMPPHGWRTQFWVVDQNNKVLVGPRAPIPPDGTRRPILVNGAEVGAVIASPVERLTRNTDINFDKQQRQTSWLIVALATLLAALATFLLARGLLAPVKRLVDGTHKLAAGDFTTRVTPTSEDELGKLAQDFNQLASTLEKNQQMRRDFMADISHELRTPLAVLRGELEAIQDGVRKFTPETVASLQAEVGTLTKLVDDLHQLSMSDEGALAYQKAPVDLIPLLEVAGGAFRERFASRGLKLQFSLPDSITVFGDRDRLMQLFNNLLENSLRYTDSGGSLQISAGQRDKTVRLTFADSAPGVSDDQLQKLFERFYRTEGSRNRASGGSGLGLAICLNIVEAHNGRIIAAHSPFGGVSITVELPLERDLQREV"},"dna_sequence":{"accession":"AP009048","fmin":"2165012","fmax":"2166416","strand":"+","sequence":"ATGAAGTTCTGGCGACCCGGTATTACCGGCAAACTGTTTCTGGCGATTTTCGCCACCTGCATTGTCTTGCTGATCAGTATGCACTGGGCGGTGCGTATCAGTTTTGAGCGTGGCTTTATTGATTACATCAAGCATGGTAATGAACAGCGATTACAACTGTTAAGTGATGCGCTTGGCGAGCAGTATGCGCAGCATGGCAACTGGCGCTTCCTGCGCAACAATGATCGCTTTGTCTTTCAGATCCTGCGTTCATTTGAACACGATAATTCGGAAGATAAACCCGGCCCGGGTATGCCACCGCACGGCTGGCGTACCCAGTTCTGGGTGGTTGATCAAAACAACAAAGTGCTGGTTGGTCCGCGAGCGCCGATTCCACCTGACGGTACACGGCGACCCATTCTGGTCAACGGTGCGGAAGTTGGCGCGGTGATCGCCTCCCCCGTTGAGCGGTTAACGCGCAATACTGATATCAATTTCGATAAACAACAGCGGCAAACCAGCTGGTTGATTGTCGCCCTGGCAACGTTACTCGCGGCACTTGCCACTTTTCTGCTGGCGCGCGGTTTACTGGCACCGGTAAAACGACTTGTCGATGGCACGCACAAACTGGCGGCGGGCGATTTCACTACCCGCGTAACGCCCACCAGTGAAGATGAACTGGGCAAACTGGCGCAAGACTTCAACCAGCTTGCCAGCACACTGGAGAAAAACCAGCAAATGCGGCGCGATTTTATGGCCGATATTTCTCACGAACTGCGTACGCCATTAGCGGTGCTGCGCGGTGAACTGGAAGCCATTCAGGATGGCGTGCGTAAATTCACGCCGGAGACGGTGGCGTCTTTACAGGCGGAGGTCGGTACACTGACCAAACTGGTTGACGATCTCCATCAGTTGTCGATGTCTGATGAAGGCGCTCTCGCCTATCAAAAAGCACCGGTAGATTTGATCCCACTGCTGGAAGTGGCGGGCGGCGCATTTCGCGAACGATTCGCCAGTCGTGGCCTGAAACTGCAATTTTCCCTGCCAGACAGTATTACCGTATTTGGCGATCGCGACCGTTTAATGCAGTTATTCAATAACTTACTGGAAAACAGCCTGCGCTACACTGACAGCGGCGGCAGCCTGCAAATCTCTGCCGGGCAGCGCGACAAAACGGTGCGCCTGACCTTTGCCGACAGTGCGCCAGGTGTCAGTGACGATCAGCTACAAAAATTGTTTGAACGTTTTTATCGCACCGAAGGTTCCCGCAACCGTGCCAGCGGCGGTTCCGGGCTGGGGCTGGCGATTTGCCTGAACATTGTTGAAGCACATAATGGTCGCATTATTGCTGCCCATTCGCCTTTTGGCGGGGTAAGCATTACAGTAGAGTTACCGCTGGAACGGGATTTACAGAGAGAAGTATGAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36839","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. W3110","NCBI_taxonomy_id":"316407"}}}},"ARO_accession":"3000829","ARO_id":"37209","ARO_name":"baeS","ARO_description":"BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity, BaeS is not necessary for overexpressed BaeR to confer resistance.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"987":{"model_id":"987","model_name":"CTX-M-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1512":{"protein_sequence":{"accession":"CAA74573.1","sequence":"MMTQSIRRSMLTVMATLPLLFSSATLHAQANSVQQQLEALEKSSGGRLGVAQINTADNSQILYVADERFAMCSTSKVMAAAAVLKQSESDKHLLNQRVEIRASDLVNYNPIAEKHVNGTMTLAELGAGALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDRTEPTLNSAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSASIRAGMPKSWGVGDKTGSGDYGTTNDIAVIWPENHAPLVLVTYFTQPEQKAESRRDILAAAAKIVTHGF"},"dna_sequence":{"accession":"Y14156","fmin":"0","fmax":"876","strand":"+","sequence":"ATGATGACTCAGAGCATTCGCCGCTCAATGTTAACGGTGATGGCGACGCTACCCCTGCTATTTAGCAGCGCAACGCTGCATGCGCAGGCGAACAGCGTGCAACAGCAGCTGGAAGCCCTGGAGAAAAGTTCGGGAGGTCGGCTTGGCGTTGCGCAGATTAACACCGCCGATAATTCGCAGATTCTCTACGTGGCCGATGAGCGTTTTGCGATGTGCAGTACCAGTAAGGTGATGGCGGCCGCGGCGGTGCTTAAACAGAGCGAGAGCGATAAGCACCTGCTAAATCAGCGCGTTGAAATCAGAGCAAGCGACCTGGTTAACTACAATCCCATTGCGGAGAAACACGTTAACGGCACGATGACGCTGGCTGAGCTTGGCGCAGGCGCCCTGCAGTATAGCGACAATACTGCCATGAATAAGCTGATTGCCCATCTGGGTGGGCCCGATAAAGTGACGGCGTTTGCTCGCTCGTTGGGTGATGAGACCTTCCGTCTGGACAGAACCGAGCCCACGCTCAATAGCGCCATTCCAGGCGACCCGCGTGATACCACCACGCCGCTCGCGATGGCGCAGACCCTGAAAAATCTGACGCTGGGTAAAGCGCTGGCGGAAACTCAGCGGGCACAGTTGGTGACGTGGCTTAAGGGCAATACTACCGGTAGCGCGAGCATTCGGGCGGGTATGCCGAAATCATGGGGAGTGGGCGATAAAACCGGCAGCGGAGATTATGGCACCACCAACGATATCGCGGTTATCTGGCCGGAAAACCACGCACCGCTGGTTCTGGTGACCTACTTTACCCAACCGGAGCAGAAGGCGGAAAGCCGTCGGGATATTCTGGCTGCGGCGGCGAAAATCGTAACCCACGGTTTCTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35732","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium","NCBI_taxonomy_id":"90371"}}}},"ARO_accession":"3001867","ARO_id":"38267","ARO_name":"CTX-M-4","ARO_description":"CTX-M-4 is a beta-lactamase found in Salmonella typhimurium","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"989":{"model_id":"989","model_name":"ErmG","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"590":{"protein_sequence":{"accession":"AAC37034.1","sequence":"MNKVNIKDSQNFITSKYHIEKIMNCISLDEKDNIFEIGAGKGHFTAELVKRCNFVTAIEIDSKLCEVTRNKLLNYPNYQIVNDDILKFTFPSHNPYKIFGSIPYNISTNIIRKIVFESSATISYLIVEYGFAKMLLDTNRSLALLLMAEVDISILAKIPRYYFHPKPKVDSTLIVLKRKPAKMAFKERKKYETFVMKWVNKEYEKLFTKNQFNKALKHARIYDINNISFEQFVSLFNSYKIFNG"},"dna_sequence":{"accession":"L42817","fmin":"201","fmax":"936","strand":"+","sequence":"ATGAACAAAGTAAATATAAAAGATAGTCAAAATTTTATTACTTCAAAATATCACATAGAAAAAATAATGAATTGCATAAGTTTAGATGAAAAAGATAACATCTTTGAAATAGGTGCAGGGAAAGGTCATTTTACTGCTGAATTGGTAAAGAGATGTAATTTTGTTACGGCGATAGAAATTGATTCTAAATTATGTGAGGTAACTCGTAATAAGCTCTTAAATTATCCTAACTATCAAATAGTAAATGATGATATACTGAAATTTACATTTCCTAGCCACAATCCATATAAAATATTTGGCAGCATACCTTACAACATAAGCACAAATATAATTCGAAAAATTGTTTTTGAAAGTTCAGCCACAATAAGTTATTTAATAGTGGAATATGGTTTTGCTAAAATGTTATTAGATACAAACAGATCACTAGCATTGCTGTTAATGGCAGAGGTAGATATTTCTATATTAGCAAAAATTCCTAGGTATTATTTCCATCCAAAACCTAAAGTGGATAGCACATTAATTGTATTAAAAAGAAAGCCAGCAAAAATGGCATTTAAAGAGAGAAAAAAATATGAAACTTTTGTAATGAAATGGGTTAACAAAGAGTACGAAAAACTGTTTACAAAAAATCAATTTAATAAAGCTTTAAAACATGCGAGAATATATGATATAAACAATATTAGTTTCGAACAATTTGTATCGCTATTTAATAGTTATAAAATATTTAACGGCTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39568","NCBI_taxonomy_name":"Bacteroides thetaiotaomicron","NCBI_taxonomy_id":"818"}}}},"ARO_accession":"3000522","ARO_id":"36661","ARO_name":"ErmG","ARO_description":"ErmG is a rRNA adenine N-6-methyltransferase that protects the ribosome from inactivation due to antibiotic binding.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35946":{"category_aro_accession":"0000027","category_aro_cvterm_id":"35946","category_aro_name":"roxithromycin","category_aro_description":"Roxithromycin is a semi-synthetic, 14-carbon ring macrolide antibiotic derived from erythromycin. It is used to treat respiratory tract, urinary and soft tissue infections. Roxithromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35974":{"category_aro_accession":"0000057","category_aro_cvterm_id":"35974","category_aro_name":"telithromycin","category_aro_description":"Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36315":{"category_aro_accession":"3000176","category_aro_cvterm_id":"36315","category_aro_name":"dirithromycin","category_aro_description":"Dirithromycin is an oxazine derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome to inhibit bacterial protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin 1A is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"vernamycin B-gamma","category_aro_description":"Vernamycin B-gamma is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"990":{"model_id":"990","model_name":"FOX-9","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1515":{"protein_sequence":{"accession":"AEK78851.1","sequence":"MQQRRAFALLTLGSLLLAPCTYASGEAPLTVTVDGIIQPMLKAYRIPGMAVAVLKDGKAHYFNYGVANRESGQRVSEQTLFEIGSVSKTLTATLGAYAAVKGGFELDDKVSQHAPWLKGSAFDGVTMAELATYSAGGLPLQFPEEVDSNDKMRTYYRSWSPVYPAGTHRQYANTSIGLFGYLAANSLGQSFEQLMSQTLLPKLGLHHTYIQVPESAMANYAYGYSKEEKPIRVTPGMLAAEAYGIKTGSADLLKFAEANMGYQGDAAVKSAIALTHTGFYSVGDMTQGLGWESYDYPVTEQVLLADNSPAVSFQANPVTRFAVPKAMGEQRLYNKTGSTGGFGAYVAFVPARGIAIVMLANRNYPIEARVKAAHAILSQLAE"},"dna_sequence":{"accession":"JF896803","fmin":"0","fmax":"1149","strand":"+","sequence":"ATGCAACAACGACGTGCGTTCGCGCTACTGACGCTGGGTAGCCTGCTGTTAGCCCCTTGTACCTATGCCAGCGGGGAGGCCCCGCTGACCGTCACTGTGGACGGCATTATCCAGCCGATGCTCAAGGCGTATCGGATCCCGGGGATGGCGGTCGCCGTACTGAAAGATGGCAAGGCCCACTATTTCAACTATGGGGTTGCCAACCGCGAGAGTGGTCAGCGCGTCAGCGAGCAGACCCTGTTCGAGATTGGCTCGGTCAGCAAAACCCTGACCGCGACCCTTGGCGCTTATGCAGCGGTCAAGGGAGGCTTTGAGCTGGATGACAAGGTGAGCCAGCACGCCCCCTGGCTGAAAGGTTCCGCCTTTGATGGGGTGACCATGGCCGAGCTTGCCACCTACAGTGCGGGTGGTTTGCCGCTGCAGTTCCCCGAAGAGGTGGATTCGAATGACAAGATGCGCACTTACTATCGGAGTTGGTCACCGGTTTATCCGGCGGGGACCCACCGTCAGTACGCCAATACCAGTATCGGTCTGTTCGGCTATCTGGCTGCCAACTCCCTGGGCCAGTCATTTGAGCAACTGATGAGCCAGACCCTGCTGCCCAAGCTGGGTTTGCACCACACCTATATCCAGGTGCCGGAGTCGGCCATGGCGAACTATGCCTACGGCTATTCGAAGGAAGAGAAGCCCATCCGGGTCACTCCGGGCATGCTGGCGGCCGAGGCTTACGGGATCAAGACCGGTTCGGCGGATCTGCTGAAGTTTGCCGAGGCAAACATGGGGTATCAGGGAGATGCCGCGGTAAAAAGCGCGATCGCGCTGACCCACACCGGTTTCTACTCGGTGGGAGACATGACTCAGGGGCTGGGCTGGGAGAGTTACGACTATCCCGTCACCGAGCAGGTGCTGCTGGCGGACAACTCACCAGCGGTGAGCTTCCAGGCCAATCCGGTTACGCGTTTTGCTGTGCCCAAAGCGATGGGCGAGCAGCGGCTCTATAACAAGACGGGCTCGACCGGCGGCTTTGGCGCCTATGTGGCGTTCGTGCCCGCCAGAGGGATAGCCATCGTCATGCTGGCCAATCGCAACTATCCCATCGAGGCCAGGGTGAAGGCGGCTCACGCCATCCTGAGTCAGTTGGCCGAGTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002163","ARO_id":"38563","ARO_name":"FOX-9","ARO_description":"FOX-9 is a beta-lactamase. From the Lahey list of FOX beta-lactamases.","ARO_category":{"36206":{"category_aro_accession":"3000067","category_aro_cvterm_id":"36206","category_aro_name":"FOX beta-lactamase","category_aro_description":"FOX beta-lactamases are plasmid-encoded AmpC-type beta-lactamase which conferred resistance to broad-spectrum cephalosporins and cephamycins","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"991":{"model_id":"991","model_name":"EreA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"183":{"protein_sequence":{"accession":"AAZ91706.1","sequence":"MTWRTTRTLLQPQNLDFNEFEILTSVIEGARIVGIGEGAHFVAEFSLARASLIRYLVERHDFNAIGLECGAIQASRLSEWLNSTAGAHELERFSDTLTFSVYGSVLIWLKSYLRESGRKLQLVGIDLPNTLNPRDDLAQLAEIIQLIDHLMKPHVDMLTHLLASIDGQSAVISSAKWGELETARQEKAISGVTRLKLRLASLAPVLKKHVNSDLFRKASDRIESIEYTLETLRMMKTFFDGTSLEGDTSVRDSYMAGVVDGMVRANPDVKIILLAHNNHLQKTPVSFSGELTAVPMGQHLAERVNYRAIAFTHLGPTVPEMHFPSPDSPLGFSVVTTPADAIREDSMEQYVIDACGTENSCLTLTDAPMEAKRMRSQSASVKTKLSEAFDAIVCVPSAGKDSLVAL"},"dna_sequence":{"accession":"DQ157752","fmin":"2699","fmax":"3920","strand":"+","sequence":"ATGACGTGGAGAACGACCAGAACACTTTTACAGCCTCAAAATCTGGACTTCAATGAGTTTGAGATTCTTACTTCCGTAATTGAGGGCGCCCGAATTGTCGGCATTGGCGAGGGCGCTCATTTTGTCGCGGAGTTTTCACTGGCTAGAGCAAGTCTTATCCGCTATTTGGTCGAAAGGCATGATTTTAATGCGATTGGTTTGGAATGTGGGGCGATTCAGGCATCCCGGTTATCTGAATGGCTCAACTCAACAGCCGGTGCTCATGAACTTGAGCGATTTTCGGATACCCTGACCTTTTCTGTGTATGGCTCAGTGCTGATCTGGCTGAAATCATATCTCCGCGAATCAGGAAGAAAACTGCAGTTAGTCGGAATCGACTTACCCAACACCCTGAACCCAAGGGACGACCTAGCGCAATTGGCCGAAATTATCCAGCTCATCGATCACCTCATGAAACCGCACGTTGATATGCTGACTCACTTGTTGGCGTCCATTGATGGCCAGTCGGCGGTTATTTCATCGGCAAAATGGGGGGAGCTAGAAACGGCTCGGCAGGAGAAAGCTATCTCAGGGGTAACCAGATTGAAGCTCCGCTTGGCGTCGCTTGCCCCTGTACTGAAAAAACACGTCAACAGCGATTTGTTCCGAAAAGCCTCTGATCGAATAGAGTCGATAGAGTATACGTTGGAAACCTTGCGTATGATGAAAACTTTCTTCGATGGTACCTCTCTTGAGGGAGATACTTCCGTACGTGACTCGTATATGGCGGGCGTAGTAGATGGAATGGTTCGAGCGAATCCGGATGTGAAGATAATTCTGCTGGCGCACAACAATCATTTACAAAAAACCCCAGTCTCCTTTTCAGGCGAGCTTACGGCTGTTCCCATGGGGCAGCACCTCGCAGAGAGGGTGAATTACCGTGCGATTGCATTCACCCATCTTGGACCCACCGTGCCGGAAATGCATTTCCCATCGCCCGACAGTCCTCTTGGATTCTCTGTTGTGACCACGCCTGCCGATGCAATCCGTGAGGATAGTATGGAACAGTATGTCATCGACGCCTGTGGTACGGAGAATTCATGTCTGACATTGACAGATGCCCCCATGGAAGCAAAGCGAATGCGGTCTCAAAGCGCCTCTGTAAAAACGAAATTGAGCGAGGCATTTGATGCCATCGTCTGTGTTCCAAGCGCCGGCAAGGACAGCCTAGTTGCCCTATAGG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000361","ARO_id":"36500","ARO_name":"EreA","ARO_description":"EreA is an erythromycin esterase that hydrolyses the drug's lactone ring.","ARO_category":{"36459":{"category_aro_accession":"3000320","category_aro_cvterm_id":"36459","category_aro_name":"macrolide esterase","category_aro_description":"Hydrolytic enzymes that cleave the macrocycle lactone ring of macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35946":{"category_aro_accession":"0000027","category_aro_cvterm_id":"35946","category_aro_name":"roxithromycin","category_aro_description":"Roxithromycin is a semi-synthetic, 14-carbon ring macrolide antibiotic derived from erythromycin. It is used to treat respiratory tract, urinary and soft tissue infections. Roxithromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"992":{"model_id":"992","model_name":"SHV-66","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1150":{"protein_sequence":{"accession":"ABA06588.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADQRFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASKRGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"DQ174306","fmin":"4","fmax":"865","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATCAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCAAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001121","ARO_id":"37501","ARO_name":"SHV-66","ARO_description":"SHV-66 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"993":{"model_id":"993","model_name":"AAC(6')-Ib9","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"463":{"protein_sequence":{"accession":"AAD02244.1","sequence":"MLRSSSRPKTKLGITKYSIVTNSNDSVTLRLMTEHDLAMLYEWLNRSHIVEWWGGEEARPTLADVQEQYLPSVLAQESVTPYIAMLNGEPIGYAQSYVALGSGDGWWEEETDPGVRGIDQSLANASQLGKGLGTKLVRALVELLFNDPEVTKIQTDPSPSNLRAIRCYEKAGFERQGTVTTPDGPAVYMVQTRQAFERTRSDA"},"dna_sequence":{"accession":"AF043381","fmin":"251","fmax":"863","strand":"+","sequence":"ATGTTACGCAGCAGCAGTCGCCCTAAAACAAAGTTAGGCATCACAAAGTACAGCATCGTGACCAACAGCAACGATTCCGTCACACTGCGCCTCATGACTGAGCATGACCTTGCGATGCTCTATGAGTGGCTAAATCGATCTCATATCGTCGAGTGGTGGGGCGGAGAAGAAGCACGCCCGACACTTGCTGACGTACAGGAACAGTACTTGCCAAGCGTTTTAGCGCAAGAGTCCGTCACTCCATACATTGCAATGCTGAATGGAGAGCCGATTGGGTATGCCCAGTCGTACGTTGCTCTTGGAAGCGGGGACGGATGGTGGGAAGAAGAAACCGATCCAGGAGTACGCGGAATAGACCAGTCACTGGCGAATGCATCACAACTGGGCAAAGGCTTGGGAACCAAGCTGGTTCGAGCTCTGGTTGAGTTGCTGTTCAATGATCCCGAGGTCACCAAGATCCAAACGGACCCGTCGCCGAGCAACTTGCGAGCGATCCGATGCTACGAGAAAGCGGGGTTTGAGAGGCAAGGTACCGTAACCACCCCAGATGGTCCAGCCGTGTACATGGTTCAAACACGCCAGGCATTCGAGCGAACACGCAGTGATGCCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002580","ARO_id":"38980","ARO_name":"AAC(6')-Ib9","ARO_description":"AAC(6')-Ib9 is an integron-encoded aminoglycoside acetyltransferase in P. aeruginosa","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"994":{"model_id":"994","model_name":"SHV-77","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"2027":{"protein_sequence":{"accession":"CAJ47132.2","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVALCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM176552","fmin":"30","fmax":"891","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGCGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001131","ARO_id":"37511","ARO_name":"SHV-77","ARO_description":"SHV-77 is a broad-spectrum beta-lactamase found in Klebsiella pneumoniae and E. coli.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"995":{"model_id":"995","model_name":"mexG","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"260"}},"model_sequences":{"sequence":{"138":{"protein_sequence":{"accession":"NP_252894.1","sequence":"MQRFIDNSLESNWLWLTARICLALMFVASGLAKLFDYQASLEEMRAAGLEPAWLFNIATAVTLLAGSALVLLDRKLWLGAGALAVFLLLTILIVHTFWSKTGVEAKLAMFFALEHIAVIGGLIATAIASAQRQRLRQDVSVAATYQKA"},"dna_sequence":{"accession":"NC_002516","fmin":"4705955","fmax":"4706402","strand":"+","sequence":"ATGCAGCGCTTCATCGATAACTCGCTCGAAAGCAACTGGCTCTGGCTGACCGCCCGGATCTGCCTGGCCCTGATGTTCGTCGCCTCGGGACTGGCGAAGCTGTTCGACTATCAGGCCAGCCTGGAGGAAATGCGCGCCGCCGGCCTGGAGCCGGCCTGGCTGTTCAACATCGCCACCGCCGTGACCCTGCTGGCCGGCTCCGCGCTGGTCCTGCTGGACCGCAAGCTATGGCTCGGCGCCGGGGCGCTGGCGGTGTTCCTGCTGCTGACCATCCTCATCGTCCACACCTTCTGGAGCAAGACCGGCGTCGAAGCCAAGCTGGCGATGTTCTTCGCCCTCGAACACATCGCGGTGATCGGCGGCCTGATCGCCACGGCCATCGCCAGCGCGCAACGCCAGCGGCTGCGCCAGGACGTCTCCGTGGCCGCCACCTACCAGAAGGCCTGAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3000806","ARO_id":"37186","ARO_name":"MexG","ARO_description":"MexG is a membrane protein required for MexGHI-OpmD efflux activity.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavin","category_aro_description":"Acriflavin is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36193":{"category_aro_accession":"3000054","category_aro_cvterm_id":"36193","category_aro_name":"acridine dye","category_aro_description":"Acridine dyes are cell permeable, basic molecules with an acridine chromophore. These compounds intercalate DNA. The image shown represents the core structure of the acridine family, with specific dyes containing varying substituents.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"996":{"model_id":"996","model_name":"CMY-77","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1739":{"protein_sequence":{"accession":"AFU25644.1","sequence":"MMKKSLCCALLLTAPLSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADITNNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWAPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKAVHVSPGQLDAEAYGVKSSVIDMARWVQVNMDASRVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"JX440353","fmin":"1026","fmax":"2172","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCCCTTTATCCACGTTTGCCGCCGCCAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCTGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCACCAATAACCACCCAGTCACGCAGCAAACTCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTACACGGCAGGCGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCGTTTTTATCAAAACTGGCAGCCGCAATGGGCCCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACAGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGGCTGTACACGTTTCTCCGGGACAACTTGATGCCGAAGCCTATGGCGTGAAATCCAGTGTTATTGATATGGCCCGCTGGGTTCAGGTCAACATGGACGCCAGCCGCGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCAATCATCAACGGTAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCTGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACTGGAGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39655","NCBI_taxonomy_name":"Citrobacter sp. W1065","NCBI_taxonomy_id":"1236704"}}}},"ARO_accession":"3002090","ARO_id":"38490","ARO_name":"CMY-77","ARO_description":"CMY-77 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"997":{"model_id":"997","model_name":"VIM-31","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1165":{"protein_sequence":{"accession":"AFK24647.1","sequence":"MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIHELSRTSAGNVADADLAEWPTSIERIQQRYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"JN982330","fmin":"245","fmax":"1046","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTCATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACGCTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAGC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3002301","ARO_id":"38701","ARO_name":"VIM-31","ARO_description":"VIM-31 is a beta-lactamase found in Enterobacter cloacae","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"998":{"model_id":"998","model_name":"SHV-134","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1231":{"protein_sequence":{"accession":"ADM25824.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLREIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASKRGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"HM559945","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCGAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCAAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001178","ARO_id":"37558","ARO_name":"SHV-134","ARO_description":"SHV-134 is an extended-spectrum beta-lactamase.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"999":{"model_id":"999","model_name":"LEN-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1580":{"protein_sequence":{"accession":"AAK69830.1","sequence":"MRYVRLCVISLLATLPLAVDAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGVEQLDRRIHYRQQDLVDYSPVSEKHLVDGMTIGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPPGWFIADKTGAGERGARGIVALLGPDGKPERIVVIYLRDTPASMAERNQHIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AY037780","fmin":"88","fmax":"949","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCACCCTGCCACTGGCGGTAGACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCAGGGGTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGTCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTTTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGCCGGGCTGGTTTATCGCCGACAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCAACGCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002455","ARO_id":"38855","ARO_name":"LEN-2","ARO_description":"LEN-2 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1000":{"model_id":"1000","model_name":"AAC(6')-Ib-Hangzhou","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"29":{"protein_sequence":{"accession":"ACL37342.1","sequence":"MTEHDLVMLYEWLNRSHIVEWWGGEEARPTLADVQEQYLPSVLAQESVTPYIAMLNGEPIGYAQSYVALGSGDGWWEEETDPGVRGIDQSLANASQLGKGLGTKLVRALVELLFNDPEVTKIQTDPSPSNLRAIRCYEKAGFERQGTVTTPDGPAVYMVQTRQAFERTRSDA"},"dna_sequence":{"accession":"FJ503047","fmin":"0","fmax":"519","strand":"+","sequence":"ATGACTGAGCATGACCTTGTGATGCTCTATGAGTGGCTAAATCGATCTCATATCGTCGAGTGGTGGGGCGGAGAAGAAGCACGCCCGACACTTGCTGACGTACAGGAACAGTACTTGCCAAGCGTTTTAGCGCAAGAGTCCGTCACTCCATACATTGCAATGCTGAATGGAGAGCCGATTGGGTATGCCCAGTCGTACGTTGCTCTTGGAAGCGGGGACGGATGGTGGGAAGAAGAAACCGATCCAGGAGTACGCGGAATAGACCAGTCACTGGCGAATGCATCACAACTGGGCAAAGGCTTGGGAACCAAGCTGGTTCGAGCTCTGGTTGAGTTGCTGTTCAATGATCCCGAGGTCACCAAGATCCAAACGGACCCGTCGCCGAGCAACTTGCGAGCGATCCGATGCTACGAGAAAGCGGGGTTTGAGAGGCAAGGTACCGTAACCACCCCAGATGGTCCAGCCGTGTACATGGTTCAAACACGCCAGGCATTCGAGCGAACACGCAGTGATGCCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3002592","ARO_id":"38992","ARO_name":"AAC(6')-Ib-Hangzhou","ARO_description":"AAC(6')-Ib-Hangzhou is an aminoglycoside acetyltransferase in A. baumannii","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1002":{"model_id":"1002","model_name":"AAC(6')-Ib4","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"401":{"protein_sequence":{"accession":"AAL38577.1","sequence":"MTNSNDSVTLRLMTEHDLAMLYEWLNRSHIVEWWGGEEARPTLADVQEQYLPSVLAQESVTPYIAMLNGEPIGYAQSYVALGSGDGWWEEETDPGVRGIDQSLANASQLGKGLGTKLVRALVELLFNDPEVTKIQTDPSPSNLRAIRCYEKAGFERQGTVTTPDGPAVYMVQTRQAFERTRSDA"},"dna_sequence":{"accession":"AF445082","fmin":"2788","fmax":"3343","strand":"+","sequence":"GTGACCAACAGCAACGATTCCGTCACACTGCGCCTCATGACTGAGCATGACCTTGCGATGCTCTATGAGTGGCTAAATCGATCTCATATCGTCGAGTGGTGGGGCGGAGAAGAAGCACGCCCGACACTTGCTGACGTACAGGAACAGTACTTGCCAAGCGTTTTAGCGCAAGAGTCCGTCACTCCATACATTGCAATGCTGAATGGAGAGCCGATTGGGTATGCCCAGTCGTACGTTGCTCTTGGAAGCGGGGACGGATGGTGGGAAGAAGAAACCGATCCAGGAGTACGCGGAATAGACCAGTCACTGGCGAATGCATCACAACTGGGCAAAGGCTTGGGAACCAAGCTGGTTCGAGCTCTGGTTGAGTTGCTGTTCAATGATCCCGAGGTCACCAAGATCCAAACGGACCCGTCGCCGAGCAACTTGCGAGCGATCCGATGCTACGAGAAAGCGGGGTTTGAGAGGCAAGGTACCGTAACCACCCCAGATGGTCCAGCCGTGTACATGGTTCAAACACGCCAGGCATTCGAGCGAACACGCAGTGATGCCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3002577","ARO_id":"38977","ARO_name":"AAC(6')-Ib4","ARO_description":"AAC(6')-Ib4 is an aminoglycoside acetyltransferase in Serratia spp.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1003":{"model_id":"1003","model_name":"OXA-18","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1206":{"protein_sequence":{"accession":"AAB58555.1","sequence":"MQRSLSMSGKRHFIFAVSFVISTVCLTFSPANAAQKLSCTLVIDEASGDLLHREGSCDKAFAPMSTFKLPLAIMGYDADILLDATTPRWDYKPEFNGYKSQQKPTDPTIWLKDSIVWYSQELTRRLGESRFSDYVQRFDYGNKDVSGDPGKHNGLTHAWLASSLKISPEEQVRFLRRFLRGELPVSEDALEMTKAVVPHFEAGDWDVQGKTGTGSLSDAKGGKAPIGWFIGWATRDDRRVVFARLTVGARKGEQPAGPAARDEFLNTLPALSENF"},"dna_sequence":{"accession":"U85514","fmin":"149","fmax":"977","strand":"+","sequence":"ATGCAACGGAGCCTGTCCATGAGCGGAAAAAGACATTTCATCTTTGCAGTATCATTTGTTATTTCAACGGTTTGCCTTACGTTCTCCCCGGCAAATGCCGCACAAAAACTGTCCTGCACGCTTGTTATCGACGAGGCGAGCGGCGACCTGCTGCACCGGGAAGGCAGTTGCGACAAGGCTTTTGCGCCGATGTCGACGTTCAAACTGCCTTTGGCCATCATGGGCTACGATGCCGATATCCTGCTCGACGCCACCACGCCGCGCTGGGATTACAAGCCGGAATTCAACGGCTACAAATCGCAGCAGAAGCCGACCGATCCGACCATCTGGCTGAAGGATTCCATCGTCTGGTATTCGCAGGAGCTGACGCGCCGCCTCGGCGAAAGCCGCTTTTCCGATTACGTGCAGCGCTTCGATTACGGCAACAAGGATGTTTCCGGCGATCCCGGCAAGCATAACGGCCTGACCCATGCCTGGCTCGCCTCGTCGCTGAAGATCTCGCCGGAGGAGCAGGTGCGTTTCCTGCGTCGTTTCCTGCGCGGCGAATTGCCGGTCTCCGAGGACGCGTTGGAGATGACGAAAGCCGTCGTGCCGCATTTCGAGGCCGGCGATTGGGACGTGCAGGGCAAGACCGGCACCGGTTCGCTTTCCGATGCCAAGGGCGGCAAGGCGCCGATCGGCTGGTTCATCGGCTGGGCGACACGCGACGACCGCCGCGTCGTCTTCGCCCGCCTAACGGTCGGGGCGAGGAAGGGCGAGCAGCCGGCCGGGCCCGCCGCTCGCGACGAGTTCCTCAACACCCTGCCGGCCCTGTCGGAAAACTTCTGAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001413","ARO_id":"37813","ARO_name":"OXA-18","ARO_description":"OXA-18 is a beta-lactamase found in P. aeruginosa and Rickettsia.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1004":{"model_id":"1004","model_name":"vanRD","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"122":{"protein_sequence":{"accession":"AAM09851.1","sequence":"MNEKILVVDDEKELADLVEVYLKNDGYTVYKFYNGRDALNCIESVELDLAILDIMLPDIDGFQICQKIREKFYFPVIMLTAKVEDGDKIMGLSVADDYITKPFNPLEVVARVKAQLRQYMRYKQPCIKQEAERTEYDIRGMTISKSSHKCILFGKEIQLTPTEFSILWYLCERQGTVVSTEELFEAVWGERYFDSNNTVMAHIGRLREKMKEPSRNPKFIKTVWGVGYTIEK"},"dna_sequence":{"accession":"AY082011","fmin":"0","fmax":"699","strand":"+","sequence":"ATGAATGAAAAAATCTTAGTGGTTGACGATGAAAAAGAGTTGGCCGACTTAGTTGAAGTGTACCTGAAAAACGATGGATATACCGTTTATAAATTTTATAATGGCAGGGACGCATTAAATTGCATTGAATCCGTGGAACTGGATTTAGCCATACTGGATATCATGCTCCCGGATATTGACGGTTTTCAAATCTGCCAGAAAATCCGGGAGAAGTTCTACTTCCCTGTTATCATGCTGACAGCGAAAGTAGAAGATGGGGATAAAATCATGGGGCTGTCCGTTGCAGATGATTATATTACGAAGCCGTTTAATCCGCTGGAAGTGGTTGCGAGGGTAAAGGCACAGCTAAGGCAGTACATGCGGTACAAGCAGCCCTGCATAAAGCAGGAGGCTGAACGCACGGAATACGATATCCGGGGGATGACAATCAGCAAGAGCAGCCATAAGTGTATCTTGTTTGGAAAGGAAATTCAACTGACACCAACGGAATTTTCGATCCTTTGGTATCTGTGCGAGCGTCAGGGAACGGTAGTTTCTACGGAGGAATTATTCGAGGCAGTATGGGGCGAGCGGTATTTTGACAGCAATAATACCGTGATGGCGCATATTGGGCGTCTCAGAGAGAAAATGAAGGAACCGTCAAGAAACCCGAAGTTCATAAAAACCGTGTGGGGAGTTGGATATACCATTGAAAAATAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002923","ARO_id":"39357","ARO_name":"vanRD","ARO_description":"vanRD is a mutated vanR variant found in the vanD gene cluster that caused constitutive expression of vanD peptidoglycan synthesis","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36713":{"category_aro_accession":"3000574","category_aro_cvterm_id":"36713","category_aro_name":"vanR","category_aro_description":"VanR is a OmpR-family transcriptional activator in the VanSR regulatory system. When activated by VanS, it promotes cotranscription of VanA, VanH, and VanX.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1007":{"model_id":"1007","model_name":"OKP-A-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1830":{"protein_sequence":{"accession":"CAJ19606.1","sequence":"MRYVRLCLISLIAALPLAAFASPPPLEQVTRSESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIRYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKSVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMAATLRKLLTSHTLSARSQQQLLQWMVDDQVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPNGKAERIVVIYLRDTPATMAERNQQIARIGAALIEHWQR"},"dna_sequence":{"accession":"AM051147","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGCATTCGCCAGCCCTCCGCCGCTCGAGCAAGTTACACGCAGCGAAAGTCAGCTGGCGGGCCGCGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGAGACGAACAGCTGGATCGGCGGATCCGCTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGAGCGTTGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAGCTCAATGAAGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCAGCCAGCATGGCCGCCACCCTGCGCAAGCTGCTAACCAGCCACACTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGACCAGGTAGCCGGTCCGCTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGCGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGAACGGCAAAGCGGAGCGCATCGTGGTGATCTATCTGCGGGATACGCCGGCGACCATGGCCGAGCGTAACCAGCAGATCGCCAGAATAGGCGCGGCGCTGATCGAGCACTGGCAGCGCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002425","ARO_id":"38825","ARO_name":"OKP-A-8","ARO_description":"OKP-A-8 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1008":{"model_id":"1008","model_name":"BEL-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1193":{"protein_sequence":{"accession":"AAZ04368.1","sequence":"MKLLLYPLLLFLVIPAFAQADFEHAISDLEAHNQAKIGVALVSENGNLIQGYRANERFAMCSTFKLPLAALVLSRIDAGEENPERKLHYDSAFLEEYAPAAKRYVATGYMTVTEAIQSALQLSDNAAANLLLKEVGGPPLLTKYFRSLGDKVSRLDRIEPTLNTNTPGDERDTTTPMSMAQTVSKLIFGDTLTYKSKGQLRRLLIGNQTGDKTIRAGLPDSWVTGDKTGSCANGGRNDVAFFITTAGKKYVLSVYTNAPELQGEERALLIASVAKLARQYVVH"},"dna_sequence":{"accession":"DQ089809","fmin":"1005","fmax":"1857","strand":"+","sequence":"ATGAAACTGCTGCTCTACCCGTTATTGCTGTTCCTTGTCATTCCAGCCTTTGCCCAGGCGGACTTTGAACATGCCATTTCAGATCTTGAGGCGCACAATCAAGCCAAGATCGGAGTGGCCCTAGTTAGTGAAAATGGCAACCTGATTCAAGGGTATCGTGCGAATGAAAGGTTCGCGATGTGCTCAACTTTCAAGTTGCCGTTGGCCGCTCTTGTTCTGAGTCGCATTGACGCTGGGGAAGAGAATCCTGAGCGCAAGCTTCATTACGATTCCGCGTTCCTTGAAGAGTACGCCCCAGCCGCAAAACGGTATGTGGCAACTGGATATATGACTGTAACTGAGGCAATTCAATCCGCCCTCCAACTCAGCGACAATGCCGCAGCTAACCTGCTGTTAAAAGAGGTTGGCGGCCCACCTTTATTGACAAAGTATTTCCGTAGCCTGGGTGATAAAGTAAGTCGCCTTGATCGTATTGAACCGACTTTGAACACCAATACGCCCGGCGATGAAAGAGATACAACAACGCCCATGTCCATGGCACAGACTGTGTCAAAGCTGATTTTTGGAGACACGTTGACATATAAATCCAAGGGGCAGCTAAGGCGATTACTCATCGGCAATCAGACCGGGGACAAAACCATTCGAGCTGGCTTGCCTGATTCATGGGTAACGGGTGACAAGACAGGCTCGTGTGCGAATGGCGGCCGTAACGATGTGGCGTTTTTTATAACCACTGCCGGAAAAAAATATGTTCTTTCTGTATATACCAATGCACCTGAATTGCAAGGCGAGGAAAGGGCGTTATTAATTGCTTCTGTAGCAAAGTTAGCACGTCAATATGTTGTTCACTGAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002385","ARO_id":"38785","ARO_name":"BEL-1","ARO_description":"BEL-1 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"38784":{"category_aro_accession":"3002384","category_aro_cvterm_id":"38784","category_aro_name":"BEL beta-lactamase","category_aro_description":"BEL beta-lactamases are class A expanded-spectrum beta-lactamases that are inhibited by clavulanic acid. They are chromosomally encoded and hydrolyze most cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1009":{"model_id":"1009","model_name":"IND-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1595":{"protein_sequence":{"accession":"AAD20273.1","sequence":"MKKSIRFFIVSILLSPFASAQVKDFVIEPPIKNNLHIYKTFGVFGGKEYSANSMYLVTKKGVVLFDVPWEKIQYQSLMDTIKKRHNLPVVAVFATHSHDDRAGDLSFFNNKGIKTYATAKTNEFLKKDGKATSTEIIKTGKPYRIGGEEFVVDFLGEGHTADNVVVWFPKYNVLDGGCLVKSNSATDLGYIKEANVEQWPKTINKLKAKYSKATLIIPGHDEWKGGGHVEHTLELLNKK"},"dna_sequence":{"accession":"AF099139","fmin":"505","fmax":"1225","strand":"+","sequence":"ATGAAAAAAAGCATCCGTTTTTTTATTGTTTCGATATTGTTGAGCCCTTTTGCAAGTGCACAGGTAAAAGATTTTGTAATAGAACCACCCATCAAAAATAACCTGCATATTTATAAAACTTTTGGAGTATTTGGTGGTAAAGAATATTCTGCAAATTCAATGTATCTGGTTACTAAAAAAGGAGTTGTTCTCTTTGATGTTCCATGGGAAAAAATACAGTACCAAAGCCTCATGGATACCATTAAAAAACGTCATAATTTACCGGTTGTAGCGGTATTTGCCACACACTCCCATGATGACCGCGCCGGTGACCTTAGTTTTTTCAATAATAAAGGGATTAAAACATATGCAACTGCCAAAACCAACGAGTTCTTGAAAAAAGACGGAAAAGCAACATCCACAGAAATCATCAAAACCGGAAAACCGTACCGCATTGGCGGAGAAGAATTTGTGGTAGATTTTCTTGGTGAAGGGCATACTGCTGATAATGTAGTGGTATGGTTCCCTAAATACAATGTATTGGATGGTGGCTGTCTTGTAAAAAGTAATTCAGCTACTGATTTAGGATATATTAAGGAAGCCAATGTAGAACAGTGGCCCAAAACTATAAATAAATTAAAAGCCAAATATTCTAAAGCAACATTAATTATTCCGGGACATGATGAATGGAAAGGCGGTGGACATGTTGAACACACTTTAGAACTTCTGAATAAAAAATAGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36916","NCBI_taxonomy_name":"Chryseobacterium indologenes","NCBI_taxonomy_id":"253"}}}},"ARO_accession":"3002256","ARO_id":"38656","ARO_name":"IND-1","ARO_description":"IND-1 is a beta-lactamase found in Chryseobacterium indologenes","ARO_category":{"36199":{"category_aro_accession":"3000060","category_aro_cvterm_id":"36199","category_aro_name":"IND beta-lactamase","category_aro_description":"IND beta-lactamases are class B carbapenem-hydrolyzing beta-lactamases","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1010":{"model_id":"1010","model_name":"TEM-209","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1001":{"protein_sequence":{"accession":"AGW25367.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLDARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"KF240808","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGATGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001386","ARO_id":"37786","ARO_name":"TEM-209","ARO_description":"From the Lahey list of beta-lactamases. Not yet released.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1011":{"model_id":"1011","model_name":"TEM-29","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2036":{"protein_sequence":{"accession":"CAA76796.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDHWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"Y17584","fmin":"0","fmax":"858","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCATTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000899","ARO_id":"37279","ARO_name":"TEM-29","ARO_description":"TEM-29 is an extended-spectrum beta-lactamase that has been found in clinical isolates.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1012":{"model_id":"1012","model_name":"KPC-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1358":{"protein_sequence":{"accession":"ABY91240.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVRWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"EU400222","fmin":"2159","fmax":"3041","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCGGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002315","ARO_id":"38715","ARO_name":"KPC-5","ARO_description":"KPC-5 is a beta-lactamase found in Klebsiella pneumoniae and Pseudomonas aeruginosa.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1013":{"model_id":"1013","model_name":"APH(2'')-IIIa","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"181":{"protein_sequence":{"accession":"AAB49832.1","sequence":"MKQNKLHYTTMIMTQFPDISIQSVESLGEGFRNYAILVNGDWVFRFPKSQQGADELNKEIQLLPLLVGCVKVNIPQYVYIGKRSDGNPFVGYRKVQGQILGEDGMAVFPDDAKDRLALQLAEFMNELSAFPVETAISAGVPVTNLKNKILLLSEAVEDQVFPLLDESLRDYLTLRFQSYMTHPVYTRYTPRLIHGDLSPDHFLTNLNSRQTPLTGIIDFGDAAISDPDYDYVYLLEDCGELFTRQVMAYRGEVDLDTHIRKVSLFVTFDQVSYLLEGLRARDQDWISEGLELLEEDKANNFGANSA"},"dna_sequence":{"accession":"U51479","fmin":"0","fmax":"921","strand":"+","sequence":"ATGAAACAAAATAAACTTCACTATACCACAATGATAATGACTCAGTTCCCAGATATAAGCATACAATCCGTCGAGTCGCTTGGTGAGGGCTTTAGGAATTACGCGATCCTCGTCAATGGAGATTGGGTTTTTCGTTTTCCCAAGAGTCAACAAGGTGCAGACGAATTGAACAAAGAAATCCAATTGCTACCTCTGTTGGTCGGTTGTGTTAAGGTGAATATTCCACAGTATGTATATATCGGAAAGCGAAGTGATGGAAATCCCTTCGTGGGCTACCGTAAAGTCCAAGGCCAAATCTTGGGTGAAGACGGGATGGCCGTTTTTCCCGATGATGCAAAAGATCGACTGGCGCTGCAACTTGCTGAGTTCATGAATGAGCTAAGCGCATTTCCTGTTGAAACTGCCATATCAGCCGGGGTTCCTGTTACAAACCTGAAAAATAAAATTCTCTTGCTATCGGAAGCTGTGGAGGATCAGGTGTTCCCTCTTCTTGATGAGTCTTTAAGGGACTATCTCACGCTGCGCTTCCAATCCTATATGACTCATCCGGTATATACACGATATACGCCGAGACTAATTCACGGCGATTTGTCACCTGATCATTTTTTGACGAATTTGAATTCACGTCAGACCCCATTAACAGGCATTATCGATTTTGGTGATGCCGCAATAAGTGATCCCGATTATGATTATGTATACCTTTTGGAAGATTGCGGCGAGCTGTTTACTCGGCAAGTGATGGCTTATAGAGGCGAGGTTGACTTGGATACTCACATCAGAAAAGTCTCCTTGTTCGTAACGTTCGATCAAGTCAGTTACCTGTTAGAAGGCTTAAGGGCAAGGGATCAGGACTGGATTTCTGAAGGGTTAGAGCTTTTGGAAGAGGATAAGGCCAACAATTTTGGTGCGAACAGTGCTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36781","NCBI_taxonomy_name":"Enterococcus gallinarum","NCBI_taxonomy_id":"1353"}}}},"ARO_accession":"3002636","ARO_id":"39036","ARO_name":"APH(2'')-IIIa","ARO_description":"APH(2'')-IIIa is a plasmid-encoded aminoglycoside phosphotransferase in Enterococcus gallinarum","ARO_category":{"36267":{"category_aro_accession":"3000128","category_aro_cvterm_id":"36267","category_aro_name":"APH(2'')","category_aro_description":"Phosphorylation of 2-deoxystreptamine aminoglycosides on the hydroxyl group at position 2''","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1014":{"model_id":"1014","model_name":"SHV-25","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1713":{"protein_sequence":{"accession":"AAF37209.2","sequence":"MRYIRLCIISLLAALPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITVSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AF208796","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCGCCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCGTGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001083","ARO_id":"37463","ARO_name":"SHV-25","ARO_description":"SHV-25 is a broad-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1015":{"model_id":"1015","model_name":"evgA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"390"}},"model_sequences":{"sequence":{"208":{"protein_sequence":{"accession":"NP_311275.1","sequence":"MNAIIIDDHPLAIAAIRNLLIKNDIEILAELTEGGSAVQRVETLKPDIVIIDVDIPGVNGIQVLETLRKRQYSGIIIIVSAKNDHFYGKHCADAGANGFVSKKEGMNNIIAAIEAAKNGYCYFPFSLNRFVGSLTSDQQKLDSLSKQEISVMRYILDGKDNNDIAEKMFISNKTVSTYKSRLMEKLECKSLMDLYTFAQRNKIG"},"dna_sequence":{"accession":"NC_002695","fmin":"3211891","fmax":"3212506","strand":"+","sequence":"ATGAACGCAATAATTATTGATGACCATCCTCTTGCTATCGCAGCAATTCGTAATTTATTGATCAAAAACGATATTGAAATCTTAGCAGAGTTGACTGAAGGCGGAAGTGCCGTTCAGCGGGTGGAAACACTTAAGCCTGATATCGTCATCATTGATGTCGATATCCCCGGAGTTAACGGTATCCAGGTGTTAGAAACGCTGAGGAAGCGCCAATATAGCGGAATTATTATTATCGTCTCCGCTAAAAATGACCATTTTTACGGGAAACATTGTGCTGATGCTGGCGCTAATGGTTTCGTGAGTAAAAAAGAAGGCATGAACAATATCATTGCGGCTATTGAAGCTGCAAAAAATGGCTACTGCTATTTCCCCTTCTCTCTCAACCGGTTTGTTGGAAGTTTAACGTCCGACCAGCAAAAACTCGACTCCTTATCGAAACAAGAAATTAGTGTCATGCGGTATATTCTTGATGGCAAGGATAATAATGACATTGCTGAAAAAATGTTCATCAGCAACAAAACTGTCAGCACTTATAAAAGTCGCCTGATGGAAAAATTAGAATGTAAATCACTGATGGATCTTTACACATTCGCACAACGTAACAAAATCGGCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36747","NCBI_taxonomy_name":"Escherichia coli O157:H7 str. Sakai","NCBI_taxonomy_id":"386585"}}}},"ARO_accession":"3000832","ARO_id":"37212","ARO_name":"evgA","ARO_description":"EvgA, when phosphorylated, is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner, it can be phosphorylated in the absence of EvgS when overexpressed.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35930":{"category_aro_accession":"0000011","category_aro_cvterm_id":"35930","category_aro_name":"cloxacillin","category_aro_description":"Cloxacillin is a semisynthetic, isoxazolyl penicillin derivative in the beta-lactam class of antibiotics. It interferes with peptidogylcan synthesis and is commonly used for treating penicillin-resistant Staphylococcus aureus infections.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1016":{"model_id":"1016","model_name":"OXA-255","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1608":{"protein_sequence":{"accession":"AGK07369.1","sequence":"MKKFILPIFSISTLLSLSACSTIQNKFEKTSDISDQQHEKAIKSYFDEAQTQGVIIIKEGKNIRIYGNNLVRAHTEYVPASTFKMLNALIGLENHKATTTEIFKWDGKKRSYPMWEKDMTLGDAMALSAVPVYQELARRTGLDLMQKEVKRVGFGNMSIGTQVNNFWLVGPLKITPIQEANFADDLANNRLPFKLETQEEVKKMLLIKEVNGSKIYAKSGWGMDVTPQVGWLTGWVEKSNGEKVPFSLNLEMKQGMSGSIRNEITYKSLENLGII"},"dna_sequence":{"accession":"KC479325","fmin":"668","fmax":"1496","strand":"+","sequence":"ATGAAAAAATTTATACTTCCTATCTTCAGCATTTCTACTCTACTTTCTCTCAGTGCATGCTCAACTATTCAAAATAAATTTGAAAAAACTTCTGATATTTCTGATCAGCAACATGAAAAAGCCATTAAAAGCTATTTTGATGAAGCTCAAACACAAGGTGTAATAATTATTAAAGAGGGAAAGAATATTAGAATCTATGGTAATAACCTGGTACGAGCACATACAGAATATGTCCCTGCGTCAACATTTAAGATGCTAAATGCCTTAATTGGATTAGAAAATCATAAAGCTACAACAACTGAGATTTTCAAATGGGATGGTAAAAAAAGATCTTATCCTATGTGGGAAAAAGATATGACTTTAGGTGATGCCATGGCACTTTCAGCAGTTCCTGTATATCAAGAACTTGCAAGACGGACTGGCTTAGATCTAATGCAAAAAGAAGTTAAACGGGTTGGTTTTGGTAATATGAGCATCGGGACACAAGTTAATAACTTCTGGTTAGTTGGCCCCCTCAAGATTACACCAATACAAGAGGCTAATTTTGCCGATGATCTTGCGAATAATCGATTACCCTTTAAATTAGAAACTCAAGAAGAAGTAAAAAAAATGCTTCTGATTAAAGAAGTCAATGGTAGTAAAATTTATGCGAAAAGTGGATGGGGAATGGATGTGACCCCTCAAGTAGGTTGGTTAACAGGTTGGGTAGAAAAATCTAATGGCGAAAAAGTTCCCTTTTCTCTAAACCTAGAAATGAAGCAAGGAATGTCTGGTTCTATTCGTAATGAAATTACTTATAAATCATTAGAAAATTTAGGGATTATATAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3001690","ARO_id":"38090","ARO_name":"OXA-255","ARO_description":"OXA-255 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1017":{"model_id":"1017","model_name":"CTX-M-86","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1413":{"protein_sequence":{"accession":"ACI29348.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPFAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"FJ214369","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGTTTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35709","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Agona","NCBI_taxonomy_id":"58095"}}}},"ARO_accession":"3001946","ARO_id":"38346","ARO_name":"CTX-M-86","ARO_description":"CTX-M-86 is a beta-lactamase found in Salmonella enterica","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1018":{"model_id":"1018","model_name":"APH(3')-IIc","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"194":{"protein_sequence":{"accession":"ADQ43421.1","sequence":"MEASNPFTDGLRLPRAWQEALADAHIERQSIGVSRADVARVHRPGQTDAFLKSEVIDAFSELGDEIARLRWLQAQGQSAPTVIATTEEGGRRWLLMSALPGRDLASSPELAPRRVAELLADALRGLHAVPVANCPFDQQLASRLQAAQARVEAGLVDADDFDDERLGQSPQQVFAELRATRPAHEDLVVSQGDACLPNLTVTDGRFTGFIDCGRLGVADRYQDLALAARSLVHNFGESRCVAALFQRYGAVPDERRLAFYRLLDEFF"},"dna_sequence":{"accession":"HQ424460","fmin":"1","fmax":"805","strand":"+","sequence":"ATGGAAGCTTCCAATCCCTTCACTGATGGCCTGCGGCTGCCGCGCGCATGGCAGGAAGCGTTGGCCGATGCGCACATCGAGCGGCAGTCGATCGGCGTGTCGCGCGCGGATGTCGCGCGGGTGCATCGTCCCGGGCAGACCGACGCCTTCCTGAAATCGGAAGTGATCGATGCCTTCAGTGAACTGGGTGATGAGATCGCCCGGCTGCGTTGGCTGCAGGCGCAGGGGCAGTCGGCGCCGACGGTGATTGCCACGACCGAGGAGGGCGGTCGGCGCTGGTTGTTGATGAGCGCGTTGCCCGGCCGCGACTTGGCCTCCTCGCCGGAGCTCGCGCCGAGACGGGTGGCAGAACTGCTGGCTGACGCACTGCGTGGCCTGCATGCCGTGCCTGTAGCCAACTGCCCGTTCGACCAGCAGTTGGCATCGCGCCTGCAGGCCGCACAGGCACGCGTCGAGGCGGGGCTGGTCGATGCCGATGACTTCGACGACGAGCGGCTGGGCCAGAGCCCGCAGCAGGTTTTCGCCGAGCTGCGCGCTACCCGGCCCGCTCATGAAGACCTGGTGGTCAGTCAGGGCGATGCCTGCCTGCCCAACCTGACGGTGACCGATGGGCGGTTCACTGGCTTCATCGATTGTGGCCGGTTGGGCGTGGCCGACCGCTATCAGGACCTGGCCCTGGCCGCGCGCAGCCTGGTCCACAATTTCGGGGAGAGCCGCTGTGTCGCCGCGCTGTTCCAGCGCTACGGTGCGGTCCCTGATGAGCGGCGGCTTGCATTCTATCGGTTGCTTGACGAGTTTTTCTGAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37076","NCBI_taxonomy_name":"Stenotrophomonas maltophilia","NCBI_taxonomy_id":"40324"}}}},"ARO_accession":"3002646","ARO_id":"39046","ARO_name":"APH(3')-IIc","ARO_description":"APH(3')-IIc is a chromosomal-encoded aminoglycoside phosphotransferase in S. maltophilia","ARO_category":{"36265":{"category_aro_accession":"3000126","category_aro_cvterm_id":"36265","category_aro_name":"APH(3')","category_aro_description":"Phosphorylation of 2-deoxystreptamine aminoglycosides on the hydroxyl group at position 3'","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1019":{"model_id":"1019","model_name":"IMP-21","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1867":{"protein_sequence":{"accession":"BAD89802.1","sequence":"MKKLFVLCIFLFCSITAAGASLPDLKIEKLEEGVYVHTSFEEVNGWGVASKHGLVVLVNTDAYLIDTPFTAKDTEKLVNWFVERGYKIKGSISSHFHSDSTGGIEWLNSQSIPTYASVLTNELLKKDGKVQAKNSFSGVSYWLVKNKIEVFYPGPGHTQDNVVVWLPKNKILFGGCFVKPYGLGNLDDANVEAWPHSAEKLISKYGNAKLVVPSHSDIGDASLLKLTWEQAVKGLNESKKSNTVH"},"dna_sequence":{"accession":"AB204557","fmin":"0","fmax":"738","strand":"+","sequence":"ATGAAAAAACTATTTGTTTTATGTATATTTTTGTTTTGTAGCATTACTGCCGCAGGAGCGTCTTTGCCTGATTTAAAAATTGAGAAGCTTGAAGAGGGTGTTTATGTTCATACATCGTTTGAAGAAGTTAACGGCTGGGGTGTTGCTTCTAAACACGGTTTGGTGGTTCTTGTAAATACTGACGCCTATCTGATTGACACTCCATTTACTGCTAAAGATACTGAAAAGTTAGTCAATTGGTTTGTGGAGCGCGGCTATAAAATCAAAGGCAGTATTTCCTCACATTTCCATAGCGACAGCACGGGTGGAATAGAGTGGCTTAATTCTCAATCTATTCCCACGTATGCATCTGTATTAACAAATGAACTTCTCAAAAAAGACGGTAAGGTGCAAGCTAAAAACTCATTTAGCGGAGTTAGCTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCAGGGCACACTCAAGATAACGTAGTGGTTTGGCTACCTAAAAATAAAATCTTATTTGGTGGTTGTTTTGTTAAACCATATGGTCTTGGTAATCTAGATGACGCAAATGTTGAAGCATGGCCACATTCGGCTGAAAAATTAATATCTAAGTATGGTAATGCAAAACTGGTTGTTCCAAGCCATAGTGACATAGGAGATGCGTCGCTCTTGAAGCTTACGTGGGAACAGGCGGTAAAAGGGCTTAATGAAAGCAAAAAAAGTAACACTGTTCATTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002212","ARO_id":"38612","ARO_name":"IMP-21","ARO_description":"IMP-21 is a beta-lactamase found in Pseudomonas and Acinetobacter spp.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1020":{"model_id":"1020","model_name":"OXA-241","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1759":{"protein_sequence":{"accession":"AFO55201.1","sequence":"MNIKALLLITSAIFISACSPYIVIANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLAHASTEYVPASTFKMLNALIGLEHHKTTTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"JX025021","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCCCTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGATTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTCTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCATGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGACAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCATTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001679","ARO_id":"38079","ARO_name":"OXA-241","ARO_description":"OXA-241 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1021":{"model_id":"1021","model_name":"CTX-M-54","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1478":{"protein_sequence":{"accession":"ABC18328.3","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEQTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"DQ303459","fmin":"2174","fmax":"3050","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCAGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001916","ARO_id":"38316","ARO_name":"CTX-M-54","ARO_description":"CTX-M-54 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1022":{"model_id":"1022","model_name":"TEM-28","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1958":{"protein_sequence":{"accession":"AAC32891.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDHWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGKRGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"U37195","fmin":"75","fmax":"936","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCATTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTAAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000898","ARO_id":"37278","ARO_name":"TEM-28","ARO_description":"TEM-28 is an extended-spectrum beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1023":{"model_id":"1023","model_name":"IMP-14","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1985":{"protein_sequence":{"accession":"AAT49068.1","sequence":"MKKLFVLCVFFFCNIAVAEESLPDLKIEKLEEGVYVHTSFEEVKGWSVVTKHGLVVLVKNDAYLIDTPITAKDTEKLVNWFVERGYKIKGSISTHFHGDSTAGIEWLNSQSIPTYASELTNELLKKDNKVQAKHSFNGVSYSLIKNKIEVFYPGPGHTQDNVVVWLPEKKILFGGCFVKPDGLGYLGDANLEAWPKSAKILMSKYGKAKLVVSSHSDIGDVSLLKRTWEQAVKGLNESKKSSQPSD"},"dna_sequence":{"accession":"AY553332","fmin":"113","fmax":"854","strand":"+","sequence":"ATGAAAAAATTATTTGTTTTATGTGTATTCTTCTTCTGCAACATTGCAGTTGCAGAAGAATCTTTGCCTGATTTAAAAATTGAGAAGCTTGAAGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAAAGGTTGGAGTGTGGTCACTAAACACGGTTTGGTGGTTCTTGTGAAAAATGACGCCTATCTGATTGATACTCCAATTACTGCTAAAGATACTGAAAAATTAGTCAATTGGTTTGTTGAGCGGGGCTATAAAATCAAAGGCAGTATTTCAACACATTTCCATGGTGACAGTACGGCTGGAATAGAGTGGCTTAATTCTCAATCTATCCCCACATATGCTTCTGAATTAACAAATGAACTTCTTAAAAAAGACAATAAGGTACAAGCTAAACACTCTTTTAATGGGGTTAGTTATTCACTAATTAAAAACAAAATTGAAGTTTTTTATCCAGGCCCAGGGCACACTCAAGATAACGTAGTGGTTTGGTTACCTGAAAAGAAAATTTTATTCGGTGGTTGCTTTGTTAAACCGGACGGTCTTGGCTATTTGGGGGACGCAAATTTAGAAGCTTGGCCAAAGTCCGCTAAAATATTAATGTCTAAATATGGTAAAGCAAAACTAGTTGTGTCGAGTCATAGTGATATTGGAGATGTATCACTCTTGAAACGTACATGGGAGCAGGCTGTTAAAGGGCTGAATGAAAGTAAAAAATCATCACAGCCAAGCGACTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002205","ARO_id":"38605","ARO_name":"IMP-14","ARO_description":"IMP-14 is a beta-lactamase found in Pseudomonas and Acinetobacter spp.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1024":{"model_id":"1024","model_name":"AAC(6')-Ib-SK","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"360":{"protein_sequence":{"accession":"BAD11815.1","sequence":"MRAHRSCCIRRRGLGHNAGVELNGEKVLLRPVLDSDVKKLDKIVREPEVAAWWSTPDDYEEMLAITLDGEVIGAVQYEEEEDPEFRHAGIDIFLTASRHGLGLGTDTVRTVARWLIDERGHHRITIDPAVANAGAIRSYSKVGFKPVGVMRSYARDHTSGVWQDALLMDLLAEELV"},"dna_sequence":{"accession":"AB164230","fmin":"35","fmax":"566","strand":"+","sequence":"ATGCGGGCACATCGGAGCTGCTGCATCCGCAGGCGCGGGCTCGGGCACAATGCAGGAGTGGAACTGAACGGTGAGAAAGTGCTGCTGCGGCCCGTGCTCGACAGCGATGTGAAGAAGCTCGACAAGATCGTCAGAGAACCCGAGGTGGCCGCTTGGTGGTCGACCCCCGATGACTACGAGGAGATGCTCGCCATCACCCTCGACGGCGAGGTCATCGGGGCAGTGCAGTACGAGGAGGAGGAAGACCCCGAGTTCCGCCACGCGGGCATCGACATCTTCCTCACGGCGAGTCGGCACGGCCTCGGCCTCGGCACGGACACCGTCCGCACCGTGGCACGTTGGCTGATCGACGAGCGGGGACACCACCGGATCACCATCGACCCGGCGGTGGCGAACGCGGGCGCGATCCGCAGCTACAGCAAGGTGGGCTTCAAGCCGGTCGGCGTCATGCGGTCATACGCCCGTGACCACACGAGCGGCGTGTGGCAGGACGCCCTGCTGATGGACCTGCTGGCCGAAGAGCTGGTCTGAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39523","NCBI_taxonomy_name":"Streptomyces kanamyceticus","NCBI_taxonomy_id":"1967"}}}},"ARO_accession":"3002593","ARO_id":"38993","ARO_name":"AAC(6')-Ib-SK","ARO_description":"AAC(6')-Ib-SK is a chromosomal-encoded aminoglycoside acetyltransferase in Streptomyces kanamyceticus","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1025":{"model_id":"1025","model_name":"TEM-136","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1073":{"protein_sequence":{"accession":"AAV83795.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGTGKRGSRGIIAALGPDGKPSRIVVIYTTGGQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AY826417","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAACCGGTAAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGGGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001000","ARO_id":"37380","ARO_name":"TEM-136","ARO_description":"TEM-136 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1026":{"model_id":"1026","model_name":"SHV-74","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1792":{"protein_sequence":{"accession":"CAJ47129.2","sequence":"MRYIRLCIISLLATLPLTVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM176549","fmin":"30","fmax":"891","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGACGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001128","ARO_id":"37508","ARO_name":"SHV-74","ARO_description":"SHV-74 is a broad-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1028":{"model_id":"1028","model_name":"SHV-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1469":{"protein_sequence":{"accession":"ACR66323.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"FJ668814","fmin":"76","fmax":"937","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001059","ARO_id":"37439","ARO_name":"SHV-1","ARO_description":"SHV-1 is a broad-spectrum beta-lactamase found in Klebsiella spp., as well as Acinetobacter spp., E. coli., Raoultella terrigena, and Yersinia pestis.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35975":{"category_aro_accession":"0000058","category_aro_cvterm_id":"35975","category_aro_name":"cefazolin","category_aro_description":"Cefazolin (INN), also known as cefazoline or cephazolin, is a first generation cephalosporin antibiotic. It is administered parenterally, and is active against a broad spectrum of bacteria.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1029":{"model_id":"1029","model_name":"CMY-102","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1360":{"protein_sequence":{"accession":"AHA80103.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNCTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGISLLHLATYTAGGLPLQIPDDVTDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"KF526115","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATTGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTAGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002114","ARO_id":"38514","ARO_name":"CMY-102","ARO_description":"CMY-102 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1030":{"model_id":"1030","model_name":"vanZA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"250"}},"model_sequences":{"sequence":{"3280":{"protein_sequence":{"accession":"AAA65959.1","sequence":"MGKILSRGLLALYLVTLIWLVLFKLQYNILSVFNYHQRSLNLTPFTATGNFREMIDNVIIFIPFGLLLNVNFKEIGFLPKFAFVLVLSLTFEIIQFIFAIGATDITDVITNTVGGFLGLKLYGLSNKHMNQKKLDRVIIFVGILLLVLLLVYRTHLRINYV"},"dna_sequence":{"accession":"M97297","fmin":"10116","fmax":"10601","strand":"+","sequence":"TTGGGAAAAATATTATCTAGAGGATTGCTAGCTTTATATTTAGTGACACTAATCTGGTTAGTGTTATTCAAATTACAATACAATATTTTATCAGTATTTAATTATCATCAAAGAAGTCTTAACTTGACTCCATTTACTGCTACTGGGAATTTCAGAGAGATGATAGATAATGTTATAATCTTTATTCCATTTGGCTTGCTTTTGAATGTCAATTTTAAAGAAATCGGATTTTTACCTAAGTTTGCTTTTGTACTGGTTTTAAGTCTTACTTTTGAAATAATTCAATTTATCTTCGCTATTGGAGCGACAGACATAACAGATGTAATTACAAATACTGTTGGAGGCTTTCTTGGACTGAAATTATATGGTTTAAGCAATAAGCATATGAATCAAAAAAAATTAGACAGAGTTATTATTTTTGTAGGTATACTTTTGCTCGTATTATTGCTCGTTTACCGTACCCATTTAAGAATAAATTACGTGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002962","ARO_id":"39396","ARO_name":"vanZA","ARO_description":"vanZA, also known as vanZ, is a vanZ variant found in the vanA gene cluster","ARO_category":{"36255":{"category_aro_accession":"3000116","category_aro_cvterm_id":"36255","category_aro_name":"vanZ","category_aro_description":"VanZ is a teicoplanin resistance gene that is an accessory protein. VanZ prevents the incorporation of the terminal D-Ala into peptidoglycan subunits.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"35948":{"category_aro_accession":"0000029","category_aro_cvterm_id":"35948","category_aro_name":"teicoplanin","category_aro_description":"Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation  and transpeptidation.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1031":{"model_id":"1031","model_name":"APH(6)-Id","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"467":{"protein_sequence":{"accession":"AAC23556.1","sequence":"MFMPPVFPAHWHVSQPVLIADTFSSLVWKVSLPDGTPAIVKGLKPIEDIADELRGADYLVWRNGRGAVRLLGRENNLMLLEYAGERMLSHIVAEHGDYQATEIAAELMAKLYAASEEPLPSALLPIRDRFAALFQRARDDQNAGCQTDYVHAAIIADQMMSNASELRGLHGDLHHENIMFSSRGWLVIDPVGLVGEVGFGAANMFYDPADRDDLCLDPRRIAQMADAFSRALDVDPRRLLDQAYAYGCLSAAWNADGEQEQRDLAIAAAIKQVRQTSY"},"dna_sequence":{"accession":"AF024602","fmin":"3155","fmax":"3992","strand":"+","sequence":"ATGTTCATGCCGCCTGTTTTTCCTGCTCATTGGCACGTTTCGCAACCTGTTCTCATTGCGGACACCTTTTCCAGCCTCGTTTGGAAAGTTTCATTGCCAGACGGGACTCCTGCAATCGTCAAGGGATTGAAACCTATAGAAGACATTGCTGATGAACTGCGCGGGGCCGACTATCTGGTATGGCGCAATGGGAGGGGAGCAGTCCGGTTGCTCGGTCGTGAGAACAATCTGATGTTGCTCGAATATGCCGGGGAGCGAATGCTCTCTCACATCGTTGCCGAGCACGGCGACTACCAGGCGACCGAAATTGCAGCGGAACTAATGGCGAAGCTGTATGCCGCATCTGAGGAACCCCTGCCTTCTGCCCTTCTCCCGATCCGGGATCGCTTTGCAGCTTTGTTTCAGCGGGCGCGCGATGATCAAAACGCAGGTTGTCAAACTGACTACGTCCACGCGGCGATTATAGCCGATCAAATGATGAGCAATGCCTCGGAACTGCGTGGGCTACATGGCGATCTGCATCATGAAAACATCATGTTCTCCAGTCGCGGCTGGCTGGTGATAGATCCCGTCGGTCTGGTCGGTGAAGTGGGCTTTGGCGCCGCCAATATGTTCTACGATCCGGCTGACAGAGACGACCTTTGTCTCGATCCTAGACGCATTGCACAGATGGCGGACGCATTCTCTCGTGCGCTGGACGTCGATCCGCGTCGCCTGCTCGACCAGGCGTACGCTTATGGGTGCCTTTCCGCAGCTTGGAACGCGGATGGAGAACAGGAGCAACGCGATCTAGCTATCGCGGCCGCGATCAAGCAGGTGCGACAGACGTCATACTAGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002660","ARO_id":"39060","ARO_name":"APH(6)-Id","ARO_description":"APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids, integrative conjugative elements and chromosomal genomic islands in K. pneumoniae, Salmonella spp., E. coli, Shigella flexneri, Providencia alcalifaciens, Pseudomonas spp., V. cholerae, Edwardsiella tarda, Pasteurella multocida and Aeromonas bestiarum","ARO_category":{"36290":{"category_aro_accession":"3000151","category_aro_cvterm_id":"36290","category_aro_name":"APH(6)","category_aro_description":"Phosphorylation of streptomycin on the hydroxyl group at position 6","category_aro_class_name":"AMR Gene Family"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1032":{"model_id":"1032","model_name":"OXA-365","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"976":{"protein_sequence":{"accession":"AHI63011.1","sequence":"MNIKTLLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEMTYKSLEQLGIL"},"dna_sequence":{"accession":"KF885217","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATGACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001552","ARO_id":"37952","ARO_name":"OXA-365","ARO_description":"OXA-365 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1033":{"model_id":"1033","model_name":"vanSN","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"78":{"protein_sequence":{"accession":"AEP40504.1","sequence":"MKNKLNDPLIKRILLRYVSTVLLAIGIYGGVLLLLLFLFRLRTWYGDEPFYLFLRTLYIRFNLIGLVSSGAFLLLLMITLVYIFKLIGYLNETITATKQLLEAPEQRIQLSTELFTVQEEMNQIRENNNQANRAAKVAEQRKNDLIVYLAHDLRTSLTSVIGYLTLLKEEPQISTELRAKYTDIALDKALRLEELIGEFFEVTQFNLTKLTINKEIVDLSIMLEQISYEFLPILNEKGLKWQLAIDKGIKAEVDPNKMGRVFDNLIRNAINYSFSNSTIHLSLEKNGQNLELKITNETHTLPEEKLTQIFEPFYRVDTSRSSSTGGTGLGLSIVKDIVEASGGRIHAQSSNNQMTFTLTLPISE"},"dna_sequence":{"accession":"JF802084","fmin":"5019","fmax":"6114","strand":"+","sequence":"TTGAAAAATAAGTTGAACGATCCTTTGATCAAAAGAATCTTACTAAGATATGTATCAACCGTTCTTCTTGCGATTGGCATTTATGGTGGAGTTTTATTGCTCCTTTTGTTTTTATTCCGTTTACGAACCTGGTATGGCGATGAACCCTTTTATTTATTTTTACGAACTTTGTATATCCGCTTCAATTTGATTGGCCTCGTCTCAAGTGGTGCGTTTCTTCTTTTGCTGATGATTACTCTCGTTTATATTTTCAAACTTATTGGCTACTTGAATGAAACTATTACGGCAACTAAACAATTATTGGAAGCACCTGAACAACGTATCCAACTATCGACCGAGCTATTCACAGTTCAAGAAGAAATGAATCAAATTAGAGAAAATAATAATCAAGCAAACCGTGCAGCGAAAGTAGCAGAACAACGAAAAAATGATCTGATTGTTTACTTAGCACATGATCTGCGTACATCATTAACTAGCGTGATCGGTTATTTGACGTTGTTAAAAGAAGAACCGCAGATCTCCACAGAATTACGAGCAAAATATACGGATATCGCCTTAGACAAAGCGTTACGTTTAGAAGAATTGATTGGTGAGTTTTTTGAAGTCACCCAATTCAATTTGACAAAGCTTACAATAAATAAAGAAATTGTGGATCTAAGTATTATGCTAGAGCAAATCAGCTATGAATTTTTACCAATTCTAAATGAAAAAGGACTTAAATGGCAATTAGCGATTGATAAAGGGATCAAAGCAGAAGTTGATCCAAACAAAATGGGACGAGTTTTTGACAATTTAATCCGTAATGCAATCAATTACAGTTTCTCAAACTCAACGATCCACCTAAGTCTAGAAAAAAATGGACAAAATTTAGAACTCAAAATCACAAACGAAACGCATACCTTACCAGAAGAAAAGCTTACGCAAATTTTCGAACCTTTTTATCGTGTCGATACTTCAAGGAGTAGCAGCACTGGTGGTACAGGACTTGGATTATCGATTGTAAAAGATATCGTGGAAGCATCCGGCGGAAGGATTCATGCTCAAAGTAGCAATAATCAAATGACATTTACGCTTACCTTGCCTATCAGTGAATAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002940","ARO_id":"39374","ARO_name":"vanSN","ARO_description":"vanSN is a vanS variant found in the vanN gene cluster","ARO_category":{"36210":{"category_aro_accession":"3000071","category_aro_cvterm_id":"36210","category_aro_name":"vanS","category_aro_description":"VanS is similar to histidine protein kinases like EnvZ and acts as a response regulator by activating VanR. VanS is required for high level transcription of other van glycopeptide resistance genes.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1034":{"model_id":"1034","model_name":"QnrA7","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"712":{"protein_sequence":{"accession":"ACV83303.2","sequence":"MDIIDKVFQQEDFSRQDLSDSRFRRCRFYQCDFSHCQLRDASFEDCSFIESGAVEGCHFSYADLRDASFKACRLSLANFSGANCFGIEFRECDLKGANFSRARFYNQISHKMYFCSAYISGCNLAYANLSGQCLEKCELFENNWSNANLSGASLMGSDLSHGTFSRDCWQQVNLRGCDLTFADLDGLDPRRVNLEGVKICAWQQEQLLEPLGVIVLPD"},"dna_sequence":{"accession":"GQ463707","fmin":"0","fmax":"657","strand":"+","sequence":"ATGGATATTATTGATAAAGTTTTTCAGCAAGAGGATTTCTCACGCCAGGATTTGAGCGACAGCCGTTTTCGCCGCTGCCGCTTTTATCAGTGTGACTTCAGCCATTGCCAGCTAAGGGATGCCAGTTTCGAGGATTGCAGTTTCATTGAAAGCGGCGCCGTCGAAGGGTGCCACTTCAGCTATGCCGATCTGCGCGATGCCAGTTTCAAGGCCTGCCGCCTGTCTTTGGCCAATTTCAGCGGTGCCAACTGCTTTGGCATAGAGTTCAGGGAGTGCGATCTCAAGGGCGCCAATTTTTCCCGGGCCCGTTTTTACAATCAAATCAGCCATAAGATGTACTTCTGCTCGGCTTATATCTCAGGCTGTAACCTGGCCTATGCCAATTTGAGCGGCCAATGCCTGGAAAAGTGCGAGCTGTTTGAAAACAACTGGAGCAATGCCAACCTCAGCGGCGCTTCCTTGATGGGCTCCGACCTCAGCCACGGCACCTTCTCCCGCGACTGCTGGCAACAGGTAAACCTGCGGGGCTGTGACCTGACCTTTGCCGATCTGGATGGGCTCGACCCCAGACGGGTCAACCTCGAAGGGGTCAAGATCTGTGCCTGGCAGCAGGAGCAACTGCTGGAACCCTTGGGAGTCATAGTGCTGCCGGATTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36891","NCBI_taxonomy_name":"Shewanella algae","NCBI_taxonomy_id":"38313"}}}},"ARO_accession":"3002713","ARO_id":"39147","ARO_name":"QnrA7","ARO_description":"QnrA7 is a plasmid-mediated quinolone resistance protein found in Shewanella algae","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1036":{"model_id":"1036","model_name":"vanWB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"3455":{"protein_sequence":{"accession":"AAB05625.1","sequence":"MNRKRLTQRFPFLLPMRQAQRKICFYAGMRFDGCCYAQTIGEKTLPYLLFETDCALYNHNTGFDMIYQENKVFNLKLAAKTLNGLLIKPGETFSFWRLVRHADKDTPYKDGLTVANGKLTTMSGGGMCQMSNLLFWVFLHTPLTIIQRSGHVVKEFPEPNSDEIKGVDATISEGWIDLKVRNDTDCTYQIWVTLDDEKIIGQVFADKQPQALYKIANGSIQYVRESGGIYEYAKVERMQVALGTGEIIDCKLLYTNKCKICYPLPESVDIQEANQ"},"dna_sequence":{"accession":"U35369","fmin":"3182","fmax":"4010","strand":"+","sequence":"ATGAACAGAAAAAGATTGACACAGCGCTTCCCGTTCCTGCTTCCAATGAGACAAGCGCAGAGAAAAATATGCTTTTATGCGGGAATGAGATTTGACGGCTGTTGCTATGCACAGACGATAGGAGAAAAAACGCTTCCCTATTTGCTCTTTGAAACGGATTGTGCGTTATACAACCACAATACCGGATTTGACATGATATACCAAGAAAACAAGGTGTTCAACTTAAAGCTGGCGGCAAAGACCTTAAACGGCCTATTGATAAAACCGGGGGAAACCTTTTCTTTCTGGCGGCTGGTACGCCATGCGGACAAAGATACCCCCTATAAAGACGGCCTTACGGTGGCCAATGGTAAGCTCACCACCATGTCGGGCGGCGGTATGTGCCAGATGAGCAATTTACTATTTTGGGTGTTCCTGCATACGCCATTGACAATTATCCAGCGCAGCGGTCACGTAGTAAAGGAGTTTCCAGAGCCAAACAGTGACGAGATCAAAGGGGTGGATGCAACCATCTCAGAGGGCTGGATTGATTTAAAAGTGCGAAACGATACCGACTGCACCTACCAAATATGGGTGACCCTAGATGATGAGAAAATCATCGGTCAGGTGTTCGCCGACAAACAGCCTCAAGCATTATACAAAATTGCAAACGGCAGTATTCAGTATGTCCGTGAAAGTGGCGGGATTTATGAATATGCCAAGGTTGAACGGATGCAAGTTGCCTTAGGTACCGGGGAAATAATAGATTGCAAGCTGCTTTATACAAACAAATGCAAAATCTGCTATCCCCTCCCGGAAAGTGTGGATATTCAGGAGGCGAACCAATGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3002964","ARO_id":"39398","ARO_name":"vanWB","ARO_description":"vanWB, also known as vanW, is a vanW variant found in the vanB gene cluster","ARO_category":{"36011":{"category_aro_accession":"3000002","category_aro_cvterm_id":"36011","category_aro_name":"vanW","category_aro_description":"vanW is an accessory gene, with unknown function, found on vancomycin resistance operons.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1037":{"model_id":"1037","model_name":"cmlA1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"617":{"protein_sequence":{"accession":"AAO15535.1","sequence":"MRSKNFSWRYSLAATVLLLSPFDLLASLGMDMYLPAVPFMPNALGTTASTIQLTLTTYLVMIGAGQLLFGPLSDRLGRRPVLLGGGLAYVVASMGLALTSSAEVFLGLRILQACGASACLVSTFATVRDIYAGREESNVIYGILGSMLAMVPAVGPLLGALVDMWLGWRAIFAFLGLGMIAASAAAWRFWPETRVQRVAGLQWSQLLLPVKCLNFWLYTLCYAAGMGSFFVFFSIAPGLMMGRQGVSQLGFSLLFATVAIAMVFTARFMGRVIPKWGSPSVLRMGMGCLIAGAVLLAITEIWASQSVLGFISPMWLVGIGVATAVSVAPNGALRGFDHVAGTVTAVYFCLGGVLLGSIGTLIISLLPRNTAWPVVVYCLTLATVVLGLSCVSRAEGSRGQGEHDVVALQSAESTSNPNR"},"dna_sequence":{"accession":"AF458080","fmin":"1504","fmax":"2764","strand":"+","sequence":"GTGCGCTCAAAAAATTTTAGTTGGCGGTACTCCCTTGCCGCCACGGTGTTGTTGTTATCACCGTTCGATTTATTGGCATCACTCGGCATGGACATGTACTTGCCGGCAGTGCCGTTTATGCCAAACGCGCTTGGTACGACAGCGAGCACAATTCAGCTTACGCTGACAACGTACTTGGTCATGATTGGTGCCGGTCAGCTCTTGTTTGGACCGCTATCGGACCGACTGGGGCGCCGCCCCGTTCTACTGGGAGGTGGCCTCGCCTACGTTGTGGCGTCAATGGGCCTCGCTCTTACGTCATCGGCTGAAGTCTTTCTGGGGCTTCGGATTCTTCAGGCTTGTGGTGCCTCGGCGTGCCTTGTTTCCACGTTTGCAACAGTACGTGACATTTACGCAGGTCGCGAGGAAAGTAATGTCATTTACGGCATACTCGGATCCATGCTGGCCATGGTCCCGGCGGTAGGCCCATTGCTCGGAGCGCTCGTCGACATGTGGCTTGGGTGGCGGGCTATCTTTGCGTTTCTAGGTTTGGGCATGATCGCTGCATCTGCAGCAGCGTGGCGATTCTGGCCTGAAACCCGGGTGCAACGAGTTGCGGGCTTGCAATGGTCGCAGCTGCTACTCCCCGTTAAGTGCCTGAACTTCTGGTTGTACACGTTGTGTTACGCCGCTGGAATGGGTAGCTTCTTCGTCTTTTTCTCCATTGCGCCCGGACTAATGATGGGCAGGCAAGGTGTGTCTCAGCTTGGCTTCAGCCTGCTGTTCGCCACAGTGGCAATTGCCATGGTGTTTACAGCTCGTTTTATGGGGCGTGTAATACCCAAGTGGGGCAGCCCAAGCGTCTTGCGAATGGGAATGGGATGCCTGATAGCTGGAGCAGTATTGCTTGCCATCACCGAAATATGGGCTTCGCAGTCCGTGTTAGGCTTTATTTCTCCAATGTGGCTAGTGGGTATTGGTGTCGCCACAGCGGTATCTGTGGCGCCCAATGGCGCTCTTCGAGGATTCGACCATGTTGCTGGAACGGTCACGGCAGTCTACTTCTGCTTGGGCGGTGTACTGCTAGGAAGCATCGGAACGTTGATCATTTCGCTGTTGCCGCGCAACACGGCTTGGCCGGTTGTCGTGTACTGTTTGACCCTTGCAACAGTCGTGCTCGGTCTGTCTTGTGTTTCCCGAGCGGAGGGCTCTCGCGGCCAGGGGGAGCATGATGTGGTCGCGCTACAAAGTGCGGAAAGTACGTCAAATCCCAATCGTTGAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002693","ARO_id":"39127","ARO_name":"cmlA1","ARO_description":"cmlA1 is a plasmid or transposon-encoded chloramphenicol exporter that is found in Pseudomonas aeruginosa and Klebsiella pneumoniae","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1038":{"model_id":"1038","model_name":"cmlB1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"731":{"protein_sequence":{"accession":"CAL30186.1","sequence":"MRSKDFSWRYSLAATLLLLSPFDLLASLGMDMYLPVVPFMAGALGAGAGTIQLTLTVYLVLLGAGQLLFGPLSDLLGRRPVLLGGGITYILASFGLAAASSPEVFLSFRILQACGASACLVSTFATVRDIYSGSEESNVIYGLLGSMLAMVPAIGPLLGALVDAWLGWRAIFGLLGIAMIGAVTAAWRFWPETRRQRTADLQWSQLLLPVKCLNFWLYTLCYSAGMGSFFVFFSTAPWLMMGRQALSQLSFSLLFATVAIAMMATARIMGRLIPRWGSLNTLRVGMGCLVVGALLLAVGETLIPNSVLGFIAPMWLVGVGIATAASVAPNGALRGFDHIAGTATAVYFCLGGLLLGGIGTFIIALLPSDTTWPIIAYCLILAIAVLCLSCFNPNRHHPSDDEHDSLATQDIGRSQSGHGHD"},"dna_sequence":{"accession":"AM296481","fmin":"775","fmax":"2041","strand":"+","sequence":"GTGCGCTCTAAAGATTTTTCTTGGCGGTATTCTCTTGCCGCCACGCTATTACTGTTATCACCATTCGACTTGTTGGCATCACTCGGCATGGATATGTATCTGCCTGTGGTGCCTTTCATGGCCGGTGCACTCGGTGCCGGTGCAGGGACGATCCAGCTGACGTTGACGGTATACCTGGTTTTGCTTGGAGCCGGTCAGCTTCTCTTTGGCCCGTTATCGGATCTGCTGGGGCGCCGCCCGGTATTACTCGGTGGTGGAATTACCTATATTTTGGCTTCATTCGGACTCGCCGCAGCTTCATCACCAGAAGTTTTCCTGAGCTTCCGTATTCTTCAAGCCTGCGGTGCTTCGGCATGTCTCGTGTCCACTTTCGCGACCGTACGCGACATATATTCGGGCAGCGAGGAAAGCAACGTTATCTATGGCTTGCTCGGCTCTATGCTTGCGATGGTTCCAGCAATAGGCCCATTGTTAGGAGCGCTGGTCGACGCTTGGCTGGGGTGGCGAGCAATCTTTGGTTTGCTGGGAATCGCAATGATAGGTGCTGTTACCGCAGCTTGGCGATTCTGGCCCGAGACCCGGCGGCAGCGAACGGCAGATTTACAGTGGTCACAGCTATTGCTTCCTGTGAAATGCCTGAACTTCTGGCTGTACACCCTCTGCTACAGCGCGGGAATGGGCAGTTTCTTTGTCTTCTTCTCGACTGCCCCTTGGCTAATGATGGGCAGGCAAGCGTTATCGCAACTTAGCTTCAGCTTGCTGTTTGCGACAGTGGCCATCGCGATGATGGCTACAGCGCGGATCATGGGACGGCTGATTCCCCGATGGGGAAGCCTGAACACTTTACGAGTTGGAATGGGTTGCCTAGTGGTCGGGGCACTGTTGCTTGCTGTCGGCGAGACACTCATACCAAACTCGGTGCTTGGCTTCATCGCCCCAATGTGGCTCGTCGGTGTTGGCATTGCCACTGCGGCCTCGGTGGCACCCAATGGTGCACTTCGAGGGTTTGATCACATCGCTGGAACCGCCACAGCAGTCTACTTCTGCTTGGGTGGGTTACTGCTAGGTGGTATCGGTACTTTCATCATTGCACTTTTACCAAGTGATACCACATGGCCGATCATTGCTTATTGCCTAATCCTCGCAATAGCAGTGCTTTGTCTATCCTGCTTCAACCCCAACAGGCACCATCCCAGCGATGACGAGCATGATTCGCTTGCGACGCAAGACATCGGCCGCTCGCAATCGGGCCATGGTCATGATTAGC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36800","NCBI_taxonomy_name":"Bordetella bronchiseptica","NCBI_taxonomy_id":"518"}}}},"ARO_accession":"3002699","ARO_id":"39133","ARO_name":"cmlB1","ARO_description":"cmlB1 is a plasmid-encoded chloramphenicol exporter that is found in Bordetella bronchiseptica","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1039":{"model_id":"1039","model_name":"dfrB3","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"392":{"protein_sequence":{"accession":"ACR57831.1","sequence":"MDQHNNGVSTLVAGQFALPSHATFGLGDRVRKKSGAAWQGQVVGWYCTKLTPEGYAVESESHPGSVQIYPVAALERVA"},"dna_sequence":{"accession":"GQ150744","fmin":"122","fmax":"359","strand":"+","sequence":"ATGGACCAACACAACAATGGAGTCAGTACTCTAGTTGCTGGCCAGTTTGCGCTCCCATCGCACGCCACGTTTGGCCTGGGAGATCGCGTGCGCAAGAAATCTGGCGCCGCTTGGCAGGGTCAAGTTGTCGGGTGGTACTGCACAAAACTGACCCCTGAAGGCTATGCCGTCGAGTCCGAGTCTCACCCCGGTTCAGTACAGATTTATCCTGTGGCTGCGCTTGAACGCGTGGCCTGAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3003022","ARO_id":"39456","ARO_name":"dfrB3","ARO_description":"dfrB3 is an integron-encoded dihydrofolate reductase found in Klebsiella oxytoca","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36408":{"category_aro_accession":"3000269","category_aro_cvterm_id":"36408","category_aro_name":"brodimoprim","category_aro_description":"Brodimoprim is a structural derivative of trimethoprim and an inhibitor of bacterial dihydrofolate reductase. The 4-methoxy group of trimethoprim is replaced with a bromine atom.","category_aro_class_name":"Antibiotic"},"36423":{"category_aro_accession":"3000284","category_aro_cvterm_id":"36423","category_aro_name":"tetroxoprim","category_aro_description":"Tetroxoprim is a trimethoprim derivative that inhibits bacterial dihydrofolate reductase.","category_aro_class_name":"Antibiotic"},"36476":{"category_aro_accession":"3000337","category_aro_cvterm_id":"36476","category_aro_name":"iclaprim","category_aro_description":"Iclaprim is a bactericidal compound that inhibits dihydrofolate reductase. It is used against clinically important Gram-positive pathogens, including methicillin-sensitive Staphylococcus aureus and methicillin-resistant S. aureus.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1040":{"model_id":"1040","model_name":"OXA-95","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1539":{"protein_sequence":{"accession":"ABF47918.1","sequence":"MNIKALFLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"DQ519089","fmin":"8","fmax":"833","strand":"+","sequence":"ATGAACATTAAAGCACTCTTCCTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001630","ARO_id":"38030","ARO_name":"OXA-95","ARO_description":"OXA-95 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1043":{"model_id":"1043","model_name":"SHV-76","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1949":{"protein_sequence":{"accession":"CAJ47131.2","sequence":"MRYIRLCIISLLAALPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVEDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM176551","fmin":"30","fmax":"891","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCGCCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGTGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGAAGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATCGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001130","ARO_id":"37510","ARO_name":"SHV-76","ARO_description":"SHV-76 is a broad-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1044":{"model_id":"1044","model_name":"CTX-M-22","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1334":{"protein_sequence":{"accession":"AAL86924.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTNGL"},"dna_sequence":{"accession":"AY080894","fmin":"3","fmax":"879","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCAACGGTTTGTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001884","ARO_id":"38284","ARO_name":"CTX-M-22","ARO_description":"CTX-M-22 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1045":{"model_id":"1045","model_name":"ErmO","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"549":{"protein_sequence":{"accession":"CAA11706.1","sequence":"MARPTQRARTLSQNFLADRAAAAHVARLTAPDRRHPPLVLEVGAGKGALTEPLARRSRELHAYEIDSRLVPGLRTRFAAAPHVRVVAGDFLAARPPRTPFSVAGNVPFSRTADIVDWCLGAPALTDATLITQLEYARKRTGDYGRWTLLTVRTWPHHEWRLVGRVSRYGFRPAPRVDAGVLRIERRATPLLTGAAQHGWRDLVELGFSGVGGSLHASLRRAHPRRRVDAAFRAARLDPGVLVGEVAPARWLRLHEELAS"},"dna_sequence":{"accession":"AJ223970","fmin":"20","fmax":"800","strand":"+","sequence":"ATGGCCCGCCCCACCCAGCGTGCGCGCACGCTCTCGCAGAACTTCCTCGCCGACCGCGCCGCCGCCGCACACGTCGCCCGGCTGACCGCCCCCGACCGTCGGCACCCGCCGCTCGTCCTGGAAGTGGGCGCCGGCAAGGGCGCCCTCACCGAGCCGCTCGCCCGCCGCAGCCGGGAGCTGCACGCCTACGAGATCGACTCCAGGCTCGTCCCCGGGCTGCGCACCCGTTTCGCCGCCGCACCCCATGTCCGCGTGGTCGCCGGTGACTTCCTCGCCGCGCGGCCTCCGCGCACGCCGTTCTCCGTCGCCGGGAACGTGCCCTTCTCCCGCACGGCGGACATCGTCGACTGGTGCCTCGGCGCGCCGGCCCTCACCGACGCCACCCTGATCACCCAGCTCGAGTACGCACGCAAACGCACCGGCGACTACGGCCGTTGGACCCTGCTGACGGTACGGACCTGGCCCCACCACGAGTGGCGCCTGGTGGGACGCGTGAGCCGCTACGGCTTCCGGCCGGCGCCCCGCGTCGACGCGGGCGTCCTCCGTATCGAGCGCCGCGCCACCCCGCTGCTCACCGGTGCCGCCCAGCACGGCTGGCGGGACCTGGTCGAGCTGGGCTTCTCCGGAGTCGGCGGCTCGCTGCACGCGTCCCTGCGCCGGGCACACCCCAGGCGCCGGGTGGACGCGGCGTTCCGGGCGGCCCGGCTGGACCCCGGGGTGCTCGTCGGCGAGGTGGCGCCGGCGCGGTGGCTGCGGCTGCACGAGGAGCTGGCGTCGTGAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36864","NCBI_taxonomy_name":"Streptomyces ambofaciens","NCBI_taxonomy_id":"1889"}}}},"ARO_accession":"3001303","ARO_id":"37702","ARO_name":"ErmO","ARO_description":"ErmO is a methyltransferase found in the spiramycin producer Streptomyces ambofaciens. Like other Erm enzymes, it catalyzes the methylation of A2058 of the 23S ribosomal RNA. Specifically, this enzyme transfers only one methyl group. The gene is responsible for self-resistance to spiramycin.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1046":{"model_id":"1046","model_name":"vgaD","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1020"}},"model_sequences":{"sequence":{"519":{"protein_sequence":{"accession":"ACX92986.2","sequence":"MLILEANHIEKSINDRKLLDVTHLQIHYEDRIGVVGRNGSGKTTLLSILAGEIEADKGEVKTSASRYFLPQLKETDTFRSGGEITKSYIDKALAMKAEILFADEPTTNLDTHNIKELEKHFSRYRGAIILVSHNRYFLDQICTKIWEIEDGEVKEIHGNYTSYVKQKELLRRQQQEEYEKYITKKKQLERAVTMKEQKAQKMIKPPSKQMGTSESRIWKMQHATKQKKMHQNIKALETRVEKLERVKKPKDYPAVKMKLSNQDQIQGRNVLRVKDLSVSFGNHVLWTDASFTIKGGEKAAIIGNNGVGKTTLLKQILERVPAVTISPAAKIGYFSQNLDTLDTHVSILENVMSTAIQDETTVRTVLARLHFYREDVYKEVQVLSGGERVKVAFAKLFVSDYNTLILDEPTNYLDIDAIEALEELLINYEGAVLFVSHDCRFVQNIASKIIELSDQKVIEFLGSYKAFRERSQETERDYMKEELLKIEIKLTQMISEMNDEASNELEKEFQMLIHERNQLRNQVNN"},"dna_sequence":{"accession":"GQ205627","fmin":"1393","fmax":"2971","strand":"+","sequence":"ATGCTCATTCTTGAAGCGAATCATATTGAAAAATCTATAAATGACCGGAAACTTTTAGATGTTACTCATCTACAAATTCATTATGAGGATCGGATTGGTGTAGTTGGTCGTAATGGAAGCGGGAAAACGACATTATTATCTATATTGGCTGGTGAAATAGAAGCAGATAAAGGTGAAGTGAAAACAAGTGCAAGTCGCTACTTTTTACCTCAATTGAAGGAGACGGATACTTTCAGAAGTGGTGGTGAGATAACAAAAAGCTATATTGACAAAGCATTAGCGATGAAGGCGGAAATATTGTTTGCCGACGAACCAACTACAAACCTTGATACCCACAATATAAAAGAACTTGAAAAGCATTTCAGTCGATATCGGGGGGCAATCATTCTTGTATCACATAACCGGTATTTTTTAGATCAAATTTGTACAAAAATATGGGAAATTGAAGATGGAGAAGTGAAAGAAATTCACGGTAACTATACAAGTTATGTAAAACAAAAAGAACTACTTCGTCGACAGCAACAAGAGGAATATGAAAAATATATAACGAAGAAAAAGCAACTGGAGCGAGCTGTTACCATGAAAGAACAAAAGGCGCAAAAAATGATTAAGCCTCCTTCTAAACAAATGGGTACTTCTGAATCTCGAATATGGAAGATGCAGCATGCGACTAAACAAAAGAAAATGCATCAAAATATTAAGGCTCTTGAAACACGTGTTGAAAAACTAGAGCGTGTGAAAAAACCAAAAGATTATCCGGCTGTCAAAATGAAGTTGTCTAACCAAGATCAAATACAGGGGCGCAATGTACTTCGGGTAAAAGACTTATCTGTTTCCTTTGGGAATCATGTGCTTTGGACAGATGCTTCTTTTACCATTAAAGGCGGGGAGAAGGCTGCCATTATTGGCAATAATGGGGTCGGTAAAACAACATTGTTGAAACAAATTTTAGAAAGGGTACCAGCGGTAACAATATCACCCGCAGCAAAAATCGGCTATTTTAGCCAGAATTTGGATACGCTTGATACGCATGTGTCGATCTTAGAAAATGTCATGTCCACCGCTATTCAAGATGAAACTACTGTACGGACTGTTCTCGCAAGATTACATTTCTACCGGGAGGATGTTTATAAGGAAGTTCAAGTCCTAAGTGGTGGGGAACGTGTGAAGGTTGCTTTTGCAAAACTATTTGTTAGCGACTATAATACGTTGATTCTGGATGAACCAACAAATTATTTAGACATTGATGCCATAGAAGCGTTAGAGGAGCTCCTAATTAACTATGAGGGGGCAGTACTATTTGTATCTCATGATTGTCGTTTCGTTCAAAATATTGCATCCAAAATTATTGAACTATCCGACCAGAAGGTTATAGAGTTTCTTGGAAGCTATAAAGCGTTTAGAGAAAGATCTCAAGAGACAGAGCGTGACTATATGAAGGAAGAACTTCTTAAAATTGAGATCAAACTCACTCAAATGATTAGTGAAATGAATGACGAGGCATCAAATGAATTAGAAAAAGAATTCCAAATGTTGATTCATGAACGTAATCAGTTAAGAAATCAAGTAAACAATTAGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002832","ARO_id":"39266","ARO_name":"vgaD","ARO_description":"vgaD is an efflux protein expressed in Enterococcus faecium that confers resistance to streptogramin A antibiotics and related compounds. It is associated with plasmid DNA.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37716":{"category_aro_accession":"3001317","category_aro_cvterm_id":"37716","category_aro_name":"pleuromutilin","category_aro_description":"Pleuromutilin is a natural product antibiotic produced by Clitopilus passeckerianus. Related antibiotics of clinical significance, such as tiamulin and retapamulin, are semi-synthetic derivatives of this compound.","category_aro_class_name":"Antibiotic"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1047":{"model_id":"1047","model_name":"catS","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"28":{"protein_sequence":{"accession":"CAA52904.1","sequence":"FTNIPCTYSMTVKLDITQIKKKRMKLYPAMLYYLATIVNRHSEFRTAINQEGELGIYDEMIPSYTIFHEDTETFSNLWTPYIPDFEAFSMAYANDMQRYGSNYGMIGKPDIPENVFNVSMIPWSTFDSFNLNLQKGYDYLIPIFTMGKYYRDDEKIILPLAIQV"},"dna_sequence":{"accession":"X74948","fmin":"0","fmax":"492","strand":"+","sequence":"TTTACGAATATACCTTGCACATACAGTATGACTGTTAAATTGGATATTACACAAATAAAAAAGAAACGAATGAAATTATACCCTGCGATGCTTTATTATCTTGCAACGATTGTAAACCGTCATTCAGAGTTTAGAACGGCAATTAATCAGGAGGGTGAACTGGGAATATATGACGAGATGATACCCAGCTATACCATATTCCATGAGGACACAGAGACATTTTCCAACCTTTGGACACCATACATACCAGATTTTGAAGCATTTTCTATGGCGTATGCGAATGATATGCAAAGGTATGGAAGCAATTATGGAATGATAGGAAAACCAGATATACCAGAAAATGTTTTTAATGTATCGATGATACCATGGTCAACCTTCGATAGCTTTAATCTGAATTTGCAGAAAGGATATGATTATTTGATTCCTATTTTTACGATGGGGAAATATTACAGAGATGATGAAAAAATCATACTTCCTCTCGCCATCCAAGTT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36764","NCBI_taxonomy_name":"Streptococcus pyogenes","NCBI_taxonomy_id":"1314"}}}},"ARO_accession":"3002688","ARO_id":"39122","ARO_name":"catS","ARO_description":"catS is a chromosome-encoded variant of the cat gene found in Streptococcus pyogenes","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. cat is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Bacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini","category_aro_class_name":"AMR Gene Family"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1048":{"model_id":"1048","model_name":"QnrB33","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"468":{"protein_sequence":{"accession":"AEL00451.1","sequence":"MTLALVSEKIDRNRFTGEKVENSTFFNCDFSGADLSSTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNASALGIEIRHCRAQGSDFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVAGATFSGSDLSGGEFSAFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDSYQAALLMERLGIAVIG"},"dna_sequence":{"accession":"JN173055","fmin":"35","fmax":"680","strand":"+","sequence":"ATGACTCTGGCATTAGTTAGCGAAAAAATTGACAGAAACCGCTTCACCGGGGAAAAAGTTGAAAACAGTACTTTTTTTAACTGTGATTTTTCAGGGGCCGATCTTAGCAGCACTGAATTTATCGGCTGTCAGTTTTATGATCGCGAAAGCCAGAAAGGGTGTAATTTTAGTCGCGCAATGCTGAAAGATGCCATTTTTAAAAGTTGCGATTTATCCATGGCGGATTTTCGCAACGCCAGTGCCCTGGGAATTGAAATTCGCCACTGCCGCGCGCAGGGTTCAGATTTTCGCGGCGCGAGTTTTATGAACATGATCACCACGCGGACCTGGTTTTGCAGCGCATACATCACGAATACCAATCTAAGCTACGCCAACTTTTCGAAGGTTGTCCTGGAAAAGTGCGAGCTGTGGGAAAACCGCTGGATGGGAACTCAGGTAGCGGGTGCAACGTTCAGTGGATCAGATCTCTCGGGCGGTGAATTTTCAGCGTTCGACTGGCGGGCCGCAAATTTCACGCACTGTGATTTGACCAATTCAGAACTGGGTGATTTAGATATTCGGGGTGTAGATTTACAAGGCGTCAAATTGGATAGCTATCAGGCAGCGTTGCTGATGGAGCGGCTTGGCATCGCGGTGATTGGTTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39584","NCBI_taxonomy_name":"Citrobacter braakii","NCBI_taxonomy_id":"57706"}}}},"ARO_accession":"3002748","ARO_id":"39182","ARO_name":"QnrB33","ARO_description":"QnrB33 is a plasmid-mediated quinolone resistance protein found in Citrobacter braakii","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1049":{"model_id":"1049","model_name":"MOX-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"961":{"protein_sequence":{"accession":"BAA02563.2","sequence":"MQQRQSILWGAVATLMWAGLAHAGEASPVDPLRPVVDASIQPLLKEHRIPGMAVAVLKDGKAHYFNYGVANRESGASVSEQTLFEIGSVSKTLTATLGAYAVVKGAMQLDDKASRHAPWLKGSVFDSITMGELATYSAGGLPLQFPEEVDSSEKMRAYYRQWAPVYSPGSHRQYSNPSIGLFGHLAASSLKQPFAQLMEQTLLPGLGMHHTYVNVPKQAMASYAYGYSKEDKPIRVNPGMLADEAYGIKTSSADLLAFVKANIGGVDDKALQQAISLTHKGHYSVGGMTQGLGWESYAYPVTEQTLLAGNSAKVILEANPTAAPRESGSQVLFNKTGSSNGFGAYVAFVPARGIGIVMLANRNYPIPARVKAAHAILAQLAG"},"dna_sequence":{"accession":"D13304","fmin":"232","fmax":"1381","strand":"+","sequence":"ATGCAACAACGACAATCCATCCTGTGGGGGGCCGTGGCCACCCTGATGTGGGCCGGTCTGGCCCATGCAGGTGAGGCTTCACCGGTCGATCCCCTGCGCCCCGTGGTGGATGCCAGCATCCAGCCGCTGCTCAAGGAGCACAGGATCCCGGGCATGGCGGTGGCCGTGCTCAAGGATGGCAAGGCCCACTATTTCAATTACGGGGTGGCCAACCGGGAGAGCGGGGCCAGCGTCAGCGAGCAGACCCTGTTCGAGATAGGATCCGTGAGCAAGACCCTGACTGCGACCCTGGGGGCCTATGCGGTGGTCAAGGGAGCGATGCAGCTGGATGACAAGGCGAGCCGGCACGCGCCCTGGCTCAAGGGATCCGTCTTTGACAGCATCACCATGGGGGAGCTTGCCACCTACAGCGCCGGAGGCCTGCCACTGCAATTCCCCGAGGAGGTGGATTCATCCGAGAAGATGCGCGCCTACTACCGCCAGTGGGCCCCTGTCTATTCGCCGGGCTCCCATCGCCAGTACTCCAACCCCAGCATAGGGCTGTTCGGCCACCTGGCGGCGAGCAGCCTGAAGCAGCCATTTGCCCAGTTGATGGAGCAGACCCTGCTGCCCGGGCTCGGCATGCACCACACCTATGTCAATGTGCCGAAGCAGGCCATGGCGAGTTATGCCTATGGCTATTCGAAAGAGGACAAGCCCATCCGGGTCAACCCTGGCATGCTGGCGGACGAGGCCTACGGCATCAAGACCAGCTCGGCGGATCTGCTCGCCTTCGTGAAGGCCAACATCGGCGGGGTTGATGACAAGGCGTTGCAGCAGGCCATCTCCCTGACCCACAAAGGGCATTACTCGGTAGGCGGGATGACCCAGGGGCTGGGTTGGGAGAGTTACGCCTATCCCGTCACCGAGCAGACATTGCTGGCGGGCAATTCGGCCAAGGTGATCCTCGAAGCCAATCCGACGGCGGCTCCCCGGGAGTCGGGGAGCCAGGTGCTCTTCAACAAGACCGGCTCGAGCAATGGCTTTGGCGCCTATGTGGCCTTCGTGCCGGCCAGGGGGATCGGCATCGTCATGCTGGCCAATCGCAACTATCCCATCCCGGCCAGGGTGAAGGCGGCCCACGCCATCCTGGCGCAGTTGGCCGGTTGAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002182","ARO_id":"38582","ARO_name":"MOX-1","ARO_description":"MOX-1 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36222":{"category_aro_accession":"3000083","category_aro_cvterm_id":"36222","category_aro_name":"MOX beta-lactamase","category_aro_description":"MOX beta-lactamases are plasmid-mediated AmpC-type beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1050":{"model_id":"1050","model_name":"AAC(6')-Ii","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"172":{"protein_sequence":{"accession":"AAB63533.1","sequence":"MIISEFDRNNPVLKDQLSDLLRLTWPEEYGDSSAEEVEEMMNPERIAVAAVDQDELVGFIGAIPQYGITGWELHPLVVESSRRKNQIGTRLVNYLEKEVASRGGITIYLGTDDLDHGTTLSQTDLYVHTFDKVASIQNLREHPYEFYEKLGYKIVGVLPNANGWDKPDIWMAKTIIPRPDSQ"},"dna_sequence":{"accession":"L12710","fmin":"0","fmax":"549","strand":"+","sequence":"ATGATAATCAGTGAATTTGACCGTAATAATCCAGTATTGAAAGATCAGCTTTCTGATTTACTGAGACTGACTTGGCCGGAAGAATATGGAGACAGCTCGGCAGAAGAAGTAGAAGAAATGATGAATCCAGAACGAATCGCGGTAGCAGCGGTAGACCAAGATGAGTTAGTAGGATTTATTGGTGCAATCCCTCAATACGGTATCACAGGTTGGGAATTGCATCCATTAGTTGTAGAAAGCTCCCGACGAAAGAACCAAATAGGTACTCGATTAGTCAATTACTTAGAAAAAGAAGTAGCTTCCAGAGGAGGAATCACGATTTATTTAGGTACGGATGATTTAGACCATGGAACAACGTTAAGTCAAACGGACCTGTATGTGCATACATTTGATAAAGTGGCTTCCATCCAGAACCTTCGTGAACATCCGTATGAATTCTATGAAAAATTAGGTTATAAAATCGTAGGTGTCTTACCAAATGCAAATGGCTGGGACAAACCGGATATTTGGATGGCAAAAACGATTATTCCTCGACCAGATTCTCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002556","ARO_id":"38956","ARO_name":"AAC(6')-Ii","ARO_description":"AAC(6')-Ii is a chromosomal-encoded aminoglycoside acetyltransferase in Enterococcus spp.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1051":{"model_id":"1051","model_name":"LEN-12","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1023":{"protein_sequence":{"accession":"CAG25817.1","sequence":"ATLPLAVYAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGLEQLDRRIHYRQQDLVDYSPVSEKHLVDGMTIGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGARGIVALLGPDGKPERIVVIYLRDTPASMAERNQHIAG"},"dna_sequence":{"accession":"AJ635406","fmin":"0","fmax":"789","strand":"+","sequence":"GCCACCCTGCCACTGGCGGTATACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGTCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGACAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002462","ARO_id":"38862","ARO_name":"LEN-12","ARO_description":"LEN-12 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1052":{"model_id":"1052","model_name":"OXA-206","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1757":{"protein_sequence":{"accession":"BAL15076.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAISVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"AB634250","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTTCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001484","ARO_id":"37884","ARO_name":"OXA-206","ARO_description":"OXA-206 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1053":{"model_id":"1053","model_name":"SHV-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1234":{"protein_sequence":{"accession":"AAD37413.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AF148851","fmin":"5","fmax":"866","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001060","ARO_id":"37440","ARO_name":"SHV-2","ARO_description":"SHV-2 is an extended-spectrum beta-lactamase found in E. coli., Klebsiella pneumoniae, and Shigella flexneri.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1056":{"model_id":"1056","model_name":"VIM-19","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1499":{"protein_sequence":{"accession":"ACY29468.1","sequence":"MLKVISSLLVYMTASVMAVASPLAHSGEPSGEYPTVNEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEAEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSAKVLYGGCAVHELSRTSAGNVADADLAEWPTSVERIQKHYPEAEVVIPGHGLPGGLDLLQHTANVVKAHKNRSVAE"},"dna_sequence":{"accession":"FJ822963","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTACATGACCGCGTCTGTCATGGCTGTCGCAAGTCCGTTAGCCCATTCCGGGGAGCCGAGTGGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGAGAGGTCCGACTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCGGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAAAAGCAAATTGGACTTCCCGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGCAGAGGGGAACGAGATTCCCACGCATTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGCTCTTCTATCCTGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAAAGTGCTATACGGTGGTTGTGCCGTTCATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCGTTGAGCGGATTCAAAAACACTACCCGGAAGCAGAGGTCGTCATTCCCGGGCACGGTCTACCGGGCGGTCTAGACTTGCTCCAGCACACAGCGAACGTTGTCAAAGCACACAAAAATCGCTCAGTCGCCGAGTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002289","ARO_id":"38689","ARO_name":"VIM-19","ARO_description":"VIM-19 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1057":{"model_id":"1057","model_name":"CTX-M-114","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1980":{"protein_sequence":{"accession":"ACU00153.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKAMAVAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"GQ351346","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGCGATGGCCGTGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36944","NCBI_taxonomy_name":"Providencia rettgeri","NCBI_taxonomy_id":"587"}}}},"ARO_accession":"3001974","ARO_id":"38374","ARO_name":"CTX-M-114","ARO_description":"CTX-M-114 is a beta-lactamase. From the Lahey list of CTX-M beta-lactamases.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1058":{"model_id":"1058","model_name":"VIM-27","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"2041":{"protein_sequence":{"accession":"ADX78234.1","sequence":"MLKVISSLLVYMTASVMAVASPLAHSGEPSGEYPTVNEIPVGEVRLYQIADGVWSHISTQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEAEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSANVLYGGCAVHELSSTSAGNVADADLAEWPTSVERIQKHYPEAEVVIPGHGLPGGLDLLQHTANVVKAHKNRSVAE"},"dna_sequence":{"accession":"HQ858608","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTACATGACCGCGTCTGTCATGGCTGTCGCAAGTCCGTTAGCCCATTCCGGGGAGCCGAGTGGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGAGAGGTCCGACTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCTCAACGCAGTCGTTTGATGGCGCGGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAAAAGCAAATTGGACTTCCCGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGCAGAGGGGAACGAGATTCCCACGCATTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGCTCTTCTATCCTGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAACGTGCTATACGGTGGTTGTGCCGTTCATGAGTTGTCAAGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCGTTGAGCGGATTCAAAAACACTACCCGGAAGCAGAGGTCGTCATTCCCGGGCACGGTCTACCGGGCGGTCTAGACTTGCTCCAGCACACAGCGAACGTTGTCAAAGCACACAAAAATCGCTCAGTCGCCGAGTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002297","ARO_id":"38697","ARO_name":"VIM-27","ARO_description":"VIM-27 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1059":{"model_id":"1059","model_name":"APH(9)-Ib","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"4377":{"protein_sequence":{"accession":"AAB66655.1","sequence":"MEDLPENLDQESLFQGLREFGISTTSASYAPLGFGDYHWHITGDDGQRWFATVSDLEHKEHCGHGAPAALRGLRRAMDTAVHLREQGGLPFVVAPRTTSDGASLVPLDSRYALTVFPHVSARPGEFGQKLTERERDQVLVLLAELHGQAPPKCTPTTDMVPTGLDGVHTALAEPSGTWTGGPFSEPARELLAEHEATLRGRMAEFGELVARVRGRGAPLVVTHGEPHPGNLILGEDGYVLVDWDTVGLAIPERDLSLISDDPAALARYTELTGHTPDPAALALYRLRWSLLDVAEFVEWFRGEHQRTSDTEAAWQSFAETLDHLNSEVPS"},"dna_sequence":{"accession":"U70376","fmin":"7525","fmax":"8518","strand":"-","sequence":"TCAGCTCGGTACTTCGGAGTTCAGATGGTCGAGAGTCTCGGCGAAGCTCTGCCAAGCGGCTTCGGTGTCGGAGGTGCGCTGGTGTTCCCCGCGGAACCACTCGACGAACTCGGCGACGTCCAGCAGGCTCCACCGCAGCCGGTAGAGCGCCAGCGCGGCCGGGTCGGGCGTGTGCCCGGTCAGTTCGGTGTAGCGGGCGAGAGCTGCCGGGTCGTCCGAGATCAGGGAGAGGTCCCGTTCGGGTATCGCGAGGCCCACCGTGTCCCAGTCCACCAGCACATAGCCGTCCTCACCAAGGATCAGGTTCCCCGGGTGCGGCTCGCCGTGTGTGACGACCAGCGGGGCGCCGCGGCCCCGTACCCGCGCCACCAGTTCGCCGAACTCCGCCATCCGCCCGCGGAGCGTCGCCTCGTGCTCGGCCAGCAACTCGCGGGCCGGCTCGGAGAACGGCCCGCCCGTCCAGGTTCCGGACGGCTCGGCCAGCGCGGTGTGCACGCCATCCAGTCCGGTCGGCACCATGTCGGTGGTCGGGGTGCACTTCGGCGGTGCCTGGCCGTGCAATTCTGCGAGCAGCACCAGCACCTGGTCCCGCTCCCGCTCCGTCAGCTTCTGGCCGAACTCCCCGGGTCGGGCCGAGACATGGGGAAATACGGTCAACGCGTACCGCGAGTCCAGCGGGACCAGTGAAGCGCCGTCACTCGTGGTCCGGGGTGCCACCACGAACGGCAGGCCGCCCTGCTCACGCAAGTGCACCGCGGTGTCCATGGCTCTCCGCAGACCTCGCAGTGCCGCCGGGGCACCGTGCCCGCAGTGCTCCTTGTGTTCGAGGTCGGAGACGGTGGCGAACCACCGCTGCCCGTCGTCACCGGTGATGTGCCAGTGATAGTCGCCGAAGCCGAGCGGCGCGTACGACGCACTGGTCGTGGAGATACCGAATTCTCGTAGTCCCTGAAATAGGCTTTCCTGGTCCAGGTTCTCAGGAAGATCTTCCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39531","NCBI_taxonomy_name":"Streptomyces netropsis","NCBI_taxonomy_id":"55404"}}}},"ARO_accession":"3002663","ARO_id":"39063","ARO_name":"APH(9)-Ib","ARO_description":"APH(9)-Ib is a chromosomal-encoded aminoglycoside phosphotransferase in S. flavopersicus","ARO_category":{"36292":{"category_aro_accession":"3000153","category_aro_cvterm_id":"36292","category_aro_name":"APH(9)","category_aro_description":"Phosphorylation of spectinomycin on the hydroxyl group at position 9","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1060":{"model_id":"1060","model_name":"SHV-103","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1772":{"protein_sequence":{"accession":"ABS72351.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNRAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"EU032604","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAGAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001152","ARO_id":"37532","ARO_name":"SHV-103","ARO_description":"SHV-103 is a beta-lactamase that has been found in clinical isolates.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1061":{"model_id":"1061","model_name":"OXY-2-10","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1140":{"protein_sequence":{"accession":"ACV44456.1","sequence":"MIKSSWRKIAMLAAAVPLLLASGALWASTDAIHQKLTDLEKRSGGRLGVALINTADNSQILYRGDERFAMCSTSKVMAAAAVLKQSESNKEVVNKRLEINAADLVVWSPITEKHLQSGMTLAELSAATLQYSDNTAMNLIIGYLGGPEKVTAFARSIGDATFRLDRTEPTLNTAIPGDERDTSTPLAMAESLRKLTLGDALGEQQRAQLVTWLKGNTTGGQSIRAGLPESWVVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKNRKEVLAAATKIVTEGL"},"dna_sequence":{"accession":"FJ785626","fmin":"131","fmax":"1004","strand":"+","sequence":"ATGATAAAAAGTTCGTGGCGTAAAATTGCAATGCTAGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGCGCACTGTGGGCCAGTACCGATGCTATCCATCAGAAGCTGACAGATCTCGAGAAGCGTTCAGGCGGCAGGTTGGGCGTGGCGCTAATCAACACGGCAGATAATTCTCAAATCTTATATCGCGGCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCCGCCGCCGCGGTATTAAAACAGAGCGAAAGCAATAAAGAGGTGGTAAATAAAAGGCTGGAGATTAACGCAGCCGATTTGGTGGTCTGGAGTCCGATTACCGAAAAACATCTCCAGAGCGGAATGACGCTGGCTGAGCTAAGCGCGGCGACGCTGCAATATAGCGACAATACGGCGATGAATCTGATCATCGGCTACCTTGGCGGGCCGGAAAAAGTCACCGCCTTCGCCCGCAGTATCGGCGATGCCACCTTTCGTCTCGATCGTACGGAGCCCACGCTGAATACCGCCATCCCGGGCGATGAGCGTGATACCAGCACGCCGCTGGCGATGGCTGAAAGCCTGCGCAAGCTGACGCTTGGCGATGCGCTGGGCGAACAGCAACGCGCCCAGTTAGTCACCTGGCTGAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCGGGCCTGCCTGAAAGCTGGGTGGTCGGCGATAAAACCGGTGCCGGAGATTACGGCACCACCAATGATATTGCGGTTATCTGGCCGGAAAATCACGCTCCGCTGGTATTAGTCACCTACTTTACCCAGCCGCAGCAGGATGCGAAAAACCGCAAAGAGGTGTTAGCCGCAGCGACAAAAATCGTGACCGAAGGGCTTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002405","ARO_id":"38805","ARO_name":"OXY-2-10","ARO_description":"OXY-2-10 is a beta-lactamase. From the Pasteur Institute (Genopole) list of OXY beta-lactamases.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1062":{"model_id":"1062","model_name":"SHV-71","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1563":{"protein_sequence":{"accession":"CAJ47126.2","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKYLADGMTVGELCAAAITMSDNSAANLLLATVGGPVGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM176546","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAATACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGTAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGGATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001125","ARO_id":"37505","ARO_name":"SHV-71","ARO_description":"SHV-71 is a broad-spectrum beta-lactamase found in Klebsiella pneumoniae and Shigella.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1063":{"model_id":"1063","model_name":"QnrB73","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"513":{"protein_sequence":{"accession":"AGT59159.1","sequence":"MSLALVSEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGSDFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVAGATFSGSDLSGGEFSAFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDSYQAALLMERLGIAIIG"},"dna_sequence":{"accession":"KF443075","fmin":"0","fmax":"645","strand":"+","sequence":"ATGAGTCTGGCACTAGTTAGCGAAAAAATTGACAGAAACCGCTTCACCGGGGAAAAAGTTGAAAACAGTACTTTTTTTAACTGTGATTTTTCAGGGGCCGATCTTAGCGGCACTGAATTTATCGGCTGTCAGTTTTATGATCGCGAAAGCCAGAAAGGGTGTAATTTTAGTCGCGCAATGCTGAAAGATGCCATTTTTAAAAGTTGCGATTTATCCATGGCGGATTTTCGCAACGTCAGTGCTCTGGGAATTGAAATTCGCCACTGCCGCGCGCAGGGTTCAGATTTTCGCGGCGCGAGTTTTATGAACATGATCACCACGCGGACCTGGTTTTGCAGCGCATACATCACGAATACCAATCTAAGCTACGCCAACTTTTCGAAGGTTGTCCTGGAAAAGTGCGAGCTGTGGGAAAATCGCTGGATGGGAACTCAGGTAGCGGGTGCAACGTTCAGTGGATCAGATCTCTCGGGCGGTGAATTTTCAGCGTTCGACTGGCGGGCCGCAAACTTCACGCACTGTGATTTGACCAATTCAGAACTGGGTGATTTAGATATTCGGGGTGTAGATTTACAAGGCGTCAAATTGGATAGCTATCAGGCAGCGTTGCTGATGGAGCGGCTTGGCATCGCGATTATTGGCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002785","ARO_id":"39219","ARO_name":"QnrB73","ARO_description":"QnrB73 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1064":{"model_id":"1064","model_name":"CTX-M-141","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1027":{"protein_sequence":{"accession":"AGN11769.1","sequence":"MMTQSIRRSMLTVMATLPLLFSSATLHAQANSVQQQLEALEKSSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKQSESDKHLLNQRVEIKKSDLVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQREQLVTWLKGNTTGSASIRAGLPKSWVVGDKTGSGDYGTTNDIAVIWPENHAPLVLVTYFTQPEQKAESRRDILAAAAKIVTHGF"},"dna_sequence":{"accession":"KC964871","fmin":"0","fmax":"876","strand":"+","sequence":"ATGATGACTCAGAGCATTCGCCGCTCAATGTTAACGGTGATGGCGACGCTACCCCTGCTATTTAGCAGCGCAACGCTGCATGCGCAGGCGAACAGCGTGCAACAGCAGCTGGAAGCCCTGGAGAAAAGTTCGGGAGGTCGGCTTGGCGTTGCGCTGATTAACACCGCCGATAATTCGCAGATTCTCTACCGTGCCGATGAACGTTTTGCGATGTGCAGTACCAGTAAGGTGATGGCGGCCGCGGCGGTGCTTAAACAGAGCGAGAGCGATAAGCACCTGCTAAATCAGCGCGTTGAAATCAAGAAGAGCGACCTGGTTAACTACAATCCCATTGCGGAGAAACACGTTAACGGCACGATGACGCTGGCTGAGCTTGGCGCAGCGGCGCTGCAGTATAGCGACAATACTGCCATGAATAAGCTGATTGCCCATCTGGGTGGTCCCGATAAAGTGACGGCGTTTGCTCGCTCGTTGGGTGATGAGACCTTCCGTCTGGACAGAACCGAGCCCACGCTCAATACCGCCATTCCAGGCGACCCGCGTGATACCACCACGCCGCTCGCGATGGCGCAGACCCTGAAAAATCTGACGCTGGGTAAAGCGCTGGCGGAAACTCAGCGGGAACAGTTGGTGACGTGGCTTAAGGGCAATACTACCGGTAGCGCGAGCATTCGGGCGGGTCTGCCGAAATCATGGGTAGTGGGCGATAAAACCGGCAGCGGAGATTATGGCACCACCAACGATATCGCGGTTATCTGGCCGGAAAACCACGCACCGCTGGTTCTGGTGACCTACTTTACCCAACCGGAGCAGAAGGCGGAAAGCCGTCGGGATATTCTGGCTGCGGCGGCGAAAATCGTAACCCACGGTTTCTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001999","ARO_id":"38399","ARO_name":"CTX-M-141","ARO_description":"CTX-M-141 is a beta-lactamase. From the Lahey list of CTX-M beta-lactamases.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1065":{"model_id":"1065","model_name":"OXA-384","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4374":{"protein_sequence":{"accession":"AHL30282.1","sequence":"MNIQALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRIGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNSEMKKGISSSVRKEITYRSLEQLGIL"},"dna_sequence":{"accession":"KF986263","fmin":"90","fmax":"915","strand":"-","sequence":"CTATAAAATACCTAATTGTTCTAAACTTCTATAAGTAATCTCTTTTCGAACAGAGCTAGATATTCCTTTTTTCATTTCTGAGTTAAGGGAGAACGCTACAATATTCCCTTGAGGCTGAACAACCCATCCAGTTAACCAGCCTACTTGTGGGTTTACATCCCATCCCCAACCACTTTTTGCGTATATTTTATTTCCATTCTTTTCTTCTATGAATAGCATGGATTGCACTTCATCTTGGACTTTTTGGCTAAATGGAAGCGTTTTATTAGCTAGCTTGTAAGCAAATTGTGCCTCTTGTTGAGGAGTAATTTTTAAAGGACCCACCAGCCAAAAATTATCGACTTGGGTACCGATATCTGCATTGCCATAACCAATACGCTTCACTTCATTAGACATGAGTTCAAGTCCAATACGACGAGCTAAATCTTGATAAACCGGAATAGCGGAAGCTTTCATAGCATCGCCTAGGGTCATGTTCTTTTCCCATTCTGGGAATAGCCTTTTTTGCCCGTCCCACTTAAATACTTCTGTAGTGGTTGCCTTATGGTGCTCAAGGCCTATCAAAGCATTAAGCATTTTGAAGGTCGAAGCAGGTACATACTCGGTCGAAGCACGAGCAAGATCATTACCATAGCTTTGTTGAGTTTGGCCTTGTTGGATAACTAAAACACCCGTAGTGTGTGCTTCGTTAAATAAATTTTTAATTTTCTCTGCTTTTTCATCAGATTTTGAAGCACTGTGATTTGGATTAGCAGTCACTATATAAGGTGAGCAGGCTGAAATAAAAATAGCGCTTGTTATAAGTAAGAGGGCTTGAATGTTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001570","ARO_id":"37970","ARO_name":"OXA-384","ARO_description":"OXA-384 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1066":{"model_id":"1066","model_name":"TEM-118","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"924":{"protein_sequence":{"accession":"AAN05029.1","sequence":"FFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDHWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYMTGSQATMDERNR"},"dna_sequence":{"accession":"AY130285","fmin":"0","fmax":"785","strand":"+","sequence":"TTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCATTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACATGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3000981","ARO_id":"37361","ARO_name":"TEM-118","ARO_description":"TEM-118 is an extended-spectrum beta-lactamase that has been found in clinical isolates.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1068":{"model_id":"1068","model_name":"AAC(6')-Ib3","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"141":{"protein_sequence":{"accession":"ACS44715.1","sequence":"MTNSNDSVTLRLMTEHDLAMLYEWLNRSHIVEWWGGEEARPTLADVQEQYLPSVLAQESVTPYIAMLNGEPIGYAQSYVALGSGDGWWEEETDPGVRGIDQLLANASQLGKGLGTKLVRALVELLFNDPEVTKIQTDPSPSNLRAIRCYEKAGFERQGTVTTPDGPAVYMVQTRQAFERTRSDA"},"dna_sequence":{"accession":"FJ854362","fmin":"1702","fmax":"2257","strand":"+","sequence":"GTGACCAACAGCAACGATTCCGTCACACTGCGCCTCATGACTGAGCATGACCTTGCGATGCTCTATGAGTGGCTAAATCGATCTCATATTGTCGAGTGGTGGGGCGGAGAAGAAGCACGCCCGACACTTGCTGACGTACAGGAACAGTACTTGCCAAGCGTTTTAGCGCAAGAGTCCGTCACTCCATACATTGCAATGCTGAATGGAGAGCCGATTGGGTATGCCCAGTCGTACGTTGCTCTTGGAAGCGGGGACGGATGGTGGGAAGAAGAAACCGATCCAGGAGTACGCGGAATAGACCAGTTACTGGCGAATGCATCACAACTGGGCAAAGGCTTGGGAACCAAGCTGGTTCGAGCTCTGGTTGAGTTGCTGTTCAATGATCCCGAGGTCACCAAGATCCAAACGGACCCGTCGCCGAGCAACTTGCGAGCGATCCGATGCTACGAGAAAGCGGGGTTTGAGAGGCAAGGTACCGTAACCACCCCAGATGGTCCAGCCGTGTACATGGTTCAAACACGCCAGGCATTCGAGCGAACACGCAGTGATGCCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3002576","ARO_id":"38976","ARO_name":"AAC(6')-Ib3","ARO_description":"AAC(6')-Ib3 is an integron-encoded aminoglycoside acetyltransferase in P. aeruginosa","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1069":{"model_id":"1069","model_name":"IMP-35","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1556":{"protein_sequence":{"accession":"AFO59566.1","sequence":"MKKIFVLFVFLFCSITAAGESLPDIKIEKLDEDVYVHTSFEEDNGWGVITKHGLVVLVNTDAYIIDTPFTAKDTEKLVRWFVGRGYKIKGSISSHFHSDSAGGIEWLNSQSIPTYASKLTNELLKKNGNAQAENSFSGVSYWLVKHKIEVFYPGPGHTQDNVVVWLPEKKILFGGCFIKPDGLGYLGDANLEAWPKSAETLMSKYGNAKLVVSSHSEIGGASLLKRTWEQAVKGLKESKKPSQPNN"},"dna_sequence":{"accession":"JF816544","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAAAAAAATATTTGTGTTATTTGTATTTTTGTTTTGCAGTATTACTGCCGCCGGAGAGTCTTTGCCTGATATAAAAATTGAGAAACTTGACGAAGATGTTTATGTTCATACTTCTTTTGAAGAAGATAACGGCTGGGGTGTTATTACTAAACACGGCTTGGTGGTTCTTGTAAATACTGATGCCTATATAATTGACACTCCATTTACAGCTAAAGATACTGAAAAATTAGTCCGCTGGTTTGTGGGGCGTGGTTATAAAATCAAAGGCAGTATTTCCTCACATTTTCATAGCGATAGCGCAGGTGGAATTGAGTGGCTTAATTCTCAATCTATCCCCACATATGCATCTAAATTAACAAATGAGCTTCTTAAAAAGAACGGTAATGCGCAAGCCGAAAACTCATTTAGTGGCGTTAGCTATTGGCTAGTTAAACATAAAATTGAAGTTTTCTATCCAGGACCAGGGCACACTCAGGATAATGTAGTGGTTTGGTTGCCTGAAAAGAAAATTTTATTTGGCGGTTGTTTTATTAAGCCGGACGGTCTTGGTTATTTGGGAGACGCAAATCTAGAAGCATGGCCTAAGTCCGCAGAAACATTAATGTCTAAGTATGGTAATGCAAAACTGGTTGTTTCGAGTCATAGTGAAATTGGGGGCGCATCACTATTGAAGCGCACTTGGGAGCAGGCTGTTAAGGGGCTAAAAGAAAGTAAAAAACCATCACAGCCAAATAACTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002226","ARO_id":"38626","ARO_name":"IMP-35","ARO_description":"IMP-35 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1070":{"model_id":"1070","model_name":"sul1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"340":{"protein_sequence":{"accession":"AEJ33969.1","sequence":"MVTVFGILNLTEDSFFDESRRLDPAGAVTAAIEMLRVGSDVVDVGPAASHPDARPVSPADEIRRIAPLLDALSDQMHRVSIDSFQPETQRYALKRGVGYLNDIQGFPDPALYPDIAEADCRLVVMHSAQRDGIATRTGHLRPEDALDEIVRFFEARVSALRRSGVAADRLILDPGMGFFLSPAPETSLHVLSNLQKLKSALGLPLLVSVSRKSFLGATVGLPVKDLGPASLAAELHAIGNGADYVRTHAPGDLRSAITFSETLAKFRSRDARDRGLDHA"},"dna_sequence":{"accession":"JF969163","fmin":"1053","fmax":"1893","strand":"+","sequence":"ATGGTGACGGTGTTCGGCATTCTGAATCTCACCGAGGACTCCTTCTTCGATGAGAGCCGGCGGCTAGACCCCGCCGGCGCTGTCACCGCGGCGATCGAAATGCTGCGAGTCGGATCAGACGTCGTGGATGTCGGACCGGCCGCCAGCCATCCGGACGCGAGGCCTGTATCGCCGGCCGATGAGATCAGACGTATTGCGCCGCTCTTAGACGCCCTGTCCGATCAGATGCACCGTGTTTCAATCGACAGCTTCCAACCGGAAACCCAGCGCTATGCGCTCAAGCGCGGCGTGGGCTACCTGAACGATATCCAAGGATTTCCTGACCCTGCGCTCTATCCCGATATTGCTGAGGCGGACTGCAGGCTGGTGGTTATGCACTCAGCGCAGCGGGATGGCATCGCCACCCGCACCGGTCACCTTCGACCCGAAGACGCGCTCGACGAGATTGTGCGGTTCTTCGAGGCGCGGGTTTCCGCCTTGCGACGGAGCGGGGTCGCTGCCGACCGGCTCATCCTCGATCCGGGGATGGGATTTTTCTTGAGCCCCGCACCGGAAACATCGCTGCACGTGCTGTCGAACCTTCAAAAGCTGAAGTCGGCGTTGGGGCTTCCGCTATTGGTCTCGGTGTCGCGGAAATCCTTCTTGGGCGCCACCGTTGGCCTTCCTGTAAAGGATCTGGGTCCAGCGAGCCTTGCGGCGGAACTTCACGCGATCGGCAATGGCGCTGACTACGTCCGCACCCACGCGCCTGGAGATCTGCGAAGCGCAATCACCTTCTCGGAAACCCTCGCGAAATTTCGCAGTCGCGACGCCAGAGACCGAGGGTTAGATCATGCCTAGC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39525","NCBI_taxonomy_name":"Vibrio fluvialis","NCBI_taxonomy_id":"676"}}}},"ARO_accession":"3000410","ARO_id":"36549","ARO_name":"sul1","ARO_description":"Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.","ARO_category":{"41402":{"category_aro_accession":"3004238","category_aro_cvterm_id":"41402","category_aro_name":"sulfonamide resistant sul","category_aro_description":"The sul genes encode forms of dihydropteroate synthase that confer resistance to sulfonamide.","category_aro_class_name":"AMR Gene Family"},"36463":{"category_aro_accession":"3000324","category_aro_cvterm_id":"36463","category_aro_name":"sulfadiazine","category_aro_description":"Sulfadiazine is a potent inhibitor of dihydropteroate synthase, interfering with the tetrahydrofolic biosynthesis pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor to many nucleotides and amino acids.","category_aro_class_name":"Antibiotic"},"36464":{"category_aro_accession":"3000325","category_aro_cvterm_id":"36464","category_aro_name":"sulfadimidine","category_aro_description":"Sulfadimidine is an alkaline sulfonamide antibiotic that inhibits dihydropteroate synthase, and enzyme in the tetrahydrofolic acid biosynthesis pathway. This interferes with the production of folate, which is a precursor to many amino acids and nucleotides.","category_aro_class_name":"Antibiotic"},"36466":{"category_aro_accession":"3000327","category_aro_cvterm_id":"36466","category_aro_name":"sulfadoxine","category_aro_description":"Sulfadoxine is an inhibitor of dihydropteroate synthase, interfering with the tetrahydrofolic biosynthesis pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor to many nucleotides and amino acids.","category_aro_class_name":"Antibiotic"},"36468":{"category_aro_accession":"3000329","category_aro_cvterm_id":"36468","category_aro_name":"sulfamethoxazole","category_aro_description":"Sulfamethoxazole is a sulfonamide antibiotic usually taken with trimethoprim, a diaminopyrimidine antibiotic. Sulfamethoxazole inhibits dihydropteroate synthase, essential to tetrahydrofolic acid biosynthesis. This pathway generates compounds used in the synthesis of many amino acids and nucleotides.","category_aro_class_name":"Antibiotic"},"36469":{"category_aro_accession":"3000330","category_aro_cvterm_id":"36469","category_aro_name":"sulfisoxazole","category_aro_description":"Sulfisoxazole is an inhibitor of dihydropteroate synthase, interfering with the tetrahydrofolic biosynthesis pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor to many nucleotides and amino acids.","category_aro_class_name":"Antibiotic"},"37027":{"category_aro_accession":"3000683","category_aro_cvterm_id":"37027","category_aro_name":"sulfacetamide","category_aro_description":"Sulfacetamide is a very soluable sulfonamide antibiotic previously used to treat urinary tract infections. Its relatively low activity and toxicity to those with Stevens-Johnson syndrome have reduced its use and availability.","category_aro_class_name":"Antibiotic"},"37028":{"category_aro_accession":"3000684","category_aro_cvterm_id":"37028","category_aro_name":"mafenide","category_aro_description":"Mafenide is a sulfonamide used topically for treating burns.","category_aro_class_name":"Antibiotic"},"37042":{"category_aro_accession":"3000698","category_aro_cvterm_id":"37042","category_aro_name":"sulfasalazine","category_aro_description":"Sulfasalazine is a derivative of the early sulfonamide sulfapyridine (salicylazosulfapyridine). It was developed to increase water solubility and is taken orally for ulcerative colitis.","category_aro_class_name":"Antibiotic"},"37043":{"category_aro_accession":"3000699","category_aro_cvterm_id":"37043","category_aro_name":"sulfamethizole","category_aro_description":"Sulfamethizole is a short-acting sulfonamide that inhibits dihydropteroate synthetase.","category_aro_class_name":"Antibiotic"},"39996":{"category_aro_accession":"3003412","category_aro_cvterm_id":"39996","category_aro_name":"dapsone","category_aro_description":"Dapsone is a sulfone in which it inhibits folic acid synthesis, such as the dihydropteroate synthase.","category_aro_class_name":"Antibiotic"},"36421":{"category_aro_accession":"3000282","category_aro_cvterm_id":"36421","category_aro_name":"sulfonamide antibiotic","category_aro_description":"Sulfonamides are broad spectrum, synthetic antibiotics that contain the sulfonamide group. Sulfonamides inhibit dihydropteroate synthase, which catalyzes the conversion of p-aminobenzoic acid to dihydropteroic acid as part of the tetrahydrofolic acid biosynthetic pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor of many nucleotides and amino acids. Many sulfamides are taken with trimethoprim, an inhibitor of dihydrofolate reductase, also disturbing the trihydrofolic acid synthesis pathway.","category_aro_class_name":"Drug Class"},"39985":{"category_aro_accession":"3003401","category_aro_cvterm_id":"39985","category_aro_name":"sulfone antibiotic","category_aro_description":"A sulfone active against a wide range of bacteria but mainly employed for its actions against mycobacterium laprae. Its mechanism of action  involves inhibition of folic acid synthesis in susceptible organisms.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1071":{"model_id":"1071","model_name":"DHA-22","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1554":{"protein_sequence":{"accession":"AIT76109.1","sequence":"MKKSLSATLISALLAFSAPGFSAADNVAAVVDSAIKPLMAQQDIPGMAVAVSVKGKPYYFNYGFADIQAKQPVTENTLFELGSVSKTFTGVLGAVSVAKKEMALNDLAAKYQPELALPQWKGITLLDLATYTAGGLPLQVPDAVKSRADLLNFYQQWQPSRKPGDMRLYANSSIGLFGALTANAAGMPYEQLLTARILAPLGLSHTFITVPESAQSQYAYGYKNKKPVRVSPGQLDAESYGVKSASKDMLRWAEMNMEPSRAGNADLEMAMYLAQTRYYKTAAINQGLGWEMYDWPQQKDMIINGVTNEVALQPHPVTDNQVQPYNRASWVHKTGATTGFGAYVAFIPEKQVAIVILANKNYPNTERVKAAQAILSALE"},"dna_sequence":{"accession":"KM087856","fmin":"0","fmax":"1140","strand":"+","sequence":"ATGAAAAAATCGTTATCTGCAACACTGATTTCCGCTCTGCTGGCGTTTTCCGCCCCGGGGTTTTCTGCCGCTGATAATGTCGCGGCGGTGGTGGACAGCGCCATTAAACCGCTGATGGCACAGCAGGATATTCCCGGGATGGCGGTTGCCGTCTCCGTAAAGGGTAAGCCCTATTATTTCAATTATGGTTTTGCCGATATTCAGGCAAAACAGCCGGTCACTGAAAATACACTATTTGAGCTCGGATCTGTAAGTAAAACTTTCACAGGTGTGCTGGGTGCAGTTTCTGTGGCGAAAAAAGAGATGGCGCTGAATGATCTGGCGGCAAAATACCAGCCGGAGCTGGCTCTGCCGCAGTGGAAGGGGATCACATTGCTGGATCTGGCTACCTATACCGCAGGCGGACTGCCGTTACAGGTGCCGGATGCGGTAAAAAGCCGTGCGGATCTGCTGAATTTCTATCAGCAGTGGCAGCCGTCCCGGAAACCGGGCGATATGCGTCTGTATGCAAACAGCAGTATCGGCCTGTTTGGTGCTCTGACCGCAAACGCGGCGGGGATGCCGTATGAGCAGTTGCTGACTGCACGGATCCTGGCACCGCTGGGGTTATCTCACACCTTTATTACTGTGCCGGAAAGTGCGCAAAGCCAGTATGCGTACGGTTATAAAAACAAAAAACCGGTCCGCGTGTCGCCGGGACAGCTTGATGCGGAATCTTACGGCGTGAAATCCGCCTCAAAAGATATGCTGCGCTGGGCGGAAATGAATATGGAGCCGTCACGGGCCGGTAATGCGGATCTGGAAATGGCAATGTATCTTGCACAGACCCGCTACTATAAAACCGCCGCGATTAACCAGGGGCTGGGCTGGGAAATGTATGACTGGCCGCAGCAGAAAGATATGATCATTAACGGCGTGACCAACGAGGTCGCATTGCAGCCGCACCCGGTAACAGACAACCAGGTTCAGCCGTATAACCGTGCTTCCTGGGTGCATAAAACGGGGGCAACAACTGGTTTCGGCGCCTATGTGGCCTTTATTCCGGAAAAACAGGTGGCGATTGTGATTCTGGCGAATAAAAACTACCCGAATACCGAAAGAGTCAAAGCCGCACAGGCTATTTTGAGTGCACTGGAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002153","ARO_id":"38553","ARO_name":"DHA-22","ARO_description":"DHA-22 is a beta-lactamase. From the Lahey list of DHA beta-lactamases.","ARO_category":{"36207":{"category_aro_accession":"3000068","category_aro_cvterm_id":"36207","category_aro_name":"DHA beta-lactamase","category_aro_description":"DHA beta-lactamases are plasmid-mediated AmpC \u03b2-lactamases that confer resistance to cephamycins and oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1072":{"model_id":"1072","model_name":"OXA-37","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1134":{"protein_sequence":{"accession":"AAG33665.1","sequence":"MIIRFLALLFSAVVLVSLGHAQDKTHESSNWGKYFSDFNAKGTIVVVDERTNGNSTSVYNESRAQQRYSPASTFKIPHTLFALDAGAVRDEFHVFRWDGAKRSFAGHNQDQNLRSAMRNSTVWVYQLFAKEIGENKARSYLEKLNYGNADPSTKSGDYWIDGNLAISANEQISILKKLYRNELPFRVEHQRLVKDLMIVEAKRDWILRAKTGWDGQMGWWVGWVEWPTGPVFFALNIDTPNRMEDLHKREAIARAILQSVNALPPN"},"dna_sequence":{"accession":"AY007784","fmin":"1122","fmax":"1923","strand":"+","sequence":"TTGATAATCCGATTTCTAGCACTGCTTTTCTCAGCTGTTGTACTTGTCTCTCTTGGTCATGCACAAGATAAAACGCATGAGAGCTCTAATTGGGGGAAATACTTTAGTGATTTCAACGCTAAAGGTACAATAGTTGTAGTAGATGAACGCACAAACGGTAATTCCACATCGGTTTATAATGAATCCCGGGCTCAGCAGCGCTATTCGCCTGCGTCCACATTCAAGATTCCGCATACCCTTTTTGCGCTGGATGCAGGGGCGGTTCGCGATGAGTTTCATGTTTTTCGATGGGACGGCGCTAAAAGAAGCTTTGCAGGTCACAATCAAGACCAAAACCTACGATCGGCAATGCGCAATTCTACCGTTTGGGTCTATCAACTATTCGCAAAAGAAATAGGCGAAAACAAAGCACGAAGCTACCTAGAAAAATTAAATTACGGCAATGCAGACCCCTCGACCAAGAGCGGTGACTACTGGATAGATGGAAATCTTGCAATTTCAGCAAATGAACAAATTTCCATCCTAAAGAAGCTTTATCGAAATGAGCTTCCTTTTAGGGTAGAGCACCAACGCTTGGTTAAAGACTTGATGATTGTCGAAGCCAAACGTGATTGGATACTACGTGCCAAAACAGGCTGGGATGGTCAAATGGGTTGGTGGGTCGGTTGGGTAGAGTGGCCTACAGGCCCAGTATTTTTTGCGTTAAATATCGACACGCCAAACAGGATGGAAGACCTTCATAAACGAGAGGCAATTGCGCGTGCTATTCTTCAATCCGTCAATGCTTTGCCACCCAACTAGC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001431","ARO_id":"37831","ARO_name":"OXA-37","ARO_description":"OXA-37 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1073":{"model_id":"1073","model_name":"OKP-B-19","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1288":{"protein_sequence":{"accession":"CAP12359.2","sequence":"MRYVRLCLISLIAALPLAVFASPQPLEQIKISEGQLAGRVGYVEMDLASGRMLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNTAGNLLLKIVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMATTLRKLLTTPSLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPDGKAERIVVIYLRDTPATMVERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM850921","fmin":"24","fmax":"885","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCAGCCGCTTGAGCAGATTAAAATCAGCGAAGGTCAGCTGGCGGGCCGGGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCATGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCTGTGCTGGCCCGGGTGGATGCCGGCGACGAACAGCTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACACCGCCGGCAATCTGCTGTTGAAGATCGTCGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGAACTCAATGAGGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCGGCCAGCATGGCCACCACCCTGCGCAAGCTGCTAACCACCCCCTCTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTTGACGACCGGGTGGCCGGCCCGTTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGTGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAAGCGGAGCGTATCGTGGTGATCTATCTGCGTGATACCCCGGCGACCATGGTCGAGCGTAACCAGCAGATCGCCGGGATAGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002452","ARO_id":"38852","ARO_name":"OKP-B-19","ARO_description":"OKP-B-19 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1074":{"model_id":"1074","model_name":"LEN-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"763":{"protein_sequence":{"accession":"AAN05030.1","sequence":"VISLLATLPLVVYAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGLEQLDRRIHYRQQDLVDYSPVSEKHLVDGMTIGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPPGWFIADKTGAGERGARGIVALLGPDGKPERIVVIYLRDTPASMAERNQQIAGIGAALI"},"dna_sequence":{"accession":"AY130286","fmin":"0","fmax":"822","strand":"+","sequence":"TGTTATCTCCCTGTTAGCCACCCTGCCACTGGTGGTATACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGTCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGCCGGGCTGGTTTATCGCCGACAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACAAATCGCCGGGATCGGCGCGGCGCTGATC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002475","ARO_id":"38875","ARO_name":"LEN-3","ARO_description":"LEN-3 is a beta-lactamase. From the Pasteur Institute list of LEN beta-lactamases.","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1075":{"model_id":"1075","model_name":"TEM-20","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1800":{"protein_sequence":{"accession":"CAA76793.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTTPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"Y17581","fmin":"78","fmax":"936","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000891","ARO_id":"37271","ARO_name":"TEM-20","ARO_description":"TEM-20 is an extended-spectrum beta-lactamase found in several species of Gram-negative bacteria.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1076":{"model_id":"1076","model_name":"IMP-37","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1632":{"protein_sequence":{"accession":"AFP97028.1","sequence":"MKKLFVLCVCFFCSITAAGAALPDLKIEKLEEGVFVHTSFEEVNGWGVVTKHGLVVLVNTDAYLIDTPFTATDTEKLVNWFVERGYEIKGTISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKSGKVQAKYSFSEVSYWLVKNKIEVFYPGPGHTQDNLVVWLPESKILFGGCFIKPHGLGNLGDANLEAWPKSAKILMSKYGKAKLVVSSHSEKGDASLMKRTWEQALKGLKESKKTSSQSTAS"},"dna_sequence":{"accession":"JX131372","fmin":"96","fmax":"843","strand":"+","sequence":"ATGAAGAAATTATTTGTTTTATGTGTATGCTTCTTTTGTAGCATTACTGCCGCAGGAGCGGCTTTACCTGATTTAAAAATCGAGAAGCTTGAAGAAGGTGTTTTTGTTCATACATCGTTCGAAGAGGTTAACGGTTGGGGGGTTGTTACTAAACACGGTTTAGTGGTGCTTGTAAACACAGACGCCTATCTAATTGACACTCCATTTACTGCTACAGACACTGAAAAATTAGTCAATTGGTTTGTGGAGCGCGGCTATGAAATCAAAGGCACTATTTCATCACATTTCCATAGCGACAGCACAGGAGGAATAGAGTGGCTTAATTCTCAATCTATTCCCACGTATGCATCTGAATTAACAAATGAACTTTTGAAAAAATCCGGTAAGGTACAAGCTAAATATTCATTTAGCGAAGTTAGCTATTGGCTAGTTAAAAATAAAATTGAAGTTTTCTACCCTGGCCCAGGTCACACTCAAGATAACCTAGTGGTTTGGTTGCCTGAAAGTAAAATTTTATTCGGTGGTTGCTTTATTAAACCTCACGGTCTTGGCAATTTAGGTGACGCAAATTTAGAAGCTTGGCCAAAGTCCGCCAAAATATTAATGTCTAAATATGGCAAAGCAAAGCTTGTTGTTTCAAGTCATAGTGAAAAAGGGGACGCATCACTAATGAAACGTACATGGGAACAAGCCCTTAAAGGGCTTAAAGAAAGTAAAAAAACATCATCACAAAGTACAGCATCGTGAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002228","ARO_id":"38628","ARO_name":"IMP-37","ARO_description":"IMP-37 is a beta-lactamase. From the Lahey list of IMP beta-lactamases.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1077":{"model_id":"1077","model_name":"OXA-420","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2012":{"protein_sequence":{"accession":"BAP28835.1","sequence":"MKLLKILSLVCLSISIGACAEHSMSRAKTSTIPQVNNSIIDQNVQALFNEISADAVFVTYDGQNIKKYGTHLDRAKTAYIPASTFKIANALIGLENHKATSTEIFKWDGKPRFFKAWDKDFTLGEAMQASTVPVYQELARRIGPSLMQSELQRIGYGNMQIGTEVDQFWLKGPLTITPIQEVKFVYDLAQGQLPFKPEVQQQVKEMLYVERRGENRLYAKSGWGMAVDPQVGWYVGFVEKADGQVVAFALNMQMKDGDDIALRKQLSLDVLDKLGVFHYL"},"dna_sequence":{"accession":"AB983359","fmin":"2425","fmax":"3268","strand":"+","sequence":"ATGAAATTATTAAAAATATTGAGTTTAGTTTGCTTAAGCATAAGTATTGGGGCTTGTGCTGAGCATAGTATGAGTCGAGCAAAAACAAGTACAATTCCACAAGTGAATAACTCAATCATCGATCAGAATGTTCAAGCGCTTTTTAATGAAATCTCAGCTGATGCTGTGTTTGTTACATATGATGGTCAAAATATTAAAAAATATGGCACGCATTTAGACCGAGCAAAAACAGCTTATATTCCTGCATCTACATTTAAAATTGCCAATGCACTAATTGGTTTAGAAAATCATAAAGCAACATCTACAGAAATATTTAAGTGGGATGGAAAGCCACGTTTTTTTAAAGCATGGGACAAAGATTTTACTTTGGGCGAAGCCATGCAAGCATCTACAGTGCCTGTATATCAAGAATTGGCACGTCGTATTGGTCCAAGCTTAATGCAAAGTGAATTGCAACGTATTGGTTATGGCAATATGCAAATAGGCACGGAAGTTGATCAATTTTGGTTGAAAGGGCCTTTGACAATTACACCTATACAAGAAGTAAAGTTTGTTTATGATTTAGCCCAAGGGCAATTGCCTTTTAAACCTGAAGTTCAGCAACAAGTGAAAGAGATGTTGTATGTAGAGCGCAGAGGGGAGAATCGTCTATATGCTAAAAGTGGCTGGGGAATGGCTGTAGACCCGCAAGTGGGTTGGTATGTGGGTTTTGTTGAAAAGGCAGATGGGCAAGTGGTGGCATTTGCTTTAAATATGCAAATGAAAGATGGTGATGATATTGCTCTACGTAAACAATTGTCTTTAGATGTGCTAGATAAGTTGGGTGTTTTTCATTATTTATAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003116","ARO_id":"39693","ARO_name":"OXA-420","ARO_description":"From the Lahey list of beta-lactamases. Not yet released.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1078":{"model_id":"1078","model_name":"VIM-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1891":{"protein_sequence":{"accession":"CAJ32502.1","sequence":"MLKVISSLLVYMTASVMAVASPLAHSGEPSGEYPTVNEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEAEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSANVLYGGCAVHELSRTSAGNVADADLAEWPTSVERIQKHYPEAEVVIPGHGLPGGLDLLQHTANVVKAHKNRSVAE"},"dna_sequence":{"accession":"AM087411","fmin":"127","fmax":"928","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTACATGACCGCGTCTGTCATGGCTGTCGCAAGTCCGTTAGCCCATTCCGGGGAGCCGAGTGGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGAGAGGTCCGACTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCGGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAAAAGCAAATTGGACTTCCCGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGCAGAGGGGAACGAGATTCCCACGCATTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGCTCTTCTATCCTGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAACGTGCTATACGGTGGTTGTGCCGTTCATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCGTTGAGCGGATTCAAAAACACTACCCGGAAGCAGAGGTCGTCATTCCCGGGCACGGTCTACCGGGCGGTCTAGACTTGCTCCAGCACACAGCGAACGTTGTCAAAGCACACAAAAATCGCTCAGTCGCCGAGTAGC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002274","ARO_id":"38674","ARO_name":"VIM-4","ARO_description":"VIM-4 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1079":{"model_id":"1079","model_name":"OXA-161","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"881":{"protein_sequence":{"accession":"ACT09125.1","sequence":"MAIRIFAILFSIFSLATFAHAQEGTLERSDWRKFFSEFQAKGTIVVADERQADRAMLVFDPVRSKKRYSPASTFKIPHTLFALDAGAVRDEFQIFRWDGVNRGFAGHNQDQDLRSAMRNSTVWVYELFAKEIGDDKARRYLKKIDYGDADPSTSNGDYWIEGSLAISAQEQIAFLRKLYRNELPFRVEHQRLVKDLMIVEAGRNWILRAKTGWEGRMGWWVGWVEWPTGSVFFALNIDTPNRMDDLFKREAIVRAILRSIEALPPNPAVNSDAAR"},"dna_sequence":{"accession":"GQ202693","fmin":"1171","fmax":"1999","strand":"+","sequence":"ATGGCAATCCGAATCTTCGCGATACTTTTCTCCATTTTTTCTCTTGCCACTTTCGCGCATGCGCAAGAAGGCACGCTAGAACGTTCTGACTGGAGGAAGTTTTTCAGCGAATTTCAAGCCAAAGGCACGATAGTTGTGGCAGACGAACGCCAAGCGGATCGTGCCATGTTGGTTTTTGATCCTGTGCGATCGAAGAAACGCTACTCGCCTGCATCGACATTCAAGATACCTCATACACTTTTTGCACTTGATGCAGGCGCTGTTCGTGATGAGTTCCAGATTTTTCGATGGGACGGCGTTAACAGGGGCTTTGCAGGCCACAATCAAGACCAAGATTTGCGATCAGCAATGCGGAATTCTACTGTTTGGGTGTATGAGCTATTTGCAAAGGAAATTGGTGATGACAAAGCTCGGCGCTATTTGAAGAAAATCGACTATGGCGACGCCGATCCTTCGACAAGTAATGGCGATTACTGGATAGAAGGCAGCCTTGCAATCTCGGCGCAGGAGCAAATTGCATTTCTCAGGAAGCTCTATCGTAACGAGCTGCCCTTTCGGGTAGAACATCAGCGCTTGGTCAAGGATCTCATGATTGTGGAAGCCGGTCGCAACTGGATACTGCGTGCAAAGACGGGCTGGGAAGGCCGTATGGGTTGGTGGGTAGGATGGGTTGAGTGGCCGACTGGCTCCGTATTCTTCGCACTGAATATTGATACGCCAAACAGAATGGATGATCTTTTCAAGAGGGAGGCAATCGTGCGGGCAATCCTTCGCTCTATTGAAGCGTTACCGCCCAACCCGGCAGTCAACTCGGACGCTGCGCGATAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001799","ARO_id":"38199","ARO_name":"OXA-161","ARO_description":"OXA-161 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1080":{"model_id":"1080","model_name":"SHV-158","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1712":{"protein_sequence":{"accession":"AFQ23964.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLAAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"JX121125","fmin":"0","fmax":"858","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGTATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001197","ARO_id":"37577","ARO_name":"SHV-158","ARO_description":"SHV-158 is a beta-lactamase.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1081":{"model_id":"1081","model_name":"IMP-30","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1174":{"protein_sequence":{"accession":"ABF70513.1","sequence":"MSKLSVFFIFLFCSIATAAESLPDLKIEKLDEGVYVHTSFKEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNESKKPSKPSN"},"dna_sequence":{"accession":"DQ522237","fmin":"1075","fmax":"1816","strand":"+","sequence":"ATGAGCAAGTTATCTGTATTCTTTATATTTTTGTTTTGCAGCATTGCTACCGCAGCAGAGTCTTTGCCAGATTTAAAAATTGAAAAGCTTGATGAAGGCGTTTATGTTCATACTTCGTTTAAAGAAGTTAACGGGTGGGGCGTTGTTCCTAAACATGGTTTGGTGGTTCTTGTAAATGCTGAGGCTTACCTAATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAGCGTGGCTATAAAATAAAAGGCAGCATTTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCGATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTGCTTAAAAAAGACGGTAAGGTTCAAGCCACAAATTCATTTAGCGGAGTTAACTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCGGGACACACTCCAGATAACGTAGTGGTTTGGTTGCCTGAAAGGAAAATATTATTCGGTGGTTGTTTTATTAAACCGTACGGTTTAGGCAATTTGGGTGACGCAAATATAGAAGCTTGGCCAAAGTCCGCCAAATTATTAAAGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAAGTCACAGTGAAGTTGGAGACGCATCACTCTTGAAACTTACATTAGAGCAGGCGGTTAAAGGGTTAAACGAAAGTAAAAAACCATCAAAACCAAGCAACTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002221","ARO_id":"38621","ARO_name":"IMP-30","ARO_description":"IMP-30 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1082":{"model_id":"1082","model_name":"CTX-M-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1432":{"protein_sequence":{"accession":"CAA06312.1","sequence":"MMTQSIRRSMLTVMATLPLLFSSATLHAQANSVQQQLEALEKSSGGRLGVALINTADNSQILYVADERFAMCSTSKVMAAAAVLKQSESDKHLLNQRVEIRASDLVNYNPIAEKHVNGTMTLAQLGAGALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDRTEPTLNSAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSASIRAGLPKSWGVGDKTGSGDYGTTNDIAVIWPENHAPLVLVTYFTQPEQKAESRRDVLAAAAKIVTHGF"},"dna_sequence":{"accession":"AJ005045","fmin":"0","fmax":"876","strand":"+","sequence":"ATGATGACTCAGAGCATTCGCCGCTCAATGTTAACGGTGATGGCGACGCTACCCCTGCTATTTAGCAGCGCAACGCTGCATGCGCAGGCGAACAGCGTGCAACAGCAGCTGGAAGCCCTGGAGAAAAGTTCGGGAGGTCGGCTTGGCGTTGCGCTGATTAACACCGCCGATAATTCGCAGATTCTCTACGTGGCCGATGAGCGTTTTGCGATGTGCAGTACCAGTAAGGTGATGGCGGCCGCGGCGGTGCTTAAACAGAGCGAGAGCGATAAGCACCTGCTAAATCAGCGCGTTGAAATCAGAGCAAGCGACCTGGTTAACTACAATCCGATTGCGGAGAAACACGTTAACGGCACGATGACGCTGGCTCAGCTTGGCGCCGGCGCCCTGCAGTATAGCGACAATACTGCCATGAATAAGCTGATTGCCCATCTGGGTGGGCCCGATAAAGTGACGGCGTTTGCTCGCTCATTGGGTGATGAGACCTTCCGTCTGGACAGAACCGAGCCCACGCTCAATAGCGCCATTCCAGGCGACCCGCGTGATACCACCACGCCGCTCGCGATGGCGCAGACCCTGAAAAATCTGACGCTGGGCAAAGCGCTGGCGGAAACTCAGCGGGCACAGTTGGTGACGTGGCTTAAGGGCAATACTACCGGTAGCGCGAGCATTCGGGCGGGTCTGCCGAAATCATGGGGAGTGGGCGATAAAACCGGCAGCGGAGATTATGGCACCACCAACGATATCGCGGTTATCTGGCCGGAAAACCACGCACCGCTGGTTCTGGTGACCTACTTTACCCAACCGGAGCAGAAGGCGGAAAGCCGTCGGGATGTTCTGGCTGCGGCGGCGAAAATCGTAACCCACGGTTTCTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35732","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium","NCBI_taxonomy_id":"90371"}}}},"ARO_accession":"3001870","ARO_id":"38270","ARO_name":"CTX-M-7","ARO_description":"CTX-M-7 is a beta-lactamase found in Salmonella typhimurium","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1083":{"model_id":"1083","model_name":"OXA-323","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2008":{"protein_sequence":{"accession":"AGW16405.1","sequence":"MYKKALIVATSILFLSACSSNTVKQNQIHSISANKNSEEIKSLFDQAQTTGVLVIKRGQTEEIYGNDLKRASTAYVPASTFKMLNALIGLEHHKATITEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNANIGSKVDNFWLVGPLKITPQQETQFAYQLAHKTLPFSQDVQEQVQSMVFIEEKNGSKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"KF203097","fmin":"0","fmax":"822","strand":"+","sequence":"ATGTATAAAAAAGCCCTTATCGTTGCAACAAGTATCCTATTTTTATCCGCCTGTTCTTCCAATACGGTAAAACAAAATCAAATACATTCTATTTCTGCCAATAAAAATTCAGAAGAAATTAAATCACTATTTGATCAAGCACAGACCACGGGTGTTTTGGTGATTAAGCGAGGACAAACAGAAGAAATTTATGGCAATGATCTTAAAAGAGCATCAACCGCCTATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTAATTGGACTTGAACATCATAAGGCAACTATAACTGAAGTGTTTAAATGGGATGGACAAAAACGCTTATTTCCTGATTGGGAAAAGGACATGACACTGGGCGATGCCATGAAAGCTTCTGCGATTCCAGTTTACCAAGAATTAGCCCGACGAATTGGTCTAGATCTTATGTCCAAAGAGGTGAAACGAATTGGTTTTGGTAATGCTAACATTGGTTCAAAAGTAGATAATTTTTGGCTTGTTGGCCCTCTAAAAATTACACCTCAACAAGAAACCCAATTTGCTTATCAATTAGCCCATAAAACGCTTCCATTTAGCCAAGATGTACAAGAACAAGTTCAATCAATGGTGTTCATAGAGGAAAAAAATGGAAGTAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTTGAACCGCAAGTTGGTTGGTTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTGGCATTTTCACTTAATTTAGAAATGAAAAAAGGAACTCCTAGCTCTATTCGCAAAGAAATTGCTTATAAAGGCTTAGAACAACTGGGTATTTTATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3001511","ARO_id":"37911","ARO_name":"OXA-323","ARO_description":"OXA-323 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1084":{"model_id":"1084","model_name":"LEN-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"874":{"protein_sequence":{"accession":"AAU25807.1","sequence":"MRYIRLCVISLLATLPLAVYAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGLEQLDRRIHYRQQDLVDYSPVSEKHLTDGMTIGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPPGWFIADKTGAGERGARGIVALLGPDGKPERIVVIYLRDTPASMAERNQHIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AY633109","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTGTTATCTCCCTGTTAGCCACCCTGCCACTGGCGGTATACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCGGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTACCGACGGGATGACGATCGGCGAACTTTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGCCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGCCGGGCTGGTTTATCGCCGACAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCAACGCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002456","ARO_id":"38856","ARO_name":"LEN-5","ARO_description":"LEN-5 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1085":{"model_id":"1085","model_name":"OKP-B-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1676":{"protein_sequence":{"accession":"CAP12356.2","sequence":"MRYVRLCLISLIAALPLAVFASPQPLEQIKISESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNTAGNLLLKIVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMATTLRKLLTTPSLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPDGKAERIVVIYLRDTPATMVERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM850918","fmin":"24","fmax":"885","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCAGCCGCTTGAGCAGATTAAAATCAGCGAAAGTCAGCTGGCGGGCCGGGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGCGACGAACAGCTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACACCGCCGGCAATCTGCTGTTGAAGATCGTCGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTCAATGAGGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCGGCCAGCATGGCCACCACCCTGCGCAAGCTGCTAACCACCCCCTCTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTTGACGACCGGGTGGCCGGCCCGTTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGTGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAAGCGGAGCGTATCGTGGTGATCTATCTGCGTGATACCCCGGCGACCATGGTCGAGCGTAACCAGCAGATCGCCGGGATAGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002438","ARO_id":"38838","ARO_name":"OKP-B-5","ARO_description":"OKP-B-5 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1086":{"model_id":"1086","model_name":"CMY-41","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1345":{"protein_sequence":{"accession":"BAG14343.1","sequence":"MMKKSICCALLLTASFSTFAATKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEEKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDEVTDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"AB429270","fmin":"14","fmax":"1160","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCGCTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCACAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACGAGGAGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAATTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTACCGCTGCAGATCCCCGATGAAGTTACGGATAAAGCCGCATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGCGGTGAAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGTTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACAGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATAGTGATGCTGGCAAACAAAAGCTACCCCAACCCGGCTCGCGTCGAGGCGGCCTGGCGCATTCTTGAAAAACTGCAATAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002052","ARO_id":"38452","ARO_name":"CMY-41","ARO_description":"CMY-41 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1087":{"model_id":"1087","model_name":"OXA-253","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1457":{"protein_sequence":{"accession":"AGK07368.1","sequence":"MKKFILPIFSISILLSLSACSSIQTKFEDTSDISDQQQGKAIKSYFDEAQTQGVIIIKEGKNISTYGNNLARAHTEYVPASTFKMLNALIGLENHKATTTEIFKWDGKKRSYPMWEKDMTLGDAMALSAVPVYQELARRTGLDLMQKEVKRVGFGNMNIGTQVDNFWLVGPLKITPIQEVNFADDLANNRLPFKLETQEEVKKMLLIKEVNGSKIYAKSGWGMDVIPQVGWLTGWVEKSNGEKVPFSLNLEMKQGMSGSIRNEITYKSLENLGII"},"dna_sequence":{"accession":"KC479324","fmin":"575","fmax":"1403","strand":"+","sequence":"ATGAAAAAATTTATACTTCCTATCTTCAGCATTTCTATTCTACTTTCTCTCAGTGCATGCTCATCTATTCAAACTAAATTTGAAGATACTTCTGATATTTCTGATCAGCAACAAGGAAAAGCCATTAAAAGCTATTTTGATGAAGCTCAAACACAAGGTGTAATCATTATTAAAGAGGGAAAGAATATTAGTACCTATGGTAATAACCTGGCACGAGCACATACAGAATATGTCCCTGCATCAACATTTAAGATGCTAAATGCCTTAATTGGATTAGAAAATCATAAAGCTACAACAACTGAGATTTTCAAATGGGATGGTAAAAAAAGATCTTATCCTATGTGGGAAAAAGATATGACTTTAGGTGATGCCATGGCACTTTCAGCAGTTCCTGTATATCAAGAACTTGCAAGACGGACTGGTTTAGACCTAATGCAAAAAGAAGTCAAACGGGTTGGTTTTGGTAATATGAACATTGGAACACAAGTTGATAACTTCTGGTTGGTTGGCCCGCTTAAAATTACACCAATACAAGAGGTTAATTTTGCCGACGATCTCGCTAATAATCGATTACCCTTTAAATTAGAAACTCAAGAAGAAGTAAAAAAAATGCTTCTGATTAAAGAAGTCAATGGTAGTAAAATTTATGCGAAAAGCGGATGGGGAATGGATGTAATCCCTCAGGTAGGTTGGTTAACAGGTTGGGTAGAAAAATCTAATGGCGAAAAAGTTCCCTTTTCTCTAAACCTAGAAATGAAGCAAGGAATGTCTGGTTCTATTCGTAATGAAATTACTTATAAGTCATTAGAAAATTTAGGGATTATATAGT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001689","ARO_id":"38089","ARO_name":"OXA-253","ARO_description":"OXA-253 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1089":{"model_id":"1089","model_name":"CMY-14","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1662":{"protein_sequence":{"accession":"CAD88479.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYARGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEINPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"AJ555825","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCCGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGATAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3002025","ARO_id":"38425","ARO_name":"CMY-14","ARO_description":"CMY-14 is a beta-lactamase found in Proteus mirabilis","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1090":{"model_id":"1090","model_name":"TEM-169","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1075":{"protein_sequence":{"accession":"ACP18864.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMLSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRGEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"FJ873740","fmin":"0","fmax":"858","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGCTGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTGGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35655","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Infantis","NCBI_taxonomy_id":"595"}}}},"ARO_accession":"3001035","ARO_id":"37415","ARO_name":"TEM-169","ARO_description":"TEM-169 is an extended spectrum beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1091":{"model_id":"1091","model_name":"IMP-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1278":{"protein_sequence":{"accession":"BAB15941.1","sequence":"MSKLSVFFIFLFCSIATAAESLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPGHSEVGDASLLKLTLEQAVKGLNESKKPSKPSN"},"dna_sequence":{"accession":"AB040994","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAGCAAGTTATCTGTATTCTTTATATTTTTGTTTTGCAGCATTGCTACCGCAGCAGAGTCTTTGCCAGATTTAAAAATTGAAAAGCTTGATGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGGTGGGGCGTTGTTCCTAAACATGGTTTGGTGGTTCTTGTAAATGCTGAGGCTTACCTAATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAGCGTGGCTATAAAATAAAAGGCAGCATTTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCGATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTGCTTAAAAAAGACGGTAAGGTTCAAGCCACAAATTCATTTAGCGGAGTTAACTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCGGGACACACTCCAGATAACGTAGTGGTTTGGTTGCCTGAAAGGAAAATATTATTCGGTGGTTGTTTTATTAAACCGTACGGTTTAGGCAATTTGGGTGACGCAAATATAGAAGCTTGGCCAAAGTCCGCCAAATTATTAAAGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAGGTCACAGTGAAGTTGGAGACGCATCACTCTTGAAACTTACATTAGAGCAGGCGGTTAAAGGGTTAAACGAAAGTAAAAAACCATCAAAACCAAGCAACTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36783","NCBI_taxonomy_name":"Serratia marcescens","NCBI_taxonomy_id":"615"}}}},"ARO_accession":"3002197","ARO_id":"38597","ARO_name":"IMP-6","ARO_description":"IMP-6 is a beta-lactamase found in Serratia marcescens","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1093":{"model_id":"1093","model_name":"AAC(6')-31","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"325"}},"model_sequences":{"sequence":{"267":{"protein_sequence":{"accession":"CAK55557.1","sequence":"MTEHDLPMLHDWLNRPHIVEWWGGEETRPTLAEVLEQYLPSALAKESVTPYIAMLDEEPIGYAQSYIALGSGDGWWEDETDPGVRGIDQSLANPSQLGKGLGTKLVCALVEMLFKDAEVTKIQTDPSPNNLRAIRCYEKAGFVAQRTINTPDGPAVYMVQTRQAFEQARSAV"},"dna_sequence":{"accession":"AM283489","fmin":"2655","fmax":"3174","strand":"+","sequence":"ATGACCGAGCACGACCTTCCGATGCTCCATGACTGGCTAAATCGGCCTCACATCGTTGAGTGGTGGGGCGGAGAAGAAACACGTCCAACACTTGCTGAAGTGCTGGAGCAATACCTACCAAGCGCCCTGGCGAAAGAGTCCGTCACTCCCTACATCGCAATGCTGGATGAAGAACCGATTGGGTACGCTCAGTCGTACATTGCACTCGGAAGCGGTGACGGATGGTGGGAAGACGAAACCGATCCAGGAGTACGCGGAATAGACCAGTCTCTGGCGAATCCATCGCAGCTGGGCAAGGGCTTGGGAACCAAGCTCGTTTGCGCGCTCGTTGAGATGCTGTTCAAAGACGCTGAGGTAACCAAGATCCAAACGGACCCGTCGCCGAACAACTTACGCGCAATCCGGTGCTACGAGAAGGCGGGTTTTGTGGCGCAAAGAACCATAAACACCCCAGATGGACCGGCCGTATACATGGTTCAAACACGTCAGGCGTTCGAGCAGGCGCGCAGTGCTGTCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36803","NCBI_taxonomy_name":"Pseudomonas putida","NCBI_taxonomy_id":"303"}}}},"ARO_accession":"3002585","ARO_id":"38985","ARO_name":"AAC(6')-31","ARO_description":"AAC(6')-31 is an integron-encoded aminoglycoside acetyltransferase in Pseudomonas putida, A. baumannii and K. pneumoniae","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1094":{"model_id":"1094","model_name":"CARB-17","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"862":{"protein_sequence":{"accession":"AIL92326.1","sequence":"MKKLFLLVGLMVCSTVSYASKLNEDISLIEKQTSGRIGVSVWDTQTDERWDYRGDERFPLMSTFKTLACATMLSDMDSGKLNKNATARIDERNIVVWSPVMDKLTGQSTRIEHACEAAMLMSDNTAANLVLNEIGGPKAVTLFLRSIGDKATRLDRLEPRLNEAKPGDKRDTTTPNAMVNTLHTLMEDNALSYESRTQLKIWMQDNKVSDSLMRSVLPKGWSIADRSGAGNYGSRGISAMIWKDNYKPVYISIYVTDTDLSLQARDQLIAQISQLILEHYKES"},"dna_sequence":{"accession":"KJ934265","fmin":"0","fmax":"852","strand":"+","sequence":"ATGAAAAAGTTATTCCTGTTGGTTGGGCTGATGGTTTGCTCAACTGTTAGTTACGCCTCCAAATTAAACGAAGACATCTCCCTCATCGAGAAACAAACATCTGGGCGAATTGGAGTGTCAGTCTGGGATACACAAACGGACGAGCGTTGGGATTATCGCGGAGACGAACGCTTCCCATTAATGAGCACATTCAAAACGTTAGCGTGTGCCACCATGCTAAGCGACATGGACAGCGGCAAACTCAACAAAAATGCCACAGCGAGAATCGATGAACGCAATATTGTGGTTTGGTCTCCGGTGATGGATAAACTGACTGGACAAAGCACACGTATCGAACACGCTTGTGAAGCCGCCATGTTGATGAGCGACAACACCGCCGCGAACTTAGTGCTAAATGAAATTGGTGGTCCTAAAGCGGTCACACTGTTTTTGCGCTCTATTGGCGACAAAGCAACGCGACTTGACCGATTGGAACCCCGTTTGAATGAAGCAAAACCGGGCGACAAGCGAGATACCACAACGCCTAACGCCATGGTAAACACCCTACATACCTTGATGGAAGATAACGCCCTATCTTACGAGTCACGCACACAGCTGAAAATCTGGATGCAAGACAACAAAGTATCGGATTCGCTCATGCGCTCTGTTCTGCCAAAAGGCTGGTCGATTGCAGACCGCTCTGGCGCAGGTAACTACGGTTCACGCGGCATTAGCGCGATGATCTGGAAAGACAACTACAAGCCAGTTTACATCAGTATTTACGTCACAGACACCGACCTTTCGCTTCAAGCTCGCGATCAACTGATCGCGCAAATCAGCCAACTGATTTTAGAGCACTACAAAGAAAGTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39615","NCBI_taxonomy_name":"Vibrio parahaemolyticus","NCBI_taxonomy_id":"670"}}}},"ARO_accession":"3002254","ARO_id":"38654","ARO_name":"CARB-17","ARO_description":"CARB-17 is a beta-lactamase. From the Lahey list of IMP beta-lactamases.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1095":{"model_id":"1095","model_name":"SHV-59","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1791":{"protein_sequence":{"accession":"AAV66328.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSVANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTLASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AY790341","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACCCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGTCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATCGTGGTGATTTATCTGCGGGATACGCTGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001114","ARO_id":"37494","ARO_name":"SHV-59","ARO_description":"SHV-59 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1096":{"model_id":"1096","model_name":"TEM-79","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"851":{"protein_sequence":{"accession":"AAF05611.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSGGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AF190692","fmin":"208","fmax":"1069","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTGGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000946","ARO_id":"37326","ARO_name":"TEM-79","ARO_description":"TEM-79 is an inhibitor-resistant beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1097":{"model_id":"1097","model_name":"Erm(38)","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"4238":{"protein_sequence":{"accession":"AAN86837.2","sequence":"MSTPHHGRHELGQNFLSDRRVIADIVEIVSRTNGPIIEIGAGDGALTIPLQRLARPLTAVEVDARRARRLAQRTARSAPGPASRPTEVVAADFLRYPLPRSPHVVVGNLPFHLTTAILRRLLHGPGWTTAVLLMQWEVARRRAAVGGATMMTAQWWPWFEFGLARKVSAASFTPRPAVDAGLLTITRRSRPLVDVADRARYQALVHRVFTGRGHGMAQILQRLPTPVPRTWLRANGIAPNSLPRQLSAAQWAALFEQTRLTGAQRVDRPRDVQHGRAHRRRGGEVDRPATHHKQTGPVVGQRQPQRGRDADADPDDQRTAPPVTRHHQGERRDEDQADHQDRPLTGEHLAGEFLWRHASFDSSASTTLVSRKARVNGPTPPGLGDT"},"dna_sequence":{"accession":"AY154657.2","fmin":"62","fmax":"1223","strand":"+","sequence":"GTGTCCACACCACATCACGGCCGGCACGAGCTCGGCCAGAACTTCCTGTCCGATCGGCGCGTCATCGCCGATATCGTCGAAATCGTCTCGCGCACAAACGGTCCGATCATCGAGATCGGGGCGGGCGACGGCGCGCTGACCATACCCTTGCAACGACTCGCCCGCCCGCTCACCGCCGTCGAGGTCGACGCGCGGCGCGCGCGGCGGTTGGCGCAGCGCACCGCGAGATCCGCCCCGGGGCCTGCCTCGCGGCCCACCGAGGTCGTCGCCGCCGACTTCCTGCGCTACCCACTGCCCCGCTCACCCCACGTGGTCGTGGGCAACCTGCCGTTCCACCTCACCACCGCGATCCTGCGGCGACTGCTGCACGGTCCGGGCTGGACCACGGCCGTGCTGCTCATGCAGTGGGAGGTGGCCCGCCGACGCGCCGCGGTGGGCGGCGCCACCATGATGACCGCCCAGTGGTGGCCGTGGTTCGAATTCGGCCTTGCCCGAAAGGTTTCCGCGGCGAGCTTCACGCCGCGGCCCGCGGTCGACGCCGGACTGCTCACCATCACGCGCCGCAGCCGGCCGCTGGTCGACGTCGCGGACCGGGCGCGTTACCAGGCGCTGGTGCACCGCGTGTTCACCGGACGCGGACACGGCATGGCGCAGATCCTGCAACGGTTGCCCACGCCGGTGCCCCGCACTTGGTTGCGGGCCAACGGGATAGCACCGAACTCCCTGCCCCGCCAGTTGTCCGCGGCGCAGTGGGCGGCGCTGTTCGAGCAGACGCGTCTAACTGGTGCCCAACGGGTCGATCGTCCACGCGATGTACAGCACGGCCGCGCTCACCGTCGCCGTGGTGGCGAAGTCGATCGCCCGGCTACGCACCACAAGCAGACCGGCCCGGTCGTCGGTCAGCGCCAACCGCAGCGCGGCCGCGACGCCGACGCCGATCCCGATGACCAGCGCACCGCGCCGCCAGTAACCCGCCACCACCAGGGCGAACGCCGCGATGAAGATCAGGCCGACCACCAGGATCGGCCATTGACCGGCGAACACCTTGCGGGCGAATTCCTTTGGCGTCACGCCAGTTTCGACTCTTCGGCTTCGACGACGTTGGTCAGCAGGAAGGCGCGGGTCAACGGGCCCACGCCACCGGGGTTGGGCGACACGTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36871","NCBI_taxonomy_name":"Mycobacterium smegmatis","NCBI_taxonomy_id":"1772"}}}},"ARO_accession":"3000601","ARO_id":"36740","ARO_name":"Erm(38)","ARO_description":"ErmD confers MLSb phenotype.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35946":{"category_aro_accession":"0000027","category_aro_cvterm_id":"35946","category_aro_name":"roxithromycin","category_aro_description":"Roxithromycin is a semi-synthetic, 14-carbon ring macrolide antibiotic derived from erythromycin. It is used to treat respiratory tract, urinary and soft tissue infections. Roxithromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35974":{"category_aro_accession":"0000057","category_aro_cvterm_id":"35974","category_aro_name":"telithromycin","category_aro_description":"Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36315":{"category_aro_accession":"3000176","category_aro_cvterm_id":"36315","category_aro_name":"dirithromycin","category_aro_description":"Dirithromycin is an oxazine derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome to inhibit bacterial protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin 1A is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"vernamycin B-gamma","category_aro_description":"Vernamycin B-gamma is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1098":{"model_id":"1098","model_name":"vanB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"650"}},"model_sequences":{"sequence":{"107":{"protein_sequence":{"accession":"AHH83938.1","sequence":"MNRIKVAIIFGGCSEEHDVSVKSAIEIAANIDTEKFDPHYIGITKNGVWKLCKKPCTEWEADSLPAILSPDRKTHGLLVMKESEYETRRIDVAFPVLHGKCGEDGAIQGLFVLSGIPYVGCDIQSSAACMDKSLAYILTKNAGIAVPEFQMIDKGDKPEAGALTYPVFVKPARSGSSFGVTKVNGTEELNAAIEAAGQYDGKILIEQAISGCEVGCAVMGNEDDLIVGEVDQIRLSHGIFRIHQENEPEKGSENAMITVPADIPVEERNRVQETAKKVYRVLGCRGLARVDLFLQEDGGIVLNEVNTLPGFTSYSRYPRMMAAAGITLPALIDSLITLALKR"},"dna_sequence":{"accession":"KF823969","fmin":"5110","fmax":"6139","strand":"+","sequence":"ATGAATAGAATAAAAGTCGCAATCATCTTCGGCGGTTGCTCGGAGGAACATGATGTGTCGGTAAAATCCGCAATAGAAATTGCTGCGAACATTGATACGGAAAAATTCGATCCGCACTACATCGGAATTACAAAAAACGGTGTATGGAAGCTATGCAAGAAGCCATGTACGGAATGGGAAGCCGACAGTCTCCCCGCCATACTCTCCCCGGATAGGAAAACGCATGGGCTGCTTGTCATGAAAGAAAGCGAATACGAAACACGGCGTATTGATGTGGCTTTCCCGGTTTTGCATGGCAAATGCGGGGAGGATGGTGCGATACAGGGGCTGTTTGTATTGTCTGGTATCCCCTATGTGGGCTGTGATATTCAAAGCTCCGCAGCTTGCATGGACAAATCACTGGCCTACATTCTTACAAAAAATGCGGGCATCGCCGTTCCCGAATTTCAAATGATTGATAAAGGTGACAAGCCGGAGGCGGGTGCGCTTACCTACCCTGTCTTTGTGAAGCCGGCACGGTCAGGTTCGTCCTTTGGCGTAACCAAAGTAAACGGTACGGAAGAACTTAACGCTGCGATAGAAGCGGCAGGACAATATGATGGAAAAATCTTAATTGAGCAAGCGATTTCGGGCTGTGAGGTCGGGTGTGCGGTCATGGGGAACGAGGATGATTTGATTGTCGGCGAAGTGGATCAAATCCGGCTGAGCCACGGTATCTTCCGCATCCATCAGGAAAACGAGCCGGAAAAAGGCTCAGAAAATGCGATGATTACAGTTCCCGCAGACATTCCGGTCGAGGAACGAAATCGGGTGCAGGAAACGGCAAAGAAAGTATATCGGGTGCTTGGATGCAGAGGGCTTGCCCGTGTTGATCTTTTTTTGCAGGAGGATGGCGGCATCGTTCTAAATGAGGTCAATACCCTGCCCGGTTTTACATCGTACAGCCGCTACCCACGTATGATGGCCGCCGCAGGAATCACGCTTCCTGCACTGATTGACAGCCTGATTACATTGGCGTTAAAGAGGTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3000013","ARO_id":"36022","ARO_name":"vanB","ARO_description":"VanB is a D-Ala-D-Ala ligase homolog similar to VanA, and can synthesize D-Ala-D-Lac, an alternative substrate for peptidoglycan synthesis that reduces vancomycin binding affinity. It has been isolated from VREs. It is associated with vancomycin resistance, but not teicoplanin resistance.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"39340":{"category_aro_accession":"3002906","category_aro_cvterm_id":"39340","category_aro_name":"van ligase","category_aro_description":"van ligases synthesize alternative substrates for peptidoglycan synthesis that reduce vancomycin binding affinity.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1099":{"model_id":"1099","model_name":"OXA-48","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1691":{"protein_sequence":{"accession":"AAP70012.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"AY236073","fmin":"2187","fmax":"2985","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGACAGTTTCTGGCTCGACGGTGGTATTCGAATTTCGGCCACGGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATGCTGACCGAAGCCAATGGTGACTATATTATTCGGGCTAAAACTGGATACTCGACTAGAATCGAACCTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001782","ARO_id":"38182","ARO_name":"OXA-48","ARO_description":"OXA-48 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"40522":{"category_aro_accession":"3003831","category_aro_cvterm_id":"40522","category_aro_name":"temocillin","category_aro_description":"Temocillin is a beta-lactamase resistant carboxypenicillin. It is primarily used for the treatment of multiple drug resistant, Gram-negative bacteria, specifically Enterobacteriaceae.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1100":{"model_id":"1100","model_name":"OXA-245","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"805":{"protein_sequence":{"accession":"AGC60013.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQYFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"JX438001","fmin":"0","fmax":"798","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTGTGCCTGTTTATCAATACTTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGACAGTTTCTGGCTCGACGGTGGTATTCGAATTTCGGCCACGGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATGCTGACCGAAGCCAATGGTGACTATATTATTCGGGCTAAAACTGGATACTCGACTAGAATCGAACCTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001787","ARO_id":"38187","ARO_name":"OXA-245","ARO_description":"OXA-245 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1101":{"model_id":"1101","model_name":"CTX-M-21","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1255":{"protein_sequence":{"accession":"CAD08929.1","sequence":"MVTKRVQRMMFAGGAGIPLLLGSAPFYAQTSAGQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"AJ416346","fmin":"556","fmax":"1432","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGGGGGGGCGGGCATTCCGCTGCTGTTGGGCAGCGCGCCGTTTTATGCGCAGACGAGTGCGGGGCAGCAAAAGCTGGCGGCGCTGGAAAAAAGCAGCGGAGGGCGGTTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001883","ARO_id":"38283","ARO_name":"CTX-M-21","ARO_description":"CTX-M-21 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1102":{"model_id":"1102","model_name":"QnrB29","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"235":{"protein_sequence":{"accession":"ADM52193.1","sequence":"MTPLLYKKTGTNMALALVGEKIDRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMVDFRNASALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"HM439649","fmin":"0","fmax":"681","strand":"+","sequence":"ATGACGCCATTACTGTATAAAAAAACAGGTACAAATATGGCACTGGCACTCGTTGGCGAAAAAATTGACAGAAACCGCTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCGATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGTGGATTTTCGCAATGCCAGTGCGCTTGGCATTGAAATTCGCCACTGTCGTGCGCAAGGCGCAGATTTCCGCGGCGCAAGCTTTATGAATATGATCACTACTCGCACCTGGTTTTGCAGCGCATATATCACTAACACAAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGCTGGAAAAATGTGAGCTGTGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTTTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTGACTTAGATATTCGGGGCGTTGATTTACAAGGCGTTAAGTTGGACAACTACCAGGCATCGTTGCTCATGGAACGTCTTGGCATCGCGGTGATTGGCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002744","ARO_id":"39178","ARO_name":"QnrB29","ARO_description":"QnrB29 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1103":{"model_id":"1103","model_name":"CMY-17","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1895":{"protein_sequence":{"accession":"AAS13399.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVAFAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"AY513266","fmin":"164","fmax":"1310","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTTGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002028","ARO_id":"38428","ARO_name":"CMY-17","ARO_description":"CMY-17 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1104":{"model_id":"1104","model_name":"acrB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1900"}},"model_sequences":{"sequence":{"4015":{"protein_sequence":{"accession":"NP_414995.1","sequence":"MPNFFIDRPIFAWVIAIIIMLAGGLAILKLPVAQYPTIAPPAVTISASYPGADAKTVQDTVTQVIEQNMNGIDNLMYMSSNSDSTGTVQITLTFESGTDADIAQVQVQNKLQLAMPLLPQEVQQQGVSVEKSSSSFLMVVGVINTDGTMTQEDISDYVAANMKDAISRTSGVGDVQLFGSQYAMRIWMNPNELNKFQLTPVDVITAIKAQNAQVAAGQLGGTPPVKGQQLNASIIAQTRLTSTEEFGKILLKVNQDGSRVLLRDVAKIELGGENYDIIAEFNGQPASGLGIKLATGANALDTAAAIRAELAKMEPFFPSGLKIVYPYDTTPFVKISIHEVVKTLVEAIILVFLVMYLFLQNFRATLIPTIAVPVVLLGTFAVLAAFGFSINTLTMFGMVLAIGLLVDDAIVVVENVERVMAEEGLPPKEATRKSMGQIQGALVGIAMVLSAVFVPMAFFGGSTGAIYRQFSITIVSAMALSVLVALILTPALCATMLKPIAKGDHGEGKKGFFGWFNRMFEKSTHHYTDSVGGILRSTGRYLVLYLIIVVGMAYLFVRLPSSFLPDEDQGVFMTMVQLPAGATQERTQKVLNEVTHYYLTKEKNNVESVFAVNGFGFAGRGQNTGIAFVSLKDWADRPGEENKVEAITMRATRAFSQIKDAMVFAFNLPAIVELGTATGFDFELIDQAGLGHEKLTQARNQLLAEAAKHPDMLTSVRPNGLEDTPQFKIDIDQEKAQALGVSINDINTTLGAAWGGSYVNDFIDRGRVKKVYVMSEAKYRMLPDDIGDWYVRAADGQMVPFSAFSSSRWEYGSPRLERYNGLPSMEILGQAAPGKSTGEAMELMEQLASKLPTGVGYDWTGMSYQERLSGNQAPSLYAISLIVVFLCLAALYESWSIPFSVMLVVPLGVIGALLAATFRGLTNDVYFQVGLLTTIGLSAKNAILIVEFAKDLMDKEGKGLIEATLDAVRMRLRPILMTSLAFILGVMPLVISTGAGSGAQNAVGTGVMGGMVTATVLAIFFVPVFFVVVRRRFSRKNEDIEHSHTVDHH"},"dna_sequence":{"accession":"NC_000913.3","fmin":"481253","fmax":"484403","strand":"-","sequence":"TCAATGATGATCGACAGTATGGCTGTGCTCGATATCTTCATTCTTGCGGCTAAAGCGGCGGCGAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTGCGCGCCGGAACCAGCACCAGTACTGATAACCAGCGGCATAACGCCGAGGATAAACGCCAGCGAGGTCATCAGGATCGGACGTAAACGCATCCGCACCGCATCAAGCGTCGCTTCAATCAGACCTTTACCTTCTTTATCCATCAAGTCTTTGGCGAATTCGACGATAAGGATCGCGTTCTTCGCCGACAACCCAATGGTTGTGAGCAGGCCTACCTGGAAGTAAACGTCATTGGTCAGGCCACGGAAGGTGGCAGCCAGCAACGCACCGATAACCCCCAGCGGAACGACCAGCATAACGGAGAACGGAATCGACCAGCTCTCGTACAGCGCCGCCAGACACAGGAACACGACAATCAACGAAATCGCGTACAGTGAAGGTGCCTGGTTGCCGGAGAGACGTTCCTGATAGGACATCCCCGTCCAGTCATAGCCAACACCGGTAGGCAGTTTGCTCGCCAGTTGTTCCATCAGCTCCATTGCTTCACCGGTACTTTTACCCGGTGCCGCCTGGCCTAAGATTTCCATGGATGGCAGGCCGTTGTAACGTTCCAGACGCGGCGAACCGTACTCCCAACGAGAAGAGGAGAACGCCGAGAATGGCACCATCTGACCATCAGCAGCACGAACATACCAGTCGCCGATATCATCCGGCAGCATACGGTATTTCGCTTCTGACATGACATAAACTTTCTTCACACGACCGCGGTCGATAAAGTCGTTCACATAGCTGCCGCCCCATGCAGCGCCCAGAGTGGTGTTAATGTCGTTGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCGGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGCTTCGCTGCTTCTGCAAGCAACTGGTTACGCGCCTGAGTCAGTTTTTCGTGACCAAGGCCAGCCTGGTCAATCAGCTCAAAGTCAAAGCCGGTTGCAGTACCCAGTTCCACGATTGCGGGCAGGTTAAAGGCGAAAACCATCGCATCTTTGATTTGCGAGAAAGCGCGTGTTGCACGCATGGTAATCGCTTCAACTTTGTTTTCTTCGCCCGGACGATCGGCCCAGTCCTTCAAGGAAACGAACGCAATACCGGTATTCTGACCACGTCCCGCAAAGCCGAAGCCGTTAACGGCGAACACCGACTCAACGTTGTTCTTTTCTTTGGTCAGATAGTAATGCGTTACCTCATTGAGCACTTTCTGTGTACGTTCCTGCGTTGCACCTGCTGGCAGCTGAACCATGGTCATAAACACGCCCTGGTCCTCATCTGGCAAGAAGGAGCTTGGCAGACGCACGAACAGATAGGCCATGCCGACCACGATGATCAGATACAGCACCAGGTAACGCCCCGTACTGCGCAGAATACCGCCTACGCTGTCGGTGTAGTGGTGCGTGCTCTTCTCGAACATGCGGTTAAACCAGCCGAAGAAGCCTTTTTTACCTTCCCCGTGATCGCCTTTGGCAATCGGTTTCAGCATGGTGGCACAAAGAGCTGGAGTCAGGATCAACGCCACCAGTACCGACAGCGCCATTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCAAACCTTCTTCCGCCATAACACGCTCAACGTTTTCTACCACAACGATGGCGTCATCCACCAACAGGCCGATGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCAAAGGCGGCAAGGACGGCAAAGGTCCCGAGCAATACCACCGGTACGGCAATGGTCGGAATCAACGTCGCGCGGAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCGTATGGGTAAACAATTTTCAGACCCGACGGGAAGAACGGTTCCATCTTCGCCAGTTCAGCACGGATTGCCGCAGCGGTATCCAGCGCGTTTGCACCGGTCGCCAGCTTGATCCCCAGACCGGAAGCCGGTTGGCCGTTAAACTCTGCGATGATGTCGTAGTTCTCACCACCCAGCTCAATCTTCGCGACGTCACGCAGCAGCACGCGGGAACCATCCTGATTCACTTTCAGCAGGATTTTGCCGAACTCTTCAGTAGAGGTCAGACGCGTCTGAGCAATAATAGAGGCGTTAAGCTGTTGGCCTTTCACCGGCGGCGTACCACCGAGCTGACCCGCCGCAACCTGGGCGTTCTGCGCTTTGATGGCGGTAATGACATCAACCGGCGTTAGCTGGAATTTGTTCAGCTCATTCGGGTTCATCCAGATACGCATCGCGTACTGTGAACCGAACAACTGAACATCACCCACGCCCGACGTACGGCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAACGCCGACAACCATCAGGAAGCTGCTGGATGATTTCTCAACGCTCACCCCTTGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTACCAGACTCAAAGGTCAGGGTGATCTGCACGGTACCCGTGGAGTCACTGTTAGAGGACATGTACATCAGGTTATCGATACCGTTCATATTCTGTTCGATAACCTGTGTCACCGTGTCCTGCACTGTTTTCGCATCAGCGCCGGGGTAGGAGGCGGAGATCGTTACTGCCGGCGGTGCAATCGTAGGATATTGCGCCACCGGCAGTTTGAGGATCGCCAGCCCCCCTGCCAACATGATGATAATGGCGATCACCCACGCAAAAATCGGGCGATCGATAAAGAAATTAGGCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3000216","ARO_id":"36355","ARO_name":"acrB","ARO_description":"Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug\/proton antiporter.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1105":{"model_id":"1105","model_name":"AAC(3)-VIa","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"659":{"protein_sequence":{"accession":"AAA16194.1","sequence":"MTDPRKNGDLHEPATAPATPWSKSELVRQLRDLGVRSGDMVMPHVSLRAVGPLADGPQTLVDALIEAVGPTGNILAFVSWRDSPYEQTLGHDAPPAAIAQSWPAFDPDHAPAYPGFGAINEFIRTYPGCRRTAHPDASMAAIGPDAAWLVAPHEMGAAYGPRSPIARFLAHAGKILSIGAGPDAVTALHYAEAVARIEGKRRVTYSMPLLREGKRVWVTTSDWDSNGILDEYAAPDGPDAVERIARDYLARTRVAQGPVGGAQSRLIDAADIVSFGIEWLEARHAAPAAAALKPKQRRD"},"dna_sequence":{"accession":"M88012","fmin":"192","fmax":"1092","strand":"+","sequence":"ATGACTGATCCCCGCAAAAACGGCGATTTGCACGAACCCGCGACGGCACCCGCGACGCCCTGGTCCAAAAGCGAGCTGGTCCGGCAATTGCGCGACCTCGGCGTGCGCTCAGGCGATATGGTGATGCCGCATGTGTCGTTGCGCGCCGTCGGGCCGCTGGCGGACGGACCGCAGACACTTGTCGATGCGCTGATCGAGGCCGTCGGCCCCACCGGGAATATTCTCGCCTTCGTCTCGTGGCGCGATTCGCCCTATGAACAGACGCTGGGTCATGATGCGCCGCCCGCCGCCATCGCCCAAAGCTGGCCTGCGTTCGACCCCGACCATGCGCCCGCCTACCCCGGCTTTGGCGCGATCAACGAATTTATCCGAACCTATCCGGGGTGTCGGCGCACGGCCCATCCCGACGCATCGATGGCGGCGATCGGGCCCGATGCGGCGTGGCTGGTGGCGCCGCACGAGATGGGCGCCGCTTATGGCCCCCGCTCGCCGATCGCGCGTTTTCTCGCCCACGCAGGAAAAATCCTGTCGATCGGCGCCGGGCCCGATGCAGTCACCGCGCTCCATTATGCCGAAGCGGTGGCGCGGATCGAGGGCAAGCGCCGCGTCACTTATTCGATGCCCTTACTGCGCGAAGGCAAGCGCGTCTGGGTCACCACGTCCGACTGGGATTCGAACGGCATCCTCGACGAATATGCCGCGCCCGACGGCCCCGACGCGGTCGAACGGATCGCCCGCGACTATCTCGCCCGCACCAGGGTTGCGCAAGGCCCGGTCGGCGGCGCGCAATCCCGGCTGATCGACGCGGCCGATATCGTTTCCTTCGGCATCGAATGGCTCGAGGCGCGCCACGCCGCGCCAGCGGCGGCAGCGCTGAAGCCGAAACAACGCCGCGACTGAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3002540","ARO_id":"38940","ARO_name":"AAC(3)-VIa","ARO_description":"AAC(3)-VIa is a plasmid-encoded aminoglycoside acetyltransferase in E. cloacae, S. enterica and E. coli","ARO_category":{"36461":{"category_aro_accession":"3000322","category_aro_cvterm_id":"36461","category_aro_name":"AAC(3)","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 3.","category_aro_class_name":"AMR Gene Family"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1106":{"model_id":"1106","model_name":"NDM-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1025":{"protein_sequence":{"accession":"AEN03071.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLLVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGLVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"JN104597","fmin":"114","fmax":"927","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGTTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGCTGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000467","ARO_id":"36606","ARO_name":"NDM-5","ARO_description":"New Delhi beta-lactamase NDM-5.","ARO_category":{"35994":{"category_aro_accession":"0000077","category_aro_cvterm_id":"35994","category_aro_name":"tazobactam","category_aro_description":"Tazobactam is a compound which inhibits the action of bacterial beta-lactamases.","category_aro_class_name":"Adjuvant"},"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35927":{"category_aro_accession":"0000008","category_aro_cvterm_id":"35927","category_aro_name":"cefoxitin","category_aro_description":"Cefoxitin is a cephamycin antibiotic often grouped with the second generation cephalosporins. Cefoxitin is bactericidal and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. Cefoxitin's 7-alpha-methoxy group and 3' leaving group make it a poor substrate for most beta-lactamases.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35987":{"category_aro_accession":"0000070","category_aro_cvterm_id":"35987","category_aro_name":"ertapenem","category_aro_description":"Ertapenem is a carbapenem antibiotic and is highly resistant to beta-lactamases like other carbapenems. It inhibits bacterial cell wall synthesis.","category_aro_class_name":"Antibiotic"},"35995":{"category_aro_accession":"0000078","category_aro_cvterm_id":"35995","category_aro_name":"piperacillin","category_aro_description":"Piperacillin is an acetylureidopenicillin and has an extended spectrum of targets relative to other beta-lactam antibiotics. It inhibits cell wall synthesis in bacteria, and is usually taken with the beta-lactamase inhibitor tazobactam to overcome penicillin-resistant bacteria.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1107":{"model_id":"1107","model_name":"PDC-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"1468":{"protein_sequence":{"accession":"ACQ82806.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTVTLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"FJ666064","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGACGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGTCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTATGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002498","ARO_id":"38898","ARO_name":"PDC-2","ARO_description":"PDC-2 is a extended-spectrum beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1109":{"model_id":"1109","model_name":"CAU-1 beta-lactamase","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"760":{"protein_sequence":{"accession":"CAC87665.1","sequence":"MKRLILAAAASLLALASAAHADDMPANWTKPTKPYRVVGNIYYVGTEGISSWLITSSEGHVVLDGGPNAETGKLVERNITALGFQLADVKILINTHAHYDHAGGLAQLKADTGAKLWISRDDAPAMAAGHHIGDNIYGPTPMPAAKPDRSFGDQTKLKLGEIAMVAHLTPGHTIGCTSWTTAVVEKGRPLTVTFPCSLSVAGNVLVGNKTHRTIVADYRASFAKLRAIPTDVMLPAHEEQGNLLAKRQKQLRGDPNAFVDPGELARFVDASEAAFNKELARQQAAGPNR"},"dna_sequence":{"accession":"AJ308331","fmin":"0","fmax":"870","strand":"+","sequence":"ATGAAGCGCCTGATCCTGGCCGCCGCTGCGTCGCTGTTGGCTCTGGCCTCGGCGGCCCACGCCGACGACATGCCGGCCAACTGGACCAAGCCGACCAAGCCCTACCGTGTGGTCGGCAACATCTATTACGTCGGCACCGAGGGCATCTCGTCCTGGCTGATCACGTCGTCCGAGGGCCATGTGGTGCTGGACGGCGGGCCGAACGCCGAGACGGGCAAGCTGGTCGAGCGCAACATCACGGCGCTGGGCTTCCAGCTTGCGGACGTGAAGATCCTGATCAACACCCACGCCCACTACGATCACGCCGGCGGTCTGGCGCAGTTGAAGGCCGACACCGGCGCCAAGCTGTGGATCTCGCGCGACGACGCCCCGGCCATGGCGGCGGGCCACCACATCGGCGACAATATCTATGGCCCAACGCCGATGCCGGCCGCCAAGCCCGACAGGAGCTTCGGCGACCAGACCAAGCTGAAGCTGGGCGAGATCGCCATGGTCGCCCACCTGACGCCGGGCCACACCATTGGCTGCACCAGCTGGACCACGGCCGTGGTCGAGAAGGGGCGGCCGCTGACCGTCACCTTCCCGTGCTCGCTGTCGGTGGCAGGCAATGTGCTCGTGGGCAACAAGACCCACCGGACCATCGTCGCCGACTATCGCGCCAGCTTCGCCAAGCTGCGCGCCATTCCTACCGACGTGATGCTGCCCGCGCACGAAGAGCAGGGGAACCTGCTGGCCAAGCGCCAGAAGCAGCTGCGCGGTGATCCCAACGCCTTTGTCGACCCAGGCGAGCTTGCCCGGTTCGTCGACGCCTCCGAAGCCGCCTTCAACAAGGAGCTCGCGCGCCAGCAGGCGGCGGGGCCCAACCGATGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39075","NCBI_taxonomy_name":"Caulobacter vibrioides","NCBI_taxonomy_id":"155892"}}}},"ARO_accession":"3000855","ARO_id":"37235","ARO_name":"CAU-1","ARO_description":"CAU-1 is a B3 metallo-beta-lactamase that is encoded by the Caulobacter crescentus chromosome","ARO_category":{"41382":{"category_aro_accession":"3004218","category_aro_cvterm_id":"41382","category_aro_name":"CAU beta-lactamase","category_aro_description":"CAU beta-lactamases are a subclass B3 family.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1110":{"model_id":"1110","model_name":"LEN-19","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1502":{"protein_sequence":{"accession":"CAP12347.2","sequence":"MRYVRLCVISLLATLPLAVYAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGLEQLDRRIHYRQQDLVDYSPVSEKHLTDGMTVGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPPGWFIADKTGAGERGARGIVALLGPDGKPERIVVIYLRDTPASMAERNQHIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM850909","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCACCCTGCCACTGGCGGTATACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTACCGACGGGATGACGGTCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGCCGGGCTGGTTTATCGCCGACAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002466","ARO_id":"38866","ARO_name":"LEN-19","ARO_description":"LEN-19 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1111":{"model_id":"1111","model_name":"AAC(6')-Ig","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"396":{"protein_sequence":{"accession":"AAA21889.1","sequence":"MNIKPASEASLKDWLELRNKLWSDSEASHLQEMHQLLAEKYALQLLAYSDHQAIAMLEASIRFEYVNGTETSPVGFLEGIYVLPAHRRSGVATMLIRQAEVWAKQFSCTEFASDAALDNVISHAMHRSLGFQETEKVVYFSKKID"},"dna_sequence":{"accession":"L09246","fmin":"543","fmax":"981","strand":"+","sequence":"ATGAATATTAAACCTGCATCAGAAGCTTCACTCAAAGATTGGTTAGAATTAAGAAATAAATTGTGGAGTGATTCGGAAGCTTCTCATTTACAAGAGATGCATCAATTATTAGCCGAAAAATATGCCCTACAATTATTGGCCTATTCCGATCACCAAGCTATTGCGATGTTAGAAGCCTCAATTCGGTTTGAATATGTGAATGGGACTGAGACTTCTCCTGTGGGTTTTTTGGAAGGTATTTACGTACTTCCGGCACATCGTCGCTCGGGCGTTGCAACGATGCTTATTCGACAGGCCGAAGTGTGGGCAAAACAATTTTCTTGCACTGAATTTGCATCTGATGCTGCATTGGACAATGTAATTAGTCATGCTATGCATCGTTCATTAGGTTTTCAAGAAACTGAAAAAGTCGTTTATTTTAGTAAAAAAATAGATTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36938","NCBI_taxonomy_name":"Acinetobacter haemolyticus","NCBI_taxonomy_id":"29430"}}}},"ARO_accession":"3002554","ARO_id":"38954","ARO_name":"AAC(6')-Ig","ARO_description":"AAC(6')-Ig is a chromosomal-encoded aminoglycoside acetyltransferase in Acinetobacter haemolyticus","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1112":{"model_id":"1112","model_name":"OXA-58","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1217":{"protein_sequence":{"accession":"YP_001840873.1","sequence":"MKLLKILSLVCLSISIGACAEHSMSRAKTSTIPQVNNSIIDQNVQALFNEISADAVFVTYDGQNIKKYGTHLDRAKTAYIPASTFKIANALIGLENHKATSTEIFKWDGKPRFFKAWDKDFTLGEAMQASTVPVYQELARRIGPSLMQSELQRIGYGNMQIGTEVDQFWLKGPLTITPIQEVKFVYDLAQGQLPFKPEVQQQVKEMLYVERRGENRLYAKSGWGMAVDPQVGWYVGFVEKADGQVVAFALNMQMKAGDDIALRKQLSLDVLDKLGVFHYL"},"dna_sequence":{"accession":"NC_010605","fmin":"13383","fmax":"14226","strand":"+","sequence":"ATGAAATTATTAAAAATATTGAGTTTAGTTTGCTTAAGCATAAGTATTGGGGCTTGTGCTGAGCATAGTATGAGTCGAGCAAAAACAAGTACAATTCCACAAGTGAATAACTCAATCATCGATCAGAATGTTCAAGCGCTTTTTAATGAAATCTCAGCTGATGCTGTGTTTGTCACATATGATGGTCAAAATATTAAAAAATATGGCACGCATTTAGACCGAGCAAAAACAGCTTATATTCCTGCATCTACATTTAAAATTGCCAATGCACTAATTGGTTTAGAAAATCATAAAGCAACATCTACAGAAATATTTAAGTGGGATGGAAAGCCACGTTTTTTTAAAGCATGGGACAAAGATTTTACTTTGGGCGAAGCCATGCAAGCATCTACAGTGCCTGTATATCAAGAATTGGCACGTCGTATTGGTCCAAGCTTAATGCAAAGTGAATTGCAACGTATTGGTTATGGCAATATGCAAATAGGCACGGAAGTTGATCAATTTTGGTTGAAAGGGCCTTTGACAATTACACCTATACAAGAAGTAAAGTTTGTGTATGATTTAGCCCAAGGGCAATTGCCTTTTAAACCTGAAGTTCAGCAACAAGTGAAAGAGATGTTGTATGTAGAGCGCAGAGGGGAGAATCGTCTATATGCTAAAAGTGGCTGGGGAATGGCTGTAGACCCGCAAGTGGGTTGGTATGTGGGTTTTGTTGAAAAGGCAGATGGGCAAGTGGTGGCATTTGCTTTAAATATGCAAATGAAAGCTGGTGATGATATTGCTCTACGTAAACAATTGTCTTTAGATGTGCTAGATAAGTTGGGTGTTTTTCATTATTTATAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35523","NCBI_taxonomy_name":"Acinetobacter baumannii ACICU","NCBI_taxonomy_id":"405416"}}}},"ARO_accession":"3001611","ARO_id":"38011","ARO_name":"OXA-58","ARO_description":"OXA-58 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1113":{"model_id":"1113","model_name":"ANT(6)-Ib","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"60":{"protein_sequence":{"accession":"CBH51824.1","sequence":"MKMRTEKQIYDTILNFAKADDRIRVVTLEGSRTNINIIPDDFQDYDITFFVTDMQSFINSDEWLNVFGERLIMQKPEDMELFPKEEKGYSYLMLFWDGVKIDLTLLPLEVLDEYFTWDKLVKLLLDKDNRVTNIPVPTDEDYYIEHPTARSFDDCCNEFWNTVTYVVKGLCRKEILFAIDHLNNIVRMELLRMISWKVGIEQGYSFSLGKNYKFLERYISPELWKKILATYNMGSYTEMWKSLELCMGIFRMVSKEVAQCLNYLYPDYDKNISNYVIRQKEKYQR"},"dna_sequence":{"accession":"FN594949","fmin":"27481","fmax":"28339","strand":"+","sequence":"ATGAAAATGAGAACAGAGAAACAAATATATGATACTATACTTAATTTTGCTAAAGCAGATGATAGAATTAGGGTGGTTACTTTAGAAGGTTCAAGAACAAATATTAATATTATACCAGATGATTTTCAAGATTATGATATTACTTTTTTTGTCACAGACATGCAGAGTTTTATTAATAGTGATGAGTGGCTTAATGTTTTTGGAGAGAGACTTATTATGCAAAAACCCGAGGATATGGAATTGTTTCCAAAAGAAGAAAAAGGGTATTCATATCTTATGTTATTTTGGGACGGAGTTAAAATAGATTTGACATTATTGCCATTAGAAGTTTTAGATGAATATTTTACTTGGGATAAATTAGTAAAATTATTATTAGATAAGGATAATCGTGTTACTAATATACCAGTACCTACAGATGAAGATTATTATATAGAACATCCGACAGCACGTTCTTTTGATGATTGCTGTAATGAATTTTGGAATACTGTAACATATGTAGTGAAAGGATTATGTCGAAAGGAAATTTTATTTGCAATCGACCATTTAAATAATATTGTGCGTATGGAATTACTGCGAATGATTTCATGGAAGGTTGGAATAGAGCAAGGTTATAGTTTTAGTCTAGGAAAAAACTATAAATTTTTAGAACGATATATTTCACCTGAATTATGGAAGAAAATTCTTGCTACATATAATATGGGGTCATATACAGAAATGTGGAAATCTTTAGAATTATGTATGGGAATTTTTAGAATGGTATCAAAAGAAGTGGCACAATGTTTAAATTATTTATATCCAGATTATGATAAAAATATTAGTAATTATGTTATAAGACAAAAAGAAAAATATCAAAGATAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36889","NCBI_taxonomy_name":"Campylobacter fetus subsp. fetus","NCBI_taxonomy_id":"32019"}}}},"ARO_accession":"3002629","ARO_id":"39029","ARO_name":"ANT(6)-Ib","ARO_description":"ANT(6)-Ib is an aminoglycoside nucleotidyltransferase gene encoded by transferable pathogenicity islands in C. fetus subsp. fetus and B. subtilis","ARO_category":{"36364":{"category_aro_accession":"3000225","category_aro_cvterm_id":"36364","category_aro_name":"ANT(6)","category_aro_description":"Nucelotidylylation of streptomycin at the hydroxyl group at position 6","category_aro_class_name":"AMR Gene Family"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1114":{"model_id":"1114","model_name":"ACT-17","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1418":{"protein_sequence":{"accession":"AHM76771.1","sequence":"MMKKSLCCALLLGISCSALATPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEALQ"},"dna_sequence":{"accession":"KF992026","fmin":"753","fmax":"1899","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCACGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGATGGTAAAGCGGTGCGTGTTTCGCCGGGTATGCTAGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAACGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAGGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001838","ARO_id":"38238","ARO_name":"ACT-17","ARO_description":"ACT-17 is a beta-lactamase. From the Lahey list of ACT beta-lactamases.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1115":{"model_id":"1115","model_name":"OXA-435","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2121":{"protein_sequence":{"accession":"AJT57878.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETPSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKPQVGWLSGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"KP144324","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGACCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCCCAATTAGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGTCCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003162","ARO_id":"39739","ARO_name":"OXA-435","ARO_description":"From the Lahey list of beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1116":{"model_id":"1116","model_name":"arr-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"250"}},"model_sequences":{"sequence":{"480":{"protein_sequence":{"accession":"AAC64366.1","sequence":"MVKDWIPISHDNYKQVQGPFYHGTKANLAIGDLLTTGFISHFEDGRILKHIYFSALMEPAVWGAELAMSLSGLEGRGYIYIVEPTGPFEDDPNLTNKKFPGNPTQSYRTCEPLRIVGVVEDWEGHPVELIRGMLDSLEDLKRRGLHVIED"},"dna_sequence":{"accession":"AF078527","fmin":"4387","fmax":"4840","strand":"+","sequence":"ATGGTAAAAGATTGGATTCCCATCTCTCATGATAATTACAAGCAGGTGCAAGGACCGTTCTATCATGGAACCAAAGCCAATTTGGCGATTGGTGACTTGCTAACCACAGGGTTCATCTCTCATTTCGAGGACGGTCGTATTCTTAAGCACATCTACTTTTCAGCCTTGATGGAGCCAGCAGTTTGGGGAGCTGAACTTGCTATGTCACTGTCTGGCCTCGAGGGTCGCGGCTACATATACATAGTTGAGCCAACAGGACCGTTCGAAGACGATCCGAATCTTACGAACAAAAAATTTCCCGGTAATCCAACACAGTCCTATAGAACCTGCGAACCCTTGAGAATTGTTGGCGTTGTTGAAGACTGGGAGGGGCATCCTGTTGAATTAATAAGGGGAATGTTGGATTCGTTAGAGGACTTAAAGCGCCGTGGTTTACACGTCATTGAAGACTAGT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002847","ARO_id":"39281","ARO_name":"arr-2","ARO_description":"arr-2 is an integron-encoded ribosyltransferase found in Pseudomonas aeruginosa","ARO_category":{"36529":{"category_aro_accession":"3000390","category_aro_cvterm_id":"36529","category_aro_name":"rifampin ADP-ribosyltransferase (Arr)","category_aro_description":"Enzyme responsible for the ADP-ribosylative inactivation of rifampin at the 23-OH position using NAD+.","category_aro_class_name":"AMR Gene Family"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36656":{"category_aro_accession":"3000517","category_aro_cvterm_id":"36656","category_aro_name":"rifaximin","category_aro_description":"Rifaximin is a semi-synthetic rifamycin used to treat traveller's diarrhea. Rifaximin inhibits RNA synthesis by binding to the beta subunit of bacterial RNA polymerase.","category_aro_class_name":"Antibiotic"},"36669":{"category_aro_accession":"3000530","category_aro_cvterm_id":"36669","category_aro_name":"rifabutin","category_aro_description":"Rifabutin is a semisynthetic rifamycin used in tuberculosis therapy. It inhibits DNA-dependent RNA synthesis.","category_aro_class_name":"Antibiotic"},"36673":{"category_aro_accession":"3000534","category_aro_cvterm_id":"36673","category_aro_name":"rifapentine","category_aro_description":"Rifapentine is a semisynthetic rifamycin that inhibits DNA-dependent RNA synthesis. It is often used in the treatment of tuberculosis and leprosy.","category_aro_class_name":"Antibiotic"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1117":{"model_id":"1117","model_name":"ErmD","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"240":{"protein_sequence":{"accession":"AAA22597.1","sequence":"MKKKNHKYRGKKLNRGESPNFSGQHLMHNKKLIEEIVDRANISIDDTVLELGAGKGALTTVLSQKAGKVLAVENDSKFVDILTRKTAQHSNTKIIHQDIMKIHLPKEKFVVVSNIPYAITTPIMKMLLNNPASGFQKGIIVMEKGAAKRFTSKFIKNSYVLAWRMWFDIGIVREISKEHFSPPPKVDSAMVRITRKKDAPLSHKHYIAFRGLAEYALKEPNIPLCVRLRGIFTPRQMKHLRKSLKINNEKTVGTLTENQWAVIFNTMTQYVMHHKWPRANKRKPGEI"},"dna_sequence":{"accession":"L08389","fmin":"390","fmax":"1254","strand":"+","sequence":"ATGAAGAAAAAAAATCATAAGTACAGAGGAAAAAAGTTAAACCGCGGGGAATCTCCGAATTTTTCCGGACAGCATTTGATGCATAATAAAAAATTAATTGAAGAAATTGTGGATCGGGCAAATATTAGCATAGACGATACGGTTTTAGAGTTAGGAGCGGGAAAAGGGGCTTTGACAACTGTGCTAAGTCAAAAAGCCGGTAAGGTATTGGCAGTGGAAAACGATTCTAAATTCGTTGATATACTCACACGTAAAACAGCACAGCATTCAAATACGAAAATTATTCATCAAGATATCATGAAGATTCATTTACCAAAAGAAAAGTTTGTGGTGGTCTCTAATATTCCCTATGCCATCACAACTCCCATCATGAAAATGCTCTTGAACAATCCTGCAAGCGGATTTCAAAAAGGGATCATCGTAATGGAAAAAGGGGCTGCTAAACGTTTCACATCAAAATTCATTAAAAATTCCTATGTTTTAGCTTGGAGAATGTGGTTTGATATTGGCATTGTCAGAGAAATATCGAAAGAGCATTTTTCTCCCCCTCCAAAAGTGGACTCGGCAATGGTCAGAATAACACGAAAAAAAGACGCGCCTCTATCACATAAACATTATATTGCGTTTCGGGGACTTGCCGAATACGCGCTAAAGGAGCCGAATATCCCTCTCTGTGTTCGTTTACGCGGAATTTTTACCCCGCGTCAAATGAAACACTTAAGAAAAAGTCTAAAAATCAACAATGAAAAAACCGTTGGAACGCTCACCGAAAACCAATGGGCGGTTATTTTTAACACGATGACTCAATATGTAATGCATCACAAATGGCCAAGAGCAAATAAGCGAAAACCCGGAGAAATATAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36786","NCBI_taxonomy_name":"Bacillus anthracis","NCBI_taxonomy_id":"1392"}}}},"ARO_accession":"3000495","ARO_id":"36634","ARO_name":"ErmD","ARO_description":"ErmD confers MLSb phenotype.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35946":{"category_aro_accession":"0000027","category_aro_cvterm_id":"35946","category_aro_name":"roxithromycin","category_aro_description":"Roxithromycin is a semi-synthetic, 14-carbon ring macrolide antibiotic derived from erythromycin. It is used to treat respiratory tract, urinary and soft tissue infections. Roxithromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35974":{"category_aro_accession":"0000057","category_aro_cvterm_id":"35974","category_aro_name":"telithromycin","category_aro_description":"Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36315":{"category_aro_accession":"3000176","category_aro_cvterm_id":"36315","category_aro_name":"dirithromycin","category_aro_description":"Dirithromycin is an oxazine derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome to inhibit bacterial protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin 1A is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"vernamycin B-gamma","category_aro_description":"Vernamycin B-gamma is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1118":{"model_id":"1118","model_name":"OXA-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4417":{"protein_sequence":{"accession":"AAB59082.1","sequence":"MAIRIFAILFSIFSLATFAHAQEGTLERSDWRKFFSEFQAKGTIVVADERQADRAMLVFDPVRSKKRYSPASTFKIPHTLFALDAGAVRDEFQIFRWDGVNRGFAGHNQDQDLRSAMRNSTVWVYELFAKEIGDDKARRYLKKIDYGNADPSTSNGDYWIEGSLAISAQEQIAFLRKLYRNELPFRVEHQRLVKDLMIVEAGRNWILRAKTGWEGRMGWWVGWVEWPTGSVFFALNIDTPNRMDDLFKREAIVRAILRSIEALPPNPAVNSDAAR"},"dna_sequence":{"accession":"M95287.4","fmin":"2455","fmax":"3283","strand":"+","sequence":"ATGGCAATCCGAATCTTCGCGATACTTTTCTCCATTTTTTCTCTTGCCACTTTCGCGCATGCGCAAGAAGGCACGCTAGAACGTTCTGACTGGAGGAAGTTTTTCAGCGAATTTCAAGCCAAAGGCACGATAGTTGTGGCAGACGAACGCCAAGCGGATCGTGCCATGTTGGTTTTTGATCCTGTGCGATCGAAGAAACGCTACTCGCCTGCATCGACATTCAAGATACCTCATACACTTTTTGCACTTGATGCAGGCGCTGTTCGTGATGAGTTCCAGATTTTTCGATGGGACGGCGTTAACAGGGGCTTTGCAGGCCACAATCAAGACCAAGATTTGCGATCAGCAATGCGGAATTCTACTGTTTGGGTGTATGAGCTATTTGCAAAGGAAATTGGTGATGACAAAGCTCGGCGCTATTTGAAGAAAATCGACTATGGCAACGCCGATCCTTCGACAAGTAATGGCGATTACTGGATAGAAGGCAGCCTTGCAATCTCGGCGCAGGAGCAAATTGCATTTCTCAGGAAGCTCTATCGTAACGAGCTGCCCTTTCGGGTAGAACATCAGCGCTTGGTCAAGGATCTCATGATTGTGGAAGCCGGTCGCAACTGGATACTGCGTGCAAAGACGGGCTGGGAAGGCCGTATGGGTTGGTGGGTAGGATGGGTTGAGTGGCCGACTGGCTCCGTATTCTTCGCACTGAATATTGATACGCCAAACAGAATGGATGATCTTTTCAAGAGGGAGGCAATCGTGCGGGCAATCCTTCGCTCTATTGAAGCGTTACCGCCCAACCCGGCAGTCAACTCGGACGCTGCGCGATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36846","NCBI_taxonomy_name":"Plasmid R46","NCBI_taxonomy_id":"2488"}}}},"ARO_accession":"3001397","ARO_id":"37797","ARO_name":"OXA-2","ARO_description":"OXA-2 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1119":{"model_id":"1119","model_name":"EBR-1 beta-lactamase","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"2046":{"protein_sequence":{"accession":"AAN32638.1","sequence":"MKKLFSLIALIGSFAFGQIKPIQIDPINNNLFVYQTFNSFNGVEYNANGMYLVTNKGIVLFDVPWQKSQYQELNDMLQEKYNLPVIAVFATHSHDDRAGDLSFYNELNIPTYATSLTNSKLKKEGKATSKFEIELGKTYKFGNEKFVFEYFGEGHTSDNVVVWFPKYKVLNGGCLIKGADAVNLGYTGEANVVEWPKTVHKLVAKHPTIKQVIPGHDNWKATGHIENTFKLLEKK"},"dna_sequence":{"accession":"AF416700","fmin":"56","fmax":"764","strand":"+","sequence":"ATGAAGAAATTATTTTCACTTATTGCATTGATAGGAAGTTTTGCATTTGGTCAAATAAAACCAATTCAAATTGATCCGATTAATAACAATCTATTTGTTTATCAAACATTCAATTCGTTTAATGGTGTTGAGTACAATGCAAATGGAATGTATTTGGTAACGAATAAAGGAATTGTTTTATTTGATGTTCCTTGGCAAAAATCGCAGTATCAAGAGTTAAATGATATGTTACAAGAAAAGTATAATTTGCCAGTTATCGCTGTCTTTGCAACACATTCGCATGATGATAGAGCAGGGGATTTGAGTTTTTATAATGAGTTGAATATTCCTACTTATGCAACTTCTTTAACCAATTCTAAATTAAAAAAAGAAGGAAAAGCGACTTCTAAATTTGAGATTGAATTAGGTAAAACATACAAGTTTGGTAACGAAAAATTTGTTTTTGAATATTTTGGAGAAGGACATACTTCTGATAATGTTGTGGTGTGGTTTCCGAAATATAAAGTGTTGAACGGAGGTTGTTTGATAAAGGGTGCTGATGCTGTAAATTTAGGTTACACAGGCGAAGCTAATGTTGTTGAATGGCCAAAAACAGTACACAAACTAGTTGCAAAACATCCAACGATTAAACAAGTTATTCCAGGCCATGATAATTGGAAAGCTACTGGACATATCGAAAATACTTTTAAACTTTTAGAAAAGAAATAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39071","NCBI_taxonomy_name":"Empedobacter brevis","NCBI_taxonomy_id":"247"}}}},"ARO_accession":"3000842","ARO_id":"37222","ARO_name":"EBR-1 beta-lactamase","ARO_description":"EBR-1 is an Ambler class B beta-lactamase found in Empedobacter brevis and is known to mediate the hydrolysis of penicillins, cephalosporins, and carbapenems efficiently but not aztreonam.","ARO_category":{"41368":{"category_aro_accession":"3004204","category_aro_cvterm_id":"41368","category_aro_name":"EBR beta-lactamase","category_aro_description":"EBR beta-lactamases are Class B beta-lactamases first isolated from Empedobacter brevis and are able to hydrolyze penicillins, cephalosporins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1120":{"model_id":"1120","model_name":"IMI-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"2107":{"protein_sequence":{"accession":"AIS19858.1","sequence":"MSLNVKPSRIAILFSSCLVSISFFSQANTKGIDEIKDLEKDFNGRIGVYALDTGSGKSFSYKANERFPLCSSFKGFLAAAVLKGSQDNQLNLNQIVNYNTRSLEFHSPITTKYKDNGMSLGDMAAAALQYSDNGATNIILERYIGGPEGMTKFMRSIGDKDFRLDRWELDLNTAIPGDERDTSTPAAVAKSLKTLALGNILNEREKETYQTWLKGNTTGAARIRASVPSDWVVGDKTGSCGAYGTANDYAVVWPKNRAPLIISVYTTKNEKEAKHEDKVIAEASRIAIDNLK"},"dna_sequence":{"accession":"KM103296","fmin":"0","fmax":"879","strand":"+","sequence":"ATGTCACTTAATGTAAAACCAAGTAGAATAGCCATCTTGTTTAGCTCTTGTTTAGTTTCAATATCATTTTTCTCACAGGCCAATACAAAGGGCATCGATGAGATTAAAGACCTTGAAAAAGATTTCAATGGTAGAATTGGTGTCTACGCTTTAGACACTGGCTCAGGCAAATCATTTTCATACAAAGCAAATGAACGATTTCCATTATGTAGTTCTTTCAAAGGTTTTTTAGCTGCTGCTGTATTAAAAGGCTCTCAAGATAATCAACTAAATCTTAATCAGATCGTGAATTATAATACAAGAAGTTTAGAGTTCCATTCACCCATCACAACTAAATATAAAGATAATGGAATGTCATTAGGTGATATGGCTGCTGCAGCTTTACAATATAGCGACAATGGTGCTACTAATATTATCCTTGAACGATATATCGGTGGTCCTGAGGGTATGACTAAATTCATGCGGTCGATTGGAGATAAAGATTTTAGACTCGATCGTTGGGAGTTAGATCTAAACACAGCTATTCCTGGCGATGAACGTGACACATCTACACCTGCAGCAGTAGCTAAGAGCCTGAAAACCCTTGCACTGGGTAACATACTCAATGAGCGTGAAAAGGAAACCTATCAGACATGGTTAAAGGGTAACACAACCGGTGCAGCGCGTATTCGTGCTAGCGTACCAAGCGATTGGGTAGTTGGCGATAAAACTGGTAGTTGCGGTGCATACGGTACGGCAAATGATTATGCGGTAGTCTGGCCAAAGAACCGAGCTCCTCTTATAATTTCTGTTTACACTACAAAAAACGAAAAAGAAGCCAAGCATGAGGATAAAGTAATCGCAGAAGCTTCAAGAATCGCAATTGATAACCTTAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3003177","ARO_id":"39754","ARO_name":"IMI-7","ARO_description":"From the Lahey list of beta-lactamases.","ARO_category":{"36027":{"category_aro_accession":"3000018","category_aro_cvterm_id":"36027","category_aro_name":"IMI beta-lactamase","category_aro_description":"IMI beta-lactamases are a group of TEM-1-like beta-lactamase that are known to hydrolyze imipenem. IMI beta-lactamases are inhibited by clavulanic acid and tazobactam.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1121":{"model_id":"1121","model_name":"APH(3')-VIa","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"368":{"protein_sequence":{"accession":"CAA30578.1","sequence":"MELPNIIQQFIGNSVLEPNKIGQSPSDVYSFNRNNETFFLKRSSTLYTETTYSVSREAKMLSWLSEKLKVPELIMTFQDEQFEFMITKAINAKPISALFLTDQELLAIYKEALNLLNSIAIIDCPFISNIDHRLKESKFFIDNQLLDDIDQDDFDTELWGDHKTYLSLWNELTETRVEERLVFSHGDITDSNIFIDKFNEIYFLDLGRAGLADEFVDISFVERCLREDASEETAKIFLKHLKNDRPDKRNYFLKLDELN"},"dna_sequence":{"accession":"X07753","fmin":"102","fmax":"882","strand":"+","sequence":"ATGGAATTGCCCAATATTATTCAACAATTTATCGGAAACAGCGTTTTAGAGCCAAATAAAATTGGTCAGTCGCCATCGGATGTTTATTCTTTTAATCGAAATAATGAAACTTTTTTTCTTAAGCGATCTAGCACTTTATATACAGAGACCACATACAGTGTCTCTCGTGAAGCGAAAATGTTGAGTTGGCTCTCTGAGAAATTAAAGGTGCCTGAACTCATCATGACTTTTCAGGATGAGCAGTTTGAATTCATGATCACTAAAGCGATCAATGCAAAACCAATTTCAGCGCTTTTTTTAACAGACCAAGAATTGCTTGCTATCTATAAGGAGGCACTCAATCTGTTAAATTCAATTGCTATTATTGATTGTCCATTTATTTCAAACATTGATCATCGGTTAAAAGAGTCAAAATTTTTTATTGATAACCAACTCCTTGACGATATAGATCAAGATGATTTTGACACTGAATTATGGGGAGACCATAAAACTTACCTAAGTCTATGGAATGAGTTAACCGAGACTCGTGTTGAAGAAAGATTGGTTTTTTCTCATGGCGATATCACGGATAGTAATATTTTTATAGATAAATTCAATGAAATTTATTTTTTAGATCTTGGTCGTGCTGGGTTAGCAGATGAATTTGTAGATATATCCTTTGTTGAACGTTGCCTAAGAGAGGATGCATCGGAGGAAACTGCGAAAATATTTTTAAAGCATTTAAAAAATGATAGACCTGACAAAAGGAATTATTTTTTAAAACTTGATGAATTGAATTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3002652","ARO_id":"39052","ARO_name":"APH(3')-VIa","ARO_description":"APH(3')-VIa is a plasmid-encoded aminoglycoside phosphotransferase in A. baumannii","ARO_category":{"36265":{"category_aro_accession":"3000126","category_aro_cvterm_id":"36265","category_aro_name":"APH(3')","category_aro_description":"Phosphorylation of 2-deoxystreptamine aminoglycosides on the hydroxyl group at position 3'","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1122":{"model_id":"1122","model_name":"OXA-180","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1293":{"protein_sequence":{"accession":"ADM26745.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAIKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"HM570036","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATAAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001474","ARO_id":"37874","ARO_name":"OXA-180","ARO_description":"OXA-180 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1123":{"model_id":"1123","model_name":"FOX-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1434":{"protein_sequence":{"accession":"ADK73994.1","sequence":"MQQRRAFALLTLGSLLLAPCTYASGEAPLTATVDGIIQPMLKEYRIPGIAVAVLKDGKAHYFNYGVANRESGQRVSEQTLFEIGSVSKTLTATLGAYAAVKGGFVLDDKVSQHAPWLKGSALDGVTMAELATYSAGGLPLQFPDKVDSNDKMQTYYRSWSPVYPAGTHRQYSNPSIGLFGHLAANSLGQPFEQLMSQTLLPKLGLHHTYIQVPESAMANYAYGYSKEDKPIRVTPGVLAAEAYGIKTGSADLLKFAEANMGYQGDALVKSAIALTHTGFYSVGEMTQGLGWESYDYPVTEQVLLAGNSPAVSLQANPVTRFAVPKAMGEQRLYNKTGSTGGFGAYVAFVPARGIAIVMLANRNYPIEARVKAAHAILSQLAE"},"dna_sequence":{"accession":"HM565917","fmin":"0","fmax":"1149","strand":"+","sequence":"ATGCAACAACGACGTGCGTTCGCGCTACTGACGCTGGGTAGCCTGCTGCTAGCCCCTTGTACTTATGCCAGCGGGGAGGCCCCGCTGACCGCCACTGTGGACGGCATTATCCAGCCGATGCTCAAGGAGTATCGGATCCCGGGGATAGCGGTCGCCGTACTGAAAGATGGCAAGGCCCACTATTTCAACTATGGGGTTGCCAACCGCGAGAGTGGCCAGCGCGTCAGCGAGCAGACCCTGTTCGAGATTGGCTCGGTCAGCAAGACCCTGACCGCGACCCTCGGTGCCTATGCTGCGGTCAAGGGGGGCTTTGTGCTGGATGACAAGGTGAGCCAGCACGCCCCCTGGCTCAAAGGTTCCGCCTTGGATGGTGTGACCATGGCCGAGCTTGCCACCTACAGTGCGGGTGGTTTGCCGCTGCAGTTCCCCGATAAGGTGGATTCGAATGACAAGATGCAAACTTACTATCGGAGCTGGTCACCGGTTTATCCGGCAGGGACTCATCGCCAGTATTCCAACCCCAGCATAGGCCTGTTTGGTCACCTGGCCGCAAATAGTCTGGGCCAGCCATTTGAGCAACTGATGAGCCAGACCCTGCTGCCCAAGCTGGGTTTGCACCACACCTATATCCAGGTGCCGGAGTCGGCCATGGCGAACTATGCCTACGGCTATTCGAAGGAAGATAAGCCCATCCGGGTCACTCCGGGCGTGCTGGCGGCCGAGGCTTACGGGATCAAGACCGGCTCGGCGGATCTGCTGAAGTTTGCCGAGGCAAACATGGGGTATCAGGGAGATGCCCTGGTAAAAAGCGCAATCGCGCTGACCCACACCGGTTTCTACTCGGTGGGGGAAATGACCCAGGGGCTGGGCTGGGAGAGTTACGACTATCCCGTCACCGAGCAGGTGCTGCTGGCGGGCAACTCCCCGGCGGTGAGCCTCCAGGCCAATCCGGTTACGCGCTTTGCGGTGCCCAAAGCGATGGGCGAGCAGCGGCTCTATAACAAGACGGGCTCGACTGGCGGCTTTGGCGCCTATGTGGCGTTCGTGCCCGCCAGAGGGATCGCCATCGTCATGCTGGCCAATCGCAACTATCCCATCGAGGCCAGGGTGAAGGCGGCTCACGCCATCCTGAGTCAGTTGGCCGAGTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002161","ARO_id":"38561","ARO_name":"FOX-8","ARO_description":"FOX-8 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36206":{"category_aro_accession":"3000067","category_aro_cvterm_id":"36206","category_aro_name":"FOX beta-lactamase","category_aro_description":"FOX beta-lactamases are plasmid-encoded AmpC-type beta-lactamase which conferred resistance to broad-spectrum cephalosporins and cephamycins","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1124":{"model_id":"1124","model_name":"TEM-186","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1883":{"protein_sequence":{"accession":"AET99222.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNNERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"JN227084","fmin":"308","fmax":"1169","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACAACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001046","ARO_id":"37426","ARO_name":"TEM-186","ARO_description":"TEM-186 is a beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1125":{"model_id":"1125","model_name":"OKP-B-11","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"877":{"protein_sequence":{"accession":"CAJ19620.1","sequence":"MRYVRLCLISLITALPLAVFASPQPLEQIKISESQLAGRVGYVEMDLASGRTLATWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKIVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMATTLRKLLTTPSLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPDGKAERIVVIYLRDTPATMVERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM051161","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTATCTCCCTGATTACCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCAGCCGCTTGAGCAGATTAAAATCAGCGAAAGTCAGCTGGCGGGCCGGGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCACCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGCGACGAACAGCTGGATCGGCGGATTCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGATCGTCGGCGGCCCTGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTCAATGAGGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCGGCCAGCATGGCCACCACCCTGCGCAAGCTGCTAACCACCCCCTCTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGACCGAGTGGCCGGCCCGTTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGTGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAAGCGGAGCGTATCGTGGTGATCTATCTGCGTGATACCCCGGCGACCATGGTCGAGCGTAACCAGCAGATCGCCGGGATAGGCGCGGCGCTGATCGAACACTGGCAGCGCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002444","ARO_id":"38844","ARO_name":"OKP-B-11","ARO_description":"OKP-B-11 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1126":{"model_id":"1126","model_name":"OXA-184","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1604":{"protein_sequence":{"accession":"AFO09968.1","sequence":"MKKILLLFSLFYSFALANDKLKDFFKDYNTSGVFITFDGKHYASNNFKRAKEPFSPASTFKIFNALIALDNGVVKDTKEIFYHYKGEKVFLPSWKQDASLSSAIKRSQVPAFKELARKIGLKTMQESLNKLSYGNTKISKIDTFWLDNSLQISAKNQADLLFKLSQNSLPFSKKSQEEVKKIILFKEDKIQKIYAKTGFNDGINLAWIVGFIESKNKILSFALNVDIKNIKNLKIREELLEKYIYSLN"},"dna_sequence":{"accession":"JQ396378","fmin":"0","fmax":"747","strand":"+","sequence":"TTGAAAAAAATACTTTTACTTTTTAGTCTTTTTTACTCTTTTGCTTTGGCAAATGATAAATTAAAAGATTTTTTTAAAGACTACAATACAAGCGGAGTTTTTATAACTTTTGATGGAAAACATTATGCAAGTAATAATTTTAAAAGAGCTAAAGAACCTTTTTCTCCTGCTTCGACTTTTAAAATTTTTAATGCTTTAATTGCGCTTGATAATGGTGTAGTTAAAGATACAAAGGAAATTTTTTATCATTATAAGGGTGAAAAAGTATTTTTGCCCTCTTGGAAACAAGATGCTAGTTTAAGCTCAGCCATAAAACGCTCTCAAGTGCCTGCTTTTAAAGAATTGGCAAGAAAAATAGGACTTAAAACCATGCAAGAAAGCTTAAATAAACTTTCCTATGGAAATACAAAAATTTCAAAAATCGATACCTTTTGGTTGGATAATTCTTTACAAATTTCTGCAAAAAATCAAGCTGATTTGCTTTTTAAACTTTCACAAAATTCTTTACCTTTTTCCAAGAAAAGTCAAGAAGAAGTTAAAAAAATTATTCTTTTTAAAGAAGATAAAATCCAAAAAATTTATGCTAAAACAGGTTTTAATGATGGTATAAATTTGGCTTGGATTGTTGGATTTATAGAGAGTAAAAACAAAATTTTATCTTTTGCCTTAAATGTTGATATAAAGAACATTAAAAATCTTAAAATAAGAGAAGAATTGCTAGAAAAATATATTTATTCTTTAAACTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3001476","ARO_id":"37876","ARO_name":"OXA-184","ARO_description":"OXA-184 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1127":{"model_id":"1127","model_name":"CTX-M-64","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"949":{"protein_sequence":{"accession":"BAF63422.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"AB284167","fmin":"225","fmax":"1101","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36790","NCBI_taxonomy_name":"Shigella sonnei","NCBI_taxonomy_id":"624"}}}},"ARO_accession":"3001925","ARO_id":"38325","ARO_name":"CTX-M-64","ARO_description":"CTX-M-64 is a beta-lactamase found in Shigella sonnei","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1128":{"model_id":"1128","model_name":"OXA-23","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"885":{"protein_sequence":{"accession":"AAV65289.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETPSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKPQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"AY795964","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGACCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCCCAATTAGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001418","ARO_id":"37818","ARO_name":"OXA-23","ARO_description":"OXA-23 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1129":{"model_id":"1129","model_name":"CMY-19","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"761":{"protein_sequence":{"accession":"BAE48233.1","sequence":"MQQRQSILWGAVATLMWAGLAHAGEASPVDPLRPVVDASIQPLLKEHRIPGMAVAVLKDGKAHYFNYGVANRESGASVSEQTLFDIGSVSKTLTATLGAYAVVKGAMQLDDKASRHAPWLKGSVFDSITMGELATYSAGGLPLQFPEEVDSSEKMRAYYRQWAPVYSPGSHRQYSNPSIGLFGHLAASSLKQPFAQLMEQTLLPGLGMHHTYVNVPKQAMASYAYGYSKEDKPIRVNPGMLADEAYGIKTSSADLLAFVKANIGGVDDKALQQAISLTHKGHYSVGGMTQGLGWESYAYPVTEQTLLAGNSAKVSLEANPTAAPRESGSQVLFNKTGSTNGFGAYVAFVPARGIGIVMLANRNYPIPARVKAAHAILAQLAG"},"dna_sequence":{"accession":"AB194410","fmin":"0","fmax":"1149","strand":"+","sequence":"ATGCAACAACGACAATCCATCCTGTGGGGGGCCGTGGCCACCCTGATGTGGGCCGGTCTGGCCCATGCAGGTGAGGCTTCACCGGTCGATCCCCTGCGCCCCGTGGTGGATGCCAGCATCCAGCCGCTGCTCAAGGAGCACAGGATCCCGGGCATGGCGGTGGCCGTGCTCAAGGATGGCAAGGCCCACTATTTCAATTACGGGGTGGCCAACCGGGAGAGCGGGGCCAGCGTCAGCGAGCAGACCCTGTTCGATATAGGATCCGTGAGCAAGACCCTGACTGCGACCCTGGGGGCCTATGCGGTGGTCAAGGGAGCGATGCAGCTGGATGACAAGGCGAGCCGGCACGCGCCCTGGCTCAAGGGATCCGTCTTTGACAGCATCACCATGGGGGAGCTTGCCACCTACAGCGCCGGAGGCCTGCCACTGCAATTCCCCGAGGAGGTGGATTCATCCGAGAAGATGCGCGCCTACTACCGCCAGTGGGCCCCTGTCTATTCGCCGGGCTCCCATCGCCAGTACTCCAACCCCAGCATAGGGCTGTTCGGCCACCTGGCGGCGAGCAGCCTGAAGCAGCCATTTGCCCAGTTGATGGAGCAGACCCTGCTGCCCGGGCTCGGCATGCACCACACCTATGTCAATGTGCCGAAGCAGGCCATGGCGAGTTATGCCTATGGCTATTCGAAAGAGGACAAGCCCATCCGGGTCAACCCTGGCATGCTGGCGGACGAGGCCTACGGCATCAAGACCAGCTCGGCGGATCTGCTCGCCTTCGTGAAGGCCAACATCGGCGGGGTTGATGACAAGGCGTTGCAGCAGGCCATCTCCCTGACCCACAAAGGGCATTACTCGGTAGGCGGGATGACCCAGGGGCTGGGTTGGGAGAGTTACGCCTATCCCGTCACCGAGCAGACATTGCTGGCGGGCAATTCGGCCAAGGTGAGCCTCGAAGCCAATCCGACGGCGGCTCCCCGGGAGTCGGGGAGCCAGGTGCTCTTCAACAAGACCGGCTCGACCAATGGCTTTGGCGCCTATGTGGCCTTCGTGCCGGCCAGGGGGATCGGCATCGTCATGCTGGCCAATCGCAACTATCCCATCCCGGCCAGGGTGAAGGCGGCCCACGCCATCCTGGCGCAGTTGGCCGGTTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002030","ARO_id":"38430","ARO_name":"CMY-19","ARO_description":"CMY-19 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1130":{"model_id":"1130","model_name":"PDC-9","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"2018":{"protein_sequence":{"accession":"ACQ82814.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAVEAPADRLKALVDAAVQPVMKANDIPGLTVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDRAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"FJ666072","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGTCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGACCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCGGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTATGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002508","ARO_id":"38908","ARO_name":"PDC-9","ARO_description":"PDC-9 is a extended-spectrum beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1131":{"model_id":"1131","model_name":"AAC(3)-Ic","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"47":{"protein_sequence":{"accession":"CAD53575.1","sequence":"MISTQTKITRLNSQDVGVMRAMLGMFGEAFEDAENYCRAQPSDSYLQDLLCGSGFIAIAALQGQEVIGGLAAYVLPKFEQQRKEIYIYDLGVQGAYRRRGIATALINELQRIAHDIGAYVIFVQADYGDDPAVALYTKLGIREDVMHFDIEPQPAA"},"dna_sequence":{"accession":"AJ511268","fmin":"1294","fmax":"1765","strand":"+","sequence":"ATGATCTCTACTCAAACCAAGATTACCCGCCTCAACTCTCAAGACGTTGGTGTAATGCGGGCAATGCTAGGCATGTTCGGCGAGGCTTTTGAGGACGCTGAGAACTATTGCCGCGCTCAACCAAGCGACAGTTACCTACAAGACTTACTGTGTGGCTCTGGCTTCATCGCAATCGCTGCGTTACAGGGGCAAGAGGTCATCGGTGGGCTCGCCGCGTATGTGCTCCCAAAGTTTGAACAACAGCGCAAAGAAATCTATATCTACGACTTAGGCGTGCAGGGAGCCTATCGCCGACGAGGCATCGCCACAGCCTTGATCAATGAACTCCAGCGTATCGCACATGATATTGGCGCTTATGTAATTTTTGTCCAGGCTGACTATGGGGACGATCCTGCGGTAGCGCTCTACACAAAACTCGGTATCCGGGAGGACGTGATGCACTTTGACATAGAACCTCAACCTGCTGCCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002531","ARO_id":"38931","ARO_name":"AAC(3)-Ic","ARO_description":"AAC(3)-Ic is an integron-encoded aminoglycoside acetyltransferase in P. aeruginosa","ARO_category":{"36461":{"category_aro_accession":"3000322","category_aro_cvterm_id":"36461","category_aro_name":"AAC(3)","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 3.","category_aro_class_name":"AMR Gene Family"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1027":{"model_id":"1027","model_name":"tet(H)","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"780"}},"model_sequences":{"sequence":{"732":{"protein_sequence":{"accession":"CAA75663.1","sequence":"MNKSIIIILLITVLDAIGIGLIMPVLPTLLNEFVSENSLATHYGVLLALYATMQVIFAPILGRLSDKYGRKPILLFSLLGAALDYLLMAFSTTLWMLYIGRIIAGITGATGAVCASAMSDVTPAKNRTRYFGFLGGAFGVGLIIGPMLGGLLGDISAHMPFIFAAISHSILLILSLLFFRETQKREALVANRTPENQTASNTVTVFFKKSLYFWLATYFIIQLIGQIPATIWVLFTQYRFDWNTTSIGMSLAVLGVLHIFFQAIVAGKLAQKWGEKTTIMISMSIDMMGCLLLAWIGHVWVILPALICLAAGGMGQPALQGYLSKSVDDNAQGKLQGTLVSLTNITGIIGPLLFAFIYSYSVAYWDGLLWLMGAILYAMLLITAYFHQRKTTPKAVISTP"},"dna_sequence":{"accession":"Y15510","fmin":"0","fmax":"1203","strand":"+","sequence":"ATGAATAAATCAATTATTATTATACTGCTGATCACCGTATTAGATGCCATTGGTATCGGGCTTATCATGCCAGTACTCCCTACTCTATTAAATGAATTTGTCAGTGAAAATTCACTGGCAACCCATTACGGTGTGCTATTAGCGCTCTATGCTACCATGCAGGTTATTTTTGCTCCTATTCTAGGACGACTGTCTGATAAATACGGCAGAAAACCCATCTTGCTGTTTTCCCTTTTAGGCGCGGCACTCGACTATCTTTTAATGGCATTCTCAACCACACTTTGGATGCTCTATATTGGGCGCATCATTGCGGGGATCACAGGCGCAACAGGTGCCGTATGTGCATCAGCGATGAGTGATGTGACTCCCGCTAAAAATCGAACTCGCTATTTTGGTTTCTTAGGTGGTGCTTTTGGTGTTGGCCTTATTATCGGCCCAATGCTAGGGGGATTATTAGGTGATATCAGTGCTCATATGCCATTTATTTTTGCCGCTATTTCACACTCGATATTATTAATACTCTCTTTGCTCTTTTTCCGAGAAACACAAAAAAGAGAAGCGCTTGTTGCCAATAGGACACCTGAAAACCAAACTGCCTCAAATACAGTCACTGTTTTTTTTAAGAAAAGCCTCTACTTTTGGTTAGCAACCTATTTTATTATCCAGCTTATCGGGCAAATTCCTGCCACCATCTGGGTGCTGTTTACACAATATCGTTTTGATTGGAACACAACTTCTATCGGTATGTCTTTGGCGGTTCTGGGTGTATTACATATTTTCTTTCAGGCGATTGTCGCTGGGAAATTGGCACAAAAATGGGGCGAAAAAACCACCATTATGATCAGTATGTCTATTGATATGATGGGCTGTTTATTATTAGCGTGGATAGGCCACGTTTGGGTCATCTTACCAGCATTAATTTGCTTAGCGGCAGGAGGTATGGGGCAACCCGCATTACAAGGTTATTTATCAAAATCTGTCGATGATAATGCGCAAGGGAAATTACAAGGTACTCTGGTGAGCCTAACCAATATTACCGGGATCATTGGTCCCCTTTTATTTGCCTTTATTTATAGTTATAGCGTCGCTTATTGGGATGGTCTGTTATGGCTGATGGGGGCAATACTTTATGCTATGTTGCTTATTACCGCTTATTTTCACCAAAGAAAAACCACACCTAAAGCTGTTATTTCAACCCCTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36867","NCBI_taxonomy_name":"Pasteurella multocida","NCBI_taxonomy_id":"747"}}}},"ARO_accession":"3000175","ARO_id":"36314","ARO_name":"tet(H)","ARO_description":"TetH is a tetracycline efflux protein expressed in Gram-negative bacteria (Actinobacillus, Acinetobacter, Gallibacterium, Histophilus, Mannheimia, Moraxella, Pasteurella, and Psychrobacter). Its gene is linked to the resistance genes sul2, and strAB, which confer resistance to sulfamethoxazole and streptomycin, respectively.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1092":{"model_id":"1092","model_name":"tet(39)","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"161":{"protein_sequence":{"accession":"AAW66497.1","sequence":"MKKSLSVILITIFLDAVGIGLIMPILPELLRSLAGAEAGGVHYGALLAVYALMQFIFAPILGALSDRFGRRPVLIISIAGATADYLLMAAAPSLLWLYIGRIFAGITGANMAVATAYVSDITPAHERAKRFGLLGAVFGIGFIAGPVIGGVLGEWNLHAPFFAAAFMNGINLIMTAVLLKESKHSNKMTEKVQEQSILKKLSYLITQPNMAPLLGIFLIITLVSQVPATLWVIYGQDRYGWSIFIAGVSLASYGICHSIAQAFAIAPMVKRFGEKNTLLCGIACDAIGLLLLSIAVEEWVPFALLPLFALGGVAVPALQAMMSRGISDERQGELQGLLSSFNSLGAIIGPVLVTSLYFMTQASAPGMVWALAAILYVITLPLLLKYRLNKYSGVP"},"dna_sequence":{"accession":"AY743590","fmin":"0","fmax":"1188","strand":"+","sequence":"GTGAAGAAATCATTGAGCGTGATTTTAATCACTATATTTCTGGATGCTGTTGGGATTGGTTTAATTATGCCGATCTTGCCTGAATTATTACGGTCATTGGCTGGAGCTGAAGCAGGCGGTGTTCACTATGGTGCTTTATTAGCTGTGTATGCTCTGATGCAGTTCATTTTTGCACCTATCCTTGGAGCGTTGAGTGACCGATTTGGACGTCGACCTGTATTAATTATTTCAATTGCTGGTGCAACGGCTGATTATCTCCTAATGGCTGCTGCTCCTTCTCTATTGTGGCTATATATTGGTCGTATTTTTGCGGGAATTACAGGTGCCAACATGGCTGTTGCAACAGCTTATGTTTCAGATATTACTCCAGCCCATGAGCGTGCAAAAAGGTTTGGTCTCCTTGGAGCTGTCTTTGGTATTGGGTTTATAGCGGGTCCGGTAATAGGTGGAGTTTTGGGTGAATGGAACTTACATGCACCGTTCTTTGCTGCTGCTTTTATGAATGGGATTAATTTAATAATGACAGCAGTCTTATTAAAAGAATCAAAACACAGCAATAAAATGACTGAGAAGGTTCAGGAGCAATCAATATTAAAGAAATTATCCTATTTGATCACTCAACCTAATATGGCTCCATTGCTTGGTATCTTTTTAATTATCACATTGGTTTCACAAGTCCCCGCAACTTTATGGGTTATCTATGGGCAGGATCGTTATGGCTGGAGTATATTTATTGCAGGTGTTTCCCTTGCTAGTTATGGAATATGCCATTCTATTGCACAGGCTTTTGCTATCGCCCCTATGGTAAAGAGGTTTGGAGAGAAAAATACGTTGTTATGTGGAATAGCTTGCGATGCAATTGGTTTACTTCTTTTATCTATTGCTGTTGAAGAATGGGTGCCTTTTGCGTTGTTACCATTGTTTGCCCTTGGTGGAGTAGCCGTTCCTGCTTTGCAAGCAATGATGTCCAGAGGTATTAGTGATGAAAGACAAGGTGAATTACAAGGGCTATTAAGCAGTTTTAATAGTCTGGGGGCTATAATTGGTCCTGTATTAGTTACTAGCCTCTATTTTATGACTCAGGCATCAGCTCCTGGAATGGTATGGGCATTAGCTGCAATACTTTATGTAATCACCCTACCCTTATTGCTTAAGTATCGCCTGAATAAATATTCTGGAGTTCCATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36811","NCBI_taxonomy_name":"Acinetobacter sp. LUH5605","NCBI_taxonomy_id":"309867"}}}},"ARO_accession":"3000566","ARO_id":"36705","ARO_name":"tet(39)","ARO_description":"Tet39 is a tetracycline efflux pump found in Gram-negative bacteria, including Brevundimonas, Stenotrophomonas, Enterobacter, Alcaligenes, Acinetobacter, and Providencia.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1067":{"model_id":"1067","model_name":"MexE","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"270":{"protein_sequence":{"accession":"NP_251183.1","sequence":"MEQSSHFSWRYPLALAAVLVLSACGKAPETTQGMAAPKVSVAEVIEQPLNEWDEFTGRLEAPESVELRPRVSGYIDRVAFHEGALVKKGDLLFQIDPRPFEAEVKRLEAQLQQARAAQARSVNEAQRGERLRASNAISAELADARTTAAQEAKAAVAATQAQLDAARLNLSFTRITAPIDGRVSRAEVTAGNLVNSGETLLTTLVSTDKVYAYFDADERVFLKYVELARQAGRDTRSESPVYLGLSSEDGNPHLGRLDFLDNQVNPRTGTIRGRAVFDNAKGEFTPGLYVRLKLVGSKTYAATLIKDEAVGTDLGKKFVLVLDGDNKTVYRTVEMGPKLEGLRIVRSGLSKGDRIVVNGLQRVRPGMQVDPQKVEMASADTLATLARLRQSVGDSEPPKVAASKDNATRNEPRG"},"dna_sequence":{"accession":"NC_002516","fmin":"2808742","fmax":"2809987","strand":"+","sequence":"ATGGAACAGTCATCCCACTTCTCCTGGCGCTACCCCCTCGCACTCGCGGCCGTACTGGTCCTGAGCGCCTGCGGCAAGGCCCCGGAAACCACCCAAGGCATGGCGGCGCCCAAGGTCAGCGTCGCCGAAGTCATCGAACAACCGCTGAACGAGTGGGACGAATTCACCGGCCGCCTGGAGGCCCCGGAGTCGGTGGAGCTGCGCCCGCGGGTGTCGGGCTACATCGACCGCGTGGCCTTCCATGAAGGCGCACTGGTGAAGAAAGGCGACCTGCTGTTCCAGATCGACCCGCGCCCGTTCGAGGCCGAGGTCAAGCGCCTCGAAGCCCAGCTGCAACAGGCCCGCGCGGCCCAGGCGCGGAGCGTCAACGAAGCCCAGCGCGGCGAACGCCTGCGCGCCAGCAACGCGATCTCCGCGGAACTCGCCGACGCCCGCACCACCGCCGCCCAGGAAGCCAAGGCGGCGGTCGCCGCGACCCAGGCGCAACTGGACGCGGCGCGCCTGAACCTGAGCTTCACCCGGATCACCGCGCCGATCGACGGTCGCGTCAGCCGCGCCGAGGTCACCGCCGGCAACCTGGTCAACTCCGGGGAGACCCTGCTCACCACCCTGGTCAGCACCGACAAGGTCTACGCCTACTTCGACGCCGACGAGCGCGTGTTCCTCAAGTACGTCGAGCTGGCCCGCCAGGCCGGTCGCGACACGCGCAGCGAGAGCCCGGTGTACCTCGGCCTGAGCAGCGAGGACGGCAACCCGCACCTGGGCCGGCTGGACTTCCTCGACAACCAGGTCAACCCGCGTACCGGCACCATCCGCGGCCGCGCCGTGTTCGACAACGCCAAGGGCGAGTTCACCCCGGGCCTCTACGTGCGCCTGAAGCTGGTCGGCAGCAAGACCTACGCCGCCACCCTGATCAAGGACGAAGCGGTCGGCACCGACCTGGGCAAGAAGTTCGTGCTGGTCCTGGATGGCGACAACAAGACCGTCTACCGCACCGTCGAGATGGGACCGAAGCTGGAGGGCCTGCGCATCGTCCGCAGCGGCCTGAGCAAGGGCGACCGGATCGTCGTGAATGGCCTGCAGCGGGTCCGCCCGGGCATGCAGGTGGATCCGCAGAAGGTCGAGATGGCCAGCGCCGACACCCTGGCCACCCTCGCGCGCCTGCGGCAGTCGGTCGGCGACAGCGAACCACCGAAGGTGGCGGCGTCCAAGGACAACGCCACTCGCAACGAGCCGCGCGGCTGAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3000803","ARO_id":"37183","ARO_name":"MexE","ARO_description":"MexE is the membrane fusion protein of the MexEF-OprN multidrug efflux complex.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1041":{"model_id":"1041","model_name":"MexS","model_type":"protein overexpression model","model_type_id":"41091","model_description":"This model detects protein overexpression based on the presence of mutations.The detection of the protein without an associated mutation indicates that the protein is likely to be expressed at low or basal levels. The detection of the protein with the mutation indicates that the protein is likely overexpressed. This model reflects how certain proteins are functional with and without mutations. For example, efflux pump subunits and regulators are functional with mutations and without mutations. Without mutations, efflux pump subunits and regulators are usually expressed at a low level. When an efflux pump regulator has a mutation, it can cause the overexpression of the efflux pump it is responsible for regulating, leading to resistance to specific drugs. Protein overexpression models have two parameters: a curated BLASTP cutoff, and a curated set of mutations (single resistance variants, frameshift mutations, indels, etc.) shown clinically to confer resistance. This model type is a combination of the protein homolog and protein variant model. A detected hit can be categorized as Perfect, Strict, or Loose with no mutation(s) or as Strict or Loose with mutation(s).","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"660"},"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"7573":"V104A","7574":"F253L","7575":"D44E","7576":"S60F","7577":"F185L","7578":"V73A","7579":"L270Q","7580":"C245G","7581":"A166P","7582":"S60P","7583":"L263Q"},"clinical":{"7573":"V104A","7574":"F253L","7575":"D44E","7576":"S60F","7577":"F185L","7578":"V73A","7579":"L270Q","7580":"C245G","7581":"A166P","7582":"S60P","7583":"L263Q"}}},"model_sequences":{"sequence":{"667":{"protein_sequence":{"accession":"ADT64081.1","sequence":"MSRVIRFHQFGPPEVLKCEELPTPAPAAGEVLVRVQAIGVSWKDVLWRQNLAPEQAALPSGLGFELAGEVLAVGAGVGDLPLGSRVASFPAHTPDHYPAYGDVVLMPRAALAVYPEVLTPVEASVYYTGLLVAYFGLVDLAGLKAGQTVLITEAARMYGPVSIQLAKALGARVIASTKSAEEREFLREQGADKVVVTDEQDLVLEVERFTEGKGVNVILDELGGPQMTLLGDVSATRGKLVLYGCNGGNESAFPACAAFKKHLQFYRHCLMDFTGHPEMGLERNDESVSKALAHIEQLTRDRLLKPVVDRVFEFDQVVEAHRYMETCPKRGRVVIHVAD"},"dna_sequence":{"accession":"HQ433550","fmin":"0","fmax":"1020","strand":"+","sequence":"ATGTCCCGAGTGATCCGTTTTCATCAGTTTGGCCCGCCAGAGGTCCTCAAATGCGAAGAGCTGCCGACCCCGGCGCCGGCCGCAGGGGAAGTCCTGGTGCGTGTCCAGGCGATCGGCGTGAGCTGGAAGGATGTGCTCTGGCGTCAGAACCTGGCCCCGGAGCAGGCTGCGCTGCCGTCCGGTCTCGGCTTCGAACTGGCCGGCGAGGTGCTGGCGGTCGGCGCCGGCGTCGGCGACCTGCCGCTGGGTTCCCGCGTGGCCAGTTTCCCCGCCCATACCCCCGATCATTATCCGGCCTATGGCGACGTGGTGCTGATGCCGCGCGCGGCCCTGGCGGTCTACCCCGAGGTACTCACCCCGGTGGAGGCCAGCGTCTACTACACCGGCCTGCTGGTGGCCTATTTCGGCCTGGTCGACCTGGCCGGGTTGAAGGCCGGGCAGACCGTGCTGATCACCGAGGCGGCGCGCATGTACGGGCCGGTCTCGATCCAGTTGGCCAAGGCTCTCGGCGCGCGGGTGATCGCTTCCACCAAGTCCGCCGAGGAGCGCGAGTTCCTCCGCGAGCAGGGCGCCGACAAGGTGGTGGTGACCGACGAGCAGGACCTGGTCCTGGAAGTCGAGCGCTTCACCGAGGGCAAGGGCGTCAATGTCATCCTCGACGAATTGGGCGGTCCGCAGATGACCCTGCTCGGCGATGTCTCCGCCACCCGCGGCAAGCTGGTGCTGTATGGCTGCAACGGCGGCAACGAGTCGGCGTTCCCGGCCTGCGCCGCGTTCAAGAAGCACCTGCAGTTCTACCGCCACTGCCTGATGGATTTCACCGGTCATCCGGAGATGGGCCTGGAACGCAACGACGAGTCGGTGAGCAAGGCCCTCGCGCACATCGAGCAACTGACCCGCGATCGCCTGCTCAAACCGGTGGTCGACCGGGTATTCGAGTTCGACCAGGTGGTCGAGGCGCACCGCTACATGGAAACCTGTCCAAAGCGCGGCCGGGTGGTGATCCACGTCGCCGATTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39594","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAK","NCBI_taxonomy_id":"1009714"}}}},"ARO_accession":"3000813","ARO_id":"37193","ARO_name":"MexS","ARO_description":"MexS is a suppressor of MexT, which is an activator of the multidrug pump MexEF-OprN. Mutations in MexS lead to multidrug resistance.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"988":{"model_id":"988","model_name":"tet(J)","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"770"}},"model_sequences":{"sequence":{"413":{"protein_sequence":{"accession":"AAD12753.1","sequence":"MNKSIIIILLVTVLDAIGIGLIMPVLPTLLNEFVSENRLANHYGILLALYATMQVIFAPILGKLSDKYGRKPILLISLLGAALDYLLMACPTSLWMLYIGRIIAGITGATGAVCASAMTDVTHPHERTRYFGFLGGAFGVGLIIGPMLGGLLGEISAHTPFIFAAISHSLLFIFSLLCFQETQTTKISTEISALNQDTAPHSTTGFIKKSLFFWLIAYFIIQLIGQIPATIWVLFTQVRFAWHTTEVGLSLAFLGVLHIFFQAVLAGKLAQKWGERNTVIISMSIDAFGCLLLAWISHVWVMLPALICLAAGGMGQPALQGYLSKSVDHHVQGQLQGTLVSLTNITGIVGPLLFSFIYSYSVEYWDGLLWFIGAMLYSGLLVASYFKQKSPILKKFPS"},"dna_sequence":{"accession":"AF038993","fmin":"0","fmax":"1197","strand":"+","sequence":"ATGAATAAATCAATTATTATCATACTGCTTGTCACAGTATTAGATGCCATTGGTATTGGCCTTATCATGCCAGTACTACCAACACTATTAAACGAGTTTGTGAGCGAAAACAGACTCGCCAATCATTACGGTATATTATTAGCACTCTATGCGACGATGCAGGTGATCTTCGCACCTATTTTAGGAAAATTATCAGATAAATATGGCAGAAAACCTATTTTATTAATTTCGCTATTGGGTGCCGCATTAGATTACCTATTAATGGCTTGCCCCACCTCATTATGGATGCTCTACATTGGACGAATAATTGCGGGTATAACAGGAGCCACTGGTGCAGTATGCGCATCAGCAATGACTGATGTAACTCATCCTCATGAAAGAACACGCTATTTCGGTTTTTTGGGTGGTGCATTTGGTGTGGGTTTAATTATTGGCCCCATGTTAGGGGGATTACTCGGTGAGATCAGCGCCCATACGCCATTTATCTTTGCGGCTATTTCTCATTCGTTATTATTTATATTTTCATTACTTTGTTTCCAAGAAACTCAAACCACAAAAATTTCGACTGAAATATCCGCATTAAATCAGGATACAGCGCCTCACTCTACCACTGGTTTTATTAAAAAGAGTCTCTTTTTTTGGCTTATTGCCTATTTTATTATTCAACTAATAGGGCAAATTCCGGCCACTATTTGGGTGCTATTCACACAAGTTCGTTTCGCTTGGCACACTACTGAAGTAGGTTTATCTCTTGCATTTCTTGGTGTATTACATATTTTTTTTCAAGCGGTTCTCGCAGGAAAACTGGCGCAAAAATGGGGAGAACGCAACACGGTTATCATTAGCATGTCAATTGATGCATTTGGTTGCTTATTATTAGCCTGGATAAGCCATGTTTGGGTTATGCTTCCCGCTTTAATCTGTTTAGCTGCGGGAGGAATGGGACAACCTGCTTTACAAGGATATTTATCAAAATCTGTTGATCATCATGTTCAAGGACAGTTACAAGGAACGTTAGTCAGTCTAACGAATATAACTGGGATTGTCGGCCCGTTACTCTTCTCTTTTATTTATAGTTACAGCGTTGAATATTGGGATGGCTTATTGTGGTTTATTGGTGCAATGCTTTACAGTGGGTTACTTGTAGCCAGTTATTTTAAACAGAAATCACCAATATTAAAAAAATTTCCCTCATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3000177","ARO_id":"36316","ARO_name":"tet(J)","ARO_description":"TetJ is a tetracycline efflux protein expressed in Gram-negative bacteria (Escherichia, Morganella, and Proteus).","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1006":{"model_id":"1006","model_name":"tet(V)","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"770"}},"model_sequences":{"sequence":{"391":{"protein_sequence":{"accession":"AAB84282.1","sequence":"MRSPRPVAGWRVLAPFRIREYRLLIAAVTLSIFAEGMWSVVMALQVIAIDNDPASLSLVATCLGVGLVAFVLVGGITADRINQRTIIIAVEVVNFVTVAVISALALLGVLKIWHMAVAAGILGIAAAFFFPAYSAILPRILPPEQLLAANGVEGVVRPVFQRSVGPAVAGMVIGATMPSIGAVVVAVLFALGLALLVATRPPAQPASEHHERPHVLRDLREGFAFVLKTPWLLWTVLFASMFVLVVLGPIEVLLPFIAQDRFADGARAYGFILAFFGIGSAMGALTVSSRRMPRRYLTTMMLMWGLGSIPLVIVGYTSSFPLMAAATFVIGVTDGAGMVIWGTLLQRRVPTEMLGRVSSLDFFVSLAFMPLSFAIVGPLSKVVSMEVIFATAGLVPVAIAAVAFTAARMHRDEVANPLL"},"dna_sequence":{"accession":"AF030344","fmin":"0","fmax":"1260","strand":"-","sequence":"TCACAGCAGTGGGTTCGCCACCTCGTCACGGTGCATGCGCGCCGCGGTGAACGCCACGGCCGCGATCGCCACGGGCACCAGACCCGCCGTCGCGAAGATCACCTCCATCGAGACCACCTTCGACAGCGGACCCACGATCGCGAATGACAACGGCATGAACGCCAGCGATACGAAGAAGTCCAGGCTCGACACGCGGCCCAGCATCTCGGTGGGCACACGCCGTTGCAGCAGCGTTCCCCAGATCACCATGCCAGCGCCGTCGGTGACGCCGATGACGAACGTCGCAGCGGCCATCAGCGGGAACGACGATGTATATCCCACGATCACAAGGGGAATCGAGCCGAGACCCCACATCAGCATCATGGTCGTGAGATAGCGGCGCGGCATGCGCCGCGACGACACCGTCAGCGCGCCCATCGCACTGCCGATACCGAAGAACGCCAGGATGAAACCGTAGGCGCGGGCGCCGTCGGCGAAGCGGTCCTGTGCGATGAACGGCAGCAGCACCTCGATGGGTCCCAGCACGACGAGCACGAACATGCTCGCGAACAGCACGGTCCACAGCAGCCACGGTGTCTTCAGGACGAAGGCGAAACCTTCACGCAGGTCCCGCAATACGTGCGGGCGCTCATGGTGCTCGGAGGCGGGCTGGGCGGGCGGACGGGTCGCGACCAGCAGCGCCAGGCCGAGCGCGAACAGCACCGCCACCACGACCGCGCCGATCGACGGCATCGTTGCACCGATGACCATGCCGGCCACCGCGGGGCCCACCGAACGCTGGAACACCGGGCGTACCACGCCCTCGACACCGTTGGCGGCCAGCAGCTGTTCGGGCGGCAGGATGCGCGGCAGGATCGCGCTGTAGGCCGGGAAGAAGAACGCCGCCGCGATGCCGAGAATGCCTGCGGCAACGGCCATGTGCCAGATCTTCAGCACGCCCAGCAGGGCCAGCGCGGAGATCACCGCGACCGTGACGAAGTTGACCACCTCGACGGCAATGATGATGGTGCGCTGGTTGATCCGGTCCGCGGTGATGCCGCCGACGAGGACGAACGCGACCAGGCCGACACCGAGGCACGTCGCGACCAGCGACAGTGACGCCGGATCGTTGTCGATCGCGATCACCTGCAGCGCCATGACCACAGACCACATGCCCTCGGCGAAGATCGACAGCGTGACCGCGGCGATCAGCAGGCGGTACTCGCGGATCCGGAACGGTGCGAGTACGCGCCAGCCTGCGACCGGACGCGGCGAGCGCAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36769","NCBI_taxonomy_name":"Mycobacterium smegmatis str. MC2 155","NCBI_taxonomy_id":"246196"}}}},"ARO_accession":"3000181","ARO_id":"36320","ARO_name":"tet(V)","ARO_description":"TetV is a tetracycline efflux protein that has been found in Mycobacterium smegmatis and M. fortuitum.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1132":{"model_id":"1132","model_name":"OXA-88","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1058":{"protein_sequence":{"accession":"ABD48715.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDKKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"DQ392963","fmin":"8","fmax":"833","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATAAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001626","ARO_id":"38026","ARO_name":"OXA-88","ARO_description":"OXA-88 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1133":{"model_id":"1133","model_name":"SHV-109","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"985":{"protein_sequence":{"accession":"ACM04459.1","sequence":"MRYIRRCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDMPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"EU418913","fmin":"16","fmax":"877","strand":"+","sequence":"ATGCGTTATATTCGCCGGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAACTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATATGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001158","ARO_id":"37538","ARO_name":"SHV-109","ARO_description":"SHV-109 is a broad-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1136":{"model_id":"1136","model_name":"MIR-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"764":{"protein_sequence":{"accession":"AFJ79785.1","sequence":"MMTKSLSCALLLSVTSAAFAAPMSETQLAEVVERTVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTSTGVLGGDAIARGEIALGDPVAKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDTASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEEAHYAWGYREGKAVHVSPGMLDAEAYGVKTNVKDMASWLIANMKPDSLQAPSLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"JQ664733","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGACAAAATCCCTAAGCTGTGCCCTGCTGCTCAGCGTCACCAGCGCTGCATTCGCCGCACCGATGTCCGAAACACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTAATTTATCAGGGTCAGCCACACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTCCACCGGCGTACTGGGCGGCGATGCCATTGCCCGGGGTGAAATAGCGCTGGGCGATCCGGTAGCAAAATACTGGCCTGAGCTCACGGGCAAGCAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTATACCGCAGGCGGTCTGCCGTTACAGGTGCCGGATGAGGTCACGGATACCGCTTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCTAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTTAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAACCCCTCAAGCTGGACCATACCTGGATTAACGTCCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGAGGGTAAAGCGGTCCACGTTTCGCCAGGGATGCTGGACGCGGAAGCCTATGGCGTAAAAACTAACGTGAAGGATATGGCGAGCTGGCTGATAGCCAACATGAAGCCGGATTCTCTTCAGGCTCCCTCACTCAAGCAAGGCATTGCTCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCTATGTATCAGGGGCTGGGCTGGGAGATGCTCAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCATTGCCCGTGGCAGAAGTGAATCCACCCGCGCCGCCGGTCAAAGCCTCCTGGGTCCATAAAACAGGCTCGACGGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3002171","ARO_id":"38571","ARO_name":"MIR-6","ARO_description":"MIR-6 is a beta-lactamase. From the Lahey list of MIR beta-lactamases.","ARO_category":{"36197":{"category_aro_accession":"3000058","category_aro_cvterm_id":"36197","category_aro_name":"MIR beta-lactamase","category_aro_description":"MIR beta-lactamases are plasmid-mediated beta-lactamases that confer resistance to oxyimino- and alpha-methoxy beta-lactams","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1137":{"model_id":"1137","model_name":"TEM-90","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1804":{"protein_sequence":{"accession":"AAK30619.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTGGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AF351241","fmin":"89","fmax":"950","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGGTGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000957","ARO_id":"37337","ARO_name":"TEM-90","ARO_description":"TEM-90 is a broad-spectrum beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1139":{"model_id":"1139","model_name":"dfrA12","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"171":{"protein_sequence":{"accession":"AHW42429.1","sequence":"MNSESVRIYLVAAMGANRVIGNGPNIPWKIPGEQKIFRRLTEGKVVVMGRKTFESIGKPLPNRHTLVISRQANYRATGCVVVSTLSHAIALASELGNELYVAGGAEIYTLALPHAHGVFLSEVHQTFEGDAFFPMLNETEFELVSTETIQAVIPYTHSVYARRNG"},"dna_sequence":{"accession":"KJ363320","fmin":"72","fmax":"570","strand":"+","sequence":"ATGAACTCGGAATCAGTACGCATTTATCTCGTTGCTGCGATGGGAGCCAATCGGGTTATTGGCAATGGTCCTAATATCCCCTGGAAAATTCCGGGTGAGCAGAAGATTTTTCGCAGACTCACTGAGGGAAAAGTCGTTGTCATGGGGCGAAAGACCTTTGAGTCTATCGGCAAGCCTCTACCGAACCGTCACACATTGGTAATCTCACGCCAAGCTAACTACCGCGCCACTGGCTGCGTAGTTGTTTCAACGCTGTCGCACGCTATCGCTTTGGCATCCGAACTCGGCAATGAACTCTACGTCGCGGGCGGAGCTGAGATATACACTCTGGCACTACCTCACGCCCACGGCGTGTTTCTATCTGAGGTACATCAAACCTTCGAGGGTGACGCCTTCTTCCCAATGCTCAACGAAACAGAATTCGAGCTTGTCTCAACCGAAACCATTCAAGCTGTAATTCCGTACACCCACTCCGTTTATGCGCGTCGAAACGGCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39097","NCBI_taxonomy_name":"Klebsiella pneumoniae subsp. pneumoniae","NCBI_taxonomy_id":"72407"}}}},"ARO_accession":"3002858","ARO_id":"39292","ARO_name":"dfrA12","ARO_description":"dfrA12 is an integron-encoded dihydrofolate reductase found in Vibrio cholerae","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36408":{"category_aro_accession":"3000269","category_aro_cvterm_id":"36408","category_aro_name":"brodimoprim","category_aro_description":"Brodimoprim is a structural derivative of trimethoprim and an inhibitor of bacterial dihydrofolate reductase. The 4-methoxy group of trimethoprim is replaced with a bromine atom.","category_aro_class_name":"Antibiotic"},"36423":{"category_aro_accession":"3000284","category_aro_cvterm_id":"36423","category_aro_name":"tetroxoprim","category_aro_description":"Tetroxoprim is a trimethoprim derivative that inhibits bacterial dihydrofolate reductase.","category_aro_class_name":"Antibiotic"},"36476":{"category_aro_accession":"3000337","category_aro_cvterm_id":"36476","category_aro_name":"iclaprim","category_aro_description":"Iclaprim is a bactericidal compound that inhibits dihydrofolate reductase. It is used against clinically important Gram-positive pathogens, including methicillin-sensitive Staphylococcus aureus and methicillin-resistant S. aureus.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1140":{"model_id":"1140","model_name":"CMY-86","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1197":{"protein_sequence":{"accession":"AHL39327.1","sequence":"MMKKSLCCALLLTAPFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADITNNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWAPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQVNMDASRVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEVAWHILEKLQ"},"dna_sequence":{"accession":"KJ207204","fmin":"579","fmax":"1725","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCCCTTTCTCCACGTTTGCCGCAGCCAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCACCAATAACCACCCAGTCACGCAGCAAACTCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTACACGGCAGGCGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCGTTTTTATCAAAACTGGCAGCCGCAATGGGCCCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACAGTTCCGCAAAGCGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGTCAACATGGACGCCAGCCGCGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGTAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACTGGAGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGTGGCCTGGCACATTCTTGAAAAGCTGCAATAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002099","ARO_id":"38499","ARO_name":"CMY-86","ARO_description":"CMY-86 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1141":{"model_id":"1141","model_name":"OXA-169","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1525":{"protein_sequence":{"accession":"ADK35873.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETPSQIVQGHNQVIHQYFDERNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKPQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"HM488990","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAGAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGACCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCCCAATTAGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001469","ARO_id":"37869","ARO_name":"OXA-169","ARO_description":"OXA-169 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1142":{"model_id":"1142","model_name":"dfrA17","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"291":{"protein_sequence":{"accession":"ABG91835.1","sequence":"MKISLISAVSENGVIGSGPDIPWSVKGEQLLFKALTYNQWLLVGRKTFDSMGVLPNRKYAVVSKNGISSSNENVLVFPSIENALKELSKVTDHVYVSGGGQIYNSLIEKADIIHLSTVHVEVEGDIKFPIMPENFNLVFEQFFMSNINYTYQIWKKG"},"dna_sequence":{"accession":"DQ838665","fmin":"0","fmax":"474","strand":"+","sequence":"TTGAAAATATCATTGATTTCTGCAGTGTCAGAAAATGGCGTAATCGGTAGTGGTCCTGATATCCCGTGGTCAGTAAAAGGTGAGCAACTACTCTTTAAAGCGCTCACATATAATCAATGGCTCCTTGTCGGAAGAAAAACATTTGACTCTATGGGTGTTCTTCCAAATCGCAAATATGCAGTAGTGTCAAAGAACGGAATTTCAAGCTCAAATGAAAACGTCCTAGTTTTTCCTTCAATAGAAAATGCTTTGAAAGAGCTATCAAAAGTTACAGATCATGTATATGTCTCTGGCGGGGGTCAAATCTATAATAGCCTTATTGAAAAAGCAGATATAATTCATTTGTCTACTGTTCACGTTGAAGTCGAAGGTGATATCAAATTCCCTATAATGCCTGAGAATTTCAATTTGGTTTTTGAACAGTTTTTTATGTCTAATATAAATTATACATACCAGATTTGGAAAAAAGGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002860","ARO_id":"39294","ARO_name":"dfrA17","ARO_description":"dfrA17 is an integron-encoded dihydrofolate reductase found in Escherichia coli","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36408":{"category_aro_accession":"3000269","category_aro_cvterm_id":"36408","category_aro_name":"brodimoprim","category_aro_description":"Brodimoprim is a structural derivative of trimethoprim and an inhibitor of bacterial dihydrofolate reductase. The 4-methoxy group of trimethoprim is replaced with a bromine atom.","category_aro_class_name":"Antibiotic"},"36423":{"category_aro_accession":"3000284","category_aro_cvterm_id":"36423","category_aro_name":"tetroxoprim","category_aro_description":"Tetroxoprim is a trimethoprim derivative that inhibits bacterial dihydrofolate reductase.","category_aro_class_name":"Antibiotic"},"36476":{"category_aro_accession":"3000337","category_aro_cvterm_id":"36476","category_aro_name":"iclaprim","category_aro_description":"Iclaprim is a bactericidal compound that inhibits dihydrofolate reductase. It is used against clinically important Gram-positive pathogens, including methicillin-sensitive Staphylococcus aureus and methicillin-resistant S. aureus.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1143":{"model_id":"1143","model_name":"OXA-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"894":{"protein_sequence":{"accession":"CAA53242.1","sequence":"MKTFAAYVITACLSSTALASSITENTFWNKEFSAEAVNGVFVLCKSSSKLACATNNLARASKEYLPASTFKIPNAIIGLETGVIKNEHQIFKWDGKPRAMKQWERDLSLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLFLNKLSASKENQLIVKEALVTEAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKGAEVYFFAFNMDIDNENKLPLRKSIPTKIMASEGIIGG"},"dna_sequence":{"accession":"X75562","fmin":"134","fmax":"935","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTACTGCGTGTCTTTCAAGTACGGCATTAGCTAGTTCAATTACAGAAAATACGTTTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTTTTCGTGCTTTGTAAAAGTAGCAGTAAATTAGCCTGCGCTACCAATAACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGATTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAACAATGGGAAAGAGACTTGAGCTTAAGAGGGGCAATACAAGTTTCAGCGGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATATCTTAAAAAATTTTCATATGGTAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAGGGTCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATTTTTAAATAAATTGTCAGCATCAAAAGAAAATCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCGCCTGAATATCTTGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGTTGGGTTGAGAAGGGAGCAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAATAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGCAAGTGAGGGCATCATTGGTGGCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001402","ARO_id":"37802","ARO_name":"OXA-7","ARO_description":"OXA-7 is a beta-lactamase found in P. aeruginosa and Enterobacteriaceae.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1144":{"model_id":"1144","model_name":"VgbB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"4415":{"protein_sequence":{"accession":"AAC61670.1","sequence":"MNFYLEEFNLSIPDSGPYGITSSEDGKVWFTQHKANKISSLDQSGRIKEFEVPTPDAKVMCLIVSSLGDIWFTENGANKIGKLSKKGGFTEYPLPQPDSGPYGITEGLNGDIWFTQLNGDRIGKLTADGTIYEYDLPNKGSYPAFITLGSDNALWFTENQNNSIGRITNTGKLEEYPLPTNAAAPVGITSGNDGALWFVEIMGNKIGRITTTGEISEYDIPTPNARPHAITAGKNSEIWFTEWGANQIGRITNDKTIQEYQLQTENAEPHGITFGKDGSVWFALKCKIGKLNLNE"},"dna_sequence":{"accession":"AF015628","fmin":"398","fmax":"1286","strand":"+","sequence":"ATGAATTTTTATTTAGAGGAGTTTAACTTGTCTATTCCCGATTCAGGTCCATACGGTATAACTTCATCAGAAGACGGAAAGGTATGGTTCACACAACATAAGGCAAACAAAATCAGCAGTCTAGATCAGAGTGGTAGGATAAAAGAATTCGAAGTTCCTACCCCTGATGCTAAAGTGATGTGTTTAATTGTATCTTCACTTGGAGACATATGGTTTACAGAGAATGGTGCAAATAAAATCGGAAAGCTCTCAAAAAAAGGTGGCTTTACAGAATATCCATTGCCACAGCCGGATTCTGGTCCTTACGGAATAACGGAAGGTCTAAATGGCGATATATGGTTTACCCAATTGAATGGAGATCGTATAGGAAAGTTGACAGCTGATGGGACTATTTATGAATATGATTTGCCAAATAAGGGATCTTATCCTGCTTTTATTACTTTAGGTTCGGATAACGCACTTTGGTTCACGGAGAACCAAAATAATTCTATTGGAAGGATTACAAATACAGGGAAATTAGAAGAATATCCTCTACCAACAAATGCAGCGGCTCCAGTGGGTATCACTAGTGGTAACGATGGTGCACTCTGGTTTGTCGAAATTATGGGCAACAAAATAGGTCGAATCACTACAACTGGTGAGATTAGCGAATATGATATTCCAACTCCAAACGCACGTCCACACGCTATAACCGCGGGGAAAAATAGCGAAATATGGTTTACTGAATGGGGGGCAAATCAAATCGGCAGAATTACAAACGACAAAACAATTCAAGAATATCAACTTCAAACAGAAAATGCGGAACCTCATGGTATTACCTTTGGAAAAGATGGATCCGTATGGTTTGCATTAAAATGTAAAATTGGGAAGCTGAATTTGAACGAATGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36766","NCBI_taxonomy_name":"Staphylococcus cohnii","NCBI_taxonomy_id":"29382"}}}},"ARO_accession":"3001308","ARO_id":"37707","ARO_name":"vgbB","ARO_description":"VgbB inactivates streptogramin B-type antibiotics by linearizing the lactone ring on the ester bond through an elimination mechanism, thus conferring resistance.","ARO_category":{"36515":{"category_aro_accession":"3000376","category_aro_cvterm_id":"36515","category_aro_name":"streptogramin vgb lyase","category_aro_description":"vgb (Virginiamycin B) lyase inactivates type B streptogramin antibiotics by linearizing the streptogramin lactone ring at the ester linkage through an elimination mechanism, thus conferring resistance to these compounds.","category_aro_class_name":"AMR Gene Family"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin 1A is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"vernamycin B-gamma","category_aro_description":"Vernamycin B-gamma is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1145":{"model_id":"1145","model_name":"CTX-M-124","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1333":{"protein_sequence":{"accession":"AFH88134.1","sequence":"MMTQSIRRSMLTVMATLPLLFSSATLHAQANSVQQQLEALEKSSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKQSESDKHLLNQRVEIKKSDLVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSASIRAGLPKSWVVGDKTGSGDYGTTNDIAIIWPENHAPLVLVTYFTQPEQKAESRRDVLAAAAKIVTHGF"},"dna_sequence":{"accession":"JQ429324","fmin":"0","fmax":"876","strand":"+","sequence":"ATGATGACTCAGAGCATTCGCCGCTCAATGTTAACGGTGATGGCGACGCTACCCCTGCTATTTAGCAGCGCAACGCTGCATGCGCAGGCGAACAGCGTGCAACAGCAGCTGGAAGCCCTGGAGAAAAGTTCGGGAGGTCGGCTTGGCGTTGCGCTGATTAACACCGCCGATAATTCGCAGATTCTCTACCGTGCCGATGAACGTTTTGCGATGTGCAGTACCAGTAAGGTGATGGCGGCCGCGGCGGTGCTTAAACAGAGCGAGAGCGATAAGCACCTGCTAAATCAGCGCGTTGAAATCAAGAAGAGCGACCTGGTTAACTACAATCCCATTGCTGAGAAACACGTTAACGGCACTATGACGCTGGCTGAGCTTGGCGCAGCGGCGCTGCAGTATAGCGACAATACTGCCATGAATAAGCTGATTGCCCATCTGGGTGGGCCCGATAAAGTGACGGCGTTTGCTCGCTCGTTGGGTGATGAGACCTTCCGTCTGGACAGAACCGAGCCCACGCTCAATACCGCCATTCCAGGCGACCCGCGTGATACCACCACGCCGCTCGCGATGGCGCAGACCCTGAAAAATCTGACGCTGGGTAAAGCGCTGGCGGAAACTCAGCGGGCACAGTTGGTGACGTGGCTTAAGGGCAATACTACCGGTAGCGCGAGCATTCGGGCGGGTCTGCCGAAATCATGGGTAGTGGGCGATAAAACCGGCAGCGGAGATTATGGCACCACCAACGATATCGCGATTATCTGGCCGGAAAACCACGCACCGCTGGTTCTGGTGACCTACTTTACCCAACCGGAGCAGAAGGCGGAAAGCCGTCGGGATGTTCTGGCTGCGGCGGCGAAAATCGTAACCCACGGTTTCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001983","ARO_id":"38383","ARO_name":"CTX-M-124","ARO_description":"CTX-M-124 is a beta-lactamase found in Escherichia coli","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1146":{"model_id":"1146","model_name":"TEM-156","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1400":{"protein_sequence":{"accession":"CAQ00120.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNIGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AM941159","fmin":"208","fmax":"1069","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATAGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3001022","ARO_id":"37402","ARO_name":"TEM-156","ARO_description":"TEM-156 is a TEM beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1147":{"model_id":"1147","model_name":"CMY-63","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1859":{"protein_sequence":{"accession":"AET07387.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADITNNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWAPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKAVHVSPGQLDAEAYGVKSSVIDMARWVQVNMDASRVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKKLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"HQ650104","fmin":"63","fmax":"1209","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCATTCTCCACGTTTGCCGCCGCCAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCACCAATAACCACCCAGTCACGCAGCAAACTCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTACACGGCAGGCGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCGTTTTTATCAAAACTGGCAGCCGCAATGGGCCCCGGGCGCTAAGAGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACAGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGGCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGTGTTATTGATATGGCCCGCTGGGTTCAGGTCAACATGGACGCCAGCCGCGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCAATCATCAACGGTAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCTGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACTGGAGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAAACTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002076","ARO_id":"38476","ARO_name":"CMY-63","ARO_description":"CMY-63 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1148":{"model_id":"1148","model_name":"OXA-363","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"890":{"protein_sequence":{"accession":"AHA11126.1","sequence":"MKTLIFLPLLNCLSLTACTLPVSSSPSHITSTQSTQAIAQLFDQAQSSGVLVIQRGQQIQVYGNDLSRADTEYVPASTFKMLNALIGLQHGKATTNEIFKWDGKKRSFSAWEKDMTLGQAMQASAVPVYQELARRIGLELMQQEVQRIQFGNQQIGQQVDNFWLVGPLKITPKQEVEFVSALAREQLAFDPQVQQQVKAMLLLQERKAYRLYAKSGWGMDVEPQVGWLTGWVETPQAEIVAFSLNMQMQNGMDPAIRLEILQQALAELGLYPKAEG"},"dna_sequence":{"accession":"KF460533","fmin":"0","fmax":"831","strand":"+","sequence":"ATGAAAACTCTGATTTTTCTGCCTTTACTTAATTGCTTGAGCCTGACGGCGTGTACCTTACCCGTTTCATCTTCCCCATCTCATATCACTTCGACTCAATCGACTCAAGCCATTGCCCAATTATTTGATCAGGCGCAAAGCTCTGGCGTTTTAGTGATTCAGCGTGGTCAACAGATACAGGTCTATGGCAATGATTTAAGCCGTGCAGATACCGAATATGTTCCCGCCTCTACTTTTAAAATGCTCAATGCCCTGATTGGCCTGCAACATGGCAAAGCCACAACCAATGAAATTTTTAAATGGGATGGTAAGAAACGTAGTTTTTCAGCCTGGGAAAAAGACATGACTCTCGGCCAAGCCATGCAAGCTTCTGCTGTACCCGTCTATCAGGAACTGGCGCGTCGTATTGGCCTTGAACTGATGCAACAGGAAGTACAACGCATCCAATTTGGTAATCAGCAGATTGGTCAGCAAGTCGATAATTTCTGGTTGGTAGGCCCTTTGAAAATCACTCCAAAACAGGAGGTCGAATTTGTCTCGGCTCTAGCCCGAGAGCAGCTTGCCTTTGATCCACAAGTCCAGCAGCAAGTCAAAGCCATGTTACTTTTACAGGAGCGGAAAGCTTATCGACTATATGCCAAATCTGGTTGGGGCATGGATGTGGAACCACAAGTCGGCTGGCTCACCGGCTGGGTTGAAACACCGCAGGCTGAAATCGTGGCATTTTCGCTGAATATGCAGATGCAAAATGGTATGGATCCGGCAATCCGCCTTGAAATTTTACAGCAGGCTTTGGCCGAATTAGGGCTTTATCCAAAAGCTGAAGGATGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36948","NCBI_taxonomy_name":"Acinetobacter lwoffii","NCBI_taxonomy_id":"28090"}}}},"ARO_accession":"3001550","ARO_id":"37950","ARO_name":"OXA-363","ARO_description":"OXA-363 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1149":{"model_id":"1149","model_name":"AER-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"901":{"protein_sequence":{"accession":"AAC09015.1","sequence":"MYVLSVEKPTLRNKFAAGIGVVLVCVVASFIPTPVFALDTTKLIQAVQSEESALHARVGMTVFDSNTGTTWNYRGDERFPLNSTHKTFSCAALLAKVDGKSLSLGQSVSISKEMLVTYSPITEKSLSPETVTFGKICQAAVSYSDNTAANVVFDAIGGATGFNAYMRSIGDEETQLDRKEPELNEGTPGDVRDTTTPNAMVNSLRKILLGDALSASSRSQLTQWMLDDQVAGALLRASLPSDWKIADKTGAGGYGSRSIVAVIWPPSKQPLVVGIYITQTKASMQASNQAIARIGVVLKDTVAP"},"dna_sequence":{"accession":"U14748","fmin":"324","fmax":"1239","strand":"+","sequence":"ATGTACGTACTTTCCGTGGAGAAACCTACATTGAGAAACAAATTTGCGGCCGGAATAGGCGTCGTGCTTGTATGTGTCGTTGCCTCGTTTATTCCAACCCCAGTATTCGCCCTAGACACCACGAAGCTGATCCAAGCCGTCCAGTCGGAAGAGAGCGCCTTGCATGCCCGAGTCGGCATGACCGTGTTTGACTCAAACACTGGAACGACTTGGAACTATCGGGGCGATGAGCGGTTTCCATTGAACAGTACGCACAAGACGTTTTCCTGTGCAGCTTTGCTCGCGAAGGTCGATGGGAAGTCCCTCTCTCTGGGCCAATCCGTATCGATCAGCAAGGAAATGCTGGTCACCTATTCGCCGATTACGGAAAAGTCGCTGTCACCCGAAACCGTTACCTTCGGCAAGATTTGTCAGGCAGCGGTGAGCTATAGCGATAACACAGCCGCAAACGTCGTCTTTGATGCCATTGGAGGAGCAACCGGATTCAACGCATACATGCGGTCTATCGGCGATGAAGAAACCCAGCTTGATCGCAAAGAACCCGAGTTGAACGAAGGTACGCCGGGCGATGTGCGTGACACCACCACTCCCAACGCCATGGTCAATAGTCTTAGGAAGATACTTCTTGGCGACGCGTTGTCAGCATCATCCCGATCCCAGCTGACGCAATGGATGCTGGACGATCAGGTTGCTGGTGCGCTCCTGCGTGCCTCACTGCCATCCGATTGGAAGATCGCCGACAAGACCGGCGCGGGGGGTTACGGCTCACGCTCGATCGTCGCAGTAATCTGGCCGCCATCGAAGCAGCCACTGGTGGTTGGCATCTATATCACGCAAACCAAAGCATCCATGCAGGCCAGCAATCAGGCGATTGCAAGGATAGGAGTGGTGCTGAAGGATACGGTCGCTCCTTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36810","NCBI_taxonomy_name":"Aeromonas hydrophila","NCBI_taxonomy_id":"644"}}}},"ARO_accession":"3002481","ARO_id":"38881","ARO_name":"AER-1","ARO_description":"AER-1 is a beta-lactamase found in Aeromonas hydrophila","ARO_category":{"36228":{"category_aro_accession":"3000089","category_aro_cvterm_id":"36228","category_aro_name":"AER beta-lactamase","category_aro_description":"AER beta-lactamases are capable of hydrolyzing arbenicillin.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1150":{"model_id":"1150","model_name":"QnrVC5","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"572":{"protein_sequence":{"accession":"AEM62764.1","sequence":"MDKTDQLYVQADFSHQDMSGQYFKNCKFFCCSFKRANLRDTQFVDCSFIERGELEGCDFSYSDLRDASFKNCSLSMSYFKGANCFGIEFRECDLKGANFSQASFMNQVSNRMYFCSAYITGCNLSYANFERQCIEKCDLFENRWIGANLSGASFKESDLSRGVFSEGCWSQCRLQGCDLSHSELYGLDPRKVDLTGVKICSWQQEQLLEQLGLIVVPD"},"dna_sequence":{"accession":"JN408080","fmin":"0","fmax":"657","strand":"+","sequence":"ATGGATAAAACAGACCAGTTATATGTACAAGCAGACTTTTCACATCAAGACATGAGTGGTCAGTATTTTAAAAATTGCAAATTTTTCTGCTGTTCCTTTAAACGAGCGAACCTCCGCGATACACAATTTGTAGATTGTTCTTTCATTGAACGAGGTGAATTAGAGGGGTGTGATTTTTCTTACTCGGATCTTAGAGATGCATCTTTTAAAAACTGCAGTCTTTCAATGTCGTATTTCAAAGGTGCAAATTGTTTTGGTATCGAGTTCAGAGAATGCGATTTAAAGGGTGCCAATTTTTCTCAAGCTAGCTTCATGAATCAGGTATCGAACAGAATGTATTTTTGTTCAGCTTATATAACAGGTTGTAATCTTTCATACGCCAACTTTGAAAGGCAGTGTATCGAAAAGTGTGATTTGTTTGAGAATAGATGGATTGGCGCAAATCTGAGTGGTGCATCATTTAAAGAGTCTGATTTAAGTCGGGGAGTATTTTCTGAAGGGTGTTGGAGCCAGTGTAGGTTGCAAGGTTGTGATTTGAGCCACTCGGAGTTGTATGGTTTAGACCCTCGGAAAGTTGACCTTACAGGTGTAAAAATCTGTTCGTGGCAGCAAGAACAACTTTTAGAGCAATTAGGTTTAATAGTAGTTCCTGACTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39525","NCBI_taxonomy_name":"Vibrio fluvialis","NCBI_taxonomy_id":"676"}}}},"ARO_accession":"3002802","ARO_id":"39236","ARO_name":"QnrVC5","ARO_description":"QnrVC5 is an integron-mediated quinolone resistance protein found in Vibrio fluvialis","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1151":{"model_id":"1151","model_name":"OXA-240","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1684":{"protein_sequence":{"accession":"AFN20670.1","sequence":"MKTFAAYVIIACLSSTALAGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMNQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG"},"dna_sequence":{"accession":"JX089628","fmin":"0","fmax":"801","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTATCGCGTGTCTTTCGAGTACGGCATTAGCTGGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTCTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATGACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAATCAATGGGAAAGAGACTTGACCTTAAGAGGGGCAATACAAGTTTCAGCTGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCCTATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAAGGCCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATATTTAAATAAATTGTCAGCATCTAAAGAAAACCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCGGCACCTGAATATCTAGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGGTGGGTTGAGAAGGAGACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAGTAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGAAAGTGAGGGCATCATTGGTGGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001499","ARO_id":"37899","ARO_name":"OXA-240","ARO_description":"OXA-240 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1152":{"model_id":"1152","model_name":"CTX-M-39","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1431":{"protein_sequence":{"accession":"AAX54694.1","sequence":"MMRKSVRRAMLMTTACVSLLLASVPLCAQANDVQQKLAALEKSSGGRLGVALINTADNTQTLYRADERFAMCSTSKVMAAAAVLKQSETQKGLLSQRVEIKPSDLINYNPIAEKHVNGTMTFGELSAAALQYSDNTAMNKLIAHLGGPDKVTAFARTIGDDTFRLDRTEPTLNTAIPGDPRDTTTPLAMAQALRNLTLGNALGDTQRAQLVMWLKGNTTGAASIQAGLPTSWVVGDKTGSGDYGTTNDIAVIWPEGRAPLVLVTYFTQSEPKAESRRDVLAAAARIVTDGY"},"dna_sequence":{"accession":"AY954516","fmin":"0","fmax":"876","strand":"+","sequence":"ATGATGAGAAAAAGCGTAAGGCGGGCGATGTTAATGACGACAGCCTGTGTTTCGCTGCTGTTGGCCAGTGTGCCGCTGTGTGCCCAGGCGAACGATGTTCAACAAAAGCTCGCGGCGCTGGAGAAAAGCAGCGGGGGACGACTGGGTGTGGCGTTGATTAACACCGCCGATAACACGCAGACGCTCTACCGCGCCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCGGCAGCGGCGGTGCTTAAGCAAAGTGAAACGCAAAAGGGCTTGTTGAGTCAGCGGGTTGAAATTAAGCCCTCAGACTTGATTAACTACAACCCCATTGCGGAAAAACACGTCAATGGCACGATGACATTCGGGGAGTTGAGCGCGGCGGCGCTACAGTACAGCGATAATACTGCCATGAATAAGCTGATTGCCCATCTCGGGGGGCCGGATAAAGTGACGGCATTTGCCCGTACGATTGGCGATGACACGTTCCGGCTCGATCGTACCGAGCCGACGCTCAACACCGCGATCCCCGGCGACCCGCGCGATACCACCACGCCGTTAGCGATGGCGCAGGCTCTGCGCAATCTGACGTTGGGCAATGCCCTGGGTGACACTCAGCGTGCGCAGCTGGTGATGTGGCTGAAAGGCAACACCACCGGCGCTGCCAGCATTCAGGCAGGGCTACCCACATCGTGGGTTGTCGGGGATAAAACCGGCAGCGGCGATTATGGTACGACGAATGATATCGCGGTTATTTGGCCGGAAGGTCGCGCGCCGCTCGTTCTGGTGACTTACTTCACCCAGTCGGAGCCGAAGGCAGAGAGCCGTCGTGACGTGCTCGCTGCTGCCGCCAGAATTGTCACCGACGGTTATTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001901","ARO_id":"38301","ARO_name":"CTX-M-39","ARO_description":"CTX-M-39 is a beta-lactamase found in Escherichia coli","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1153":{"model_id":"1153","model_name":"KPC-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1192":{"protein_sequence":{"accession":"AAL05630.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"AF395881","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002313","ARO_id":"38713","ARO_name":"KPC-3","ARO_description":"KPC-3 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1154":{"model_id":"1154","model_name":"TEM-146","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1797":{"protein_sequence":{"accession":"AAZ14084.2","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLPDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSHGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"DQ105529","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTCCGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCACGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001013","ARO_id":"37393","ARO_name":"TEM-146","ARO_description":"TEM-146 is a beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1155":{"model_id":"1155","model_name":"ACT-9","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"819":{"protein_sequence":{"accession":"AEI70575.1","sequence":"MKTKSLCCALLLSTSCSVLAAPMSEKQLSDVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVTANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNTSLLRFYQHWQPQWKPGTTRLYANASIGLFGALAVKPSGMNFEQAMTKRVFKPLKLDHTWINVPKEEEAHYAWGYRDGKAIHVSPGMLDAEAYGVKTNIQDMASWLKANMNPDALSDSTLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLLVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEAAYRILSAL"},"dna_sequence":{"accession":"HQ693810","fmin":"1008","fmax":"2151","strand":"+","sequence":"ATGAAGACAAAATCCCTTTGCTGTGCCCTGCTGCTCAGCACCTCCTGCTCTGTTCTCGCCGCGCCGATGTCAGAGAAACAGCTGTCTGACGTGGTGGAACGTACCGTTACCCCCCTGATGAAAGCGCAAGCCATTCCGGGCATGGCGGTGGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGAAAGGCCGATGTTACGGCGAACAAACCTGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTATTAGGTGGCGATGCGATTGCGCGCGGAGAAATATCGCTGGGCGACCCCGTGACAAAGTACTGGCCCGAGCTAACAGGCAAGCAGTGGCAGGGTATTCGCATGTTGGATCTGGCGACCTACACCGCGGGTGGCCTGCCGCTACAGGTGCCGGATGAGGTCACGGATAACACCTCCCTGCTGCGTTTCTATCAACACTGGCAACCGCAGTGGAAACCAGGCACAACGCGTCTTTATGCGAACGCCAGCATCGGGCTTTTTGGCGCCCTCGCGGTTAAACCCTCCGGTATGAACTTTGAACAGGCCATGACGAAGCGGGTCTTCAAGCCACTCAAACTGGACCATACATGGATTAACGTTCCGAAAGAAGAAGAGGCGCATTACGCCTGGGGATACCGTGATGGTAAAGCAATCCACGTTTCACCGGGAATGCTGGATGCCGAAGCGTATGGTGTCAAAACCAACATCCAGGATATGGCGAGCTGGCTGAAGGCCAACATGAACCCTGACGCCCTTTCGGATTCAACGTTGAAACAGGGTATTGCCCTGGCACAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTCGTGGAGGGCAGCGATAACAAGGTGGCTCTTGCACCGTTACTGGTGGCAGAAGTGAACCCTCCAGCTCCGCCAGTAAAAGCATCATGGGTACATAAAACAGGCTCGACGGGTGGATTCGGCAGCTATGTCGCATTTATTCCTGAAAAGGAACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCGCGCGTGGAAGCGGCATACCGTATTTTGAGCGCTCTGTAGT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36950","NCBI_taxonomy_name":"Pantoea agglomerans","NCBI_taxonomy_id":"549"}}}},"ARO_accession":"3001826","ARO_id":"38226","ARO_name":"ACT-9","ARO_description":"ACT-9 is a beta-lactamase found in Pantoea agglomerans","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1156":{"model_id":"1156","model_name":"Erm(31)","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"249":{"protein_sequence":{"accession":"AAC69327.1","sequence":"MAFSPQGGRHELGQNFLVDRSVIDEIDGLVARTKGPILEIGPGDGALTLPLSRHGRPITAVELDGRRAQRLGARTPGHVTVVHHDFLQYPLPRNPHVVVGNVPFHLTTAIMRRLLDAQHWHTAVLLVQWEVARRRAGVGGSTLLTAGWAPWYEFDLHSRVPARAFRPMPGVDGGVLAIRRRSAPLVGQVKTYQDFVRQVFTGKGNGLKEILRRTGRISQRDLATWLRRNEISPHALPKDLKPGQWASLWELTGGTADGSFDGTAGGGAAGSHGAARVGAGHPGGRVSASRRGVPQARRGRGHAVRSSTGTEPRWGRGRAESA"},"dna_sequence":{"accession":"AF079138","fmin":"153","fmax":"1122","strand":"+","sequence":"ATGGCATTTTCCCCGCAGGGCGGCCGACACGAGCTCGGTCAGAACTTCCTCGTCGACCGGTCAGTGATCGACGAGATCGACGGCCTGGTGGCCAGGACCAAGGGTCCGATACTGGAGATCGGTCCGGGTGACGGCGCCCTGACCCTGCCGCTGAGCAGGCACGGCAGGCCGATCACCGCCGTCGAGCTCGACGGCCGGCGCGCGCAGCGCCTCGGTGCCCGCACCCCCGGTCATGTGACCGTGGTGCACCACGACTTCCTGCAGTACCCGCTGCCGCGCAACCCGCATGTGGTCGTCGGCAACGTCCCCTTCCATCTGACGACGGCGATCATGCGGCGGCTGCTCGACGCCCAGCACTGGCACACCGCCGTCCTCCTCGTCCAGTGGGAGGTCGCCCGGCGCCGGGCCGGCGTCGGCGGGTCGACGCTGCTGACGGCCGGCTGGGCGCCCTGGTACGAGTTCGACCTGCACTCCCGGGTCCCCGCGCGGGCCTTCCGTCCGATGCCGGGCGTGGACGGAGGAGTACTGGCCATCCGGCGGCGGTCCGCGCCGCTCGTGGGCCAGGTGAAGACGTACCAGGACTTCGTACGCCAGGTGTTCACCGGCAAGGGGAACGGGCTGAAGGAGATCCTGCGGCGGACCGGGCGGATCTCGCAGCGGGACCTGGCGACCTGGCTGCGGAGGAACGAGATCTCGCCGCACGCGCTGCCCAAGGACCTGAAGCCCGGGCAGTGGGCGTCGCTGTGGGAGCTGACCGGCGGCACGGCCGACGGATCCTTCGACGGTACGGCGGGCGGTGGCGCGGCCGGATCGCACGGGGCGGCTCGGGTCGGGGCCGGTCACCCGGGCGGCCGGGTGTCCGCGAGCCGGCGGGGCGTGCCGCAGGCGCGGCGCGGCCGGGGGCATGCGGTACGGAGCTCCACGGGGACCGAGCCGAGGTGGGGCAGGGGGCGGGCGGAGAGCGCGTGAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36873","NCBI_taxonomy_name":"Streptomyces venezuelae","NCBI_taxonomy_id":"54571"}}}},"ARO_accession":"3000598","ARO_id":"36737","ARO_name":"Erm(31)","ARO_description":"Erm(31) confers a MLSb resistant phenotype. Along with erm(30), these genes are responsible for self-resistance in the pikromycin\/narbomycin\/methymycin\/neomethymycin producer, Streptomyces venezuelae.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35946":{"category_aro_accession":"0000027","category_aro_cvterm_id":"35946","category_aro_name":"roxithromycin","category_aro_description":"Roxithromycin is a semi-synthetic, 14-carbon ring macrolide antibiotic derived from erythromycin. It is used to treat respiratory tract, urinary and soft tissue infections. Roxithromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35974":{"category_aro_accession":"0000057","category_aro_cvterm_id":"35974","category_aro_name":"telithromycin","category_aro_description":"Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36315":{"category_aro_accession":"3000176","category_aro_cvterm_id":"36315","category_aro_name":"dirithromycin","category_aro_description":"Dirithromycin is an oxazine derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome to inhibit bacterial protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin 1A is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"vernamycin B-gamma","category_aro_description":"Vernamycin B-gamma is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1157":{"model_id":"1157","model_name":"vanG","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"650"}},"model_sequences":{"sequence":{"300":{"protein_sequence":{"accession":"ABA71731.1","sequence":"MQNKKIAVIFGGNSTEYEVSLQSASAVFENINTNKFDIIPIGITRSGEWYHYTGEKEKILNNTWFEDSKNLCPVVVSQNRSVKGFLEIASDKYRIIKVDLVFPVLHGKNGEDGTLQGIFELAGIPVVGCDTLSSALCMDKDRAHKLVSLAGISVPKSVTFKRFNEEAAMKEIEANLTYPLFIKPVRAGSSFGITKVIEKQELDAAIELAFEHDTEVIVEETINGFEVGCAVLGIDELIVGRVDEIELSSGFFDYTEKYTLKSSKIYMPARIDAEAEKRIQEAAVTIYKALGCSGFSRVDMFYTPSGEIVFNEVNTIPGFTSHSRYPNMMKGIGLSFSQMLDKLIGLYVE"},"dna_sequence":{"accession":"DQ212986","fmin":"5984","fmax":"7034","strand":"+","sequence":"ATGCAAAATAAAAAAATAGCAGTTATTTTTGGAGGCAATTCAACAGAGTACGAGGTGTCATTGCAATCGGCATCCGCTGTTTTTGAAAATATCAATACCAATAAATTTGACATAATTCCAATAGGAATTACAAGAAGTGGTGAATGGTATCACTATACGGGAGAAAAGGAGAAAATCCTAAACAATACTTGGTTTGAAGATAGCAAAAATCTATGCCCTGTTGTCGTTTCCCAAAATCGTTCCGTTAAAGGCTTTTTAGAAATTGCTTCAGACAAATACCGTATTATAAAAGTTGATTTGGTATTCCCCGTATTGCATGGCAAAAACGGCGAAGATGGTACTTTGCAGGGCATATTTGAATTGGCAGGAATACCTGTTGTTGGCTGCGATACACTCTCATCAGCTCTTTGTATGGATAAGGACAGGGCACATAAACTCGTTAGCCTTGCGGGTATATCTGTTCCTAAATCGGTAACATTCAAACGCTTTAACGAAGAAGCAGCGATGAAAGAGATTGAAGCGAATTTAACTTATCCGCTGTTTATTAAACCTGTTCGTGCAGGCTCTTCCTTTGGAATAACAAAAGTAATTGAAAAGCAAGAGCTTGATGCTGCCATAGAGTTGGCATTTGAACACGATACAGAAGTCATCGTTGAAGAAACAATAAACGGCTTTGAAGTCGGTTGTGCCGTACTTGGCATAGATGAGCTCATTGTTGGCAGAGTTGATGAAATCGAACTGTCAAGCGGCTTTTTTGATTATACAGAGAAATATACGCTTAAATCTTCAAAGATATATATGCCTGCAAGGATTGATGCCGAAGCAGAAAAACGGATACAAGAAGCGGCTGTAACCATATATAAAGCTCTGGGCTGTTCGGGTTTTTCCAGAGTGGATATGTTTTATACACCGTCTGGCGAAATTGTATTTAATGAGGTAAACACAATACCAGGCTTTACCTCGCACAGTCGCTATCCAAATATGATGAAAGGCATTGGTCTATCGTTCTCCCAAATGTTGGATAAGCTGATAGGTCTGTATGTGGAATGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3002909","ARO_id":"39343","ARO_name":"vanG","ARO_description":"VanG is a D-Ala-D-Ala ligase homolog that can synthesize D-Ala-D-Ser, an alternative substrate for peptidoglycan synthesis that reduces vancomycin binding affinity in Enterococcus faecalis","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"39340":{"category_aro_accession":"3002906","category_aro_cvterm_id":"39340","category_aro_name":"van ligase","category_aro_description":"van ligases synthesize alternative substrates for peptidoglycan synthesis that reduce vancomycin binding affinity.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1158":{"model_id":"1158","model_name":"SHV-22","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1474":{"protein_sequence":{"accession":"AAF34336.1","sequence":"MLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDKVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASKRGARGIVALLGPNNKAERIVVIYLRDTPASMAERN"},"dna_sequence":{"accession":"AF117746","fmin":"0","fmax":"780","strand":"+","sequence":"CTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAAGGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCAAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001080","ARO_id":"37460","ARO_name":"SHV-22","ARO_description":"SHV-22 is a broad-spectrum beta-lactamase that has been found in clinical isolates.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1159":{"model_id":"1159","model_name":"TEM-129","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1796":{"protein_sequence":{"accession":"CAG34105.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AJ746225","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3000993","ARO_id":"37373","ARO_name":"TEM-129","ARO_description":"TEM-129 is an extended-spectrum beta-lactamase found in Klebsiella oxytoca.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1160":{"model_id":"1160","model_name":"QnrB34","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"512":{"protein_sequence":{"accession":"AEL00452.1","sequence":"MMTLALVGEKIDRNRFTGAKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAILKDAIFKSCDLSMAGFRNVSALGIEIRHCRAQGSDFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFSSFDWRAANFTHCDLTNSELGDLDVRGVDLQGVKLDSYQASLILERLGIAVIG"},"dna_sequence":{"accession":"JN173056","fmin":"35","fmax":"683","strand":"+","sequence":"ATGATGACTCTGGCGTTAGTTGGCGAAAAAATTGACAGAAACAGATTCACTGGTGCGAAAGTTGAAAATAGCACATTTTTCAACTGTGATTTTTCGGGTGCCGACCTCAGCGGTACTGAGTTTATTGGCTGCCAGTTCTATGATCGAGAGAGCCAGAAAGGGTGTAATTTTAGTCGCGCTATCCTGAAAGATGCCATTTTCAAAAGTTGTGATCTCTCCATGGCGGGTTTCAGGAATGTGAGCGCGCTGGGAATCGAAATTCGCCACTGCCGCGCACAAGGTTCAGATTTTCGCGGCGCAAGCTTTATGAATATGATTACCACACGCACCTGGTTTTGTAGCGCCTATATCACCAATACCAACTTAAGCTACGCCAACTTTTCAAAAGTCGTACTGGAAAAGTGCGAGCTGTGGGAAAACCGTTGGATGGGTACTCAGGTACTGGGGGCGACGTTCAGTGGTTCAGATCTTTCCGGCGGTGAGTTTTCGTCGTTCGACTGGCGGGCCGCAAACTTTACGCACTGTGATTTGACCAATTCAGAACTGGGCGATCTCGATGTCCGGGGTGTTGATTTGCAAGGCGTCAAACTGGACAGCTACCAGGCATCGTTGATCCTGGAACGTCTTGGCATCGCTGTCATTGGTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39583","NCBI_taxonomy_name":"Citrobacter werkmanii","NCBI_taxonomy_id":"67827"}}}},"ARO_accession":"3002749","ARO_id":"39183","ARO_name":"QnrB34","ARO_description":"QnrB34 is a plasmid-mediated quinolone resistance protein found in Citrobacter werkmanii","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1161":{"model_id":"1161","model_name":"lsaB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"990"}},"model_sequences":{"sequence":{"5":{"protein_sequence":{"accession":"NP_899166.1","sequence":"MSMIHVQNLTFSYPSSFDNIFEDVSFQIDTDWKLGFIGRNGRGKTTLFNLLLDKFEYRGKIISSVDFNYFPYPVEDKSKYTHEILEEICPQAEDWEFLREIAYLNVDAEAMYRPFETLSNGEQTKVLLVALFLNEGQFLLIDEPTNHLDTEARKTVSNYLRKKKGNILISHDRNFLDGSVDHILSINRADIEVQSGNYSSWKLNFDRQQGHEQATNERLQKDIGRLEQSTKRSAGWSNRVEASKNGTTNSGSKLDKGFVGHKAAKMMKRSKNLEARQQKSIEEKSKLLKNIEKTESLQFEPVEYKSKELIQLTDVSVIYDGQVVNKPISFNVEQGDRIVLDGKNGSGKSSILKLILGDPIQYTGTLNTGSNLITSYVQQDTSHLKGMLADFIEENEIDESLFKAILRKLDFDRVQFEKDISHYSGGQKKKLLIAKSLCEKAHLYIWDEPLNFIDIYSRMQIEELIQTFNPTMVFVEHDQTFQETISTKIIKI"},"dna_sequence":{"accession":"NC_005076","fmin":"4149","fmax":"5628","strand":"+","sequence":"ATGTCAATGATACATGTACAAAATTTAACTTTCTCTTATCCGAGTAGTTTTGATAATATCTTTGAAGATGTAAGCTTTCAAATTGATACAGATTGGAAGCTTGGATTTATTGGTCGAAATGGACGAGGGAAAACAACCCTTTTTAATTTATTACTAGATAAATTTGAATATAGGGGGAAAATCATTTCTTCGGTCGATTTTAACTACTTCCCATATCCAGTAGAAGATAAAAGTAAGTATACACATGAAATTTTAGAAGAAATATGCCCTCAAGCTGAGGACTGGGAATTTCTTCGAGAAATAGCTTATTTAAATGTGGATGCCGAAGCCATGTACCGTCCTTTTGAAACTTTATCAAACGGTGAACAAACAAAGGTATTGCTTGTTGCTCTATTTTTAAACGAAGGACAATTTTTATTAATTGATGAACCAACAAATCATTTAGATACTGAAGCTCGTAAGACGGTTTCGAATTACTTGAGGAAGAAAAAAGGGAATATTTTAATTTCTCATGACCGTAACTTTTTAGATGGCAGTGTTGATCATATCTTGTCTATAAATAGAGCAGATATTGAGGTTCAAAGTGGAAATTATTCCTCATGGAAGTTGAACTTTGACCGACAGCAGGGACATGAACAAGCAACAAATGAACGCTTGCAGAAGGATATTGGAAGGTTAGAACAATCTACAAAACGTTCGGCTGGTTGGTCTAACCGAGTCGAAGCTTCAAAAAATGGAACAACGAATTCTGGTTCTAAATTGGACAAAGGTTTTGTAGGACATAAAGCAGCAAAAATGATGAAACGATCTAAGAACCTTGAGGCTCGACAGCAAAAATCGATTGAAGAAAAGTCAAAGCTTCTAAAAAACATTGAAAAAACGGAGTCCCTACAGTTTGAACCAGTGGAATATAAATCGAAGGAACTCATTCAATTAACAGATGTGTCTGTCATATATGATGGGCAAGTTGTCAACAAACCAATAAGTTTTAATGTTGAACAAGGAGATAGAATTGTACTGGATGGAAAGAACGGCAGTGGAAAAAGTAGTATTTTAAAATTAATCTTAGGCGATCCAATACAGTATACAGGCACGTTAAATACGGGTTCTAACCTGATAACTTCTTATGTTCAGCAAGACACCTCTCATTTAAAGGGGATGCTAGCTGACTTTATTGAAGAAAATGAGATTGATGAATCGTTGTTTAAGGCCATCCTGAGAAAGCTAGATTTTGACCGAGTACAGTTTGAAAAAGATATATCTCATTATTCAGGTGGTCAGAAGAAAAAATTGCTTATCGCTAAAAGTTTATGTGAAAAAGCTCACCTATATATTTGGGATGAACCATTAAACTTTATTGATATTTACTCTCGAATGCAAATTGAAGAGCTTATTCAAACCTTTAATCCGACTATGGTTTTTGTTGAACATGACCAGACCTTCCAAGAGACAATATCAACAAAAATAATAAAAATATAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36794","NCBI_taxonomy_name":"Staphylococcus sciuri","NCBI_taxonomy_id":"1296"}}}},"ARO_accession":"3003111","ARO_id":"39687","ARO_name":"lsaB","ARO_description":"LsaB is an ABC efflux pump expressed in Staphylococcus sciuri. It confers resistance to clindamycin.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"37716":{"category_aro_accession":"3001317","category_aro_cvterm_id":"37716","category_aro_name":"pleuromutilin","category_aro_description":"Pleuromutilin is a natural product antibiotic produced by Clitopilus passeckerianus. Related antibiotics of clinical significance, such as tiamulin and retapamulin, are semi-synthetic derivatives of this compound.","category_aro_class_name":"Antibiotic"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1162":{"model_id":"1162","model_name":"aadA15","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"116":{"protein_sequence":{"accession":"ABD58917.1","sequence":"MREAVIAEVSTQLSEVVGVIERHLEPTLLAVHLYGSAVDGGLKPHSDIDLLVTVTVRLDETTRRALINDLLETSASPGESEILRAVEVTIVVHDDIIPWRYPAKRELQFGEWQRNDILAGIFEPATIDIDLAILLTKAREHSVALVGPAAEELFDPVPEQDLFEALNETLTLWNSPPDWAGDERNVVLTLSRIWYSAITGKIAPKDVAADWAIKRLPAQYQPVLLEAKQAYLGQKEDHLASRADHLEEFIRFVKGEIIKSVGK"},"dna_sequence":{"accession":"DQ393783","fmin":"1799","fmax":"2591","strand":"+","sequence":"ATGAGGGAAGCGGTGATCGCCGAAGTATCGACTCAACTATCAGAGGTAGTTGGCGTCATCGAGCGCCATCTCGAACCGACGTTGCTGGCCGTCCATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCACACAGTGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCGAGCTTTGATCAACGACCTTTTGGAAACTTCGGCTTCCCCTGGAGAGAGCGAGATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCCGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAATAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATAAAACGCCTACCTGCCCAGTATCAGCCCGTCTTACTTGAAGCTAAGCAAGCTTATCTGGGACAAAAAGAAGATCACTTGGCCTCACGCGCAGATCACTTGGAAGAATTTATTCGCTTTGTGAAAGGCGAGATCATCAAGTCAGTTGGTAAATGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002615","ARO_id":"39015","ARO_name":"aadA15","ARO_description":"aadA15 is an integron-encoded aminoglycoside nucleotidyltransferase gene in P. aeruginosa","ARO_category":{"41439":{"category_aro_accession":"3004275","category_aro_cvterm_id":"41439","category_aro_name":"ANT(3'')","category_aro_description":"Nucleotidylylation of streptomycin at the hydroxyl group at position 3''","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1163":{"model_id":"1163","model_name":"CMY-94","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1626":{"protein_sequence":{"accession":"AGC54798.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVASAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"JX514368","fmin":"271","fmax":"1417","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATCGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002107","ARO_id":"38507","ARO_name":"CMY-94","ARO_description":"CMY-94 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1164":{"model_id":"1164","model_name":"MIR-9","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"875":{"protein_sequence":{"accession":"AIT76113.1","sequence":"MMTKSLSCALLLSVASSAFAAPMSEKQLAEVVERTVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEIALGDPVAKYWPELTGKQWQSIRMLDLATYTAGGLPLQVPDEVTDTASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEEAHYAWGYREGKAVHVSPGMLDAEAYGVKTNVKDMASWVIANMKPDSLQAPSLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"KM087860","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGACAAAATCCCTAAGCTGTGCCCTGCTGCTCAGCGTCGCCAGTTCTGCATTCGCCGCACCGATGTCCGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTAATTTATCAGGGTCAGCCACACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGCGGCGATGCCATTGCCCGGGGTGAAATAGCGCTGGGCGATCCGGTAGCAAAATACTGGCCTGAGCTCACGGGCAAGCAGTGGCAGAGCATTCGCATGCTGGATCTGGCAACCTATACCGCAGGCGGTCTGCCGTTACAGGTGCCGGATGAGGTCACGGATACCGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCTAACGCCAGCATCGGTCTTTTTGGTGCGTTGGCGGTTAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAACCCCTCAAGCTGGACCATACCTGGATTAACGTCCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGAGGGTAAAGCGGTCCACGTTTCGCCAGGGATGCTGGACGCGGAAGCCTATGGCGTAAAAACTAACGTGAAGGATATGGCGAGCTGGGTGATAGCCAACATGAAGCCGGATTCTCTTCAGGCTCCCTCACTCAAGCAAGGCATTGCTCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCTATGTATCAGGGGTTGGGCTGGGAGATGCTCAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCATTGCCCGTGGCAGAAGTGAATCCACCCGCACCGCCGGTCAAGGCCTCCTGGGTCCATAAAACAGGCTCGACGGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTTGACGCGCTGCAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36926","NCBI_taxonomy_name":"Enterobacter asburiae","NCBI_taxonomy_id":"61645"}}}},"ARO_accession":"3002174","ARO_id":"38574","ARO_name":"MIR-9","ARO_description":"MIR-9 is a beta-lactamase. From the Lahey list of MIR beta-lactamases.","ARO_category":{"36197":{"category_aro_accession":"3000058","category_aro_cvterm_id":"36197","category_aro_name":"MIR beta-lactamase","category_aro_description":"MIR beta-lactamases are plasmid-mediated beta-lactamases that confer resistance to oxyimino- and alpha-methoxy beta-lactams","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1165":{"model_id":"1165","model_name":"OKP-A-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1520":{"protein_sequence":{"accession":"CAJ19601.1","sequence":"MRYVRLCLFSLIAALPLAVFASPPPLEQITRSESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIRYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKSVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMAATLRKLLTSHTLSARSQQQLLQWMVDDQVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPNGKAERIVVIYLRDTPATMAERNQQIARIGAALIEHWQR"},"dna_sequence":{"accession":"AM051142","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTTTCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCCGCCACTTGAGCAAATTACACGCAGCGAAAGTCAGCTGGCGGGCCGCGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGAGACGAACAGCTGGATCGGCGGATCCGCTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGAGCGTTGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAGCTCAATGAAGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCAGCCAGCATGGCCGCCACCCTGCGCAAGCTGCTAACCAGCCACACTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGACCAGGTAGCCGGTCCGCTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGCGAGCGGGGCTCACGTGGCATTGTCGCCCTGCTCGGCCCGAACGGCAAAGCGGAGCGCATCGTGGTGATCTATCTGCGGGATACGCCGGCGACCATGGCCGAGCGTAACCAGCAGATCGCCAGAATAGGCGCGGCGCTGATCGAGCACTGGCAGCGCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002421","ARO_id":"38821","ARO_name":"OKP-A-4","ARO_description":"OKP-A-4 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1167":{"model_id":"1167","model_name":"norB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"900"}},"model_sequences":{"sequence":{"4379":{"protein_sequence":{"accession":"CCQ22388.1","sequence":"MTSTAYKGTNKLIVGIVFGVITFWLFAQSMVNIVPAVQSDLGISSDLLSIAISLTALFSGIFIVVAGGMADKFGRVKLTYIGLILSIIGSLLLVVTQGSTLLIIGRIIQGLSAACIMPATLALMKTYFDGADRQRALSYWSIGSWGGSGICSFAGGAIATYMGWRWIFIISIVFALLGMLLIKGTPESKVVQNTKAKFDSFGLVLFVIAMVCLNLIITRGATFGWTSPITITMLVVFLVSAGLFFRVELRQANGFIDFSLFKNKAYTGATLSNFLLNAAAGTLVVANTYVQIGRGFTAFQSGLLSIGYLVCVLGMIRIGEKILQRVGARKPMILGSGITAVGIALMALTFIPGTLYTVLVFIGFALFGIGLGMYATPSTDTAISNAPEDKVGVASGIYKMASSLGGSFGVAISATIYGVIALSGNIDLAAMVGLLTNVGFCVVSLISVAITTPSAKKALELKAAKE"},"dna_sequence":{"accession":"HE999704","fmin":"2734780","fmax":"2736181","strand":"-","sequence":"CTATTCTTTTGCGGCTTTTAATTCGAGCGCTTTTTTCGCAGATGGTGTTGTTATAGCAACGGAAATAAGTGAAACGACACAAAAACCGACGTTCGTTAAAAGCCCCACCATTGCGGCTAAATCAATATTTCCTGAAAGTGCAATCACACCATAAATCGTAGCAGATATCGCCACGCCGAATGAGCCACCTAGCGAACTTGCCATTTTGTAAATACCAGATGCTACTCCGACTTTATCTTCTGGAGCATTAGAAATGGCTGTATCTGTTGAAGGAGTCGCATACATGCCAAGTCCAATCCCGAATAAAGCAAAACCGATAAATACAAGCACTGTATAAAGGGTTCCCGGAATAAACGTCAGCGCCATTAGTGCAATACCAACAGCCGTAATACCAGAGCCTAAAATCATTGGTTTACGCGCACCAACACGTTGAAGAATTTTTTCACCGATGCGAATCATTCCGAGCACACAGACAAGATATCCGATAGAAAGTAAACCGGATTGGAACGCCGTAAAACCGCGACCAATTTGCACATAAGTGTTTGCGACAACCAGTGTTCCAGCTGCTGCGTTTAGCAAGAAGTTCGAAAGTGTTGCGCCTGTATAAGCTTTATTTTTAAATAACGAGAAATCAATAAATCCGTTTGCTTGTCGCAGTTCCACTCGGAAGAATAATCCCGCAGAAACTAGGAAAACAACGAGCATTGTAATAGTAATTGGGCTTGTCCAGCCAAATGTTGCGCCACGAGTAATAATAAGGTTCAAACAAACCATTGCGATAACAAAAAGAACAAGACCAAATGAATCAAATTTTGCTTTTGTATTTTGAACGACTTTACTTTCTGGAGTACCTTTAATAAGTAGCATTCCAAGCAGTGCGAATACGATGGAAATAATGAAAATCCAGCGCCAGCCCATATATGTTGCGATAGCGCCACCTGCGAACGAACAAATACCTGATCCGCCCCATGAGCCAATTGACCAGTAACTAAGTGCTCTTTGTCTATCTGCCCCGTCAAAATAAGTTTTCATTAAGGCAAGGGTTGCTGGCATAATACAAGCAGCTGAAAGACCTTGAATAATCCGGCCGATAATAAGTAGCGTCGACCCTTGAGTGACAACAAGTAGCAGTGAACCGATGATACTAAGAATAAGTCCGATATAAGTTAATTTCACACGACCAAATTTGTCAGCCATCCCACCTGCTACAACGATAAAAATACCTGAAAATAGCGCGGTTAAACTGATGGCAATACTAAGTAAATCAGAGGAAATTCCAAGGTCAGATTGCACGGCCGGAACAATATTCACCATAGATTGAGCAAAAAGCCAAAACGTGATAACCCCGAAAACAATTCCAACGATTAGTTTATTTGTACCTTTATACGCTGTTGAAGTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36757","NCBI_taxonomy_name":"Listeria monocytogenes","NCBI_taxonomy_id":"1639"}}}},"ARO_accession":"3000421","ARO_id":"36560","ARO_name":"norB","ARO_description":"NorB is a multidrug efflux pump in Staphylococcus aureus that confers resistance to fluoroquinolones and other structurally unrelated antibiotics like tetracycline. It shares 30% similarity with NorB, and is a structural homolog of Blt of Bacillus subtilis. It is regulated by mgrA, also known as NorR.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1168":{"model_id":"1168","model_name":"NDM-9","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1349":{"protein_sequence":{"accession":"AGU91756.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQKGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"KC999080","fmin":"379","fmax":"1192","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAAAGGGGATGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39097","NCBI_taxonomy_name":"Klebsiella pneumoniae subsp. pneumoniae","NCBI_taxonomy_id":"72407"}}}},"ARO_accession":"3002359","ARO_id":"38759","ARO_name":"NDM-9","ARO_description":"NDM-9 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1169":{"model_id":"1169","model_name":"OXA-360","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1932":{"protein_sequence":{"accession":"AGZ83156.1","sequence":"MKILILLPLLSCLSLTACSFAVSNSPSQITSTQSIQAIVKLFDQAQSSGVLVIQRGPHLQVYGNELSRAHTEYVPASTFKMLNALIGLQHGKATTNEIFKWDRKKRSFAAWEKDMTLGQAMQASAVPVYQELARRIGLELMQQEVQRIQFGNQQIGQHIDNFWLVGPLKVTPKQEVKFASALAQEQLAFDPRFQQQVKTMLLLQERQAYRLYAKSGWGMDVEPQVGWLTGWIETPQDEIVAFSLNMQMQSNMDPAIRLKILQQALAELGLYPKAEG"},"dna_sequence":{"accession":"KF421163","fmin":"0","fmax":"831","strand":"+","sequence":"ATGAAAATTCTTATTTTGTTGCCTTTACTCAGTTGCTTGAGCCTGACAGCCTGTAGCTTCGCTGTTTCAAATTCGCCCTCTCAAATCACTTCAACTCAATCTATTCAAGCTATTGTAAAGTTATTTGATCAGGCACAAAGCTCTGGCGTTTTAGTAATTCAACGGGGTCCACATCTACAAGTCTATGGCAATGAGTTGAGTCGTGCACATACCGAATATGTTCCTGCTTCAACCTTTAAAATGCTTAATGCTCTGATTGGCCTGCAACATGGTAAAGCTACGACCAATGAAATTTTTAAATGGGATCGCAAGAAGCGCAGTTTTGCAGCCTGGGAAAAAGACATGACTCTCGGCCAAGCCATGCAAGCTTCTGCTGTACCGGTCTATCAGGAACTGGCACGTCGCATTGGTCTGGAATTAATGCAACAGGAAGTGCAACGCATCCAATTTGGTAATCAGCAGATTGGTCAGCATATCGACAACTTCTGGTTGGTCGGACCTTTGAAAGTTACTCCAAAACAGGAAGTCAAATTTGCCTCTGCGCTTGCTCAAGAGCAACTTGCCTTTGATCCTCGGTTTCAGCAGCAAGTTAAAACCATGTTACTGTTACAGGAGCGACAAGCTTATCGACTATATGCCAAATCTGGTTGGGGTATGGATGTGGAGCCGCAAGTCGGCTGGCTCACCGGCTGGATCGAAACACCTCAGGACGAAATTGTGGCATTTTCACTGAATATGCAGATGCAAAGTAATATGGATCCGGCGATCCGCCTTAAAATTTTGCAGCAGGCCTTGGCCGAATTAGGGCTTTATCCCAAAGCTGAAGGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39096","NCBI_taxonomy_name":"Acinetobacter schindleri","NCBI_taxonomy_id":"108981"}}}},"ARO_accession":"3001547","ARO_id":"37947","ARO_name":"OXA-360","ARO_description":"OXA-360 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1170":{"model_id":"1170","model_name":"CMY-46","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1738":{"protein_sequence":{"accession":"CBH19182.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADITNNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWAPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPKNEQKDYAWGYREGKAVHVSPGQLDAEAYGVKSSVIDMARWVQVNMDASRVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"FN556186","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCATTCTCCACGTTTGCCGCCGCCAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCTGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCACCAATAACCACCCAGTCACGCAGCAAACTCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTACACGGCAGGCGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCGTTTTTATCAAAACTGGCAGCCGCAATGGGCCCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACAGTTCCGAAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGGCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGTCAACATGGACGCCAGCCGCGTTCAGGAGAAAACACTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGTAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACTGGAGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002057","ARO_id":"38457","ARO_name":"CMY-46","ARO_description":"CMY-46 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1171":{"model_id":"1171","model_name":"tet44","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1200"}},"model_sequences":{"sequence":{"410":{"protein_sequence":{"accession":"CBH51823.1","sequence":"MKIINIGILAHVDAGKTTLTESLLYTSGAILELGSVDKGTTRTDTMFLERQRGITIQAAVTSFNWNDYKINIVDTPGHTDFITEVYRSLSVLDGAILVISAKDGVQAQTRILFHALQKMNIPTIIFINKIDQDGINLNNIYQNIKEKLSNDIIVMQNVTLTPEISIKNIIDLDDWDPVISKNDKLLEKYIVGEKLTIQELMYEEYRCVKKGSLFPIYHGSARNNIGTQQLIEAISNLFCSEMNENDSELCGRVFKIEYTDHKQRLVYLRLYSGTLHLRDTIILPEKKKVKLTEIYIPSNGEMIQTKTVCSGDIFIIPNNTLRLNDIIGNEKLLPCNVWNDKTVPILRTRIEPIKIEEREKLLDALTEIADTDPLLRYYVDTITHEIIISFLGTVQLEVICSLLIEKYHINIRIEDPTVIYLEKPLQKADYTIHIEVPPNPFWASIGLSITPLPIGSGIQYESKVSLGYLNQSFQNAVREGINYGLEQGLYGWEVTDCKICFEYGVYYSPVSTPSDFRFLAPIVLEQTLKKAGTQLLEPYLSFILFTPQGYFSRAYKDAQKHCAIIETSQSKNDEVIFTGHIPVRCINEYRNTLTLYTNGQAVFLTELKDYQIATCEPVIQSRRPNNRIDKVRHMFNKKEN"},"dna_sequence":{"accession":"FN594949","fmin":"25244","fmax":"27167","strand":"+","sequence":"ATGAAAATAATCAACATTGGTATTCTTGCTCATGTAGATGCAGGAAAGACGACCTTAACGGAAAGTCTGCTTTATACAAGTGGAGCAATTTTAGAATTAGGCAGTGTAGATAAGGGAACAACAAGGACAGATACTATGTTTTTAGAACGTCAGCGTGGAATCACAATTCAGGCAGCAGTTACTTCTTTTAATTGGAATGACTACAAAATCAATATTGTAGATACTCCTGGACATACAGATTTTATAACAGAAGTGTATCGTTCCTTATCTGTTCTTGATGGAGCAATTTTAGTAATTTCTGCTAAAGATGGTGTACAAGCACAAACCCGAATACTATTCCATGCACTTCAAAAAATGAATATACCAACAATTATTTTTATAAATAAAATAGATCAGGATGGAATTAACTTAAATAATATTTATCAAAATATCAAAGAAAAACTTTCAAATGATATTATTGTTATGCAAAATGTAACATTAACTCCAGAAATATCAATTAAAAATATCATTGATTTAGATGATTGGGATCCTGTAATTTCCAAAAATGATAAACTTTTAGAAAAATATATTGTAGGAGAAAAATTGACTATACAAGAATTAATGTATGAAGAATATAGGTGTGTTAAAAAAGGTTCGTTGTTTCCTATATACCATGGAAGTGCTAGAAATAATATAGGGACTCAACAACTTATCGAAGCTATTTCAAATCTTTTTTGTTCTGAAATGAATGAGAATGATTCAGAACTATGTGGAAGAGTTTTTAAAATTGAATATACAGACCATAAGCAAAGATTAGTTTATTTGCGTCTTTATAGTGGAACATTACACTTACGAGATACAATTATATTGCCAGAAAAAAAGAAAGTGAAACTTACAGAAATATATATTCCTTCAAATGGAGAAATGATACAGACAAAAACAGTTTGTTCTGGAGATATTTTTATTATACCTAACAATACATTAAGATTGAACGATATTATAGGAAATGAAAAGCTTTTGCCATGCAATGTATGGAATGACAAGACTGTACCAATACTACGAACAAGAATTGAACCGATAAAAATAGAAGAGAGAGAAAAATTATTGGATGCTCTTACAGAAATTGCAGATACTGATCCTCTTTTACGTTATTATGTTGATACGATAACACATGAAATCATCATTTCTTTTTTAGGAACAGTGCAGTTAGAAGTTATCTGTTCTCTGTTGATTGAAAAATATCACATAAACATAAGAATCGAAGATCCAACCGTAATTTATTTGGAAAAACCATTACAAAAGGCAGATTATACTATTCATATTGAAGTACCACCAAATCCATTTTGGGCATCGATTGGATTATCAATAACTCCACTTCCAATTGGCAGTGGAATACAGTACGAAAGCAAAGTTTCACTCGGTTATTTAAATCAAAGTTTCCAAAATGCAGTAAGAGAAGGTATTAATTATGGACTGGAGCAAGGTTTGTATGGTTGGGAAGTAACAGATTGTAAAATATGTTTTGAATATGGTGTTTATTATAGCCCTGTTAGTACTCCCTCGGATTTTCGCTTTCTTGCCCCAATTGTACTTGAACAAACATTGAAAAAAGCGGGAACGCAATTATTAGAGCCATATCTTTCGTTTATACTTTTTACGCCACAGGGATACTTTTCTCGTGCATATAAAGATGCACAAAAACATTGTGCAATAATTGAAACAAGTCAATCAAAAAATGATGAAGTTATTTTTACAGGACATATTCCTGTACGTTGTATTAATGAATATCGTAATACTTTAACTCTATATACAAATGGGCAAGCAGTTTTTTTGACAGAATTAAAAGATTATCAAATTGCTACTTGTGAACCAGTTATTCAATCACGTAGACCAAATAATCGAATAGATAAAGTACGCCATATGTTTAATAAAAAAGAAAATTAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36889","NCBI_taxonomy_name":"Campylobacter fetus subsp. fetus","NCBI_taxonomy_id":"32019"}}}},"ARO_accession":"3000556","ARO_id":"36695","ARO_name":"tet44","ARO_description":"Tet44 is a tetracycline resistance gene found in Campylobacter fetus, and binds to the ribosome to confer antibiotic resistance as a ribosomal protection protein.","ARO_category":{"35921":{"category_aro_accession":"0000002","category_aro_cvterm_id":"35921","category_aro_name":"tetracycline-resistant ribosomal protection protein","category_aro_description":"A family of proteins known to bind to the 30S ribosomal subunit. This interaction prevents tetracycline and tetracycline derivatives from inhibiting ribosomal function. Thus, these proteins confer elevated resistance to tetracycline derivatives as a ribosomal protection protein.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1172":{"model_id":"1172","model_name":"OXA-194","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1925":{"protein_sequence":{"accession":"AEB98920.1","sequence":"MNIKALFLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWVVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"HQ425492","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAACATTAAAGCCCTCTTCCTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGGTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36949","NCBI_taxonomy_name":"Acinetobacter nosocomialis","NCBI_taxonomy_id":"106654"}}}},"ARO_accession":"3001479","ARO_id":"37879","ARO_name":"OXA-194","ARO_description":"OXA-194 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1173":{"model_id":"1173","model_name":"TEM-54","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1959":{"protein_sequence":{"accession":"AAD22539.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSLGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AF104442","fmin":"193","fmax":"1054","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCTCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000923","ARO_id":"37303","ARO_name":"TEM-54","ARO_description":"TEM-54 is an inhibitor-resistant beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1174":{"model_id":"1174","model_name":"QnrB22","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"689":{"protein_sequence":{"accession":"ACS71746.1","sequence":"MMTLALVGEKIDRNRFTGEKVENSTFFNCDFSGADLCGTEFIGCQFYDRESQKGCNFSRANLKDAIFKSCDLSMADFRNINALGIEIRHCRAQGSDFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFSSFDWRAANVTHCDLTNSELGDLDIRVVDLQGVKLDSYQASLLLERLGIAVMG"},"dna_sequence":{"accession":"FJ981621","fmin":"0","fmax":"648","strand":"+","sequence":"ATGATGACTCTGGCGTTAGTTGGCGAAAAAATTGACAGAAACAGGTTCACCGGTGAAAAAGTCGAAAATAGCACATTTTTCAACTGTGATTTTTCGGGTGCCGACCTTTGCGGTACTGAATTTATTGGCTGCCAGTTTTATGATCGAGAAAGCCAGAAAGGGTGTAATTTTAGTCGCGCTAACCTGAAGGATGCCATTTTCAAAAGTTGTGATCTCTCCATGGCGGATTTCAGAAATATCAATGCGCTGGGAATCGAAATTCGCCACTGCCGGGCACAAGGGTCAGATTTTCGCGGCGCAAGCTTTATGAATATGATCACCACCCGCACCTGGTTTTGTAGCGCTTATATCACCAATACCAACTTAAGCTACGCCAACTTTTCTAAAGTCGTACTGGAAAAGTGCGAGCTGTGGGAGAACCGCTGGATGGGTACTCAGGTGCTGGGCGCAACGTTCAGTGGATCAGACCTCTCTGGCGGCGAGTTTTCATCCTTCGACTGGCGAGCAGCAAACGTAACGCACTGTGATTTGACCAATTCGGAACTGGGCGATTTAGATATCCGGGTAGTTGATTTGCAAGGCGTCAAACTGGACAGCTACCAGGCATCGTTGCTCCTGGAACGTCTTGGTATCGCTGTCATGGGTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39583","NCBI_taxonomy_name":"Citrobacter werkmanii","NCBI_taxonomy_id":"67827"}}}},"ARO_accession":"3002737","ARO_id":"39171","ARO_name":"QnrB22","ARO_description":"QnrB22 is a plasmid-mediated quinolone resistance protein found in Citrobacter werkmanii","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1177":{"model_id":"1177","model_name":"KPC-12","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1786":{"protein_sequence":{"accession":"ADZ75467.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELEMNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"HQ641421","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGATGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002322","ARO_id":"38722","ARO_name":"KPC-12","ARO_description":"KPC-12 is a beta-lactamase. From the Lahey list of KPC beta-lactamases.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1178":{"model_id":"1178","model_name":"CMY-81","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"823":{"protein_sequence":{"accession":"AFK73452.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIVNNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDYVTDKAELLRFYQNWQPQWTPGAKRLYANSSIGLFGALVVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"JQ733578","fmin":"1007","fmax":"2153","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCGCTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGTCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATTACGTTACGGATAAAGCCGAATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGTGGTAAAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACAGGATCCACAGGCGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTAATGTTGGCAAACAAAAGCTACCCCAACCCGGCTCGCGTCGAGGCGGCCTGGCGCATTCTTGAAAAACTGCAATAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002094","ARO_id":"38494","ARO_name":"CMY-81","ARO_description":"CMY-81 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1179":{"model_id":"1179","model_name":"IMP-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1785":{"protein_sequence":{"accession":"AAK13078.1","sequence":"MSKLSVFFIFLFCSIATAAEPLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVDAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKDGKVQAKNSFGGVNYWLVKNKIEVFYPGPGHTPDNLVVWLPERKILFGGCFIKPYGLGNLGDANLEAWPKSAKLLISKYGKAKLVVPSHSEAGDASLLKLTLEQAVKGLNESKKPSKLSN"},"dna_sequence":{"accession":"AF244145","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAGCAAGTTATCTGTATTCTTTATATTTTTGTTTTGTAGCATTGCTACCGCAGCAGAGCCTTTGCCAGATTTAAAAATTGAAAAACTTGATGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGGTGGGGCGTTGTTCCTAAACATGGTTTGGTTGTTCTTGTAGATGCTGAAGCTTATCTAATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAACGTGGCTATAAAATAAAAGGCAGTATTTCCTCTCATTTTCATAGTGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCAATCCATCCCCACGTATGCGTCTGAATTAACTAATGAGCTGCTTAAAAAAGACGGTAAGGTTCAAGCTAAAAATTCATTTGGCGGGGTTAACTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCAGGACACACTCCAGATAACCTAGTAGTTTGGCTGCCTGAAAGGAAAATATTATTCGGTGGTTGTTTTATTAAACCGTACGGTCTAGGTAATTTGGGTGACGCAAATTTAGAAGCTTGGCCAAAGTCCGCTAAATTATTAATATCCAAATATGGTAAGGCAAAACTGGTTGTTCCAAGTCACAGTGAAGCTGGAGACGCATCACTCTTGAAACTTACATTAGAGCAGGCGGTTAAAGGGTTAAACGAAAGTAAAAAACCATCAAAACTAAGCAACTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3002195","ARO_id":"38595","ARO_name":"IMP-4","ARO_description":"IMP-4 is a beta-lactamase found in Acinetobacter baumannii","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1180":{"model_id":"1180","model_name":"mdsC","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"940"}},"model_sequences":{"sequence":{"4393":{"protein_sequence":{"accession":"NP_459345.3","sequence":"MRTALIRMISKHNDGNGIMKITFTGYRQTATLATLAFVTTLAGCTMAPKHERPASPTAMVYPYATSTVSGAPDAADIGWRDFFHDPLLQELIAIALRNNRDLRKAGLNVEAARALYRIQRAEMLPTLGIATAMDASRTPADLSVMDESEINRRYEAAGATTAWELDLWGRVRSLSDQALAAYMALDETYIAARMSLVSEVASAWLTLRADRELLRLTEDTLAAQKSSYTLTTQLARTGNATQLDLRMAEIALRSAEINRAAYTRQLARDRNALELLLGQPLTPELSRRLNEAVTLTEGAIPTTLPGGLPSDLLVRRPDIRAAEYRLRGANARIGAARAAFFPTISLTGSAGTASASLSGLFEPGSGSWRFLPQITLPLFHGGALRADLDRAHVQKQIEIARYENVIQQAFRDVADGLAGQRTLNDQVQSEQRAVEASQIAYELAGLRFQEGVDDYLTLLDTHRMLYGAQQRLVRTRLMQQLNIINLYKALGGGWREYSEKKQG"},"dna_sequence":{"accession":"NC_003197.2","fmin":"392419","fmax":"393931","strand":"-","sequence":"CTAACCTTGCTTTTTCTCACTGTATTCCCGCCAACCGCCGCCTAATGCTTTATACAGGTTAATGATATTTAACTGTTGCATGAGACGTGTGCGTACCAGGCGCTGTTGTGCGCCATAAAGCATACGATGGGTATCAAGCAGCGTAAGGTAGTCATCGACGCCTTCCTGAAAACGGAGTCCGGCCAGCTCATAGGCGATTTGACTGGCTTCAACCGCGCGTTGTTCTGATTGCACCTGGTCATTCAGCGTACGCTGTCCCGCCAGACCATCCGCCACGTCGCGAAAGGCTTGCTGAATAACGTTTTCATACCTGGCGATTTCAATCTGTTTTTGGACATGCGCCCTATCCAGGTCAGCGCGTAATGCGCCGCCGTGAAAGAGAGGCAAGGTGATTTGCGGTAGAAAACGCCAGCTTCCCGATCCCGGTTCAAAGAGTCCGCTAAGAGACGCGCTGGCCGTTCCCGCCGAGCCTGTCAGGCTGATGGTCGGGAAGAAGGCGGCGCGCGCTGCGCCTATCCGGGCGTTTGCGCCGCGCAGCCTGTACTCGGCGGCGCGAATATCCGGGCGGCGTACCAGCAGATCTGACGGTAATCCGCCTGGCAGTGTGGTCGGGATCGCGCCTTCTGTAAGCGTGACCGCTTCGTTTAGTCGACGCGACAGTTCAGGCGTGAGCGGCTGGCCCAACAGCAATTCCAGCGCGTTACGATCCCGCGCCAACTGTCGCGTATACGCCGCGCGATTGATTTCGGCAGAACGCAGCGCGATCTCCGCCATACGCAGATCGAGCTGTGTGGCGTTACCTGTCCGGGCAAGCTGGGTCGTCAATGTGTATGAACTTTTTTGCGCGGCCAGCGTATCCTCGGTTAAGCGCAGCAGCTCCCGGTCAGCCCGTAGCGTCAGCCAGGCGCTGGCGACTTCGGAAACCAGGCTCATTCGCGCCGCAATGTACGTCTCATCAAGCGCCATATAGGCGGCTAATGCCTGGTCGCTAAGGCTTCGCACTCGCCCCCAGAGATCCAGTTCCCAGGCCGTCGTCGCCCCAGCCGCCTCGTAGCGTCGGTTAATCTCAGACTCGTCCATGACGCTGAGATCGGCGGGAGTGCGACTGGCGTCCATGGCGGTGGCGATGCCGAGCGTCGGCAGCATCTCCGCGCGCTGAATGCGGTATAACGCCCGGGCGGCTTCAACATTGAGCCCTGCCTTGCGTAAATCCCGATTATTGCGTAACGCGATCGCAATCAGTTCCTGTAGAAGCGGATCGTGGAAGAAATCACGCCAGCCAATGTCAGCGGCATCCGGCGCGCCAGAAACGGTTGACGTTGCGTAGGGATAGACCATCGCAGTCGGCGATGCGGGGCGTTCGTGCTTCGGCGCCATCGTACAGCCAGCAAGCGTGGTGACGAAAGCAAGCGTCGCCAGCGTGGCGGTCTGCCGATAGCCTGTAAAAGTGATCTTCATTATGCCATTCCCATCATTATGCTTGCTGATCATGCGAATCAACGCGGTTCTCAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35734","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium str. LT2","NCBI_taxonomy_id":"99287"}}}},"ARO_accession":"3000791","ARO_id":"37171","ARO_name":"mdsC","ARO_description":"MdsC is the outer membrane channel of the multidrug and metal efflux complex MdsABC.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1181":{"model_id":"1181","model_name":"cmeA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"710"}},"model_sequences":{"sequence":{"431":{"protein_sequence":{"accession":"ABS43901.1","sequence":"MKLFQKNTILVLGVVFLLTACSKEEAPKIQMPPQPVTTMSAKSEDLPLNFTYPAKLVSDYDVIIKPQVSGVIVNKLFKAGDKVKRGQTLFIIEQAKFKASVDSAYGQALMAKATFENASKDFNRSEALFSKNAISQKEYDSSLATFNNAKASLASARAQLANARIDLDHTEIKAPFDGTIGDALVNIGDYVSTSTTELVRVTNLNPIYADFFISDTDKLNLVRNTQSGKWDLDSIHANLNLNGETVQGKLYFIDSVIDANSGTVKAKAVFDNNNSTLLPGAFATITSEGFIQKNGFKVPQIAIKQDQNDVYVLLVKNGKVEKSSVHISYQNNEYAIIDKGLQNGDKIILDNFKKIQVGSEVKEIGAQ"},"dna_sequence":{"accession":"CP000768","fmin":"1405391","fmax":"1406495","strand":"+","sequence":"ATGAAATTATTTCAAAAAAATACTATTTTAGTTTTAGGTGTTGTGTTTTTACTCACTGCTTGCAGCAAAGAAGAAGCGCCAAAAATACAAATGCCGCCTCAACCTGTAACAACCATGAGTGCTAAATCTGAAGATTTACCACTTAATTTTACCTATCCTGCCAAACTTGTCAGTGATTATGATGTTATTATAAAACCTCAAGTTAGCGGTGTGATAGTAAATAAACTTTTTAAGGCTGGAGATAAGGTAAAAAGAGGACAAACATTATTTATTATAGAACAAGCCAAATTTAAAGCTAGCGTTGATTCAGCCTACGGACAAGCGTTAATGGCTAAAGCAACTTTCGAAAATGCAAGTAAAGATTTTAATCGCTCTGAGGCTCTTTTTAGCAAAAACGCAATCTCTCAAAAAGAATACGACTCTTCTCTTGCTACATTTAATAATGCAAAAGCTAGTCTAGCAAGTGCTAGAGCACAGCTTGCAAATGCAAGAATTGATCTAGATCATACCGAAATAAAAGCTCCTTTTGATGGTACTATAGGAGATGCTTTAGTTAATATAGGAGATTATGTAAGCACTTCAACAACTGAACTAGTTAGAGTTACAAATTTAAATCCTATTTACGCAGATTTCTTTATTTCAGATACAGATAAACTAAATTTAGTCCGCAATACTCAAAGTGGAAAATGGGATTTAGACAGCATTCATGCAAATTTAAATCTTAACGGAGAAACTGTTCAAGGCAAACTTTATTTTATTGATTCTGTTATAGATGCCAATAGTGGAACAGTAAAAGCCAAAGCTGTATTTGATAACAACAACTCGACACTTTTACCAGGTGCTTTTGCAACGATTACCTCAGAAGGTTTTATACAAAAAAATGGCTTTAAGGTACCTCAAATAGCTATTAAACAAGATCAAAATGATGTTTATGTTCTTCTTGTTAAAAATGGAAAAGTAGAAAAATCTTCTGTACATATAAGCTACCAAAACAATGAATACGCTATTATTGACAAAGGATTGCAAAATGGCGATAAAATCATTTTGGATAATTTTAAAAAAATTCAAGTTGGTAGCGAAGTTAAAGAAATTGGAGCACAATAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37595","NCBI_taxonomy_name":"Campylobacter jejuni subsp. doylei 269.97","NCBI_taxonomy_id":"360109"}}}},"ARO_accession":"3000783","ARO_id":"37163","ARO_name":"cmeA","ARO_description":"CmeA is the membrane fusion protein of the CmeABC multidrug efflux complex.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"36989":{"category_aro_accession":"3000645","category_aro_cvterm_id":"36989","category_aro_name":"cefotaxime","category_aro_description":"Cefotaxime is a semisynthetic cephalosporin taken parenterally. It is resistant to most beta-lactamases and active against Gram-negative rods and cocci due to its aminothiazoyl and methoximino functional groups.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"37139":{"category_aro_accession":"3000759","category_aro_cvterm_id":"37139","category_aro_name":"fusidic acid","category_aro_description":"Fusidic acid is the only commercially available fusidane, a group of steroid-like antibiotics. It is most active against Gram-positive bacteria, and acts by inhibiting elongation factor G to  block protein synthesis.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1182":{"model_id":"1182","model_name":"CTX-M-105","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1184":{"protein_sequence":{"accession":"ADY02554.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAVAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQREQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGGYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"HQ833651","fmin":"244","fmax":"1120","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGTCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGAGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGGCTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001965","ARO_id":"38365","ARO_name":"CTX-M-105","ARO_description":"CTX-M-105 is a beta-lactamase found in Escherichia coli","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1183":{"model_id":"1183","model_name":"tetQ","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1200"}},"model_sequences":{"sequence":{"476":{"protein_sequence":{"accession":"CAA79727.1","sequence":"MRFDNASIVVYYCLIQMNIINLGILAHIDAGKTSVTENLLFASGATEKCGRVDNGDTITDSMDIEKRRGITVRASTTSIIWNGVKCNIIDTPGHMDFIAEVERTFKMLDGAVLILSAKEGIQAQTKLLFNTLQKLQIPTIIFINKIDRDGVNLERLYLDIKTNLSQDVLFMQTVVDGLVYPICSQTYIKEEYKEFVCNHDDNILERYLADSEISPADYWNTIIDLVAKAKVYPVLHGSAMFNIGINELLDAISSFILPPESVSNRLSAYLYKIEHDPKGHKRSFLKIIDGSLRLRDIVRINDSEKFIKIKNLKTIYQGREINVDEVGANDIAIVEDMEDFRIGDYLGTKPCLIQGLSHQHPALKSSVRPDRSEERSKVISALNTLWIEDPSLSFSINSYSDELEISLYGLTQKEIIQTLLEERFSVKVHFDEIKTIYKERPVKKVNKIIQIEVPPNPYWATIGLTLEPLPLGTGLQIESDISYGYLNHSFQNAVFEGIRMSCQSGLHGWEVTDLKVTFTQAEYYSPVSTPADFRQLTPYVFRLALQQSGVDILEPMLYFELQIPQAASSKAITDLQKMMSEIEDISCNNEWCHIKGKVPLNTSKDYASEVSSYTKGLGVFMVKPCGYQITKGDYSDNIRMNEKDKLLFMFQKSMSSK"},"dna_sequence":{"accession":"Z21523","fmin":"0","fmax":"1974","strand":"+","sequence":"GTGCGTTTCGACAATGCATCTATTGTAGTATATTATTGCTTAATCCAAATGAATATTATAAATTTAGGAATTCTTGCTCACATTGATGCAGGAAAAACTTCCGTAACCGAGAATCTGCTGTTTGCCAGTGGAGCAACGGAAAAGTGCGGCCGTGTGGATAATGGTGACACCATAACAGACTCTATGGATATAGAGAAACGTAGAGGAATTACTGTTCGGGCTTCTACGACATCTATTATCTGGAATGGAGTGAAATGCAATATCATTGACACTCCGGGACACATGGATTTTATTGCGGAAGTGGAGCGGACATTCAAAATGCTTGATGGAGCAGTCCTCATCTTATCCGCAAAGGAAGGCATACAAGCGCAAACAAAGTTGCTGTTCAATACTTTACAAAAACTGCAAATCCCGACAATTATATTTATCAATAAAATTGACCGTGACGGTGTGAATTTAGAGCGTTTGTATCTGGATATAAAAACAAATCTGTCTCAAGATGTCCTGTTTATGCAAACTGTTGTCGATGGATTGGTTTATCCGATTTGCTCCCAAACATATATAAAGGAAGAATACAAAGAATTTGTATGCAACCATGACGACAATATATTAGAACGATATTTGGCGGATAGCGAAATTTCACCGGCTGATTATTGGAATACGATAATCGATCTTGTGGCAAAAGCCAAAGTCTATCCGGTACTACATGGATCAGCAATGTTCAATATCGGTATCAATGAGTTGTTGGACGCCATCTCTTCTTTTATACTTCCTCCAGAATCAGTCTCAAACAGACTTTCAGCTTATCTCTATAAGATAGAGCATGACCCCAAAGGACATAAAAGAAGTTTTCTAAAAATAATTGACGGAAGTCTGAGACTTCGAGACATTGTAAGAATCAACGATTCGGAAAAATTCATCAAGATTAAAAATCTAAAGACTATTTATCAGGGCAGAGAGATAAATGTTGATGAAGTGGGGGCCAATGATATCGCGATTGTAGAAGATATGGAAGATTTTCGAATCGGAGATTATTTAGGTACTAAACCTTGTTTGATTCAAGGGTTATCTCATCAGCATCCCGCTCTCAAATCCTCCGTCCGGCCAGACAGGTCCGAAGAGAGAAGCAAGGTGATATCCGCTCTGAATACATTGTGGATTGAAGACCCGTCTTTGTCCTTTTCCATAAACTCATATAGTGATGAATTGGAAATCTCGTTATATGGTTTGACACAAAAGGAAATCATACAGACATTGCTGGAAGAACGATTTTCCGTAAAGGTCCATTTTGATGAGATCAAGACTATCTACAAAGAACGACCTGTAAAAAAGGTCAATAAGATTATTCAGATCGAAGTGCCACCCAACCCTTACTGGGCCACAATAGGGCTGACGCTTGAACCCTTGCCGTTAGGGACAGGGTTGCAAATCGAAAGTGACATCTCCTATGGTTATCTGAACCATTCTTTTCAAAATGCCGTTTTTGAAGGGATTCGTATGTCTTGCCAATCTGGTTTACATGGATGGGAAGTGACTGATCTGAAAGTAACTTTTACTCAAGCCGAGTATTATAGCCCGGTAAGTACACCTGCTGATTTCAGACAGCTGACCCCTTATGTCTTCAGGCTGGCCTTGCAACAGTCAGGTGTGGACATTCTCGAACCGATGCTCTATTTTGAGTTGCAGATACCCCAAGCGGCAAGTTCCAAAGCTATTACAGATTTGCAAAAAATGATGTCTGAGATTGAAGACATCAGTTGCAATAATGAGTGGTGTCATATTAAAGGGAAAGTTCCATTAAATACAAGTAAAGACTACGCCTCAGAAGTAAGTTCATACACTAAGGGCTTAGGCGTTTTTATGGTCAAGCCATGCGGGTATCAAATAACAAAAGGCGATTATTCTGATAATATCCGCATGAACGAAAAAGATAAACTTTTATTCATGTTCCAAAAATCAATGTCATCAAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35916","NCBI_taxonomy_name":"Bacteroides fragilis","NCBI_taxonomy_id":"817"}}}},"ARO_accession":"3000191","ARO_id":"36330","ARO_name":"tetQ","ARO_description":"TetQ is a ribosomal protection protein. Its gene is associated with a conjugative transposon and has been found in both Gram-positive and Gram-negative bacteria.","ARO_category":{"35921":{"category_aro_accession":"0000002","category_aro_cvterm_id":"35921","category_aro_name":"tetracycline-resistant ribosomal protection protein","category_aro_description":"A family of proteins known to bind to the 30S ribosomal subunit. This interaction prevents tetracycline and tetracycline derivatives from inhibiting ribosomal function. Thus, these proteins confer elevated resistance to tetracycline derivatives as a ribosomal protection protein.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1184":{"model_id":"1184","model_name":"OXA-182","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1453":{"protein_sequence":{"accession":"ADK92148.1","sequence":"MKKFILPIFSISILLSLSACSSIQTKFEDTFHISNQKHEKAIKSYFDEAQTQGVIIIKEGKNISSYGNNLVRAHTEYVPASTFKMLNALIGLENHKATTNEIFKWDGKKRSYPMWEKDMTLGEAMALSAVPVYQDLARRIGLNLMQKEVKRVGFGNMNIGTQVDNFWLIGPLKITPIQEVNFADDLANNRLPFKLETQEEVKKMLLIKEVNGSKIYAKSGWGMDVSPQVGWLTGWVEKSNGEKVSFSLNIEMKQGMSGSIRNEITYKSLENLGII"},"dna_sequence":{"accession":"HM640278","fmin":"0","fmax":"828","strand":"+","sequence":"ATGAAAAAATTTATACTTCCTATCTTCAGCATTTCTATTCTACTTTCTCTCAGTGCATGCTCATCTATTCAAACTAAATTTGAAGATACTTTTCATATTTCTAATCAGAAACATGAAAAAGCTATTAAAAGCTATTTTGATGAAGCTCAAACACAAGGTGTAATTATTATTAAGGAAGGTAAAAATATTAGCTCCTATGGTAATAACCTTGTACGAGCACATACAGAATATGTCCCTGCATCAACATTTAAGATGCTAAATGCTTTAATCGGACTAGAAAATCATAAAGCGACAACAAATGAGATTTTTAAATGGGATGGTAAAAAAAGATCTTATCCTATGTGGGAGAAAGATATGACTTTGGGTGAGGCCATGGCACTTTCAGCTGTTCCTGTATATCAAGATCTTGCGAGACGGATTGGCTTAAATCTCATGCAAAAAGAAGTTAAACGCGTTGGTTTTGGTAATATGAACATTGGAACACAAGTTGATAATTTCTGGTTGATTGGTCCTCTTAAGATTACACCAATACAAGAAGTGAATTTTGCCGATGATCTTGCGAATAATCGATTACCCTTTAAATTAGAAACTCAAGAAGAAGTAAAAAAGATGCTTCTGATTAAAGAAGTCAATGGTAGTAAAATTTATGCTAAAAGCGGATGGGGAATGGATGTAAGCCCACAAGTAGGTTGGTTAACAGGTTGGGTAGAAAAATCTAATGGAGAAAAAGTTTCCTTTTCTTTAAATATAGAAATGAAGCAAGGAATGTCTGGTTCTATTCGTAATGAGATTACTTATAAGTCGTTAGAAAATTTAGGGATCATCTAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001709","ARO_id":"38109","ARO_name":"OXA-182","ARO_description":"OXA-182 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1185":{"model_id":"1185","model_name":"OXA-176","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"882":{"protein_sequence":{"accession":"ADI58620.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDSKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWVVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"HM113562","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATAGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGGTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001660","ARO_id":"38060","ARO_name":"OXA-176","ARO_description":"OXA-176 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1186":{"model_id":"1186","model_name":"OXA-327","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1052":{"protein_sequence":{"accession":"AGW16409.1","sequence":"MYKKALIVATSILFLSACSSNTVKQHQIHSISANKNSEEIKSLFDQAQTTGVLVIKRGQTEEIYGNDLKRASTAYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNANIGSKVDNFWLVGPLKITPQQETQFAYQLAHKTLPFSQDVQEQVQSMVFIEEKNGSKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGVL"},"dna_sequence":{"accession":"KF203101","fmin":"0","fmax":"822","strand":"+","sequence":"ATGTACAAAAAAGCCCTTATCGTTGCAACAAGTATCCTATTTTTATCCGCCTGTTCTTCCAATACGGTAAAACAACATCAAATACACTCTATTTCTGCCAATAAAAATTCAGAAGAAATTAAATCACTGTTTGATCAAGCACAGACCACGGGAGTTTTGGTGATTAAGCGAGGGCAAACAGAAGAAATTTATGGCAATGATCTTAAAAGAGCATCAACCGCCTATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTAATTGGACTTGAACATCATAAGGCAACTACAACTGAAGTGTTTAAATGGAATGGACAAAAACGCTTATTTCCTGATTGGGAAAAGGACATGACATTGGGCGATGCCATGAAAGCTTCTGCGATTCCAGTTTACCAAGAATTAGCCCGACGAATTGGTCTAGATCTTATGTCCAAAGAGGTGAAACGAATTGGTTTTGGTAATGCTAACATTGGTTCAAAAGTAGATAATTTTTGGCTTGTTGGCCCTCTAAAAATTACACCTCAACAAGAAACCCAATTTGCTTATCAATTAGCCCATAAAACGCTTCCATTTAGCCAAGATGTACAAGAACAAGTTCAATCAATGGTGTTCATAGAGGAAAAAAATGGAAGTAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTTGAACCGCAAGTTGGTTGGTTAACAGGTTGGGTCGTTCAACCACAAGGAGAAATTGTCGCATTCTCACTTAATTTAGAAATGAAAAAAGGAACTCCTAGCTCTATTCGCAAAGAAATTGCTTATAAAGGATTAGAACAACTCGGTGTTTTATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3001515","ARO_id":"37915","ARO_name":"OXA-327","ARO_description":"OXA-327 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1187":{"model_id":"1187","model_name":"OXA-248","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1050":{"protein_sequence":{"accession":"CCJ32596.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGEKRLFPEWEKNMTLGDAMKASAMPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"HE963769","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAATGGGATGGGGAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATGCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTCTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001673","ARO_id":"38073","ARO_name":"OXA-248","ARO_description":"OXA-248 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1188":{"model_id":"1188","model_name":"ErmV","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"420":{"protein_sequence":{"accession":"AAB51440.1","sequence":"MARPSRVSRALSQNFLADRAAAGQLARLAAPHGLPVPLLLEVGAGKGALTELLAPRCRSLLAYEIDPRLVPVLRSRFADAPHVRVLGEDFLRARAPRTPFSVAGNVPFSRTAAVVAWCLRAPHLTDATLLTQLEYARRRTGDYGSWTRLTVLTWPRHEWRLAGRVGRRSFRPVPRVDAGIVRIERRRTPLLAPGADAGWRELVDLGFSGAGGSLHASLRRARPRRRVDAAFRAAGLDRDVLVGEVPPWTWLRLHEVLGS"},"dna_sequence":{"accession":"U59450","fmin":"396","fmax":"1176","strand":"+","sequence":"ATGGCCCGCCCCAGTCGCGTATCCCGCGCGCTCTCGCAGAACTTCCTCGCCGACCGCGCCGCCGCCGGACAGCTCGCCCGGCTCGCCGCGCCCCACGGCCTCCCCGTCCCGCTGCTGCTCGAAGTCGGCGCGGGCAAAGGCGCGTTGACCGAGCTGCTCGCCCCGCGCTGTCGCAGTCTCCTCGCCTACGAGATCGACCCACGGCTCGTCCCCGTCCTGCGCTCGCGCTTCGCGGACGCCCCGCACGTCCGCGTCCTCGGCGAGGACTTCCTGCGCGCCAGGGCGCCGCGCACCCCGTTCTCCGTCGCCGGGAACGTCCCCTTCTCCCGTACCGCCGCCGTCGTCGCGTGGTGTCTGCGGGCCCCGCACCTCACCGACGCCACCCTGCTCACCCAGCTGGAGTACGCCCGCAGACGCACCGGCGACTACGGCAGCTGGACGCGGCTGACCGTGCTGACTTGGCCCCGCCACGAGTGGCGGCTCGCCGGGCGGGTCGGGCGCCGCAGCTTCCGTCCCGTGCCCCGGGTGGACGCGGGGATCGTCCGTATCGAGCGGCGTCGCACCCCGCTGCTCGCGCCCGGTGCCGACGCCGGCTGGCGGGAGCTGGTCGACCTCGGCTTCTCCGGGGCCGGCGGCTCCCTGCACGCCTCGCTGCGGCGGGCCCGCCCGAGACGGCGGGTGGACGCGGCGTTCCGCGCGGCGGGGCTCGACCGGGACGTCCTGGTGGGGGAGGTGCCGCCGTGGACGTGGCTGAGGCTGCACGAGGTGCTGGGCTCGTGAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39570","NCBI_taxonomy_name":"Streptomyces viridochromogenes","NCBI_taxonomy_id":"1938"}}}},"ARO_accession":"3002824","ARO_id":"39258","ARO_name":"ErmV","ARO_description":"ErmV is a plasmid-mediated methyltransferase found in Streptomyces viridochromogenes","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1189":{"model_id":"1189","model_name":"vatB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"3345":{"protein_sequence":{"accession":"AAA86871.1","sequence":"MKYGPDPNSIYPHEEIKSVCFIKNTITNPNIIVGDYTYYSDVNGAEKFEEHVTHHYEFRGDKLVIGKFCAIAEGIEFIMNGANHRMNSITTYPFNIMGNGWEKATPSLEDLPFKGDTVVGNDVWIGQNVTVMPGIQIGDGAIVAANSVVTKDVPPYRIIGGNPSRIIKKRFEDELIDYLLQIKWWDWSAQKIFSNLETLCSSDLEKIKSIRD"},"dna_sequence":{"accession":"U19459","fmin":"66","fmax":"705","strand":"+","sequence":"ATGAAATATGGCCCTGATCCAAATAGCATATATCCACATGAAGAAATAAAAAGTGTTTGTTTTATTAAAAATACAATTACCAATCCAAATATTATAGTTGGAGATTATACTTACTATTCCGATGTTAACGGAGCTGAAAAATTTGAAGAACATGTGACACATCATTATGAATTTAGGGGTGATAAACTTGTAATTGGCAAGTTTTGTGCAATAGCTGAAGGTATAGAATTTATTATGAATGGAGCAAACCATAGAATGAATTCAATAACAACTTATCCTTTTAATATAATGGGAAATGGTTGGGAAAAAGCAACTCCATCTCTTGAAGATTTACCATTTAAGGGAGATACTGTTGTTGGAAATGATGTGTGGATTGGTCAGAATGTTACTGTTATGCCAGGAATTCAAATAGGAGATGGAGCAATTGTTGCTGCGAATTCAGTTGTTACAAAAGATGTACCACCATATCGTATTATTGGTGGAAATCCGAGTAGAATTATAAAGAAAAGGTTTGAAGATGAATTGATAGATTATTTATTGCAAATAAAATGGTGGGATTGGTCAGCACAAAAAATATTTTCTAATCTTGAAACACTTTGTAGCTCTGATTTAGAGAAAATAAAATCTATTCGAGATTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3002841","ARO_id":"39275","ARO_name":"vatB","ARO_description":"vatB is a plasmid-mediated acetyltransferase found in Staphylococcus aureus","ARO_category":{"36592":{"category_aro_accession":"3000453","category_aro_cvterm_id":"36592","category_aro_name":"streptogramin vat acetyltransferase","category_aro_description":"vat (Virginiamycin acetyltransferases) enzymes catalyze the transfer of an acetyl group from acetyl-CoA to the secondary alcohol of streptogramin A compounds, thus inactivating virginiamycin-like antibiotics and conferring resistance to these compounds.","category_aro_class_name":"AMR Gene Family"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1190":{"model_id":"1190","model_name":"OXA-354","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1378":{"protein_sequence":{"accession":"AGW83452.1","sequence":"MYKKALIVATSILFLSACSSNSVKQHQIHSISANKNSEEIKSLFDQAQTTGVLVIKRGQTEEIYGNDLKRASTDYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNANIGSKVDDFWLVGPLKITPQQETQFAYQLAHKMLPFSKDVQEQVQSMVFIEEKNGRKIYAKSGWGWDIEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"KF297583","fmin":"0","fmax":"822","strand":"+","sequence":"ATGTATAAAAAAGCCCTTATCGTTGCAACAAGTATCCTATTTTTATCCGCCTGTTCTTCTAATTCAGTAAAACAACATCAAATACACTCTATTTCTGCCAATAAAAATTCAGAAGAAATTAAATCACTGTTTGATCAGGCACAAACCACGGGTGTTTTGGTGATTAAGCGAGGACAAACAGAAGAAATTTATGGCAATGATCTTAAAAGAGCATCAACAGACTATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTAATTGGACTTGAACATCATAAGGCAACTACAACTGAAGTATTTAAATGGGATGGGCAGAAACGTTTATTTCCTGATTGGGAAAAGGACATGACACTGGGTGATGCCATGAAAGCTTCTGCAATCCCAGTTTACCAAGAATTAGCCCGACGAATTGGTCTGGATCTTATGTCTAAAGAGGTAAAGCGAATTGGTTTCGGTAATGCTAACATTGGCTCAAAAGTAGATGATTTCTGGCTTGTTGGTCCTCTAAAAATTACACCTCAACAAGAAACCCAATTTGCTTATCAATTAGCCCATAAAATGCTTCCATTTAGTAAAGATGTACAAGAACAAGTTCAATCAATGGTGTTCATAGAAGAAAAAAATGGACGTAAAATTTATGCAAAAAGCGGTTGGGGATGGGATATTGAGCCACAAGTTGGTTGGTTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTGGCATTCTCACTTAATTTAGAAATGAAAAAAGGAACTCCTAGCTCTATTCGCAAAGAAATTGCTTATAAAGGCTTAGAACAACTGGGTATCTTATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3001541","ARO_id":"37941","ARO_name":"OXA-354","ARO_description":"OXA-354 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1191":{"model_id":"1191","model_name":"mdtM","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"4381":{"protein_sequence":{"accession":"AAC77293.1","sequence":"MPRFFTRHAATLFFPMALILYDFAAYLSTDLIQPGIINVVRDFNADVSLAPAAVSLYLAGGMALQWLLGPLSDRIGRRPVLITGALIFTLACAATMFTTSMTQFLIARAIQGTSICFIATVGYVTVQEAFGQTKGIKLMAIITSIVLIAPIIGPLSGAALMHFMHWKVLFAIIAVMGFISFVGLLLAMPETVKRGAVPFSAKSVLRDFRNVFCNRLFLFGAATISLSYIPMMSWVAVSPVILIDAGSLTTSQFAWTQVPVFGAVIVANAIVARFVKDPTEPRFIWRAVPIQLVGLSLLIVGNLLSPHVWLWSVLGTSLYAFGIGLIFPTLFRFTLFSNKLPKGTVSASLNMVILMVMSVSVEIGRWLWFNGGRLPFHLLAVVAGVIVVFTLAGLLNRVRQHQAAELVEEQ"},"dna_sequence":{"accession":"U00096","fmin":"4567286","fmax":"4568519","strand":"-","sequence":"TCACTGCTCCTCCACTAGCTCGGCTGCCTGATGCTGGCGCACGCGATTGAGCAATCCCGCCAGGGTGAAAACGACGATAACGCCCGCCACAACGGCTAACAGATGAAACGGCAAGCGACCGCCGTTAAACCATAGCCAGCGGCCGATTTCGACCGAGACCGACATCACCATCAGGATCACCATATTTAGCGATGCGGAGACGGTCCCTTTCGGTAACTTATTGGAAAACAGCGTAAAGCGGAATAAGGTCGGGAAAATCAAACCAATCCCGAAAGCATACAGACTGGTGCCCAGCACCGACCACAGCCAGACGTGCGGCGACAGCAGATTGCCGACAATCAACAGCGAGAGGCCGACCAGTTGAATGGGTACGGCACGCCAGATAAACCGCGGTTCGGTCGGATCTTTAACAAAACGCGCCACGATGGCATTCGCAACAATCACCGCGCCGAACACCGGAACCTGTGTCCAGGCGAACTGCGAAGTTGTTAAGCTGCCTGCATCGATAAGGATCACCGGCGAGACAGCCACCCAGCTCATCATCGGGATATAGCTTAAAGAGATGGTTGCTGCGCCAAAGAGGAACAGCCGATTGCAAAAGACATTACGAAAATCGCGCAAGACGCTTTTGGCGCTAAACGGAACCGCGCCGCGCTTCACCGTCTCTGGCATCGCCAACAGTAAGCCAACAAATGAGATAAAACCCATAACCGCAATGATGGCAAAAAGGACTTTCCAGTGCATAAAGTGCATCAGAGCTGCGCCGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATGGAGGTGATAATCGCCATCAACTTGATCCCTTTTGTCTGTCCGAACGCCTCCTGCACCGTGACATAACCAACGGTGGCAATAAAACAGATACTGGTGCCCTGAATTGCACGCGCGATAAGAAACTGTGTCATAGACGTTGTGAACATTGTCGCGGCGCAGGCAAGGGTAAAAATTAGCGCCCCGGTAATCAGCACCGGCCTGCGGCCAATTCTGTCGGAAAGCGGCCCCAGCAGCCACTGTAACGCCATACCGCCAGCAAGATAGAGACTGACGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3001214","ARO_id":"37613","ARO_name":"mdtM","ARO_description":"Multidrug resistance protein MdtM","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavin","category_aro_description":"Acriflavin is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35965":{"category_aro_accession":"0000047","category_aro_cvterm_id":"35965","category_aro_name":"puromycin","category_aro_description":"Puromycin is an aminonucleoside antibiotic, derived from Streptomyces alboniger, that causes premature chain termination during ribosomal protein translation.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36193":{"category_aro_accession":"3000054","category_aro_cvterm_id":"36193","category_aro_name":"acridine dye","category_aro_description":"Acridine dyes are cell permeable, basic molecules with an acridine chromophore. These compounds intercalate DNA. The image shown represents the core structure of the acridine family, with specific dyes containing varying substituents.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1192":{"model_id":"1192","model_name":"VEB-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"4382":{"protein_sequence":{"accession":"YP_001715362.1","sequence":"MKIVKRILLVLLSLFFTIVYSNAQTDNLTLKIENVLKAKNARIGVAIFNSNEKDTLKINNDFHFPMQSVMKFPIALAVLSEIDKGNLSFEQKIEITPQDLLPKTWSPIKEEFPNGTTLTIEQILNYTVSESDNIGCDILLKLIGGTDSVQKFLNANHFTDISIKANEEQMHKDWNTQYQNWATPTAMNKLLIDTYNNKNQLLSKKSYDFIWKIMRETTTGSNRLKGQLPKNTIVAHKTGTSGINNGIAAATNDVGVITLPNGQLIFISVFVAESKETSEINEKIISDIAKITWNYYLNK"},"dna_sequence":{"accession":"NC_010410","fmin":"3660736","fmax":"3661636","strand":"-","sequence":"TTATTTATTCAAATAGTAATTCCACGTTATTTTTGCAATGTCTGAAATAATCTTTTCATTAATTTCCGAAGTTTCTTTGGACTCTGCAACAAATACGCTTATAAAAATTAATTGTCCATTCGGTAAAGTAATTACCCCAACATCATTAGTGGCTGCTGCAATTCCATTATTTATTCCGGAAGTCCCTGTTTTATGAGCAACAATTGTATTCTTTGGTAATTGTCCTTTTAATCGGTTACTTCCTGTTGTTGTTTCTCTCATAATTTTCCAAATAAAATCATAACTTTTTTTAGAAAGTAATTGGTTCTTATTATTATAAGTATCTATTAACAGTTTGTTCATCGCTGTTGGGGTTGCCCAATTTTGATATTGGGTATTCCAATCCTTGTGCATTTGTTCTTCGTTTGCTTTGATTGAAATATCAGTGAAATGATTAGCATTCAAGAATTTTTGAACAGAATCAGTTCCTCCGATTAATTTTAGCAAAATATCACAACCAATATTGTCGCTCTCTGATACTGTATAATTTAGTATTTGTTCAATCGTCAAAGTTGTTCCATTAGGGAATTCCTCTTTAATCGGACTCCACGTTTTAGGCAAAAGGTCTTGAGGGGTAATCTCTATTTTTTGTTCAAAAGAAAGATTCCCTTTATCTATCTCAGACAAAACGGCTAAAGCAATCGGAAATTTCATAACGCTTTGCATCGGGAAATGGAAGTCGTTATTAATCTTCAAAGTATCCTTCTCATTGCTGTTGAATATTGCTACTCCTATTCTGGCATTTTTTGCCTTTAAAACATTCTCAATTTTCAAAGTTAAGTTGTCAGTTTGAGCATTTGAATACACAATTGTAAAAAATAAACTTAACAATACTAATAATATCCTTTTTACGATTTTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35535","NCBI_taxonomy_name":"Acinetobacter baumannii AYE","NCBI_taxonomy_id":"509173"}}}},"ARO_accession":"3002370","ARO_id":"38770","ARO_name":"VEB-1","ARO_description":"VEB-1 is a beta-lactamase found in Escherichia coli and Pseudomonas aeruginosa.","ARO_category":{"36182":{"category_aro_accession":"3000043","category_aro_cvterm_id":"36182","category_aro_name":"VEB beta-lactamase","category_aro_description":"VEB beta-lactamases or Vietnamese extended-spectrum beta-lactamases are class A beta-lactamases that confer high-level resistance to oxyimino cephalosporins and to aztreonam","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1193":{"model_id":"1193","model_name":"ErmH","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"63":{"protein_sequence":{"accession":"AAC32026.1","sequence":"MAALLKRILRRRMAEKRSGRGRMAAARTTGAQSRKTAQRSGRSEADRRRRVHGQNFLVDRETVQRFVRFADPDPGEVVLEVGAGNGAITRELARLCRRVVAYEIDRHFADRLREATAEDPRIEVVAGDFLKTSQPKVPFSVVGNIPFGNTADIVDWCLNARRLRTTTLVTQLEYARKRTGGYRRWSRLTVATWPEVEWRMGERISRRWFRPVPAVDSAVLRLERRPVPLIPPGLMHDFRDLVETGFTGKGGSLDASLRRRFPARRVAAGFRRARLEQGVVVAYVTPGQWITLFEELHGR"},"dna_sequence":{"accession":"M16503","fmin":"243","fmax":"1143","strand":"+","sequence":"ATGGCTGCGCTCCTGAAGCGCATACTTAGGAGACGCATGGCTGAAAAGAGGTCAGGACGCGGGCGCATGGCCGCAGCGCGTACAACCGGAGCTCAGTCGCGTAAAACGGCACAGCGGTCGGGCCGGAGTGAGGCTGACCGTAGAAGAAGAGTCCACGGGCAGAATTTCCTCGTCGACCGGGAAACAGTACAACGGTTTGTGCGTTTCGCCGATCCGGACCCCGGGGAGGTCGTTCTCGAGGTCGGTGCCGGTAATGGTGCGATCACGCGCGAGCTGGCGCGATTATGCCGACGAGTGGTGGCGTATGAGATCGACCGGCACTTCGCGGACCGATTACGTGAGGCGACCGCCGAGGATCCGCGGATCGAGGTCGTCGCCGGCGACTTCCTGAAGACCTCGCAGCCCAAGGTCCCGTTCTCCGTGGTCGGCAACATCCCGTTCGGCAACACCGCGGACATAGTGGACTGGTGCCTGAACGCGCGGCGGCTGCGTACGACCACCCTGGTCACCCAGCTCGAATACGCCCGCAAGCGCACCGGCGGCTATCGGCGCTGGTCACGGCTCACCGTGGCCACCTGGCCCGAGGTGGAGTGGCGGATGGGCGAGCGGATCAGCCGCCGCTGGTTCCGGCCCGTCCCCGCCGTCGACTCCGCGGTACTGCGACTGGAACGGCGACCGGTGCCGCTGATCCCACCCGGTCTGATGCACGACTTCCGGGACCTGGTGGAGACCGGGTTCACGGGAAAGGGCGGTTCGCTGGACGCCTCGCTGCGCCGGCGCTTCCCGGCCCGGCGGGTGGCCGCCGGGTTCCGCAGGGCCCGCCTGGAGCAGGGCGTGGTCGTCGCCTACGTCACCCCGGGCCAATGGATCACACTCTTCGAGGAACTCCACGGGCGCTGAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36843","NCBI_taxonomy_name":"Streptomyces thermotolerans","NCBI_taxonomy_id":"80858"}}}},"ARO_accession":"3002823","ARO_id":"39257","ARO_name":"ErmH","ARO_description":"ErmH is a plasmid-mediated methyltransferase found in Streptomyces thermotolerans","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1194":{"model_id":"1194","model_name":"OXA-16","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2001":{"protein_sequence":{"accession":"AAB97924.1","sequence":"IACLSSTALAGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQITREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEDQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG"},"dna_sequence":{"accession":"AF043100","fmin":"0","fmax":"774","strand":"+","sequence":"TATCGCGTGTCTTTCGAGTACGGCATTAGCTGGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTCTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATGACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAGCAATGGGAAAGAGACTTGACCTTAAGAGGGGCAATACAAGTTTCAGCTGTTCCCGTATTTCAACAAATCACCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCCTATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAAGACCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATATTTAAATAAATTGTCAGCATCTAAAGAAAACCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCGGCACCTGAATATCTAGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGGTGGGTTGAGAAGGAGACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAGTAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGAAAGTGAGGGCATCATTGGTGGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001411","ARO_id":"37811","ARO_name":"OXA-16","ARO_description":"OXA-16 is a beta-lactamase found in P. aeruginosa.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1195":{"model_id":"1195","model_name":"SHV-55","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1562":{"protein_sequence":{"accession":"CAI10727.2","sequence":"MRFIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASKRGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AJ863560","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTTTATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGAGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCAAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATCGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001111","ARO_id":"37491","ARO_name":"SHV-55","ARO_description":"SHV-55 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1196":{"model_id":"1196","model_name":"OXA-71","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1057":{"protein_sequence":{"accession":"AAW81342.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKTTTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"AY750913","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCCCTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTCTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGACAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCATTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001619","ARO_id":"38019","ARO_name":"OXA-71","ARO_description":"OXA-71 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1198":{"model_id":"1198","model_name":"mefB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"4383":{"protein_sequence":{"accession":"ACJ63262.1","sequence":"MNRIKNWKKQFAVIYTGQAFSILGSAAVQFAVIWWLTIQTESAITLTIASLVAFLPNMLIGPFAGVWIDRYNRRTVMILADGLVAVSSIILGAAFLLVETPPIWFIYIVLFLRGLGNTFHGPAMQAAIPMFVPADMLTKAGGWGNMIQSISNMMGPVLGAALMSFLPISSIMIVDILGAAFAIVCLLFVIIPDITQTNEKMSVLSDMKQGFIAMKANKPLMAVFSPMLLMTILYMPLGSLFPLLARSHFMGEAWHNSIVEFVFAGGLLLSSLVIGVWGGMKRRFFMASLAIGLMGLATLISGALPTSGFWIFVICCFFLGASGTFMNVPVMAYVQESIAPEMMGKVFSLLMTAMTLSMPIGLLVAGPVVEVIGVNTWFFWSGVALIVNAVLCRILTRRYDKVTMKPQVD"},"dna_sequence":{"accession":"FJ196385","fmin":"11083","fmax":"12313","strand":"-","sequence":"TCAGTCCACTTGCGGTTTCATTGTTACTTTGTCATAGCGTCGTGTCAGAATGCGGCAGAGAACAGCGTTTACTATCAACGCAACACCAGACCAGAAAAACCATGTATTAACACCTATAACCTCAACAACCGGACCTGCAACAAGTAAGCCTATCGGCATAGAAAGAGTCATGGCGGTCATCAAAAGGGAAAACACCTTGCCCATCATTTCAGGGGCAATGCTTTCTTGAACATAAGCCATAACAGGAACATTCATAAATGTGCCAGAGGCGCCCAAGAAGAAGCAGCATATAACAAATATCCAAAAACCGCTTGTCGGTAGCGCTCCGCTAATCAGTGTAGCCAGACCCATTAAGCCAATAGCTAAGGATGCCATGAAAAACCTTCTTTTCATGCCGCCCCATACACCGATAACCAAAGATGAAAGAAGCAATCCACCTGCAAAGACAAATTCCACAATGCTATTGTGCCAGGCTTCACCCATAAAGTGGCTGCGTGCCAGTAGAGGGAACAGAGAACCTAATGGCATATAAAGTATGGTCATCAGCAGCATGGGGGAAAACACAGCCATTAAAGGTTTATTTGCTTTCATTGCGATAAAGCCCTGCTTCATGTCAGACAATACACTCATCTTCTCATTGGTTTGCGTAATGTCTGGAATTATAACAAATAGGAGGCAAACTATCGCAAAAGCGGCTCCCAGTATATCCACAATCATAATGGAGGAAATAGGTAGAAATGACATAAGCGCAGCACCCAGCACAGGCCCCATCATGTTGGATATTGATTGGATCATATTTCCCCAGCCCCCTGCTTTGGTCAACATATCTGCTGGCACAAACATGGGTATCGCCGCTTGCATAGCTGGACCGTGAAAGGTATTCCCCAATCCACGCAAAAATAAAACAATGTAGATAAACCAAATAGGGGGTGTTTCCACAAGTAAAAATGCTGCCCCAAGGATGATGCTGGATACAGCTACCAGACCGTCAGCTAAAATCATTACTGTTCGGCGGTTGTATCGGTCGATCCACACACCGGCAAAGGGTCCGATTAACATATTGGGGAGAAAGGCAACTAAGGATGCAATCGTCAAGGTGATTGCGGATTCAGTCTGGATGGTCAGCCACCAGATAACAGCGAACTGCACTGCGGCAGAACCCAAGATTGAAAAAGCCTGCCCTGTGTATATTACAGCAAATTGTTTCTTCCAATTTTTTATTCTGTTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3003107","ARO_id":"39681","ARO_name":"mef(B)","ARO_description":"mef(B) is a macrolide efflux gene located in the vicinity of sul3 in Escherichia coli. There is also a mefB found in Streptococcus agalactiae that confers resistance to macrolides.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1199":{"model_id":"1199","model_name":"SHV-168","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1233":{"protein_sequence":{"accession":"AFW16978.1","sequence":"MRYFRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPVGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"JX870080","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATTTTCGCCTGTGTATTATCTCTCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGTAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGGATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001352","ARO_id":"37752","ARO_name":"SHV-168","ARO_description":"From the Lahey list of beta-lactamases.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1200":{"model_id":"1200","model_name":"msrA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"4185":{"protein_sequence":{"accession":"YP_008709794.1","sequence":"MEQYTIKFNQINHKLTDLRSLNIDHLYAYQFEKIALIGGNGTGKTTLLNMIAQKTKPESGTVETNGEIQYFEQLNMDVENDFNTLDGSLMSELHIPMHTTDSMSGGEKAKYKLANVISNYSPILLLDEPTNHLDKIGKDYLNNILKYYYGTLIIVSHDRALIDQIADTIWDIQEDGTIRVFKGNYTQYQNQYEQEQLEQQRKYEQYISEKQRLSQASKAKRNQAQQMAQASSKQKNKSIAPDRLSASKQKGTVEKAAQKQAKHIEKRMEHLEEVEKPQSYHEFNFPQNKIYDIHNNYPIIAQNLTLVKGSQKLLTQVRFQIPYGKNIALVGANGVGKTTLLEAIYHQIEGIDCSPKVQMAYYRQLAYEDMRDVSLLQYLMDETDSSESFSRAILNNLGLNEALERSCNVLSGGERTKLSLAVLFSTKANMLILDEPTNFLDIKTLEALEMFMNKYPGIILFTSHDTRFVKHVSDKKWELTGQSIHDIT"},"dna_sequence":{"accession":"NC_022598.1","fmin":"14791","fmax":"16258","strand":"+","sequence":"ATGGAACAATATACAATTAAATTTAACCAAATCAATCATAAATTGACAGATTTACGATCACTTAACATCGATCATCTTTATGCTTACCAATTTGAAAAAATAGCACTTATTGGGGGTAATGGTACTGGCAAAACCACATTACTAAATATGATTGCTCAAAAAACAAAACCAGAATCTGGAACAGTTGAAACGAATGGCGAAATTCAATATTTTGAACAGCTTAACATGGATGTGGAAAATGATTTTAACACGTTAGACGGTAGTTTAATGAGTGAACTCCATATACCTATGCATACAACCGACAGTATGAGTGGTGGTGAAAAAGCAAAATATAAATTAGCTAATGTCATATCAAATTATAGTCCGATATTACTTTTAGATGAACCTACAAATCACTTGGATAAAATTGGTAAAGATTATCTGAATAATATTTTAAAATATTACTATGGTACTTTAATTATAGTAAGTCACGATAGAGCACTTATAGACCAAATTGCTGACACAATTTGGGATATACAAGAAGATGGCACAATAAGAGTGTTTAAAGGTAATTACACACAGTATCAAAATCAATATGAACAAGAACAGTTAGAACAACAACGTAAATATGAACAGTATATAAGTGAAAAACAAAGATTGTCCCAAGCCAGTAAAGCTAAACGAAATCAAGCGCAACAAATGGCACAAGCATCATCAAAACAAAAAAATAAAAGTATAGCACCAGATCGTTTAAGTGCATCAAAACAAAAAGGCACGGTTGAGAAGGCTGCTCAAAAACAAGCTAAGCATATTGAAAAAAGAATGGAACATTTGGAAGAAGTTGAAAAACCACAAAGTTATCATGAATTCAATTTTCCACAAAATAAAATTTATGATATCCATAATAATTATCCAATCATTGCACAAAATCTAACATTGGTTAAAGGAAGTCAAAAACTGCTAACACAAGTACGATTCCAAATACCATATGGCAAAAATATAGCGCTCGTAGGTGCAAATGGTGTAGGTAAGACAACTTTACTTGAAGCTATTTACCACCAAATAGAGGGAATTGATTGTTCTCCTAAAGTGCAAATGGCATACTATCGTCAACTTGCTTATGAAGACATGCGTGACGTTTCATTATTGCAATATTTAATGGATGAAACGGATTCATCAGAATCATTCAGTAGAGCTATTTTAAATAACTTGGGTTTAAATGAAGCACTTGAGCGTTCTTGTAATGTTTTGAGTGGTGGGGAAAGAACGAAATTATCGTTAGCAGTATTATTTTCAACGAAAGCGAATATGTTAATTTTGGATGAACCAACTAATTTTTTAGATATTAAAACATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATGATACAAGGTTTGTTAAACATGTATCAGATAAAAAATGGGAATTAACAGGACAATCTATTCATGATATAACTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3000251","ARO_id":"36390","ARO_name":"msrA","ARO_description":"MsrA is an ABC-efflux pump expressed to Staphylococcus species that confers resistance to erythromycin and streptogramin B antibiotics. It is associated with plasmid DNA.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1201":{"model_id":"1201","model_name":"CARB-22","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4384":{"protein_sequence":{"accession":"BAC61820.1","sequence":"MKKLFLLVGLMVCSTVSYASKLNEDISLIEKQTSGRIGVSVWDTQTDKRWDYRGDERFPLMSTFKTLACATMLSDMDSGKLNKNATAKIDERNIVVWSPVMDKLAGQSTRIEHACEAAMLMSDNTAANLVLNEIGGPKAVTQFLRSIGDKATRLDRLEPRLNEAKPGDKRDTTTPNAMVNTLHTLMEDNALSYESRTQLKIWMQDNKVSDSLMRSVLPKGWSIADRSGAGNYGSRGISAMIWKDNYKPVYISIYVTDTDLSLQARDQLIAQISQLILEHYKES"},"dna_sequence":{"accession":"BA000032","fmin":"476707","fmax":"477559","strand":"-","sequence":"TTAACTTTCTTTGTAGTGCTCTAAAATCAGTTGGCTGATTTGCGCGATCAGTTGATCGCGAGCTTGAAGCGAAAGGTCTGTGTCTGTGACGTAAATACTGATGTAAACCGGCTTGTAGTTGTCTTTCCAGATCATCGCGCTAATGCCGCGTGAACCGTAGTTACCTGCGCCAGAGCGGTCTGCAATCGACCAGCCTTTTGGCAGAACAGAGCGCATGAGAGAATCCGATACTTTGTTGTCTTGCATCCAGATTTTCAGCTGTGTGCGTGACTCGTAAGATAGGGCGTTATCTTCCATCAAGGTGTGTAGGGTGTTTACCATGGCGTTAGGCGTTGTGGTGTCTCGCTTGTCGCCCGGTTTTGCTTCATTCAAACGGGGTTCCAATCGGTCAAGTCGCGTTGCTTTGTCGCCAATAGATCGCAAAAACTGCGTGACCGCTTTAGGACCACCAATTTCATTTAACACTAAGTTCGCGGCGGTGTTGTCGCTCATCAACATGGCGGCTTCACAAGCGTGTTCGATGCGTGTGCTTTGTCCAGCCAGTTTATCCATCACCGGAGACCAAACCACAATATTGCGTTCATCGATTTTCGCTGTGGCATTTTTGTTGAGTTTGCCGCTGTCCATGTCGCTTAGCATGGTGGCACACGCTAACGTTTTGAATGTGCTCATTAATGGGAAACGTTCGTCTCCGCGATAATCCCAACGCTTGTCCGTTTGTGTATCCCAGACTGACACTCCAATTCGCCCAGATGTTTGTTTCTCGATGAGGGAGATGTCTTCGTTTAATTTGGAGGCGTAACTAACAGTTGAGCAAACCATCAGCCCAACCAACAGGAATAACTTTTTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39776","NCBI_taxonomy_name":"Vibrio parahaemolyticus RIMD 2210633","NCBI_taxonomy_id":"223926"}}}},"ARO_accession":"3003151","ARO_id":"39728","ARO_name":"CARB-22","ARO_description":"From the Lahey list of beta-lactamases.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1202":{"model_id":"1202","model_name":"CTX-M-28","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1780":{"protein_sequence":{"accession":"CAD70280.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTNGL"},"dna_sequence":{"accession":"AJ549244","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGTCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCAACGGTTTGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001890","ARO_id":"38290","ARO_name":"CTX-M-28","ARO_description":"CTX-M-28 is a beta-lactamase found in Salmonella enterica","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1204":{"model_id":"1204","model_name":"tcmA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"3313":{"protein_sequence":{"accession":"AAA67509.1","sequence":"MSTETHDEPSGVAHTPASGLRGRPWPTLLAVAVGVMMVALDSTIVAIANPAIQQDLHASLADVQWITNGYLLALAVSLITAGKLGDRFGHRQTFLVGVAGFAVTSAAIGLSGSVAAIVVFRVLQGLFGALMQPSALGLLRVTFPPGKLNMAIGIWSGVVGASTAAGPIIGGLLVQHVGWEAVFFINVPVGLAALVAGLVILTDARAERAPKSFDVSGIVLLSGAMFCLVWGLIKAPAWGWGDLRTLGFLAAAVLAFAGFTLRESRATEPLMPLAMFRSVPLSAGTVLMVLMAFSFIGGLFFVTFYLQNVHGMSPVESGVHLLPLTGMMIVGAPVSGIVISRFGPGGPLVVGMLLTAASLWGMSTLEADSGMGITSLWFVLLGLGLAPVMVGTTDVIVSNAPAELAGVAGGLQQSAMQVGGSLGTAVLGVLMASRVGDVFPDKWAEANLPRVGPREAAAIEDAAEVGAVPPAGTLPGRHAGTLSEVVHSSFISGMGLAFTVAGAVALVAAAVALFTRKAEPDERAPEEFPVPASTAGRG"},"dna_sequence":{"accession":"M80674","fmin":"877","fmax":"2494","strand":"+","sequence":"ATGAGCACGGAAACGCACGACGAGCCGTCAGGCGTCGCACACACCCCCGCTTCCGGTCTGCGTGGACGTCCCTGGCCGACCCTGCTCGCGGTCGCGGTCGGCGTGATGATGGTGGCTCTGGACAGCACCATCGTCGCCATCGCCAACCCGGCCATCCAGCAGGACCTCCACGCCTCGCTGGCCGATGTGCAGTGGATCACCAACGGCTACCTGCTGGCGCTCGCGGTCTCCCTGATCACCGCCGGCAAACTGGGCGACAGGTTCGGGCACCGGCAGACCTTCCTGGTCGGAGTGGCGGGCTTCGCCGTCACCTCCGCGGCCATCGGCCTGTCCGGCAGCGTCGCGGCGATCGTCGTCTTCCGCGTTCTCCAGGGCCTGTTCGGCGCTCTGATGCAGCCGTCGGCGCTGGGCCTGCTGCGGGTCACGTTCCCGCCCGGCAAGCTCAACATGGCGATCGGCATCTGGAGCGGCGTGGTCGGCGCCTCGACCGCAGCCGGACCGATCATCGGCGGGCTCCTGGTGCAGCACGTCGGCTGGGAGGCGGTCTTCTTCATCAATGTGCCGGTCGGCCTCGCGGCACTCGTCGCCGGCCTCGTCATCCTGACCGACGCGCGCGCCGAACGCGCCCCGAAGTCCTTCGACGTCTCCGGCATCGTGCTCCTGTCCGGGGCCATGTTCTGCCTGGTGTGGGGTCTGATCAAGGCTCCGGCCTGGGGCTGGGGCGACCTGCGGACGCTGGGCTTCCTGGCCGCCGCCGTGCTCGCCTTCGCCGGATTCACACTGCGGGAGAGCAGGGCCACCGAGCCGCTGATGCCGCTCGCCATGTTCCGTTCCGTGCCGCTGTCCGCGGGCACCGTGCTCATGGTCCTGATGGCGTTCTCGTTCATCGGCGGACTCTTCTTCGTCACCTTCTACCTGCAGAACGTCCATGGCATGAGCCCGGTCGAGAGCGGTGTGCACCTGCTGCCGCTCACCGGCATGATGATCGTCGGCGCCCCCGTGTCCGGCATCGTGATCAGCCGGTTCGGACCAGGCGGGCCGCTGGTGGTGGGCATGCTCCTGACGGCGGCGTCCCTGTGGGGGATGTCGACGCTGGAAGCGGACAGCGGTATGGGGATCACCTCGCTCTGGTTCGTGCTGCTGGGTCTCGGTCTCGCGCCGGTGATGGTGGGGACGACGGACGTCATCGTCAGCAACGCCCCGGCCGAACTGGCCGGTGTGGCCGGTGGTCTTCAGCAGTCCGCGATGCAGGTCGGCGGAAGTCTCGGCACCGCCGTACTCGGTGTCCTCATGGCCTCCCGGGTCGGCGACGTCTTCCCCGACAAGTGGGCGGAGGCGAACCTGCCGCGGGTGGGTCCGCGGGAGGCCGCGGCGATCGAGGACGCGGCCGAGGTGGGAGCCGTCCCGCCGGCCGGCACCCTCCCCGGCCGGCACGCCGGGACGCTCTCCGAGGTGGTCCACTCCTCGTTCATCTCGGGGATGGGGCTGGCCTTCACCGTGGCCGGTGCCGTCGCGCTCGTGGCCGCCGCCGTCGCCCTGTTCACCAGGAAGGCCGAGCCCGACGAGAGGGCCCCGGAGGAATTCCCGGTCCCGGCGTCCACGGCAGGGCGGGGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36901","NCBI_taxonomy_name":"Streptomyces glaucescens","NCBI_taxonomy_id":"1907"}}}},"ARO_accession":"3003554","ARO_id":"40157","ARO_name":"tcmA","ARO_description":"Major facilitator superfamily transporter. Resistance to tetracenomycin C by an active tetracenomycin C efflux system which is probably energized by transmembrane electrochemical gradients.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1205":{"model_id":"1205","model_name":"VIM-39","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1807":{"protein_sequence":{"accession":"AGS82586.1","sequence":"MLKVISSLLVYMTASVMAVASPLAHSGEPSGEYPAVNEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEAEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSANVLYGGCAVLELSSTSAGNVADADLAEWPTSVERIQKHYPEAEVVIPGHGLPGGLDLLQHTANVVKAHKNRSVAE"},"dna_sequence":{"accession":"KF131539","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTACATGACCGCGTCTGTCATGGCTGTCGCAAGTCCGTTAGCCCATTCCGGGGAGCCGAGTGGTGAGTATCCGGCAGTCAACGAAATTCCGGTCGGAGAGGTCCGACTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCGGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAAAAGCAAATTGGACTTCCCGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGCAGAGGGGAACGAGATTCCCACGCATTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGCTCTTCTATCCTGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAACGTGCTATACGGTGGTTGTGCCGTTCTTGAGTTGTCAAGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCGTTGAGCGGATTCAAAAACACTACCCGGAAGCAGAGGTCGTCATTCCCGGGCACGGTCTACCGGGCGGTCTAGACTTGCTCCAGCACACAGCGAACGTTGTCAAAGCACACAAAAATCGCTCAGTCGCCGAGTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002309","ARO_id":"38709","ARO_name":"VIM-39","ARO_description":"VIM-39 is a beta-lactamase. From the Lahey list of VIM beta-lactamases.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1206":{"model_id":"1206","model_name":"qepA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"900"}},"model_sequences":{"sequence":{"398":{"protein_sequence":{"accession":"AEZ36150.1","sequence":"MSATLHDTAADRRKATRREWIGLAVVALPCLVYAMDLTVLNLALPVLSRELQPSSAQLLWILDIYGFFVAGFLITMGTLGDRIGRRRLLLIGAAFFAFASVLAALADTAALLIAARALLGLAGATIAPSTMALVRNMFHDPRQRQFAIGVWIAAFSLGSAIGPLVGGVLLEFFHWGAVFWLNVPVMLLTLALGPRFLPEYRDPDAGHLDLASVLLSLAAVLLTIYGLKQLAEHGEGLASMAALLAGLAVGALFLRRQGHIAYPLLDLRLFAHALFRAALAAYALAALAMFGVYIFMTQYLQLVLGLSPLQAGLATLPCSLCFVIGSLLSPQLAARWPAARILVVGLSAAAFGFAVLGLGQGLWWLVPATIVKGLGLAPVFTIGNEIIITSAPSERAGAASALSETVSEFSGALGIALFGSVGLVVYRQALTSAALPGLPADALQTAGASLGGAVHLADTLPAWQGAALLAAARAGFTDALQATAWAGAVLVLVAAGLVARLLRKRPALASG"},"dna_sequence":{"accession":"JQ064560","fmin":"0","fmax":"1536","strand":"+","sequence":"ATGTCCGCCACGCTCCACGACACCGCAGCGGATCGTCGGAAGGCCACCCGCCGCGAATGGATCGGCCTGGCCGTGGTCGCCCTGCCGTGCCTGGTCTACGCCATGGACCTCACGGTGCTGAACCTGGCGCTGCCGGTGCTCAGCCGTGAACTGCAGCCCTCCAGCGCCCAGCTTCTCTGGATCCTGGACATCTACGGCTTCTTCGTCGCCGGCTTCCTGATCACCATGGGCACGCTGGGCGACCGCATCGGCCGGCGCCGGCTGTTGTTGATCGGCGCGGCGTTCTTCGCATTCGCCTCGGTGCTCGCGGCGCTGGCCGATACCGCCGCGCTGTTGATCGCGGCGCGCGCCTTGCTCGGCCTGGCCGGCGCCACCATCGCGCCGTCCACCATGGCGCTGGTCCGCAACATGTTCCACGACCCGCGCCAGCGCCAGTTCGCCATCGGCGTGTGGATCGCCGCGTTTTCGCTGGGCAGCGCGATCGGTCCGCTGGTCGGCGGCGTGTTGCTGGAGTTCTTCCACTGGGGCGCCGTGTTCTGGCTCAACGTGCCGGTGATGCTGCTGACGCTGGCGCTCGGCCCTCGCTTCCTGCCCGAGTATCGTGATCCGGACGCGGGGCACCTGGACCTGGCCAGCGTGCTGCTGTCGCTGGCGGCGGTGCTGCTGACGATCTACGGGCTCAAGCAGTTGGCCGAGCATGGAGAGGGCCTCGCCTCGATGGCTGCGCTGCTGGCCGGGCTGGCGGTCGGGGCGCTGTTCCTGCGCCGCCAGGGCCACATCGCCTACCCGCTGCTGGACCTGCGGCTGTTCGCGCACGCGCTGTTCCGCGCGGCGCTGGCGGCGTATGCGCTGGCCGCGCTGGCCATGTTCGGCGTCTACATCTTCATGACGCAGTACCTGCAGCTCGTGCTGGGGCTGTCGCCGCTGCAGGCCGGGCTGGCCACGCTGCCCTGCTCCCTGTGCTTCGTCATCGGTTCGCTGTTGTCGCCGCAGCTCGCGGCGCGCTGGCCGGCGGCGCGCATCCTCGTCGTGGGCCTGTCGGCAGCGGCGTTCGGCTTCGCCGTGCTGGGGCTGGGGCAGGGCCTGTGGTGGCTGGTGCCGGCCACGATCGTCAAGGGCCTGGGCCTGGCGCCGGTGTTCACCATCGGCAACGAGATCATCATCACCAGCGCGCCGTCCGAGCGCGCGGGCGCGGCCTCGGCCTTGTCGGAGACGGTGTCCGAATTCAGCGGCGCGCTGGGCATCGCGCTGTTCGGCAGCGTCGGCCTGGTGGTCTACCGGCAGGCGCTGACCAGCGCGGCGCTGCCCGGCCTGCCGGCCGATGCGCTGCAGACGGCCGGTGCCTCGCTCGGGGGCGCCGTGCACCTGGCCGACACCCTGCCGGCGTGGCAGGGCGCGGCCTTGCTGGCGGCCGCACGCGCGGGCTTCACCGATGCGCTGCAGGCCACGGCCTGGGCCGGCGCGGTGCTGGTGCTGGTGGCCGCTGGGCTGGTGGCGCGCCTGCTGCGCAAGCGCCCAGCGCTCGCATCTGGTTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36770","NCBI_taxonomy_name":"Enterobacter aerogenes","NCBI_taxonomy_id":"548"}}}},"ARO_accession":"3000448","ARO_id":"36587","ARO_name":"QepA1","ARO_description":"QepA1 is a plasmid-mediated efflux pump in E. coli, shown to contribute to fluoroquinolone resistance. It is regulated by sox genes, also known as global stress regulators.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1207":{"model_id":"1207","model_name":"DHA-13","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"770":{"protein_sequence":{"accession":"AIT76108.1","sequence":"MKKSLSATLISALLAFSAPGFSAADNVAAVVDSTIKPLMAQQDIPGMAVAVSVKGKPYYFNYGFADVQAKQPVTENTLFELGSVSKTFTGVLGAVSVAKKEMALNDPAAKYQPELALPQWKGITLLDLATYTAGGLPLQVPDAVKSRADLLNFYQQWQPSWKPGDMRLYANSSIGLFGALTANAAGMPYEQLLTARILAPLGLSHTFITVPESAQSQYAYGYKNKKPVRVSPGQLDAESYGVKSASKDMLRWAEMNMEPSRAGNADLEMAMYLAQTRYYKTAAINQGLGWEMYDWPQQKDMIINGVTNEVALQPHPVTDNQVQPYNRASWVHKTGATTGFGAYVAFIPEKQVAIVILANKNYPNTERVKAAQAILSALE"},"dna_sequence":{"accession":"KM087855","fmin":"0","fmax":"1140","strand":"+","sequence":"ATGAAAAAATCGTTATCTGCAACACTGATTTCCGCTCTGCTGGCGTTTTCCGCCCCGGGGTTTTCTGCCGCTGATAATGTCGCGGCGGTGGTGGACAGCACCATTAAACCGCTGATGGCACAGCAGGATATTCCCGGGATGGCGGTTGCCGTCTCCGTAAAGGGTAAGCCCTATTATTTCAATTACGGTTTTGCCGATGTTCAGGCAAAACAGCCTGTCACTGAAAATACACTATTTGAGCTCGGATCTGTAAGTAAAACTTTCACAGGTGTGCTGGGTGCGGTTTCCGTGGCGAAAAAAGAGATGGCGCTGAATGATCCGGCGGCAAAATATCAGCCGGAGCTGGCTCTGCCGCAGTGGAAGGGGATCACGCTGCTGGATCTGGCCACCTATACCGCAGGCGGGCTGCCGTTACAGGTACCGGATGCGGTGAAAAGCCGTGCGGATCTGCTGAATTTCTATCAGCAGTGGCAGCCATCATGGAAACCGGGCGATATGCGTCTGTATGCAAACAGCAGTATCGGCCTGTTTGGTGCTCTGACCGCCAACGCGGCGGGGATGCCGTATGAGCAGTTGCTGACTGCACGGATCCTGGCACCGCTGGGGTTATCTCACACCTTTATTACTGTGCCGGAAAGTGCGCAAAGCCAGTATGCGTACGGTTATAAAAACAAAAAACCGGTCCGCGTGTCGCCGGGACAGCTTGATGCGGAATCTTACGGCGTGAAATCCGCCTCAAAAGATATGCTGCGCTGGGCGGAAATGAATATGGAGCCGTCACGGGCCGGTAATGCGGATCTGGAAATGGCAATGTATCTTGCACAGACCCGCTACTATAAAACCGCCGCGATTAACCAGGGGCTGGGCTGGGAAATGTATGACTGGCCGCAGCAGAAAGATATGATCATTAACGGCGTGACCAACGAGGTCGCATTGCAGCCGCACCCGGTAACAGACAACCAGGTTCAGCCGTATAACCGTGCTTCCTGGGTGCATAAAACGGGGGCAACAACTGGTTTCGGCGCCTATGTGGCCTTTATTCCGGAAAAACAGGTGGCGATTGTGATTCTGGCGAATAAAAACTACCCGAATACCGAAAGAGTCAAAGCCGCACAGGCTATTTTGAGTGCACTGGAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36917","NCBI_taxonomy_name":"Morganella morganii","NCBI_taxonomy_id":"582"}}}},"ARO_accession":"3002144","ARO_id":"38544","ARO_name":"DHA-13","ARO_description":"DHA-13 is a beta-lactamase. From the Lahey list of DHA beta-lactamases.","ARO_category":{"36207":{"category_aro_accession":"3000068","category_aro_cvterm_id":"36207","category_aro_name":"DHA beta-lactamase","category_aro_description":"DHA beta-lactamases are plasmid-mediated AmpC \u03b2-lactamases that confer resistance to cephamycins and oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1208":{"model_id":"1208","model_name":"SHV-173","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1390":{"protein_sequence":{"accession":"AHA80959.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDQASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"KF513178","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCAGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001357","ARO_id":"37757","ARO_name":"SHV-173","ARO_description":"From the Lahey list of beta-lactamases.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1209":{"model_id":"1209","model_name":"QnrB45","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"635":{"protein_sequence":{"accession":"AFA52644.1","sequence":"MTPLLYKKTGTNMALALVGEKIDRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRTMLKDAIFKSCDLSMADFRNASALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"JQ349152","fmin":"0","fmax":"680","strand":"+","sequence":"ATGACGCCATTACTGTATAAAAAAACAGGTACAAATATGGCTCTGGCACTCGTTGGCGAAAAAATTGACAGAAACCGCTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTACGATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATGCCAGTGCGCTTGGCATTGAAATTCGCCACTGTCGTGCGCAAGGCGCAGATTTCCGCGGCGCAAGCTTTATGAATATGATCACTACTCGCACCTGGTTTTGTAGTGCATATATCACTAACACAAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGCTGGAAAAGTGTGAGCTGTGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTGACTTAGATATTCGGGGCGTTGATTTACAAGGCGTTAAGTTGGACAACTACCAGGCATCGTTGCTCATGGAACGTCTTGGCATCGCGGTGATTGGTTA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002760","ARO_id":"39194","ARO_name":"QnrB45","ARO_description":"QnrB45 is a plasmid-mediated quinolone resistance protein found in Escherichia coli","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1210":{"model_id":"1210","model_name":"novA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1190"}},"model_sequences":{"sequence":{"344":{"protein_sequence":{"accession":"AAF67494.2","sequence":"MKSALSTWKPSDRPPDPTLPEPPAQLRRIFRLFRPYRGRLAVVGLLVGASSLVAVASPFMLREILDTAIPQGRTGLLSLLALGMILTAVLSSVFGVVQTLISTTVGQRVMHDLRTAVYAQLQRMPLAFFTRTRTGEVQSRIANDIGGMQATVTSTATSLVSNLTAVIATVVAMLALDWRLTVVSLLLLPVFVWISRRVGRERKRITLQRQKQMATMAATVTESLSVSGILLGRTMGRADSLTRSFAEESERLVDLEVRSNMAGRWRMSVIGIVMAAMPAVIYWAAGFVLQSGGTVVSIGTLVAFVSLQQGLFRPAVSLLATGVQMQTSLALFQRIFEYLDLPVDITEPERPVALDKVRGEVRFDGVDFSYEEKDGNTLHGLDLTVPAGGSLAVVGPTGSGKSTLSYLVPRLYDVTGGRVLLDGVDVRDLAFDTLARAVGVVSQETYLFHASVADNLRFAKPDATDEEIEKAARAAQIHEHIVTLPDGYDTLVGERGYRFSGGEKQRLAIARTILRDPPVLVLDEATSALDTRTEHAVQQAIDSLSEGRTTITIAHRLSTVRDADQIVVLDAGRIAERGTHEELIDRDGRYAALVRRDGAPAPAPVPARDERVGAA"},"dna_sequence":{"accession":"AF170880","fmin":"0","fmax":"1848","strand":"+","sequence":"ATGAAGTCCGCACTCTCGACCTGGAAGCCCTCGGACCGGCCGCCGGATCCGACACTGCCCGAGCCGCCGGCCCAGCTGCGCCGCATCTTCCGGCTCTTCCGCCCGTACCGCGGCAGGCTCGCCGTCGTCGGCCTGCTCGTCGGCGCCTCGTCGCTGGTGGCCGTCGCCTCGCCGTTCATGCTGCGCGAGATCCTCGACACCGCGATCCCGCAGGGCCGCACCGGGCTGCTCAGCCTGCTCGCCCTCGGCATGATCCTGACCGCCGTCCTCAGCAGCGTCTTCGGCGTCGTCCAGACCCTCATCTCCACGACGGTCGGCCAGCGCGTCATGCACGACCTGCGCACCGCCGTCTACGCGCAGCTCCAGCGCATGCCCCTCGCGTTCTTCACCCGCACCCGCACCGGTGAGGTCCAGTCCCGGATAGCCAACGACATCGGCGGCATGCAGGCGACCGTCACCTCAACCGCCACGTCGCTGGTCTCCAACCTCACCGCCGTCATCGCCACCGTCGTCGCGATGCTCGCGCTGGACTGGCGGCTGACCGTCGTCTCGCTGCTCCTGCTGCCGGTGTTCGTCTGGATCAGCCGCCGCGTCGGCCGTGAGCGCAAACGGATCACCCTGCAACGGCAGAAGCAGATGGCCACGATGGCCGCCACGGTCACGGAGTCGCTGTCGGTCAGCGGCATCCTCCTCGGCCGCACGATGGGGCGCGCCGACTCGCTCACCAGATCCTTCGCCGAGGAGTCCGAGCGACTCGTCGACCTGGAGGTCCGCTCCAACATGGCCGGGCGGTGGCGGATGTCCGTCATCGGCATCGTCATGGCCGCCATGCCCGCCGTCATCTACTGGGCGGCCGGCTTCGTCCTCCAGTCCGGCGGCACGGTCGTCTCCATCGGCACACTCGTCGCCTTCGTCTCCCTCCAGCAGGGCCTCTTCCGCCCGGCCGTGAGCCTGCTCGCCACCGGCGTGCAGATGCAGACGTCCCTCGCGCTCTTCCAGCGCATCTTCGAATATCTCGACCTGCCCGTCGACATCACCGAACCCGAGCGTCCGGTGGCCCTCGACAAGGTCCGGGGCGAAGTGCGCTTCGACGGCGTCGACTTCAGTTACGAGGAGAAGGACGGCAACACCCTCCACGGCCTGGATCTGACCGTCCCGGCCGGCGGCAGCCTCGCCGTCGTCGGTCCCACCGGATCGGGCAAGTCGACCCTGAGCTATCTCGTGCCGCGTCTGTACGACGTGACGGGCGGCCGGGTCCTGCTCGACGGCGTCGACGTACGCGACCTGGCCTTCGACACCCTCGCCCGCGCGGTGGGCGTCGTGTCGCAGGAGACGTATCTCTTCCACGCCTCCGTCGCCGACAACCTCCGCTTCGCCAAACCGGACGCGACGGACGAGGAGATCGAGAAGGCGGCCAGGGCCGCCCAGATCCACGAGCACATCGTCACCCTGCCCGACGGGTACGACACACTGGTCGGCGAGCGCGGATACCGGTTCTCCGGCGGCGAGAAACAGCGCCTCGCGATCGCCCGCACCATCCTGCGCGACCCGCCCGTCCTCGTGCTGGACGAGGCGACGAGCGCGCTCGACACCCGTACCGAACACGCGGTCCAGCAGGCCATCGACTCCCTCTCCGAGGGCCGTACGACCATCACCATCGCCCACCGGCTCTCCACGGTGCGCGACGCCGACCAGATCGTCGTCCTCGACGCCGGTCGCATAGCCGAGCGCGGCACGCACGAGGAGCTGATCGACCGGGACGGCAGGTACGCGGCGCTCGTCCGCCGGGACGGCGCGCCGGCGCCCGCGCCCGTGCCCGCCCGGGACGAGCGCGTGGGCGCCGCCTGAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39503","NCBI_taxonomy_name":"Streptomyces niveus","NCBI_taxonomy_id":"193462"}}}},"ARO_accession":"3002522","ARO_id":"38922","ARO_name":"novA","ARO_description":"A type III ABC transporter, identified on the novobiocin biosynthetic gene cluster, involved in the transport and resistance of novobiocin.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1211":{"model_id":"1211","model_name":"VIM-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1962":{"protein_sequence":{"accession":"AAN63496.1","sequence":"MLKVISSLLVYMTASVMAVASPLAHSGEPSGEYPTVNEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEAEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSANVLYGGCAVHELSSTSAGNVADADLAEWPTSVERIQKHYPEAEVVIPGHGLPGGLDLLQHTANVVKAHKNRSVAE"},"dna_sequence":{"accession":"AF317511","fmin":"187","fmax":"988","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTACATGACCGCGTCTGTCATGGCTGTCGCAAGTCCGTTAGCCCATTCCGGGGAGCCGAGTGGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGAGAGGTCCGACTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCGGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAAAAGCAAATTGGACTTCCCGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGCAGAGGGGAACGAGATTCCCACGCATTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGCTCTTCTATCCTGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAACGTGCTATACGGTGGTTGTGCCGTTCATGAGTTGTCAAGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCGTTGAGCGGATTCAAAAACACTACCCGGAAGCAGAGGTCGTCATTCCCGGGCACGGTCTACCGGGCGGTCTAGACTTGCTCCAGCACACAGCGAACGTTGTCAAAGCACACAAAAATCGCTCAGTCGCCGAGTAGC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002271","ARO_id":"38671","ARO_name":"VIM-1","ARO_description":"VIM-1 is a beta-lactamase found in Pseudomonas spp.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1212":{"model_id":"1212","model_name":"OXA-141","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1124":{"protein_sequence":{"accession":"ABQ15112.1","sequence":"MAIRIFAILFSIFSLATFAHAQEGTLERSDWRKFFSEFQAKGTIVVADERQADRAMLVFDPVRSKKRYSPASTFKIPHTLFALDAGAVRDEFQIFRWDGVNRGFAGHNQDQDLRSAMRNSTVWVYELFAKEIGDDKARRYLKKIDYGNADPSTSNGDYWIESSLAISAQEQIAFLRKLYRNELPFRVEHQRLVKDLMIVEAGRNWILRAKTGWEGRMGWWVGWVEWPTGSVFFALNIDTPNRMDDLFKREAIVRAILRSIEALPPNPAVNSDAAR"},"dna_sequence":{"accession":"EF552405","fmin":"12","fmax":"840","strand":"+","sequence":"ATGGCAATCCGAATCTTCGCGATACTTTTCTCCATTTTTTCTCTTGCCACTTTCGCGCATGCGCAAGAAGGCACGCTAGAACGTTCTGACTGGAGGAAGTTTTTCAGCGAATTTCAAGCCAAAGGCACGATAGTTGTGGCAGACGAACGCCAAGCGGATCGTGCCATGTTGGTTTTTGATCCTGTGCGATCGAAGAAACGCTACTCGCCTGCATCGACATTCAAGATACCTCATACACTTTTTGCACTTGATGCAGGCGCTGTTCGTGATGAGTTCCAGATTTTTCGATGGGACGGCGTTAACAGGGGCTTTGCAGGCCACAATCAAGACCAAGATTTGCGATCAGCAATGCGGAATTCTACTGTTTGGGTGTATGAGCTATTTGCAAAGGAAATTGGTGATGACAAAGCTCGGCGCTATTTGAAGAAAATCGACTATGGCAACGCCGATCCTTCGACAAGTAATGGCGATTACTGGATAGAAAGCAGCCTTGCAATCTCGGCGCAGGAGCAAATTGCATTTCTCAGGAAGCTCTATCGTAACGAGCTGCCCTTTCGGGTAGAACATCAGCGCTTGGTCAAGGATCTCATGATTGTGGAAGCCGGTCGCAACTGGATACTGCGTGCAAAGACGGGCTGGGAAGGCCGTATGGGTTGGTGGGTAGGATGGGTTGAGTGGCCGACTGGCTCCGTATTCTTCGCACTGAATATTGATACGCCAAACAGAATGGATGATCTTTTCAAGAGGGAGGCAATCGTGCGGGCAATCCTTCGCTCTATTGAAGCGTTACCGCCCAACCCGGCAGTCAACTCGGACGCTGCGCGATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001802","ARO_id":"38202","ARO_name":"OXA-141","ARO_description":"OXA-141 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1214":{"model_id":"1214","model_name":"TEM-134","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"925":{"protein_sequence":{"accession":"AAS79107.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDHWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AY574271","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCATTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36934","NCBI_taxonomy_name":"Citrobacter koseri","NCBI_taxonomy_id":"545"}}}},"ARO_accession":"3000998","ARO_id":"37378","ARO_name":"TEM-134","ARO_description":"TEM-134 is an extended-spectrum beta-lactamase found in Citrobacter koseri.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1215":{"model_id":"1215","model_name":"FosC","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"481":{"protein_sequence":{"accession":"CAA83855.1","sequence":"MMTSIMFSMLSDITRIFVEQGLRVYPFQSSALLGVDEEGRVTLHARQLATAMASGYMPLLTGDLLLRGEQEAQVFSSDNIAPLLAADFEVRRVLYYSDVAGVYDQGNALVPWVGNANAACMEACVGASSMTDLTGGMRNKFMQQRQLARLGVVSEVLSFECFDRVHLSLCGLRQFGTVFLSE"},"dna_sequence":{"accession":"Z33413","fmin":"386","fmax":"935","strand":"+","sequence":"ATGATGACATCGATCATGTTTTCGATGTTGTCGGACATCACGCGGATTTTTGTCGAGCAGGGGCTACGGGTCTATCCCTTTCAAAGCAGTGCCTTGCTGGGCGTCGATGAAGAGGGGCGTGTCACGCTTCATGCGCGCCAGCTGGCAACGGCCATGGCATCGGGTTACATGCCCTTGCTCACTGGGGATCTGCTGCTGCGCGGCGAGCAGGAGGCGCAGGTCTTTTCAAGTGACAATATCGCCCCGTTGCTCGCTGCGGACTTCGAAGTGCGTCGGGTCTTGTATTACTCCGATGTGGCCGGTGTCTACGACCAGGGCAATGCCTTGGTCCCTTGGGTTGGCAATGCCAACGCCGCGTGCATGGAGGCTTGTGTGGGGGCGTCGTCGATGACGGACCTGACCGGTGGCATGCGCAACAAGTTCATGCAGCAGCGCCAGTTGGCACGCCTGGGCGTGGTTTCGGAGGTCTTGTCATTCGAGTGCTTCGACAGGGTGCATCTGTCGTTGTGCGGGTTGCGTCAATTTGGAACCGTGTTCTTGAGCGAGTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37078","NCBI_taxonomy_name":"Pseudomonas syringae","NCBI_taxonomy_id":"317"}}}},"ARO_accession":"3000380","ARO_id":"36519","ARO_name":"FosC","ARO_description":"FosC is an enzyme that phosphorylates fosfomycin to confer resistance","ARO_category":{"41409":{"category_aro_accession":"3004245","category_aro_cvterm_id":"41409","category_aro_name":"fosC phosphotransferase family","category_aro_description":"The fosC family of phosphotransferases phosphorylate fosfomycin to confer resistance and have been found in various bacterial isolates.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1216":{"model_id":"1216","model_name":"SHV-119","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1387":{"protein_sequence":{"accession":"AIG51284.1","sequence":"MRHIRLCIISLLATLPLAVQASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"KJ776406","fmin":"16","fmax":"877","strand":"+","sequence":"ATGCGTCATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACAAGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTTACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001340","ARO_id":"37740","ARO_name":"SHV-119","ARO_description":"From the Lahey list of beta-lactamases. Not yet released.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1217":{"model_id":"1217","model_name":"OXA-139","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"966":{"protein_sequence":{"accession":"CAQ51348.1","sequence":"MKKFILPIFSISILVSLSACSSIKTKSEDNFHISSQQHEKAIKSYFDEAQTQGVIIIKEGKNLSTYGNALARANKEYVPASTFKMLIALIGLENHKATTNEIFKWDGKKRTYPMWEKDMTLGEAMALSAVPVYQELARRTGLELMQKEVKRVNFGNTNIGTQVDNFWLVGPLKITPVQEVNFADDLAHNRLPFKLETQEEVKKMLLIKEVNGSKIYAKSGWGMGVTPQVGWLTGWVEQANGKKIPFSLNLEMKEGMSGSIRNEITYKSLENLGII"},"dna_sequence":{"accession":"AM991978","fmin":"0","fmax":"828","strand":"+","sequence":"ATGAAAAAATTTATACTTCCTATATTCAGCATTTCTATTCTAGTTTCTCTCAGTGCATGTTCATCTATTAAAACTAAATCTGAAGATAATTTTCATATTTCTTCTCAGCAACATGAAAAAGCTATTAAAAGCTATTTTGATGAAGCTCAAACACAGGGTGTAATTATTATTAAAGAGGGTAAAAATCTTAGCACCTATGGTAATGCTCTTGCACGAGCAAATAAAGAATATGTCCCTGCATCAACATTTAAGATGCTAATTGCTTTAATCGGGCTAGAAAATCATAAAGCAACAACAAATGAGATTTTCAAATGGGATGGTAAAAAAAGAACTTATCCTATGTGGGAGAAAGATATGACTTTAGGTGAGGCAATGGCATTGTCAGCAGTTCCAGTATATCAAGAGCTTGCAAGACGGACTGGCCTAGAGCTAATGCAGAAAGAAGTAAAGCGGGTTAATTTTGGAAATACAAATATTGGAACACAGGTCGATAATTTTTGGTTAGTTGGCCCCCTTAAAATTACACCAGTACAAGAAGTTAATTTTGCCGATGACCTTGCACATAACCGATTACCTTTTAAATTAGAAACTCAAGAAGAAGTTAAAAAAATGCTTCTAATTAAAGAAGTAAATGGTAGTAAGATTTATGCAAAAAGTGGATGGGGAATGGGTGTTACTCCACAGGTAGGTTGGTTGACTGGTTGGGTGGAGCAAGCTAATGGAAAAAAAATCCCCTTTTCGCTCAACTTAGAAATGAAAGAAGGAATGTCTGGTTCTATTCGTAATGAAATTACTTATAAGTCGCTAGAAAATCTTGGAATCATTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001451","ARO_id":"37851","ARO_name":"OXA-139","ARO_description":"OXA-139 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1218":{"model_id":"1218","model_name":"TEM-219","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1649":{"protein_sequence":{"accession":"AIS39742.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVFIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"KM114268","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTATTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3003157","ARO_id":"39734","ARO_name":"TEM-219","ARO_description":"From the Lahey list of beta-lactamases.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1219":{"model_id":"1219","model_name":"vanRN","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"379":{"protein_sequence":{"accession":"AEP40503.1","sequence":"MDTIVIVDDEKEIANLMTTFLENEGFKVMTFYSGKEALDYIDQNGASLAILDVMLPDLDGFQILQHIRQTFFFPVLMLTAKGENLDKITGLTLGADDYITKPFNPLEVVARVKTQLRRTQRYDQPSHSQSDEEFTKEGLVLKKNSHQVFLFDQEVLITPLEFKILLYLFEHQGTVVSSETLFEEVWQEKYLDNNNTVMAHIARLREKLGEKPRKPKYIKTVWGVGYIIEK"},"dna_sequence":{"accession":"JF802084","fmin":"4337","fmax":"5030","strand":"+","sequence":"ATGGATACAATTGTAATCGTTGATGATGAGAAAGAAATTGCCAATTTAATGACGACCTTTCTAGAAAATGAAGGATTCAAGGTCATGACCTTTTATAGCGGAAAGGAAGCACTGGATTATATTGATCAAAACGGTGCTTCCTTGGCCATTTTGGATGTGATGTTACCTGATTTAGATGGCTTCCAAATATTACAACACATCCGTCAAACATTCTTTTTCCCCGTATTGATGTTGACCGCAAAAGGAGAAAACTTAGATAAAATCACCGGACTGACTCTAGGCGCAGATGACTACATTACGAAACCTTTCAACCCGCTGGAAGTCGTGGCGCGAGTAAAAACACAACTGCGACGTACTCAGCGTTACGATCAGCCTTCCCATAGTCAATCGGATGAAGAATTTACAAAGGAAGGTTTGGTACTGAAAAAAAACAGCCACCAAGTTTTCTTATTTGATCAAGAAGTGTTGATTACACCCTTGGAGTTTAAGATCCTGCTCTACCTATTTGAGCATCAAGGGACAGTAGTCTCTTCTGAAACATTATTTGAAGAAGTTTGGCAAGAAAAATATTTAGACAATAATAATACAGTAATGGCACATATTGCTCGTTTAAGAGAAAAATTAGGCGAAAAACCAAGAAAACCAAAATATATTAAAACAGTTTGGGGGGTAGGCTATATCATTGAAAAATAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002929","ARO_id":"39363","ARO_name":"vanRN","ARO_description":"vanRN is a vanR variant found in the vanN gene cluster","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36713":{"category_aro_accession":"3000574","category_aro_cvterm_id":"36713","category_aro_name":"vanR","category_aro_description":"VanR is a OmpR-family transcriptional activator in the VanSR regulatory system. When activated by VanS, it promotes cotranscription of VanA, VanH, and VanX.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1220":{"model_id":"1220","model_name":"OCH-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1734":{"protein_sequence":{"accession":"CAC17625.1","sequence":"MRKSTTLLIGFLTTAAIIPNNGALAASKANDGDLRRIVDETVRPLMAEQKIPGMAVAITIDGKSHFFGYGVASKESGQKVTEDTIFEIGSVSKTFTAMLGGYGLATGAFSLSDPATKWAPELAGSSFDKITMLDLGTYTPGGLPLQFPDAVTDDSSMLAYFKKWRPDYPAGTQHRYSNPSIGLFGYLAARSMDKPFDVLMEQKLLPAFGLKNTFINVPESQMKNYAYGYSKANKPIRVSGGTLDAQAYGIKTTALDLARFVELNIDSSSLEPDFQKAVAATHTGYYHVDANNQGLGWEFYNYPTALKTLLAGNSSDMALKSHKIEKFDTPRQPSADVLINKTGSTNGFGAYAAFIPAKKIGIVVLANRNYPIDERVKAAYRILQALDNKQ"},"dna_sequence":{"accession":"AJ295343","fmin":"0","fmax":"1173","strand":"+","sequence":"ATGAGAAAATCTACGACACTTTTGATCGGTTTCCTCACCACTGCCGCTATTATCCCGAATAACGGCGCGCTGGCTGCGAGCAAGGCGAATGATGGCGACTTGCGCCGTATTGTCGATGAAACGGTGCGCCCGCTCATGGCCGAGCAGAAAATCCCCGGCATGGCGGTTGCCATAACCATCGACGGCAAGAGCCACTTCTTCGGTTATGGTGTGGCATCGAAGGAAAGCGGGCAAAAAGTCACTGAAGACACGATTTTCGAGATCGGCTCGGTCAGCAAGACCTTCACTGCAATGCTTGGCGGCTACGGGCTGGCGACGGGCGCGTTCTCCCTGTCCGATCCCGCGACCAAATGGGCTCCTGAACTGGCAGGCAGCAGCTTCGACAAGATCACCATGCTTGATCTTGGGACCTACACGCCGGGCGGATTGCCCCTCCAGTTTCCCGATGCTGTCACCGATGACAGTTCGATGCTGGCATATTTCAAGAAATGGAGGCCGGACTATCCGGCAGGCACGCAGCATCGCTATTCGAATCCCAGCATCGGCCTGTTCGGCTATCTGGCGGCACGAAGCATGGACAAGCCGTTCGACGTTTTGATGGAGCAAAAGCTTCTGCCTGCATTCGGCCTGAAGAACACCTTCATCAATGTGCCGGAAAGCCAGATGAAGAACTACGCCTACGGCTATTCCAAAGCCAACAAGCCGATCCGGGTATCGGGCGGGACGCTGGATGCACAAGCCTATGGCATCAAGACCACCGCGCTTGATCTTGCCCGCTTCGTCGAACTGAACATTGACAGCTCATCTCTGGAGCCTGATTTCCAGAAAGCCGTCGCCGCAACACACACGGGTTACTACCATGTCGATGCGAACAATCAGGGACTTGGCTGGGAGTTCTACAACTATCCGACTGCGCTCAAGACACTTCTTGCCGGCAATTCGTCGGACATGGCGCTGAAGTCGCACAAAATCGAGAAATTCGATACACCTCGCCAACCGTCAGCTGATGTGCTGATCAATAAGACAGGCTCAACCAACGGCTTTGGCGCTTATGCGGCCTTTATTCCTGCGAAGAAGATCGGAATTGTTGTGCTTGCCAACCGGAATTATCCGATCGATGAGCGCGTAAAGGCTGCCTATCGGATATTGCAGGCGCTCGACAACAAGCAATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37077","NCBI_taxonomy_name":"Ochrobactrum anthropi","NCBI_taxonomy_id":"529"}}}},"ARO_accession":"3002518","ARO_id":"38918","ARO_name":"OCH-5","ARO_description":"OCH-5 beta-lactamase is an Ambler class C chromosomal-encoded beta-lactamases in Ochrobactrum anthropi","ARO_category":{"36233":{"category_aro_accession":"3000094","category_aro_cvterm_id":"36233","category_aro_name":"OCH beta-lactamase","category_aro_description":"OCH beta-lactamases are Ambler class C chromosomal-encoded beta-lactamases in Ochrobactrum anthropi","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1221":{"model_id":"1221","model_name":"OXA-231","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1049":{"protein_sequence":{"accession":"AFG29918.1","sequence":"MKKFILPILSISTLLSVSACSSIQTKFEDTFHTSNQQHEKAIKSYFDEAQTQGVIIIKKGKNISTYGNNLTRAHTEYVPASTFKMLNALIGLENHKATTTEIFKWDGKKRSYPMWEKDMTLGDAMALSAVPVYQELARRTGLDLMQKEVKRVGFGNMNIGTQVDNFWLVGPLKITPIQEVNFADDFANNRLPFKLETQEEVKKMLLIKEFNGSKIYAKSGWGMAVTPQVGWLTGWVEKSNGEKVAFSLNIEMKQGMPGSIRNEITYKSLENLGII"},"dna_sequence":{"accession":"JQ326200","fmin":"193","fmax":"1021","strand":"+","sequence":"ATGAAAAAATTTATACTTCCTATTCTCAGCATTTCTACTCTACTTTCTGTCAGTGCATGCTCATCTATTCAAACTAAATTTGAAGACACTTTTCATACTTCTAATCAGCAACATGAAAAAGCCATTAAAAGCTATTTTGATGAAGCTCAAACACAGGGTGTAATCATTATTAAAAAGGGAAAAAATATTAGTACCTATGGTAATAACCTGACACGAGCACATACAGAATATGTCCCTGCATCAACATTTAAGATGCTAAATGCCTTAATTGGACTAGAAAATCATAAAGCTACAACAACTGAGATTTTCAAATGGGACGGTAAAAAGAGATCTTATCCCATGTGGGAAAAAGATATGACTTTAGGTGATGCCATGGCACTTTCAGCAGTTCCTGTATATCAAGAACTTGCAAGACGGACTGGCTTAGACCTAATGCAAAAAGAAGTTAAACGGGTTGGTTTTGGTAATATGAACATTGGAACACAAGTTGATAACTTCTGGTTGGTTGGCCCCCTCAAGATTACACCAATACAAGAGGTTAATTTTGCCGATGATTTTGCAAATAATCGATTACCCTTTAAATTAGAGACTCAAGAAGAAGTTAAAAAAATGCTTCTGATTAAAGAATTCAATGGTAGTAAAATTTATGCAAAAAGCGGCTGGGGAATGGCTGTAACCCCTCAAGTAGGTTGGTTAACAGGTTGGGTAGAAAAATCTAATGGAGAAAAAGTTGCCTTTTCTCTAAACATAGAAATGAAGCAAGGAATGCCTGGTTCTATTCGTAATGAAATTACTTATAAATCATTAGAGAATTTAGGGATTATATAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001670","ARO_id":"38070","ARO_name":"OXA-231","ARO_description":"OXA-231 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1223":{"model_id":"1223","model_name":"viomycin phosphotransferase","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"62":{"protein_sequence":{"accession":"CAA26235.1","sequence":"MRIIETHRDLLSRLLPGDTVGGLAVHEGQFHHVVIGSHRVVCFARTRAAADRLPGRADVLRALAGIDLGFRTPQPLSEGGAQGTDEPPYLVLSRIPGAPLEDDVLTSPEVAEAVARQYATLLSGLAAAGDEEKVRAALPEAPANEWQEFATGVRTELFPLMSDGGRERAERELAALDALPHLTSAVVHGDLGGENVLWETVDGVPRMSGVVDWDEVGIGDPAEDLAAIGASYGEELLGRVLALGGWADNGTAERISAIRGTFALQQALYAQRDGDEEELADGLSGYR"},"dna_sequence":{"accession":"X02393","fmin":"96","fmax":"960","strand":"+","sequence":"ATGAGAATCATTGAGACGCACCGCGATCTGCTGAGCCGGCTCCTGCCCGGGGACACCGTGGGCGGACTCGCCGTCCACGAGGGGCAGTTCCACCATGTGGTGATCGGATCGCACCGGGTGGTCTGCTTCGCCCGCACCCGGGCGGCCGCCGACCGTCTGCCCGGCAGGGCGGACGTCCTGCGCGCTCTTGCCGGGATCGACCTCGGGTTTCGCACGCCGCAGCCGCTGTCCGAGGGCGGCGCCCAGGGCACGGACGAGCCGCCGTACCTGGTGCTGAGCCGCATTCCCGGAGCACCGTTGGAGGACGATGTGCTCACCAGCCCGGAGGTGGCGGAGGCCGTCGCCCGACAGTACGCGACCCTGCTGTCCGGGCTCGCGGCGGCGGGCGACGAGGAGAAGGTGCGCGCCGCGCTGCCGGAGGCTCCCGCGAACGAGTGGCAGGAGTTCGCCACGGGGGTGCGTACCGAACTGTTCCCGCTGATGTCCGACGGCGGCCGGGAGCGTGCCGAGCGCGAGCTCGCCGCGCTCGACGCCCTGCCCCATCTCACCTCCGCGGTGGTCCACGGTGACCTCGGCGGCGAGAACGTCCTGTGGGAGACGGTGGACGGAGTGCCGCGCATGAGCGGCGTCGTCGACTGGGACGAGGTCGGCATCGGCGACCCGGCTGAGGACCTGGCCGCCATCGGGGCGAGCTACGGCGAGGAACTGCTGGGCCGAGTGCTCGCGCTCGGCGGCTGGGCCGACAACGGAACGGCCGAGCGGATCTCGGCGATCCGAGGCACCTTCGCACTCCAGCAGGCCCTCTACGCGCAGCGCGACGGCGACGAGGAGGAACTCGCCGACGGCCTCAGCGGCTACCGGTAGG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39588","NCBI_taxonomy_name":"Streptomyces vinaceus","NCBI_taxonomy_id":"1960"}}}},"ARO_accession":"3003061","ARO_id":"39495","ARO_name":"vph","ARO_description":"vph is a phosphotransferase that confers resistance to viomycin in Streptomyces vinaceus","ARO_category":{"41425":{"category_aro_accession":"3004261","category_aro_cvterm_id":"41425","category_aro_name":"viomycin phosphotransferase","category_aro_description":"Viomycin family of phosphotransferases confer resistance to viomycin antibiotics.","category_aro_class_name":"AMR Gene Family"},"35937":{"category_aro_accession":"0000018","category_aro_cvterm_id":"35937","category_aro_name":"viomycin","category_aro_description":"Viomycin sulfate (Viocin) is an polypeptide antibiotic used in the treatment of tuberculosis. It is produced by the actinomycete Streptomyces puniceus and binds to the bacterial ribosome, inhibiting prokaryotic protein synthesis and certain forms of RNA splicing.","category_aro_class_name":"Antibiotic"},"36629":{"category_aro_accession":"3000490","category_aro_cvterm_id":"36629","category_aro_name":"tuberactinomycin","category_aro_description":"Tuberactinomycins are a family of cyclic peptide antibiotics that are important in the treatment of tuberculosis. Tuberactinomycins contain nonproteinogenic amino acids and inhibit group I self-splicing RNA to disrupt prokaryotic protein synthesis.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1224":{"model_id":"1224","model_name":"Erm(30)","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"4386":{"protein_sequence":{"accession":"AAC69328.1","sequence":"MAMRDSIPRRADRDTLRRELGQNFLQDDRAVRNLVTHVEGDGRNVLEIGPGKGAITEELVRSFDTVTVVEMDPHWAAHVRRKFEGERVTVFQGDFLDFRIPRDIDTVVGNVPFGITTQILRSLLESTNWQSAALIVQWEVARKRAGRSGGSLLTTSWAPWYEFAVHDRVRASSFRPMPRVDGGVLTIRRRPQPLLPESASRAFQNFAEAVFTGPGRGLAEILRRHIPKRTYRSLADRHGIPDGGLPKDLTLTQWIALFQASQPSYAPGAPGTRMPGQGGGAGGRDYDSETSRAAVPGSRRYGPTRGGEPCAPRAQVRQTKGRQGARGSSYGRRTGR"},"dna_sequence":{"accession":"AF079138","fmin":"1282","fmax":"2293","strand":"-","sequence":"CTAACGGCCCGTGCGGCGTCCGTACGACGAGCCTCGCGCGCCCTGGCGGCCCTTGGTCTGCCGGACCTGTGCGCGGGGTGCGCAGGGTTCGCCGCCGCGCGTGGGGCCGTATCTGCGGCTCCCGGGCACGGCGGCCCTGCTCGTCTCCGAGTCATAGTCCCTGCCGCCGGCGCCACCGCCCTGGCCCGGCATGCGCGTGCCGGGCGCCCCCGGCGCGTAACTCGGCTGGGAGGCCTGGAAAAGGGCGATCCATTGGGTGAGCGTGAGGTCCTTCGGCAGTCCGCCGTCCGGAATTCCGTGGCGGTCGGCGAGGGAACGGTAGGTCCGCTTGGGGATGTGGCGCCGGAGGATCTCCGCGAGGCCCCGTCCGGGGCCGGTGAAGACGGCTTCGGCGAAGTTCTGGAAGGCGCGGCTCGCGCTCTCGGGCAGCAGGGGCTGGGGGCGTCGCCTGATCGTCAGGACGCCGCCGTCGACGCGGGGCATCGGACGGAACGACGAGGCGCGGACGCGGTCGTGGACCGCGAACTCGTACCAGGGGGCCCAGGAGGTCGTGAGGAGCGATCCGCCGCTGCGACCGGCGCGTTTGCGGGCGACCTCCCACTGCACTATCAGGGCCGCCGACTGCCAGTTCGTCGATTCCAGGAGACTCCGGAGAATCTGGGTCGTGATGCCGAAGGGAACGTTTCCGACGACGGTGTCGATATCGCGCGGAATGCGGAAGTCGAGGAAATCACCCTGGAATACGGTGACCCTCTCCCCTTCGAATTTCCGCCGCACATGCGCGGCCCAGTGCGGGTCCATCTCCACGACCGTCACGGTGTCGAAGGAGCGCACCAACTCCTCGGTTATCGCGCCCTTTCCGGGGCCGATTTCGAGAACGTTCCTACCGTCCCCCTCGACATGCGTGACGAGATTGCGCACGGCTCTGTCGTCCTGAAGGAAGTTCTGGCCTAATTCGCGGCGAAGGGTGTCGCGGTCCGCTCGCCTCGGTATGGAGTCGCGCATTGCCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36873","NCBI_taxonomy_name":"Streptomyces venezuelae","NCBI_taxonomy_id":"54571"}}}},"ARO_accession":"3001265","ARO_id":"37664","ARO_name":"Erm(30)","ARO_description":"Erm(30) confers a MLSb resistant phenotype. Along with erm(31), these genes are responsible for self-resistance in the pikromycin\/narbomycin\/methymycin\/neomethymycin producer, Streptomyces venezuelae.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1225":{"model_id":"1225","model_name":"TEM-178","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1492":{"protein_sequence":{"accession":"CAA65888.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGSTSGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGSQELTAFLHNMGDHVTRLDRWEPELNEAIPNDEADTTMPAAMATTLRKLLTGELLTLASRQQLIDWMADKVAGPLLRSALPAGWFIADKSGARERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"X97254","fmin":"153","fmax":"1011","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTTCGACGAGTGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGATCGCAAGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGGCTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCCGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATCGGTGCTTCCCTTATCAAACATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36783","NCBI_taxonomy_name":"Serratia marcescens","NCBI_taxonomy_id":"615"}}}},"ARO_accession":"3001043","ARO_id":"37423","ARO_name":"TEM-178","ARO_description":"TEM-178 is an inhibitor-resistant, extended-spectrum beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1226":{"model_id":"1226","model_name":"adeG","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"2100"}},"model_sequences":{"sequence":{"4251":{"protein_sequence":{"accession":"CAJ77857.1","sequence":"MSFSRKQFALSAIFVAILATGGSFMLLHENADAKAAPTAAQQAATVDVAPVVSKTITDWQEYSGRLEAIDQVDIRPQVSGKLIAVHFKDGSLVKKGDLLFTIDPRPFEAELNRAKAQLASAEAQVTYTASNLSRIQRLIQSNAVSRQELDLAENDARSANANLQAARAAVQSARLNLEYTRITAPVSGRISRAEVTVGNVVSAGNGAQVLTSLVSVSRLYASFDVDEQTYLKYISNQRNSAQVPVYMGLANETGFTREGTINSIDNNLNTTSGTIRVRATFDNPNGVLLPGLYARIRLGGGQPRPAILISPTAVGVDQDKRFVVVVDAKNQTAYREVKLGAQQDGLQIVNSGLQAGDRIVVNGLQRIRPGDPVTPHLVPMPNSQITASATPPQPQPTDKTSTPAKG"},"dna_sequence":{"accession":"CT025800.2","fmin":"0","fmax":"1221","strand":"+","sequence":"ATGTCATTTTCCCGCAAACAGTTTGCACTGTCTGCCATCTTTGTCGCTATTTTAGCAACCGGTGGCAGTTTTATGTTGTTACATGAAAATGCCGATGCAAAAGCTGCACCAACCGCTGCCCAACAAGCTGCTACTGTTGATGTAGCCCCAGTAGTAAGCAAAACCATTACCGATTGGCAAGAATATTCCGGTCGTTTAGAAGCAATTGATCAAGTTGATATTCGGCCTCAAGTTTCAGGAAAACTTATTGCCGTACATTTCAAAGATGGAAGCCTCGTTAAAAAAGGTGATTTACTTTTCACAATCGACCCTCGTCCTTTTGAAGCAGAACTGAACCGTGCAAAAGCCCAACTTGCTTCAGCTGAAGCACAGGTAACATATACCGCAAGCAATCTTTCGCGTATTCAACGTCTCATTCAGAGTAATGCTGTTTCTCGCCAAGAACTGGATTTAGCCGAAAATGATGCACGTTCAGCGAATGCTAACCTACAAGCCGCTAGAGCTGCTGTCCAATCTGCACGTTTAAATCTAGAATACACCCGTATTACAGCACCTGTCAGCGGCCGGATTTCACGAGCTGAAGTCACCGTTGGTAATGTAGTTTCTGCAGGTAACGGCGCACAGGTTTTAACAAGTTTAGTGTCTGTATCCCGCCTTTATGCATCTTTCGATGTTGATGAACAAACTTACCTGAAATATATCAGTAATCAGCGTAATTCAGCACAAGTACCTGTCTATATGGGACTTGCCAATGAAACAGGCTTTACTCGTGAAGGTACAATCAACTCAATCGATAACAATCTGAATACAACCTCAGGTACGATCCGTGTTCGCGCAACTTTTGACAATCCAAACGGTGTTTTATTACCAGGCCTATATGCACGAATTCGTTTAGGTGGAGGCCAACCTCGCCCAGCGATTCTGATTAGTCCAACCGCGGTTGGTGTCGACCAAGATAAACGTTTTGTCGTAGTAGTAGATGCGAAAAATCAAACTGCTTATCGCGAAGTAAAACTCGGTGCCCAACAAGATGGCTTGCAAATCGTAAATAGCGGATTACAAGCGGGTGATCGTATTGTAGTGAATGGTTTACAACGGATTCGTCCGGGTGACCCTGTTACACCGCATCTCGTCCCTATGCCAAATTCACAAATCACTGCTAGCGCTACTCCTCCTCAACCTCAGCCAACAGATAAAACATCAACTCCGGCAAAAGGTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35535","NCBI_taxonomy_name":"Acinetobacter baumannii AYE","NCBI_taxonomy_id":"509173"}}}},"ARO_accession":"3000778","ARO_id":"37158","ARO_name":"adeG","ARO_description":"AdeG is the inner membrane transporter of the AdeFGH multidrug efflux complex.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1227":{"model_id":"1227","model_name":"aadA2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"3404":{"protein_sequence":{"accession":"AAF27727.1","sequence":"MTIEISNQLSEVLSVIERHLESTLLAVHLYGSAVDGGLKPYSDIDLLVTVAVKLDETTRRALLNDLMEASAFPGESETLRAIEVTLVVHDDIIPWRYPAKRELQFGEWQRNDILAGIFEPAMIDIDLAILLTKAREHSVALVGPAAEEFFDPVPEQDLFEALRETLKLWNSQPDWAGDERNVVLTLSRIWYSAITGKIAPKDVAADWAIKRLPAQYQPVLLEAKQAYLGQKEDHLASRADHLEEFIRFVKGEIIKSVGK"},"dna_sequence":{"accession":"AF156486","fmin":"5012","fmax":"5792","strand":"+","sequence":"GTGACCATCGAAATTTCGAACCAACTATCAGAGGTGCTAAGCGTCATTGAGCGCCATCTGGAATCAACGTTGCTGGCCGTGCATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCATACAGCGATATTGATTTGTTGGTTACTGTGGCCGTAAAGCTTGATGAAACGACGCGGCGAGCATTGCTCAATGACCTTATGGAGGCTTCGGCTTTCCCTGGCGAGAGCGAGACGCTCCGCGCTATAGAAGTCACCCTTGTCGTGCATGACGACATCATCCCGTGGCGTTATCCGGCTAAGCGCGAGCTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCGGGTATCTTCGAGCCAGCCATGATCGACATTGATCTAGCTATCCTGCTTACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCGGCAGCGGAGGAATTCTTTGACCCGGTTCCTGAACAGGATCTATTCGAGGCGCTGAGGGAAACCTTGAAGCTATGGAACTCGCAGCCCGACTGGGCCGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAATAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATAAAACGCCTACCTGCCCAGTATCAGCCCGTCTTACTTGAAGCTAAGCAAGCTTATCTGGGACAAAAAGAAGATCACTTGGCCTCACGCGCAGATCACTTGGAAGAATTTATTCGCTTTGTGAAAGGCGAGATCATCAAGTCAGTTGGTAAATGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002602","ARO_id":"39002","ARO_name":"aadA2","ARO_description":"aadA2 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids and integrons in K. pneumoniae, Salmonella spp., Corynebacterium glutamicum, C. freundii and Aeromonas spp.","ARO_category":{"41439":{"category_aro_accession":"3004275","category_aro_cvterm_id":"41439","category_aro_name":"ANT(3'')","category_aro_description":"Nucleotidylylation of streptomycin at the hydroxyl group at position 3''","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1228":{"model_id":"1228","model_name":"CMY-30","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1700":{"protein_sequence":{"accession":"ABS12249.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHGSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"EF685372","fmin":"0","fmax":"1143","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGGTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002041","ARO_id":"38441","ARO_name":"CMY-30","ARO_description":"CMY-30 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1229":{"model_id":"1229","model_name":"CTX-M-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1863":{"protein_sequence":{"accession":"CAA06311.1","sequence":"MMTQSIRRSMLTVMATLPLLFSSATLHAQANSVQQQLEALEKSSGGRLGVALINTADNSQILYLADERFAMCSTSKVMAAAAVLKQSESDKHLLNQRVEIKASDLVNYNPIAEKHVNGTMTLAELGAGALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDRTEPTLNSAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSASIRAGLPKCWVVGDKTGSGDYGTTNDIAVIWPENHAPLVLVTYFTQPEQKAESRRDVLAAAAKIVTHGF"},"dna_sequence":{"accession":"AJ005044","fmin":"0","fmax":"876","strand":"+","sequence":"ATGATGACTCAGAGCATTCGCCGCTCAATGTTAACGGTGATGGCGACGCTACCCCTGCTATTTAGCAGCGCAACGCTGCATGCGCAGGCGAACAGCGTGCAACAGCAGCTGGAAGCCCTGGAGAAAAGTTCGGGAGGTCGGCTTGGCGTTGCGCTGATTAACACCGCCGATAATTCGCAGATTCTCTACCTGGCCGATGAGCGTTTTGCGATGTGCAGTACCAGTAAGGTGATGGCGGCCGCGGCGGTGCTTAAACAGAGCGAGAGCGATAAGCACCTGCTAAATCAGCGCGTTGAAATCAAGGCGAGCGACCTGGTTAACTACAATCCCATTGCGGAGAAACACGTTAACGGCACGATGACGCTGGCTGAGCTTGGCGCAGGCGCCCTGCAGTATAGCGACAATACTGCCATGAATAAGCTGATTGCCCATCTGGGTGGGCCCGATAAAGTGACGGCGTTTGCCCGCTCGTTGGGTGATGAGACCTTCCGTCTGGACAGAACCGAGCCCACGCTCAATAGCGCCATTCCAGGCGACCCGCGTGATACCACCACGCCGCTCGCGATGGCGCAGACCCTGAAAAATCTGACGCTGGGTAAAGCGCTGGCGGAAACTCAGCGGGCACAGTTGGTGACGTGGCTTAAGGGCAATACTACCGGTAGCGCGAGCATTCGGGCGGGTCTGCCGAAATGTTGGGTAGTGGGCGATAAAACCGGCAGCGGAGATTATGGCACCACCAACGATATCGCGGTTATCTGGCCGGAAAACCACGCACCGCTGGTTCTGGTGACCTACTTTACCCAACCGGAGCAGAAGGCGGAAAGCCGTCGGGATGTTCTGGCTGCGGCGGCGAAAATCGTAACCCACGGTTTCTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35732","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium","NCBI_taxonomy_id":"90371"}}}},"ARO_accession":"3001869","ARO_id":"38269","ARO_name":"CTX-M-6","ARO_description":"CTX-M-6 is a beta-lactamase found in Salmonella typhimurium","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1230":{"model_id":"1230","model_name":"CTX-M-33","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4401":{"protein_sequence":{"accession":"AAO88912.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYSPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"AY238472","fmin":"12","fmax":"888","strand":"-","sequence":"TTACAAACCGTCGGTGACGATTTTAGCCGCCGACGCTAATACATCGCGACGGCTTTCTGCCTTAGGTTGAGGCTGGGTGAAGTAAGTGACCAGAATCAGCGGCGCACGATCTTTTGGCCAGATCACCGCGATATCGTTGGTGGTGCCATAGCCACCGCTGCCGGTTTTATCCCCCACAACCCAGGAAGCAGGCAGTCCAGCCTGAATGCTCGCTGCACCGGTGGTATTGCCTTTCATCCATGTCACCAGCTGCGCCCGTTGGCTGTCGCCCAATGCTTTACCCAGCGTCAGATTCCGCAGAGTTTGCGCCATTGCCCGAGGTGAAGTGGTATCACGCGGATCGCCCGGAATGGCGGTGTTTAACGTCGGCTCGGTACGGTCGAGACGGAACGTTTCGTCTCCCAGCTGTCGGGCGAACGCGGTGACGCTAGCCGGGCCGCCAACGTGAGCAATCAGCTTATTCATCGCCACGTTATCGCTGTACTGTAGCGCGGCCGCGCTAAGCTCAGCCAGTGACATCGTCCCATTGACGTGCTTTTCCGCAATCGGACTATAGTTAACAAGGTCAGATTTTTTGATCTCAACTCGCTGATTTAACAGATTCGGTTCGCTTTCACTTTTCTTCAGCACCGCGGCCGCGGCCATCACTTTACTGGTGCTGCACATCGCAAAGCGCTCATCAGCACGATAAAGTATTTGCGAATTATCTGCTGTGTTAATCAATGCCACACCCAGTCTGCCTCCCGACTGCCGCTCTAATTCGGCAAGTTTTTGCTGTACGTCCGCCGTTTGCGCATACAGCGGCACACTTCCTAACAACAGCGTGACGGTTGCCGTCGCCATCAGCGTGAACTGGCGCAGTGATTTTTTAACCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001895","ARO_id":"38295","ARO_name":"CTX-M-33","ARO_description":"CTX-M-33 is a beta-lactamase found in Salmonella enterica","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1231":{"model_id":"1231","model_name":"mel","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"950"}},"model_sequences":{"sequence":{"4387":{"protein_sequence":{"accession":"YP_002743273.1","sequence":"MELILKAKDIRVEFKGRDVLDINELEVYDYDRIGLVGANGAGKSTLLRVLLGELTPPGCKMNRLGELAYIPQLDEVTLQEEKDFALVGKLGVEQLNIQTMSGGEETRLKIAQALSAQVHGILADEPTSHLDREGIDFLIGQLKYFTGALLVISHDRYFLDEIVDKIWELKDGKITEYWGNYSDYLRQKEEERKSQAAEYEQFIAERARLERAAEEKRKQARKIEQKAKGSSKKKSTEDGGRLAHQKSIGSKEKKMYNAAKTLEHRIAALGKVEAPEGIRRIRFRQSKALELHNPYPIVGAEINKVFGDKALFENASFQIPLGAKVALTGGNGIGKTTLIQMILNHEEGISISPKAKIGYFAQNGYKYNSNQNVMEFMQKDCDYNISEIRSVLASMGFKQNDIGKSLSVLSGGEIIKLLLAKMLMGRYNILIMDEPSNFLDIPSLEALEILMKEYTGTIVFITHDKRLLENVADVVYEIRDKKINLKH"},"dna_sequence":{"accession":"NC_012469","fmin":"1800927","fmax":"1802391","strand":"-","sequence":"TTAATGTTTCAGATTTATTTTCTTATCTCTAATTTCATAAACTACATCTGCTACATTTTCGAGTAATCGTTTATCGTGGGTGATAAACACGATAGTTCCGGTGTACTCCTTCATTAGTATTTCCAAAGCCTCTAAACTTGGTATGTCAAGGAAGTTACTGGGTTCATCCATTATTAGGATGTTATATCTACCCATGAGCATTTTAGCAAGCAACAATTTTATAATTTCTCCACCGCTTAAAACAGATAAACTTTTTCCAATATCGTTCTGTTTGAACCCCATAGATGCTAGCACTGAACGAATTTCTGATATATTGTAGTCACAATCCTTCTGCATAAACTCCATAACATTCTGATTACTGTTGTACTTGTAACCATTCTGTGCAAAGTAACCTATTTTTGCCTTAGGCGAAATAGAAATTCCTTCTTCATGGTTTAAGATCATTTGGATTAAAGTTGTTTTTCCGATTCCATTACCACCAGTTAACGCCACTTTTGCTCCTAACGGAATTTGAAAAGATGCATTTTCAAACAGAGCCTTATCCCCAAATACTTTATTAATTTCTGCACCGACTATAGGGTATGGATTATGGAGCTCCAATGCTTTACTTTGCCTGAAACGAATTCTGCGAATGCCTTCCGGAGCTTCTACTTTTCCTAAGGCCGCAATCCTGTGCTCTAGGGTTTTAGCAGCATTATACATCTTTTTTTCCTTACTTCCTATTGATTTTTGATGAGCTAAACGCCCTCCGTCTTCAGTACTTTTTTTCTTTGAAGAACCTTTTGCCTTCTGTTCTATTTTACGAGCCTGTTTTCGCTTTTCCTCCGCAGCCCTTTCCAATCGGGCACGTTCCGCAATAAATTGTTCGTATTCTGCAGCTTGGCTCTTACGTTCTTCCTCTTTCTGACGAAGATAATCAGAATAGTTTCCCCAATACTCAGTGATTTTGCCATCTTTCAGTTCCCATATTTTATCTACTATTTCATCAAGAAAATAGCGGTCATGGCTAATAACTAACAGTGCACCTGTAAAATATTTTAGCTGTCCTATTAGAAAATCAATTCCTTCACGGTCTAAATGGCTCGTAGGTTCATCCGCTAAAATACCATGAACCTGTGCCGATAAGGCCTGTGCTATTTTAAGCCTTGTTTCTTCACCACCGCTCATAGTCTGTATATTTAATTGCTCAACACCTAGCTTGCCTACAAGTGCAAAATCTTTTTCCTCCTGCAGAGTTACTTCGTCCAACTGGGGAATATAGGCAAGTTCACCCAGACGATTCATTTTACATCCTGGGGGAGTTAATTCTCCTAAAAGTACCCTGAGTAAAGTGCTTTTTCCAGCACCATTTGCTCCTACTAAACCAATACGGTCATAATCATATACTTCTAATTCATTTATATCTAAAACATCGCGTCCTTTGAATTCCACACGAATGTCTTTTGCTTTTAATATTAATTCCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36914","NCBI_taxonomy_name":"Streptococcus pneumoniae Taiwan19F-14","NCBI_taxonomy_id":"487213"}}}},"ARO_accession":"3000616","ARO_id":"36910","ARO_name":"mel","ARO_description":"Mel, a homolog of MsrA, is an ABC transporter associated with macrolide resistance. It is expressed on the same operon as mefA and mefE, both MFS-type efflux proteins that confer macrolide resistance.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35974":{"category_aro_accession":"0000057","category_aro_cvterm_id":"35974","category_aro_name":"telithromycin","category_aro_description":"Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1232":{"model_id":"1232","model_name":"cmeR","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"4388":{"protein_sequence":{"accession":"YP_002343805.1","sequence":"MNSNRTPSQKVLARQEKIKAVALELFLTKGYQETSLSDIIKLSGGSYSNIYDGFKSKEGLFFEILDDICKKHFHLIYSKTQEIENGTLKEILTSFGLAFIEIFNQPEAVAFGKIIYSQVYDKDRHLANWIENNQQNFSYNILMGFFKQQNNSYMKKNAEKLAVLFCTMLKEPYHHLNVLINAPLKNKKEQKEHVEFVVNVFLNGINSSKA"},"dna_sequence":{"accession":"NC_002163","fmin":"336915","fmax":"337548","strand":"-","sequence":"TTAAGCTTTGGAGCTATTGATTCCATTTAGAAAAACATTTACAACAAATTCAACATGTTCTTTTTGTTCTTTTTTATTTTTCAAAGGAGCGTTAATTAAAACATTAAGATGATGATAAGGTTCTTTTAACATAGTGCAAAAAAGAACAGCAAGTTTTTCTGCATTTTTTTTCATATAAGAATTATTTTGTTGCTTGAAAAAACCCATAAGTATGTTATAGGAAAAATTTTGTTGATTATTTTCTATCCAATTGGCAAGATGTCTATCTTTGTCATAAACTTGAGAATAGATAATTTTACCAAAAGCTACAGCTTCTGGTTGATTGAAAATTTCTATAAAAGCTAAACCAAAAGAAGTTAAAATTTCTTTTAAAGTGCCATTTTCAATTTCTTGTGTTTTGGAATAAATAAGATGAAAGTGTTTTTTACATATGTCATCTAAAATTTCAAAGAATAGCCCTTCTTTACTTTTAAAACCATCATAAATATTAGAATAAGATCCTCCAGATAATTTAATAATATCACTCAAACTTGTTTCTTGGTATCCTTTTGTTAAAAAAAGCTCTAAGGCCACTGCTTTGATTTTTTCTTGTCTGGCTAAAACTTTTTGTGATGGTGTTCTATTTGAGTTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36956","NCBI_taxonomy_name":"Campylobacter jejuni subsp. jejuni NCTC 11168","NCBI_taxonomy_id":"192222"}}}},"ARO_accession":"3000526","ARO_id":"36665","ARO_name":"cmeR","ARO_description":"CmeR is a repressor for the CmeABC multidrug efflux pump, binding to the cmeABC promoter region.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"36989":{"category_aro_accession":"3000645","category_aro_cvterm_id":"36989","category_aro_name":"cefotaxime","category_aro_description":"Cefotaxime is a semisynthetic cephalosporin taken parenterally. It is resistant to most beta-lactamases and active against Gram-negative rods and cocci due to its aminothiazoyl and methoximino functional groups.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"37139":{"category_aro_accession":"3000759","category_aro_cvterm_id":"37139","category_aro_name":"fusidic acid","category_aro_description":"Fusidic acid is the only commercially available fusidane, a group of steroid-like antibiotics. It is most active against Gram-positive bacteria, and acts by inhibiting elongation factor G to  block protein synthesis.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1233":{"model_id":"1233","model_name":"tet32","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1200"}},"model_sequences":{"sequence":{"4245":{"protein_sequence":{"accession":"CAC41371.2","sequence":"MKIINLGILAHVDAGKTTLTESLLYTSGAIAELGSVDEGTTRTDTMNLERQRGITIQTAVTSFQWEDVKVNIIDTPGHMDFLTEAYRSLSVLDGAVLVISAKDGVQAQTRILFHALQKMNIPTIIFINKIDQNGIDLQRVYQSIKDKLTSDMIVMQEVSLSPKITMTDISDLDKWDMIISGSDELLERYVAEDSLDIQELQYEKCKRTRCCSLFPVYHGSAKDNLGTEKLIEAITETFITETDDIQSELCGYVFKVEYTERKKRLSYLRLYHGTLHLRDTLLLSKKEKIKITEMCIPSNGEIVPVDHACPGEIVILADDTLKLNDILGNEKLLPHKTRIDNPMPLLRTTVEPQKPEQREALLNALTEIADTDPLLHFDIDTVTHEIILSFLGKVQLEVICSLLEEKYHVGVAMKEPSVIYLERPLRKAEYTIHIEVPPNPFWASVGLSIEPLPIGSGVQYESRVSLGYLNQSFQNAVMEGVLYGCEQGLYGWKVTDCKICFEYGLYYSPVSTPADFRLLSPIVLEQALKKAGTELLEPYLHFEIYAPQEYLSRAYHDAPRYCADIVSTQIKNDEVILKGEIPARCIQEYRNDLTYFTNGQGVCLTELKGYQPAIGKFICQPRRPNSRIDKVRHMFHKLA"},"dna_sequence":{"accession":"AJ295238.3","fmin":"163","fmax":"2083","strand":"+","sequence":"ATGAAAATAATTAACTTAGGCATTCTGGCTCACGTTGACGCAGGAAAGACAACATTAACGGAAAGTTTATTGTATACCAGTGGTGCAATTGCAGAACTAGGGAGCGTAGATGAAGGCACAACAAGGACAGATACAATGAATTTGGAGCGTCAAAGGGGAATCACTATCCAGACAGCAGTGACATCTTTTCAGTGGGAGGATGTAAAAGTCAACATTATAGATACGCCAGGCCATATGGATTTTTTAACCGAAGCATACCGCTCTTTATCTGTCCTTGACGGAGCTGTTTTAGTCATTTCGGCAAAAGACGGCGTACAGGCACAGACGCGTATATTATTCCATGCGCTTCAGAAAATGAACATTCCGACAATTATCTTTATAAATAAGATAGACCAAAATGGAATCGACCTACAGCGTGTTTACCAAAGCATTAAAGACAAACTTACCAGTGATATGATTGTCATGCAGGAGGTTTCCCTGTCGCCAAAGATAACCATGACCGATATTTCTGATTTGGACAAATGGGATATGATTATTTCCGGAAGCGATGAACTATTAGAACGATATGTTGCAGAGGATTCTTTGGATATACAGGAATTACAATATGAAAAGTGCAAAAGAACCAGATGCTGCTCTTTGTTTCCTGTTTATCATGGGAGTGCAAAAGACAATTTAGGAACAGAAAAACTGATTGAAGCGATTACAGAAACTTTCATTACAGAAACAGACGATATTCAGTCTGAATTATGTGGATATGTTTTTAAGGTTGAGTATACAGAGCGGAAAAAACGGCTTTCTTATTTACGCCTGTATCATGGGACGCTCCATTTACGGGATACCCTGCTGCTGTCAAAAAAGGAAAAAATAAAGATTACAGAAATGTGTATTCCGTCAAATGGTGAAATCGTCCCGGTTGACCATGCCTGTCCGGGAGAAATTGTTATTTTAGCTGATGATACTTTGAAACTGAACGACATTCTGGGAAATGAAAAACTCCTGCCTCACAAAACACGGATTGATAATCCCATGCCATTACTTCGGACAACGGTAGAGCCGCAAAAGCCGGAGCAAAGGGAAGCCCTGTTAAATGCCCTCACAGAGATTGCTGATACAGACCCTCTTTTGCATTTTGACATTGATACTGTTACACATGAGATTATATTATCTTTTTTGGGAAAAGTACAGTTAGAAGTTATTTGTTCGCTATTAGAAGAAAAATATCATGTGGGCGTGGCTATGAAAGAGCCTTCGGTTATTTATCTGGAAAGACCGCTTAGAAAAGCAGAATATACCATCCACATAGAAGTCCCGCCAAATCCTTTCTGGGCTTCTGTCGGGTTGTCCATAGAGCCGCTCCCTATTGGAAGCGGAGTGCAGTATGAAAGCAGAGTTTCACTTGGATATTTAAATCAATCGTTCCAAAATGCGGTTATGGAGGGGGTTCTTTATGGCTGCGAGCAGGGGCTGTATGGATGGAAAGTGACAGACTGTAAAATCTGTTTTGAATATGGATTGTATTATAGTCCTGTAAGTACCCCCGCAGACTTTCGGCTGCTTTCCCCTATCGTATTGGAGCAGGCTTTAAAAAAAGCAGGGACAGAACTATTAGAGCCATATCTCCACTTTGAAATTTATGCACCGCAGGAATATCTCTCACGGGCGTATCATGATGCTCCAAGGTATTGTGCAGATATTGTAAGTACTCAGATAAAGAATGACGAGGTCATTCTGAAAGGAGAAATCCCTGCTAGATGTATTCAAGAATACAGGAACGATTTAACTTATTTCACAAATGGGCAGGGAGTCTGCTTGACAGAGTTAAAAGGATACCAGCCAGCTATTGGTAAATTTATTTGCCAACCCCGCCGCCCGAATAGCCGTATAGATAAGGTTCGGCATATGTTCCACAAGTTAGCTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36797","NCBI_taxonomy_name":"Clostridiaceae bacterium K10","NCBI_taxonomy_id":"185309"}}}},"ARO_accession":"3000196","ARO_id":"36335","ARO_name":"tet32","ARO_description":"Tet32 is a tetracycline resistance gene similar to Tet(O), and binds to the ribosome to confer tetracycline resistance as a ribosomal protection protein.","ARO_category":{"35921":{"category_aro_accession":"0000002","category_aro_cvterm_id":"35921","category_aro_name":"tetracycline-resistant ribosomal protection protein","category_aro_description":"A family of proteins known to bind to the 30S ribosomal subunit. This interaction prevents tetracycline and tetracycline derivatives from inhibiting ribosomal function. Thus, these proteins confer elevated resistance to tetracycline derivatives as a ribosomal protection protein.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1234":{"model_id":"1234","model_name":"MIR-13","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"1348":{"protein_sequence":{"accession":"AIT76115.1","sequence":"MMTKSLSCALLLSVTSSAFAAPMSEKQLAEVVERTVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEIALGDPVAKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDTASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEEAHYAWGYREGKAVHVSPGMLNAEAYGVKTNVKDMASWVIANMKPDSLQAPSLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"KM087862","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGACAAAATCCCTAAGCTGTGCCCTGCTGCTCAGCGTCACCAGCTCTGCATTCGCCGCACCGATGTCCGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTAATTTATCAGGGTCAGCCACACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGCGGCGATGCCATTGCCCGGGGTGAAATAGCGCTGGGCGATCCGGTTGCAAAATACTGGCCTGAGCTCACGGGCAAGCAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTATACCGCAGGCGGTCTGCCGTTACAGGTGCCGGATGAGGTCACGGATACCGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCTAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTTAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAACCCCTCAAGCTGGACCATACCTGGATTAACGTCCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGAGGGTAAAGCGGTCCACGTTTCGCCAGGGATGCTGAACGCAGAAGCCTATGGCGTAAAAACTAACGTGAAGGATATGGCGAGCTGGGTGATAGCCAACATGAAGCCGGATTCTCTTCAGGCTCCCTCACTCAAGCAAGGCATTGCTCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCCATGTATCAGGGGTTGGGCTGGGAGATGCTCAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCATTGCCCGTGGCAGAAGTGAATCCACCCGCGCCGCCGGTTAAGGCCTCCTGGGTCCATAAAACAGGCTCGACGGGTGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36926","NCBI_taxonomy_name":"Enterobacter asburiae","NCBI_taxonomy_id":"61645"}}}},"ARO_accession":"3002178","ARO_id":"38578","ARO_name":"MIR-13","ARO_description":"MIR-13 is a beta-lactamase. From the Lahey list of MIR beta-lactamases.","ARO_category":{"36197":{"category_aro_accession":"3000058","category_aro_cvterm_id":"36197","category_aro_name":"MIR beta-lactamase","category_aro_description":"MIR beta-lactamases are plasmid-mediated beta-lactamases that confer resistance to oxyimino- and alpha-methoxy beta-lactams","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1235":{"model_id":"1235","model_name":"AAC(6')-Ib'","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"3393":{"protein_sequence":{"accession":"AAT74613.1","sequence":"MTNSNDSVTLRLMTEHDLAMLYEWLNRSHIVEWWGGEEARPTLADVQEQYLPSVLAQESVTPYIAMLNGEPIGYAQSYVALGSGDGWWEEETDPGVRGIDQSLANASQLGKGLGTKLVRALVELLFNDPEVTKIQTDPSPSNLRAIRCYEKAGFERQGTVTTPDGPAVYMVQTRQAFERTRSVA"},"dna_sequence":{"accession":"AY660529.1","fmin":"0","fmax":"3902","strand":"+","sequence":"GGCATCCAAGCAGCAAGCGCGTTACGCCGTGGGTCGATGTTTGATGTTATGGAGCAGCAACGATGTTACGCAGCAGGGCAGTCGCCCTAAAACAAAGTTAGGCATCACAAAGTACAGCATCGTGACCAACAGCAACGATTCCGTCACACTGCGCCTCATGACTGAGCATGACCTTGCGATGCTCTATGAGTGGCTAAATCGATCTCATATCGTCGAGTGGTGGGGCGGAGAAGAAGCACGCCCGACACTTGCTGACGTACAGGAACAGTACTTGCCAAGCGTTTTAGCGCAAGAGTCCGTCACTCCATACATTGCAATGCTGAATGGAGAGCCGATTGGGTATGCCCAGTCGTACGTTGCTCTTGGAAGCGGGGACGGATGGTGGGAAGAAGAAACCGATCCAGGAGTACGCGGAATAGACCAGTCACTGGCGAATGCATCACAACTGGGCAAAGGCTTGGGAACCAAGCTGGTTCGAGCTCTGGTTGAGTTGCTGTTCAATGATCCCGAGGTCACCAAGATCCAAACGGACCCGTCGCCGAGCAACTTGCGAGCGATCCGATGCTACGAGAAAGCGGGGTTTGAGAGGCAAGGTACCGTAACCACCCCAGATGGTCCAGCCGTGTACATGGTTCAAACACGCCAGGCATTCGAGCGAACACGCAGTGTTGCCTAACCCTTCCATCGAGGGGGACGTCCAAGGGCTGGCGCCCTTGGCCGCCCCTCATGTCAAACGTTAGCCACCAAGAAGGTGCCATGAAAACATTTGCCGCATATGTAATTACTGCGTGTCTTTCAAGTACGGCATTAGCTAGTTCAATTACAGAAAATACGTTTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTTTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATAACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGATTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAACAATGGGAAAGAGACTTGAGCTTAAGAGGGGCAATACAAGTTTCAGCGGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATATCTTAAAAAATTTTCATATGGTAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAGGGTCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATTTTTAAATAAATTGTCAGCATCAAAAGAAAATCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCTGCGCCTGAATATCTTGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGTTGGGTTGAGAAGGGAGCAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAATAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGCAAGTGAGGGCATCATTGGTGGCTAACAATTCGCTGCAGGCGCGACGGCCCTGACGGGTCCGCGGCCTGAGCTCAAACGTTAGACATCATGAGTGAAAAAGTGCCCGCCGAGATTTCGGTGCAACTATCACAAGCACTCAACGTCATCGGGCGCCACTTGGAGTCGACGTTGCTGGCCGTGCATTTGTACGGCTCCGCACTGGATGGCGGATTGAAACCGTACAGTGATATTGATTTGCTGGTGGCTGTAGCTGCACCGCTCAATGATGCCGTGCGGCAAGCCCTGCTCGTCGATCTCTTGGAGGTTTCAGCTTCCCCTGGCCAAAACAAGGCACTCCGCGCCTTGGAAGTGACCATCGTCGTGCACAGTGACATCGTACCTTGGCGTTATCCGGCCAGGCGGGAACTGCAGTTCGGAGAGTGGCAGCGCAAAGACATCCTTGCGGGCATCTTCGAGCCCGCCACAACCGATTCTGACTTGGCGATTCTGCTAACAAAGGCAAAGCAACATAGCATCGTCTTGGCAGGTTCAGCAGCGAAGGATCTCTTCAGCTCAGTCCCAGAAAGCGATCTATTCAAGGCACTGGCCGATACTCTGAAGCTATGGAACTCGCCGCCAGATTGGGCGGGCGATGAGCGGAATGTAGTGCTTACTTTGTCTCGTATCTGGTACACCGCAGCAACCGGCAAGATCGCGCCAAAGGATGTTGCTGCCACTTGGGCAATGGCACGCTTGCCAGCTCAACATCAGCCCATCCTGTTGAATGCCAAGCGGGCTTATCTTGGGCAAGAAGAAGATTATTTGCCCGCTCGTGCGGATCAGGTGGCGGCGCTCATTAAATTCGTGAAGTATGAAGCAGTTAAACTGCTTGGTGCCAGCCAATGATGTCTAACAATTCATATATGGACTCTCCCCACAAGCAGTGAGGAAAGCTTTTTTCGATCCTGTCGTCAGCGCGGTTGCATTCGTATATCCGGCCTTGTCGTGGGCAGTGCCCTGGCCATGCTGTAGTTCGCGCAGCGGGGGCCAAGCGTTCAAACGATCCCGAAGATCATGATTGTTATCGGCCTTGTACCGCTGCAGGACTCGCCTGTTCCGACAGTCTCGCTTCTCACCACAACCGCAAGAAATAACGCGTCTTCCTGATTACCCCGCCGTCAGGCGGGCCTTGCACTCTGCCAGTCGCCACTGAAGCGGCGTTCGTGGCACCACACCGCCCAGCAGATCCTCACCAGTTTGTTCGCCAGGGCCACGGCAGCCTTGTTGTGGCCGATGCGTTCGGCCGTCTGCAGGGCCCAGCGCTGCAGCTGGGTCAGGCGTTGCGGCGTTCGTGCCTGGCAGCGCTTGGCGGCCAGCAACGCCGCGCGGGCGCCGTGGATCAGCAGCGTTCGCACGTAAACATTGCCCTTGCAGCTGATGCGGCCGAGCTTGCGGCGCTCGCCGCTGCTGTATTCGTTGGGCGTCATGCCCAGCCAGGCGCTCAGATGCCGGCCGCTGGCAAAGCGTTCGGGTTTGCCCACAGCGGTTTTCAGGGCGCTGGCGGTGAGCAGGCCGATGCCGCTGACTTCATCGAGCTTGTGCACGATGTCGTCGTCGGCATGCCAGCGCGCCAGTTGGTCTTCGCACTCACGCATCGACTGTTCGTAGAGGTTGATTTCAGCCAGTACCACTTGCAGGACACCACGCAGAGCCTGCACCTCGGGCTGCTCGATCAACGCGCAGGCCTGGCGCAGAAACGCCTGGGTGCCGTTGGGCGCGGCCACGCCCATCTCGCGCAGGATGCCGCGCAACAGGTTGATGCGCTGGACCCGGGTCTTCTTCCAGGCCTCGCGCATTTTGTGCAGCTGCTGCACCTGTTGCTGCTGCACGCTTTTGACCGGCACCGGACGGATACCCTCGCAACGAGCCGCCTCCAGGATCGCATCGCAGTCGTTGCGATCGGTCTTACTGCGCCGGCGATAGGCCCGCACGTAGCGCGGATGCAGCAGCACCACGCGATGCCCCGCCGCCTGCATCAACCGGCCCCAGTGGTGAGCCGTGCCGCAGGCCTCCATCACCCACTCGACAGGCGCCGGCTGCTCCTGTACATAACGCCAGAACGCCTCCGGATCGAGCCGCCTGCGACGATCCACCCGACCGACATGGATACTTTCGGCAACTTGGTAAACGGACTTGGCCAAATCAATTGCAATGCGTTTCATCTTCACTCTCCCGGCAAACAGACACCTCGTGTCTTATAGAAGAAACGCGGTGCGGGGAGAGTCCATTACAGCCTTCAAGCCGACGCCGCTTCGCGGCGCGGCTTAATTCAAGCGTTAGATGCACTAAGCACATAATTGCTCACAGCCAAACTATCAGGTCAAGTCTGCT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3003676","ARO_id":"40308","ARO_name":"AAC(6')-Ib'","ARO_description":"AAC(6')-Ib' is an aminoglycoside acetyltransferase encoded by plasmids, transposons, integrons in P. aeruginosa and P. fluorescens.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1236":{"model_id":"1236","model_name":"CMY-53","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"958":{"protein_sequence":{"accession":"ADQ38362.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGICLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"HQ336940","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCTGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAATAAAAGCTATCCTAACCCTGCCCGCGTCGAGGCGGCCTGGCGTATTCTTGAAAAACTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002064","ARO_id":"38464","ARO_name":"CMY-53","ARO_description":"CMY-53 is a beta-lactamase found in Escherichia coli","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1238":{"model_id":"1238","model_name":"OXA-397","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1535":{"protein_sequence":{"accession":"AIT76118.1","sequence":"MKLLKILSLVCLSISIGACAEHSMSRAKTSTIPQVNNSIIDQNVQALFNEISADAVFVTYDGQNIKKYGTHLDRAKTAYIPASTFKIANALIGLENHKATSTEIFKWDGKPRFFKAWDKDFTLGEAMQASAVPVYQELARRIGPSLMQSELQRIGYGNMQIGTEVDQFWLKGPLTITPIQEVKFVYDLAQGQLPFKPEVQQQVKEMLYVERRGENRLYAKSGWGMAVDPQVGWYVGFVEKADGQVVAFALNMQMKAGDDIALRKQLSLDVLDKLGVFHYL"},"dna_sequence":{"accession":"KM087865","fmin":"0","fmax":"843","strand":"+","sequence":"ATGAAATTATTAAAAATATTGAGTTTAGTTTGCTTAAGCATAAGTATTGGGGCTTGTGCTGAGCATAGTATGAGTCGAGCAAAAACAAGTACAATTCCACAAGTGAATAACTCAATCATCGATCAGAATGTTCAAGCGCTTTTTAATGAAATCTCAGCTGATGCTGTGTTTGTCACATATGATGGTCAAAATATTAAAAAATATGGCACGCATTTAGACCGAGCAAAAACAGCTTATATTCCTGCATCTACATTTAAAATTGCCAATGCACTAATTGGTTTAGAAAATCATAAAGCAACATCTACAGAAATATTTAAGTGGGATGGAAAGCCACGTTTTTTTAAAGCATGGGACAAAGATTTTACTTTGGGCGAAGCCATGCAAGCATCTGCAGTGCCTGTATATCAAGAATTGGCACGTCGTATTGGTCCAAGCTTAATGCAAAGTGAATTGCAACGTATTGGTTATGGCAATATGCAAATAGGCACGGAAGTTGATCAATTTTGGTTGAAAGGGCCTTTGACAATTACACCTATACAAGAAGTAAAGTTTGTGTATGATTTAGCCCAAGGGCAATTGCCTTTTAAACCTGAAGTTCAGCAACAAGTGAAAGAGATGTTGTATGTAGAGCGCAGAGGGGAGAATCGTCTATATGCTAAAAGTGGCTGGGGAATGGCTGTAGACCCGCAAGTGGGTTGGTATGTGGGTTTTGTTGAAAAGGCAGATGGGCAAGTGGTGGCATTTGCTTTAAATATGCAAATGAAAGCTGGTGATGATATTGCTCTACGTAAACAATTGTCTTTAGATGTGCTAGATAAGTTGGGTGTTTTTCATTATTTATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001583","ARO_id":"37983","ARO_name":"OXA-397","ARO_description":"OXA-397 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1239":{"model_id":"1239","model_name":"SHV-81","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1151":{"protein_sequence":{"accession":"CAJ47136.2","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGSPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM176556","fmin":"25","fmax":"886","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCAGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001135","ARO_id":"37515","ARO_name":"SHV-81","ARO_description":"SHV-81 is a broad-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1241":{"model_id":"1241","model_name":"TEM-144","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1645":{"protein_sequence":{"accession":"CAJ17558.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDCWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGKRGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AM049399","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATTGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTAAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35667","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Derby","NCBI_taxonomy_id":"28144"}}}},"ARO_accession":"3001007","ARO_id":"37387","ARO_name":"TEM-144","ARO_description":"TEM-144 is an extended-spectrum beta-lactamase found in Salmonella enterica.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1242":{"model_id":"1242","model_name":"aadA6\/aadA10","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"409":{"protein_sequence":{"accession":"CAJ32491.1","sequence":"MSNAVPAEISVQLSLALNAIERHLESTLLAVHLYGSALDGGLKPYSDIDLLVTVAARLDETVRQALVVDLLEISASPGQSEALRALEVTIVVHGDVVPWRYPARRELQFGEWQRKDILAGIFEPATTDVDLAILLTKVRQHSLALAGSAAEDFFNPVPEGDLFKALSDTLKLWNSQPDWEGDERNVVLTLSRIWYSAATGKIAPKDIVANWAMERLPDQHKPVLLEARQAYLGQGEDCLASRADQLAAFVHFVKHEATKLLSAMPVMSKTKLDALST"},"dna_sequence":{"accession":"AM087405","fmin":"1748","fmax":"2582","strand":"+","sequence":"ATGAGTAACGCAGTACCCGCCGAGATTTCGGTACAGCTATCACTGGCTCTCAACGCCATCGAGCGTCATCTGGAATCAACGTTGCTGGCCGTGCATTTGTACGGCTCTGCACTGGACGGTGGCCTGAAGCCATACAGTGATATTGATTTGCTGGTTACTGTGGCTGCACGGCTCGATGAGACTGTCCGACAAGCCCTGGTCGTAGATCTCTTGGAAATTTCTGCCTCCCCTGGCCAAAGTGAGGCTCTCCGCGCCTTGGAAGTTACCATCGTCGTGCATGGTGATGTTGTCCCTTGGCGTTATCCGGCCAGACGGGAACTGCAATTCGGGGAGTGGCAGCGTAAGGACATTCTTGCGGGCATCTTCGAGCCCGCCACAACCGATGTTGATCTGGCTATTCTGCTAACTAAAGTAAGGCAGCATAGCCTTGCATTGGCAGGTTCGGCCGCAGAGGATTTCTTTAACCCAGTTCCGGAAGGCGATCTATTCAAGGCATTGAGCGACACTCTGAAACTATGGAATTCGCAGCCGGATTGGGAAGGCGATGAGCGGAATGTAGTGCTTACCTTGTCTCGCATTTGGTACAGCGCAGCAACCGGCAAGATCGCACCGAAGGATATCGTTGCCAACTGGGCAATGGAGCGTCTGCCAGATCAACATAAGCCCGTACTGCTTGAAGCCCGGCAGGCTTATCTTGGACAAGGAGAAGATTGCTTGGCCTCACGCGCGGATCAGTTGGCGGCGTTCGTTCACTTCGTGAAACATGAAGCCACTAAATTGCTTAGTGCCATGCCAGTGATGTCTAAAACAAAGTTAGATGCACTAAGCACATAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002622","ARO_id":"39022","ARO_name":"aadA6\/aadA10","ARO_description":"aadA6\/aadA10 is an integron-encoded aminoglycoside nucleotidyltransferase gene cassette in P. aeruginosa","ARO_category":{"41439":{"category_aro_accession":"3004275","category_aro_cvterm_id":"41439","category_aro_name":"ANT(3'')","category_aro_description":"Nucleotidylylation of streptomycin at the hydroxyl group at position 3''","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1243":{"model_id":"1243","model_name":"mphA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4035":{"protein_sequence":{"accession":"BAA03776.1","sequence":"MTVVTTADTSQLYALAARHGLKLHGPLTVNELGLDYRIVIATVDDGRRWVLRIPRRAEVSAKVEPEARVLAMLKNRLPFAVPDWRVANAELVAYPMLEDSTAMVIQPGSSTPDWVVPQDSEVFAESFATALAALHAVPISAAVDAGMLIRTPTQARQKVADDVDRVRREFVVNDKRLHRWQRWLDDDSSWPDFSVVVHGDLYVGHVLIDNTERVSGMIDWSEARVDDPAIDMAAHLMVFGEEGLAKLLLTYEAAGGRVWPRLAHHIAERLAFGAVTYALFALDSGNEEYLAAAKAQLAAAE"},"dna_sequence":{"accession":"D16251.1","fmin":"1625","fmax":"2531","strand":"-","sequence":"TCATTCCGCTGCGGCGAGCTGCGCCTTCGCCGCAGCGAGGTACTCTTCGTTACCCGAGTCGAGGGCGAAGAGTGCGTAGGTGACCGCCCCGAACGCAAGGCGCTCCGCGATGTGGTGGGCGAGCCGCGGCCACACCCGGCCACCGGCCGCTTCATACGTGAGGAGGAGCTTCGCGAGCCCCTCTTCACCAAAGACCATAAGGTGCGCGGCCATGTCGATGGCAGGGTCATCAACGCGGGCCTCGCTCCAGTCGATCATCCCGCTGACGCGCTCCGTGTTGTCGATGAGCACATGGCCCACGTAGAGATCGCCATGCACCACCACGGAGAAATCTGGCCACGACGAATCGTCGTCGAGCCAGCGCTGCCACCGGTGGAGGCGCTTGTCGTTCACCACGAACTCGCGTCGGACGCGGTCAACGTCGTCGGCCACCTTCTGACGGGCCTGCGTCGGTGTACGGATGAGCATCCCCGCATCCACGGCGGCGGAAATGGGGACGGCATGCAGGGCGGCGAGCGCGGTCGCGAAGCTCTCCGCGAAGACCTCCGAGTCCTGCGGCACGACCCAGTCGGGCGTGGACGAACCAGGCTGGATGACCATCGCAGTCGAGTCTTCGAGCATGGGATAGGCAACGAGCTCGGCGTTGGCCACGCGCCAGTCCGGCACCGCGAACGGCAGGCGATTCTTGAGCATTGCCAGCACCCGCGCCTCTGGTTCGACCTTCGCGCTTACCTCGGCTCGGCGCGGGATGCGCAGCACCCACCGACGTCCATCGTCGACGGTGGCGATCACGATCCTATAGTCGAGCCCAAGCTCATTGACAGTCAGCGGGCCATGGAGCTTGAGCCCATGTCGGGCTGCAAGTGCGTACAGTTGGGAGGTATCGGCGGTCGTGACTACGGTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000316","ARO_id":"36455","ARO_name":"mphA","ARO_description":"The mphA gene encodes for resistance enzyme MPH(2')-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin, telithromycin, roxithromycin) over 16-membered macrolides (e.g.tylosin, spiramycin). It phosphorylates macrolides at 2'-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.","ARO_category":{"36472":{"category_aro_accession":"3000333","category_aro_cvterm_id":"36472","category_aro_name":"macrolide phosphotransferase (MPH)","category_aro_description":"Macrolide phosphotransferases (MPH) are enzymes encoded by macrolide phosphotransferase genes (mph genes). These enzymes phosphorylate macrolides in GTP dependent manner at 2'-OH of desosamine sugar thereby inactivating them. Characterized MPH's are differentiated based on their substrate specificity.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35946":{"category_aro_accession":"0000027","category_aro_cvterm_id":"35946","category_aro_name":"roxithromycin","category_aro_description":"Roxithromycin is a semi-synthetic, 14-carbon ring macrolide antibiotic derived from erythromycin. It is used to treat respiratory tract, urinary and soft tissue infections. Roxithromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35974":{"category_aro_accession":"0000057","category_aro_cvterm_id":"35974","category_aro_name":"telithromycin","category_aro_description":"Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36315":{"category_aro_accession":"3000176","category_aro_cvterm_id":"36315","category_aro_name":"dirithromycin","category_aro_description":"Dirithromycin is an oxazine derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome to inhibit bacterial protein synthesis.","category_aro_class_name":"Antibiotic"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1244":{"model_id":"1244","model_name":"OXY-5-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2017":{"protein_sequence":{"accession":"CAI43417.1","sequence":"MLKSSWRKTALMAAAVPLLLASGSLWASADAIQQKLADLEKHSGGRLGVALINTADDSQTLYRGDERFAMCSTGKVMAAAAVLKQSESNPEVVNKRLEIKKADLVVWSPITEKHLQSGMTLAELSAAALQYSDNTAMNKIIGYLGGPEKVTAFAQSIGDVTFRLDRMEPALNSAIPGDKRDTTTPLAMAESLRKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPASWAVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKSRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"AJ871869","fmin":"0","fmax":"873","strand":"+","sequence":"ATGTTGAAAAGTTCGTGGCGTAAAACCGCCCTGATGGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGTTCATTATGGGCCAGTGCCGATGCTATCCAGCAAAAGCTGGCTGATTTAGAAAAACATTCCGGCGGTCGGCTGGGCGTAGCGCTGATTAATACGGCAGATGATTCGCAAACCCTCTATCGCGGCGATGAACGGTTTGCCATGTGCAGCACCGGTAAAGTGATGGCCGCCGCCGCGGTGTTAAAACAGAGCGAAAGCAATCCAGAGGTAGTGAATAAAAGGCTGGAGATTAAAAAAGCGGATTTAGTAGTCTGGAGCCCGATTACCGAAAAACATCTGCAAAGCGGAATGACCCTGGCGGAACTCAGCGCGGCGGCGCTGCAGTACAGCGACAATACCGCGATGAATAAGATTATCGGTTACCTTGGCGGGCCGGAAAAAGTCACCGCATTCGCCCAGAGTATCGGTGACGTTACTTTTCGTCTCGATCGCATGGAGCCGGCGCTGAACAGCGCGATTCCCGGCGATAAGCGCGATACCACCACCCCGTTGGCGATGGCCGAAAGCCTGCGCAAGCTGACGCTGGGCAATGCGCTGGGCGAACAGCAGCGCGCCCAGTTAGTGACGTGGCTAAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCAGGCCTGCCCGCAAGCTGGGCGGTCGGGGATAAAACCGGCGCCGGAGATTACGGCACCACCAACGATATTGCGGTGATCTGGCCGGAAAATCATGCCCCGCTGGTGCTGGTGACCTATTTTACCCAGCCGCAGCAGGATGCGAAAAGCCGCAAAGAGGTGTTAGCCGCGGCGGCAAAAATCGTCACCGAAGGGCTTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002411","ARO_id":"38811","ARO_name":"OXY-5-1","ARO_description":"OXY-5-1 is a beta-lactamase found in Klebsiella oxytoca","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1245":{"model_id":"1245","model_name":"TEM-114","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1879":{"protein_sequence":{"accession":"AAS89984.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGTGKRGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AY589495","fmin":"181","fmax":"1042","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAACCGGTAAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36770","NCBI_taxonomy_name":"Enterobacter aerogenes","NCBI_taxonomy_id":"548"}}}},"ARO_accession":"3000977","ARO_id":"37357","ARO_name":"TEM-114","ARO_description":"TEM-114 is an extended-spectrum beta-lactamase found in Enterobacter aerogenes.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1246":{"model_id":"1246","model_name":"AAC(2')-Ic","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"4277":{"protein_sequence":{"accession":"CCP42991.1","sequence":"MHTQVHTARLVHTADLDSETRQDIRQMVTGAFAGDFTETDWEHTLGGMHALIWHHGAIIAHAAVIQRRLIYRGNALRCGYVEGVAVRADWRGQRLVSALLDAVEQVMRGAYQLGALSSSARARRLYASRGWLPWHGPTSVLAPTGPVRTPDDDGTVFVLPIDISLDTSAELMCDWRAGDVW"},"dna_sequence":{"accession":"AL123456","fmin":"314308","fmax":"314854","strand":"-","sequence":"TTACCAGACGTCGCCCGCGCGCCAATCGCACATCAGCTCCGCCGAGGTGTCCAGGCTGATGTCGATGGGCAGGACGAACACCGTTCCGTCGTCATCGGGTGTACGGACTGGACCGGTTGGTGCCAGTACCGATGTCGGGCCGTGCCAGGGCAGCCAGCCGCGTGAGGCGTACAGTCTGCGGGCCCGCGCCGAGGAACTGAGCGCTCCGAGCTGGTAAGCGCCGCGCATCACCTGCTCGACGGCGTCCAACAGCGCGCTCACCAGGCGTTGGCCCCGCCAGTCCGCCCGCACCGCAACGCCTTCGACGTACCCGCAGCGCAGCGCGTTGCCGCGGTAGATCAGTCGCCGCTGGATCACCGCGGCATGCGCGATGATCGCCCCGTGATGCCAGATCAGGGCGTGCATCCCACCCAGCGTGTGCTCCCAGTCGGTCTCGGTGAAGTCACCGGCAAACGCGCCGGTGACCATCTGACGGATGTCCTGGCGGGTCTCGCTGTCAAGATCGGCGGTGTGGACCAGGCGGGCCGTGTGTACCTGGGTGTGCAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3002525","ARO_id":"38925","ARO_name":"AAC(2')-Ic","ARO_description":"AAC(2')-Ic is a chromosomal-encoded aminoglycoside acetyltransferase in M. tuberculosis and M. bovis","ARO_category":{"36480":{"category_aro_accession":"3000341","category_aro_cvterm_id":"36480","category_aro_name":"AAC(2')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 2'.","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1247":{"model_id":"1247","model_name":"CMY-72","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1346":{"protein_sequence":{"accession":"AFU25641.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDDVTDKAELLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVKSSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYLEGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"JX440352","fmin":"1027","fmax":"2173","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCGCTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGAATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGCGGTGAAATCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAACTATGCCTGGGGCTATCTCGAAGGGAAGCCTGTGCACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACAGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATAGTGATGCTGGCAAACAAAAGCTATCCTAACCCGGCTCGCGTAGAGGCGGCCTGGCGCATTCTTGAAAAACTGCAATAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002085","ARO_id":"38485","ARO_name":"CMY-72","ARO_description":"CMY-72 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1248":{"model_id":"1248","model_name":"H-NS","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"240"}},"model_sequences":{"sequence":{"4390":{"protein_sequence":{"accession":"NP_309766.1","sequence":"MSEALKILNNIRTLRAQARECTLETLEEMLEKLEVVVNERREEESAAAAEVEERTRKLQQYREMLIADGIDPNELLNSLAAVKSGTKAKRAQRPAKYSYVDENGETKTWTGQGRTPAVIKKAMDEQGKSLDDFLIKQ"},"dna_sequence":{"accession":"NC_002695","fmin":"1737553","fmax":"1737967","strand":"-","sequence":"TTATTGCTTGATCAGGAAATCGTCGAGGGATTTACCTTGCTCATCCATTGCTTTTTTGATTACAGCTGGAGTACGGCCCTGGCCAGTCCAGGTTTTAGTTTCGCCGTTTTCGTCAACGTAGCTATATTTTGCCGGACGCTGAGCACGTTTAGCTTTGGTGCCAGATTTAACGGCGGCAAGGCTATTCAGCAGCTCGTTCGGGTCAATACCGTCAGCGATCAGCATTTCGCGATATTGCTGCAGTTTACGAGTGCGCTCTTCAACTTCAGCAGCAGCCGCGCTTTCTTCTTCGCGACGTTCGTTAACAACAACTTCTAATTTTTCCAGCATTTCTTCCAGCGTTTCAAGTGTACATTCTCTTGCCTGCGCACGAAGAGTACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36747","NCBI_taxonomy_name":"Escherichia coli O157:H7 str. Sakai","NCBI_taxonomy_id":"386585"}}}},"ARO_accession":"3000676","ARO_id":"37020","ARO_name":"H-NS","ARO_description":"H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE, mdtE, and emrK as well as nearby genes of many RND-type multidrug exporters.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35930":{"category_aro_accession":"0000011","category_aro_cvterm_id":"35930","category_aro_name":"cloxacillin","category_aro_description":"Cloxacillin is a semisynthetic, isoxazolyl penicillin derivative in the beta-lactam class of antibiotics. It interferes with peptidogylcan synthesis and is commonly used for treating penicillin-resistant Staphylococcus aureus infections.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1249":{"model_id":"1249","model_name":"FOX-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1276":{"protein_sequence":{"accession":"AAG12974.1","sequence":"MQQRRAFALLTLGSLLLAPCTYASGEAPLTAAVDGIIQPMLKAYRIPGMAVAVLKDGKAHYFNYGVANRESGQRVSEQTLFEIGSVSKTLTATLGAYAAVKGGFELDDKVSQHAPWLKGSALDGVTMAELATYSAGGLPLQFPDEVDSNDKMRTYYRSWSPVYPAGTHRQYSNPSIGLFGHLAANSLGQPFEQLMSQTLLPKLGLHHTYIQVPESAMVNYAYGYSKEDKPVRVTPGVLAAEAYGIKTGSADLLKFAEANMGYQGDAAVKSAIALTHTGFYSVGDMTQGLGWESYAYPVTEQTLLAGNAPAVSFQANPVTRFAVPKAMGEQRLYNKTGSTGGFGAYVAFVPARGIAIVMLANRNYPIEARVKAAHAILSQLAE"},"dna_sequence":{"accession":"AY007369","fmin":"0","fmax":"1149","strand":"+","sequence":"ATGCAACAACGGCGTGCGTTCGCGCTACTGACGCTGGGTAGCCTGCTGTTAGCCCCTTGTACTTATGCCAGCGGGGAGGCTCCGTTGACCGCCGCTGTGGACGGCATTATCCAGCCGATGCTCAAGGCGTATCGGATCCCGGGGATGGCGGTCGCCGTACTGAAAGATGGCAAAGCCCACTATTTCAACTATGGGGTTGCCAACCGGGAGAGTGGCCAGCGCGTCAGCGAGCAGACCCTGTTCGAGATTGGCTCGGTCAGCAAGACCCTGACTGCGACCCTCGGTGCCTATGCCGCGGTCAAGGGGGGCTTTGAGCTGGATGACAAGGTGAGCCAGCACGCCCCCTGGCTCAAAGGTTCCGCCTTGGATGGTGTGACCATGGCCGAGCTTGCCACCTACAGTGCGGGTGGTTTGCCGCTGCAGTTCCCCGATGAGGTGGATTCGAATGACAAGATGCGCACTTACTATCGGAGCTGGTCACCGGTTTATCCGGCGGGGACCCATCGCCAGTATTCCAACCCCAGCATCGGCCTGTTTGGTCACCTGGCCGCAAATAGTCTGGGCCAGCCATTTGAGCAACTGATGAGCCAGACCCTGCTGCCCAAGCTGGGTTTGCACCACACCTATATCCAGGTACCGGAGTCGGCTATGGTGAACTATGCCTACGGCTATTCGAAGGAAGATAAGCCCGTCCGGGTCACTCCGGGCGTGCTGGCAGCCGAGGCTTACGGGATCAAGACCGGCTCGGCGGATCTGCTGAAGTTTGCCGAGGCAAACATGGGGTATCAGGGAGATGCCGCGGTAAAAAGCGCGATCGCGCTGACCCACACCGGTTTCTACTCGGTGGGAGACATGACCCAGGGACTGGGCTGGGAGAGTTACGCCTATCCGGTGACCGAGCAGACATTGCTGGCGGGTAACGCACCGGCGGTGAGCTTCCAGGCCAATCCGGTTACGCGCTTTGCGGTGCCCAAGGCGATGGGCGAGCAGCGGCTCTATAACAAGACGGGCTCGACTGGCGGCTTTGGCGCCTATGTGGCGTTCGTGCCCGCCAGAGGGATCGCCATCGTCATGCTGGCCAATCGCAACTATCCCATCGAGGCCAGGGTGAAGGCGGCTCACGCCATCCTGAGTCAGTTGGCCGAGTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002159","ARO_id":"38559","ARO_name":"FOX-5","ARO_description":"FOX-5 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36206":{"category_aro_accession":"3000067","category_aro_cvterm_id":"36206","category_aro_name":"FOX beta-lactamase","category_aro_description":"FOX beta-lactamases are plasmid-encoded AmpC-type beta-lactamase which conferred resistance to broad-spectrum cephalosporins and cephamycins","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1250":{"model_id":"1250","model_name":"CTX-M-96","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"950":{"protein_sequence":{"accession":"CAG28417.1","sequence":"MVKKSLRQFTLMATAAVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPSLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDILASAAKIVTDGL"},"dna_sequence":{"accession":"AJ704396","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAGCCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCGGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTCGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAGTCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTGGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCAGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATTTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATATATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001956","ARO_id":"38356","ARO_name":"CTX-M-96","ARO_description":"CTX-M-96 is a beta-lactamase. From the Lahey list of CTX-M beta-lactamases.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1251":{"model_id":"1251","model_name":"CTX-M-157","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1819":{"protein_sequence":{"accession":"AIS67613.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTAPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"KM211510","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGCGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3003165","ARO_id":"39742","ARO_name":"CTX-M-157","ARO_description":"From the Lahey list of beta-lactamases.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1252":{"model_id":"1252","model_name":"ceoB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"2030"}},"model_sequences":{"sequence":{"121":{"protein_sequence":{"accession":"AAB58161.1","sequence":"MNISKFFIDRPIFAGVLSVIILLGGVIAMFLLPISEYPEVVPPSVIVKAQYPGANPKVIAETVASPLEEQINGVENMLYMQSQANSDGNMTITVTFKLGTDPDKATQLVQNRVNQALPRLPEDVQRLGITTVKSSPTLTMVVHLISPDNRYDMTYLRNYALINVKDRLSRIQGVGQVQLWGSGDYAMRVWLDPQKVAQRGLSAEDVVQAIREQNVQVAAGVIGASPSLPGTPLQLSVNARGRLQTEDEFGDIVVKTTPDGGVTHLRDIARIQLDASEYGLRSLLDNKPAVAMAINQSPGANSLQISDEVRKTMAELKQDMPAGVDYKIVYDPTQFVRSSIKAVVHTLLEAIALVVIVVIVFLQTWRASLIPLIAVPVSIIGTFSLLLAFGYSINALSLFGMVLAIGIVVDDAIVVVENVERNIENGMNARQATYKAMQEVSGPIIAIALTLVAVFVPLAFMSGLTGQFYKQFAMTIAISTVISAFNSLTLSPALSAILLKGHGDKEDWLTRVMNRVLGGFFRGFNKVFHRGAENYGRGVRGVLSRKTLMLGVYLVLVGATVLVSKVVPGGFVPAQDKEYLIAFAQLPNGASLDRTEKVIRDMGSIALKQPGVESAVAFPGLSVNGFTNSSSAGIVFVTLKPFAERHGKALSAGAIAGALNQKYGAMKDSFVAVFPPPPVLGLGTLGGFKMQIEDRGAVGYAKLSDATNDFIKRAQQAPELGPLFTSYQINVPQLNVDLDRVKAKQLGVPVTDVFNTMQVYLGSLYVNDFNRFGRVYQVRVQADAPFRQRADDILQLKTRNDKGEMVPLSSLVTVTPTFGPEMVVRYNGYTAADINGGPAPGFSSGQAQAAVERIADETLPRGVRFEWTDLTYQQILAGDSAMWVFPISVLLVFLVLAALYESLTLPLAVILIVPMSILSALTGVWLTQGDNNIFTQIGLMVLVGLSAKNAILIVEFARELEHDGRTPLEAAIEASRLRLRPILMTSIAFIMGVVPLVTSTGAGSEMRHAMGVAVFFGMLGVTLFGLI"},"dna_sequence":{"accession":"U97042","fmin":"1263","fmax":"4347","strand":"+","sequence":"ATGAACATTTCCAAATTCTTTATCGACCGGCCGATCTTTGCAGGAGTCCTATCGGTGATCATCCTGCTCGGCGGGGTGATCGCGATGTTCCTGCTGCCGATTTCGGAATATCCGGAAGTCGTGCCGCCTTCGGTGATCGTGAAGGCGCAGTACCCGGGCGCGAACCCGAAAGTGATCGCCGAGACGGTCGCGTCGCCACTTGAAGAGCAGATCAACGGCGTCGAGAACATGCTCTACATGCAGTCGCAGGCGAACAGCGACGGCAACATGACGATCACCGTCACGTTCAAGCTGGGCACCGATCCGGACAAGGCCACGCAGCTCGTGCAGAACCGCGTGAACCAGGCGCTGCCGCGCTTGCCGGAAGACGTGCAGCGGCTCGGCATCACCACGGTGAAGAGCTCGCCGACGCTGACGATGGTGGTCCACCTGATCTCGCCGGACAACCGCTACGACATGACCTACCTGCGCAACTACGCGCTGATCAACGTGAAGGATCGCCTGTCGCGGATCCAGGGCGTCGGCCAGGTGCAGCTGTGGGGTTCGGGCGACTACGCGATGCGCGTGTGGCTCGATCCGCAGAAGGTCGCGCAGCGCGGGCTGTCGGCCGAGGACGTCGTGCAGGCGATCCGCGAGCAGAACGTGCAGGTCGCGGCCGGCGTGATCGGCGCATCGCCGTCGCTGCCCGGCACGCCGCTGCAGCTGTCGGTGAACGCGCGCGGCCGTCTGCAGACGGAAGACGAATTCGGCGACATCGTCGTGAAGACGACGCCGGATGGCGGCGTCACGCACCTGCGCGACATCGCGCGGATCCAGCTCGACGCGTCCGAGTACGGGCTGCGCTCGCTGCTCGACAACAAGCCGGCCGTCGCGATGGCGATCAACCAGTCGCCGGGCGCGAACTCGCTGCAGATCTCGGACGAAGTGCGCAAGACGATGGCCGAACTGAAGCAGGACATGCCGGCGGGCGTCGACTACAAGATCGTCTATGACCCGACGCAGTTCGTGCGCTCGTCGATCAAGGCCGTCGTGCACACGCTGCTCGAAGCGATCGCGCTGGTCGTGATCGTCGTGATCGTGTTCCTGCAGACCTGGCGCGCGTCGCTGATTCCGCTGATCGCGGTGCCGGTGTCGATCATCGGCACGTTCTCGCTGCTGCTCGCGTTCGGGTATTCGATCAACGCGTTGTCGCTGTTCGGGATGGTGCTCGCGATCGGGATCGTGGTCGACGATGCGATCGTCGTCGTCGAGAACGTCGAGCGCAACATCGAGAACGGGATGAACGCGCGGCAGGCGACCTACAAGGCGATGCAGGAAGTGAGCGGGCCGATCATCGCGATCGCGCTGACGCTGGTCGCCGTGTTCGTGCCGCTCGCGTTCATGTCGGGCCTGACCGGCCAGTTCTACAAGCAGTTCGCGATGACCATCGCGATCTCGACGGTGATCTCGGCGTTCAACTCGCTGACGCTGTCGCCGGCGCTGTCCGCGATCCTGCTGAAGGGGCACGGCGACAAGGAAGACTGGCTCACGCGTGTGATGAACCGCGTGCTCGGCGGCTTCTTCCGCGGCTTCAACAAGGTGTTCCATCGCGGGGCGGAGAACTACGGCCGCGGCGTGCGCGGCGTGCTGTCGCGCAAGACGCTGATGCTCGGCGTGTATCTCGTGCTGGTGGGCGCGACGGTGCTCGTGTCGAAGGTCGTGCCGGGCGGCTTCGTGCCCGCGCAGGACAAGGAATACCTGATCGCGTTCGCGCAGCTGCCGAACGGTGCGTCGCTCGACCGCACCGAGAAGGTGATCCGCGACATGGGTTCGATCGCGCTGAAGCAGCCGGGCGTCGAGAGCGCGGTCGCGTTCCCGGGGCTGTCGGTGAACGGCTTCACCAACAGCTCGAGCGCGGGCATCGTGTTCGTCACGCTCAAGCCGTTCGCGGAACGGCACGGCAAGGCGCTGTCGGCCGGCGCCATCGCGGGTGCGCTGAACCAGAAGTACGGCGCGATGAAGGATTCGTTCGTCGCGGTGTTCCCGCCGCCGCCGGTGCTCGGCCTCGGTACGCTCGGCGGGTTCAAGATGCAGATCGAGGATCGCGGCGCGGTCGGCTACGCGAAGCTGTCGGATGCGACCAACGACTTCATCAAGCGCGCGCAGCAGGCGCCTGAACTCGGCCCGCTGTTCACGAGCTACCAGATCAACGTGCCGCAGCTCAACGTCGATCTCGACCGCGTGAAGGCGAAGCAGCTCGGCGTGCCGGTGACCGACGTGTTCAACACGATGCAGGTGTATCTGGGTTCGCTGTACGTGAACGACTTCAACCGCTTCGGACGCGTGTACCAGGTGCGCGTGCAGGCCGATGCGCCGTTCCGCCAGCGCGCGGACGACATCCTGCAACTGAAGACGCGCAACGACAAGGGCGAGATGGTGCCGCTGTCGTCGCTGGTCACCGTGACGCCGACGTTCGGCCCGGAAATGGTCGTGCGCTACAACGGCTACACGGCGGCCGACATCAACGGCGGCCCGGCGCCCGGCTTCTCGTCGGGGCAGGCGCAGGCCGCGGTCGAGCGCATCGCCGACGAGACGCTGCCGCGCGGCGTGCGCTTCGAGTGGACCGACCTCACGTACCAGCAGATCCTCGCGGGCGATTCGGCGATGTGGGTGTTCCCGATCAGCGTGCTGCTCGTGTTCCTCGTGCTCGCCGCGCTGTATGAAAGCCTGACGCTGCCGCTCGCGGTGATCCTGATCGTGCCGATGAGCATTCTGTCGGCGCTGACGGGCGTGTGGCTCACGCAGGGCGACAACAACATCTTCACGCAGATCGGCCTGATGGTGCTGGTGGGGCTGTCGGCGAAGAACGCGATCCTGATCGTCGAATTCGCGCGCGAGCTCGAACACGACGGCAGGACGCCGCTCGAGGCCGCGATCGAGGCGAGCCGGCTGCGGCTGCGCCCGATCCTGATGACGTCGATCGCTTTCATCATGGGCGTGGTGCCGCTCGTCACGTCGACCGGCGCGGGTTCGGAAATGCGTCATGCGATGGGGGTCGCGGTGTTCTTCGGGATGCTCGGCGTGACGCTGTTCGGGCTGATCTGAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36822","NCBI_taxonomy_name":"Burkholderia cepacia","NCBI_taxonomy_id":"292"}}}},"ARO_accession":"3003010","ARO_id":"39444","ARO_name":"ceoB","ARO_description":"ceoB is a cytoplasmic membrane component of the CeoAB-OpcM efflux pump","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1253":{"model_id":"1253","model_name":"GES-23","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1481":{"protein_sequence":{"accession":"AGT20529.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGELVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMGDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"KF179354","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGCTTCATCCACGCCCTGCTGCTGGCCGGCATCGCCCACAGCGCCTACGCCAGCGAGAAGCTGACCTTCAAGACCGACCTGGAGAAGCTGGAGCGCGAGAAGGCCGCCCAGATCGGCGTGGCCATCGTGGACCCGCAGGGCGAGCTGGTGGCCGGCCACCGCATGGCCCAGCGCTTCGCCATGTGCAGCACCTTCAAGTTCCCGCTGGCCGCCCTGGTGTTCGAGCGCATCGACAGCGGCACCGAGCGCGGCGACCGCAAGCTGAGCTACGGCCCGGACATGATCGTGGAGTGGAGCCCGGCCACCGAGCGCTTCCTGGCCAGCGGCCACATGACCGTGCTGGAGGCCGCCCAGGCCGCCGTGCAGCTGAGCGACAACGGCGCCACCAACCTGCTGCTGCGCGAGATCGGCGGCCCGGCCGCCATGACCCAGTACTTCCGCAAGATCGGCGACAGCGTGAGCCGCCTGGACCGCAAGGAGCCGGAGATGGGCGACAACACCCCGGGCGACCTGCGCGACACCACCACCCCGATCGCCATGGCCCGCACCGTGGCCAAGGTGCTGTACGGCGGCGCCCTGACCAGCACCAGCACCCACACCATCGAGCGCTGGCTGATCGGCAACCAGACCGGCGACGCCACCCTGCGCGCCGGCTTCCCGAAGGACTGGGTGGTGGGCGAGAAGACCGGCACCTGCGCCAACGGCGGCCGCAACGACATCGGCTTCTTCAAGGCCCAGGAGCGCGACTACGCCGTGGCCGTGTACACCACCGCCCCGAAGCTGAGCGCCGTGGAGCGCGACGAGCTGGTGGCCAGCGTGGGCCAGGTGATCACCCAGCTGATCCTGAGCACCGACAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002352","ARO_id":"38752","ARO_name":"GES-23","ARO_description":"GES-23 is a beta-lactamase. From the Lahey list of GES beta-lactamases.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1254":{"model_id":"1254","model_name":"CTX-M-46","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"768":{"protein_sequence":{"accession":"AAV97956.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTNAVQQKLAALEKSSGGRLGVPLIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"AY847147","fmin":"81","fmax":"957","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAATGCGGTGCAACAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCCCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001908","ARO_id":"38308","ARO_name":"CTX-M-46","ARO_description":"CTX-M-46 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1255":{"model_id":"1255","model_name":"OXA-119","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1043":{"protein_sequence":{"accession":"AAN41427.1","sequence":"MAIRFLTILLSTFFLTSFVHAQEHVLERSDWKKFFSDLRAEGAIVISDERQAEHALLVFGQERAAKRYSPASTFKLPHTLFALDADAVRDEFQVFRWDGVKRSFAGHNQDQDLRSAMRNSAVWVYELFAKEIGEDKARRYLKQIDYGNADPSTIKGDYWIDGNLEISAHEQISFLRKLYRNQLPFQVEHQRLVKDLMITEAGRNWILRAKTGWEGRFGWWVGWVEWPTGPVFFALNIDTPNRTDDLFKREAIARAILRSIDALPPN"},"dna_sequence":{"accession":"AY139598","fmin":"1486","fmax":"2287","strand":"+","sequence":"ATGGCAATCCGATTCCTCACCATACTGCTATCTACTTTTTTTCTTACCTCATTCGTGCATGCGCAAGAACACGTGCTAGAGCGTTCTGACTGGAAGAAGTTCTTCAGCGACCTCCGGGCCGAAGGTGCAATCGTTATTTCAGACGAACGTCAAGCGGAGCATGCTTTATTGGTTTTTGGTCAAGAGCGAGCAGCAAAGCGTTACTCGCCTGCTTCAACCTTCAAGCTTCCACACACACTTTTTGCACTCGATGCAGACGCCGTTCGTGATGAGTTCCAGGTTTTTCGATGGGACGGCGTTAAACGGAGCTTTGCGGGCCATAATCAAGACCAAGACTTGCGATCAGCGATGCGAAATTCTGCGGTCTGGGTTTATGAGCTATTTGCAAAAGAGATCGGAGAGGACAAAGCAAGACGCTATTTAAAGCAAATTGATTATGGCAACGCCGACCCTTCGACAATCAAGGGCGATTACTGGATAGATGGCAATCTTGAAATCTCAGCGCACGAACAGATTTCGTTTCTCAGAAAACTCTATCGAAATCAGCTGCCATTTCAGGTGGAACATCAGCGCTTGGTCAAAGATCTCATGATTACGGAAGCCGGGCGCAATTGGATACTACGCGCAAAGACCGGCTGGGAAGGCAGGTTTGGCTGGTGGGTAGGGTGGGTGGAGTGGCCAACCGGTCCCGTATTCTTCGCGCTGAATATTGATACGCCAAACAGAACGGATGATCTTTTCAAAAGAGAGGCAATCGCGCGGGCAATCCTTCGCTCTATCGACGCATTGCCGCCCAACTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3001775","ARO_id":"38175","ARO_name":"OXA-119","ARO_description":"OXA-119 is a beta-lactamase found in Enterobacteriaceae","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1256":{"model_id":"1256","model_name":"bmr","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"86":{"protein_sequence":{"accession":"AAA22277.1","sequence":"MEKKNITLTILLTNLFIAFLGIGLVIPVTPTIMNELHLSGTAVGYMVACFAITQLIVSPIAGRWVDRFGRKIMIVIGLLFFSVSEFLFGIGKTVEMLFISRMLGGISAPFIMPGVTAFIADITTIKTRPKALGYMSAAISTGFIIGPGIGGFLAEVHSRLPFFFAAAFALLAAILSILTLREPERNPENQEIKGQKTGFKRIFAPMYFIAFLIILISSFGLASFESLFALFVDHKFGFTASDIAIMITGGAIVGAITQVVLFDRFTRWFGEIHLIRYSLILSTSLVFLLTTVHSYVAILLVTVTVFVGFDLMRPAVTTYLSKIAGNEQGFAGGMNSMFTSIGNVFGPIIGGMLFDIDVNYPFYFATVTLAIGIALTIAWKAPAHLKAST"},"dna_sequence":{"accession":"M33768","fmin":"194","fmax":"1364","strand":"+","sequence":"ATGGAGAAGAAAAATATTACCTTAACTATATTATTAACCAATTTATTTATTGCTTTTTTGGGGATCGGGCTTGTGATTCCAGTAACGCCGACCATTATGAATGAATTGCATTTATCGGGGACCGCGGTCGGCTATATGGTTGCCTGCTTCGCTATTACACAGCTCATTGTCTCACCAATAGCCGGACGATGGGTTGATCGCTTCGGGCGCAAGATCATGATCGTAATCGGCCTGTTGTTCTTTAGTGTGTCGGAGTTTTTGTTCGGCATTGGAAAAACAGTTGAGATGTTATTTATCTCCCGTATGCTGGGCGGTATCAGCGCACCGTTCATTATGCCCGGGGTCACGGCTTTTATTGCAGATATCACGACCATTAAAACACGGCCAAAAGCGCTCGGTTATATGTCAGCCGCTATTTCAACAGGATTTATTATCGGCCCCGGCATCGGGGGATTTTTAGCAGAAGTCCATTCCCGGCTGCCTTTTTTCTTTGCGGCAGCTTTTGCACTGTTAGCAGCCATTTTATCAATCCTCACGCTGCGCGAGCCGGAACGAAACCCTGAAAATCAGGAAATAAAAGGACAGAAGACAGGCTTTAAACGAATTTTTGCCCCCATGTATTTCATAGCTTTTCTCATTATCTTAATTTCGTCTTTTGGTTTAGCATCATTTGAATCTTTATTTGCATTATTCGTGGATCATAAATTCGGATTTACGGCCAGCGACATTGCCATTATGATTACAGGAGGAGCGATTGTTGGCGCCATTACGCAAGTCGTCTTATTCGACCGCTTCACAAGATGGTTTGGCGAAATTCATTTAATTCGGTACAGCTTAATTCTCTCGACGAGTCTGGTATTCTTGCTGACAACGGTACATTCATATGTTGCGATTCTGCTGGTGACAGTCACCGTATTTGTCGGATTTGATCTCATGCGGCCTGCGGTAACGACTTACCTGTCAAAGATTGCGGGAAATGAACAGGGGTTTGCCGGCGGTATGAATTCAATGTTTACAAGTATCGGCAATGTATTCGGGCCTATTATCGGCGGAATGCTGTTCGATATAGATGTAAACTATCCTTTCTACTTTGCAACGGTCACCTTAGCCATAGGGATTGCACTGACCATTGCTTGGAAAGCGCCTGCACATCTTAAAGCCAGCACGTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36833","NCBI_taxonomy_name":"Bacillus subtilis","NCBI_taxonomy_id":"1423"}}}},"ARO_accession":"3003007","ARO_id":"39441","ARO_name":"bmr","ARO_description":"bmr is an MFS antibiotic efflux pump that confers resistance to multiple drugs including acridine dyes, fluoroquinolone antibiotics, chloramphenicol, and puromycin","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavin","category_aro_description":"Acriflavin is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35965":{"category_aro_accession":"0000047","category_aro_cvterm_id":"35965","category_aro_name":"puromycin","category_aro_description":"Puromycin is an aminonucleoside antibiotic, derived from Streptomyces alboniger, that causes premature chain termination during ribosomal protein translation.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36193":{"category_aro_accession":"3000054","category_aro_cvterm_id":"36193","category_aro_name":"acridine dye","category_aro_description":"Acridine dyes are cell permeable, basic molecules with an acridine chromophore. These compounds intercalate DNA. The image shown represents the core structure of the acridine family, with specific dyes containing varying substituents.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1257":{"model_id":"1257","model_name":"QnrB68","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"236":{"protein_sequence":{"accession":"AGL43629.1","sequence":"MTLALVGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVMGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"KC580657","fmin":"0","fmax":"645","strand":"+","sequence":"ATGACTCTGGCATTAGTTGGCGAAAAAATTGACAGAAATCGCTTCACCGGTGAGAAAGTTGAAAATAGTACATTTTTTAACTGCGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGCCAGTTCTATGATCGCGAAAGTCAGAAAGGATGCAATTTTAGTCGCGCAATGCTGAAAGATGCCATTTTCAAAAGCTGTGATTTATCAATGGCAGATTTCCGCAACGTCAGCGCATTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGTGCAAGCTTTATGAATATGATCACCACGCGCACCTGGTTTTGCAGCGCATATATCACTAATACCAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAGCTATGGGAAAACCGCTGGATGGGGACTCAGGTAATGGGTGCGACGTTTAGTGGTTCAGATCTCTCCGGTGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTAGGTGACTTAGATATTCGGGGTGTTGATTTACAAGGCGTTAAGTTAGACAACTACCAGGCATCGTTGCTCATGGAGCGGCTTGGCATCGCTGTGATTGGTTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39584","NCBI_taxonomy_name":"Citrobacter braakii","NCBI_taxonomy_id":"57706"}}}},"ARO_accession":"3002780","ARO_id":"39214","ARO_name":"QnrB68","ARO_description":"QnrB68 is a plasmid-mediated quinolone resistance protein found in Citrobacter braakii","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1258":{"model_id":"1258","model_name":"OXA-55","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"979":{"protein_sequence":{"accession":"AAR03105.1","sequence":"MNKGLHRKRLSKRLLLPMLLCLLAQQTQAVAAEQTKVSDVCSEVTAEGWQEVRRWDKLFESAGVKGSLLLWDQKRSLGLSNNLSRAAEGFIPASTFKLPSSLIALETGAVRDETSRFSWDGKVREIAVWNRDQSFRTAMKYSVVPVYQQLAREIGPKVMAAMVRQLEYGNQDIGGQADSFWLDGQLRITAFQQVDFLRQLHDNKLPVSERSQRIVKQMMLTEASTDYIIRAKTGYGVRRTPAIGWWVGWLELDDNTVYFAVNLDLASASQLPLRQQLVKQVLKQEQLLP"},"dna_sequence":{"accession":"AY343493","fmin":"76","fmax":"946","strand":"+","sequence":"ATGAATAAAGGTTTGCACAGAAAGCGCCTGAGTAAGCGTTTGCTGCTGCCCATGTTGCTGTGTTTATTGGCTCAACAAACGCAGGCTGTGGCAGCTGAGCAGACCAAGGTCAGTGACGTCTGCTCTGAGGTCACGGCTGAGGGTTGGCAAGAGGTACGCCGCTGGGACAAGCTGTTCGAATCCGCAGGAGTTAAAGGCAGTTTGCTGCTTTGGGATCAAAAGCGTTCTTTGGGGCTCTCCAACAATCTAAGTCGCGCCGCCGAAGGCTTTATTCCGGCTTCCACCTTCAAGCTCCCCTCCAGCCTTATTGCGTTGGAAACCGGGGCGGTGCGCGATGAAACCAGTCGTTTTAGCTGGGACGGAAAGGTTCGCGAAATTGCCGTCTGGAACAGGGACCAGAGTTTTCGCACCGCAATGAAGTACTCTGTGGTGCCTGTATATCAGCAGTTGGCCAGGGAGATAGGCCCCAAAGTGATGGCAGCTATGGTGCGGCAGCTGGAATATGGCAATCAGGATATCGGTGGCCAAGCGGACAGCTTCTGGCTCGACGGCCAACTGAGAATTACAGCATTTCAACAAGTGGATTTTCTAAGGCAACTGCATGACAACAAGTTGCCTGTGTCCGAGCGCAGCCAGCGAATTGTCAAACAGATGATGCTGACCGAAGCGAGTACTGACTATATTATTCGCGCCAAGACAGGCTATGGTGTGCGGCGTACGCCGGCCATAGGTTGGTGGGTCGGTTGGTTGGAGTTGGACGACAACACTGTCTATTTCGCCGTTAACCTGGATCTGGCCTCGGCCAGCCAGTTACCGTTGCGCCAACAACTGGTGAAACAGGTGCTCAAGCAGGAACAGCTGCTGCCTTGAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36891","NCBI_taxonomy_name":"Shewanella algae","NCBI_taxonomy_id":"38313"}}}},"ARO_accession":"3001813","ARO_id":"38213","ARO_name":"OXA-55","ARO_description":"OXA-55 is a beta-lactamase found in Shewanella spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1259":{"model_id":"1259","model_name":"SHV-31","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"990":{"protein_sequence":{"accession":"AAP33454.2","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGKRGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AY277255","fmin":"66","fmax":"927","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCAAACGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001089","ARO_id":"37469","ARO_name":"SHV-31","ARO_description":"SHV-31 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1260":{"model_id":"1260","model_name":"APH(3')-IVa","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"237":{"protein_sequence":{"accession":"CAA27061.1","sequence":"MNESTRNWPEELLELLGQTELTVNKIGYSGDHVYHVKEYRGTPAFLKIAPSVWWRTLRPEIEALAWLDGKLPVPKILYTAEHGGMDYLLMEALGGKDGSHETIQAKRKLFVKLYAEGLRSVHGLDIRECPLSNGLEKKLRDAKRIVDESLVDPADIKEEYDCTPEELYGLLLESKPVTEDLVFAHGDYCAPNLIIDGEKLSGFIDLGRAGVADRYQDISLAIRSLRHDYGDDRYKALFLELYGLDGLDEDKVRYYIRLDEFF"},"dna_sequence":{"accession":"X03364","fmin":"0","fmax":"789","strand":"+","sequence":"ATGAACGAAAGTACGCGTAATTGGCCGGAGGAACTTCTTGAGCTTCTCGGGCAGACGGAACTAACCGTCAACAAAATCGGATATTCCGGAGATCACGTCTATCACGTGAAAGAGTACAGGGGCACCCCCGCATTTCTGAAAATCGCCCCCAGTGTATGGTGGAGAACGCTCCGGCCCGAAATTGAAGCGCTCGCTTGGCTGGACGGGAAGCTCCCGGTTCCCAAAATTTTGTACACGGCCGAACACGGCGGGATGGACTACTTGCTGATGGAGGCGCTAGGCGGAAAAGACGGCTCCCACGAAACGATCCAGGCGAAGCGGAAACTGTTTGTGAAGCTGTACGCGGAAGGGCTCCGAAGCGTGCATGGCCTCGATATCCGCGAATGTCCGCTGTCGAACGGGCTGGAGAAGAAGCTCCGGGATGCGAAAAGAATAGTCGATGAGAGCCTGGTGGACCCGGCCGATATAAAAGAGGAGTACGATTGCACGCCGGAGGAATTGTACGGGCTATTGCTTGAGAGTAAGCCGGTAACCGAAGATCTGGTTTTTGCGCACGGAGATTACTGTGCTCCGAATCTGATTATCGACGGTGAGAAGCTGTCGGGATTTATCGATCTCGGACGTGCGGGCGTGGCGGACCGTTATCAGGACATCAGCCTGGCGATCCGCAGCCTCCGGCACGATTACGGCGACGACCGCTACAAAGCGCTCTTCCTGGAACTTTACGGGCTGGACGGGCTTGACGAGGACAAGGTCCGGTATTACATCCGGCTGGATGAATTTTTTTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36858","NCBI_taxonomy_name":"Bacillus circulans","NCBI_taxonomy_id":"1397"}}}},"ARO_accession":"3002648","ARO_id":"39048","ARO_name":"APH(3')-IVa","ARO_description":"APH(3')-IVa is a chromosomal-encoded aminoglycoside phosphotransferase in B. circulans","ARO_category":{"36265":{"category_aro_accession":"3000126","category_aro_cvterm_id":"36265","category_aro_name":"APH(3')","category_aro_description":"Phosphorylation of 2-deoxystreptamine aminoglycosides on the hydroxyl group at position 3'","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1261":{"model_id":"1261","model_name":"rosA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"770"}},"model_sequences":{"sequence":{"4391":{"protein_sequence":{"accession":"AAC60781.1","sequence":"MTDRSETELPPSVNTQPFDNTKVKRTSFSILGAISVSHLLNDMIQSLILAIYPLLQAEFSLSFAQIGLITLTYQLTASLLQPLIGLYTDKHPQPYSLPIGMGFTLSGILLLAVATTFPGGFTWHAALVGTGSSVFHPESSRVAARLPVAATVWLSLFLGGRQFRQRLGPLLAAILIAPYGKGNVGWFSLAALLAIVVLLQVSKWYQQQQRATYGKVVKVSSAKILPKKTVISALAILMVLIFSKYFYLTSISSYYTFYLMHKFGVSVQNAQIHLFVFLFAVAAGTIIGGPLGDRIGRKYVIWGSILGVAPFTLILPYVSLYWTGVLTVIIGLILASAFSAILVYAQELIPGKVGMVSGLFFGFAFGMGGLGAAVLGYVADLTSIELVYQICAFLPLLGIITVFLPNIEDK"},"dna_sequence":{"accession":"U46859","fmin":"24294","fmax":"25527","strand":"-","sequence":"TTACTTATCTTCTATATTGGGCAGGAAGACCGTAATTATCCCCAGTAATGGTAAGAAGGCGCATATTTGATAAACCAGTTCAATACTGGTTAAATCAGCAACATACCCTAGTACAGCCGCACCTAACCCCCCCATACCGAAAGCAAAACCGAAGAATAGACCGGATACCATGCCCACTTTACCCGGAATAAGCTCTTGCGCATACACCAGTATTGCCGAGAAGGCAGAGGCAAGGATAAGGCCAATGATCACGGTTAAAACCCCGGTCCAATACAGAGAAACGTAGGGTAAAATAAGGGTAAATGGCGCAACGCCCAATATTGACCCCCAAATAACATACTTTCGACCTATCCTATCGCCAAGAGGGCCGCCAATGATGGTGCCAGCGGCCACTGCGAATAAGAAGACAAATAAATGTATTTGGGCATTTTGTACCGAAACACCAAACTTATGCATCAAATAAAAGGTGTAATAGCTACTAATACTGGTCAAGTAGAAGTATTTAGAGAATATCAGCACCATTAAGATAGCTAGGGCGCTAATAACCGTCTTTTTAGGCAGTATTTTGGCCGATGAGACTTTTACTACTTTGCCATAGGTTGCTCTTTGTTGTTGCTGATACCATTTACTGACCTGCAACAGCACCACAATAGCCAGCAGTGCCGCGAGTGAAAACCAACCTACATTGCCTTTACCGTAAGGTGCGATAAGGATCGCGGCTAATAGTGGGCCAAGGCGCTGCCGAAATTGCCTCCCACCCAAAAATAGACTGAGCCATACCGTGGCGGCCACCGGTAGCCTAGCGGCTACGCGTGAGGATTCTGGGTGGAAGACCGAAGAACCGGTTCCGACTAATGCCGCATGCCATGTAAAACCACCTGGGAAAGTCGTGGCAACCGCAAGCAGCAAGATACCTGATAAGGTGAAACCCATGCCAATCGGCAGTGAATAGGGCTGCGGATGCTTATCGGTATAAAGACCAATAAGTGGCTGTAATAATGAGGCGGTAAGCTGATAAGTGAGGGTGATTAATCCAATCTGCGCAAAACTCAGCGAAAACTCGGCTTGTAATAGCGGATAAATCGCCAGAATCAGCGACTGGATCATATCGTTAAGTAAGTGAGATACGCTAATAGCACCTAATATAGAGAAAGAGGTGCGTTTTACCTTGGTATTATCGAAGGGCTGGGTATTGACGGAGGGAGGGAGCTCCGTCTCAGAACGATCGGTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39589","NCBI_taxonomy_name":"Yersinia enterocolitica (type O:8)","NCBI_taxonomy_id":"34054"}}}},"ARO_accession":"3003048","ARO_id":"39482","ARO_name":"rosA","ARO_description":"rosA is part of an efflux pump\/potassium antiporter system (RosAB) in Yersinia that confers resistance to cationic antimicrobial peptides such as polymyxin B.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1262":{"model_id":"1262","model_name":"SHV-149","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"915":{"protein_sequence":{"accession":"AFQ23955.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESRLSGSVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTASLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"JX121116","fmin":"0","fmax":"858","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCGGCTGTCGGGCAGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTCTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001188","ARO_id":"37568","ARO_name":"SHV-149","ARO_description":"SHV-149 is a beta-lactamase.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1263":{"model_id":"1263","model_name":"QnrB56","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"425":{"protein_sequence":{"accession":"AFR46587.1","sequence":"MTPLLYKNTGIDMTLALVGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFSTFDWRAGNFTHCDLTNSELGDLDIRGVDLQGVKLDSYQASLLMERLGIAIIG"},"dna_sequence":{"accession":"JX259317","fmin":"0","fmax":"681","strand":"+","sequence":"ATGACGCCATTACTGTATAAAAACACAGGCATAGATATGACTCTGGCATTAGTTGGCGAAAAAATTGACAGAAACCGCTTCACCGGTGAGAAAGTTGAAAATAGTACATTTTTTAACTGCGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGCCAGTTCTATGATCGCGAAAGTCAGAAAGGGTGCAATTTTAGTCGCGCAATGCTGAAAGATGCCATTTTCAAAAGCTGTGATTTATCAATGGCAGATTTCCGCAACGTCAGCGCATTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTTCGCGGTGCAAGCTTTATGAATATGATCACCACGCGTACCTGGTTTTGCAGCGCATATATCACTAATACCAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAGCTATGGGAAAACCGCTGGATGGGGACTCAGGTACTGGGTGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGGAAACTTCACACATTGCGATCTGACCAATTCGGAGTTAGGTGACTTAGATATTCGGGGTGTTGATTTACAAGGCGTTAAGTTAGACAGCTACCAGGCATCGTTGCTCATGGAGCGGCTTGGCATCGCGATTATTGGCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002769","ARO_id":"39203","ARO_name":"QnrB56","ARO_description":"QnrB56 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1264":{"model_id":"1264","model_name":"smeC","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"900"}},"model_sequences":{"sequence":{"155":{"protein_sequence":{"accession":"AAD51346.1","sequence":"MKPMLLRALAAATMTTVLGGCVSMAPHYQRPEAPVPAQFGNAAIGAAEPALAMPAWRDVFLEPRLQQVIALALQNNRDLRVAVLQVEKERAQYRIQRAALLPSVDASGSVTRSRVSDANSETGVTQVTESDAVQVGISSWELDLFGRIRSLKNEALQNWLASAENQRAVRTSLVAEVATAWLALAADEQSLAFTQQTLDSQHQTLQRTEARHAQGLASGLDLSQVQTSVEAARGALAKLQAQQAQDRDALQLLVGAPLDPALLPTAQALDGSVALAPLPANLPSSVLLQRPDVLSAEHALQAANADIGAARAAFFPTLALTANYGHSSTALSTLFSAGTRGWSFAPSITAPIFHAGALKASLDASKIGKDIGIAQYEKAIQQAFSEVADALATRDHLTAQLDAQRALVADSQRSYTLADARYRTGLDGYLQSLDAQRSLYAAQQDLIALQQQEAGNRVTLFKVLGGGADAR"},"dna_sequence":{"accession":"AF173226","fmin":"6913","fmax":"8329","strand":"+","sequence":"ATGAAGCCGATGCTGCTGCGCGCCCTGGCGGCCGCAACGATGACCACCGTGCTGGGCGGCTGCGTGAGCATGGCCCCGCACTACCAGCGTCCCGAGGCACCGGTGCCGGCGCAGTTCGGCAATGCTGCCATCGGCGCGGCCGAACCGGCACTGGCGATGCCGGCCTGGCGCGACGTGTTCCTGGAACCGCGCCTGCAGCAGGTCATCGCGCTGGCGCTGCAGAACAACCGCGATCTGCGCGTGGCGGTGCTGCAGGTGGAGAAGGAGCGCGCGCAGTACCGCATCCAGCGCGCGGCACTGCTGCCGTCGGTGGATGCCAGCGGCAGTGTCACCCGTTCGCGGGTGAGCGATGCCAACAGCGAGACCGGCGTCACCCAGGTGACCGAATCCGATGCCGTGCAGGTGGGCATCAGCAGCTGGGAGCTGGACCTGTTCGGGCGTATCCGCAGCTTGAAGAACGAGGCGCTGCAGAACTGGCTGGCCAGCGCCGAGAACCAGCGCGCCGTGCGCACCAGCCTGGTGGCTGAAGTGGCGACGGCGTGGCTGGCGCTGGCGGCCGACGAGCAGTCGCTGGCATTCACGCAACAGACGCTGGACAGCCAGCACCAGACCCTGCAGCGCACCGAGGCCCGCCATGCACAGGGGCTGGCCTCGGGCCTGGACCTGTCGCAGGTGCAGACCAGCGTGGAAGCCGCGCGCGGGGCGCTGGCGAAGCTGCAGGCCCAGCAGGCGCAGGATCGCGATGCATTGCAGCTGTTGGTGGGGGCACCGCTGGATCCGGCCCTGCTGCCAACCGCGCAGGCGCTGGATGGCAGCGTCGCATTGGCGCCGCTGCCCGCCAACCTGCCGTCCAGCGTGTTGCTGCAGCGCCCGGACGTGCTGTCCGCCGAGCATGCATTGCAGGCAGCCAACGCCGATATCGGTGCCGCGCGCGCCGCATTCTTTCCGACGCTGGCGTTGACCGCCAACTACGGCCACAGTTCCACCGCGTTGTCGACGCTGTTCTCGGCCGGCACCCGTGGCTGGTCGTTCGCGCCCAGCATCACCGCGCCGATCTTCCATGCCGGTGCACTGAAGGCCTCGCTGGATGCCTCGAAGATCGGCAAGGACATCGGCATCGCGCAGTACGAGAAGGCGATCCAGCAGGCCTTCAGTGAGGTGGCCGATGCGCTGGCCACGCGCGATCACCTGACCGCGCAGCTGGACGCGCAACGCGCGTTGGTGGCTGACAGCCAGCGCAGCTACACCTTGGCCGATGCGCGCTACCGCACCGGACTGGATGGCTACCTGCAGTCGTTGGATGCGCAGCGCAGCCTGTATGCCGCGCAGCAGGACCTGATCGCCCTGCAGCAGCAGGAGGCGGGCAACCGGGTGACGTTGTTCAAGGTGCTGGGTGGTGGCGCGGACGCGCGGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37076","NCBI_taxonomy_name":"Stenotrophomonas maltophilia","NCBI_taxonomy_id":"40324"}}}},"ARO_accession":"3003053","ARO_id":"39487","ARO_name":"smeC","ARO_description":"smeC is an outer membrane multidrug efflux protein of the smeABC complex in Stenotrophomonas maltophilia","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1265":{"model_id":"1265","model_name":"MIR-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"1899":{"protein_sequence":{"accession":"ABN69112.2","sequence":"MMTKSLSCALLLSVASAAFAAPMFEKQLAEVVERTVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEIALGDPVAKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDTASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEEAHYAWGYREGKAVHVSPGMLDAEAYGVKTNVKDMASWLIANMKPDSLHAPSLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"EF417572","fmin":"29","fmax":"1175","strand":"+","sequence":"ATGATGACAAAATCCCTAAGCTGTGCCCTGCTGCTCAGCGTCGCCAGCGCTGCATTCGCCGCACCGATGTTCGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTAATTTATCAGGGTCAGCCACACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGCGGCGATGCCATTGCCCGGGGTGAAATAGCGCTGGGCGATCCGGTAGCAAAATACTGGCCTGAGCTCACGGGCAAGCAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTATACCGCAGGCGGTCTGCCGTTACAGGTGCCGGATGAGGTCACGGATACCGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCTAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAACCCCTCAAGCTGGACCATACCTGGATTAACGTCCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGAGGGTAAAGCGGTCCACGTTTCGCCAGGGATGCTGGACGCGGAAGCCTATGGCGTAAAAACTAACGTGAAGGATATGGCGAGCTGGCTGATAGCCAACATGAAGCCGGATTCTCTTCACGCTCCCTCACTCAAGCAAGGCATTGCTCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCTATGTATCAGGGGTTAGGCTGGGAGATGCTCAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCATTGCCCGTGGCAGAAGTGAATCCACCCGCGCCGCCGGTCAAAGCCTCCTGGGTCCATAAAACAGGCTCGACGGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTAGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002167","ARO_id":"38567","ARO_name":"MIR-4","ARO_description":"MIR-4 is a beta-lactamase found in Escherichia coli","ARO_category":{"36197":{"category_aro_accession":"3000058","category_aro_cvterm_id":"36197","category_aro_name":"MIR beta-lactamase","category_aro_description":"MIR beta-lactamases are plasmid-mediated beta-lactamases that confer resistance to oxyimino- and alpha-methoxy beta-lactams","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1266":{"model_id":"1266","model_name":"ANT(4')-IIa","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"190":{"protein_sequence":{"accession":"AAA25717.1","sequence":"MHLTITYWIDRLREAYPHAVAILLKGSYARGEASAWSDIDFDVLVSDEEVEEYRTWIEPVGERLVHISVAVEWVTGWERDSADPSSWSYGLPTQETTQLLWAADENIRRRLDRPFKVHPAAEPEVEDTVEALGKIRNAMVRGDDLAVYQAAQVVGKLIPTLLVPINPPTYARFAREAIDRILAFPNVPEGFAADWLTCMGLVDRRTHDPQPTRPNEWCAARSRFCRRMRTSSVRISRGCWKQDWYLRISART"},"dna_sequence":{"accession":"M98270","fmin":"0","fmax":"759","strand":"+","sequence":"ATGCACCTCACCATTACCTACTGGATCGATCGTCTGCGAGAAGCGTATCCCCATGCGGTCGCGATTTTGCTGAAGGGAAGCTATGCCCGGGGCGAGGCGAGTGCGTGGAGCGATATCGATTTCGATGTGCTCGTGAGCGACGAGGAAGTGGAGGAGTATCGCACCTGGATCGAGCCTGTGGGCGAGCGGCTGGTGCATATCTCGGTCGCGGTGGAGTGGGTCACCGGGTGGGAGCGCGATTCGGCAGATCCATCGAGTTGGAGTTATGGCCTGCCTACGCAGGAGACCACCCAGCTGCTTTGGGCAGCTGATGAGAATATTCGCCGACGTCTCGATCGACCGTTCAAGGTGCATCCGGCCGCCGAACCAGAGGTGGAAGACACGGTAGAAGCGCTCGGGAAGATCCGGAATGCGATGGTTCGGGGTGACGACCTTGCGGTCTATCAAGCTGCGCAGGTCGTGGGGAAATTGATTCCGACACTCCTGGTTCCCATCAATCCGCCCACGTACGCACGGTTCGCACGCGAGGCGATCGACAGGATTCTCGCCTTCCCGAATGTACCCGAAGGGTTCGCGGCCGATTGGCTGACGTGCATGGGTCTGGTCGATCGGCGGACGCACGATCCACAGCCGACGCGGCCGAACGAATGGTGCGCGGCACGATCTCGCTTCTGCCGGCGGATGCGGACATCGTCGGTGAGGATATCGCGCGGTTGCTGGAAGCAGGATTGGTACTTGCGTATATCGGCCAGAACGTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002624","ARO_id":"39024","ARO_name":"ANT(4')-IIa","ARO_description":"ANT(4')-IIa is a plasmid-encoded aminoglycoside nucleotidyltransferase in P. aeruginosa and Enterobacteriaceae","ARO_category":{"36368":{"category_aro_accession":"3000229","category_aro_cvterm_id":"36368","category_aro_name":"ANT(4')","category_aro_description":"Nucleotidylylation of 2-deoxystreptamine aminoglycosides at the hydroxyl group at position 4'","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1267":{"model_id":"1267","model_name":"QnrB40","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"644":{"protein_sequence":{"accession":"AEL31271.1","sequence":"NTGIDMTLALVGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLRDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGTTFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"JN166689","fmin":"0","fmax":"660","strand":"+","sequence":"AACACAGGCATAGATATGACTCTGGCATTAGTTGGCGAAAAAATTGACAGAAATCGCTTCACTGGTGAGAAAGTTGAAAATAGTACATTTTTTAACTGCGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGCCAGTTCTATGATCGCGAAAGTCAGAAAGGATGCAATTTTAGTCGCGCAATGCTGAGAGATGCCATTTTCAAAAGCTGTGATTTATCAATGGCAGATTTCCGCAACGTCAGCGCATTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGTGCAAGCTTTATGAATATGATCACCACGCGCACCTGGTTTTGCAGCGCATATATCACTAATACCAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAGCTATGGGAAAACCGCTGGATGGGGACTCAGGTACTGGGTACGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTAGGTGACTTAGATATTCGGGGTGTTGATTTACAAGGCGTTAAGTTAGACAACTACCAGGCATCGTTGCTCATGGAGCGGCTTGGCATCGCTGTGATTGGTTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39584","NCBI_taxonomy_name":"Citrobacter braakii","NCBI_taxonomy_id":"57706"}}}},"ARO_accession":"3002755","ARO_id":"39189","ARO_name":"QnrB40","ARO_description":"QnrB40 is a plasmid-mediated quinolone resistance protein found in Citrobacter braakii","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1268":{"model_id":"1268","model_name":"CMY-115","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1020":{"protein_sequence":{"accession":"AIT76092.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYKGKPYYFTWGKADIANNHPVTQHTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDDITDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMAHWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"KM087839","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCACTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACAAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCATACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGACATTACGGATAAAGCCGCATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGCGGTGAAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAACTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTGCACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCACTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACAGGATCCACAGGCGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTAATGTTGGCAAACAAAAGCTATCCCAACCCGGCTCGCGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002126","ARO_id":"38526","ARO_name":"CMY-115","ARO_description":"CMY-115 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1269":{"model_id":"1269","model_name":"OXA-192","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1756":{"protein_sequence":{"accession":"ADZ54048.1","sequence":"MSKKNFILIFIFVILISCKNTEKTSNETTLIDNIFTNSNAEGTLVIYNLNDDKYIIHNKERAEQRFYPASTFKIYNSLIGLNEKAVKDVDEVFYKYNGEKVFLESWAKDSNLRYAIKNSQVPAYKELARRIGLEKMKENIEKLDFGNKNIGDSVDTFWLEGPLEISAMEQVKLLTKLAQNELPYPIEIQKAVSDITILEQTDNYTLHGKTGLADSENMTTEPIGWLVGWLEENNNIYVFALNIDNINSDDLAKRINIVKESLKALNLLK"},"dna_sequence":{"accession":"JF273470","fmin":"0","fmax":"810","strand":"+","sequence":"ATGTCTAAAAAAAATTTTATATTAATATTTATTTTTGTTATTTTAATATCTTGTAAAAATACAGAAAAAACATCAAATGAAACTACATTAATAGATAATATATTTACTAATAGCAATGCTGAAGGAACATTAGTTATATATAATTTAAATGATGATAAATACATAATTCATAATAAAGAAAGAGCTGAACAAAGATTTTATCCAGCATCAACATTTAAAATATATAATAGTTTAATAGGCTTAAATGAAAAAGCAGTTAAAGATGTAGATGAAGTATTTTATAAATATAATGGCGAAAAAGTTTTTCTTGAATCTTGGGCTAAGGACTCTAATTTAAGATATGCAATTAAAAATTCACAAGTACCGGCATATAAAGAATTAGCAAGAAGAATAGGGCTTGAAAAGATGAAAGAGAATATAGAAAAACTAGATTTTGGTAATAAAAATATAGGTGATAGTGTAGATACTTTTTGGCTTGAAGGACCTTTGGAAATAAGTGCGATGGAGCAAGTTAAATTATTAACTAAATTAGCTCAAAATGAATTGCCGTATCCTATAGAAATACAAAAAGCTGTTTCTGATATTACTATACTAGAGCAAACTGACAATTATACGCTTCATGGAAAAACTGGATTAGCTGATTCTGAAAACATGACAACTGAGCCTATTGGTTGGTTAGTAGGCTGGCTTGAAGAAAATAATAATATATACGTCTTTGCTTTAAATATTGATAATATCAATTCAGATGACCTTGCAAAAAGGATAAATATAGTAAAAGAAAGTTTAAAAGCATTAAATTTATTAAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36935","NCBI_taxonomy_name":"Brachyspira pilosicoli","NCBI_taxonomy_id":"52584"}}}},"ARO_accession":"3001766","ARO_id":"38166","ARO_name":"OXA-192","ARO_description":"OXA-192 is a beta-lactamase found in Brachyspira spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1270":{"model_id":"1270","model_name":"QnrS3","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"175":{"protein_sequence":{"accession":"ABU52984.1","sequence":"ETYNHTYRHRNFSHKDLSDLTFTACTFIRSDFRRANLRDTTFVNCKFIEQGDIEGCHFDVADLRDASFQQCQLAMANFSNANCYGIEFRACDLKGANFSRTNFAHQVSNRMYFCSAFISGCNLSYANMERVCLEKCELFENRWIGTNLAGASLKESDLSRGVFSEDVWGQFSLQGANLCHAELDGLDPRKVDTSGIKIAAWQQELILEALGIVVYPD"},"dna_sequence":{"accession":"EU077611","fmin":"0","fmax":"654","strand":"+","sequence":"TGGAAACCTACAATCATACATATCGGCACCGCAACTTTTCACATAAAGACTTAAGTGATCTCACCTTCACCGCTTGCACATTCATTCGCAGCGACTTTCGACGTGCTAACTTGCGTGATACGACATTCGTCAACTGCAAGTTCATTGAACAGGGTGATATCGAAGGCTGCCACTTTGATGTCGCAGATCTTCGTGATGCAAGTTTCCAACAATGCCAACTTGCGATGGCAAACTTCAGTAATGCCAATTGCTACGGTATAGAGTTCCGTGCGTGTGATTTAAAAGGTGCCAACTTTTCCCGAACAAACTTTGCCCATCAAGTGAGTAATCGTATGTACTTTTGCTCAGCATTTATTTCTGGATGTAATCTTTCCTATGCCAATATGGAGAGGGTTTGTTTAGAAAAATGTGAGTTGTTTGAAAATCGCTGGATAGGAACGAACCTAGCGGGTGCATCACTGAAAGAGTCAGACTTAAGTCGAGGTGTTTTTTCCGAAGATGTCTGGGGGCAATTTAGCCTACAGGGTGCCAATTTATGCCACGCCGAACTCGACGGTTTAGATCCCCGCAAAGTCGATACATCAGGTATCAAAATTGCAGCCTGGCAGCAAGAACTGATTCTCGAAGCACTGGGTATTGTTGTTTATCCTGACTA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002792","ARO_id":"39226","ARO_name":"QnrS3","ARO_description":"QnrS3 is a plasmid-mediated quinolone resistance protein found in Escherichia coli","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1271":{"model_id":"1271","model_name":"AAC(6')-Iw","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"139":{"protein_sequence":{"accession":"AAD03495.1","sequence":"MKIMPISEALLADWLQLRILLWPDHEDAHLLEMRQLLTRTDSLQLLAYSETQQPIAMLEASIRHEYVNGTQTSPVAFLEGIYVLPEHRRSGIATQLVQQVEQWAKQYACTEFASDAAIDNTISHAMHQALGFHETERVVYFKKNIS"},"dna_sequence":{"accession":"AF031331","fmin":"0","fmax":"441","strand":"+","sequence":"ATGAAAATTATGCCTATATCTGAAGCATTATTGGCAGATTGGTTACAATTAAGAATTTTGCTGTGGCCTGATCATGAAGATGCGCATTTATTGGAAATGCGTCAGTTACTTACACGAACAGATAGTTTGCAGTTATTGGCATATTCAGAAACGCAACAGCCGATTGCGATGTTAGAAGCATCCATTCGACATGAATATGTGAACGGTACACAAACCTCACCTGTGGCGTTTCTGGAAGGGATTTATGTCCTGCCTGAGCACCGACGTTCAGGTATTGCCACTCAATTGGTTCAACAAGTAGAACAATGGGCAAAACAATATGCATGTACTGAATTTGCTTCAGATGCAGCAATTGATAATACCATCAGTCATGCAATGCATCAGGCTTTAGGTTTTCATGAAACTGAACGCGTGGTTTATTTCAAGAAAAATATCAGTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39518","NCBI_taxonomy_name":"Acinetobacter sp. 640","NCBI_taxonomy_id":"70350"}}}},"ARO_accession":"3002567","ARO_id":"38967","ARO_name":"AAC(6')-Iw","ARO_description":"AAC(6')-Iw is a chromosomal-encoded aminoglycoside acetyltransferase in Acinetobacter sp.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1272":{"model_id":"1272","model_name":"CTX-M-67","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1187":{"protein_sequence":{"accession":"ABS90365.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYSPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"EF581888","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAGTCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001928","ARO_id":"38328","ARO_name":"CTX-M-67","ARO_description":"CTX-M-67 is a beta-lactamase found in Escherichia coli","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1274":{"model_id":"1274","model_name":"VIM-10","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"2040":{"protein_sequence":{"accession":"AAS13761.1","sequence":"MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQYVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"AY524989","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTACGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002280","ARO_id":"38680","ARO_name":"VIM-10","ARO_description":"VIM-10 is a beta-lactamase found in Pseudomonas spp.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1275":{"model_id":"1275","model_name":"ErmT","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"367":{"protein_sequence":{"accession":"AAA98096.1","sequence":"MNKKNIKDSQNFITSKHHINEILRNVHLNTNDNIIEIGSGKGHFSFELAKRCNYVTAIEIDPKLCRITKNKLIEYENFQVINKDILQFKFPKNKSYKIFGNIPYNISTDIIRKIVFESTATESYLIVEYGFAKRLLNTNRSLALFLMTEVDISILSKIPREYFHPKPRVNSSLIVLKRHPSKISLKDRKQYENFVMKWVNKEYIKLFSKNQFYQALKYARIDDLNNISFEQFLSLFNSYKLFNR"},"dna_sequence":{"accession":"M64090","fmin":"0","fmax":"735","strand":"+","sequence":"ATGAACAAAAAAAATATAAAAGATAGTCAAAACTTTATTACTTCAAAGCATCATATAAATGAAATTTTGAGAAATGTACATTTAAATACAAATGATAATATTATTGAGATTGGTTCAGGGAAAGGTCATTTCTCGTTTGAATTAGCTAAAAGGTGTAATTATGTAACCGCCATTGAAATAGATCCTAAATTATGTAGGATAACTAAAAACAAACTTATTGAATATGAGAACTTCCAGGTTATCAATAAAGATATTTTACAATTTAAGTTTCCTAAAAATAAGTCATATAAGATATTTGGAAATATACCCTACAATATAAGTACAGATATAATTCGAAAAATTGTTTTTGAAAGCACAGCTACAGAAAGTTATTTAATAGTGGAATATGGATTTGCTAAAAGGTTGCTAAATACAAATCGTTCACTAGCACTATTTTTAATGACAGAAGTTGATATATCCATATTAAGTAAAATCCCTAGAGAATACTTTCATCCAAAACCTAGAGTTAATAGCTCGTTAATTGTATTAAAAAGACACCCTTCAAAAATATCACTCAAAGATAGAAAACAATATGAAAATTTTGTTATGAAATGGGTTAACAAAGAATACATAAAACTATTTTCCAAAAACCAATTTTATCAAGCCTTAAAATATGCAAGAATTGACGATTTAAACAATATTAGCTTTGAACAATTCTTGTCTCTTTTCAATAGCTATAAATTATTTAATAGATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36841","NCBI_taxonomy_name":"Plasmid pGT633","NCBI_taxonomy_id":"28406"}}}},"ARO_accession":"3000595","ARO_id":"36734","ARO_name":"ErmT","ARO_description":"ErmT confers MLSb phenotype.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35946":{"category_aro_accession":"0000027","category_aro_cvterm_id":"35946","category_aro_name":"roxithromycin","category_aro_description":"Roxithromycin is a semi-synthetic, 14-carbon ring macrolide antibiotic derived from erythromycin. It is used to treat respiratory tract, urinary and soft tissue infections. Roxithromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35974":{"category_aro_accession":"0000057","category_aro_cvterm_id":"35974","category_aro_name":"telithromycin","category_aro_description":"Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36315":{"category_aro_accession":"3000176","category_aro_cvterm_id":"36315","category_aro_name":"dirithromycin","category_aro_description":"Dirithromycin is an oxazine derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome to inhibit bacterial protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin 1A is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"vernamycin B-gamma","category_aro_description":"Vernamycin B-gamma is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1276":{"model_id":"1276","model_name":"OXA-210","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"884":{"protein_sequence":{"accession":"AEE61368.1","sequence":"MAIRIFAILFSIFSLATFAHAQEGTLERSDWRKFFSEFQAKGTIVVADERQADRAMLVFDPVRSKKRYSPASTFKIPHTLFALDAGAVRDEFQIFRWDGVNRGFAGHNQDQDLRSAMRNSTVWVYELFAKEIGDDKARRYLKKIDYGNADPSTSNGDCWIEGSLAISAQEQIAFLRKLYRNELPFRVEHQRLVKDLMIVEAGRNWILRAKTGWEGRMGWWVGWVEWPTGSVFFALNIDTPNRMDDLFKREAIVRAILRSIEALPPNPAVNSDAAR"},"dna_sequence":{"accession":"JF795487","fmin":"0","fmax":"828","strand":"+","sequence":"ATGGCAATCCGAATCTTCGCGATACTTTTCTCCATTTTTTCTCTTGCCACTTTCGCGCATGCGCAAGAAGGCACGCTAGAACGTTCTGACTGGAGGAAGTTTTTCAGCGAATTTCAAGCCAAAGGCACGATAGTTGTGGCAGACGAACGCCAAGCGGATCGTGCCATGTTGGTTTTTGATCCTGTGCGATCGAAGAAACGCTACTCGCCTGCATCGACATTCAAGATACCTCATACACTTTTTGCACTTGATGCAGGCGCTGTTCGTGATGAGTTCCAGATTTTTCGATGGGACGGCGTTAACAGGGGCTTTGCAGGCCACAATCAAGACCAAGATTTGCGATCAGCAATGCGGAATTCTACTGTTTGGGTGTATGAGCTATTTGCAAAGGAAATTGGTGATGACAAAGCTCGGCGCTATTTGAAGAAAATCGACTATGGCAACGCCGATCCTTCGACAAGTAATGGCGATTGCTGGATAGAAGGCAGCCTTGCAATCTCGGCGCAGGAGCAAATTGCATTTCTCAGGAAGCTCTATCGTAACGAGCTGCCCTTTCGGGTAGAACATCAGCGCTTGGTCAAGGATCTCATGATTGTGGAAGCCGGTCGCAACTGGATACTGCGTGCAAAGACGGGCTGGGAAGGCCGTATGGGTTGGTGGGTAGGATGGGTTGAGTGGCCGACTGGCTCCGTATTCTTCGCACTGAATATTGATACGCCAAACAGAATGGATGATCTTTTCAAGAGGGAGGCAATCGTGCGGGCAATCCTTCGCTCTATTGAAGCGTTACCGCCCAACCCGGCAGTCAACTCGGACGCTGCGCGATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001487","ARO_id":"37887","ARO_name":"OXA-210","ARO_description":"OXA-210 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1277":{"model_id":"1277","model_name":"GES-16","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"835":{"protein_sequence":{"accession":"ADJ94120.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAEIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMSDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"HM173356","fmin":"511","fmax":"1375","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTGAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGAGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACGCTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAGT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36783","NCBI_taxonomy_name":"Serratia marcescens","NCBI_taxonomy_id":"615"}}}},"ARO_accession":"3002345","ARO_id":"38745","ARO_name":"GES-16","ARO_description":"GES-16 is a beta-lactamase. From the Lahey list of GES beta-lactamases.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1278":{"model_id":"1278","model_name":"TEM-45","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1495":{"protein_sequence":{"accession":"CAA64682.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMLSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDEQNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"X95401","fmin":"208","fmax":"1069","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGTTGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACAAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000914","ARO_id":"37294","ARO_name":"TEM-45","ARO_description":"TEM-45 is an inhibitor-resistant beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1279":{"model_id":"1279","model_name":"TEM-104","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"995":{"protein_sequence":{"accession":"AAM61952.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIVEIGASLIKHW"},"dna_sequence":{"accession":"AF516719","fmin":"214","fmax":"1075","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGTCGAGATAGGTGCCTCACTGATTAAGCATTGGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000967","ARO_id":"37347","ARO_name":"TEM-104","ARO_description":"TEM-104 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1280":{"model_id":"1280","model_name":"QnrB12","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"176":{"protein_sequence":{"accession":"CAO82104.1","sequence":"MMTLALVGEKIDRNRFTGAKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAILKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGSDFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFSSFDWRAANFTHCDLTNSELGDLDVRGVDLQGVKLDSYQASLILERLGIAVIG"},"dna_sequence":{"accession":"AM774474","fmin":"2431","fmax":"3079","strand":"+","sequence":"ATGATGACTCTGGCATTAGTTGGCGAAAAAATTGACAGAAACAGATTCACTGGTGCGAAAGTTGAAAATAGCACATTTTTCAACTGTGATTTTTCGGGTGCCGACCTCAGCGGCACTGAGTTTATTGGCTGTCAGTTCTATGATCGAGAGAGCCAGAAAGGGTGTAATTTTAGTCGCGCTATCCTGAAAGATGCCATTTTCAAAAGTTGTGATCTCTCCATGGCGGATTTCAGGAATGTGAGCGCGCTGGGAATCGAAATTCGCCACTGCCGCGCACAAGGTTCAGATTTTCGCGGCGCAAGCTTTATGAATATGATTACCACACGCACCTGGTTTTGTAGCGCCTATATCACCAATACCAACTTAAGCTACGCCAACTTTTCAAAAGTCGTACTGGAAAAGTGCGAGCTGTGGGAAAACCGTTGGATGGGTACTCAGGTACTGGGGGCGACGTTCAGTGGTTCAGATCTTTCCGGCGGTGAGTTTTCGTCGTTCGACTGGCGGGCCGCAAACTTTACGCACTGTGATTTGACCAATTCAGAACTGGGCGATCTCGATGTCCGGGGTGTTGATTTGCAAGGCGTCAAACTGGACAGCTACCAGGCATCGTTGATCCTGGAACGTCTTGGCATCGCTGTCATTGGTTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39583","NCBI_taxonomy_name":"Citrobacter werkmanii","NCBI_taxonomy_id":"67827"}}}},"ARO_accession":"3002726","ARO_id":"39160","ARO_name":"QnrB12","ARO_description":"QnrB12  is a plasmid-mediated quinolone resistance protein found in Citrobacter werkmanii","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1281":{"model_id":"1281","model_name":"OXA-110","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1600":{"protein_sequence":{"accession":"ABV31690.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGEKRLFPEWEKNMTLGDAMKASALPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"EF650036","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAATGGGATGGGGAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTCTTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTCTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001641","ARO_id":"38041","ARO_name":"OXA-110","ARO_description":"OXA-110 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1282":{"model_id":"1282","model_name":"SIM-1 beta-lactamase","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1152":{"protein_sequence":{"accession":"ACT66697.1","sequence":"MRTLLILCLFGTLNTAFAEEAQPDLKIEKIEEGIYLHTSFQEYKGFGIVKKQGLVVLDNHKAYLIDTPASAGDTEKLVNWLEKNDFTVNGSISTHFHDDSTAGIEWLNTKSIPTYASKLTNELLNKNGKTQAKHSFDKESFWLVKNKIEIFYPGPGHTQDNEVVWIPNKKILFGGCFIKPNGLGNLSDANLEAWPGSAKKMISKYSKAKLVIPSHSEIGDASLLKLTWEQAIKGLNESKSKPPLIN"},"dna_sequence":{"accession":"GQ288397","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAGAACTTTATTGATTTTATGTTTATTCGGCACTTTAAATACCGCGTTTGCGGAAGAAGCCCAGCCAGATTTAAAAATTGAAAAAATAGAAGAAGGGATCTATCTTCATACATCTTTTCAAGAGTACAAGGGATTCGGCATCGTTAAAAAACAAGGCTTAGTAGTTCTTGACAATCACAAGGCATATCTCATCGACACTCCAGCTTCCGCAGGAGATACTGAAAAGCTAGTAAACTGGCTCGAAAAAAATGATTTCACTGTCAATGGAAGCATTTCAACACATTTCCACGACGACAGTACTGCTGGGATAGAGTGGCTTAATACAAAGTCCATCCCCACATATGCATCTAAATTGACAAATGAATTGCTAAATAAAAATGGCAAAACTCAAGCCAAGCACTCTTTTGATAAAGAGAGCTTTTGGTTGGTCAAAAATAAAATTGAAATTTTTTATCCAGGCCCAGGACACACTCAAGATAACGAAGTTGTCTGGATACCTAATAAAAAAATCCTATTCGGGGGCTGTTTTATAAAACCGAATGGCCTTGGCAATCTAAGTGACGCAAATTTGGAAGCTTGGCCAGGCTCCGCAAAAAAAATGATATCAAAATACAGTAAGGCAAAACTTGTTATCCCAAGCCACAGTGAAATCGGAGACGCATCACTATTGAAACTCACATGGGAACAGGCCATTAAAGGTTTAAATGAAAGCAAATCAAAACCGCCGCTCATTAATTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39090","NCBI_taxonomy_name":"Acinetobacter bereziniae","NCBI_taxonomy_id":"106648"}}}},"ARO_accession":"3000846","ARO_id":"37226","ARO_name":"SIM-1","ARO_description":"SIM-1 is an integron-encoded Ambler class B beta-lactamase isolated from Acinetobacter baumannii","ARO_category":{"41370":{"category_aro_accession":"3004206","category_aro_cvterm_id":"41370","category_aro_name":"SIM beta-lactamase","category_aro_description":"SIM beta-lactamases are Class B beta-lactamases that are capable of hydrolyzing a wide variety of beta-lactams, including penicillins, narrow- to expanded-spectrum cephalosporins, and carbapenem. The SIM family of beta-lactamases appear to be transferable through integrons.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1283":{"model_id":"1283","model_name":"KPC-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1437":{"protein_sequence":{"accession":"ACB71165.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGGYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"EU555534","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGGGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002316","ARO_id":"38716","ARO_name":"KPC-6","ARO_description":"KPC-6 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1284":{"model_id":"1284","model_name":"IND-15","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1987":{"protein_sequence":{"accession":"BAJ14288.1","sequence":"MKKSIQLLMMSMFLSPLINAQVKDFVIEPPVKPNLYLYKSFGVFGGKEYSANAVYLTTKKGVVLFDVPWQKEQYQTLMDTIQKRHHLPVIAVFATHSHDDRAGDLSFYNQKGIKTYATAKTNELLKKDGKATSTEIIKTGKPYKIGGEEFMVDFLGEGHTVDNVVVRFPKYKVLDGGCLVKSRTATDLGYTGEANVKQWPETMRKLKMKYAQATLVIPGHDEWKGGGHVQHTLDLLDKNKKPE"},"dna_sequence":{"accession":"AB563173","fmin":"32","fmax":"764","strand":"+","sequence":"ATGAAAAAAAGTATTCAGCTTTTGATGATGTCAATGTTTTTAAGCCCATTGATCAATGCCCAGGTTAAAGATTTTGTAATTGAGCCGCCTGTTAAACCCAACCTGTATCTTTATAAAAGTTTCGGAGTTTTCGGGGGTAAAGAATATTCTGCCAATGCTGTATATCTTACCACTAAGAAAGGAGTGGTCTTATTTGATGTCCCATGGCAAAAGGAACAATATCAAACCCTTATGGACACTATACAAAAGCGTCATCACCTTCCTGTAATTGCTGTATTTGCCACCCACTCTCATGATGACAGAGCGGGCGATCTAAGCTTTTACAATCAAAAAGGAATTAAAACATATGCGACCGCCAAGACCAATGAACTGTTGAAAAAAGACGGAAAAGCAACCTCAACCGAAATTATAAAAACAGGAAAACCTTACAAAATTGGTGGTGAAGAATTTATGGTAGACTTTCTTGGAGAAGGACATACAGTTGATAATGTTGTTGTACGGTTCCCCAAATATAAAGTACTGGACGGAGGATGTCTTGTAAAAAGCAGGACAGCCACTGACCTGGGATATACCGGTGAAGCAAACGTAAAACAATGGCCGGAAACCATGCGAAAACTAAAAATGAAATATGCTCAGGCTACTCTGGTAATCCCGGGACACGACGAATGGAAAGGCGGTGGTCATGTACAGCATACTCTGGATCTTCTGGATAAGAATAAAAAGCCGGAATAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36916","NCBI_taxonomy_name":"Chryseobacterium indologenes","NCBI_taxonomy_id":"253"}}}},"ARO_accession":"3002270","ARO_id":"38670","ARO_name":"IND-15","ARO_description":"IND-15 is a beta-lactamase found in Escherichia coli","ARO_category":{"36199":{"category_aro_accession":"3000060","category_aro_cvterm_id":"36199","category_aro_name":"IND beta-lactamase","category_aro_description":"IND beta-lactamases are class B carbapenem-hydrolyzing beta-lactamases","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1286":{"model_id":"1286","model_name":"SHV-34","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1235":{"protein_sequence":{"accession":"AAK64187.1","sequence":"MRYFRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGSVGMIEMDLASGRTLTAWRADGRFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AY036620","fmin":"88","fmax":"949","strand":"+","sequence":"ATGCGTTATTTTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCAGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGGACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGGATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001092","ARO_id":"37472","ARO_name":"SHV-34","ARO_description":"SHV-34 is an extended-spectrum beta-lactamase found in E. coli.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1287":{"model_id":"1287","model_name":"CTX-M-110","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1665":{"protein_sequence":{"accession":"AEM44648.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEEHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGNL"},"dna_sequence":{"accession":"JF274242","fmin":"0","fmax":"877","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAGAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGAATCTCT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36952","NCBI_taxonomy_name":"Shigella sp. SH165","NCBI_taxonomy_id":"1074431"}}}},"ARO_accession":"3001970","ARO_id":"38370","ARO_name":"CTX-M-110","ARO_description":"CTX-M-110 is a beta-lactamase found in Shigella spp.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1288":{"model_id":"1288","model_name":"OXA-82","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1846":{"protein_sequence":{"accession":"ABV71248.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWVVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"EU019536","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCAAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGGTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001635","ARO_id":"38035","ARO_name":"OXA-82","ARO_description":"OXA-82 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1289":{"model_id":"1289","model_name":"OKP-B-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1831":{"protein_sequence":{"accession":"CAJ19615.1","sequence":"MRYVRLCLISLIAALPLAVFASPQPLEQIKISESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKIVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMATTLRKLLTTPSLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPDGKAERIVVIYLRDTAATMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM051156","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCAGCCGCTTGAGCAGATTAAAATCAGCGAAAGTCAGCTGGCGGGCCGGGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGCGACGAACAGCTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGATCGTCGGCGGCCCCGCGGGATTGACAGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGATCGCTGGGAAACGGAACTCAATGAGGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCGGCCAGCATGGCCACCACCCTGCGCAAGCTGCTAACCACCCCCTCTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTTGACGACCGGGTGGCCGGCCCGTTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGTGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAAGCGGAGCGTATCGTGGTGATCTATCTGCGGGATACCGCAGCGACCATGGCCGAACGTAACCAGCAGATCGCCGGGATAGGCGCGGCGCTGATCGAGCACTGGCAGCGCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002440","ARO_id":"38840","ARO_name":"OKP-B-7","ARO_description":"OKP-B-7 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1290":{"model_id":"1290","model_name":"TEM-141","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1399":{"protein_sequence":{"accession":"AAX56615.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVEDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AY956335","fmin":"38","fmax":"899","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAGAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001004","ARO_id":"37384","ARO_name":"TEM-141","ARO_description":"TEM-141 is a broad-spectrum beta-lactamase found in Enterobacter cloacae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1291":{"model_id":"1291","model_name":"TEM-177","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1401":{"protein_sequence":{"accession":"CBJ06718.1","sequence":"MSIKHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTTPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGTGKRGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"FN652295","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTAAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAACCGGTAAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3001042","ARO_id":"37422","ARO_name":"TEM-177","ARO_description":"TEM-177 is an extended-spectrum beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1292":{"model_id":"1292","model_name":"CTX-M-109","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1510":{"protein_sequence":{"accession":"AEM44654.1","sequence":"VKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSRILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTK"},"dna_sequence":{"accession":"JF274248","fmin":"0","fmax":"864","strand":"-","sequence":"TTTGGTGACGATTTTAGCCGCCGACGCTAATACATCGCGACGGCTTTCTGCCTTAGGTTGAGGCTGGGTGAAGTAAGTGACCAGAATCAGCGGCGCACGATCTTTTGGCCAGATCACCGCGATATCGTTGGTGGTGCCATAGCCACCGCTGCCGGTTTTATCCCCCACAACCCAGGAAGCAGGCAGTCCAGCCTGAATGCTCGCTGCACCGGTGGTATTGCCTTTCATCCATGTCACCAGCTGCGCCCGTTGGCTGTCGCCCAATGCTTTACCCAGCGTCAGATTCCGCAGAGTTTGCGCCATTGCCCGAGGTGAAGTGGTATCACGCGGATCGCCCGGAATGGCGGTGTTTAACGTCGGCTCGGTACGGTCGAGACGGAACGTTTCGTCTCCCAGCTGTCGGGCGAACGCGGTGACGCTAGCCGGGCCGCCAACGTGAGCAATCAGCTTATTCATCGCCACGTTATCGCTGTACTGTAGCGCGGCCGCGCTAAGCTCAGCCAGTGACATCGTCCCATTGACGTGCTTTTCCGCAATCGGATTATAGTTAACAAGGTCAGATTTTTTGATCTCAACTCGCTGATTTAACAGATTCGGTTCGCTTTCACTTTTCTTCAGCACCGCGGCCGCGGCCATCACTTTACTGGTGCTGCACATCGCAAAGCGCTCATCAGCACGATAAAGTATTCGCGAATTATCTGCTGTGTTAATCAATGCCACACCCAGTCTGCCTCCCGACTGCCGCTCTAATTCGGCAAGTTTTTGCTGTACGTCCGCCGTTTGCGCATACAGCGGCACACTTCCTAACAACAGCGTGACGGTTGCCGTCGCCATCAGCGTGAACTGACGCAGTGATTTTTTAACC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39658","NCBI_taxonomy_name":"Shigella sp. SH361","NCBI_taxonomy_id":"1074437"}}}},"ARO_accession":"3001969","ARO_id":"38369","ARO_name":"CTX-M-109","ARO_description":"CTX-M-109 is a beta-lactamase found in Shigella spp.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1293":{"model_id":"1293","model_name":"OXA-197","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"883":{"protein_sequence":{"accession":"AEB98923.1","sequence":"MNIKALFLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWVVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEIAYKSLEQLGIL"},"dna_sequence":{"accession":"HQ425495","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAACATTAAAGCCCTCTTCCTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGGTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTGCTTATAAAAGCTTAGAACAATTAGGTATTTTA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36949","NCBI_taxonomy_name":"Acinetobacter nosocomialis","NCBI_taxonomy_id":"106654"}}}},"ARO_accession":"3001482","ARO_id":"37882","ARO_name":"OXA-197","ARO_description":"OXA-197 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1294":{"model_id":"1294","model_name":"Sed1 beta-lactamase","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"3310":{"protein_sequence":{"accession":"AAK63223.1","sequence":"MLKERFRQTVFIAAAVMPFIFSSTSLHAQATSDVQQVQKKLAALEKQSGGRLGVALINTADNSQVLYRADERFAMCSTSKVMTAAAVLKQSETHDGILQQKMTIKKADLTNWNPVTEKYVGNTMTLAELSAATLQYSDNTAMNKLLAHLGGPGNVTAFARSIGDTTFRLDRKEPELNTAIPGDERDTTSPLAMAKSLRKLTLGDALAGPQRAQLVDWLKGNTTGGQSIRAGLPAHWVVGDKTGAGDYGTTNDIAVIWPEDRAPLVLVTYFTQPQQDAKWRKDVLAAAAKIVTEGK"},"dna_sequence":{"accession":"AF321608","fmin":"0","fmax":"888","strand":"+","sequence":"ATGCTTAAGGAACGGTTTCGCCAGACGGTATTTATCGCTGCCGCTGTTATGCCCTTCATTTTTAGTAGCACTTCACTGCATGCGCAGGCGACGTCAGACGTGCAGCAGGTTCAGAAAAAGCTGGCGGCGCTGGAAAAGCAATCTGGCGGACGCCTGGGCGTGGCGCTGATTAATACCGCGGATAATTCGCAGGTGCTGTACCGCGCAGACGAGCGTTTTGCGATGTGCAGCACCAGTAAGGTCATGACCGCCGCCGCGGTATTAAAACAGAGTGAAACCCATGACGGTATTTTGCAGCAAAAAATGACCATTAAAAAAGCCGATCTGACCAACTGGAATCCCGTAACAGAGAAATATGTGGGTAATACGATGACATTAGCTGAGCTAAGCGCAGCGACGTTACAGTACAGCGATAATACCGCCATGAATAAACTGCTGGCGCATCTTGGCGGCCCCGGCAACGTCACGGCGTTTGCACGTTCCATTGGCGACACGACGTTTCGTCTCGATCGCAAAGAGCCGGAATTAAACACCGCCATTCCCGGCGATGAGCGCGACACAACATCGCCGCTGGCCATGGCCAAAAGTCTGCGTAAACTCACGCTGGGCGACGCGCTGGCAGGGCCCCAGCGCGCGCAGCTTGTCGACTGGCTGAAAGGCAACACCACCGGAGGCCAGAGCATTCGTGCCGGCCTTCCTGCACACTGGGTGGTGGGCGATAAAACCGGGGCGGGTGATTACGGCACCACGAATGACATCGCAGTGATCTGGCCGGAAGACCGCGCCCCGCTGGTGCTGGTAACCTATTTCACACAGCCACAGCAGGATGCGAAATGGCGTAAAGATGTCCTGGCCGCGGCGGCGAAAATTGTGACGGAAGGAAAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40168","NCBI_taxonomy_name":"Citrobacter sedlakii","NCBI_taxonomy_id":"67826"}}}},"ARO_accession":"3003561","ARO_id":"40167","ARO_name":"Sed-1","ARO_description":"Sed-1 is a chromosomal-encoded class A beta-lactamase identified in Citrobacter sedlakii.","ARO_category":{"41357":{"category_aro_accession":"3004193","category_aro_cvterm_id":"41357","category_aro_name":"Sed beta-lactamase","category_aro_description":"Sed beta-lactamases are Class A beta-lactamases that are capable of hydrolyzing benzypenicillin, cephalothin, and cloxacillin.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1285":{"model_id":"1285","model_name":"SAT-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"584":{"protein_sequence":{"accession":"BAD95494.1","sequence":"MKISVIPEQVAETLDAENHFIVREVFDVHLSDQGFELSTRSVSPYRKDYISDDDSDEDSACYGAFIDQELVGKIELNSTWNDLASIEHIVVSHTHRGKGVAHSLIEFAKKWALSRQLLGIRLETQTNNVPACNLYAKCGFTLGGIDLFTYKTRPQVSNETAMYWYWFSGAQDDA"},"dna_sequence":{"accession":"AB211124","fmin":"0","fmax":"525","strand":"+","sequence":"ATGAAGATTTCGGTGATCCCTGAGCAGGTGGCGGAAACATTGGATGCTGAGAACCATTTCATTGTTCGTGAAGTGTTCGATGTGCACCTATCCGACCAAGGCTTTGAACTATCTACCAGAAGTGTGAGCCCCTACCGGAAGGATTACATCTCGGATGATGACTCTGATGAAGACTCTGCTTGCTATGGCGCATTCATCGACCAAGAGCTTGTCGGGAAGATTGAACTCAACTCAACATGGAACGATCTAGCCTCTATCGAACACATTGTTGTGTCGCACACGCACCGAGGCAAAGGAGTCGCGCACAGTCTCATCGAATTTGCGAAAAAGTGGGCACTAAGCAGACAGCTCCTTGGCATACGATTAGAGACACAAACGAACAATGTACCTGCCTGCAATTTGTACGCAAAATGTGGCTTTACTCTCGGCGGCATTGACCTGTTCACGTATAAAACTAGACCTCAAGTCTCGAACGAAACAGCGATGTACTGGTACTGGTTCTCGGGAGCACAGGATGACGCCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002895","ARO_id":"39329","ARO_name":"SAT-2","ARO_description":"SAT-2 is a plasmid-mediated streptothricin acetyltransferase, which confers resistance to streptothricin, a nucleoside antibiotic. Originally described from an E. coli plasmid sequence by Heim et al., 1989.","ARO_category":{"37249":{"category_aro_accession":"3000869","category_aro_cvterm_id":"37249","category_aro_name":"streptothricin acetyltransferase (SAT)","category_aro_description":"AcetylCoA dependent acetyltransferase that acetylate streptothricins such as nourseothricin at position 16 (beta position of beta-lysine).","category_aro_class_name":"AMR Gene Family"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1273":{"model_id":"1273","model_name":"otr(A)","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1200"}},"model_sequences":{"sequence":{"660":{"protein_sequence":{"accession":"CAA37477.1","sequence":"MNKLNLGILAHVDAGKTSLTERLLHRTGVIDEVGSVDAGTTTTDSMELERQRGITIRSAVATFVLDDLKVNLIDTPGHSDFISEVERALGVLDGAVLVVSAVEGVQPQTRILMRTLRRLGIPTLVFVNKIDRGGARPDGVLREIRDRLTPAAVALSAVADAGTPRARAIALGPDTDPDFAVRVGELLADHDDAFLTAYLDEEHVLTEKEYAEELAAQTARGLVHPVYFGSALTGEGLDHLVHGIRELLPSVHASQDAPLRATVFKVDRGARGEAVAYLRLVSGTLGTRDSVTLHRVDHTGRVTEHAGRITALRVFEHGSATSETRATAGDIAQAWGLKDVRVGDRAGHLDGPPPRNFFAPPSLETVIRPERPEEAGRLHAALRMLDEQDPSIDLRQDEENAAGAVVRLYGEVQKEILGSTLAESFGVRVRFDPTRTVCIEKPVGTGEALIELDTRTHNYFWGAPWVCASDRPSPARAITFRLAVELGSLPLAFHKAIEETVHTTLRHGLYGWQVTDCAVTLTRTGVRSPVSAADDFRKANARLVLMDALGRAGTEVHEPVSSFELEVPAARLSPVLAKLAELGATPGVPTAEGDVFRLEGTMPTSLVHDFNQRVPGLTQGEGVFLAEHRGYRPAVGQPPVRPRPEGPNPLNRDEYILHVLKRV"},"dna_sequence":{"accession":"X53401","fmin":"0","fmax":"1992","strand":"+","sequence":"ATGAACAAGCTGAATCTGGGCATCCTGGCCCACGTTGACGCCGGCAAGACCAGCCTCACCGAGCGCCTGCTGCACCGCACCGGTGTGATCGACGAGGTCGGCAGCGTGGACGCCGGCACCACGACGACCGACTCGATGGAGCTGGAGCGGCAGCGCGGCATCACCATCCGGTCCGCCGTGGCCACGTTCGTCCTGGACGATCTCAAGGTCAACCTCATCGACACCCCGGGCCACTCCGACTTCATCTCCGAGGTCGAGCGGGCGCTCGGGGTGCTCGACGGCGCGGTCCTGGTGGTCTCGGCCGTCGAGGGCGTCCAGCCGCAGACCCGCATCCTGATGCGGACCCTGCGCAGGCTGGGCATTCCCACGCTGGTCTTCGTCAACAAGATCGACCGGGGCGGCGCGCGTCCCGACGGTGTGCTGCGGGAGATCCGCGACCGGCTCACCCCCGCCGCGGTGGCACTGTCCGCCGTGGCGGACGCCGGCACGCCGCGGGCCCGCGCGATCGCGCTCGGCCCGGACACCGACCCGGACTTCGCCGTCCGGGTCGGTGAGCTGCTGGCCGACCACGACGACGCGTTCCTCACCGCCTACCTGGACGAGGAACACGTACTGACCGAGAAGGAGTACGCGGAGGAACTGGCCGCGCAGACCGCGCGCGGTCTGGTGCACCCGGTGTACTTCGGGTCCGCGCTGACCGGCGAGGGCCTGGACCATCTGGTGCACGGCATCCGGGAGTTGCTGCCGTCCGTGCACGCGTCGCAGGACGCGCCGCTGCGGGCCACCGTGTTCAAGGTGGACCGTGGCGCGCGCGGCGAGGCCGTCGCGTACCTGCGGCTGGTCTCCGGCACGCTGGGCACCCGCGATTCGGTGACGCTGCACCGCGTCGACCACACCGGCCGGGTCACCGAGCACGCCGGACGCATCACCGCGCTGCGGGTCTTCGAGCACGGGTCGGCCACCAGCGAGACCCGGGCGACCGCCGGGGACATCGCGCAGGCGTGGGGCCTGAAGGACGTACGGGTCGGTGACCGGGCCGGGCACCTCGACGGTCCCCCGCCGCGCAACTTCTTCGCGCCGCCCAGCCTGGAGACCGTGATCAGGCCGGAGCGCCCGGAGGAAGCGGGACGGCTGCACGCCGCGCTGCGCATGCTGGACGAGCAGGACCCCTCGATCGACCTGCGGCAGGACGAGGAGAACGCGGCCGGCGCGGTGGTCCGCCTCTACGGGGAGGTGCAGAAGGAGATCCTCGGCAGCACGCTCGCGGAGTCCTTCGGCGTACGGGTGCGCTTCGACCCGACCCGTACGGTCTGCATCGAAAAGCCCGTGGGGACCGGCGAGGCGCTGATCGAGCTGGACACGCGGACGCACAACTACTTCTGGGGCGCACCGTGGGTCTGCGCGTCGGACCGGCCGAGCCCGGCGCGGGCGATCACGTTCCGTTTGGCGGTGGAACTGGGCTCGCTCCCCCTGGCCTTCCACAAGGCCATCGAGGAGACGGTGCACACCACCCTGCGGCACGGTCTGTACGGCTGGCAGGTCACCGACTGCGCCGTCACCCTGACCCGTACCGGCGTTCGCAGTCCGGTCAGCGCGGCCGACGACTTCCGCAAGGCCAACGCGCGCTTGGTCCTGATGGACGCGCTCGGCAGGGCCGGTACGGAGGTGCACGAGCCGGTCAGCTCCTTCGAACTGGAGGTGCCCGCCGCCCGGCTCAGCCCGGTACTTGCGAAACTCGCGGAACTGGGCGCGACGCCCGGTGTGCCCACGGCCGAGGGGGACGTCTTCCGCCTGGAGGGCACGATGCCGACCAGCCTCGTGCACGACTTCAACCAGCGGGTTCCCGGACTGACCCAGGGCGAGGGCGTGTTCCTGGCCGAGCACCGGGGCTACCGGCCCGCCGTCGGACAGCCGCCCGTGCGGCCGCGGCCCGAGGGGCCCAACCCGCTCAACCGCGACGAGTACATCCTGCACGTGCTCAAGCGCGTGTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36773","NCBI_taxonomy_name":"Streptomyces rimosus","NCBI_taxonomy_id":"1927"}}}},"ARO_accession":"3002891","ARO_id":"39325","ARO_name":"otr(A)","ARO_description":"otr(A) is an oxytetracycline resistance ribosomal protection protein found in Streptomyces rimosus","ARO_category":{"35921":{"category_aro_accession":"0000002","category_aro_cvterm_id":"35921","category_aro_name":"tetracycline-resistant ribosomal protection protein","category_aro_description":"A family of proteins known to bind to the 30S ribosomal subunit. This interaction prevents tetracycline and tetracycline derivatives from inhibiting ribosomal function. Thus, these proteins confer elevated resistance to tetracycline derivatives as a ribosomal protection protein.","category_aro_class_name":"AMR Gene Family"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1138":{"model_id":"1138","model_name":"tet(D)","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"250"}},"model_sequences":{"sequence":{"4378":{"protein_sequence":{"accession":"CAE51745.1","sequence":"MYIEQHSRYQNKANNIQLRYDDKQFHTTVIKDVLLWIEHNLDQSLLLDDVANKAGYTKWYFQRLFKKVTGVTLASYIRARRLTKAAVELRLTKKTILEIALKYQFDSQQSFTRRFKYIFKVTPSYYRRNKLWELEAMH"},"dna_sequence":{"accession":"BX664015","fmin":"204137","fmax":"204554","strand":"-","sequence":"TCAGTGCATTGCCTCCAATTCCCATAATTTATTACGCCGATAATAACTTGGTGTAACCTTAAAAATGTACTTAAATCGACGTGTAAAAGATTGTTGGGAATCAAATTGATATTTTAATGCGATCTCAAGGATAGTTTTTTTCGTCAACCTCAACTCAACAGCCGCTTTCGTCAAACGACGAGCACGAATATAGCTAGCCAGTGTGACCCCTGTTACTTTTTTGAACAGCCGCTGAAAATACCACTTGGTATAACCCGCTTTATTCGCCACATCATCAAGCAGTAAAGACTGATCTAAATTATGTTCAATCCATAATAGAACATCTTTGATAACCGTTGTATGAAACTGCTTATCATCATATCTTAATTGGATGTTATTAGCTTTATTTTGATAGCGAGAATGCTGTTCAATATACAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36783","NCBI_taxonomy_name":"Serratia marcescens","NCBI_taxonomy_id":"615"}}}},"ARO_accession":"3000168","ARO_id":"36307","ARO_name":"tet(D)","ARO_description":"TetD is a tetracycline efflux pump found exclusively in Gram-negative bacteria.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1222":{"model_id":"1222","model_name":"fosA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"3366":{"protein_sequence":{"accession":"NP_249820.1","sequence":"MLTGLNHLTLAVADLPASIAFYRDLLGFRLEARWDQGAYLELGSLWLCLSREPQYGGPAADYTHYAFGIAAADFARFAAQLRAHGVREWKQNRSEGDSFYFLDPDGHRLEAHVGDLRSRLAACRQAPYAGMRFAD"},"dna_sequence":{"accession":"NC002516","fmin":"1221690","fmax":"1222098","strand":"+","sequence":"ATGCTTACCGGTCTCAATCACCTGACCCTGGCGGTCGCCGACCTGCCGGCCAGCATCGCCTTCTACCGCGATCTTCTCGGCTTTCGCCTGGAAGCGCGCTGGGACCAGGGCGCCTATCTCGAACTGGGTTCGCTGTGGCTGTGCCTGTCCCGGGAGCCGCAGTACGGCGGGCCGGCCGCGGACTACACGCACTACGCCTTCGGCATCGCCGCCGCGGATTTCGCCCGCTTCGCCGCGCAGCTGCGCGCGCATGGCGTGCGCGAATGGAAGCAGAACCGCAGCGAGGGCGATTCGTTCTACTTCCTCGACCCGGACGGCCATCGCCTGGAGGCCCACGTCGGCGACCTGCGCAGCCGGCTCGCGGCGTGCCGGCAAGCGCCCTATGCGGGAATGCGTTTCGCCGACTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3000149","ARO_id":"36288","ARO_name":"FosA","ARO_description":"An enzyme that confers resistance to fosfomycin in Serratia marcescens by breaking the epoxide ring of the molecule. It depends on the cofactors Manganese (II) and Potassium and uses Glutathione (GSH) as the nucleophilic molecule. In Pseudomonas aeruginosa, FosA catalyzes the conjugation of glutathione to carbon-1 of fosfomycin, rendering it ineffective as an antibacterial drug.","ARO_category":{"36272":{"category_aro_accession":"3000133","category_aro_cvterm_id":"36272","category_aro_name":"fosfomycin thiol transferase","category_aro_description":"Catalyzes the addition of a thiol group from a nucleophilic molecule to fosfomycin.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1295":{"model_id":"1295","model_name":"catII","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"742":{"protein_sequence":{"accession":"CAA37806.1","sequence":"MNFTRIDLNTWNRREHFALYRQQIKCGFSLTTKLDITAFRTALAETDYKFYPVMIYLISRVVNQFPEFRMAMKDNALIYWDQTDPVFTVFHKETETFSALFCRYCPDISEFMAGYNAVMAEYQHNTALFPQGALPENHLNISSLPWVSFDGFNLNITGNDDYFAPVFTMAKFQQEDNRVLLPVSVQVHHAVCDGFHAARFINTLQMMCDNILK"},"dna_sequence":{"accession":"X53797","fmin":"133","fmax":"775","strand":"+","sequence":"ATGAATTTTACCAGAATTGATCTGAACACCTGGAACCGCAGAGAACATTTTGCTCTTTATCGTCAGCAGATAAAATGCGGATTCAGCCTGACCACAAAACTCGATATTACAGCTTTTCGTACCGCACTGGCGGAAACGGATTATAAATTTTATCCGGTGATGATTTATCTGATCTCCCGGGTTGTTAATCAGTTTCCGGAGTTCCGGATGGCAATGAAAGATAATGCACTGATTTACTGGGATCAGACCGATCCTGTATTTACTGTTTTTCATAAAGAGACTGAAACATTTTCTGCGCTCTTCTGCCGTTATTGTCCGGATATCAGTGAATTTATGGCGGGCTATAATGCGGTGATGGCAGAATATCAGCATAATACTGCATTGTTCCCGCAGGGAGCGTTACCAGAGAACCACCTGAATATATCATCATTACCCTGGGTGAGTTTTGACGGATTTAACCTGAATATCACCGGTAATGATGATTATTTTGCTCCGGTGTTTACTATGGCGAAATTTCAGCAGGAAGATAACCGCGTATTATTACCTGTTTCTGTACAGGTACATCATGCCGTTTGTGATGGCTTTCATGCAGCCAGGTTTATTAATACACTTCAGATGATGTGTGATAACATACTGAAATAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36768","NCBI_taxonomy_name":"Haemophilus influenzae","NCBI_taxonomy_id":"727"}}}},"ARO_accession":"3002684","ARO_id":"39118","ARO_name":"catII","ARO_description":"catII is a plasmid-encoded variant of the cat gene found in Haemophilus influenzae, Agrobacterium tumefaciens and Escherichia coli","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. cat is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Bacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini","category_aro_class_name":"AMR Gene Family"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1296":{"model_id":"1296","model_name":"OKP-B-12","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"963":{"protein_sequence":{"accession":"CAG25831.1","sequence":"TALPLAVFASPQPLEQIKISEGQLAGRVGYVEMDLASGRMLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKSVGGPAGLTTFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMATTLRKLLTTPSLSARSQQQLLQWMVDDQVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPDGKAERIVVIYLRDTAATMAERNQQIAG"},"dna_sequence":{"accession":"AJ635420","fmin":"0","fmax":"789","strand":"+","sequence":"ACCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCAGCCGCTTGAGCAGATTAAAATCAGCGAAGGTCAGCTGGCGGGCCGGGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCATGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCTGTGCTGGCCCGGGTGGATGCCGGCGACGAACAGCTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGATAACAGCGCCGGCAATCTGCTGTTGAAGAGCGTCGGCGGCCCCGCGGGATTGACCACTTTTCTGCGCCAGATCGGTGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTCAATGAGGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCGGCCAGCATGGCCACCACCCTGCGCAAGTTGCTAACCACCCCCTCTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGACCAGGTGGCCGGCCCGTTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGTGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAAGCGGAGCGTATCGTGGTGATCTATCTGCGGGATACCGCTGCGACCATGGCCGAACGTAACCAGCAGATCGCCGGG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002445","ARO_id":"38845","ARO_name":"OKP-B-12","ARO_description":"OKP-B-12 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1297":{"model_id":"1297","model_name":"CTX-M-80","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"909":{"protein_sequence":{"accession":"ABW86620.2","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTVDVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"EU202673","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACCGTGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001941","ARO_id":"38341","ARO_name":"CTX-M-80","ARO_description":"CTX-M-80 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1298":{"model_id":"1298","model_name":"lsaA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"71":{"protein_sequence":{"accession":"AAT46077.1","sequence":"MSKIELKQLSFAYDNQEVLLFDQANITMDTNWKLGLIGRNGRGKTTLLRLLQKQLDYQGEILHQVDFVYFPQTVAEEQQLTYYVLQEVTSFEQWELERELTLLNVDPEVLWRPFSSLSGGEKTKVLLGLLFIEENAFPLIDEPTNHLDLAGRQQVAEYLKKKKHGFILVSHDRAFVDEVVDHILAIEKSQLTLYQGNFSIYEEQKKLRDAFELAENEKIKKEVNRLKETARKKAEWSMNREGDKYGNAKEKGSGAIFDTGAIGARAARVMKRSKHIQQRAETQLAEKEKLLKDLEYIDPLSMDYQPTHHKTLLTVEELRLGYEKNWLFAPLSFSINAGEIVGITGKNGSGKSSLIQYLLDNFSGDSEGEATLAHQLTISYVRQDYEDNQGTLSEFAEKNQLDYTQFLNNLRKLGMERAVFTNRIEQMSMGQRKKVEVAKSLSQSAELYIWDEPLNYLDVFNHQQLEALILSVKPAMLVIEHDAHFMKKITDKKIVLKS"},"dna_sequence":{"accession":"AY587982","fmin":"309","fmax":"1806","strand":"+","sequence":"ATGTCGAAAATTGAACTAAAACAACTATCTTTTGCCTATGATAATCAAGAAGTATTGCTTTTTGATCAGGCAAATATCACGATGGATACCAATTGGAAATTAGGATTGATTGGCCGCAATGGCCGTGGGAAAACAACCTTATTAAGATTGTTACAAAAACAGTTGGATTACCAAGGAGAGATTCTTCATCAAGTCGATTTCGTCTATTTTCCACAAACAGTTGCAGAAGAACAACAGCTCACTTATTATGTCTTACAAGAGGTGACTTCTTTTGAACAGTGGGAATTAGAACGAGAATTAACGCTTTTAAACGTTGATCCTGAAGTTTTATGGCGGCCCTTTTCTTCTTTATCAGGCGGCGAAAAGACGAAAGTTTTATTAGGTCTTCTTTTTATTGAAGAAAATGCCTTTCCTTTAATTGACGAGCCAACAAATCATTTAGATCTAGCTGGCAGACAACAAGTGGCTGAATATTTGAAGAAAAAGAAACACGGGTTTATTTTAGTCAGCCACGATCGGGCATTTGTTGATGAAGTGGTTGATCATATTTTGGCGATTGAAAAAAGTCAATTGACGCTGTATCAAGGGAATTTTTCTATTTATGAAGAGCAAAAAAAATTAAGAGATGCTTTTGAACTAGCAGAAAATGAAAAAATCAAAAAAGAAGTCAATCGCTTGAAAGAAACCGCTCGTAAAAAAGCGGAATGGTCGATGAACCGTGAAGGTGATAAGTACGGCAACGCTAAGGAAAAAGGGAGCGGGGCGATTTTTGATACAGGAGCCATTGGTGCCCGGGCAGCGCGCGTAATGAAGCGCTCGAAACACATTCAACAACGCGCCGAAACACAATTAGCAGAAAAAGAAAAACTATTAAAAGATCTTGAGTATATTGATCCTTTGTCAATGGATTATCAGCCAACGCATCACAAAACATTATTGACGGTGGAAGAGCTTCGTCTAGGCTACGAGAAAAATTGGCTATTTGCGCCACTTTCTTTTTCAATAAACGCGGGAGAAATTGTTGGAATAACAGGGAAAAATGGCTCAGGAAAATCGAGCTTAATTCAGTATTTATTGGATAATTTTTCTGGGGATTCAGAAGGCGAAGCCACTTTGGCTCACCAATTAACCATTTCTTATGTGCGCCAAGATTATGAAGACAATCAAGGAACTTTATCCGAATTTGCAGAGAAAAATCAGTTAGATTACACTCAATTTTTAAATAACTTACGAAAACTTGGGATGGAGCGTGCCGTTTTCACTAATCGAATTGAACAAATGAGTATGGGGCAACGGAAAAAAGTCGAAGTAGCCAAATCATTGTCTCAATCAGCTGAACTTTATATTTGGGATGAACCCCTTAATTACTTGGATGTATTTAATCATCAACAATTAGAAGCGCTAATCTTATCTGTGAAGCCTGCAATGCTAGTGATTGAGCATGATGCACATTTCATGAAGAAAATAACAGATAAAAAAATTGTCTTGAAATCATAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3000300","ARO_id":"36439","ARO_name":"lsaA","ARO_description":"LsaA is an ABC efflux pump expressed in Enterococcus faecalis. It confers resistance to clindamycin, quinupristin-dalfopristin, and dalfopristin.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37716":{"category_aro_accession":"3001317","category_aro_cvterm_id":"37716","category_aro_name":"pleuromutilin","category_aro_description":"Pleuromutilin is a natural product antibiotic produced by Clitopilus passeckerianus. Related antibiotics of clinical significance, such as tiamulin and retapamulin, are semi-synthetic derivatives of this compound.","category_aro_class_name":"Antibiotic"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1299":{"model_id":"1299","model_name":"AAC(6')-Ic","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"306":{"protein_sequence":{"accession":"AAA26549.1","sequence":"MIVICDHDNLDAWLALRTALWPSGSPEDHRAEMREILASPHHTAFMARGLDGAFVAFAEVALRYDYVNGCESSPVAFLEGIYTAERARRQGWAARLIAQVQEWAKQQGCSELASDTDIANLDSQRLHAALGFAETERVVFYRKTLG"},"dna_sequence":{"accession":"M94066","fmin":"1553","fmax":"1994","strand":"+","sequence":"ATGATCGTCATCTGCGACCACGACAACCTCGACGCCTGGCTGGCGCTGCGCACCGCGCTGTGGCCCTCCGGCTCGCCTGAAGATCACCGCGCGGAAATGCGCGAGATATTGGCTTCGCCGCACCACACCGCGTTTATGGCGCGGGGGCTGGACGGCGCTTTCGTTGCCTTTGCCGAGGTCGCGCTGCGCTACGATTACGTCAACGGCTGCGAATCGTCGCCGGTGGCGTTTTTGGAAGGAATTTATACCGCCGAACGCGCCCGCCGCCAGGGCTGGGCCGCGCGCCTGATCGCGCAGGTGCAGGAGTGGGCGAAGCAACAGGGGTGCAGCGAGCTGGCGTCGGATACCGATATCGCCAATCTGGACTCCCAGCGCCTGCATGCGGCGCTGGGCTTTGCCGAAACGGAGCGAGTAGTGTTTTACCGCAAAACGCTGGGCTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36783","NCBI_taxonomy_name":"Serratia marcescens","NCBI_taxonomy_id":"615"}}}},"ARO_accession":"3002549","ARO_id":"38949","ARO_name":"AAC(6')-Ic","ARO_description":"AAC(6')-Ic is a chromosomal-encoded aminoglycoside acetyltransferase in S. marcescens","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1302":{"model_id":"1302","model_name":"tet34","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"3346":{"protein_sequence":{"accession":"BAB59035.1","sequence":"MSKKFIITWDAMQNYCRQLAEKQMPAEQWKGIWAVSRGGLVPGAILARELGIRHVDTICISSYDHDHQRDMTVLKAPEGDGEGYLIVEDLVDSGDTARKLREMYPKAKLIAVCAKPSGATLLDDYVVDIAQDTWIEQPWDTTVQFVEPINRKQK"},"dna_sequence":{"accession":"AB061440","fmin":"305","fmax":"770","strand":"-","sequence":"TTACTTTTGCTTGCGATTAATTGGTTCCACAAATTGCACTGTGGTATCCCATGGCTGCTCAATCCATGTATCTTGAGCAATATCAACCACGTAATCATCAAGAAGAGTGGCACCTGATGGCTTAGCGCAAACAGCAATCAGTTTCGCTTTCGGGTACATTTCACGTAGTTTACGCGCTGTATCACCGCTATCCACTAGGTCTTCGACGATTAGGTAACCTTCGCCATCACCTTCTGGCGCTTTTAGCACGGTCATATCACGCTGGTGATCATGATCGTAGCTAGAGATACAAATGGTATCAACGTGACGAATACCAAGTTCACGCGCAAGAATAGCACCCGGTACTAGACCGCCACGGCTCACCGCCCAAATACCTTTCCACTGTTCAGCTGGCATCTGTTTTTCAGCAAGCTGACGACAGTAATTTTGCATGGCGTCCCAAGTGATAATGAATTTTTTGCTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36750","NCBI_taxonomy_name":"Vibrio sp. No.6","NCBI_taxonomy_id":"159729"}}}},"ARO_accession":"3002870","ARO_id":"39304","ARO_name":"tet34","ARO_description":"tet34 causes the activation of Mg2+-dependent purine nucleotide synthesis, which protects the protein synthesis pathway. It is found in Gram-negative Vibrio","ARO_category":{"36176":{"category_aro_accession":"3000036","category_aro_cvterm_id":"36176","category_aro_name":"tetracycline inactivation enzyme","category_aro_description":"Enzymes or other gene products which hydroxylate tetracycline and other tetracycline derivatives. Hydroxylation inactivates tetracycline-like antibiotics, thus conferring resistance to these compounds.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1303":{"model_id":"1303","model_name":"BEL-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1280":{"protein_sequence":{"accession":"ACV69996.1","sequence":"MKLLLYPLLLFLVIPAFAQADFEHAISDLEAHNQAKIGVALVSENGNLIQGYRANERFAMCSTFKLPLAALVLSRIDAGEENPERKLHYDSAFLEEYAPAAKRYVATGYMTVTEAIQSALQLSDNAAANLLLKEVGGPPLLTKYFRSLGDKVSRFDRIEPTLNTNTPGDERDTTTPMSMAQTVSKLIFGDTLTYKSKGQLRRLLIGNQTGDKTIRAGLPDSWVTGDKTGSCANGGRNDVAFFITTAGKKYVLSVYTNAPELQGEERALLIASVAKLARQYVVH"},"dna_sequence":{"accession":"FJ666063","fmin":"0","fmax":"852","strand":"+","sequence":"ATGAAACTGCTGCTCTACCCGTTATTGCTGTTCCTTGTCATTCCAGCCTTTGCCCAGGCGGACTTTGAACATGCCATTTCAGATCTTGAGGCGCACAATCAAGCCAAGATCGGAGTGGCCCTAGTTAGTGAAAATGGCAACCTGATTCAAGGGTATCGTGCGAATGAAAGGTTCGCGATGTGCTCAACTTTCAAGTTGCCGTTGGCCGCTCTTGTTCTGAGTCGCATTGACGCTGGGGAAGAGAATCCTGAGCGCAAGCTTCATTACGATTCCGCGTTCCTTGAAGAGTACGCCCCAGCCGCAAAACGGTATGTGGCAACTGGATATATGACTGTAACTGAGGCAATTCAATCCGCCCTCCAACTCAGCGACAATGCCGCAGCTAACCTGCTGTTAAAAGAGGTTGGCGGCCCACCTTTATTGACAAAGTATTTCCGTAGCCTGGGTGATAAAGTAAGTCGCTTTGATCGTATTGAACCGACTTTGAACACCAATACGCCCGGCGATGAAAGAGATACAACAACGCCCATGTCCATGGCACAGACTGTGTCAAAGCTGATTTTTGGAGACACGTTGACATATAAATCCAAGGGGCAGCTAAGGCGATTACTCATCGGCAATCAGACCGGGGACAAAACCATTCGAGCTGGCTTGCCTGATTCATGGGTAACGGGTGACAAGACAGGCTCGTGTGCGAATGGCGGCCGTAACGATGTGGCGTTTTTTATAACCACTGCCGGAAAAAAATATGTTCTTTCTGTATATACCAATGCACCTGAATTGCAAGGCGAGGAAAGGGCGTTATTAATTGCTTCTGTAGCAAAGTTAGCACGTCAATATGTTGTTCACTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002386","ARO_id":"38786","ARO_name":"BEL-2","ARO_description":"BEL-2 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"38784":{"category_aro_accession":"3002384","category_aro_cvterm_id":"38784","category_aro_name":"BEL beta-lactamase","category_aro_description":"BEL beta-lactamases are class A expanded-spectrum beta-lactamases that are inhibited by clavulanic acid. They are chromosomally encoded and hydrolyze most cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1304":{"model_id":"1304","model_name":"CTX-M-85","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1336":{"protein_sequence":{"accession":"ACI29347.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTPAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"FJ214368","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCCGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35772","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Albany","NCBI_taxonomy_id":"211968"}}}},"ARO_accession":"3002495","ARO_id":"38895","ARO_name":"CTX-M-85","ARO_description":"CTX-M-85 is a beta-lactamase found in Salmonella enterica","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1306":{"model_id":"1306","model_name":"IND-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1093":{"protein_sequence":{"accession":"AAS78754.1","sequence":"MKKRIQFFMVSMMLAPMFNAQVKDFVIEPPIKNNLHIYKTFGVFGGKEYSANSVYLVTKKGVVLFDVPWEKAQYQSLMDTIKKRHNLPVIAVFATHSHDDRAGDLSFFNNKGIKTYATSKTNEFLKKDGKATSTEIIKTGKPYRIGGEEFTVDFLGEGHTADNVVVWFPKYNVLDGGCLVKSNSATDLGYIKEANVEQWPITIDKLKAKYSKATLIIPGHDDWKGGGHVEHTLELLNKK"},"dna_sequence":{"accession":"AY504627","fmin":"0","fmax":"720","strand":"+","sequence":"ATGAAAAAAAGAATTCAGTTCTTTATGGTTTCAATGATGCTTGCTCCAATGTTTAATGCGCAGGTAAAGGATTTTGTAATTGAGCCACCCATTAAAAATAACTTACATATTTATAAAACATTTGGAGTATTTGGTGGTAAAGAATATTCTGCCAACTCAGTATATCTTGTCACTAAAAAAGGAGTCGTTTTATTTGATGTTCCCTGGGAAAAAGCACAATACCAAAGCCTGATGGATACAATCAAAAAACGTCATAACCTACCGGTTATTGCTGTATTTGCTACGCATTCCCATGATGACCGCGCTGGAGATCTAAGCTTTTTCAATAATAAAGGGATTAAAACCTATGCTACCAGCAAAACCAATGAGTTTTTGAAAAAAGACGGAAAAGCAACATCCACTGAAATCATAAAAACAGGAAAGCCTTACCGCATTGGAGGCGAAGAATTTACTGTTGATTTTCTGGGTGAAGGGCATACTGCTGATAATGTAGTGGTATGGTTTCCAAAATACAATGTACTGGATGGTGGTTGTCTGGTAAAAAGTAATTCAGCTACTGATTTAGGATATATTAAAGAAGCCAATGTGGAACAATGGCCAATAACCATAGATAAACTGAAGGCTAAATATTCAAAGGCAACATTGATTATTCCAGGACATGATGACTGGAAAGGCGGAGGACATGTTGAGCACACTCTTGAACTTCTTAACAAAAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36916","NCBI_taxonomy_name":"Chryseobacterium indologenes","NCBI_taxonomy_id":"253"}}}},"ARO_accession":"3002261","ARO_id":"38661","ARO_name":"IND-5","ARO_description":"IND-5 is a beta-lactamase found in Chryseobacterium indologenes","ARO_category":{"36199":{"category_aro_accession":"3000060","category_aro_cvterm_id":"36199","category_aro_name":"IND beta-lactamase","category_aro_description":"IND beta-lactamases are class B carbapenem-hydrolyzing beta-lactamases","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1307":{"model_id":"1307","model_name":"OXY-1-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"982":{"protein_sequence":{"accession":"CAB42615.1","sequence":"MLKSSWRKTALMAAAAVPLLLASGSLWASADAIQQKLADLEKRSGGRLGVALINTADDSQTLYRGDERFAMCSTGKVMAAAAVLKQSESNPEVVNKRLEIKKSDLVVWSPITEKHLQSGMTLAELSAAALQYSDNTAMNKMISYLGGPEKVTAFAQSIGDVTFRLDRTEPALNSAIPGDKRDTTTPLAMAESLRKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPASWAVGDKTGAGDYGTTNDIAVIWPENHAPLVPVTYFTQPQQDAKSRKKVLAAAAKIVTEGL"},"dna_sequence":{"accession":"Y17715","fmin":"146","fmax":"1022","strand":"+","sequence":"ATGTTGAAAAGTTCGTGGCGTAAAACCGCCCTGATGGCCGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGTTCATTATGGGCCAGTGCCGATGCTATCCAGCAAAAGCTGGCTGATTTAGAAAAACGTTCCGGCGGTCGGCTGGGCGTAGCGCTGATTAACACGGCAGATGATTCGCAAACCCTCTATCGCGGCGATGAACGTTTTGCCATGTGCAGCACCGGTAAAGTGATGGCCGCCGCCGCGGTGTTAAAACAGAGCGAAAGCAATCCAGAGGTGGTGAATAAAAGGCTGGAGATTAAAAAATCGGATTTAGTGGTCTGGAGCCCGATCACCGAAAAACATCTGCAAAGCGGAATGACCCTGGCGGAACTCAGCGCGGCGGCGCTGCAGTACAGCGACAATACCGCGATGAATAAGATGATTAGCTACCTTGGCGGACCGGAAAAGGTGACCGCATTCGCCCAGAGTATCGGGGATGTCACTTTTCGTCTCGATCGTACGGAGCCGGCGCTGAACAGCGCGATTCCCGGCGATAAGCGCGATACCACCACCCCGTTGGCGATGGCCGAAAGCCTGCGCAAGCTGACGCTGGGCAATGCGCTGGGCGAACAGCAGCGCGCCCAGTTAGTGACGTGGCTAAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCAGGCCTGCCCGCAAGCTGGGCGGTCGGGGATAAAACCGGCGCCGGAGATTACGGCACCACCAACGATATTGCGGTGATCTGGCCGGAAAATCATGCCCCGCTGGTGCCGGTGACCTATTTTACCCAGCCGCAGCAAGATGCGAAAAGCCGCAAAAAGGTGTTAGCCGCGGCGGCAAAAATCGTCACCGAAGGGCTTTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002394","ARO_id":"38794","ARO_name":"OXY-1-6","ARO_description":"OXY-1-6 is a beta-lactamase found in Klebsiella oxytoca","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1308":{"model_id":"1308","model_name":"vanTE","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1300"}},"model_sequences":{"sequence":{"180":{"protein_sequence":{"accession":"AAL27444.1","sequence":"MKHRANGIDLFRIFAATMVVAIHTFPFQSIAPFLDEVITLTVFRVAVPFFFMITGYFLLGRLSLNFSYNNNQRVKKYLYKIGMIYLYSILLYFPLSLLNGTISLKMNILLLLKVFIFDGTFYHLWYFPASIIGTILVTLLLRSIGFKLTVAFSTCLYLVGLGGDSWYGITNQVPLLNKLYTFIFSWSDYTRSGVFFTPVFLCLGIFAYRVSKKLTASKILNLLFYVFIIGMTFESIFLHRFTNVKHDSMYLLLPSCALILFLMLLNWQPKLKVKESADLTLLVYILHPLVIVIVHSISKYIPILKNSLLNFLLVVVCSFILAQLLLNLKRKLRVSKQKIPFERASKEISASAIHHNINEIRKIIPKNTNIMGVVKANAYGCGMVEVAYELEKIGISFFCVATIEEAIALRKSGNQGDILILGYTHPNRINDIKKYNLIQSIVSEEHGKVLNLKKIPIRCHLQVDTGMHRLGVTPNVTIIQQMYLFSNLKIEGIYSHLGSSDSLEQESIARTNTQIFLFNNILSDLEQMGISYGYTHIQSSYGILNYPELSFDFVRIGILCYGFLSDYNSPTKIPIDLQPIVKVKASLITERIVEAGEYVGYGLGAKVEKRTRIGVVSIGYADGIPRALSNAKLTLEFKGQSIKQIGNICMDMMLVDLSEVEDISLNDELIVLPNISKIADEEQTITNELLSRLGSRLGTELN"},"dna_sequence":{"accession":"FJ872411","fmin":"41336","fmax":"43445","strand":"+","sequence":"ATGAAGCATAGAGCTAACGGCATTGATCTATTTCGAATATTCGCTGCTACTATGGTTGTTGCTATCCATACATTCCCTTTTCAATCAATAGCACCTTTTTTAGACGAAGTCATAACGTTAACTGTGTTTCGGGTAGCTGTCCCTTTTTTCTTTATGATTACAGGATATTTTTTGTTAGGAAGATTGTCATTAAATTTTTCGTATAATAATAATCAGAGAGTGAAAAAATATCTATACAAAATTGGAATGATTTATTTATATTCTATTTTATTGTATTTCCCATTATCTTTACTAAATGGCACTATTTCATTAAAAATGAACATACTTTTACTTTTAAAGGTTTTCATTTTTGACGGTACCTTTTATCACCTATGGTACTTTCCAGCTAGTATAATTGGAACGATTTTAGTAACCCTACTGTTACGTAGTATAGGATTTAAATTAACAGTCGCATTTTCTACATGTCTATATCTAGTTGGACTTGGTGGAGACAGCTGGTACGGGATAACCAATCAAGTTCCATTGCTAAATAAACTGTATACATTTATTTTTAGTTGGTCGGACTATACGCGTTCAGGTGTTTTCTTTACGCCTGTGTTTCTTTGCCTAGGAATATTTGCCTATAGAGTATCTAAAAAGTTAACTGCATCAAAGATATTAAACTTGCTTTTTTATGTGTTTATCATAGGTATGACTTTTGAGAGTATATTTCTACACCGATTTACGAACGTCAAACACGATAGTATGTATCTCTTATTGCCTTCATGTGCATTAATTTTGTTTTTAATGTTATTAAACTGGCAACCAAAACTAAAGGTAAAAGAATCAGCCGATTTAACGTTACTGGTTTATATTCTCCATCCATTAGTTATTGTAATTGTCCATTCTATAAGTAAGTATATTCCGATATTAAAAAACAGTTTGCTAAATTTCTTGTTAGTAGTCGTGTGCAGCTTTATACTAGCTCAGCTTCTGTTAAACTTAAAAAGAAAGCTAAGAGTTAGTAAGCAAAAAATACCATTTGAACGTGCTAGTAAAGAAATATCAGCTAGTGCAATACACCATAATATTAATGAAATACGAAAGATAATTCCCAAAAATACAAATATTATGGGTGTTGTGAAGGCAAATGCGTATGGCTGTGGCATGGTAGAGGTAGCTTATGAATTAGAAAAAATCGGTATTTCATTTTTCTGCGTAGCTACTATAGAAGAAGCAATTGCTTTAAGGAAATCAGGAAACCAAGGGGATATTTTAATTTTAGGGTATACACATCCCAATCGCATTAATGATATAAAAAAATATAATTTGATTCAATCGATTGTAAGTGAAGAACATGGGAAAGTGTTGAATCTAAAAAAAATACCTATTCGTTGTCATTTACAGGTTGATACTGGGATGCATCGTTTAGGTGTTACACCGAACGTAACAATTATTCAGCAGATGTATCTTTTTTCCAATCTTAAGATTGAGGGGATATACTCACACTTAGGTTCTTCAGACTCATTAGAGCAAGAATCAATCGCTCGAACAAATACTCAAATTTTTTTATTCAATAATATACTAAGTGATTTGGAACAAATGGGTATTTCCTACGGTTATACTCATATCCAAAGCAGCTATGGTATTTTAAATTACCCAGAATTAAGCTTTGATTTTGTGAGAATAGGAATTCTCTGTTATGGATTTTTAAGTGACTATAATAGTCCGACTAAAATCCCTATAGATTTACAACCTATAGTAAAAGTAAAAGCCTCTTTGATTACAGAAAGAATTGTGGAGGCAGGTGAATATGTTGGCTATGGATTAGGCGCTAAAGTTGAAAAAAGAACAAGAATAGGTGTCGTTAGTATTGGGTATGCGGACGGTATACCAAGGGCATTATCCAATGCTAAACTTACGTTAGAGTTTAAAGGTCAATCAATAAAACAGATTGGGAATATTTGTATGGATATGATGCTTGTTGATCTGTCCGAAGTGGAAGATATTTCCTTGAATGATGAACTAATCGTGTTACCTAATATTAGTAAAATCGCTGATGAAGAACAAACAATTACCAATGAGCTATTGAGTCGATTAGGTTCGAGGTTAGGTACAGAGTTAAATTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3002971","ARO_id":"39405","ARO_name":"vanTE","ARO_description":"vanTE is a vanT variant found in the vanE gene cluster","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36511":{"category_aro_accession":"3000372","category_aro_cvterm_id":"36511","category_aro_name":"vanT","category_aro_description":"VanT is a membrane bound serine racemase, converting L-serine to D-serine. It is associated with VanC, which incorporated D-serine into D-Ala-D-Ser terminal end of peptidoglycan subunits that have a decreased binding affinity with vancomycin. It was isolated from Enterococcus gallinarum.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1309":{"model_id":"1309","model_name":"ACT-20","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1853":{"protein_sequence":{"accession":"AHA80105.1","sequence":"MMKKSLCCALLLGLSCSALAAPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKSHYYTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPEKVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYHILEALQ"},"dna_sequence":{"accession":"KF526117","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTGGGCCTCTCTTGCTCTGCTCTCGCCGCGCCAGTATCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAATCGCACTATTACACGTTCGGTAAAGCCGATGTTGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAAGGTTGCCGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAAGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTACCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGTTCTACCGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39098","NCBI_taxonomy_name":"Enterobacter hormaechei","NCBI_taxonomy_id":"158836"}}}},"ARO_accession":"3001841","ARO_id":"38241","ARO_name":"ACT-20","ARO_description":"ACT-20 is a beta-lactamase. From the Lahey list of ACT beta-lactamases.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1310":{"model_id":"1310","model_name":"IMP-10","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1671":{"protein_sequence":{"accession":"BAB72069.1","sequence":"MSKLSVFFIFLFCSIATAAESLPDLKIEKLDEGVYVHTSFEEVNGWGVFPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNESKKPSKPSN"},"dna_sequence":{"accession":"AB074433","fmin":"16","fmax":"757","strand":"+","sequence":"ATGAGCAAGTTATCTGTATTCTTTATATTTTTGTTTTGCAGCATTGCTACCGCAGCAGAGTCTTTGCCAGATTTAAAAATTGAAAAGCTTGATGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGGTGGGGCGTTTTTCCTAAACATGGTTTGGTGGTTCTTGTAAATGCTGAGGCTTACCTAATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAGCGTGGCTATAAAATAAAAGGCAGCATTTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCGATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTGCTTAAAAAAGACGGTAAGGTTCAAGCCACAAATTCATTTAGCGGAGTTAACTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCGGGACACACTCCAGATAACGTAGTGGTTTGGTTGCCTGAAAGGAAAATATTATTCGGTGGTTGTTTTATTAAACCGTACGGTTTAGGCAATTTGGGTGACGCAAATATAGAAGCTTGGCCAAAGTCCGCCAAATTATTAAAGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAAGTCACAGTGAAGTTGGAGACGCATCACTCTTGAAACTTACATTAGAGCAGGCGGTTAAAGGGTTAAACGAAAGTAAAAAACCATCAAAACCAAGCAACTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002201","ARO_id":"38601","ARO_name":"IMP-10","ARO_description":"IMP-10 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1311":{"model_id":"1311","model_name":"OXY-5-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"816":{"protein_sequence":{"accession":"CAI43419.1","sequence":"MLKSSWRKTALMAAAVPLLLASGSLWASADAIQQKLADLEKRSGGRLGVALINTADDSQTLYRGDERFAMCSTGKVMAAAAVLKQSESNPEVVNKRLEIKKADLVVWSPITEKHLQSGMTLAELSAAALQYSDNTAMNKIIGYLGGPEKVTAFALSIGDVTFRLDRMEPALNSAIPGDKRDTTTPLAMAESLRKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPASWAVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKSRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"AJ871871","fmin":"0","fmax":"873","strand":"+","sequence":"ATGTTGAAAAGTTCGTGGCGTAAAACCGCCCTGATGGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGTTCATTATGGGCCAGTGCCGATGCTATCCAGCAAAAGCTGGCTGATTTAGAAAAACGTTCCGGCGGTCGGCTGGGCGTAGCGCTGATTAACACGGCAGATGATTCGCAAACCCTCTATCGCGGCGATGAACGGTTTGCCATGTGCAGCACCGGTAAAGTGATGGCCGCCGCCGCGGTGTTAAAACAGAGCGAAAGCAATCCAGAGGTAGTGAATAAAAGGCTGGAGATTAAAAAAGCGGATTTAGTAGTCTGGAGCCCGATTACCGAAAAACATCTGCAAAGCGGAATGACCCTGGCGGAACTCAGCGCGGCGGCGCTGCAGTACAGCGACAATACCGCGATGAATAAGATTATCGGTTACCTTGGCGGGCCGGAAAAAGTCACCGCATTCGCCCTGAGTATCGGTGACGTTACTTTTCGTCTCGATCGCATGGAGCCGGCGCTGAACAGCGCGATTCCCGGCGATAAGCGCGATACCACCACCCCGTTGGCGATGGCCGAAAGCCTGCGCAAGCTGACGCTGGGCAATGCGCTGGGCGAACAGCAGCGCGCCCAGTTAGTGACGTGGCTAAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCAGGCCTGCCCGCAAGCTGGGCGGTCGGGGATAAAACCGGCGCCGGAGATTACGGCACCACCAACGATATCGCGGTGATCTGGCCGGAAAATCATGCCCCGCTGGTGCTGGTGACCTATTTTACCCAGCCGCAGCAGGATGCGAAAAGCCGCAAAGAGGTGTTAGCCGCGGCGGCAAAAATCGTCACCGAAGGGCTTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002412","ARO_id":"38812","ARO_name":"OXY-5-2","ARO_description":"OXY-5-2 is a beta-lactamase found in Klebsiella oxytoca","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1312":{"model_id":"1312","model_name":"OXA-111","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1677":{"protein_sequence":{"accession":"ABV31691.1","sequence":"MNIKTLLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEMNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"EF650037","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCATCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGCCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAATGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001642","ARO_id":"38042","ARO_name":"OXA-111","ARO_description":"OXA-111 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1313":{"model_id":"1313","model_name":"adeA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"4256":{"protein_sequence":{"accession":"AAL14439.1","sequence":"MQKHLLLPLFLSIGLILQGCDSKEVAQAEPPPAKVSVLSIQPQSVNFSENLPARVHAFRTAEIRPQVGGIIEKVLFKQGSEVRAGQALYKINSETFEADVNSNRASLNKAEAEVARLKVQLERYEQLLPSNAISKQEVSNAQAQYRQALADVAQMKALLARQNLNLQYATVRAPISGRIGQSFVTEGALVGQGDTNTMATIQQIDKVYVDVKQSVSEYERLQAALQSGELSANSDKTVRITNSHGQPYNVTAKMLFEDINVDPETGDVTFRIEVNNTERKLLPGMYVRVNIDRASIPQALLVPAQAIQRNISGEPQVYVINAQGTAEIRPIEIGQQYEQFYIANKGLKVGDRVVVEGIERIKPNQKLALAAWKAPAVANHASSVETKTSIAEGAQP"},"dna_sequence":{"accession":"AF370885.1","fmin":"3438","fmax":"4629","strand":"+","sequence":"ATGCAAAAGCATCTTTTACTTCCTTTATTTTTATCTATTGGGCTGATATTACAGGGGTGTGATTCAAAAGAAGTCGCTCAAGCTGAGCCACCACCGGCTAAAGTCAGTGTATTAAGCATTCAACCGCAATCGGTAAATTTTAGTGAAAATCTTCCTGCACGTGTACATGCATTCCGTACGGCGGAAATCCGTCCGCAAGTCGGAGGTATCATTGAAAAGGTTCTATTTAAACAAGGTAGTGAAGTTAGAGCAGGGCAAGCCTTATATAAAATTAATTCCGAGACTTTTGAGGCCGATGTAAATAGCAATAGAGCTTCTCTCAATAAAGCTGAAGCTGAGGTGGCAAGACTCAAAGTTCAGTTAGAACGTTATGAGCAGTTATTACCAAGTAATGCAATTAGTAAGCAAGAAGTAAGTAATGCTCAAGCTCAGTATCGTCAGGCTCTAGCCGATGTCGCTCAAATGAAAGCATTGCTGGCCAGACAAAACTTGAATCTGCAATATGCAACAGTTCGAGCGCCTATTTCTGGGCGTATTGGGCAATCTTTTGTCACTGAAGGTGCATTGGTCGGTCAGGGCGATACCAATACGATGGCAACCATTCAACAGATTGATAAAGTCTATGTTGATGTAAAGCAATCGGTTAGTGAGTATGAACGCCTACAGGCTGCGCTACAAAGCGGCGAATTATCAGCAAATAGTGACAAAACCGTTCGTATTACCAATAGCCACGGACAGCCCTATAACGTCACAGCAAAAATGTTGTTTGAAGATATTAATGTTGACCCGGAAACAGGCGATGTCACATTCCGTATTGAAGTTAATAACACTGAACGAAAATTACTTCCGGGCATGTATGTGCGTGTCAATATTGATCGTGCTTCTATTCCTCAAGCGCTATTGGTTCCGGCGCAAGCGATCCAACGTAATATCAGTGGCGAGCCTCAGGTATATGTCATTAACGCCCAAGGGACAGCGGAAATTCGTCCTATCGAAATTGGACAGCAATATGAGCAGTTCTATATCGCTAACAAAGGCTTGAAAGTCGGTGACAGAGTCGTTGTTGAAGGTATTGAACGTATTAAGCCAAATCAAAAATTGGCATTGGCAGCATGGAAAGCACCAGCCGTCGCGAATCATGCTTCAAGTGTAGAAACCAAAACTTCTATAGCTGAAGGGGCACAACCATGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3000774","ARO_id":"37154","ARO_name":"adeA","ARO_description":"AdeA is the membrane fusion protein of the multidrug efflux complex AdeABC.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1314":{"model_id":"1314","model_name":"OXA-214","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1208":{"protein_sequence":{"accession":"AEV91553.1","sequence":"MKLSKLYTLTVLIGFGLSGVACQHIHTPVSFNQIENDQTKQIASLFENVQTTGVLITFDGQAYKAYGNDLNRAKTAYIPASTFKILNALIGIEHDKTSPNEVFKWDGQKRAFESWEKDLTLAEAMQASAVPVYQALAQRIGLDLMAKEVKRVGFGNTRIGTQVDNFWLIGPLKITPIEEAQFAYRLAKQELPFTPKTQQQVIDMLLVDEIRGTKVYAKSGWGMDITPQVGWWTGWIEDPNGKVIAFSLNMEMNQPAHAAARKEIVYQALTQLKLL"},"dna_sequence":{"accession":"JN861782","fmin":"0","fmax":"828","strand":"+","sequence":"ATGAAGCTATCAAAATTATACACCCTCACTGTGCTCATAGGATTTGGATTAAGCGGTGTCGCCTGCCAGCATATCCATACTCCAGTCTCGTTCAATCAAATTGAAAACGATCAAACAAAGCAGATCGCTTCCTTGTTTGAGAATGTTCAAACAACAGGTGTTCTAATTACCTTTGATGGACAGGCGTATAAAGCATACGGTAATGATCTGAATCGTGCCAAAACTGCGTATATCCCAGCATCTACTTTCAAAATATTAAATGCTTTGATTGGCATTGAACATGATAAAACTTCACCAAATGAAGTATTTAAGTGGGATGGTCAGAAGCGTGCTTTTGAAAGTTGGGAAAAAGATCTGACTTTAGCTGAAGCCATGCAAGCTTCTGCTGTACCTGTTTATCAAGCGCTTGCCCAGAGAATCGGATTGGATTTGATGGCAAAGGAAGTCAAAAGAGTCGGCTTCGGTAATACACGCATCGGAACACAAGTTGATAACTTCTGGCTCATTGGACCTTTAAAGATCACGCCAATCGAAGAAGCTCAATTTGCTTACAGGCTTGCAAAACAGGAGTTACCGTTTACCCCAAAAACACAACAGCAAGTGATTGATATGCTGTTGGTGGATGAAATACGGGGAACGAAAGTTTACGCCAAAAGTGGTTGGGGAATGGATATTACCCCGCAAGTAGGATGGTGGACTGGATGGATTGAAGATCCGAACGGAAAAGTGATCGCTTTTTCTCTCAATATGGAAATGAATCAACCTGCGCATGCAGCTGCACGTAAAGAAATTGTTTATCAGGCACTTACGCAATTGAAATTATTGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36938","NCBI_taxonomy_name":"Acinetobacter haemolyticus","NCBI_taxonomy_id":"29430"}}}},"ARO_accession":"3001713","ARO_id":"38113","ARO_name":"OXA-214","ARO_description":"OXA-214 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1315":{"model_id":"1315","model_name":"mdtC","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1800"}},"model_sequences":{"sequence":{"257":{"protein_sequence":{"accession":"AAC75137.1","sequence":"MKFFALFIYRPVATILLSVAITLCGILGFRMLPVAPLPQVDFPVIIVSASLPGASPETMASSVATPLERSLGRIAGVSEMTSSSSLGSTRIILQFDFDRDINGAARDVQAAINAAQSLLPSGMPSRPTYRKANPSDAPIMILTLTSDTYSQGELYDFASTQLAPTISQIDGVGDVDVGGSSLPAVRVGLNPQALFNQGVSLDDVRTAVSNANVRKPQGALEDGTHRWQIQTNDELKTAAEYQPLIIHYNNGGAVRLGDVATVTDSVQDVRNAGMTNAKPAILLMIRKLPEANIIQTVDSIRAKLPELQETIPAAIDLQIAQDRSPTIRASLEEVEQTLIISVALVILVVFLFLRSGRATIIPAVSVPVSLIGTFAAMYLCGFSLNNLSLMALTIATGFVVDDAIVVLENIARHLEAGMKPLQAALQGTREVGFTVLSMSLSLVAVFLPLLLMGGLPGRLLREFAVTLSVAIGISLLVSLTLTPMMCGWMLKASKPREQKRLRGFGRMLVALQQGYGKSLKWVLNHTRLVGVVLLGTIALNIWLYISIPKTFFPEQDTGVLMGGIQADQSISFQAMRGKLQDFMKIIRDDPAVDNVTGFTGGSRVNSGMMFITLKPRDERSETAQQIIDRLRVKLAKEPGANLFLMAVQDIRVGGRQSNASYQYTLLSDDLAALREWEPKIRKKLATLPELADVNSDQQDNGAEMNLVYDRDTMARLGIDVQAANSLLNNAFGQRQISTIYQPMNQYKVVMEVDPRYTQDISALEKMFVINNEGKAIPLSYFAKWQPANAPLSVNHQGLSAASTISFNLPTGKSLSDASAAIDRAMTQLGVPSTVRGSFAGTAQVFQETMNSQVILIIAAIATVYIVLGILYESYVHPLTILSTLPSAGVGALLALELFNAPFSLIALIGIMLLIGIVKKNAIMMVDFALEAQRHGNLTPQEAIFQACLLRFRPIMMTTLAALFGALPLVLSGGDGSELRQPLGITIVGGLVMSQLLTLYTTPVVYLFFDRLRLRFSRKPKQTVTE"},"dna_sequence":{"accession":"U00096","fmin":"2158385","fmax":"2161463","strand":"+","sequence":"GTGAAGTTTTTTGCCCTCTTCATTTACCGCCCGGTGGCGACGATTTTACTGTCGGTTGCCATTACCCTGTGCGGCATACTGGGCTTCCGTATGCTGCCGGTCGCCCCGCTGCCGCAGGTCGATTTTCCGGTGATTATCGTCAGCGCCTCGCTGCCCGGTGCGTCACCAGAAACAATGGCGTCTTCCGTTGCCACGCCGCTGGAGCGCTCACTTGGGCGCATTGCCGGAGTCAGTGAAATGACCTCCAGCAGTTCGCTCGGCAGCACGCGTATTATTTTGCAGTTTGATTTTGACCGGGATATCAACGGCGCAGCGCGTGATGTGCAGGCGGCGATCAACGCTGCACAAAGTTTGCTGCCCAGTGGGATGCCCAGCCGCCCGACCTATCGCAAAGCGAACCCGTCGGATGCGCCAATTATGATCCTCACGCTGACGTCCGATACTTATTCGCAGGGTGAACTGTACGATTTCGCCTCGACGCAGCTGGCTCCGACGATTTCGCAAATCGACGGTGTTGGTGATGTCGATGTCGGAGGCAGCTCACTGCCCGCCGTACGCGTCGGGCTGAATCCGCAGGCGCTGTTTAATCAGGGCGTGTCGCTGGACGACGTACGCACCGCCGTCAGCAATGCCAACGTGCGTAAACCGCAGGGCGCGCTGGAAGATGGCACTCACCGCTGGCAGATCCAGACCAATGATGAGCTAAAAACCGCCGCTGAATATCAGCCGTTGATTATTCACTACAACAACGGCGGCGCGGTTCGTCTGGGCGATGTGGCGACGGTGACCGACTCAGTGCAGGATGTGCGCAACGCCGGGATGACCAACGCCAAACCGGCTATTTTACTGATGATCCGCAAACTGCCGGAAGCCAATATTATCCAGACGGTTGACAGCATCCGGGCAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGCTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCGGTGGCGCTGGTGATTCTGGTGGTGTTTTTATTCCTGCGCTCGGGTCGCGCCACTATTATTCCCGCCGTTTCGGTGCCGGTTTCGCTGATTGGTACGTTTGCGGCGATGTACCTGTGCGGATTCAGTCTCAATAACCTTTCGTTAATGGCGCTCACCATCGCTACTGGTTTCGTGGTGGATGACGCCATCGTGGTGCTGGAAAACATTGCACGTCATCTGGAAGCGGGAATGAAACCGTTGCAAGCCGCACTGCAAGGTACTCGCGAAGTCGGTTTTACGGTGCTGTCGATGAGTCTGTCACTGGTGGCGGTGTTCCTGCCGCTGCTGTTGATGGGCGGATTGCCGGGCCGACTGTTACGCGAATTTGCCGTGACGCTTTCTGTCGCCATTGGTATATCGTTGCTGGTTTCTCTGACATTAACGCCAATGATGTGTGGCTGGATGCTGAAAGCCAGCAAGCCGCGCGAGCAAAAGCGACTGCGTGGTTTTGGTCGCATGTTGGTAGCCCTGCAACAAGGCTACGGCAAGTCACTAAAATGGGTGCTCAATCATACCCGTCTGGTGGGCGTGGTGCTGCTTGGCACCATTGCGCTGAATATCTGGCTGTATATCTCGATCCCGAAAACCTTCTTCCCGGAGCAGGACACTGGCGTGTTGATGGGCGGGATTCAGGCGGATCAGAGTATTTCGTTTCAGGCGATGCGCGGTAAGTTGCAGGATTTCATGAAAATTATCCGTGACGATCCGGCAGTGGATAATGTCACCGGCTTTACAGGCGGTTCGCGAGTGAACAGCGGGATGATGTTTATCACCCTCAAGCCACGCGACGAACGCAGCGAAACGGCGCAGCAAATTATCGACCGTCTGCGCGTAAAACTGGCGAAAGAACCGGGGGCGAATCTGTTCCTGATGGCGGTACAGGATATTCGCGTTGGTGGGCGTCAGTCGAACGCCAGCTACCAGTACACGTTGTTATCCGACGACCTGGCGGCACTGCGAGAATGGGAGCCGAAAATCCGCAAAAAACTGGCGACGTTGCCGGAACTGGCGGACGTGAACTCCGATCAGCAGGATAACGGCGCGGAGATGAATCTGGTTTACGACCGCGACACCATGGCACGGCTGGGAATCGACGTACAAGCCGCCAACAGTCTGTTAAATAACGCCTTCGGTCAGCGGCAAATCTCGACCATTTACCAGCCGATGAACCAGTATAAAGTGGTGATGGAAGTGGATCCGCGCTATACCCAGGACATCAGTGCGCTGGAAAAAATGTTCGTTATCAATAACGAAGGCAAAGCGATCCCGCTGTCGTATTTCGCTAAATGGCAACCGGCGAATGCCCCACTATCGGTGAATCATCAGGGATTATCGGCGGCCTCGACCATTTCGTTTAACCTGCCGACCGGAAAATCGCTCTCGGACGCCAGTGCGGCGATCGATCGCGCAATGACCCAGCTTGGTGTGCCTTCGACGGTGCGCGGCAGTTTTGCCGGCACGGCGCAGGTGTTCCAGGAGACGATGAACTCGCAGGTGATCCTGATTATCGCCGCCATCGCCACGGTGTATATCGTGCTGGGTATCCTTTACGAGAGTTACGTACATCCGCTGACGATTCTCTCCACCCTGCCCTCGGCGGGCGTTGGAGCGCTGTTGGCGCTGGAGCTGTTCAATGCCCCGTTCAGCCTAATCGCCCTGATAGGGATCATGCTATTAATCGGCATCGTGAAGAAAAACGCCATTATGATGGTCGATTTTGCGCTTGAAGCCCAACGGCACGGTAACCTGACGCCGCAGGAAGCTATTTTCCAGGCCTGTCTGCTGCGTTTTCGCCCGATTATGATGACTACCCTGGCGGCGCTGTTTGGTGCGCTGCCGCTGGTATTGTCGGGCGGCGACGGCTCGGAGCTGCGGCAACCCCTGGGGATCACCATTGTCGGCGGACTGGTAATGAGCCAGCTCCTTACGCTGTATACCACGCCGGTGGTGTATCTCTTTTTCGACCGTCTGCGGCTGCGTTTTTCGCGTAAACCTAAACAAACGGTAACCGAGTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3000794","ARO_id":"37174","ARO_name":"mdtC","ARO_description":"MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB, MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC\/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1317":{"model_id":"1317","model_name":"CTX-M-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1965":{"protein_sequence":{"accession":"CAA71321.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"Y10278","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3001866","ARO_id":"38266","ARO_name":"CTX-M-3","ARO_description":"CTX-M-3 is a beta-lactamase found in Citrobacter freundii","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35979":{"category_aro_accession":"0000062","category_aro_cvterm_id":"35979","category_aro_name":"ceftriaxone","category_aro_description":"Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1318":{"model_id":"1318","model_name":"evgS","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"2300"}},"model_sequences":{"sequence":{"178":{"protein_sequence":{"accession":"AAC75429.1","sequence":"MKFLPYIFLLCCGLWSTISFADEDYIEYRGISSNNRVTLDPLRLSNKELRWLASKKNLVIAVHKSQTATLLHTDSQQRVRGINADYLNLLKRALNIKLTLREYADHQKAMDALAEGEVDIVLSHLVTSPPLNNDIAATKPLIITFPALVTTLHDSMRPLTSPKPVNIARVANYPPDEVIHQSFPKATIISFTNLYQALASVSAGHNDYFIGSNIITSSMISRYFTHSLNVVKYYNSPRQYNFFLTRKESVILNEVLNRFVDALTNEVRYEVSQNWLDTGNLAFLNKPLELTEHEKQWIKQHPNLKVLENPYSPPYSMTDENGSVRGVMGDILNIITLQTGLNFSPITVSHNIHAGTQLSPGGWDIIPGAIYSEDRENNVLFAEAFITTPYVFVMQKAPDSEQTLKKGMKVAIPYYYELHSQLKEMYPEVEWIQVDNASAAFHKVKEGELDALVATQLNSRYMIDHYYPNELYHFLIPGVPNASLSFAFPRGEPELKDIINKALNAIPPSEVLRLTEKWIKMPNVTIDTWDLYSEQFYIVTTLSVLLVGSSLLWGFYLLRSVRRRKVIQGDLENQISFRKALSDSLPNPTYVVNWQGNVISHNSAFEHYFTADYYKNAMLPLENSDSPFKDVFSNAHEVTAETKENRTIYTQVFEIDNGIEKRCINHWHTLCNLPASDNAVYICGWQDITETRDLINALEVEKNKAIKATVAKSQFLATMSHEIRTPISSIMGFLELLSGSGLSKEQRVEAISLAYATGQSLLGLIGEILDVDKIESGNYQLQPQWVDIPTLVQNTCHSFGAIAASKSIALSCSSTFPEHYLVKIDPQAFKQVLSNLLSNALKFTTEGAVKITTSLGHIDDNHAVIKMTIMDSGSGLSQEEQQQLFKRYSQTSAGRQQTGSGLGLMICKELIKNMQGDLSLESHPGIGTTFTITIPVEISQQVATVEAKAEQPITLPEKLSILIADDHPTNRLLLKRQLNLLGYDVDEATDGVQALHKVSMQHYDLLITDVNMPNMDGFELTRKLREQNSSLPIWGLTANAQANEREKGLSCGMNLCLFKPLTLDVLKTHLSQLHQVAHIAPQYRHLDIEALKNNTANDLQLMQEILMTFQHETHKDLPAAFQALEAGDNRTFHQCIHRIHGAANILNLQKLINISHQLEITPVSDDSKPEILQLLNSVKEHIAELDQEIAVFCQKND"},"dna_sequence":{"accession":"U00096","fmin":"2484373","fmax":"2487967","strand":"+","sequence":"ATGAAGTTTTTACCCTATATTTTTCTTCTCTGTTGTGGTCTTTGGTCGACCATAAGTTTCGCAGACGAAGATTACATCGAATATCGTGGCATCAGTAGTAACAACCGTGTCACACTTGATCCACTACGTCTGAGCAACAAGGAATTACGTTGGTTAGCGAGCAAAAAAAATCTTGTGATTGCAGTACATAAGTCCCAAACGGCTACGTTGTTGCATACCGATTCGCAGCAACGGGTTCGTGGTATTAATGCTGATTATTTAAATCTTTTAAAAAGAGCGTTAAATATCAAATTAACACTCCGGGAATACGCAGATCATCAAAAAGCAATGGACGCGCTTGCAGAAGGTGAAGTCGATATAGTGTTATCACATTTAGTTACTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGATTACTTTATTGGTAGTAACATCATTACCAGCAGTATGATTTCCCGCTATTTCACTCACTCCTTAAATGTAGTGAAATATTATAACTCGCCGCGTCAATATAATTTTTTCTTGACCAGAAAAGAATCTGTCATTCTTAATGAAGTACTCAATAGATTTGTTGATGCTTTAACAAATGAAGTTCGCTATGAAGTATCACAAAATTGGCTTGATACAGGAAACCTGGCCTTTCTGAACAAACCATTAGAACTCACTGAACATGAAAAACAGTGGATTAAGCAGCATCCCAATTTAAAGGTGCTGGAAAATCCTTACTCGCCCCCCTATTCTATGACGGATGAAAATGGCTCGGTTCGGGGCGTTATGGGGGACATTCTTAATATTATTACCTTGCAAACAGGTTTAAATTTTTCTCCGATCACCGTTTCACACAATATCCATGCTGGAACACAGCTTAGCCCCGGAGGATGGGATATAATACCTGGCGCTATTTATAGTGAAGATCGAGAAAATAATGTTTTATTTGCTGAAGCCTTCATAACAACGCCTTACGTTTTTGTCATGCAAAAAGCGCCTGACAGTGAACAAACATTAAAAAAAGGAATGAAAGTTGCCATTCCATATTATTATGAGCTGCATTCGCAATTAAAAGAGATGTATCCGGAGGTTGAATGGATACAGGTCGATAATGCCAGCGCTGCATTTCACAAGGTTAAGGAAGGTGAACTTGATGCTCTGGTCGCGACACAGCTAAATTCGCGTTACATGATCGATCATTACTATCCTAATGAACTTTATCATTTTCTTATTCCTGGCGTTCCGAATGCATCGCTTTCGTTCGCTTTTCCTCGCGGAGAACCGGAACTTAAGGATATTATTAATAAAGCACTGAATGCAATTCCCCCAAGCGAAGTTCTGCGCCTGACGGAAAAATGGATTAAAATGCCCAATGTGACCATTGACACATGGGACCTATATAGCGAGCAATTTTATATTGTTACGACATTATCCGTTTTATTAGTTGGCAGTAGCCTTTTATGGGGATTCTACCTGTTACGCTCAGTTCGTCGTCGTAAAGTCATTCAGGGTGATTTAGAAAACCAAATATCATTCCGAAAAGCACTCTCGGATTCCTTACCGAATCCAACTTATGTTGTAAACTGGCAAGGTAATGTCATTAGTCATAATAGTGCTTTTGAACATTATTTCACTGCGGATTACTACAAAAATGCAATGTTACCATTAGAAAACAGTGACTCACCCTTTAAAGATGTTTTTTCTAATGCGCATGAAGTCACAGCAGAAACGAAAGAAAATCGAACAATATACACACAGGTATTTGAAATTGATAATGGCATCGAGAAAAGATGCATTAATCACTGGCATACATTATGCAATCTTCCTGCAAGTGACAATGCAGTATATATTTGTGGTTGGCAAGATATTACTGAAACGCGTGATCTAATTAATGCACTCGAGGTAGAAAAAAATAAAGCGATAAAGGCTACCGTAGCAAAAAGTCAGTTTCTGGCAACGATGAGTCACGAAATAAGAACACCAATAAGCTCTATTATGGGCTTCCTGGAACTTCTGTCGGGTTCTGGTCTTAGCAAGGAGCAACGGGTGGAGGCGATTTCACTTGCCTACGCCACCGGACAATCACTCCTCGGCTTAATTGGTGAAATCCTTGATGTCGACAAAATTGAATCGGGTAACTATCAACTTCAACCACAATGGGTCGATATCCCTACTTTAGTCCAGAACACTTGTCACTCTTTCGGTGCGATTGCTGCAAGCAAATCGATCGCATTAAGTTGCAGCAGTACGTTTCCTGAACATTACCTGGTTAAGATCGACCCTCAGGCGTTTAAGCAGGTCTTATCAAATTTACTGAGTAATGCTCTCAAATTTACCACCGAGGGGGCAGTAAAAATTACGACCTCCCTGGGTCACATTGATGACAACCACGCTGTTATCAAAATGACGATTATGGATTCTGGAAGTGGATTATCGCAGGAAGAACAACAACAACTGTTTAAACGCTACAGCCAAACAAGTGCAGGTCGTCAGCAAACAGGTTCTGGTTTAGGCTTAATGATCTGCAAAGAATTAATTAAAAATATGCAGGGCGATTTGTCATTAGAAAGTCATCCAGGCATAGGAACAACATTTACGATCACAATCCCGGTAGAAATTAGCCAGCAAGTGGCGACTGTCGAGGCAAAAGCAGAACAACCCATCACACTACCTGAAAAGTTGAGCATATTAATCGCGGATGATCATCCGACCAACAGGCTATTACTCAAACGCCAGCTAAATCTATTAGGATATGATGTTGATGAAGCCACTGATGGTGTGCAAGCGCTACACAAAGTCAGTATGCAACATTATGATCTGCTTATTACTGACGTTAATATGCCGAATATGGATGGTTTTGAGTTGACTCGCAAACTCCGTGAGCAAAATTCTTCCTTACCCATCTGGGGGCTTACAGCCAACGCACAGGCTAACGAACGTGAAAAAGGGTTAAGTTGCGGCATGAACTTATGTTTGTTCAAACCGTTGACCCTGGATGTACTGAAAACACATTTAAGTCAGTTACACCAAGTTGCGCATATTGCACCTCAGTATCGCCACCTTGATATCGAAGCCCTGAAAAATAATACGGCGAACGATCTACAACTGATGCAGGAGATTCTCATGACTTTCCAGCATGAAACGCATAAAGATCTACCCGCTGCGTTTCAAGCACTAGAAGCTGGCGATAACAGAACTTTCCATCAGTGTATTCATCGCATCCACGGTGCGGCTAACATCCTGAATTTGCAAAAGTTGATTAATATTAGCCATCAGTTAGAAATAACACCTGTTTCAGATGACAGTAAGCCTGAAATTCTTCAGTTGCTGAACTCTGTAAAAGAACACATTGCAGAGCTGGACCAGGAGATTGCTGTTTTCTGTCAGAAAAATGACTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3000833","ARO_id":"37213","ARO_name":"evgS","ARO_description":"EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35930":{"category_aro_accession":"0000011","category_aro_cvterm_id":"35930","category_aro_name":"cloxacillin","category_aro_description":"Cloxacillin is a semisynthetic, isoxazolyl penicillin derivative in the beta-lactam class of antibiotics. It interferes with peptidogylcan synthesis and is commonly used for treating penicillin-resistant Staphylococcus aureus infections.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1319":{"model_id":"1319","model_name":"SHV-147","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"2021":{"protein_sequence":{"accession":"AFQ23953.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSAFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTSASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"JX121114","fmin":"0","fmax":"858","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCGCCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGTCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001186","ARO_id":"37566","ARO_name":"SHV-147","ARO_description":"SHV-147 is a beta-lactamase.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1321":{"model_id":"1321","model_name":"mecA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1250"}},"model_sequences":{"sequence":{"227":{"protein_sequence":{"accession":"AGC51118.1","sequence":"MKKIKIVPLILIVVVVGFGIYFYASKDKEINNTIDAIEDKNFKQVYKDSSYISKSDNGEVEMTERPIKIYNSLGVKDINIQDRKIKKVSKNKKRVDAQYKIKTNYGNIDRNVQFNFVKEDGMWKLDWDHSVIIPGMQKDQSIHIENLKSERGKILDRNNVELANTGTAYEIGIVPKNVSKKDYKAIAKELSISEDYIKQQMDQNWVQDDTFVPLKTVKKMDEYLSDFAKKFHLTTNETKSRNYPLEKATSHLLGYVGPINSEELKQKEYKGYKDDAVIGKKGLEKLYDKKLQHEDGYRVTIVDDNSNTIAHTLIEKKKKDGKDIQLTIDAKVQKSIYNNMKNDYGSGTAIHPQTGELLALVSTPSYDVYPFMYGMSNEEYNKLTEDKKEPLLNKFQITTSPGSTQKILTAMIGLNNKTLDDKTSYKIDGKGWQKDKSWGGYNVTRYEVVNGNIDLKQAIESSDNIFFARVALELGSKKFEKGMKKLGVGEDIPSDYPFYNAQISNKNLDNEILLADSGYGQGEILINPVQILSIYSALENNGNINAPHLLKDTKNKVWKKNIISKENINLLTDGMQQVVNKTHKEDIYRSYANLIGKSGTAELKMKQGETGRQIGWFISYDKDNPNMMMAINVKDVQDKGMASYNAKISGKVYDELYENGNKKYDIDE"},"dna_sequence":{"accession":"KC243783","fmin":"0","fmax":"2007","strand":"+","sequence":"ATGAAAAAGATAAAAATTGTTCCACTTATTTTAATAGTTGTAGTTGTCGGGTTTGGTATATATTTTTATGCTTCAAAAGATAAAGAAATTAATAATACTATTGATGCAATTGAAGATAAAAATTTCAAACAAGTTTATAAAGATAGCAGTTATATTTCTAAAAGCGATAATGGTGAAGTAGAAATGACTGAACGTCCGATAAAAATATATAATAGTTTAGGCGTTAAAGATATAAACATTCAGGATCGTAAAATAAAAAAAGTATCTAAAAATAAAAAACGAGTAGATGCTCAATATAAAATTAAAACAAACTACGGTAACATTGATCGCAACGTTCAATTTAATTTTGTTAAAGAAGATGGTATGTGGAAGTTAGATTGGGATCATAGCGTCATTATTCCAGGAATGCAGAAAGACCAAAGCATACATATTGAAAATTTAAAATCAGAACGTGGTAAAATTTTAGACCGAAACAATGTGGAATTGGCCAATACAGGAACAGCATATGAGATAGGCATCGTTCCAAAGAATGTATCTAAAAAAGATTATAAAGCAATCGCTAAAGAACTAAGTATTTCTGAAGACTATATCAAACAACAAATGGATCAAAATTGGGTACAAGATGATACCTTCGTTCCACTTAAAACCGTTAAAAAAATGGATGAATATTTAAGTGATTTCGCAAAAAAATTTCATCTTACAACTAATGAAACAAAAAGTCGTAACTATCCTCTAGAAAAAGCGACTTCACATCTATTAGGTTATGTTGGTCCCATTAACTCTGAAGAATTAAAACAAAAAGAATATAAAGGCTATAAAGATGATGCAGTTATTGGTAAAAAGGGACTCGAAAAACTTTACGATAAAAAGCTCCAACATGAAGATGGCTATCGTGTCACAATCGTTGACGATAATAGCAATACAATCGCACATACATTAATAGAGAAAAAGAAAAAAGATGGCAAAGATATTCAACTAACTATTGATGCTAAAGTTCAAAAGAGTATTTATAACAACATGAAAAATGATTATGGCTCAGGTACTGCTATCCACCCTCAAACAGGTGAATTATTAGCACTTGTAAGCACACCTTCATATGACGTCTATCCATTTATGTATGGCATGAGTAACGAAGAATATAATAAATTAACCGAAGATAAAAAAGAACCTCTGCTCAACAAGTTCCAGATTACAACTTCACCAGGTTCAACTCAAAAAATATTAACAGCAATGATTGGGTTAAATAACAAAACATTAGACGATAAAACAAGTTATAAAATCGATGGTAAAGGTTGGCAAAAAGATAAATCTTGGGGTGGTTACAACGTTACAAGATATGAAGTGGTAAATGGTAATATCGACTTAAAACAAGCAATAGAATCATCAGATAACATTTTCTTTGCTAGAGTAGCACTCGAATTAGGCAGTAAGAAATTTGAAAAAGGCATGAAAAAACTAGGTGTTGGTGAAGATATACCAAGTGATTATCCATTTTATAATGCTCAAATTTCAAACAAAAATTTAGATAATGAAATATTATTAGCTGATTCAGGTTACGGACAAGGTGAAATACTGATTAACCCAGTACAGATCCTTTCAATCTATAGCGCATTAGAAAATAATGGCAATATTAACGCACCTCACTTATTAAAAGACACGAAAAACAAAGTTTGGAAGAAAAATATTATTTCCAAAGAAAATATCAATCTATTAACTGATGGTATGCAACAAGTCGTAAATAAAACACATAAAGAAGATATTTATAGATCTTATGCAAACTTAATTGGCAAATCCGGTACTGCAGAACTCAAAATGAAACAAGGAGAAACTGGCAGACAAATTGGGTGGTTTATATCATATGATAAAGATAATCCAAACATGATGATGGCTATTAATGTTAAAGATGTACAAGATAAAGGAATGGCTAGCTACAATGCCAAAATCTCAGGTAAAGTGTATGATGAGCTATATGAGAACGGTAATAAAAAATACGATATAGATGAATAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3000617","ARO_id":"36911","ARO_name":"mecA","ARO_description":"A foreign PBP2a acquired by lateral gene transfer that able to perform peptidoglycan synthesis in the presence of beta-lactams.","ARO_category":{"37589":{"category_aro_accession":"3001208","category_aro_cvterm_id":"37589","category_aro_name":"methicillin resistant PBP2","category_aro_description":"In methicillin sensitive S. aureus (MSSA), beta-lactams bind to native penicillin-binding proteins (PBPs) and disrupt synthesis of the cell membrane's peptidoglycan layer. In methicillin resistant S. aureus (MRSA), foreign PBP2a acquired by lateral gene transfer is able to perform peptidoglycan synthesis in the presence of beta-lactams.","category_aro_class_name":"AMR Gene Family"},"35927":{"category_aro_accession":"0000008","category_aro_cvterm_id":"35927","category_aro_name":"cefoxitin","category_aro_description":"Cefoxitin is a cephamycin antibiotic often grouped with the second generation cephalosporins. Cefoxitin is bactericidal and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. Cefoxitin's 7-alpha-methoxy group and 3' leaving group make it a poor substrate for most beta-lactamases.","category_aro_class_name":"Antibiotic"},"35930":{"category_aro_accession":"0000011","category_aro_cvterm_id":"35930","category_aro_name":"cloxacillin","category_aro_description":"Cloxacillin is a semisynthetic, isoxazolyl penicillin derivative in the beta-lactam class of antibiotics. It interferes with peptidogylcan synthesis and is commonly used for treating penicillin-resistant Staphylococcus aureus infections.","category_aro_class_name":"Antibiotic"},"35934":{"category_aro_accession":"0000015","category_aro_cvterm_id":"35934","category_aro_name":"methicillin","category_aro_description":"Derived from penicillin to combat penicillin-resistance, methicillin is insensitive to beta-lactamases (also known as penicillinases) secreted by many penicillin-resistant bacteria. Methicillin is bactericidal, and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Antibiotic"},"35961":{"category_aro_accession":"0000043","category_aro_cvterm_id":"35961","category_aro_name":"carbenicillin","category_aro_description":"Carbenicillin is a semi-synthetic antibiotic belonging to the carboxypenicillin subgroup of the penicillins. It has gram-negative coverage which includes Pseudomonas aeruginosa but limited gram-positive coverage. The carboxypenicillins are susceptible to degradation by beta-lactamase enzymes. Carbenicillin antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Antibiotic"},"35971":{"category_aro_accession":"0000054","category_aro_cvterm_id":"35971","category_aro_name":"penicillin","category_aro_description":"Penicillin (sometimes abbreviated PCN) is a beta-lactam antibiotic used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms. It works by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Antibiotic"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35975":{"category_aro_accession":"0000058","category_aro_cvterm_id":"35975","category_aro_name":"cefazolin","category_aro_description":"Cefazolin (INN), also known as cefazoline or cephazolin, is a first generation cephalosporin antibiotic. It is administered parenterally, and is active against a broad spectrum of bacteria.","category_aro_class_name":"Antibiotic"},"35976":{"category_aro_accession":"0000059","category_aro_cvterm_id":"35976","category_aro_name":"cefepime","category_aro_description":"Cefepime (INN) is a fourth-generation cephalosporin antibiotic developed in 1994. It contains an aminothiazolyl group that decreases its affinity with beta-lactamases. Cefepime shows high binding affinity with penicillin-binding proteins and has an extended spectrum of activity against Gram-positive and Gram-negative bacteria, with greater activity against both Gram-negative and Gram-positive organisms than third-generation agents.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35978":{"category_aro_accession":"0000061","category_aro_cvterm_id":"35978","category_aro_name":"ceftobiprole","category_aro_description":"Ceftobiprole (Zeftera\/Zevtera) is a next generation (5th generation) cephalosporin antibiotic with activity against methicillin-resistant Staphylococcus aureus, penicillin-resistant Streptococcus pneumoniae, Pseudomonas aeruginosa, and Enterococci. Ceftobiprole inhibits transpeptidases essential to building cell walls, and is a poor substrate for most beta-lactamases.","category_aro_class_name":"Antibiotic"},"35979":{"category_aro_accession":"0000062","category_aro_cvterm_id":"35979","category_aro_name":"ceftriaxone","category_aro_description":"Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"35980":{"category_aro_accession":"0000063","category_aro_cvterm_id":"35980","category_aro_name":"cefuroxime","category_aro_description":"Cefuroxime is a second-generation cephalosporin antibiotic with increased stability with beta-lactamases than first-generation cephalosporins. Cefuroxime is active against Gram-positive organisms but less active against methicillin-resistant strains.","category_aro_class_name":"Antibiotic"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"35987":{"category_aro_accession":"0000070","category_aro_cvterm_id":"35987","category_aro_name":"ertapenem","category_aro_description":"Ertapenem is a carbapenem antibiotic and is highly resistant to beta-lactamases like other carbapenems. It inhibits bacterial cell wall synthesis.","category_aro_class_name":"Antibiotic"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"35995":{"category_aro_accession":"0000078","category_aro_cvterm_id":"35995","category_aro_name":"piperacillin","category_aro_description":"Piperacillin is an acetylureidopenicillin and has an extended spectrum of targets relative to other beta-lactam antibiotics. It inhibits cell wall synthesis in bacteria, and is usually taken with the beta-lactamase inhibitor tazobactam to overcome penicillin-resistant bacteria.","category_aro_class_name":"Antibiotic"},"36309":{"category_aro_accession":"3000170","category_aro_cvterm_id":"36309","category_aro_name":"imipenem","category_aro_description":"Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.","category_aro_class_name":"Antibiotic"},"36689":{"category_aro_accession":"3000550","category_aro_cvterm_id":"36689","category_aro_name":"aztreonam","category_aro_description":"Aztreonam was the first monobactam discovered, and is greatly effective against Gram-negative bacteria while inactive against Gram-positive bacteria. Artreonam is a poor substrate for beta-lactamases, and may even act as an inhibitor. In Gram-negative bacteria, Aztreonam interferes with filamentation, inhibiting cell division and leading to cell death.","category_aro_class_name":"Antibiotic"},"36976":{"category_aro_accession":"3000632","category_aro_cvterm_id":"36976","category_aro_name":"benzylpenicillin","category_aro_description":"Benzylpenicillin, commonly referred to as penicillin G, is effective against both Gram-positive and Gram-negative bacteria. It is unstable in acid.","category_aro_class_name":"Antibiotic"},"36977":{"category_aro_accession":"3000633","category_aro_cvterm_id":"36977","category_aro_name":"phenoxymethylpenicillin","category_aro_description":"Phenoxymethylpenicillin, or penicillin V, is a penicillin derivative that is acid stable but less active than benzylpenicillin (penicillin G).","category_aro_class_name":"Antibiotic"},"36978":{"category_aro_accession":"3000634","category_aro_cvterm_id":"36978","category_aro_name":"propicillin","category_aro_description":"Propicillin is an orally taken penicillin derivative that has high absorption but poor activity.","category_aro_class_name":"Antibiotic"},"36979":{"category_aro_accession":"3000635","category_aro_cvterm_id":"36979","category_aro_name":"dicloxacillin","category_aro_description":"Dicloxacillin is a penicillin derivative that has an extra chlorine atom in comparison to cloxacillin. While more active than cloxacillin, its high affinity for serum protein reduces its activity in human serum in vitro.","category_aro_class_name":"Antibiotic"},"36980":{"category_aro_accession":"3000636","category_aro_cvterm_id":"36980","category_aro_name":"flucloxacillin","category_aro_description":"Flucloxacillin is similar to cloxacillin, with an extra additional fluorine atom.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"36982":{"category_aro_accession":"3000638","category_aro_cvterm_id":"36982","category_aro_name":"azlocillin","category_aro_description":"Azlocillin is a semisynthetic derivative of penicillin that is notably active against Ps. aeruginosa and other Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36983":{"category_aro_accession":"3000639","category_aro_cvterm_id":"36983","category_aro_name":"mezlocillin","category_aro_description":"Mezlocillin is a penicillin derivative taken parenterally.","category_aro_class_name":"Antibiotic"},"36984":{"category_aro_accession":"3000640","category_aro_cvterm_id":"36984","category_aro_name":"doripenem","category_aro_description":"Doripenem is a carbapenem with a broad range of activity against Gram-positive and Gram-negative bacteria, and along with meropenem, it is the most active beta-lactam antibiotic against Pseudomonas aeruginosa. It inhibits bacterial cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36985":{"category_aro_accession":"3000641","category_aro_cvterm_id":"36985","category_aro_name":"cefalexin","category_aro_description":"Cefalexin is a cephalosporin antibiotic that causes filamentation. It is resistant to staphylococcal beta-lactamase, but degraded by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"36986":{"category_aro_accession":"3000642","category_aro_cvterm_id":"36986","category_aro_name":"cefadroxil","category_aro_description":"Cefadroxil, or p-hydroxycephalexin, is an cephalosporin antibiotic similar to cefalexin.","category_aro_class_name":"Antibiotic"},"36987":{"category_aro_accession":"3000643","category_aro_cvterm_id":"36987","category_aro_name":"cefotiam","category_aro_description":"Cefotiam is a cephalosporin antibiotic with similar activity to cefuroxime but more active against enterobacteria. It is consumed orally as the prodrug cefotiam hexetil.","category_aro_class_name":"Antibiotic"},"36988":{"category_aro_accession":"3000644","category_aro_cvterm_id":"36988","category_aro_name":"cefaclor","category_aro_description":"Cefaclor is a semisynthetic cephalosporin derived from cephalexin. It has broad-spectrum antibiotic activity.","category_aro_class_name":"Antibiotic"},"36989":{"category_aro_accession":"3000645","category_aro_cvterm_id":"36989","category_aro_name":"cefotaxime","category_aro_description":"Cefotaxime is a semisynthetic cephalosporin taken parenterally. It is resistant to most beta-lactamases and active against Gram-negative rods and cocci due to its aminothiazoyl and methoximino functional groups.","category_aro_class_name":"Antibiotic"},"36990":{"category_aro_accession":"3000646","category_aro_cvterm_id":"36990","category_aro_name":"cefixime","category_aro_description":"Cefixime is a cephalosporin resistant to most beta-lactamases. It is active against many enterobacteria, but activity against staphylococci is poor.","category_aro_class_name":"Antibiotic"},"36991":{"category_aro_accession":"3000647","category_aro_cvterm_id":"36991","category_aro_name":"cefpodoxime","category_aro_description":"Cefpodoxime is a semisynthetic cephalosporin that acts similarly to cefotaxime with broad-spectrum activity. It is stable to many plasmid-mediated beta-lactamses. Cefpodoxime is consumed as the prodrug cefpodoxime proxetil.","category_aro_class_name":"Antibiotic"},"36992":{"category_aro_accession":"3000648","category_aro_cvterm_id":"36992","category_aro_name":"ceftibuten","category_aro_description":"Ceftibuten is a semisynthetic cephalosporin active against Gram-negative bacilli. It is resistant against many plasmid-mediated beta-lactamases.","category_aro_class_name":"Antibiotic"},"36993":{"category_aro_accession":"3000649","category_aro_cvterm_id":"36993","category_aro_name":"cefditoren","category_aro_description":"Cefditoren is a semisynthetic cephalosporin active against staphylococci, streptococci, and and most enterobacteria. It is resistant to staphylococcal and most enterobacterial beta-lactamases, and is usually taken as the prodrug cefditoren pivoxil.","category_aro_class_name":"Antibiotic"},"36994":{"category_aro_accession":"3000650","category_aro_cvterm_id":"36994","category_aro_name":"cefdinir","category_aro_description":"Cefdinir is similar to cefixime with a modified side-chain at its 7-amino position. It also shares similar activity with cefixime but is more active against staphylococci. It has also be shown to enhance phagocytosis.","category_aro_class_name":"Antibiotic"},"36995":{"category_aro_accession":"3000651","category_aro_cvterm_id":"36995","category_aro_name":"ceftaroline","category_aro_description":"Ceftaroline is a novel cephalosporin active against methicillin resistant Staphylococcus aureus. Like other cephalosporins it binds penicillin-binding proteins to inhibit cell wall synthesis. It strongly binds with PBP2a, associated with methicillin resistance. It is taken orally as the prodrug ceftaroline fosamil.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"37085":{"category_aro_accession":"3000705","category_aro_cvterm_id":"37085","category_aro_name":"isopenicillin N","category_aro_description":"Isopenicillin N is a natural penicillin derivative produced by Penicillium chrysogenum with activity similar to penicillin N.","category_aro_class_name":"Antibiotic"},"37086":{"category_aro_accession":"3000706","category_aro_cvterm_id":"37086","category_aro_name":"penicillin N","category_aro_description":"Penicillin N is a penicillin derivative produced by Cephalosporium acremonium.","category_aro_class_name":"Antibiotic"},"37141":{"category_aro_accession":"3000761","category_aro_cvterm_id":"37141","category_aro_name":"mecillinam","category_aro_description":"Mecillinam is a broad-spectrum beta-lactam antibiotic that was semi-synthetically derived to have a different drug centre, being a 6-alpha-amidinopenicillanate instead of a 6-alpha-acylaminopenicillanate. Contrasting most beta-lactam drugs, mecillinam is most active against Gram-negative bacteria. It binds specifically to penicillin binding protein 2 (PBP2).","category_aro_class_name":"Antibiotic"},"40928":{"category_aro_accession":"3004001","category_aro_cvterm_id":"40928","category_aro_name":"cefmetazole","category_aro_description":"Cefmetazole is a semi-synthetic cephamycin antibiotic with broad spectrum antibiotic activity against both gram-positive and gram-negative bacteria, that disrupt cell wall synthesis through binding to PBPs causing cell lysis.","category_aro_class_name":"Antibiotic"},"40929":{"category_aro_accession":"3004002","category_aro_cvterm_id":"40929","category_aro_name":"cefonicid","category_aro_description":"Cefonicid is a second-generation cephalosporin-class beta-lactam antibiotic with broad spectrum activity. Particularly used against urinary tract infections and lower respiratory infections. Causes cell lysis by inactivation of PBPs through binding, inhibiting peptidoglycan synthesis.","category_aro_class_name":"Antibiotic"},"40932":{"category_aro_accession":"3004005","category_aro_cvterm_id":"40932","category_aro_name":"cefprozil","category_aro_description":"Cefprozil is a cephalosporin and beta-lactam antibiotic with bactericidal activity. It selectively binds to PBPs and inhibits peptidoglycan synthesis, a major cell wall component, resulting in cell lysis.","category_aro_class_name":"Antibiotic"},"40933":{"category_aro_accession":"3004006","category_aro_cvterm_id":"40933","category_aro_name":"ceftiofur","category_aro_description":"Ceftiofur is a third-generation broad spectrum cephalosporin and beta-lactam antibiotic. It causes cell lysis by disrupting peptidoglycan cross-linkage and cell wall formation by binding to PBPs.","category_aro_class_name":"Antibiotic"},"40934":{"category_aro_accession":"3004007","category_aro_cvterm_id":"40934","category_aro_name":"ceftizoxime","category_aro_description":"Ceftizoxime is a third-generation cephalosporin and broad spectrum beta-lactam antibiotic. Ceftizoxime causes bacterial cell lysis through peptidoglycan cross-linking inhibition by binding to PBPs.","category_aro_class_name":"Antibiotic"},"40935":{"category_aro_accession":"3004008","category_aro_cvterm_id":"40935","category_aro_name":"cephapirin","category_aro_description":"Cephapirin is a first-generation cephalosporin and broad spectrum beta-lactam antibiotic. Inactivation of penicillin-binding proteins through cephapirin binding disrupts peptidoglycan cross-linking, resulting in cell lysis.","category_aro_class_name":"Antibiotic"},"40936":{"category_aro_accession":"3004009","category_aro_cvterm_id":"40936","category_aro_name":"cefradine","category_aro_description":"Cefradine is a first-generation cephalosporin and broad spectrum beta-lactam antibiotic. Cefradine binding to penicillin-binding proteins disrupts cell wall peptidoglycan cross-linkage, resulting in cell lysis.","category_aro_class_name":"Antibiotic"},"40943":{"category_aro_accession":"3004016","category_aro_cvterm_id":"40943","category_aro_name":"loracarbef","category_aro_description":"Loracarbef is a second-generation cephalosporin (carbacephem) and broad spectrum beta-lactam antibiotic. Loracarbef inhibits PBPs through binding, disrupting peptidoglycan cell wall cross-linkage and resulting in cell death.","category_aro_class_name":"Antibiotic"},"40944":{"category_aro_accession":"3004017","category_aro_cvterm_id":"40944","category_aro_name":"moxalactam","category_aro_description":"Moxalactam (Latamoxef) is a broad spectrum cephalosporin (oxacephem) and beta-lactam antibiotic. Moxalactam binding to PBPs inhibits peptidoglycan cross-linkage in the cell wall, resulting in cell death. Moxalactam is proposed to be effective against meningitides as it passes the blood-brain barrier.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1322":{"model_id":"1322","model_name":"SHV-65","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1068":{"protein_sequence":{"accession":"ABA06587.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCTAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"DQ174305","fmin":"4","fmax":"865","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACCCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCACCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001120","ARO_id":"37500","ARO_name":"SHV-65","ARO_description":"SHV-65 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1324":{"model_id":"1324","model_name":"LRA-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"4394":{"protein_sequence":{"accession":"ACH58985.1","sequence":"MMDGIKKKTAAGAAAGSLLMMLGVFATPAAGGEAAFKDCPQCAQWNQQRKPFRIYGNTYFVGTAGLSSILVTSDYGHVLIDGGLAQSAPLIKANIEALGFKLTDVKAILVSHVHPDHAGGVAELQRQSGAQVYALRTAEAVLRTGRLTQDDPQSASKTATITPVPQVWVVQDDQLLGVGALRMRAIATPGHTPGGTSWTWDACEDGNCLKMIYADSLSAVAAGKYRFKDHPEVLQAFASSFSRAESAPCDVLLTPHPDASQLFQRLDPEGGTRAASIKDDTACRRYVQAARDTLARKLASEG"},"dna_sequence":{"accession":"EU408347","fmin":"10174","fmax":"11083","strand":"-","sequence":"TCAGCCCTCGCTGGCGAGTTTCCGGGCAAGCGTGTCCCGCGCTGCCTGCACGTATCGCCGGCATGCCGTGTCGTCCTTGATGCTGGCTGCCCGGGTGCCGCCCTCCGGATCCAGCCGCTGGAACAACTGCGAAGCATCCGGATGCGGCGTGAGCAGTACATCGCAGGGTGCGGACTCCGCCCGGGAGAAGCTGCTGGCAAAGGCCTGCAGCACTTCGGGGTGATCCTTGAAGCGATACTTGCCGGCAGCTACGGCGGACAGGCTGTCTGCATAGATCATCTTCAGGCAGTTGCCGTCTTCGCAGGCGTCCCAGGTCCAGCTGGTACCGCCAGGCGTGTGACCGGGGGTCGCGATGGCCCGCATCCGCAGCGCGCCGACGCCGAGCAGCTGGTCATCCTGCACCACCCAGACCTGCGGCACCGGTGTGATGGTTGCCGTCTTGCTGGCGGATTGGGGATCGTCCTGCGTGAGCCTGCCCGTTCGCAGCACGGCTTCTGCGGTTCGCAATGCATAGACCTGCGCACCGCTCTGCCGCTGCAGCTCGGCGACGCCACCCGCATGGTCTGGATGCACATGCGAGACCAGGATGGCCTTTACATCGGTGAGCTTGAAGCCCAGTGCTTCGATGTTTGCCTTGATGAGCGGCGCGGATTGCGCGAGCCCGCCGTCGATCAGCACATGGCCGTAGTCGGAGGTGACGAGAATCGAGCTGAGACCGGCGGTGCCGACGAAATAGGTATTACCGTAGATGCGAAACGGCTTGCGCTGCTGATTCCACTGGGCGCACTGCGGGCAATCCTTGAATGCCGCTTCACCGCCCGCGGCGGGCGTGGCAAAAACACCCAGCATCATCAGCAGTGAACCTGCTGCAGCGCCGGCCGCCGTCTTCTTCTTTATTCCATCCATCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39080","NCBI_taxonomy_name":"uncultured bacterium BLR2","NCBI_taxonomy_id":"506520"}}}},"ARO_accession":"3002485","ARO_id":"38885","ARO_name":"LRA-2","ARO_description":"LRA-2 is a beta-lactamase isolated from soil samples in Alaska","ARO_category":{"41390":{"category_aro_accession":"3004226","category_aro_cvterm_id":"41390","category_aro_name":"subclass B3 LRA beta-lactamase","category_aro_description":"Beta-lactamases that are part of the LRA gene family and are classified as B3 (metallo-) beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1325":{"model_id":"1325","model_name":"OXA-65","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1767":{"protein_sequence":{"accession":"AAW81337.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"AY750908","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001614","ARO_id":"38014","ARO_name":"OXA-65","ARO_description":"OXA-65 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1326":{"model_id":"1326","model_name":"OXA-170","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1680":{"protein_sequence":{"accession":"ADK35874.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETPSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEKSNGYKIFGKTGWAMDIKPQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"HM488991","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGACCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCCCAATTAGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAAAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001470","ARO_id":"37870","ARO_name":"OXA-170","ARO_description":"OXA-170 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1327":{"model_id":"1327","model_name":"AAC(6')-Iq","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"343":{"protein_sequence":{"accession":"AAC25500.1","sequence":"MDYSICDIAESNELILEAAKILRKSFLDAGNESWVDIKKAIEEVEDCIEHPNLCLGICLDDKLIGWTGLRPMYDKTWELHPMVIKTEYQCRGIGKVLIKELEKRAKGRGIIGIALGTDDEYQKTSLSMIDINERNIFDEIGNIKNVTNHPYEFYKKCGYMIVGIIPNANGKRKPDIWMWKDIS"},"dna_sequence":{"accession":"AF047556","fmin":"126","fmax":"678","strand":"+","sequence":"TTGGACTATTCAATATGCGATATAGCGGAATCAAATGAATTAATCCTTGAAGCAGCAAAAATACTTAGGAAAAGCTTTCTTGATGCTGGAAATGAATCATGGGTAGATATCAAAAAGGCTATTGAAGAAGTTGAGGATTGTATAGAACACCCAAATCTATGCTTGGGAATATGTCTGGATGATAAACTGATTGGCTGGACCGGATTAAGGCCGATGTACGATAAGACCTGGGAACTTCATCCCATGGTTATAAAAACTGAGTATCAATGCAGGGGTATTGGGAAAGTCTTAATAAAAGAACTAGAGAAGAGAGCGAAGGGTAGGGGAATTATCGGAATAGCTCTTGGAACTGATGATGAATATCAGAAAACTAGTTTGTCTATGATTGATATAAACGAACGAAACATCTTCGATGAAATCGGGAACATAAAGAACGTTACTAATCATCCATATGAGTTTTATAAGAAATGTGGTTATATGATCGTTGGAATAATCCCTAATGCTAATGGAAAAAGAAAACCAGATATTTGGATGTGGAAAGATATTAGCTAGG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002560","ARO_id":"38960","ARO_name":"AAC(6')-Iq","ARO_description":"AAC(6')-Iq is a aminoglycoside acetyltransferase encoded by plasmids and integrons in K. pneumoniae","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1328":{"model_id":"1328","model_name":"vanSM","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"44":{"protein_sequence":{"accession":"ACL82958.1","sequence":"MAKMRSSFRTKIILLFAVSMLLAGMVTYLLFKGLQLYYHTMIHRGNPLAELRDFIESIGDFNFFFLLFILLSLSVFYILTKPYSAYFDEISTGIQYLALGDFKRRVNIQSNDEFGDIAQAINQASEKLEEAIQRGDFSENSKEQLVVNLAHDLRTPLTSVLGYLDLVLKDEKLTKEQVRHFLTIAFTKSQRLEKLIDELFEITRMNYGMLSIEKKPINLTDLLLQLKEELYPIFEKNGLTARMNTLPHLPVSADGEMLARVFENLLTNANRYGHDGQFVDINGFVDEEEVVVQVVNYGDSIPPNELPYLFDMFYTGDKARTHKEDSTGLGLFIAKNIVEQHNGTVTAESSLIRTVFEVRLPLESAPIDQV"},"dna_sequence":{"accession":"FJ349556","fmin":"1672","fmax":"2785","strand":"+","sequence":"ATGGCTAAAATGAGAAGCAGTTTTCGCACCAAAATCATCTTGTTATTTGCTGTAAGCATGCTTCTGGCTGGTATGGTAACTTACTTACTTTTTAAAGGACTACAGCTTTATTATCATACTATGATTCATCGTGGTAACCCATTAGCCGAACTTCGCGATTTCATAGAGAGTATTGGAGACTTTAACTTCTTTTTCCTATTATTTATCTTACTGTCGCTGTCGGTTTTCTATATACTCACTAAGCCCTATTCTGCTTATTTCGATGAAATATCAACCGGAATTCAATACCTCGCACTTGGCGACTTTAAACGCCGGGTTAATATCCAATCAAATGATGAATTTGGGGATATTGCTCAAGCTATTAATCAGGCAAGTGAAAAATTAGAAGAAGCCATACAAAGAGGTGATTTTTCAGAAAACAGCAAAGAACAATTAGTTGTAAATTTGGCTCATGATTTGCGTACGCCGCTAACTTCTGTTTTAGGTTATTTAGATTTAGTTCTTAAGGATGAGAAGTTGACAAAAGAACAAGTCAGGCATTTTTTAACGATCGCCTTTACGAAATCACAGCGTTTAGAAAAACTGATTGATGAATTATTCGAAATCACGAGAATGAACTATGGCATGCTATCAATTGAAAAAAAGCCAATTAATTTAACTGATCTGCTTCTTCAATTGAAAGAAGAATTGTATCCGATTTTCGAGAAAAACGGTTTGACCGCTCGAATGAATACACTGCCTCATTTACCTGTTTCGGCTGATGGAGAGATGTTGGCTCGAGTGTTTGAAAATCTGTTGACCAATGCCAATCGTTACGGACATGACGGTCAGTTTGTAGATATTAATGGGTTTGTTGATGAAGAAGAAGTGGTTGTTCAAGTTGTGAATTATGGAGATAGCATTCCTCCGAACGAACTTCCGTATCTTTTTGATATGTTCTATACCGGTGATAAAGCACGAACCCATAAAGAGGATAGCACTGGTCTTGGACTATTTATTGCGAAGAATATTGTGGAACAGCATAATGGAACGGTTACGGCTGAAAGCAGTCTAATACGTACGGTATTTGAAGTTCGTTTACCGCTGGAAAGTGCTCCTATTGACCAAGTTTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002939","ARO_id":"39373","ARO_name":"vanSM","ARO_description":"vanSM is a vanS variant found in the vanM gene cluster","ARO_category":{"36210":{"category_aro_accession":"3000071","category_aro_cvterm_id":"36210","category_aro_name":"vanS","category_aro_description":"VanS is similar to histidine protein kinases like EnvZ and acts as a response regulator by activating VanR. VanS is required for high level transcription of other van glycopeptide resistance genes.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1329":{"model_id":"1329","model_name":"ANT(4')-IIb","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"234":{"protein_sequence":{"accession":"AAM76670.1","sequence":"MQHTIARWVDRLREEYADAVAILLKGSYARGDAATWSDIDFDVLVSTQDVEDYRTWIEPVGDRLVHISAAVEWVTGWERDTVDPSSWSYGLPTQETTRLMWAINDETRRRMDRPYKTHPAAEPEVENTVEALGKIRNAIARGDDLGVYQSAQTVAKLVPTLLIPINPPVTVSHARQAIEAILAFPRVPVGFAADWLTCLGLVEERSARSTAAAAERMVRGVLEMLPTDPDLLGEDIARLMNAGLLEKYVQQ"},"dna_sequence":{"accession":"AY114142","fmin":"1060","fmax":"1816","strand":"+","sequence":"GTGCAACATACTATCGCCCGTTGGGTTGATCGCCTTCGCGAGGAGTACGCCGATGCCGTCGCGATTCTACTGAAGGGCAGTTACGCCCGGGGCGATGCTGCGACGTGGAGCGATATCGATTTCGATGTATTGGTAAGCACGCAGGATGTGGAGGATTACCGCACCTGGATAGAGCCGGTCGGCGATCGGCTGGTGCATATCTCGGCGGCGGTCGAGTGGGTCACCGGTTGGGAGCGCGATACCGTCGATCCATCCAGTTGGAGTTACGGCCTGCCAACGCAGGAAACCACCCGACTTATGTGGGCGATTAATGACGAGACTCGGCGGCGCATGGATCGTCCTTACAAAACGCATCCGGCCGCCGAACCCGAGGTGGAGAATACCGTTGAGGCGCTAGGCAAAATTCGCAATGCCATTGCTCGCGGCGATGACCTGGGCGTGTATCAATCCGCACAGACCGTGGCAAAGTTAGTGCCGACATTGTTGATCCCCATCAATCCACCGGTGACCGTGTCGCACGCACGGCAGGCGATCGAGGCGATTCTCGCGTTTCCCCGCGTGCCCGTGGGGTTTGCAGCAGATTGGCTCACCTGCCTCGGATTGGTGGAAGAGCGAAGTGCGCGCTCGACCGCCGCAGCGGCCGAGCGCATGGTTCGTGGCGTGCTCGAAATGCTCCCTACCGATCCCGACCTCCTAGGCGAGGATATCGCCCGATTGATGAACGCCGGGTTGCTCGAGAAATACGTGCAGCAGTGAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002625","ARO_id":"39025","ARO_name":"ANT(4')-IIb","ARO_description":"ANT(4')-IIb is a transposon-encoded aminoglycoside nucleotidyltransferase in P. aeruginosa","ARO_category":{"36368":{"category_aro_accession":"3000229","category_aro_cvterm_id":"36368","category_aro_name":"ANT(4')","category_aro_description":"Nucleotidylylation of 2-deoxystreptamine aminoglycosides at the hydroxyl group at position 4'","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1330":{"model_id":"1330","model_name":"emrR","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"280"}},"model_sequences":{"sequence":{"3621":{"protein_sequence":{"accession":"NP_417169.1","sequence":"MDSSFTPIEQMLKFRASRHEDFPYQEILLTRLCMHMQSKLLENRNKMLKAQGINETLFMALITLESQENHSIQPSELSCALGSSRTNATRIADELEKRGWIERRESDNDRRCLHLQLTEKGHEFLREVLPPQHNCLHQLWSALSTTEKDQLEQITRKLLSRLDQMEQDGVVLEAMS"},"dna_sequence":{"accession":"NC_000913.3","fmin":"2810769","fmax":"2811300","strand":"+","sequence":"ATGGATAGTTCGTTTACGCCCATTGAACAAATGCTAAAATTTCGCGCCAGCCGCCACGAAGATTTTCCTTATCAGGAGATCCTTCTGACTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCTTCTGAATTAAGTTGTGCTCTTGGATCATCCCGTACCAACGCGACGCGTATTGCCGATGAACTGGAAAAACGCGGTTGGATCGAACGTCGTGAAAGCGATAACGATCGCCGCTGCCTGCATCTGCAATTAACGGAAAAAGGTCACGAGTTTTTGCGCGAGGTTTTACCACCGCAGCATAACTGCCTGCATCAACTCTGGTCCGCGCTCAGCACAACAGAAAAAGATCAGCTCGAGCAAATCACCCGCAAATTGCTCTCCCGTCTCGACCAGATGGAACAAGACGGTGTGGTTCTCGAAGCGATGAGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3000516","ARO_id":"36655","ARO_name":"emrR","ARO_description":"EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1331":{"model_id":"1331","model_name":"CTX-M-52","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1335":{"protein_sequence":{"accession":"ABB17185.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAVAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTESTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"DQ223685","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGTGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGTCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001914","ARO_id":"38314","ARO_name":"CTX-M-52","ARO_description":"CTX-M-52 is a beta-lactamase found in Escherichia coli","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1332":{"model_id":"1332","model_name":"APH(3')-IIIa","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"233":{"protein_sequence":{"accession":"AGV10830.1","sequence":"MAKMRISPELKKLIEKYRCVKDTEGMSPAKVYKLVGENENLYLKMTDSRYKGTTYDVEREKDMMLWLEGKLPVPKVLHFERHDGWSNLLMSEADGVLCSEEYEDEQSPEKIIELYAECIRLFHSIDISDCPYTNSLDSRLAELDYLLNNDLADVDCENWEEDTPFKDPRELYDFLKTEKPEEELVFSHGDLGDSNIFVKDGKVSGFIDLGRSGRADKWYDIAFCVRSIREDIGEEQYVELFFDLLGIKPDWEKIKYYILLDELF"},"dna_sequence":{"accession":"CP004067","fmin":"52914","fmax":"53709","strand":"+","sequence":"ATGGCTAAAATGAGAATATCACCGGAATTGAAAAAACTGATCGAAAAATACCGCTGCGTAAAAGATACGGAAGGAATGTCTCCTGCTAAGGTATATAAGCTGGTGGGAGAAAATGAAAACCTATATTTAAAAATGACGGACAGCCGGTATAAAGGGACCACCTATGATGTGGAACGGGAAAAGGACATGATGCTATGGCTGGAAGGAAAGCTGCCTGTTCCAAAGGTCCTGCACTTTGAACGGCATGATGGCTGGAGCAATCTGCTCATGAGTGAGGCCGATGGCGTCCTTTGCTCGGAAGAGTATGAAGATGAACAAAGCCCTGAAAAGATTATCGAGCTGTATGCGGAGTGCATCAGGCTCTTTCACTCCATCGACATATCGGATTGTCCCTATACGAATAGCTTAGACAGCCGCTTAGCCGAATTGGATTACTTACTGAATAACGATCTGGCCGATGTGGATTGCGAAAACTGGGAAGAAGACACTCCATTTAAAGATCCGCGCGAGCTGTATGATTTTTTAAAGACGGAAAAGCCCGAAGAGGAACTTGTCTTTTCCCACGGCGACCTGGGAGACAGCAACATCTTTGTGAAAGATGGCAAAGTAAGTGGCTTTATTGATCTTGGGAGAAGCGGCAGGGCGGACAAGTGGTATGACATTGCCTTCTGCGTCCGGTCGATCAGGGAGGATATCGGGGAAGAACAGTATGTCGAGCTATTTTTTGACTTACTGGGGATCAAGCCTGATTGGGAGAAAATAAAATATTATATTTTACTGGATGAATTGTTTTAGT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39528","NCBI_taxonomy_name":"Campylobacter coli CVM N29710","NCBI_taxonomy_id":"1273173"}}}},"ARO_accession":"3002647","ARO_id":"39047","ARO_name":"APH(3')-IIIa","ARO_description":"APH(3')-IIIa is a plasmid-encoded aminoglycoside phosphotransferase in S. aureus and Enterococcus spp.","ARO_category":{"36265":{"category_aro_accession":"3000126","category_aro_cvterm_id":"36265","category_aro_name":"APH(3')","category_aro_description":"Phosphorylation of 2-deoxystreptamine aminoglycosides on the hydroxyl group at position 3'","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37044":{"category_aro_accession":"3000700","category_aro_cvterm_id":"37044","category_aro_name":"lividomycin A","category_aro_description":"Lividomycin A is a pentasaccharide antibiotic which interferes with bacterial protein synthesis.","category_aro_class_name":"Antibiotic"},"37045":{"category_aro_accession":"3000701","category_aro_cvterm_id":"37045","category_aro_name":"lividomycin B","category_aro_description":"Lividomycin B is a derivative of lividomycin A with a removed mannose group (demannosyllividomycin A). Livodomycins interfere with bacterial protein synthesis.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1333":{"model_id":"1333","model_name":"vanHD","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"428":{"protein_sequence":{"accession":"AAM09850.1","sequence":"MQEKIDITVFGCERDEAAVFRKLSSEYGVTVSLIEDVVSEHNAKLADGCQCVSVSHKAELSEQLLLALKHAGVKYISTRSIGFNHIDIQAAGQLGMAVGTVAYSPGSVADYTVMLMLMLLRGTKSVLRGTQKQNYCLNDCRGKELQDLTVGVLGTGRIGQAVMERLEGIGCKVLAYDRTHKAGANYVSFCELLKSSDIVTLHVPLAEDTRHMIGREQLEMMKREALLINTARGALVDTAALVAALKEQKIGGAALDVLEGEEGIFYHECTQKTIGHPYLSVLQKMPNVIVTPHTAYHTDRVLVDTVSNTIRNCLNFERSLGNV"},"dna_sequence":{"accession":"AY082011","fmin":"4936","fmax":"5908","strand":"+","sequence":"ATGCAGGAAAAAATAGATATTACGGTTTTTGGGTGTGAGCGGGATGAAGCGGCGGTATTCCGTAAACTTTCATCTGAGTATGGCGTCACAGTTTCGCTCATCGAAGATGTCGTATCAGAGCACAATGCAAAATTAGCGGACGGATGCCAGTGTGTCAGCGTAAGCCATAAGGCGGAGCTGTCGGAGCAGCTTCTCCTTGCGCTGAAACACGCAGGAGTGAAATACATCAGTACCCGGAGCATTGGATTCAACCATATTGATATACAGGCTGCAGGTCAGTTGGGTATGGCTGTTGGCACAGTGGCATACTCACCGGGAAGCGTGGCCGATTATACCGTCATGCTGATGCTCATGCTGCTGCGCGGCACAAAGTCGGTTCTACGAGGAACCCAGAAGCAGAATTATTGTCTGAATGACTGCCGTGGAAAAGAACTGCAGGATTTGACGGTTGGCGTCCTGGGAACCGGACGAATCGGACAGGCAGTCATGGAACGCCTGGAGGGAATCGGCTGCAAGGTGTTGGCCTATGACCGAACTCACAAAGCCGGAGCAAATTATGTTTCGTTTTGTGAATTATTGAAGAGCAGCGACATTGTTACGCTGCATGTGCCTCTGGCAGAGGATACCCGCCATATGATTGGGCGCGAGCAGCTAGAGATGATGAAGAGGGAGGCACTTCTGATCAACACGGCACGGGGGGCTTTAGTGGATACGGCTGCACTGGTTGCTGCGCTGAAAGAACAAAAAATCGGCGGAGCCGCCTTAGATGTCCTGGAAGGGGAAGAAGGCATCTTTTACCATGAATGCACACAAAAAACGATAGGGCATCCTTACCTCTCCGTTTTGCAGAAAATGCCCAATGTCATTGTTACGCCGCATACGGCCTATCATACGGATCGGGTACTGGTCGATACCGTGAGCAATACCATCCGAAATTGTCTGAATTTTGAAAGGAGTCTTGGAAATGTATAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002944","ARO_id":"39378","ARO_name":"vanHD","ARO_description":"vanHD is a vanH variant in the vanD gene cluster","ARO_category":{"36015":{"category_aro_accession":"3000006","category_aro_cvterm_id":"36015","category_aro_name":"vanH","category_aro_description":"VanH is a D-specific alpha-ketoacid dehydrogenase that synthesizes D-lactate. D-lactate is incorporated into the end of the peptidoglycan subunits, decreasing vancomycin binding affinity.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1334":{"model_id":"1334","model_name":"SHV-126","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"2020":{"protein_sequence":{"accession":"ACV32636.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGKRGARGIVALLGPNNKAERTVVIYLRDTPASMAERNQ"},"dna_sequence":{"accession":"GQ390808","fmin":"0","fmax":"813","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCAAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCACCGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001173","ARO_id":"37553","ARO_name":"SHV-126","ARO_description":"SHV-126 is a beta-lactamase that has been found in clinical isolates.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1335":{"model_id":"1335","model_name":"QnrB8","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"592":{"protein_sequence":{"accession":"ABW03157.2","sequence":"MTLALVGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAILKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKAVLEKCELWENRWMGTQVLGATLSGSDLSGGEFSSFDWRTANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQAALLMERLGIAVIG"},"dna_sequence":{"accession":"EU043312","fmin":"0","fmax":"645","strand":"+","sequence":"ATGACTCTGGCATTAGTTGGCGAAAAAATTGACAGAAACCGCTTCACCGGTGAAAAAGTTGAAAATAGCACTTTTTTTAACTGTGATTTTTCGGGTGCCGACCTTAGCGGTACTGAATTTATCGGCTGTCAGTTCTATGATCGAGAAAGCCAGAAAGGGTGCAATTTCAGTCGCGCAATACTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAACGTCAGTGCGTTGGGCATAGAAATTCGCCACTGCCGCGCACAGGGTGCAGATTTTCGCGGCGCAAGTTTCATGAATATGATCACCACGCGCACCTGGTTTTGCAGCGCATATATCACTAATACCAATCTAAGCTACGCCAACTTTTCGAAGGCCGTGCTTGAAAAGTGCGAATTGTGGGAAAATCGCTGGATGGGAACTCAGGTACTGGGTGCGACGTTGAGTGGTTCCGATCTCTCCGGTGGCGAGTTTTCGTCGTTCGACTGGCGGACGGCAAATTTCACGCACTGTGATTTGACCAATTCAGAACTGGGTGATTTAGATATTCGGGGCGTCGATTTACAAGGTGTCAAATTGGACAACTATCAGGCCGCATTGCTCATGGAACGTCTTGGCATCGCTGTGATTGGCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002722","ARO_id":"39156","ARO_name":"QnrB8","ARO_description":"QnrB8 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1336":{"model_id":"1336","model_name":"BcII","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"1699":{"protein_sequence":{"accession":"AAA22562.1","sequence":"MKNTLLKLGVCVSLLGITPFVSTISSVQAERTVEHKVIKNETGTISISQLNKNVWVHTELGYFSGEAVPSNGLVLNTSKGLVLVDSSWDDKLTKELIEMVEKKFKKRVTDVIITHAHADRIGGMKTLKERGIKAHSTALTAELAKKNGYEEPLGDLQSVTNLKFGNMKVETFYPGKGHTEDNIVVWLPQYQILAGGCLVKSASSKDLGNVADAYVNEWSTSIENVLKRYGNINLVVPGHGEVGDRGLLLHTLDLLK"},"dna_sequence":{"accession":"M19530","fmin":"415","fmax":"1186","strand":"+","sequence":"ATGAAAAATACATTATTAAAATTAGGGGTATGTGTTAGTTTACTAGGAATAACTCCATTTGTTAGTACAATTTCTTCTGTACAAGCAGAACGAACGGTAGAGCATAAAGTAATAAAAAATGAGACAGGAACTATTTCGATTTCTCAGTTAAACAAAAATGTATGGGTTCATACGGAGTTAGGTTATTTTAGCGGAGAAGCAGTTCCTTCGAACGGTTTAGTCCTTAATACTTCTAAAGGGTTAGTACTTGTCGATTCTTCTTGGGATGATAAGTTAACGAAGGAATTAATAGAGATGGTAGAAAAGAAATTTAAGAAGCGCGTAACAGATGTCATTATTACACATGCACACGCTGATCGAATTGGTGGAATGAAAACATTGAAAGAAAGGGGCATTAAAGCGCATAGTACAGCGTTAACTGCGGAATTAGCAAAGAAAAATGGATATGAAGAACCACTTGGAGACTTACAAAGCGTTACAAATTTGAAGTTTGGAAATATGAAAGTAGAAACATTTTATCCAGGGAAGGGACATACAGAAGATAATATTGTTGTTTGGTTGCCACAATATCAAATTTTAGCTGGAGGCTGTTTAGTTAAATCTGCGTCCTCTAAAGATTTAGGAAACGTTGCTGATGCGTATGTAAATGAATGGTCCACATCGATTGAAAATGTGCTGAAGCGATATGGAAATATAAATTTAGTAGTGCCTGGTCATGGAGAAGTAGGGGATAGAGGATTACTTTTACATACATTGGATTTGTTGAAATAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36751","NCBI_taxonomy_name":"Bacillus cereus","NCBI_taxonomy_id":"1396"}}}},"ARO_accession":"3002878","ARO_id":"39312","ARO_name":"BcII","ARO_description":"Bacillus cereus beta-lactamase II is a zinc metallo-beta-lactamase that hydrolyzes a large number of penicillins and cephalosporins in the Bacillus cereus strain 5\/B\/6","ARO_category":{"36716":{"category_aro_accession":"3000577","category_aro_cvterm_id":"36716","category_aro_name":"Bc beta-lactamase","category_aro_description":"Bacillus cereus beta-lactamases are zinc metallo-beta-lactamases that hydrolyze a large number of penicillins and cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1337":{"model_id":"1337","model_name":"baeR","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"676":{"protein_sequence":{"accession":"YP_490321.1","sequence":"MTELPIDENTPRILIVEDEPKLGQLLIDYLRAASYAPTLISHGDQVLPYVRQTPPDLILLDLMLPGTDGLTLCREIRRFSDIPIVMVTAKIEEIDRLLGLEIGADDYICKPYSPREVVARVKTILRRCKPQRELQQQDAESPLIIDEGRFQASWRGKMLDLTPAEFRLLKTLSHEPGKVFSREQLLNHLYDDYRVVTDRTIDSHIKNLRRKLESLDAEQSFIRAVYGVGYRWEADACRIV"},"dna_sequence":{"accession":"NC_007779","fmin":"2166412","fmax":"2167135","strand":"+","sequence":"ATGACCGAGTTACCAATCGACGAAAACACACCGCGTATTTTGATCGTGGAAGATGAACCGAAGCTGGGGCAGTTGCTCATTGATTATCTGCGTGCTGCGAGCTATGCGCCGACGCTTATCAGCCACGGCGATCAGGTACTGCCGTATGTGCGCCAGACACCACCGGATCTGATCCTGTTAGATCTGATGCTCCCTGGCACCGATGGCCTGACGCTGTGCCGGGAAATTCGTCGTTTTTCTGACATTCCGATCGTGATGGTGACGGCAAAAATCGAAGAGATCGATCGCCTGCTGGGGCTGGAGATTGGCGCAGATGATTATATCTGTAAGCCGTACAGCCCACGGGAAGTGGTAGCGCGCGTCAAAACCATTTTGCGCCGTTGCAAACCGCAGCGCGAGTTGCAGCAACAGGATGCTGAAAGCCCGTTGATTATCGACGAAGGTCGTTTTCAGGCTTCATGGCGCGGTAAAATGCTTGACCTGACGCCTGCGGAATTTCGTCTGCTGAAAACGCTCTCTCACGAACCAGGAAAAGTGTTCTCCCGCGAGCAATTGCTCAATCATCTTTATGACGACTACCGCGTAGTAACCGACCGCACCATCGACAGCCACATTAAAAACCTGCGCCGCAAGCTGGAATCTCTCGACGCCGAACAGTCATTTATCCGCGCCGTTTATGGCGTCGGTTACCGCTGGGAAGCCGACGCCTGCCGCATCGTTTAGT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36839","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. W3110","NCBI_taxonomy_id":"316407"}}}},"ARO_accession":"3000828","ARO_id":"37208","ARO_name":"baeR","ARO_description":"BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1338":{"model_id":"1338","model_name":"BLA1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"1545":{"protein_sequence":{"accession":"AAR20595.1","sequence":"MIVLKNKKMLKIGMCVGILGLSITSLVTFTGGALQVEAKEKTGQVKHKNQATHKEFSQLEKKFDARLGVYAIDTGTNQTIAYRPNERFAFASTYKALAAGVLLQQNSTKKLDEVITYTKEDLVDYSPVTEKHVDTGMTLGEIAEAAVRYSDNTAGNILFHKIGGPKGYEKALRQMGDRVTMSDRFETELNEAIPGDIRDTSTAKAIATNLKAFTAGNALPNHKRNILTKWMKGNATGDKLIRAGVPTNWVVADKSGAGSYGTRNDIAIVWPPNRAPIIIAILSSKDEKGATYDNQLIAEAAEVIVNAFR"},"dna_sequence":{"accession":"AY453161","fmin":"500","fmax":"1430","strand":"+","sequence":"ATGATAGTTTTGAAAAACAAGAAAATGCTAAAAATAGGGATGTGTGTTGGTATATTAGGTTTAAGTATTACAAGCCTAGTAACTTTTACAGGAGGTGCATTGCAAGTTGAAGCGAAAGAAAAGACTGGACAAGTGAAACATAAAAATCAGGCGACGCATAAAGAGTTCTCTCAACTTGAGAAAAAATTTGATGCTCGATTAGGTGTATATGCGATTGATACTGGTACAAATCAAACAATCGCTTATCGACCTAACGAAAGGTTTGCCTTTGCATCAACTTACAAGGCTTTAGCGGCAGGGGTATTACTGCAACAGAACTCTACTAAGAAATTAGATGAAGTTATTACTTATACGAAAGAAGACTTAGTGGATTATTCACCTGTTACAGAGAAACATGTAGATACTGGAATGACACTAGGAGAAATTGCGGAGGCTGCTGTTCGTTACAGTGATAATACTGCAGGGAACATTTTATTTCATAAAATAGGCGGACCGAAAGGATATGAAAAAGCGCTTAGACAGATGGGGGACCGGGTTACTATGTCTGATCGTTTTGAAACAGAATTAAACGAGGCTATTCCAGGAGACATTCGTGACACCAGTACAGCGAAAGCAATTGCTACGAATCTTAAAGCTTTTACGGCCGGAAATGCGCTTCCAAATCATAAACGTAACATTCTTACAAAGTGGATGAAAGGAAATGCTACAGGAGACAAACTTATTCGTGCAGGTGTGCCTACTAACTGGGTAGTTGCAGATAAATCAGGAGCTGGAAGTTACGGGACACGAAATGATATTGCTATCGTTTGGCCACCAAATAGAGCACCTATTATCATCGCAATTTTATCTAGTAAAGATGAAAAAGGGGCTACCTATGATAATCAACTCATTGCAGAGGCGGCTGAAGTTATAGTTAATGCTTTTAGGTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36786","NCBI_taxonomy_name":"Bacillus anthracis","NCBI_taxonomy_id":"1392"}}}},"ARO_accession":"3000090","ARO_id":"36229","ARO_name":"Bla1","ARO_description":"Bla1 is a chromosomal-encoded beta-lactamase, found in Bacillus anthracis, which hydrolyzes penicillins.","ARO_category":{"41393":{"category_aro_accession":"3004229","category_aro_cvterm_id":"41393","category_aro_name":"class A Bacillus anthracis Bla beta-lactamase","category_aro_description":"Beta-lactamases belonging to the Bla genes from Bacillus anthracis that are classified as class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1340":{"model_id":"1340","model_name":"mtrC","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"790"}},"model_sequences":{"sequence":{"4396":{"protein_sequence":{"accession":"NP_274719.1","sequence":"MAFYAFKAMRAAALAAAVALVLSSCGKGGDAAQGGQPAGREAPAPVVGVVTVHPQTVALTVELPGRLESLRTADVRAQVGGIIQKRLFQEGSYVRAGQPLYQIDSSTYEAGLESARAQLATAQATLAKADADLARYKPLVAAEAVSRQEYDAAVTAKRSAEAGVKAAQAAIKSAGISLNRSRITAPISGFIGQSKVSEGTLLNAGDATVLATIRQTNPMYVNVTQSASEVMKLRRQIAEGKLLAADGVIAVGIKFDDGTVYPEKGRLLFADPAVNESTGQITLRAAVPNDQNILMPGLYVRVLMDQVAVDNAFVVPQQAVTRGAKDTVMIVNAQGGMEPREVTVAQQQGTNWIVTSGLKDGDKVVVEGISIAGITGAKKVTPKEWASSENQAAAPQSGVQTASEAKPASEAK"},"dna_sequence":{"accession":"NC_003112","fmin":"1795181","fmax":"1796420","strand":"-","sequence":"TTATTTCGCTTCAGAAGCAGGTTTGGCTTCAGATGCCGTCTGAACGCCGGATTGAGGCGCGGCGGCTTGGTTTTCAGACGACGCCCATTCTTTGGGCGTTACCTTTTTCGCACCCGTTATACCGGCGATACTGATGCCTTCCACAACCACCTTGTCCCCGTCCTTCAGACCCGACGTAACAATCCAATTCGTACCCTGCTGTTGCGCAACCGTTACCTCGCGGGGTTCCATACCGCCTTGGGCATTCACAATCATCACGGTATCTTTCGCACCGCGCGTTACCGCCTGCTGCGGCACAACAAATGCGTTATCCACCGCCACTTGGTCCATCAGCACGCGCACATACAGACCGGGCATCAAGATATTCTGATCGTTCGGTACGGCGGCGCGCAGGGTAATCTGACCGGTCGATTCGTTGACGGCCGGATCGGCAAACAGCAGGCGGCCTTTTTCAGGGTAAACTGTGCCGTCGTCAAATTTGATGCCGACCGCAATCACACCATCCGCCGCCAGCAGTTTGCCTTCGGCTATCTGACGGCGCAATTTCATCACTTCGGATGCAGACTGGGTAACGTTCACATACATCGGATTGGTTTGGCGGATGGTCGCCAGTACGGTCGCATCGCCAGCGTTCAGCAACGTACCTTCGGAAACTTTGGACTGACCGATAAAGCCGGAAATCGGCGCGGTAATGCGCGAACGGTTCAGGCTGATGCCGGCGGATTTGATTGCCGCCTGCGCCGCTTTAACGCCTGCCTCGGCAGAACGTTTCGCCGTTACCGCAGCATCGTATTCCTGCCGGCTGACGGCTTCGGCGGCAACCAAAGGCTTGTATCGCGCCAAATCCGCATCCGCTTTGGCAAGCGTTGCCTGAGCCGTTGCCAGTTGCGCGCGCGCGCTTTCCAGACCTGCTTCATAAGTGGAACTGTCGATCTGATACAGCGGCTGTCCGGCACGGACATAACTGCCTTCTTGGAACAGGCGTTTTTGGATGATGCCGCCGACTTGGGCGCGGACATCGGCGGTACGCAGCGATTCCAAACGCCCCGGCAACTCGACGGTCAATGCGACGGTTTGCGGATGGACGGTTACGACACCGACGACGGGCGCAGGGGCTTCCCGACCAGCAGGCTGCCCGCCCTGCGCCGCGTCTCCGCCTTTACCGCAAGACGACAGTACCAATGCAACGGCGGCAGCCAACGCGGCCGCACGCATCGCCTTAAAAGCATAAAAAGCCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39597","NCBI_taxonomy_name":"Neisseria meningitidis MC58","NCBI_taxonomy_id":"122586"}}}},"ARO_accession":"3000810","ARO_id":"37190","ARO_name":"mtrC","ARO_description":"MtrC is the membrane fusion protein of the MtrCDE multidrug efflux complex.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35971":{"category_aro_accession":"0000054","category_aro_cvterm_id":"35971","category_aro_name":"penicillin","category_aro_description":"Penicillin (sometimes abbreviated PCN) is a beta-lactam antibiotic used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms. It works by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1341":{"model_id":"1341","model_name":"OXA-53","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"812":{"protein_sequence":{"accession":"AAP43641.1","sequence":"MAIQIFAILFSTFVLATFAHAQDGTLERSDWGKFFSDFQAKGTIVVADERQADHAILVFDQARSMKRYSPASTFKIPHTLFALDAGAVRDEFQIFRWDGVKRSFAGHNKDQDLRSAMRNSTVWVYELFAKEIGDGKARRYLKQIGYGNADPSTSHGDYWIEGSLAISAQEQIAFLRKLYQNDLPFRVEHQRLVKDLMIVEAGRNWILRAKTGWEGSMGWWVGWVEWPTGPVFFALNIDTPNRMDDLFKREAIARAILLSIEALPPNPAVHSDAAR"},"dna_sequence":{"accession":"AY289608","fmin":"616","fmax":"1444","strand":"+","sequence":"ATGGCAATCCAAATCTTCGCAATACTTTTCTCCACTTTTGTTCTTGCCACTTTTGCACATGCGCAAGATGGCACGCTGGAACGTTCTGACTGGGGGAAATTTTTCAGCGATTTTCAGGCCAAAGGTACGATAGTTGTGGCAGACGAACGCCAAGCGGATCATGCGATATTGGTTTTTGATCAAGCACGGTCAATGAAACGCTACTCGCCTGCGTCGACATTCAAGATTCCACATACACTTTTTGCACTTGATGCAGGCGCCGTTCGCGATGAGTTTCAGATTTTCCGCTGGGACGGCGTCAAAAGGAGCTTTGCAGGTCACAATAAAGACCAAGATTTGCGATCAGCAATGCGAAATTCTACTGTCTGGGTTTATGAGCTATTTGCAAAGGAAATCGGTGATGGCAAGGCTCGACGCTATTTGAAGCAAATCGGCTATGGCAACGCCGATCCTTCGACAAGTCATGGCGATTACTGGATAGAAGGCAGCCTTGCAATCTCAGCACAGGAACAGATCGCGTTTCTCAGAAAGCTCTATCAAAACGATCTGCCCTTTAGGGTGGAACATCAGCGCTTGGTCAAGGATCTGATGATTGTGGAAGCGGGACGCAACTGGATTCTGCGCGCGAAGACGGGCTGGGAAGGCAGCATGGGTTGGTGGGTGGGGTGGGTTGAATGGCCAACCGGTCCCGTATTCTTTGCCTTGAATATCGATACGCCAAACAGAATGGACGATCTTTTCAAGAGGGAAGCAATAGCGCGAGCGATACTTCTCTCTATCGAAGCGTTGCCGCCCAACCCGGCAGTCCACTCGGACGCTGCGCGATGAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35709","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Agona","NCBI_taxonomy_id":"58095"}}}},"ARO_accession":"3001810","ARO_id":"38210","ARO_name":"OXA-53","ARO_description":"OXA-53 is a beta-lactamase found in Salmonella enterica","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1343":{"model_id":"1343","model_name":"OXA-166","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1292":{"protein_sequence":{"accession":"ADK35870.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETPSQIVQGHNQVIHQYFDEKNTSGALVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKPQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"HM488987","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGCGCTGGTTATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGACCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCCCAATTAGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001466","ARO_id":"37866","ARO_name":"OXA-166","ARO_description":"OXA-166 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1344":{"model_id":"1344","model_name":"mexH","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"650"}},"model_sequences":{"sequence":{"294":{"protein_sequence":{"accession":"NP_252895.1","sequence":"MQKPVLIASAALICAAVIGIAVYATGSAKKDAGGFAGYPPVKVALASVERRVVPRVFDGVGELEAGRQVQVAAEAAGRITRIAFESGQQVQQGQLLVQLNDAVEQAELIRLKAQLRNAEILHARARKLVERNVASQEQLDNAVAARDMALGAVRQTQALIDQKAIRAPFSGQLGIRRVHLGQYLGVAEPVASLVDARTLKSNFSLDESTSPELKLGQPLEVLVDAYPGRSFPARISAIDPLIGKSRTVQVQALLDNPEGLLAAGMFASIRVSRKADAPSLSVPETAVTYTAYGDTVFVAHQDGDRPLSAKRVSVRIGERWDGRVEILQGLAEGDRVVTSGQINLSDGMAVEPVKEDTLSSAAPPVPVAGR"},"dna_sequence":{"accession":"NC_002516","fmin":"4706409","fmax":"4707522","strand":"+","sequence":"ATGCAGAAACCCGTCCTGATCGCCAGTGCCGCGCTCATCTGCGCGGCGGTTATCGGCATCGCCGTCTACGCCACCGGCTCGGCGAAGAAAGACGCCGGCGGTTTCGCCGGCTACCCGCCGGTGAAGGTCGCCCTCGCCTCGGTGGAGCGGCGGGTGGTGCCGCGCGTCTTCGATGGCGTCGGCGAGCTGGAGGCCGGTCGCCAGGTCCAGGTGGCCGCCGAAGCGGCAGGACGGATCACCCGCATCGCCTTCGAATCGGGCCAGCAGGTGCAGCAAGGGCAGTTGCTGGTGCAACTCAACGACGCGGTGGAACAGGCCGAGCTGATCCGTCTCAAGGCGCAGTTGCGCAATGCCGAGATCCTCCATGCCCGTGCGCGCAAGCTGGTAGAGCGCAACGTCGCCTCGCAGGAACAGCTGGACAACGCCGTCGCCGCCCGCGACATGGCGCTCGGCGCGGTGCGCCAGACCCAGGCGCTGATCGACCAGAAGGCGATCCGCGCGCCCTTCTCCGGCCAGCTCGGCATCCGCCGCGTGCACCTCGGCCAGTACCTCGGCGTCGCCGAGCCGGTGGCCAGCCTGGTGGATGCGCGGACCCTGAAAAGCAATTTCTCCCTGGACGAAAGCACCAGTCCCGAGCTGAAGCTCGGCCAGCCCCTCGAGGTCCTGGTCGACGCCTATCCGGGGCGCAGCTTCCCGGCGCGCATCAGCGCCATCGACCCGCTGATCGGCAAGTCGCGCACGGTGCAGGTCCAGGCCTTGCTGGACAACCCCGAAGGCCTGCTCGCCGCCGGCATGTTCGCCAGCATCCGGGTCTCGCGCAAAGCCGACGCGCCGTCGCTGAGCGTGCCGGAAACCGCGGTCACCTATACCGCCTACGGCGACACCGTGTTCGTCGCCCACCAGGACGGCGACCGGCCGCTCAGCGCCAAGCGCGTCTCGGTGCGGATCGGCGAGCGCTGGGACGGTCGCGTGGAAATCCTCCAGGGCCTCGCCGAGGGCGACCGGGTAGTGACTTCCGGACAGATCAACCTGAGCGACGGGATGGCCGTGGAACCGGTCAAGGAAGACACCCTGAGCAGTGCCGCGCCCCCCGTGCCGGTCGCCGGCCGCTGAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3000807","ARO_id":"37187","ARO_name":"MexH","ARO_description":"MexH is the membrane fusion protein of the efflux complex MexGHI-OpmD.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavin","category_aro_description":"Acriflavin is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36193":{"category_aro_accession":"3000054","category_aro_cvterm_id":"36193","category_aro_name":"acridine dye","category_aro_description":"Acridine dyes are cell permeable, basic molecules with an acridine chromophore. These compounds intercalate DNA. The image shown represents the core structure of the acridine family, with specific dyes containing varying substituents.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1346":{"model_id":"1346","model_name":"SHV-94","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1950":{"protein_sequence":{"accession":"ABN49111.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQHLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"EF373970","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGCATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGATGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001146","ARO_id":"37526","ARO_name":"SHV-94","ARO_description":"SHV-94 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1347":{"model_id":"1347","model_name":"OXA-425","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1136":{"protein_sequence":{"accession":"AJA32743.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTLKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASALPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KM588353","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCCTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTCTTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003148","ARO_id":"39725","ARO_name":"OXA-425","ARO_description":"OXA-425 is a \u00df-lactamase found in clinical isolates of Acinetobacter baumannii. It is carbapenem-resistant","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1349":{"model_id":"1349","model_name":"IND-2a","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"838":{"protein_sequence":{"accession":"AAG29760.1","sequence":"MKKSIQLLMMSMFLSPLINAQVKDFVIEPPVKPNLYLYKSFGVFGGKEYSANAVYLTTKKGVVLFDVPWQKEQYQTLMDTIQKRHHLPVIAVFATHSHDDRAGDLSFYNQKGIKTYATAKTNELLKKDGKATSTEIIKTGKPYKIGGEEFMVDFLGEGHTVDNVVVWFPKYKVLDGGCLVKSRTATDLGYTGEANVKQWPETMRKLKTKYAQATLVIPGHEEWKGGGHVQHTLDLLDKNKKPE"},"dna_sequence":{"accession":"AF219130","fmin":"0","fmax":"732","strand":"+","sequence":"ATGAAAAAAAGTATTCAGCTTTTGATGATGTCAATGTTTTTAAGCCCATTGATCAATGCCCAGGTTAAAGATTTTGTAATTGAGCCGCCTGTTAAACCCAACCTGTATCTTTATAAAAGTTTCGGAGTTTTCGGGGGTAAAGAATATTCTGCCAATGCTGTATATCTTACCACTAAGAAAGGAGTTGTCTTATTTGATGTCCCATGGCAAAAGGAACAATATCAAACCCTTATGGACACTATACAAAAGCGTCATCACCTTCCTGTAATTGCTGTATTTGCCACCCACTCTCATGATGACAGAGCGGGCGATCTAAGCTTTTACAATCAAAAAGGAATTAAAACATATGCGACCGCCAAGACCAATGAACTGTTGAAAAAAGACGGAAAAGCAACCTCAACCGAAATTATAAAAACAGGAAAACCTTACAAAATTGGTGGTGAAGAATTTATGGTAGACTTTCTTGGAGAAGGACATACAGTTGATAATGTTGTTGTATGGTTCCCCAAATATAAAGTACTGGACGGAGGATGTCTTGTAAAAAGCAGGACAGCCACTGACCTGGGATATACCGGTGAAGCAAACGTAAAACAATGGCCGGAAACCATGCGAAAACTAAAAACGAAATATGCTCAGGCCACTCTGGTAATCCCGGGACACGAGGAATGGAAAGGCGGTGGCCATGTACAGCATACTCTGGATCTTCTGGATAAGAATAAAAAGCCGGAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36916","NCBI_taxonomy_name":"Chryseobacterium indologenes","NCBI_taxonomy_id":"253"}}}},"ARO_accession":"3002258","ARO_id":"38658","ARO_name":"IND-2a","ARO_description":"IND-2a is a beta-lactamase found in Chryseobacterium indologenes","ARO_category":{"36199":{"category_aro_accession":"3000060","category_aro_cvterm_id":"36199","category_aro_name":"IND beta-lactamase","category_aro_description":"IND beta-lactamases are class B carbapenem-hydrolyzing beta-lactamases","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1350":{"model_id":"1350","model_name":"TEM-93","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2039":{"protein_sequence":{"accession":"CAC85660.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTTPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASKRGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AJ318093","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTAAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000960","ARO_id":"37340","ARO_name":"TEM-93","ARO_description":"TEM-93 is an extended-spectrum beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1351":{"model_id":"1351","model_name":"QnrVC1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"423":{"protein_sequence":{"accession":"ACC54440.2","sequence":"MEKSKQLYNQVNFSHQDLQEHIFSNCTFIHCNFKRSNLRDTQFINCTFIEQGALEGCDFSYADLRDASFKNCQLSMSHFKGANCFGIELRDCDLKGANFSQVSFVNQVSNKMYFCSAYITGCNLSYANFEQQLIEKCDLFENRWIGANLRGASFKESDLSRGVFSEDCWEQFRVQGCDLSHSELYGLDPRKIDLTGVKICSWQQEQLLEQLGVIIVPD"},"dna_sequence":{"accession":"EU436855","fmin":"1401","fmax":"2058","strand":"+","sequence":"ATGGAAAAATCAAAGCAATTATATAATCAAGTGAACTTCTCACATCAGGACTTGCAAGAACATATCTTTAGCAATTGTACTTTTATACATTGTAATTTTAAGCGCTCAAACCTCCGAGATACACAGTTCATTAACTGTACTTTCATAGAGCAGGGGGCATTGGAAGGGTGCGATTTTTCTTATGCTGATCTTCGAGATGCTTCATTTAAAAACTGTCAGCTTTCAATGTCCCATTTTAAGGGGGCAAATTGCTTTGGTATTGAACTGAGAGATTGTGATCTTAAAGGAGCAAATTTTAGTCAAGTTAGTTTTGTAAATCAGGTTTCGAATAAAATGTACTTTTGTTCTGCATACATAACAGGTTGTAACTTATCCTATGCCAATTTTGAGCAGCAGCTTATTGAAAAATGTGACCTGTTCGAAAATAGATGGATTGGTGCAAATCTTCGAGGCGCTTCATTTAAAGAATCAGATTTAAGCCGTGGTGTTTTTTCGGAAGACTGCTGGGAACAGTTTAGAGTACAAGGCTGTGATTTAAGCCATTCAGAGCTTTATGGTTTAGATCCTCGAAAGATTGATCTTACGGGTGTAAAAATATGCTCGTGGCAACAGGAACAGTTACTGGAGCAATTAGGGGTAATCATTGTTCCTGACTAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36789","NCBI_taxonomy_name":"Vibrio cholerae","NCBI_taxonomy_id":"666"}}}},"ARO_accession":"3002799","ARO_id":"39233","ARO_name":"QnrVC1","ARO_description":"QnrVC1 is an integron-mediated quinolone resistance protein found in Vibrio cholerae","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1352":{"model_id":"1352","model_name":"OXA-251","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1375":{"protein_sequence":{"accession":"AER57903.1","sequence":"MKTFAAYVIIACLSSTALAGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVDEVRMQKYLKNFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLTVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG"},"dna_sequence":{"accession":"JN118546","fmin":"1761","fmax":"2562","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTATCGCGTGTCTTTCGAGTACGGCATTAGCTGGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTCTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATGACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAGCAATGGGAAAGAGACTTGACCTTAAGAGGGGCAATACAAGTTTCAGCTGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGACGAAGTAAGAATGCAGAAATACCTTAAAAACTTTTCCTATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAAGGCCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATATTTAAATAAATTGTCAGCATCTAAAGAAAACCAGCTAACAGTAAAAGAGGCTTTGGTAACGGAGGCGGCACCTGAATATCTAGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGGTGGGTTGAGAAGGAGACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAGTAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGAAAGTGAGGGCATCATTGGTGGCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001500","ARO_id":"37900","ARO_name":"OXA-251","ARO_description":"OXA-251 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1353":{"model_id":"1353","model_name":"GES-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1866":{"protein_sequence":{"accession":"AAR97270.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMSDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"AY494717","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCATCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGAGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002334","ARO_id":"38734","ARO_name":"GES-5","ARO_description":"GES-5 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1355":{"model_id":"1355","model_name":"TEM-149","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2032":{"protein_sequence":{"accession":"ABC96711.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTTPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGVRGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"DQ369751","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGTGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36770","NCBI_taxonomy_name":"Enterobacter aerogenes","NCBI_taxonomy_id":"548"}}}},"ARO_accession":"3001016","ARO_id":"37396","ARO_name":"TEM-149","ARO_description":"TEM-149 is an extended-spectrum beta-lactamase found in Enterobacter aerogenes.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1356":{"model_id":"1356","model_name":"dfrA22","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"419":{"protein_sequence":{"accession":"CAX16467.1","sequence":"MNPESVRIYLVAAMGANRVIGNGPDIPWNIPGEQKIFRRLTEGKVVVMGRKTFESIGKPLPNRRTVVLSRQASYSAAGCAVVSTLSQAIAIAAEHGKELYVAGGAEVYALALPRADGVFLSEVHQTFEGDAFFPALDAAEFDVVSAETVQATITYTHSVYARRNG"},"dna_sequence":{"accession":"FM957884","fmin":"87","fmax":"585","strand":"+","sequence":"ATGAACCCGGAATCGGTCCGCATTTATCTGGTCGCTGCCATGGGTGCCAATCGGGTTATTGGCAATGGCCCTGATATCCCTTGGAATATCCCTGGTGAGCAAAAGATTTTTCGCAGGCTCACCGAGGGCAAAGTGGTCGTTATGGGCCGCAAGACGTTTGAGTCCATAGGCAAGCCCTTACCAAACCGTCGCACAGTGGTGCTCTCGCGCCAAGCTAGTTATAGCGCTGCTGGTTGTGCAGTTGTTTCAACGCTGTCGCAGGCTATTGCCATCGCAGCCGAACACGGCAAGGAACTCTACGTGGCCGGCGGAGCCGAGGTATATGCACTGGCACTACCTCGTGCCGATGGCGTCTTTCTATCTGAGGTACATCAAACCTTCGAGGGTGACGCCTTCTTCCCAGCGCTCGACGCAGCAGAATTCGACGTTGTCTCAGCCGAAACCGTTCAAGCCACAATCACGTACACGCACTCCGTCTATGCACGTCGTAACGGCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3003018","ARO_id":"39452","ARO_name":"dfrA22","ARO_description":"dfrA22 is an integron-encoded dihydrofolate reductase found in Salmonella enterica","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36408":{"category_aro_accession":"3000269","category_aro_cvterm_id":"36408","category_aro_name":"brodimoprim","category_aro_description":"Brodimoprim is a structural derivative of trimethoprim and an inhibitor of bacterial dihydrofolate reductase. The 4-methoxy group of trimethoprim is replaced with a bromine atom.","category_aro_class_name":"Antibiotic"},"36423":{"category_aro_accession":"3000284","category_aro_cvterm_id":"36423","category_aro_name":"tetroxoprim","category_aro_description":"Tetroxoprim is a trimethoprim derivative that inhibits bacterial dihydrofolate reductase.","category_aro_class_name":"Antibiotic"},"36476":{"category_aro_accession":"3000337","category_aro_cvterm_id":"36476","category_aro_name":"iclaprim","category_aro_description":"Iclaprim is a bactericidal compound that inhibits dihydrofolate reductase. It is used against clinically important Gram-positive pathogens, including methicillin-sensitive Staphylococcus aureus and methicillin-resistant S. aureus.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1357":{"model_id":"1357","model_name":"CTX-M-132","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1861":{"protein_sequence":{"accession":"AFQ94051.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"JX313020","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001991","ARO_id":"38391","ARO_name":"CTX-M-132","ARO_description":"CTX-M-132 is a beta-lactamase. From the Lahey list of CTX-M beta-lactamases.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1358":{"model_id":"1358","model_name":"VIM-24","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1806":{"protein_sequence":{"accession":"ADL27533.1","sequence":"MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSLTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"HM855205","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACTCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002294","ARO_id":"38694","ARO_name":"VIM-24","ARO_description":"VIM-24 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1359":{"model_id":"1359","model_name":"OXA-233","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1209":{"protein_sequence":{"accession":"AID67109.1","sequence":"MKTFAAYVIIACLSSTALAGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPSAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAFPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG"},"dna_sequence":{"accession":"KJ657570","fmin":"0","fmax":"801","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTATCGCGTGTCTTTCGAGTACGGCATTAGCTGGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTCTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATGACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAGCGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAGCAATGGGAAAGAGACTTGACCTTAAGAGGGGCAATACAAGTTTCAGCTTTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCCTATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAAGGCCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATATTTAAATAAATTGTCAGCATCTAAAGAAAACCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCGGCACCTGAATATCTAGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGGTGGGTTGAGAAGGAGACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAGTAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGAAAGTGAGGGCATCATTGGTGGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3001495","ARO_id":"37895","ARO_name":"OXA-233","ARO_description":"OXA-233 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1361":{"model_id":"1361","model_name":"OXA-223","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1683":{"protein_sequence":{"accession":"AEL88491.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEYHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"JN248564","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGTACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCCTTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001669","ARO_id":"38069","ARO_name":"OXA-223","ARO_description":"OXA-223 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1362":{"model_id":"1362","model_name":"IMP-31","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1260":{"protein_sequence":{"accession":"AGS82587.1","sequence":"MKKIFVLFVFLFCSITAAGESLPDIKIEKLDEDVYVHTSFEKITGWGVITKHGLVVLVNTDAYIIDTPFTAKDTEKLVRWFVGRGYKIKGSISSHFHSDSAGGIEWLNSQSIPTYASKLTNELLKKNGNAQAENSFSGVSYWLVKHKIEVFYPGPGHTQDNVVVWLPEKKILFGGCFIKPDGLGYLGDANLEAWPKSAETLMSKYGNAKLVVSSHSEIGGASLLKRTWEQAVKGLKESKNHHSPK"},"dna_sequence":{"accession":"KF148593","fmin":"0","fmax":"738","strand":"+","sequence":"ATGAAAAAAATATTTGTGTTATTTGTATTTTTGTTTTGCAGTATTACTGCCGCCGGAGAGTCTTTGCCTGATATAAAAATTGAGAAACTTGACGAAGATGTTTATGTTCATACTTCTTTTGAAAAGATAACCGGCTGGGGTGTTATTACTAAACACGGCTTGGTGGTTCTTGTAAATACTGATGCCTATATAATTGACACTCCATTTACAGCTAAAGATACTGAAAAATTAGTCCGCTGGTTTGTGGGGCGTGGTTATAAAATCAAAGGCAGTATTTCCTCACATTTTCATAGCGATAGCGCAGGTGGAATTGAGTGGCTTAATTCTCAATCTATCCCCACATATGCATCTAAATTAACAAATGAGCTTCTTAAAAAGAACGGTAATGCGCAAGCCGAAAACTCATTTAGTGGCGTTAGCTATTGGCTAGTTAAACATAAAATTGAAGTTTTCTATCCAGGACCAGGGCACACTCAGGATAATGTAGTGGTTTGGTTGCCTGAAAAGAAAATTTTATTTGGCGGTTGTTTTATTAAGCCGGACGGTCTTGGTTATTTGGGAGACGCAAATCTAGAAGCATGGCCTAAGTCCGCAGAAACATTAATGTCTAAGTATGGTAATGCAAAACTGGTTGTTTCGAGTCATAGTGAAATTGGGGGCGCATCACTATTGAAGCGCACTTGGGAGCAGGCTGTTAAGGGGCTAAAAGAAAGTAAAAACCATCACAGCCCCAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002222","ARO_id":"38622","ARO_name":"IMP-31","ARO_description":"IMP-31 is a beta-lactamase. From the Lahey list of IMP beta-lactamases.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1363":{"model_id":"1363","model_name":"CARB-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1855":{"protein_sequence":{"accession":"AAK96394.1","sequence":"MKFLLAFSLLIPSVVFASSSKFQQVEQDVKAIEVSLSARIGVSVLDTQNGEYWDYNGNQRFPLTSTFKTIACAKLLYDAEQGKVNPNSTVEIKKADLVTYSPVIEKQVGQAITLDDACFATMTTSDNTAANIILSAVGGPKGVTDFLRQIGDKETRLDRIEPDLNEGKLGDLRDTTTPKAIASTLNKFLFGSALSEMNQKKLESWMVNNQVTGNLLRSVLPAGWNIADRSGAGGFGARSITAVVWSEHQAPIIVSIYLAQTQASMEERNDAIVKIGHSIFDVYTSQSR"},"dna_sequence":{"accession":"AF313471","fmin":"1421","fmax":"2288","strand":"+","sequence":"ATGAAGTTTTTATTGGCATTTTCGCTTTTAATACCATCCGTGGTTTTTGCAAGTAGTTCAAAGTTTCAGCAAGTTGAACAAGACGTTAAGGCAATTGAAGTTTCTCTTTCTGCTCGTATAGGTGTTTCCGTTCTTGATACTCAAAATGGAGAATATTGGGATTACAATGGCAATCAGCGCTTCCCGTTAACAAGTACTTTTAAAACAATAGCTTGCGCTAAATTACTATATGATGCTGAGCAAGGAAAAGTTAATCCCAATAGTACAGTCGAGATTAAGAAAGCAGATCTTGTGACCTATTCCCCTGTAATAGAAAAGCAAGTAGGGCAGGCAATCACACTCGATGATGCGTGCTTCGCAACTATGACTACAAGTGATAATACTGCGGCAAATATCATCCTAAGTGCTGTAGGTGGCCCCAAAGGCGTTACTGATTTTTTAAGACAAATTGGGGACAAAGAGACTCGTCTAGACCGTATTGAGCCTGATTTAAATGAAGGTAAGCTCGGTGATTTGAGGGATACGACAACTCCTAAGGCAATAGCCAGTACTTTGAATAAATTTTTATTTGGTTCCGCGCTATCTGAAATGAACCAGAAAAAATTAGAGTCTTGGATGGTGAACAATCAAGTCACTGGTAATTTACTACGTTCAGTATTGCCGGCGGGATGGAACATTGCGGATCGCTCAGGTGCTGGCGGATTTGGTGCTCGGAGTATTACAGCAGTTGTGTGGAGTGAGCATCAAGCCCCAATTATTGTGAGCATCTATCTAGCTCAAACACAGGCTTCAATGGAAGAGCGAAATGATGCGATTGTTAAAATTGGTCATTCAATTTTTGACGTTTATACATCACAGTCGCGCTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002240","ARO_id":"38640","ARO_name":"CARB-1","ARO_description":"CARB-1 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1364":{"model_id":"1364","model_name":"CMY-101","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1281":{"protein_sequence":{"accession":"AHA80102.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYQGKPYYFTWGKADIANNRPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTHYWPELTGKQWQGISLLHLATYTAGGLPLQVPDDVTDKAALLRFYQNWQPQWAPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTKRVLHPLKLAHTWITVPQSEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMTRWVQANMDASQVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPVKADSIISGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"KF526114","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCGCTGCTGCTGACAGCTTCTTTCTCCACGTTTGCCGCCGCCAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCGCTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCGATTATCTATCAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCGTCCAGTCACGCAACAAACGCTGTTTGAACTCGGATCGGTCAGTAAAACGTTCAACGGCGTGCTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGCATTACTGGCCTGAACTGACTGGTAAGCAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTACACGGCAGGCGGCCTGCCGCTTCAGGTTCCGGACGACGTTACGGATAAAGCCGCGTTACTACGCTTTTATCAAAACTGGCAGCCGCAATGGGCCCCAGGCGCTAAACGTCTTTATGCTAACTCCAGCATTGGTCTGTTTGGCGCCCTGGCGGTGAAACCCTCAGGCATGAGCTACGAAGAGGCGATGACCAAACGCGTCCTGCACCCCTTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAGCGAACAAAAAGATTATGCCTGGGGTTATCGCGAAGGAAAGCCAGTGCATGTATCCCCTGGCCAACTTGATGCCGAAGCATACGGGGTGAAATCGAGCGTTATCGATATGACCCGTTGGGTTCAGGCCAACATGGACGCCAGCCAGGTTCAGGAGAAAACGCTCCAGCAGGGCATCGAGCTTGCGCAGTCACGTTACTGGCGTATTGGCGATATGTACCAGGGCCTGGGTTGGGAGATGCTGAACTGGCCGGTGAAAGCCGACTCGATAATTAGCGGTAGCGACAGCAAAGTGGCACTGGCAGCGCTTCCTGCCGTTGAGGTAAACCCGCCCGCGCCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGCGGATTCGGCAGCTACGTTGCTTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAGAGCTACCCAAACCCTGTTCGCGTCGAGGCCGCCTGGCGCATTCTTGAAAAACTGCAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002113","ARO_id":"38513","ARO_name":"CMY-101","ARO_description":"CMY-101 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1365":{"model_id":"1365","model_name":"AAC(6')-I30","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"399":{"protein_sequence":{"accession":"AAP43642.1","sequence":"MAYAFCEIGESNEYIIQAARILTKSFLDIGNDSWPDMKSATKEVEECIEKPNICLGIHENEKLLGWIGLRPMYKLTWELHPLVISTQYQNKGIGRLLINELEKQAKQNGIIGIVLGTDDEYFKTSLSDVDLSGKNILDEIRNIKNIRNHPYEFYQRCGYSIVGVIPDANGKRKPDIWMWKKISD"},"dna_sequence":{"accession":"AY289608","fmin":"1523","fmax":"2078","strand":"+","sequence":"ATGGCATATGCGTTCTGCGAAATTGGAGAATCAAATGAATATATTATTCAGGCAGCTAGAATCTTAACGAAATCATTCCTTGATATTGGAAATGATTCCTGGCCTGATATGAAAAGTGCCACCAAAGAAGTTGAAGAATGTATTGAGAAGCCAAACATATGTCTTGGAATACATGAAAACGAAAAACTACTTGGATGGATTGGTCTTAGGCCCATGTACAAATTAACATGGGAATTACATCCCTTGGTAATAAGTACGCAATATCAGAATAAAGGTATTGGAAGACTTCTAATAAATGAATTGGAAAAACAAGCAAAGCAAAATGGAATAATCGGAATAGTATTGGGAACTGACGATGAATACTTTAAGACTTCATTATCAGATGTGGATCTTTCCGGGAAAAATATACTTGATGAGATAAGGAATATTAAAAATATAAGGAATCATCCGTACGAATTCTATCAACGATGTGGTTATTCCATTGTCGGAGTAATACCCGATGCAAATGGCAAAAGAAAGCCAGATATTTGGATGTGGAAGAAGATTAGTGATTAGG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35709","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Agona","NCBI_taxonomy_id":"58095"}}}},"ARO_accession":"3002588","ARO_id":"38988","ARO_name":"AAC(6')-I30","ARO_description":"AAC(6')-I30 is an integron-encoded aminoglycoside acetyltransferase in S. enterica","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1366":{"model_id":"1366","model_name":"cmx","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3":{"protein_sequence":{"accession":"AAG03380.1","sequence":"MPFALYMLALAVFVMGTSEFMLAGLLPAIATELDVSVGTAGLLTSAFAVGMVVGAPVMAAFARRWPPRLTLIVCLLVFAGSHVIGAMTPVFSLLLITRVLSALANAGFLAVALSTATTLVPANQKGRALSILLSGTTIATVVGVPAGALLGTALGWRTTFWAIAILCIPAAVGVIRGVTNNVGRSETSATSPRLRVELSQLATPRLILAMALGALINGGTFAAFTFLAPIVTETAGLAEAWVSVALVMFGIGSFLGVTIAGRLSDQRPGLVLAVGGPLLLTGWIVLAVVASHPVALIVLVLVQGFLSFGVGSTLITRVLYAASGAPTMGGSYATAALNIGAAAGPVLGALGLATGLGLLAPVWVASVLTAIALVIMLLTRRALTKTAAEAN"},"dna_sequence":{"accession":"AF024666","fmin":"35934","fmax":"37110","strand":"+","sequence":"ATGCCTTTTGCCCTCTACATGCTTGCCCTGGCGGTCTTCGTCATGGGCACTTCAGAATTCATGCTCGCGGGATTGCTCCCCGCGATCGCGACCGAACTTGACGTCTCGGTCGGCACTGCGGGCCTGCTGACCTCCGCATTCGCAGTCGGTATGGTCGTCGGCGCGCCAGTGATGGCGGCATTCGCTCGCCGTTGGCCACCGCGGCTCACATTGATCGTTTGCCTTCTCGTGTTCGCGGGAAGCCACGTCATCGGAGCGATGACACCAGTGTTCTCTCTCCTGCTCATCACCCGGGTGCTCAGCGCTCTCGCAAACGCAGGATTCCTCGCCGTAGCACTGAGCACGGCCACTACCCTCGTGCCAGCGAACCAGAAGGGGCGTGCACTGTCGATCCTGCTCTCCGGCACGACGATCGCAACCGTCGTGGGCGTCCCCGCCGGGGCACTGCTCGGCACAGCGCTGGGCTGGCGAACGACGTTCTGGGCGATCGCCATCCTCTGTATTCCCGCGGCCGTTGGAGTCATTCGTGGCGTCACGAACAATGTTGGTCGGAGCGAGACTAGCGCGACCTCACCAAGGCTCCGTGTCGAGCTCAGCCAGTTGGCGACGCCGCGGCTCATCCTGGCCATGGCACTCGGAGCGCTGATCAACGGAGGGACCTTTGCGGCATTCACCTTCCTGGCACCCATCGTGACCGAGACCGCGGGCTTGGCCGAAGCGTGGGTGTCCGTCGCGCTGGTGATGTTCGGCATCGGATCGTTCCTTGGCGTCACGATCGCAGGACGACTATCAGATCAACGACCTGGCCTCGTGCTCGCAGTCGGCGGACCGCTATTGCTGACAGGCTGGATCGTGTTGGCAGTGGTCGCATCTCATCCCGTTGCGCTTATCGTCCTCGTCCTCGTTCAGGGATTCCTGTCGTTCGGCGTCGGCAGTACTCTGATCACGCGTGTGCTGTATGCAGCATCGGGTGCGCCAACGATGGGCGGTTCGTACGCAACCGCAGCATTGAATATCGGAGCTGCAGCGGGGCCCGTGCTTGGTGCGCTCGGGCTCGCGACCGGGCTGGGGCTGCTCGCGCCGGTTTGGGTCGCTTCGGTGCTGACAGCGATCGCTCTCGTCATCATGCTTCTCACCAGACGCGCGCTTACGAAGACCGCGGCGGAGGCCAATTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39554","NCBI_taxonomy_name":"Corynebacterium striatum","NCBI_taxonomy_id":"43770"}}}},"ARO_accession":"3002703","ARO_id":"39137","ARO_name":"cmx","ARO_description":"cmx is a plasmid or transposon-encoded chloramphenicol exporter that is found in Corynebacterium striatum and Pseudomonas aeruginosa.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1367":{"model_id":"1367","model_name":"oleD","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"4240":{"protein_sequence":{"accession":"ABA42119.2","sequence":"MTTQTTPAHIAMFSIAAHGHVNPSLEVIRELVARGHRVTYAIPPVFADKVAATGARPVLYHSTLPGPDADPEAWGSTLLDNVEPFLNDAIQALPQLADAYADDIPDLVLHDITSYPARVLARRWGVPAVSLSPNLVAWKGYEEEVAEPMWREPRQTERGRAYYARFEAWLKENGITEHPDTFASHPPRSLVLIPKALQPHADRVDEDVYTFVGACQGDRAEEGGWQRPAGAEKVVLVSLGSAFTKQPAFYRECVRAFGNLPGWHLVLQIGRKVTPAELGELPDNVEVHDWVPQLAILRQADLFVTHAGAGGSQEGLATATPMIAVPQAVDQFGNADMLQGLGVARKLATEEATADLLRETALALVDDPEVARRLRRIQAEMAQEGGTRRAADLIEAELPARHERQEPVGDRPNGG"},"dna_sequence":{"accession":"DQ195536.2","fmin":"0","fmax":"1248","strand":"+","sequence":"ATGACCACCCAGACCACTCCCGCCCACATCGCCATGTTCTCCATCGCCGCCCACGGCCATGTGAACCCCAGCCTGGAGGTGATCCGTGAACTCGTCGCCCGCGGCCACCGGGTCACGTACGCCATTCCGCCCGTCTTCGCCGACAAGGTGGCCGCCACCGGCGCCCGGCCCGTCCTCTACCACTCCACCCTGCCCGGCCCCGACGCCGACCCGGAGGCATGGGGAAGCACCCTGCTGGACAACGTCGAACCGTTCCTGAACGACGCGATCCAGGCGCTCCCGCAGCTCGCCGATGCCTACGCCGACGACATCCCCGATCTCGTCCTGCACGACATCACCTCCTACCCGGCCCGCGTCCTGGCCCGCCGCTGGGGCGTCCCGGCGGTCTCCCTCTCCCCGAACCTCGTCGCCTGGAAGGGTTACGAGGAGGAGGTCGCCGAGCCGATGTGGCGCGAACCCCGGCAGACCGAGCGCGGACGGGCCTACTACGCCCGGTTCGAGGCATGGCTGAAGGAGAACGGGATCACCGAGCACCCGGACACGTTCGCCAGTCATCCGCCGCGCTCCCTGGTGCTCATCCCGAAGGCGCTCCAGCCGCACGCCGACCGGGTGGACGAAGACGTGTACACCTTCGTCGGCGCCTGCCAGGGAGACCGCGCCGAGGAAGGCGGCTGGCAGCGGCCCGCCGGCGCGGAGAAGGTCGTCCTGGTGTCGCTCGGCTCGGCGTTCACCAAGCAGCCCGCCTTCTACCGGGAGTGCGTGCGCGCCTTCGGGAACCTGCCCGGCTGGCACCTCGTCCTCCAGATCGGCCGGAAGGTGACCCCCGCCGAACTGGGGGAGCTGCCGGACAACGTGGAGGTGCACGACTGGGTGCCGCAGCTCGCGATCCTGCGCCAGGCCGATCTGTTCGTCACCCACGCGGGCGCCGGCGGCAGCCAGGAGGGGCTGGCCACCGCGACGCCCATGATCGCCGTACCGCAGGCCGTCGACCAGTTCGGCAACGCCGACATGCTCCAAGGGCTCGGCGTCGCCCGGAAGCTGGCGACCGAGGAGGCCACCGCCGACCTGCTCCGCGAGACCGCCCTCGCTCTGGTGGACGACCCGGAGGTCGCGCGCCGGCTCCGGCGGATCCAGGCGGAGATGGCCCAGGAGGGCGGCACCCGGCGGGCGGCCGACCTCATCGAGGCCGAACTGCCCGCGCGCCACGAGCGGCAGGAGCCGGTGGGCGACCGACCCAACGGTGGGTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36823","NCBI_taxonomy_name":"Streptomyces antibioticus","NCBI_taxonomy_id":"1890"}}}},"ARO_accession":"3000865","ARO_id":"37245","ARO_name":"oleD","ARO_description":"OleD is a glycotransferase found in Streptomyces antibioticus, a natural producer  of oleandomycin. OleD can glycosylate a wide range of macrolides. Unlike oleI, oleD is not found in the oleandomycin biosynthetic cluster.","ARO_category":{"36604":{"category_aro_accession":"3000465","category_aro_cvterm_id":"36604","category_aro_name":"ole glycosyltransferase","category_aro_description":"OleI and OleD are glycosyltransferases found in Streptomyces antibioticus which is a natural producer of antibiotic oleandomycin. OleI glycosylates antibiotic oleandomycin whereas OleD can glycosylate a wide variety of macrolides.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1368":{"model_id":"1368","model_name":"abeM","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"850"}},"model_sequences":{"sequence":{"671":{"protein_sequence":{"accession":"BAD89844.2","sequence":"MSNVTSFRSELKQLFHLMLPILITQFAQAGFGLIDTIMAGHLSAADLAAIAVGVGLWIPVMLLFSGIMIATTPLVAEAKGARNTEQIPVIVRQSLWVAVILGVLAMLILQLMPFFLHVFGVPESLQPKASLFLHAIGLGMPAVTMYAALRGYSEALGHPRPVTVISLLALVVLIPLNMIFMYGLGPIPALGSAGCGFATSILQWLMLITLAGYIYKASAYRNTSIFSRFDKISLTWVKRILQLGLPIGLAVFFEVSIFSTGALVLSPLGEVFIAAHQVAISVTSVLFMIPLSLAIALTIRVGTYYGEKNWASMYQVQKIGLSTAVFFALLTMSFIALGREQIVSVYTQDINVVPVAMYLLWFAMAYQLMDALQVSAAGCLRGMQDTQAPMWITLMAYWVIAFPIGLYLARYTDWGVAGVWLGLIIGLSIACVLLLSRLYLNTKRLSQT"},"dna_sequence":{"accession":"AB204810","fmin":"186","fmax":"1533","strand":"+","sequence":"GTGTCGAATGTCACGTCGTTTCGGTCTGAATTAAAACAACTCTTCCATTTAATGTTACCTATTTTAATTACGCAGTTTGCTCAAGCAGGGTTCGGGTTAATTGATACCATTATGGCTGGGCATTTATCTGCCGCAGACTTAGCCGCTATTGCGGTAGGTGTAGGCTTATGGATTCCAGTCATGCTCTTGTTCAGTGGCATCATGATTGCAACCACACCATTAGTTGCCGAAGCAAAAGGCGCTAGAAATACAGAGCAAATTCCAGTGATTGTCCGCCAATCATTATGGGTTGCAGTAATTCTAGGGGTATTGGCAATGCTCATTTTGCAGCTTATGCCATTTTTCTTACATGTGTTTGGCGTACCAGAAAGTTTACAACCTAAAGCCAGTTTATTCTTACATGCAATTGGTTTGGGTATGCCCGCTGTAACCATGTATGCAGCGCTCCGAGGCTATTCCGAAGCATTAGGCCATCCCCGCCCTGTCACGGTCATTAGCTTACTAGCCTTAGTGGTTTTAATCCCGCTTAACATGATTTTTATGTATGGCTTAGGACCAATACCTGCTTTGGGTAGCGCAGGCTGTGGTTTTGCAACATCCATTTTACAGTGGCTGATGCTCATTACGTTAGCAGGCTATATTTATAAGGCTTCGGCTTATCGAAACACATCTATTTTTAGCAGATTCGATAAAATTAGCCTGACTTGGGTTAAAAGAATTTTACAGCTCGGCCTGCCAATTGGTTTAGCTGTGTTTTTTGAAGTGAGTATTTTTAGTACAGGGGCATTGGTCCTTAGCCCTCTAGGGGAAGTCTTTATTGCCGCACACCAAGTAGCAATTTCAGTCACTTCGGTACTGTTTATGATTCCACTTTCTCTTGCCATTGCTTTAACCATTCGCGTGGGGACGTATTATGGTGAAAAGAACTGGGCTTCCATGTACCAAGTACAGAAAATTGGTCTAAGCACAGCAGTATTTTTTGCTCTATTGACCATGTCTTTTATTGCTTTAGGCCGTGAACAAATTGTCTCGGTTTATACTCAAGATATAAATGTTGTGCCGGTTGCCATGTATTTGCTCTGGTTTGCAATGGCATATCAATTAATGGATGCTCTACAAGTCAGCGCTGCCGGCTGTTTAAGAGGTATGCAAGATACTCAGGCACCGATGTGGATCACCTTAATGGCGTATTGGGTAATTGCTTTTCCAATCGGTCTTTATTTAGCGCGTTATACCGATTGGGGCGTAGCTGGTGTGTGGTTAGGTTTAATTATTGGTTTAAGTATTGCCTGTGTTTTATTGCTATCACGACTCTATTTGAATACCAAACGTTTAAGTCAAACCTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3000753","ARO_id":"37133","ARO_name":"abeM","ARO_description":"AbeM is an multidrug efflux pump found in Acinetobacter baumannii.","ARO_category":{"36251":{"category_aro_accession":"3000112","category_aro_cvterm_id":"36251","category_aro_name":"multidrug and toxic compound extrusion (MATE) transporter","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Multidrug and toxic compound extrusion (MATE) transporters utilize the cationic gradient across the membrane as an energy source. Although there is a diverse substrate specificity, almost all MATE transporters recognize fluoroquinolones. Arciflavine, ethidium and aminoglycosides are also good substrates.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavin","category_aro_description":"Acriflavin is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36193":{"category_aro_accession":"3000054","category_aro_cvterm_id":"36193","category_aro_name":"acridine dye","category_aro_description":"Acridine dyes are cell permeable, basic molecules with an acridine chromophore. These compounds intercalate DNA. The image shown represents the core structure of the acridine family, with specific dyes containing varying substituents.","category_aro_class_name":"Drug Class"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1369":{"model_id":"1369","model_name":"QnrB69","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"278":{"protein_sequence":{"accession":"AGL43630.1","sequence":"MTLALVGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAILKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGSDFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFSSFDWRAANFTHCDLTNSELGDLDVRGVDLQGVKLDSYQASLILERLGIAVIG"},"dna_sequence":{"accession":"KC580658","fmin":"0","fmax":"645","strand":"+","sequence":"ATGACTCTGGCGTTAGTTGGCGAAAAAATTGACAGAAACAGGTTCACCGGTGAGAAAGTCGAAAATAGCACATTTTTCAACTGTGATTTTTCGGGTGCCGACCTTAGCGGTACTGAGTTTATTGGCTGCCAATTTTATGATCGAGAGAGCCAGAAAGGGTGTAATTTTAGCCGCGCTATCCTGAAAGATGCCATTTTCAAAAGTTGCGATCTCTCCATGGCGGATTTCAGAAATGTGAGTGCGCTGGGAATCGAAATTCGCCACTGCCGCGCACAAGGTTCAGATTTTCGCGGCGCAAGCTTTATGAATATGATTACCACACGCACCTGGTTTTGTAGCGCCTATATCACCAATACCAACTTAAGCTACGCCAACTTTTCAAAAGTCGTACTGGAAAAGTGCGAGCTGTGGGAAAACCGCTGGATGGGTACTCAGGTACTTGGCGCAACGTTCAGTGGATCGGACCTCTCTGGCGGCGAGTTTTCATCGTTCGACTGGCGGGCAGCAAACTTTACGCACTGTGATTTGACCAATTCAGAACTGGGCGATCTCGATGTCCGGGGTGTTGATTTGCAAGGCGTTAAACTGGACAGCTACCAGGCATCGTTGATCCTGGAACGTCTTGGCATCGCTGTCATTGGTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002781","ARO_id":"39215","ARO_name":"QnrB69","ARO_description":"QnrB69 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1370":{"model_id":"1370","model_name":"AAC(6')-Ib10","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"314":{"protein_sequence":{"accession":"AAC46343.1","sequence":"MLRSSSRPKTKLGITKYSIVTNSNDSVTLRLMTEHDLAMLYEWLNRSHIVEWWGGEEARPTLADVQEQYLPSVLAQESVTPYIAMLNGEPIGYAQSYVALGSGDGWWEEETDPGVRGIDQLLANASQLGKGLGTKLVRALVELLFNDPEVTKIQTDPSPSNLRAIRCYEKAGFERQGTVTTPDGPAVYMVQTRQAFERTRSDA"},"dna_sequence":{"accession":"U59183","fmin":"247","fmax":"859","strand":"+","sequence":"ATGTTACGCAGCAGCAGTCGCCCTAAAACAAAGTTAGGCATCACAAAGTACAGCATCGTGACCAACAGCAACGATTCCGTCACACTGCGCCTCATGACTGAGCATGACCTTGCGATGCTCTATGAGTGGCTAAATCGATCTCATATCGTCGAGTGGTGGGGCGGAGAAGAAGCACGCCCGACACTTGCTGACGTACAGGAACAGTACTTGCCAAGCGTTTTAGCGCAAGAGTCCGTCACTCCATACATTGCAATGCTGAATGGAGAGCCGATTGGGTATGCCCAGTCGTACGTTGCTCTTGGAAGCGGGGACGGATGGTGGGAAGAAGAAACCGATCCAGGAGTACGCGGAATAGACCAGTTACTGGCGAATGCATCACAACTGGGCAAAGGCTTGGGAACCAAGCTGGTTCGAGCTCTGGTTGAGTTGCTGTTCAATGATCCCGAGGTCACCAAGATCCAAACGGACCCGTCGCCGAGCAACTTGCGAGCGATCCGATGCTACGAGAAAGCGGGGTTTGAGAGGCAAGGTACCGTAACCACCCCAGATGGTCCAGCCGTGTACATGGTTCAAACACGCCAGGCATTCGAGCGAACACGCAGTGATGCCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002581","ARO_id":"38981","ARO_name":"AAC(6')-Ib10","ARO_description":"AAC(6')-Ib10 is an integron-encoded aminoglycoside acetyltransferase in P. aeruginosa","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1371":{"model_id":"1371","model_name":"CTX-M-26","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1628":{"protein_sequence":{"accession":"AAN75444.1","sequence":"MMRKSVRRAMLMTTACVSLLLASVPLCAQANDVQQKLAALEKSSGGRLGVALINTADNTQTLYRADERFAMCSTSKVMAAAAVLKQSETQKGLLSQRVEIKPSDLINYNPIAEKHVNGTMTFGELSAAALQYSDNTAMNKLIAHLGGPDKVTAFARTIGDDTFRLDRTEPTLNTAIPGDPRDTTTPLAMAQALRNLTLGNALGDTQRAQLVMWLKGNTTGAASIRAGLPTSWVVGDKTGSGDYGTTNDIAVIWPEGRAPLVLVTYFTQSEPKAESRRDVLAAAARIVTDGY"},"dna_sequence":{"accession":"AY157676","fmin":"0","fmax":"876","strand":"+","sequence":"ATGATGAGAAAAAGCGTAAGGCGGGCGATGTTAATGACGACAGCCTGTGTTTCGCTGCTGTTGGCCAGTGTGCCGCTGTGTGCCCAGGCGAACGATGTTCAACAAAAGCTCGCGGCGCTGGAGAAAAGCAGCGGGGGACGACTGGGTGTGGCGTTGATTAACACCGCCGATAACACGCAGACGCTCTACCGCGCCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCGGCAGCGGCGGTGCTTAAGCAAAGTGAAACGCAAAAGGGCTTGTTGAGTCAGCGGGTTGAAATTAAGCCCTCAGACTTGATTAACTACAACCCCATTGCGGAAAAACACGTCAATGGCACGATGACATTCGGGGAGTTGAGCGCGGCGGCGCTACAGTACAGCGATAATACTGCCATGAATAAGCTGATTGCCCATCTCGGGGGGCCGGATAAAGTGACGGCATTTGCCCGTACGATTGGCGATGACACGTTCCGGCTCGATCGTACCGAGCCGACGCTCAACACCGCGATCCCCGGCGACCCGCGCGATACCACCACGCCGTTAGCGATGGCGCAGGCTCTGCGCAATCTGACGTTGGGCAATGCCCTGGGTGACACTCAGCGTGCGCAGCTGGTGATGTGGCTGAAAGGCAACACCACCGGCGCTGCCAGCATTCGGGCAGGGCTACCCACATCGTGGGTTGTCGGGGATAAAACCGGCAGCGGCGATTATGGTACGACGAATGATATCGCGGTTATTTGGCCGGAAGGTCGCGCGCCGCTCGTTCTGGTGACTTACTTCACCCAGTCGGAGCCGAAGGCAGAGAGCCGTCGTGACGTGCTCGCTGCTGCCGCCAGAATTGTCACCGACGGTTATTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001888","ARO_id":"38288","ARO_name":"CTX-M-26","ARO_description":"CTX-M-26 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1372":{"model_id":"1372","model_name":"ANT(2'')-Ia","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"457":{"protein_sequence":{"accession":"AAC64365.1","sequence":"MDTTQVTLIHKILAAADERNLPLWIGGGWAIDARLGRVTRKHDDIDLTFPGERRGELEAIVEMLGGRVMEELDYGFLAEIGDELLDCEPAWWADEAYEIAEAPQGSCPEAAEGVIAGRPVRCNSWEAIIWDYFYYADEVPPVDWPTKHIESYRLACTSLGAEKVEVLRAAFRSRYAA"},"dna_sequence":{"accession":"AF078527","fmin":"3769","fmax":"4303","strand":"+","sequence":"ATGGACACAACGCAGGTCACATTGATACACAAAATTCTAGCTGCGGCAGATGAGCGAAATCTGCCGCTCTGGATCGGTGGGGGCTGGGCGATCGATGCACGGCTAGGGCGTGTAACACGCAAGCACGATGATATTGATCTGACGTTTCCCGGCGAGAGGCGCGGCGAGCTCGAGGCAATAGTTGAAATGCTCGGCGGGCGCGTCATGGAGGAGTTGGACTATGGATTCTTAGCGGAGATCGGGGATGAGTTACTTGACTGCGAACCTGCTTGGTGGGCAGACGAAGCGTATGAAATCGCGGAGGCTCCGCAGGGCTCGTGCCCAGAGGCGGCTGAGGGCGTCATCGCCGGGCGGCCAGTCCGTTGTAACAGCTGGGAGGCGATCATCTGGGATTACTTTTACTATGCCGATGAAGTACCACCAGTGGACTGGCCTACAAAGCACATAGAGTCCTACAGGCTCGCATGCACCTCACTCGGGGCGGAAAAGGTTGAGGTCTTGCGTGCCGCTTTCAGGTCGCGATATGCGGCCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3000230","ARO_id":"36369","ARO_name":"ANT(2'')-Ia","ARO_description":"Plasmid or integron-encoded nucleotidylylation of 2-deoxystreptamine aminoglycosides at the hydroxyl group at position 2'' in P. aeruginosa, K. pneumoniae, Morganella morganii, E. coli, S. typhimurium, C. freundii and A. baumannii","ARO_category":{"41440":{"category_aro_accession":"3004276","category_aro_cvterm_id":"41440","category_aro_name":"ANT(2'')","category_aro_description":"Nucelotidylylation of streptomycin at the hydroxyl group at position 2''.","category_aro_class_name":"AMR Gene Family"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1373":{"model_id":"1373","model_name":"CMY-26","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1361":{"protein_sequence":{"accession":"BAF56185.1","sequence":"MMKKSLCCALLLTASFSTFASAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKTYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQDISLLHLATYTAGGLPLQIPDDVTDKTALLHFYQNWQPQWAPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSNVTDMARWVQVNMDASRVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"AB300358","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACGTTTGCCTCCGCCAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAAACCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGATATCAGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTACGGATAAAACCGCATTACTGCACTTTTATCAAAACTGGCAGCCGCAATGGGCTCCGGGCGCTAAGAGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAGCCATTAAAACTGGCGCATACCTGGATTACAGTTCCGCAAAGCGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGACAACTTGATGCCGAAGCCTATGGCGTGAAATCCAACGTTACCGATATGGCACGCTGGGTTCAGGTCAACATGGACGCCAGCCGCGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGTAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCGGCAGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACTGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002037","ARO_id":"38437","ARO_name":"CMY-26","ARO_description":"CMY-26 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1374":{"model_id":"1374","model_name":"blaI","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"4397":{"protein_sequence":{"accession":"ABU39978.1","sequence":"MSNQTPSISEAEWEVMKVLWKKGPQTANQVISAIQEQTDWKPKTIRTLLDRLTKKKVVGVDKEQKIYVFFPLYSEEACKHAEAQSFVKRVYGGTVKPLLVQFLEEESLTKEELDELYAILDQKRKE"},"dna_sequence":{"accession":"EF540343","fmin":"1059","fmax":"1440","strand":"-","sequence":"TTATTCTTTCCGTTTTTGATCTAAGATCGCATACAGTTCATCCAGCTCTTCTTTTGTTAGTGACTCTTCCTCCAAGAACTGGACCAACAATGGTTTTACTGTTCCCCCGTAAACTCTCTTTACGAAAGACTGTGCTTCTGCATGCTTACACGCTTCTTCTGAGTATAGGGGAAAGAAGACATAGATTTTCTGCTCTTTATCTACGCCTACTACTTTCTTCTTCGTTAATCGATCGAGTAACGTCCGAATCGTTTTTGGTTTCCAGTCCGTTTGCTCTTGGATCGCGGAAATGACTTGATTGGCTGTTTGCGGCCCCTTTTTCCACAAAACTTTCATAACTTCCCATTCTGCTTCCGATATGCTAGGTGTTTGGTTTGACAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36882","NCBI_taxonomy_name":"Bacillus clausii","NCBI_taxonomy_id":"79880"}}}},"ARO_accession":"3000160","ARO_id":"36299","ARO_name":"blaI","ARO_description":"blaI acts as a repressor of transcription of the blaZ\/blaR1\/blaI operon.","ARO_category":{"41361":{"category_aro_accession":"3004197","category_aro_cvterm_id":"41361","category_aro_name":"blaZ beta-lactamase","category_aro_description":"blaZ beta-lactamases are Class A beta-lactamases. These beta-lactamases are responsible for penicillin resistance in Staphylococcus aures.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1375":{"model_id":"1375","model_name":"CMY-11","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1857":{"protein_sequence":{"accession":"AAK31370.1","sequence":"MQQRQSILWGAVATLMWAGLAHAGEASPVDPLRPVVDASIQPLLKEHRIPGMAVAVLKDGKAHYFNYGVANRESGAGVSEQTLFEIGSVSKTLTATLGAYAVVKGAMQLDDKASRHAPWLKGSAFDSITMGELATYSAGGLPLQFPEEVDSSEKMRAYYRQWAPVYSPGSHRQYSNPSIGLFGHLAASSLKQPFAPLMEQTLLPGLGMHHTYVNVPKQAMASYAYGYSKEDKPIRVNPGMLADEAYGIKTSSADLLRFVKANIGGVDDKALQQAISLTHQGHYSVGGMTQGLGWESYAYPVTEQTLLAGNSAKVSLEANPTAAPRESGSQVLFNKTGSTNGFGAYVAFVPARGIGIVMLANRNYPIEARIKAAHAILAQLAG"},"dna_sequence":{"accession":"AF357599","fmin":"253","fmax":"1402","strand":"+","sequence":"ATGCAACAACGACAATCCATCCTGTGGGGGGCCGTGGCCACCCTGATGTGGGCCGGTCTGGCCCATGCAGGTGAGGCTTCACCGGTCGATCCCCTGCGCCCCGTGGTGGATGCCAGCATCCAGCCGCTGCTCAAGGAGCACAGGATCCCGGGCATGGCGGTGGCCGTGCTCAAGGATGGCAAGGCCCACTACTTCAATTACGGGGTGGCCAACCGGGAGAGCGGGGCCGGCGTCAGCGAGCAGACCCTGTTCGAGATAGGATCCGTGAGCAAGACCCTGACTGCGACCCTGGGGGCCTATGCGGTGGTCAAGGGAGCGATGCAGCTGGATGACAAGGCGAGCCGGCACGCGCCCTGGCTCAAGGGATCCGCCTTTGACAGCATCACCATGGGGGAGCTTGCCACCTACAGCGCCGGAGGCCTGCCACTGCAATTCCCCGAGGAGGTGGATTCATCCGAGAAGATGCGCGCCTACTACCGCCAGTGGGCCCCTGTCTATTCGCCGGGCTCCCATCGCCAGTACTCCAACCCCAGCATAGGGCTGTTCGGCCACCTGGCGGCGAGCAGCCTGAAGCAGCCGTTTGCCCCCTTGATGGAGCAGACCCTGCTGCCCGGGCTCGGCATGCACCACACCTATGTCAATGTGCCGAAGCAGGCCATGGCGAGTTATGCCTATGGCTATTCGAAAGAGGACAAGCCCATCCGTGTCAACCCTGGCATGCTGGCGGACGAGGCCTATGGCATCAAGACCAGCTCGGCGGATCTGCTGCGTTTTGTGAAGGCCAACATCGGCGGGGTTGATGACAAGGCGTTGCAGCAGGCCATCTCCCTGACCCACCAAGGGCATTACTCGGTAGGCGGGATGACCCAGGGGCTGGGTTGGGAGAGTTACGCCTATCCCGTCACCGAGCAGACATTGCTGGCGGGCAATTCGGCCAAGGTGAGCCTCGAAGCCAATCCGACGGCGGCGCCCCGGGAGTCGGGGAGCCAGGTGCTCTTCAACAAGACCGGCTCGACCAATGGCTTTGGCGCCTATGTGGCCTTCGTGCCGGCCAGGGGGATCGGCATCGTCATGCTGGCCAATCGCAACTACCCCATCGAGGCGCGCATCAAGGCGGCCCACGCCATCCTGGCGCAGTTGGCCGGTTGAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002022","ARO_id":"38422","ARO_name":"CMY-11","ARO_description":"CMY-11 is a beta-lactamase found in Escherichia coli","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1376":{"model_id":"1376","model_name":"MOX-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1364":{"protein_sequence":{"accession":"ACS44784.1","sequence":"MQQRQSILWGVLPTLMWAGLAHAGDRAATDPLRPVVDASIRPLLKEHRIPGMAVAVLKDGKAHYFNYGVADRERAVGVSEQTLFEIGSVSKTLTATLGAYAVVQGSFELDDKASLFAPWLKGSVFDNITMGELATYSAGGLPLQFPEEVDSLEKMQAYYRQWTPAYSPGSHRQYANPSIGLFGYLAASSMKQPFDRLMEQTILPGLGLYHTYLNVPEQAMGHYAYGYSKEDKPIRVTPGMLADEAYGIKTSSADLLRFVKANISGVDNAAMQQAIDLTHQGQYAVGEMTQGLGWERYAYPVSEQTLLAGNSAAMIYNANPAAPAPAARGHPVLFNKTGSTNGFGAYVAFVPAKGIGIVMLANRNSPIEGTLKAGHAILTQLAR"},"dna_sequence":{"accession":"GQ152601","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCAACAACGACAATCCATCCTGTGGGGCGTTCTGCCCACCCTGATGTGGGCCGGCCTGGCCCATGCAGGTGACAGGGCGGCGACCGATCCCCTGCGCCCCGTGGTGGATGCCAGCATCCGGCCGCTGCTCAAGGAGCACAGGATCCCGGGCATGGCGGTGGCCGTGCTCAAGGATGGCAAGGCCCACTATTTCAACTACGGTGTGGCCGATCGGGAGCGCGCAGTCGGTGTCAGCGAGCAGACCCTGTTCGAGATAGGTTCCGTGAGCAAGACCCTGACCGCGACGCTGGGGGCCTACGCCGTGGTGCAGGGGAGCTTCGAGCTCGATGACAAGGCGAGTCTGTTCGCCCCCTGGCTCAAGGGATCCGTCTTTGACAACATCACCATGGGGGAGCTGGCTACCTACAGCGCGGGCGGCTTGCCGCTGCAATTCCCCGAGGAGGTGGATTCGCTCGAGAAGATGCAGGCCTACTACCGCCAGTGGACCCCAGCCTACTCGCCGGGTTCCCATCGCCAGTACGCCAACCCCAGCATCGGGCTCTTTGGCTATCTGGCGGCGAGCAGCATGAAGCAGCCGTTCGATCGCCTGATGGAGCAGACGATCCTGCCGGGGCTTGGCCTGTACCATACCTACCTCAATGTGCCCGAGCAGGCCATGGGGCACTACGCCTACGGCTACTCGAAGGAGGACAAGCCCATCCGCGTCACTCCCGGCATGCTGGCGGACGAGGCCTACGGCATCAAGACCAGCTCGGCGGATCTGCTGCGCTTTGTGAAGGCCAACATCAGCGGGGTGGATAATGCGGCCATGCAGCAGGCCATCGACCTGACTCACCAGGGGCAGTATGCGGTGGGGGAGATGACCCAGGGACTGGGCTGGGAGCGTTACGCCTATCCCGTCAGCGAGCAGACGCTGCTGGCGGGCAACTCCGCGGCGATGATTTACAATGCGAACCCGGCTGCGCCCGCGCCCGCTGCAAGGGGGCACCCTGTGCTCTTCAACAAGACCGGCTCGACCAACGGCTTCGGGGCCTATGTGGCCTTCGTGCCGGCCAAAGGGATCGGCATCGTCATGCTGGCCAATCGCAACTCTCCCATCGAGGGCACGCTCAAGGCGGGCCACGCCATCCTGACGCAACTGGCCAGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36936","NCBI_taxonomy_name":"Aeromonas caviae","NCBI_taxonomy_id":"648"}}}},"ARO_accession":"3002185","ARO_id":"38585","ARO_name":"MOX-6","ARO_description":"MOX-6 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36222":{"category_aro_accession":"3000083","category_aro_cvterm_id":"36222","category_aro_name":"MOX beta-lactamase","category_aro_description":"MOX beta-lactamases are plasmid-mediated AmpC-type beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1377":{"model_id":"1377","model_name":"CTX-M-60","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1966":{"protein_sequence":{"accession":"CAL80726.1","sequence":"MVKKSLRQFTLMATAAVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAVAAVLKKSESEPSLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDILASAAKIVTDGL"},"dna_sequence":{"accession":"AM411407","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAGCCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCGGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTCGCGATGTGCAGCACCAGTAAAGTGATGGCCGTGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAGTCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTGGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCAGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATTTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATATATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001921","ARO_id":"38321","ARO_name":"CTX-M-60","ARO_description":"CTX-M-60 is a beta-lactamase. From the Lahey list of CTX-M beta-lactamases.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1378":{"model_id":"1378","model_name":"AAC(3)-IIc","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"616":{"protein_sequence":{"accession":"CAA38525.1","sequence":"MHTRKAITEALQKLGVQTGDLLMVHASLKAIGPVEGGAETVVAALRSAVGPTGTVMGYASWDRSPYEETRNGARLDDKTRRTWPPFDPATAGTYRGFGLLNQFLVQAPGARRSAHPDASMVAVGPLAETLTEPHKLGHALGEGSPVERFVRLGGKALLLGAPLNSVTALHYAEAVADIPNKRRVTYEMPMLGSNGEVAWKTASDYDSNGILDCFAIEGKPDAVETIANAYVKLGRHREGVVGFAQCYLFDAQDIVTFGVTYLEKHFGTTPIVPAHEVAECSCEPSG"},"dna_sequence":{"accession":"X54723","fmin":"818","fmax":"1679","strand":"+","sequence":"ATGCATACGCGGAAGGCAATAACGGAGGCGCTTCAAAAACTCGGAGTCCAAACCGGTGACCTATTGATGGTGCATGCCTCACTTAAAGCGATTGGTCCGGTCGAAGGAGGAGCGGAGACGGTCGTTGCCGCGTTACGCTCCGCGGTTGGGCCGACTGGCACTGTGATGGGATACGCATCGTGGGACCGATCACCCTACGAGGAGACTCGTAATGGCGCTCGGTTGGATGACAAAACCCGCCGTACCTGGCCGCCGTTCGATCCCGCAACGGCCGGGACTTACCGTGGGTTCGGCCTGCTGAATCAGTTTCTGGTTCAAGCCCCCGGCGCGCGGCGCAGCGCGCACCCCGATGCATCGATGGTCGCGGTTGGTCCACTGGCTGAAACGCTGACGGAGCCTCACAAGCTCGGTCACGCCTTGGGGGAAGGGTCGCCCGTCGAGCGGTTCGTTCGCCTTGGCGGGAAGGCCCTGCTGTTGGGTGCGCCGCTAAACTCCGTTACCGCATTGCACTACGCCGAGGCGGTTGCCGATATCCCCAACAAACGGCGGGTGACGTATGAGATGCCGATGCTTGGAAGCAACGGCGAAGTCGCCTGGAAAACGGCATCGGATTACGATTCAAACGGCATTCTCGATTGCTTTGCTATCGAAGGAAAGCCGGATGCGGTCGAAACTATAGCAAATGCTTACGTGAAGCTCGGTCGCCATCGAGAAGGTGTCGTGGGCTTTGCTCAGTGCTACCTGTTCGACGCGCAGGACATCGTGACGTTCGGCGTCACCTATCTTGAGAAGCATTTCGGAACCACTCCGATCGTGCCAGCACACGAAGTCGCCGAGTGCTCTTGCGAGCCTTCAGGTTAGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002535","ARO_id":"38935","ARO_name":"AAC(3)-IIc","ARO_description":"AAC(3)-IIc is a plasmid-encoded aminoglycoside acetyltransferase in E. coli and P. aeruginosa","ARO_category":{"36461":{"category_aro_accession":"3000322","category_aro_cvterm_id":"36461","category_aro_name":"AAC(3)","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 3.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1379":{"model_id":"1379","model_name":"OXA-313","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1376":{"protein_sequence":{"accession":"AGU69251.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKTTTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIQVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KF057030","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCCCTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTCTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGACAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCAGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCATTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001684","ARO_id":"38084","ARO_name":"OXA-313","ARO_description":"OXA-313 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1380":{"model_id":"1380","model_name":"TEM-193","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1245":{"protein_sequence":{"accession":"AFC75523.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAAHLFLTTIGGPKELTAFLHNMGDHVTRLDCWGPKLTEAIPHDERDTTMPAAVANTLRKLLTGELLTLASRQQLIDWMEADKVAGPILRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"JN935135","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCCACTTATTTCTGACAACGATCGGAGGACCGAAGGAGCTCACCGCTTTTTTGCACAACATGGGGGATCATGTCACCCGCCTTGATTGTTGGGGACCGAAGCTGACTGAGGCCATACCACACGACGAGCGTGACACCACGATGCCTGCAGCAGTGGCCAACACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCAATTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001053","ARO_id":"37433","ARO_name":"TEM-193","ARO_description":"TEM-193 is a beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1381":{"model_id":"1381","model_name":"CcrA beta-lactamase","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"1275":{"protein_sequence":{"accession":"AAA22904.1","sequence":"MKTVFILISMLFPVAVMAQKSVKISDDISITQLSDKVYTYVSLAEIEGWGMVPSNGMIVINNHQAALLDTPINDAQTEMLVNWVTDSLHAKVTTFIPNHWHGDCIGGLGYLQRKGVQSYANQMTIDLAKEKGLPVPEHGFTDSLTVSLDGMPLQCYYLGGGHATDNIVVWLPTENILFGGCMLKDNQATSIGNISDADVTAWPKTLDKVKAKFPSARYVVPGHGDYGGTELIEHTKQIVNQYIESTSKP"},"dna_sequence":{"accession":"M63556","fmin":"90","fmax":"840","strand":"+","sequence":"ATGAAAACAGTATTTATCCTTATCTCCATGCTTTTCCCTGTCGCAGTTATGGCACAGAAAAGCGTAAAAATATCCGATGACATCAGTATCACCCAACTCTCGGACAAAGTGTACACTTATGTATCCCTCGCCGAAATCGAAGGATGGGGTATGGTACCTTCCAACGGGATGATTGTTATCAACAACCACCAGGCAGCGTTGCTGGACACACCGATCAATGACGCACAAACGGAAATGCTGGTCAACTGGGTGACAGACTCTTTGCATGCCAAAGTCACCACGTTTATCCCGAACCACTGGCACGGCGATTGTATTGGCGGACTGGGTTACCTGCAAAGGAAAGGTGTCCAATCATACGCGAACCAGATGACGATAGACCTCGCCAAGGAAAAAGGGTTGCCCGTACCGGAACATGGATTCACCGATTCACTGACCGTCAGCTTGGACGGCATGCCTCTCCAATGTTATTATTTAGGAGGCGGACATGCGACCGACAATATCGTGGTTTGGCTGCCGACAGAGAATATCCTTTTTGGCGGATGTATGCTTAAAGACAACCAGGCGACAAGCATCGGCAACATCTCGGACGCGGACGTGACGGCATGGCCGAAAACTCTCGATAAGGTAAAAGCCAAGTTCCCCTCGGCCCGTTACGTCGTGCCCGGACATGGCGACTATGGCGGAACCGAACTGATAGAGCATACCAAGCAGATCGTGAACCAATATATAGAAAGCACTTCAAAGCCATAGC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35916","NCBI_taxonomy_name":"Bacteroides fragilis","NCBI_taxonomy_id":"817"}}}},"ARO_accession":"3000578","ARO_id":"36717","ARO_name":"CcrA","ARO_description":"This CcrA beta-lactamases is found in Bacteroides fragilis.","ARO_category":{"41364":{"category_aro_accession":"3004200","category_aro_cvterm_id":"41364","category_aro_name":"CcrA beta-lactamase","category_aro_description":"CcrA beta-lactamases are chromosomal-encoded carbapenemase commonly found in Bacteroides fragilis isolates.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1382":{"model_id":"1382","model_name":"rmtG","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"93":{"protein_sequence":{"accession":"AGE00988.1","sequence":"MRDPLFEKLAASKKYRDVCPDTIARILTECRAKYRREKEIDKAAREKLHGITAAFMTDAEYRRAMEIAVRGGELAELMECHASTRERLPLEETDAVYARLLGAPDESALDLACGLNPAYLQNRYPEMRVTGIDISGQCVRVLRALGVDARLGDLLAENAIPRARYSVALLFKILPLLDRQSAGAARRILEAVNADALICSFPTRSLSGRNVGMAVHYAAWMRDQLPEKWRIERTVETDNELYYVLKEKQDGEAVRGGDSHRESE"},"dna_sequence":{"accession":"JX486113","fmin":"0","fmax":"795","strand":"+","sequence":"ATGCGTGATCCGTTGTTTGAAAAGCTGGCGGCTTCGAAGAAATACCGCGATGTGTGTCCGGATACGATCGCGCGCATTTTAACGGAATGCCGCGCGAAGTACCGGCGGGAAAAGGAAATCGATAAAGCGGCGCGCGAAAAGCTGCACGGCATCACCGCTGCGTTCATGACGGATGCGGAATACAGGCGCGCGATGGAAATTGCAGTGCGGGGCGGCGAACTGGCTGAATTGATGGAATGCCACGCCTCCACGCGCGAACGGCTGCCGCTGGAAGAAACAGATGCCGTGTATGCGCGTCTGTTGGGTGCGCCCGACGAATCGGCGCTGGATCTGGCGTGCGGGCTGAATCCCGCGTATCTGCAAAATCGATACCCCGAAATGCGCGTTACCGGAATCGATATCAGCGGCCAATGCGTGCGCGTGCTGCGCGCGCTGGGCGTGGATGCGCGCCTCGGCGATCTGCTTGCGGAGAACGCGATTCCGCGGGCGCGGTATTCCGTCGCGCTGCTGTTTAAAATTCTGCCGCTGCTGGATCGCCAGTCGGCGGGCGCGGCGCGGCGCATCCTGGAAGCGGTGAACGCCGATGCGCTGATCTGTTCGTTCCCCACGCGCAGCCTGTCCGGCAGAAATGTGGGCATGGCGGTGCATTACGCCGCGTGGATGCGGGATCAGCTGCCCGAAAAATGGCGAATCGAACGCACCGTGGAAACGGATAACGAGCTATATTACGTTCTGAAGGAGAAACAGGATGGCGAAGCTGTACGTGGTGGCGACTCCCATCGGGAATCTGAATGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002668","ARO_id":"39068","ARO_name":"rmtG","ARO_description":"RmtG is a 16S rRNA methyltransferase found in Pseudomonas aeruginosa which methylates G1405 of the 16S rRNA. It confers high level resistance to many aminoglycosides.","ARO_category":{"41435":{"category_aro_accession":"3004271","category_aro_cvterm_id":"41435","category_aro_name":"16S rRNA methyltransferase (G1405)","category_aro_description":"Methyltransferases that methylate the G1405 position of 16S rRNA, which is part of an aminoglycoside binding site.","category_aro_class_name":"AMR Gene Family"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1383":{"model_id":"1383","model_name":"IMI-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1435":{"protein_sequence":{"accession":"AHE78014.1","sequence":"MSLNVKPSRIAILFSSCLVSISFFSQANTKGIDEIKDLETDFNGRIGVYALDTGSGKSFSYKANERFPLCSSFKGFLAAAVLKGSQDNQLNLNQIVNYNTRSLEFHSPITTKYKDNGMSLGDMAAAALQYSDNGATNIILERYIGGPEGMTKFMRSIGDKDFRLDRWELDLNTAIPGDERDTSTPAAVAKSLKTLALGNILNEREKETYQTWLKGNTTGAARIRASVPSDWVVGDKTGSCGAYGTANDYAVVWPKNRAPLIISVYTTKYEKEAKHEDKVIAEASRIAIDNLK"},"dna_sequence":{"accession":"KF958750","fmin":"0","fmax":"879","strand":"+","sequence":"ATGTCACTTAATGTAAAACCAAGTAGAATAGCCATCTTGTTTAGCTCTTGTTTAGTTTCAATATCATTTTTCTCACAGGCCAATACAAAGGGCATCGATGAGATTAAAGACCTTGAAACAGATTTCAATGGTAGAATTGGTGTCTACGCTTTAGACACTGGCTCAGGCAAATCATTTTCATACAAAGCAAATGAACGATTTCCATTATGTAGTTCTTTCAAAGGTTTTTTAGCTGCTGCTGTATTAAAAGGCTCTCAAGATAATCAACTAAATCTTAATCAGATCGTGAATTATAATACAAGAAGTTTAGAGTTCCATTCACCCATCACAACTAAATATAAAGATAATGGAATGTCATTAGGTGATATGGCTGCTGCAGCTTTACAATATAGCGACAATGGTGCTACTAATATTATCCTTGAACGATATATCGGTGGTCCTGAGGGTATGACTAAATTCATGCGGTCGATTGGAGATAAAGATTTTAGACTCGATCGTTGGGAGTTAGATCTAAACACAGCTATTCCTGGCGATGAACGTGACACATCTACACCTGCAGCAGTAGCTAAGAGCCTGAAAACCCTTGCACTGGGTAACATACTCAATGAGCGTGAAAAGGAAACCTATCAGACATGGTTAAAGGGTAACACAACCGGTGCAGCGCGTATTCGTGCTAGCGTACCAAGCGATTGGGTAGTTGGCGATAAAACTGGTAGTTGCGGTGCATACGGTACGGCAAATGATTATGCGGTAGTCTGGCCAAAGAACCGAGCTCCTCTTATAATTTCTGTATACACTACAAAATACGAAAAAGAAGCCAAGCATGAGGATAAAGTAATCGCAGAAGCTTCAAGAATCGCAATTGATAACCTTAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001861","ARO_id":"38261","ARO_name":"IMI-4","ARO_description":"IMI-4 is a beta-lactamase. From the Lahey list of IMI beta-lactamases.","ARO_category":{"36027":{"category_aro_accession":"3000018","category_aro_cvterm_id":"36027","category_aro_name":"IMI beta-lactamase","category_aro_description":"IMI beta-lactamases are a group of TEM-1-like beta-lactamase that are known to hydrolyze imipenem. IMI beta-lactamases are inhibited by clavulanic acid and tazobactam.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1384":{"model_id":"1384","model_name":"OXA-382","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2011":{"protein_sequence":{"accession":"AHL30286.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKTDKKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFTYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KJ135345","fmin":"14","fmax":"839","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAAACTGATAAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGGCTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTACTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001568","ARO_id":"37968","ARO_name":"OXA-382","ARO_description":"OXA-382 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1385":{"model_id":"1385","model_name":"mdsB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"2090"}},"model_sequences":{"sequence":{"4402":{"protein_sequence":{"accession":"NP_459346.1","sequence":"MKFTHFFIARPIFAIVLSLLMLLAGAIAFLKLPLSEYPAVTPPTVQVSASYPGANPQVIADTVAAPLEQVINGVDGMLYMNTQMAIDGRMVISIAFEQGTDPDMAQIQVQNRVSRALPRLPEEVQRIGVVTEKTSPDMLMVVHLVSPQKRYDSLYLSNFAIRQVRDELARLPGVGDVLVWGAGEYAMRVWLDPAKIANRGLTASDIVTALREQNVQVAAGSVGQQPEASAAFQMTVNTLGRLTSEEQFGEIVVKIGADGEVTRLRDVARVTLGADAYTLRSLLNGEAAPALQIIQSPGANAIDVSNAIRGKMDELQQNFPQDIEYRIAYDPTVFVRASLQSVAITLLEALVLVVLVVVMFLQTWRASIIPLVAVPVSLVGTFALMHLFGFSLNTLSLFGLVLSIGIVVDDAIVVVENVERHISQGKSPGEAAKKAMDEVTGPILSITSVLTAVFIPSAFLAGLQGEFYRQFALTIAISTILSAINSLTLSPALAAILLRPHHDTAKADWLTRLMGTVTGGFFHRFNRFFDSASNRYVSAVRRAVRGSVIVMVLYAGFVGLTWLGFHQVPNGFVPAQDKYYLVGIAQLPSGASLDRTEAVVKQMSAIALAEPGVESVVVFPGLSVNGPVNVPNSALMFAMLKPFDEREDPSLSANAIAGKLMHKFSHIPDGFIGIFPPPPVPGLGATGGFKLQIEDRAELGFEAMTKVQSEIMSKAMQTPELANMLASFQTNAPQLQVDIDRVKAKSMGVSLTDIFETLQINLGSLYVNDFNRFGRAWRVMAQADAPFRMQQEDIGLLKVRNAKGEMIPLSAFVTIMRQSGPDRIIHYNGFPSVDISGGPAPGFSSGQATDAIEKIVRETLPEGMVFEWTDLVYQEKQAGNSALAIFALAVLLAFLILAAQYNSWSLPFAVLLIAPMSLLSAIVGVWVSGGDNNIFTQIGFVVLVGLAAKNAILIVEFARAKEHDGADPLTAVLEASRLRLRPILMTSFAFIAGVVPLVLATGAGAEMRHAMGIAVFAGMLGVTLFGLLLTPVFYVVVRRMALKRENRVDSHDQQA"},"dna_sequence":{"accession":"NC_003197.2","fmin":"393893","fmax":"397061","strand":"-","sequence":"TTATGCTTGCTGATCATGCGAATCAACGCGGTTCTCACGCTTTAATGCCATCCTGCGAACCACCACGTAAAATACAGGCGTCAATAACAGGCCGAAGAGCGTGACGCCCAACATGCCGGCAAACACGGCGATGCCCATCGCATGTCGCATTTCCGCGCCGGCACCCGTCGCGAGTACCAGTGGTACTACACCTGCGATAAAGGCGAATGAGGTCATCAGGATAGGACGCAGACGCAGGCGGGACGCTTCCAGTACGGCGGTCAGCGGGTCTGCGCCGTCGTGTTCTTTGGCGCGGGCAAACTCGACAATCAAAATGGCGTTCTTGGCCGCCAGGCCGACCAGCACCACGAAACCAATCTGCGTAAAGATATTGTTATCTCCGCCAGATACCCACACGCCGACAATGGCTGAGAGTAATGACATAGGCGCAATAAGCAGGACGGCGAAGGGCAGCGACCAACTGTTGTACTGCGCCGCCAGGATCAGGAAGGCCAGCAGCACCGCCAGCGCAAAGATAGCAAGCGCAGAGTTGCCGGCCTGTTTTTCCTGATAAACCAGATCGGTCCATTCGAAGACCATCCCTTCCGGTAACGTTTCACGCACGATCTTTTCAATCGCGTCCGTCGCCTGTCCGGAGGAGAAGCCCGGAGCCGGTCCACCGCTAATATCTACCGAGGGGAAGCCGTTGTAATGGATGATTCTGTCCGGCCCCGACTGGCGCATAATCGTGACGAAAGCGCTAAGCGGGATCATCTCGCCCTTCGCATTGCGGACTTTAAGCAGGCCGATATCCTCTTGCTGCATACGGAATGGCGCATCGGCCTGCGCCATCACCCGCCAGGCACGGCCAAATCGGTTGAAATCGTTGACGTAAAGCGAGCCGAGGTTAATTTGCAACGTTTCAAAGATGTCGGTGAGCGATACCCCCATTGATTTCGCCTTTACCCGGTCGATATCCACCTGTAATTGCGGGGCGTTTGTCTGGAAACTGGCCAGCATATTGGCCAGTTCGGGCGTCTGCATCGCCTTAGACATAATCTCGCTTTGCACCTTTGTCATCGCTTCAAATCCCAGTTCCGCACGATCTTCAATCTGCAATTTAAAGCCGCCCGTCGCGCCAAGCCCTGGAACCGGCGGTGGCGGGAAGATGCCAATAAATCCGTCGGGAATGTGGCTAAATTTGTGCATTAGCTTTCCGGCGATAGCGTTAGCGGAAAGCGAAGGATCTTCACGCTCGTCAAAGGGTTTCAGCATGGCGAACATCAGCGCCGAATTTGGCACATTTACCGGGCCGTTAACCGACAGACCGGGGAAGACGACGACGCTTTCAACGCCGGGTTCCGCCAGCGCGATAGCGGACATCTGTTTCACGACCGCCTCTGTGCGATCCAACGATGCGCCGCTTGGGAGCTGGGCGATGCCGACGAGATAGTATTTATCCTGCGCAGGCACAAACCCGTTCGGCACCTGATGGAAGCCAAGCCAGGTCAGCCCCACAAAGCCAGCATAGAGCACCATCACAATGACGCTGCCGCGCACGGCCCGACGGACGGCGCTAACATAGCGGTTCGACGCGCTGTCGAAGAAACGGTTAAAGCGATGGAAAAAACCGCCAGTGACCGTGCCCATCAACCGCGTTAGCCAGTCAGCCTTCGCAGTATCGTGGTGCGGTCTTAGCAAAATGGCAGCCAGCGCAGGGGAGAGCGTCAGCGAGTTAATGGCCGAAAGGATGGTCGAAATAGCGATGGTCAACGCGAACTGACGATAAAACTCACCCTGCAGGCCCGCCAGGAATGCGGAAGGGATAAAGACCGCCGTTAGCACCGAGGTAATAGAAAGAATGGGACCAGTGACTTCATCCATCGCCTTCTTTGCCGCCTCTCCGGGACTTTTGCCCTGCGAGATATGCCGTTCCACGTTTTCGACCACAACGATGGCGTCATCGACAACGATACCTATCGACAGGACCAAACCAAACAGCGAAAGCGTATTCAGCGAAAAGCCAAACAGGTGCATCAAGGCAAAGGTGCCGACCAGCGAAACGGGAACCGCCACCAGAGGAATAATGGACGCCCGCCAGGTTTGCAGGAACATCACCACGACAAGGACGACCAGCACGAGGGCTTCCAGCAACGTAATCGCCACCGATTGTAGCGATGCGCGCACGAAGACCGTAGGATCATAGGCAATCCGGTATTCGATATCCTGCGGGAAGTTTTGCTGCAACTCATCCATTTTGCCGCGAATCGCGTTAGAAACGTCAATCGCATTGGCGCCCGGACTTTGAATAATCTGTAACGCTGGCGCCGCTTCGCCATTCAGTAAACTGCGCAGCGTATAGGCATCTGCGCCCAGCGTGACGCGGGCGACATCACGCAGACGCGTCACCTCGCCGTCAGCGCCGATTTTTACCACAATCTCGCCGAACTGTTCTTCGCTGGTCAGGCGGCCCAGCGTGTTTACCGTCATCTGAAAAGCGGCGGAGGCCTCCGGCTGTTGCCCGACGGAACCGGCGGCGACCTGTACGTTTTGTTCCCGCAACGCCGTAACGATATCACTGGCGGTAAGACCGCGGTTGGCGATTTTCGCCGGGTCCAGCCAGACGCGCATGGCGTACTCGCCCGCGCCCCAGACGAGAACATCGCCGACGCCGGGTAAACGGGCCAGTTCGTCGCGAACCTGCCGGATGGCGAAGTTAGACAGGTAAAGCGAGTCATAGCGTTTTTGCGGCGAGACAAGATGAACCACCATCAACATATCGGGGGACGTTTTCTCCGTTACAACGCCAATTCGCTGGACTTCTTCGGGCAGGCGAGGCAGCGCGCGGGATACCCGGTTTTGCACCTGAATTTGCGCCATATCAGGATCGGTTCCCTGTTCGAAGGCGATAGAGATAACCATGCGACCATCAATGGCCATCTGGGTATTCATATACAACATGCCGTCAACGCCGTTGATCACCTGTTCCAGCGGCGCGGCTACCGTATCGGCAATCACTTGCGGGTTAGCGCCGGGGTAGCTGGCGCTAACCTGTACCGTGGGCGGCGTAACGGCCGGATATTCACTCAGCGGCAGTTTTAAAAAGGCGATAGCGCCAGCCAGCAGCATTAACAGCGACAGGACGATGGCGAAGATGGGGCGTGCAATGAAAAAGTGGGTGAATTTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35734","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium str. LT2","NCBI_taxonomy_id":"99287"}}}},"ARO_accession":"3000790","ARO_id":"37170","ARO_name":"mdsB","ARO_description":"MdsB is the inner membrane transporter of the multidrug and metal efflux complex MdsABC. mdsB corresponds to 1 locus in Pseudomonas aeruginosa PAO1 (gene name: mexQ) and 2 loci in Pseudomonas aeruginosa LESB58.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1386":{"model_id":"1386","model_name":"ANT(9)-Ia","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"495":{"protein_sequence":{"accession":"AFU35063.1","sequence":"MLIGVYLYGSAVMGGLRMNSDVDILVITNQSLSEKTRRNLTNRLMLISGKIGNIKDMRPLEVTVINQKDIVPWHFPPKYEFMYGEWLREQFEKGEIPESTYDPDLAILLAQLRKNSINLLGPKATEVIEPVPMTDIRKAIKESLPGLIASINGDERNVILTLARMWLTASTGEIRSKDLAAEWAIPQLPDEHATLLNKAREAYLGECVDKWEGMESEVAELVNHMKKSIESSLNIQLPFRIV"},"dna_sequence":{"accession":"JX560992","fmin":"8592","fmax":"9321","strand":"+","sequence":"ATGTTAATTGGGGTGTATTTGTATGGTTCGGCAGTAATGGGTGGTTTACGTATGAATAGCGATGTAGATATTTTGGTAATAACAAATCAAAGTTTATCTGAAAAAACTCGAAGGAATCTTACAAATAGGTTAATGCTTATATCTGGGAAAATAGGAAACATAAAAGATATGAGGCCTCTTGAAGTTACGGTCATAAATCAAAAGGATATTGTCCCTTGGCATTTCCCCCCCAAATATGAATTTATGTATGGCGAGTGGCTAAGAGAGCAGTTTGAAAAGGGAGAAATTCCTGAGTCGACTTATGATCCGGATTTAGCAATACTTTTAGCACAACTAAGAAAAAATAGTATTAACCTTTTGGGACCAAAGGCAACAGAAGTAATTGAGCCTGTGCCAATGACAGATATTCGAAAAGCAATTAAAGAATCGTTGCCCGGGTTGATAGCTAGCATTAACGGTGACGAACGCAATGTGATTTTAACTTTAGCCAGAATGTGGCTGACAGCATCTACTGGTGAAATTCGCTCAAAAGATCTGGCAGCTGAATGGGCGATACCTCAATTACCCGATGAGCATGCTACTTTACTCAACAAAGCGAGAGAGGCTTATTTAGGAGAGTGTGTTGACAAGTGGGAAGGAATGGAATCTGAGGTGGCTGAACTCGTTAATCATATGAAAAAGTCTATAGAGTCTTCCCTTAATATCCAATTACCTTTTCGAATAGTTTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3002630","ARO_id":"39030","ARO_name":"ANT(9)-Ia","ARO_description":"ANT(9)-Ia is an aminoglycoside nucleotidyltransferase encoded by plasmids and transposons in S. aureus, Enterococcus spp., Staphylococcus sciuri and E. faecalis","ARO_category":{"36367":{"category_aro_accession":"3000228","category_aro_cvterm_id":"36367","category_aro_name":"ANT(9)","category_aro_description":"Nucleotidylylation of spectinomycin at the hydroxyl group at position 9","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1387":{"model_id":"1387","model_name":"OXA-99","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1847":{"protein_sequence":{"accession":"ABI53716.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIRQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEMNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"DQ888718","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCGACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAATGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001649","ARO_id":"38049","ARO_name":"OXA-99","ARO_description":"OXA-99 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1388":{"model_id":"1388","model_name":"oleB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1100"}},"model_sequences":{"sequence":{"3347":{"protein_sequence":{"accession":"AAA50325.1","sequence":"MQNAHRSDTGAAALTGTPEKLLPTQPETGSFQVVLDDVVRAPGGRPLLDGVNQSVALGERVGIIGENGSGKSTLLRMLAGVDRPDGGQVLVRAPGGCGYLPQTPDLPPEDTVQDAIDHALAELRSLERGLREAEQALAGAEPEELEGLLGAYGDLLEAFEARDGYAADARVDAAMHGLGLAGITGDRRLGSLSGGEQARLNLACLLAASPQLMLLDEPTNHLDVGALEWLEERLRAHRGSVLVVSHDRVFLERVATALWEVDGERRTVNRHGGGYAGYLQAKAAARRRWEQAYQDWLEDLARQRELARSAADHLATGPRRNTERSNQRHQRNVEKQISARVRNAKERVRRLEENPVPRPPQPMRFRARVEGGGTVGRGGALAELYKVTVGTRLDVPSFTVDPGERILITGHNGAGKSTLLRVLAGDLAPDQGECERPERIGWLPQETEITDRQQSLLAAFAAGLPGIAEEHRGALLGFGLFRPSALGTAVGDLSTGQLRRLALARLLRDPADLLLLDEPTNHLSPALVEDLEEALAHYRGALVVVSHDRMFAQRFTGRRMHMEGGRFVE"},"dna_sequence":{"accession":"L36601","fmin":"1420","fmax":"3130","strand":"+","sequence":"ATGCAGAACGCACACCGTTCCGATACCGGCGCCGCGGCGCTCACCGGCACGCCGGAAAAGCTCCTTCCCACGCAACCTGAGACCGGTTCCTTCCAGGTCGTCCTCGACGACGTCGTCCGGGCACCCGGCGGACGGCCGCTGTTGGACGGCGTCAACCAGTCGGTGGCACTCGGCGAGCGCGTCGGCATCATCGGTGAGAACGGATCGGGCAAGTCGACCCTGCTCCGCATGCTCGCCGGCGTGGACCGCCCGGACGGTGGCCAGGTCCTCGTCCGGGCTCCCGGCGGCTGCGGCTACCTCCCCCAGACACCGGACCTGCCCCCGGAGGACACCGTTCAGGACGCCATCGACCACGCCCTCGCCGAACTGCGCTCCCTGGAGCGGGGGTTGCGTGAGGCGGAGCAGGCGCTGGCCGGGGCGGAGCCCGAGGAGCTGGAGGGCCTGCTCGGCGCCTACGGCGACCTGCTGGAGGCGTTCGAGGCCCGCGACGGCTACGCGGCGGACGCCCGTGTCGACGCGGCGATGCACGGCCTCGGTCTGGCGGGCATCACGGGCGACCGGCGGCTCGGCAGCCTCTCCGGAGGTGAGCAGGCGCGTCTCAACCTGGCCTGCCTGCTGGCCGCGTCCCCGCAGCTGATGCTGCTCGACGAACCCACCAACCACCTCGACGTCGGGGCGCTGGAGTGGCTGGAGGAGCGCCTGCGGGCCCACCGCGGCAGCGTGCTGGTCGTCTCGCACGACCGGGTCTTCCTGGAGCGCGTGGCCACCGCCCTGTGGGAGGTGGACGGCGAGCGGCGCACCGTCAACCGGCACGGCGGCGGTTACGCGGGATACCTGCAAGCCAAGGCGGCCGCGCGGCGCCGCTGGGAGCAGGCTTACCAGGACTGGCTGGAGGACCTGGCACGCCAGCGGGAACTGGCCCGCAGCGCCGCCGACCACCTGGCCACCGGCCCGCGGCGCAACACCGAGCGGTCGAACCAGCGCCACCAGCGCAACGTGGAGAAGCAGATCTCCGCGCGGGTCCGCAACGCCAAGGAGCGGGTCCGCCGGCTGGAGGAGAACCCGGTGCCGCGGCCCCCTCAACCCATGCGTTTCCGGGCCCGGGTGGAGGGTGGCGGCACGGTCGGGCGCGGCGGGGCACTCGCCGAGCTGTACAAGGTCACCGTCGGCACGCGGCTCGACGTCCCGTCCTTCACCGTCGACCCCGGTGAGCGCATCCTGATCACGGGGCACAACGGCGCGGGCAAGAGCACCCTGCTGCGCGTGCTGGCCGGTGACCTGGCGCCCGATCAGGGCGAGTGCGAGCGCCCGGAGCGCATCGGCTGGCTGCCGCAGGAGACGGAGATCACCGACCGGCAGCAGAGCCTGCTGGCGGCCTTCGCGGCGGGGCTGCCCGGCATCGCGGAGGAACACCGGGGCGCGCTCCTGGGATTCGGGCTCTTCCGGCCCTCGGCGCTGGGCACCGCGGTGGGAGACCTGTCCACCGGGCAGTTGAGGCGGCTGGCCCTGGCCCGTCTGCTGCGCGACCCGGCGGACCTGCTGCTGCTCGACGAGCCGACGAACCACCTGTCGCCCGCGCTCGTGGAGGACCTGGAGGAGGCGCTGGCGCACTACCGGGGCGCACTGGTCGTGGTCTCCCACGACCGCATGTTCGCGCAGCGGTTCACCGGTCGCCGCATGCACATGGAGGGTGGCCGCTTCGTGGAGTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36823","NCBI_taxonomy_name":"Streptomyces antibioticus","NCBI_taxonomy_id":"1890"}}}},"ARO_accession":"3003036","ARO_id":"39470","ARO_name":"oleB","ARO_description":"oleB is an ABC transporter in Streptomyces antibioticus and is involved in oleandomycin secretion","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1389":{"model_id":"1389","model_name":"KPC-22","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1112":{"protein_sequence":{"accession":"AIX87991.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPGSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQLVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"KM379100","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGGGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGCTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3003180","ARO_id":"39757","ARO_name":"KPC-22","ARO_description":"From the Lahey list of beta-lactamases.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1390":{"model_id":"1390","model_name":"arlR","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"410"}},"model_sequences":{"sequence":{"4399":{"protein_sequence":{"accession":"YP_001332362.1","sequence":"MTQILIVEDEQNLARFLELELTHENYNVDTEYDGQDGLDKALSHYYDLIILDLMLPSINGLEICRKIRQQQSTPIIIITAKSDTYDKVAGLDYGADDYIVKPFDIEELLARIRAILRRQPQKDIIDVNGITIDKNAFKVTVNGAEIELTKTEYDLLYLLAENKNHVMQREQILNHVWGYNSEVETNVVDVYIRYLRNKLKPYDRDKMIETVRGVGYVIR"},"dna_sequence":{"accession":"NC_009641","fmin":"1461588","fmax":"1462248","strand":"-","sequence":"TCATCGTATCACATACCCAACGCCACGAACTGTTTCAATCATTTTGTCACGATCGTATGGTTTTAACTTGTTTCGTAAATATCTTATATAAACATCTACGACATTTGTTTCTACTTCACTATTATAACCCCATACATGATTTAAAATTTGTTCCCGTTGCATAACATGGTTTTTATTTTCAGCTAGAAGATATAGTAAATCATACTCTGTTTTTGTTAATTCAATTTCTGCGCCATTTACCGTCACTTTAAAAGCGTTCTTATCAATTGTAATACCGTTGACATCGATAATATCCTTTTGTGGCTGACGACGTAAAATTGCACGAATTCTTGCTAAAAGTTCTTCAATATCAAACGGCTTAACTATATAATCGTCTGCACCGTAATCAAGCCCAGCAACTTTGTCATACGTATCACTTTTCGCTGTAATTATAATGATAGGTGTAGATTGTTGTTGTCTAATTTTGCGACAAATTTCTAAGCCATTAATTGACGGCAACATTAAATCTAATATGATTAAATCATAGTAATGGCTAAGCGCTTTATCTAAACCGTCTTGTCCATCATACTCTGTGTCCACATTGTAATTTTCATGTGTGAGTTCCAATTCAAGAAATCTTGCTAAGTTTTGTTCATCTTCTACTATTAAAATTTGCGTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35525","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus str. Newman","NCBI_taxonomy_id":"426430"}}}},"ARO_accession":"3000838","ARO_id":"37218","ARO_name":"arlR","ARO_description":"ArlR is a response regulator that binds to the norA promoter to activate expression. ArlR must first be phosphorylated by ArlS.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavin","category_aro_description":"Acriflavin is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36193":{"category_aro_accession":"3000054","category_aro_cvterm_id":"36193","category_aro_name":"acridine dye","category_aro_description":"Acridine dyes are cell permeable, basic molecules with an acridine chromophore. These compounds intercalate DNA. The image shown represents the core structure of the acridine family, with specific dyes containing varying substituents.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1391":{"model_id":"1391","model_name":"CTX-M-92","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1967":{"protein_sequence":{"accession":"ACY74743.1","sequence":"MMTQSIRRSMLTVMATLPLLFSSATLHAQANSVQQQLEALEKSSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKQSESDKHLLNQRVEIKKSDLVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRTQLVTWLKGNTTGSASIRAGLPKSWVVGDKTGSGDYGTTNDIAVIWPENHAPLVLVTYFTQPEQKAESRRDILAAAAKIVTHGF"},"dna_sequence":{"accession":"GU127598","fmin":"0","fmax":"876","strand":"+","sequence":"ATGATGACTCAGAGCATTCGCCGCTCAATGTTAACGGTGATGGCGACGCTACCCCTGCTATTTAGCAGCGCAACGCTGCATGCGCAGGCGAACAGCGTGCAACAGCAGCTGGAAGCCCTGGAGAAAAGTTCGGGAGGTCGGCTTGGCGTTGCGCTGATTAACACCGCCGATAATTCGCAGATTCTCTACCGTGCCGATGAACGTTTTGCGATGTGCAGTACCAGTAAGGTGATGGCGGCCGCGGCGGTGCTTAAACAGAGCGAGAGCGATAAGCACCTGCTAAATCAGCGCGTTGAAATCAAGAAGAGCGACCTGGTTAACTACAATCCCATTGCGGAGAAACACGTTAACGGCACGATGACGCTGGCTGAGCTTGGCGCAGCGGCGCTGCAGTATAGCGACAATACTGCCATGAATAAGCTGATTGCCCATCTGGGTGGTCCCGATAAAGTGACGGCGTTTGCTCGCTCGTTGGGTGATGAGACCTTCCGTCTGGACAGAACCGAGCCCACGCTCAATACCGCCATTCCAGGCGACCCGCGTGATACCACCACGCCGCTCGCGATGGCGCAGACCCTGAAAAATCTGACGCTGGGTAAAGCGCTGGCGGAAACTCAGCGGACACAGTTGGTGACGTGGCTTAAGGGCAATACTACCGGTAGCGCGAGCATTCGGGCGGGTCTGCCGAAATCATGGGTAGTGGGCGATAAAACCGGCAGCGGAGATTATGGCACCACCAACGATATCGCGGTTATCTGGCCGGAAAACCACGCACCGCTGGTTCTGGTGACCTACTTTACCCAACCGGAGCAGAAGGCGGAAAGCCGTCGGGATATTCTGGCTGCGGCGGCGAAAATCGTAACCCACGGTTTCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001952","ARO_id":"38352","ARO_name":"CTX-M-92","ARO_description":"CTX-M-92 is a beta-lactamase found in Escherichia coli","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1392":{"model_id":"1392","model_name":"aadA22","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"238":{"protein_sequence":{"accession":"CAK12750.1","sequence":"MRVAVTIEISNQLSEVLSVIERHLESTLLAVHLYGSAVDGGLKPYSDIDLLVTVTVRLDETTRRALINDLLETSASPGESEILRAVEVTIVVHDDIIPWRYPAKRELQFGEWQRNDILAGIFEPATIDIDLAILLTKAREHSVALVGPAAEELFDPVPEQDLFEALNETLTLWNSPPDWAGDERNVVLTLSRIWYSAVTGKIAPKDVAADWAMERLPAQYQPVILEARQAYLGQEEDRLASRADQLEEFVHYVKGEITKVIGK"},"dna_sequence":{"accession":"AM261837","fmin":"73","fmax":"865","strand":"+","sequence":"ATGAGGGTAGCGGTGACCATCGAAATTTCGAACCAACTATCAGAGGTGCTAAGCGTCATTGAGCGCCATCTGGAATCAACGTTGCTGGCCGTGCATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCATACAGCGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCGAGCTTTGATCAACGACCTTTTGGAAACTTCGGCTTCCCCTGGAGAGAGCGAGATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCTGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAGTAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATGGAGCGCCTGCCGGCCCAGTATCAGCCCGTCATACTTGAAGCTAGACAGGCTTATCTTGGACAAGAAGAAGATCGCTTGGCCTCGCGCGCAGATCAGTTGGAAGAATTTGTCCACTACGTGAAAGGCGAGATCACCAAGGTAATCGGCAAATAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35732","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium","NCBI_taxonomy_id":"90371"}}}},"ARO_accession":"3002619","ARO_id":"39019","ARO_name":"aadA22","ARO_description":"aadA22 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids and integrons in S. enterica and E. coli","ARO_category":{"41439":{"category_aro_accession":"3004275","category_aro_cvterm_id":"41439","category_aro_name":"ANT(3'')","category_aro_description":"Nucleotidylylation of streptomycin at the hydroxyl group at position 3''","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1393":{"model_id":"1393","model_name":"THIN-B beta-lactamase","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"1081":{"protein_sequence":{"accession":"CAC33832.1","sequence":"MTLLAKLMLATVATMSAATVQAKTPAPKPDTPVDCDSCKAWNGEVTPFNVFGNTWYVGTAGLSAVLVTSPQGHVLLDGALPQSAPLIIANIAALGFRIEDVKFILNSHAHWDHAGGIAALQAASGATVVASASGALGLQSGTNGKDDPQFQAKPVVHVAKVEKVKVVGEGDAIKLGPLNLTAHMTPGHTPGATTWTWTSCEGQRCLDVVYADSLNPYSSGDFTYTGKGDGPDISASFAASIAKVAALPCDIILSVHPDSTGVLDKAAKRSGEHNPFIDANACRAYAATADAMLTKRLAKERGVALPAAAPAAQHAH"},"dna_sequence":{"accession":"AJ250876","fmin":"36","fmax":"987","strand":"+","sequence":"ATGACACTATTGGCGAAGTTGATGCTGGCGACGGTTGCGACCATGTCGGCGGCTACGGTGCAGGCAAAGACACCGGCGCCCAAGCCGGATACCCCTGTCGATTGCGACAGCTGCAAGGCGTGGAACGGGGAAGTCACACCATTCAACGTATTTGGCAATACCTGGTATGTGGGCACGGCCGGCTTGTCCGCCGTGCTGGTGACCAGCCCGCAAGGCCACGTCCTGCTCGACGGCGCGCTGCCGCAATCGGCGCCACTGATCATCGCGAACATCGCGGCGCTGGGTTTCCGCATCGAGGATGTGAAATTCATCCTCAATTCCCACGCGCATTGGGATCACGCCGGCGGCATCGCCGCGCTGCAGGCCGCCAGCGGCGCCACCGTGGTGGCCAGCGCCTCGGGCGCCCTGGGATTGCAAAGCGGCACCAACGGCAAGGATGATCCGCAATTCCAGGCCAAGCCTGTCGTGCATGTGGCAAAGGTGGAGAAGGTCAAGGTGGTGGGCGAGGGCGATGCCATCAAGCTGGGGCCGTTGAACCTGACGGCGCACATGACGCCAGGCCACACGCCAGGCGCCACCACCTGGACCTGGACCTCGTGCGAAGGGCAGCGCTGCCTGGACGTGGTGTATGCCGACAGCCTGAATCCGTATTCCAGCGGCGACTTTACGTACACGGGCAAAGGGGACGGACCCGATATCTCGGCCTCGTTTGCCGCCAGCATCGCCAAGGTGGCGGCCCTGCCGTGCGACATCATTCTTTCCGTGCATCCCGATTCGACGGGCGTGCTGGACAAGGCGGCCAAGCGCAGCGGCGAACACAATCCCTTCATCGATGCGAACGCCTGCCGCGCCTATGCGGCCACGGCGGACGCCATGCTGACGAAACGGCTGGCGAAGGAGCGCGGCGTGGCCCTGCCTGCGGCGGCCCCGGCTGCCCAGCACGCGCACTAGG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39074","NCBI_taxonomy_name":"Janthinobacterium lividum","NCBI_taxonomy_id":"29581"}}}},"ARO_accession":"3000851","ARO_id":"37231","ARO_name":"THIN-B","ARO_description":"THIN-B, isolated from Janthinobacterium lividum, hydrolyzes a broad spectrum of beta-lactams including penicillins, cephalosporins, and carbapenems.","ARO_category":{"41378":{"category_aro_accession":"3004214","category_aro_cvterm_id":"41378","category_aro_name":"THIN-B beta-lactamase","category_aro_description":"Beta-lactamases that are part of the THIN-B family, which is a subclass B3 beta-lactamase family and hydrolyze a broad spectrum of beta-lactams including penicillins, cephalosporins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1394":{"model_id":"1394","model_name":"OXA-257","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1760":{"protein_sequence":{"accession":"AGK07370.1","sequence":"MKFKMKGLFYVILSSLAFSGCVYDSKLQRPVISERETEIPLLFNQAQTQAVFVTYDGIHLKSYGNDLSRAKTEYIPASTFKMLNALIGLQNAKATNTEVFHWNGEKRAFSAWEKDMTLAEAMQASAVPVYQELARRIGLELMREEVKRVGFGNAEIGQQVDNFWLVGPLKISPEQEVQFAYQLAMKQLPFDRNVQQQVKDMLYIERRGDSKLYAKSGWGMDVEPQVGWYTGWVEQPNGKVTAFALNMKMQAGDDLAERKQLTLSILDKLGLFFYLR"},"dna_sequence":{"accession":"KC567681","fmin":"1210","fmax":"2041","strand":"+","sequence":"ATGAAGTTTAAAATGAAAGGTTTATTTTATGTCATCCTCAGTAGTTTGGCATTTTCAGGTTGTGTTTATGATTCAAAACTACAACGCCCAGTCATATCAGAGCGAGAAACTGAGATTCCTTTATTATTTAATCAAGCACAGACTCAAGCTGTGTTTGTTACTTATGATGGGATTCATCTAAAAAGTTATGGTAATGATCTAAGCCGAGCAAAGACTGAATATATTCCTGCATCTACATTTAAGATGTTGAATGCTTTAATTGGCTTGCAAAATGCAAAAGCAACCAATACTGAAGTATTTCATTGGAATGGTGAAAAGCGCGCTTTTTCAGCATGGGAAAAAGATATGACTTTGGCAGAAGCGATGCAGGCTTCAGCTGTTCCCGTATATCAGGAGCTTGCTCGACGTATTGGCTTGGAATTGATGCGTGAAGAAGTGAAGCGTGTAGGTTTTGGCAATGCGGAGATTGGTCAGCAAGTCGATAATTTTTGGTTGGTGGGTCCTTTAAAAATCTCCCCTGAACAAGAAGTTCAATTTGCCTATCAACTGGCGATGAAGCAATTACCTTTTGATCGAAATGTACAGCAACAAGTCAAAGATATGCTTTATATCGAGAGACGTGGTGACAGTAAACTGTATGCTAAAAGTGGTTGGGGAATGGATGTTGAACCTCAAGTGGGTTGGTATACGGGATGGGTTGAACAACCCAATGGCAAGGTGACTGCATTTGCGTTAAATATGAAAATGCAAGCAGGTGATGATCTAGCTGAACGTAAACAATTAACCTTAAGTATTTTGGACAAATTGGGTCTATTTTTTTATTTAAGATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39090","NCBI_taxonomy_name":"Acinetobacter bereziniae","NCBI_taxonomy_id":"106648"}}}},"ARO_accession":"3001694","ARO_id":"38094","ARO_name":"OXA-257","ARO_description":"OXA-257 is a beta-lactamase found in A. bereziniae","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1396":{"model_id":"1396","model_name":"OXA-11","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1522":{"protein_sequence":{"accession":"CAA80304.1","sequence":"MKTFAAYVIIACLSSTALAGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGSQNISGGIDKFWLEDQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG"},"dna_sequence":{"accession":"Z22590","fmin":"154","fmax":"955","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTATCGCGTGTCTTTCGAGTACGGCATTAGCTGGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTCTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATGACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAGCAATGGGAAAGAGACTTGACCTTAAGAGGGGCAATACAAGTTTCAGCTGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCCTATGGCAGCCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAAGACCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATATTTAAATAAATTGTCAGCATCTAAAGAAAACCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCGGCACCTGAATATCTAGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGGTGGGTTGAGAAGGAGACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAGTAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGAAAGTGAGGGCATCATTGGTGGCTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001406","ARO_id":"37806","ARO_name":"OXA-11","ARO_description":"OXA-11 is a beta-lactamase found in P. aeruginosa.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1397":{"model_id":"1397","model_name":"dfrC","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"4400":{"protein_sequence":{"accession":"AAO04716.1","sequence":"MTLSIIVAHDKQRVIGYQNQLPWHLPNDLKHVKQLTTGNTLVMGRKTFNSIGKPLPNRRNVVLTNQASFHHEGVDVINSLDEIKELSGHVFIFGGQTLFEAMIDQVDDMYITVIDGKFQGDTFFPPYTFENWEVESSVEGQLDEKNTIPHTFLHLVRRKGK"},"dna_sequence":{"accession":"AE015929","fmin":"1128933","fmax":"1129419","strand":"-","sequence":"CTATTTCCCTTTTCTACGCACTAAATGTAAGAATGTATGCGGTATAGTATTTTTTTCATCTAGTTGACCTTCTACTGAAGATTCGACTTCCCAGTTTTCGAATGTGTATGGTGGAAAGAATGTGTCTCCTTGAAACTTTCCATCTATTACTGTGATATACATATCATCTACCTGGTCAATCATTGCCTCGAATAACGTTTGTCCTCCAAATATAAAAACATGACCAGATAACTCTTTAATTTCATCAAGAGAGTTTATAACATCTACCCCTTCATGGTGAAATGAAGCTTGGTTAGTGAGTACGACGTTACGTCTATTTGGCAATGGTTTCCCTATAGAATTAAAAGTTTTCCGTCCCATTACAAGTGTATTCCCAGTGGTCAGTTGTTTAACATGCTTTAAATCATTTGGTAAGTGCCAAGGTAATTGATTTTGGTACCCAATGACTCTTTGTTTATCGTGAGCGACAATTATTGATAATGTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37591","NCBI_taxonomy_name":"Staphylococcus epidermidis ATCC 12228","NCBI_taxonomy_id":"176280"}}}},"ARO_accession":"3002865","ARO_id":"39299","ARO_name":"dfrC","ARO_description":"dfrC is a chromosome-encoded dihydrofolate reductase found in Staphylococcus aureus","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36408":{"category_aro_accession":"3000269","category_aro_cvterm_id":"36408","category_aro_name":"brodimoprim","category_aro_description":"Brodimoprim is a structural derivative of trimethoprim and an inhibitor of bacterial dihydrofolate reductase. The 4-methoxy group of trimethoprim is replaced with a bromine atom.","category_aro_class_name":"Antibiotic"},"36423":{"category_aro_accession":"3000284","category_aro_cvterm_id":"36423","category_aro_name":"tetroxoprim","category_aro_description":"Tetroxoprim is a trimethoprim derivative that inhibits bacterial dihydrofolate reductase.","category_aro_class_name":"Antibiotic"},"36476":{"category_aro_accession":"3000337","category_aro_cvterm_id":"36476","category_aro_name":"iclaprim","category_aro_description":"Iclaprim is a bactericidal compound that inhibits dihydrofolate reductase. It is used against clinically important Gram-positive pathogens, including methicillin-sensitive Staphylococcus aureus and methicillin-resistant S. aureus.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1398":{"model_id":"1398","model_name":"OXA-108","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1367":{"protein_sequence":{"accession":"ABV31688.1","sequence":"MNIKALLLITSAIFISACSPYIVTTNPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNTDIGTQVDNFWVVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"EF650034","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTACTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATACAGATATCGGTACCCAAGTCGATAATTTTTGGGTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001639","ARO_id":"38039","ARO_name":"OXA-108","ARO_description":"OXA-108 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1399":{"model_id":"1399","model_name":"OXA-315","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1531":{"protein_sequence":{"accession":"AGU69253.1","sequence":"MNIQALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPIYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPHGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KF057032","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTCAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCGATTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCATGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001686","ARO_id":"38086","ARO_name":"OXA-315","ARO_description":"OXA-315 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1400":{"model_id":"1400","model_name":"CTX-M-74","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1668":{"protein_sequence":{"accession":"ACS32293.1","sequence":"MMTQSIRRSMLTVMATLPLLFSSATLHAQANSVQQQLEALEKSSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKQSESDKHLLNQRVEIKKSDLVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDRTETTLNTAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSASIRAGLPKSWVVGDKTGSGDYGTTNDIAVIWPENHAPLVLVTYFTQPEQKAESRRDILAAAAKIVTHGF"},"dna_sequence":{"accession":"GQ149243","fmin":"0","fmax":"873","strand":"+","sequence":"ATGATGACCCAGAGCATTCGCCGCAGCATGCTGACCGTGATGGCGACCCTGCCGCTGCTGTTTAGCAGCGCGACCCTGCATGCGCAGGCGAACAGCGTGCAGCAGCAGCTGGAAGCGCTGGAAAAAAGCAGCGGCGGCCGCCTGGGCGTGGCGCTGATTAACACCGCGGATAACAGCCAGATTCTGTATCGCGCGGATGAACGCTTTGCGATGTGCAGCACCAGCAAAGTGATGGCGGCGGCGGCGGTGCTGAAACAGAGCGAAAGCGATAAACATCTGCTGAACCAGCGCGTGGAAATTAAAAAAAGCGATCTGGTGAACTATAACCCGATTGCGGAAAAACATGTGAACGGCACCATGACCCTGGCGGAACTGGGCGCGGCGGCGCTGCAGTATAGCGATAACACCGCGATGAACAAACTGATTGCGCATCTGGGCGGCCCGGATAAAGTGACCGCGTTTGCGCGCAGCCTGGGCGATGAAACCTTTCGCCTGGATCGCACCGAAACCACCCTGAACACCGCGATTCCGGGCGATCCGCGCGATACCACCACCCCGCTGGCGATGGCGCAGACCCTGAAAAACCTGACCCTGGGCAAAGCGCTGGCGGAAACCCAGCGCGCGCAGCTGGTGACCTGGCTGAAAGGCAACACCACCGGCAGCGCGAGCATTCGCGCGGGCCTGCCGAAAAGCTGGGTGGTGGGCGATAAAACCGGCAGCGGCGATTATGGCACCACCAACGATATTGCGGTGATTTGGCCGGAAAACCATGCGCCGCTGGTGCTGGTGACCTATTTTACCCAGCCGGAACAGAAAGCGGAAAGCCGCCGCGATATTCTGGCGGCGGCGGCGAAAATTGTGACCCATGGCTTT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001935","ARO_id":"38335","ARO_name":"CTX-M-74","ARO_description":"CTX-M-74 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1401":{"model_id":"1401","model_name":"mefE","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"26":{"protein_sequence":{"accession":"NP_358565.1","sequence":"MKIDKKNEAFLIVSRGISRIGDIMFDFANNTFLAGLNPTSLSLVAVYQSLESVIGVLFNLFGGVIADSFKRKKIIIVANILCGIACIILSFISQEQWMVFAIVITNIILAFMSAFSGPSYKAFTKEIVKKDSISQLNSLLEITSTIIKVTIPMVAILLYKLLGIHGVLLLDGFSFLIAASLISFIVPVNDEVVTKDKMTIGGVLNDLKIGFKYIYSHKTIFMIIILSAFVNFFLAAYNLLLPYSNQMFGEISDGLYGVFLTAEAIGGFIGAILSGVINKTLSSKRLMVFLSCSGLMLMLSTPLYFLFQNFIILAFSPALFSLFISIFNIQFFSIVQREVDTEFLGRVFGIIFTVAILFMPVGSGFFSVVLNPNNTFNLFIIGVSITILSLIFSTLLKRYDKNS"},"dna_sequence":{"accession":"NC_003098","fmin":"953382","fmax":"954594","strand":"+","sequence":"TTGAAAATAGATAAAAAAAACGAGGCTTTCCTTATTGTAAGTAGAGGCATATCTCGAATTGGAGATATTATGTTTGACTTTGCGAATAATACCTTTCTTGCAGGATTAAATCCAACATCTTTATCATTGGTTGCAGTATATCAGTCACTAGAAAGTGTGATAGGTGTTCTTTTTAATTTATTTGGTGGAGTCATTGCAGATAGTTTCAAGCGGAAAAAAATTATTATTGTTGCAAATATCTTATGTGGTATTGCTTGTATAATTCTTTCATTCATATCACAAGAGCAGTGGATGGTCTTTGCAATTGTCATCACTAATATTATCTTGGCATTTATGAGTGCTTTTTCTGGACCGTCCTATAAAGCATTTACAAAAGAAATTGTAAAAAAGGATAGTATATCACAACTTAATTCATTGCTAGAGATAACAAGTACTATAATTAAAGTAACAATACCAATGGTAGCAATTTTATTATATAAGCTACTTGGGATACATGGTGTTTTACTATTGGATGGATTCTCATTTCTAATTGCTGCATCACTGATTTCCTTTATTGTACCCGTTAATGACGAAGTGGTCACAAAGGATAAAATGACAATAGGAGGAGTTTTAAATGACTTAAAAATAGGGTTTAAGTATATTTATAGTCATAAGACAATATTTATGATTATTATTCTCTCTGCTTTTGTTAATTTTTTTCTAGCAGCTTATAATTTATTGTTACCTTATAGTAATCAAATGTTTGGAGAAATTTCAGATGGGCTTTATGGTGTTTTTCTAACTGCGGAAGCAATTGGAGGATTTATTGGAGCGATATTAAGTGGTGTTATAAATAAAACCTTGTCAAGCAAACGTTTAATGGTCTTCTTATCATGTTCAGGATTGATGTTAATGCTATCAACGCCACTCTATTTTTTGTTTCAAAACTTCATTATTCTAGCCTTTTCTCCGGCATTATTTAGTCTATTTATTTCTATTTTTAATATTCAATTTTTCTCTATTGTTCAAAGAGAAGTTGATACTGAGTTTCTCGGTAGAGTCTTTGGAATCATCTTTACGGTAGCTATTCTTTTTATGCCAGTTGGGTCTGGATTTTTCTCAGTAGTTTTAAATCCTAACAATACTTTTAATCTTTTTATTATTGGTGTATCTATTACGATATTATCGCTAATATTCAGCACGCTATTGAAGAGGTATGATAAAAATAGCTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39596","NCBI_taxonomy_name":"Streptococcus pneumoniae R6","NCBI_taxonomy_id":"171101"}}}},"ARO_accession":"3000614","ARO_id":"36908","ARO_name":"mefE","ARO_description":"mefE is a proton motive efflux pump in Streptococcus pneumoniae that confers resistance to macrolides. It is found on the same operon as mefA and the ABC-efflux pump mel.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1402":{"model_id":"1402","model_name":"OXA-390","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4370":{"protein_sequence":{"accession":"AHL30283.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFTEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KJ135342","fmin":"48","fmax":"873","strand":"-","sequence":"CTATAAAATACCTAATTGTTCTAAACTTTTATAAGTAATCTCTTTTCGAACAGAGCTAGGTATTCCTTTTTTCATTTCTAAGTTAAGGGAGAACGCTACAATATTCCCTTGAGGCTGAACAACCCATCCAGTTAACCAGCCTACTTGTGGGTCTACATCCCATCCCCAACCACTTTTTGCGTATATTTTATTTCCATTCTTTTCTTCTATGAATAGCATGGATTGCACTTCATCTTGGACTTTTTGGCTAAATGGAAGCGTTTTATTAGCTAGCTTGTAAGCAAATTGTGCCTCTTGCTGAGGAGTAATTTTTAAAGGACCCACCAGCCAAAAATTATCGACTTGGGTACCGATATCTGCATTGCCATAACCAACACGCTTCACTTCATTAGACATGAGTTCAAGTCCAATACGACGAGCTAAATCTTGATAAACCGGAATAGCGGAAGCTTTCATAGCATCGCCTAGGGTCATGTCCTTTTCCCATTCTGGGAACAGCCTTTTTTGCCCGTTCCACTTAAATACTTCTGTGGTGGTTGCCTTATGGTGCTCAAGGCCGATCAAAGCATTAAGCATTTTGAAGGTCGAAGCAGGTACATACTCGGTCGAAGCACGAGCAAGATCATTACCATAGCTTTGTTGAGTTTGACCTTGATGGATAACTAAAACACCCGTAGTGTGTGCTTCGGTAAATAAATTTTTAATTTTCTCTGCTTTGTCATCAGATTTTGAAGCACTGTGATTTGGATTAGCAGTCACTATATAAGGTGAGCAGGCTGAAATAAAAATAGCGCTTGTTATAAGTAAGAGTGCTTTAATGTTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001576","ARO_id":"37976","ARO_name":"OXA-390","ARO_description":"OXA-390 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1403":{"model_id":"1403","model_name":"OXA-388","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1215":{"protein_sequence":{"accession":"AHL30284.1","sequence":"MNIQALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKYLFNEAHTTGVLVIQQGQIQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRIGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KJ135343","fmin":"14","fmax":"839","strand":"+","sequence":"ATGAACATTCAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAATATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATTCAACAAGGCCAAATTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTATTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001574","ARO_id":"37974","ARO_name":"OXA-388","ARO_description":"OXA-388 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1404":{"model_id":"1404","model_name":"IMP-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1092":{"protein_sequence":{"accession":"BAA77393.1","sequence":"MSKLSVFFIFLFCSIATAAESLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIGWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPGHSEVGDASLLKLTLEQAVKGLNESKKPSKPSN"},"dna_sequence":{"accession":"AB010417","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAGCAAGTTATCTGTATTCTTTATATTTTTGTTTTGCAGCATTGCTACCGCAGCAGAGTCTTTGCCAGATTTAAAAATTGAAAAGCTTGATGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGGTGGGGCGTTGTTCCTAAACATGGTTTGGTGGTTCTTGTAAATGCTGAGGCTTATTTAATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAGCGTGGCTATAAAATAAAAGGCAGTATTTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGGGTGGCTTAATTCTCGATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTGCTTAAAAAAGACGGTAAGGTTCAAGCCACAAATTCATTTAGCGGAGTTAACTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCGGGACACACTCCAGATAACGTAGTGGTTTGGCTGCCTGAAAGGAAAATATTATTCGGTGGTTGTTTTATTAAACCGTACGGTTTAGGCAATTTGGGTGACGCAAATATAGAAGCTTGGCCAAAGTCCGCCAAATTATTAAAGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAGGTCACAGTGAAGTTGGAGACGCATCACTCTTGAAACTTACATTAGAGCAGGCGGTTAAAGGATTAAACGAAAGTAAAAAACCATCAAAACCAAGCAACTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36870","NCBI_taxonomy_name":"Shigella flexneri","NCBI_taxonomy_id":"623"}}}},"ARO_accession":"3002194","ARO_id":"38594","ARO_name":"IMP-3","ARO_description":"IMP-3 is a beta-lactamase found in Acinetobacter baumannii","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1405":{"model_id":"1405","model_name":"armA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"3397":{"protein_sequence":{"accession":"ADC55560.1","sequence":"MDKNDVVKKILESKKYENLDSDIVEKVVSISEKKYKLKEVENYSKKKLHQIWGSYYSAYPNWDKLLKKYNQGQLSIEDLLKIHSSTNERVATLNDFYTYVFGNIKHVSSILDFGCGFNPLALYQWNENEKIIYHAYDIDRAEIAFLSSIIGKLKTTIKYRFLNKESDVYKGTYDVVFLLKMLPVLKQQDVNILDFLQLFHTQNFVISFPIKSLSGKEKGMEENYQLWFESFTKGWIKILDSKVIGNELVYITSGFQK"},"dna_sequence":{"accession":"GU437214.1","fmin":"0","fmax":"774","strand":"+","sequence":"ATGGATAAGAATGATGTTGTTAAGAAGATACTTGAATCAAAAAAGTACGAAAACCTTGATTCAGATATTGTTGAAAAGGTTGTTTCCATTTCTGAGAAGAAATATAAATTAAAGGAAGTTGAGAATTATTCTAAAAAGAAATTGCATCAAATATGGGGGTCTTACTATTCTGCCTATCCTAATTGGGATAAATTATTAAAAAAGTACAATCAGGGGCAGTTATCAATAGAAGATTTACTAAAGATTCATTCTTCGACGAATGAAAGAGTCGCAACATTAAATGACTTTTACACTTATGTATTTGGAAATATCAAACATGTCTCATCTATTTTAGATTTTGGTTGTGGCTTCAATCCATTAGCTTTATACCAATGGAATGAAAATGAAAAAATAATATATCATGCATACGATATTGATAGAGCTGAGATAGCTTTTTTGAGTAGCATTATTGGGAAGTTAAAGACGACGATAAAGTATAGGTTTTTGAATAAAGAGAGTGATGTCTACAAAGGTACTTATGATGTAGTATTCCTTTTAAAGATGCTTCCTGTGCTAAAACAGCAAGATGTAAATATCTTGGATTTCCTACAGCTTTTTCATACTCAAAACTTTGTAATATCTTTTCCAATAAAGTCTTTATCTGGAAAGGAGAAGGGAATGGAAGAGAATTACCAGCTATGGTTTGAATCTTTTACAAAAGGTTGGATAAAAATCCTTGATTCGAAGGTTATAGGGAATGAGTTAGTATATATTACTAGTGGATTTCAGAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3000858","ARO_id":"37238","ARO_name":"armA","ARO_description":"ArmA is a 16S rRNA methyltransferase that targets mature or nearly mature 30S subunits. It transfers a methyl group from S-adenosyl-L-methionine to N7-G1405 of the 16S rRNA, an aminoglycoside binding site.","ARO_category":{"41435":{"category_aro_accession":"3004271","category_aro_cvterm_id":"41435","category_aro_name":"16S rRNA methyltransferase (G1405)","category_aro_description":"Methyltransferases that methylate the G1405 position of 16S rRNA, which is part of an aminoglycoside binding site.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1406":{"model_id":"1406","model_name":"OXA-121","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1290":{"protein_sequence":{"accession":"AGU69248.1","sequence":"MNIKALLLITNAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKTTTTEVFKWDGQKRLCPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KF057027","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCCCTCTTACTTATAACAAACGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTCTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGACAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATGCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCATTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001443","ARO_id":"37843","ARO_name":"OXA-121","ARO_description":"OXA-121 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1407":{"model_id":"1407","model_name":"CMY-62","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1777":{"protein_sequence":{"accession":"AEM97674.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFSALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"JF460796","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTAGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002075","ARO_id":"38475","ARO_name":"CMY-62","ARO_description":"CMY-62 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1408":{"model_id":"1408","model_name":"TEM-124","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1398":{"protein_sequence":{"accession":"AAQ93491.1","sequence":"MSIKHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTTPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIALGPDGKPSRIVVIYTTGSQATMDEANRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AY327540","fmin":"0","fmax":"858","strand":"+","sequence":"ATGAGTATTAAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAAGCAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36917","NCBI_taxonomy_name":"Morganella morganii","NCBI_taxonomy_id":"582"}}}},"ARO_accession":"3000986","ARO_id":"37366","ARO_name":"TEM-124","ARO_description":"TEM-124 is an extended-spectrum beta-lactamase found in Morganella morganii.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1409":{"model_id":"1409","model_name":"CMY-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1548":{"protein_sequence":{"accession":"CAB36902.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYALGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"AJ011293","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTTGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002017","ARO_id":"38417","ARO_name":"CMY-6","ARO_description":"CMY-6 is a beta-lactamase found in Escherichia coli","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1410":{"model_id":"1410","model_name":"OXA-19","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1681":{"protein_sequence":{"accession":"AAD02245.1","sequence":"MKTFAAYVITACLSSTALASSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNNLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLSLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEDQLRISAVNQVEFLESLFLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKGTEVYFFAFNMDIDNENKLPLRKSIPTKIMASEGIIGG"},"dna_sequence":{"accession":"AF043381","fmin":"943","fmax":"1744","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTACTGCGTGTCTTTCAAGTACGGCATTAGCTAGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTTTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATAACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAACAATGGGAAAGAGACTTGAGCTTAAGAGGGGCAATACAAGTTTCAGCGGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCATATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAGGATCAGCTAAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATTTTTAAATAAATTGTCAGCATCAAAAGAAAATCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCTGCGCCTGAATATCTTGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGTTGGGTTGAGAAGGGAACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAATAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGCAAGTGAGGGCATCATTGGTGGCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001414","ARO_id":"37814","ARO_name":"OXA-19","ARO_description":"OXA-19 is a beta-lactamase found in P. aeruginosa.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1411":{"model_id":"1411","model_name":"OXA-62","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1537":{"protein_sequence":{"accession":"AAR32134.1","sequence":"MNTIISRRWRAGLWRRLVGAVVLPATLAATPAAYAADVPKAALGRITERADWGKLFAAEGVKGTIVVLDARTQTYQAYDAARAEKRMSPASTYKIFNSLLALDSGALDNERAIIPWDGKPRRIKNWNAAMDLRTAFRVSCLPCYQVVSHKIGRRYAQAKLNEVGYGNRTIGGAPDAYWVDDSLQISAREQVDFVQRLARGTLPFSARSQDIVRQMSIVEATPDYVLHGKTGWFVDKKPDIGWWVGWIERDGNITSVAINIDMLSEADAPKRARIVKAVLKDLKLI"},"dna_sequence":{"accession":"AY423074","fmin":"0","fmax":"858","strand":"+","sequence":"ATGAATACGATAATCTCTCGCCGGTGGCGTGCCGGCCTGTGGCGGCGGCTGGTCGGCGCGGTCGTCTTGCCCGCAACGCTCGCCGCCACCCCTGCGGCCTATGCGGCCGACGTGCCGAAAGCCGCGTTGGGGCGCATCACCGAGCGCGCCGACTGGGGCAAGCTGTTCGCCGCGGAGGGCGTGAAGGGCACGATCGTGGTGCTCGACGCACGCACGCAAACCTATCAGGCCTACGACGCCGCACGTGCCGAGAAGCGCATGTCGCCGGCGTCGACCTACAAGATATTCAACAGCCTGCTGGCGCTCGACTCCGGGGCGCTGGACAACGAACGCGCGATCATTCCCTGGGATGGCAAGCCGCGACGCATCAAGAACTGGAACGCGGCGATGGACCTGAGGACCGCGTTTCGCGTGTCATGCCTGCCCTGCTATCAGGTCGTCTCGCACAAGATCGGGCGCCGGTACGCGCAGGCGAAGCTGAACGAGGTCGGGTATGGCAACCGCACCATTGGCGGCGCGCCGGACGCCTATTGGGTCGACGACAGTCTGCAGATTTCGGCGCGTGAGCAGGTGGACTTCGTGCAGCGTCTCGCGCGTGGCACGTTGCCGTTCTCTGCGCGCTCGCAGGACATCGTGCGCCAGATGTCGATCGTCGAAGCCACGCCGGACTATGTGCTTCACGGCAAGACGGGTTGGTTCGTCGACAAGAAGCCCGATATCGGCTGGTGGGTAGGGTGGATCGAGCGCGACGGCAACATCACCAGCGTCGCGATCAACATCGACATGCTGTCGGAGGCGGACGCCCCGAAACGGGCACGCATCGTGAAGGCGGTGCTGAAGGACCTGAAGCTGATCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36932","NCBI_taxonomy_name":"Pandoraea pnomenusa","NCBI_taxonomy_id":"93220"}}}},"ARO_accession":"3001792","ARO_id":"38192","ARO_name":"OXA-62","ARO_description":"OXA-62 is a beta-lactamase found in Pandoraea pnomenusa","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1412":{"model_id":"1412","model_name":"SHV-167","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1146":{"protein_sequence":{"accession":"BAM28879.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDADDEQLERKIHYRQQDLVDYSPVSEKYLADGMTVGELCAAAITMSDNSAANLLLATVGGPVGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIE"},"dna_sequence":{"accession":"AB733453","fmin":"3","fmax":"849","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGATGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAATACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGTAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001204","ARO_id":"37584","ARO_name":"SHV-167","ARO_description":"SHV-167 is a beta-lactamase.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1413":{"model_id":"1413","model_name":"OXA-172","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1835":{"protein_sequence":{"accession":"ADI58616.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAVPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGLDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"HM113558","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTGTTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATTGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001656","ARO_id":"38056","ARO_name":"OXA-172","ARO_description":"OXA-172 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1414":{"model_id":"1414","model_name":"QnrB15","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"297":{"protein_sequence":{"accession":"ABX72227.1","sequence":"MTPLLYKKTGTNMALALVGEKIDRNRFTGEKIESSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNANALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAIIG"},"dna_sequence":{"accession":"EU302865","fmin":"0","fmax":"681","strand":"+","sequence":"ATGACGCCATTACTGTATAAAAAAACAGGTACAAATATGGCTCTGGCACTCGTTGGCGAAAAAATTGACAGAAACCGTTTCACCGGTGAGAAAATTGAAAGTAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCGATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATGCCAATGCGCTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGCGCAAGTTTTATGAATATGATCACTACTCGCACCTGGTTTTGTAGTGCATATATCACTAACACAAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAGCTGTGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTGACTTAGATATTCGGGGCGTTGATTTACAAGGCGTTAAGCTGGACAACTACCAGGCGTCGTTGCTCATGGAGCGGCTTGGCATCGCGATTATTGGCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002730","ARO_id":"39164","ARO_name":"QnrB15","ARO_description":"QnrB15 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1415":{"model_id":"1415","model_name":"AAC(2')-Id","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"228":{"protein_sequence":{"accession":"AAB41701.1","sequence":"MLTQHVSEARTRGAIHTARLIHTSDLDQETRDGARRMVIEAFRDPSGDSDFTDDFTDDDWDHALGGMHALISHHGALIAHGAVVQRRLMYRGPDGRGHALRCGYVEAVAVREDRRGDGLGTAVLDALEQVIRGAYQIGALSASDIARPMYIARGWLSWEGPTSVLTPTEGIVRTPEDDRSLFVLPVDLPDGLELDTAREITCDWRSGDPW"},"dna_sequence":{"accession":"U72743","fmin":"385","fmax":"1018","strand":"+","sequence":"GTGCTCACCCAGCATGTCAGTGAGGCTCGCACGCGCGGTGCGATCCACACCGCGCGTCTGATCCACACCTCCGATCTGGACCAGGAAACCCGCGACGGCGCGCGCCGCATGGTGATCGAGGCGTTCCGCGATCCGTCCGGAGACAGTGATTTCACCGACGATTTCACCGACGACGACTGGGACCACGCGCTCGGCGGCATGCACGCGCTGATCTCTCACCACGGTGCGCTCATCGCGCACGGCGCCGTCGTCCAACGTCGGTTGATGTACCGGGGACCCGACGGTAGAGGTCACGCGCTGCGCTGCGGTTACGTCGAGGCCGTCGCGGTGCGCGAGGACCGGCGGGGCGACGGTCTGGGCACCGCCGTGCTCGACGCGCTCGAGCAGGTGATCCGCGGCGCCTATCAGATCGGCGCGCTGAGCGCGTCGGACATCGCCCGGCCGATGTACATTGCCAGGGGCTGGCTGTCGTGGGAGGGTCCGACATCGGTGCTGACCCCCACCGAGGGCATCGTTCGCACCCCTGAGGACGACCGGTCGCTGTTCGTCCTGCCGGTCGATCTCCCGGACGGCCTCGAGTTGGACACCGCGCGCGAGATCACGTGCGACTGGCGCTCCGGCGACCCCTGGTGAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36769","NCBI_taxonomy_name":"Mycobacterium smegmatis str. MC2 155","NCBI_taxonomy_id":"246196"}}}},"ARO_accession":"3002526","ARO_id":"38926","ARO_name":"AAC(2')-Id","ARO_description":"AAC(2')-Id is a chromosomal-encoded aminoglycoside acetyltransferase in M. smegmatis","ARO_category":{"36480":{"category_aro_accession":"3000341","category_aro_cvterm_id":"36480","category_aro_name":"AAC(2')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 2'.","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1416":{"model_id":"1416","model_name":"OXA-89","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1139":{"protein_sequence":{"accession":"ABE03012.1","sequence":"MNIKTLLLITSAIFISACSHYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFTYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"DQ445683","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACATTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCATCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTACTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001625","ARO_id":"38025","ARO_name":"OXA-89","ARO_description":"OXA-89 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1417":{"model_id":"1417","model_name":"OXA-131","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1678":{"protein_sequence":{"accession":"ACD84989.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAVPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNQQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"EU547446","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTGTTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCAACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001652","ARO_id":"38052","ARO_name":"OXA-131","ARO_description":"OXA-131 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1418":{"model_id":"1418","model_name":"DHA-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1783":{"protein_sequence":{"accession":"ADT91161.1","sequence":"MKKSLSATLISALLAFSAPGFSAADNVAAVVDSTIKPLMAQQDIPGMAVAVSVKGKPYYFNYGFADIQAKQPVTENTLFELGSVSKTFTGVLGAVSVAKKEMALNDPAAKYQPELALPQWKGITLLDLATYTAGGLPLQVPDAVKSRADLLNFYQQWQPSRKPGDMRLYANSSIGLFGALTANAAGMPYEQLLTARILAPLGLSHTFITVPESAQSQYAYGYKNKKPVRVSPGQLDAESYGVKSTSKDMLRWAEMNMEPSRAGNADLEMAMYLAQTRYYKTAAINQGLGWEMYDWPQQKDMIINGVTNEVALQPHPVTDNQVQPYNRASWVHKTGATTGFGAYVAFIPEKQVAIVILANKNYPNTERVKAAQAILSALE"},"dna_sequence":{"accession":"HQ322612","fmin":"0","fmax":"1140","strand":"+","sequence":"ATGAAAAAATCGTTATCTGCAACACTGATTTCCGCTCTGCTGGCGTTTTCCGCCCCGGGGTTTTCTGCCGCTGATAATGTCGCGGCGGTGGTGGACAGCACCATTAAACCGCTGATGGCACAGCAGGATATTCCCGGGATGGCGGTTGCCGTCTCCGTAAAGGGTAAGCCCTATTATTTCAATTATGGTTTTGCCGATATTCAGGCAAAACAGCCGGTCACTGAAAATACACTATTTGAGCTCGGATCTGTAAGTAAAACTTTCACAGGTGTGCTGGGTGCGGTTTCTGTGGCGAAAAAAGAGATGGCGCTGAATGATCCGGCGGCAAAATACCAGCCGGAGCTGGCTCTGCCGCAGTGGAAGGGGATCACATTGCTGGATCTGGCTACCTATACCGCAGGCGGACTGCCGTTACAGGTGCCGGATGCGGTAAAAAGCCGTGCGGATCTGCTGAATTTCTATCAGCAGTGGCAGCCGTCCCGGAAACCGGGCGATATGCGTCTGTATGCAAACAGCAGTATCGGCCTGTTTGGTGCTCTGACCGCAAACGCGGCGGGGATGCCGTATGAGCAGTTGCTGACTGCACGGATCCTGGCACCGCTGGGGTTATCTCACACCTTTATTACTGTGCCGGAAAGTGCGCAAAGCCAGTATGCGTACGGTTATAAAAACAAAAAACCGGTCCGCGTGTCGCCGGGACAGCTTGATGCGGAATCTTACGGCGTGAAATCCACCTCAAAAGATATGCTGCGCTGGGCGGAAATGAATATGGAGCCGTCACGGGCCGGTAATGCGGATCTGGAAATGGCAATGTATCTCGCCCAGACCCGCTACTATAAAACCGCCGCGATTAACCAGGGGCTGGGCTGGGAAATGTATGACTGGCCGCAGCAGAAAGATATGATCATTAACGGTGTGACCAACGAGGTCGCATTGCAGCCGCATCCGGTAACAGACAACCAGGTTCAGCCGTATAACCGTGCTTCCTGGGTGCATAAAACGGGCGCAACAACTGGTTTCGGCGCCTATGTCGCCTTTATTCCGGAAAAACAGGTGGCGATTGTGATTCTGGCGAATAAAAACTACCCGAATACCGAAAGAGTCAAAGCTGCACAGGCTATTTTGAGTGCACTGGAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002135","ARO_id":"38535","ARO_name":"DHA-6","ARO_description":"DHA-6 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36207":{"category_aro_accession":"3000068","category_aro_cvterm_id":"36207","category_aro_name":"DHA beta-lactamase","category_aro_description":"DHA beta-lactamases are plasmid-mediated AmpC \u03b2-lactamases that confer resistance to cephamycins and oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1419":{"model_id":"1419","model_name":"OXA-454","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2122":{"protein_sequence":{"accession":"BAR45714.1","sequence":"MKTFAAYVIIACLSSTALAGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIENEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLKGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG"},"dna_sequence":{"accession":"LC037981","fmin":"0","fmax":"801","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTATCGCGTGTCTTTCGAGTACGGCATTAGCTGGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTCTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATGACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAGAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAGCAATGGGAAAGAGACTTGACCTTAAGAGGGGCAATACAAGTTTCAGCTGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCCTATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGAAAGGCCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATATTTAAATAAATTGTCAGCATCTAAAGAAAACCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCGGCACCTGAATATCTAGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGGTGGGTTGAGAAGGAGACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAGTAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGAAAGTGAGGGCATCATTGGTGGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40276","NCBI_taxonomy_name":"Delftia acidovorans","NCBI_taxonomy_id":"80866"}}}},"ARO_accession":"3003610","ARO_id":"40220","ARO_name":"OXA-454","ARO_description":"Assigned by Lahey's list of beta-lactamases, no accessions or other information available","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1420":{"model_id":"1420","model_name":"aadA5","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"471":{"protein_sequence":{"accession":"AAF17880.1","sequence":"MGEFFPAQVFKQLSHARAVIERHLAATLDTIHLFGSAIDGGLKPDSDIDLLVTVSAAPNDSLRQALMLDLLKVSSPPGDGGTWRPLELTVVARSEVVPWRYPARRELQFGEWLRHDILSGTFEPAVLDHDLAILLTKARQHSLALLGPSAATFFEPVPKEHFSKALFDTIAQWNAESDWKGDERNVVLALARIWYSASTGLIAPKDVAAAWVSERLPAEHRPLICKARAAYLGSEDDDLAMRVEETAAFVRYAKATIERILR"},"dna_sequence":{"accession":"AF137361","fmin":"63","fmax":"852","strand":"+","sequence":"ATGGGTGAATTTTTCCCTGCACAAGTTTTCAAGCAGCTGTCCCACGCTCGCGCGGTGATCGAGCGCCATCTGGCTGCGACACTGGACACAATCCACCTGTTCGGATCTGCGATCGATGGAGGGCTGAAGCCGGACAGCGACATAGACTTGCTCGTGACCGTCAGCGCCGCACCTAACGATTCGCTCCGGCAGGCGCTAATGCTCGATTTGCTGAAAGTCTCATCACCGCCAGGCGATGGCGGAACATGGCGACCGCTGGAGCTAACTGTTGTCGCTCGAAGCGAAGTAGTGCCTTGGCGCTATCCGGCGCGGCGTGAGCTTCAGTTCGGTGAGTGGCTCCGCCACGACATCCTTTCCGGAACGTTCGAGCCTGCCGTTCTGGATCACGATCTTGCGATTTTGCTGACCAAGGCGAGGCAACACAGCCTTGCGCTTCTAGGCCCATCCGCAGCCACGTTTTTCGAGCCGGTGCCGAAGGAGCATTTCTCCAAGGCGCTTTTCGACACTATTGCCCAGTGGAATGCAGAGTCGGATTGGAAGGGTGACGAGCGGAACGTCGTTCTTGCTCTTGCTCGCATTTGGTACAGCGCTTCAACTGGTCTCATTGCTCCTAAGGACGTTGCTGCCGCATGGGTATCGGAGCGTTTGCCTGCCGAGCATCGGCCCCTCATCTGCAAGGCACGCGCGGCGTACCTGGGTAGCGAGGACGACGACCTAGCAATGCGCGTCGAAGAGACGGCCGCGTTCGTTCGATATGCCAAAGCAACGATTGAGAGAATCTTGCGTTGAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002605","ARO_id":"39005","ARO_name":"aadA5","ARO_description":"aadA5 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids, transposons and integrons in E. coli, K. pneumoniae, Kluyvera georgiana, P. aeruginosa and E. cloacae","ARO_category":{"41439":{"category_aro_accession":"3004275","category_aro_cvterm_id":"41439","category_aro_name":"ANT(3'')","category_aro_description":"Nucleotidylylation of streptomycin at the hydroxyl group at position 3''","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1421":{"model_id":"1421","model_name":"TEM-85","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1405":{"protein_sequence":{"accession":"CAC43229.1","sequence":"MSIQHFRVALIPFFAAFCFPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGKRGSRGIIAALGPDGKPSRIVVIYMTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AJ277414","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCTTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTAAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACATGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000952","ARO_id":"37332","ARO_name":"TEM-85","ARO_description":"TEM-85 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1422":{"model_id":"1422","model_name":"ACC-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1910":{"protein_sequence":{"accession":"AAF86697.1","sequence":"MRKKMQNTLKMLSVITCLALTAQGAMASEMDQAKIKDTVDSLIQPLMQKNNIPGMSVAVTLNGKNYIYNYGLASKQPQQPVTDNTLFEVGSLSKTFAATLASYAQVSGKLSLDKSISHYVPELRGSSFDHISVLNAGTHTTGLALFMPEEVKNTDQLMAYLKAWKPADPAGTHRVYSNIGTGLLGMIAAQSMGMTYEDAIEKTLLPKLGMTHTYLNVPADQAENYAWGYNKKNEPIHVNMEVLGNEAYGIRTNASDLIRYVQANMGQLKLDGNSTLQKALTDTHIGYFKSGKITQDLMWEQLPYPVSLPDLLTGNDMAMTKSVATPIVPPLPPQENVWINKTGSTNGFGAYIAFVPAKKMGIVMLANKNYSIDQRVT"},"dna_sequence":{"accession":"AF180958","fmin":"0","fmax":"1131","strand":"+","sequence":"ATGCGTAAAAAAATGCAGAACACCTTGAAGATGTTATCCGTGATTACCTGTCTGGCTTTAACGGCTCAGGGTGCCATGGCGTCAGAAATGGATCAGGCCAAAATTAAAGACACCGTTGATAGCCTGATCCAGCCGCTGATGCAGAAGAATAATATTCCGGGCATGTCGGTGGCAGTTACGCTGAACGGTAAAAATTATATTTATAACTATGGCTTAGCCTCCAAACAGCCCCAGCAGCCCGTAACGGACAACACGCTATTTGAAGTTGGCTCGCTGAGCAAAACCTTTGCAGCGACGCTGGCGTCTTATGCACAGGTCAGCGGCAAGTTATCGCTGGATAAAAGCATTAGCCATTATGTTCCAGAACTGCGCGGCAGCAGCTTCGATCACATTAGCGTGCTGAATGCGGGAACGCATACCACAGGTTTAGCGCTGTTCATGCCTGAAGAAGTGAAAAACACCGATCAGCTGATGGCTTATCTGAAAGCGTGGAAACCCGCCGATCCTGCGGGGACTCACCGTGTTTATTCCAATATTGGTACCGGCTTGTTGGGCATGATTGCCGCGCAAAGCATGGGAATGACTTACGAAGATGCGATTGAGAAAACGCTCCTTCCGAAGTTGGGCATGACGCACACCTATCTTAATGTTCCAGCAGACCAAGCGGAAAATTATGCTTGGGGCTATAACAAAAAGAATGAGCCGATCCACGTTAATATGGAAGTGTTGGGCAACGAAGCCTATGGCATTAGAACCAATGCGAGTGACCTGATTCGCTATGTGCAAGCCAATATGGGGCAGCTAAAACTTGATGGAAATTCGACGCTGCAAAAAGCGCTCACCGACACGCATATCGGTTACTTCAAGTCAGGCAAAATCACTCAGGATCTGATGTGGGAACAGCTGCCATATCCGGTATCTCTGCCGGATCTGCTCACTGGCAACGATATGGCGATGACAAAAAGCGTTGCTACGCCGATTGTTCCACCGCTGCCACCACAGGAAAATGTATGGATTAACAAAACCGGTTCCACCAATGGTTTTGGTGCCTACATCGCATTTGTTCCGGCTAAAAAGATGGGTATCGTGATGCTGGCGAACAAGAACTACTCTATCGATCAGCGTGTAACG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36784","NCBI_taxonomy_name":"Hafnia alvei","NCBI_taxonomy_id":"569"}}}},"ARO_accession":"3001817","ARO_id":"38217","ARO_name":"ACC-3","ARO_description":"ACC-3 is a beta-lactamase found in Hafnia alvei","ARO_category":{"36212":{"category_aro_accession":"3000073","category_aro_cvterm_id":"36212","category_aro_name":"ACC beta-lactamase","category_aro_description":"ACC beta-lactamases or Ambler class C beta-lactamases are AmpC beta-lactamases. They possess an interesting resistance phenotype due to their low activity against cephamycins.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1423":{"model_id":"1423","model_name":"TEM-15","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"845":{"protein_sequence":{"accession":"CAO98721.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AM849805","fmin":"262","fmax":"1123","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36927","NCBI_taxonomy_name":"Haemophilus parainfluenzae","NCBI_taxonomy_id":"729"}}}},"ARO_accession":"3000886","ARO_id":"37266","ARO_name":"TEM-15","ARO_description":"TEM-15 is an extended-spectrum beta-lactamase that has been found in Haemophilus parainfluenzae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1424":{"model_id":"1424","model_name":"OXY-2-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1384":{"protein_sequence":{"accession":"CAB42614.1","sequence":"MIKSSWRKIAMLAAVPLLLASGALWASTDAIHQKLTDLEKRSGGRLGVALINTADNSQILYRGDERFAMCSTSKVMAAAAVLKQSESNKEVVNKRLEINAADLVVWSPITEKHLQSGMTLAELSAATLQYSDNTAMNLIIGYLGGPEKVTAFARSIGDATFRLDRTEPTLNTAIPGDERDTSTPLAMAESLRKLTLGDALGEQQRAQLVTWLKGNTTGGQSIRAGLPESWVVGDKTGAGDYGTTNDIAVIWPEDHAPLVLVTYFTQPQQDAKNRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"Y17714","fmin":"146","fmax":"1016","strand":"+","sequence":"ATGATAAAAAGTTCGTGGCGTAAAATTGCAATGCTAGCCGCCGTTCCGCTGCTGCTGGCGAGCGGCGCACTGTGGGCCAGTACCGATGCTATCCATCAGAAGCTGACAGATCTCGAGAAGCGTTCAGGCGGCAGGTTGGGCGTGGCGCTAATCAACACGGCAGATAATTCTCAAATCTTATATCGCGGCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCCGCCGCCGCGGTATTAAAACAGAGCGAAAGCAATAAAGAGGTGGTAAATAAAAGGCTGGAGATTAACGCAGCCGATTTGGTGGTCTGGAGTCCGATTACCGAAAAACATCTCCAGAGCGGAATGACGCTGGCTGAGCTAAGCGCGGCGACGCTGCAATATAGCGACAATACGGCGATGAATCTGATCATCGGCTACCTTGGCGGGCCGGAAAAAGTCACCGCCTTCGCCCGCAGTATCGGCGATGCCACCTTTCGTCTCGATCGTACGGAGCCCACGCTGAATACCGCCATCCCGGGCGATGAGCGTGATACCAGCACGCCGCTGGCGATGGCTGAAAGCCTACGCAAGCTGACGCTTGGCGATGCGCTGGGCGAACAGCAACGCGCCCAGTTAGTCACCTGGCTGAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCGGGCCTGCCTGAAAGCTGGGTGGTCGGCGATAAAACCGGCGCCGGAGATTACGGCACCACCAATGATATTGCGGTTATCTGGCCGGAAGATCACGCTCCGCTGGTATTAGTCACCTACTTTACCCAGCCGCAGCAGGATGCGAAAAACCGCAAAGAAGTGTTAGCCGCAGCGGCAAAAATCGTGACCGAAGGGCTTTAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002399","ARO_id":"38799","ARO_name":"OXY-2-4","ARO_description":"OXY-2-4 is a beta-lactamase found in Klebsiella oxytoca","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1425":{"model_id":"1425","model_name":"RbpA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"356":{"protein_sequence":{"accession":"ADV91011.1","sequence":"MADRVLRGSRLGAVSYETDRNHDLAPRQVARYRTDNGEEFDVPFADDAEIPGTWLCRNGLEGTLIEGDVPEPKKVKPPRTHWDMLLERRSVEELEELLKERLDLIKAKRRGTGS"},"dna_sequence":{"accession":"HQ203032","fmin":"0","fmax":"345","strand":"+","sequence":"ATGGCTGATCGTGTCCTGCGGGGCAGTCGCCTCGGAGCCGTGAGCTACGAGACCGACCGCAACCATGACCTGGCGCCGCGTCAGGTCGCCCGCTACCGCACGGATAACGGCGAGGAGTTCGACGTACCTTTCGCCGACGACGCCGAGATCCCCGGTACGTGGCTCTGCCGCAACGGTCTGGAGGGCACCCTCATCGAGGGTGACGTGCCGGAGCCCAAGAAGGTCAAGCCGCCGCGTACGCACTGGGACATGCTGTTGGAGCGCCGGTCCGTCGAGGAGCTCGAAGAGCTGCTCAAGGAGCGTCTCGACCTGATCAAGGCCAAGCGGCGCGGAACCGGAAGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36769","NCBI_taxonomy_name":"Mycobacterium smegmatis str. MC2 155","NCBI_taxonomy_id":"246196"}}}},"ARO_accession":"3000245","ARO_id":"36384","ARO_name":"RbpA","ARO_description":"RNA-polymerase binding protein which confers resistance to rifampin.","ARO_category":{"41407":{"category_aro_accession":"3004243","category_aro_cvterm_id":"41407","category_aro_name":"RbpA bacterial RNA polymerase-binding protein","category_aro_description":"RbpA is a family of bacterial RNA polymerase-binding proteins, which acts as a transcription factor and binds to the sigma subunit of RNA polymerase.","category_aro_class_name":"AMR Gene Family"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36656":{"category_aro_accession":"3000517","category_aro_cvterm_id":"36656","category_aro_name":"rifaximin","category_aro_description":"Rifaximin is a semi-synthetic rifamycin used to treat traveller's diarrhea. Rifaximin inhibits RNA synthesis by binding to the beta subunit of bacterial RNA polymerase.","category_aro_class_name":"Antibiotic"},"36669":{"category_aro_accession":"3000530","category_aro_cvterm_id":"36669","category_aro_name":"rifabutin","category_aro_description":"Rifabutin is a semisynthetic rifamycin used in tuberculosis therapy. It inhibits DNA-dependent RNA synthesis.","category_aro_class_name":"Antibiotic"},"36673":{"category_aro_accession":"3000534","category_aro_cvterm_id":"36673","category_aro_name":"rifapentine","category_aro_description":"Rifapentine is a semisynthetic rifamycin that inhibits DNA-dependent RNA synthesis. It is often used in the treatment of tuberculosis and leprosy.","category_aro_class_name":"Antibiotic"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1426":{"model_id":"1426","model_name":"IMP-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1357":{"protein_sequence":{"accession":"AAK12087.1","sequence":"MKKLSVFFMFLFCSIAASGEALPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNTDAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKDGKVQAKNSFSGASYWLVKKKIEIFYPGPGHTPDNVVVWLPEHRVLFGGCFVKPYGLGNLGDANLEAWPKSAKLLVSKYGKAKLVVPSHSEVGDASLLKRTLEQAVKGLNESKKLSKPSN"},"dna_sequence":{"accession":"AF318077","fmin":"1147","fmax":"1888","strand":"+","sequence":"ATGAAAAAGTTATCAGTATTCTTTATGTTTTTGTTTTGTAGCATTGCTGCCTCAGGAGAGGCTTTGCCAGATTTAAAAATTGAGAAGCTTGACGAAGGCGTTTATGTTCATACTTCGTTTGAGGAAGTTAACGGCTGGGGCGTGGTTCCTAAACACGGCTTGGTGGTTCTTGTAAATACTGACGCTTATTTGATTGACACTCCATTTACAGCTAAAGATACTGAAAAGTTAGTTACTTGGTTTGTAGAGCGCGGCTATAAAATAAAAGGCAGTATCTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCAATCTATTCCAACATATGCATCTGAATTAACAAATGAACTTCTTAAAAAAGACGGTAAGGTACAAGCTAAAAATTCATTTAGCGGAGCCAGCTATTGGTTAGTTAAGAAAAAGATTGAAATTTTTTATCCTGGCCCAGGGCACACTCCAGATAACGTAGTGGTTTGGCTACCTGAACATAGAGTTTTGTTTGGTGGTTGTTTTGTTAAACCGTATGGTCTAGGTAATTTGGGTGACGCAAATTTAGAAGCTTGGCCAAAGTCTGCCAAATTATTAGTGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAAGTCACAGTGAAGTTGGAGATGCATCACTCTTGAAACGTACATTAGAACAGGCTGTTAAAGGATTAAACGAAAGTAAAAAGCTATCAAAACCAAGTAACTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002198","ARO_id":"38598","ARO_name":"IMP-7","ARO_description":"IMP-7 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1427":{"model_id":"1427","model_name":"acrD","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1900"}},"model_sequences":{"sequence":{"664":{"protein_sequence":{"accession":"YP_490697.1","sequence":"MANFFIDRPIFAWVLAILLCLTGTLAIFSLPVEQYPDLAPPNVRVTANYPGASAQTLENTVTQVIEQNMTGLDNLMYMSSQSSGTGQASVTLSFKAGTDPDEAVQQVQNQLQSAMRKLPQAVQNQGVTVRKTGDTNILTIAFVSTDGSMDKQDIADYVASNIQDPLSRVNGVGDIDAYGSQYSMRIWLDPAKLNSFQMTAKDVTDAIESQNAQIAVGQLGGTPSVDKQALNATINAQSLLQTPEQFRDITLRVNQDGSEVRLGDVATVEMGAEKYDYLSRFNGKPASGLGVKLASGANEMATAELVLNRLDELAQYFPHGLEYKVAYETTSFVKASIEDVVKTLLEAIALVFLVMYLFLQNFRATLIPTIAVPVVLMGTFSVLYAFGYSVNTLTMFAMVLAIGLLVDDAIVVVENVERIMSEEGLTPREATRKSMGQIQGALVGIAMVLSAVFVPMAFFGGTTGAIYRQFSITIVAAMVLSVLVAMILTPALCATLLKPLKKGEHHGQKGFFAWFNQMFNRNAERYEKGVAKILHRSLRWIVIYVLLLGGMVFLFLRLPTSFLPLEDRGMFTTSVQLPSGSTQQQTLKVVEQIEKYYFTHEKDNIMSVFATVGSGPGGNGQNVARMFIRLKDWSERDSKTGTSFAIIERATKAFNQIKEARVIASSPPAISGLGSSAGFDMELQDHAGAGHDALMAARNQLLALAAENPELTRVRHNGLDDSPQLQIDIDQRKAQALGVAIDDINDTLQTAWGSSYVNDFMDRGRVKKVYVQAAAPYRMLPDDINLWYVRNKDGGMVPFSAFATSRWETGSPRLERYNGYSAVEIVGEAAPGVSTGTAMDIMESLVKQLPNGFGLEWTAMSYQERLSGAQAPALYAISLLVVFLCLAALYESWSVPFSVMLVVPLGVIGALLATWMRGLENDVYFQVGLLTVIGLSAKNAILIVEFANEMNQKGHDLFEATLHACRQRLRPILMTSLAFIFGVLPMATSTGAGSGGQHAVGTGVMGGMISATILAIYFVPLFFVLVRRRFPLKPRPE"},"dna_sequence":{"accession":"NC_007779","fmin":"2586250","fmax":"2589364","strand":"+","sequence":"ATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCGCCACCGAATGTGCGAGTGACCGCTAACTATCCCGGCGCATCGGCCCAGACGCTGGAAAACACCGTGACCCAGGTTATCGAGCAAAATATGACCGGCCTCGATAATCTCATGTATATGTCATCTCAGAGCAGTGGCACCGGTCAGGCATCTGTCACTTTAAGTTTTAAAGCAGGCACCGATCCGGACGAAGCCGTGCAGCAAGTACAAAACCAGCTGCAATCAGCCATGCGAAAGTTACCGCAGGCGGTGCAAAATCAGGGCGTGACGGTGCGTAAAACCGGCGATACCAACATTCTGACCATTGCCTTCGTCTCTACCGATGGTTCGATGGATAAACAGGATATTGCTGATTATGTTGCCAGTAATATTCAGGACCCGTTAAGCCGCGTGAATGGCGTCGGGGATATCGATGCCTATGGTTCGCAATATTCCATGCGTATCTGGCTGGACCCGGCGAAACTCAACAGTTTCCAGATGACGGCTAAAGATGTCACTGATGCCATTGAGTCACAGAACGCGCAGATTGCGGTTGGGCAACTTGGTGGTACACCTTCCGTCGATAAGCAGGCGCTCAACGCCACCATTAACGCCCAGTCACTGCTGCAAACACCAGAACAGTTCCGCGATATCACCTTGCGGGTCAATCAGGACGGCTCAGAGGTAAGGCTGGGCGATGTCGCCACCGTCGAAATGGGGGCGGAGAAATACGATTATCTTAGCCGCTTCAATGGTAAGCCAGCCTCCGGGCTGGGGGTAAAACTGGCCTCCGGCGCTAACGAAATGGCGACAGCGGAGCTGGTGCTCAATCGTCTCGACGAGCTGGCGCAGTATTTCCCGCATGGACTGGAATACAAGGTGGCGTATGAAACCACCTCGTTTGTTAAAGCCTCCATTGAAGACGTGGTGAAAACGCTGCTGGAAGCTATCGCTCTGGTTTTCCTCGTTATGTATCTGTTCCTGCAAAACTTCCGCGCCACGCTGATACCCACTATCGCCGTGCCGGTGGTGTTGATGGGAACCTTCTCCGTACTTTACGCCTTCGGTTACAGCGTCAACACCTTAACCATGTTCGCGATGGTGCTGGCGATCGGTCTGCTGGTGGATGACGCCATCGTGGTGGTGGAAAACGTCGAACGTATTATGAGTGAGGAAGGACTCACTCCTCGCGAAGCCACACGTAAATCGATGGGGCAGATCCAGGGGGCACTGGTCGGGATTGCGATGGTTCTTTCGGCGGTATTTGTACCAATGGCCTTCTTCGGCGGCACCACCGGTGCCATCTATCGCCAGTTCTCTATTACCATTGTTGCGGCGATGGTGCTGTCAGTACTGGTAGCGATGATCCTCACTCCGGCTCTGTGTGCCACACTACTTAAGCCACTGAAAAAAGGTGAGCATCATGGGCAAAAAGGCTTTTTTGCCTGGTTTAACCAGATGTTTAACCGCAACGCCGAACGCTACGAAAAAGGGGTGGCGAAAATTCTCCACCGTAGCCTGCGCTGGATTGTGATTTATGTCCTGCTGCTTGGCGGCATGGTGTTCCTGTTCCTGCGTTTGCCGACGTCGTTCTTACCGCTGGAAGACCGTGGCATGTTTACTACCTCGGTACAGTTGCCCAGCGGTTCAACGCAACAACAGACCCTGAAAGTCGTTGAGCAAATCGAGAAATACTACTTCACCCATGAAAAAGACAACATCATGTCGGTGTTTGCCACCGTTGGTTCTGGCCCTGGGGGTAACGGGCAAAACGTGGCGCGAATGTTTATCCGCCTGAAAGACTGGAGCGAACGCGACAGTAAGACCGGCACCTCGTTTGCCATTATCGAGCGTGCAACGAAGGCGTTTAACCAAATTAAAGAAGCTCGCGTTATCGCCAGCAGCCCGCCAGCAATTAGCGGTCTTGGTAGTTCTGCAGGTTTTGATATGGAGTTGCAGGACCACGCTGGAGCGGGTCACGATGCGCTGATGGCAGCACGTAATCAGTTGCTGGCGCTGGCGGCGGAAAACCCGGAGCTAACCCGTGTGCGCCATAACGGCCTCGACGACAGTCCGCAGTTGCAGATTGATATCGACCAGCGTAAAGCTCAGGCGCTGGGCGTTGCTATCGACGATATTAACGACACACTGCAAACCGCCTGGGGTTCGAGCTATGTGAATGACTTTATGGATCGCGGTCGCGTGAAGAAAGTCTATGTGCAGGCAGCTGCGCCGTATCGCATGCTGCCAGATGACATCAATCTCTGGTATGTCCGAAATAAAGATGGCGGCATGGTGCCCTTCTCTGCTTTCGCGACCTCACGCTGGGAAACAGGCTCGCCGCGTCTGGAACGCTATAACGGTTATTCTGCGGTTGAGATTGTTGGGGAAGCCGCACCGGGGGTCAGTACCGGTACGGCGATGGATATTATGGAATCGTTAGTGAAGCAGCTGCCAAACGGCTTTGGTCTGGAGTGGACGGCGATGTCGTATCAGGAGCGGCTTTCCGGCGCGCAGGCTCCGGCGCTGTACGCCATTTCCTTGCTGGTGGTATTCCTGTGTCTGGCTGCGTTGTATGAAAGCTGGTCGGTGCCGTTCTCGGTAATGCTGGTCGTGCCGCTGGGGGTAATCGGCGCGCTGCTGGCAACCTGGATGCGCGGGCTGGAAAACGACGTTTACTTCCAGGTGGGCCTGTTAACGGTCATTGGTTTATCGGCGAAAAACGCCATCCTGATCGTCGAGTTTGCTAACGAGATGAACCAAAAAGGCCACGACCTGTTTGAAGCGACGCTCCACGCCTGCCGTCAGCGTTTACGCCCGATTCTGATGACCTCGCTGGCATTTATCTTCGGCGTATTGCCAATGGCAACCAGCACGGGTGCCGGTTCCGGTGGTCAGCATGCGGTGGGTACTGGCGTAATGGGCGGGATGATTTCGGCCACTATTCTGGCTATTTACTTCGTGCCGCTGTTCTTTGTGCTGGTGCGCCGCCGCTTCCCGCTGAAGCCGCGCCCGGAATAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36839","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. W3110","NCBI_taxonomy_id":"316407"}}}},"ARO_accession":"3000491","ARO_id":"36630","ARO_name":"acrD","ARO_description":"AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole, and is regulated by baeRS and cpxAR.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1428":{"model_id":"1428","model_name":"cphA2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"3364":{"protein_sequence":{"accession":"AAB03413.1","sequence":"MMKGWMKCGLAGAVVLMASFWGGSVRAAGMSLTQVSGPVYVVEDNYYVQENSMVYFGAKGVTVVGATWTPDTARELHKLIKRVSRQPVLEVINTNYHTDRAGGNAYWKSIGAKVVSTRQTRDLMKSDWAEIVAFTRKGLPEYPDLPLVLPNVVHEGDFTLQEGKLRAFYAGPAHTPDGIFVYFPDQQVLYGNCILKEKLGNLSFADVKAYPRTLERLKAMKLPIKTVVGGHDSPLHGPELIDHYEALIKAAPQS"},"dna_sequence":{"accession":"U60294","fmin":"0","fmax":"765","strand":"+","sequence":"ATGATGAAAGGTTGGATGAAGTGTGGATTGGCCGGGGCCGTGGTGCTGATGGCGAGTTTCTGGGGTGGCAGCGTGCGGGCGGCGGGGATGTCGCTGACGCAGGTGAGCGGCCCTGTCTATGTGGTAGAGGACAATTACTACGTGCAGGAAAACTCCATGGTCTATTTCGGGGCCAAGGGAGTGACTGTTGTAGGGGCGACCTGGACGCCGGATACCGCCCGCGAGCTGCACAAGCTGATCAAACGAGTCAGCCGCCAGCCGGTGCTGGAGGTGATCAACACCAACTACCACACCGACCGGGCGGGCGGTAACGCCTACTGGAAGTCCATCGGGGCCAAGGTGGTATCGACCCGCCAGACCCGGGATCTGATGAAGAGCGACTGGGCCGAGATTGTTGCCTTTACCCGCAAGGGGTTGCCGGAGTACCCGGATCTGCCCCTGGTGCTGCCCAACGTGGTGCACGAGGGCGACTTCACGCTGCAAGAGGGCAAGCTGCGCGCCTTCTATGCGGGCCCGGCCCACACGCCGGATGGCATCTTTGTCTACTTCCCCGACCAGCAGGTGCTCTATGGCAACTGCATCCTCAAGGAGAAGCTGGGCAACCTGAGCTTTGCCGATGTGAAGGCCTATCCGCGCACGCTTGAGCGGCTCAAGGCGATGAAGCTGCCAATCAAGACGGTGGTGGGCGGTCACGACTCGCCGCTGCATGGGCCTGAGCTTATCGATCACTACGAGGCGCTGATCAAGGCCGCACCCCAGTCATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36810","NCBI_taxonomy_name":"Aeromonas hydrophila","NCBI_taxonomy_id":"644"}}}},"ARO_accession":"3003099","ARO_id":"39665","ARO_name":"cphA2","ARO_description":"CphA2 is an Ambler Class B MBL; subclass B2 originally isolated from Aeromonas hydrophila. This enzyme has specific activity against carbapenems and is active as a mono-zinc protein","ARO_category":{"36720":{"category_aro_accession":"3000581","category_aro_cvterm_id":"36720","category_aro_name":"CphA beta-lactamase","category_aro_description":"CphA is an Ambler Class B MBL; subclass B2 originally isolated from Aeromonas hydrophilia.  This enzyme has specific activity against carbapenems and is active as a mono-zinc protein.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1429":{"model_id":"1429","model_name":"SHV-60","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1948":{"protein_sequence":{"accession":"BAF92780.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMTATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AB302939","fmin":"8","fmax":"869","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGACCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001115","ARO_id":"37495","ARO_name":"SHV-60","ARO_description":"SHV-60 is a broad-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1430":{"model_id":"1430","model_name":"SHV-125","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1942":{"protein_sequence":{"accession":"ACV32635.1","sequence":"MRYIRLNIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQ"},"dna_sequence":{"accession":"GQ390807","fmin":"0","fmax":"813","strand":"+","sequence":"ATGCGTTATATTCGCCTGAATATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001172","ARO_id":"37552","ARO_name":"SHV-125","ARO_description":"SHV-125 is a beta-lactamase that has been found in clinical isolates.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1431":{"model_id":"1431","model_name":"GES-15","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"771":{"protein_sequence":{"accession":"ACZ98826.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKESEMSDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"GU208678","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGTCGGAGATGAGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002344","ARO_id":"38744","ARO_name":"GES-15","ARO_description":"GES-15 is a beta-lactamase. From the Lahey list of GES beta-lactamases.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1433":{"model_id":"1433","model_name":"CMY-18","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1974":{"protein_sequence":{"accession":"AAU95778.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGNGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"AY743434","fmin":"46","fmax":"1198","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002029","ARO_id":"38429","ARO_name":"CMY-18","ARO_description":"CMY-18 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1434":{"model_id":"1434","model_name":"Erm(35)","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"4237":{"protein_sequence":{"accession":"AAK07612.2","sequence":"MTKKKLPVRFTGQHFTIDKVLIKDAIKESNINQHDTVLDIGAGKGFLTVHLLKNVDKVIAIENDVALSQHLRKKFIHAQNVQVVSCDYRNFVVPKVPFKVVSNIPFGITSDIFSSLMFENVEYFLCGSIILQSEPAKKLFSSKVYNPLTVLYHTYYDLKFLYEINPESFLPPPTVKSALLRIERKQISLDIGLKVKYLNFVSYMLQKPDLTVKTAMKSIFRKKQVRSISEKFGVDLNSKIVCLTPNQWKNCFLEMLEVVPEKFHPS"},"dna_sequence":{"accession":"AF319779.2","fmin":"32","fmax":"833","strand":"+","sequence":"ATGACAAAAAAGAAATTGCCCGTTCGTTTTACGGGTCAGCACTTTACTATTGACAAAGTGCTTATTAAAGATGCAATAAAAGAATCAAATATAAATCAACACGATACAGTTTTAGATATTGGAGCTGGTAAGGGTTTTCTAACTGTTCATCTCTTAAAAAATGTCGATAAAGTTATTGCCATTGAAAACGATGTTGCATTAAGTCAACATTTGCGCAAAAAATTCATTCACGCTCAAAACGTTCAAGTGGTTAGTTGTGATTATAGAAATTTTGTGGTTCCGAAAGTTCCATTTAAAGTAGTTTCAAATATTCCTTTTGGTATTACATCTGATATTTTTAGTAGTCTGATGTTTGAAAATGTCGAATATTTTCTATGCGGTTCAATTATCCTTCAGTCAGAACCGGCAAAAAAATTGTTTTCAAGTAAGGTTTATAACCCATTGACAGTACTTTATCATACCTATTATGATTTGAAATTCCTGTATGAGATAAATCCTGAAAGTTTTTTGCCACCACCAACTGTCAAATCAGCACTTTTGAGAATTGAAAGAAAACAGATTTCATTAGATATTGGGCTTAAGGTTAAGTACTTAAATTTTGTTTCGTATATGTTACAAAAACCTGATTTAACAGTCAAAACAGCTATGAAGTCTATTTTTAGAAAAAAACAAGTTAGGTCAATTTCAGAAAAATTTGGAGTTGACCTTAACTCCAAAATTGTCTGTTTGACTCCAAATCAATGGAAGAATTGTTTTTTAGAAATGCTCGAAGTTGTTCCTGAAAAGTTTCATCCGTCATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36798","NCBI_taxonomy_name":"Bacteroides coprosuis DSM 18011","NCBI_taxonomy_id":"679937"}}}},"ARO_accession":"3000604","ARO_id":"36743","ARO_name":"Erm(35)","ARO_description":"ErmD confers MLSb phenotype.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35946":{"category_aro_accession":"0000027","category_aro_cvterm_id":"35946","category_aro_name":"roxithromycin","category_aro_description":"Roxithromycin is a semi-synthetic, 14-carbon ring macrolide antibiotic derived from erythromycin. It is used to treat respiratory tract, urinary and soft tissue infections. Roxithromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35974":{"category_aro_accession":"0000057","category_aro_cvterm_id":"35974","category_aro_name":"telithromycin","category_aro_description":"Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36315":{"category_aro_accession":"3000176","category_aro_cvterm_id":"36315","category_aro_name":"dirithromycin","category_aro_description":"Dirithromycin is an oxazine derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome to inhibit bacterial protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin 1A is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"vernamycin B-gamma","category_aro_description":"Vernamycin B-gamma is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1435":{"model_id":"1435","model_name":"cmlA6","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"728":{"protein_sequence":{"accession":"AAK52606.1","sequence":"MRSKNFSWRYSLAATVLLLSPFDLLASLGMDMYLPAVPFMPNALGTTASTIQLTLTTYLVMIGAGQLLFGPLSDRLGRRPVLLGGGLAYVVASMGLALTSSAEVFLGLRILQACGASACLVSTFATVRDIYAGREESNVIYGILGSMLAIVPAVGPLLGALVDMWLGWRAIFAFLGLGMIAASAAAWRFWPETRVQRVAGLQWSQLLLPVKCLNFWLYTLCYAAGMGSFFVFFSIAPGLMMGRQGVSQLGFSLLFATVAIAMVFTARFMGRVIPKWGSPSVLRMGMGCLIAGAVLLAITEIWALQSVLGFIAPMWLVGIGVATAVSVAPNGALRGFDHVAGTVTAVYFCLGGVLLGSIGTLIISLLPRNTAWPVVVYCLTLATVVLGLSCVSRVKGSRGQGEHDVVALQSAESTSNPNR"},"dna_sequence":{"accession":"AF294653","fmin":"2749","fmax":"4009","strand":"+","sequence":"GTGCGCTCAAAAAACTTTAGTTGGCGGTACTCCCTTGCCGCCACGGTGTTGTTGTTATCACCGTTCGATTTATTGGCATCACTCGGCATGGACATGTACTTGCCAGCAGTGCCGTTTATGCCAAACGCGCTTGGTACGACAGCGAGCACAATTCAGCTTACGCTGACAACGTACTTGGTCATGATTGGTGCCGGTCAGCTCTTGTTTGGACCGCTATCGGACCGACTGGGGCGCCGCCCCGTTCTACTGGGAGGTGGCCTCGCCTACGTTGTGGCGTCAATGGGCCTCGCTCTTACGTCATCGGCTGAAGTCTTTCTGGGGCTTCGGATTCTTCAGGCTTGTGGTGCCTCGGCGTGCCTTGTTTCCACATTTGCAACAGTACGTGACATTTACGCAGGTCGCGAGGAAAGTAATGTCATTTACGGCATACTCGGATCCATGCTGGCCATAGTCCCGGCGGTAGGCCCATTGCTCGGAGCGCTCGTCGACATGTGGCTTGGGTGGCGGGCTATCTTTGCGTTTCTAGGTTTGGGCATGATCGCTGCATCTGCAGCAGCGTGGCGATTCTGGCCTGAAACCCGGGTGCAACGAGTTGCGGGCTTGCAATGGTCGCAGCTGCTACTCCCCGTTAAGTGCCTGAACTTCTGGTTGTACACGTTGTGTTACGCCGCTGGAATGGGTAGCTTCTTCGTCTTTTTCTCCATTGCGCCCGGACTAATGATGGGCAGGCAAGGTGTGTCTCAGCTTGGCTTCAGCCTGCTGTTCGCCACAGTGGCAATTGCCATGGTGTTTACGGCTCGTTTTATGGGGCGTGTGATACCCAAGTGGGGCAGCCCAAGTGTCTTGCGAATGGGAATGGGATGCCTGATAGCTGGAGCAGTATTGCTTGCCATCACCGAAATATGGGCTTTGCAGTCCGTGTTAGGCTTTATTGCTCCAATGTGGCTAGTGGGTATTGGTGTCGCCACAGCGGTATCTGTGGCGCCCAATGGCGCTCTTCGAGGATTCGACCATGTTGCTGGAACGGTCACGGCAGTCTACTTCTGCTTGGGCGGTGTACTGCTAGGAAGCATCGGAACGTTGATCATTTCGCTGTTGCCGCGCAACACGGCTTGGCCGGTTGTCGTGTACTGTTTGACCCTTGCAACAGTCGTGCTCGGTCTGTCTTGTGTTTCCCGAGTGAAGGGCTCTCGCGGCCAGGGGGAGCATGATGTGGTCGCGCTACAAAGTGCGGAAAGTACATCAAATCCCAATCGTTGAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002696","ARO_id":"39130","ARO_name":"cmlA6","ARO_description":"cmlA6 is a plasmid-encoded chloramphenicol exporter that is found in Pseudomonas aeruginosa","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1436":{"model_id":"1436","model_name":"TEM-40","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1247":{"protein_sequence":{"accession":"CBX53726.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMISTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"FR717535","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATAAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000910","ARO_id":"37290","ARO_name":"TEM-40","ARO_description":"TEM-40 is an inhibitor-resistant beta-lactamase that has been found in clinical isolates.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1437":{"model_id":"1437","model_name":"acrF","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1900"}},"model_sequences":{"sequence":{"700":{"protein_sequence":{"accession":"AAC76298.1","sequence":"MANFFIRRPIFAWVLAIILMMAGALAILQLPVAQYPTIAPPAVSVSANYPGADAQTVQDTVTQVIEQNMNGIDNLMYMSSTSDSAGSVTITLTFQSGTDPDIAQVQVQNKLQLATPLLPQEVQQQGISVEKSSSSYLMVAGFVSDNPGTTQDDISDYVASNVKDTLSRLNGVGDVQLFGAQYAMRIWLDADLLNKYKLTPVDVINQLKVQNDQIAAGQLGGTPALPGQQLNASIIAQTRFKNPEEFGKVTLRVNSDGSVVRLKDVARVELGGENYNVIARINGKPAAGLGIKLATGANALDTAKAIKAKLAELQPFFPQGMKVLYPYDTTPFVQLSIHEVVKTLFEAIMLVFLVMYLFLQNMRATLIPTIAVPVVLLGTFAILAAFGYSINTLTMFGMVLAIGLLVDDAIVVVENVERVMMEDKLPPKEATEKSMSQIQGALVGIAMVLSAVFIPMAFFGGSTGAIYRQFSITIVSAMALSVLVALILTPALCATLLKPVSAEHHENKGGFFGWFNTTFDHSVNHYTNSVGKILGSTGRYLLIYALIVAGMVVLFLRLPSSFLPEEDQGVFLTMIQLPAGATQERTQKVLDQVTDYYLKNEKANVESVFTVNGFSFSGQAQNAGMAFVSLKPWEERNGDENSAEAVIHRAKMELGKIRDGFVIPFNMPAIVELGTATGFDFELIDQAGLGHDALTQARNQLLGMAAQHPASLVSVRPNGLEDTAQFKLEVDQEKAQALGVSLSDINQTISTALGGTYVNDFIDRGRVKKLYVQADAKFRMLPEDVDKLYVRSANGEMVPFSAFTTSHWVYGSPRLERYNGLPSMEIQGEAAPGTSSGDAMALMENLASKLPAGIGYDWTGMSYQERLSGNQAPALVAISFVVVFLCLAALYESWSIPVSVMLVVPLGIVGVLLAATLFNQKNDVYFMVGLLTTIGLSAKNAILIVEFAKDLMEKEGKGVVEATLMAVRMRLRPILMTSLAFILGVLPLAISNGAGSGAQNAVGIGVMGGMVSATLLAIFFVPVFFVVIRRCFKG"},"dna_sequence":{"accession":"U00096","fmin":"3415032","fmax":"3418137","strand":"+","sequence":"ATGGCAAACTTTTTTATTCGACGACCGATATTTGCATGGGTGCTGGCCATTATTCTGATGATGGCGGGCGCACTGGCGATCCTACAATTGCCCGTCGCTCAGTATCCAACAATTGCACCGCCTGCGGTTTCTGTTTCAGCAAACTATCCGGGCGCTGATGCGCAGACCGTGCAGGATACGGTGACGCAGGTTATCGAACAGAATATGAACGGTATCGATAACCTGATGTATATGTCCTCCACCAGCGATTCCGCCGGTAGCGTGACAATTACCCTTACCTTCCAGTCCGGGACCGATCCTGATATCGCGCAAGTGCAGGTGCAGAACAAACTCCAGCTCGCCACGCCGTTGCTGCCGCAGGAGGTTCAGCAGCAGGGGATCAGTGTTGAAAAGTCCAGTAGCAGCTATTTGATGGTGGCGGGCTTTGTCTCTGATAACCCAGGCACCACACAGGACGATATCTCGGACTATGTGGCCTCTAACGTTAAAGATACGCTTAGCCGTCTGAATGGCGTCGGTGACGTACAGCTTTTCGGCGCACAGTATGCGATGCGTATCTGGCTGGATGCCGATCTGCTAAACAAATATAAACTGACACCGGTTGATGTGATTAACCAGTTGAAGGTACAGAACGATCAGATCGCTGCCGGACAGTTGGGCGGAACGCCAGCGTTACCAGGGCAACAATTGAACGCCTCGATTATTGCTCAGACGCGGTTTAAAAATCCGGAAGAATTCGGCAAAGTGACCCTGCGCGTAAACAGTGACGGCTCGGTGGTACGCCTGAAAGATGTCGCACGGGTTGAACTTGGCGGTGAAAACTATAACGTTATCGCTCGTATCAACGGAAAACCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGAATGCTCTCGATACCGCGAAAGCCATTAAGGCAAAACTGGCGGAATTACAGCCATTCTTCCCGCAGGGAATGAAGGTTCTCTACCCTTATGACACCACGCCATTCGTCCAGCTTTCTATTCACGAAGTGGTAAAAACGCTGTTCGAAGCCATTATGCTGGTGTTCCTGGTGATGTATCTGTTCTTGCAGAATATGCGAGCAACGCTGATCCCCACCATTGCGGTACCCGTGGTGTTGTTAGGGACGTTTGCCATCCTCGCCGCTTTTGGTTACTCCATCAACACACTAACGATGTTCGGGATGGTGCTTGCCATCGGGCTGCTCGTCGATGATGCGATAGTGGTGGTGGAGAACGTCGAGCGCGTGATGATGGAGGATAAGCTCCCGCCAAAAGAAGCGACGGAAAAATCGATGTCGCAAATTCAGGGCGCACTGGTGGGTATCGCGATGGTGCTGTCAGCGGTATTTATTCCGATGGCATTCTTCGGCGGTTCTACTGGGGCAATTTATCGCCAGTTCTCTATCACCATCGTTTCGGCAATGGCGCTTTCTGTTCTGGTGGCATTGATTCTTACCCCTGCGTTATGTGCAACGCTGCTTAAACCCGTCTCTGCTGAGCATCACGAAAATAAGGGCGGTTTCTTCGGTTGGTTTAATACCACCTTCGATCATAGCGTTAACCACTACACCAACAGCGTCGGCAAAATCCTCGGATCCACAGGACGATATTTACTGATCTATGCGCTGATTGTTGCAGGAATGGTGGTGTTGTTTTTACGTCTTCCGTCTTCCTTCTTACCTGAAGAGGATCAGGGTGTCTTTCTGACCATGATTCAGTTACCCGCTGGCGCGACGCAAGAGCGGACGCAAAAAGTGTTGGATCAAGTTACGGATTACTATCTGAAGAACGAGAAAGCGAACGTTGAAAGTGTCTTTACGGTTAACGGCTTTAGCTTCAGCGGCCAGGCACAAAACGCCGGTATGGCCTTCGTCAGTCTGAAACCGTGGGAAGAGCGTAATGGTGACGAAAACAGTGCGGAAGCGGTAATCCATCGTGCCAAAATGGAATTGGGCAAGATCCGCGACGGTTTTGTCATTCCATTCAATATGCCAGCCATTGTTGAACTGGGCACGGCAACGGGTTTCGACTTTGAGTTAATTGATCAGGCTGGGCTGGGTCACGATGCCCTAACCCAGGCCCGTAACCAGTTGCTTGGTATGGCGGCGCAACATCCTGCCAGCTTAGTCAGCGTGCGCCCTAATGGCCTGGAAGACACCGCGCAGTTTAAACTGGAAGTTGACCAGGAAAAGGCGCAGGCATTAGGTGTTTCACTTTCTGACATCAATCAGACCATTTCAACGGCGCTGGGTGGGACTTACGTTAACGACTTCATCGACCGTGGCCGCGTGAAAAAGTTGTATGTTCAGGCGGATGCCAAATTCCGTATGCTGCCAGAAGATGTCGATAAACTTTATGTCCGCAGCGCCAACGGCGAAATGGTGCCATTCTCGGCCTTTACCACTTCACATTGGGTGTATGGCTCTCCGCGACTGGAACGCTACAACGGTCTGCCGTCAATGGAGATTCAGGGGGAAGCCGCGCCAGGAACCAGTTCCGGCGATGCCATGGCGTTGATGGAAAACCTTGCGTCAAAATTACCTGCGGGCATTGGTTATGACTGGACGGGTATGTCGTATCAGGAACGCTTATCGGGAAACCAGGCTCCCGCTCTGGTAGCAATTTCCTTTGTGGTTGTTTTCCTGTGCCTTGCTGCACTCTATGAAAGCTGGTCAATTCCTGTCTCGGTTATGTTGGTAGTGCCGTTAGGGATTGTCGGCGTGCTGCTGGCGGCGACACTCTTTAATCAAAAAAATGACGTCTACTTTATGGTGGGCTTGCTAACGACAATTGGCTTGTCGGCCAAAAACGCTATTTTGATCGTTGAGTTCGCTAAAGATCTCATGGAGAAAGAGGGTAAAGGTGTTGTTGAAGCGACACTGATGGCAGTACGTATGCGTCTGCGTCCTATCCTGATGACCTCTCTCGCCTTTATTCTCGGCGTATTACCGCTAGCTATCAGTAACGGTGCCGGCAGTGGCGCGCAGAACGCTGTGGGTATCGGGGTAATGGGAGGAATGGTCTCTGCAACGTTGCTGGCAATCTTCTTCGTACCGGTGTTCTTTGTGGTGATCCGCCGTTGCTTTAAAGGATAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3000502","ARO_id":"36641","ARO_name":"AcrF","ARO_description":"AcrF is a inner membrane transporter, similar to AcrB.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1438":{"model_id":"1438","model_name":"SHV-19","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1147":{"protein_sequence":{"accession":"AAF34333.1","sequence":"MLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEAFPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERN"},"dna_sequence":{"accession":"AF117743","fmin":"0","fmax":"780","strand":"+","sequence":"CTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGTTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001077","ARO_id":"37457","ARO_name":"SHV-19","ARO_description":"SHV-19 is a broad-spectrum beta-lactamase that has been found in clinical isolates.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1439":{"model_id":"1439","model_name":"SHV-80","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1069":{"protein_sequence":{"accession":"CAJ47135.2","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPTGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM176555","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCACAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001134","ARO_id":"37514","ARO_name":"SHV-80","ARO_description":"SHV-80 is a broad-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1440":{"model_id":"1440","model_name":"CTX-M-103","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1026":{"protein_sequence":{"accession":"CDG50843.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGNGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"HG423149","fmin":"39","fmax":"915","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAACGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001962","ARO_id":"38362","ARO_name":"CTX-M-103","ARO_description":"CTX-M-103 is a beta-lactamase found in Escherichia coli","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1442":{"model_id":"1442","model_name":"mdtN","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"3298":{"protein_sequence":{"accession":"BAE78084.1","sequence":"MESTPKKAPRSKFPALLVVALALVALVFVIWRVDSAPSTNDAYASADTIDVVPEVSGRIVELAVTDNQAVKQGDLLFRIDPRPYEANLAKAEASLAALDKQIMLTQRSVDAQQFGADSVNATVEKARAAAKQATDTLRRTEPLLKEGFVSAEDVDRARTAQRAAEADLNAVLLQAQSAASAVSGVDALVAQRAAVEADIALTKLHLEMATVRAPFDGRVISLKTSVGQFASAMRPIFTLIDTRHWYVIANFRETDLKNIRSGTPATIRLMSDSGKTFEGKVDSIGYGVLPDDGGLVLGGLPKVSRSINWVRVAQRFPVKIMVDKPDPEMFRIGASAVANLEPQ"},"dna_sequence":{"accession":"AP009048","fmin":"4306556","fmax":"4307588","strand":"-","sequence":"TTATTGCGGCTCAAGATTAGCGACTGCCGAAGCGCCGATGCGGAACATTTCCGGGTCAGGTTTATCGACCATGATTTTGACCGGAAAACGCTGGGCAACGCGGACCCAGTTAATAGAACGAGACACTTTCGGCAGGCCGCCCAGCACCAGGCCGCCGTCATCCGGTAGCACGCCGTAGCCAATCGAATCCACTTTACCCTCGAAGGTTTTGCCGCTGTCACTCATCAGGCGAATCGTTGCGGGTGTACCTGAGCGAATATTTTTCAGATCGGTTTCGCGGAAGTTGGCGATCACATACCAGTGACGAGTGTCGATTAGGGTAAAAATAGGGCGCATGGCAGAAGCAAATTGCCCGACGGAGGTTTTGAGGGAAATGACCCGGCCATCAAACGGCGCGCGAACGGTCGCCATTTCCAGATGCAGTTTGGTCAGGGCAATATCCGCTTCGACCGCCGCACGCTGGGCAACTAATGCATCCACGCCGCTGACGGCGCTGGCGGCTGACTGCGCCTGTAACAATACGGCATTAAGATCCGCTTCTGCGGCGCGCTGCGCCGTTCTTGCACGGTCAACATCTTCCGCTGAGACAAAACCTTCTTTCAGTAATGGCTCGGTGCGGCGTAATGTATCTGTGGCCTGTTTCGCGGCGGCACGGGCTTTTTCTACCGTGGCATTAACCGAGTCGGCACCAAACTGTTGCGCGTCAACGCTACGCTGGGTGAGCATAATTTGCTTATCCAGCGCCGCGAGGGAGGCTTCAGCTTTCGCCAGATTGGCTTCGTACGGGCGCGGGTCGATGCGGAACAGCAAATCGCCCTGTTTGACTGCCTGGTTGTCGGTGACCGCCAGTTCTACAATGCGGCCGCTGACTTCCGGTACCACATCAATGGTATCTGCTGACGCGTAAGCGTCATTAGTTGATGGCGCACTGTCTACGCGCCAGATAACGAAAACAAGGGCAACCAGCGCCAACGCAACCACTAACAGAGCAGGGAATTTACTGCGAGGAGCTTTTTTCGGCGTACTTTCCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36839","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. W3110","NCBI_taxonomy_id":"316407"}}}},"ARO_accession":"3003548","ARO_id":"40150","ARO_name":"mdtN","ARO_description":"Multidrug resistance efflux pump. Could be involved in resistance to puromycin, acriflavine and tetraphenylarsonium chloride.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavin","category_aro_description":"Acriflavin is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35965":{"category_aro_accession":"0000047","category_aro_cvterm_id":"35965","category_aro_name":"puromycin","category_aro_description":"Puromycin is an aminonucleoside antibiotic, derived from Streptomyces alboniger, that causes premature chain termination during ribosomal protein translation.","category_aro_class_name":"Antibiotic"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36193":{"category_aro_accession":"3000054","category_aro_cvterm_id":"36193","category_aro_name":"acridine dye","category_aro_description":"Acridine dyes are cell permeable, basic molecules with an acridine chromophore. These compounds intercalate DNA. The image shown represents the core structure of the acridine family, with specific dyes containing varying substituents.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1443":{"model_id":"1443","model_name":"CARB-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1814":{"protein_sequence":{"accession":"AAM74565.1","sequence":"MKSLLVFALLMPSVVFASSSKFQSVEQEIKGIESSLSARIGVAILDTQNGESWDYNGDQRFPLTSTFKTIACAKLLYDAEHGKVNLNSTVEIKKADLVTYSPVLEKQVGKPITLSDACLATMTTSDNTAANIVINAVGDPKSITDFLRQIGDKETRLDRVEPELNEGKLGDLRDTTTPNAITSTLNQLLFGSTLSEASQKKLESWMVNNQVTGNLLRSVLPVKWSIADRSGAGGFGARSITAIVWSEEKKPIIVSIYLAQTEASMAERNDAIVKIGRSIFEVYTSQSR"},"dna_sequence":{"accession":"AF409092","fmin":"887","fmax":"1754","strand":"+","sequence":"ATGAAGTCTTTGTTGGTATTTGCGCTTTTAATGCCATCTGTAGTTTTTGCAAGCAGTTCAAAATTTCAATCAGTTGAACAAGAAATTAAGGGAATTGAGTCTTCACTCTCTGCTCGTATAGGAGTCGCCATTTTGGATACTCAAAATGGCGAAAGCTGGGATTATAATGGTGATCAACGATTTCCATTAACAAGTACTTTCAAAACAATAGCTTGTGCTAAGTTGCTGTATGATGCAGAGCATGGGAAAGTTAATCTCAATAGTACAGTTGAGATTAAGAAAGCAGATCTTGTTACGTATTCGCCTGTATTAGAAAAGCAAGTAGGTAAACCAATAACGCTCTCTGATGCATGCCTTGCTACTATGACAACAAGCGACAATACAGCAGCCAATATTGTTATAAATGCTGTCGGTGATCCTAAAAGCATTACTGATTTTCTGAGACAAATTGGTGACAAAGAAACTCGTCTAGATCGTGTCGAGCCTGAGCTCAATGAAGGTAAACTCGGTGATTTGAGGGATACGACAACGCCTAATGCAATAACCAGCACGTTAAATCAATTATTATTTGGTTCCACATTATCTGAAGCTAGTCAGAAAAAATTAGAGTCTTGGATGGTGAACAATCAAGTTACGGGTAATTTATTGAGGTCAGTATTGCCAGTGAAGTGGAGTATTGCTGATCGCTCAGGAGCAGGTGGATTTGGTGCTAGGAGTATTACAGCGATTGTGTGGAGTGAAGAAAAAAAACCGATTATCGTAAGTATTTATCTAGCTCAAACCGAGGCTTCAATGGCAGAACGAAATGATGCGATAGTTAAGATTGGTCGTTCAATTTTTGAAGTTTATACATCACAGTCGCGTTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36920","NCBI_taxonomy_name":"Vibrio cholerae non-O1\/non-O139","NCBI_taxonomy_id":"156539"}}}},"ARO_accession":"3002246","ARO_id":"38646","ARO_name":"CARB-7","ARO_description":"CARB-7 is a beta-lactamase found in Vibrio cholerae.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1444":{"model_id":"1444","model_name":"IND-12","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1826":{"protein_sequence":{"accession":"ADK25051.1","sequence":"MKKSIQLLMMSMFLSPLINAQVKDFVIEPPVKPNLYLYKSFGVFGGKEYSANAVYLTTKKGVVLFDVPWQKEQYQTLMDTIQKRHHLPVIAVFATHSHDDRAGDLSFYNQKGIKTYATAKTNELLKKDGKATSTEIIKTGKPYKIGGEEFMVDFLGEGHTVDNVVVWFPKYKVLDGGCLVKSRTATDLGYTGEANVKQWPETMRKLKTKYAQATLVIPGHDEWKGGGHVQHSLDLLDKNKKPE"},"dna_sequence":{"accession":"HM245380","fmin":"27","fmax":"759","strand":"+","sequence":"ATGAAAAAAAGTATTCAGCTTTTGATGATGTCAATGTTTTTAAGCCCATTGATCAATGCCCAGGTTAAAGATTTTGTAATTGAGCCGCCTGTTAAACCCAACCTGTATCTTTATAAAAGTTTCGGAGTTTTCGGGGGTAAAGAATATTCTGCCAATGCTGTATATCTTACCACTAAGAAAGGAGTTGTCTTATTTGATGTCCCATGGCAAAAGGAACAATATCAAACCCTTATGGACACCATACAAAAGCGTCATCACCTTCCTGTAATTGCTGTATTTGCCACCCACTCTCATGATGACAGAGCGGGTGATCTAAGCTTTTACAATCAAAAAGGAATTAAAACATATGCGACCGCCAAGACCAATGAACTGTTGAAAAAAGACGGAAAAGCAACCTCAACCGAAATTATAAAAACAGGAAAACCTTACAAAATTGGTGGTGAAGAATTTATGGTAGACTTTCTTGGAGAAGGACATACAGTTGATAATGTTGTTGTATGGTTCCCCAAATATAAAGTACTGGACGGAGGATGTCTTGTAAAAAGCAGGACAGCCACTGACCTGGGATATACCGGTGAAGCAAATGTAAAACAATGGCCGGAAACCATGCGAAAACTAAAAACGAAATATGCTCAGGCCACTCTGGTAATCCCGGGACACGACGAATGGAAAGGCGGTGGCCATGTACAGCATTCTCTGGATCTTCTGGATAAGAATAAAAAGCCGGAATAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36916","NCBI_taxonomy_name":"Chryseobacterium indologenes","NCBI_taxonomy_id":"253"}}}},"ARO_accession":"3002268","ARO_id":"38668","ARO_name":"IND-12","ARO_description":"IND-12 is a beta-lactamase found in Escherichia coli","ARO_category":{"36199":{"category_aro_accession":"3000060","category_aro_cvterm_id":"36199","category_aro_name":"IND beta-lactamase","category_aro_description":"IND beta-lactamases are class B carbapenem-hydrolyzing beta-lactamases","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1445":{"model_id":"1445","model_name":"acrE","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"675"}},"model_sequences":{"sequence":{"333":{"protein_sequence":{"accession":"AAC76297.1","sequence":"MTKHARFFLLPSFILISAALIAGCNDKGEEKAHVGEPQVTVHIVKTAPLEVKTELPGRTNAYRIAEVRPQVSGIVLNRNFTEGSDVQAGQSLYQIDPATYQANYDSAKGELAKSEAAAAIAHLTVKRYVPLVGTKYISQQEYDQAIADARQADAAVIAAKATVESARINLAYTKVTAPISGRIGKSTVTEGALVTNGQTTELATVQQLDPIYVDVTQSSNDFMRLKQSVEQGNLHKENATSNVELVMENGQTYPLKGTLQFSDVTVDESTGSITLRAVFPNPQHTLLPGMFVRARIDEGVQPDAILIPQQGVSRTPRGDATVLIVNDKSQVEARPVVASQAIGDKWLISEGLKSGDQVIVSGLQKARPGEQVKATTDTPADTASK"},"dna_sequence":{"accession":"U00096","fmin":"3413863","fmax":"3415021","strand":"+","sequence":"ATGACGAAACATGCCAGGTTTTTCCTCCTGCCCTCCTTTATTCTGATCTCCGCGGCTTTAATCGCCGGTTGTAACGATAAGGGAGAAGAGAAAGCTCACGTCGGTGAACCGCAGGTTACCGTTCATATTGTAAAAACGGCCCCGTTAGAAGTTAAGACTGAATTACCAGGCCGCACCAATGCTTATCGTATAGCCGAAGTTCGCCCACAGGTTAGCGGGATCGTACTGAATCGCAATTTCACTGAAGGCAGCGATGTGCAAGCAGGCCAGTCCCTGTACCAGATCGATCCCGCGACCTATCAGGCAAATTATGACAGCGCGAAAGGCGAACTGGCGAAAAGTGAAGCCGCCGCCGCCATCGCGCATTTGACGGTAAAACGTTACGTTCCGCTCGTGGGTACGAAATACATCAGCCAGCAGGAGTACGACCAGGCCATTGCTGATGCTCGTCAGGCCGATGCCGCCGTGATTGCCGCAAAAGCCACAGTCGAAAGCGCTCGCATCAATCTTGCTTATACCAAAGTCACTGCGCCAATTAGCGGACGTATCGGCAAATCGACTGTGACCGAAGGCGCTCTTGTCACTAATGGGCAAACGACTGAACTGGCGACTGTCCAGCAGCTCGATCCTATCTACGTTGATGTGACCCAATCCAGCAACGATTTTATGAGGCTGAAGCAATCCGTAGAGCAAGGAAATTTGCATAAGGAAAACGCCACCAGCAACGTAGAGTTGGTCATGGAAAACGGTCAAACCTATCCCCTGAAAGGTACGCTGCAATTCTCCGATGTGACCGTTGATGAAAGCACCGGCTCCATAACCCTACGTGCTGTCTTCCCTAACCCGCAACATACGCTTTTGCCGGGTATGTTTGTGCGTGCACGGATTGATGAAGGCGTCCAACCTGACGCCATTCTTATCCCGCAACAAGGCGTTAGCCGCACACCGCGTGGTGATGCAACCGTGCTGATTGTTAACGATAAAAGTCAGGTTGAAGCGCGCCCTGTCGTTGCCAGTCAGGCGATTGGCGATAAATGGTTGATTAGTGAAGGACTGAAATCTGGCGATCAAGTCATTGTCAGCGGCCTGCAAAAAGCGCGTCCGGGAGAGCAGGTTAAAGCCACTACCGATACCCCCGCAGATACTGCATCGAAGTAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3000499","ARO_id":"36638","ARO_name":"AcrE","ARO_description":"AcrE is a membrane fusion protein, similar to AcrA.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1446":{"model_id":"1446","model_name":"PDC-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"1771":{"protein_sequence":{"accession":"ACQ82811.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"FJ666069","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTATGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002505","ARO_id":"38905","ARO_name":"PDC-6","ARO_description":"PDC-6 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1447":{"model_id":"1447","model_name":"OKP-A-10","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"794":{"protein_sequence":{"accession":"CAJ19608.1","sequence":"MRCVRLCLIPLIAALPLAVFASPPPLEQITLSESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIRYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKSVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMAATLRKLLTSHALSDRSQQQLLQWMVDDQVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPNGKAERIVMIYLRDTPATMAERNQQIAKIGAALIEHWQR"},"dna_sequence":{"accession":"AM051149","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTGTGTTCGCCTGTGCCTTATCCCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCCGCCGCTTGAGCAAATTACACTCAGCGAAAGTCAGCTGGCGGGCCGCGTGGGCTATGTTGAAATGGATCTGGCGAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGAGACGAACAGCTGGATCGGCGGATCCGCTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGAGCGTTGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAGCTCAATGAAGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCAGCCAGCATGGCCGCCACCCTGCGCAAGCTGCTAACCAGCCACGCGCTGAGCGACCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGATCAGGTGGCCGGTCCGCTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGCGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGAACGGCAAAGCGGAGCGCATCGTGATGATCTATCTGCGGGATACGCCGGCGACCATGGCCGAGCGTAACCAGCAGATCGCCAAAATAGGCGCGGCGCTGATCGAGCACTGGCAGCGCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002427","ARO_id":"38827","ARO_name":"OKP-A-10","ARO_description":"OKP-A-10 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1448":{"model_id":"1448","model_name":"SHV-26","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1789":{"protein_sequence":{"accession":"AAF36719.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMTATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AF227204","fmin":"73","fmax":"934","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGACCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001084","ARO_id":"37464","ARO_name":"SHV-26","ARO_description":"SHV-26 is an inhibitor-resistant beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1449":{"model_id":"1449","model_name":"OXA-59","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1304":{"protein_sequence":{"accession":"CAG15145.1","sequence":"MKFRHALSSAFVLLGCIAASAHAKTICTAIADAGTGKLLVQDGDCGRRASPASTFKIAISLMGYDAGFLRNEHDPVLPYRDSYIAWGGEAWKQPTDPTRWLKYSVVWYSQQVAHHLGAQRFAQYAKAFGYGNADVSGDPGQNNGLDRAWIGSSLQISPLEQLEFLGKMLNRKLPVSPTAVDMTERIVESTTLADGTVVHGKTGVSYPLLADGTRDWARGSGWFVGWIVRGKQTLVFARLTQDERKQPVSAGIRTREAFLRDLPRLLAAR"},"dna_sequence":{"accession":"AJ632249","fmin":"0","fmax":"810","strand":"+","sequence":"ATGAAATTCCGACACGCGCTGTCGAGCGCATTCGTTTTGCTGGGTTGCATCGCCGCGTCGGCGCATGCGAAGACGATCTGCACGGCGATCGCCGATGCGGGCACGGGCAAGCTGCTGGTGCAGGACGGCGATTGCGGCCGCCGCGCATCGCCCGCGTCGACGTTCAAGATCGCGATCAGCCTGATGGGCTACGACGCAGGCTTCCTGCGCAACGAGCATGACCCGGTGCTGCCGTATCGCGACAGTTACATCGCGTGGGGTGGCGAAGCATGGAAGCAGCCGACCGATCCGACGCGCTGGCTCAAGTATTCGGTCGTGTGGTATTCGCAGCAGGTGGCGCACCATCTCGGCGCGCAGCGCTTCGCGCAGTATGCGAAGGCGTTCGGCTACGGCAATGCGGACGTGTCCGGCGATCCCGGCCAGAACAACGGCCTCGATCGCGCGTGGATCGGCTCGTCGCTGCAGATCTCGCCGCTCGAACAATTGGAATTCCTCGGCAAGATGCTCAATCGCAAGCTGCCCGTGTCGCCCACAGCCGTCGACATGACGGAGCGGATCGTCGAATCGACGACGCTTGCCGACGGAACGGTGGTGCACGGCAAGACCGGCGTGTCCTATCCGCTGCTGGCCGACGGCACACGCGACTGGGCGCGTGGATCCGGCTGGTTCGTCGGCTGGATCGTGCGTGGCAAGCAGACGCTGGTGTTCGCGCGCCTCACGCAGGACGAGCGCAAGCAGCCCGTTTCAGCCGGCATACGGACGCGCGAGGCCTTCCTGCGCGACTTGCCCCGGCTTCTCGCCGCGCGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36923","NCBI_taxonomy_name":"Burkholderia pseudomallei","NCBI_taxonomy_id":"28450"}}}},"ARO_accession":"3001772","ARO_id":"38172","ARO_name":"OXA-59","ARO_description":"OXA-59 is a beta-lactamase found in Burkholderia pseudomallei","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1451":{"model_id":"1451","model_name":"MIR-17","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"1658":{"protein_sequence":{"accession":"CEA29752.1","sequence":"MMTKSLSCALLLSVTSAAFAAPMSEKQLAEVVERTVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEVALGDPVAKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDTASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEEAHYAWGYREGKAVHVSPGMLDAEAYGVKTNVKDMASWVIANMKPDSLQAPSLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"LN515535","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGACAAAATCCCTAAGCTGTGCCCTGCTGCTCAGCGTCACCAGCGCTGCATTCGCCGCACCGATGTCCGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTAATTTATCAGGGTCAGCCACACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGCGGCGATGCCATTGCCCGGGGTGAAGTAGCGCTGGGCGATCCGGTAGCAAAATACTGGCCTGAGCTCACGGGCAAGCAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTATACCGCAGGCGGTCTGCCGTTACAGGTGCCGGATGAGGTCACGGATACCGCTTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCTAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTTAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAACCCCTCAAGCTGGACCATACCTGGATTAACGTCCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGAGGGTAAAGCGGTCCACGTTTCGCCAGGGATGCTGGACGCGGAAGCCTATGGCGTAAAAACTAACGTGAAGGATATGGCGAGCTGGGTGATAGCCAACATGAAGCCGGATTCTCTTCAGGCTCCCTCACTCAAGCAAGGCATTGCTCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCTATGTATCAGGGGTTAGGCTGGGAGATGCTCAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCATTGCCCGTGGCAGAAGTGAATCCACCCGCGCCGCCGGTCAAGGCCTCCTGGGTCCATAAAACAGGCTCGACGGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3003173","ARO_id":"39750","ARO_name":"MIR-17","ARO_description":"From the Lahey list of beta-lactamases.","ARO_category":{"36197":{"category_aro_accession":"3000058","category_aro_cvterm_id":"36197","category_aro_name":"MIR beta-lactamase","category_aro_description":"MIR beta-lactamases are plasmid-mediated beta-lactamases that confer resistance to oxyimino- and alpha-methoxy beta-lactams","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1452":{"model_id":"1452","model_name":"TEM-216","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1494":{"protein_sequence":{"accession":"AHJ78622.1","sequence":"MSIQHFRVSLIPFFAAFCLPVFAHPETLVKVKDAEDQLGAPVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"KF944358","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCTCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACCAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001393","ARO_id":"37793","ARO_name":"TEM-216","ARO_description":"From the Lahey list of beta-lactamases. Not yet released.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1453":{"model_id":"1453","model_name":"vanYD","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"250"}},"model_sequences":{"sequence":{"338":{"protein_sequence":{"accession":"AAM09853.1","sequence":"MERQNNNENQYGRNRRKDKRKKLFFYRAACAMLGLLIVCVIFGAVYFLRESKDPVLPSKENTKTGKDYSFLADGQSEDESPISEPAISNRANAIDLNIIAANAIVMNKDTDALLYQKKRHGQNCAGQYSKDDYGVDRA"},"dna_sequence":{"accession":"AY082011","fmin":"3848","fmax":"4265","strand":"+","sequence":"GTGGAACGTCAAAATAACAATGAAAACCAGTATGGAAGGAATCGCAGAAAAGACAAAAGAAAAAAATTGTTTTTTTACAGAGCAGCATGTGCCATGCTCGGTCTGCTCATAGTCTGTGTAATTTTTGGAGCTGTGTATTTTCTCAGAGAGAGTAAAGATCCGGTTCTTCCATCCAAAGAAAATACAAAGACAGGCAAGGACTATTCATTTTTGGCCGACGGTCAGAGTGAGGATGAGTCTCCGATTTCGGAGCCAGCCATATCCAACCGGGCGAATGCGATTGACCTGAACATCATAGCAGCAAATGCCATTGTGATGAATAAAGACACCGATGCGTTATTGTATCAAAAAAAACGGCACGGACAGAATTGCGCCGGCCAGTACAGCAAAGATGATTACGGCGTTGACCGTGCTTGAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002957","ARO_id":"39391","ARO_name":"vanYD","ARO_description":"vanYD is a vanY variant found in the vanD gene cluster","ARO_category":{"36216":{"category_aro_accession":"3000077","category_aro_cvterm_id":"36216","category_aro_name":"vanY","category_aro_description":"VanY is a D,D-carboxypeptidase that cleaves removes the terminal D-Ala from peptidoglycan for the addition of D-Lactate. The D-Ala-D-Lac peptidoglycan subunits have reduced binding affinity with vancomycin compared to D-Ala-D-Ala.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1454":{"model_id":"1454","model_name":"CMY-112","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"781":{"protein_sequence":{"accession":"AIT76090.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEEKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDEVTDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"KM087837","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCGCTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACGAGGAGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAATTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTACCGCTGCAGATCCCCGATGAAGTTACGGATAAAGCCGCATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGCGGTGAAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGTTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACAGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATAGTGATGCTGGCAAACAAAAGCTACCCCAACCCGGCTCGCGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002123","ARO_id":"38523","ARO_name":"CMY-112","ARO_description":"CMY-112 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1455":{"model_id":"1455","model_name":"IND-9","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1417":{"protein_sequence":{"accession":"ACZ65153.1","sequence":"MKKSIQFFIVSLLLSPFANAQVKDFVIEPPISKNLYIYKTFGVFGGKEYSANAVYLVTKKGVVLFDVPWEKVQYQSLMDTIKKRHNLPVVAVFATHSHDDRAGDLSFFNKKGIKTYATAKTNELLKKEGKAVSSNIINTGKAYHIGGEEFVVDFIGEGHTVDNVVVWFPKYKVLDGGCLVKSTSATDLGYIKEANVEQWPQTMNTLKSKYSQATLIIPGHDEWKGGGHVEHTLELLNKK"},"dna_sequence":{"accession":"GU186045","fmin":"34","fmax":"754","strand":"+","sequence":"ATGAAAAAAAGCATACAGTTTTTTATTGTTTCCCTATTATTAAGTCCGTTTGCTAATGCTCAGGTAAAGGATTTTGTAATAGAACCTCCTATCAGCAAGAACTTATATATTTATAAAACTTTTGGTGTATTCGGAGGAAAAGAATATTCTGCCAACGCTGTTTACCTTGTCACAAAAAAAGGAGTAGTCCTGTTTGATGTTCCCTGGGAAAAAGTTCAGTACCAAAGCTTGATGGATACCATAAAAAAACGTCATAATTTACCTGTAGTGGCAGTATTTGCTACCCATTCTCATGATGACAGAGCCGGAGATTTAAGCTTCTTCAACAAAAAAGGGATTAAGACCTATGCCACGGCAAAAACCAATGAGTTATTGAAAAAAGAAGGTAAAGCGGTGTCCAGCAATATTATAAATACAGGGAAAGCTTATCATATAGGCGGAGAAGAATTTGTGGTTGATTTTATTGGAGAAGGACATACCGTAGATAATGTAGTGGTATGGTTTCCAAAATATAAAGTTCTTGATGGCGGCTGCTTAGTAAAAAGTACTTCTGCAACAGATTTAGGATATATCAAGGAAGCAAACGTTGAACAATGGCCACAAACTATGAATACTTTAAAATCCAAATACTCTCAGGCAACCTTAATCATTCCGGGACATGACGAATGGAAAGGCGGCGGACATGTAGAACATACATTAGAGCTTTTGAATAAAAAATAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36916","NCBI_taxonomy_name":"Chryseobacterium indologenes","NCBI_taxonomy_id":"253"}}}},"ARO_accession":"3002265","ARO_id":"38665","ARO_name":"IND-9","ARO_description":"IND-9 is a beta-lactamase found in Escherichia coli","ARO_category":{"36199":{"category_aro_accession":"3000060","category_aro_cvterm_id":"36199","category_aro_name":"IND beta-lactamase","category_aro_description":"IND beta-lactamases are class B carbapenem-hydrolyzing beta-lactamases","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1456":{"model_id":"1456","model_name":"IMP-15","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"772":{"protein_sequence":{"accession":"AAT49070.1","sequence":"MNKLSVFFMFMFCSITAAGESLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNTEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKDGKVQAKNSFSGGSYWLVNNKIEVFYPGPGHTPDNVVVWLPENRVLFGGCFVKPYGLGNLGDANLEAWPKSAKILMSKYGKAKLVVSSHSETGNASLLKLTWEQAVKGLKESKKPSLPSN"},"dna_sequence":{"accession":"AY553333","fmin":"113","fmax":"854","strand":"+","sequence":"ATGAACAAGTTATCTGTATTCTTTATGTTTATGTTTTGTAGCATTACTGCCGCAGGAGAGTCTTTGCCAGATTTAAAAATTGAGAAGCTTGACGAAGGTGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGTTGGGGTGTTGTTCCTAAACACGGCTTGGTGGTTCTTGTAAATACTGAGGCCTATCTGATTGACACTCCATTTACGGCAAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAGCGCGGCTATAAAATAAAAGGCAGTATTTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCAATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTTCTTAAAAAAGACGGTAAGGTACAAGCTAAAAATTCATTTAGCGGAGGTAGCTATTGGCTAGTTAATAATAAGATTGAAGTTTTTTATCCTGGTCCAGGGCACACTCCAGATAACGTAGTGGTTTGGCTACCTGAAAATAGAGTTTTGTTCGGTGGTTGTTTTGTTAAACCGTACGGTCTTGGTAATTTGGGTGACGCAAATTTAGAAGCTTGGCCAAAGTCCGCCAAAATATTAATGTCTAAATATGGTAAAGCAAAGTTGGTTGTTTCAAGTCATAGTGAAACTGGGAACGCATCACTCTTGAAACTTACTTGGGAGCAGGCTGTTAAAGGGCTAAAAGAAAGTAAAAAACCATCACTGCCAAGTAACTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002206","ARO_id":"38606","ARO_name":"IMP-15","ARO_description":"IMP-15 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1457":{"model_id":"1457","model_name":"CTX-M-13","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1627":{"protein_sequence":{"accession":"AAF72531.1","sequence":"MVTKRMQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTKDNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFAREIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"AF252623","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAATGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCAAAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGAGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001876","ARO_id":"38276","ARO_name":"CTX-M-13","ARO_description":"CTX-M-13 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1458":{"model_id":"1458","model_name":"TEM-157","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1491":{"protein_sequence":{"accession":"ABI81768.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQSDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"DQ909059","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGAGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTATTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAGTGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001023","ARO_id":"37403","ARO_name":"TEM-157","ARO_description":"TEM-157 is an extended-spectrum beta-lactamase found in Enterobacter cloacae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1459":{"model_id":"1459","model_name":"CTX-M-78","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1982":{"protein_sequence":{"accession":"CAQ42481.2","sequence":"MMRKSVRRAILMTTACVSLLLASVPLYAQANDIQQKLAALEKSSGGRLGVALINTADNTQTLYRADERFAMCSTSKVMAAAAVLKQSETQKDLLSQRVEIKSSDLINYNPIAEKHVNGTMTLGELSAAALQYSDNTAMNKLIAHLGGPGKVTAFARVIGDDTFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLRNLTLGNALGDTQRAQLVTWLKGNTTGAASIQAGLPTSWVVGDKTGSGDYGTTNDIAVIWPEGRAPLVLVTYFTQPEPKAESRRDVLAAAARIVTDGY"},"dna_sequence":{"accession":"AM982522","fmin":"0","fmax":"876","strand":"+","sequence":"ATGATGAGAAAAAGCGTAAGGCGGGCGATATTAATGACGACAGCCTGTGTTTCGCTGCTGTTGGCCAGTGTGCCGCTGTATGCCCAAGCGAACGATATTCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGGGGACGACTGGGTGTGGCGTTGATTAACACCGCCGATAACACGCAGACGCTCTACCGCGCCGACGAGCGTTTTGCTATGTGCAGCACCAGTAAAGTGATGGCGGCGGCGGCGGTGCTTAAGCAAAGTGAAACGCAAAAAGACTTACTGAGTCAGCGGGTTGAAATTAAGTCCTCAGACTTGATTAACTACAACCCAATCGCTGAAAAGCACGTCAATGGCACGATGACACTCGGGGAGCTGAGCGCGGCGGCGCTGCAGTACAGCGATAATACTGCCATGAATAAGCTGATTGCCCATCTCGGGGGGCCGGGTAAAGTGACGGCATTTGCTCGCGTGATTGGCGATGACACTTTCCGGCTCGATCGTACCGAGCCGACGCTCAACACCGCGATCCCCGGCGACCCGCGCGATACCACCACGCCGTTAGCGATGGCGCAGACTCTACGCAATCTCACATTGGGCAATGCCCTGGGTGACACTCAGCGTGCGCAGCTGGTGACGTGGCTGAAAGGCAACACCACCGGCGCTGCCAGCATTCAGGCAGGGCTACCCACATCGTGGGTTGTCGGGGATAAAACCGGCAGCGGCGATTATGGTACGACGAATGATATCGCGGTTATTTGGCCGGAAGGTCGCGCGCCGCTCGTTCTGGTGACTTACTTCACCCAGCCGGAGCCGAAGGCAGAGAGCCGTCGTGACGTGCTCGCTGCTGCCGCCAGAATAGTCACCGACGGTTATTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36929","NCBI_taxonomy_name":"Kluyvera georgiana","NCBI_taxonomy_id":"73098"}}}},"ARO_accession":"3001939","ARO_id":"38339","ARO_name":"CTX-M-78","ARO_description":"CTX-M-78 is a beta-lactamase found in Kluyvera georgiana","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1460":{"model_id":"1460","model_name":"FosB3","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"250"}},"model_sequences":{"sequence":{"418":{"protein_sequence":{"accession":"ADX95999.1","sequence":"MIKGINHITYSVSNIAKSIEFYRDILGADILVESETLAYFNLGGIWLALNEEKNIPRSEIKYSYTHIAFTISDNDFEDWYNWLKENEVNILEGRDRDIRDKKSIYFTDLDGHKLELHTGSLEDRLSYYKEAKPHMNFYI"},"dna_sequence":{"accession":"HQ219726","fmin":"385","fmax":"805","strand":"+","sequence":"ATGATTAAAGGAATAAATCATATTACTTATTCGGTTTCTAATATAGCTAAATCAATTGAATTTTACAGAGATATTTTAGGGGCTGACATTTTAGTTGAAAGTGAGACCTTGGCCTATTTTAATTTAGGTGGTATATGGTTAGCTTTGAACGAAGAAAAAAATATTCCTAGAAGCGAAATTAAATATTCGTATACTCATATAGCATTTACAATTTCAGATAACGATTTTGAAGATTGGTATAACTGGTTGAAAGAAAATGAAGTAAATATTCTTGAAGGTAGAGATAGAGATATTAGAGATAAAAAATCAATATATTTCACTGATTTAGATGGTCATAAATTAGAATTGCATACAGGAAGTTTAGAAGATAGATTGAGTTATTATAAAGAGGCTAAACCTCATATGAATTTTTATATTTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002873","ARO_id":"39307","ARO_name":"FosB3","ARO_description":"A thiol transferase that leads to the resistance of fosfomycin in Enterococcus faecium. Contrasting FosA, FosB is dependent on the cofactor Magnesium (II) and uses either bacillithiol to open up the epoxide ring of fosfomycin.","ARO_category":{"36272":{"category_aro_accession":"3000133","category_aro_cvterm_id":"36272","category_aro_name":"fosfomycin thiol transferase","category_aro_description":"Catalyzes the addition of a thiol group from a nucleophilic molecule to fosfomycin.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1342":{"model_id":"1342","model_name":"plasmid-encoded cat (pp-cat)","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"486":{"protein_sequence":{"accession":"BAA03718.1","sequence":"MEKKITGYTTVDISQWHRKEHFEAFQSVAQCTYNQTVQLDITAFLKTVKKNKHKFYPAFIHILARLMNAHPEFRMAMKDGELVIWDSVHPCYTVFHEQTETFSSLWSEYHDDFRQFLHIYSQDIACYGENLAYFPKGFIENMFFVSANPWVSFTSFDLNVANMDNFFAPVFTMGKYYTQGDKVLMPLAIQVHHAVCDGFHVGRMLNELQQYCDEWQGGA"},"dna_sequence":{"accession":"D16171","fmin":"382","fmax":"1042","strand":"+","sequence":"ATGGAGAAAAAAATCACTGGATATACCACCGTTGATATATCCCAATGGCATCGTAAAGAACATTTTGAGGCATTTCAGTCAGTTGCTCAATGTACCTATAACCAGACCGTTCAGCTGGATATTACGGCTTTCTTAAAAACCGTAAAGAAAAATAAGCACAAATTTTATCCGGCCTTTATTCACATTCTTGCCCGCCTGATGAATGCTCATCCGGAATTCCGTATGGCAATGAAAGACGGTGAGCTGGTGATATGGGATAGTGTTCACCCTTGTTACACCGTATTCCATGAGCAAACTGAAACGTTTTCATCGCTCTGGAGTGAATACCACGACGATTTCCGGCAGTTTCTACACATATATTCGCAAGATATAGCGTGTTACGGTGAAAACCTGGCCTATTTCCCCAAAGGGTTCATTGAGAATATGTTTTTCGTCTCAGCCAATCCCTGGGTGAGTTTCACCAGTTTTGATTTAAACGTGGCCAATATGGACAACTTCTTCGCCCCCGTTTTCACCATGGGCAAATATTATACGCAAGGCGACAAGGTGCTGATGCCGCTGGCGATTCAGGTTCATCATGCCGTTTGTGATGGCTTCCATGTCGGCAGAATGCTTAATGAATTACAACAGTACTGCGATGAGTGGCAGGGCGGGGCGTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39539","NCBI_taxonomy_name":"Photobacterium damselae subsp. piscicida","NCBI_taxonomy_id":"38294"}}}},"ARO_accession":"3002689","ARO_id":"39123","ARO_name":"plasmid-encoded cat (pp-cat)","ARO_description":"pp-cat is a plasmid-encoded variant of the cat gene found in Photobacterium damselae subsp. piscicida","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. cat is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Bacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini","category_aro_class_name":"AMR Gene Family"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1345":{"model_id":"1345","model_name":"tet(K)","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"850"}},"model_sequences":{"sequence":{"96":{"protein_sequence":{"accession":"YP_003283625.1","sequence":"MFSLYKKFKGLFYSVLFWLCILSFFSVLNEMVLNVSLPDIANHFNTTPGITNWVNTAYMLTFSIGTAVYGKLSDYINIKKLLIIGISLSCLGSLIAFIGHNHFFILIFGRLVQGVGSAAFPSLIMVVVARNITRKKQGKAFGFIGSIVALGEGLGPSIGGIIAHYIHWSYLLILPMITIVTIPFLIKVMVPGKSTKNTLDIVGIVLMSISIICFMLFTTNYNWTFLILFTIFFVIFIKHISRVSNPFINPKLGKNIPFMLGLFSGGLIFSIVAGFISMVPYMMKTIYHVNVATIGNSVIFPGTMSVIVFGYFGGFLVDRKGSLFVFILGSLSISISFLTIAFFVEFSMWLTTFMFIFVMGGLSFTKTVISKIVSSSLSEEEVASGMSLLNFTSFLSEGTGIAIVGGLLSLQLINRKLVLEFINYSSGVYSNILVAMAILIILCCLLTIIVFKRSEKQFE"},"dna_sequence":{"accession":"NC_013452","fmin":"2917","fmax":"4297","strand":"+","sequence":"TTGTTTAGTTTATATAAAAAATTTAAAGGTTTGTTTTATAGCGTTTTATTTTGGCTTTGTATTCTTTCATTTTTTAGTGTATTAAATGAAATGGTTTTAAATGTTTCTTTACCTGATATTGCAAATCATTTTAATACTACTCCTGGAATTACAAACTGGGTAAACACTGCATATATGTTAACTTTTTCGATAGGAACAGCAGTATATGGAAAATTATCTGATTATATAAATATAAAAAAATTGTTAATTATTGGTATTAGTTTGAGCTGTCTTGGTTCATTGATTGCTTTTATTGGTCACAATCACTTTTTTATTTTGATTTTTGGTAGGTTAGTACAAGGAGTAGGATCTGCTGCATTCCCTTCACTGATTATGGTGGTTGTAGCTAGAAATATTACAAGAAAAAAACAAGGCAAAGCCTTTGGTTTTATAGGATCAATTGTAGCTTTAGGTGAAGGGTTAGGTCCTTCAATAGGGGGAATAATAGCACATTATATTCATTGGTCTTACCTACTTATACTTCCTATGATTACAATAGTAACTATACCTTTTCTTATTAAAGTAATGGTACCTGGTAAATCAACAAAAAATACATTAGATATCGTAGGTATTGTTTTAATGTCTATAAGTATTATATGTTTTATGTTATTTACGACAAATTATAATTGGACTTTTTTAATACTCTTCACAATCTTTTTTGTGATTTTTATTAAACATATTTCAAGAGTTTCTAACCCTTTTATTAATCCTAAACTAGGGAAAAACATTCCGTTTATGCTTGGTTTGTTTTCTGGTGGGCTAATATTTTCTATAGTAGCTGGTTTTATATCAATGGTGCCTTATATGATGAAAACTATTTATCATGTAAATGTAGCGACAATAGGTAATAGTGTTATTTTTCCTGGAACCATGAGTGTTATTGTTTTTGGTTATTTTGGTGGTTTTTTAGTGGATAGAAAAGGATCATTATTTGTTTTTATTTTAGGATCATTGTCTATCTCTATAAGTTTTTTAACTATTGCATTTTTTGTTGAGTTTAGTATGTGGTTGACTACTTTTATGTTTATATTTGTTATGGGCGGATTATCTTTTACTAAAACAGTTATATCAAAAATAGTATCAAGTAGTCTTTCTGAAGAAGAAGTTGCTTCTGGAATGAGTTTGCTAAATTTCACAAGTTTTTTATCAGAGGGAACAGGTATAGCAATTGTAGGAGGTTTATTGTCACTACAATTGATTAATCGTAAACTAGTTCTGGAATTTATAAATTATTCTTCTGGAGTGTATAGTAATATTCTTGTAGCCATGGCTATCCTTATTATTTTATGTTGTCTTTTGACGATTATTGTATTTAAACGTTCTGAAAAGCAGTTTGAATAGT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35647","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus ED98","NCBI_taxonomy_id":"681288"}}}},"ARO_accession":"3000178","ARO_id":"36317","ARO_name":"tet(K)","ARO_description":"TetK is a tetracycline efflux protein found in both Gram-negative (Haemophilus and Gallibacterium) and Gram-positive (many species, including mycobacteria) bacteria.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1316":{"model_id":"1316","model_name":"Pseudomonas aeruginos catB6","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"295":{"protein_sequence":{"accession":"CAA11473.1","sequence":"MENYFDSPFKGKLLSEQVTNRNIKVGRYSYYSGYYHGHSFDDCARYLLPDRDDVDKLIIGSFCSIGSGASFIMAGNQGHRHDWVTSFPFFYMQEEPAFSSSTDAFQKAGDTIVGNDVWIGSEAMIMPGIKIGDGAVIGSRSLVTRDVEPYTIIGGNPAKQIKKRFSDEEISLLMEMEWWNWPLDKIKTAMPLLCSSDIFGLHRHWRGIAV"},"dna_sequence":{"accession":"AJ223604","fmin":"3017","fmax":"3650","strand":"+","sequence":"ATGGAAAATTACTTTGACAGTCCCTTCAAAGGGAAACTACTTTCAGAGCAAGTGACTAACCGCAACATCAAAGTTGGTCGGTACAGCTACTACTCTGGTTACTATCACGGGCATTCATTTGATGACTGCGCACGATACTTGCTCCCAGACCGTGATGACGTTGACAAACTAATCATCGGCAGCTTTTGCTCCATCGGAAGCGGGGCTTCTTTCATCATGGCGGGCAATCAGGGTCACCGGCATGACTGGGTAACATCTTTCCCTTTCTTCTACATGCAAGAAGAGCCAGCTTTTTCAAGTTCAACGGACGCCTTTCAAAAGGCCGGTGACACCATCGTCGGCAATGATGTCTGGATAGGATCAGAGGCAATGATTATGCCCGGCATCAAGATTGGAGATGGCGCGGTAATAGGCAGCCGATCGTTGGTGACGAGAGATGTAGAACCCTATACCATCATTGGCGGAAACCCTGCAAAGCAAATTAAAAAGCGATTCTCTGACGAGGAGATTTCATTACTCATGGAAATGGAGTGGTGGAACTGGCCGTTAGATAAAATCAAAACAGCTATGCCCCTTCTCTGCTCTTCAGACATTTTTGGTCTGCACAGGCATTGGCGTGGGATTGCCGTCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002678","ARO_id":"39112","ARO_name":"Pseudomonas aeruginosa catB6","ARO_description":"catB6 is a plasmid-encoded variant of the cat gene found in Pseudomonas aeruginosa","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. cat is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Bacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini","category_aro_class_name":"AMR Gene Family"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1461":{"model_id":"1461","model_name":"SHV-63","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"920":{"protein_sequence":{"accession":"ABY56290.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGENVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTNQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"EU342351","fmin":"172","fmax":"1033","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGAAAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAACCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001118","ARO_id":"37498","ARO_name":"SHV-63","ARO_description":"SHV-63 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1462":{"model_id":"1462","model_name":"LRA-19","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1748":{"protein_sequence":{"accession":"ACH59005.1","sequence":"MNSEMSQTSFKIRILVTCLLSIAQLTMAQQVQVTEPPITNQDWVKPYPPFRIVGNLYYVGTYDLACYLIVTPQGNILINTGLASSAPMIEASIKALGFKFSDTKILLTTQAHYDHVGAMAAIKKSTNAQLMIDEKDSPVMADGGSSDYELFGSTGSTYEPVKADRLLKNGDKITLGGTTLVMLHHPGHTKGSCSFLFDVKDESKSYKVLIANMPSIITSKKFSDIPTYPGIAEDYTYTFDAMKKVHFDIWLSSHASQFGMHSKHKPGEAYNPGVFIDRAGYDKAVGDLEDKFSKKKQADK"},"dna_sequence":{"accession":"EU408359","fmin":"3791","fmax":"4694","strand":"+","sequence":"ATGAACTCAGAAATGTCTCAAACTTCTTTTAAAATCAGGATATTGGTGACCTGCCTCCTATCCATTGCCCAGTTAACAATGGCGCAACAAGTACAGGTAACTGAACCCCCGATCACAAATCAGGATTGGGTCAAACCCTATCCTCCATTCCGTATAGTCGGCAATTTGTATTATGTGGGCACTTACGATTTAGCCTGTTACCTCATTGTCACCCCACAGGGGAATATCCTTATCAATACAGGACTCGCTTCCTCCGCGCCTATGATCGAGGCAAGCATCAAAGCATTAGGCTTCAAGTTTTCCGACACGAAAATTCTGTTGACAACCCAGGCCCATTACGATCATGTGGGCGCCATGGCCGCAATTAAAAAGTCAACCAACGCGCAACTTATGATTGATGAAAAAGATTCACCCGTGATGGCTGATGGTGGAAGCTCGGATTATGAATTGTTTGGAAGTACCGGCAGCACCTATGAACCGGTTAAGGCCGATAGGCTTTTAAAGAATGGCGATAAAATAACATTGGGAGGTACCACCCTTGTCATGCTCCATCACCCCGGTCACACCAAAGGCTCATGTAGTTTTCTGTTTGATGTGAAAGACGAGAGCAAATCCTACAAAGTACTTATCGCCAACATGCCATCGATCATCACATCTAAAAAGTTTTCCGACATACCCACATATCCTGGCATTGCCGAAGACTATACCTACACGTTCGATGCAATGAAAAAAGTGCACTTCGATATCTGGCTCTCCTCACATGCTAGTCAGTTTGGGATGCATTCAAAACACAAACCAGGTGAAGCCTACAACCCTGGTGTCTTCATAGACCGGGCCGGATATGACAAGGCTGTGGGTGATCTGGAAGATAAATTTTCAAAAAAGAAGCAGGCGGACAAATAGG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39089","NCBI_taxonomy_name":"uncultured bacterium BLR19","NCBI_taxonomy_id":"506519"}}}},"ARO_accession":"3002513","ARO_id":"38913","ARO_name":"LRA-19","ARO_description":"LRA-19 is a beta-lactamase isolated from soil samples in Alaska","ARO_category":{"41390":{"category_aro_accession":"3004226","category_aro_cvterm_id":"41390","category_aro_name":"subclass B3 LRA beta-lactamase","category_aro_description":"Beta-lactamases that are part of the LRA gene family and are classified as B3 (metallo-) beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1463":{"model_id":"1463","model_name":"GES-19","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1090":{"protein_sequence":{"accession":"AEZ05107.1","sequence":"MRFIHALLLAAIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMGDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGARNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"JN596280","fmin":"1918","fmax":"2782","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGCGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGGGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGCCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAGT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002348","ARO_id":"38748","ARO_name":"GES-19","ARO_description":"GES-19 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1464":{"model_id":"1464","model_name":"aadA7","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"516":{"protein_sequence":{"accession":"BAD00739.1","sequence":"MSEKVPAEISVQLSQALNGIGRHLESTLLAVHLYGSALDGGLKPYSDIDLLVTVAAPLNDAVRQALLVDLLEVSASPGQNKALRALEVTIVVHSDIVPWRYPARRELQFGEWQRKDILAGIFEPATTDSDLAILLTKAKQHSVVLAGSAAKDLFSSVPESDLFKALADTLKLWNSPPDWAGDERNVVLTLSRIWYTAATGKIAPKDVAATWAMARLPAQHQPILLNAKRAYLGQEEDYLPARADQVAALIKFVKYEAVKLLGASQ"},"dna_sequence":{"accession":"AB114632","fmin":"655","fmax":"1453","strand":"+","sequence":"ATGAGTGAAAAAGTGCCCGCCGAGATTTCGGTGCAACTATCACAAGCACTCAACGGCATCGGGCGCCACTTGGAGTCGACGTTGCTGGCCGTGCATTTGTACGGCTCCGCACTGGATGGCGGATTGAAACCGTACAGTGATATTGATTTGCTGGTGACTGTAGCTGCACCGCTCAATGATGCCGTGCGGCAAGCCCTGCTCGTCGATCTCTTGGAGGTTTCAGCTTCCCCTGGCCAAAACAAGGCACTCCGCGCCTTGGAAGTGACCATCGTCGTGCACAGTGACATCGTACCTTGGCGTTATCCGGCCAGGCGGGAACTGCAGTTCGGAGAGTGGCAGCGCAAAGACATCCTTGCGGGCATCTTCGAGCCCGCCACAACCGATTCTGACTTGGCGATTCTGCTAACAAAGGCAAAGCAACATAGCGTCGTCTTGGCAGGTTCAGCAGCGAAGGATCTCTTCAGCTCAGTCCCAGAAAGCGATCTATTCAAGGCACTGGCCGATACTCTGAAGCTATGGAACTCGCCGCCAGATTGGGCGGGCGATGAGCGGAATGTAGTGCTTACTTTGTCTCGTATCTGGTACACCGCAGCAACCGGCAAGATCGCGCCAAAGGATGTTGCTGCCACTTGGGCAATGGCACGCTTGCCAGCTCAACATCAGCCCATCCTGTTGAATGCCAAGCGGGCTTATCTTGGGCAAGAAGAAGATTATTTGCCCGCTCGTGCGGATCAGGTGGCGGCGCTCATTAAATTCGTGAAGTATGAAGCAGTTAAACTGCTTGGTGCCAGCCAATGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39525","NCBI_taxonomy_name":"Vibrio fluvialis","NCBI_taxonomy_id":"676"}}}},"ARO_accession":"3002607","ARO_id":"39007","ARO_name":"aadA7","ARO_description":"aadA7 is an integron-encoded aminoglycoside nucleotidyltransferase gene in V. fluvialis, P. aeruginosa, E. coli, V. cholerae and S. enterica","ARO_category":{"41439":{"category_aro_accession":"3004275","category_aro_cvterm_id":"41439","category_aro_name":"ANT(3'')","category_aro_description":"Nucleotidylylation of streptomycin at the hydroxyl group at position 3''","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1466":{"model_id":"1466","model_name":"SHV-13","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1063":{"protein_sequence":{"accession":"AAD43815.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAAERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AF164577","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGCCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001072","ARO_id":"37452","ARO_name":"SHV-13","ARO_description":"SHV-13 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1467":{"model_id":"1467","model_name":"LEN-22","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1809":{"protein_sequence":{"accession":"CAP12350.2","sequence":"MRYVRLCVISLLATLPLAVDAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGLEQLDRRIHYRQQDLVDYSPVSEKHLVDGMTIGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSPRSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGARGIVALLGPDGKPERIVVIYLRDTPASMAERNQHIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM850912","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCACCCTGCCACTGGCGGTAGACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGTCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCCCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGACAAGACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002469","ARO_id":"38869","ARO_name":"LEN-22","ARO_description":"LEN-22 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1468":{"model_id":"1468","model_name":"SHV-135","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1311":{"protein_sequence":{"accession":"ADR66517.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLKQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMTATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"HQ637576","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTAAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGACCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001179","ARO_id":"37559","ARO_name":"SHV-135","ARO_description":"SHV-135 is a beta-lactamase.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1469":{"model_id":"1469","model_name":"facT","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1050"}},"model_sequences":{"sequence":{"687":{"protein_sequence":{"accession":"AFK80333.1","sequence":"MNKAGQAEKPAAAGPPATPETPEPDPKRWLALTVLLVATFMDLLDANIITVAIPSIQRDLGASTFAIQAMTAGYTLSFAVLLITGGRLGDIFGRKRMFLVGVGGFVLASAMCAAAPSTDLLVVARALQGLTAAVMVPQVLALIHVSFAPQEIGRVVSLYASMVGLAIVSGPLIGGALISWNPLDLGWRSIFVVNLPVGVLALVGAAKWMRESSSPHAKRLDIAGMLLIVLGLLLLMVPLTLGRELDWPVWSIVSLVAAAPVLVLFVVYERHKTAKDGSPLVTLSLFKVRAFGAGIGVQLLFSAIPAGFFLSWTLYLQAGLGWSALHTGLTAIPFSLCVPIVGGLAVRRLSPLYGRYCLLAGAVLMLAGILSYAWAADRFGTDITSWHAIPSMLLIGSGMGMLMPPLTALVLREVQPQEAGAASGIINATGQLGAALGVAVIGSLFFAALAGNAGPQAERVAPTVQSVSPRQASDLRDCATEALGQDDLAKVPDICSTLVQGADDGTRDTINGALGEIRAKTFVSTYSETLYWAAGGLVPVTALVLLLPHHRVRREEPAQ"},"dna_sequence":{"accession":"JQ768046","fmin":"7760","fmax":"9440","strand":"+","sequence":"ATGAACAAGGCAGGGCAGGCAGAAAAGCCGGCGGCAGCCGGCCCACCTGCCACTCCCGAGACGCCCGAGCCCGACCCGAAGCGGTGGCTCGCGCTGACAGTCCTGCTGGTCGCCACCTTCATGGACCTGCTCGACGCGAACATCATCACCGTGGCCATCCCGAGCATCCAACGCGACCTCGGCGCCTCGACCTTCGCCATCCAGGCGATGACGGCCGGCTACACCCTGAGCTTCGCGGTCCTGCTGATCACCGGCGGCCGGCTCGGCGACATCTTCGGCCGCAAGCGCATGTTCCTCGTCGGCGTCGGCGGCTTCGTCCTCGCGTCCGCGATGTGCGCCGCCGCGCCGAGCACCGACTTACTCGTCGTCGCCCGCGCGCTCCAGGGCCTCACCGCCGCCGTCATGGTGCCCCAGGTGCTCGCGCTCATCCACGTCTCCTTCGCGCCCCAGGAGATCGGCCGCGTCGTCAGCCTGTACGCGAGCATGGTCGGTCTGGCCATCGTCTCCGGGCCCCTCATCGGCGGTGCGCTGATCAGCTGGAACCCGCTGGACCTCGGCTGGCGCAGCATCTTCGTGGTGAACCTGCCGGTCGGCGTGCTCGCCCTGGTCGGCGCCGCGAAGTGGATGCGGGAGTCGAGCTCCCCCCATGCGAAGCGCCTGGACATCGCCGGCATGCTGCTGATCGTGCTCGGCCTGCTGCTGCTCATGGTGCCGCTGACCCTCGGCCGCGAGCTCGACTGGCCGGTGTGGAGCATCGTCTCGCTCGTCGCCGCCGCCCCCGTCCTCGTGCTGTTCGTCGTCTACGAGCGCCACAAGACCGCCAAGGACGGCTCGCCCCTGGTGACGCTGTCCCTGTTCAAGGTCCGCGCGTTCGGCGCCGGCATCGGCGTCCAGCTCCTCTTCAGCGCCATCCCCGCGGGCTTCTTCCTCAGCTGGACCCTCTACCTCCAGGCCGGCCTCGGCTGGTCGGCCCTGCACACGGGCCTGACCGCCATCCCGTTCTCCCTGTGCGTCCCGATCGTCGGCGGTCTCGCCGTCCGCAGGCTCTCGCCGCTCTACGGCCGCTACTGCCTGCTCGCCGGTGCCGTCCTGATGCTCGCGGGCATCCTCTCCTACGCCTGGGCGGCCGACCGCTTCGGCACGGACATCACCTCCTGGCACGCGATCCCGTCCATGCTCCTGATCGGCTCCGGCATGGGCATGCTGATGCCCCCGCTGACGGCGCTGGTGCTCAGGGAGGTCCAGCCGCAGGAGGCCGGCGCCGCCTCCGGCATCATCAACGCCACCGGCCAGCTCGGTGCCGCGCTCGGCGTGGCGGTCATCGGCAGCCTCTTCTTCGCGGCCCTCGCCGGCAACGCCGGGCCGCAGGCCGAACGCGTCGCCCCCACCGTGCAGTCGGTCTCACCCCGGCAGGCCTCCGACCTCCGGGACTGCGCGACCGAGGCGCTGGGCCAGGACGACCTGGCCAAGGTCCCGGACATCTGCTCCACCCTGGTGCAGGGCGCCGACGACGGCACCCGGGATACGATCAATGGCGCGCTCGGCGAGATCCGCGCGAAGACGTTCGTGTCCACCTACAGCGAGACGCTGTACTGGGCGGCCGGTGGCCTCGTCCCGGTCACCGCCCTCGTCCTGCTCCTGCCGCACCACCGCGTCCGGCGGGAGGAACCGGCCCAGTGAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37730","NCBI_taxonomy_name":"Streptomyces sp. WAC5292","NCBI_taxonomy_id":"1194538"}}}},"ARO_accession":"3001313","ARO_id":"37712","ARO_name":"facT","ARO_description":"Efflux protein facT confers resistance to factumycin. The gene has been heterologously expressed in S. coelicolor and its function was confirmed (Thaker et al. Med. Chem. Commun. 2012, 3: 1020). It is possible that this gene can efflux other kirromycin-like elfamycins, but this has not been tested.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"37619":{"category_aro_accession":"3001220","category_aro_cvterm_id":"37619","category_aro_name":"factumycin","category_aro_description":"Factumycin is a kirromycin-like antibiotic produced by Kitasatospora setae and Streptomyces strains. Its biosynthetic cluster has been characterized which has interesting acetyl transferase domains in trans, or outside of the polyketide synthase domains. Factumycin has specific, rather than broad spectrum,  antibacterial properties, especially targeting various Acinetobacter baumanii strains.","category_aro_class_name":"Antibiotic"},"37618":{"category_aro_accession":"3001219","category_aro_cvterm_id":"37618","category_aro_name":"elfamycin antibiotic","category_aro_description":"Elfamycins are molecules that inhibit bacterial elongation factor Tu (EF-Tu), a key protein which brings aminoacyl-tRNA (aa-tRNA) to the ribosome during protein synthesis. Elfamycins defined by their target (EF-Tu), rather than a conserved chemical backbone. Elfamycins follow two mechanisms to disrupt protein synthesis: 1. kirromycins and enacyloxin fix EF-Tu in the GTP bound conformation and lock EF-Tu onto the ribosome, and 2. pulvomycin and GE2270 cover the binding site of aa-tRNA disallowing EF-Tu from being charged with aa-tRNA. All elfamycins cause increased the affinity of EF-Tu for GTP.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1470":{"model_id":"1470","model_name":"QnrB26","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"114":{"protein_sequence":{"accession":"AEH59666.1","sequence":"MTPLLYKKTGTNMALALVGVKIDRNRFTGEKIENGTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNASALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"HQ386846","fmin":"0","fmax":"681","strand":"+","sequence":"ATGACGCCATTACTGTATAAAAAAACAGGTACAAATATGGCTCTGGCACTCGTTGGCGTAAAAATTGACAGAAACCGTTTCACCGGTGAGAAAATTGAAAATGGTACATTTTTTAATTGTGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCGATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATGCCAGTGCGCTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGCGCAAGCTTTATGAATATGATCACCACGCGCACCTGGTTTTGTAGCGCATATATCACGAATACCAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAGCTGTGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCGAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTGACTTAGATATTCGGGGCGTTGATTTACAAGGCGTTAAGCTGGACAACTACCAGGCGTCGTTGCTCATGGAGCGGCTTGGCATCGCGGTGATTGGTTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36943","NCBI_taxonomy_name":"Proteus vulgaris","NCBI_taxonomy_id":"585"}}}},"ARO_accession":"3002741","ARO_id":"39175","ARO_name":"QnrB26","ARO_description":"QnrB26 is a plasmid-mediated quinolone resistance protein found in Proteus vulgaris","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1471":{"model_id":"1471","model_name":"adeI","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"526":{"protein_sequence":{"accession":"YP_002320475.1","sequence":"MMSAKLWAPALTACALATSIALVGCSKGSDEKQQAAAAQKMPPAEVGVIVAQPQSVEQSVELSGRTSAYQISEVRPQTSGVILKRLFAEGSYVREGQALYELDSRTNRATLENAKASLLQQQANLASLRTKLNRYKQLVSSNAVSKQEYDDLLGQVNVAEAQVAAAKAQVTNANVDLGYSTIRSPISGQSGRSSVTAGALVTANQTDPLVTIQQLDPIYVDINQSSAELLRLRQQLSKGSLNNSNNTKVKLKLEDGSTYPIEGQLAFSDASVNQDTGTITLRAVFSNPNHLLLPGMYTTAQIVQGVVPNAYLIPQAAITRLPTGQAVAMLVNAKGVVESRPVETSGVQGQNWIVTNGLKAGDKVIVDGVAKVKEGQEVSAKPYQAQPANSQGAAPNAAKPAQSGKPQAEQKAASNA"},"dna_sequence":{"accession":"NC_011586","fmin":"3278907","fmax":"3280158","strand":"+","sequence":"ATGATGTCGGCTAAGCTTTGGGCACCAGCCCTTACTGCTTGCGCATTAGCAACAAGTATCGCGCTTGTTGGTTGTAGCAAAGGCTCCGATGAGAAACAGCAAGCTGCTGCTGCTCAGAAAATGCCGCCTGCAGAAGTAGGTGTTATTGTTGCTCAACCACAAAGTGTTGAACAAAGCGTTGAGCTTTCAGGCCGTACTTCAGCATATCAAATTTCTGAAGTTCGTCCTCAAACAAGTGGCGTGATTTTAAAACGTTTATTTGCTGAAGGAAGCTATGTTCGTGAAGGTCAGGCGCTTTATGAGCTCGACTCTAGAACGAACCGTGCAACGTTAGAAAATGCAAAAGCATCACTCCTACAACAACAGGCAAATCTAGCTTCACTACGTACCAAGTTAAATCGTTATAAACAACTTGTTTCTAGTAATGCTGTGTCTAAACAGGAATATGATGACTTACTTGGTCAAGTCAATGTTGCAGAAGCACAAGTTGCAGCAGCTAAGGCTCAAGTAACAAATGCAAATGTAGATCTTGGTTATTCTACAATTCGCTCTCCTATTTCTGGCCAATCTGGTCGTTCTTCAGTAACGGCTGGTGCTTTGGTTACTGCAAACCAGACTGACCCGTTGGTAACGATTCAACAATTAGATCCTATCTATGTTGATATTAATCAGTCTAGTGCTGAGTTATTGCGTTTACGTCAACAACTAAGCAAAGGCAGTTTAAATAACAGTAACAACACGAAAGTAAAATTAAAGCTTGAAGATGGTTCTACCTATCCAATCGAAGGGCAACTTGCTTTCTCTGACGCTTCTGTAAACCAAGATACAGGAACAATTACATTACGTGCCGTATTCTCTAACCCGAATCATTTATTGCTTCCGGGTATGTATACCACTGCGCAAATTGTTCAGGGCGTTGTTCCAAATGCTTACCTGATTCCTCAAGCTGCCATTACTCGTTTACCTACAGGACAAGCTGTAGCGATGCTTGTTAATGCTAAAGGGGTTGTTGAGAGCCGTCCTGTTGAAACCTCTGGTGTTCAAGGACAAAACTGGATTGTGACTAACGGCTTAAAAGCCGGCGATAAAGTCATTGTTGATGGTGTTGCCAAAGTTAAAGAAGGGCAAGAAGTATCAGCAAAACCTTATCAAGCTCAACCAGCAAACTCTCAAGGTGCAGCACCAAATGCTGCGAAACCGGCTCAATCAGGTAAACCTCAAGCAGAACAGAAAGCAGCTTCAAATGCATAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35531","NCBI_taxonomy_name":"Acinetobacter baumannii AB0057","NCBI_taxonomy_id":"480119"}}}},"ARO_accession":"3000780","ARO_id":"37160","ARO_name":"adeI","ARO_description":"AdeI is the membrane fusion protein of the AdeIJK multidrug efflux complex.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36309":{"category_aro_accession":"3000170","category_aro_cvterm_id":"36309","category_aro_name":"imipenem","category_aro_description":"Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"40523":{"category_aro_accession":"3003832","category_aro_cvterm_id":"40523","category_aro_name":"ticarcillin","category_aro_description":"Ticarcillin is a carboxypenicillin used for the treatment of Gram-negative bacteria, particularly P. aeruginosa. Ticarcillin's antibiotic properties arise from its ability to prevent cross-linking of peptidoglycan during cell wall synthesis, when the bacteria try to divide, causing cell death.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1472":{"model_id":"1472","model_name":"DHA-18","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1171":{"protein_sequence":{"accession":"AIT76094.1","sequence":"MKKSLSATLISALLAFSAPGFSAADNVAAVVDSTIKPLMAQQDIPGMAVAVSVKGKPYYFNYGFADVQAKQPVTENTLFELGSVSKTFTGVLGAVSVAKKETALNDPAAKYQPELALPQWKGITLLDLATYTAGGLPLQVPDAVKSRADLLNFYQQWQPSWKPGDMRLYANSSIGLFGALTANAAGMPYEQLLTARILAPLGLSHTFITVPESVQSRYAYGYKNKKPVRVSPGQLDAESYGVKSASKDMLRWAEMNMEPSRAGNADLEMAMYLAQTRYYKTAAINQGLGWEMYDWPQQKDMIINGVTNEVALQPHPVTDNQVQPYNRASWVHKTGATTGFGAYVAFIPEKQVAIVILANKNYPNTERVKAAQAILSALE"},"dna_sequence":{"accession":"KM087841","fmin":"0","fmax":"1140","strand":"+","sequence":"ATGAAAAAATCGTTATCTGCAACACTGATTTCTGCCCTGCTGGCGTTTTCCGCCCCGGGGTTTTCTGCCGCTGATAATGTCGCAGCGGTGGTGGACAGCACTATTAAACCGCTGATGGCACAGCAGGATATTCCCGGGATGGCGGTTGCCGTATCCGTAAAGGGCAAGCCCTATTATTTTAACTATGGTTTTGCCGATGTTCAGGCAAAACAGCCGGTCACTGAAAATACACTATTTGAGCTCGGATCTGTAAGTAAAACTTTCACAGGTGTGCTGGGTGCGGTTTCTGTGGCGAAAAAAGAGACGGCGCTGAATGATCCGGCGGCAAAATATCAGCCGGAGCTGGCTCTGCCGCAGTGGAAGGGGATCACGCTGCTGGATCTGGCCACCTATACCGCAGGCGGGCTGCCGTTACAGGTACCGGATGCGGTGAAAAGCCGTGCGGATCTGCTGAATTTCTATCAGCAGTGGCAGCCATCATGGAAACCGGGCGATATGCGTCTGTATGCAAACAGCAGTATCGGCCTGTTTGGTGCTCTGACCGCCAATGCGGCGGGGATGCCGTATGAGCAGTTGCTGACCGCGCGGATCCTGGCACCGCTGGGATTATCTCACACCTTTATTACCGTGCCGGAAAGTGTGCAAAGCCGGTATGCGTACGGCTATAAAAACAAAAAACCGGTCCGCGTGTCGCCGGGACAGCTTGATGCGGAATCTTACGGCGTGAAATCCGCCTCAAAAGATATGCTGCGCTGGGCGGAAATGAATATGGAGCCGTCACGGGCCGGTAATGCGGATCTGGAAATGGCAATGTATCTCGCCCAGACCCGCTACTATAAAACCGCCGCGATTAACCAGGGGCTGGGCTGGGAAATGTATGACTGGCCGCAGCAGAAAGATATGATCATTAACGGTGTGACCAACGAGGTCGCATTGCAGCCGCATCCGGTAACAGACAACCAGGTTCAGCCGTATAACCGTGCTTCCTGGGTGCATAAAACGGGGGCAACAACTGGTTTCGGCGCCTATGTGGCCTTTATTCCGGAAAAACAGGTGGCGATTGTGATTCTGGCGAATAAAAACTACCCGAATACCGAAAGAGTCAAAGCTGCACAGGCTATTTTGAGTGCACTGGAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36917","NCBI_taxonomy_name":"Morganella morganii","NCBI_taxonomy_id":"582"}}}},"ARO_accession":"3002149","ARO_id":"38549","ARO_name":"DHA-18","ARO_description":"DHA-18 is a beta-lactamase. From the Lahey list of DHA beta-lactamases.","ARO_category":{"36207":{"category_aro_accession":"3000068","category_aro_cvterm_id":"36207","category_aro_name":"DHA beta-lactamase","category_aro_description":"DHA beta-lactamases are plasmid-mediated AmpC \u03b2-lactamases that confer resistance to cephamycins and oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1473":{"model_id":"1473","model_name":"CTX-M-44","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1903":{"protein_sequence":{"accession":"BAA07082.1","sequence":"MMTQSIRRSMLTVMATLPLLFSSATLHAQANSVQQQLEALEKSSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKQSESDKHLLNQRVEIKKSDLVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSASIRAGLPKSWVVGDKTGSGDYGTTNDIAVIWPENHAPLVLVTYFTQPEQKAERRRDILAAAAKIVTHGF"},"dna_sequence":{"accession":"D37830","fmin":"90","fmax":"966","strand":"+","sequence":"ATGATGACTCAGAGCATTCGCCGCTCAATGTTAACGGTGATGGCGACGCTACCCCTGCTATTTAGCAGCGCAACGCTGCATGCGCAGGCGAACAGCGTGCAACAGCAGCTGGAAGCCCTGGAGAAAAGTTCGGGAGGTCGGCTTGGCGTTGCGCTGATTAACACCGCCGATAATTCGCAGATTCTCTACCGTGCCGATGAACGTTTTGCGATGTGCAGTACCAGTAAGGTGATGGCGGCCGCGGCGGTGCTTAAACAGAGCGAGAGCGATAAGCACCTGCTAAATCAGCGCGTTGAAATCAAGAAGAGCGACCTGGTTAACTACAATCCCATTGCGGAGAAACACGTTAACGGCACGATGACGCTGGCTGAGCTTGGCGCAGCGGCGCTGCAGTATAGCGACAATACTGCCATGAATAAGCTGATTGCCCATCTGGGTGGTCCCGATAAAGTGACGGCGTTTGCTCGCTCGTTGGGTGATGAGACCTTCCGTCTGGACAGAACCGAGCCCACGCTCAATACCGCCATTCCAGGCGACCCGCGTGATACCACCACGCCGCTCGCGATGGCGCAGACCCTGAAAAATCTGACGCTGGGTAAAGCGCTGGCGGAAACTCAGCGGGCACAGTTGGTGACGTGGCTTAAGGGCAATACTACCGGTAGCGCGAGCATTCGGGCGGGTCTGCCGAAATCATGGGTAGTGGGCGATAAAACCGGCAGCGGAGATTATGGCACCACCAACGATATCGCGGTTATCTGGCCGGAAAACCACGCACCGCTGGTTCTGGTGACCTACTTTACCCAACCGGAGCAGAAGGCGGAAAGGCGTCGGGATATTCTGGCTGCGGCGGCGAAAATCGTAACCCACGGTTTCTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001906","ARO_id":"38306","ARO_name":"CTX-M-44","ARO_description":"CTX-M-44 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1475":{"model_id":"1475","model_name":"SHV-99","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1070":{"protein_sequence":{"accession":"CAQ03504.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVGYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM941845","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGGCTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATCGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001337","ARO_id":"37737","ARO_name":"SHV-99","ARO_description":"SHV-99 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1476":{"model_id":"1476","model_name":"TEM-199","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1648":{"protein_sequence":{"accession":"AFN69127.1","sequence":"QHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNIGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"JX050178","fmin":"0","fmax":"852","strand":"+","sequence":"TCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATTGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3001058","ARO_id":"37438","ARO_name":"TEM-199","ARO_description":"TEM-199 is a beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1477":{"model_id":"1477","model_name":"SHV-39","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1638":{"protein_sequence":{"accession":"AAN77730.1","sequence":"ALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASERGARGIVALLGPNNKAERIVVIYLRDS"},"dna_sequence":{"accession":"AY150585","fmin":"0","fmax":"285","strand":"+","sequence":"GCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATTCC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001097","ARO_id":"37477","ARO_name":"SHV-39","ARO_description":"SHV-39 is an extended-spectrum beta-lactamase that has been found in clinical isolates.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1478":{"model_id":"1478","model_name":"CARB-10","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1856":{"protein_sequence":{"accession":"ACJ61335.1","sequence":"MDVRQHKASFFSVVITFLCLTLSLNANATDSVLEAVTNAETELGARIGLAAHDLETGKRWEHKSNERFPLTSTFKTLACANVLQRVDLGKERIDRVVRFSESNLVTYSPVTEKHVGKKGMSLAELCQATLSTSDNSAANFILQAIGGPKALTKFLRSIGDDTTRLDRWETELNEAVPGDKRDTTTPIAMVTTLEKLLIDETLSIKSRQQLESWLKGNEVGDALFRKGVPSDWIVADRTGAGGYGSRAITAVMWPPNRKPIVAALYITETDASFEERNAVIAKIGEQIAKTVLMENSRN"},"dna_sequence":{"accession":"EU850412","fmin":"2269","fmax":"3166","strand":"+","sequence":"ATGGACGTACGTCAACACAAGGCTAGTTTTTTTAGCGTAGTAATTACTTTTTTATGTCTCACGCTATCATTAAATGCTAATGCAACAGACTCAGTACTTGAAGCGGTTACCAATGCTGAAACTGAATTAGGCGCTAGAATTGGTCTAGCTGCGCATGATTTGGAAACGGGAAAACGTTGGGAACATAAATCTAATGAACGTTTTCCTCTAACTAGTACCTTTAAAACACTTGCCTGTGCAAACGTTCTTCAAAGAGTTGATCTAGGTAAAGAAAGAATTGATAGAGTTGTGAGATTCTCTGAAAGCAATCTCGTTACATACTCACCTGTAACAGAAAAACATGTGGGTAAAAAAGGGATGTCGCTCGCAGAGCTGTGTCAGGCCACATTATCAACCAGTGATAATTCAGCTGCCAATTTTATTCTACAAGCGATTGGGGGACCTAAGGCTCTAACGAAATTTTTGCGTTCCATTGGCGACGATACTACGCGCCTTGATCGCTGGGAAACAGAACTTAACGAAGCGGTGCCTGGAGATAAGCGAGACACGACAACACCAATTGCAATGGTAACGACACTTGAAAAGTTACTAATTGACGAAACACTATCTATCAAATCTCGTCAACAACTAGAATCTTGGCTTAAAGGTAATGAGGTTGGCGATGCATTGTTTCGTAAAGGCGTTCCAAGTGACTGGATAGTAGCAGATAGAACAGGCGCTGGTGGTTATGGGTCGCGTGCTATTACTGCGGTGATGTGGCCTCCAAATCGCAAGCCTATCGTAGCCGCTCTATACATTACAGAGACAGACGCCTCGTTTGAAGAAAGAAATGCTGTCATTGCAAAAATTGGTGAGCAAATAGCGAAGACAGTATTAATGGAGAATAGCCGTAACTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3002249","ARO_id":"38649","ARO_name":"CARB-10","ARO_description":"CARB-10 is a beta-lactamase found in Acinetobacter baumannii","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1479":{"model_id":"1479","model_name":"IMP-40","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1868":{"protein_sequence":{"accession":"BAM62794.1","sequence":"MSKLSVFFIFLFCSIATAAESLPDLKIEKLDEGVYVHTSFEEVNGWGVFPKHGLVVLVNAEAYLIDTPSTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNESKKPSKPSN"},"dna_sequence":{"accession":"AB753457","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAGCAAGTTATCTGTATTCTTTATATTTTTGTTTTGCAGCATTGCTACCGCAGCAGAGTCTTTGCCAGATTTAAAAATTGAAAAGCTTGATGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGGTGGGGCGTTTTTCCTAAACATGGTTTGGTGGTTCTTGTAAATGCTGAGGCTTACCTAATTGACACTCCATCTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAGCGTGGCTATAAAATAAAAGGCAGCATTTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCGATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTGCTTAAAAAAGACGGTAAGGTTCAAGCCACAAATTCATTTAGCGGAGTTAACTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCGGGACACACTCCAGATAACGTAGTGGTTTGGTTGCCTGAAAGGAAAATATTATTCGGTGGTTGTTTTATTAAACCGTACGGTTTAGGCAATTTGGGTGACGCAAATATAGAAGCTTGGCCAAAGTCCGCCAAATTATTAAAGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAAGTCACAGTGAAGTTGGAGACGCATCACTCTTGAAACTTACATTAGAGCAGGCGGTTAAAGGGTTAAACGAAAGTAAAAAACCATCAAAACCAAGCAACTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002231","ARO_id":"38631","ARO_name":"IMP-40","ARO_description":"IMP-40 is a beta-lactamase found in Pseudomonas and Acinetobacter spp.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1480":{"model_id":"1480","model_name":"EXO beta-lactamase","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"3292":{"protein_sequence":{"accession":"AAA26775.1","sequence":"MHPSTSRPSRRTLLTATAGAALAAATLVPGTAHASSGGRGHGSGSVSDAERRLAGLERASGARLGVYAYDTGSGRTVAYRADELFPMCSVFKTLSSAAVLRDLDRNGEFLSRRILYTQDDVEQADGAGPETGKPQNLANAQLTVEELCEVSITASDNCAANLMLRELGGPAAVTRFVRSLGDRVTRLDRWEPELNSAEPGRVTDTTSPRAITRTYGRLVLGDALNPRDRRLLTSWLLANTTSGDRFRAGLPDDWTLGDKTGAGRYGTNNDAGVTWPPGRAPIVLTVLTAKTEQDAARDDGLVADAARVLAETLG"},"dna_sequence":{"accession":"M28303","fmin":"242","fmax":"1187","strand":"+","sequence":"GTGCACCCCAGCACTTCCCGTCCCTCCCGCCGCACCCTGTTGACCGCCACGGCGGGCGCAGCCCTGGCCGCCGCCACACTCGTACCCGGTACCGCGCACGCCTCCTCCGGCGGGCGGGGCCACGGTTCCGGTTCCGTCTCCGACGCCGAACGGCGGCTCGCGGGGCTGGAGCGGGCCAGTGGGGCGCGGCTCGGGGTGTACGCGTACGACACGGGGAGCGGGCGGACGGTCGCGTACCGGGCCGACGAGCTGTTCCCGATGTGTTCGGTGTTCAAGACGCTGTCGTCGGCGGCCGTTCTGCGGGACCTCGACCGGAACGGGGAGTTCCTGTCCCGCCGGATCTTGTACACGCAGGACGACGTGGAGCAGGCCGACGGCGCCGGCCCCGAGACAGGCAAGCCGCAGAACCTGGCCAACGCGCAATTGACCGTCGAGGAGTTGTGCGAGGTCTCCATCACCGCCTCCGACAACTGCGCCGCCAACCTCATGCTGCGCGAGCTGGGCGGGCCCGCCGCCGTCACCCGGTTCGTCCGCTCGCTCGGTGACCGGGTCACCCGGCTCGACCGCTGGGAGCCGGAGCTGAACTCCGCCGAGCCCGGCCGCGTCACCGACACCACCTCGCCGCGCGCCATCACCCGCACCTACGGCCGCCTCGTCCTCGGCGACGCCCTGAACCCGCGCGACCGCCGCCTGCTCACCAGCTGGCTCCTGGCCAACACCACGAGCGGCGACCGGTTCCGCGCGGGGCTCCCGGACGACTGGACCCTCGGCGACAAGACCGGCGCCGGCCGCTACGGCACCAACAACGACGCGGGCGTCACCTGGCCCCCCGGCCGCGCGCCGATCGTCCTGACCGTCCTCACGGCCAAGACCGAGCAGGACGCCGCCCGCGACGACGGGCTCGTCGCGGACGCGGCCCGGGTACTGGCGGAGACGCTGGGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40173","NCBI_taxonomy_name":"Streptomyces albus","NCBI_taxonomy_id":"1888"}}}},"ARO_accession":"3003564","ARO_id":"40172","ARO_name":"EXO-1","ARO_description":"Class A beta-lactamase found in Streptomyces albus G","ARO_category":{"41398":{"category_aro_accession":"3004234","category_aro_cvterm_id":"41398","category_aro_name":"EXO beta-lactamase","category_aro_description":"Beta-lactamases part of this family discovered in Streptomyces albus G.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1481":{"model_id":"1481","model_name":"OXY-1-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"896":{"protein_sequence":{"accession":"AAL78276.1","sequence":"MLKSSWRKTALMAAAVPLLLASGSLWASADAIQQKLADLEKRSGGRLGVALINTADDSQTLYRGDERFAMCSTGKVMAAAAVLKQSESNPEVVNKRLEIKKSDLVVWSPITEKHLQSGMTLAELSAAALQYSDNTAMNKMISYLGGPEKVTAFAQSIGDVTFRLDRTEPALNSAIPGDKRDTTTPLAMAESLRKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPASWVVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKSRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"AY077483","fmin":"182","fmax":"1055","strand":"+","sequence":"ATGTTGAAAAGTTCGTGGCGTAAAACCGCCCTGATGGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGTTCATTATGGGCCAGTGCCGATGCTATCCAGCAAAAGCTGGCTGATTTAGAAAAACGTTCCGGCGGTCGGCTGGGCGTAGCGCTGATTAACACGGCAGATGATTCGCAAACCCTCTATCGCGGCGATGAACGTTTTGCCATGTGCAGCACCGGTAAAGTGATGGCCGCCGCCGCGGTGTTAAAACAGAGCGAAAGCAATCCAGAGGTGGTGAATAAAAGGCTGGAGATTAAAAAATCGGATTTAGTGGTCTGGAGCCCGATCACCGAAAAACATCTGCAAAGCGGAATGACCCTGGCGGAACTCAGCGCGGCGGCGCTGCAGTACAGCGACAATACCGCGATGAATAAGATGATTAGCTACCTTGGCGGACCGGAAAAGGTGACCGCATTCGCCCAGAGTATCGGGGATGTCACTTTTCGTCTCGATCGTACGGAGCCGGCGCTGAACAGCGCGATTCCCGGCGATAAGCGCGATACCACCACCCCGTTGGCGATGGCCGAAAGCCTGCGCAAGCTGACGCTGGGCAATGCGCTGGGCGAACAGCAGCGCGCCCAGTTAGTGACGTGGCTAAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCAGGCCTGCCCGCAAGCTGGGTGGTCGGGGATAAAACCGGCGCCGGAGATTACGGCACCACCAACGATATCGCGGTGATCTGGCCGGAAAATCATGCCCCGCTGGTGCTGGTGACCTATTTTACCCAGCCGCAGCAGGATGCGAAAAGCCGCAAAGAGGTGTTAGCCGCGGCGGCAAAAATCGTCACCGAAGGGCTTTAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002392","ARO_id":"38792","ARO_name":"OXY-1-4","ARO_description":"OXY-1-4 is a beta-lactamase found in Klebsiella oxytoca","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1482":{"model_id":"1482","model_name":"SME-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"1319":{"protein_sequence":{"accession":"CAA82281.1","sequence":"MSNKVNFKTASFLFSVCLALSAFNAHANKSDAAAKQIKKLEEDFDGRIGVFAIDTGSGNTFGYRSDERFPLCSSFKGFLAAAVLERVQQKKLDINQKVKYESRDLEYHSPITTKYKGSGMTLGDMASAALQYSDNGATNIIMERFLGGPEGMTKFMRSIGDNEFRLDRWELELNTAIPGDKRDTSTPKAVANSLNKLALGNVLNAKVKAIYQNWLKGNTTGDARIRASVPADWVVGDKTGSCGAIGTANDYAVIWPKNRAPLIVSIYTTRKSKDDKHSDKTIAEASRIAIQAID"},"dna_sequence":{"accession":"Z28968","fmin":"0","fmax":"885","strand":"+","sequence":"ATGTCAAACAAAGTAAATTTTAAAACGGCTTCATTTTTGTTTAGTGTTTGTTTAGCTTTGTCGGCATTTAATGCTCATGCTAACAAAAGTGATGCTGCGGCAAAACAAATAAAAAAATTAGAGGAAGACTTTGATGGGAGGATTGGCGTCTTTGCAATAGATACAGGATCGGGTAATACATTTGGGTATAGATCAGATGAGCGGTTCCCTTTATGCAGTTCATTTAAAGGTTTTTTGGCGGCTGCTGTTTTAGAGAGGGTGCAACAAAAAAAACTAGATATCAACCAAAAGGTTAAATATGAGAGTAGGGATCTAGAATATCATTCACCTATTACAACAAAATATAAAGGCTCAGGTATGACATTAGGTGATATGGCTTCTGCTGCATTGCAATATAGCGACAATGGGGCAACAAATATAATTATGGAACGATTTCTTGGCGGTCCTGAGGGGATGACTAAATTTATGCGTTCTATTGGAGATAATGAGTTTAGGTTAGATCGCTGGGAACTGGAACTTAACACTGCAATCCCAGGAGATAAACGTGACACTTCAACGCCAAAAGCTGTTGCAAATAGTTTGAATAAACTAGCTTTGGGGAATGTTCTCAATGCTAAAGTGAAAGCGATTTATCAAAATTGGTTAAAAGGTAATACAACTGGTGATGCTCGAATTCGTGCTAGTGTTCCTGCTGATTGGGTTGTAGGTGACAAAACTGGGAGCTGTGGGGCTATAGGTACTGCGAATGATTATGCCGTCATTTGGCCTAAAAATAGAGCACCATTAATTGTCTCTATATATACAACACGAAAATCGAAAGATGATAAGCACAGTGATAAAACTATTGCGGAAGCATCACGTATTGCAATTCAGGCAATTGATTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36783","NCBI_taxonomy_name":"Serratia marcescens","NCBI_taxonomy_id":"615"}}}},"ARO_accession":"3002379","ARO_id":"38779","ARO_name":"SME-1","ARO_description":"SME-1 is a beta-lactamase found in Serratia marcescens","ARO_category":{"36194":{"category_aro_accession":"3000055","category_aro_cvterm_id":"36194","category_aro_name":"SME beta-lactamase","category_aro_description":"SME beta-lactamases are chromosome-mediated class A beta-lactamases that hydrolyze carbapenems in Serratia marcescens.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1483":{"model_id":"1483","model_name":"AAC(3)-Xa","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"4278":{"protein_sequence":{"accession":"BAA78619.1","sequence":"MDETELLRRSDGPVTRDRIRHDLAALGLVPGDTVMFHTRLSAIGYVSGGPQTVIDALLDVVGPTGTLLVTCGWNDAPPYDFTDWPPAWQEAVRAHHPAFDPRTSEAEHANGRLPEALRRRPGAVRSRHPDVSLAALGASAPALMDAHPWDDPHGPGSPLARLVALGGRVLLLGAPRDTMTLLHHAEALAQAPGKRFVTYEQPIEVAGERVWRTFRDIDSEHGAFDYSSAVPEGQDPFAVIVGSMLAAGIGREGFVGAARSRLFDAAPAVEFGVRWIEEHLNRDR"},"dna_sequence":{"accession":"AB028210","fmin":"2710","fmax":"3565","strand":"-","sequence":"TCAGCGGTCCCGGTTCAGGTGCTCCTCGATCCAGCGGACGCCGAACTCGACGGCCGGGGCGGCGTCGAACAGCCGGCTCCTGGCCGCCCCGACGAAGCCCTCCCGTCCGATGCCCGCGGCGAGCATGGAACCGACGATCACCGCGAAGGGGTCCTGCCCCTCGGGCACGGCCGAGGAGTAGTCGAACGCACCGTGCTCGGAGTCGATGTCCCGGAAGGTGCGCCAGACCCGCTCGCCCGCCACCTCGATGGGCTGCTCGTACGTCACGAACCGCTTGCCGGGGGCCTGGGCCAGCGCCTCGGCGTGGTGCAGCAGCGTCATCGTGTCCCGGGGCGCGCCGAGCAGCAGCACCCGGCCGCCGAGGGCGACCAGGCGCGCCAGCGGGCTGCCGGGACCGTGCGGATCGTCCCAGGGGTGGGCGTCCATCAGAGCGGGGGCCGAGGCGCCGAGCGCCGCGAGACTCACGTCGGGGTGGCGACTGCGTACGGCCCCCGGTCTGCGGCGCAGGGCCTCCGGAAGGCGGCCGTTGGCGTGCTCGGCCTCGCTCGTCCGCGGGTCGAACGCGGGGTGGTGGGCGCGTACGGCCTCCTGCCAGGCGGGAGGCCAGTCGGTGAAGTCGTAGGGCGGAGCGTCGTTCCAGCCGCAGGTGACCAACAGAGTGCCGGTCGGTCCCACCACGTCCAGCAGGGCGTCGATGACGGTCTGGGGGCCTCCGGAGACGTAGCCGATCGCGGACAGCCGCGTATGGAACATCACGGTGTCGCCCGGGACGAGGCCGAGCGCGGCCAGGTCGTGCCGGATCCGGTCCCGGGTCACGGGCCCGTCGGAGCGTCGCAGCAGTTCCGTCTCGTCCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36903","NCBI_taxonomy_name":"Streptomyces griseus","NCBI_taxonomy_id":"1911"}}}},"ARO_accession":"3002544","ARO_id":"38944","ARO_name":"AAC(3)-Xa","ARO_description":"AAC(3)-Xa is a chromosomal-encoded aminoglycoside acetyltransferase in Streptomyces griseus","ARO_category":{"36461":{"category_aro_accession":"3000322","category_aro_cvterm_id":"36461","category_aro_name":"AAC(3)","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 3.","category_aro_class_name":"AMR Gene Family"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1484":{"model_id":"1484","model_name":"ACT-27","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"941":{"protein_sequence":{"accession":"AHL39340.1","sequence":"MMKKSLCCALLLGISCSALAAPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVVEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEALQ"},"dna_sequence":{"accession":"KJ207209","fmin":"454","fmax":"1600","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCGCGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCAGAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAACGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAGGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTGCCCGTGGTAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001847","ARO_id":"38247","ARO_name":"ACT-27","ARO_description":"ACT-27 is a beta-lactamase. From the Lahey list of ACT beta-lactamases.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1485":{"model_id":"1485","model_name":"MOX-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1519":{"protein_sequence":{"accession":"AGH56079.1","sequence":"MQQRQSILWGALATLMWAGLAHAGDKAATDPLRPVVDASIRPLLKEHRIPGMAVAVLKDGKAHYFNYGVADRERAVGVSEQTLFEIGSVSKPLTATLGAYAVVKGAMQLDDKASRHAPWLKGSAFDSITMGELATYSAGGLPLQFPEEVDSLEKMQAYYRQWTPAYSPGSHRQYSNPSIGLFGHLAASSMKQPFAQLMEQTLLPGLGLHHTYVNVPKQAMASYAYGYSKEDKPIRVSPGMLADEAYGIKTSSADLLRFVKANISGVDDKALQQAISLTHKGHYSVGGMTQGLGWESYAYPVSEQTLLAGNSPAMIYNANPAAPAPAAAGHPVLFNKTGSTSGFGAYVAFVPAKGIGIVMLANRNYPIPARVKAAHAILTQLAR"},"dna_sequence":{"accession":"JX173956","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCAACAACGACAATCCATCCTGTGGGGCGCTTTGGCCACCCTGATGTGGGCCGGTCTGGCTCATGCCGGTGACAAGGCGGCGACCGATCCCCTGCGCCCCGTGGTGGATGCCAGCATCCGGCCGCTGCTCAAGGAGCACAGGATCCCGGGCATGGCGGTGGCCGTGCTCAAGGATGGCAAGGCCCACTATTTCAACTACGGTGTGGCCGATCGGGAGCGCGCGGTCGGTGTCAGCGAGCAGACCCTGTTCGAGATAGGCTCCGTGAGCAAGCCCCTGACCGCGACCCTAGGAGCCTATGCGGTGGTCAAGGGAGCGATGCAACTGGATGACAAGGCGAGCCGGCACGCCCCCTGGCTCAAGGGATCCGCCTTTGACAGCATCACCATGGGGGAGCTGGCTACCTACAGCGCGGGCGGCTTGCCGCTGCAATTCCCCGAGGAGGTGGATTCGCTCGAGAAGATGCAGGCCTACTACCGCCAGTGGACCCCAGCCTACTCGCCGGGTTCCCATCGCCAGTACTCTAACCCCAGCATAGGGCTGTTCGGCCACCTGGCGGCGAGCAGCATGAAGCAGCCGTTTGCCCAGTTGATGGAGCAGACGCTCCTGCCGGGGCTTGGCCTGCACCACACCTATGTCAATGTGCCGAAGCAGGCCATGGCGAGTTATGCCTATGGCTATTCGAAAGAGGACAAGCCCATCAGGGTCAGCCCCGGCATGCTGGCGGACGAGGCCTACGGCATCAAGACCAGCTCGGCGGATCTGCTGCGCTTTGTGAAGGCCAACATCAGCGGGGTTGATGACAAGGCGTTGCAGCAGGCCATCTCCCTGACCCACAAAGGGCACTACTCGGTAGGCGGGATGACCCAGGGACTGGGTTGGGAGAGTTACGCCTATCCCGTCAGCGAGCAGACATTGCTGGCGGGCAACTCCCCGGCGATGATTTACAATGCCAACCCGGCGGCGCCCGCGCCCGCTGCGGCAGGGCACCCTGTGCTCTTCAACAAGACCGGCTCGACCAGCGGCTTCGGCGCCTATGTGGCCTTCGTGCCGGCCAAAGGGATCGGCATCGTCATGCTGGCCAACCGCAACTATCCTATCCCGGCCAGGGTGAAAGCGGCCCACGCCATCCTGACGCAACTGGCCAGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36936","NCBI_taxonomy_name":"Aeromonas caviae","NCBI_taxonomy_id":"648"}}}},"ARO_accession":"3002190","ARO_id":"38590","ARO_name":"MOX-8","ARO_description":"MOX-8 is a beta-lactamase. From the Lahey list of MOX beta-lactamases.","ARO_category":{"36222":{"category_aro_accession":"3000083","category_aro_cvterm_id":"36222","category_aro_name":"MOX beta-lactamase","category_aro_description":"MOX beta-lactamases are plasmid-mediated AmpC-type beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1486":{"model_id":"1486","model_name":"CARB-12","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1912":{"protein_sequence":{"accession":"BAA02497.1","sequence":"MKFLLVFSLLIPSVVFASSSKFRQVEQDVKAIEVSLSARIGVSVLDTQNGEYWDYNGNQRFPLTSTFKTIACAKLLYDAEQGKVNPNSTVEIKKADLVTYSPVIEKQVGQAITLDDACFATMTTSDNTAANIILSAVGGSKGVTDFLRQIGDKETRLDRIEPDLNEGKLGDLRDTTTPKAIASTLNKFLFGSALSEMNKKKLESWMVNNQVTGNLLRSVLPAGWNIADRSGAGGFGARSITAVVWSEHQAPIIVSIYLAQTQASMAERNDAIVKIGRSIFDVYTSQSR"},"dna_sequence":{"accession":"D13210","fmin":"231","fmax":"1098","strand":"+","sequence":"ATGAAGTTTTTATTGGTATTTTCGCTTTTAATACCATCCGTGGTTTTTGCAAGTAGTTCAAAGTTTCGGCAAGTTGAACAAGACGTTAAGGCAATTGAAGTTTCTCTTTCTGCTCGTATAGGTGTTTCCGTTCTTGATACTCAAAATGGAGAATACTGGGATTACAATGGCAATCAGCGCTTCCCGTTGACAAGTACTTTTAAAACAATAGCTTGCGCTAAATTACTATATGATGCTGAGCAAGGAAAAGTTAATCCCAATAGTACAGTCGAGATTAAGAAAGCAGATCTTGTGACCTATTCCCCTGTAATAGAAAAGCAAGTAGGGCAGGCAATCACACTCGATGATGCGTGCTTCGCAACTATGACTACAAGTGATAATACTGCGGCAAATATCATCCTAAGTGCTGTAGGTGGCTCCAAAGGCGTTACTGATTTTTTAAGACAAATTGGGGACAAAGAGACTCGTCTAGACCGTATTGAGCCTGATTTAAATGAAGGTAAGCTCGGTGATTTGAGGGATACGACAACTCCTAAGGCAATAGCCAGTACTTTGAATAAATTTTTATTTGGTTCAGCGCTATCTGAAATGAACAAAAAAAAATTAGAGTCTTGGATGGTGAACAATCAAGTCACTGGTAATTTACTACGTTCAGTATTGCCGGCGGGATGGAACATTGCGGATCGTTCAGGTGCTGGCGGATTTGGTGCTCGGAGTATTACAGCAGTTGTGTGGAGTGAGCATCAAGCCCCAATTATTGTGAGCATCTATCTAGCTCAAACACAGGCTTCAATGGCAGAGCGAAATGATGCGATTGTTAAAATTGGTCGTTCAATTTTTGACGTTTATACATCACAGTCGCGCTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3002250","ARO_id":"38650","ARO_name":"CARB-12","ARO_description":"CARB-12 is a beta-lactamase. From the Lahey list of IMP beta-lactamases.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1487":{"model_id":"1487","model_name":"SHV-48","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"991":{"protein_sequence":{"accession":"AAP03063.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTIGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AY263404","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGATCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCAGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001105","ARO_id":"37485","ARO_name":"SHV-48","ARO_description":"SHV-48 is a broad-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1488":{"model_id":"1488","model_name":"TEM-75","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1803":{"protein_sequence":{"accession":"AAN05028.1","sequence":"FFAAFCFPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDHWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYMTGSQATMDERNR"},"dna_sequence":{"accession":"AY130284","fmin":"0","fmax":"785","strand":"+","sequence":"TTTTTTGCGGCATTTTGCTTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCATTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACATGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000941","ARO_id":"37321","ARO_name":"TEM-75","ARO_description":"TEM-75 is an extended-spectrum beta-lactamase that has been found in clinical isolates.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1489":{"model_id":"1489","model_name":"CMY-37","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"944":{"protein_sequence":{"accession":"BAF36388.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWSELTGKQWQGISLLHLATYTAGGLPLQIPDDVTDKTALLHFYQNWQPQWAPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASRVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAAIPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPIRVEAAWRILEKLQ"},"dna_sequence":{"accession":"AB280919","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCATTCTCCACGTTTGCCGCCGCCAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGTCAGAACTGACAGGCAAACAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTACGGATAAAACCGCATTACTGCACTTTTATCAAAACTGGCAGCCTCAATGGGCTCCGGGCGCTAAGAGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAGCCATTAAAACTGGCGCATACCTGGATTACAGTTCCGCAGAGCGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGACAACTTGATGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCACGCTGGGTTCAGGCCAACATGGATGCCAGCCGCGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAGGCTGATTCGATCATCAACGGTAGCGACAGCAAAGTGGCATTGGCAGCGATTCCCGCCGTTGAGGTAAACCCGCCCGCCCCGGCAGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACTGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTATCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002048","ARO_id":"38448","ARO_name":"CMY-37","ARO_description":"CMY-37 is a beta-lactamase found in Citrobacter freundii","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1490":{"model_id":"1490","model_name":"SHV-107","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"818":{"protein_sequence":{"accession":"CAQ03507.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKAGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM941848","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGGCCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001156","ARO_id":"37536","ARO_name":"SHV-107","ARO_description":"SHV-107 is an inhibitor-resistant beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1491":{"model_id":"1491","model_name":"lnuF","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"61":{"protein_sequence":{"accession":"CAD91132.1","sequence":"MLQQKMIERFKEACHEDARIIAALMFGSFAIGEGDEFSDIEFAVFIQNNHFENFDQRSWLNAVSPVAAYFPDDFGHHTALFENGIRGEFHFMRKSDIPVISTWQGYGWFPSLEEAVLLDRSGELSRYASALVGSPPKREGAPLVEGLVLNLISLMLFGANLLNRGEYARAWALLSKAHENLLKLVRLHEGATDHWPTPSRALEKDVSEDSYNRYLACTGSAEPKALCVAYHETWKWSLELFRSVAGPLNIELPRIVIAQTKRLLNESATPHNK"},"dna_sequence":{"accession":"AJ561197","fmin":"1320","fmax":"2142","strand":"+","sequence":"ATGCTTCAGCAGAAAATGATCGAACGCTTCAAGGAAGCTTGCCATGAGGATGCACGAATAATCGCGGCGCTGATGTTCGGCTCATTTGCTATCGGAGAGGGTGACGAGTTCTCTGATATCGAATTTGCAGTGTTCATCCAGAATAATCATTTTGAAAATTTCGATCAGCGCTCGTGGCTTAATGCTGTAAGTCCGGTTGCAGCTTACTTTCCGGATGACTTCGGCCACCACACCGCGCTTTTTGAAAACGGCATTCGCGGTGAATTCCATTTCATGCGAAAATCGGACATACCGGTCATTTCCACTTGGCAAGGCTACGGGTGGTTTCCCTCGCTTGAGGAGGCTGTTTTGTTGGACCGATCAGGAGAGTTGTCAAGGTACGCGAGTGCTCTCGTGGGCAGTCCCCCGAAACGTGAAGGCGCGCCGCTGGTGGAAGGACTTGTATTGAACCTCATCAGCCTGATGCTCTTTGGGGCAAATCTTTTAAATCGGGGAGAGTATGCTCGCGCCTGGGCTTTGCTCAGCAAAGCACATGAAAACTTACTCAAGTTGGTTCGCCTCCATGAAGGGGCAACAGACCACTGGCCGACACCTTCACGCGCGCTCGAAAAGGATGTCTCGGAGGACTCGTATAATCGCTACCTGGCATGCACAGGCAGCGCGGAACCAAAAGCACTATGTGTAGCCTATCATGAAACGTGGAAGTGGAGTCTCGAATTGTTCAGGAGTGTGGCTGGACCTCTGAATATCGAGCTTCCGAGAATTGTAATTGCGCAGACAAAAAGGTTGCTAAATGAATCTGCGACGCCGCACAACAAGTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002839","ARO_id":"39273","ARO_name":"lnuF","ARO_description":"lnuF is an integron-mediated nucleotidyltransferase found in Escherichia coli","ARO_category":{"36360":{"category_aro_accession":"3000221","category_aro_cvterm_id":"36360","category_aro_name":"lincosamide nucleotidyltransferase (LNU)","category_aro_description":"Resistance to the lincosamide antibiotic by ATP-dependent modification of the 3' and\/or 4'-hydroxyl groups of the methylthiolincosamide sugar.","category_aro_class_name":"AMR Gene Family"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1492":{"model_id":"1492","model_name":"MOX-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1119":{"protein_sequence":{"accession":"ACA30419.1","sequence":"MQQRQSILWGAVATLMWAGLAHAGETSPVDPLRPVVDASIQPLLKEHRIPGMAVAVLKDGKAHYFNYGVADRERAVGVSEQTLFEIGSVSKPLTATLGAYAVVKGAMQLDDKASRHAPWLKGSAFDSITMGELATYSAGGLPLQFPEEVDSLEKMQAYYRQWTPAYSPGSHRQYSNPSIGLFGHLAASSLKQPFAQLMEQTLLPGLGLHHTYVNVPKQAMASYAYGYSKEDKPIRVSPGMLADEAYGIKTSSADLLRFVKANISGVDDKALQQAISLTHKGHYSVGGMTQGLGWERYAYPVSEQTLLAGNSAKVILEANPTAAPRESGSQMLFNKTGSTSGFGAYVAFVPAKGIGIVMLANRNYPIPARVKAAHAILTQLAR"},"dna_sequence":{"accession":"EU515248","fmin":"0","fmax":"1149","strand":"+","sequence":"ATGCAACAACGACAATCCATCCTGTGGGGGGCCGTGGCCACCCTGATGTGGGCCGGTCTGGCCCATGCAGGTGAGACTTCACCGGTCGATCCCCTGCGCCCCGTGGTGGATGCCAGCATCCAGCCGCTGCTCAAGGAGCACAGGATCCCGGGCATGGCGGTGGCCGTGCTCAAGGATGGCAAGGCCCACTATTTCAACTACGGTGTGGCCGATCGGGAGCGCGCAGTCGGTGTCAGCGAGCAGACCCTGTTCGAGATAGGCTCCGTGAGCAAGCCCCTGACCGCGACCCTAGGAGCCTATGCGGTGGTCAAGGGAGCGATGCAACTGGATGACAAGGCGAGCCGGCACGCCCCCTGGCTCAAGGGATCCGCCTTTGACAGCATCACCATGGGGGAGCTGGCTACCTACAGCGCGGGCGGCTTGCCGCTGCAATTCCCCGAGGAGGTGGATTCGCTCGAGAAGATGCAGGCCTACTACCGCCAGTGGACCCCAGCCTACTCGCCGGGTTCCCATCGCCAGTACTCTAACCCCAGCATAGGGCTGTTCGGCCACCTGGCGGCGAGCAGCCTGAAGCAGCCGTTTGCCCAGTTGATGGAGCAGACGCTCCTGCCGGGGCTTGGCCTGCACCACACCTATGTCAATGTGCCGAAGCAGGCCATGGCGAGTTATGCCTATGGCTATTCGAAAGAGGACAAGCCCATCAGGGTCAGCCCCGGCATGCTGGCGGACGAGGCCTACGGCATCAAAACCAGCTCGGCGGATCTGCTGCGCTTTGTGAAGGCCAACATCAGCGGGGTTGATGACAAGGCGTTGCAGCAGGCCATCTCCCTGACCCACAAAGGGCACTACTCGGTAGGCGGGATGACCCAGGGACTGGGTTGGGAGCGTTACGCCTATCCCGTCAGCGAGCAGACATTGCTGGCGGGCAATTCGGCCAAGGTGATCCTCGAAGCCAATCCGACGGCGGCGCCCCGGGAGTCGGGGAGCCAGATGCTCTTCAACAAGACCGGCTCGACCAGCGGCTTCGGCGCCTATGTGGCCTTCGTGCCGGCCAAAGGGATCGGCATCGTCATGCTGGCCAACCGCAACTATCCTATCCCGGCCAGGGTGAAAGCGGCCCACGCCATCCTGACGCAACTGGCCAGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36942","NCBI_taxonomy_name":"Aeromonas sp. HCUZ 2422275","NCBI_taxonomy_id":"505724"}}}},"ARO_accession":"3002186","ARO_id":"38586","ARO_name":"MOX-3","ARO_description":"MOX-3 is a beta-lactamase. From the Lahey list of MOX beta-lactamases.","ARO_category":{"36222":{"category_aro_accession":"3000083","category_aro_cvterm_id":"36222","category_aro_name":"MOX beta-lactamase","category_aro_description":"MOX beta-lactamases are plasmid-mediated AmpC-type beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1493":{"model_id":"1493","model_name":"PER-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1229":{"protein_sequence":{"accession":"ADD80743.1","sequence":"MNVIAKGVFTTTALLMLSLSSWVVSAQSPLLKEQIETIVTGKKATVGVAVWGPDDLEPLLVNPFEKFPMQSVFKMHLAMLVLHQVDQGKLDLNKTVAVNRAAVLQNTWSPMMKDHQGDEFTVTVQQLLQYSVSHSDNVACDLLFELVGGPAALHAYIQSLGIKETEVVANEAQMHADDQVQYKNWTSMKAAAQLLRKFEQKKQLSETSQALLWKWMVETTTGPQRLKGLLPAGTVVAHKTGTSGVRAGKTAATNDIGVIMLPDGRPLLVAVFVKDSAESARTNEAIIAQVAQAAYQFELKKLSAVSPD"},"dna_sequence":{"accession":"GQ396303","fmin":"0","fmax":"927","strand":"+","sequence":"ATGAATGTCATCGCAAAAGGTGTTTTTACTACTACAGCTCTGCTGATGTTGAGTTTAAGTTCATGGGTCGTCTCTGCCCAATCCCCGCTGTTAAAAGAGCAAATTGAGACCATAGTGACAGGTAAAAAAGCCACTGTAGGTGTTGCCGTATGGGGCCCTGATGATCTGGAGCCTTTGCTGGTTAATCCTTTTGAGAAATTCCCGATGCAAAGCGTATTTAAGATGCATTTAGCCATGCTGGTTCTGCATCAGGTGGATCAGGGCAAACTGGATTTAAATAAAACTGTTGCTGTTAATCGTGCTGCAGTATTACAAAATACCTGGTCGCCTATGATGAAAGATCATCAAGGCGATGAATTTACCGTTACTGTGCAGCAGTTGCTGCAGTATTCGGTGTCGCACAGTGATAACGTGGCCTGTGATTTATTGTTCGAACTGGTTGGAGGGCCTGCAGCTCTGCATGCTTACATTCAGTCTTTAGGTATTAAAGAAACTGAAGTGGTAGCAAATGAAGCACAAATGCATGCTGATGATCAGGTGCAATATAAAAACTGGACCTCGATGAAAGCAGCAGCGCAACTTTTGCGAAAGTTTGAACAAAAAAAGCAGTTGTCTGAAACCTCTCAGGCTTTATTGTGGAAGTGGATGGTGGAAACCACCACAGGACCACAGCGGTTAAAAGGCCTGTTACCTGCCGGAACTGTAGTAGCGCATAAAACCGGTACGTCCGGTGTCAGAGCAGGAAAAACGGCGGCGACCAATGATATAGGCGTCATTATGTTGCCTGATGGGCGGCCTTTATTGGTGGCGGTATTTGTCAAAGATTCCGCCGAATCAGCAAGAACCAATGAAGCCATTATCGCGCAGGTGGCTCAAGCTGCTTATCAGTTTGAGCTGAAAAAACTCTCCGCAGTAAGTCCGGATTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36947","NCBI_taxonomy_name":"Aeromonas allosaccharophila","NCBI_taxonomy_id":"656"}}}},"ARO_accession":"3002368","ARO_id":"38768","ARO_name":"PER-6","ARO_description":"PER-6 is a beta-lactamase found in Aeromonas allosaccharophila","ARO_category":{"36195":{"category_aro_accession":"3000056","category_aro_cvterm_id":"36195","category_aro_name":"PER beta-lactamase","category_aro_description":"PER beta-lactamases are plasmid-mediated extended spectrum beta-lactamases found in the Enterobacteriaceae family.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1494":{"model_id":"1494","model_name":"LAT-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1988":{"protein_sequence":{"accession":"CAA55007.1","sequence":"MMKKSLCSALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDCIARGEIKLSDPVTKYWPELTGKKWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGRLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"X78117","fmin":"141","fmax":"1287","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTCCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAACCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGGAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACTGTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAAAAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCTTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACGACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001857","ARO_id":"38257","ARO_name":"LAT-1","ARO_description":"LAT-1 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1495":{"model_id":"1495","model_name":"ACT-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1813":{"protein_sequence":{"accession":"ABZ81086.1","sequence":"MMTKSLCCALLLSTSCSVLAAPMSEKQLAEVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVADNASLLRFYQNWQPQWKPGTTRLYANTSIGLFGALAVKPSGMSYEQAITTRVFKPLKLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMVNMKPDSLQDNSLRQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVEGSDNKVALAPLPAREVNPPAPPVNASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILSAL"},"dna_sequence":{"accession":"EU427302","fmin":"1475","fmax":"2618","strand":"+","sequence":"ATGATGACTAAATCCCTTTGCTGCGCCCTGCTGCTCAGCACCTCCTGCTCGGTATTGGCTGCACCGATGTCAGAAAAACAGCTGGCTGAGGTGGTGGAACGGACCGTTACGCCGCTGATGAAAGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTGATTTATCAGGGCCAGCCGCACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCTGTCACCCCACAAACCTTGTTCGAACTGGGTTCTATAAGTAAAACCTTTACCGGCGTACTGGGTGGCGATGCCATTGCTCGGGGTGAAATATCGCTGGGCGATCCGGTGACAAAATACTGGCCTGAGCTGACGGGCAAGCAGTGGCAGGGGATCCGCATGCTGGATCTGGCAACCTATACCGCAGGCGGTCTGCCGTTACAGGTACCGGATGAGGTCGCGGATAACGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGTACCACGCGTCTTTACGCCAATACCAGCATCGGCCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAACAGGCCATAACGACGCGGGTCTTTAAGCCGCTCAAGCTGGACCATACGTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGCGACGGTAAAGCGGTACACGTTTCGCCAGGCATGCTGGACGCTGAAGCCTATGGCGTAAAAACCAACGTGCAGGATATGGCAAGCTGGGTGATGGTCAACATGAAGCCGGACTCCCTTCAGGATAATTCACTCAGGCAAGGCATTGCCCTGGCGCAGTCTCGCTACTGGCGCGTAGGGGCCATGTATCAGGGGTTAGGCTGGGAAATGCTTAACTGGCCGGTCGATGCCAAAACCGTGGTTGAAGGTAGCGACAATAAGGTGGCACTGGCACCGCTGCCCGCAAGAGAAGTGAATCCTCCGGCGCCTCCGGTCAACGCGTCCTGGGTCCATAAAACAGGCTCTACCGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCCAACCCAGCACGCGTTGAGGCGGCTTACCGTATTTTGAGCGCGCTGTAGT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36926","NCBI_taxonomy_name":"Enterobacter asburiae","NCBI_taxonomy_id":"61645"}}}},"ARO_accession":"3001829","ARO_id":"38229","ARO_name":"ACT-4","ARO_description":"ACT-4 is a beta-lactamase. From the Lahey list of ACT beta-lactamases.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1496":{"model_id":"1496","model_name":"OXA-224","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1758":{"protein_sequence":{"accession":"AEQ73521.1","sequence":"MKNTIHINFAIFLIIANIIYSSASASTDISTVASPLFEGTEGCFLLYDVSTNTEIAQFNKAKCATQMAPDSTFKIALSLMAFDAEIIDQKTIFKWDKTPKGMEIWNSNHTPKTWMQFSVVWVSQEITQKIGLNKIKNYLKDFDYGNQDFSGDKERNNGLTEAWLESSLKISPEEQIQFLRKIINHNLPVKNSAIENTIENMYLQDLENSTKLYGKTGAGFTANRTLQNGWFEGFIISKSGHKYVFVSALTGNLGSNLTSSIKAKKNAITILNTLNL"},"dna_sequence":{"accession":"JN596991","fmin":"2280","fmax":"3111","strand":"+","sequence":"ATGAAAAACACAATACATATCAACTTCGCTATTTTTTTAATAATTGCAAATATTATCTACAGCAGCGCCAGTGCATCAACAGATATCTCTACTGTTGCATCTCCATTATTTGAAGGAACTGAAGGTTGTTTTTTACTTTACGATGTATCCACAAACACTGAAATTGCTCAATTCAATAAAGCAAAGTGTGCAACGCAAATGGCACCAGATTCAACTTTCAAGATCGCATTATCACTTATGGCATTTGATGCGGAAATAATAGATCAGAAAACCATATTCAAATGGGATAAAACCCCCAAAGGAATGGAGATCTGGAACAGCAATCATACACCAAAGACGTGGATGCAATTTTCTGTTGTTTGGGTTTCGCAAGAAATAACCCAAAAAATTGGATTAAATAAAATCAAGAATTATCTCAAAGATTTTGATTATGGAAATCAAGACTTCTCTGGAGATAAAGAAAGAAACAACGGATTAACAGAAGCATGGCTCGAAAGTAGCTTAAAAATTTCACCAGAAGAACAAATTCAATTCCTGCGTAAAATTATTAATCACAATCTCCCAGTTAAAAACTCAGCCATAGAAAACACCATAGAGAACATGTATCTACAAGATCTGGAGAATAGTACAAAACTGTATGGGAAAACTGGTGCAGGATTCACAGCAAATAGAACCTTACAAAACGGATGGTTTGAAGGGTTTATTATAAGCAAATCAGGACATAAATATGTTTTTGTGTCCGCACTTACAGGAAACTTGGGGTCGAATTTAACATCAAGCATAAAAGCCAAGAAAAATGCGATCACCATTCTAAACACACTAAATTTATAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001806","ARO_id":"38206","ARO_name":"OXA-224","ARO_description":"OXA-224 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1497":{"model_id":"1497","model_name":"dfrA10","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"686":{"protein_sequence":{"accession":"AHG97174.1","sequence":"MNISLIFANELITRAFGNQGKLPWQFIKEDMQFFQKTTENSVVVMGLNTWRSLPKMKKLGRDFIVISSTITEHEVLNNNIQIFKSFESFLEAFRDTTKPINVIGGVGLLSEAIEHASTVYMSSIHMVKPVHADVYVPVELMNKLYSDFKYPENILWVGDPIDSVYSLSIDKFVRPASLVGVPNDINT"},"dna_sequence":{"accession":"KF976462","fmin":"111558","fmax":"112122","strand":"+","sequence":"ATGAATATATCACTTATCTTTGCCAATGAATTAATTACCAGAGCATTCGGTAATCAAGGCAAATTACCTTGGCAATTCATTAAAGAAGATATGCAGTTCTTCCAGAAGACTACAGAAAATTCTGTAGTCGTTATGGGATTAAATACATGGAGATCTCTACCTAAGATGAAGAAGCTTGGTAGAGACTTCATTGTCATATCTTCAACTATCACAGAGCACGAAGTGCTCAACAATAATATCCAAATATTCAAATCATTTGAGAGCTTCTTAGAAGCATTCAGAGACACAACCAAACCAATCAATGTCATTGGTGGTGTTGGTTTATTATCTGAAGCGATAGAACATGCTAGCACTGTTTACATGAGTTCTATTCATATGGTTAAACCTGTTCATGCTGATGTGTATGTACCGGTAGAACTAATGAATAAACTCTATAGTGATTTCAAATATCCAGAAAATATTCTATGGGTAGGTGATCCAATAGATTCTGTGTATAGCTTGTCTATTGATAAGTTTGTTAGACCAGCTTCGCTGGTTGGGGTGCCAAATGATATTAATACGTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3003011","ARO_id":"39445","ARO_name":"dfrA10","ARO_description":"dfrA10 is an integron-encoded dihydrofolate reductase found in Klebsiella pneumoniae","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36408":{"category_aro_accession":"3000269","category_aro_cvterm_id":"36408","category_aro_name":"brodimoprim","category_aro_description":"Brodimoprim is a structural derivative of trimethoprim and an inhibitor of bacterial dihydrofolate reductase. The 4-methoxy group of trimethoprim is replaced with a bromine atom.","category_aro_class_name":"Antibiotic"},"36423":{"category_aro_accession":"3000284","category_aro_cvterm_id":"36423","category_aro_name":"tetroxoprim","category_aro_description":"Tetroxoprim is a trimethoprim derivative that inhibits bacterial dihydrofolate reductase.","category_aro_class_name":"Antibiotic"},"36476":{"category_aro_accession":"3000337","category_aro_cvterm_id":"36476","category_aro_name":"iclaprim","category_aro_description":"Iclaprim is a bactericidal compound that inhibits dihydrofolate reductase. It is used against clinically important Gram-positive pathogens, including methicillin-sensitive Staphylococcus aureus and methicillin-resistant S. aureus.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1498":{"model_id":"1498","model_name":"cphA8","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"1731":{"protein_sequence":{"accession":"AAP97129.1","sequence":"MMKGWIKCTLAGAVVLMASFWGGSVRAAGMSLMQVSGPVYVVEDNYYVKENSMVYFGAKGVTVVGATWTPDTARELHKLIKRVSSKPVLEVINTNYHTDRAGGNAYWKSIGAKVVSTRQTRDLMKSDWAEIVAFTRKGLPEYPDLPLVLPNVVHDGDFKLQEGKVRAFYAGPAHTPDGIFVYFPDQQVFYGNCILKEKLGNLSFANVKEYPQTIERLKAMKLPIKTVIGGHDSPLHGPELIDHYEELIKAATHS"},"dna_sequence":{"accession":"AY261375","fmin":"0","fmax":"765","strand":"+","sequence":"ATGATGAAAGGTTGGATAAAGTGCACATTGGCCGGGGCCGTGGTGCTGATGGCGAGTTTCTGGGGTGGCAGCGTGCGGGCGGCGGGGATGTCGCTGATGCAGGTGAGCGGCCCTGTCTATGTTGTTGAAGATAACTACTACGTCAAAGAGAACTCCATGGTCTATTTCGGGGCCAAGGGGGTGACGGTGGTGGGGGCGACCTGGACGCCGGATACCGCCCGCGAGCTGCACAAGCTGATCAAACGGGTCAGCAGCAAACCGGTGCTGGAGGTGATCAACACCAACTACCACACCGACCGAGCGGGCGGTAACGCCTACTGGAAGTCCATCGGGGCCAAGGTGGTATCGACTCGCCAGACCCGGGATCTGATGAAGAGCGACTGGGCCGAGATTGTCGCCTTTACCCGCAAGGGGCTGCCGGAGTATCCGGATCTACCGCTGGTGCTGCCCAACGTGGTGCACGATGGCGACTTCAAGCTGCAAGAGGGCAAGGTGCGCGCCTTCTACGCAGGCCCGGCCCACACGCCGGACGGCATCTTTGTCTACTTCCCCGACCAGCAGGTGTTCTATGGCAACTGCATCCTCAAGGAGAAGCTGGGCAACCTGAGCTTTGCCAATGTGAAGGAGTATCCGCAGACCATCGAGCGGCTCAAGGCGATGAAGCTGCCGATCAAGACGGTAATCGGCGGTCACGACTCACCGCTGCACGGGCCTGAGCTGATTGATCACTATGAAGAGCTGATCAAGGCGGCAACTCATTCATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36957","NCBI_taxonomy_name":"Aeromonas sobria","NCBI_taxonomy_id":"646"}}}},"ARO_accession":"3003104","ARO_id":"39670","ARO_name":"cphA8","ARO_description":"cphA8 is an Ambler Class B MBL; subclass B2 originally isolated from Aeromonas sobria. This enzyme has specific activity against carbapenems and is active as a mono-zinc protein.","ARO_category":{"36720":{"category_aro_accession":"3000581","category_aro_cvterm_id":"36720","category_aro_name":"CphA beta-lactamase","category_aro_description":"CphA is an Ambler Class B MBL; subclass B2 originally isolated from Aeromonas hydrophilia.  This enzyme has specific activity against carbapenems and is active as a mono-zinc protein.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1499":{"model_id":"1499","model_name":"VEB-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"4367":{"protein_sequence":{"accession":"ACA34904.1","sequence":"MKIVKRILLVLLSLFFTVVYSNAQADNLTLKIENVLKAKNARIGVAIFNSNEKDTLKINNDFHFPMQSVMKFPIALAVLSEIDKGNLSFEQKIEITPQDLLPKMWSPIKEEFPNGTTLTIEQILNYTVSESDNIGCDILLKLIGGTDSVQKFLNANHFTDISIKANEEQMHKDWNTQYQNWATPTAMNKLLIDTYNNKNQLLSKKSYDFIWKIMRETTTGSNRLKGQLPKNTIVAHKTGTSGINNGIAAATNDVGVITLPNGQLIFISVFVAESKETSEINEKIISDIAKITWNYYLNK"},"dna_sequence":{"accession":"EU259884","fmin":"6411","fmax":"7311","strand":"-","sequence":"TTATTTATTCAAATAGTAATTCCACGTTATTTTTGCAATGTCTGAAATAATCTTTTCATTAATTTCCGAAGTTTCTTTGGACTCTGCAACAAATACGCTTATAAAAATTAATTGTCCATTCGGTAAAGTAATTACCCCAACATCATTAGTGGCTGCTGCAATTCCATTATTTATTCCGGAAGTCCCTGTTTTATGAGCAACAATTGTATTCTTTGGTAATTGTCCTTTTAATCGGTTACTTCCTGTTGTTGTTTCTCTCATAATTTTCCAAATAAAATCATAACTTTTTTTAGAAAGTAATTGGTTCTTATTATTATAAGTATCTATTAACAGTTTGTTCATCGCTGTTGGGGTTGCCCAATTTTGATATTGGGTATTCCAATCCTTGTGCATTTGTTCTTCGTTTGCTTTGATTGAAATATCAGTGAAATGATTAGCATTCAAGAATTTTTGAACAGAATCAGTTCCTCCGATTAATTTTAGCAAAATATCACAACCAATATTGTCGCTCTCTGATACTGTATAATTTAGTATTTGTTCAATCGTCAAAGTTGTTCCATTAGGGAATTCCTCTTTAATCGGACTCCACATTTTAGGCAAAAGGTCTTGAGGGGTAATCTCTATTTTTTGTTCAAAAGAAAGATTCCCTTTATCTATCTCAGACAAAACGGCTAAAGCAATCGGAAATTTCATAACGCTTTGCATCGGGAAATGGAAGTCGTTATTAATCTTCAAAGTATCCTTCTCATTGCTGTTGAATATTGCTACTCCTATTCTGGCATTTTTTGCCTTTAAAACATTCTCAATTTTCAAAGTTAAGTTGTCAGCTTGAGCATTTGAATACACAACTGTAAAAAATAAACTTAACAATACTAATAATATCCTTTTTACGATTTTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3002374","ARO_id":"38774","ARO_name":"VEB-6","ARO_description":"VEB-6 is a beta-lactamase found in Proteus mirabilis","ARO_category":{"36182":{"category_aro_accession":"3000043","category_aro_cvterm_id":"36182","category_aro_name":"VEB beta-lactamase","category_aro_description":"VEB beta-lactamases or Vietnamese extended-spectrum beta-lactamases are class A beta-lactamases that confer high-level resistance to oxyimino cephalosporins and to aztreonam","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1500":{"model_id":"1500","model_name":"APH(6)-Ia","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"94":{"protein_sequence":{"accession":"CAA68516.1","sequence":"MSSSDHIHVPDGLAESYSRSGGEEGRAWIAGLPALVARCVDRWELKRDGGVRSGEASLVVPVLRADGTRAALKLQMPREETTAALIGLRAWGGDGMVRLLDHDEESSTMLLERLDGSRTLASVEDDDEAMGVLAGLLNRLHSVPAPPGLRGLGEIAGAMVEEVPSAVDSLADPEDRSRLRGWASAVAELVGEPGDRVLHWDLHYENVLAAEREPWLAIDPEPLVGDPGFDLWPALDTGWERIEATGDARRVVRRRFDLLTESLELDRGRAAGWTLARLLQNTLWDIEDGLTAIAPSQIAVAEALAKP"},"dna_sequence":{"accession":"Y00459","fmin":"2824","fmax":"3748","strand":"+","sequence":"ATGAGTTCGTCGGACCACATCCACGTCCCGGACGGCCTGGCCGAGTCGTACAGCAGAAGCGGTGGCGAGGAAGGGCGCGCCTGGATCGCCGGACTTCCCGCTCTCGTCGCGCGATGCGTCGACCGCTGGGAGCTGAAGAGGGACGGCGGCGTCCGCTCCGGTGAGGCCTCCCTCGTGGTGCCGGTGCTGCGTGCTGACGGCACCCGGGCGGCGCTCAAACTCCAGATGCCCCGGGAAGAGACGACGGCCGCGCTGATCGGCCTGCGAGCCTGGGGCGGGGACGGCATGGTGCGGCTGCTCGACCACGACGAGGAGAGCAGCACGATGCTGCTGGAACGCCTGGACGGTTCGCGGACGCTGGCGTCGGTCGAGGACGACGACGAGGCCATGGGCGTCCTCGCCGGGCTGCTGAACCGGCTGCACTCCGTTCCGGCACCTCCGGGGCTGCGGGGTCTGGGAGAGATCGCCGGCGCCATGGTGGAGGAAGTTCCCTCCGCTGTCGACTCGTTGGCGGATCCGGAGGACCGTAGCCGGTTGCGCGGCTGGGCGTCGGCCGTGGCCGAGCTGGTGGGCGAGCCCGGTGACCGCGTCCTGCACTGGGACCTGCACTACGAGAACGTGCTGGCCGCCGAGCGCGAACCGTGGCTGGCCATCGACCCCGAGCCGCTGGTCGGCGACCCGGGGTTCGACCTGTGGCCGGCCCTGGACACCGGTTGGGAGCGGATCGAGGCCACCGGTGACGCGCGGCGGGTGGTCCGGCGGCGCTTCGACCTGCTGACGGAATCGCTGGAGCTGGACCGCGGGAGGGCGGCCGGGTGGACCCTGGCCCGGCTCCTGCAGAACACCCTGTGGGACATCGAGGACGGGCTGACGGCGATCGCCCCCTCCCAGATCGCCGTGGCCGAAGCGCTGGCGAAGCCCTGAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36903","NCBI_taxonomy_name":"Streptomyces griseus","NCBI_taxonomy_id":"1911"}}}},"ARO_accession":"3002657","ARO_id":"39057","ARO_name":"APH(6)-Ia","ARO_description":"APH(6)-Ia is a chromosomal-encoded aminoglycoside phosphotransferase in S. griseus","ARO_category":{"36290":{"category_aro_accession":"3000151","category_aro_cvterm_id":"36290","category_aro_name":"APH(6)","category_aro_description":"Phosphorylation of streptomycin on the hydroxyl group at position 6","category_aro_class_name":"AMR Gene Family"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1501":{"model_id":"1501","model_name":"CMY-49","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1975":{"protein_sequence":{"accession":"ACV32310.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVTPGQLDAEAYGVKSNVTDMARWIQVNMDASRVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALHTVEVNPPAPAVKASWVHKTGSTGGFGSYVAFIPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"GQ402541","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCATTCTCCACGTTTGCCGCCGCCAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCATTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTACAGATAAAGCCGCATTACTGCGTTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACAGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTACTCCTGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAACGTTACCGATATGGCCCGTTGGATTCAGGTCAACATGGACGCCAGCCGCGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGTAGTGACAGCAAAGTGGCATTGGCAGCGCTTCACACCGTTGAGGTAAACCCGCCCGCCCCGGCAGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACTGGAGGATTTGGCAGCTACGTAGCCTTCATTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002060","ARO_id":"38460","ARO_name":"CMY-49","ARO_description":"CMY-49 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1502":{"model_id":"1502","model_name":"OXA-209","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4365":{"protein_sequence":{"accession":"AEM66528.1","sequence":"MKKTFILLNLILLVNLNGYCQTKSLKSNEIVKPEFRNILDSLKVKGAILIYDVKNKTYYSNDFSWTKTGIIPASTFKIPNSIIALETGIIKNDSTIFKWNGEKRKFKNWEEDLTFKKAFQVSCVPCYQEIARKIGVKRMKRYLKKLNYRGMVFDTLTIDQFWLEGESKITQMQQIDFLERLYFSKFPISDRTIKIVKNIMEIERTENYILSGKTGLSSIEEKYNGWFVGYVETKSNVYFFATNVIPTDGLNVDDFISSRINVTKNALKQMNIMK"},"dna_sequence":{"accession":"JF268688","fmin":"5407","fmax":"6232","strand":"-","sequence":"TCATTTCATTATATTCATTTGCTTTAACGCATTTTTTGTTACATTAATTCTCGATGAAATAAAATCATCAACATTCAATCCGTCTGTCGGAATTACATTTGTTGCAAAAAAATAAACATTAGATTTTGTTTCAACATAACCAACAAACCAACCATTATATTTTTCTTCTATCGAACTTAATCCAGTCTTACCGCTTAAAATGTAATTTTCAGTTCGCTCAATTTCCATAATATTTTTGACAATCTTTATTGTCCTATCAGAAATTGGAAATTTTGAAAAGTATAATCGTTCTAAAAAATCTATTTGTTGCATTTGAGTAATTTTAGATTCTCCTTCTAACCAAAATTGATCAATCGTCAAAGTATCGAAAACCATTCCTCTGTAATTTAATTTTTTCAAATATCTTTTCATCCTTTTCACACCAATTTTTCTGGCAATTTCTTGATAACAAGGAACACAAGAAACTTGAAATGCTTTTTTAAAAGTCAAATCTTCTTCCCAATTTTTAAATTTGCGTTTTTCACCATTCCATTTAAAAATTGTAGAGTCATTTTTGATTATTCCTGTTTCTAACGCAATAATTGAATTTGGTATTTTGAAAGTCGATGCAGGAATTATTCCAGTTTTTGTCCAAGAAAAATCATTTGAATAATAAGTTTTGTTTTTTACATCATAAATTAAAATTGCTCCTTTTACCTTTAAACTATCTAATATATTTCTAAATTCAGGTTTTACAATTTCATTTGATTTTAAACTTTTAGTTTGACAATATCCATTAAGATTTACTAATAAAATTAGATTCAGAAGTATAAATGTTTTTTTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36951","NCBI_taxonomy_name":"Riemerella anatipestifer","NCBI_taxonomy_id":"34085"}}}},"ARO_accession":"3001809","ARO_id":"38209","ARO_name":"OXA-209","ARO_description":"OXA-209 is a beta-lactamase found in Riemerella anatipestifer","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1503":{"model_id":"1503","model_name":"LEN-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"793":{"protein_sequence":{"accession":"AAN05031.1","sequence":"VISLLATLPLAVDAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGLEQLDRRIHYRQQDLVDYSPVSEKHLTDGMTIGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPPGWFIADKTGAGERGARGIVALLGPDGKPERIVVIYLRDTPASMAERNQQIAGIGAALI"},"dna_sequence":{"accession":"AY130287","fmin":"0","fmax":"822","strand":"+","sequence":"TGTTATCTCCCTGTTAGCCACCCTGCCACTGGCGGTAGACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTACCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGCCGGGCTGGTTTATCGCCGACAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACAAATCGCCGGGATCGGCGCGGCGCTGATC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002472","ARO_id":"38872","ARO_name":"LEN-4","ARO_description":"LEN-4 is a beta-lactamase found in Escherichia coli","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1504":{"model_id":"1504","model_name":"CMY-108","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1775":{"protein_sequence":{"accession":"AGZ20169.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWAPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQVNMDASRVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWHILEKLQ"},"dna_sequence":{"accession":"KF564648","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCATTCTCCACGTTTGCCGCCGCCAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTACTGATAAAGCCGCATTACTGCGTTTTTATCAAAACTGGCAGCCGCAATGGGCCCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACAGTTCCGCAAAGCGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGTCAACATGGACGCCAGCCGCGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGTAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAGGCCTCATGGGTGCATAAAACGGGATCCACTGGAGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCACATTCTTGAAAAGCTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002120","ARO_id":"38520","ARO_name":"CMY-108","ARO_description":"CMY-108 is a beta-lactamase present in plasmids of clinical Escherichia coli from humans and companion animals in the upper Midwestern USA . From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1506":{"model_id":"1506","model_name":"ACT-12","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1017":{"protein_sequence":{"accession":"AFU25650.1","sequence":"MMKKSLCCALLLSTSCAALAAPLSETQLAKVVERTVTPLMKAQSIPGMAVAVIYQGQPHYFTFGKADVAANTPVTAQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGVRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQSWQPQWAPGTTRLYANASIGLFGALAVKPSGMRFEQAMTERVLKPLNLNHTWINVPKAEEQHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVKDMASWVVANMAPDGVQDASLKQGMVLAQSRYWRTGSMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEAAYRILSALQ"},"dna_sequence":{"accession":"JX440355","fmin":"751","fmax":"1897","strand":"+","sequence":"ATGATGAAAAAATCCCTGTGCTGCGCCCTGCTGCTCAGCACCTCCTGCGCTGCATTAGCCGCACCTCTGTCAGAAACACAGCTGGCGAAGGTCGTGGAACGTACCGTTACGCCCCTGATGAAAGCGCAGTCTATTCCGGGTATGGCGGTCGCCGTGATCTATCAGGGCCAGCCGCACTACTTCACCTTCGGCAAGGCCGATGTCGCCGCGAACACACCCGTCACTGCACAAACGCTGTTTGAGCTGGGCTCAATCAGCAAAACCTTCACCGGCGTTCTGGGTGGCGATGCTATTGCTCGCGGTGAAATTTCGCTGGGCGATCCGGTGACCAAATACTGGCCTGAACTGACCGGCAAACAGTGGCAGGGCGTTCGCATGCTGGACCTGGCAACCTATACTGCCGGTGGCCTGCCGTTACAGGTGCCCGATGAGGTTACCGATAATGCCTCGCTGCTGCGTTTTTACCAGTCCTGGCAACCACAGTGGGCGCCAGGCACCACGCGTCTTTATGCGAATGCCAGCATCGGTCTGTTTGGGGCTCTGGCAGTGAAACCTTCTGGCATGCGCTTTGAGCAGGCGATGACGGAGCGGGTCCTGAAGCCGCTTAACCTGAACCATACGTGGATTAACGTTCCGAAGGCAGAAGAACAGCATTACGCCTGGGGTTATCGTGACGGTAAAGCGGTTCACGTTTCGCCGGGCATGCTCGATGCCGAAGCATATGGCGTGAAAACCAACGTGAAGGATATGGCGAGCTGGGTGGTGGCTAACATGGCCCCCGATGGGGTACAGGATGCCTCACTGAAGCAGGGCATGGTGCTTGCACAGTCTCGCTACTGGCGCACAGGCTCGATGTACCAGGGCCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTGGTGGAGGGCAGCGACAACAAGGTAGCGCTTGCACCGTTGCCCGTGGCAGAAGTGAACCCTCCGGCTCCACCGGTAAAAGCGTCATGGGTACATAAAACAGGCTCGACGGGCGGATTTGGCAGCTACGTGGCATTTATCCCTGAGAAGGAACTCGGCATCGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCACGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001834","ARO_id":"38234","ARO_name":"ACT-12","ARO_description":"ACT-12 is a beta-lactamase. From the Lahey list of ACT beta-lactamases.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1507":{"model_id":"1507","model_name":"smeA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"496":{"protein_sequence":{"accession":"AAD51344.1","sequence":"MSLLRPLSRSPRPLLLPLLLALAACSADRTDAPAMPEVGVIIASAQPLALQQTLPGRAVPFEISEVRPQIGGLIRQRLFTEGQQVKAGQLLYQVDPAPYQAAFDTARGQLAQAEATVLSAQPKAERTRALVSMDAASKQDADDATSALKQAQANVIAARAALQAARINLDYTRVTAPIDGRIGTSSVTAGALVAAGQDTALTTIQRLDPVYLDVTQSSTQMLALRKRLDAGLVKAIDGKAQVKVLLEDGSTYAHEGTLEFVGSAVDPGTGNVKLRAVIPNPDGLLLPGMYLKAVLPMATDARALLVPQKAVVRNERGEPLLRLLDAKDHVVERRVSTGQVVGNQWQITSGLKAGERVIVSNGSAVSLGQQVKAVAPTTAQLAAMPAVDPNGNTDEKSH"},"dna_sequence":{"accession":"AF173226","fmin":"2558","fmax":"3755","strand":"+","sequence":"ATGTCTCTCCTGCGCCCGCTGTCCCGTTCCCCGCGTCCCCTGCTGTTGCCCCTGCTGCTGGCCCTGGCGGCCTGTTCGGCGGACAGGACCGACGCCCCGGCCATGCCCGAAGTGGGCGTCATCATCGCCAGCGCGCAGCCGCTGGCACTCCAGCAGACCTTGCCCGGCCGTGCCGTGCCGTTCGAGATCTCCGAGGTGCGGCCGCAGATCGGCGGCCTGATCCGCCAGCGGTTGTTCACCGAAGGCCAGCAGGTCAAGGCAGGGCAGCTGCTGTACCAGGTCGACCCGGCACCGTACCAGGCGGCCTTCGATACCGCCCGCGGGCAGCTGGCGCAGGCCGAGGCCACCGTGTTGTCGGCACAGCCGAAGGCCGAGCGTACCCGCGCGCTGGTGAGCATGGATGCAGCCAGCAAGCAGGACGCCGACGATGCCACCTCGGCGTTGAAGCAGGCGCAGGCCAACGTGATTGCCGCGCGCGCTGCATTGCAGGCTGCCCGCATCAACCTCGACTACACCCGGGTGACCGCCCCCATCGACGGTCGCATCGGCACCTCCAGCGTCACCGCCGGCGCGCTGGTCGCGGCCGGCCAGGATACGGCGTTGACCACCATCCAGCGGCTGGACCCGGTGTACCTGGATGTCACCCAGTCCAGCACGCAGATGCTGGCGCTGCGCAAGCGGCTCGATGCGGGCCTAGTGAAGGCCATCGATGGCAAGGCACAGGTTAAGGTGCTGCTGGAGGACGGCAGCACCTACGCGCATGAAGGCACGTTGGAGTTCGTCGGCAGCGCAGTGGATCCGGGCACCGGAAACGTGAAGCTGCGCGCGGTCATTCCGAACCCGGACGGCCTGCTGTTGCCGGGCATGTACCTGAAGGCGGTGCTGCCGATGGCCACCGACGCGCGTGCCCTGCTGGTGCCGCAGAAGGCAGTGGTGCGCAACGAACGCGGCGAACCGCTGCTGCGCCTGCTCGACGCCAAGGATCATGTGGTCGAGCGCCGCGTCAGCACCGGCCAGGTGGTCGGTAACCAGTGGCAGATCACCAGCGGCCTCAAGGCTGGCGAACGGGTGATCGTCAGCAACGGCAGCGCGGTATCGCTCGGTCAGCAGGTGAAAGCGGTGGCGCCCACGACGGCGCAGTTGGCGGCGATGCCGGCGGTCGATCCGAACGGCAACACCGACGAAAAGTCGCACTGAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37076","NCBI_taxonomy_name":"Stenotrophomonas maltophilia","NCBI_taxonomy_id":"40324"}}}},"ARO_accession":"3003051","ARO_id":"39485","ARO_name":"smeA","ARO_description":"smeA is the membrane fusion protein of the smeABC multidrug efflux complex in Stenotrophomonas maltophilia","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1508":{"model_id":"1508","model_name":"QnrA2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"465":{"protein_sequence":{"accession":"ADU33193.1","sequence":"MDIIDKVFQQEDFSRQDLSDSRFRRCRFYQCDFSHCQLRDASFEDCSFIESGAVEGCHFSYADLRDASFKACRLSLANFSGANCFGIEFRECDLKGANFSRARFYNQVSHKMYFCAAYISGCNLAYANLSGQCLEKCELFENNWSNANLSGASLMGSDLSRGTFSRDCWQQVNLRGCDLTFADLDGLDPRRVNLEGVKICAWQQEQLLEPLGIIVLPD"},"dna_sequence":{"accession":"HQ449669","fmin":"0","fmax":"657","strand":"+","sequence":"ATGGATATTATCGATAAAGTTTTTCAACAAGAGGATTTCTCACGCCAGGATTTGAGTGACAGCCGTTTTCGCCGCTGCCGCTTCTATCAGTGTGACTTCAGCCACTGTCAGCTAAGGGATGCCAGTTTCGAGGATTGCAGTTTCATTGAAAGCGGCGCCGTTGAAGGGTGCCACTTCAGCTATGCCGATCTGCGCGATGCCAGTTTCAAGGCTTGCCGTCTGTCTTTGGCTAACTTCAGCGGTGCCAACTGCTTTGGCATAGAGTTCAGGGAATGCGATCTCAAGGGCGCCAACTTTTCCCGGGCCCGCTTTTACAATCAAGTCAGCCATAAAATGTACTTTTGTGCGGCTTATATCTCAGGCTGCAACCTGGCCTATGCCAATTTGAGTGGCCAATGCCTGGAAAAGTGCGAGCTGTTTGAAAATAACTGGAGCAATGCCAATCTCAGCGGTGCTTCCTTGATGGGCTCCGACCTCAGCCGCGGCACCTTCTCCCGCGACTGTTGGCAACAGGTCAATCTGCGGGGCTGTGACCTGACCTTTGCCGATCTGGATGGACTCGATCCCAGGCGGGTCAACCTCGAGGGGGTCAAGATCTGTGCCTGGCAACAGGAGCAACTGTTAGAGCCTCTGGGGATAATAGTGCTTCCGGATTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36891","NCBI_taxonomy_name":"Shewanella algae","NCBI_taxonomy_id":"38313"}}}},"ARO_accession":"3002708","ARO_id":"39142","ARO_name":"QnrA2","ARO_description":"QnrA2 is a plasmid-mediated quinolone resistance protein found in Klebsiella oxytoca","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1509":{"model_id":"1509","model_name":"vanXF","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"375"}},"model_sequences":{"sequence":{"685":{"protein_sequence":{"accession":"AAF36804.1","sequence":"MEKDFVFLDEILHGVRWDSKYATWDNFTGKPVDGYEVNRIAGTYALAVALLEVKKQAAALGYGLLLWDGYRPQRAVNCFLHWSAQPEDGRTKERYYPNIDRIEMVTKGYVASKSSHSRGSAIDLTLYRLDTGALVPMGSGFDFMDERSHHTSKGISSNEAQNRQLLCSIMEYSGFESYVYEWWHYVLRNEPYPSSYFDFPIGGNHLDPFSNFCGTVPLDALSP"},"dna_sequence":{"accession":"AF155139","fmin":"6976","fmax":"7648","strand":"+","sequence":"ATGGAAAAAGATTTTGTTTTTTTAGATGAAATATTGCATGGAGTTCGTTGGGACTCCAAATATGCCACATGGGACAATTTCACTGGAAAACCGGTAGACGGATATGAAGTCAATCGCATAGCGGGGACATATGCTTTGGCTGTTGCGCTGCTGGAGGTAAAGAAGCAGGCGGCTGCTCTAGGGTACGGCTTGCTCCTGTGGGATGGCTATCGTCCTCAACGTGCGGTAAACTGTTTCTTGCATTGGTCTGCGCAGCCGGAAGACGGCCGCACAAAAGAAAGATATTATCCCAATATTGATCGGATCGAGATGGTTACAAAGGGATATGTGGCTTCAAAATCAAGCCACAGTCGCGGAAGCGCGATTGACCTTACGCTTTATCGATTGGACACGGGTGCGCTTGTCCCTATGGGGAGCGGCTTCGATTTTATGGATGAACGTTCACATCATACCTCAAAAGGAATTTCAAGTAACGAAGCGCAAAATCGCCAGTTATTATGTTCTATTATGGAATACAGCGGATTTGAATCATATGTATATGAATGGTGGCACTACGTATTAAGAAACGAACCATACCCCAGCAGCTATTTTGATTTTCCCATTGGCGGGAACCATCTAGACCCATTTTCCAACTTTTGTGGGACAGTGCCACTTGATGCGTTGTCGCCCTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39542","NCBI_taxonomy_name":"Paenibacillus popilliae ATCC 14706","NCBI_taxonomy_id":"1212764"}}}},"ARO_accession":"3002952","ARO_id":"39386","ARO_name":"vanXF","ARO_description":"vanXF is a vanX variant found in the vanF gene cluster","ARO_category":{"36020":{"category_aro_accession":"3000011","category_aro_cvterm_id":"36020","category_aro_name":"vanX","category_aro_description":"VanX is a D,D-dipeptidase that cleaves D-Ala-D-Ala but not D-Ala-D-Lac, ensuring that the latter dipeptide that has reduced binding affinity with vancomycin is used to synthesize peptidoglycan substrate.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1510":{"model_id":"1510","model_name":"vanTrL","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"353":{"protein_sequence":{"accession":"ABX54690.1","sequence":"MVENKMRAYKEFYVESLLHNVQVIKKNIPKSTKIMAVVKANAYGINAVNVAIILEYIGIDFFAVATIDEAIALRKNGITSNILILGYTTPTKVDDLIHYELTQTIVSKEHAYFLNKTGKKIMCHLKVDTGMHRLGVEPTLEEICPIFNYPFLKIKGVYSHLGSADDLSEEGKQRTIKQISRYNTIIAELKRKRVDVGLTHLQSSYGILNYSELAYDYVRPGIILYGLLSNNDHNVKLHLDLQPVVAVKAQLISKKKIAPGEYIGYGTDTQLTSSKTIGVLSIGYADGIPRNLSNGEYCVVFEDKQIPQIGRICMDMMLVDLSNCSDIPLGVMVDVLPNIEEISQIQSTITNEIISCLGSRLGMEVK"},"dna_sequence":{"accession":"EU250284","fmin":"3557","fmax":"4658","strand":"+","sequence":"ATGGTAGAAAACAAAATGAGAGCCTACAAAGAATTCTATGTAGAATCATTGTTGCATAATGTACAAGTTATCAAAAAAAACATACCCAAGTCTACTAAAATAATGGCAGTAGTGAAAGCAAATGCCTATGGAATAAATGCAGTGAATGTAGCTATTATCTTAGAATATATAGGAATTGACTTTTTTGCAGTTGCTACTATAGATGAAGCTATTGCTTTAAGAAAAAATGGCATTACAAGTAATATTTTAATTTTAGGATACACTACACCAACCAAGGTAGATGATCTTATCCATTACGAACTTACCCAAACAATAGTAAGCAAAGAACACGCGTATTTTCTTAATAAAACAGGAAAGAAGATAATGTGTCATTTAAAAGTCGACACAGGGATGCATCGGTTAGGTGTTGAACCTACGTTAGAAGAAATCTGTCCTATTTTTAACTACCCTTTTTTAAAGATAAAGGGTGTTTATTCTCACTTGGGCTCAGCAGACGATTTATCTGAGGAAGGCAAACAACGAACTATAAAACAAATTAGCCGATACAATACCATTATTGCAGAATTAAAACGAAAACGTGTTGACGTAGGGCTAACCCATCTCCAAAGTAGTTATGGTATACTTAATTATTCTGAGTTAGCGTATGACTATGTTCGTCCTGGAATTATTTTATATGGGCTTTTAAGTAATAATGACCACAACGTCAAATTGCATTTGGATCTCCAGCCTGTAGTAGCGGTTAAAGCTCAGTTAATTTCAAAAAAAAAGATAGCTCCTGGTGAATATATTGGCTACGGTACAGATACACAATTAACTTCTTCCAAAACTATAGGGGTATTAAGCATTGGGTATGCTGACGGAATCCCTAGAAATTTATCAAATGGAGAATATTGTGTCGTGTTTGAAGATAAGCAAATCCCTCAAATTGGACGTATTTGTATGGACATGATGTTAGTAGATTTGTCAAATTGTTCAGATATCCCTTTAGGTGTAATGGTTGATGTATTACCTAATATTGAAGAAATATCTCAAATCCAAAGCACCATAACGAATGAAATAATAAGTTGTTTGGGTAGTCGCTTGGGGATGGAAGTAAAGTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3002974","ARO_id":"39408","ARO_name":"vanTrL","ARO_description":"vanTrL is a vanT variant found in the vanL gene cluster. vanTrL codes for the racemase component of vanT","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36511":{"category_aro_accession":"3000372","category_aro_cvterm_id":"36511","category_aro_name":"vanT","category_aro_description":"VanT is a membrane bound serine racemase, converting L-serine to D-serine. It is associated with VanC, which incorporated D-serine into D-Ala-D-Ser terminal end of peptidoglycan subunits that have a decreased binding affinity with vancomycin. It was isolated from Enterococcus gallinarum.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1511":{"model_id":"1511","model_name":"OXA-423","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"978":{"protein_sequence":{"accession":"AIY30332.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETPSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAAPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKPQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"KM433672","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCGTTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGCCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGACCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCCCAATTAGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003161","ARO_id":"39738","ARO_name":"OXA-423","ARO_description":"From the Lahey list of beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1512":{"model_id":"1512","model_name":"SME-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"1487":{"protein_sequence":{"accession":"AAS92558.1","sequence":"MSNKVNFKTASFLFSVCLALSAFNAHANKSDAAAKQIKKLEEDFDGRIGVFAIDTGSGNTFGYRSDERFPLCSSFKGFLAAAVLERVQQKKLDINQKVKYESRDLEYYSPITTKYKGSGMTLGDMASAALQYSDNGATNIIMERFLGGPEGMTKFMRSIGDNEFRLDRWELELNTAIPGDKRDTSTPKAVANSLNKLALGNVLNAKVKAIYQNWLKGNTTGDARIRASVPADWVVGDKTGSCGAYGTANDYAVIWPKNRAPLIVSIYTTRKSKDDKHSDKTIAEASRIAIQAID"},"dna_sequence":{"accession":"AY584237","fmin":"123","fmax":"1008","strand":"+","sequence":"ATGTCAAACAAAGTAAATTTTAAAACGGCTTCATTTTTGTTTAGTGTTTGTTTAGCTTTGTCGGCATTTAATGCTCATGCTAACAAAAGTGATGCTGCGGCAAAACAAATAAAAAAATTAGAGGAAGACTTTGATGGGAGGATTGGCGTCTTTGCAATAGATACAGGATCGGGTAATACATTTGGGTATAGATCAGATGAGCGGTTCCCTTTATGCAGTTCATTTAAAGGTTTTTTGGCGGCTGCTGTTTTAGAGAGGGTGCAACAAAAAAAACTAGATATCAACCAAAAGGTTAAATATGAGAGTAGGGATCTAGAATATTATTCACCTATTACAACAAAATATAAAGGCTCAGGTATGACATTAGGTGATATGGCTTCTGCTGCATTGCAATATAGCGACAATGGGGCAACAAATATAATTATGGAACGATTTCTTGGCGGTCCTGAGGGGATGACTAAATTTATGCGTTCTATTGGAGATAATGAGTTTAGGTTAGATCGCTGGGAACTGGAACTTAACACTGCAATCCCAGGAGATAAACGTGACACTTCAACGCCAAAAGCTGTTGCAAATAGTTTGAATAAACTAGCTTTGGGGAATGTTCTCAATGCTAAAGTGAAAGCGATTTATCAAAATTGGTTAAAAGGTAATACAACTGGTGATGCTCGAATTCGTGCTAGTGTTCCTGCTGATTGGGTTGTAGGTGACAAAACTGGGAGCTGTGGGGCATATGGTACTGCGAATGATTATGCCGTCATTTGGCCTAAAAATAGAGCACCATTAATTGTCTCTATATATACAACACGAAAATCGAAAGATGATAAGCACAGTGATAAAACTATTGCGGAAGCATCACGTATTGCAATTCAGGCAATTGATTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36783","NCBI_taxonomy_name":"Serratia marcescens","NCBI_taxonomy_id":"615"}}}},"ARO_accession":"3002381","ARO_id":"38781","ARO_name":"SME-3","ARO_description":"SME-3 is a beta-lactamase found in Serratia marcescens","ARO_category":{"36194":{"category_aro_accession":"3000055","category_aro_cvterm_id":"36194","category_aro_name":"SME beta-lactamase","category_aro_description":"SME beta-lactamases are chromosome-mediated class A beta-lactamases that hydrolyze carbapenems in Serratia marcescens.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1513":{"model_id":"1513","model_name":"QnrB64","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"74":{"protein_sequence":{"accession":"AGL43625.1","sequence":"MALALVGDKIDRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNASALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRRVDLQGVKLDNYQASLLMERLGIAIIG"},"dna_sequence":{"accession":"KC580653","fmin":"0","fmax":"645","strand":"+","sequence":"ATGGCTCTGGCACTCGTTGGCGATAAAATTGACAGAAACCGTTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCGATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATGCCAGTGCGCTGGGCATTGAAATTCGTCACTGCCGCGCACAAGGCGCAGATTTCCGCGGCGCAAGCTTTATGAATATGATCACTACTCGCACCTGGTTTTGCAGCGCATATATCACTAACACAAATCTAAGCTATGCCAATTTTTCGAAAGTCGTGCTGGAAAAATGTGAGCTGTGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTGACTTAGATATTCGGCGCGTTGATTTACAAGGCGTTAAGTTGGACAACTACCAGGCATCGTTGCTCATGGAACGTCTTGGCATCGCGATTATTGGCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002776","ARO_id":"39210","ARO_name":"QnrB64","ARO_description":"QnrB64 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1514":{"model_id":"1514","model_name":"IMP-28","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"913":{"protein_sequence":{"accession":"AFG73659.1","sequence":"MSKLFVFFMFLFCSITAAAESLPDLKIERLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNTEAYLIDTPFTAKDTEKLVTWFVGRGYKIKGSISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKDGKVQAKNSFGGVSYWLVKNKIEVFYPGPGHTPDNVVVWLPENRVLFGGCFVKPYGLGNLGDANLEAWPKSAKLLMSKYGKAKLVVPSHSEVGDASLLKRTLEHAVKGLNESKKPSKPSN"},"dna_sequence":{"accession":"JQ407409","fmin":"1168","fmax":"1909","strand":"+","sequence":"ATGAGCAAGTTATTTGTATTCTTTATGTTTTTGTTTTGTAGCATTACTGCCGCAGCAGAGTCTTTGCCAGATTTAAAAATTGAGAGGCTTGATGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGTTGGGGTGTTGTTCCTAAACACGGCTTGGTGGTTCTTGTAAATACTGAGGCCTATCTGATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGGACGCGGCTATAAAATAAAAGGCAGTATTTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCAATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTTCTTAAAAAAGACGGTAAGGTACAAGCTAAAAATTCATTTGGCGGAGTTAGCTATTGGCTAGTTAAGAATAAGATTGAAGTTTTTTATCCTGGTCCAGGGCACACTCCAGATAACGTAGTGGTTTGGCTACCTGAAAATAGAGTTTTGTTCGGTGGTTGTTTTGTTAAACCGTACGGTCTTGGTAATTTGGGTGACGCAAATTTAGAAGCTTGGCCAAAGTCCGCCAAATTATTAATGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAAGTCACAGTGAAGTTGGAGACGCATCACTCTTGAAGCGAACATTAGAACATGCGGTTAAAGGGTTAAATGAAAGTAAAAAACCATCAAAACCAAGTAACTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002219","ARO_id":"38619","ARO_name":"IMP-28","ARO_description":"IMP-28 is a beta-lactamase found in Klebsiella oxytoca","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1515":{"model_id":"1515","model_name":"NDM-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"859":{"protein_sequence":{"accession":"AFK80349.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTNDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"JQ734687","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCAATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGATGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002354","ARO_id":"38754","ARO_name":"NDM-3","ARO_description":"NDM-3 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1516":{"model_id":"1516","model_name":"CMY-45","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1663":{"protein_sequence":{"accession":"CBB16411.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLKIPDDVRDKAALLHFYQNWQPQWTPGAKRLYSNSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYARGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTVGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"FN546177","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGAAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACTCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCCGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGTTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3002056","ARO_id":"38456","ARO_name":"CMY-45","ARO_description":"CMY-45 is a beta-lactamase found in Proteus mirabilis","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1517":{"model_id":"1517","model_name":"OXA-33","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1299":{"protein_sequence":{"accession":"AAG23871.1","sequence":"ANIIYSSASASTDISTVASPLFEGTEGCFLLYDVSTNAEIAQFNKAKCATQMAPDSTFKIALSLMAFDAEIIDQKTIFKWDKTPKGMEIWNSNHTPKTWMQFSVVWVSQEITQKIGLNKIKNYLKDFDYGNQDFSGDKERNNGLTEAWLESSLKISPEEQIQFLRKIINHNLPVKNSAIENTIENMYLQDLENSTKLYGKTGAGFTANRTLQNGWFEGFIISKSGHKYVFVSALTGNLGSNLTSSIKAKKNAITIL"},"dna_sequence":{"accession":"AY008291","fmin":"0","fmax":"769","strand":"+","sequence":"GCAAATATTATCTACAGCAGCGCCAGTGCATCAACAGATATCTCTACTGTTGCATCTCCATTATTTGAAGGAACTGAAGGTTGTTTTTTACTTTACGATGTATCCACAAACGCTGAAATTGCTCAATTCAATAAAGCAAAGTGTGCAACGCAAATGGCACCAGATTCAACTTTCAAGATCGCATTATCACTTATGGCATTTGATGCGGAAATAATAGATCAGAAAACCATATTCAAATGGGATAAAACCCCCAAAGGAATGGAGATCTGGAACAGCAATCATACACCAAAGACGTGGATGCAATTTTCTGTTGTTTGGGTTTCGCAAGAAATAACCCAAAAAATTGGATTAAATAAAATCAAGAATTATCTCAAAGATTTTGATTATGGAAATCAAGACTTCTCTGGAGATAAAGAAAGAAACAACGGATTAACAGAAGCATGGCTCGAAAGTAGCTTAAAAATTTCACCAGAAGAACAAATTCAATTCCTGCGTAAAATTATTAATCACAATCTCCCAGTTAAAAACTCAGCCATAGAAAACACCATAGAGAACATGTATCTACAAGATCTGGAGAATAGTACAAAACTGTATGGGAAAACTGGTGCAGGATTCACAGCAAATAGAACCTTACAAAACGGATGGTTTGAAGGGTTTATTATAAGCAAATCAGGACATAAATATGTTTTTGTGTCCGCACTTACAGGAAACTTGGGGTCGAATTTAACATCAAGCATAAAAGCCAAGAAAAATGCGATCACCATTCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001427","ARO_id":"37827","ARO_name":"OXA-33","ARO_description":"OXA-33 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1518":{"model_id":"1518","model_name":"EreA2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"219":{"protein_sequence":{"accession":"AAC78336.1","sequence":"MTWRTTRTLLQPQKLEFNEFEILNPVVEGARIVGIGEGAHFVAEFSLARASLIRYFVERHDFNAIGLECGAIQASRLSEWLNSTAGAHELERFSDTLTFSLYGSVLIWVKSYLRESGRKLQLVGIDLPNTLNPRDDLAQLAEIIQVIDHLMKPHVDALTQLLTSIDGQSAVISSAKWGELETAQQEKAISGVTRLKLRLASLAPVLKNHVNSDFFRKASDRIESIEYTLETLRVMKAFFDGTSLEGDTSVRDSYMAGVVDGMVRANPDVRIILLAHNNHLQKTPVSFSGELTAVPMGQHLAEREEGDYRAIAFTHLGLTVPEMHFPSPDSPLGFSVVTTPADAIREDSVEQYVIDACGKEDSCLTLTDDPMEAKRMRSQSASVETNLSEAFDAIVCVPSAGKDSLVAL"},"dna_sequence":{"accession":"AF099140","fmin":"136","fmax":"1363","strand":"+","sequence":"ATGACATGGAGAACGACCAGAACACTTTTACAGCCTCAAAAGCTGGAGTTCAATGAGTTTGAGATTCTTAATCCCGTAGTTGAGGGCGCCCGAATTGTCGGCATTGGCGAGGGTGCTCACTTTGTCGCGGAGTTCTCACTGGCTAGAGCTAGTCTTATTCGCTATTTTGTCGAGAGGCATGATTTTAATGCGATTGGTTTGGAATGTGGGGCGATTCAGGCATCCCGGCTATCTGAATGGCTCAACTCAACAGCCGGTGCTCATGAACTTGAGCGATTTTCGGATACCCTGACCTTTTCTTTGTATGGCTCAGTGCTGATTTGGGTTAAATCATATCTACGCGAATCAGGAAGAAAACTGCAGTTAGTCGGAATCGATTTACCCAACACCTTGAATCCAAGGGACGACCTAGCGCAATTGGCCGAAATTATCCAGGTCATCGACCACCTCATGAAACCCCACGTTGATGCGCTGACTCAGTTGTTGACGTCCATTGATGGCCAGTCGGCGGTTATTTCATCGGCAAAATGGGGGGAGTTGGAAACGGCTCAGCAGGAGAAAGCTATCTCAGGGGTAACCAGATTGAAGCTCCGTTTGGCGTCGCTTGCCCCTGTCCTGAAAAATCACGTCAACAGCGATTTTTTCCGAAAAGCCTCTGATCGAATAGAGTCGATAGAGTATACGTTGGAAACCTTGCGTGTAATGAAAGCTTTCTTCGATGGTACCTCTCTTGAGGGAGATACTTCCGTACGTGACTCGTATATGGCGGGCGTGGTGGATGGAATGGTTCGAGCGAATCCGGATGTAAGGATAATTCTGCTGGCGCACAACAATCATTTACAAAAAACTCCAGTTTCCTTTTCAGGCGAGCTTACGGCTGTTCCCATGGGACAGCATCTCGCAGAGAGGGAGGAGGGGGATTACCGTGCGATTGCATTCACCCATCTTGGACTCACCGTGCCGGAAATGCATTTCCCATCGCCCGACAGTCCTCTTGGATTCTCTGTTGTGACCACGCCTGCCGATGCAATCCGTGAGGATAGTGTGGAACAGTATGTCATCGATGCCTGTGGTAAGGAGGATTCATGCCTGACATTGACAGATGACCCCATGGAAGCAAAGCGAATGCGGTCCCAAAGCGCCTCTGTAGAAACGAATTTGAGCGAGGCATTTGATGCCATCGTCTGCGTTCCCAGCGCCGGCAAGGACAGCCTGGTTGCCCTATAGG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36946","NCBI_taxonomy_name":"Providencia stuartii","NCBI_taxonomy_id":"588"}}}},"ARO_accession":"3002826","ARO_id":"39260","ARO_name":"EreA2","ARO_description":"EreA2 is an integron-encoded erythromycin esterase that hydrolyses the drug's lactone ring. EreA2 is found in Providencia stuartii","ARO_category":{"36459":{"category_aro_accession":"3000320","category_aro_cvterm_id":"36459","category_aro_name":"macrolide esterase","category_aro_description":"Hydrolytic enzymes that cleave the macrocycle lactone ring of macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1519":{"model_id":"1519","model_name":"vatE","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"507":{"protein_sequence":{"accession":"AAF86220.1","sequence":"MTIPDANAIYPNSAIKEVVFIKNVIKSPNIEIGDYTYYDDPVNPTDFEKHVTHHYEFLGDKLIIGKFCSIASGIEFIMNGANHVMKGISTYPFNILGGDWQQYTPELTDLPLKGDTVVGNDVWFGQNVTVLPGVKIGDGAIIGANSVVTKDVAPYTIVGGNPIQLIGPRFEPEVIQALENLAWWNKDIEWITANVPKLMQTTPTLELINSLMEK"},"dna_sequence":{"accession":"AF242872","fmin":"3579","fmax":"4224","strand":"+","sequence":"ATGACTATACCTGACGCAAATGCAATCTATCCTAACTCAGCCATCAAAGAGGTTGTCTTTATCAAGAACGTGATCAAAAGTCCCAATATTGAAATTGGGGACTACACCTATTATGATGACCCAGTAAATCCCACCGATTTTGAGAAACACGTTACCCATCACTATGAATTTCTAGGCGACAAATTAATCATCGGTAAATTTTGTTCTATCGCCAGTGGCATTGAATTTATCATGAACGGTGCCAACCACGTAATGAAAGGTATTTCGACTTATCCATTTAATATTTTAGGTGGCGATTGGCAACAATACACTCCTGAACTGACTGATTTGCCGTTGAAAGGTGATACTGTAGTCGGAAATGACGTGTGGTTTGGGCAAAATGTGACCGTCCTACCAGGCGTAAAAATAGGTGACGGTGCCATTATCGGAGCAAATAGTGTTGTAACAAAAGACGTCGCTCCATATACAATTGTCGGTGGCAATCCAATTCAACTCATCGGACCAAGATTTGAACCGGAAGTTATTCAAGCATTAGAAAATCTGGCATGGTGGAATAAAGATATTGAATGGATAACTGCTAATGTTCCTAAACTAATGCAAACAACACCCACACTTGAATTGATAAACAGTTTAATGGAAAAATAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002844","ARO_id":"39278","ARO_name":"vatE","ARO_description":"vatE is a transposon-mediated acetyltransferase found in Enterococcus faecium","ARO_category":{"36592":{"category_aro_accession":"3000453","category_aro_cvterm_id":"36592","category_aro_name":"streptogramin vat acetyltransferase","category_aro_description":"vat (Virginiamycin acetyltransferases) enzymes catalyze the transfer of an acetyl group from acetyl-CoA to the secondary alcohol of streptogramin A compounds, thus inactivating virginiamycin-like antibiotics and conferring resistance to these compounds.","category_aro_class_name":"AMR Gene Family"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1520":{"model_id":"1520","model_name":"SHV-85","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1486":{"protein_sequence":{"accession":"ABC54571.1","sequence":"MRYIRLCIISLLATMPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"DQ322460","fmin":"15","fmax":"876","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCATGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATCGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001139","ARO_id":"37519","ARO_name":"SHV-85","ARO_description":"SHV-85 is a broad-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1521":{"model_id":"1521","model_name":"VIM-32","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1252":{"protein_sequence":{"accession":"AEZ49857.1","sequence":"MLKVISSLLVYMTASVMAVASPLAHSGEPSGEYPTVNEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEAAGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSANVLYGGCAVHELSSTSAGNVADADLAEWPTSVERIQKHYPEAEVVIPGHGLPGGLDLLQHTANVVKAHKNRSVAE"},"dna_sequence":{"accession":"JN676230","fmin":"1549","fmax":"2350","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTACATGACCGCGTCTGTCATGGCTGTCGCAAGTCCGTTAGCCCATTCCGGGGAGCCGAGTGGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGAGAGGTCCGACTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCGGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAAAAGCAAATTGGACTTCCCGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGCAGCGGGGAACGAGATTCCCACGCATTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGCTCTTCTATCCTGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAACGTGCTATACGGTGGTTGTGCCGTTCATGAGTTGTCAAGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCGTTGAGCGGATTCAAAAACACTACCCGGAAGCAGAGGTCGTCATTCCCGGGCACGGTCTACCGGGCGGTCTAGACTTGCTCCAGCACACAGCGAACGTTGTCAAAGCACACAAAAATCGCTCAGTCGCCGAGTAGC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002302","ARO_id":"38702","ARO_name":"VIM-32","ARO_description":"VIM-32 is a beta-lactamase. From the Lahey list of VIM beta-lactamases.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1522":{"model_id":"1522","model_name":"IMP-38","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1709":{"protein_sequence":{"accession":"AEN75249.1","sequence":"MSKLSVFFIFLFCSIATAAEPLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVDAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKDGKVQAKNSFGGVNYWLVKNKIEVFYPGPGHTPDNLVVWLPERKILFGGCFIKPYGLGNLGDANLEAWPKSAKLLISKYGKAKLVVPGHSEAGDASLLKLTLEQAVKGLNESKKPSKLSN"},"dna_sequence":{"accession":"HQ875573","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAGCAAGTTATCTGTATTCTTTATATTTTTGTTTTGTAGCATTGCTACCGCAGCAGAGCCTTTGCCAGATTTAAAAATTGAAAAACTTGATGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGGTGGGGCGTTGTTCCTAAACATGGTTTGGTTGTTCTTGTAGATGCTGAAGCTTATCTAATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAACGTGGCTATAAAATAAAAGGCAGTATTTCCTCTCATTTTCATAGTGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCAATCCATCCCCACGTATGCGTCTGAATTAACTAATGAGCTGCTTAAAAAAGACGGTAAGGTTCAAGCTAAAAATTCATTTGGCGGGGTTAACTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCAGGACACACTCCAGATAACCTAGTAGTTTGGCTGCCTGAAAGGAAAATATTATTCGGTGGTTGTTTTATTAAACCGTACGGTCTAGGTAATTTGGGTGACGCAAATTTAGAAGCTTGGCCAAAGTCCGCTAAATTATTAATATCCAAATATGGTAAGGCAAAACTGGTTGTTCCAGGTCACAGTGAAGCTGGAGACGCATCACTCTTGAAACTTACATTAGAGCAGGCGGTTAAAGGGTTAAACGAAAGTAAAAAACCATCAAAACTAAGCAACTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002229","ARO_id":"38629","ARO_name":"IMP-38","ARO_description":"IMP-38 is a beta-lactamase. From the Lahey list of IMP beta-lactamases.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1525":{"model_id":"1525","model_name":"TEM-160","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1798":{"protein_sequence":{"accession":"ABM54870.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMVSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"EF136377","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGGTGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3001026","ARO_id":"37406","ARO_name":"TEM-160","ARO_description":"TEM-160 is an inhibitor-resistant beta-lactamase found in Proteus mirabilis.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1526":{"model_id":"1526","model_name":"AAC(6')-Iaa","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"308":{"protein_sequence":{"accession":"NP_460578.1","sequence":"MDIRQMNRTHLDHWRGLRKQLWPGHPDDAHLADGEEILQADHLASFIAMADGVAIGFADASIRHDYVNGCDSSPVVFLEGIFVLPSFRQRGVAKQLIAAVQRWGTNKGCREMASDTSPENTISQKVHQALGFEETERVIFYRKRC"},"dna_sequence":{"accession":"NC_003197","fmin":"1707357","fmax":"1707795","strand":"+","sequence":"ATGGACATCAGGCAAATGAACAGAACCCATCTGGATCACTGGCGCGGATTGCGAAAACAGCTCTGGCCTGGTCACCCGGATGACGCCCATCTGGCGGACGGCGAAGAAATTCTGCAAGCCGATCATCTGGCATCATTTATTGCGATGGCAGACGGGGTGGCGATTGGCTTTGCGGATGCCTCAATCCGCCACGATTATGTCAATGGCTGTGACAGTTCGCCCGTGGTTTTCCTTGAAGGTATTTTTGTTCTCCCCTCATTCCGTCAACGCGGCGTAGCGAAACAATTGATTGCAGCGGTGCAACGATGGGGAACGAATAAAGGGTGTCGGGAAATGGCCTCCGATACCTCGCCGGAAAATACAATTTCCCAGAAAGTTCATCAGGCGTTAGGATTTGAGGAAACAGAGCGCGTCATTTTCTACCGAAAGCGTTGTTGAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35734","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium str. LT2","NCBI_taxonomy_id":"99287"}}}},"ARO_accession":"3002571","ARO_id":"38971","ARO_name":"AAC(6')-Iaa","ARO_description":"AAC(6')-Iaa is a chromosomal-encoded aminoglycoside acetyltransferase in S. typhimurium","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1527":{"model_id":"1527","model_name":"SHV-51","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1316":{"protein_sequence":{"accession":"AAP41944.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGLAGLTAFLRQIGDNVTRLDRWETELNEALPADARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AY289548","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCTCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGCCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001108","ARO_id":"37488","ARO_name":"SHV-51","ARO_description":"SHV-51 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1528":{"model_id":"1528","model_name":"TEM-168","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"999":{"protein_sequence":{"accession":"ACR22829.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYMTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"FJ919776","fmin":"208","fmax":"1069","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACATGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001034","ARO_id":"37414","ARO_name":"TEM-168","ARO_description":"TEM-168 is an extended-spectrum beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1529":{"model_id":"1529","model_name":"TEM-130","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1880":{"protein_sequence":{"accession":"CAI29263.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKPAEDKLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGTGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AJ866988","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAACCTGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAACCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000994","ARO_id":"37374","ARO_name":"TEM-130","ARO_description":"TEM-130 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1530":{"model_id":"1530","model_name":"OXA-67","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1936":{"protein_sequence":{"accession":"ABF50983.1","sequence":"MNIKALLLITSTIFISACSPYIVTANPNHSTSKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEIFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSLKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"DQ491200","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCACTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCACTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAATATTTAAGTGGGACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGTGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCTAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001437","ARO_id":"37837","ARO_name":"OXA-67","ARO_description":"OXA-67 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1531":{"model_id":"1531","model_name":"TEM-81","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1080":{"protein_sequence":{"accession":"AAL29433.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMLSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAVTMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AF427127","fmin":"208","fmax":"1069","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGCTGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCGTAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000948","ARO_id":"37328","ARO_name":"TEM-81","ARO_description":"TEM-81 is an inhibitor-resistant beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1532":{"model_id":"1532","model_name":"OXA-249","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1130":{"protein_sequence":{"accession":"CCJ32597.1","sequence":"MNIKALLLITSAIFISACSPYIVTTNPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIQVYQDLARRIGLELMSKEVKRVGYGNTDIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"HE963770","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTACTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCAAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATACAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001674","ARO_id":"38074","ARO_name":"OXA-249","ARO_description":"OXA-249 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1533":{"model_id":"1533","model_name":"SHV-143","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"4364":{"protein_sequence":{"accession":"AFQ32277.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDLWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"JQ341060","fmin":"881","fmax":"1742","strand":"-","sequence":"TTAGCGTTGCCAGTGCTCGATCAGCGCCGCGCCGATCCCGGCGATTTGCTGATTTCGCTCGGCCATGCTCGCCGGGGTATCCCGCAGATAAATCACCACAATGCGCTCTGCTTTGTTATTCGGGCCAAGCAGGGCGACAATCCCGCGCGCACCCCGTTCGCCAGCTCCGGTCTTATCGGCGATAAACCAGCCCGCCGGCAGCACGGAGCGGATCAACGGTCCGGCGACCCGATCGTCCACCATCCACTGCAGCAGCTGCCGTTGCGAACGGGCGCTCAGACGCTGGCTGGTCAGCAGCTTGCGCAGGGTCGCGGCCATGCTGGCCGGGGTAGTGGTGTCGCGGGCGTCGCCGGGAAGCGCCTCATTCAGTTCCGTTTCCCAGAGGTCAAGGCGGGTGACGTTGTCGCCGATCTGGCGCAAAAAGGCAGTCAATCCTGCGGGGCCGCCGACGGTGGCCAGTAGCAGATTGGCGGCGCTGTTATCGCTCATGGTAATGGCGGCGGCGCAGAGTTCGCCGACCGTCATGCCGTCGGCAAGGTGTTTTTCGCTGACCGGCGAGTAGTCCACCAGATCCTGCTGGCGATAGTGGATCTTTCGCTCCAGCTGTTCGTCACCGGCATCCACCCGCGCCAGCACTGCGCCGCAGAGCACTACTTTAAAGGTGCTCATCATGGGAAAGCGTTCATCGGCGCGCCAGGCGGTCAGCGTGCGGCCGCTGGCCAGATCCATTTCTATCATGCCTACGCGGCCCGACAGCTGGCTTTCGCTTAGTTTAATTTGCTCAAGCGGCTGCGGGCTGGCGTGTACCGCCAGCGGCAGGGTGGCTAACAGGGAGATAATACACAGGCGAATATAACGCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001344","ARO_id":"37744","ARO_name":"SHV-143","ARO_description":"From the Lahey list of beta-lactamases.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1534":{"model_id":"1534","model_name":"PER-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1142":{"protein_sequence":{"accession":"ACN22483.1","sequence":"MNVIIKAVVTASTLLMVSFSSFETSAQSPLLKGQIESIVIGKKATVGVAVWGPDDLEPLLINPFEKFPMQSVFKLHLAMLVLHQVDQGKLDLNQTVIVNRAKVLQNTWAPIMKAYQGDEFSVPVQQLLQYSVSHSDNVACDLLFELVGGPAALHDYIQSMGIKETAVVANEAQMHADDQVQYQNWTSMKGAAEILKKFEQKTQLSETSQALLWKWMVETTTGPERLKGLLPAGTVVAHKTGTSGIKAGKTAATNDLGIILLPDGRPLLVAVFVKDSAESSRTNEAIIAQVAQTAYQFELKKLSALSPN"},"dna_sequence":{"accession":"FJ627180","fmin":"0","fmax":"926","strand":"+","sequence":"ATGAATGTCATTATAAAAGCTGTAGTTACTGCCTCGACGCTACTGATGGTATCTTTTAGTTCATTCGAAACCTCAGCGCAATCCCCACTGTTAAAAGGGCAAATTGAATCCATAGTCATTGGAAAAAAAGCCACTGTAGGCGTTGCAGTGTGGGGGCCTGACGATCTGGAACCTTTACTGATTAATCCTTTTGAAAAATTCCCAATGCAAAGTGTATTTAAATTGCATTTAGCTATGTTGGTACTGCATCAGGTTGATCAGGGAAAGTTGGATTTAAATCAGACCGTTATCGTAAACAGGGCTAAGGTTTTACAGAATACCTGGGCTCCGATAATGAAAGCGTATCAGGGAGACGAGTTTAGTGTTCCAGTGCAGCAACTGCTGCAATACTCGGTCTCGCACAGCGATAACGTGGCCTGTGATTTGTTATTTGAACTGGTTGGTGGACCAGCTGCTTTGCATGACTATATCCAGTCTATGGGTATAAAGGAGACCGCTGTGGTCGCAAATGAAGCGCAGATGCACGCCGATGATCAGGTGCAGTATCAAAACTGGACCTCGATGAAAGGTGCTGCAGAGATCCTGAAAAAGTTTGAGCAAAAAACACAGCTGTCTGAAACCTCGCAGGCTTTGTTATGGAAGTGGATGGTCGAAACCACCACAGGACCAGAGCGGTTAAAAGGTTTGTTACCAGCTGGTACTGTGGTCGCACATAAAACTGGTACTTCGGGTATCAAAGCCGGAAAAACTGCGGCCACTAATGATTTAGGTATCATTCTGTTGCCTGATGGACGGCCCTTGCTGGTTGCTGTTTTTGTGAAAGACTCAGCCGAGTCAAGCCGAACCAATGAAGCTATCATTGCGCAGGTTGCTCAGACTGCGTATCAATTTGAATTGAAAAAGCTTTCTGCCCTAAGCCCAAATTA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36944","NCBI_taxonomy_name":"Providencia rettgeri","NCBI_taxonomy_id":"587"}}}},"ARO_accession":"3002367","ARO_id":"38767","ARO_name":"PER-5","ARO_description":"PER-5 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36195":{"category_aro_accession":"3000056","category_aro_cvterm_id":"36195","category_aro_name":"PER beta-lactamase","category_aro_description":"PER beta-lactamases are plasmid-mediated extended spectrum beta-lactamases found in the Enterobacteriaceae family.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1535":{"model_id":"1535","model_name":"CMY-16","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1815":{"protein_sequence":{"accession":"CAH03679.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYSNSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYARGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"AJ781421","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACTCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCCGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3002027","ARO_id":"38427","ARO_name":"CMY-16","ARO_description":"CMY-16 is a beta-lactamase found in Proteus mirabilis","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1536":{"model_id":"1536","model_name":"OXA-421","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4363":{"protein_sequence":{"accession":"AIZ00987.1","sequence":"MTKKTLFFAIGTMFLSACSFNTVEQHQIQSISTNKNSEKIQSLFDQAQTTGVLIIKRGQTEEVYGNDLKRASTEYVPASTFKMLNALIGLEHHKATPTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIDFGNADIGSKIDNFWLVGPLKITPQQEAQFAYELAHKTLPFSKNVQEQVQSMLFIEEKNGRKIYAKSGWGWDVEPQVGWFTGWVVQPQGEIVAFALNLEMKKGIPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"KM401566","fmin":"1211","fmax":"2033","strand":"-","sequence":"TTATAAAATACCTAATTGTTCTAATCCTTTATAAGCAATTTCTTTTCGAATAGAACTAGGTATTCCTTTTTTCATTTCTAAATTAAGTGCGAACGCTACAATTTCTCCTTGTGGTTGAACCACCCAGCCTGTAAACCAACCAACTTGTGGTTCAACATCCCATCCCCAACCACTTTTAGCATAAATTTTTCGTCCATTTTTTTCTTCTATGAACAACATAGATTGAACTTGTTCTTGCACATTTTTGCTAAAGGGAAGAGTTTTGTGGGCTAGTTCATAAGCAAACTGGGCTTCTTGTTGAGGTGTAATTTTAAGTGGGCCAACAAGCCAAAAATTATCTATTTTTGAACCAATATCAGCATTACCGAAATCAATACGCTTTACCTCTTTAGACATAAGATCAAGGCCAATTCGTCGAGCTAGTTCCTGATAAACTGGAATAGCAGAAGCTTTCATAGCATCGCCTAATGTCATGTCTTTTTCCCAATCGGGAAATAAACGCTTTTGCCCATCCCATTTAAATACTTCAGTTGGTGTTGCTTTATGATGCTCAAGGCCGATCAAAGCATTTAACATTTTAAAGGTAGAGGCGGGAACATATTCGGTTGATGCTCTTTTAAGATCATTACCATAGACTTCCTCTGTTTGGCCACGTTTTATAATTAAAACACCTGTAGTTTGTGCTTGATCAAACAATGATTGAATTTTCTCTGAGTTTTTATTGGTAGAAATTGACTGTATTTGATGTTGTTCTACGGTATTAAAAGAACACGCCGATAAAAACATCGTACCAATGGCAAAGAAAAGAGTTTTTTTAGTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3003117","ARO_id":"39694","ARO_name":"OXA-421","ARO_description":"From the Lahey list of beta-lactamases. Not yet released.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1537":{"model_id":"1537","model_name":"GES-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1172":{"protein_sequence":{"accession":"AAK58421.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMNDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"AF326355","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGAACGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002331","ARO_id":"38731","ARO_name":"GES-2","ARO_description":"GES-2 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1538":{"model_id":"1538","model_name":"SHV-104","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1850":{"protein_sequence":{"accession":"ABX71158.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSASSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"EU274581","fmin":"0","fmax":"861","strand":"+","sequence":"TTGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCAGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001153","ARO_id":"37533","ARO_name":"SHV-104","ARO_description":"SHV-104 is an extended-spectrum beta-lactamase that has been found in clinical isolates.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1539":{"model_id":"1539","model_name":"aadA3","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"372":{"protein_sequence":{"accession":"AAC14728.1","sequence":"MRVAVTIEISNQLSEVLSVIERHLESTLLAVHLYGSAVDGGLKPYSDIDLLVTVAVKLDETTRRALLNDLMEASAFPGESETLRAIEVTLVVHDDIIPWRYPAKRELQFGEWQRNDILAGIFEPAMIDIDLAILLTKAREHSVALVGPAAEEFFDPVPEQDLFEALRETLKLWNSQPDWAGDERNVVLTLSRIWYSAITGKIAPKDVAADWAIKRLPAQYQPVLLEAKQAYLGQKEDHLASRADHLEEFIHYVKGEITKVVGK"},"dna_sequence":{"accession":"AF047479","fmin":"1295","fmax":"2087","strand":"+","sequence":"ATGAGGGTAGCGGTGACCATCGAAATTTCGAACCAACTATCAGAGGTGCTAAGCGTCATTGAGCGCCATCTGGAATCAACGTTGCTGGCCGTGCATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCATACAGCGATATTGATTTGTTGGTTACTGTGGCCGTAAAGCTTGATGAAACGACGCGGCGAGCATTGCTCAATGACCTTATGGAGGCTTCGGCTTTCCCTGGCGAGAGCGAGACGCTCCGCGCTATAGAAGTCACCCTTGTCGTGCATGACGACATCATCCCGTGGCGTTATCCGGCTAAGCGCGAGCTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCGGGTATCTTCGAGCCAGCCATGATCGACATTGATCTAGCTATCCTGCTTACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCGGCAGCGGAGGAATTCTTTGACCCGGTTCCTGAACAGGATCTATTCGAGGCGCTGAGGGAAACCTTGAAGCTATGGAACTCGCAGCCCGACTGGGCCGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAATAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATAAAACGCCTACCTGCCCAGTATCAGCCCGTCTTACTTGAAGCTAAGCAAGCTTATCTGGGACAAAAAGAAGATCACTTGGCCTCACGCGCAGATCACTTGGAAGAATTTATTCACTACGTGAAAGGCGAGATCACCAAGGTAGTCGGCAAATAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36872","NCBI_taxonomy_name":"Plasmid NR79","NCBI_taxonomy_id":"2468"}}}},"ARO_accession":"3002603","ARO_id":"39003","ARO_name":"aadA3","ARO_description":"aadA3 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids, transposons and integrons in E. coli","ARO_category":{"41439":{"category_aro_accession":"3004275","category_aro_cvterm_id":"41439","category_aro_name":"ANT(3'')","category_aro_description":"Nucleotidylylation of streptomycin at the hydroxyl group at position 3''","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1540":{"model_id":"1540","model_name":"rmtC","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"3396":{"protein_sequence":{"accession":"AIA09786.1","sequence":"MKTNDNYIEEVTAKVLTSGKYSTLYPPTVRRVTERLFDRYPPKQLEKEVRKKLHQAYGAYIGGIDGKRLEKKIEKIIHEIPNPTTDEATRTEWEKEICLKILNLHTSTNERTVAYDELYQKIFEVTGVPTSITDAGCALNPFSFPFFTEAGMLGQYIGFDLDKGMIEAIEHSLRTLNAPEGIVVKQGDILSDPSGESDLLLMFKLYTLLDRQEEASGLKILQEWKYKNAVISFPIKTISGRDVGMEENYTVKFENDLVGSDLRIMQKLKLGNEMYFIVSRL"},"dna_sequence":{"accession":"KJ476816.1","fmin":"79","fmax":"925","strand":"+","sequence":"ATGAAAACCAACGATAATTATATCGAAGAAGTAACAGCCAAAGTACTCACAAGTGGTAAATACTCCACACTTTATCCACCAACTGTACGACGTGTAACTGAGAGGCTTTTCGATCGATACCCTCCCAAGCAGCTAGAGAAGGAGGTTCGCAAGAAATTGCATCAAGCATATGGTGCTTATATTGGTGGGATCGATGGGAAAAGGTTGGAGAAGAAGATTGAGAAGATAATTCATGAGATACCAAATCCAACTACGGATGAAGCAACTCGTACGGAGTGGGAAAAAGAGATCTGCCTGAAAATATTGAACTTGCACACTTCAACAAATGAGCGAACGGTGGCTTACGATGAGCTTTACCAAAAGATCTTTGAGGTAACAGGGGTTCCAACAAGTATCACCGATGCAGGTTGCGCTTTGAATCCATTTTCTTTTCCATTCTTTACGGAGGCTGGCATGCTTGGGCAATACATAGGTTTCGATCTTGATAAAGGTATGATCGAAGCGATCGAACACTCGTTGAGAACGCTTAACGCCCCAGAGGGTATTGTTGTCAAACAGGGAGATATATTATCCGATCCGTCAGGCGAGAGTGATCTTCTACTTATGTTCAAGCTATATACTCTACTCGATCGGCAGGAAGAGGCCTCTGGTTTGAAAATTCTTCAAGAGTGGAAATACAAAAATGCTGTGATCTCTTTTCCTATTAAAACTATAAGTGGGAGAGATGTTGGGATGGAAGAGAATTACACTGTTAAGTTCGAGAATGATCTTGTTGGGTCAGATCTGAGAATCATGCAAAAATTGAAATTAGGAAACGAGATGTATTTTATCGTATCGAGATTGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3000861","ARO_id":"37241","ARO_name":"rmtC","ARO_description":"RmtC is a rRNA methyltransferase found in Proteus mirabilis with high level resistance to similar to aminoglycosides, with the exception of non-4,6-disubstituted deoxystreptamines (streptomycin and neomycin). It has also been isolated in Salmonella enterica ser. Virchow. It is hypothesized to methylate G1405, like related methyltransferases RmtA, RmtB, and ArmA.","ARO_category":{"41435":{"category_aro_accession":"3004271","category_aro_cvterm_id":"41435","category_aro_name":"16S rRNA methyltransferase (G1405)","category_aro_description":"Methyltransferases that methylate the G1405 position of 16S rRNA, which is part of an aminoglycoside binding site.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1541":{"model_id":"1541","model_name":"ACT-14","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1176":{"protein_sequence":{"accession":"AFU25647.1","sequence":"MMKKSLCCALLLGISCSALAAPVSEKQLAEVVANTVTPLMKAQSIPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNAALLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMGYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPEKVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVIEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYLAFIPEKQIGIVMLANKSYPNPARVEAAYHILDALQ"},"dna_sequence":{"accession":"JX440354","fmin":"756","fmax":"1902","strand":"+","sequence":"ATGATGAAAAAATCTCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCGCGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCGATTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGTAAACCGCACTATTACACGTTTGGCAAAGCAGATATCGCGGCTAATAAACCCGTTACGCCTCAGACTCTGTTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGGGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTAACGGGCAAGCAGTGGCAGGGGATTCGTATGCTGGATCTCGCAACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAATGCCGCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGTATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGGGCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAAGGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGATCGAGGGCAGCGACAGTAAGGTGGCGCTGGCACCGCTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACTTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGACGCGCTACAGTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001836","ARO_id":"38236","ARO_name":"ACT-14","ARO_description":"ACT-14 is a beta-lactamase. From the Lahey list of ACT beta-lactamases.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1542":{"model_id":"1542","model_name":"amrA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4080":{"protein_sequence":{"accession":"YP_108403.1","sequence":"MKYEWARTRRLSAALAVAAFVAAGCGKHESEHDAAAPREASVVTVKKTSVPLSVELPGRLDAYRQAEVRARVAGIVTARTYEEGQEVKRGAVLFRIDPAPFKAARDAAAGALEKARAAHLAALDKRRRYDELVRDRAVSERDHTEALADERQAKAAVASARAELARAQLQLDYATVTAPIDGRARRALVTEGALVGQDQATPLTTVEQLDPIYVNFSQPAADVESLRRAVKSGRAAGIAQQDVEVTLVRPDGSTYARKGKLLFADLAVDPSTDTVAMRALFPNPERELLPGAYVRIALDRAVARDAILVPRDALLRTADSATVKVVGQNGKIRDVTVEAAQMKGRDWIVTRGLAGGERVVVVDAAQFEAGTTVKALERGAAAQPASGAAAASAPGRRST"},"dna_sequence":{"accession":"NC_006350.1","fmin":"2150965","fmax":"2152165","strand":"-","sequence":"TCAGGTTGAGCGCCGGCCGGGCGCGGAAGCCGCGGCGGCGCCGGAGGCCGGCTGCGCGGCGGCGCCGCGCTCGAGCGCCTTCACCGTCGTGCCTGCTTCGAATTGCGCGGCGTCGACGACGACGACGCGCTCGCCGCCCGCGAGCCCGCGCGTGACGATCCAGTCGCGGCCTTTCATCTGCGCGGCCTCGACCGTCACGTCGCGTATCTTGCCGTTCTGGCCGACGACCTTGACGGTCGCGCTGTCGGCCGTGCGCAGCAGCGCGTCGCGCGGCACGAGGATCGCGTCGCGCGCGACCGCGCGATCGAGCGCGATCCGCACGTACGCGCCGGGCAGCAGTTCGCGCTCCGGGTTCGGAAAGAGCGCACGCATCGCCACCGTGTCGGTGGACGGGTCGACGGCAAGATCCGCGAACAGCAGCTTGCCCTTGCGCGCGTACGTGCTGCCGTCCGGGCGCACGAGCGTCACCTCGACGTCCTGCTGCGCGATGCCCGCCGCGCGTCCGCTCTTCACCGCGCGCCGCAGCGATTCGACGTCGGCCGCGGGCTGCGAGAAGTTCACGTAGATCGGATCGAGCTGCTCGACGGTCGTGAGCGGCGTCGCCTGATCCTGGCCGACGAGCGCGCCTTCGGTCACGAGCGCGCGGCGCGCGCGGCCGTCGATCGGCGCGGTGACGGTCGCGTAATCGAGCTGCAGTTGCGCGCGCGCGAGCTCCGCGCGCGCCGACGCGACGGCCGCCTTCGCCTGCCGTTCGTCGGCGAGCGCCTCGGTGTGGTCGCGCTCGCTGACCGCGCGGTCGCGCACGAGCTCGTCATAGCGGCGGCGCTTGTCGAGCGCCGCGAGGTGCGCGGCCCGCGCCTTCTCGAGCGCGCCCGCGGCCGCGTCGCGCGCCGCCTTGAACGGCGCGGGATCGATCCTGAACAGCACCGCGCCGCGCTTGACTTCCTGCCCTTCCTCGTAGGTGCGCGCGGTCACGATGCCCGCGACCCGCGCGCGCACCTCGGCCTGCCGGTACGCGTCGAGCCGGCCCGGCAATTCGACCGACAGCGGCACCGATGTCTTCTTCACCGTGACGACGCTCGCCTCGCGCGGCGCGGCGGCGTCGTGCTCGCTTTCGTGCTTGCCGCAGCCGGCCGCGACGAACGCCGCGACCGCGAGCGCCGCCGACAAGCGGCGCGTGCGTGCCCATTCGTATTTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41211","NCBI_taxonomy_name":"Burkholderia pseudomallei K96243","NCBI_taxonomy_id":"272560"}}}},"ARO_accession":"3002982","ARO_id":"39416","ARO_name":"amrA","ARO_description":"amrA is the efflux pump subunit of the AmrAB-OprM multidrug efflux complex. amrA corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1543":{"model_id":"1543","model_name":"CMY-22","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1035":{"protein_sequence":{"accession":"ABB72431.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAYWRILEKLQ"},"dna_sequence":{"accession":"DQ256079","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGTACTGGCGCATTCTTGAAAAGCTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002033","ARO_id":"38433","ARO_name":"CMY-22","ARO_description":"CMY-22 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1544":{"model_id":"1544","model_name":"dfrE","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"4233":{"protein_sequence":{"accession":"EOD99669.1","sequence":"MLAAIWAQDEQGVIGKEGKLPWHLPNDLKFFKEKTIHNTLVLGRATFEGMGCRPLPNRTTIVLTSNPDYRAEGVLVMHSVEEILAYADNYEGVTVIGGGSVVFKELIPACDVLYRTMIHETFEGDTFFPEIDWFVWEKVATVPGVVDEKNLYAHDYETYHRNDK"},"dna_sequence":{"accession":"AIIS01000002.1","fmin":"233812","fmax":"234307","strand":"-","sequence":"TTATTTATCGTTTCGATGATACGTTTCATAGTCATGTGCATAGAGATTTTTCTCGTCCACGACGCCGGGAACAGTGGCAACTTTTTCCCAAACAAACCAGTCGATTTCTGGAAAGAAAGTGTCGCCTTCAAACGTTTCATGAATCATCGTCCGATATAAGACATCGCATGCGGGAATCAGTTCTTTAAAAACGACAGAACCTCCACCAATAACGGTCACACCTTCATAGTTGTCAGCATACGCAAGAATTTCCTCTACGGAATGCATAACCAAAACGCCTTCAGCTCGGTAATCCGGATTACTGGTTAGGACAATCGTTGTTCGATTTGGTAGCGGACGACATCCCATGCCTTCGAAAGTTGCACGTCCTAAGACCAATGTATTATGAATTGTTTTTTCCTTGAAAAATTTCAAGTCATTGGGTAAATGCCAAGGCAATTTGCCTTCTTTACCAATCACTCCTTGTTCATCTTGGGCCCAAATAGCTGCTAACAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41527","NCBI_taxonomy_name":"Enterococcus faecalis EnGen0074","NCBI_taxonomy_id":"1151194"}}}},"ARO_accession":"3002875","ARO_id":"39309","ARO_name":"dfrE","ARO_description":"dfrE is a chromosome-encoded dihydrofolate reductase found in Enterococcus faecalis","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36408":{"category_aro_accession":"3000269","category_aro_cvterm_id":"36408","category_aro_name":"brodimoprim","category_aro_description":"Brodimoprim is a structural derivative of trimethoprim and an inhibitor of bacterial dihydrofolate reductase. The 4-methoxy group of trimethoprim is replaced with a bromine atom.","category_aro_class_name":"Antibiotic"},"36423":{"category_aro_accession":"3000284","category_aro_cvterm_id":"36423","category_aro_name":"tetroxoprim","category_aro_description":"Tetroxoprim is a trimethoprim derivative that inhibits bacterial dihydrofolate reductase.","category_aro_class_name":"Antibiotic"},"36476":{"category_aro_accession":"3000337","category_aro_cvterm_id":"36476","category_aro_name":"iclaprim","category_aro_description":"Iclaprim is a bactericidal compound that inhibits dihydrofolate reductase. It is used against clinically important Gram-positive pathogens, including methicillin-sensitive Staphylococcus aureus and methicillin-resistant S. aureus.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1546":{"model_id":"1546","model_name":"Erm(43)","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"3291":{"protein_sequence":{"accession":"CCF55073.1","sequence":"MNNKNPKDTQNFITSKKCINEILKNIIITADDNIVEIGTGKGHFTKALSKVVKSVIGVEIDKSLYYNLKKDSKLQDNIQLINQDILNFQFPDNKDYKIFGSIPYNISTEIIKKILYESKAEYNYLIVELGFAKRIQDKNKALSLLLLPKMDVEILKVIPNKYFHPKPKVESALILLKKHKPLISAKDEKNYQFFVYKWVNKEYKKLFTKNQFKKALKNANVQNLNKISKQQFISIFYSYKLFN"},"dna_sequence":{"accession":"HE650138","fmin":"2186","fmax":"2918","strand":"+","sequence":"ATGAATAACAAAAATCCCAAAGATACGCAGAACTTTATAACCTCTAAGAAATGTATAAATGAAATATTAAAAAATATTATTATTACAGCAGATGATAACATTGTTGAAATTGGAACTGGGAAAGGTCATTTTACGAAAGCTTTATCAAAAGTAGTTAAGTCTGTAATTGGCGTAGAAATCGATAAGTCTTTATATTATAACTTGAAAAAGGATAGTAAACTACAAGATAATATACAACTTATTAATCAAGATATATTAAATTTTCAATTCCCTGATAATAAAGATTATAAAATTTTTGGTAGTATTCCTTATAATATTAGTACTGAAATTATTAAAAAAATACTGTATGAGAGTAAAGCAGAATACAATTATTTAATTGTAGAATTAGGATTTGCTAAACGGATTCAAGATAAAAATAAAGCGTTAAGCCTACTATTATTGCCTAAAATGGATGTTGAAATCTTGAAAGTAATTCCTAACAAATATTTTCATCCCAAACCTAAAGTAGAATCGGCATTAATATTATTAAAAAAACATAAACCTTTAATTTCGGCAAAAGATGAAAAAAATTATCAATTCTTTGTATATAAGTGGGTAAACAAAGAATATAAGAAATTGTTTACAAAAAACCAGTTTAAGAAAGCATTAAAAAATGCAAATGTACAAAACTTAAATAAAATATCGAAACAACAATTTATCTCTATTTTTTATAGTTATAAATTATTTAATTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39555","NCBI_taxonomy_name":"Staphylococcus lentus","NCBI_taxonomy_id":"42858"}}}},"ARO_accession":"3003205","ARO_id":"39789","ARO_name":"Erm(43)","ARO_description":"Erm(43) is a macrolide, lincosamide, and streptogramin B resistance gene found in Staphylococcus lentus chromosome isolated from human, dog and chicken.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1547":{"model_id":"1547","model_name":"vanRC","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"105":{"protein_sequence":{"accession":"AAF86641.1","sequence":"MSEKIVVVDDEKEIADLVTTFLQNEGFSVQPFYDGTSAIAYIEKEAIDLAVLDVMLPDIDGFQLLQQIRKTHFFPVLMLTAKGEDLDKITGLSLGADDYVTKPFNPLEVVARVKTQLRRYQRYNHSTASPTVEEYEKDGLILKINSHQCILYGKEVFLTPIEFKILLYLFEHQGSVVSSETLFEAVWKEKYLDNNNTVMAHIARLREKLHEEPRKPKLIKTVWGVGYIIEK"},"dna_sequence":{"accession":"AF162694","fmin":"5192","fmax":"5888","strand":"+","sequence":"ATGTCAGAAAAAATAGTCGTTGTTGATGATGAAAAAGAAATTGCGGACTTAGTCACGACCTTTTTGCAAAACGAAGGATTTAGTGTGCAGCCGTTTTATGATGGTACTAGTGCCATCGCCTATATTGAAAAAGAAGCCATTGATTTGGCCGTTTTAGATGTCATGTTGCCGGACATTGATGGTTTTCAACTGTTACAGCAGATCCGCAAGACCCATTTTTTCCCAGTGTTGATGCTGACTGCCAAGGGAGAGGATCTAGACAAAATCACTGGATTGAGTTTGGGAGCGGATGACTATGTCACCAAACCTTTTAATCCTTTAGAAGTTGTGGCTCGGGTAAAAACCCAATTGCGGCGCTACCAGCGATACAATCATTCCACTGCTTCTCCAACAGTAGAAGAATATGAAAAAGACGGCTTGATACTCAAAATCAACAGTCATCAATGCATTCTCTACGGCAAAGAAGTTTTCCTGACTCCCATTGAGTTCAAAATATTGCTTTATTTATTTGAGCACCAAGGATCCGTCGTCTCTTCCGAAACACTTTTCGAAGCGGTTTGGAAAGAAAAATATTTAGATAACAATAATACTGTCATGGCACACATTGCTCGTTTAAGAGAAAAATTGCATGAAGAACCTCGTAAACCTAAATTAATCAAAACCGTATGGGGGGTCGGCTATATCATTGAAAAATAGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36781","NCBI_taxonomy_name":"Enterococcus gallinarum","NCBI_taxonomy_id":"1353"}}}},"ARO_accession":"3002922","ARO_id":"39356","ARO_name":"vanRC","ARO_description":"vanRC is a vanR variant found in the vanC gene cluster","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36713":{"category_aro_accession":"3000574","category_aro_cvterm_id":"36713","category_aro_name":"vanR","category_aro_description":"VanR is a OmpR-family transcriptional activator in the VanSR regulatory system. When activated by VanS, it promotes cotranscription of VanA, VanH, and VanX.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1548":{"model_id":"1548","model_name":"APH(3')-Vb","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"407":{"protein_sequence":{"accession":"AAC32025.1","sequence":"MESTLRRTYPHHTWHLVNEGDSGAFVYRLTGHGPELYAKIAPRTPENSAFHLDGEADRLDWLARHGISVPRVVERGADDTTAWLVTEAVPGAAASEEWPEDERAAVVDAIAEMARTLHELPVSECPFDRRLDVTGEARHNVREGLVDLDDLQEEPAGWTGDQLLAELDLTRPEKEDLVVCHGDLCPNNVLLDPETHRITGLIDVGRLRLATCHADLALAARELAIDEDPWFGPAYAERFLERYGAHHVDQEKMAFYQLLDEFF"},"dna_sequence":{"accession":"M22126","fmin":"372","fmax":"1164","strand":"+","sequence":"ATGGAAAGCACGTTGCGCCGGACATACCCGCACCACACTTGGCACCTCGTGAACGAAGGAGACTCGGGCGCCTTCGTCTACCGCCTCACCGGACACGGGCCCGAGCTCTACGCGAAGATCGCCCCCCGCACCCCCGAGAACTCCGCCTTCCACCTCGACGGCGAGGCCGACCGCCTCGACTGGCTCGCCCGCCATGGCATCTCGGTCCCCCGTGTCGTCGAGCGCGGTGCCGACGACACCACCGCCTGGCTCGTCACCGAGGCCGTGCCCGGCGCCGCGGCCTCCGAGGAGTGGCCCGAGGACGAGCGGGCGGCCGTTGTCGACGCGATCGCCGAAATGGCCCGCACCCTCCATGAACTCCCCGTGTCCGAGTGCCCCTTCGACCGCCGCCTCGACGTCACCGGCGAGGCCCGGCACAACGTCCGCGAGGGCCTGGTCGACCTCGACGACCTCCAGGAGGAGCCGGCCGGCTGGACCGGCGACCAACTCCTGGCCGAACTCGACCTGACGCGGCCCGAGAAGGAGGACTTGGTCGTCTGCCATGGCGACCTGTGCCCCAACAACGTGCTGCTCGACCCCGAGACCCACCGGATCACCGGGCTGATCGACGTCGGCCGCCTCCGGCTCGCCACCTGCCACGCCGACCTCGCCCTCGCCGCCCGCGAACTGGCGATCGACGAGGACCCGTGGTTCGGCCCCGCATACGCCGAACGGTTCCTCGAACGGTACGGGGCCCACCACGTCGACCAGGAGAAGATGGCCTTCTACCAGCTGCTCGACGAGTTCTTCTAGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39530","NCBI_taxonomy_name":"Streptomyces ribosidificus","NCBI_taxonomy_id":"80859"}}}},"ARO_accession":"3002650","ARO_id":"39050","ARO_name":"APH(3')-Vb","ARO_description":"APH(3')-Vb is a chromosomal-encoded aminoglycoside phosphotransferase in Streptomyces ribosidificus","ARO_category":{"36265":{"category_aro_accession":"3000126","category_aro_cvterm_id":"36265","category_aro_name":"APH(3')","category_aro_description":"Phosphorylation of 2-deoxystreptamine aminoglycosides on the hydroxyl group at position 3'","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1549":{"model_id":"1549","model_name":"ErmB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"323":{"protein_sequence":{"accession":"AAF86219.1","sequence":"MNKNIKYSQNFLTSEKVLNQIIKQLNLKETDTVYEIGTGKGHLTTKLAKISKQVTSIELDSHLFNLSSEKLKLNTRVTLIHQDILQFQFPNKQRYKIVGSIPYNLSTQIIKKVVFESRASDIYLIVEEGFYKRTLDIHRTLGLLLHTQVSIQQLLKLPAECFHPKPKVNSVLIKLTRHTTDVPDKYWKLYTYFVSKWVNREYRQLFTKNQFHQAMKHAKVNNLSTITYEQVLSIFNSYLLFNGRKLIL"},"dna_sequence":{"accession":"AF242872","fmin":"2131","fmax":"2878","strand":"+","sequence":"ATGAACAAAAATATAAAATATTCTCAAAACTTTTTAACGAGTGAAAAAGTACTCAACCAAATAATAAAACAATTGAATTTAAAAGAAACCGATACCGTTTACGAAATTGGAACAGGTAAAGGGCATTTAACGACGAAACTGGCTAAAATAAGTAAACAGGTAACGTCTATTGAATTAGACAGTCATCTATTCAACTTATCGTCAGAAAAATTAAAACTGAATACTCGTGTCACTTTAATTCACCAAGATATTCTACAGTTTCAATTCCCTAACAAACAGAGGTATAAAATTGTTGGGAGTATTCCTTACAATTTAAGCACACAAATTATTAAAAAAGTGGTTTTTGAAAGCCGTGCGTCTGACATCTATCTGATTGTTGAAGAAGGATTCTACAAGCGTACCTTGGATATTCACCGAACACTAGGGTTGCTCTTGCACACTCAAGTCTCGATTCAGCAATTGCTTAAGCTGCCAGCGGAATGCTTTCATCCTAAACCAAAAGTAAACAGTGTCTTAATAAAACTTACCCGCCATACCACAGATGTTCCAGATAAATATTGGAAGCTATATACGTACTTTGTTTCAAAATGGGTCAATCGAGAATATCGTCAACTGTTTACTAAAAATCAGTTTCATCAAGCAATGAAACACGCCAAAGTAAACAATTTAAGTACCATTACTTATGAGCAAGTATTGTCTATTTTTAATAGTTATCTATTATTTAACGGGAGGAAATTAATTCTATGAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3000375","ARO_id":"36514","ARO_name":"ErmB","ARO_description":"ErmB confers the MLSb phenotype. Similar to ErmC, expression of ErmB is inducible by erythromycin. The leader peptide causes attenuation of the mRNA and stabilizes the structure preventing further translation. When erythromycin is present, it binds the leader peptide causing a change in conformation allowing for the expression of ErmB.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35946":{"category_aro_accession":"0000027","category_aro_cvterm_id":"35946","category_aro_name":"roxithromycin","category_aro_description":"Roxithromycin is a semi-synthetic, 14-carbon ring macrolide antibiotic derived from erythromycin. It is used to treat respiratory tract, urinary and soft tissue infections. Roxithromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35974":{"category_aro_accession":"0000057","category_aro_cvterm_id":"35974","category_aro_name":"telithromycin","category_aro_description":"Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36315":{"category_aro_accession":"3000176","category_aro_cvterm_id":"36315","category_aro_name":"dirithromycin","category_aro_description":"Dirithromycin is an oxazine derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome to inhibit bacterial protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin 1A is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"vernamycin B-gamma","category_aro_description":"Vernamycin B-gamma is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1550":{"model_id":"1550","model_name":"smeR","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"420"}},"model_sequences":{"sequence":{"4360":{"protein_sequence":{"accession":"AAD51348.1","sequence":"MSTSPATSTKILIVEDEPRLASVLRDYLAAAGMASEWVDDGGQVIDAFARYQPDLVLLDLMLPQRDGVDLCRELRASSDVPVIMVTARVEEIDRLLGLEIGADDYICKPFSPREVVARVMAVLRRYRPDPGARANGGLHIDEPAARATWNGKGLDLTPVEYRLLRTLLATPGRIWARDELLDRLYLDHRVVVDRTVDSHVRNLRRKLADAGMEGEPIRSVYGMGYSYEP"},"dna_sequence":{"accession":"AF173226","fmin":"351","fmax":"1041","strand":"-","sequence":"TCAGGGCTCGTAGCTGTAGCCCATGCCGTACACCGAACGGATCGGCTCGCCTTCCATGCCGGCGTCGGCCAGCTTGCGGCGCAGGTTGCGCACATGGCTGTCGACGGTGCGGTCGACCACCACGCGATGGTCCAGGTACAGCCGGTCGAGCAGTTCATCGCGCGCCCAGATCCGGCCTGGGGTGGCCAGCAGCGTGCGCAGCAGGCGGTACTCCACCGGCGTCAGGTCCAGGCCCTTGCCGTTCCAGGTGGCGCGTGCGGCCGGCTCGTCGATGTGCAGGCCACCGTTGGCGCGCGCACCCGGGTCCGGGCGGTAGCGGCGCAGCACCGCCATTACCCGCGCGACCACTTCGCGCGGACTGAACGGCTTGCAGATGTAGTCGTCGGCGCCGATCTCCAGGCCCAGCAGGCGGTCGATCTCTTCCACCCGTGCGGTGACCATGATGACCGGTACATCGCTGCTGGCACGCAGTTCGCGGCACAGGTCCACGCCGTCGCGCTGCGGCAGCATCAGGTCCAGCAGCACCAGGTCGGGCTGGTAGCGCGCGAATGCGTCGATCACCTGGCCACCGTCGTCCACCCACTCGCTGGCCATGCCGGCGGCGGCCAGGTAGTCGCGCAGTACCGAGGCCAGGCGTGGCTCGTCCTCGACGATCAGGATCTTCGTGGACGTGGCGGGCGACGTGCTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37076","NCBI_taxonomy_name":"Stenotrophomonas maltophilia","NCBI_taxonomy_id":"40324"}}}},"ARO_accession":"3003066","ARO_id":"39500","ARO_name":"smeR","ARO_description":"smeR is the responder component of a two component signal transduction system that includes smeS","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1551":{"model_id":"1551","model_name":"OXA-78","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1616":{"protein_sequence":{"accession":"AAW81358.1","sequence":"MNIKALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTAVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGTPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"AY862132","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGCAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTAGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAACACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001645","ARO_id":"38045","ARO_name":"OXA-78","ARO_description":"OXA-78 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1552":{"model_id":"1552","model_name":"MUS-1 beta-lactamase","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1597":{"protein_sequence":{"accession":"AAN63647.1","sequence":"MHRILSVITMLICTTLVHAQSDKLKIKQLNDNMYIYTTYQEFQGVTYSSNSMYVLTDEGVILIDTPWDKDQYEPLLEYIRSNHNKEVKWVITTHFHEDRSGGLGYFNSIGAQTYTYALTNEILKERNEPQAQHSFNKEKQFTFGNEKLAVYFLGEGHSLDNTVVWFPKEEVLYGGCLIKSAEATTIGNIADGNVIAWPKTIEAVKQKFKNAKVIIPGHDEWDMTGHIENTERILSAYNQQHSTKND"},"dna_sequence":{"accession":"AF441286","fmin":"224","fmax":"965","strand":"+","sequence":"ATGCACAGAATACTTAGTGTCATAACGATGTTAATCTGTACTACATTAGTACACGCTCAATCTGACAAACTAAAAATCAAACAACTCAATGATAATATGTATATATACACTACTTATCAAGAGTTTCAAGGAGTAACATACTCTTCTAATTCGATGTACGTACTGACAGACGAAGGCGTTATTCTAATAGACACACCTTGGGATAAAGATCAGTACGAACCTCTATTAGAGTACATCAGATCGAATCATAACAAAGAGGTTAAATGGGTCATCACTACCCACTTCCACGAAGATCGTTCTGGTGGATTAGGTTACTTTAACAGTATAGGAGCACAGACGTATACCTATGCATTGACCAATGAAATATTAAAAGAACGCAATGAACCACAAGCTCAACATTCTTTTAATAAAGAAAAACAGTTTACCTTTGGCAATGAGAAGTTGGCTGTATACTTTTTAGGAGAAGGACATTCACTAGATAATACCGTAGTCTGGTTTCCAAAAGAAGAAGTATTATACGGAGGATGCCTGATTAAGAGTGCCGAAGCTACCACTATAGGTAATATAGCCGATGGTAACGTGATAGCTTGGCCTAAGACTATCGAAGCCGTAAAACAAAAATTTAAGAATGCTAAAGTCATTATACCAGGACATGATGAATGGGATATGACAGGCCATATCGAGAATACTGAGCGTATATTATCAGCATACAATCAACAACATTCAACTAAAAACGATTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39072","NCBI_taxonomy_name":"Myroides odoratimimus","NCBI_taxonomy_id":"76832"}}}},"ARO_accession":"3000843","ARO_id":"37223","ARO_name":"MUS-1","ARO_description":"MUS-1 is a chromosome-encoded beta-lactamase from Myroides odoratus and Myroides odoratimimus.","ARO_category":{"41143":{"category_aro_accession":"3004067","category_aro_cvterm_id":"41143","category_aro_name":"MUS beta-lactamase","category_aro_description":"Subclass B1 (metallo-) beta-lactamases found in Myroides spp., which confer resistance to carbapenam class beta-lactamase antibiotics.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1553":{"model_id":"1553","model_name":"tetS","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1200"}},"model_sequences":{"sequence":{"619":{"protein_sequence":{"accession":"AAA25293.1","sequence":"MKIINIGILAHVDAGKTTLTESLLYSSGAIKELGSVDSGTTKTDTMFLERQRGITIQTAITSFQRENVKVNIVDTPGHMDFLADVYRSLSVLDGAILLISAKDGVQSQTRILFHALRKMNIPIIFFINKIDQNGINLPDVYQDIKDKLSDDIIIKQTVNLNLKPYVIDYTEPEQWETVIVGNDYLLEKYTIGKTLNIAELEKEENERIQSCSLYPVYHGSAKNNIGIKQLIEVITSKLFSPTQLNSDKLCGNVFKVEYSDDGQRLVYVRLYSGTLHLRDSVNISEKEKIKVTEMYTSINGELRQIDKAEPGEIIILKNELLKLNNVLGDKKRLPHREILENPLPMLQTTIEPCKSVQREKLLDALFEISDSDPLLQYYVDTVTHEIVLSFLGEVQMEVTCTLIQEKYHIEIETRKPTVIYMERPLKKSEFTIDIEVPPNPFWASIGLSVTPLPLGSGIQYESLVSLGYLNQSFQNAVMEGIRYGCEQGLYGWKLTDCKICFKYGLYYSPVSTPADFRMLAPIVLEQAFRKSGTELLEPYLSFEIYVPQEYLSRAYNDASKYCANILNTKLKGNEVILIGEIPARCIQEYRNSLTFFTNGRSVCLTELKGYQVTNIKSAFQPRRPNNRIDKVRHMFNKINLH"},"dna_sequence":{"accession":"L09756","fmin":"0","fmax":"1926","strand":"+","sequence":"TTGAAAATTATTAATATCGGTATCTTAGCACATGTTGATGCAGGAAAAACTACTTTGACAGAAAGCTTACTATACAGTAGCGGAGCAATTAAAGAGTTAGGAAGTGTAGATAGCGGTACAACGAAAACGGATACTATGTTTTTGGAACGCCAGAGAGGTATTACTATTCAGACCGCAATAACATCTTTTCAACGGGAAAATGTTAAAGTAAATATTGTAGATACTCCTGGACACATGGATTTTTTGGCAGATGTATACCGTTCATTATCTGTTTTGGATGGAGCTATTTTGCTAATCTCTGCAAAAGATGGAGTACAGTCACAAACTCGTATACTATTCCATGCACTTAGAAAGATGAACATACCTATAATATTTTTTATTAACAAAATTGATCAAAATGGAATAAATTTGCCAGATGTTTATCAAGATATTAAGGACAAACTTTCTGACGACATCATAATTAAGCAGACTGTGAATCTAAATTTGAAACCTTATGTAATAGATTATACTGAACCAGAACAATGGGAGACAGTAATTGTGGGAAATGATTATTTATTAGAAAAATATACCATTGGGAAAACATTGAATATTGCAGAACTTGAAAAGGAGGAAAACGAAAGAATTCAAAGTTGCTCCTTATATCCTGTTTATCACGGAAGTGCAAAGAATAATATTGGAATTAAACAACTTATAGAGGTAATTACTAGCAAATTATTTTCACCCACACAACTCAATTCAGATAAACTTTGTGGAAATGTTTTTAAAGTAGAATATTCAGATGATGGTCAACGGCTTGTCTATGTACGTCTTTATAGTGGAACGCTACATTTGCGAGACTCAGTCAATATATCAGAAAAGGAAAAAATAAAAGTTACAGAAATGTATACTTCAATAAATGGAGAATTACGCCAGATAGATAAGGCAGAGCCTGGTGAGATTATTATTTTAAAAAATGAGCTTTTAAAACTAAATAACGTACTTGGAGATAAAAAAAGATTACCACATAGAGAAATTCTTGAGAATCCTCTTCCTATGTTACAAACAACAATTGAACCATGTAAATCAGTACAAAGAGAAAAGTTACTAGATGCACTTTTTGAAATATCCGATAGTGATCCCCTTCTACAATATTATGTAGATACAGTAACTCACGAAATTGTGCTATCTTTTTTAGGTGAGGTCCAAATGGAGGTAACTTGTACTCTGATTCAAGAAAAATATCATATTGAGATAGAAACAAGAAAACCAACTGTCATTTATATGGAAAGACCATTAAAAAAATCTGAATTTACCATTGATATCGAAGTACCTCCAAATCCTTTCTGGGCTTCTATTGGTTTATCTGTAACACCACTTCCTTTGGGTAGTGGCATTCAGTATGAGAGCCTGGTTTCTCTAGGTTATTTAAATCAATCATTTCAAAATGCAGTTATGGAAGGTATACGCTATGGGTGTGAACAAGGATTGTACGGTTGGAAATTAACAGACTGTAAGATCTGTTTTAAGTATGGTCTATATTACAGCCCTGTCAGTACGCCAGCAGATTTCCGAATGCTTGCGCCTATTGTACTAGAGCAGGCTTTTAGAAAGAGTGGTACAGAGTTATTAGAGCCATATCTTAGCTTCGAAATTTATGTACCACAAGAATATCTTTCGAGAGCATATAATGATGCTTCCAAATATTGTGCAAATATTTTAAATACTAAGTTAAAAGGTAACGAGGTCATTCTCATTGGTGAAATTCCAGCCCGTTGTATTCAAGAGTATCGAAACAGTTTAACTTTCTTTACAAATGGACGCAGTGTCTGTTTAACAGAGTTAAAAGGTTATCAGGTTACTAACATTAAGTCTGCTTTCCAACCACGTCGTCCAAATAATAGAATAGACAAAGTAAGGCATATGTTTAATAAAATCAACTTACATTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36757","NCBI_taxonomy_name":"Listeria monocytogenes","NCBI_taxonomy_id":"1639"}}}},"ARO_accession":"3000192","ARO_id":"36331","ARO_name":"tetS","ARO_description":"Tet(S) is a ribosomal protection protein found in Gram-positive and Gram-negative strains. It is similar to tet(M) and tet(O).","ARO_category":{"35921":{"category_aro_accession":"0000002","category_aro_cvterm_id":"35921","category_aro_name":"tetracycline-resistant ribosomal protection protein","category_aro_description":"A family of proteins known to bind to the 30S ribosomal subunit. This interaction prevents tetracycline and tetracycline derivatives from inhibiting ribosomal function. Thus, these proteins confer elevated resistance to tetracycline derivatives as a ribosomal protection protein.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1554":{"model_id":"1554","model_name":"norA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"268":{"protein_sequence":{"accession":"AAS68233.1","sequence":"MKKQLFILYFNIFLIFLGIGLVIPVLPVYLKDLGLKGSDLGMLVAAFALSQMIISPFGGTLADKLGKKLIICIGLVFFAVSEFMFAAGQSFTILIISRVLGGFSAGMVMPGVTGMIADISPGADKAKNFGYMSAIINSGFILGPGFGGFLAEISHRLPFYVAGTLGVVAFIMSVLLIHNPQKATTDGFHQYQPELFTKINWKVFITPVILTLVLAFGLSAFETLFSLYTADKVNYTPKDISIAIIGGGVFGALFQVFFFDKFMKYMSELNFIAWSLLYSAIVLVMLVLANGYWTIMIISFVVFIGFDMIRPALTNYFSNIAGKRQGFAGGLNSTFTSMGNFIGPLVAGALFDVNLEFPLYMAIAVSLSGIIIIFIEKGLKSRRKEAN"},"dna_sequence":{"accession":"AY566250","fmin":"391","fmax":"1555","strand":"+","sequence":"ATGAAAAAACAATTATTCATTCTTTATTTTAATATATTTCTTATATTTTTAGGGATTGGATTAGTTATTCCTGTACTTCCTGTATATTTGAAGGATTTAGGATTAAAAGGTAGTGACTTAGGAATGCTAGTTGCTGCTTTTGCATTATCACAAATGATTATTTCACCATTTGGTGGGACACTAGCTGATAAATTGGGTAAAAAATTAATTATATGTATCGGTTTAGTATTCTTTGCTGTCTCTGAATTTATGTTCGCAGCCGGTCAAAGTTTTACCATTTTAATCATTTCACGTGTTTTAGGTGGCTTTAGTGCAGGCATGGTCATGCCTGGTGTAACAGGTATGATTGCAGATATTTCTCCAGGAGCTGATAAAGCTAAAAACTTTGGTTACATGTCGGCAATTATTAATTCAGGTTTTATATTAGGACCTGGATTTGGAGGCTTTTTAGCTGAAATTTCACATAGATTACCTTTCTATGTTGCTGGAACATTAGGTGTTGTTGCATTCATTATGTCAGTTTTATTAATTCATAATCCTCAAAAAGCAACTACAGATGGATTCCACCAATATCAACCTGAATTATTCACTAAAATTAATTGGAAAGTATTTATTACTCCAGTCATATTAACACTTGTATTAGCATTTGGTTTATCTGCTTTTGAAACATTATTTTCTTTATATACAGCTGACAAAGTAAATTATACTCCTAAAGATATTTCGATAGCTATTATCGGTGGAGGCGTGTTTGGCGCATTATTCCAAGTATTCTTCTTTGATAAATTTATGAAATATATGAGTGAACTTAATTTTATTGCATGGTCATTACTATATTCAGCCATTGTTCTCGTTATGTTAGTGCTTGCAAACGGTTATTGGACGATTATGATTATTAGCTTTGTTGTTTTTATAGGTTTTGATATGATTAGACCAGCTTTAACCAATTACTTCTCGAATATAGCAGGCAAACGGCAAGGTTTTGCAGGTGGATTGAATTCAACTTTTACCAGTATGGGTAACTTTATAGGTCCTCTTGTAGCTGGTGCATTATTCGATGTTAATTTAGAGTTTCCTTTATATATGGCTATTGCGGTTTCATTAAGTGGAATTATCATTATTTTTATTGAAAAAGGACTTAAGTCACGCCGTAAAGAAGCAAATTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36868","NCBI_taxonomy_name":"Staphylococcus epidermidis","NCBI_taxonomy_id":"1282"}}}},"ARO_accession":"3000391","ARO_id":"36530","ARO_name":"norA","ARO_description":"NorA is a multidrug efflux pump in Staphylococcus aureus that confers resistance to fluoroquinolones and other structurally unrelated antibiotics like acriflavine. It shares 30% similarity with NorA, and is a structural homolog of Bmr of Bacillus subtilis. It is regulated by arlRS and mgrA, the latter also known as NorR.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavin","category_aro_description":"Acriflavin is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36193":{"category_aro_accession":"3000054","category_aro_cvterm_id":"36193","category_aro_name":"acridine dye","category_aro_description":"Acridine dyes are cell permeable, basic molecules with an acridine chromophore. These compounds intercalate DNA. The image shown represents the core structure of the acridine family, with specific dyes containing varying substituents.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1555":{"model_id":"1555","model_name":"SHV-140","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1544":{"protein_sequence":{"accession":"AEK80394.1","sequence":"KRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYSQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"JN051143","fmin":"0","fmax":"861","strand":"+","sequence":"AAGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCCCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATAGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGGATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001182","ARO_id":"37562","ARO_name":"SHV-140","ARO_description":"SHV-140 is a broad-spectrum beta-lactamase.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1556":{"model_id":"1556","model_name":"VIM-13","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1005":{"protein_sequence":{"accession":"ABC94518.1","sequence":"MLKVISSLLFYMTASLMAVASPLAHSGESRGEYPTVSEIPVGEVRLYQIDDGVWSHIATHTFDGVVYPSNGLIVRDGDELLLIDTAWGTKNTVALLAEIEKQIGLPVTRSVSTHFHDDRVGGVDALRAAGVATYASPSTRRLAEAEGNEVPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSANVLYGGCAVLELSRTSAGNVADADLAEWPGSVERIQQHYPEAEVVIPGHGLPGGLDLLQHTANVVKAHTNRSVAE"},"dna_sequence":{"accession":"DQ365886","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGTTCTACATGACCGCCTCTCTAATGGCTGTAGCTAGTCCGTTAGCCCATTCCGGGGAGTCGAGAGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGAGAAGTTCGGCTGTACCAGATTGACGATGGTGTTTGGTCGCATATCGCAACGCATACGTTTGATGGCGTGGTGTACCCGTCCAATGGTCTCATTGTCCGTGATGGCGATGAGTTGCTTTTGATTGATACAGCTTGGGGTACGAAAAACACAGTGGCCCTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCCGTAACGCGTTCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGAGTTGATGCCCTTAGGGCGGCTGGAGTGGCGACGTACGCATCGCCCTCGACACGCCGTCTAGCCGAGGCAGAGGGGAACGAGGTTCCCACACACTCTCTAGAAGGGCTCTCATCGAGTGGGGACGCAGTGCGTTTCGGTCCAGTAGAGCTCTTCTATCCTGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAACGTGCTATACGGTGGTTGTGCCGTTCTGGAATTGTCACGCACATCCGCGGGAAACGTGGCCGATGCCGACCTGGCTGAATGGCCCGGTTCCGTTGAGCGGATTCAACAACATTACCCAGAAGCAGAGGTGGTCATTCCCGGGCACGGTCTACCGGGCGGTCTAGACTTGCTCCAGCACACAGCGAACGTTGTCAAAGCACACACAAATCGCTCAGTCGCCGAGTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002283","ARO_id":"38683","ARO_name":"VIM-13","ARO_description":"VIM-13 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1557":{"model_id":"1557","model_name":"SHV-187","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"917":{"protein_sequence":{"accession":"CEA29750.1","sequence":"MVKRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"LN515533","fmin":"0","fmax":"867","strand":"+","sequence":"GTGGTTAAGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGGATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3003154","ARO_id":"39731","ARO_name":"SHV-187","ARO_description":"From the Lahey list of beta-lactamases.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1559":{"model_id":"1559","model_name":"mtrA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"420"}},"model_sequences":{"sequence":{"4359":{"protein_sequence":{"accession":"CCP46065.1","sequence":"MDTMRQRILVVDDDASLAEMLTIVLRGEGFDTAVIGDGTQALTAVRELRPDLVLLDLMLPGMNGIDVCRVLRADSGVPIVMLTAKTDTVDVVLGLESGADDYIMKPFKPKELVARVRARLRRNDDEPAEMLSIADVEIDVPAHKVTRNGEQISLTPLEFDLLVALARKPRQVFTRDVLLEQVWGYRHPADTRLVNVHVQRLRAKVEKDPENPTVVLTVRGVGYKAGPP"},"dna_sequence":{"accession":"AL123456.3","fmin":"3626662","fmax":"3627349","strand":"-","sequence":"TCACGGAGGTCCGGCCTTGTACCCCACTCCTCGAACGGTCAGCACCACAGTCGGGTTCTCGGGATCCTTTTCGACCTTGGCCCGCAGACGCTGGACATGCACGTTCACCAGCCTGGTATCGGCTGGGTGCCGGTAACCCCATACCTGTTCGAGCAGCACATCACGAGTAAACACCTGGCGCGGCTTGCGCGCCAATGCGACCAACAGGTCGAATTCCAGCGGTGTCAACGAGATCTGCTCACCGTTGCGAGTGACCTTGTGCGCCGGTACGTCGATTTCTACGTCGGCGATGGACAGCATCTCGGCGGGTTCGTCGTCGTTGCGGCGCAGCCGCGCCCGCACCCGCGCAACCAGCTCCTTGGGCTTGAACGGCTTCATGATGTAGTCGTCGGCGCCCGACTCCAGACCCAGCACCACATCCACGGTGTCGGTCTTTGCGGTGAGCATCACGATCGGAACACCGGAATCGGCGCGCAACACCCGGCACACGTCGATGCCGTTCATACCGGGCAGCATCAAATCCAATAACACCAGATCGGGGCGCAGCTCGCGCACCGCGGTCAGAGCCTGAGTACCGTCGCCGATGACCGCGGTGTCGAAGCCTTCCCCCCGCAGCACGATGGTGAGCATCTCAGCCAACGAAGCGTCGTCGTCAACGACCAAAATCCTTTGCCTCATGGTGTCCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3000816","ARO_id":"37196","ARO_name":"mtrA","ARO_description":"MtrA is a transcriptional activator of the MtrCDE multidrug efflux pump of Neisseria gonorrhoeae.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35971":{"category_aro_accession":"0000054","category_aro_cvterm_id":"35971","category_aro_name":"penicillin","category_aro_description":"Penicillin (sometimes abbreviated PCN) is a beta-lactam antibiotic used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms. It works by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1560":{"model_id":"1560","model_name":"OKP-B-20","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1448":{"protein_sequence":{"accession":"CAP12360.2","sequence":"MRYVRLCLISLIAALPLAVFASPQPLEQIKISESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNTAGNLLLKIVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMATTLRKLLTTPSLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPDGKAERIVVIYLRDTAATMVERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM850922","fmin":"24","fmax":"885","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCAGCCGCTTGAGCAGATTAAAATCAGCGAAAGTCAGCTGGCGGGCCGTGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGCGACGAACAGCTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACACCGCCGGCAATCTGCTGTTGAAGATCGTCGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGAACTCAATGAGGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCGGCCAGCATGGCCACCACCCTGCGCAAGCTGCTAACCACCCCCTCTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTTGACGACCGGGTGGCCGGCCCGTTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGTGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAAGCGGAGCGTATCGTGGTGATCTATCTGCGTGATACCGCGGCGACCATGGTCGAGCGTAACCAGCAGATCGCCGGGATAGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002453","ARO_id":"38853","ARO_name":"OKP-B-20","ARO_description":"OKP-B-20 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1561":{"model_id":"1561","model_name":"vanTG","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1300"}},"model_sequences":{"sequence":{"217":{"protein_sequence":{"accession":"ABA71733.1","sequence":"MTKNESYSGIDYFRFIAALLIVAIHTSPLSSFSETGNFIFTRIVARVAVPFFFMTSGFFLISRYTCNAEKLGAFIKKTTLIYGVAILLYIPINVYNGYFKMDNLLPNIIKDIVFDGTLYHLWYLPASIIGAAIAWYLVKKVHYRKAFLIASILYIIGLFGDSYYGIVKSVSCLNVFYNLIFQLTDYTRNGIFFAPIFFVLGGYISDSQNRLSLKRSIVGFIVCFALMFGEALTLHHFDIQKHDSMYVLLLPSVYCLFNLLLHFRGKRRTGLRTISLIIYIIHPFMIVVIRLFAKLLHLQSLLVENSLVHYIAVCFASVVLAVVITALLSSLKPKKAKHTADTDRAYLEINLNNLEHNVNTLQKAMSPKCELMAVVKAEAYGHGMYEVTTYLEQIGVSSFAVATIDEGIRLRKYGISSEILILGYTSPSRAKELCKYELTQTLIDYRYSLLLNKQGYDIKAHIKIDTGMHRLGFSTEDKDKILAAFSLKHIKVAGIFTHLCAADSLEENDVAFTNKQIGSFYKVLDWLKSSGLNIPKVHIQSSYGLLNYPELECDYIRVGVALYGVLSSTNDKTKLELDLRPVLSLKAKVVLIRKIKQGESVGYSRAFTATRDSLIAILPIGYADGFPRNLSCGNSYVLIGGRQAPIVGKICMDQLAVDVTDIPNVKTGSIATLIGKDGKEEITAPMVAESAESITNELLSRMGHRLNIIRRA"},"dna_sequence":{"accession":"DQ212986","fmin":"7787","fmax":"9926","strand":"+","sequence":"ATGACTAAAAACGAAAGCTATTCTGGCATTGATTATTTTAGATTTATTGCAGCCTTATTGATTGTTGCTATTCATACTTCGCCTCTCTCTTCTTTTAGTGAAACAGGCAACTTTATATTTACACGCATTGTAGCCCGTGTAGCCGTTCCGTTCTTTTTTATGACATCTGGATTTTTTCTGATTTCCAGATATACCTGTAATGCCGAAAAGCTGGGAGCTTTTATAAAAAAGACAACCTTAATTTACGGGGTTGCAATACTCTTATACATACCTATCAATGTTTATAACGGTTATTTCAAAATGGACAACCTTTTGCCAAATATCATAAAAGATATTGTATTTGATGGTACTTTATATCACTTGTGGTATCTTCCTGCATCTATTATCGGAGCTGCGATTGCTTGGTATCTGGTAAAGAAAGTTCATTATCGCAAAGCCTTTTTGATAGCTTCTATACTCTATATCATAGGCTTATTTGGAGATAGTTATTATGGAATTGTGAAAAGCGTTTCCTGCTTAAATGTTTTTTACAATCTAATCTTCCAATTAACAGATTACACAAGAAACGGAATATTTTTTGCCCCAATCTTTTTTGTGCTTGGTGGATATATCTCTGATAGTCAAAACAGACTATCGTTAAAAAGAAGTATAGTAGGATTTATAGTTTGTTTTGCCCTTATGTTTGGAGAAGCCCTTACTTTACATCATTTTGATATACAGAAACATGACAGTATGTATGTGCTTTTACTTCCGAGTGTGTATTGCTTATTTAATCTTCTTCTGCACTTTAGAGGAAAACGCCGCACAGGATTACGGACAATATCATTGATTATCTATATCATTCATCCGTTTATGATTGTTGTAATACGATTGTTTGCCAAATTACTGCATCTGCAAAGCCTGCTTGTTGAAAACAGCCTTGTTCATTATATTGCGGTCTGCTTTGCATCGGTAGTATTAGCAGTGGTTATAACAGCGTTATTGAGCAGTCTGAAACCGAAAAAGGCAAAACATACCGCCGATACGGATAGAGCGTATCTGGAAATCAACCTAAATAATTTAGAGCATAATGTAAACACTTTGCAAAAAGCAATGTCACCTAAATGTGAATTGATGGCGGTTGTAAAAGCGGAAGCCTATGGTCACGGTATGTATGAAGTGACGACATATCTTGAGCAGATAGGAGTTTCTTCATTTGCGGTAGCTACCATTGATGAAGGTATCCGATTGAGAAAATATGGCATCTCTAGCGAAATCCTAATTTTAGGCTATACATCGCCTTCAAGGGCAAAAGAACTTTGTAAGTATGAGCTGACACAAACCTTGATAGATTATAGGTATTCGTTGCTTTTGAATAAACAGGGATATGACATTAAAGCACATATTAAAATTGACACAGGTATGCATAGACTTGGATTTAGCACAGAAGATAAGGATAAAATCCTTGCAGCTTTTTCTTTGAAGCACATCAAAGTTGCGGGAATTTTTACACATTTGTGTGCGGCTGACAGCCTTGAAGAAAATGATGTTGCATTTACAAACAAGCAAATAGGCAGTTTCTATAAAGTGCTTGATTGGCTGAAAAGCAGCGGTTTGAATATACCTAAAGTACATATCCAAAGTAGTTATGGATTATTGAATTATCCAGAGCTTGAATGTGATTATATCAGAGTGGGTGTTGCTCTGTATGGTGTTTTAAGCTCTACTAATGACAAAACAAAATTAGAACTTGATTTAAGACCTGTACTTTCTTTGAAAGCAAAAGTTGTTTTAATTCGGAAGATAAAGCAGGGCGAAAGTGTTGGTTATAGCAGGGCTTTTACTGCAACCCGAGATAGTTTAATTGCCATATTACCAATTGGATATGCAGATGGTTTTCCAAGAAATCTGTCTTGTGGAAATAGTTATGTGCTGATTGGTGGACGACAAGCCCCTATTGTCGGAAAAATCTGTATGGATCAACTTGCAGTTGATGTAACAGATATTCCCAATGTTAAGACTGGAAGTATTGCAACGCTGATTGGTAAAGATGGAAAGGAAGAAATTACAGCACCGATGGTAGCTGAAAGTGCAGAAAGCATAACCAATGAATTGTTAAGCCGTATGGGACACAGATTAAATATTATTCGTAGAGCGTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3002972","ARO_id":"39406","ARO_name":"vanTG","ARO_description":"vanTG is a vanT variant found in the vanG gene cluster","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36511":{"category_aro_accession":"3000372","category_aro_cvterm_id":"36511","category_aro_name":"vanT","category_aro_description":"VanT is a membrane bound serine racemase, converting L-serine to D-serine. It is associated with VanC, which incorporated D-serine into D-Ala-D-Ser terminal end of peptidoglycan subunits that have a decreased binding affinity with vancomycin. It was isolated from Enterococcus gallinarum.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1562":{"model_id":"1562","model_name":"aad(6)","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4434":{"protein_sequence":{"accession":"AAU10334.1","sequence":"EGSRANINIPKDEFQDYDITYFVSDIEPFISNDDWLNQFGNIIMMQKPEDMELFPPEEKGFSYLMLFDDYNKIDLTLLPLEELDNYLKGDKLIKVLIDKDCRIKRDIVPTDIDYHVRKPSAREYDDCCNEFWNVTPYVIKGLCRKEILFAIDHFNQIVRHELLRMISWKVGIETGFKLSVGKNYKFIERYISEDLWEKLLSTYRMDSYENIWEALFLCHQLFRAVSGEVAERLHYAYPEYDRNITKYTRDMYKKYTGKTGCLDSTYAADIEERREQ"},"dna_sequence":{"accession":"AY712687","fmin":"0","fmax":"831","strand":"+","sequence":"GAGGGGTCACGCGCAAATATTAATATACCTAAAGATGAATTTCAGGATTATGATATTACATATTTTGTAAGTGATATAGAACCGTTTATATCTAATGATGACTGGCTTAATCAATTTGGGAATATAATAATGATGCAAAAGCCGGAGGATATGGAATTATTCCCACCTGAAGAAAAGGGATTTTCCTATCTTATGCTATTTGATGATTACAATAAAATTGATCTTACCTTATTGCCCTTGGAAGAGTTAGATAATTACCTAAAGGGCGATAAATTAATAAAGGTTCTAATTGATAAAGATTGTAGAATTAAAAGGGACATAGTTCCGACTGATATAGATTATCATGTAAGAAAGCCAAGCGCAAGGGAGTATGATGATTGCTGCAATGAATTTTGGAATGTAACACCTTATGTTATTAAAGGATTGTGCCGTAAGGAAATTTTATTTGCTATTGATCATTTTAATCAGATTGTTCGCCATGAGCTGCTGAGAATGATATCATGGAAGGTCGGCATCGAAACAGGCTTTAAATTAAGTGTAGGCAAGAACTATAAGTTTATTGAAAGGTATATATCCGAGGATTTGTGGGAGAAACTTTTGTCCACCTACCGGATGGATTCCTATGAAAACATATGGGAAGCATTATTTCTATGCCATCAATTGTTCAGGGCGGTATCCGGTGAGGTGGCGGAAAGGCTTCATTATGCCTATCCGGAGTATGATAGGAATATAACAAAATATACCAGGGACATGTATAAAAAATACACTGGTAAAACCGGCTGCCTGGATAGCACATATGCCGCTGATATAGAAGAGAGGCGGGAACAGTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39527","NCBI_taxonomy_name":"Streptococcus oralis","NCBI_taxonomy_id":"1303"}}}},"ARO_accession":"3002628","ARO_id":"39028","ARO_name":"aad(6)","ARO_description":"aad(6) is a plasmid-encoded aminoglycoside nucleotidyltransferase gene in E. faecalis and Streptococcus oralis","ARO_category":{"36364":{"category_aro_accession":"3000225","category_aro_cvterm_id":"36364","category_aro_name":"ANT(6)","category_aro_description":"Nucelotidylylation of streptomycin at the hydroxyl group at position 6","category_aro_class_name":"AMR Gene Family"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1563":{"model_id":"1563","model_name":"CTX-M-63","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"868":{"protein_sequence":{"accession":"BAD90119.1","sequence":"MRHRVKRMMLMTTACISLLLGSAPLYAQANDVQQKLAALEKSSGGRLGVALIDTADNAQTLYRADERFAMCSTSKVMAAAAVLKQSETQKNVLSQKVEIKSSDLINYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAHLGGPDKVTAFARAIGDDTFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLRHLTLGSALGETQRAQLVTWLKGNTTGAASIQAGLPTSWVVGDKTGSGDYGTTNDIAVIWPEGRAPLILVTYFTQPEQKAENRRDVLAAAAKIVTDGY"},"dna_sequence":{"accession":"AB205197","fmin":"3","fmax":"876","strand":"+","sequence":"ATGAGACATCGCGTTAAGCGGATGATGCTAATGACAACGGCCTGTATTTCGCTGTTGCTGGGGAGTGCGCCGCTGTATGCGCAGGCGAACGACGTTCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGGGGGCGGTTGGGAGTGGCGCTGATTGACACCGCCGATAACGCACAGACGCTCTACCGCGCCGACGAGCGCTTTGCCATGTGCAGCACCAGTAAGGTGATGGCAGCCGCGGCGGTGCTCAAGCAAAGTGAAACGCAAAAGAACGTGTTGAGTCAGAAGGTTGAGATTAAATCCTCGGACCTGATTAACTACAATCCCATCGCTGAAAAACACGTCAACGGCACGATGACGCTGGCGGAATTGAGCGCCGCGGCGTTGCAGTACAGCGATAATACGGCCATGAACAAGCTGATTGCCCATCTTGGGGGGCCGGATAAAGTGACGGCGTTTGCCCGTGCGATTGGGGATGACACCTTCCGGCTCGATCGTACTGAGCCGACGCTCAACACCGCGATCCCCGGCGACCCGCGCGATACCACCACGCCATTAGCGATGGCGCAGACGCTTCGCCATCTGACGTTGGGCAGTGCCTTAGGTGAAACTCAGCGTGCGCAACTGGTAACGTGGCTGAAAGGCAACACCACCGGTGCTGCCAGCATTCAGGCTGGGCTACCCACATCGTGGGTTGTCGGGGATAAAACCGGCAGCGGTGATTATGGTACGACGAATGACATCGCCGTCATCTGGCCGGAAGGGCGTGCGCCGCTTATTCTGGTCACTTACTTCACCCAACCGGAGCAGAAGGCAGAAAATCGTCGTGACGTGCTCGCGGCTGCCGCGAAAATCGTCACCGACGGTTATTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001924","ARO_id":"38324","ARO_name":"CTX-M-63","ARO_description":"CTX-M-63 is a beta-lactamase found in Salmonella enterica","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1564":{"model_id":"1564","model_name":"QnrB16","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"349":{"protein_sequence":{"accession":"ABV66096.1","sequence":"MTPLLYIKTGTNMALALVGEKIDRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNASALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAIIG"},"dna_sequence":{"accession":"EU136183","fmin":"0","fmax":"681","strand":"+","sequence":"ATGACGCCATTACTGTATATAAAAACAGGTACAAATATGGCTCTGGCACTCGTTGGCGAAAAAATTGACAGAAACCGCTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCGATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATGCCAGTGCGCTTGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGCGCAAGCTTTATGAATATGATCACCACGCGCACCTGGTTTTGTAGCGCATATATCACGAATACAAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGCTGGAAAAGTGTGAGCTGTGGGAAAACCGTTGGATGGGTACCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTGACTTAGATATTCGGGGGGTTGATTTACAAGGCGTTAAGTTGGACAACTACCAGGCATCGTTGCTCATGGAACGTCTTGGCATCGCGATTATTGGCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002731","ARO_id":"39165","ARO_name":"QnrB16","ARO_description":"QnrB16 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1565":{"model_id":"1565","model_name":"ACT-18","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1505":{"protein_sequence":{"accession":"AHM76777.1","sequence":"MMKKSLCCALLLGISCSALAAPVSEKQLAEVVANTITPLMKAQSIPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNAALLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMGYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPEKVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVIEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYHILDALQ"},"dna_sequence":{"accession":"KF992028","fmin":"761","fmax":"1907","strand":"+","sequence":"ATGATGAAAAAATCTCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCGCGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGATTACCCCGCTGATGAAAGCCCAGTCGATTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGTAAACCGCACTATTATACGTTTGGCAAAGCCGATATCGCGGCTAATAAACCCGTTACGCCTCAGACTCTGTTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGGGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGGATTCGTATGCTGGATCTCGCAACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAATGCCGCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGTATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGGGCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAAGGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGATCGAGGGCAGCGACAGTAAGGTGGCGCTGGCACCGCTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGACGCGCTACAGTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001839","ARO_id":"38239","ARO_name":"ACT-18","ARO_description":"ACT-18 is a beta-lactamase. From the Lahey list of ACT beta-lactamases.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1566":{"model_id":"1566","model_name":"vanXD","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"375"}},"model_sequences":{"sequence":{"652":{"protein_sequence":{"accession":"AAM09852.1","sequence":"MEKNFVFLDEMLPGIRWDAKYATWDNFTGKPVDGYEVNRIVGTKELGAALRKAQKAAEKLGYGLLLWDGYRPQCAVDCFLTWASLPENNLTKKRYYPNIKRNEMITKGYVASQSSHSRGSAIDLTIFRLDTGMLVPMGGDFDFMDVRSHHAASGLSEEEAGNRERLRDIMERSGFEAYRYEWWHYVLADEPYPDTYFDFCIA"},"dna_sequence":{"accession":"AY082011","fmin":"6937","fmax":"7546","strand":"+","sequence":"ATGGAAAAGAACTTTGTCTTTTTGGATGAAATGCTGCCGGGCATCCGGTGGGATGCCAAATATGCCACATGGGACAATTTCACCGGGAAACCGGTAGACGGATACGAGGTAAACCGCATTGTGGGAACGAAAGAGCTTGGTGCCGCTTTACGTAAGGCACAGAAGGCGGCGGAGAAACTGGGATACGGTCTGCTCTTATGGGACGGCTACCGTCCCCAGTGTGCAGTGGACTGCTTTTTGACTTGGGCTTCCCTGCCGGAGAACAATCTGACGAAAAAGCGTTACTACCCAAATATCAAAAGGAACGAGATGATCACGAAAGGGTATGTGGCTTCTCAGTCCAGCCACAGTCGCGGGAGCGCGATTGATCTCACGATTTTTCGTTTGGACACGGGTATGCTTGTGCCAATGGGCGGAGATTTCGACTTTATGGATGTACGGTCGCATCATGCCGCCAGTGGTCTGAGCGAAGAGGAGGCCGGAAACCGTGAGCGCCTGCGTGATATCATGGAGCGCAGCGGATTTGAAGCCTACCGATATGAATGGTGGCATTATGTCTTGGCAGACGAGCCATACCCGGATACATATTTTGATTTTTGCATTGCCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3003070","ARO_id":"39600","ARO_name":"vanXD","ARO_description":"vanXD is a vanX variant found in the vanD gene cluster","ARO_category":{"36020":{"category_aro_accession":"3000011","category_aro_cvterm_id":"36020","category_aro_name":"vanX","category_aro_description":"VanX is a D,D-dipeptidase that cleaves D-Ala-D-Ala but not D-Ala-D-Lac, ensuring that the latter dipeptide that has reduced binding affinity with vancomycin is used to synthesize peptidoglycan substrate.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1567":{"model_id":"1567","model_name":"FosB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"225"}},"model_sequences":{"sequence":{"3613":{"protein_sequence":{"accession":"NP_831795.1","sequence":"MLRGINHICFSVSNLENSIMFYEKVLEGELLVKGRKLAYFNICGVWIALNEETHIPRNEVHQSYTHIAFSVEQEDFKCLIQRLEENDVHILQGRERDVRDCESIYFVDPDGHKFEFHSGTLQDRLNYYRDEKPHMTFY"},"dna_sequence":{"accession":"NC_004722.1","fmin":"1972251","fmax":"1972668","strand":"+","sequence":"TTGTTAAGGGGAATCAATCATATTTGTTTTTCGGTATCTAATTTAGAAAACTCTATTATGTTTTATGAAAAAGTATTAGAAGGAGAATTATTAGTTAAAGGAAGAAAATTGGCTTATTTTAACATATGTGGAGTATGGATAGCGCTTAATGAAGAGACGCATATTCCGAGAAATGAGGTTCATCAATCTTATACGCACATTGCATTTTCTGTTGAACAAGAAGACTTTAAATGTCTAATACAGCGATTAGAAGAAAATGATGTTCATATTTTACAAGGAAGAGAACGTGATGTAAGAGATTGCGAATCTATATACTTTGTTGATCCTGACGGTCATAAATTTGAGTTTCACTCAGGGACACTGCAAGACCGTTTAAATTATTATAGAGATGAGAAACCTCATATGACATTTTATTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40539","NCBI_taxonomy_name":"Bacillus cereus ATCC 14579","NCBI_taxonomy_id":"226900"}}}},"ARO_accession":"3000172","ARO_id":"36311","ARO_name":"FosB","ARO_description":"A thiol transferase that leads to the resistance of fosfomycin. Contrasting FosA, FosB is dependent on the cofactor Magnesium (II) and uses either bacillithiol or  L-cysteine to open up the epoxide ring of fosfomycin.","ARO_category":{"36272":{"category_aro_accession":"3000133","category_aro_cvterm_id":"36272","category_aro_name":"fosfomycin thiol transferase","category_aro_description":"Catalyzes the addition of a thiol group from a nucleophilic molecule to fosfomycin.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1568":{"model_id":"1568","model_name":"OXA-183","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1526":{"protein_sequence":{"accession":"ADV41666.1","sequence":"MKTFAAYVITACLSSTALASSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNNLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLSLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGTDKFWLEDQLRISAVNQVEFLESLFLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKGTEVYFFAFNMDIDNENKLPLRKSIPTKIMASEGIIGG"},"dna_sequence":{"accession":"HQ111474","fmin":"1056","fmax":"1857","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTACTGCGTGTCTTTCAAGTACGGCATTAGCTAGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTTTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATAACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAACAATGGGAAAGAGACTTGAGCTTAAGAGGGGCAATACAAGTTTCAGCGGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCATATGGCAACCAGAATATCAGTGGTGGCACTGACAAATTCTGGTTGGAGGATCAGCTAAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATTTTTAAATAAATTGTCAGCATCAAAAGAAAATCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCTGCGCCTGAATATCTTGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGTTGGGTTGAGAAGGGAACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAATAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGCAAGTGAGGGCATCATTGGTGGCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001475","ARO_id":"37875","ARO_name":"OXA-183","ARO_description":"OXA-183 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1569":{"model_id":"1569","model_name":"catD","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"3590":{"protein_sequence":{"accession":"AAF66228.1","sequence":"MVFEKIDKNSWNRKEYFDHYFASVPCTYSMTVKVDITQIKEKGMKLYPAMLYYIAMIVNRHSEFRTAINQDGELGIYDEMIPSYTIFHNDTETFSSLWTECKSDFKSFLADYESDTQRYGNNHRMEGKPNAPENIFNVSMIPWSTFDGFNLNLQKGYDYLIPIFTMGKYYKEDNKIILPLAIQVHHAVCDGFHICRFVNELQELINS"},"dna_sequence":{"accession":"AF226276.1","fmin":"3583","fmax":"4207","strand":"+","sequence":"ATGGTATTTGAAAAAATTGATAAAAATAGTTGGAACAGAAAAGAGTATTTTGACCACTACTTTGCAAGTGTACCTTGTACATACAGCATGACCGTTAAAGTGGATATCACACAAATAAAGGAAAAGGGAATGAAACTATATCCTGCAATGCTTTATTATATTGCAATGATTGTAAACCGCCATTCAGAGTTTAGGACGGCAATCAATCAAGATGGTGAATTGGGGATATATGATGAGATGATACCAAGCTATACAATATTTCACAATGATACTGAAACATTTTCCAGCCTTTGGACTGAGTGTAAGTCTGACTTTAAATCATTTTTAGCAGATTATGAAAGTGATACGCAACGGTATGGAAACAATCATAGAATGGAAGGAAAGCCAAATGCTCCGGAAAACATTTTTAATGTATCTATGATACCGTGGTCAACCTTCGATGGCTTTAATCTGAATTTGCAGAAAGGATATGATTATTTGATTCCTATTTTTACTATGGGGAAATATTATAAAGAAGATAACAAAATTATACTTCCTTTGGCAATTCAAGTTCATCACGCAGTATGTGACGGATTTCACATTTGCCGTTTTGTAAACGAATTGCAGGAATTGATAAATAGTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36807","NCBI_taxonomy_name":"Clostridium difficile","NCBI_taxonomy_id":"1496"}}}},"ARO_accession":"3002682","ARO_id":"39116","ARO_name":"catD","ARO_description":"catD is a chromosome and transposon-encoded variant of the cat gene found in Clostridium difficile","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. cat is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Bacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini","category_aro_class_name":"AMR Gene Family"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1570":{"model_id":"1570","model_name":"oprA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"890"}},"model_sequences":{"sequence":{"315":{"protein_sequence":{"accession":"BAM10414.1","sequence":"MPLSKLSASSLALCLGLLGACSLAPRYQRPEAPIPTTYPAVPASQQAGDRARLDDWQQQFTDPVLRQMIGQALEHNRNLRVAALRIEEARALYGVQASERLPTLEASGRYERERMRGETREAGEVEQRYRVAAGISAFELDFFGRVKNLGDAALADYLASEEAQRSARIALIAEVAGGYVQERALYAQQRLAERTLHARENGLALVRKRYAAGMSTRIDLRSEEMLVESARATHAALVRERSQAVSGLQLLLGDFTGDWQDSQLDLEHLQLQPLPAGLPSELLARRPDIRQAEQQLRAANANIGAARAAFFPSLRLSTDLGSASSGLHGLFRGGSRVWTFSPQMTLPIFDGGRNRANLDLAEVRKDIAVNRYEESIQVAFREVADALSAGDQLELQLRAQRAVRDADRERLQLVRKRYAKGVANYLEMLDAQRSLFDSEQQLIHLRGLRLNNGVALYRALGGGWSQG"},"dna_sequence":{"accession":"AB639410","fmin":"0","fmax":"1404","strand":"+","sequence":"ATGCCCCTTTCGAAACTCTCGGCCTCCTCCCTGGCGCTGTGCCTGGGCCTGCTCGGCGCCTGTTCGCTGGCGCCCCGCTACCAGCGCCCGGAGGCGCCGATCCCGACGACCTATCCGGCCGTCCCGGCGAGCCAGCAGGCTGGCGACCGGGCCAGGCTGGACGACTGGCAACAACAGTTCACCGACCCGGTGCTGCGCCAGATGATCGGCCAGGCCCTGGAGCACAACCGCAACCTGCGCGTCGCCGCCCTGCGCATCGAGGAAGCCCGCGCGCTATATGGCGTACAGGCCTCGGAGCGCTTGCCGACGCTGGAGGCCAGCGGTCGCTACGAGCGCGAGCGCATGCGCGGCGAAACCCGCGAGGCCGGCGAGGTCGAACAACGCTATCGGGTCGCAGCCGGCATCAGCGCCTTCGAGCTGGACTTCTTCGGCCGGGTGAAAAACCTCGGCGACGCCGCCCTGGCCGACTACCTGGCCAGCGAGGAGGCCCAGCGCAGCGCGCGGATCGCCCTGATCGCCGAGGTCGCCGGCGGCTACGTGCAGGAACGGGCGCTGTACGCACAGCAACGGCTGGCGGAACGCACCCTGCACGCGCGGGAAAACGGCCTGGCGCTGGTGCGCAAGCGCTACGCCGCCGGGATGAGCACGCGCATCGACCTGCGCAGCGAGGAAATGCTGGTGGAAAGCGCCCGCGCCACCCACGCCGCGCTGGTTCGCGAACGCAGCCAGGCGGTCAGCGGTCTGCAGCTGCTGCTCGGCGACTTCACCGGCGACTGGCAGGATAGCCAGCTGGACCTGGAACACCTCCAGCTGCAGCCACTGCCCGCCGGACTGCCCTCGGAGCTGCTCGCGCGGCGTCCGGACATCCGCCAGGCCGAACAACAACTGCGCGCGGCCAACGCCAACATCGGCGCGGCGCGCGCGGCGTTCTTCCCGAGCCTGCGCCTGAGCACCGACCTGGGCTCGGCCAGTTCAGGCCTGCACGGCCTGTTCAGGGGCGGCAGCCGGGTCTGGACCTTCAGCCCGCAGATGACCCTGCCGATCTTCGACGGCGGACGCAACCGCGCCAATCTCGACCTCGCCGAAGTGCGCAAGGACATCGCCGTCAACCGCTACGAGGAAAGCATCCAGGTCGCCTTCCGCGAGGTCGCCGACGCGCTCAGCGCCGGCGACCAGCTGGAGCTCCAGCTGCGCGCGCAGCGCGCTGTCCGCGACGCCGACCGTGAACGCCTGCAACTGGTACGCAAGCGCTATGCCAAGGGTGTCGCCAATTACCTGGAAATGCTCGACGCCCAGCGCAGCCTGTTCGACTCGGAACAGCAACTGATCCACCTGCGGGGCCTGCGCCTGAACAATGGCGTCGCCCTCTATCGCGCCCTCGGCGGCGGCTGGTCGCAAGGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3003039","ARO_id":"39473","ARO_name":"OprA","ARO_description":"OprA is an outer membrane factor protein found in Pseudomonas aeruginosa. It is part of the MexXY-OprA complex.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1571":{"model_id":"1571","model_name":"vanSE","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"649":{"protein_sequence":{"accession":"AAL27446.1","sequence":"MKNNLTVQITKKYFYTMIIITTILVILPLVAKMFLSLRVWQGTEFFYPILYILNRSLGVWLIVTPLFIWLIVTYMFFRKMISYLEEMIVATKSLIETPNEKIVLRVELAEFENEINHIRIDSLENKKMAEEAGKKRDDLLTYLAHDLRTPLTSIIGYISLLQNEQTYLELDSTKRKNYIDIISDKANRLEHLLNDFFEIAKTGKSREEVYKEEVDLSLMLSQISSEFLPLLDEKKLEWDFKIEPNVFVQLNINKFERVLDNLIRNAISYSLNDTTIKLTLEKVDEKVVVSVGNITDKVSEKDIDQLFEPFYRGDKSRNTKTGNAGLGLAIAKQIISEHGGTIEAELQNNDFKVSIIL"},"dna_sequence":{"accession":"FJ872411","fmin":"44192","fmax":"45266","strand":"+","sequence":"TTGAAAAATAATCTAACAGTGCAGATTACAAAAAAATATTTCTATACAATGATCATAATAACAACTATTCTAGTGATCCTTCCTTTGGTAGCCAAAATGTTTCTTTCTCTTCGAGTATGGCAGGGTACTGAATTTTTTTACCCAATATTATATATTTTAAATAGATCATTAGGAGTCTGGTTGATTGTAACACCGTTATTTATTTGGTTGATAGTGACTTATATGTTCTTTAGAAAAATGATTAGCTATTTAGAGGAAATGATAGTGGCTACTAAGAGTTTAATTGAAACACCGAATGAAAAAATAGTGTTAAGAGTTGAATTAGCAGAGTTTGAGAATGAAATTAATCATATTCGTATAGATAGTTTAGAGAATAAAAAGATGGCCGAAGAAGCAGGAAAAAAAAGAGATGATCTTCTAACCTATTTAGCACATGACTTGAGAACTCCTTTGACGAGTATTATTGGATATATCTCACTACTTCAAAATGAACAAACCTACTTGGAATTAGATTCTACAAAAAGGAAAAATTATATAGACATCATTTCAGACAAAGCTAACAGATTAGAGCATCTGCTCAATGATTTTTTTGAAATTGCAAAAACAGGCAAAAGTAGAGAAGAGGTGTATAAAGAAGAAGTAGATTTAAGCTTGATGTTAAGCCAAATTAGTTCTGAATTTTTGCCTCTTTTAGACGAGAAGAAGCTTGAGTGGGATTTTAAGATTGAACCAAATGTCTTTGTCCAATTAAATATTAATAAATTTGAACGAGTGTTGGATAATCTTATTAGAAATGCTATATCATACTCGCTCAATGATACAACGATAAAACTTACATTAGAGAAAGTAGATGAGAAAGTAGTAGTATCTGTAGGAAATATAACTGATAAGGTATCAGAAAAGGACATAGACCAGCTATTTGAACCATTTTACAGAGGAGATAAATCGAGAAATACAAAAACAGGGAATGCTGGTCTAGGGTTAGCAATTGCCAAACAAATTATTAGTGAGCATGGTGGAACTATCGAGGCAGAACTACAAAATAATGATTTCAAAGTATCAATTATTTTGTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3002935","ARO_id":"39369","ARO_name":"vanSE","ARO_description":"vanSE is a vanS variant found in the vanE gene cluster","ARO_category":{"36210":{"category_aro_accession":"3000071","category_aro_cvterm_id":"36210","category_aro_name":"vanS","category_aro_description":"VanS is similar to histidine protein kinases like EnvZ and acts as a response regulator by activating VanR. VanS is required for high level transcription of other van glycopeptide resistance genes.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1572":{"model_id":"1572","model_name":"OXA-205","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1682":{"protein_sequence":{"accession":"AEO92079.1","sequence":"MAIRFLTILLSTFFLTSFVHAQEHVVVRSDWKKFFSDLQAEGAIVIADERQAEHALLVFGQERAAKRYSPASTFKLPHTLFALDAGAVRDEFQVFRWDGVKRSFAGHNQDQDLRSAMRNSAVWVYELFAKEIGEDNARRYLKQIDYGNADPSTIKGNYWIDGNLEISAHEQISFLRKLYRNQLPFQVEHQRLVKYLMITEAGRNWILRAKTGWEGRFGWWIGWVEWPTGPVFFALNIDTPNRTDDLFKREAIARAILRSIDALPPN"},"dna_sequence":{"accession":"JF800667","fmin":"657","fmax":"1458","strand":"+","sequence":"ATGGCAATCCGATTCCTCACCATACTGCTATCTACTTTTTTTCTTACCTCATTCGTGCATGCGCAAGAACACGTGGTAGTCCGTTCTGACTGGAAGAAGTTCTTCAGCGACCTCCAGGCCGAAGGTGCAATCGTTATTGCAGACGAACGTCAAGCGGAGCATGCTTTATTGGTTTTTGGTCAAGAGCGAGCAGCAAAGCGTTACTCGCCTGCTTCAACCTTCAAGCTTCCACACACACTTTTTGCACTCGATGCAGGCGCCGTTCGTGATGAGTTCCAGGTTTTTCGATGGGATGGCGTTAAGCGGAGCTTTGCGGGCCACAATCAAGACCAAGACTTGCGATCAGCGATGCGAAATTCTGCGGTCTGGGTTTATGAGCTATTTGCAAAAGAGATCGGAGAGGACAACGCAAGACGCTATTTAAAGCAAATTGACTATGGCAACGCCGACCCTTCGACAATTAAGGGCAATTACTGGATAGATGGCAATCTTGAAATCTCAGCGCACGAACAGATTTCGTTTCTCAGAAAACTTTATCGAAATCAGCTGCCATTTCAGGTGGAACACCAGCGCTTGGTCAAATATCTCATGATTACGGAAGCCGGGCGCAACTGGATACTACGCGCAAAGACTGGCTGGGAAGGCAGGTTTGGCTGGTGGATAGGGTGGGTTGAATGGCCAACCGGTCCCGTATTCTTCGCGCTGAATATTGATACGCCAAACAGAACGGATGATCTTTTCAAAAGAGAGGCAATCGCGCGGGCAATCCTTCGCTCTATCGACGCGTTGCCGCCCAACTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001483","ARO_id":"37883","ARO_name":"OXA-205","ARO_description":"OXA-205 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1573":{"model_id":"1573","model_name":"SHV-110","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1143":{"protein_sequence":{"accession":"AEK48094.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIDDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"HQ877615","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGACGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001159","ARO_id":"37539","ARO_name":"SHV-110","ARO_description":"SHV-110 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1575":{"model_id":"1575","model_name":"OXA-91","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1383":{"protein_sequence":{"accession":"ABF47914.1","sequence":"MNIKALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"DQ519086","fmin":"1198","fmax":"2023","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001627","ARO_id":"38027","ARO_name":"OXA-91","ARO_description":"OXA-91 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1576":{"model_id":"1576","model_name":"OXA-17","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1603":{"protein_sequence":{"accession":"AAC15074.1","sequence":"IACLSSTALAGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPSAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG"},"dna_sequence":{"accession":"AF060206","fmin":"0","fmax":"774","strand":"+","sequence":"TATCGCGTGTCTTTCGAGTACGGCATTAGCTGGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTCTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATGACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAGCGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAGCAATGGGAAAGAGACTTGACCTTAAGAGGGGCAATACAAGTTTCAGCTGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCCTATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAAGGCCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATATTTAAATAAATTGTCAGCATCTAAAGAAAACCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCGGCACCTGAATATCTAGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGGTGGGTTGAGAAGGAGACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAGTAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGAAAGTGAGGGCATCATTGGTGGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001412","ARO_id":"37812","ARO_name":"OXA-17","ARO_description":"OXA-17 is a beta-lactamase found in P. aeruginosa and Klebsiella pneumoniae.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1577":{"model_id":"1577","model_name":"AAC(6')-32","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"310":{"protein_sequence":{"accession":"ABR10839.1","sequence":"MSPSKTPVTLRLMTERDLPMLHAWLNRPHIVEWWGGEEERPTLHEVVKHYLPRVLAEEAVTPYIAMLGDEPIGYAQSYVALGSGDGWWEDETDPGVRGIDQFLSNHTQLNQGLGTKLVQALVELLFSDPTVTKIQTDPAPNNHRAIRCYEKAGFVQQNVITTPDGPAVYMVQTRQAFERVRSAA"},"dna_sequence":{"accession":"EF614235","fmin":"2246","fmax":"2801","strand":"+","sequence":"ATGTCCCCGAGCAAAACACCCGTTACCTTGCGCCTCATGACCGAGCGCGACCTACCGATGCTGCATGCATGGCTGAACCGGCCGCACATTGTCGAGTGGTGGGGTGGAGAAGAAGAACGCCCGACTCTTCATGAAGTGGTCAAACACTACCTGCCGAGGGTTTTGGCAGAAGAAGCCGTCACACCATACATCGCGATGTTGGGCGACGAACCCATCGGCTACGCTCAGTCATACGTCGCACTCGGAAGCGGTGATGGATGGTGGGAGGATGAAACCGACCCAGGCGTACGAGGGATAGACCAATTCCTGTCGAACCATACACAGTTGAACCAGGGCCTAGGTACAAAGCTCGTCCAGGCACTCGTTGAACTGCTGTTCTCAGATCCTACCGTGACGAAGATCCAAACCGACCCGGCGCCAAACAACCATCGAGCGATTCGCTGCTACGAGAAAGCTGGCTTTGTTCAGCAAAACGTCATCACCACACCAGACGGCCCAGCCGTCTACATGGTTCAAACCAGGCAGGCCTTCGAGCGTGTGCGCAGTGCTGCCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002586","ARO_id":"38986","ARO_name":"AAC(6')-32","ARO_description":"AAC(6')-32 is an aminoglycoside acetyltransferase encoded by plasmids and integrons in P. aeruginosa","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1578":{"model_id":"1578","model_name":"SHV-123","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1773":{"protein_sequence":{"accession":"ACV32633.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASKRGARGIVALLGGNIKAERIVVIYLRDTPASMAERNQ"},"dna_sequence":{"accession":"GQ390805","fmin":"0","fmax":"813","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCAAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCGGGAATATCAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001170","ARO_id":"37550","ARO_name":"SHV-123","ARO_description":"SHV-123 is a beta-lactamase that has been found in clinical isolates.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1579":{"model_id":"1579","model_name":"QnrB9","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"681":{"protein_sequence":{"accession":"ABP88094.1","sequence":"MALALVGEKIDRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNASALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAIIG"},"dna_sequence":{"accession":"EF526508","fmin":"0","fmax":"645","strand":"+","sequence":"ATGGCTCTGGCACTCGTTGGCGAAAAAATTGACAGAAACCGTTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTAAGTGGTACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCAATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATGCCAGTGCGCTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGCGCAAGCTTTATGAATATGATCACTACACGCACCTGGTTTTGCAGCGCATATATCACTAACACAAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGCTGGAAAAGTGTGAGCTGTGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTGACTTAGATATTCGGGGCGTTGATTTACAAGGCGTTAAGTTGGACAACTACCAGGCATCGTTGCTCATGGAACGTCTTGGCATCGCGATTATTGGCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002723","ARO_id":"39157","ARO_name":"QnrB9","ARO_description":"QnrB9 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1580":{"model_id":"1580","model_name":"catIII","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"528":{"protein_sequence":{"accession":"CAA30695.1","sequence":"MNYTKFDVKNWVRREHFEFYRHRLPCGFSLTSKIDITTLKKSLDDSAYKFYPVMIYLIAQAVNQFDELRMAIKDDELIVWDSVDPQFTVFHQETETFSALSCPYSSDIDQFMVNYLSVMERYKSDTKLFPQGVTPENHLNISALPWVNFDSFNLNVANFTDYFAPIITMAKYQQEGDRLLLPLSVQVHHAVCDGFHVARFINRLQELCNSKLK"},"dna_sequence":{"accession":"X07848","fmin":"271","fmax":"913","strand":"+","sequence":"ATGAACTATACAAAATTTGATGTAAAAAATTGGGTTCGCCGTGAGCATTTTGAGTTTTATCGGCATCGTTTACCATGTGGTTTTAGCTTAACAAGCAAAATTGATATCACGACGTTAAAAAAGTCATTGGATGATTCAGCGTATAAGTTTTATCCGGTAATGATCTATCTGATTGCTCAGGCCGTGAATCAATTTGATGAGTTGAGAATGGCGATAAAAGATGATGAATTGATCGTATGGGATTCAGTCGACCCACAATTCACCGTATTCCATCAAGAAACAGAGACATTTTCAGCACTGAGTTGCCCATACTCATCCGATATTGATCAATTTATGGTGAATTATTTATCGGTAATGGAACGTTATAAAAGTGATACCAAGTTATTTCCTCAAGGGGTAACACCAGAAAATCATTTAAATATTTCAGCATTACCTTGGGTTAATTTTGATAGCTTTAATTTAAATGTTGCTAATTTTACCGATTATTTTGCACCCATTATAACAATGGCAAAATATCAGCAAGAAGGGGATAGACTGTTATTGCCGCTCTCAGTACAGGTTCATCATGCAGTTTGTGATGGCTTCCATGTTGCACGCTTTATTAATCGGCTACAAGAGTTGTGTAACAGTAAATTAAAATAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39545","NCBI_taxonomy_name":"Plasmid R387","NCBI_taxonomy_id":"2486"}}}},"ARO_accession":"3002685","ARO_id":"39119","ARO_name":"catIII","ARO_description":"catIII is a plasmid-encoded variant of the cat gene found in Shigella flexneri","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. cat is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Bacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini","category_aro_class_name":"AMR Gene Family"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1581":{"model_id":"1581","model_name":"ACT-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1177":{"protein_sequence":{"accession":"ABL67017.1","sequence":"MMMTKSLCCALLLSTSCSVLATPMSEKQLAEVVERTVTPLMKAQAIPGMAVAVIYEGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAITTRVFKPLKLDHTWINVPKAEEAHYAWGYRDGKAIHVSPGMLDAEAYGVKTNVQDMASWVMVNMKPDSLQDNSLRKGLTLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVEGSDNKVALAPLPAREVNPPAPPVNASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILSAL"},"dna_sequence":{"accession":"EF125013","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGATGACTAAATCCCTTTGCTGCGCCCTGCTGCTCAGCACCTCCTGCTCGGTATTGGCTACCCCGATGTCAGAAAAACAGCTGGCTGAGGTGGTGGAGCGGACCGTTACGCCGCTGATGAAAGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTGATTTATGAGGGTCAGCCGCACTACTTCACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCTGTCACTCCACAAACCTTGTTCGAACTGGGTTCTATAAGTAAAACCTTCACCGGCGTACTCGGTGGCGATGCCATTGCTCGGGGTGAAATATCGCTGGGCGATCCGGTGACAAAATACTGGCCTGAGCTGACAGGCAAGCAGTGGCAGGGGATCCGCATGCTGGATCTGGCAACCTATACCGCAGGAGGTTTGCCGTTACAGGTACCGGATGAGGTCACGGATAACGCCTCTCTGTTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCCAATGCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATAACGACGCGGGTCTTTAAGCCGCTCAAGCTGGACCATACGTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGCGACGGTAAAGCGATACACGTTTCGCCAGGAATGCTGGACGCTGAAGCCTATGGCGTAAAAACCAACGTGCAGGATATGGCAAGCTGGGTGATGGTCAACATGAAGCCGGACTCCCTTCAGGATAATTCACTCAGGAAAGGCCTTACCCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCCATGTATCAGGGGTTAGGCTGGGAAATGCTTAACTGGCCGGTCGATGCCAAAACCGTGGTTGAAGGTAGCGACAATAAGGTTGCACTGGCACCGCTGCCTGCGAGAGAAGTGAATCCACCAGCGCCCCCGGTCAATGCATCCTGGGTCCATAAAACAGGCTCTACCGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGTATTGTGATGCTGGCAAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATTTTGAGCGCGCTGTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001823","ARO_id":"38223","ARO_name":"ACT-3","ARO_description":"ACT-3 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1582":{"model_id":"1582","model_name":"dfrA5","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"2104":{"protein_sequence":{"accession":"ABB89122.1","sequence":"MKVSLMAAKAKNGVIGCGPHIPWSAKGEQLLFKALTYNQWLLVGRKTFESMGALPNRKYAVVTRSAWTADNDNVIVFPSIEEAMYGLAELTDHVIVSGGGEIYRETLPMASTLHISTIDIEPEGDVFFPNIPNTFEVVFEQHFSSNINYCYQIWQKG"},"dna_sequence":{"accession":"DQ278190","fmin":"0","fmax":"474","strand":"+","sequence":"GTGAAAGTATCATTAATGGCTGCAAAAGCGAAAAACGGAGTGATTGGTTGCGGTCCACACATACCCTGGTCCGCGAAAGGAGAGCAGCTACTCTTTAAAGCCTTGACGTACAACCAGTGGCTTTTGGTGGGCCGCAAGACGTTCGAATCTATGGGAGCACTCCCTAATAGGAAATACGCGGTCGTTACTCGCTCAGCCTGGACGGCCGATAATGACAACGTAATAGTATTCCCGTCGATCGAAGAGGCCATGTACGGGCTGGCTGAACTCACCGATCACGTTATAGTGTCTGGTGGCGGGGAGATTTACAGAGAAACATTGCCCATGGCCTCTACGCTCCATATATCGACGATTGATATTGAGCCGGAAGGAGATGTTTTCTTTCCGAATATTCCCAATACCTTCGAAGTTGTTTTTGAGCAACACTTTAGCTCAAACATTAACTATTGCTATCAAATTTGGCAAAAGGGTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35750","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Enteritidis","NCBI_taxonomy_id":"149539"}}}},"ARO_accession":"3002861","ARO_id":"39295","ARO_name":"dfrA5","ARO_description":"dfrA5 is an integron-encoded dihydrofolate reductase found in Vibrio cholerae","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36408":{"category_aro_accession":"3000269","category_aro_cvterm_id":"36408","category_aro_name":"brodimoprim","category_aro_description":"Brodimoprim is a structural derivative of trimethoprim and an inhibitor of bacterial dihydrofolate reductase. The 4-methoxy group of trimethoprim is replaced with a bromine atom.","category_aro_class_name":"Antibiotic"},"36423":{"category_aro_accession":"3000284","category_aro_cvterm_id":"36423","category_aro_name":"tetroxoprim","category_aro_description":"Tetroxoprim is a trimethoprim derivative that inhibits bacterial dihydrofolate reductase.","category_aro_class_name":"Antibiotic"},"36476":{"category_aro_accession":"3000337","category_aro_cvterm_id":"36476","category_aro_name":"iclaprim","category_aro_description":"Iclaprim is a bactericidal compound that inhibits dihydrofolate reductase. It is used against clinically important Gram-positive pathogens, including methicillin-sensitive Staphylococcus aureus and methicillin-resistant S. aureus.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1583":{"model_id":"1583","model_name":"QnrVC6","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"631":{"protein_sequence":{"accession":"AGH08253.1","sequence":"MEKSKQLYNQVNFSHQDLQEHIFSNCTFIHCNFKRSNLRDTQFINCTFIEQGALEGCDFSYADLRDASFKDCQLSMSHFKGANCFGIELRDCDLKGANFSQVSFVNQVSNKMYFCSAYITGCNLSYANFEQQLIEKCDLFENRWIGANLRGASFKESDLSRGVFSEDCWEQFRVQGCDLSHSELYGLDPRKIDLTGVKICSWQQEQLLEQLGVIIVPD"},"dna_sequence":{"accession":"KC202804","fmin":"3874","fmax":"4531","strand":"+","sequence":"ATGGAAAAATCAAAGCAATTATATAATCAAGTGAACTTCTCACATCAGGACTTGCAAGAACATATCTTTAGCAATTGTACTTTTATACATTGTAATTTTAAGCGCTCAAACCTTCGAGATACACAGTTCATTAACTGTACTTTCATAGAGCAGGGGGCACTGGAAGGGTGCGATTTTTCTTATGCTGATCTTCGAGATGCTTCATTTAAAGATTGTCAGCTTTCAATGTCCCATTTTAAGGGGGCAAATTGCTTTGGTATTGAACTGAGAGATTGTGATCTTAAAGGGGCAAATTTTAGCCAAGTTAGTTTTGTAAATCAGGTTTCGAATAAAATGTACTTTTGCTCTGCATACATAACAGGTTGTAACTTATCCTATGCCAATTTTGAGCAGCAGCTTATTGAAAAATGTGACCTGTTCGAAAATAGATGGATTGGTGCAAATCTTCGAGGCGCTTCATTTAAAGAATCAGATTTAAGTCGTGGCGTTTTTTCAGAAGACTGCTGGGAACAGTTTAGAGTACAAGGCTGTGATTTAAGTCATTCAGAGCTTTATGGTTTAGATCCTCGAAAGATTGATCTTACAGGTGTAAAAATATGCTCGTGGCAACAGGAGCAGTTACTGGAGCAATTAGGGGTAATCATTGTTCCTGACTAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39615","NCBI_taxonomy_name":"Vibrio parahaemolyticus","NCBI_taxonomy_id":"670"}}}},"ARO_accession":"3002803","ARO_id":"39237","ARO_name":"QnrVC6","ARO_description":"QnrVC6 is an integron-mediated quinolone resistance protein found in Acinetobacter baumannii","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1585":{"model_id":"1585","model_name":"CMY-73","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1423":{"protein_sequence":{"accession":"ACU00152.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVLYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYLPELTGKQWQGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVTPGQLDAEAYGVKSNVTDMARWIQVNMDASRVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPTVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"GQ351345","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCATTCTCCACGTTTGCCGCCGCCAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTCTCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTTGCCAGAACTGACAGGCAAGCAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTACAGATAAAGCCGCATTACTGCGTTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACAGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTACTCCTGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAACGTTACCGATATGGCCCGTTGGATTCAGGTCAACATGGACGCCAGCCGCGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGTGACAGCAAAGTGGCATTGGCAGCGCTTCCCACCGTTGAGGTAAACCCGCCCGCCCCGGCAGTGAAAGCCTCATGGGTGCATAAAACGGGTTCCACTGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTACAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002086","ARO_id":"38486","ARO_name":"CMY-73","ARO_description":"CMY-73 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1586":{"model_id":"1586","model_name":"CTX-M-32","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"867":{"protein_sequence":{"accession":"CAD89606.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAVAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVDGTMSLAELSAAALQYSDNVAMNKLISHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTNGL"},"dna_sequence":{"accession":"AJ557142","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGTCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGAAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGTGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACTTGGTTAACTATAATCCGATTGCGGAAAAGCACGTCGATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTTCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGTAATCTGACGCTGGGTAAAGCATTGGGTGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCAACGGTTTGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001894","ARO_id":"38294","ARO_name":"CTX-M-32","ARO_description":"CTX-M-32 is a beta-lactamase found in Escherichia coli","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1587":{"model_id":"1587","model_name":"OXA-10","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"878":{"protein_sequence":{"accession":"AAG45720.1","sequence":"MKTFAAYVIIACLSSTALAGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG"},"dna_sequence":{"accession":"AF205943","fmin":"7511","fmax":"8312","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTATCGCGTGTCTTTCGAGTACGGCATTAGCTGGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTCTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATGACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAGCAATGGGAAAGAGACTTGACCTTAAGAGGGGCAATACAAGTTTCAGCTGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCCTATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAAGGCCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATATTTAAATAAATTGTCAGCATCTAAAGAAAACCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCGGCACCTGAATATCTAGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGGTGGGTTGAGAAGGAGACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAGTAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGAAAGTGAGGGCATCATTGGTGGCTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001405","ARO_id":"37805","ARO_name":"OXA-10","ARO_description":"OXA-10 is a beta-lactamase found in Acinetobacter baumannii and P. aeruginosa.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1588":{"model_id":"1588","model_name":"QnrB50","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"298":{"protein_sequence":{"accession":"AFU25656.1","sequence":"MTLALVGEKIDRKRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"JX440357","fmin":"135","fmax":"780","strand":"+","sequence":"ATGACTCTGGCATTAGTTGGCGAAAAAATTGACAGAAAGCGCTTCACCGGTGAGAAAGTTGAAAATAGTACATTTTTTAACTGCGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGCCAGTTCTATGATCGCGAAAGTCAGAAAGGATGCAATTTTAGTCGCGCAATGCTGAAAGATGCCATTTTCAAAAGCTGTGATTTATCAATGGCAGATTTCCGCAACGTCAGCGCATTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGTGCAAGCTTTATGAATATGATCACCACGCGCACCTGGTTTTGCAGCGCATATATCACTAATACCAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAGCTATGGGAAAACCGCTGGATGGGGACTCAGGTACTGGGTGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTAGGTGACTTAGATATTCGGGGTGTTGATTTACAAGGCGTTAAGTTAGACAACTACCAGGCATCGTTGCTCATGGAGCGGCTTGGCATCGCTGTGATTGGTTAGC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002765","ARO_id":"39199","ARO_name":"QnrB50","ARO_description":"QnrB50 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1589":{"model_id":"1589","model_name":"PER-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"984":{"protein_sequence":{"accession":"AAU89132.1","sequence":"MNVIIKAVVTASTLLMVSFSSFETSAQSPLLKEQIESIVIGKKATVGVAVWGPDDLEPLLINPFEKFPMQSVFKLHLAMLVLHQVDQGKLDLNQTVIVNRAKVLQNTWAPIMKAYQGDEFSVPVQQLLQYSVSLSDNVACDLLFELVGGPAALHDYIQSMGIKETAVVANEAQMHADDQVQYQNWTSMKGAAEILKKFEQKTQLSETSQALLWKWMVETTTGPERLKGLLPAGTVVAHKTGTSGIKAGKTAATNDLGIILLPDGRPLLVAVFVKDSAESSRTNEAIIAQVAQTAYQFELKKLSALSPN"},"dna_sequence":{"accession":"AY740681","fmin":"7102","fmax":"8029","strand":"+","sequence":"ATGAATGTCATTATAAAAGCTGTAGTTACTGCCTCGACGCTACTGATGGTATCTTTTAGTTCATTCGAAACCTCAGCGCAATCCCCACTGTTAAAAGAGCAAATTGAATCCATAGTCATTGGAAAAAAAGCCACTGTAGGCGTTGCAGTGTGGGGGCCTGACGATCTGGAACCTTTACTGATTAATCCTTTTGAAAAATTCCCAATGCAAAGTGTATTTAAATTGCATTTAGCTATGTTGGTACTGCATCAGGTTGATCAGGGAAAGTTGGATTTAAATCAGACCGTTATCGTAAACAGGGCTAAGGTTTTACAGAATACCTGGGCTCCGATAATGAAAGCGTATCAGGGAGACGAGTTTAGTGTTCCAGTGCAGCAACTGCTGCAATACTCGGTCTCGCTCAGCGATAACGTGGCCTGTGATTTGTTATTTGAACTGGTTGGTGGACCAGCTGCTTTGCATGACTATATCCAGTCTATGGGTATAAAGGAGACCGCTGTGGTCGCAAATGAAGCGCAGATGCACGCCGATGATCAGGTGCAGTATCAAAACTGGACCTCGATGAAAGGTGCTGCAGAGATCCTGAAAAAGTTTGAGCAAAAAACACAGCTGTCTGAAACCTCGCAGGCTTTGTTATGGAAGTGGATGGTCGAAACCACCACAGGACCAGAGCGGTTAAAAGGTTTGTTACCAGCTGGTACTGTGGTCGCACATAAAACTGGTACTTCGGGTATCAAAGCCGGAAAAACTGCGGCCACTAATGATTTAGGTATCATTCTGTTGCCTGATGGACGGCCCTTGCTGGTTGCTGTTTTTGTGAAAGACTCAGCCGAGTCAAGCCGAACCAATGAAGCTATCATTGCGCAGGTTGCTCAGACTGCGTATCAATTTGAATTGAAAAAGCTTTCTGCCCTAAGCCCAAATTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36936","NCBI_taxonomy_name":"Aeromonas caviae","NCBI_taxonomy_id":"648"}}}},"ARO_accession":"3002365","ARO_id":"38765","ARO_name":"PER-3","ARO_description":"PER-3 is a beta-lactamase found in Aeromonas spp.","ARO_category":{"36195":{"category_aro_accession":"3000056","category_aro_cvterm_id":"36195","category_aro_name":"PER beta-lactamase","category_aro_description":"PER beta-lactamases are plasmid-mediated extended spectrum beta-lactamases found in the Enterobacteriaceae family.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1590":{"model_id":"1590","model_name":"QnrB27","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"156":{"protein_sequence":{"accession":"ADM52186.1","sequence":"MTLALVSEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNASALGIEIRHCRAQGSDFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVAGATFSGSDLSGGEFSAFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDSYQAALLMERLGIAVIG"},"dna_sequence":{"accession":"HM439641","fmin":"0","fmax":"645","strand":"+","sequence":"ATGACTCTGGCATTAGTTAGCGAAAAAATTGACAGAAACCGCTTCACCGGGGAAAAAGTTGAAAACAGTACTTTTTTTAACTGTGATTTTTCAGGGGCCGATCTTAGCGGCACTGAATTTATCGGCTGTCAGTTTTATGATCGCGAAAGCCAGAAAGGGTGTAATTTTAGTCGCGCAATGCTGAAAGATGCCATTTTTAAAAGTTGCGATTTATCCATGGCGGATTTTCGCAACGCCAGTGCCCTGGGAATTGAAATTCGCCACTGCCGCGCGCAGGGTTCAGATTTTCGCGGCGCGAGTTTTATGAACATGATCACCACGCGGACCTGGTTTTGCAGCGCATACATCACGAATACCAATCTAAGCTACGCCAACTTTTCGAAGGTTGTCCTGGAAAAGTGCGAGCTGTGGGAAAACCGCTGGATGGGAACTCAGGTAGCGGGTGCAACGTTCAGTGGATCAGATCTCTCGGGCGGTGAATTTTCAGCGTTCGACTGGCGGGCCGCAAACTTCACGCACTGTGATTTGACCAATTCAGAACTGGGTGATTTAGATATTCGGGGTGTAGATTTACAAGGCGTCAAATTGGATAGCTATCAGGCAGCGTTGCTGATGGAGCGGCTTGGCATCGCGGTGATTGGCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39584","NCBI_taxonomy_name":"Citrobacter braakii","NCBI_taxonomy_id":"57706"}}}},"ARO_accession":"3002742","ARO_id":"39176","ARO_name":"QnrB27","ARO_description":"QnrB27 is a plasmid-mediated quinolone resistance protein found in Citrobacter braakii","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1591":{"model_id":"1591","model_name":"CMY-64","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1915":{"protein_sequence":{"accession":"ADW84690.1","sequence":"MMKKSLCCALLLTASLSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAIAVIYQGKPYYFTWGKADITNNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWAPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKAVHVSPGQLDAEAYGVKSSVIDMARWVQVNMDASRVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"HQ832678","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTATCCACGTTTGCCGCCGCCAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCTATTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCACCAATAACCACCCAGTCACGCAGCAAACTCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTACACGGCAGGCGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCGTTTTTATCAAAACTGGCAGCCGCAATGGGCCCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACAGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGGCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGTGTTATTGATATGGCCCGCTGGGTTCAGGTCAACATGGACGCCAGCCGCGTTCAAGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCAATCATCAACGGTAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCTGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACTGGAGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002077","ARO_id":"38477","ARO_name":"CMY-64","ARO_description":"CMY-64 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1592":{"model_id":"1592","model_name":"dfrA14","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"206":{"protein_sequence":{"accession":"ACI32877.1","sequence":"MRTLKVSLIAAKAKNGVIGCGPDIPWSAKGEQLLFKALTYNQWLLVGRKTFESMGALPNRKYAVVTRSGWTSNDDNVVVFQSIEEAMDRLAEFTGHVIVSGGGEIYRETLPMASTLHLSTIDIEPEGDVFFPSIPNTFEVVFEQHFTSNINYCYQIWKKG"},"dna_sequence":{"accession":"EU780012","fmin":"2162","fmax":"2645","strand":"+","sequence":"ATGAGAACCTTGAAAGTATCATTGATAGCTGCGAAAGCGAAAAACGGCGTGATTGGTTGCGGTCCAGACATACCCTGGTCCGCGAAAGGGGAGCAGCTACTTTTTAAAGCATTGACCTACAATCAGTGGCTTCTGGTGGGTCGCAAGACGTTTGAATCTATGGGCGCACTCCCCAATAGGAAATACGCGGTCGTTACCCGCTCAGGTTGGACATCAAATGATGACAATGTAGTTGTATTTCAGTCAATCGAAGAGGCCATGGACAGGCTAGCTGAATTCACCGGTCACGTTATAGTGTCTGGTGGCGGAGAAATTTACCGAGAAACATTACCCATGGCCTCTACGCTCCACTTATCGACGATCGACATCGAGCCAGAGGGGGATGTTTTCTTCCCGAGTATTCCAAATACCTTCGAAGTTGTTTTTGAGCAACACTTTACTTCAAACATTAACTATTGCTATCAAATTTGGAAAAAGGGTTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002859","ARO_id":"39293","ARO_name":"dfrA14","ARO_description":"dfrA14 is an integron-encoded dihydrofolate reductase found in Escherichia coli","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36408":{"category_aro_accession":"3000269","category_aro_cvterm_id":"36408","category_aro_name":"brodimoprim","category_aro_description":"Brodimoprim is a structural derivative of trimethoprim and an inhibitor of bacterial dihydrofolate reductase. The 4-methoxy group of trimethoprim is replaced with a bromine atom.","category_aro_class_name":"Antibiotic"},"36423":{"category_aro_accession":"3000284","category_aro_cvterm_id":"36423","category_aro_name":"tetroxoprim","category_aro_description":"Tetroxoprim is a trimethoprim derivative that inhibits bacterial dihydrofolate reductase.","category_aro_class_name":"Antibiotic"},"36476":{"category_aro_accession":"3000337","category_aro_cvterm_id":"36476","category_aro_name":"iclaprim","category_aro_description":"Iclaprim is a bactericidal compound that inhibits dihydrofolate reductase. It is used against clinically important Gram-positive pathogens, including methicillin-sensitive Staphylococcus aureus and methicillin-resistant S. aureus.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1593":{"model_id":"1593","model_name":"CMY-99","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1860":{"protein_sequence":{"accession":"AGU59995.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYSNSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYARGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPATAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"KF305673","fmin":"17","fmax":"1163","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACTCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCCGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCACCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3002070","ARO_id":"38470","ARO_name":"CMY-99","ARO_description":"CMY-99 is a beta-lactamase found in Proteus mirabilis","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1594":{"model_id":"1594","model_name":"VgbA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"4416":{"protein_sequence":{"accession":"AAA98349.1","sequence":"MEFKLQELNLTNQDTGPYGITVSDKGKVWITQHKANMISCINLDGKITEYPLPTPDAKVMCLTISSDGEVWFTENAANKIGRITKKGIIKEYTLPNPDSAPYGITEGPNGDIWFTEMNGNRIGRITDDGKIREYELPNKGSYPSFITLGSDNALWFTENQNNAIGRITESGDITEFKIPTPASGPVGITKGNDDALWFVEIIGNKIGRITPLGEITEFKIPTPNARPHAITAGAGIDLWFTEWGANKIGRLTSNNIIEEYPIQIKSAEPHGICFDGETIWFAMECDKIGKLTLIKDNME"},"dna_sequence":{"accession":"M20129","fmin":"640","fmax":"1540","strand":"+","sequence":"ATGGAATTTAAATTACAAGAATTAAATCTTACTAACCAAGATACAGGACCATATGGTATAACCGTTTCAGATAAGGGGAAAGTTTGGATTACACAACATAAAGCAAATATGATAAGTTGCATCAATTTAGATGGAAAAATTACAGAGTACCCACTACCGACACCAGATGCAAAAGTCATGTGTTTAACTATATCCTCAGATGGGGAAGTTTGGTTTACTGAGAATGCAGCAAACAAAATAGGGAGGATTACAAAAAAAGGGATTATTAAGGAATATACATTGCCTAACCCAGATTCAGCACCCTACGGTATTACAGAAGGACCAAATGGAGATATATGGTTTACAGAAATGAATGGCAACCGTATTGGACGTATTACGGACGACGGTAAAATTCGTGAATACGAGCTGCCTAATAAAGGATCTTACCCTTCTTTTATCACTTTGGGTTCTGATAATGCCCTGTGGTTCACAGAAAATCAAAATAATGCTATTGGTAGAATTACAGAAAGTGGGGATATTACAGAGTTTAAAATTCCTACACCTGCATCAGGACCAGTTGGTATTACAAAGGGGAACGACGATGCTTTATGGTTTGTGGAAATTATCGGTAATAAGATAGGGCGAATAACTCCTCTGGGGGAAATTACCGAATTCAAAATTCCAACGCCAAACGCTCGACCTCATGCAATTACTGCTGGAGCAGGAATTGATTTATGGTTTACTGAATGGGGGGCTAATAAAATAGGAAGGCTGACAAGCAATAATATAATTGAGGAATACCCAATTCAAATCAAAAGTGCTGAACCACATGGCATTTGTTTCGATGGTGAAACAATTTGGTTTGCAATGGAGTGTGACAAGATAGGCAAATTAACTCTCATTAAGGATAATATGGAGTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3001307","ARO_id":"37706","ARO_name":"vgbA","ARO_description":"vgbA inactivates streptogramin B-type antibiotics by linearizing the lactone ring on the ester bond using an elimination mechanism, thus conferring resistance to these compounds.","ARO_category":{"36515":{"category_aro_accession":"3000376","category_aro_cvterm_id":"36515","category_aro_name":"streptogramin vgb lyase","category_aro_description":"vgb (Virginiamycin B) lyase inactivates type B streptogramin antibiotics by linearizing the streptogramin lactone ring at the ester linkage through an elimination mechanism, thus conferring resistance to these compounds.","category_aro_class_name":"AMR Gene Family"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin 1A is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"vernamycin B-gamma","category_aro_description":"Vernamycin B-gamma is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1595":{"model_id":"1595","model_name":"mecB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1300"}},"model_sequences":{"sequence":{"3282":{"protein_sequence":{"accession":"BAI83385.1","sequence":"MKNKALAILIICICLLIAYNFVKKDEVDKIFDAIELRDSEYLNEHATFLSKSLYDKDQRYKRMDKIDASLGIKEVKVSNVRLVQKKKNKRQYSANLNFRTKYGNFSREGNYSFEKDEITKKWLLDWSPEVIIPGLTDRNQISIETLESFRGKILDRNGIDIAKDGIHYEVGIDIKNLNKKNKKNISKLLSISESTLNKKLKQTWVKEGVFLPLKSYIELDDELKLGIQKYHLTVNQTKGRVYPLREATVHLLGYVGEINAEELKNKKFKDYDEHSIVGKSGIELQYDKQLQNKDGYKVVITSDDALNNDEDVLLEKKPKNGQDIILTIDSKVQRSIYSHLKEDNGSGVAMNPKTGELLALVSYPAYDPYEFMFGISDENYKKIVNDKKEPLLNKFQTTSSPGSTQKLITSIIGLKNGTIDASTSYNIVTKGWQRNSSWGGYEVTRFEEVNGDIDLEKAIAHSDNIFFARATLDMGSEKFIKGMKALDIGRNIPSDYYFQKGQIANPESLKNNFKNEILLADSGYGQGEILISPVQILSIYSSLINEGKMMKPKLFETTKEDIWKNHIISKDDVDILTRSMRKVVTGTHRLDAERNYAQFAGKTGTAELKTSREEGLGAQIGWFVGYDQNNPNMMLGISVKNVENKGMSSYNARKFAEIMDELYENGTKKYEIDR"},"dna_sequence":{"accession":"AB498758","fmin":"3738","fmax":"5762","strand":"+","sequence":"ATGAAAAATAAAGCTTTAGCAATTTTAATTATATGTATTTGCCTTTTAATAGCATATAATTTTGTGAAAAAAGATGAAGTTGATAAAATATTTGATGCTATTGAATTAAGGGATTCGGAATATCTGAATGAACATGCGACATTCTTATCTAAAAGTCTTTACGACAAAGATCAGAGATATAAAAGAATGGATAAGATTGATGCTTCTCTTGGTATTAAAGAAGTGAAAGTTAGTAATGTACGACTCGTGCAAAAGAAAAAAAATAAACGTCAATATAGTGCAAATTTAAATTTTAGAACTAAATATGGTAATTTTTCTAGAGAAGGGAACTATTCTTTTGAAAAGGATGAAATAACAAAAAAATGGCTTTTGGATTGGTCACCTGAGGTTATAATACCGGGATTGACTGATAGAAATCAAATCAGTATAGAAACCTTGGAATCTTTCAGAGGGAAAATACTAGACAGAAACGGGATTGATATAGCGAAAGACGGAATTCATTACGAAGTTGGAATAGATATTAAAAATTTAAATAAAAAAAATAAGAAAAATATTTCAAAATTGTTATCAATAAGTGAATCGACACTAAATAAAAAGTTAAAACAAACATGGGTAAAAGAAGGTGTTTTTTTACCTTTAAAATCGTACATAGAGTTGGATGATGAACTTAAATTGGGTATCCAAAAATATCATTTGACGGTTAATCAAACAAAAGGTAGGGTTTATCCATTAAGAGAAGCAACAGTACATCTTTTAGGGTATGTTGGAGAAATTAATGCTGAAGAATTAAAGAATAAAAAGTTTAAGGATTATGATGAACACTCAATCGTAGGAAAAAGTGGTATCGAACTACAATATGATAAACAATTGCAAAATAAAGATGGTTATAAAGTTGTCATAACTAGTGATGATGCATTAAATAATGATGAAGATGTCTTGTTAGAAAAGAAACCAAAAAATGGACAGGACATTATATTAACAATTGATAGCAAAGTACAAAGAAGTATATATAGTCATTTAAAAGAAGATAATGGTTCAGGAGTAGCCATGAATCCTAAAACTGGTGAATTATTAGCTTTAGTTAGTTATCCTGCATATGACCCCTATGAGTTTATGTTCGGCATTTCCGACGAAAACTACAAAAAGATAGTTAATGATAAGAAAGAGCCCCTGTTAAATAAATTTCAGACAACCTCTTCCCCAGGATCTACTCAGAAATTAATAACATCTATCATAGGTTTGAAAAATGGGACTATAGACGCATCAACCAGCTACAACATAGTAACTAAGGGATGGCAGAGAAATTCTTCATGGGGAGGATATGAAGTTACAAGGTTTGAGGAAGTTAATGGAGATATTGATTTAGAAAAAGCGATAGCACATTCTGATAATATATTTTTTGCAAGAGCTACCCTCGATATGGGTTCCGAAAAATTTATTAAGGGCATGAAAGCTTTAGACATTGGGAGAAATATTCCTTCTGATTATTATTTTCAAAAAGGACAAATTGCAAATCCAGAAAGTTTAAAAAATAATTTTAAAAATGAAATATTACTAGCTGATTCAGGATATGGCCAGGGAGAAATACTTATAAGTCCAGTACAAATATTATCTATTTATAGTTCTTTAATTAATGAAGGTAAAATGATGAAACCTAAATTATTTGAAACAACAAAAGAAGATATTTGGAAAAATCATATTATTTCAAAAGATGACGTAGATATATTAACAAGAAGCATGAGAAAAGTAGTTACTGGGACACATAGATTGGATGCAGAAAGAAATTATGCACAGTTTGCTGGAAAAACTGGCACTGCAGAATTGAAAACCTCTAGAGAAGAGGGGTTAGGAGCTCAAATCGGTTGGTTTGTTGGATATGATCAAAATAATCCCAATATGATGTTAGGTATAAGTGTGAAGAATGTAGAGAATAAAGGTATGTCGAGTTATAATGCAAGAAAGTTTGCCGAGATAATGGATGAATTATATGAAAATGGAACGAAAAAATATGAAATAGATAGGTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40025","NCBI_taxonomy_name":"Macrococcus caseolyticus","NCBI_taxonomy_id":"69966"}}}},"ARO_accession":"3003440","ARO_id":"40024","ARO_name":"mecB","ARO_description":"A foreign PBP2 acquired by lateral gene transfer that able to perform peptidoglycan synthesis in the presence of beta-lactams.","ARO_category":{"37589":{"category_aro_accession":"3001208","category_aro_cvterm_id":"37589","category_aro_name":"methicillin resistant PBP2","category_aro_description":"In methicillin sensitive S. aureus (MSSA), beta-lactams bind to native penicillin-binding proteins (PBPs) and disrupt synthesis of the cell membrane's peptidoglycan layer. In methicillin resistant S. aureus (MRSA), foreign PBP2a acquired by lateral gene transfer is able to perform peptidoglycan synthesis in the presence of beta-lactams.","category_aro_class_name":"AMR Gene Family"},"35927":{"category_aro_accession":"0000008","category_aro_cvterm_id":"35927","category_aro_name":"cefoxitin","category_aro_description":"Cefoxitin is a cephamycin antibiotic often grouped with the second generation cephalosporins. Cefoxitin is bactericidal and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. Cefoxitin's 7-alpha-methoxy group and 3' leaving group make it a poor substrate for most beta-lactamases.","category_aro_class_name":"Antibiotic"},"35930":{"category_aro_accession":"0000011","category_aro_cvterm_id":"35930","category_aro_name":"cloxacillin","category_aro_description":"Cloxacillin is a semisynthetic, isoxazolyl penicillin derivative in the beta-lactam class of antibiotics. It interferes with peptidogylcan synthesis and is commonly used for treating penicillin-resistant Staphylococcus aureus infections.","category_aro_class_name":"Antibiotic"},"35934":{"category_aro_accession":"0000015","category_aro_cvterm_id":"35934","category_aro_name":"methicillin","category_aro_description":"Derived from penicillin to combat penicillin-resistance, methicillin is insensitive to beta-lactamases (also known as penicillinases) secreted by many penicillin-resistant bacteria. Methicillin is bactericidal, and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Antibiotic"},"35961":{"category_aro_accession":"0000043","category_aro_cvterm_id":"35961","category_aro_name":"carbenicillin","category_aro_description":"Carbenicillin is a semi-synthetic antibiotic belonging to the carboxypenicillin subgroup of the penicillins. It has gram-negative coverage which includes Pseudomonas aeruginosa but limited gram-positive coverage. The carboxypenicillins are susceptible to degradation by beta-lactamase enzymes. Carbenicillin antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Antibiotic"},"35971":{"category_aro_accession":"0000054","category_aro_cvterm_id":"35971","category_aro_name":"penicillin","category_aro_description":"Penicillin (sometimes abbreviated PCN) is a beta-lactam antibiotic used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms. It works by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Antibiotic"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35975":{"category_aro_accession":"0000058","category_aro_cvterm_id":"35975","category_aro_name":"cefazolin","category_aro_description":"Cefazolin (INN), also known as cefazoline or cephazolin, is a first generation cephalosporin antibiotic. It is administered parenterally, and is active against a broad spectrum of bacteria.","category_aro_class_name":"Antibiotic"},"35976":{"category_aro_accession":"0000059","category_aro_cvterm_id":"35976","category_aro_name":"cefepime","category_aro_description":"Cefepime (INN) is a fourth-generation cephalosporin antibiotic developed in 1994. It contains an aminothiazolyl group that decreases its affinity with beta-lactamases. Cefepime shows high binding affinity with penicillin-binding proteins and has an extended spectrum of activity against Gram-positive and Gram-negative bacteria, with greater activity against both Gram-negative and Gram-positive organisms than third-generation agents.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35978":{"category_aro_accession":"0000061","category_aro_cvterm_id":"35978","category_aro_name":"ceftobiprole","category_aro_description":"Ceftobiprole (Zeftera\/Zevtera) is a next generation (5th generation) cephalosporin antibiotic with activity against methicillin-resistant Staphylococcus aureus, penicillin-resistant Streptococcus pneumoniae, Pseudomonas aeruginosa, and Enterococci. Ceftobiprole inhibits transpeptidases essential to building cell walls, and is a poor substrate for most beta-lactamases.","category_aro_class_name":"Antibiotic"},"35979":{"category_aro_accession":"0000062","category_aro_cvterm_id":"35979","category_aro_name":"ceftriaxone","category_aro_description":"Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"35980":{"category_aro_accession":"0000063","category_aro_cvterm_id":"35980","category_aro_name":"cefuroxime","category_aro_description":"Cefuroxime is a second-generation cephalosporin antibiotic with increased stability with beta-lactamases than first-generation cephalosporins. Cefuroxime is active against Gram-positive organisms but less active against methicillin-resistant strains.","category_aro_class_name":"Antibiotic"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"35987":{"category_aro_accession":"0000070","category_aro_cvterm_id":"35987","category_aro_name":"ertapenem","category_aro_description":"Ertapenem is a carbapenem antibiotic and is highly resistant to beta-lactamases like other carbapenems. It inhibits bacterial cell wall synthesis.","category_aro_class_name":"Antibiotic"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"35995":{"category_aro_accession":"0000078","category_aro_cvterm_id":"35995","category_aro_name":"piperacillin","category_aro_description":"Piperacillin is an acetylureidopenicillin and has an extended spectrum of targets relative to other beta-lactam antibiotics. It inhibits cell wall synthesis in bacteria, and is usually taken with the beta-lactamase inhibitor tazobactam to overcome penicillin-resistant bacteria.","category_aro_class_name":"Antibiotic"},"36309":{"category_aro_accession":"3000170","category_aro_cvterm_id":"36309","category_aro_name":"imipenem","category_aro_description":"Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.","category_aro_class_name":"Antibiotic"},"36689":{"category_aro_accession":"3000550","category_aro_cvterm_id":"36689","category_aro_name":"aztreonam","category_aro_description":"Aztreonam was the first monobactam discovered, and is greatly effective against Gram-negative bacteria while inactive against Gram-positive bacteria. Artreonam is a poor substrate for beta-lactamases, and may even act as an inhibitor. In Gram-negative bacteria, Aztreonam interferes with filamentation, inhibiting cell division and leading to cell death.","category_aro_class_name":"Antibiotic"},"36976":{"category_aro_accession":"3000632","category_aro_cvterm_id":"36976","category_aro_name":"benzylpenicillin","category_aro_description":"Benzylpenicillin, commonly referred to as penicillin G, is effective against both Gram-positive and Gram-negative bacteria. It is unstable in acid.","category_aro_class_name":"Antibiotic"},"36977":{"category_aro_accession":"3000633","category_aro_cvterm_id":"36977","category_aro_name":"phenoxymethylpenicillin","category_aro_description":"Phenoxymethylpenicillin, or penicillin V, is a penicillin derivative that is acid stable but less active than benzylpenicillin (penicillin G).","category_aro_class_name":"Antibiotic"},"36978":{"category_aro_accession":"3000634","category_aro_cvterm_id":"36978","category_aro_name":"propicillin","category_aro_description":"Propicillin is an orally taken penicillin derivative that has high absorption but poor activity.","category_aro_class_name":"Antibiotic"},"36979":{"category_aro_accession":"3000635","category_aro_cvterm_id":"36979","category_aro_name":"dicloxacillin","category_aro_description":"Dicloxacillin is a penicillin derivative that has an extra chlorine atom in comparison to cloxacillin. While more active than cloxacillin, its high affinity for serum protein reduces its activity in human serum in vitro.","category_aro_class_name":"Antibiotic"},"36980":{"category_aro_accession":"3000636","category_aro_cvterm_id":"36980","category_aro_name":"flucloxacillin","category_aro_description":"Flucloxacillin is similar to cloxacillin, with an extra additional fluorine atom.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"36982":{"category_aro_accession":"3000638","category_aro_cvterm_id":"36982","category_aro_name":"azlocillin","category_aro_description":"Azlocillin is a semisynthetic derivative of penicillin that is notably active against Ps. aeruginosa and other Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36983":{"category_aro_accession":"3000639","category_aro_cvterm_id":"36983","category_aro_name":"mezlocillin","category_aro_description":"Mezlocillin is a penicillin derivative taken parenterally.","category_aro_class_name":"Antibiotic"},"36984":{"category_aro_accession":"3000640","category_aro_cvterm_id":"36984","category_aro_name":"doripenem","category_aro_description":"Doripenem is a carbapenem with a broad range of activity against Gram-positive and Gram-negative bacteria, and along with meropenem, it is the most active beta-lactam antibiotic against Pseudomonas aeruginosa. It inhibits bacterial cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36985":{"category_aro_accession":"3000641","category_aro_cvterm_id":"36985","category_aro_name":"cefalexin","category_aro_description":"Cefalexin is a cephalosporin antibiotic that causes filamentation. It is resistant to staphylococcal beta-lactamase, but degraded by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"36986":{"category_aro_accession":"3000642","category_aro_cvterm_id":"36986","category_aro_name":"cefadroxil","category_aro_description":"Cefadroxil, or p-hydroxycephalexin, is an cephalosporin antibiotic similar to cefalexin.","category_aro_class_name":"Antibiotic"},"36987":{"category_aro_accession":"3000643","category_aro_cvterm_id":"36987","category_aro_name":"cefotiam","category_aro_description":"Cefotiam is a cephalosporin antibiotic with similar activity to cefuroxime but more active against enterobacteria. It is consumed orally as the prodrug cefotiam hexetil.","category_aro_class_name":"Antibiotic"},"36988":{"category_aro_accession":"3000644","category_aro_cvterm_id":"36988","category_aro_name":"cefaclor","category_aro_description":"Cefaclor is a semisynthetic cephalosporin derived from cephalexin. It has broad-spectrum antibiotic activity.","category_aro_class_name":"Antibiotic"},"36989":{"category_aro_accession":"3000645","category_aro_cvterm_id":"36989","category_aro_name":"cefotaxime","category_aro_description":"Cefotaxime is a semisynthetic cephalosporin taken parenterally. It is resistant to most beta-lactamases and active against Gram-negative rods and cocci due to its aminothiazoyl and methoximino functional groups.","category_aro_class_name":"Antibiotic"},"36990":{"category_aro_accession":"3000646","category_aro_cvterm_id":"36990","category_aro_name":"cefixime","category_aro_description":"Cefixime is a cephalosporin resistant to most beta-lactamases. It is active against many enterobacteria, but activity against staphylococci is poor.","category_aro_class_name":"Antibiotic"},"36991":{"category_aro_accession":"3000647","category_aro_cvterm_id":"36991","category_aro_name":"cefpodoxime","category_aro_description":"Cefpodoxime is a semisynthetic cephalosporin that acts similarly to cefotaxime with broad-spectrum activity. It is stable to many plasmid-mediated beta-lactamses. Cefpodoxime is consumed as the prodrug cefpodoxime proxetil.","category_aro_class_name":"Antibiotic"},"36992":{"category_aro_accession":"3000648","category_aro_cvterm_id":"36992","category_aro_name":"ceftibuten","category_aro_description":"Ceftibuten is a semisynthetic cephalosporin active against Gram-negative bacilli. It is resistant against many plasmid-mediated beta-lactamases.","category_aro_class_name":"Antibiotic"},"36993":{"category_aro_accession":"3000649","category_aro_cvterm_id":"36993","category_aro_name":"cefditoren","category_aro_description":"Cefditoren is a semisynthetic cephalosporin active against staphylococci, streptococci, and and most enterobacteria. It is resistant to staphylococcal and most enterobacterial beta-lactamases, and is usually taken as the prodrug cefditoren pivoxil.","category_aro_class_name":"Antibiotic"},"36994":{"category_aro_accession":"3000650","category_aro_cvterm_id":"36994","category_aro_name":"cefdinir","category_aro_description":"Cefdinir is similar to cefixime with a modified side-chain at its 7-amino position. It also shares similar activity with cefixime but is more active against staphylococci. It has also be shown to enhance phagocytosis.","category_aro_class_name":"Antibiotic"},"36995":{"category_aro_accession":"3000651","category_aro_cvterm_id":"36995","category_aro_name":"ceftaroline","category_aro_description":"Ceftaroline is a novel cephalosporin active against methicillin resistant Staphylococcus aureus. Like other cephalosporins it binds penicillin-binding proteins to inhibit cell wall synthesis. It strongly binds with PBP2a, associated with methicillin resistance. It is taken orally as the prodrug ceftaroline fosamil.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"37085":{"category_aro_accession":"3000705","category_aro_cvterm_id":"37085","category_aro_name":"isopenicillin N","category_aro_description":"Isopenicillin N is a natural penicillin derivative produced by Penicillium chrysogenum with activity similar to penicillin N.","category_aro_class_name":"Antibiotic"},"37086":{"category_aro_accession":"3000706","category_aro_cvterm_id":"37086","category_aro_name":"penicillin N","category_aro_description":"Penicillin N is a penicillin derivative produced by Cephalosporium acremonium.","category_aro_class_name":"Antibiotic"},"37141":{"category_aro_accession":"3000761","category_aro_cvterm_id":"37141","category_aro_name":"mecillinam","category_aro_description":"Mecillinam is a broad-spectrum beta-lactam antibiotic that was semi-synthetically derived to have a different drug centre, being a 6-alpha-amidinopenicillanate instead of a 6-alpha-acylaminopenicillanate. Contrasting most beta-lactam drugs, mecillinam is most active against Gram-negative bacteria. It binds specifically to penicillin binding protein 2 (PBP2).","category_aro_class_name":"Antibiotic"},"40928":{"category_aro_accession":"3004001","category_aro_cvterm_id":"40928","category_aro_name":"cefmetazole","category_aro_description":"Cefmetazole is a semi-synthetic cephamycin antibiotic with broad spectrum antibiotic activity against both gram-positive and gram-negative bacteria, that disrupt cell wall synthesis through binding to PBPs causing cell lysis.","category_aro_class_name":"Antibiotic"},"40929":{"category_aro_accession":"3004002","category_aro_cvterm_id":"40929","category_aro_name":"cefonicid","category_aro_description":"Cefonicid is a second-generation cephalosporin-class beta-lactam antibiotic with broad spectrum activity. Particularly used against urinary tract infections and lower respiratory infections. Causes cell lysis by inactivation of PBPs through binding, inhibiting peptidoglycan synthesis.","category_aro_class_name":"Antibiotic"},"40932":{"category_aro_accession":"3004005","category_aro_cvterm_id":"40932","category_aro_name":"cefprozil","category_aro_description":"Cefprozil is a cephalosporin and beta-lactam antibiotic with bactericidal activity. It selectively binds to PBPs and inhibits peptidoglycan synthesis, a major cell wall component, resulting in cell lysis.","category_aro_class_name":"Antibiotic"},"40933":{"category_aro_accession":"3004006","category_aro_cvterm_id":"40933","category_aro_name":"ceftiofur","category_aro_description":"Ceftiofur is a third-generation broad spectrum cephalosporin and beta-lactam antibiotic. It causes cell lysis by disrupting peptidoglycan cross-linkage and cell wall formation by binding to PBPs.","category_aro_class_name":"Antibiotic"},"40934":{"category_aro_accession":"3004007","category_aro_cvterm_id":"40934","category_aro_name":"ceftizoxime","category_aro_description":"Ceftizoxime is a third-generation cephalosporin and broad spectrum beta-lactam antibiotic. Ceftizoxime causes bacterial cell lysis through peptidoglycan cross-linking inhibition by binding to PBPs.","category_aro_class_name":"Antibiotic"},"40935":{"category_aro_accession":"3004008","category_aro_cvterm_id":"40935","category_aro_name":"cephapirin","category_aro_description":"Cephapirin is a first-generation cephalosporin and broad spectrum beta-lactam antibiotic. Inactivation of penicillin-binding proteins through cephapirin binding disrupts peptidoglycan cross-linking, resulting in cell lysis.","category_aro_class_name":"Antibiotic"},"40936":{"category_aro_accession":"3004009","category_aro_cvterm_id":"40936","category_aro_name":"cefradine","category_aro_description":"Cefradine is a first-generation cephalosporin and broad spectrum beta-lactam antibiotic. Cefradine binding to penicillin-binding proteins disrupts cell wall peptidoglycan cross-linkage, resulting in cell lysis.","category_aro_class_name":"Antibiotic"},"40943":{"category_aro_accession":"3004016","category_aro_cvterm_id":"40943","category_aro_name":"loracarbef","category_aro_description":"Loracarbef is a second-generation cephalosporin (carbacephem) and broad spectrum beta-lactam antibiotic. Loracarbef inhibits PBPs through binding, disrupting peptidoglycan cell wall cross-linkage and resulting in cell death.","category_aro_class_name":"Antibiotic"},"40944":{"category_aro_accession":"3004017","category_aro_cvterm_id":"40944","category_aro_name":"moxalactam","category_aro_description":"Moxalactam (Latamoxef) is a broad spectrum cephalosporin (oxacephem) and beta-lactam antibiotic. Moxalactam binding to PBPs inhibits peptidoglycan cross-linkage in the cell wall, resulting in cell death. Moxalactam is proposed to be effective against meningitides as it passes the blood-brain barrier.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1596":{"model_id":"1596","model_name":"OXA-24","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1607":{"protein_sequence":{"accession":"AAM34291.1","sequence":"MKKFILPIFSISILVSLSACSSIKTKSEDNFHISSQQHEKAIKSYFDEAQTQGVIIIKEGKNLSTYGNALARANKEYVPASTFKMLNALIGLENHKATTNEIFKWDGKKRTYPMWEKDMTLGEAMALSAVPVYQELARRTGLELMQKEVKRVNFGNTNIGTQVDNFWLVGPLKITPVQEVNFADDLAHNRLPFKLETQEEVKKMLLIKEVNGSKIYAKSGWGMGVTPQVGWLTGWVEQANGKKIPFSLNLEMKEGMSGSIRNEITYKSLENLGII"},"dna_sequence":{"accession":"AF509241","fmin":"0","fmax":"828","strand":"+","sequence":"ATGAAAAAATTTATACTTCCTATATTCAGCATTTCTATTCTAGTTTCTCTCAGTGCATGTTCATCTATTAAAACTAAATCTGAAGATAATTTTCATATTTCTTCTCAGCAACATGAAAAAGCTATTAAAAGCTATTTTGATGAAGCTCAAACACAGGGTGTAATTATTATTAAAGAGGGTAAAAATCTTAGCACCTATGGTAATGCTCTTGCACGAGCAAATAAAGAATATGTCCCTGCATCAACATTTAAGATGCTAAATGCTTTAATCGGGCTAGAAAATCATAAAGCAACAACAAATGAGATTTTCAAATGGGATGGTAAAAAAAGAACTTATCCTATGTGGGAGAAAGATATGACTTTAGGTGAGGCAATGGCATTGTCAGCAGTTCCAGTATATCAAGAGCTTGCAAGACGGACTGGCCTAGAGCTAATGCAGAAAGAAGTAAAGCGGGTTAATTTTGGAAATACAAATATTGGAACACAGGTCGATAATTTTTGGTTAGTTGGCCCCCTTAAAATTACACCAGTACAAGAAGTTAATTTTGCCGATGACCTTGCACATAACCGATTACCTTTTAAATTAGAAACTCAAGAAGAAGTTAAAAAAATGCTTCTAATTAAAGAAGTAAATGGTAGTAAGATTTATGCAAAAAGTGGATGGGGAATGGGTGTTACTCCACAGGTAGGTTGGTTGACTGGTTGGGTGGAGCAAGCTAATGGAAAAAAAATCCCCTTTTCGCTCAACTTAGAAATGAAAGAAGGAATGTCTGGTTCTATTCGTAATGAAATTACTTATAAGTCGCTAGAAAATCTTGGAATCATTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001419","ARO_id":"37819","ARO_name":"OXA-24","ARO_description":"OXA-24 is a beta-lactamase found in A. baumannii and P. aeruginosa.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"40512":{"category_aro_accession":"3003821","category_aro_cvterm_id":"40512","category_aro_name":"BAL30072","category_aro_description":"BAL30072 is a monocyclic beta-lactam antibiotic belonging to the sulfactams. BAL30072 was found to trigger the spheroplasting and lysis of Escherichia coli rather than the formation of extensive filaments.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1597":{"model_id":"1597","model_name":"SHV-2A","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"833":{"protein_sequence":{"accession":"CAA66730.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"X98102","fmin":"73","fmax":"934","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGTTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001061","ARO_id":"37441","ARO_name":"SHV-2A","ARO_description":"SHV-2A is an extended-spectrum beta-lactamase found in Enterobacter cloacae, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Salmonella enterica.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1598":{"model_id":"1598","model_name":"OXA-101","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1042":{"protein_sequence":{"accession":"CAL85435.1","sequence":"MKTFAAYVITACLSSTALASSITENTFWNKEFSAEAVNGVFVLCKSSSKSCATNNLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLSLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLFLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKGTEVYFFAFNMDIDNENKLPLRKSIPTKIMASEGIIGG"},"dna_sequence":{"accession":"AM412777","fmin":"117","fmax":"918","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTACTGCGTGTCTTTCAAGTACGGCATTAGCTAGTTCAATTACAGAAAATACGTTTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTTTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATAACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAACAATGGGAAAGAGACTTGAGCTTAAGAGGGGCAATACAAGTTTCAGCGGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATATCTTAAAAAATTTTCATATGGTAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAGGGTCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATTTTTAAATAAATTGTCAGCATCAAAAGAAAATCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCTGCGCCTGAATATCTTGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGTTGGGTTGAGAAGGGAACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAATAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGCAAGTGAGGGCATCATTGGTGGCTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3001439","ARO_id":"37839","ARO_name":"OXA-101","ARO_description":"OXA-101 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1599":{"model_id":"1599","model_name":"SHV-23","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1560":{"protein_sequence":{"accession":"AAF34337.1","sequence":"MLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGEFCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAGTLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASKRGARGIVALLGPNNKAERIVVIYLRDTPASMAERN"},"dna_sequence":{"accession":"AF117747","fmin":"0","fmax":"780","strand":"+","sequence":"CTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAATTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGGGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCAAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001081","ARO_id":"37461","ARO_name":"SHV-23","ARO_description":"SHV-23 is an extended-spectrum beta-lactamase that has been found in clinical isolates.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1601":{"model_id":"1601","model_name":"LRA-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"4355":{"protein_sequence":{"accession":"ACH58980.1","sequence":"MNPPIHRRTLLLAASVLPLASACTAWSAKGPQQDASAQLAALEAASGSRLGVVGFNTATGARVQHRAEERFPFCSTFKLMLAAAVLERSAKEGDLLARRVNYSKGDLVSYSPITEKNVATGMTVAELCAATVQYSDNGAANLLMKILGGPSAVTAFARASGDEVFRLDRWETELNTAIPGDLRDTTTPAAMAASVQRLVLGNALGAAQREQLKTWLLGNTTSTQRFLAGVPAGWKVGDKTGSGSYGTTNDVGVLWPPAGAPLVLAVYLTFPQKEAKGRSDVVASATRIAVSALAS"},"dna_sequence":{"accession":"EU408346.1","fmin":"4825","fmax":"5713","strand":"-","sequence":"TCAGCTCGCCAGCGCGCTCACCGCAATGCGCGTCGCCGACGCAACCACATCGCTGCGCCCCTTCGCCTCCTTCTGCGGAAACGTCAGGTAGACCGCCAGCACCAGCGGCGCGCCGGCCGGCGGCCACAGCACGCCCACGTCGTTCGTGGTGCCGTAGGAGCCCGAACCGGTCTTGTCGCCCACCTTCCAGCCGGCGGGCACGCCGGCCAGGAAGCGCTGGGTGCTCGTGGTGTTGCCCAGCAACCAGGTCTTGAGCTGCTCGCGCTGTGCCGCGCCCAGCGCGTTGCCCAGCACCAGCCGCTGCACGCTTGCCGCCATGGCCGCGGGCGTGGTGGTGTCGCGCAGGTCGCCGGGGATGGCGGTGTTGAGTTCGGTCTCCCAGCGGTCCAGCCTGAAGACCTCGTCGCCGGAGGCACGCGCAAAGGCCGTCACGGCGGACGGGCCGCCCAGGATCTTCATCAGCAGGTTGGCCGCGCCGTTGTCGCTGTACTGGACGGTGGCGGCGCACAGCTCGGCCACCGTCATGCCGGTCGCCACATTCTTTTCGGTGATGGGCGAGTAGGAGACCAGGTCGCCCTTGCTGTAGTTGACGCGGCGCGCGAGCAGGTCGCCCTCTTTCGCGCTGCGTTCGAGGACGGCCGCGGCCAGCATGAGCTTGAAGGTGCTGCAGAACGGAAAGCGTTCCTCGGCACGGTGCTGCACGCGCGCGCCGGTGGCGGTGTTGAAACCGACCACACCGAGCCGGCTGCCCGATGCGGCTTCGAGCGCGGCGAGCTGCGCCGATGCGTCTTGCTGCGGCCCCTTGGCGGACCACGCGGTGCAGGCGCTTGCGAGCGGGAGGACCGAGGCGGCGAGCAACAGGGTGCGGCGATGGATTGGAGGATTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39079","NCBI_taxonomy_name":"uncultured bacterium BLR1","NCBI_taxonomy_id":"506512"}}}},"ARO_accession":"3002482","ARO_id":"38882","ARO_name":"LRA-1","ARO_description":"LRA-1 is a beta-lactamase isolated from soil samples in Alaska","ARO_category":{"41392":{"category_aro_accession":"3004228","category_aro_cvterm_id":"41392","category_aro_name":"class A LRA beta-lactamase","category_aro_description":"Beta-lactamases that are part of the LRA gene family and are classified as Class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1602":{"model_id":"1602","model_name":"AAC(6')-Iai","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"708":{"protein_sequence":{"accession":"ACI28880.1","sequence":"MKYTIIDIKDSETYITQAAEILFDVFSEISPESWPTLQKAKEDVIECIEGENICIGIIINKELIGWIGLREMYKKTWELHPMVIKKTHHNMGFGKILINEIEKKARERNLEGIVLGTDDETYRTSLSMIELNNENILQEIKNIRNLENHPYEFYKKCGYCIIGVIPNANGKNKPDILMWKNIMEENCG"},"dna_sequence":{"accession":"EU886977","fmin":"543","fmax":"1110","strand":"+","sequence":"ATGAAATACACTATTATTGATATTAAAGATTCAGAAACGTACATTACTCAAGCTGCAGAAATATTATTTGATGTATTTTCAGAAATAAGCCCAGAATCATGGCCAACACTCCAAAAAGCAAAAGAAGATGTTATTGAATGTATAGAAGGTGAAAACATTTGCATTGGCATTATAATAAATAAAGAATTAATTGGATGGATTGGATTAAGAGAAATGTATAAAAAAACATGGGAATTACATCCTATGGTTATCAAGAAAACACATCATAATATGGGATTTGGAAAAATACTAATTAATGAAATAGAAAAAAAAGCAAGAGAAAGAAATTTAGAAGGTATTGTACTTGGAACAGATGATGAAACATATAGAACTTCATTATCAATGATTGAATTAAATAATGAAAATATTTTGCAAGAAATAAAGAATATTAGAAATTTAGAAAATCATCCTTATGAATTTTATAAAAAATGTGGATATTGTATTATTGGTGTAATTCCAAACGCAAATGGGAAGAATAAGCCAGATATATTAATGTGGAAAAATATTATGGAAGAAAATTGCGGCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002575","ARO_id":"38975","ARO_name":"AAC(6')-Iai","ARO_description":"AAC(6')-Iai is an aminoglycoside acetyltransferase encoded by plasmids and integrons in P. aeruginosa","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1603":{"model_id":"1603","model_name":"SHV-86","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1564":{"protein_sequence":{"accession":"ABC58727.1","sequence":"MRFIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASRRGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"DQ328802","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTTTATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCAGGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001140","ARO_id":"37520","ARO_name":"SHV-86","ARO_description":"SHV-86 is an extended-spectrum beta-lactamase that has been found in clinical isolates.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1604":{"model_id":"1604","model_name":"CTX-M-84","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1257":{"protein_sequence":{"accession":"ACI29346.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVAWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"FJ214367","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGGCGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35667","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Derby","NCBI_taxonomy_id":"28144"}}}},"ARO_accession":"3001945","ARO_id":"38345","ARO_name":"CTX-M-84","ARO_description":"CTX-M-84 is a beta-lactamase found in Salmonella enterica","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1605":{"model_id":"1605","model_name":"cphA5","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"1501":{"protein_sequence":{"accession":"AAP69913.1","sequence":"MMKGWIKCGLAGAVVLVASFWGGSVHAAAISLTQVSGPVYVVEDNYYVKENSMVYFGAKGVTIVGATWTPDTARELHKLIKRVNNKPVLEVINTNYHTGQAGGNAYWKSIGAKVVSTRQTRDLMKSDWAEIVAFTRKGLPEYPDLPLVLPNVVHDGDFNLQEGKVRAFYAGPAHTPDGIFVYFPDQQVLYGNCILKEKLGNLSFADVKAYPQTLERLKAMKLPIKIVVGGHDSPLHGPELIDHYQALIKAATHS"},"dna_sequence":{"accession":"AY227051","fmin":"0","fmax":"765","strand":"+","sequence":"ATGATGAAAGGTTGGATAAAGTGCGGGCTGGCCGGAGCTGTGGTGCTGGTGGCGAGTTTCTGGGGCGGCAGCGTGCATGCGGCGGCGATCTCCCTCACTCAGGTAAGCGGCCCTGTCTATGTGGTGGAGGATAACTACTACGTCAAAGAGAACTCCATGGTTTATTTCGGAGCCAAGGGAGTGACGATAGTGGGGGCGACCTGGACGCCGGATACCGCCCGCGAGCTGCACAAGCTGATCAAACGGGTCAACAACAAGCCTGTGCTGGAGGTGATCAACACCAACTACCACACCGGACAGGCAGGGGGTAACGCCTACTGGAAGTCCATCGGTGCCAAGGTGGTCTCGACCCGCCAGACCCGGGATCTGATGAAGAGCGACTGGGCCGAGATCGTCGCCTTTACCCGCAAGGGGCTGCCGGAGTACCCGGACTTGCCGCTGGTGCTGCCGAACGTGGTGCACGATGGTGACTTCAATCTGCAAGAGGGCAAGGTGCGCGCCTTCTATGCGGGCCCGGCCCACACGCCGGACGGCATCTTTGTCTACTTCCCTGACCAGCAGGTGCTCTATGGCAACTGCATCCTCAAGGAGAAGCTGGGCAACCTGAGCTTTGCCGATGTGAAGGCGTATCCGCAGACGCTGGAGCGGCTGAAAGCGATGAAGCTGCCCATCAAGATTGTGGTTGGCGGTCACGACTCGCCGCTGCACGGCCCCGAGTTGATTGATCACTACCAGGCGCTGATCAAGGCCGCTACTCACTCATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36795","NCBI_taxonomy_name":"Aeromonas salmonicida","NCBI_taxonomy_id":"645"}}}},"ARO_accession":"3003101","ARO_id":"39667","ARO_name":"cphA5","ARO_description":"cphA5 is an Ambler Class B MBL; subclass B2 originally isolated from Aeromonas salmonicida. This enzyme has specific activity against carbapenems and is active as a mono-zinc protein.","ARO_category":{"36720":{"category_aro_accession":"3000581","category_aro_cvterm_id":"36720","category_aro_name":"CphA beta-lactamase","category_aro_description":"CphA is an Ambler Class B MBL; subclass B2 originally isolated from Aeromonas hydrophilia.  This enzyme has specific activity against carbapenems and is active as a mono-zinc protein.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1606":{"model_id":"1606","model_name":"CTX-M-16","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"767":{"protein_sequence":{"accession":"AAK32961.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTAGDKTGSGGYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"AY029068","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAGCTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCACAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGCAGGTGATAAGACCGGCAGCGGCGGCTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001879","ARO_id":"38279","ARO_name":"CTX-M-16","ARO_description":"CTX-M-16 is a beta-lactamase found in Escherichia coli","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1609":{"model_id":"1609","model_name":"QnrC","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"508":{"protein_sequence":{"accession":"ACK75961.1","sequence":"MNYSHKTYDQIDFSGQDLSSHHFSHCKFFGCNFNRVNLRDAKFMGCTFIESNDFEGCNFIYADLRDASFMNCMLSMANFQGANCFGLELRECDLKGANFSQANFVNHVSNKMYFCSAYITGCNLSYANFDKQCLEKCDLFENKWVGASLQGASFKESDLSRGSFSDDFWEQCRIQGCDLTHSELNGLEPRKVDLTGVKICSWQQEQLLEQLGVIVIPDKVF"},"dna_sequence":{"accession":"EU917444","fmin":"1716","fmax":"2382","strand":"+","sequence":"TTGAATTATTCCCATAAAACGTACGATCAAATTGATTTTTCCGGCCAAGATTTGAGCTCTCATCACTTTTCTCACTGTAAATTTTTTGGTTGTAATTTTAATCGAGTGAATTTACGTGATGCTAAATTCATGGGTTGTACATTTATTGAATCGAATGATTTTGAAGGATGTAATTTTATCTATGCAGACCTACGAGATGCTTCATTTATGAATTGCATGCTTTCAATGGCGAATTTCCAAGGGGCAAACTGTTTTGGCCTTGAATTGAGAGAATGCGATTTAAAAGGTGCTAATTTCTCACAGGCAAACTTTGTTAATCATGTTTCTAACAAAATGTATTTTTGCTCTGCTTACATTACGGGTTGTAATTTGTCTTATGCTAATTTCGATAAGCAATGCCTTGAAAAGTGTGATTTATTTGAAAATAAATGGGTAGGTGCAAGCCTGCAAGGGGCCTCTTTTAAAGAGTCAGACTTAAGTAGGGGATCATTTTCTGATGACTTTTGGGAGCAATGCAGAATTCAGGGGTGTGATCTCACTCATTCAGAATTAAATGGCTTAGAACCTCGTAAAGTGGATTTAACTGGCGTGAAAATTTGTTCATGGCAACAAGAGCAGCTTTTGGAGCAGTTGGGGGTGATTGTTATTCCAGACAAAGTGTTTTGAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3002787","ARO_id":"39221","ARO_name":"QnrC","ARO_description":"QnrC is a plasmid-mediated quinolone resistance protein found in Proteus mirabilis","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1610":{"model_id":"1610","model_name":"OXA-74","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1305":{"protein_sequence":{"accession":"CAH69530.1","sequence":"MKTFAAYVIIACLSSTALAGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPVSTFKIPSAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG"},"dna_sequence":{"accession":"AJ854182","fmin":"0","fmax":"801","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTATCGCGTGTCTTTCGAGTACGGCATTAGCTGGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTCTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATGACTTAGCTCGTGCATCAAAGGAATATCTTCCAGTATCAACATTTAAGATCCCCAGCGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAGCAATGGGAAAGAGACTTGACCTTAAGAGGGGCAATACAAGTTTCAGCTGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCCTATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAAGGCCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATATTTAAATAAATTGTCAGCATCTAAAGAAAACCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCGGCACCTGAATATCTAGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGGTGGGTTGAGAAGGAGACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAGTAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGAAAGTGAGGGCATCATTGGTGGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001798","ARO_id":"38198","ARO_name":"OXA-74","ARO_description":"OXA-74 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1611":{"model_id":"1611","model_name":"SME-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"1565":{"protein_sequence":{"accession":"AHA49908.1","sequence":"MSNKVNFKTASFLFSVCLALSAFNAHANKSDAAAKQIKKLEEDFDGRIGVFAIDTGSGNTFGYRSDERFPLCSSFKGFLAAAVLERVQQKKLDINQKVKYESRDLEYHSPITTKYKGSGMTLGDMASAALQYSDNGATNIIMERFLGGPEGMTKFMRSIGDNEFRLDRWELELNTAIPGDKRDTSTPKAVANSLNKLALGNVLNAKVKAIYQNWLKGNTTGDARIRASVPADWVVGDKTGSCGAYGTANDYAVIWPKNRAPLIVSIYTTRKSKDDKHSDKTIAEASRIAIQAID"},"dna_sequence":{"accession":"KF481967","fmin":"0","fmax":"885","strand":"+","sequence":"ATGTCAAACAAAGTAAATTTTAAAACGGCTTCATTTTTGTTTAGTGTTTGTTTAGCTTTGTCGGCATTTAATGCTCATGCTAACAAAAGTGATGCTGCGGCAAAACAAATAAAAAAATTAGAGGAAGACTTTGATGGGAGGATTGGCGTCTTTGCAATAGATACAGGATCGGGTAATACATTTGGGTATAGATCAGATGAGCGGTTCCCTTTATGCAGTTCATTTAAAGGTTTTTTGGCGGCTGCTGTTTTAGAGAGGGTGCAACAAAAAAAACTAGATATCAACCAAAAGGTTAAATATGAGAGTAGGGATCTAGAATATCATTCACCTATTACAACAAAATATAAAGGCTCAGGTATGACATTAGGTGATATGGCTTCTGCTGCATTGCAATATAGCGACAATGGGGCAACAAATATAATTATGGAACGATTTCTTGGCGGTCCTGAGGGGATGACTAAATTTATGCGTTCTATTGGAGATAATGAGTTTAGGTTAGATCGCTGGGAACTGGAACTTAACACTGCAATCCCAGGAGATAAACGTGACACTTCAACGCCAAAAGCTGTTGCAAATAGTTTGAATAAACTAGCTTTGGGGAATGTTCTCAATGCTAAAGTGAAAGCGATTTATCAAAATTGGTTAAAAGGTAATACAACTGGTGATGCTCGAATTCGTGCTAGTGTTCCTGCTGATTGGGTTGTAGGTGACAAAACTGGGAGCTGTGGGGCATATGGTACTGCGAATGATTATGCCGTCATTTGGCCTAAAAATAGAGCACCATTAATTGTCTCTATATATACAACACGAAAATCGAAAGATGATAAGCACAGTGATAAAACTATTGCGGAAGCATCACGTATTGCAATTCAGGCAATTGATTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36783","NCBI_taxonomy_name":"Serratia marcescens","NCBI_taxonomy_id":"615"}}}},"ARO_accession":"3002382","ARO_id":"38782","ARO_name":"SME-4","ARO_description":"SME-4 is a beta-lactamase. From the Lahey list of SME beta-lactamases.","ARO_category":{"36194":{"category_aro_accession":"3000055","category_aro_cvterm_id":"36194","category_aro_name":"SME beta-lactamase","category_aro_description":"SME beta-lactamases are chromosome-mediated class A beta-lactamases that hydrolyze carbapenems in Serratia marcescens.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1612":{"model_id":"1612","model_name":"ErmR","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"3582":{"protein_sequence":{"accession":"ALX06067.1","sequence":"MAGPQDRPRGRGPSSGRPQRPVGGRSQRDRDRRVLGQNFLRDPATIRRIADAADVDPDGLVVEAGPGEGLLTRELARRAGRVRTYELDQRLARRLSTDLAQETSIEVVHADFLTAPHPEEPFQFVGAIPYGITSAIVDWCLTAPTLTSATLVTQQEFARKRTGDYGRWTALTVTTWPTFEWQYVAKVDRTLFTPVPRVHSAIMRLRRRPQPLLRDAAARSRFADMVEIGFVGKGGSLYRSLTREWPRSKVDSAFARADVHHDEIVAFVHPDQWITLFQLLDGSRGGAARGPGDQRGRRGRPGGGPRPDGRAGGGPRRDAGGRRTGDGRGGRPRPPRGGQA"},"dna_sequence":{"accession":"CP011502.1","fmin":"3324540","fmax":"3325563","strand":"+","sequence":"ATGGCAGGTCCGCAAGACCGTCCGCGAGGGCGCGGACCCTCCTCCGGTCGCCCGCAGCGGCCGGTGGGCGGCCGCAGCCAGCGCGACCGCGACCGGCGGGTCCTCGGCCAGAACTTCCTGCGCGACCCGGCGACCATCCGGCGCATCGCCGACGCCGCCGACGTCGACCCCGACGGGCTCGTCGTCGAGGCGGGTCCCGGCGAAGGGCTGCTCACCCGCGAGCTCGCCCGACGCGCCGGGCGGGTACGCACCTACGAGCTGGACCAGCGCCTCGCGCGACGACTCTCGACCGACCTGGCCCAGGAGACGAGCATCGAGGTCGTCCACGCCGACTTCCTGACCGCGCCTCACCCCGAGGAGCCGTTCCAGTTCGTCGGCGCGATCCCCTACGGCATCACCTCCGCCATCGTCGACTGGTGCCTGACCGCCCCGACCCTGACGTCGGCGACCCTCGTGACCCAGCAGGAGTTCGCGCGCAAGCGGACGGGTGACTACGGACGGTGGACGGCCCTCACCGTCACCACGTGGCCGACCTTCGAGTGGCAGTACGTCGCCAAGGTCGACCGCACGCTGTTCACACCGGTGCCGCGCGTGCACTCCGCGATCATGCGGCTGCGCCGCCGCCCACAGCCCCTCCTGCGCGACGCGGCGGCGAGGTCGCGCTTCGCGGACATGGTGGAGATCGGCTTCGTCGGCAAGGGCGGCAGCCTCTACCGGTCGCTGACCCGGGAGTGGCCGCGCTCGAAGGTCGACAGCGCGTTCGCGCGCGCCGACGTCCACCACGACGAGATCGTCGCCTTCGTGCACCCCGACCAGTGGATCACGCTGTTCCAGCTCCTCGACGGGTCCCGTGGCGGCGCCGCGCGCGGACCGGGCGACCAGCGGGGGCGGCGCGGCCGCCCAGGCGGAGGCCCCCGGCCGGACGGTCGCGCGGGCGGCGGCCCGCGCCGCGACGCGGGCGGGCGCCGCACGGGTGACGGACGCGGAGGTCGCCCCCGTCCCCCGCGCGGCGGCCAGGCCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40506","NCBI_taxonomy_name":"Aeromicrobium erythreum","NCBI_taxonomy_id":"2041"}}}},"ARO_accession":"3000594","ARO_id":"36733","ARO_name":"ErmR","ARO_description":"ErmR is a methyltransferase found in the erythromycin producer Aeromicrobium erythreum. Like other Erm enzymes, it catalyzes the methylation of A2058 of the 23S ribosomal RNA. The gene is found within the erythromycin biosynthetic cluster and is responsible for self-resistance.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35946":{"category_aro_accession":"0000027","category_aro_cvterm_id":"35946","category_aro_name":"roxithromycin","category_aro_description":"Roxithromycin is a semi-synthetic, 14-carbon ring macrolide antibiotic derived from erythromycin. It is used to treat respiratory tract, urinary and soft tissue infections. Roxithromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35974":{"category_aro_accession":"0000057","category_aro_cvterm_id":"35974","category_aro_name":"telithromycin","category_aro_description":"Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36315":{"category_aro_accession":"3000176","category_aro_cvterm_id":"36315","category_aro_name":"dirithromycin","category_aro_description":"Dirithromycin is an oxazine derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome to inhibit bacterial protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin 1A is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"vernamycin B-gamma","category_aro_description":"Vernamycin B-gamma is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1613":{"model_id":"1613","model_name":"CMY-38","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1021":{"protein_sequence":{"accession":"CAP60699.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYARGYREGKPVHVSPGQLNAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKNYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"AM931008","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCCGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTAACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAACTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3002049","ARO_id":"38449","ARO_name":"CMY-38","ARO_description":"CMY-38 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1614":{"model_id":"1614","model_name":"TEM-194","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1325":{"protein_sequence":{"accession":"AFC75524.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSRNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANILLTTIGGPKELTAFLHNMRDHVTRLDRWEPELNEAIPHDERDTTMPAPVATTLRTLLTVELLTLASRPRLIDWMEADKVAGPILRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"JN935136","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCGGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACATACTTCTGACAACGATCGGAGGACCGAAGGAGCTCACCGCTTTTTTGCACAACATGAGAGATCATGTCACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCACACGACGAGCGTGACACCACGATGCCTGCTCCAGTGGCCACAACGTTGCGCACACTATTAACTGTCGAACTACTTACTCTAGCTTCCCGGCCACGATTAATAGACTGGATGGAGGCGGATAAAGTGGCAGGACCAATTCTGCGCTCGGCCCTTCCGGCCGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001054","ARO_id":"37434","ARO_name":"TEM-194","ARO_description":"TEM-194 is a beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1615":{"model_id":"1615","model_name":"APH(2'')-IIa","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"696":{"protein_sequence":{"accession":"AAK63040.1","sequence":"MVNLDAEIYEHLNKQIKINELRYLSSGDDSDTFLCNEQYVVKVPKRDSVRISQKRELELYRFLENCKLSYQIPAVVYQSDRFNIMKYIKGERITYEQYHKLSEKEKDALAYDEATFLKELHSIEIDCSVSLFSDALVNKKDKFLQDKKLLISILEKEQLLTDEMLEHIETIYENILSNAVLFKYTPCLVHNDFSANNMIFRNNRLFGVIDFGDFNVGDPDNDFLCLLDCSTDDFGKEFGRKVLKYYQHKAPEVAERKAELNDVYWSIDQIIYGYERKDREMLIKDVSELLQTQAEMFIF"},"dna_sequence":{"accession":"AF337947","fmin":"271","fmax":"1171","strand":"+","sequence":"ATGGTTAACTTGGACGCTGAGATATATGAGCACTTAAATAAACAGATAAAAATAAATGAACTCCGTTATTTATCGTCCGGCGATGATAGTGATACTTTTTTGTGTAATGAACAATATGTTGTGAAAGTTCCTAAACGAGATTCTGTTAGAATTTCTCAGAAACGAGAGCTTGAATTGTATCGTTTTTTAGAAAACTGTAAGCTATCTTATCAAATCCCTGCGGTAGTGTATCAAAGTGACCGATTTAATATTATGAAATATATTAAAGGGGAACGTATTACTTATGAGCAGTATCATAAGTTGAGTGAAAAGGAAAAGGATGCCCTTGCATATGATGAAGCGACGTTTTTGAAAGAGTTACATTCCATAGAGATTGATTGTTCTGTCAGTTTGTTTTCAGATGCTCTGGTGAATAAGAAAGATAAGTTTTTGCAAGATAAAAAATTACTTATAAGTATTCTGGAAAAGGAGCAGCTGTTAACTGATGAGATGTTGGAACATATCGAAACAATATATGAAAACATATTAAGCAATGCTGTTTTATTTAAATATACCCCTTGTTTGGTACATAATGATTTCAGTGCAAATAACATGATTTTTAGAAATAATAGACTGTTTGGAGTTATTGATTTTGGCGATTTTAATGTAGGTGACCCGGATAATGATTTTTTGTGCTTGCTGGATTGTAGTACAGATGATTTCGGGAAAGAATTTGGCAGGAAGGTATTAAAATACTATCAGCATAAGGCGCCGGAAGTAGCAGAAAGAAAAGCAGAGCTTAATGATGTATATTGGTCGATAGACCAAATCATTTATGGTTATGAAAGAAAAGATAGGGAAATGTTGATTAAGGATGTTTCTGAATTGCTACAAACACAAGCAGAGATGTTTATATTTTAGC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002635","ARO_id":"39035","ARO_name":"APH(2'')-IIa","ARO_description":"APH(2'')-IIa is a chromosomal-encoded aminoglycoside phosphotransferase in E. faecium and E. coli","ARO_category":{"36267":{"category_aro_accession":"3000128","category_aro_cvterm_id":"36267","category_aro_name":"APH(2'')","category_aro_description":"Phosphorylation of 2-deoxystreptamine aminoglycosides on the hydroxyl group at position 2''","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1616":{"model_id":"1616","model_name":"CTX-M-152","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1589":{"protein_sequence":{"accession":"AHY20039.1","sequence":"MRKSVRRAILMTTACVSLLLASVPLYAHANDVQQKLAALEKSSGGRLGVALINTADNTQTLYRADERFAMCSTSKVMAAAAVLKQSETQKDLLSQRVEIKSSDLINYNPIAEKHVNGTMTLGELSAAALQYSDNTAMNKLIAHLGGPGKVTAFARAIGDDTFRLDRTEPTLNTAIPGDPRDTTTPLAMAQALRNLTLGNALGDTQRAQLVMWLKGNTTGAASIQAGLPTSWVVGDKTGSGDYGTTNDIAVIWPEGRAPLVLVTYFTQSEPKAESRRDVLAAAARIVTDGY"},"dna_sequence":{"accession":"KJ461948","fmin":"3","fmax":"876","strand":"+","sequence":"ATGAGAAAAAGCGTAAGGCGGGCGATATTAATGACGACAGCCTGTGTTTCGCTGCTGTTGGCCAGTGTGCCGCTGTATGCCCACGCGAACGATGTTCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGGGGACGACTGGGTGTGGCGTTGATTAACACCGCCGATAACACGCAGACGCTCTACCGCGCCGACGAGCGTTTTGCTATGTGCAGCACCAGTAAAGTGATGGCGGCGGCGGCGGTGCTTAAGCAAAGTGAAACGCAAAAGGACTTACTGAGTCAGCGGGTTGAAATTAAGTCCTCAGACTTGATTAACTACAACCCAATCGCTGAAAAGCACGTCAATGGCACGATGACACTCGGGGAGCTGAGCGCGGCGGCGCTGCAGTACAGCGATAATACTGCCATGAATAAGCTGATTGCCCATCTCGGGGGGCCGGGTAAAGTGACGGCATTTGCTCGTGCGATTGGCGATGACACTTTCCGGCTCGATCGTACCGAGCCGACGCTCAACACCGCGATCCCCGGCGACCCGCGCGATACCACCACGCCGTTAGCGATGGCGCAGGCTCTGCGCAATCTGACGTTGGGCAATGCCCTGGGTGACACTCAGCGTGCGCAGCTGGTGATGTGGCTGAAAGGCAACACCACCGGCGCTGCCAGCATTCAGGCAGGGCTACCCACATCGTGGGTTGTCGGGGATAAAACCGGCAGCGGCGATTATGGTACGACGAATGATATCGCGGTTATTTGGCCGGAAGGTCGCGCGCCGCTCGTTCTGGTGACTTACTTCACCCAGTCGGAGCCGAAGGCAGAGAGCCGTCGTGACGTGCTCGCTGCTGCCGCCAGAATTGTCACCGACGGTTATTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39100","NCBI_taxonomy_name":"Kluyvera sp. MRB7","NCBI_taxonomy_id":"1491392"}}}},"ARO_accession":"3002009","ARO_id":"38409","ARO_name":"CTX-M-152","ARO_description":"CTX-M-152 is a beta-lactamase. From the Lahey list of CTX-M beta-lactamases.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1617":{"model_id":"1617","model_name":"vanE","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"650"}},"model_sequences":{"sequence":{"216":{"protein_sequence":{"accession":"AAL27442.1","sequence":"MKTVAIIFGGVSSEYEVSLKSAVAIIKNMESIDYNVMKIGITEEGHWYLFEGTTDKIKKDRWFLDESCEEIVVDFAKKSFVLKNSKKIIKPDILFPVLHGGYGENGAMQGVFELLDIPYVGCGIGAAAISMNKIMLHQFAEAIGVKSTPSMIIEKGQDLQKVDAFAKIHGFPLYIKPNEAGSSKGISKVERKSDLYKAIDEASKYDSRILIQKEVKGVEIGCGILGNEQLVVGECDQISLVDGFFDYEEKYNLVTAEILLPAKLSIDKKEDIQMKAKKLYRLLGCKGLARIDFFLTDDGEILLNEINTMPGFTEHSRFPMMMNEIGMDYKEIIENLLVLAVENHEKKLSTID"},"dna_sequence":{"accession":"FJ872411","fmin":"39735","fmax":"40794","strand":"+","sequence":"ATGAAGACAGTTGCGATTATCTTTGGCGGAGTTTCTTCTGAATATGAAGTTTCACTGAAATCTGCTGTAGCGATTATTAAAAATATGGAATCTATTGATTATAACGTAATGAAAATAGGGATCACCGAAGAAGGTCATTGGTATCTATTTGAAGGAACGACAGACAAAATAAAGAAAGATCGTTGGTTTTTAGATGAAAGCTGTGAAGAAATCGTAGTTGATTTCGCAAAAAAAAGCTTTGTATTGAAAAACAGTAAAAAAATAATCAAGCCTGATATTTTATTCCCAGTTTTACATGGAGGTTATGGTGAGAATGGTGCTATGCAGGGAGTATTTGAGTTATTAGATATTCCATATGTAGGTTGTGGTATCGGAGCTGCAGCAATCTCTATGAATAAAATAATGCTCCATCAATTTGCTGAAGCAATTGGTGTAAAAAGCACCCCTAGTATGATTATAGAAAAGGGACAAGACCTACAAAAAGTCGATGCGTTTGCGAAAATACATGGATTTCCTTTATATATTAAACCGAATGAGGCAGGCTCATCAAAAGGAATTAGCAAGGTAGAACGAAAAAGTGATTTATATAAAGCAATAGACGAAGCTTCAAAATATGATAGTCGTATTTTAATTCAAAAGGAAGTGAAAGGGGTAGAAATTGGTTGTGGTATTTTAGGAAATGAACAATTGGTCGTTGGAGAATGTGACCAAATCAGTCTTGTGGATGGCTTTTTCGATTATGAAGAGAAATACAATTTAGTAACAGCAGAAATTTTGTTACCAGCTAAACTATCAATAGACAAAAAAGAAGATATTCAGATGAAAGCAAAAAAACTATACAGACTATTAGGATGCAAAGGATTAGCGAGAATCGACTTTTTCTTAACTGATGACGGAGAAATTTTATTAAATGAAATCAATACAATGCCTGGTTTTACAGAGCATTCGAGATTTCCAATGATGATGAATGAGATTGGGATGGACTACAAAGAGATTATAGAAAACCTATTAGTATTGGCGGTGGAAAATCATGAAAAAAAATTATCTACGATTGATTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3002907","ARO_id":"39341","ARO_name":"vanE","ARO_description":"VanE is a D-Ala-D-Ala ligase homolog that can synthesize D-Ala-D-Ser, an alternative substrate for peptidoglycan synthesis that reduces vancomycin binding affinity in Enterococcus faecalis","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"39340":{"category_aro_accession":"3002906","category_aro_cvterm_id":"39340","category_aro_name":"van ligase","category_aro_description":"van ligases synthesize alternative substrates for peptidoglycan synthesis that reduce vancomycin binding affinity.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1618":{"model_id":"1618","model_name":"OXA-362","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"809":{"protein_sequence":{"accession":"AHA11125.1","sequence":"MKILILLPLLSCLGLTACTSPVSSFPSHITSTQSTQAIAQLFDQAQSSGVLVIQRGQKVQVYGNDLSRAGTEYVPASTFKMLNALIGLQHGKATTNEIFKWDGKKRSFAAWEKDMTLGEAMQASAVPVYQELARRIGLELMQQEVRRIQFGNQQIGQQVDNFWLVGPLKITPKQEVEFVSALAREQLAFDPQVQQQVKAMLLLQERKAYRLYAKSGWGMDVEPQVGWLTGWVETPQAEIVAFSLNMQMQNGMDPAIRLEILQQALAELGLYPKAEG"},"dna_sequence":{"accession":"KF460532","fmin":"0","fmax":"831","strand":"+","sequence":"ATGAAAATTCTGATTTTGCTACCTTTACTGAGTTGCTTGGGCCTGACAGCGTGTACCTCACCTGTTTCATCTTTCCCTTCTCATATCACTTCGACTCAATCGACTCAAGCCATTGCCCAATTATTTGATCAGGCGCAAAGTTCTGGCGTTTTAGTGATTCAGCGTGGTCAAAAAGTACAGGTCTATGGCAATGATTTAAGCCGTGCAGGTACCGAATATGTTCCAGCCTCTACTTTCAAAATGCTCAATGCCCTGATTGGCCTGCAACATGGCAAAGCCACAACCAATGAAATTTTTAAATGGGATGGCAAGAAACGCAGTTTTGCAGCCTGGGAAAAAGACATGACTCTCGGCGAAGCCATGCAAGCTTCTGCTGTACCCGTGTATCAGGAACTGGCACGTCGCATTGGCCTTGAACTGATGCAACAGGAAGTGAGACGTATTCAATTCGGCAATCAGCAGATTGGGCAGCAGGTTGATAACTTCTGGTTGGTAGGCCCTTTGAAAATCACTCCAAAACAGGAGGTCGAATTTGTCTCGGCTCTAGCCCGAGAGCAGCTTGCCTTTGATCCACAAGTCCAGCAGCAAGTCAAAGCCATGTTACTTTTACAGGAGCGGAAAGCTTATCGACTATATGCCAAATCTGGTTGGGGCATGGATGTGGAACCACAAGTCGGCTGGCTCACCGGCTGGGTTGAAACACCGCAGGCTGAAATCGTGGCATTTTCGCTGAATATGCAGATGCAAAATGGTATGGATCCGGCAATCCGCCTTGAAATTTTACAGCAGGCTTTGGCCGAATTAGGGCTTTATCCAAAAGCTGAAGGATGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36948","NCBI_taxonomy_name":"Acinetobacter lwoffii","NCBI_taxonomy_id":"28090"}}}},"ARO_accession":"3001549","ARO_id":"37949","ARO_name":"OXA-362","ARO_description":"OXA-362 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1619":{"model_id":"1619","model_name":"L1 beta-lactamase","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1909":{"protein_sequence":{"accession":"CAB75346.1","sequence":"MRSTLLAFALSSLALAATLFTFDGAAADASLPQLQAYTVDPSWLQTMAPLQIADHTWQIGTHDLTALLVQTADGLVLIDGGMPQMASYLLTNMKARGTNTGPLRMVLLSHAHTDHAGPVAEIKRRTGAQVVVNAETAVLLARGGSDDLHFGDEITFPPVNADRIVMDREVVKLGGIAFTAHFMPGHTPGSTAWTWTDTRDGKPVRIAYADSLSAPGYQLQGNARYPRLVEDYRRSFATVRGLPCDLLLTPHPGASNWNYAAGSNASEKVLSCKAYADAAEKKFDAQLAKETAGAR"},"dna_sequence":{"accession":"AJ272109","fmin":"0","fmax":"888","strand":"+","sequence":"ATGCGTTCTACCCTGCTCGCCTTCGCCCTCTCGTCGCTCGCCCTGGCCGCCACGCTCTTCACCTTCGACGGCGCCGCCGCCGACGCATCGCTGCCACAGCTGCAGGCCTACACGGTGGACCCTTCCTGGCTGCAAACGATGGCGCCGTTGCAGATTGCCGATCACACCTGGCAGATCGGCACGCATGACCTGACGGCACTGCTGGTCCAGACGGCTGATGGCCTCGTCCTGATCGATGGTGGCATGCCGCAAATGGCCTCTTACCTGCTGACCAACATGAAGGCCAGGGGAACCAATACCGGTCCCCTGCGCATGGTCCTGCTCAGCCACGCGCACACCGATCACGCCGGCCCTGTGGCCGAGATCAAGCGCCGCACGGGGGCGCAGGTGGTCGTGAACGCCGAAACCGCAGTGCTGCTGGCCCGAGGCGGCAGCGACGACCTTCATTTCGGCGACGAAATCACGTTTCCACCGGTCAATGCAGACCGCATCGTCATGGATCGGGAGGTCGTCAAGCTGGGCGGCATCGCGTTCACCGCCCATTTCATGCCCGGGCACACGCCGGGGAGCACCGCCTGGACCTGGACCGATACGCGCGATGGCAAGCCGGTGCGCATCGCCTATGCCGACAGCCTGAGCGCGCCGGGCTACCAGCTGCAGGGCAATGCCCGCTATCCCCGCCTGGTTGAGGACTACCGACGCAGCTTCGCTACGGTGCGCGGCCTGCCCTGCGACCTGTTGCTGACCCCGCATCCGGGCGCCAGCAACTGGAACTATGCTGCTGGCAGCAACGCCAGCGAGAAGGTACTGAGCTGCAAAGCCTACGCGGATGCGGCCGAGAAGAAGTTCGACGCGCAGCTGGCCAAGGAAACGGCCGGGGCCCGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37076","NCBI_taxonomy_name":"Stenotrophomonas maltophilia","NCBI_taxonomy_id":"40324"}}}},"ARO_accession":"3000582","ARO_id":"36721","ARO_name":"L1 beta-lactamase","ARO_description":"L1 is an Ambler class B MBL; subclass B3 originally isolated from Stenotrophomonas maltophilia.  It has activity against a broad range of beta-lactams and is only active with two Zn(II) ions in the active site.","ARO_category":{"41379":{"category_aro_accession":"3004215","category_aro_cvterm_id":"41379","category_aro_name":"L1 family beta-lactamase","category_aro_description":"This subclass B3 of beta-lactamses have the ability to hydrolyze cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1620":{"model_id":"1620","model_name":"CTX-M-156","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1741":{"protein_sequence":{"accession":"AIS67612.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPNAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"KM211509","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAACGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3003164","ARO_id":"39741","ARO_name":"CTX-M-156","ARO_description":"From the Lahey list of beta-lactamases.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1621":{"model_id":"1621","model_name":"SHV-45","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"834":{"protein_sequence":{"accession":"AAN39364.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIDDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASKRGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AF547625","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGACGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCAAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001103","ARO_id":"37483","ARO_name":"SHV-45","ARO_description":"SHV-45 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1505":{"model_id":"1505","model_name":"SAT-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"459":{"protein_sequence":{"accession":"AAB53445.1","sequence":"MITEMKAEHLKDIDKPSEPFEVIGKIIPRYENENWTFTELLYEAPYLKSYQDEEDEEDEEADCLEYIDNTDKIIYLYYQDDKCVGKVKLRKNWNRYAYIEDIAVCKDFRGQGIGSALINISIEWAKHKNLHGLMLETQDNNLIACKFYHNCGFKIGSVDTMLYANFENNFEKAVFWYLRF"},"dna_sequence":{"accession":"U01945","fmin":"373","fmax":"916","strand":"+","sequence":"GTGATTACAGAAATGAAAGCAGAGCACCTGAAAGATATCGATAAACCCAGCGAACCATTTGAGGTGATAGGTAAGATTATACCGAGGTATGAAAACGAGAATTGGACCTTTACAGAATTACTCTATGAAGCGCCATATTTAAAAAGCTACCAAGACGAAGAGGATGAAGAGGATGAGGAGGCAGATTGCCTTGAATATATTGACAATACTGATAAGATAATATATCTTTACTACCAAGACGATAAATGCGTCGGAAAAGTTAAACTGCGAAAAAATTGGAACCGGTACGCTTATATAGAAGATATCGCCGTATGTAAGGATTTCAGGGGGCAAGGCATAGGCAGCGCGCTTATCAATATATCTATAGAATGGGCAAAGCATAAAAACTTGCATGGACTAATGCTTGAAACCCAGGACAATAACCTTATAGCTTGTAAATTCTATCATAATTGTGGTTTCAAAATCGGCTCCGTCGATACTATGTTATACGCCAACTTTGAAAACAACTTTGAAAAAGCTGTTTTCTGGTATTTAAGGTTTTAGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36835","NCBI_taxonomy_name":"Campylobacter coli","NCBI_taxonomy_id":"195"}}}},"ARO_accession":"3002897","ARO_id":"39331","ARO_name":"SAT-4","ARO_description":"SAT-4 is a plasmid-mediated streptothricin acetyltransferase and streptothricin (a nucleoside antibiotic) resistant determinant. Originally described from a Campylobacter coli BE\/G4 plasmid gene sequence by Jacob et al, 1994.","ARO_category":{"37249":{"category_aro_accession":"3000869","category_aro_cvterm_id":"37249","category_aro_name":"streptothricin acetyltransferase (SAT)","category_aro_description":"AcetylCoA dependent acetyltransferase that acetylate streptothricins such as nourseothricin at position 16 (beta position of beta-lysine).","category_aro_class_name":"AMR Gene Family"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1608":{"model_id":"1608","model_name":"MexT","model_type":"protein overexpression model","model_type_id":"41091","model_description":"This model detects protein overexpression based on the presence of mutations.The detection of the protein without an associated mutation indicates that the protein is likely to be expressed at low or basal levels. The detection of the protein with the mutation indicates that the protein is likely overexpressed. This model reflects how certain proteins are functional with and without mutations. For example, efflux pump subunits and regulators are functional with mutations and without mutations. Without mutations, efflux pump subunits and regulators are usually expressed at a low level. When an efflux pump regulator has a mutation, it can cause the overexpression of the efflux pump it is responsible for regulating, leading to resistance to specific drugs. Protein overexpression models have two parameters: a curated BLASTP cutoff, and a curated set of mutations (single resistance variants, frameshift mutations, indels, etc.) shown clinically to confer resistance. This model type is a combination of the protein homolog and protein variant model. A detected hit can be categorized as Perfect, Strict, or Loose with no mutation(s) or as Strict or Loose with mutation(s).","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"7570":"G258D","7571":"Y138D"},"clinical":{"7570":"G258D","7571":"Y138D"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4032":{"protein_sequence":{"accession":"NP_251182.1","sequence":"MPVSDPMPLRHLARPRPVSHARLDGEPPRLQPLAPGNEERHEPKRPAPRRSEPADRVRDPDARTQRDPRRRETVPRPAGQPAISAALSRLRTLFDDPLFVRTGRSMEPTARAQEIFAHLSPALDSISTAMSRASEFDPATSTAVFRIGLSDDVEFGLLPPLLRRLRAEAPGFVLVVRRANYLLMPNLLASGEISVGVSYTDELPANAKRKTVRRSKPKILRADSAPGQLTLDDYCARPHALVSFAGDLSGFVDEELEKFGRKRKVVLAVPQFNGLGTLLAGTDIIATVPDYAAQALIAAGGLRAEDPPFETRAFELSMAWRGAQDNDPAERWLRSRISMFIGDPDSL"},"dna_sequence":{"accession":"NC_002516.2","fmin":"2807468","fmax":"2807469","strand":"+","sequence":"A"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3000814","ARO_id":"37194","ARO_name":"MexT","ARO_description":"MexT is a LysR-type transcriptional activator that positively regulates the expression of MexEF-OprN, OprD, and MexS.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1523":{"model_id":"1523","model_name":"MexD","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1800"}},"model_sequences":{"sequence":{"335":{"protein_sequence":{"accession":"AAB41957.1","sequence":"MSEFFIKRPNFAWVVALFISLGGLLVISKLPVAQYPNVAPPQITITATYPGASAKVLVDSVTSVLEESLNGAKGLLYFESTNNSNGTAEIVVTFEPGTDPDLAQVDVQNRLKKAEARMPQAVLTQGLQVEQTSAGFLLIYALSYKEGAQRSDTTALGDYAARNINNELRRLPGVGKLQFFSSEAAMRVWIDPQKLVGFGLSIDDVSNAIRGQNVQVPAGAFGSAPGSSAQELTATLAVKGTLDDPQEFGQVVLRANEDGSLVPARRCRAPGTRQGELQHFLATERHAHRGRGYPAVARGQRDPDPTLVKQRLAELSAFFPEDMQYSVPYDTSRFVDVAIEKVIHTLIEAMVLVFLVMFLFLENVRYTLIPSIVVPVCLLGTLMVMYLLGFSVNMMTMFGMVLAIGILVDDAIVVVENVERIMAEEGISPAEATVKAMKQVSGAIVGITLVLSAVFLPLAFMAGSVGVIYQQFSVSLAVSILFSGFLALTFTPALCATLFKPIPEGHHEKRGFFGAFNRGFARVTERYSLLNSKLVARAGRFMLVYAGLVAMLGYFYLRLPEAFVPAEDLGYMVVDVQLPPGASRVRTDATGEELERFLKSREAVASVFLISGFSFSGQGDNAALAFPTFKDWSERGAEQSSAAEIAALNEHFALPDDGTVMAVSPPPINGLGNSGGFALRLMDRSGVGREALLQARDTLLGEIQTNPKFLYAMMEGLAEAPQLRLLIDREKARALGVSFETISGTLSAAFGSEVINDFTNAGRQQRVVIQAEQGNRMTPESVLELYVPNAAGNLVPLSAFVSVKWEEGPVQLVRYNGYPSIRIVGDAAPGFSTGEAMAEMERLASQLPAGIGYEWTGLSYQEKVSAGQATSLFALAILVVFLLLVALYESWSIPLSVMLIVPIGAIGAVLAVMVSGMSNDVYFKVGLITIIGLSAKNAILIVEFAKELWEQGHSLRDAAIEAARLRFRPIIMTSMAFILGVIPLALASGAGAASQRAIGTGVIGGMLSATFLGVLFVPICFVWLLSLLRSKPAPIEQAASAGE"},"dna_sequence":{"accession":"U57969","fmin":"1485","fmax":"4617","strand":"+","sequence":"ATGTCCGAATTCTTCATCAAGCGGCCGAACTTCGCCTGGGTGGTGGCCCTGTTCATCTCCCTGGGCGGCCTGCTGGTCATTTCCAAATTGCCGGTAGCGCAGTACCCCAATGTCGCGCCGCCACAGATCACCATCACCGCCACCTATCCCGGCGCCTCGGCGAAGGTGCTGGTGGACTCCGTCACCAGTGTGCTCGAGGAGTCGCTGAACGGCGCCAAGGGCCTGCTCTACTTCGAGTCGACCAACAACTCCAACGGCACCGCCGAGATCGTCGTCACCTTCGAGCCGGGCACCGATCCGGACCTGGCCCAGGTGGACGTGCAGAACCGCCTGAAGAAAGCCGAGGCGCGCATGCCGCAGGCGGTGCTGACCCAGGGCCTGCAGGTCGAGCAGACCAGCGCCGGTTTCCTGCTGATCTATGCGCTCAGCTACAAGGAAGGCGCTCAGCGCAGCGACACCACCGCCCTCGGCGACTACGCCGCGCGCAATATCAACAACGAGCTGCGGCGCCTGCCGGGCGTCGGCAAGCTGCAATTCTTCTCTTCCGAGGCGGCCATGCGGGTCTGGATCGATCCGCAGAAGCTGGTGGGCTTCGGCCTCTCCATCGACGACGTGAGCAATGCCATCCGCGGGCAGAACGTGCAGGTGCCGGCCGGCGCCTTCGGCAGCGCACCGGGCAGTTCCGCGCAGGAGCTGACGGCGACCCTGGCGGTGAAGGGCACCCTGGACGATCCGCAGGAGTTCGGCCAGGTAGTGCTGCGCGCCAACGAGGACGGCTCGCTGGTCCCGGCTCGCCGATGTCGCGCGCCTGGAACTCGGCAAGGAGAGCTACAACATTTCCTCGCGACTGAACGGCACGCCCACCGTGGGCGGGGCTATCCAGCTGTCGCCCGGGGCCAACGCGATCCAGACCCTACCCTGGTGAAACAGCGTCTCGCCGAACTGTCGGCGTTCTTCCCCGAGGACATGCAGTACAGCGTGCCCTACGACACCTCGCGCTTCGTCGACGTGGCCATCGAGAAGGTGATCCACACCCTGATCGAAGCGATGGTCCTGGTGTTCCTGGTGATGTTCCTGTTCCTGGAGAACGTCCGCTACACCCTGATCCCGTCCATCGTGGTGCCGGTGTGCCTGCTGGGTACGCTGATGGTGATGTACCTGCTGGGGTTCTCGGTGAACATGATGACCATGTTCGGCATGGTCCTGGCGATCGGCATCCTGGTGGACGACGCCATCGTGGTGGTGGAGAACGTCGAGCGGATCATGGCGGAGGAGGGGATTTCCCCGGCCGAGGCCACGGTCAAGGCGATGAAGCAGGTATCCGGCGCCATCGTCGGCATCACCCTGGTGCTCTCGGCGGTGTTCCTGCCGCTGGCTTTCATGGCCGGTTCGGTGGGGGTGATCTACCAGCAGTTCTCGGTGTCGCTGGCGGTCTCGATCCTGTTCTCCGGCTTCCTCGCCCTGACCTTCACCCCGGCGCTGTGCGCCACGCTGTTCAAGCCCATTCCCGAAGGGCACCACGAGAAGCGCGGCTTCTTCGGCGCCTTCAACCGTGGCTTCGCCCGCGTCACCGAGCGCTATTCGCTGCTCAACTCGAAGCTGGTGGCGCGCGCCGGACGCTTCATGCTGGTGTACGCCGGCCTGGTGGCCATGCTCGGCTACTTCTACCTGCGCCTGCCGGAAGCCTTCGTGCCGGCGGAAGACCTCGGCTACATGGTGGTCGACGTGCAACTGCCGCCTGGCGCTTCGCGCGTGCGCACCGATGCCACCGGCGAGGAGCTCGAGCGCTTCCTCAAGTCCCGCGAGGCGGTGGCTTCGGTGTTCCTGATCTCGGGCTTCAGCTTCTCCGGCCAGGGCGACAATGCCGCGCTGGCCTTCCCAACCTTCAAGGACTGGTCCGAGCGAGGCGCCGAGCAGTCGTCCGCCGCCGAGATCGCCGCGCTGAACGAGCATTTCGCGCTGCCCGACGATGGCACGGTCATGGCCGTGTCGCCGCCACCGATCAACGGTCTGGGTAACTCCGGCGGCTTCGCATTGCGCCTGATGGACCGTAGCGGGGTCGGCCGCGAAGCGCTGCTGCAGGCTCGCGATACTCTTCTTGGCGAGATCCAGACCAACCCGAAATTCCTTTACGCGATGATGGAAGGACTGGCCGAAGCGCCGCAACTGCGCCTGTTGATCGACCGGGAGAAGGCCCGTGCCCTGGGGGTGAGCTTCGAGACCATCAGCGGCACGCTGTCCGCTGCCTTCGGCTCGGAGGTGATCAACGACTTCACCAATGCGGGGCGCCAACAGCGGGTGGTGATCCAGGCCGAACAGGGCAACCGGATGACCCCGGAAAGCGTGCTCGAGCTATACGTGCCTAACGCTGCTGGCAACCTGGTACCGCTCAGCGCCTTCGTCAGCGTGAAATGGGAAGAGGGACCGGTGCAATTGGTGCGCTATAACGGCTACCCGTCGATCCGCATCGTCGGTGACGCCGCGCCCGGCTTCAGTACCGGCGAAGCCATGGCGGAAATGGAGCGCCTGGCCTCGCAGCTGCCGGCCGGCATCGGCTACGAGTGGACCGGCCTGTCCTATCAGGAGAAGGTCTCCGCCGGGCAGGCCACCAGCCTGTTCGCCCTCGCCATCCTGGTGGTGTTCCTGTTGCTGGTGGCGCTCTACGAGAGCTGGTCGATCCCGCTGTCGGTGATGCTGATCGTGCCGATCGGCGCCATCGGCGCGGTGCTCGCGGTGATGGTCAGCGGTATGTCCAACGACGTGTATTTCAAGGTCGGCCTGATCACCATCATCGGTCTTTCGGCGAAGAACGCGATCCTCATCGTCGAGTTCGCCAAGGAACTCTGGGAACAGGGACATAGCCTGCGCGACGCCGCCATCGAGGCCGCGCGCCTGCGCTTCCGGCCGATCATCATGACTTCCATGGCGTTCATCCTCGGCGTGATACCCCTGGCCCTGGCCAGCGGTGCCGGCGCGGCGAGCCAGCGTGCCATCGGCACCGGAGTGATCGGCGGGATGCTCAGCGCCACCTTCCTCGGCGTGCTGTTCGTACCTATCTGTTTCGTCTGGCTGCTGTCGCTGCTGCGCAGCAAGCCGGCACCCATCGAACAGGCCGCTTCGGCCGGGGAGTGAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3000801","ARO_id":"37181","ARO_name":"MexD","ARO_description":"MexD is the multidrug inner membrane transporter of the MexCD-OprJ complex.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1584":{"model_id":"1584","model_name":"tet(41)","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"4357":{"protein_sequence":{"accession":"AAP93922.1","sequence":"MKKPMLVILLTVLLDAVGIGLIMPILPALLRSLGGLDAGSVHYGALLAAYALMQFLFSPILGALSDRFGRRPVLLISLAGAAADYLLMAFAPTLAWLYLGRLLAGITGANMAVATAYVTDITPVGQRARRFGLVGAVFGVGFIVGPLLGGSLGEWHLHAPFLAAAMMNALNLVMAFFLLPESRKSRPRAAEKIRLNPFSSLRRLHGKPGLLPLAGIYLVMALVSQAPATLWILYGQDRFGWSMMVAGLSLAGYGACHALSQAFAIGPLVARLGERKALLIGLAADAVGLALLSVATRGWAPFALLPFFAAGGMALPALQALMAHKVDDDHQGELQGTLASMGSLIGVAGPLVATALYAATRDVWPGLVWALAAALYLVVPPLLARSRARDAAP"},"dna_sequence":{"accession":"AY264780.2","fmin":"1824","fmax":"3006","strand":"-","sequence":"TTATGGCGCCGCATCCCTGGCGCGTGAGCGTGCCAGCAGCGGCGGCACCACCAGGTACAGGGCGGCGGCCAACGCCCACACCAGCCCAGGCCAGACATCGCGCGTGGCGGCATACAGCGCCGTCGCCACCAGCGGCCCCGCGACGCCGATCAGGCTGCCCATGCTGGCGAGCGTCCCTTGCAGCTCGCCCTGATGATCGTCGTCCACCTTGTGCGCCATCAGCGCCTGCAGTGCGGGCAACGCCATGCCGCCCGCGGCGAAGAACGGCAGCAGGGCGAACGGCGCCCAGCCGCGCGTGGCGACAGACAACAGCGCCAGGCCCACGGCGTCGGCGGCCAGGCCGATCAGCAGCGCCTTGCGCTCGCCGAGCCGCGCGACCAGCGGGCCGATGGCAAAGGCCTGCGACAGCGCGTGGCAGGCGCCGTAGCCGGCCAGCGACAGGCCCGCCACCATCATGCTCCAGCCGAAACGATCCTGACCGTATAAAATCCACAGCGTGGCCGGCGCCTGCGAAACCAGCGCCATAACCAGATAAATGCCGGCCAGCGGCAGCAGGCCAGGCTTGCCGTGCAGCCGGCGCAATGACGAGAAGGGATTAAGGCGAATTTTCTCGGCGGCGCGGGGGCGGGATTTACGCGATTCGGGCAGCAGGAAAAACGCCATCACCAGGTTGAGGGCATTCATCATCGCCGCCGCCAGGAAGGGCGCATGCAGATGCCATTCGCCCAGCGATCCGCCGAGCAGCGGGCCGACGATAAAGCCGACGCCGAACACCGCGCCCACCAGGCCGAAACGCCGAGCGCGCTGGCCGACGGGGGTAATATCGGTGACGTAAGCGGTGGCGACCGCCATGTTGGCGCCGGTGATGCCCGCCAGCAACCGCCCCAGATAGAGCCAGGCCAGCGTCGGCGCGAACGCCATCAGCAGGTAGTCGGCCGCCGCGCCGGCGAGCGAAATCAACAGCACCGGCCGCCGCCCGAAACGATCGCTCAGCGCGCCGAGGATCGGCGAAAACAGGAATTGCATCAACGCATAGGCCGCCAGCAGGGCGCCGTAATGCACGCTGCCGGCATCGAGACCGCCCAGCGAGCGCAACAGCGCCGGTAGAATAGGCATGATCAGACCGATGCCCACCGCATCCAGCAACACCGTCAACAAAATAACCAGCATGGGTTTTTTCAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36783","NCBI_taxonomy_name":"Serratia marcescens","NCBI_taxonomy_id":"615"}}}},"ARO_accession":"3000569","ARO_id":"36708","ARO_name":"tet(41)","ARO_description":"Tet41 is a tetracycline efflux pump found in Serratia, a Gram-negative bacterium.  It is related to Acinetobacter Tet(39).","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1524":{"model_id":"1524","model_name":"Lactobacillus reuteri cat-TC","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"688":{"protein_sequence":{"accession":"AAB53259.1","sequence":"MNFNKIDLDNWKRKEIFNHYLNQQTTFSITTEIDISVLYRNIKQEGYKFYPAFIFLVTRVINSNTAFRTGYNSDGELGYWDKLEPLYTIFDGVSKTFSGIWTSVKNDFKEFYDLYLSDVEKYNGSGKLFPKTPIPENAFSLSIIPWTSFTGFNLNINNNSNYLLPIITAGKFINKGNSIYLPLSLQVHHSVCDGYHAGLFMNSIRNCQIGLMTGFYNIDKPTVLFTVGFLMSLTCPLI"},"dna_sequence":{"accession":"U75299","fmin":"0","fmax":"717","strand":"+","sequence":"ATGAACTTTAATAAAATTGATTTAGACAATTGGAAGAGAAAAGAGATATTTAATCATTATTTGAACCAACAAACGACTTTTAGTATAACCACAGAAATTGATATTAGTGTTTTATACCGAAACATAAAACAAGAAGGATATAAATTTTACCCTGCATTTATTTTCTTAGTGACAAGGGTGATAAACTCAAATACAGCTTTTAGAACTGGTTACAATAGCGACGGAGAGTTAGGTTATTGGGATAAGTTAGAGCCACTTTATACAATTTTTGATGGTGTATCTAAAACATTCTCTGGTATTTGGACTTCTGTAAAGAATGACTTCAAAGAGTTTTATGATTTATACCTTTCTGATGTAGAGAAATATAATGGTTCGGGGAAATTGTTTCCCAAAACACCTATACCTGAAAATGCTTTTTCTCTTTCTATTATTCCATGGACTTCATTTACTGGGTTTAACTTAAATATCAATAATAATAGTAATTACCTTCTACCCATTATTACAGCAGGAAAATTCATTAATAAAGGTAATTCAATATATTTACCGCTATCTTTACAGGTACATCATTCTGTTTGTGATGGTTATCATGCAGGATTGTTTATGAACTCTATCAGGAATTGTCAGATAGGCCTAATGACTGGCTTTTATAATATAGATAAGCCGACTGTACTTTTTACAGTCGGTTTTCTAATGTCACTAACCTGCCCGTTAATTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36855","NCBI_taxonomy_name":"Lactobacillus reuteri","NCBI_taxonomy_id":"1598"}}}},"ARO_accession":"3002671","ARO_id":"39105","ARO_name":"Lactobacillus reuteri cat-TC","ARO_description":"cat-TC is a plasmid-encoded variant of the cat gene found in Lactobacillus reuteri","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. cat is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Bacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini","category_aro_class_name":"AMR Gene Family"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1622":{"model_id":"1622","model_name":"vanWG","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"535":{"protein_sequence":{"accession":"ABA71730.1","sequence":"MIEVYKLTQRKRLTQLFPFLLPLRKWQRKKYFYFKMKFDGNRYAKKTSEKLLPNTVFETSSLMLNENSGFDMKYQINKVHNLKLAAKTINKVIIEPKETFSFWQLVRWADRHEKYKDGLNLVNGKIVGSYGGGLCQLSNMLFWLFLHTPLVIVERHGHAVESFPSTTEDLPCGTDATINEGWLDLKLRNDTDNTFQIEISFDDNFMYGRILSQSSVNIEYTVFNSSVSYFKREEKVYQIASVCRTEKDKMTGSQTEKELYVNQCEIAYKLPDDVKIEERGV"},"dna_sequence":{"accession":"DQ212986","fmin":"5137","fmax":"5983","strand":"+","sequence":"GTGATTGAGGTGTATAAATTAACACAAAGAAAAAGACTAACGCAGTTGTTTCCTTTTTTGCTACCTCTCCGCAAATGGCAAAGAAAAAAATATTTTTATTTCAAAATGAAATTTGACGGCAATAGATACGCAAAAAAGACATCTGAGAAATTGTTACCAAACACAGTATTTGAAACATCATCACTTATGCTAAATGAAAATAGTGGATTTGATATGAAGTACCAAATCAATAAGGTACACAACCTAAAACTTGCCGCAAAAACAATCAATAAAGTGATTATTGAGCCGAAAGAAACATTTTCATTTTGGCAGCTTGTACGATGGGCAGACCGTCACGAGAAATATAAGGACGGATTAAATCTTGTTAATGGAAAGATTGTAGGCTCTTATGGCGGAGGTTTGTGTCAATTGAGTAATATGCTATTTTGGCTTTTTTTACACACGCCGCTTGTTATTGTCGAGCGACACGGACACGCAGTTGAGTCTTTCCCATCAACAACCGAAGATTTGCCCTGCGGTACTGATGCTACGATTAACGAAGGTTGGTTAGACCTAAAACTCCGTAACGACACGGACAATACTTTCCAGATTGAGATTAGTTTTGATGACAACTTTATGTATGGTCGAATTTTGTCGCAAAGCTCCGTAAATATTGAATATACGGTTTTTAATTCGTCTGTTTCCTATTTCAAGCGAGAGGAAAAAGTATATCAAATAGCTTCTGTTTGTCGTACAGAAAAAGACAAAATGACTGGTAGTCAGACGGAAAAAGAATTGTATGTCAACCAATGTGAAATAGCCTATAAGCTACCCGATGATGTAAAAATTGAAGAAAGAGGTGTGTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3002965","ARO_id":"39399","ARO_name":"vanWG","ARO_description":"vanWG is a vanW variant found in the vanG gene cluster","ARO_category":{"36011":{"category_aro_accession":"3000002","category_aro_cvterm_id":"36011","category_aro_name":"vanW","category_aro_description":"vanW is an accessory gene, with unknown function, found on vancomycin resistance operons.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1623":{"model_id":"1623","model_name":"GIM-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"2106":{"protein_sequence":{"accession":"AIY26289.1","sequence":"MKNVLVFLILLVALPALAQGHKPLEVIKIEDGVYLHTSFKNIEGYGLVDSNGLVVLDNNQAYIIDTPWSEEDTKLLLSWATDRGYQVMASISTHSHGDRTAGIKLLNSKSIPTYTSELTKKLLAREGKPVPTHYFKDDEFTLGNGLIELYYPGAGHTEDNIVAWLPKSKILFGGCLVRSHEWEGLGYVGDASISSWADSIKNIVSKKYPIQMVVPGHGKVGSSDILDHTIDLAESASNKLMQPTAEASAD"},"dna_sequence":{"accession":"KM659858","fmin":"401","fmax":"1154","strand":"+","sequence":"ATGAAAAATGTATTAGTGTTTTTAATATTACTTGTAGCGTTGCCAGCTTTAGCTCAGGGTCATAAACCGCTAGAAGTTATAAAAATTGAAGATGGAGTATATCTTCATACCTCCTTTAAGAATATTGAAGGCTATGGGTTAGTTGATTCGAATGGGTTGGTAGTTCTGGATAATAATCAAGCCTATATTATCGACACACCTTGGTCTGAAGAAGACACGAAGTTGTTATTATCCTGGGCGACTGACAGGGGATACCAGGTTATGGCTAGCATCTCAACTCATTCTCATGGAGATCGCACTGCTGGTATCAAGTTGCTAAATTCAAAGTCAATTCCTACATACACATCAGAGTTAACTAAAAAGCTTCTTGCCCGTGAAGGAAAGCCGGTTCCTACCCACTACTTTAAAGACGACGAATTCACACTGGGAAATGGGCTTATAGAGCTCTACTATCCAGGTGCTGGGCATACAGAGGATAATATTGTTGCTTGGTTACCCAAAAGCAAAATACTATTTGGTGGCTGCCTCGTGAGGAGTCATGAGTGGGAAGGCTTAGGTTACGTAGGCGACGCCTCAATTAGCTCTTGGGCTGACTCAATTAAAAATATTGTATCGAAAAAATATCCCATTCAAATGGTCGTTCCGGGGCATGGCAAAGTTGGAAGTTCAGATATATTAGATCACACCATTGATCTTGCTGAATCAGCTTCTAACAAATTAATGCAACCGACCGCTGAAGCGTCGGCTGATTAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3003194","ARO_id":"39771","ARO_name":"GIM-2","ARO_description":"GIM-2 is a metallo-beta-lactamase present on an integron found in clinical isolates of Enterobacter cloacae in Germany","ARO_category":{"39772":{"category_aro_accession":"3003195","category_aro_cvterm_id":"39772","category_aro_name":"GIM beta-lactamase","category_aro_description":"The GIM beta-lactamases are isolated from Pseudomonas aeruginosa. They are located in a distinct integron structure. They confers high broad spectrum resistant, including all \u00df-lactams, aminoglycosides and quinolones.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1624":{"model_id":"1624","model_name":"lmrD","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1320"}},"model_sequences":{"sequence":{"718":{"protein_sequence":{"accession":"ABF66027.1","sequence":"ENTKSTRKMSDTTRAIRFFYLYLKRYKLQFAVIMIFIILATWLQVVSPSLLGDAITNLTKYVTDFFTHQHAGQSQDALQQIAQQLSQQMHQTVDWHNVPEVVKSLPQAAQDQITANLPKGTTLETLKTVATSHAASTSTFMKGMWQLLAVYVATGVSMLIYTLLFSRIVAHSTNRMRKGLFGKLERLTISYFDRHQDGDILARFTSDLDNIQNTLNQALVSVISNAAVFVGVIIQIFNKDVTFAWLTVAASPVAILSAVIIIRQSKKATDKQQEEVSQLNAYMDEKISGQKAIIVEGLQEDSINGFLEHNENVKKRTFAAQAWSGMIFPLMNGFQLLSIAIVIFGGTAYVLNDDSMSIATGLGLLVAFVQYVQSYYNPIMQISSNFGQLQLAITGATRLNVMFDEPEEVRPENGKKFDTIKDGIQIENLDFEYLPGKPVLKKVNIDVKKGQMVALVGPTGSGKTTVMNLMNRFYDVNGGAIKFDGTDIREFDLDSLRSNVGIVLQESVLFDGTIADNIKFGKPNATQEEIETVAKTTHIHDFIDSLPDKYETHVSDDESVFSVGQKQQISIARTILTNPELLILDEATSNVDTVTEQQIQWAMEAAIAGRTSFVIAHRLKTILNADKIVVLKDGEVIEEGNHHELVAQGGFYSELYHNQFVF"},"dna_sequence":{"accession":"DQ516970","fmin":"0","fmax":"1987","strand":"+","sequence":"GAAAATACCAAATCAACAAGAAAAATGTCTGACACCACACGTGCCATCCGATTTTTTTACCTCTATCTGAAAAGATATAAACTCCAATTTGCTGTAATTATGATTTTCATCATTTTAGCAACTTGGTTACAGGTTGTTTCTCCATCACTTTTGGGGGACGCCATCACTAATTTGACTAAATATGTGACTGACTTCTTTACACATCAACATGCTGGTCAATCCCAAGATGCACTACAACAAATTGCTCAACAATTAAGCCAACAAATGCACCAAACAGTAGATTGGCACAATGTTCCTGAAGTTGTGAAATCTTTGCCACAAGCAGCACAAGACCAAATCACTGCTAATCTTCCTAAAGGAACAACTTTAGAAACACTTAAAACAGTGGCAACTTCACATGCAGCCAGCACTTCTACATTCATGAAAGGAATGTGGCAATTGCTTGCAGTCTATGTAGCAACAGGTGTATCAATGTTGATTTATACCTTGCTCTTTAGTCGTATCGTTGCTCATTCAACAAATCGCATGCGTAAAGGTTTGTTTGGTAAACTTGAACGTTTGACAATTTCATATTTTGACCGTCATCAAGATGGTGATATCCTTGCTCGTTTCACATCTGACTTGGATAACATTCAAAATACTTTAAACCAAGCACTCGTTTCGGTTATTTCAAATGCTGCGGTCTTTGTGGGTGTCATTATCCAGATTTTCAATAAAGATGTGACATTTGCTTGGTTGACAGTTGCTGCTTCTCCAGTTGCCATTTTATCTGCTGTGATTATCATTCGTCAATCGAAAAAAGCAACAGACAAACAACAAGAAGAAGTTTCACAACTTAATGCCTATATGGATGAAAAAATCTCTGGGCAAAAAGCAATTATCGTTGAAGGTTTACAAGAAGATTCTATTAATGGATTCTTGGAACACAATGAAAATGTTAAAAAACGTACCTTTGCTGCTCAAGCATGGTCTGGTATGATTTTCCCATTGATGAATGGTTTCCAACTTTTATCAATTGCCATTGTTATCTTTGGTGGAACGGCCTATGTTCTTAACGATGATAGCATGTCAATTGCCACAGGTTTAGGGCTTTTGGTTGCCTTTGTTCAATACGTTCAAAGTTACTACAACCCAATCATGCAAATTTCATCAAACTTTGGTCAACTTCAACTTGCCATCACAGGGGCAACTCGTCTGAATGTCATGTTTGATGAACCAGAAGAAGTTCGTCCTGAAAATGGTAAGAAATTTGATACGATTAAAGACGGAATTCAAATCGAAAATCTTGATTTTGAATATCTTCCAGGAAAACCAGTCCTCAAAAAAGTTAATATTGATGTTAAAAAAGGACAAATGGTTGCCCTCGTTGGTCCAACTGGTTCAGGTAAAACAACAGTTATGAACTTGATGAACCGTTTCTACGATGTTAATGGTGGAGCAATTAAATTTGATGGAACTGATATTCGTGAATTTGATTTAGATAGCTTGCGTTCAAATGTCGGAATTGTTTTGCAAGAGTCTGTTCTCTTTGATGGAACGATTGCTGATAATATCAAGTTTGGTAAACCAAATGCTACTCAAGAAGAAATTGAAACAGTGGCTAAGACAACTCACATTCATGATTTCATTGATAGCTTACCTGACAAGTACGAAACACATGTTTCAGATGATGAATCAGTCTTCTCAGTTGGTCAAAAACAACAAATTTCTATCGCACGTACCATTTTGACAAATCCAGAACTTTTGATTTTGGATGAAGCAACTTCAAATGTGGATACAGTAACTGAACAACAAATTCAATGGGCGATGGAAGCTGCTATTGCTGGTCGTACTTCATTCGTTATTGCTCACCGTTTGAAAACAATTCTTAATGCAGATAAGATTGTTGTTCTTAAAGATGGTGAAGTTATCGAAGAAGGAAATCACCATGAACTTGTTGCTCAAGGTGGCTTCTACTCTGAACTTTATCACAATCAATTTGTTTTTG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39574","NCBI_taxonomy_name":"Lactococcus lactis subsp. lactis","NCBI_taxonomy_id":"1360"}}}},"ARO_accession":"3002882","ARO_id":"39316","ARO_name":"lmrD","ARO_description":"lmrD is a chromosomally-encoded efflux pump that confers resistance to lincosamides in Streptomyces lincolnensis and Lactococcus lactis. It can dimerize with lmrC","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1625":{"model_id":"1625","model_name":"OXA-179","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1126":{"protein_sequence":{"accession":"ADM26744.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIAVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"HM570035","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCCCTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTCTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTGCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001473","ARO_id":"37873","ARO_name":"OXA-179","ARO_description":"OXA-179 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1626":{"model_id":"1626","model_name":"vgaE","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1020"}},"model_sequences":{"sequence":{"562":{"protein_sequence":{"accession":"CBY88983.1","sequence":"MLLFEGTSLKKHIQDRLLFDIDLIQVHEHQRIGLVGRNGTGKTSLLKIITGEELVDGGNVNHFTSVKLVPQFKETRSEKSGGEITQQYLQLAFNEKPGLLILDEPTTHLDTQRIDWLEKKLANYQGAFVVVSHDRTFLNNVCTEIWEIEDGSLNAFKGDYNAYAEQKELIKTQQQIAFEKYEREKKQLEKAIRQKEERAQRATKKPKNLSSSEARITGAKTHYANIQKKLRGSAKALETRLEQLDRIDKVKELPEIKMDILNKESLTNQSVLRAENIKGEVDGRKLWNPFSLYLYGGDKVAIIGKNGTGKTTLLKKIVERDERIAIPEKVRIGYFSQHLTILDDDKTIIENIQLTSSQDETLIRTVLARMHFWDEDVYKKVGILSGGEKVKVALAKLFLSDVNMLVLDEPTNFLDIESLEALETLMKSYHGTILFVTHDRTLVTNIATKIIDIKDGKITVFDGSYEAYEEWLENQTKSNNDDQLLLIETKISDVLGRLSLEPSRELEDEFQRLLKEKKELTKKL"},"dna_sequence":{"accession":"FR772051","fmin":"8740","fmax":"10315","strand":"+","sequence":"ATGTTATTATTTGAAGGTACATCATTGAAAAAACACATACAAGACAGATTATTATTTGATATAGATTTAATACAAGTACATGAACATCAGCGAATAGGATTAGTAGGTAGGAATGGAACGGGGAAAACAAGTCTATTAAAAATTATTACAGGTGAAGAACTAGTTGATGGAGGGAATGTTAATCATTTTACCTCTGTAAAATTAGTACCACAATTTAAAGAAACAAGATCGGAGAAAAGTGGTGGAGAAATAACGCAACAATATTTGCAATTAGCATTTAATGAAAAGCCAGGATTATTAATTTTAGATGAACCAACGACTCATTTAGATACACAAAGAATTGATTGGTTAGAAAAGAAATTAGCAAACTATCAAGGAGCATTTGTTGTCGTATCACATGATCGGACATTTCTAAATAATGTGTGTACTGAAATATGGGAAATAGAAGATGGTAGTCTAAACGCGTTTAAAGGGGATTATAATGCTTATGCGGAACAAAAGGAATTAATAAAAACACAGCAGCAGATTGCATTTGAAAAGTACGAACGAGAGAAAAAGCAATTAGAAAAAGCAATACGACAAAAAGAGGAAAGAGCACAGCGAGCAACAAAGAAACCTAAAAATCTGAGTTCTTCAGAGGCAAGAATAACAGGAGCTAAAACCCATTATGCCAATATACAGAAAAAGTTGAGGGGTTCTGCAAAAGCATTAGAAACAAGGTTGGAACAACTGGATAGGATTGACAAGGTGAAAGAACTACCTGAAATTAAGATGGATATATTAAATAAAGAAAGTCTAACAAACCAGTCTGTGTTACGCGCTGAAAACATTAAGGGAGAGGTTGACGGACGTAAGCTTTGGAATCCCTTTAGTTTATATTTATATGGCGGCGATAAAGTTGCTATCATTGGGAAAAATGGCACGGGTAAAACAACCTTACTTAAAAAAATAGTTGAGCGAGATGAAAGAATAGCAATCCCAGAAAAGGTGAGGATAGGTTATTTTTCCCAACACCTCACAATTCTCGATGATGATAAAACAATCATAGAAAATATACAATTGACCTCTAGTCAGGATGAAACATTAATTAGAACAGTTTTAGCAAGAATGCATTTTTGGGATGAAGATGTCTATAAAAAGGTCGGCATATTAAGTGGTGGTGAAAAAGTAAAAGTAGCACTAGCTAAACTATTCTTAAGTGACGTGAATATGCTGGTGTTAGATGAACCTACAAATTTTTTAGATATTGAATCTTTAGAAGCGCTAGAAACATTAATGAAAAGTTATCATGGAACGATTCTATTTGTTACTCACGACCGAACGTTAGTAACAAATATAGCTACAAAAATAATTGATATAAAAGATGGTAAGATAACAGTATTCGATGGATCATACGAAGCATATGAAGAGTGGTTAGAGAATCAAACAAAGTCCAACAATGATGATCAACTTTTACTAATCGAAACTAAAATATCTGACGTTCTGGGTAGGTTGAGTTTGGAGCCTTCACGAGAGTTAGAAGATGAATTTCAAAGATTATTGAAAGAAAAGAAAGAACTGACTAAAAAACTATAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35536","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus ST398","NCBI_taxonomy_id":"523796"}}}},"ARO_accession":"3002833","ARO_id":"39267","ARO_name":"vgaE","ARO_description":"vgaE is an efflux protein expressed in staphylococci that confers resistance to streptogramin A antibiotics and related compounds. It is associated with transposon DNA.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37716":{"category_aro_accession":"3001317","category_aro_cvterm_id":"37716","category_aro_name":"pleuromutilin","category_aro_description":"Pleuromutilin is a natural product antibiotic produced by Clitopilus passeckerianus. Related antibiotics of clinical significance, such as tiamulin and retapamulin, are semi-synthetic derivatives of this compound.","category_aro_class_name":"Antibiotic"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1627":{"model_id":"1627","model_name":"CTX-M-95","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"869":{"protein_sequence":{"accession":"CBL80615.1","sequence":"MMTQSIRRSMLTVMATLPLLFSSATLHAQTNSVQQQLEALEKSSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAALLKQSESDKHLLNQRVEIKKSDLVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSASIQAGLPKSWVVGDKTGSGDYGTTNDIAVIWPENHAPLVLVTYFTQPEQKAESRRDVLAAAAKIVTHGF"},"dna_sequence":{"accession":"FN813245","fmin":"1911","fmax":"2787","strand":"+","sequence":"ATGATGACTCAGAGCATTCGCCGCTCAATGTTAACGGTGATGGCGACGCTACCCCTGCTATTTAGCAGCGCAACGCTGCATGCGCAAACGAACAGCGTGCAACAGCAGCTGGAAGCCCTGGAGAAAAGTTCGGGAGGTCGGCTTGGCGTTGCGCTGATTAACACCGCCGATAATTCGCAGATTCTCTACCGTGCCGATGAACGTTTTGCGATGTGCAGTACCAGTAAGGTGATGGCGGCCGCGGCGTTGCTTAAACAGAGCGAGAGCGATAAGCACCTGCTAAATCAGCGCGTTGAAATCAAGAAGAGCGACCTGGTTAACTACAATCCCATTGCGGAGAAACACGTTAACGGCACGATGACGCTGGCTGAGCTTGGCGCAGCGGCGCTGCAGTATAGCGACAATACTGCCATGAATAAGCTGATTGCCCATCTGGGTGGGCCCGATAAAGTGACGGCGTTTGCTCGCTCGTTGGGTGATGAGACCTTCCGTCTGGACAGAACCGAGCCCACGCTCAATACCGCCATTCCAGGCGACCCGCGTGATACTACCACGCCGCTCGCGATGGCGCAGACCCTGAAAAATCTGACGCTGGGTAAAGCGCTGGCGGAAACCCAGCGGGCACAGTTGGTGACGTGGCTTAAGGGCAATACTACCGGTAGCGCGAGCATTCAGGCGGGTCTGCCGAAATCATGGGTAGTGGGCGATAAAACCGGCAGCGGAGATTATGGCACCACCAACGATATCGCGGTTATCTGGCCGGAAAACCACGCACCGCTGGTTCTGGTGACCTACTTTACCCAACCGGAGCAGAAGGCGGAAAGCCGTCGGGATGTTCTGGCTGCGGCAGCGAAAATCGTAACCCACGGTTTCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36928","NCBI_taxonomy_name":"Kluyvera ascorbata","NCBI_taxonomy_id":"51288"}}}},"ARO_accession":"3001955","ARO_id":"38355","ARO_name":"CTX-M-95","ARO_description":"CTX-M-95 is a beta-lactamase found in Kluyvera spp.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1628":{"model_id":"1628","model_name":"SHV-154","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1389":{"protein_sequence":{"accession":"AFQ23960.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGSVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASKRGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"JX121121","fmin":"0","fmax":"858","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCAGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCAAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGGATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001193","ARO_id":"37573","ARO_name":"SHV-154","ARO_description":"SHV-154 is a beta-lactamase.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1629":{"model_id":"1629","model_name":"TEM-197","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1493":{"protein_sequence":{"accession":"AEK48085.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"HQ877606","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001056","ARO_id":"37436","ARO_name":"TEM-197","ARO_description":"TEM-197 is an extended-spectrum beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1630":{"model_id":"1630","model_name":"IMP-13","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1906":{"protein_sequence":{"accession":"CAD80251.1","sequence":"MKKLFVLCVCFFCSITAAGAALPDLKIEKLEEGVFVHTSFEEVNGWGVVTKHGLVVLVNTDAYLIDTPFTATDTEKLVNWFVERGYEIKGTISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKSGKVQAKYSFSEVSYWLVKNKIEVFYPGPGHTQDNLVVWLPESKILFGGCFIKPHGLGNLGDANLEAWPKSAKILMSKYGKAKLVVSSHSEKGDASLMKRTWEQALKGLKESKKTSSPSN"},"dna_sequence":{"accession":"AJ550807","fmin":"2242","fmax":"2983","strand":"+","sequence":"ATGAAGAAATTATTTGTTTTATGTGTATGCTTCTTTTGTAGCATTACTGCCGCAGGAGCGGCTTTACCTGATTTAAAAATCGAGAAGCTTGAAGAAGGTGTTTTTGTTCATACATCGTTCGAAGAGGTTAACGGTTGGGGGGTTGTTACTAAACACGGTTTAGTGGTGCTTGTAAACACAGACGCCTATCTAATTGACACTCCATTTACTGCTACAGACACTGAAAAATTAGTCAATTGGTTTGTGGAGCGCGGCTATGAAATCAAAGGCACTATTTCATCACATTTCCATAGCGACAGCACAGGAGGAATAGAGTGGCTTAATTCTCAATCTATTCCCACGTATGCATCTGAATTAACAAATGAACTTTTGAAAAAATCCGGTAAGGTACAAGCTAAATATTCATTTAGCGAAGTTAGCTATTGGCTAGTTAAAAATAAAATTGAAGTTTTCTACCCTGGCCCAGGTCACACTCAAGATAACCTAGTGGTTTGGTTGCCTGAAAGTAAAATTTTATTCGGTGGTTGCTTTATTAAACCTCACGGTCTTGGCAATTTAGGTGACGCAAATTTAGAAGCTTGGCCAAAGTCCGCCAAAATATTAATGTCTAAATATGGCAAAGCAAAGCTTGTTGTTTCAAGTCATAGTGAAAAAGGGGACGCATCACTAATGAAACGTACATGGGAACAAGCCCTTAAAGGGCTTAAAGAAAGTAAAAAAACATCATCACCAAGTAACTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002204","ARO_id":"38604","ARO_name":"IMP-13","ARO_description":"IMP-13 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1631":{"model_id":"1631","model_name":"CTX-M-71","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1513":{"protein_sequence":{"accession":"ACV92002.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSCGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"FJ815436","fmin":"195","fmax":"1071","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCTGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001932","ARO_id":"38332","ARO_name":"CTX-M-71","ARO_description":"CTX-M-71 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1632":{"model_id":"1632","model_name":"CTX-M-53","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1412":{"protein_sequence":{"accession":"ABB72225.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTVDVQQKLAELEQQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAVAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVIYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"DQ268764","fmin":"5891","fmax":"6767","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGTGGACGTACAGCAAAAACTTGCCGAATTAGAGCAGCAGTCGGGAGGAAGGCTGGGTGTGGCATTGATTAACACGGCGGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGTGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTCGAGATCAAAAAATCTGACCTGGTTAACTATAATCCGATTGCGGAAAAACACGTCAATGGGACGATGTCACTGGCTGAGCTCAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTTACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCTGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACGCTGCGTAATCTGACGCTGGGTAAAGCATTGGGTGACAGCCAACGGGCGCAGCTGGTGACGTGGATGAAAGGCAATACTACCGGTGCAGCGAGTATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGTACCACCAACGATATCGCGGTGATTTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCATTTACTTCACCCAGCCCCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAGC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35809","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Westhampton","NCBI_taxonomy_id":"356621"}}}},"ARO_accession":"3001915","ARO_id":"38315","ARO_name":"CTX-M-53","ARO_description":"CTX-M-53 is a beta-lactamase found in Salmonella enterica","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1633":{"model_id":"1633","model_name":"catQ","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"607":{"protein_sequence":{"accession":"AAA23215.1","sequence":"MKFNLIDIEDWNRKPYFEHYLNAVRCTYSMTANIEITGLLREIKLKGLKLYPTLIYIITTVVNRHKEFRTCFDQKGKLGYWDSMNPSYTVFHKDNETFSSIWTEYDENFPRFYYNYLEDIRNYSDVLNFMPKTGEPANTINVSSIPWVNFTGFNLNIYNDATYLIPIFTLGKYFQQDNKILLPMSVQVHHAVCDGYHISRFFNEAQELASNYETWLGEK"},"dna_sequence":{"accession":"M55620","fmin":"0","fmax":"660","strand":"+","sequence":"ATGAAATTTAATTTGATAGATATTGAGGATTGGAATAGAAAGCCATACTTTGAGCATTATTTAAATGCGGTTAGGTGCACTTACAGTATGACTGCAAATATAGAGATAACTGGTTTACTGCGTGAAATTAAACTTAAGGGCCTGAAACTGTACCCTACGCTTATTTATATCATCACAACTGTGGTTAACCGTCACAAGGAGTTCCGCACCTGTTTTGATCAAAAAGGTAAGTTAGGATACTGGGATAGTATGAACCCAAGTTATACTGTCTTTCATAAGGATAACGAAACTTTTTCAAGTATTTGGACAGAGTATGACGAGAACTTCCCACGTTTTTACTATAATTACCTTGAGGATATTAGAAACTATAGCGACGTTTTGAATTTCATGCCTAAGACAGGTGAACCTGCTAATACAATTAATGTGTCCAGCATTCCTTGGGTGAATTTTACCGGATTCAACCTGAATATATACAATGATGCAACATATCTAATCCCTATTTTTACTTTGGGTAAGTATTTTCAGCAGGATAATAAAATTTTATTACCTATGTCTGTACAGGTGCATCATGCGGTTTGCGACGGTTATCATATAAGCAGATTTTTTAATGAGGCACAGGAATTAGCGTCAAATTATGAGACATGGTTAGGAGAAAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36812","NCBI_taxonomy_name":"Clostridium perfringens","NCBI_taxonomy_id":"1502"}}}},"ARO_accession":"3002687","ARO_id":"39121","ARO_name":"catQ","ARO_description":"catQ is a chromosome-encoded variant of the cat gene found in Clostridium perfringens","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. cat is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Bacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini","category_aro_class_name":"AMR Gene Family"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1634":{"model_id":"1634","model_name":"CMY-78","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1817":{"protein_sequence":{"accession":"AFK73443.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPGDVTDKAELLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVKSSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYLEGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"JQ733575","fmin":"1027","fmax":"2173","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCGCTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGGTGACGTTACGGATAAAGCCGAATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGCGGTGAAATCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAACTATGCCTGGGGCTATCTCGAAGGGAAGCCTGTGCACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACAGGATCCACAGGCGGATTTGGCAGCTACGTTGCTTTCGTTCCAGAAAAAAACCTTGGCATCGTAATGTTGGCAAACAAAAGCTACCCCAACCCGGCTCGCGTCGAGGCGGCCTGGCGCATTCTTGAAAAACTGCAATAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002091","ARO_id":"38491","ARO_name":"CMY-78","ARO_description":"CMY-78 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1635":{"model_id":"1635","model_name":"vanRG","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"246":{"protein_sequence":{"accession":"ABA71727.1","sequence":"MNEKILIVDDEKEIADLIELYLKNDGYKVYKFYNGIDALKCVESEKMDLAILDVMLPDVDGFHICQKIRERYFYPIIMLTAKVEDADKIMGLTIGADDYITKPFNPLEVAARVKTQLRRYVCYNNAADIEKENVLVTEYDINGLVINKNTHKCTLYGKAVTLTPIEFSVLWYLCENRGKVISSEELFENVWGEKFLDNNNTVMAHIGRLREKLKEPARNPKFIKTVWGVGYTIEE"},"dna_sequence":{"accession":"DQ212986","fmin":"2258","fmax":"2966","strand":"+","sequence":"ATGAATGAAAAGATTTTAATTGTTGATGATGAAAAAGAGATAGCAGATTTAATTGAGCTTTATCTGAAAAATGACGGTTATAAAGTGTATAAATTTTACAATGGTATAGACGCATTAAAATGTGTGGAATCAGAAAAAATGGATTTGGCAATTTTAGATGTTATGCTTCCTGATGTCGATGGTTTCCATATCTGTCAAAAGATTCGGGAACGATATTTTTATCCAATTATTATGCTGACGGCAAAGGTAGAAGATGCTGATAAGATTATGGGGCTGACGATTGGAGCGGATGATTATATTACAAAGCCATTTAATCCACTAGAGGTTGCTGCAAGGGTCAAGACACAGCTTCGCCGTTATGTATGTTACAATAATGCCGCAGATATAGAAAAAGAAAATGTATTGGTTACGGAATATGATATTAACGGACTTGTCATTAATAAGAATACTCATAAATGCACACTGTATGGAAAGGCAGTCACATTAACCCCGATAGAATTTTCTGTTCTTTGGTATTTGTGTGAAAATAGGGGAAAAGTGATTTCTTCAGAGGAACTTTTTGAAAATGTCTGGGGCGAGAAATTCCTTGATAATAATAATACAGTTATGGCTCATATCGGGAGGTTACGGGAAAAATTGAAAGAACCTGCCAGAAATCCGAAATTTATAAAAACCGTATGGGGAGTGGGATATACCATTGAAGAATGAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3002926","ARO_id":"39360","ARO_name":"vanRG","ARO_description":"vanRG is a vanR variant found in the vanG gene cluster","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36713":{"category_aro_accession":"3000574","category_aro_cvterm_id":"36713","category_aro_name":"vanR","category_aro_description":"VanR is a OmpR-family transcriptional activator in the VanSR regulatory system. When activated by VanS, it promotes cotranscription of VanA, VanH, and VanX.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1636":{"model_id":"1636","model_name":"QnrB57","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"485":{"protein_sequence":{"accession":"AFR46588.1","sequence":"MTPLLYKKTGTNMALALVGEKIDRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNASALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGNLDIRGVDLQGVKLDNYQASLLMERLGIAIIG"},"dna_sequence":{"accession":"JX259318","fmin":"0","fmax":"681","strand":"+","sequence":"ATGACGCCATTACTGTATAAAAAAACAGGTACAAATATGGCTCTGGCACTCGTTGGCGAAAAAATTGACAGAAACCGCTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCGATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATGCCAGTGCGCTTGGCATTGAAATTCGCCACTGTCGTGCGCAAGGCGCAGATTTCCGCGGCGCAAGCTTTATGAATATGATCACTACTCGCACCTGGTTTTGCAGCGCATATATCACTAACACAAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAATGTGAGCTGTGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTTTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTAACTTAGATATTCGGGGCGTTGATTTACAAGGCGTTAAGTTGGACAACTACCAGGCATCGCTGCTCATGGAACGTCTTGGCATCGCGATTATTGGCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002770","ARO_id":"39204","ARO_name":"QnrB57","ARO_description":"QnrB57 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1637":{"model_id":"1637","model_name":"MOX-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1446":{"protein_sequence":{"accession":"ACS44785.1","sequence":"MQQRQSILWGALATLMWAGLVHAGDKAATDPLRPVVDASIRPLLKEHRIPGMAVAVLKDGKAHYFNYGVADRERAVGVSEQTLFEIGSVSKTLTATLGAYAVVQGSFELDDKASLFAPWLKGSVFDNITMGELATYSAGGLPLQFPEEVDSLEKMQAYYRQWTPAYSPGSHRQYANPSIGLFGYLAASSMKQPFDRLMEQTMLPGLGLYHTYLTVPEQAMGHYAYGYSKEDKPIRVTPGMLADEAYGIKTSSADLLRFVKANIGGVDNAAMQQAIDLTHQGQYAVGEMTQGLGWERYAYPVSEQTLLAGNSPAMIYNAIPAVPAPAAAGHPVLFNKTGSTNGFGAYVAFVPAKGIGIVMLANRNSPIEARIKAAHAILTQLAR"},"dna_sequence":{"accession":"GQ152602","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCAACAACGACAATCCATCCTGTGGGGCGCTCTGGCCACCTTGATGTGGGCCGGCTTGGTTCATGCCGGTGACAAGGCGGCGACCGATCCCCTGCGCCCCGTGGTGGATGCCAGCATCCGGCCGCTGCTCAAGGAGCACAGGATCCCGGGCATGGCGGTGGCCGTGCTCAAGGATGGCAAGGCCCACTATTTCAACTACGGTGTGGCCGATCGGGAGCGCGCAGTCGGTGTCAGCGAGCAGACCCTGTTCGAGATAGGTTCCGTGAGCAAGACCCTGACCGCGACGCTGGGGGCCTACGCCGTGGTGCAGGGGAGCTTCGAGCTCGATGACAAGGCGAGTCTGTTCGCCCCCTGGCTCAAGGGATCCGTCTTTGACAACATCACCATGGGGGAGCTGGCTACCTACAGCGCAGGCGGCTTGCCGCTGCAATTCCCCGAGGAGGTGGATTCGCTCGAGAAGATGCAGGCCTACTACCGCCAGTGGACTCCAGCCTACTCGCCGGGTTCCCATCGCCAGTACGCCAACCCCAGCATCGGGCTCTTTGGCTATCTGGCGGCGAGCAGCATGAAGCAGCCGTTCGATCGCCTGATGGAGCAGACGATGCTGCCGGGGCTAGGCCTGTACCATACTTACCTCACTGTGCCCGAGCAGGCCATGGGGCACTACGCCTACGGCTACTCGAAGGAGGACAAGCCGATCCGCGTCACTCCCGGCATGCTGGCGGACGAGGCCTACGGCATCAAGACCAGTTCGGCGGATCTGCTGCGCTTTGTGAAGGCGAACATCGGCGGGGTGGATAATGCGGCCATGCAGCAGGCCATCGACCTGACTCACCAGGGCCAGTATGCGGTGGGGGAGATGACCCAGGGACTGGGCTGGGAGCGTTACGCCTATCCCGTCAGCGAGCAGACGCTGCTGGCGGGCAACTCCCCGGCGATGATTTACAATGCCATCCCGGCTGTGCCCGCGCCCGCTGCGGCAGGCCACCCTGTGCTTTTCAACAAGACCGGCTCGACCAATGGCTTCGGGGCTTATGTGGCCTTCGTGCCGGCCAAAGGGATCGGCATCGTCATGCTGGCCAATCGCAACTCTCCCATCGAGGCGCGCATCAAGGCGGCTCACGCAATCCTGACGCAACTGGCCAGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36936","NCBI_taxonomy_name":"Aeromonas caviae","NCBI_taxonomy_id":"648"}}}},"ARO_accession":"3002189","ARO_id":"38589","ARO_name":"MOX-7","ARO_description":"MOX-7 is a beta-lactamase. From the Lahey list of MOX beta-lactamases.","ARO_category":{"36222":{"category_aro_accession":"3000083","category_aro_cvterm_id":"36222","category_aro_name":"MOX beta-lactamase","category_aro_description":"MOX beta-lactamases are plasmid-mediated AmpC-type beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1638":{"model_id":"1638","model_name":"CMY-111","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1992":{"protein_sequence":{"accession":"AHW47897.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDVEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"KJ155695","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGTCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36783","NCBI_taxonomy_name":"Serratia marcescens","NCBI_taxonomy_id":"615"}}}},"ARO_accession":"3002122","ARO_id":"38522","ARO_name":"CMY-111","ARO_description":"CMY-111 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1639":{"model_id":"1639","model_name":"SHV-84","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1395":{"protein_sequence":{"accession":"CAJ32371.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADRTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIG"},"dna_sequence":{"accession":"AM087453","fmin":"25","fmax":"856","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAGGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCAGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001138","ARO_id":"37518","ARO_name":"SHV-84","ARO_description":"SHV-84 is an inhibitor-resistant beta-lactamase that has been found in clinical isolates.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1640":{"model_id":"1640","model_name":"MIR-14","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"1425":{"protein_sequence":{"accession":"AIT76117.1","sequence":"MMTKSLSCALLLSVASSAFAAPMSEKQLAEVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIHMLELATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAMTTRIFKPLNLNHTWINVPKTEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMVNMKPDSLQDSSLRKGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVEGSDNKVALAPLPAREVNPPAPLVNASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"KM087864","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGACAAAATCCCTAAGCTGTGCCCTGCTGCTCAGCGTTGCCAGCTCTGCATTCGCCGCACCGATGTCCGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAAAGCGCAGGCCATTCCGGGCATGGCGGTGGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCAAACAAACCCGTCACCCCACAAACCTTGTTCGAACTGGGTTCTATAAGTAAAACCTTCACCGGCGTACTGGGTGGCGATGCCATTGCTCGCGGTGAAATATCGCTCGGCGATCCGGTGACAAAATACTGGCCTGAACTGACGGGCAAGCAGTGGCAGGGCATTCACATGCTGGAGCTGGCAACCTATACCGCAGGCGGTCTGCCGTTACAGGTACCGGATGAGGTCACGGATAACGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCCAATGCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTTAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGAATCTTTAAGCCGCTCAATCTGAACCATACCTGGATTAACGTTCCGAAAACGGAAGAGGCGCATTACGCCTGGGGATACCGCGACGGTAAAGCGGTCCACGTTTCGCCAGGAATGCTGGATGCAGAAGCCTATGGCGTAAAAACCAACGTGCAGGATATGGCAAGCTGGGTGATGGTCAACATGAAGCCGGACTCGCTTCAGGATAGTTCACTCAGGAAAGGCATTGCCCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCCATGTATCAAGGGTTAGGTTGGGAAATGCTTAACTGGCCGGTCGATGCCAAAACCGTGGTTGAAGGCAGCGACAATAAGGTGGCGCTGGCACCGCTGCCTGCGAGAGAAGTGAATCCACCGGCACCGCTGGTCAACGCGTCCTGGGTCCATAAAACAGGCTCAACCGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAACAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCTGCCCGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36926","NCBI_taxonomy_name":"Enterobacter asburiae","NCBI_taxonomy_id":"61645"}}}},"ARO_accession":"3002179","ARO_id":"38579","ARO_name":"MIR-14","ARO_description":"MIR-14 is a beta-lactamase. From the Lahey list of MIR beta-lactamases.","ARO_category":{"36197":{"category_aro_accession":"3000058","category_aro_cvterm_id":"36197","category_aro_name":"MIR beta-lactamase","category_aro_description":"MIR beta-lactamases are plasmid-mediated beta-lactamases that confer resistance to oxyimino- and alpha-methoxy beta-lactams","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1641":{"model_id":"1641","model_name":"OXA-203","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1527":{"protein_sequence":{"accession":"ADX07748.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"HQ998857","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGTTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCATTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001664","ARO_id":"38064","ARO_name":"OXA-203","ARO_description":"OXA-203 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1642":{"model_id":"1642","model_name":"clbC","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"4249":{"protein_sequence":{"accession":"BAD63613.1","sequence":"MKVVNHATKYERLKHFLNALNEPTYRYKQITEAIFKHRIGAFNKMTTLPKALRESLINEFGPSILTVEPVLETTSQQVTKVLLKVAGNNQVEAVRMHYEAGWESFCISSQCGCGLGCTFCSTGAIGLKQNLSADEMTDQLLYFYLKGHSLDSVSFMGMGEALANVRIFDALNVLVDRQLFALSPRRITVSTVGIIPNIQRMTSSFPQMNLTFSLHSPFHDQRSELMPINNKYPLDQVMNVLDQHIHETGRKVYIAYVMLRGVNDSEKHAEALVKRILNNRYPHLYHVNLIRYNPTVGTPENYGQTIEEKLQTFYRVVKSARIPVTIRSQFGREIDAACGQLYGQYQAKKR"},"dna_sequence":{"accession":"AP006627.1","fmin":"1162417","fmax":"1163470","strand":"+","sequence":"ATGAAAGTTGTCAATCATGCGACAAAATACGAACGATTAAAACATTTTTTGAATGCTTTAAATGAACCAACGTACCGGTATAAACAGATTACTGAAGCGATTTTCAAACATCGTATTGGTGCGTTTAATAAAATGACCACATTGCCAAAAGCACTGAGAGAATCGCTCATAAACGAATTTGGTCCTTCCATCCTTACAGTAGAGCCGGTGCTAGAAACAACGTCTCAACAAGTCACTAAAGTGTTGCTAAAAGTAGCGGGAAACAATCAAGTGGAAGCCGTAAGAATGCATTATGAAGCAGGGTGGGAGTCGTTTTGCATTTCTTCTCAATGTGGCTGTGGGTTAGGGTGTACGTTTTGTTCGACAGGAGCCATTGGGTTAAAACAAAACTTATCAGCAGACGAGATGACAGACCAGTTGCTCTATTTTTATCTGAAGGGGCATTCCTTAGATAGTGTCTCTTTTATGGGCATGGGCGAAGCGCTAGCCAATGTAAGGATATTTGATGCTTTGAATGTGCTTGTCGATCGGCAACTATTTGCATTAAGTCCTAGAAGAATAACGGTCTCTACGGTTGGCATCATACCAAACATCCAAAGAATGACTAGCAGCTTTCCTCAGATGAACCTAACGTTTTCACTGCACTCTCCTTTTCATGATCAGCGCAGCGAGTTGATGCCGATTAACAACAAGTACCCGTTAGACCAGGTAATGAATGTATTGGATCAGCATATTCACGAGACAGGGAGAAAAGTATATATTGCTTATGTCATGCTTCGGGGTGTCAATGATTCGGAGAAACATGCAGAAGCACTTGTTAAACGGATTCTAAACAATCGCTATCCCCATCTCTATCATGTCAATTTGATTCGCTACAATCCGACTGTGGGTACGCCTGAAAACTATGGCCAAACCATAGAAGAGAAACTGCAAACTTTTTACCGTGTCGTAAAATCAGCTCGAATTCCTGTAACGATTCGGAGTCAATTTGGAAGAGAAATTGATGCCGCCTGCGGCCAATTATATGGTCAGTATCAGGCGAAAAAAAGGTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39605","NCBI_taxonomy_name":"Bacillus clausii KSM-K16","NCBI_taxonomy_id":"66692"}}}},"ARO_accession":"3002816","ARO_id":"39250","ARO_name":"clbC","ARO_description":"clbC is a plasmid-encoded cfr gene found in Bacillus clausii","ARO_category":{"36341":{"category_aro_accession":"3000202","category_aro_cvterm_id":"36341","category_aro_name":"Cfr 23S ribosomal RNA methyltransferase","category_aro_description":"Cfr genes produce enzymes which catalyze the methylation of the 23S rRNA subunit at position 8 of adenine-2503. Methylation of 23S rRNA at this site confers resistance to some classes of antibiotics, including streptogramins, chloramphenicols, florfenicols, linezolids and clindamycin.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"35989":{"category_aro_accession":"0000072","category_aro_cvterm_id":"35989","category_aro_name":"linezolid","category_aro_description":"Linezolid is a synthetic antibiotic used for the treatment of serious infections caused by Gram-positive bacteria that are resistant to several other antibiotics. It inhibits protein synthesis by binding to domain V of the 23S rRNA of the 50S subunit of bacterial ribosomes.","category_aro_class_name":"Antibiotic"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37015":{"category_aro_accession":"3000671","category_aro_cvterm_id":"37015","category_aro_name":"tiamulin","category_aro_description":"Tiamulin is a pleuromutilin derivative currently used in veterinary medicine. It binds to the 23 rRNA of the 50S ribosomal subunit to inhibit protein translation.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"36218":{"category_aro_accession":"3000079","category_aro_cvterm_id":"36218","category_aro_name":"oxazolidinone antibiotic","category_aro_description":"Oxazolidinones are a class of synthetic antibiotics discovered the the 1980's.  They inhibit protein synthesis by binding to domain V of the 23S rRNA of the 50S subunit of bacterial ribosomes.  Linezolid is the only member of this class currently in clinical use.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1643":{"model_id":"1643","model_name":"arnA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1200"}},"model_sequences":{"sequence":{"3373":{"protein_sequence":{"accession":"NP_252244","sequence":"MTSKAVVFAYHDIGCTGIEALLNAGYEIAAVFTHADDPRENTFYASVARLCAERGIPLHAPEDVNHPLWLERIRQLRPDFLFSFYYRRLLGAELLACAARGAYNLHGSLLPRYRGRAPANWVLVNGETQTGVTLHRMIERADAGPILAQQAVAIDPEDTALSLHGKLRKAAGALLRDSLPLLALGVLPEVEQDESQASHFGRRTPADGLLDWHRPARQLYDLVRAVTQPYPGAFCQVGEQKLIVWSAEVVAGNHGREPGSVLSCDPLRIACGEDSLVLRFGQRGERGLYLAGTQLATELGLVEGARLRGAACSPQRRTRVLILGVNGFIGNHLSERLLRDGRYEVHGMDIGSDAIERLKADPHFHFVEGDIGIHSEWLEYHVKKCDVILPLVAIATPIEYTRNPLRVFELDFEENLRIVRYCVKYGKRVVFPSTSEVYGMCQDPDFDEDRSNLVVGPINKQRWIYSVSKQLLDRVIWAYGQQGLRFTLFRPFNWMGPRLDRLDSARIGSSRAITQLILHLVEGTPIRLVDGGAQKRCFTDVDDGIEALARIIDNRDGRCDGQIVNIGNPDNEASIRQLGEELLRQFEAHPLRAQFPPFAGFREVESRSFYGDGYQDVAHRKPSIDNARRLLDWQPTIELRETIGKTLDFFLHEALREREAQA"},"dna_sequence":{"accession":"NC_002516.2","fmin":"3982020","fmax":"3984009","strand":"+","sequence":"ATGACCTCGAAAGCCGTCGTCTTCGCCTACCACGACATCGGTTGCACCGGTATCGAAGCCCTGCTCAATGCCGGCTACGAGATCGCCGCCGTCTTCACCCATGCCGACGACCCACGGGAAAACACCTTCTACGCCTCGGTCGCACGCCTCTGCGCCGAGCGCGGCATTCCGCTGCACGCGCCCGAGGACGTGAACCATCCGCTGTGGCTGGAGCGTATCCGCCAACTGCGCCCGGACTTCCTGTTCTCCTTCTACTACCGCCGCCTGCTCGGCGCCGAGCTGCTCGCCTGCGCCGCACGCGGCGCCTACAACCTGCACGGTTCGCTGCTGCCGCGCTACCGCGGACGCGCCCCGGCGAACTGGGTGCTGGTCAACGGCGAAACGCAGACCGGGGTGACCCTGCATCGCATGATCGAGCGCGCCGACGCCGGGCCGATCCTCGCCCAGCAGGCCGTCGCCATCGACCCCGAGGACACCGCCCTGAGCCTGCACGGCAAGCTGCGCAAGGCCGCCGGCGCCCTGCTGCGCGACAGCCTGCCGCTGCTCGCCCTCGGCGTGCTGCCGGAAGTCGAGCAGGACGAGAGCCAGGCCAGCCACTTCGGCCGGCGCACCCCGGCGGACGGCCTGCTCGACTGGCACAGGCCGGCACGGCAGTTGTACGACCTGGTGCGCGCGGTGACCCAGCCCTACCCTGGCGCCTTCTGCCAGGTCGGCGAACAGAAGCTGATCGTCTGGAGCGCCGAGGTGGTCGCCGGCAACCACGGCCGCGAGCCGGGCAGCGTACTGTCCTGCGACCCGCTGCGGATCGCCTGCGGCGAGGACTCGCTGGTGCTGCGCTTCGGCCAGCGCGGCGAGCGCGGCCTGTACCTGGCCGGCACGCAACTGGCCACCGAGCTGGGCCTGGTCGAGGGCGCGCGCCTGCGTGGCGCGGCATGCAGTCCGCAGCGCCGCACGCGGGTGCTGATCCTCGGGGTCAACGGCTTCATCGGCAACCACCTGTCCGAACGCCTGCTGCGCGACGGTCGCTACGAGGTCCACGGCATGGACATCGGCTCCGACGCCATCGAACGGCTCAAGGCCGACCCGCATTTCCACTTCGTCGAAGGCGACATCGGCATCCATTCGGAGTGGCTCGAATACCATGTGAAGAAATGCGACGTGATCCTGCCGCTGGTGGCCATCGCCACGCCCATCGAGTACACGCGCAACCCGCTGCGGGTGTTCGAACTGGACTTCGAGGAAAACCTGCGGATCGTCCGCTACTGCGTGAAATACGGCAAACGCGTGGTGTTCCCTTCCACCTCCGAGGTCTACGGCATGTGCCAGGACCCGGACTTCGACGAAGACCGCTCGAACCTGGTGGTCGGGCCGATCAACAAGCAGCGCTGGATCTACTCGGTGTCCAAGCAGTTGCTCGACCGGGTGATCTGGGCCTACGGCCAGCAGGGCCTGCGCTTCACCCTGTTCCGTCCGTTCAACTGGATGGGCCCGCGCCTGGACCGCCTGGATTCGGCGCGGATCGGCAGCTCGCGGGCGATCACCCAGCTCATCCTGCACCTGGTCGAAGGCACGCCGATCCGCCTGGTCGACGGCGGCGCGCAGAAGCGCTGCTTCACCGACGTCGACGACGGCATCGAGGCCCTCGCGCGGATCATCGACAACCGCGACGGCCGCTGCGACGGGCAGATCGTCAACATCGGCAACCCGGACAACGAGGCGAGCATCCGCCAGCTCGGCGAGGAACTGCTGCGCCAGTTCGAGGCCCACCCGCTGCGCGCGCAGTTCCCGCCCTTCGCCGGCTTCCGCGAGGTGGAGAGCCGCAGCTTCTACGGCGACGGCTACCAGGACGTGGCCCACCGCAAGCCGAGCATCGACAACGCCCGGCGCCTGCTCGACTGGCAGCCCACCATCGAACTGCGCGAGACCATCGGCAAGACCCTCGACTTCTTCCTCCACGAAGCGCTCCGCGAGCGCGAGGCACAGGCGTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3002985","ARO_id":"39419","ARO_name":"arnA","ARO_description":"arnA modifies lipid A with 4-amino-4-deoxy-L-arabinose (Ara4N) which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. arnA is found in E. coli and P. aeruginosa.","ARO_category":{"41433":{"category_aro_accession":"3004269","category_aro_cvterm_id":"41433","category_aro_name":"pmr phosphoethanolamine transferase","category_aro_description":"This family of phosphoethanolamine transferase catalyze the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine to lipid A, which impedes the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1644":{"model_id":"1644","model_name":"SHV-70","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1485":{"protein_sequence":{"accession":"AAY42633.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGVTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"DQ013287","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGAGTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001124","ARO_id":"37504","ARO_name":"SHV-70","ARO_description":"SHV-70 is an extended-spectrum beta-lactamase found in Enterobacter cloacae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1645":{"model_id":"1645","model_name":"ACT-23","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1990":{"protein_sequence":{"accession":"AGU38146.1","sequence":"MMKKSLCCALLLGISCSALAAPVSEKQLAEVVANTVTPLMKAQSIPGMAVAVIYQGKPHYYTFGKADIAASKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNAALLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMGYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMVPEKVADASLKQGISLAQSRYWRIGSMYQGLGWEMLNWPVEANTVIEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYHILDALQ"},"dna_sequence":{"accession":"KF515536","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCTCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCGCGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCGATTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGTAAACCGCACTATTACACGTTTGGCAAAGCCGATATCGCGGCCAGCAAACCCGTTACGCCTCAGACTCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGGGTTTTAGGAGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTAACGGGCAAGCAGTGGCAGGGGATTCGTATGCTGGATCTCGCAACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAATGCCGCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGTATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGGGCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGTGCCGGAGAAGGTTGCTGATGCCTCACTTAAGCAGGGCATCTCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGATCGAGGGCAGCGACAGTAAGGTGGCGCTGGCACCGCTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGACGCGCTACAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001828","ARO_id":"38228","ARO_name":"ACT-23","ARO_description":"ACT-23 is a beta-lactamase found in Escherichia coli","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1646":{"model_id":"1646","model_name":"TEM-139","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1322":{"protein_sequence":{"accession":"AAZ23494.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIEMDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"DQ072853","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGATGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001003","ARO_id":"37383","ARO_name":"TEM-139","ARO_description":"TEM-139 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1647":{"model_id":"1647","model_name":"mexI","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1900"}},"model_sequences":{"sequence":{"163":{"protein_sequence":{"accession":"NP_252896.1","sequence":"MTFTDLFVRRPVLALVVSTLILLLGLFSLGKLPIRQYPLLESSTITVTTEYPGASADLMQGFVTQPIAQAVSSVEGIDYLSSTSVQGRSVVTIRMLLNRDSTQAMTETMAKVNSVRYKLPERAYDSVIERSSGETTAVAYVGFSSKTLPIPALTDYLSRVVEPMFSSIDGVAKVQTFGGQRLAMRLWLDADRLAGRGLTASDVAEAIRRNNYQAAPGMVKGQYVLSNVRVNTDLTNVDDFREMVIRNDGNGLVRLRDVGTVELGAAATETSALMDGDPAVHLGLFPTPTGNPLVIVDGIRKLLPEIQKTLPPDVRVDLAYETSRFIQASIDEVVRTLVEALLIVVLVIYLCLGSLRSVLIPVATIPLSMLGAAALMLAFGFSVNLLTLLAMVLAIGLVVDDAIVVVENVHRHIEEGKSPVAAALIGAREVAGPVIAMTITLAAVYTPIGLMGGLTGALFREFALTLAGAVIVSGVVALTLSPVMSSLLLQAHQNEGRMGRAAEWFFGGLTRRYGQVLEFSLGHRWLTGGLALLVCISLPLLYSMPKRELAPTEDQAAVLTAIKAPQHANLDYVELFARKLDQVYTSIPETVSTWIINGTDGPAASFGGINLAAWEKRERDASAIQSELQGKVGDVEGSSIFAFQLAALPGSTGGLPVQMVLRSPQDYPVLYRTMEEIKQKARQSGLFVVVDSDLDYNNPVVQVRIDRAKANSLGIRMQDIGESLAVLVGENYVNRFGMEGRSYDVIPQSLRDQRFTPQALARQFVRTQDGNLVPLSTVVRVALQVEPNKLIQFDQQNAATLQAIPAPGVSMGQAVAFLDDVARGLPAGFSHDWQSDSRQYTQEGNTLVFAFLAALVVIYLVLAAQYESLADPLIILITVPLSICGALLPLALGYATMNIYTQIGLVTLIGLISKHGILMVEFANELQLHERLDRRAAILRAAQIRLRPVLMTTAAMVFGLVPLLFASGAGAASRFGLGVVIVSGMLVGTLFTLFVLPTVYTLLARNHAEVDKSPRSRQLAEADLLVNKA"},"dna_sequence":{"accession":"NC_002516","fmin":"4707534","fmax":"4710624","strand":"+","sequence":"ATGACCTTTACCGACCTGTTCGTCCGCCGGCCGGTGCTGGCGCTGGTGGTCAGCACGCTGATCCTGCTGCTCGGCCTGTTCTCCCTGGGCAAGCTGCCGATCCGCCAGTACCCGCTGCTGGAAAGCTCGACCATCACCGTCACCACCGAGTACCCCGGCGCCTCCGCCGATCTCATGCAAGGCTTCGTCACCCAGCCGATCGCCCAGGCGGTGTCGTCGGTGGAGGGCATCGACTACCTTTCCTCGACCTCGGTGCAGGGGCGTAGCGTGGTGACCATCCGCATGCTGCTCAACCGCGATTCGACCCAGGCGATGACCGAGACCATGGCCAAGGTCAACTCGGTGCGCTACAAGCTGCCCGAGCGTGCCTACGACTCGGTGATCGAACGCTCTTCCGGCGAGACCACCGCGGTAGCCTACGTCGGCTTTTCCAGCAAGACCCTGCCGATCCCGGCGTTGACCGACTACCTGTCGCGGGTGGTCGAGCCGATGTTCTCTTCCATCGACGGCGTGGCCAAGGTCCAGACCTTTGGCGGCCAGCGCCTGGCCATGCGCCTCTGGCTCGACGCCGACCGCCTCGCCGGGCGCGGCCTGACCGCCTCCGACGTGGCCGAGGCGATCCGCCGCAACAACTACCAGGCGGCGCCGGGGATGGTGAAGGGGCAGTACGTGCTGTCCAACGTGCGGGTCAACACCGACCTGACCAACGTCGACGACTTCCGCGAGATGGTCATCCGCAACGATGGCAACGGCCTGGTGCGCCTGCGCGACGTCGGTACCGTCGAACTGGGCGCCGCGGCCACCGAGACCAGCGCACTGATGGACGGCGACCCGGCGGTGCACCTGGGGTTGTTCCCGACGCCCACCGGCAACCCGCTGGTGATCGTCGACGGCATCCGCAAGCTGCTGCCGGAGATCCAGAAGACCCTGCCGCCGGATGTCCGCGTCGACCTCGCCTACGAGACTTCGCGCTTCATCCAGGCCTCCATCGACGAGGTGGTGCGGACCCTGGTGGAAGCGCTGCTGATCGTGGTGCTGGTGATCTACCTCTGCCTCGGCTCGCTGCGCAGCGTGCTGATCCCGGTGGCGACCATTCCCCTGTCGATGCTCGGCGCCGCCGCGCTGATGCTGGCCTTCGGCTTCAGCGTCAACCTGCTGACCCTGCTGGCGATGGTGCTGGCCATCGGGCTGGTGGTGGACGACGCCATCGTGGTGGTGGAGAACGTCCACCGCCACATCGAGGAAGGCAAGTCGCCGGTGGCGGCGGCGCTGATCGGCGCCCGCGAAGTGGCCGGCCCGGTGATCGCCATGACCATCACCCTGGCCGCCGTGTACACCCCCATCGGCCTGATGGGCGGCCTCACCGGCGCGCTGTTCCGCGAGTTCGCCCTGACCCTGGCGGGCGCGGTGATCGTGTCCGGGGTGGTGGCGCTGACCCTGTCGCCGGTGATGAGTTCGCTGCTGCTCCAGGCGCACCAGAACGAGGGGCGCATGGGCCGCGCCGCCGAGTGGTTCTTCGGCGGCCTGACGCGGCGCTACGGGCAGGTCCTGGAGTTCTCCCTGGGCCACCGCTGGCTGACCGGCGGCCTGGCATTGCTGGTGTGCATCAGCCTGCCGCTGCTGTATTCGATGCCCAAGCGCGAACTGGCGCCGACCGAGGACCAGGCCGCGGTGCTCACCGCGATCAAGGCGCCGCAGCACGCCAACCTCGACTATGTCGAACTGTTCGCGCGCAAGCTCGACCAGGTCTACACCAGCATCCCGGAAACCGTGAGCACCTGGATCATCAACGGCACCGACGGACCGGCGGCGAGCTTCGGCGGGATCAACCTGGCGGCCTGGGAAAAACGCGAGCGCGACGCCTCGGCGATCCAGTCCGAGCTGCAAGGCAAGGTCGGCGATGTCGAGGGCAGCAGCATCTTCGCCTTCCAGTTGGCCGCCCTGCCCGGCTCCACCGGCGGCCTGCCGGTGCAGATGGTGCTGCGCAGCCCGCAGGACTATCCAGTGCTCTACCGGACCATGGAAGAGATCAAGCAGAAGGCCCGACAGAGCGGGCTGTTCGTGGTGGTCGACAGCGACCTCGACTACAACAACCCGGTGGTCCAGGTCCGCATCGACCGCGCCAAGGCCAACAGCCTGGGCATCCGCATGCAGGACATCGGCGAGTCGCTGGCGGTGCTGGTGGGCGAGAACTACGTCAACCGCTTCGGCATGGAGGGCCGCTCCTACGACGTGATCCCACAGAGCCTGCGCGACCAGCGTTTCACTCCGCAAGCGCTGGCACGACAGTTCGTGCGCACCCAGGACGGCAACCTGGTGCCGCTGTCGACGGTGGTCCGGGTGGCGCTTCAGGTCGAACCGAACAAGCTGATCCAGTTCGACCAGCAGAACGCCGCGACCCTCCAGGCGATCCCCGCGCCCGGCGTCTCCATGGGCCAGGCGGTGGCCTTCCTCGACGACGTGGCGCGCGGCCTGCCGGCCGGCTTCAGCCACGACTGGCAATCCGACTCGCGGCAATACACCCAGGAAGGCAACACCCTGGTGTTCGCCTTCCTCGCCGCCCTGGTGGTGATCTACCTGGTGCTCGCCGCGCAGTACGAGAGCCTGGCCGACCCGCTGATCATCCTGATCACCGTGCCGCTGTCGATCTGCGGCGCGCTGCTGCCGCTGGCGCTGGGCTACGCGACGATGAACATCTATACGCAGATCGGCCTGGTCACCCTGATCGGCCTGATCAGCAAGCACGGCATCCTCATGGTCGAGTTCGCCAACGAACTGCAACTCCACGAGCGCCTCGACCGCCGCGCGGCGATCCTGCGCGCCGCGCAGATCCGCCTGCGGCCGGTGCTGATGACCACCGCGGCAATGGTCTTCGGCCTGGTGCCGCTGCTCTTCGCCAGCGGCGCCGGCGCCGCCAGCCGCTTCGGCCTGGGCGTGGTGATCGTCTCCGGGATGCTGGTCGGCACCCTCTTCACCCTGTTCGTGCTGCCCACCGTCTATACCCTGCTGGCGCGCAACCACGCGGAAGTCGACAAGAGCCCGCGCAGCCGGCAACTGGCCGAGGCCGATCTGCTGGTGAACAAGGCATGAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3000808","ARO_id":"37188","ARO_name":"MexI","ARO_description":"MexI is the inner membrane transporter of the efflux complex MexGHI-OpmD.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavin","category_aro_description":"Acriflavin is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36193":{"category_aro_accession":"3000054","category_aro_cvterm_id":"36193","category_aro_name":"acridine dye","category_aro_description":"Acridine dyes are cell permeable, basic molecules with an acridine chromophore. These compounds intercalate DNA. The image shown represents the core structure of the acridine family, with specific dyes containing varying substituents.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1648":{"model_id":"1648","model_name":"CTX-M-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1086":{"protein_sequence":{"accession":"AAZ95872.1","sequence":"MMTQSIRRSMLTVMATLPLLFSSATLHAQANSVQQQLEALEKSSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKQSESDKHLLNQRVEIKKSDLVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSASIRAGLPKSWVVGDKTGSGDYGTTNDIAVIWPENHAPLVLVTYFTQPEQKAESRRDILAAAAKIVTHGF"},"dna_sequence":{"accession":"DQ125241","fmin":"0","fmax":"876","strand":"+","sequence":"ATGATGACTCAGAGCATTCGCCGCTCAATGTTAACGGTGATGGCGACGCTACCCCTGCTATTTAGCAGCGCAACGCTGCATGCGCAGGCGAACAGCGTGCAACAGCAGCTGGAAGCCCTGGAGAAAAGTTCGGGAGGTCGGCTTGGCGTTGCGCTGATTAACACCGCCGATAATTCGCAGATTCTCTACCGTGCCGATGAACGTTTTGCGATGTGCAGTACCAGTAAGGTGATGGCGGCCGCGGCGGTGCTTAAACAGAGCGAGAGCGATAAGCACCTGCTAAATCAGCGCGTTGAAATCAAGAAGAGCGACCTGGTTAACTACAATCCCATTGCGGAGAAACACGTTAACGGCACGATGACGCTGGCTGAGCTTGGCGCAGCGGCGCTGCAGTATAGCGACAATACTGCCATGAATAAGCTGATTGCCCATCTGGGTGGTCCCGATAAAGTGACGGCGTTTGCTCGCTCGTTGGGTGATGAGACCTTCCGTCTGGACAGAACCGAGCCCACGCTCAATACCGCCATTCCAGGCGACCCGCGTGATACCACCACGCCGCTCGCGATGGCGCAGACCCTGAAAAATCTGACGCTGGGTAAAGCGCTGGCGGAAACTCAGCGGGCACAGTTGGTGACGTGGCTTAAGGGCAATACTACCGGTAGCGCGAGCATTCGGGCGGGTCTGCCGAAATCATGGGTAGTGGGCGATAAAACCGGCAGCGGAGATTATGGCACCACCAACGATATCGCGGTTATCTGGCCGGAAAACCACGCACCGCTGGTTCTGGTGACCTACTTTACCCAACCGGAGCAGAAGGCGGAAAGCCGTCGGGATATTCTGGCTGCGGCGGCGAAAATCGTAACCCACGGTTTCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001865","ARO_id":"38265","ARO_name":"CTX-M-2","ARO_description":"CTX-M-2 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1649":{"model_id":"1649","model_name":"DHA-21","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1480":{"protein_sequence":{"accession":"AIT76100.1","sequence":"MKKSLSATLISALLAFSAPGFSAADNVAAVVDSTIKPLMAQQDIPGMAVAVSVKGKPYYFNYGFADVQAKQPVTENTLFELGSVSKTFTGVLGAVSVAKKEMTLNDPAEKYQPELALPQWKGITLLDLATYTAGGLPLQVPDAVKSRADLLHFYQQWQPSRKPGDMRLYANSSIGLFGALTANAAGMPYEQLLTARILAPLGLSHTFITVPESAQSQYAYGYKNKKPVRVSPGQLDAESYGVKSASKDMLRWAEMNMEPSRAGNADLEMAMYLAQTRYYKTAAINQGLGWEMYDWPQQKDMIINGVTNEVALQPHPVTDNQVQPYNRASWVHKTGATTGFGAYVAFIPEKQVAIVILANKNYPNTERVKAAQAILSALE"},"dna_sequence":{"accession":"KM087847","fmin":"0","fmax":"1140","strand":"+","sequence":"ATGAAAAAATCGTTATCTGCAACACTGATTTCCGCTCTGCTGGCGTTTTCCGCCCCGGGGTTTTCTGCCGCTGATAATGTCGCGGCGGTGGTGGACAGCACCATTAAACCGCTGATGGCACAGCAGGATATTCCTGGGATGGCGGTTGCCGTCTCCGTAAAGGGTAAGCCCTATTATTTCAATTACGGTTTTGCCGATGTTCAGGCAAAACAGCCTGTCACTGAAAATACACTATTTGAGCTCGGATCTGTAAGTAAAACTTTCACAGGTGTGCTGGGTGCGGTTTCCGTGGCGAAAAAAGAGATGACGTTGAATGACCCGGCAGAAAAATACCAGCCGGAGCTGGCTCTGCCGCAGTGGAAGGGGATCACACTGCTGGATCTGGCTACCTACACCGCAGGCGGGCTGCCGTTACAGGTGCCGGATGCGGTGAAAAGCCGTGCGGATCTGCTGCATTTCTATCAGCAGTGGCAGCCGTCCCGGAAACCGGGCGATATGCGTCTGTATGCAAACAGCAGTATCGGCCTGTTTGGTGCTCTGACCGCCAACGCGGCGGGGATGCCGTATGAGCAGTTGCTGACTGCACGGATCCTGGCACCGCTGGGGTTATCTCACACCTTTATTACTGTGCCGGAAAGTGCGCAAAGCCAGTATGCGTACGGTTATAAAAACAAAAAACCGGTCCGCGTGTCGCCGGGACAGCTTGATGCGGAATCTTACGGCGTGAAATCCGCCTCAAAAGATATGCTGCGCTGGGCGGAAATGAATATGGAGCCGTCACGGGCCGGTAATGCGGATCTGGAAATGGCAATGTATCTTGCACAGACCCGCTACTATAAAACCGCCGCGATTAACCAGGGGCTGGGCTGGGAAATGTATGACTGGCCGCAGCAGAAAGATATGATCATTAACGGCGTGACCAACGAGGTCGCATTGCAGCCGCACCCGGTAACAGACAACCAGGTTCAGCCGTATAACCGTGCTTCCTGGGTGCATAAAACGGGGGCAACAACGGGTTTCGGCGCCTATGTGGCCTTTATTCCGGAAAAACAGGTGGCGATTGTGATTCTGGCGAATAAAAACTACCCGAATACCGAAAGAGTCAAAGCCGCACAGGCTATTTTGAGTGCACTGGAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36917","NCBI_taxonomy_name":"Morganella morganii","NCBI_taxonomy_id":"582"}}}},"ARO_accession":"3002152","ARO_id":"38552","ARO_name":"DHA-21","ARO_description":"DHA-21 is a beta-lactamase. From the Lahey list of DHA beta-lactamases.","ARO_category":{"36207":{"category_aro_accession":"3000068","category_aro_cvterm_id":"36207","category_aro_name":"DHA beta-lactamase","category_aro_description":"DHA beta-lactamases are plasmid-mediated AmpC \u03b2-lactamases that confer resistance to cephamycins and oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1650":{"model_id":"1650","model_name":"CMY-15","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1737":{"protein_sequence":{"accession":"CAD88477.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYARGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKNYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"AJ555823","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCCGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAACTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3002026","ARO_id":"38426","ARO_name":"CMY-15","ARO_description":"CMY-15 is a beta-lactamase found in Proteus mirabilis","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1651":{"model_id":"1651","model_name":"AAC(6')-If","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"358":{"protein_sequence":{"accession":"CAA39038.1","sequence":"MDEASLSMWVGLRSQLWPDHSYEDHILDSQHILSCPDKYVSFLAINNQSQAIAFADAAVRHDYVNGCESSPVVYLEGIFVIPEQRGHGVAKLLVAAVQDWGVAKGCTEMASDAALDNHISYQMHQALGFEETERVVFFRKRIAG"},"dna_sequence":{"accession":"X55353","fmin":"278","fmax":"713","strand":"+","sequence":"ATGGATGAAGCTTCTTTGAGCATGTGGGTTGGGCTTCGAAGTCAGCTATGGCCAGACCATAGCTATGAAGATCATATTCTGGATAGCCAACACATTTTATCTTGTCCCGATAAATATGTTTCATTCCTGGCAATAAATAACCAGAGTCAGGCAATAGCGTTTGCCGATGCCGCGGTTCGCCATGATTATGTGAATGGTTGTGAAAGCAGTCCGGTGGTTTATCTTGAAGGGATTTTTGTTATTCCGGAGCAGAGAGGCCATGGCGTTGCCAAACTACTGGTTGCAGCCGTACAGGATTGGGGAGTGGCGAAAGGTTGCACCGAGATGGCAAGCGATGCGGCTTTAGATAACCATATATCCTATCAAATGCATCAGGCTTTAGGCTTTGAAGAAACCGAACGCGTGGTATTTTTCAGAAAAAGAATAGCTGGTTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3002553","ARO_id":"38953","ARO_name":"AAC(6')-If","ARO_description":"AAC(6')-If is a plasmid-encoded aminoglycoside acetyltransferase in E. cloacae","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1652":{"model_id":"1652","model_name":"IMP-20","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1173":{"protein_sequence":{"accession":"BAD81061.1","sequence":"MKKLFVLCVCFLCSITAAGAALPDLKIEKLEEGVYVHTSFEEVNGWGVFSKHGLVVLVNTDAYLIDTPFTATDTEKLVNWFVERGYKIKGTISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKDGKVQAKNSFSGVSYWLVKNKIEVFYPGPGHTQDNVVVWLPEKKILFGGCFVKPDGLGNLGDANLEAWPKSAKILMSKYVKAKLVVSSHSEIGDASLLKRTWEQAVKGLNESKKPSQPSN"},"dna_sequence":{"accession":"AB196988","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAAGAAATTATTTGTTTTATGTGTATGCTTCCTTTGTAGCATTACTGCCGCAGGAGCGGCTTTGCCTGATTTAAAAATCGAGAAGCTTGAAGAAGGTGTTTATGTTCATACATCGTTCGAAGAAGTTAACGGTTGGGGTGTTTTTTCTAAACACGGTTTGGTGGTTCTTGTAAACACTGACGCCTATCTGATTGACACTCCATTTACTGCTACAGATACTGAAAAGTTAGTCAATTGGTTTGTGGAGCGCGGCTATAAAATCAAAGGCACTATTTCCTCACATTTCCATAGCGACAGCACAGGGGGAATAGAGTGGCTTAATTCTCAATCTATTCCCACGTATGCATCTGAATTAACAAATGAACTTCTTAAAAAAGACGGTAAGGTGCAAGCTAAAAACTCATTTAGCGGAGTTAGTTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCCGGCCCGGGGCACACTCAAGATAACGTAGTGGTTTGGTTACCTGAAAAGAAAATTTTATTCGGTGGTTGTTTTGTTAAACCGGACGGTCTTGGTAATTTGGGTGACGCAAATTTAGAAGCTTGGCCAAAGTCCGCCAAAATATTAATGTCTAAATATGTTAAAGCAAAACTGGTTGTTTCAAGTCATAGTGAAATTGGGGACGCATCACTCTTGAAACGTACATGGGAACAGGCTGTTAAAGGGCTAAATGAAAGTAAAAAACCATCACAGCCAAGTAACTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002211","ARO_id":"38611","ARO_name":"IMP-20","ARO_description":"IMP-20 is a beta-lactamase found in Pseudomonas and Acinetobacter spp.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1653":{"model_id":"1653","model_name":"AAC(6')-Ip","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"4422":{"protein_sequence":{"accession":"WP_069453146.1","sequence":"MNYSICDIAESNELILEAAKMLKKSFLDAGNESWGDIKNAIEEVEECIEHPNICLGICLDDKLIGWTGLRPMYDKTWELHPMVIKTEYQGKGFGKVLLRELETRAKSRGIIGIALGTDDEYQKTSLSMIDINERNIFDEIGNIKNVNNHPYEFYKKCGYMIVGIIPNANGKRKPDIWMWQILARKNSPTIAST"},"dna_sequence":{"accession":"NG_047307.2","fmin":"100","fmax":"682","strand":"+","sequence":"TTGAACTATTCAATATGCGATATAGCTGAATCAAATGAATTAATCCTTGAAGCAGCAAAGATGCTTAAGAAAAGCTTTCTTGATGCTGGAAATGAATCATGGGGAGATATTAAAAATGCTATTGAAGAAGTTGAAGAATGTATAGAACATCCAAATATATGCTTGGGAATATGTCTGGATGATAAACTGATTGGATGGACCGGATTAAGGCCGATGTACGATAAGACCTGGGAACTTCATCCCATGGTTATAAAAACTGAATATCAAGGCAAGGGTTTTGGGAAAGTACTACTAAGAGAACTAGAGACGAGAGCGAAGAGTAGGGGAATTATCGGAATAGCTCTTGGAACTGATGACGAATATCAGAAAACTAGTTTGTCTATGATTGATATAAACGAACGAAATATCTTCGATGAAATCGGGAATATAAAGAACGTTAATAATCATCCATATGAGTTTTATAAGAAATGTGGTTATATGATCGTTGGAATAATCCCTAATGCTAATGGAAAAAGAAAACCAGATATATGGATGTGGCAGATATTAGCTAGGAAGAACAGCCCAACAATCGCTTCAACCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002559","ARO_id":"38959","ARO_name":"AAC(6')-Ip","ARO_description":"AAC(6')-Ip is a aminoglycoside acetyltransferase encoded by plasmids and integrons in C. freundii, E. coli, E. faecium and Enterobacter aerogenes","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1654":{"model_id":"1654","model_name":"SHV-95","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"2028":{"protein_sequence":{"accession":"ABN49113.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARLQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"EF373972","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGATGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTTGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGAGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3001147","ARO_id":"37527","ARO_name":"SHV-95","ARO_description":"SHV-95 is a beta-lactamase found in Citrobacter freundii.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1655":{"model_id":"1655","model_name":"TEM-117","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"843":{"protein_sequence":{"accession":"AAN05026.1","sequence":"FFAAFCFPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQA"},"dna_sequence":{"accession":"AY130282","fmin":"0","fmax":"764","strand":"+","sequence":"TTTTTTGCGGCATTTTGCTTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000980","ARO_id":"37360","ARO_name":"TEM-117","ARO_description":"TEM-117 is a beta-lactamase that has been found in clinical isolates.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1656":{"model_id":"1656","model_name":"CTX-M-79","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"769":{"protein_sequence":{"accession":"ABO09821.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAVAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTNGL"},"dna_sequence":{"accession":"EF426798","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGTGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCAACGGTTTGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001940","ARO_id":"38340","ARO_name":"CTX-M-79","ARO_description":"CTX-M-79 is a beta-lactamase found in Escherichia coli","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1657":{"model_id":"1657","model_name":"AAC(6')-IIa","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"460":{"protein_sequence":{"accession":"AAM92464.1","sequence":"MSASTPPITLRLMTERDLPMLHDWLNRPHIVEWWGGDEERPTLDEVLEHYLPRAMAEESVTPYIAMLGEEPIGYAQSYVALGSGDGWWEDETDPGVRGIDQSLADPTQLNKGLGTRLVRALVELLFSDPTVTKIQTDPTPNNHRAIRCYEKAGFVREKIITTPDGPAVYMVQTRQAFERKRGVA"},"dna_sequence":{"accession":"AY123251","fmin":"2950","fmax":"3505","strand":"+","sequence":"ATGTCCGCGAGCACCCCCCCCATAACTCTTCGCCTCATGACCGAGCGCGACCTGCCGATGCTCCATGATTGGCTCAACCGGCCGCACATCGTTGAGTGGTGGGGTGGTGACGAAGAGCGACCGACTCTTGATGAAGTGCTGGAACACTACCTGCCCAGAGCGATGGCGGAAGAGTCCGTAACACCGTACATCGCAATGCTGGGCGAGGAACCGATCGGCTATGCTCAGTCGTACGTCGCGCTCGGAAGCGGTGATGGCTGGTGGGAAGATGAAACTGATCCAGGAGTGCGAGGAATAGACCAGTCTCTGGCTGACCCGACACAGTTGAACAAAGGCCTAGGAACAAGGCTTGTCCGCGCTCTCGTTGAACTACTGTTCTCGGACCCCACCGTGACGAAGATTCAGACCGACCCGACTCCGAACAACCATCGAGCCATACGCTGCTATGAGAAGGCAGGATTCGTGCGGGAGAAGATCATCACCACGCCTGACGGGCCGGCGGTTTACATGGTTCAAACACGACAAGCCTTCGAGAGAAAGCGCGGTGTTGCCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35731","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhi","NCBI_taxonomy_id":"90370"}}}},"ARO_accession":"3002594","ARO_id":"38994","ARO_name":"AAC(6')-IIa","ARO_description":"AAC(6')-IIa is an aminoglycoside acetyltransferase encoded by plasmids and integrons in P. aeruginosa and S. enterica","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1658":{"model_id":"1658","model_name":"OKP-B-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1599":{"protein_sequence":{"accession":"CAJ19612.1","sequence":"MRYVRLCLISLIAALPLAVFASPQPLEQIKISESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKSVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMATTLRKLLTTPSLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPDGKAERIVVIYLRDTPATMVERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM051153","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCAGCCGCTTGAGCAGATTAAAATCAGCGAAAGTCAGCTGGCGGGCCGGGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGCGACGAACAGCTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGAGCGTCGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTCAATGAGGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCGGCCAGCATGGCCACCACCCTGCGCAAGTTGCTAACCACCCCCTCTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGACCGGGTGGCCGGCCCGTTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGTGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAAGCGGAGCGTATCGTGGTGATCTATCTGCGTGATACCCCGGCGACCATGGTCGAGCGTAACCAGCAGATCGCCGGGATAGGCGCGGCGCTGATCGAGCACTGGCAGCGCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002437","ARO_id":"38837","ARO_name":"OKP-B-4","ARO_description":"OKP-B-4 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1659":{"model_id":"1659","model_name":"OXA-258","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1839":{"protein_sequence":{"accession":"CCE73593.2","sequence":"MTVRLVSRALGAVLFASALTLPARADVLCTLVADAADGRILFQQGTRQDCTQRYTPASTFKLPIALMGADAGILQGPHQPVWNYQPAYPDWGGEAWRQPTDPARWIKYSVVWYSQLTARALGQERFQRYTSAFGYGNADVSGEPGKHNGTDGAWIISSLRISPFEQVDFLRKFVNRQLPVKAAAYDLAENLFEVGEADGWRLYGKTGTGSPGSHGVYTPANAYGWFVGWARKDDRQLVFARLLQDEGATQPNAGLRARDGLMRDWAAMVAAPRK"},"dna_sequence":{"accession":"HE614014","fmin":"0","fmax":"825","strand":"+","sequence":"ATGACAGTTCGACTCGTTTCGCGCGCCCTGGGCGCAGTCCTCTTTGCGTCCGCCCTGACCCTGCCCGCCCGGGCGGACGTCCTGTGCACCCTGGTGGCCGACGCCGCCGACGGCCGCATCCTGTTCCAGCAGGGCACGCGGCAGGACTGCACGCAGCGCTACACCCCCGCCTCGACCTTCAAGCTGCCCATCGCCCTGATGGGCGCGGATGCCGGCATCCTGCAGGGCCCGCACCAGCCCGTCTGGAACTACCAGCCCGCTTATCCCGACTGGGGCGGCGAGGCCTGGCGCCAGCCCACCGATCCGGCTCGCTGGATCAAGTATTCGGTGGTCTGGTACTCGCAGTTGACCGCCAGGGCGCTGGGGCAGGAGCGCTTCCAGCGCTACACCTCCGCGTTCGGTTATGGCAACGCGGACGTCTCGGGTGAACCCGGCAAGCACAACGGCACCGATGGCGCGTGGATCATCTCCTCGCTGCGCATTTCGCCGTTTGAGCAGGTGGACTTCCTGCGCAAGTTCGTCAACCGGCAACTGCCCGTCAAGGCGGCTGCCTATGACCTGGCCGAGAACCTGTTCGAGGTCGGCGAAGCCGACGGCTGGCGTCTGTACGGCAAGACCGGAACCGGCTCGCCCGGCAGCCACGGCGTCTACACGCCGGCCAACGCCTATGGCTGGTTCGTCGGCTGGGCGCGCAAGGACGACCGCCAACTGGTGTTTGCCCGCCTGCTGCAGGACGAGGGGGCGACCCAGCCCAATGCCGGCCTGCGCGCCCGCGACGGCCTGATGCGCGACTGGGCCGCCATGGTCGCGGCGCCCCGCAAATGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39091","NCBI_taxonomy_name":"Achromobacter ruhlandii","NCBI_taxonomy_id":"72557"}}}},"ARO_accession":"3001503","ARO_id":"37903","ARO_name":"OXA-258","ARO_description":"OXA-258 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1660":{"model_id":"1660","model_name":"OXA-375","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4354":{"protein_sequence":{"accession":"AHL30275.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLVRASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFREWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KF986256.1","fmin":"40","fmax":"865","strand":"-","sequence":"CTATAAAATACCTAATTGTTCTAAGCTTTTATAAGTAATCTCTTTTCGAACAGAGCTAGGTATTCCTTTTTTCATTTCTAAGTTAAGGGAGAACGCTACAATATTCCCTTGAGGCTGAACAACCCATCCAGTTAACCAGCCTACTTGTGGGTTTACATCCCATCCCCAACCACTTTTTGCGTATATTTTATTTCCATTCTTTTCTTCTATGAATAGCATGGATTGCACTTCATCTTGGACTTTTTGGCTAAATGGAAGCGTTTTATTAGCTAGCTTGTAAGCAAATTGTGCCTCTTGCTGAGGAGTAATTTTTAAAGGACCCACCAGCCAAAAATTATCGACTTGGGTACCGATATCTGCATTGCCATAACCAACACGCTTCACTTCATTAGACATGAGTTCAAGTCCAATACGACGAGCTAAATCTTGATAAACTGGAATAGCGGAAGCTTTCATGGCATCGCCTAGGGTCATGTCCTTTTCCCATTCTCGGAATAACCTTTTTTTACCATCCCACTTAAATACTTCTGTGGTGGTTGCCTTATGGTGCTCAAGGCCGATCAAAGCATTAAGCATTTTGAAGGTCGAAGCAGGTACATACTCGGTCGAAGCACGAACAAGATCATTACCATAGCTTTGTTGAGTTTGGCCTTGTTGGATAACTAAAACACCCGTAGTGTGTGCTTCGTTAAATAAATTTTTAATTTTCTCTGCTTTTTCATCAGATTTTGAAGCGCTGTGATTTGGATTAGCAGTCACTATATAAGGTGAGCAGGCTGAAATAAAAATAGCGCTTGTTATAAGTAAGAGTGCTTTAATGTTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001561","ARO_id":"37961","ARO_name":"OXA-375","ARO_description":"OXA-375 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1661":{"model_id":"1661","model_name":"CARB-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1894":{"protein_sequence":{"accession":"AAO59455.1","sequence":"MDVRKHKASFFSVVITFLCLTLSLNANATDSVLEAVTNAETELGARIGLAVHDLETGKRWEHKSNERFPLSSTFKTLACANVLQRVDLGKERIDRVVRFSESNLVTYSPVTEKHVGKKGMSLAELCQATLSTSDNSAANFILQAIGGPKALTKFLRSIGDDTTRLDRWETELNEAVPGDKRDTTTPIAMVTTLEKLLIDETLSIKSRQQLESWLKGNEVGDALFRKGVPSDWIVADRTGAGGYGSRAITAVMWPPNRKPIVAALYITETDASFEERNAVIAKIGEQIAKTILMENSRN"},"dna_sequence":{"accession":"AY178993","fmin":"574","fmax":"1471","strand":"+","sequence":"ATGGACGTACGTAAACACAAGGCTAGTTTTTTTAGCGTAGTAATTACTTTTTTATGTCTCACGCTATCATTAAATGCTAATGCAACAGACTCAGTACTTGAAGCGGTTACCAATGCTGAAACTGAATTAGGCGCTAGAATTGGTCTAGCTGTGCATGATTTGGAAACGGGAAAACGTTGGGAACATAAATCTAATGAACGTTTTCCTCTAAGTAGTACCTTTAAAACACTTGCCTGTGCAAACGTTCTTCAAAGAGTTGATCTAGGTAAAGAAAGAATTGATAGAGTTGTGAGATTCTCTGAAAGCAATCTCGTTACATACTCACCTGTAACAGAAAAACATGTGGGTAAAAAAGGGATGTCGCTCGCAGAGCTGTGTCAGGCCACATTATCAACCAGTGATAATTCAGCTGCCAATTTTATTCTACAAGCGATTGGTGGACCTAAGGCTCTAACGAAATTTTTGCGTTCCATTGGCGACGATACTACGCGCCTTGATCGCTGGGAAACAGAACTTAACGAAGCGGTGCCTGGAGATAAGCGAGACACGACAACACCAATTGCAATGGTAACGACACTTGAAAAGTTACTAATTGACGAAACACTATCTATCAAATCTCGTCAACAACTAGAATCTTGGCTTAAAGGTAATGAGGTTGGCGATGCATTGTTTCGTAAAGGCGTTCCAAGTGACTGGATAGTAGCAGATAGAACAGGTGCTGGTGGTTATGGGTCGCGTGCTATTACTGCGGTGATGTGGCCTCCAAATCGCAAGCCTATCGTAGCCGCTCTATACATTACAGAGACAGACGCCTCGTTTGAAGAAAGAAATGCTGTCATTGCAAAAATTGGTGAGCAAATAGCGAAGACAATATTAATGGAGAATAGCCGTAACTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36930","NCBI_taxonomy_name":"Oligella urethralis","NCBI_taxonomy_id":"90245"}}}},"ARO_accession":"3002247","ARO_id":"38647","ARO_name":"CARB-8","ARO_description":"CARB-8 is a beta-lactamase found in Oligella urethralis","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1662":{"model_id":"1662","model_name":"OKP-B-17","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1121":{"protein_sequence":{"accession":"CAP12357.2","sequence":"MRYVRLCLISLIAALPLAVFASPQPLEQIKISEGQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKSVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMATTLRKLLTTPSLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPDGKAERIVVIYLRDTPATMVERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM850919","fmin":"24","fmax":"885","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCAGCCGCTTGAGCAGATTAAAATCAGCGAAGGTCAGCTGGCGGGCCGGGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGCGACGAACAGCTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGAGCGTCGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTCAATGAGGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCGGCCAGCATGGCCACCACCCTGCGCAAGCTGCTAACCACCCCCTCTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGACCGGGTGGCCGGCCCGTTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGTGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAAGCGGAGCGTATCGTGGTGATCTATCTGCGTGATACCCCGGCGACCATGGTCGAGCGTAACCAGCAGATCGCCGGGATAGGCGCGGCGCTGATCGAGCACTGGCAGCGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002450","ARO_id":"38850","ARO_name":"OKP-B-17","ARO_description":"OKP-B-17 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1663":{"model_id":"1663","model_name":"ACC-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"856":{"protein_sequence":{"accession":"CAB46491.1","sequence":"MQNTLKLLSVITCLAATVQGALAANIDESKIKDTVDDLIQPLMQKNNIPGMSVAVTVNGKNYIYNYGLAAKQPQQPVTENTLFEVGSLSKTFAATLASYAQVSGKLSLDQSVSHYVPELRGSSFDHVSVLNVGTHTSGLQLFMPEDIKNTTQLMAYLKAWKPADAAGTHRVYSNIGTGLLGMIAAKSLGVSYEDAIEKTLLPQLGMHHSYLKVPADQMENYAWGYNKKDEPVHVNMEILGNEAYGIKTTSSDLLRYVQANMGQLKLDANAKMQQALTATHTGYFKSGEITQDLMWEQLPYPVSLPNLLTGNDMAMTKSVATPIVPPLPPQENVWINKTGSTNGFGAYIAFVPAKKMGIVMLANKNYSIDQRVTVAYKILSSLEGNK"},"dna_sequence":{"accession":"AJ133121","fmin":"649","fmax":"1810","strand":"+","sequence":"ATGCAGAACACATTGAAGCTGTTATCCGTGATTACCTGTCTGGCAGCAACTGTCCAAGGTGCTCTGGCTGCTAATATCGATGAGAGCAAAATTAAAGACACCGTTGATGACCTGATCCAGCCGCTGATGCAGAAGAATAATATTCCCGGTATGTCGGTCGCAGTGACCGTCAACGGTAAAAACTACATTTATAACTATGGGTTAGCGGCAAAACAGCCTCAGCAGCCGGTTACGGAAAATACGTTATTTGAAGTGGGTTCGCTGAGTAAAACGTTTGCTGCCACCTTGGCGTCCTATGCGCAGGTGAGCGGTAAGCTGTCTTTGGATCAAAGCGTTAGCCATTACGTTCCAGAGTTGCGTGGCAGCAGCTTTGACCACGTTAGCGTACTCAATGTGGGCACGCATACCTCAGGCCTACAGCTATTTATGCCGGAAGATATTAAAAATACCACACAGCTGATGGCTTATCTAAAAGCATGGAAACCTGCCGATGCGGCTGGAACCCATCGCGTTTATTCCAATATCGGTACTGGTTTGCTAGGGATGATTGCGGCGAAAAGTCTGGGTGTGAGCTATGAAGATGCGATTGAGAAAACCCTCCTTCCTCAGTTAGGCATGCATCACAGCTACTTGAAGGTTCCGGCTGACCAGATGGAAAACTATGCGTGGGGCTACAACAAGAAAGATGAGCCAGTGCACGTGAATATGGAGATTTTGGGTAACGAAGCTTATGGTATCAAAACCACCTCCAGCGACTTGTTACGCTACGTGCAAGCCAATATGGGGCAGTTAAAGCTTGATGCTAATGCCAAGATGCAACAGGCTCTGACAGCCACCCACACCGGCTATTTCAAATCGGGTGAGATTACTCAGGATCTGATGTGGGAGCAGCTGCCATATCCGGTTTCTCTGCCGAATTTGCTCACCGGTAACGATATGGCGATGACGAAAAGCGTGGCTACGCCGATTGTTCCGCCGTTACCGCCACAGGAAAATGTGTGGATTAATAAGACCGGATCAACTAACGGCTTCGGTGCCTATATTGCGTTTGTTCCTGCTAAGAAGATGGGGATCGTGATGCTGGCTAACAAAAACTACTCAATCGATCAGCGAGTGACGGTGGCGTATAAAATCCTGAGCTCATTGGAAGGGAATAAGTAGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001815","ARO_id":"38215","ARO_name":"ACC-1","ARO_description":"ACC-1 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36212":{"category_aro_accession":"3000073","category_aro_cvterm_id":"36212","category_aro_name":"ACC beta-lactamase","category_aro_description":"ACC beta-lactamases or Ambler class C beta-lactamases are AmpC beta-lactamases. They possess an interesting resistance phenotype due to their low activity against cephamycins.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1664":{"model_id":"1664","model_name":"adeK","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"950"}},"model_sequences":{"sequence":{"674":{"protein_sequence":{"accession":"AAX14803.1","sequence":"MQKVWSISGRSIAVSALALALAACQSMRGPEPVVKTDIPQSYAYNSASGTSIAEQGYKQFFADPRLLEVIDLALANNRDLRTATLNIERAQQQYQITQNNQLPTIGASGSAIRQVSQSRDPNNPYSTYQVGLGVTAYELDFWGRVRSLKDAALDSYLATQSARDSTQISLISQVAQAWLNYSFATANLRLAEQTLKAQLDSYNLNKKRFDVGIDSEVPLRQAQISVETARNDVANYKTQIAQAQNLLNLLVGQPVPQNLLPTQPVKRIAQQNVFTAGLPSDLLNNRPDVKAAEYNLSAAGANIGAAKARLFPTISLTGSAGYASTDLSDLFKSGGFVWSVGPSLDLPIFDWGTRRANVKISETDQKIALSDYEKSVQSAFREVNDALATRANIGERLTAQQRLVEATNRNYTLSNARFRAGIDSYLTVLDAQRSSYAAEQGLLLLQQANLNNQIELYKTLGGGLKANTSDTVVHQPSSAELKKQ"},"dna_sequence":{"accession":"AY769962","fmin":"5610","fmax":"7065","strand":"+","sequence":"ATGCAAAAAGTATGGTCTATTTCAGGTCGTAGCATTGCGGTGTCTGCACTTGCGCTTGCTTTGGCAGCTTGTCAAAGCATGCGCGGCCCAGAACCAGTCGTGAAAACCGATATACCACAAAGCTATGCATATAACAGCGCTTCTGGTACGTCTATTGCTGAACAGGGTTATAAACAGTTCTTTGCTGACCCGCGTTTGCTTGAAGTGATTGATTTGGCTCTTGCCAATAACCGTGACTTACGTACAGCAACGCTCAATATTGAACGTGCTCAACAGCAATATCAGATTACACAGAACAACCAGCTTCCAACAATCGGAGCAAGTGGTAGTGCAATTCGTCAGGTTTCTCAAAGCCGTGATCCGAATAACCCCTACTCTACTTATCAAGTAGGTTTGGGTGTAACTGCTTATGAGCTAGATTTCTGGGGTCGTGTTCGTAGCCTCAAAGATGCTGCTTTAGATAGTTATCTTGCAACACAAAGTGCTCGTGATTCGACTCAAATCAGTCTGATTAGCCAAGTTGCTCAAGCATGGTTAAATTATTCGTTTGCAACAGCAAACTTAAGACTGGCAGAGCAAACGCTTAAAGCACAGTTAGATTCTTACAATCTCAACAAAAAACGTTTTGATGTAGGTATTGACAGTGAAGTTCCATTACGTCAAGCACAGATTTCTGTAGAAACTGCGCGTAATGATGTAGCGAACTACAAAACTCAAATTGCTCAAGCACAAAACTTGTTGAACTTGCTTGTAGGCCAACCTGTTCCACAAAACTTGTTACCTACACAACCTGTAAAACGCATTGCTCAACAAAATGTGTTTACTGCCGGTTTACCAAGTGACTTGTTAAATAACCGTCCGGATGTAAAAGCTGCTGAATACAACTTAAGCGCTGCGGGTGCGAATATCGGTGCTGCAAAAGCACGTTTATTCCCAACCATTAGCTTAACGGGTTCGGCTGGTTATGCATCAACTGACTTAAGTGATCTATTTAAGTCTGGTGGTTTTGTATGGTCAGTTGGTCCAAGCTTAGATTTACCAATCTTTGACTGGGGTACACGCCGTGCCAATGTAAAAATTTCTGAAACCGATCAGAAAATTGCATTGTCTGATTATGAAAAATCAGTTCAGTCGGCGTTCCGTGAAGTTAATGACGCGCTTGCAACTCGTGCCAATATTGGTGAGCGTTTAACAGCACAACAACGTCTAGTAGAAGCAACTAACCGCAACTACACACTTTCAAATGCCCGCTTCCGTGCCGGTATTGATAGTTACTTGACTGTTCTTGATGCACAGCGTTCTTCATATGCAGCTGAACAAGGTTTGTTATTGCTTCAACAAGCAAACTTAAACAACCAAATCGAGTTATACAAAACTCTAGGTGGTGGTTTAAAAGCAAATACTTCAGATACAGTGGTTCACCAACCATCTAGTGCTGAACTTAAAAAGCAATAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3000782","ARO_id":"37162","ARO_name":"adeK","ARO_description":"AdeK is the outer membrane factor protein in the adeIJK multidrug efflux complex.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36309":{"category_aro_accession":"3000170","category_aro_cvterm_id":"36309","category_aro_name":"imipenem","category_aro_description":"Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"40523":{"category_aro_accession":"3003832","category_aro_cvterm_id":"40523","category_aro_name":"ticarcillin","category_aro_description":"Ticarcillin is a carboxypenicillin used for the treatment of Gram-negative bacteria, particularly P. aeruginosa. Ticarcillin's antibiotic properties arise from its ability to prevent cross-linking of peptidoglycan during cell wall synthesis, when the bacteria try to divide, causing cell death.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1665":{"model_id":"1665","model_name":"ramA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"230"}},"model_sequences":{"sequence":{"289":{"protein_sequence":{"accession":"AFK13828.1","sequence":"MINQEAEGESSMTISAQIIDTIVEWIDDNLHQPLRIEEIARHAGYSKWHLQRLFMQYKGESLGRYIRERKLLLAARDLRESDARVYDICLRYGFDSQQTFTRIFTRTFNQPPGAYRKENHSRAH"},"dna_sequence":{"accession":"JQ727668","fmin":"0","fmax":"375","strand":"+","sequence":"ATGATCAATCAGGAAGCTGAAGGGGAGAGCAGTATGACCATTTCCGCTCAAATCATCGACACTATCGTCGAGTGGATCGACGATAACCTGCACCAGCCATTACGTATCGAAGAGATTGCCCGCCATGCGGGTTACTCGAAATGGCACCTGCAGCGGCTGTTTATGCAATACAAAGGGGAGAGTCTGGGGCGCTATATCCGTGAACGCAAGCTGCTGCTGGCGGCGCGGGATCTGCGCGAATCAGACGCCCGGGTATACGACATCTGCCTGCGTTACGGGTTTGACTCGCAGCAGACCTTCACTCGCATCTTCACCCGCACGTTCAACCAGCCGCCTGGGGCGTATCGTAAAGAGAACCACAGCCGCGCGCACTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3000823","ARO_id":"37203","ARO_name":"ramA","ARO_description":"RamA (\"resistance antibiotic multiple\") is a positive regulator of AcrAB-TolC and leads to high level multidrug resistance in Klebsiella pneumoniae, Salmonella enterica, and Enterobacter aerugenes, increasing the expression of both the mar operon as well as AcrAB. RamA also decreases OmpF expression.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"41445":{"category_aro_accession":"3004281","category_aro_cvterm_id":"41445","category_aro_name":"General Bacterial Porin with reduced permeability to beta-lactams","category_aro_description":"These are GBPs that are associated with decreased susceptibility to beta-lactams either through mutations in the porin protein, absence of the porin protein, or expression of the porin protein.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"},"36383":{"category_aro_accession":"3000244","category_aro_cvterm_id":"36383","category_aro_name":"reduced permeability to antibiotic","category_aro_description":"Reduction in permeability to antibiotic, generally through reduced production of porins, can provide resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1666":{"model_id":"1666","model_name":"vanXB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"375"}},"model_sequences":{"sequence":{"3456":{"protein_sequence":{"accession":"AAB05628.1","sequence":"MENGFLFLDEMLHGVRWDAKYATWDNFTGKPVDGYEVNRIIGTKAVALALREAQIHAARLGYGLLLWDGYRPKSAVDCFLRWAAQPEDNLTKEKYYPNIERAELITKGYVASQSSHSRGSTIDLTLYHLDTGELVSMGSNFDFMDERSHHTAKGIGNAEAQNRRCLRKIMESSGFQSYRFEWWHYKLIDEPYPDTYFNFAVS"},"dna_sequence":{"accession":"U35369","fmin":"6004","fmax":"6613","strand":"+","sequence":"ATGGAAAATGGTTTTTTGTTTTTAGATGAAATGTTGCATGGTGTTCGTTGGGATGCCAAGTACGCTACATGGGATAACTTCACGGGAAAACCAGTGGATGGGTATGAGGTGAATCGCATCATCGGCACAAAGGCCGTGGCGCTTGCTCTGCGCGAAGCACAAATCCATGCGGCACGCCTTGGCTACGGCTTGCTTTTATGGGATGGATATCGGCCAAAATCTGCGGTGGACTGTTTCCTGCGTTGGGCGGCGCAGCCGGAGGACAACCTCACAAAAGAAAAATATTACCCCAATATTGAGCGAGCCGAGTTGATTACAAAGGGCTATGTGGCCTCACAATCCAGCCATAGCCGTGGAAGCACAATTGATCTTACGCTCTACCACTTGGATACAGGGGAACTTGTTTCAATGGGAAGCAACTTCGATTTTATGGACGAACGGTCGCACCATACAGCAAAAGGGATAGGGAATGCAGAGGCACAAAATCGAAGATGCTTGCGTAAAATCATGGAAAGCAGCGGATTTCAGTCCTATCGCTTTGAATGGTGGCACTATAAGTTGATTGATGAGCCATACCCCGATACCTATTTTAATTTTGCTGTTTCATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3002950","ARO_id":"39384","ARO_name":"vanXB","ARO_description":"vanXB is a vanX variant found in the vanB gene cluster","ARO_category":{"36020":{"category_aro_accession":"3000011","category_aro_cvterm_id":"36020","category_aro_name":"vanX","category_aro_description":"VanX is a D,D-dipeptidase that cleaves D-Ala-D-Ala but not D-Ala-D-Lac, ensuring that the latter dipeptide that has reduced binding affinity with vancomycin is used to synthesize peptidoglycan substrate.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1667":{"model_id":"1667","model_name":"TEM-80","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1003":{"protein_sequence":{"accession":"AAM15527.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMLSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAVTMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERDRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AF347054","fmin":"208","fmax":"1069","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGCTGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCGTAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAGATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3000947","ARO_id":"37327","ARO_name":"TEM-80","ARO_description":"TEM-80 is an inhibitor-resistant beta-lactamase found in Enterobacter cloacae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1668":{"model_id":"1668","model_name":"CMY-68","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"945":{"protein_sequence":{"accession":"AEZ49855.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGIAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDEVTDKAELLRFYQNWQPQWTPGAKRLYANSSIGLFGALVVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"JN714480","fmin":"1039","fmax":"2185","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCACTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGCATTGCCGTGGCAATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAATTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGAAGTTACGGATAAAGCCGAATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGTTGGTGGTAAAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACAGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATAGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGCGTCGAGGCGGCCTGGCGCATTCTTGAAAAACTGCAATAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002081","ARO_id":"38481","ARO_name":"CMY-68","ARO_description":"CMY-68 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1669":{"model_id":"1669","model_name":"vanZF","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"566":{"protein_sequence":{"accession":"AAF36806.1","sequence":"MLTPLTVLYTYFCTIIFCIVFQIGFFFKALKNISIRHFLWVYVFLFYLALVYMMTGIGNVWVVGRYETLIRVSEINLLPFSSEGVTTYILNIILFMPLGFLLPTIWPQFRTIKNTACTGFFFSLAIELTQLLNHRITDIDDLLMNTLGAIIGYLLYRAFKMIYTRDEKKLDNKSSLVIKYEAIFYIVCSFIGMILLYYPFLLRKII"},"dna_sequence":{"accession":"AF155139","fmin":"4338","fmax":"4959","strand":"+","sequence":"ATGCTTACACCACTTACAGTTTTATATACTTATTTTTGTACTATTATTTTTTGTATTGTGTTTCAAATTGGATTTTTTTTTAAAGCGCTAAAAAATATATCTATTAGGCATTTTCTATGGGTGTATGTTTTTCTGTTCTACCTTGCGCTAGTGTATATGATGACGGGGATAGGGAATGTATGGGTAGTAGGAAGATATGAAACATTGATTCGTGTAAGTGAAATCAACTTACTTCCATTTTCTTCTGAAGGTGTTACTACGTATATTTTGAACATTATTCTGTTTATGCCGTTAGGTTTTTTATTGCCAACTATTTGGCCGCAGTTTAGAACAATTAAAAATACTGCATGTACTGGATTCTTTTTTTCATTGGCTATTGAGCTAACTCAATTGCTAAATCATAGAATTACAGATATTGATGATTTACTTATGAACACCCTGGGGGCGATTATTGGGTATTTATTATATAGAGCTTTTAAAATGATATATACAAGAGATGAAAAAAAGCTTGATAATAAATCTTCTCTAGTAATAAAATACGAGGCTATTTTTTATATAGTTTGCTCGTTTATAGGTATGATATTACTTTATTATCCATTTTTATTACGAAAAATTATTTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39542","NCBI_taxonomy_name":"Paenibacillus popilliae ATCC 14706","NCBI_taxonomy_id":"1212764"}}}},"ARO_accession":"3002963","ARO_id":"39397","ARO_name":"vanZF","ARO_description":"vanZF is a vanZ variant found in the vanF gene cluster","ARO_category":{"36255":{"category_aro_accession":"3000116","category_aro_cvterm_id":"36255","category_aro_name":"vanZ","category_aro_description":"VanZ is a teicoplanin resistance gene that is an accessory protein. VanZ prevents the incorporation of the terminal D-Ala into peptidoglycan subunits.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1672":{"model_id":"1672","model_name":"TEM-211","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1159":{"protein_sequence":{"accession":"AHA80960.1","sequence":"MSIKHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMTDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTTPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDELNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"KF513179","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTAAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGACTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACTAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3001388","ARO_id":"37788","ARO_name":"TEM-211","ARO_description":"From the Lahey list of beta-lactamases. Not yet released.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1673":{"model_id":"1673","model_name":"QnrA6","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"3348":{"protein_sequence":{"accession":"AAZ78355.1","sequence":"MDIIDKVFQQEDFSRQDLSDSRFRRCRFYQCDFSHCQLRDASFEDCSFIESGAIEGCHFSYADLRDASFKACRLSLANFSGANCFGIEFRECDLKGANFSRARFYNQISHKMYFCSAYISGCNLAYANLSGQCLEKCELFENNWSNANLSGASLMGSDLSHGTFSRDCWQQVNLRGCDLTFADLDGLDPRRVNLEGVKICAWQQEQLLEPLGVIVLPD"},"dna_sequence":{"accession":"DQ151889","fmin":"0","fmax":"657","strand":"+","sequence":"ATGGATATTATTGATAAAGTTTTTCAGCAAGAGGATTTCTCACGCCAGGATTTGAGTGACAGCCGTTTTCGCCGCTGCCGCTTTTATCAGTGTGACTTCAGCCATTGCCAGCTAAGGGATGCCAGTTTCGAGGATTGCAGTTTCATTGAAAGCGGCGCCATCGAAGGGTGCCACTTCAGCTATGCCGATCTGCGCGATGCCAGTTTCAAGGCCTGCCGCCTGTCTTTGGCCAATTTCAGCGGTGCCAACTGCTTTGGCATAGAGTTCAGGGAGTGCGATCTCAAGGGCGCCAATTTTTCCCGGGCCCGTTTTTACAATCAAATCAGCCATAAGATGTACTTCTGCTCGGCTTATATCTCAGGCTGTAACCTGGCCTATGCCAATTTGAGCGGCCAATGCCTGGAAAAGTGCGAGCTGTTTGAAAACAACTGGAGCAATGCCAACCTCAGCGGCGCTTCCTTGATGGGCTCCGACCTCAGCCACGGCACCTTCTCCCGCGACTGCTGGCAACAGGTAAACCTGCGGGGCTGTGACCTGACCTTTGCCGATCTGGATGGGCTCGACCCCAGACGGGTCAACCTCGAAGGGGTCAAGATCTGTGCCTGGCAGCAGGAGCAACTGCTGGAACCCTTGGGAGTAATAGTGCTGCCGGATTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3002712","ARO_id":"39146","ARO_name":"QnrA6","ARO_description":"QnrA6 is a plasmid-mediated quinolone resistance protein found in Proteus mirabilis","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1674":{"model_id":"1674","model_name":"AAC(6')-It","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"736":{"protein_sequence":{"accession":"AAD03492.1","sequence":"MHIMPITESQLSDWLVLRCLLWPDHEDADLQEMRQLITQAHCLQLLAYTNTQKAIGMLEASIRYEYVNGTQTSPVAFLEGIYVLPEYRRSGIATGLVQHVEIWAKQFACTEFASDATLDNQISHAMHRALGFHETERVVYFKKNIG"},"dna_sequence":{"accession":"AF031328","fmin":"0","fmax":"441","strand":"+","sequence":"ATGCATATTATGCCGATAACTGAATCACAATTATCAGATTGGCTAGTATTGAGATGCTTACTCTGGCCTGATCATGAAGATGCAGATTTACAGGAAATGCGCCAACTGATCACACAGGCACATTGCTTACAATTATTGGCTTATACCAACACCCAAAAAGCAATTGGCATGTTGGAAGCTTCGATTCGATATGAATATGTGAATGGTACGCAAACCTCACCCGTGGCTTTTCTTGAAGGGATTTATGTATTACCTGAATATCGCCGTTCAGGTATCGCAACAGGTTTGGTTCAGCATGTCGAAATCTGGGCTAAACAGTTTGCATGTACAGAGTTTGCTTCAGACGCAACGCTGGACAATCAGATCAGCCATGCAATGCATCGAGCGCTCGGTTTTCATGAAACTGAACGTGTGGTGTATTTTAAGAAAAATATCGGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39515","NCBI_taxonomy_name":"Acinetobacter genomosp. 16BJ","NCBI_taxonomy_id":"70347"}}}},"ARO_accession":"3002564","ARO_id":"38964","ARO_name":"AAC(6')-It","ARO_description":"AAC(6')-It is a chromosomal-encoded aminoglycoside acetyltransferase in Acinetobacter genomosp. 16","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1675":{"model_id":"1675","model_name":"CTX-M-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1087":{"protein_sequence":{"accession":"AAC32890.1","sequence":"MMTQSIRRSMLTVMATLPLLFSSATLHAQTNSVQQQLEALEKSSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKQSESDKHLLNQRVEIKKSDLVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSASIRAGLPKSWGVGDKTGSGDYGTTNDIAVIWPANHAPLVLVTYFTQPEQKAESRRDVLAAAAKIVTHGF"},"dna_sequence":{"accession":"U95364","fmin":"5","fmax":"881","strand":"+","sequence":"ATGATGACTCAGAGCATTCGCCGCTCAATGTTAACGGTGATGGCGACGCTACCCCTGCTATTTAGCAGCGCAACGCTGCACGCGCAGACGAACAGCGTGCAGCAGCAGCTGGAAGCCCTGGAGAAAAGTTCGGGAGGTCGGCTTGGCGTTGCGCTGATTAACACCGCCGATAATTCGCAGATTCTCTACCGTGCCGATGAACGTTTTGCGATGTGCAGTACCAGTAAGGTGATGGCGGCCGCGGCGGTGCTTAAACAGAGCGAGAGCGATAAGCACCTGCTAAATCAGCGCGTTGAAATCAAGAAGAGCGACCTGGTTAACTACAATCCCATTGCGGAGAAACACGTTAACGGCACGATGACGCTGGCTGAGCTTGGCGCAGCGGCGCTGCAGTATAGCGACAATACTGCCATGAATAAGCTGATTGCCCATCTGGGTGGGCCCGATAAAGTGACGGCGTTTGCTCGCTCGTTGGGTGATGAGACCTTCCGTCTGGACAGAACCGAGCCCACGCTCAATACCGCCATTCCAGGCGACCCGCGTGATACCACCACGCCGCTCGCGATGGCGCAGACCCTGAAAAATCTGACGCTGGGTAAAGCGCTGGCGGAAACTCAGCGGGCACAGTTGGTGACGTGGCTTAAGGGCAATACTACCGGTAGCGCGAGCATTCGGGCGGGTCTGCCGAAATCATGGGGAGTGGGCGATAAAACCGGCAGCGGAGATTATGGCACCACCAACGATATCGCGGTTATCTGGCCGGCAAACCACGCACCGCTGGTTCTGGTGACCTACTTTACCCAACCGGAGCAGAAGGCGGAAAGCCGTCGGGATGTTCTGGCTGCGGCGGCGAAAATCGTAACCCACGGTTTCTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35732","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium","NCBI_taxonomy_id":"90371"}}}},"ARO_accession":"3001868","ARO_id":"38268","ARO_name":"CTX-M-5","ARO_description":"CTX-M-5 is a beta-lactamase found in Salmonella typhimurium","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1676":{"model_id":"1676","model_name":"GES-18","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1013":{"protein_sequence":{"accession":"AEX59144.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALIFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMSDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"JQ028729","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGATCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGGGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGAGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002347","ARO_id":"38747","ARO_name":"GES-18","ARO_description":"GES-18 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1677":{"model_id":"1677","model_name":"cepA beta-lactamase","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"3285":{"protein_sequence":{"accession":"AAA21532.1","sequence":"MQKRLIHLSIIFFLLCPALVVAQNSPLETQLKKAIEGKKAEIGIAVIIDGQDTITVNNDIHYPMMSVFKFHQALALADYMHHQKQPLETRLLIKKSDLKPDTYSPLRETYPQGGIEMSIADLLKYTLQQSDNNACDILFNYQGGPDAVNKYLHSLGIRECAVIHTENDMHKNLEFCYQNWTTPLAAAKLLEIFRNENLFDKEYKNFIYQTMVECQTGQDRLIAPLLDKKVTMGHKTGTGDRNAKGQQIGCNDIGFILLPDGHAYSIAVFVKDSEADNRENSEIIAEISRIVYEYVTQQID"},"dna_sequence":{"accession":"U05883","fmin":"555","fmax":"1458","strand":"+","sequence":"ATGCAAAAAAGACTTATACATTTATCCATTATCTTCTTTCTGCTATGTCCTGCCCTGGTAGTTGCGCAGAACAGTCCTCTTGAAACTCAACTCAAGAAAGCCATAGAAGGGAAAAAAGCCGAAATAGGAATTGCAGTCATTATCGACGGGCAAGATACGATAACAGTCAATAATGATATTCATTATCCCATGATGAGTGTTTTCAAATTTCATCAGGCATTGGCATTGGCCGATTACATGCATCATCAAAAGCAACCTTTGGAAACCCGATTATTGATTAAAAAGTCGGATTTAAAGCCGGACACCTATAGTCCGCTTCGAGAAACATACCCGCAGGGAGGAATCGAAATGAGCATTGCCGATCTACTGAAATATACGCTTCAGCAAAGTGACAATAATGCCTGCGATATTCTTTTTAATTATCAAGGTGGTCCGGATGCCGTGAATAAGTATCTTCATTCATTGGGAATTCGTGAATGTGCTGTCATCCATACAGAAAACGATATGCATAAAAATCTGGAGTTCTGTTACCAAAACTGGACTACTCCATTAGCAGCCGCCAAATTACTGGAAATATTTCGCAATGAAAACCTTTTTGACAAAGAATACAAGAATTTCATTTATCAAACAATGGTGGAATGTCAGACAGGACAAGACCGCCTGATTGCTCCACTGCTCGATAAAAAAGTAACAATGGGGCATAAAACCGGAACAGGCGACCGTAATGCGAAAGGACAACAGATCGGTTGCAATGACATCGGGTTTATTCTTCTTCCCGACGGACATGCCTATAGTATAGCCGTCTTCGTGAAAGATTCCGAAGCAGATAACAGAGAAAACAGTGAGATTATCGCAGAAATTTCGCGCATCGTTTACGAATACGTAACGCAACAGATAGATTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35916","NCBI_taxonomy_name":"Bacteroides fragilis","NCBI_taxonomy_id":"817"}}}},"ARO_accession":"3003559","ARO_id":"40165","ARO_name":"cepA","ARO_description":"A beta-lactamase found in Bacteroides fragilis producing either low or high levels of the endogenous cephalosporinase activity","ARO_category":{"41356":{"category_aro_accession":"3004192","category_aro_cvterm_id":"41356","category_aro_name":"cepA beta-lactamase","category_aro_description":"cepA beta-lactamases are Class A beta-lactamases found in Bateroides fragilis and have the ability to hydrolyze cephalosporin.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1678":{"model_id":"1678","model_name":"AAC(6')-Ib-cr","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"272":{"protein_sequence":{"accession":"ABC17627.1","sequence":"MSNAKTKLGITKYSIVTNSNDSVTLRLMTEHDLAMLYEWLNRSHIVEWWGGEEARPTLADVQEQYLPSVLAQESVTPYIAMLNGEPIGYAQSYVALGSGDGRWEEETDPGVRGIDQLLANASQLGKGLGTKLVRALVELLFNDPEVTKIQTDPSPSNLRAIRCYEKAGFERQGTVTTPYGPAVYMVQTRQAFERTRSDA"},"dna_sequence":{"accession":"DQ303918","fmin":"0","fmax":"600","strand":"+","sequence":"ATGAGCAACGCAAAAACAAAGTTAGGCATCACAAAGTACAGCATCGTGACCAACAGCAACGATTCCGTCACACTGCGCCTCATGACTGAGCATGACCTTGCGATGCTCTATGAGTGGCTAAATCGATCTCATATCGTCGAGTGGTGGGGCGGAGAAGAAGCACGCCCGACACTTGCTGACGTACAGGAACAGTACTTGCCAAGCGTTTTAGCGCAAGAGTCCGTCACTCCATACATTGCAATGCTGAATGGAGAGCCGATTGGGTATGCCCAGTCGTACGTTGCTCTTGGAAGCGGGGACGGACGGTGGGAAGAAGAAACCGATCCAGGAGTACGCGGAATAGACCAGTTACTGGCGAATGCATCACAACTGGGCAAAGGCTTGGGAACCAAGCTGGTTCGAGCTCTGGTTGAGTTGCTGTTCAATGATCCCGAGGTCACCAAGATCCAAACGGACCCGTCGCCGAGCAACTTGCGAGCGATCCGATGCTACGAGAAAGCGGGGTTTGAGAGGCAAGGTACCGTAACCACCCCATATGGTCCAGCCGTGTACATGGTTCAAACACGCCAGGCATTCGAGCGAACACGCAGTGATGCCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002547","ARO_id":"38947","ARO_name":"AAC(6')-Ib-cr","ARO_description":"AAC(6')-Ib-cr is an aminoglycoside acetyltransferase encoded by plasmids, transposons, integrons in Enterobacteriaceae. The aac(6')-Ib-cr variant gene can induce resistance against aminoglycoside and fluoroquinolone simultaneously","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1679":{"model_id":"1679","model_name":"OXA-49","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1766":{"protein_sequence":{"accession":"AAP40270.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETPSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVERIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAAMDIKPQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"AY288523","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAGAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGACCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCCCAATTAGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001671","ARO_id":"38071","ARO_name":"OXA-49","ARO_description":"OXA-49 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1680":{"model_id":"1680","model_name":"macA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"760"}},"model_sequences":{"sequence":{"578":{"protein_sequence":{"accession":"AAV85981.1","sequence":"MAKMMKWSAVAAVAAAAVWGGWHYLKPEPQAAYITETVRRGGISRTVSATGEISPSNLVSVGAQASGQIKKLYVKLGQQVKKGDLIAEINSTTQTNTLNMEKSKLETYQAKLVSAQIALGSAEKKYKRQTALWKDDATSKEDLESAQDALAAAKANVAELKALIRQSKISINTAESDLGYTRITATMDGTVVAIPVEEGQTVNAAQSTPTIVQLANLDMMLNKMQIAEGDITKVKAGQDISFTILSEPDTPIKAKLDSVDPGLTTMSSGGYNSSTDTASNAVYYYARSFVPNPDGKLATGMTTQNTVEIDGVKNVLLIPSLTVKNRGGKAFVRVLGADGKAAEREIRTGMRDSMNTEVKSGLKEGDKVVISEITAAEQQESGERALGGPPRR"},"dna_sequence":{"accession":"AY768531","fmin":"0","fmax":"1179","strand":"+","sequence":"ATGGCGAAAATGATGAAATGGTCGGCTGTTGCGGCAGTCGCGGCGGCAGCGGTTTGGGGCGGATGGCATTATCTGAAGCCCGAACCGCAGGCTGCTTATATTACGGAAACGGTCAGGCGCGGCGGCATCAGCCGGACGGTTTCCGCGACGGGCGAGATTTCGCCGTCGAATCTGGTATCGGTCGGCGCGCAGGCTTCGGGGCAGATTAAAAAGCTTTATGTCAAACTCGGGCAACAGGTCAAAAAGGGAGATTTGATTGCGGAAATCAATTCGACCACGCAGACCAACACGCTCAATATGGAAAAATCTAAATTGGAAACGTATCAGGCGAAGCTGGTGTCGGCACAGATTGCATTGGGCAGCGCGGAGAAGAAATATAAGCGTCAGACGGCGTTGTGGAAGGATGATGCGACCTCTAAAGAAGATTTGGAAAGCGCGCAGGATGCGCTTGCCGCCGCCAAAGCCAATGTTGCCGAGTTGAAGGCTTTAATCAGACAGAGCAAAATTTCCATCAATACCGCCGAGTCGGATTTGGGCTACACGCGCATTACCGCGACGATGGACGGCACGGTGGTGGCGATTCCCGTGGAAGAGGGGCAAACCGTGAACGCGGCGCAGTCTACGCCGACGATTGTCCAATTGGCGAATCTGGATATGATGTTGAACAAAATGCAGATTGCCGAGGGCGATATTACCAAGGTGAAGGCGGGGCAGGATATTTCGTTTACGATTTTGTCCGAACCGGATACGCCGATTAAGGCGAAGCTCGACAGCGTCGACCCCGGGCTGACCACGATGTCGTCGGGCGGCTACAACAGCAGTACGGATACGGCTTCCAATGCGGTCTATTATTATGCCCGTTCGTTTGTGCCGAATCCGGACGGCAAACTCGCCACGGGGATGACGACGCAGAATACGGTTGAAATCGACGGTGTGAAAAATGTGTTGCTTATTCCGTCGCTGACCGTGAAAAATCGCGGCGGCAAGGCGTTCGTACGCGTGTTGGGTGCGGACGGCAAGGCGGCGGAACGCGAAATCCGGACCGGTATGAGAGACAGTATGAATACCGAAGTGAAAAGCGGGTTGAAAGAGGGGGACAAAGTGGTCATCTCCGAAATAACCGCCGCCGAGCAGCAGGAAAGCGGCGAACGCGCCCTAGGCGGCCCGCCGCGCCGATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36806","NCBI_taxonomy_name":"Neisseria gonorrhoeae","NCBI_taxonomy_id":"485"}}}},"ARO_accession":"3000533","ARO_id":"36672","ARO_name":"macA","ARO_description":"MacA is a membrane fusion protein that forms an antibiotic efflux complex with MacB and TolC. macA corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1681":{"model_id":"1681","model_name":"APH(4)-Ib","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"262":{"protein_sequence":{"accession":"CAA52372.1","sequence":"MLQTSKKKSGHDESWANADAHKWRGERKRDNRKIVLSGTTKLLFVAEEQFQLIPPPSYCVSLVPKLPSNVTQPLFEYCFAPRILFFYALKKMTQHTKLCKLSSLIWREMWAISSRLQWQCVCAARRITMRNGGWKFIEMLSCWSDMVHKHESVLISTLPSFINFLVGPFRSAGAEPGGMHRRVDPPRPLSPALIEAFDGVMQLSGAPSRGVTPTPRGPDALGRITDSRGGSEAGYRFNMCNRAVPSAALPIGEVLDIGEFSGKRTYLAAVHRAREQDLPETELPAVLQPCTGMAHAIAAADLSHTSGFAPFGPQGMGQETPWRDKRDCYFDPQVYYWLSQMGDTLRASVAQGFEKRMLWAEDCPEARHLRIHVKGSNAALPEPGPKTWAGDGSQAVWAGRLRPTQDSRYVVASIFPWRPW"},"dna_sequence":{"accession":"X74325","fmin":"645","fmax":"1908","strand":"+","sequence":"ATGCTGCAAACTTCTAAAAAAAAATCTGGGCACGATGAAAGTTGGGCTAACGCTGACGCTCACAAATGGCGTGGCGAAAGGAAGCGAGACAATCGGAAAATTGTTCTCTCGGGCACCACAAAGCTGTTGTTTGTCGCTGAAGAACAATTCCAACTGATTCCGCCGCCTTCCTATTGCGTCAGCCTTGTACCTAAGCTGCCGAGTAACGTCACTCAACCTCTCTTTGAATACTGCTTTGCTCCGCGAATACTTTTCTTCTATGCGCTCAAGAAAATGACACAGCACACCAAGCTCTGCAAACTTTCTTCGCTCATCTGGCGCGAAATGTGGGCCATTTCTTCTCGCCTGCAATGGCAATGCGTCTGTGCGGCGAGGAGAATCACGATGCGGAATGGGGGCTGGAAGTTCATAGAGATGCTGAGTTGTTGGAGCGACATGGTACATAAGCATGAGTCTGTCCTGATTTCCACCCTCCCGTCTTTCATCAACTTTCTCGTCGGACCCTTCCGATCGGCGGGCGCAGAACCAGGCGGTATGCACCGTAGGGTGGACCCACCGCGGCCACTGTCGCCAGCCTTGATCGAGGCCTTCGACGGGGTCATGCAGCTCTCGGGCGCCCCCTCTCGTGGGGTCACACCAACCCCACGAGGGCCAGATGCTTTGGGCCGGATAACAGATAGCCGCGGGGGGTCCGAGGCTGGCTATAGGTTTAATATGTGTAATCGGGCAGTACCATCGGCCGCGCTCCCGATTGGGGAAGTGCTTGACATTGGGGAATTCAGCGGGAAGCGGACCTACCTGGCCGCCGTGCACAGGGCCCGCGAGCAAGACCTGCCTGAAACCGAACTGCCCGCTGTTCTGCAGCCCTGCACGGGCATGGCACATGCGATCGCTGCGGCCGATCTTAGCCACACGAGCGGGTTCGCCCCATTCGGACCGCAAGGAATGGGTCAAGAGACTCCATGGCGTGATAAGCGCGATTGCTATTTCGATCCCCAGGTGTATTATTGGCTCTCTCAAATGGGCGACACCCTACGGGCGTCCGTCGCGCAGGGTTTCGAAAAGCGGATGCTTTGGGCCGAGGACTGCCCCGAAGCCCGGCACCTCCGGATTCACGTAAAGGGGTCCAACGCTGCCCTGCCGGAACCCGGCCCCAAAACGTGGGCGGGGGACGGGAGCCAAGCGGTGTGGGCAGGCCGGCTGCGTCCCACCCAGGATTCCCGGTACGTGGTCGCCAGCATCTTCCCCTGGAGGCCGTGGTGAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36923","NCBI_taxonomy_name":"Burkholderia pseudomallei","NCBI_taxonomy_id":"28450"}}}},"ARO_accession":"3002656","ARO_id":"39056","ARO_name":"APH(4)-Ib","ARO_description":"APH(4)-Ib is a chromosomal-encoded aminoglycoside phosphotransferase in Pseudomonas pseudomallei","ARO_category":{"36294":{"category_aro_accession":"3000155","category_aro_cvterm_id":"36294","category_aro_name":"APH(4)","category_aro_description":"Phosphorylation of hygromycin on the hydroxyl group at position 4","category_aro_class_name":"AMR Gene Family"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1682":{"model_id":"1682","model_name":"aadA24","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"330":{"protein_sequence":{"accession":"ABG72894.1","sequence":"MTIEISNQLSEVLSVIERHLEPTLLAVHLYGSAVDGGLKPHSDIDLLVTVTVRLDETTRRALINDLLETSASPGESEILRAVEVTIVVHDDIIPWRYPAKRELQFGEWQRNDILAGIFEPATIDIDLAILLTKAREHSVALVGPAAEELFDPVPEQDLFEALNETLTLWNSPPDWAGDERNVVLTLSRIWYSAVTGKIAPKDVAADWAMERLPAQYQPVILEARQAYLGQEEDRLASRADQLEEFVHYVKGEITKVVGK"},"dna_sequence":{"accession":"DQ677333","fmin":"0","fmax":"780","strand":"+","sequence":"GTGACCATCGAAATTTCGAACCAACTATCAGAGGTGCTAAGCGTCATTGAGCGCCATCTCGAACCGACGTTGCTGGCCGTACATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCACACAGTGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCGAGCTTTGATCAACGACCTTTTGGAAACTTCGGCTTCCCCTGGAGAGAGCGAGATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCTGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAGTAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATGGAGCGCCTGCCGGCCCAGTATCAGCCCGTCATACTTGAAGCTAGACAGGCTTATCTTGGACAAGAAGAAGATCGCTTGGCCTCCCGCGCAGATCAGTTGGAAGAATTTGTTCACTACGTGAAAGGCGAGATCACCAAGGTAGTCGGCAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35735","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Newport","NCBI_taxonomy_id":"108619"}}}},"ARO_accession":"3002621","ARO_id":"39021","ARO_name":"aadA24","ARO_description":"aadA24 is an integron-encoded aminoglycoside nucleotidyltransferase gene in Salmonella spp.","ARO_category":{"41439":{"category_aro_accession":"3004275","category_aro_cvterm_id":"41439","category_aro_name":"ANT(3'')","category_aro_description":"Nucleotidylylation of streptomycin at the hydroxyl group at position 3''","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1683":{"model_id":"1683","model_name":"QnrB67","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"192":{"protein_sequence":{"accession":"AGL43628.1","sequence":"MTLALVCEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"KC580656","fmin":"0","fmax":"645","strand":"+","sequence":"ATGACTCTGGCATTAGTTTGCGAAAAAATTGACAGAAATCGCTTCACCGGTGAGAAAGTTGAAAATAGTACATTTTTTAACTGCGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGCCAGTTCTATGATCGCGAAAGTCAGAAAGGATGCAATTTTAGTCGCGCAATGCTGAAAGATGCCATTTTCAAAAGCTGTGATTTATCAATGGCAGATTTCCGCAACGTCAGCGCATTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGTGCAAGCTTTATGAATATGATCACCACGCGCACCTGGTTTTGCAGCGCATATATCACTAATACCAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAACTATGGGAAAACCGCTGGATGGGGACTCAGGTACTGGGTGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACTAATTCGGAGTTAGGTGACTTAGATATTCGGGGTGTTGATTTACAAGGCGTTAAGTTAGACAACTACCAGGCATCGTTGCTCATGGAGCGGCTTGGCATCGCTGTGATTGGTTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39584","NCBI_taxonomy_name":"Citrobacter braakii","NCBI_taxonomy_id":"57706"}}}},"ARO_accession":"3002779","ARO_id":"39213","ARO_name":"QnrB67","ARO_description":"QnrB67 is a plasmid-mediated quinolone resistance protein found in Citrobacter braakii","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1684":{"model_id":"1684","model_name":"LEN-18","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1424":{"protein_sequence":{"accession":"CAP12346.2","sequence":"MRYVRLCVISLLATLPLAVDAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGLEQLDRRIHYRQQDLVDYSPVSEKHLTDGMTVGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPPGWFIADKTGAGERGARGIVALLGPDGKPERIVVLYLRDTPASMAERNQHIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM850908","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTTTGTGTTATCTCCCTGTTAGCCACCCTGCCACTGGCGGTAGACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTACCGACGGGATGACGGTCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGCCGGGCTGGTTTATCGCCGACAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGCTCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002465","ARO_id":"38865","ARO_name":"LEN-18","ARO_description":"LEN-18 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1685":{"model_id":"1685","model_name":"SHV-40","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1714":{"protein_sequence":{"accession":"AAN04882.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGGRGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AF535128","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGGGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATCGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001098","ARO_id":"37478","ARO_name":"SHV-40","ARO_description":"SHV-40 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1686":{"model_id":"1686","model_name":"OXA-34","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1931":{"protein_sequence":{"accession":"AAK15582.1","sequence":"MAIRIFAILFSIFSLATFAHAQEGTLERSDWRKFFSEFQAKGTIVVADERQADRAMLVFDPVRSKKRYSPASTFKIPHTLFALDAGAVRDEFQIFRWDGVNRGFAGHNQDQDLRSAMRNSTVWVYELFAKEIGDDKARRYLKKIDYGNADPSTSNGDYCIEGSLAISAQEQIAFLRKLYRNELPFRVEHQRLVKDLMIVEAGRNWILRAKTGWEGRMGWWVGWVEWPTGSVFFALNIDTPNRMDDLFKREAIVRAIL"},"dna_sequence":{"accession":"AF350424","fmin":"0","fmax":"771","strand":"+","sequence":"ATGGCAATCCGAATCTTCGCGATACTTTTCTCCATTTTTTCTCTTGCCACTTTCGCGCATGCGCAAGAAGGCACGCTAGAACGTTCTGACTGGAGGAAGTTTTTCAGCGAATTTCAAGCCAAAGGCACGATAGTTGTGGCAGACGAACGCCAAGCGGATCGTGCCATGTTGGTTTTTGATCCTGTGCGATCGAAGAAACGCTACTCGCCTGCATCGACATTCAAGATACCTCATACACTTTTTGCACTTGATGCAGGCGCTGTTCGTGATGAGTTCCAGATTTTTCGATGGGACGGCGTTAACAGGGGCTTTGCAGGCCACAATCAAGACCAAGATTTGCGATCAGCAATGCGGAATTCTACTGTTTGGGTGTATGAGCTATTTGCAAAGGAAATTGGTGATGACAAAGCTCGGCGCTATTTGAAGAAAATCGACTATGGCAACGCCGATCCTTCGACAAGTAATGGCGATTACTGTATAGAAGGCAGCCTTGCAATCTCGGCGCAGGAGCAAATTGCATTTCTCAGGAAGCTCTATCGTAACGAGCTGCCCTTTCGGGTAGAACATCAGCGCTTGGTCAAGGATCTCATGATTGTGGAAGCCGGTCGCAACTGGATACTGCGTGCAAAGACGGGCTGGGAAGGCCGTATGGGTTGGTGGGTAGGATGGGTTGAGTGGCCGACTGGCTCCGTATTCTTCGCACTGAATATTGATACGCCAAACAGAATGGATGATCTTTTCAAGAGGGAGGCAATCGTGCGGGCAATCCTT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001428","ARO_id":"37828","ARO_name":"OXA-34","ARO_description":"OXA-34 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1687":{"model_id":"1687","model_name":"CEPH-A3","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"475"}},"model_sequences":{"sequence":{"820":{"protein_sequence":{"accession":"AAM63403.1","sequence":"MMKGWIKCTLAGAVVLMASFWGGSVRAAGIELKQVSGPVYVVEDNYYVKENSMVYFGAKGVTVVGATWTPDTARELHKLIKRVSSKPVLEVINTNYHTDRAGGNAYWKSIGAKVVATRQTRDLMKSDWAEIVAFTRKGLPEYPDLPLVLPNVVHDGDFTLQEGKVRAFYAGPAHTPDGIFVYFPDEQVLYGNCILKEKLGNLSFANVKAYPQTIERLKAMKLPIKTVIGGHDSPLHGPELIDHYEELIKAVPQS"},"dna_sequence":{"accession":"AY112998","fmin":"196","fmax":"961","strand":"+","sequence":"ATGATGAAAGGTTGGATAAAGTGCACATTGGCCGGGGCCGTGGTGCTGATGGCGAGTTTCTGGGGTGGCAGCGTGCGGGCGGCGGGGATCGAGCTCAAGCAGGTGAGTGGCCCTGTCTATGTTGTTGAAGACAACTACTACGTCAAAGAGAACTCCATGGTCTATTTCGGGGCCAAGGGAGTGACGGTGGTGGGGGCGACCTGGACGCCGGATACTGCTCGCGAGCTGCACAAGCTGATTAAACGGGTCAGCAGCAAGCCGGTGCTGGAGGTGATCAACACCAACTACCACACCGACCGGGCGGGCGGTAACGCCTACTGGAAGTCCATCGGGGCCAAGGTGGTGGCGACGCGCCAGACCCGGGATCTGATGAAGAGCGACTGGGCCGAGATTGTCGCCTTTACCCGCAAGGGGCTGCCGGAGTACCCGGATCTGCCGCTGGTGCTGCCAAACGTGGTGCACGATGGCGACTTCACTCTGCAAGAGGGCAAGGTGCGCGCTTTCTACGCGGGCCCGGCCCACACGCCGGACGGCATCTTTGTCTACTTCCCCGACGAGCAGGTGCTCTATGGCAACTGCATCCTCAAGGAGAAGCTGGGCAACTTGAGTTTTGCCAATGTGAAGGCGTATCCGCAGACCATCGAGCGGCTCAAAGCGATGAAGCTGCCGATCAAGACGGTGATTGGCGGCCACGATTCGCCGCTGCACGGCCCCGAGTTGATTGATCACTATGAAGAGCTGATCAAGGCCGTGCCGCAGTCATAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39653","NCBI_taxonomy_name":"Aeromonas veronii bv. sobria","NCBI_taxonomy_id":"114517"}}}},"ARO_accession":"3003093","ARO_id":"39646","ARO_name":"cphA3","ARO_description":"CEPH-A3 is an Ambler Class B MBL; subclass B2 originally isolated from Aeromonas veronii. This enzyme has specific activity against carbapenems and is active as a mono-zinc protein.","ARO_category":{"36720":{"category_aro_accession":"3000581","category_aro_cvterm_id":"36720","category_aro_name":"CphA beta-lactamase","category_aro_description":"CphA is an Ambler Class B MBL; subclass B2 originally isolated from Aeromonas hydrophilia.  This enzyme has specific activity against carbapenems and is active as a mono-zinc protein.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1688":{"model_id":"1688","model_name":"CTX-M-90","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1782":{"protein_sequence":{"accession":"ACQ99521.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAVAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"FJ907381","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGTCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36945","NCBI_taxonomy_name":"Salmonella sp. YLD3","NCBI_taxonomy_id":"644616"}}}},"ARO_accession":"3001950","ARO_id":"38350","ARO_name":"CTX-M-90","ARO_description":"CTX-M-90 is a beta-lactamase found in Proteus mirabilis","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1689":{"model_id":"1689","model_name":"vanRO","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"4351":{"protein_sequence":{"accession":"AHA41505.1","sequence":"MASMRVLVVEDERFMAEAIRDGLRLEAIAADIAGDGDTALDLLGVNAYDIAVLDRDIPGPSGDEIAQRIVASGGGIPILMLTAADRMDDKASGFELGADDYLTKPFELQELVLRLRALDRRRAHSRPPVREIAGLQLDPFRREVYRDGRYVALTRKQFAVLEVLVAAEGGVISAEELLERAWDENADPFTNAVRITVSTLRKRLGEPWLIATVPGVGYRIDTEPDARGGGDGG"},"dna_sequence":{"accession":"KF478993","fmin":"6002","fmax":"6704","strand":"-","sequence":"CTATCCACCGTCGCCCCCGCCTCTGGCGTCCGGTTCGGTATCGATGCGGTACCCGACCCCCGGCACCGTGGCGATCAGCCACGGTTCGCCGAGCCGCTTGCGCAACGTCGAGACCGTGATGCGCACGGCATTCGTGAACGGATCGGCGTTCTCGTCCCACGCCCGCTCCAGCAACTCCTCGGCGCTGATCACACCGCCCTCGGCAGCGACGAGAACTTCGAGCACCGCGAACTGCTTCCGGGTCAGCGCGACGTACCGGCCGTCCCGGTAGACCTCGCGACGGAACGGGTCCAGCTGCAGACCAGCGATCTCCCGCACGGGCGGCCTGCTGTGCGCGCGCCTGCGGTCGAGGGCCCGGAGACGGAGCACGAGCTCCTGCAGCTCGAAAGGCTTGGTGAGGTAGTCGTCGGCACCGAGCTCGAACCCGGAGGCCTTGTCGTCCATCCGGTCCGCGGCAGTGAGCATCAGGATTGGTATGCCGCCACCGGAAGCGACGATGCGCTGGGCGATCTCGTCACCGGAGGGGCCGGGGATATCACGGTCGAGGACGGCGATGTCGTAGGCGTTGACGCCCAACAGATCCAGGGCAGTGTCCCCATCACCGGCGATGTCGGCCGCGATCGCTTCCAGGCGCAGCCCATCGCGGATGGCTTCCGCCATGAACCGCTCGTCCTCGACGACCAACACACGCATGCTCGCCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36897","NCBI_taxonomy_name":"Rhodococcus equi","NCBI_taxonomy_id":"43767"}}}},"ARO_accession":"3002930","ARO_id":"39364","ARO_name":"vanRO","ARO_description":"vanRO is a vanR variant found in the vanO gene cluster","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36713":{"category_aro_accession":"3000574","category_aro_cvterm_id":"36713","category_aro_name":"vanR","category_aro_description":"VanR is a OmpR-family transcriptional activator in the VanSR regulatory system. When activated by VanS, it promotes cotranscription of VanA, VanH, and VanX.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1690":{"model_id":"1690","model_name":"OXA-317","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1686":{"protein_sequence":{"accession":"AGU69255.1","sequence":"MNIKALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQEEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KF057034","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACGCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCCTTTAGCCAAAAAGTCCAAGAAGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001688","ARO_id":"38088","ARO_name":"OXA-317","ARO_description":"OXA-317 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1691":{"model_id":"1691","model_name":"CMY-31","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1776":{"protein_sequence":{"accession":"ABR18736.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGRLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"EF622224","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACGACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002042","ARO_id":"38442","ARO_name":"CMY-31","ARO_description":"CMY-31 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1692":{"model_id":"1692","model_name":"tetM","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1200"}},"model_sequences":{"sequence":{"560":{"protein_sequence":{"accession":"CAJ67339.1","sequence":"MKIINIGVLAHVDAGKTTLTESLLYTSGAIAESGSVDTGTTRTDTTFLERQRGITIQTAVTSFQWKDIKVNIIDTPGHMDFLAEVYRSLSVLDGAILLISARDGVQAQTRILFHALNKMGIPTIFFINKIDQNGIDLSTVYQDIKEKLSMEIIIKQKVELHPNMCVMSCTEPEQWDVVIEGNDYLLEKYTLGKSLEILELEQEEIRRFQNCSLYPVYHGSAKSNIGIEQLIEVITNKFYSSTYRKKSELCGNVFKIEYSEERQRLAYVRLYGGILHLRDSVRISEKEKIKITEMYTSINGELCKIDKAYSGEIVILQNEFLKLNSVLGDTKLLPQRERIENPLPLLQTTVEPSKPQQREMLLDALLEISDSDPLLQYYVDSTTHEIILSFLGKVQMEVTCALLQEKYHVEVKIKKPTVIYMERPLKKAEYTIHIEVPPNPFWASIGLSVAPLPLGSGVQYESSVSLGYLNQSFQNAVMEGIRYGCEQGLYGWNVTDCKICFKYGLYYSPVSTPADFRMLAPIVLEQVLKKAGTELLEPYLSFKIYAPQEYLSRAYNDAPKYCANIVDTQLKNNEVILSGEIPARCIQEYRNDLTFFTNGRSVCLTELKGYYVTTGESVCQPRRPNSRIDKVRYMFNKIT"},"dna_sequence":{"accession":"AM180355","fmin":"600033","fmax":"601953","strand":"+","sequence":"ATGAAAATTATTAATATAGGTGTTTTAGCTCATGTTGACGCAGGAAAAACTACTTTGACAGAAAGCTTACTATATACTAGTGGAGCGATTGCGGAGTCAGGAAGCGTGGATACAGGCACAACAAGAACGGATACTACATTTTTAGAACGTCAGCGAGGAATTACAATTCAGACAGCAGTAACCTCTTTTCAGTGGAAAGATATTAAGGTAAATATCATAGATACTCCAGGACATATGGATTTTTTAGCAGAAGTATATCGCTCGTTATCAGTTTTAGATGGGGCAATCCTACTAATTTCTGCGAGAGATGGAGTACAAGCACAAACTCGGATATTATTTCATGCACTAAATAAAATGGGTATTCCCACAATCTTTTTTATCAATAAGATTGACCAAAATGGGATTGATTTATCAACGGTTTATCAAGATATTAAAGAGAAACTTTCTATGGAAATTATAATCAAACAGAAAGTAGAGCTGCACCCTAATATGTGTGTGATGAGCTGTACGGAACCTGAGCAATGGGATGTGGTAATAGAAGGAAATGATTATCTTTTGGAGAAATATACACTTGGGAAATCATTGGAGATATTAGAACTCGAACAAGAGGAAATCAGAAGATTTCAGAATTGCTCCTTGTACCCTGTTTATCATGGAAGCGCAAAAAGCAACATAGGGATTGAGCAGCTTATAGAAGTGATAACGAATAAATTTTATTCATCAACATACAGAAAGAAGTCTGAACTTTGCGGAAATGTCTTCAAAATTGAATATTCGGAAGAAAGACAACGTCTTGCATATGTACGCCTTTATGGCGGAATCCTGCATTTGCGGGATTCGGTTAGAATATCGGAAAAGGAAAAAATAAAAATTACAGAAATGTATACTTCAATAAATGGTGAATTATGTAAAATTGATAAGGCTTATTCCGGGGAAATTGTTATTTTGCAAAATGAGTTTTTGAAGCTAAATAGTGTTCTTGGAGATACAAAGCTATTGCCACAGAGAGAGAGAATTGAAAATCCGCTCCCTCTGCTGCAAACAACTGTTGAACCGAGCAAACCTCAACAAAGGGAAATGTTACTTGATGCACTTTTAGAAATCTCCGACAGTGACCCGCTTCTACAATATTATGTGGATTCTACGACACATGAAATCATACTTTCTTTCTTAGGGAAAGTACAAATGGAAGTGACTTGTGCTCTATTGCAAGAAAAGTATCATGTGGAGGTAAAAATAAAAAAGCCTACAGTCATTTATATGGAAAGACCGTTAAAAAAAGCAGAGTATACCATTCACATCGAAGTGCCACCGAATCCCTTCTGGGCTTCCATTGGTCTTTCTGTAGCACCGCTTCCATTAGGGAGCGGAGTACAGTATGAGAGCTCGGTTTCTCTTGGATACTTAAATCAATCGTTTCAAAATGCAGTTATGGAAGGGATACGATATGGCTGTGAACAAGGATTGTATGGTTGGAATGTGACGGACTGTAAAATCTGTTTTAAGTATGGCTTATACTATAGCCCTGTTAGTACCCCAGCAGATTTTCGGATGCTTGCTCCTATTGTATTGGAACAAGTTTTAAAAAAAGCTGGAACAGAATTGTTAGAGCCATATCTTAGTTTTAAAATTTATGCACCACAAGAATATCTTTCACGAGCATATAACGATGCTCCTAAATATTGTGCGAACATCGTAGACACTCAACTGAAAAATAATGAGGTCATTCTTAGTGGAGAAATTCCTGCTCGGTGTATTCAAGAATATCGTAATGATTTAACTTTCTTTACAAATGGACGTAGCGTTTGTTTAACAGAGTTAAAAGGGTACTATGTTACTACTGGTGAATCTGTTTGTCAGCCCCGTCGTCCAAATAGTCGGATAGATAAAGTACGATATATGTTCAATAAAATAACTTAGC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37603","NCBI_taxonomy_name":"Clostridium difficile 630","NCBI_taxonomy_id":"272563"}}}},"ARO_accession":"3000186","ARO_id":"36325","ARO_name":"tetM","ARO_description":"TetM is a ribosomal protection protein that confers tetracycline resistance. It is found on transposable DNA elements and its horizontal transfer between bacterial species has been documented.","ARO_category":{"35921":{"category_aro_accession":"0000002","category_aro_cvterm_id":"35921","category_aro_name":"tetracycline-resistant ribosomal protection protein","category_aro_description":"A family of proteins known to bind to the 30S ribosomal subunit. This interaction prevents tetracycline and tetracycline derivatives from inhibiting ribosomal function. Thus, these proteins confer elevated resistance to tetracycline derivatives as a ribosomal protection protein.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1693":{"model_id":"1693","model_name":"TEM-143","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1568":{"protein_sequence":{"accession":"AAY85632.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDCWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"DQ075245","fmin":"217","fmax":"1078","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATTGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001006","ARO_id":"37386","ARO_name":"TEM-143","ARO_description":"TEM-143 is an extended-spectrum beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1694":{"model_id":"1694","model_name":"OXA-353","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1300":{"protein_sequence":{"accession":"AGW83451.1","sequence":"MYKKTLIVTTSILFLSACSSNMVKQHQIHSMSANKNSEEIKSLFDQAQTTGVLVIKRGKTEEIYGNDLKRASTAYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPDWKKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNANIGSKVDDFWLVGPLKITPQQETQFAYQLAHKTLPFSKNVQEQVQSMVFIEKKNGSKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTSSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"KF297582","fmin":"0","fmax":"822","strand":"+","sequence":"ATGTATAAAAAAACCCTTATCGTTACAACAAGTATCCTATTTTTATCCGCCTGTTCTTCCAATATGGTAAAACAACATCAAATACACTCTATGTCTGCCAATAAAAATTCAGAAGAAATTAAATCACTGTTTGATCAAGCACAAACCACGGGTGTTTTGGTAATTAAGCGAGGGAAAACAGAAGAAATTTATGGCAATGATCTTAAAAGAGCATCAACCGCCTATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTAATTGGACTTGAACATCATAAGGCAACTACAACTGAAGTATTTAAATGGAATGGGCAAAAACGTTTATTTCCTGATTGGAAAAAGGACATGACACTGGGCGATGCCATGAAAGCTTCTGCAATTCCAGTTTACCAAGAATTAGCCCGACGAATTGGTCTGGATCTTATGTCCAAAGAGGTGAAACGAATTGGTTTCGGTAATGCTAACATTGGCTCAAAAGTAGATGATTTCTGGCTTGTTGGCCCTCTAAAAATTACACCTCAACAAGAAACCCAATTTGCTTATCAATTAGCCCATAAAACGCTTCCATTTAGCAAAAATGTACAAGAGCAAGTTCAATCAATGGTGTTCATAGAGAAAAAAAATGGAAGTAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTTGAACCACAAGTTGGTTGGCTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTGGCATTCTCACTTAATTTAGAAATGAAAAAAGGAACTTCTAGCTCTATTCGCAAAGAAATTGCTTATAAAGGCTTAGAACAACTGGGTATCTTATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3001540","ARO_id":"37940","ARO_name":"OXA-353","ARO_description":"OXA-353 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1695":{"model_id":"1695","model_name":"DHA-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1707":{"protein_sequence":{"accession":"AEL22919.1","sequence":"MKKSLSATLISALLAFSAPGFSAADNVAAVVDSTIKPLMAQQDIPGMAVAVSVKGRPYYFNYGFADVQAKQPVTENTLFELGSVSKTFTGVLGAVSVAKKEMALNDPAAKYQPELALPQWKGITLLDLATYTAGGLPLQVPDAVKSRADLLHFYQQWQPSRKPGDMRLYANSSIGLFGALTANAAGMPYEQLLTARILAPLGLSHTFITVPESAQSQYAYGYKNKKPVRVSPGQLDAESYGVKSASKDMLRWAEMNMEPSRAGNADLEMAMYLAQTRYYKTAAINQGLGWEMYDWPQQKDMIINGVTNEVALQPHPVTDNQVQPYNRASWVHKTGATTGFGAYVAFIPEKQVAIVILANKNYPNTERVKAAQAILSALE"},"dna_sequence":{"accession":"JF273491","fmin":"745","fmax":"1885","strand":"+","sequence":"ATGAAAAAATCGTTATCTGCAACACTGATTTCCGCTCTGCTGGCGTTTTCCGCCCCGGGGTTTTCTGCCGCTGATAATGTCGCGGCGGTGGTGGACAGCACCATTAAACCGCTGATGGCACAGCAGGACATTCCCGGGATGGCGGTTGCCGTCTCTGTAAAGGGCAGGCCCTATTATTTCAATTACGGTTTTGCCGATGTTCAGGCAAAACAGCCGGTCACTGAAAATACACTATTTGAGCTCGGATCTGTAAGTAAAACTTTCACAGGTGTGCTGGGTGCGGTTTCTGTGGCGAAAAAAGAGATGGCGCTGAATGATCCGGCGGCAAAATACCAGCCGGAGCTGGCTCTGCCGCAGTGGAAGGGGATCACATTGCTGGATCTGGCTACCTATACCGCAGGCGGACTGCCGTTACAGGTGCCGGATGCGGTAAAAAGCCGTGCGGATCTGCTGCACTTCTATCAGCAGTGGCAGCCGTCCCGGAAACCGGGCGATATGCGTCTGTATGCAAACAGCAGCATCGGCCTGTTTGGTGCTCTGACCGCAAACGCGGCGGGGATGCCGTATGAGCAGTTGCTGACTGCACGGATCCTGGCACCGCTGGGGTTATCTCACACCTTTATTACTGTGCCGGAAAGTGCGCAAAGCCAGTATGCGTACGGTTATAAAAACAAAAAACCGGTCCGCGTGTCGCCGGGACAGCTTGATGCGGAATCTTACGGCGTGAAATCCGCCTCAAAAGATATGCTGCGCTGGGCGGAAATGAATATGGAGCCGTCACGGGCCGGTAATGCGGATCTGGAAATGGCAATGTATCTCGCCCAGACCCGTTACTATAAAACCGCCGCGATTAATCAGGGGCTGGGCTGGGAAATGTATGACTGGCCGCAGCAGAAAGATATGATCATTAACGGCGTGACCAACGAGGTCGCATTGCAGCCGCACCCGGTAACAGACAACCAGGTTCAGCCGTATAACCGTGCTTCCTGGGTGCATAAAACGGGGGCAACAACTGGTTTCGGCGCCTATGTGGCCTTTATTCCGGAAAAACAGGTGGCGATTGTGATTCTGGCGAATAAAAACTACCCGAATACCGAAAGAGTCAAAGCTGCACAGGCTATTTTGAGTGCACTGGAATAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36917","NCBI_taxonomy_name":"Morganella morganii","NCBI_taxonomy_id":"582"}}}},"ARO_accession":"3002138","ARO_id":"38538","ARO_name":"DHA-5","ARO_description":"DHA-5 is a beta-lactamase. From the Lahey list of DHA beta-lactamases.","ARO_category":{"36207":{"category_aro_accession":"3000068","category_aro_cvterm_id":"36207","category_aro_name":"DHA beta-lactamase","category_aro_description":"DHA beta-lactamases are plasmid-mediated AmpC \u03b2-lactamases that confer resistance to cephamycins and oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1697":{"model_id":"1697","model_name":"TEM-135","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"997":{"protein_sequence":{"accession":"CAG25427.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTTPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AJ634602","fmin":"0","fmax":"861","strand":"-","sequence":"TTACCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCTGACTCCCCGTCGTGTAGATAACTACGATACGGGAGGGCTTACCATCTGGCCCCAGTGCTGCAATGATACCGCGAGACCCACGCTCACCGGCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGTTTGCGCAACGTTGTTGCCATTGCTGCAGGCGTCGTGGTGTCACGCTCGTCGTTTGGTATGGCTTCATTCAGCTCCGGTTCCCAACGATCAAGGCGAGTTACATGATCCCCCATGTTGTGCAAAAAAGCGGTTAGCTCCTTCGGTCCTCCGATCGTTGTCAGAAGTAAGTTGGCAGCAGTGTTATCACTCATGGTTATGGCAGCACTGCATAATTCTCTTACTGTCATGCCATCCGTAAGATGCTTTTCTGTGACTGGTGAGTACTCAACCAAGTCATTCTGAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGCCCGGCGTCAACACGGGATAATACCGCACCACATAGCAGAACTTTAAAAGTGCTCATCATTGGAAAACGTTCTTCGGGGCGAAAACTCTCAAGGATCTTACCGCTGTTGAGATCCAGTTCGATGTAACCCACTCGTGCACCCAACTGATCTTCAGCATCTTTTACTTTCACCAGCGTTTCTGGGTGAGCAAAAACAGGAAGGCAAAATGCCGCAAAAAAGGGAATAAGGGCGACACGAAAATGTTGAATACTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35732","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium","NCBI_taxonomy_id":"90371"}}}},"ARO_accession":"3000999","ARO_id":"37379","ARO_name":"TEM-135","ARO_description":"TEM-135 is a broad-spectrum beta-lactamase found in Salmonella enterica.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1698":{"model_id":"1698","model_name":"OCH-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1811":{"protein_sequence":{"accession":"CAC17626.1","sequence":"MRKSTTLLIGFLTTAAIIPNNGALAASKANDGDLRRIVDETVRPLMAEQKIPGMAVAITIDGKSHFFGYGVASKESGQKVTEDTIFEIGSVSKTFTAMLGGYGLATGAFSLSDPATKWAPELAGSSFDKITMRDLGTYTPGGLPLQFPDAVTDDSSMLAYFKKWKPDYPAGTQRRYSNPSIGLFGYLAARSMDKPFDVLMEQKLLPAFGLKNTFINVPESQMKNYAYGYSKANKPIRVSGGALDAQAYGIKTTALDLARFVELNIDSSSLEPDFQKAVAATHTGYYHVGANNQGLGWEFYNYPTALKTLLAGNSSDMALKSHKIEKFDTPRQPSADVWLNKTGSTNGFGAYAAFIPAKKTGIVLLANRNYPIDERVKAAYRILQALDNKQ"},"dna_sequence":{"accession":"AJ295344","fmin":"0","fmax":"1173","strand":"+","sequence":"ATGAGAAAATCTACGACACTTTTGATCGGTTTCCTCACCACTGCCGCTATTATCCCGAATAATGGCGCGCTGGCTGCGAGCAAGGCGAATGATGGCGACTTGCGCCGTATTGTCGATGAAACGGTGCGCCCGCTCATGGCCGAGCAGAAAATCCCCGGCATGGCCGTCGCTATAACCATCGACGGCAAGAGCCACTTCTTCGGTTATGGTGTGGCATCGAAAGAAAGCGGGCAAAAAGTCACTGAAGACACGATTTTCGAGATCGGTTCGGTCAGCAAGACCTTCACTGCAATGCTTGGCGGTTACGGGCTGGCGACAGGCGCGTTCTCCCTGTCCGATCCCGCGACCAAATGGGCTCCTGAACTGGCAGGCAGCAGCTTCGACAAGATCACCATGCGTGATCTTGGGACCTACACGCCGGGCGGATTGCCCCTCCAGTTTCCCGATGCTGTCACCGATGACAGTTCGATGCTGGCATATTTCAAGAAATGGAAGCCGGACTATCCGGCAGGCACGCAGCGTCGCTATTCGAATCCCAGCATCGGCCTGTTCGGCTATCTGGCGGCACGAAGCATGGACAAGCCGTTCGACGTTTTGATGGAGCAAAAGCTTCTGCCTGCATTCGGCCTGAAGAACACCTTCATCAATGTGCCGGAAAGCCAGATGAAGAACTACGCCTACGGCTATTCCAAAGCCAACAAGCCGATCCGGGTATCGGGCGGGGCGCTGGATGCACAAGCCTATGGCATCAAGACCACCGCGCTTGATCTTGCCCGCTTCGTCGAACTGAACATCGACAGCTCATCTCTGGAGCCTGATTTCCAGAAAGCCGTCGCCGCAACGCATACCGGTTACTACCATGTCGGAGCGAACAATCAGGGACTTGGCTGGGAGTTCTACAACTATCCGACTGCGCTCAAGACACTTCTTGCCGGCAATTCGTCGGACATGGCGCTGAAGTCGCACAAAATCGAGAAATTCGATACACCTCGCCAACCGTCAGCTGATGTGTGGCTCAACAAGACAGGCTCAACCAACGGCTTTGGCGCTTATGCGGCCTTTATTCCTGCGAAGAAGACCGGAATTGTTCTGCTTGCCAATCGGAATTATCCGATCGATGAGCGCGTAAAGGCTGCCTATCGGATATTGCAGGCGCTCGACAACAAGCAATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37077","NCBI_taxonomy_name":"Ochrobactrum anthropi","NCBI_taxonomy_id":"529"}}}},"ARO_accession":"3002519","ARO_id":"38919","ARO_name":"OCH-6","ARO_description":"OCH-6 beta-lactamase is an Ambler class C chromosomal-encoded beta-lactamases in Ochrobactrum anthropi","ARO_category":{"36233":{"category_aro_accession":"3000094","category_aro_cvterm_id":"36233","category_aro_name":"OCH beta-lactamase","category_aro_description":"OCH beta-lactamases are Ambler class C chromosomal-encoded beta-lactamases in Ochrobactrum anthropi","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1699":{"model_id":"1699","model_name":"vanXO","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"375"}},"model_sequences":{"sequence":{"23":{"protein_sequence":{"accession":"AHA41501.1","sequence":"MNDDFVYVDDWVPGVRWDAKYATWDNFTGKPVDGYLANRIVGTRALCAALEQAREKAASLGFGLLLWDGYRPRRAVDSFLRWSEQPEDGQTKQRHYPNIDRPEMLEKGYVATQSGHSRGGAVDLTLYHLATGELAPMGGDHDLMDPISHHRARGIKPIESKNRELLRSIMEDCGFDRYDCEWWHYTLKREPYPDVYFDFPIT"},"dna_sequence":{"accession":"KF478993","fmin":"2576","fmax":"3185","strand":"+","sequence":"ATGAACGACGACTTCGTCTACGTCGACGACTGGGTGCCCGGAGTCCGCTGGGATGCCAAGTACGCCACGTGGGACAACTTCACCGGCAAACCGGTAGACGGCTACCTCGCGAATCGAATCGTCGGCACCCGGGCTTTGTGCGCGGCCCTCGAGCAAGCACGCGAGAAGGCAGCTTCCCTCGGCTTCGGATTGCTTCTCTGGGACGGCTACCGTCCTCGACGCGCCGTCGACAGCTTCCTACGCTGGTCAGAACAGCCGGAGGATGGCCAGACGAAGCAGCGACACTATCCCAATATCGACAGACCCGAGATGCTCGAAAAGGGATACGTGGCAACCCAGTCGGGCCACAGTAGGGGCGGCGCCGTTGACCTGACGCTCTATCACCTTGCGACCGGTGAACTTGCTCCTATGGGTGGCGACCACGACCTCATGGACCCGATCTCACATCATCGAGCGCGAGGAATCAAGCCAATCGAGTCCAAGAATCGTGAGCTTCTTCGTTCCATCATGGAGGACTGCGGATTTGATCGGTACGACTGCGAGTGGTGGCACTACACGCTGAAACGCGAACCATATCCAGATGTCTACTTCGACTTTCCGATCACGTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36897","NCBI_taxonomy_name":"Rhodococcus equi","NCBI_taxonomy_id":"43767"}}}},"ARO_accession":"3002954","ARO_id":"39388","ARO_name":"vanXO","ARO_description":"vanXO is a vanX variant found in the vanO gene cluster","ARO_category":{"36020":{"category_aro_accession":"3000011","category_aro_cvterm_id":"36020","category_aro_name":"vanX","category_aro_description":"VanX is a D,D-dipeptidase that cleaves D-Ala-D-Ala but not D-Ala-D-Lac, ensuring that the latter dipeptide that has reduced binding affinity with vancomycin is used to synthesize peptidoglycan substrate.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1700":{"model_id":"1700","model_name":"ACT-28","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1018":{"protein_sequence":{"accession":"AHL39333.1","sequence":"MKTKSLCCALLLSTSCSVLAAPMSEKQLSDVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQHWQPQWKPGATRLYANASIGLFGALAVKPSGMSFEQAMTKRVFKPLKLDHTWINVPKEEEAHYAWGYRDGKAIHVSPGMLDAEAYGVKTNIQDMASWLKANMNPDALPDSTLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEAAYRILSALQ"},"dna_sequence":{"accession":"KJ207206","fmin":"751","fmax":"1897","strand":"+","sequence":"ATGAAGACAAAATCCCTTTGCTGTGCCCTGCTGCTCAGCACCTCCTGCTCTGTTCTCGCCGCGCCGATGTCAGAGAAACAGCTGTCTGACGTGGTGGAACGTACCGTTACCCCCCTGATGAAAGCGCAAGCCATTCCGGGCATGGCGGTAGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGAAAGGCCGATGTTGCGGCGAACAAACCTGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTATTAGGTGGCGATGCGATTGCGCGCGGAGAAATATCGCTGGGCGACCCCGTGACAAAGTACTGGCCCGAGCTAACAGGCAAGCAGTGGCAGGGTATTCGCATGTTGGATCTGGCGACCTACACCGCGGGTGGCCTGCCGCTACAGGTGCCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGTTTCTATCAACACTGGCAACCGCAGTGGAAACCAGGCGCAACGCGTCTTTATGCGAACGCCAGCATCGGGCTTTTTGGCGCCCTCGCGGTTAAACCCTCCGGCATGAGCTTTGAACAGGCCATGACGAAGCGGGTCTTCAAGCCACTCAAACTGGACCATACATGGATTAACGTTCCGAAAGAAGAAGAGGCGCATTACGCCTGGGGATACCGTGATGGTAAAGCAATCCACGTTTCACCGGGAATGCTGGATGCCGAAGCGTATGGTGTCAAAACCAACATCCAGGATATGGCGAGCTGGCTGAAGGCCAACATGAACCCTGACGCCCTTCCGGATTCAACGTTGAAACAGGGTATTGCCCTGGCACAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTCGTGGAGGGCAGCGATAACAAGGTGGCTCTTGCACCGTTACCGGTGGCAGAAGTGAACCCTCCAGCTCCGCCAGTAAAAGCATCATGGGTACATAAAACAGGCTCGACGGGTGGATTCGGCAGCTATGTCGCATTTATTCCTGAAAAGGAACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCGCGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001848","ARO_id":"38248","ARO_name":"ACT-28","ARO_description":"ACT-28 is a beta-lactamase. From the Lahey list of ACT beta-lactamases.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1701":{"model_id":"1701","model_name":"Erm(39)","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"274":{"protein_sequence":{"accession":"AAR92235.1","sequence":"MSSVHHGRHENGQNFLRDRRVVGDIVRMVSHTAGPIVEIGAGDGALTLPLQRLGRPLTAIEIDLHRARRLADRTTAEVIATDFLRYRLPRTPHVVVGNLPFHLTTAILRRLLHENGWTDAILLVQWEVARRRAGVGGATMMTAQWWPWFEFGLARKVSADAFRPRPSVDAGLLTIQRRAEPLLPWADRRAYQALVHRVFTGRGRGLAQILRPHVHPRWLSANGIHPSALPRALTARQWVALFDAAG"},"dna_sequence":{"accession":"AY487229","fmin":"2152","fmax":"2893","strand":"+","sequence":"GTGTCTTCAGTTCATCACGGCCGGCATGAGAACGGCCAGAATTTTCTGCGCGACCGTCGAGTGGTCGGCGACATCGTGAGGATGGTCTCGCACACAGCGGGTCCCATCGTCGAGATCGGGGCCGGAGACGGCGCCCTCACCCTGCCGTTACAGCGGCTGGGCCGACCGTTGACCGCCATCGAGATCGACCTCCACCGTGCCCGACGGCTCGCCGACCGAACCACTGCCGAGGTGATCGCAACCGACTTCCTGCGGTACCGGCTGCCGCGCACGCCGCACGTGGTGGTGGGCAACCTGCCGTTCCATCTGACCACCGCCATCCTCCGGCGCCTACTGCACGAGAACGGCTGGACCGATGCGATCCTGTTGGTGCAGTGGGAGGTGGCTCGACGGCGGGCCGGTGTCGGCGGCGCCACCATGATGACCGCCCAGTGGTGGCCGTGGTTCGAATTCGGCCTGGCGCGAAAGGTTTCGGCCGACGCGTTCCGGCCGCGGCCGAGTGTGGATGCCGGGCTGCTGACCATTCAGCGCCGAGCTGAGCCGCTACTCCCGTGGGCCGACCGTCGTGCGTATCAGGCGCTGGTCCACAGGGTTTTCACCGGGCGCGGGCGTGGTCTGGCCCAGATTCTGCGGCCCCACGTGCACCCACGGTGGCTGTCTGCCAACGGAATTCACCCGTCGGCTCTGCCCAGAGCGCTGACGGCTCGACAGTGGGTGGCGTTGTTCGATGCCGCCGGCTAGC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36886","NCBI_taxonomy_name":"Mycobacterium fortuitum","NCBI_taxonomy_id":"1766"}}}},"ARO_accession":"3000602","ARO_id":"36741","ARO_name":"Erm(39)","ARO_description":"ErmD confers MLSb phenotype.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35946":{"category_aro_accession":"0000027","category_aro_cvterm_id":"35946","category_aro_name":"roxithromycin","category_aro_description":"Roxithromycin is a semi-synthetic, 14-carbon ring macrolide antibiotic derived from erythromycin. It is used to treat respiratory tract, urinary and soft tissue infections. Roxithromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35974":{"category_aro_accession":"0000057","category_aro_cvterm_id":"35974","category_aro_name":"telithromycin","category_aro_description":"Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36315":{"category_aro_accession":"3000176","category_aro_cvterm_id":"36315","category_aro_name":"dirithromycin","category_aro_description":"Dirithromycin is an oxazine derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome to inhibit bacterial protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin 1A is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"vernamycin B-gamma","category_aro_description":"Vernamycin B-gamma is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1702":{"model_id":"1702","model_name":"MIR-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"1024":{"protein_sequence":{"accession":"AAD22636.1","sequence":"MMTKSLSCALLLSVASSAFAAPMSEKQLAEVVERTVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEIALGDPVAKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDTASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEEAHFAWGYREGKAVHVSPGMLDAEAYGVKTNVKDMASWLIANMKPDSLQAPSLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"M37839","fmin":"927","fmax":"2073","strand":"+","sequence":"ATGATGACAAAATCCCTAAGCTGTGCCCTGCTGCTCAGCGTCGCCAGTTCTGCATTCGCCGCACCGATGTCCGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTAATTTATCAGGGTCAGCCACACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGCGGCGATGCCATTGCCCGGGGTGAAATAGCGCTGGGCGATCCGGTAGCAAAATACTGGCCTGAGCTCACGGGCAAGCAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTATACCGCAGGCGGTCTGCCGTTACAGGTGCCGGATGAGGTCACGGATACCGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCTAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTTAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAACCCCTCAAGCTGGACCATACCTGGATTAACGTCCCGAAAGCGGAAGAGGCGCATTTCGCCTGGGGATACCGTGAGGGTAAAGCGGTCCACGTTTCGCCAGGGATGCTGGACGCGGAAGCCTATGGCGTAAAAACTAACGTGAAGGATATGGCGAGCTGGCTGATAGCCAACATGAAGCCGGATTCTCTTCAGGCTCCCTCACTCAAGCAAGGCATTGCTCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCTATGTATCAGGGGTTAGGCTGGGAGATGCTCAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCATTGCCCGTGGCAGAAGTGAATCCACCCGCGCCGCCGGTCAAGGCCTCCTGGGTCCATAAAACAGGCTCGACGGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002166","ARO_id":"38566","ARO_name":"MIR-1","ARO_description":"MIR-1 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36197":{"category_aro_accession":"3000058","category_aro_cvterm_id":"36197","category_aro_name":"MIR beta-lactamase","category_aro_description":"MIR beta-lactamases are plasmid-mediated beta-lactamases that confer resistance to oxyimino- and alpha-methoxy beta-lactams","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1703":{"model_id":"1703","model_name":"FosK","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"3294":{"protein_sequence":{"accession":"BAO79518.1","sequence":"MITGINHITFSVRDLSSSIEFYRDLLGMRLHVTWEAGAYFTAGDTWVCLSVGEPKPANDYTHVAFSVGERELVELHARLKEAGVEEWKQNTSEGNSVYLLDPNGHRIELHCGTLATRLAELEKSPYKRLVWC"},"dna_sequence":{"accession":"AB917040","fmin":"736","fmax":"1135","strand":"+","sequence":"ATGATCACTGGTATCAATCACATCACCTTTTCCGTCAGGGACTTGAGCTCTTCAATCGAGTTCTATCGTGACTTGCTGGGAATGAGGCTGCACGTGACCTGGGAAGCAGGTGCTTATTTTACAGCGGGTGATACGTGGGTATGTCTGAGCGTCGGGGAACCTAAACCCGCCAACGACTACACGCATGTGGCATTCAGTGTTGGCGAAAGAGAGCTTGTTGAGCTGCACGCTAGGCTAAAAGAAGCCGGGGTTGAGGAGTGGAAGCAGAATACAAGTGAGGGTAACTCCGTGTATCTGCTTGATCCAAACGGCCATCGCATTGAGCTTCACTGCGGAACGTTGGCAACCCGCTTAGCTGAGTTGGAGAAGTCGCCCTATAAAAGGTTGGTCTGGTGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39070","NCBI_taxonomy_name":"Acinetobacter soli","NCBI_taxonomy_id":"487316"}}}},"ARO_accession":"3003207","ARO_id":"39791","ARO_name":"FosK","ARO_description":"FosK is a fosfomycin thiol transferase isolated from Acinetobacter soli. It is integrin-mediated. It confers a high level of resistance to fosfomycin.","ARO_category":{"36272":{"category_aro_accession":"3000133","category_aro_cvterm_id":"36272","category_aro_name":"fosfomycin thiol transferase","category_aro_description":"Catalyzes the addition of a thiol group from a nucleophilic molecule to fosfomycin.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1704":{"model_id":"1704","model_name":"CMY-57","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1283":{"protein_sequence":{"accession":"ADP37961.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQFDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"HQ285243","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAATTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002068","ARO_id":"38468","ARO_name":"CMY-57","ARO_description":"CMY-57 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1705":{"model_id":"1705","model_name":"SHV-111","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1230":{"protein_sequence":{"accession":"BAF95849.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALSGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AB372881","fmin":"8","fmax":"869","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTTCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGGATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001160","ARO_id":"37540","ARO_name":"SHV-111","ARO_description":"SHV-111 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1706":{"model_id":"1706","model_name":"OXA-142","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1204":{"protein_sequence":{"accession":"ABY79006.1","sequence":"MKTFAAYVIIACLSSTALAGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPSAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEDQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG"},"dna_sequence":{"accession":"EU358785","fmin":"720","fmax":"1521","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTATCGCGTGTCTTTCGAGTACGGCATTAGCTGGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTCTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATGACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAGCGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAGCAATGGGAAAGAGACTTGACCTTAAGAGGGGCAATACAAGTTTCAGCTGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCCTATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAAGACCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATATTTAAATAAATTGTCAGCATCTAAAGAAAACCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCGGCACCTGAATATCTAGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGGTGGGTTGAGAAGGAGACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAGTAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGAAAGTGAGGGCATCATTGGTGGCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001803","ARO_id":"38203","ARO_name":"OXA-142","ARO_description":"OXA-142 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1707":{"model_id":"1707","model_name":"QnrB4","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"748":{"protein_sequence":{"accession":"ABC17630.2","sequence":"MMTLALVGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRANLKDAIFKSCDLSMADFRNINALGIEIRHCRAQGSDFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFSSFDWRAANVTHCDLTNSELGDLDIRGVDLQGVKLDSYQASLLLERLGIAVMG"},"dna_sequence":{"accession":"DQ303921","fmin":"0","fmax":"648","strand":"+","sequence":"ATGATGACTCTGGCGTTAGTTGGCGAAAAAATTGACAGAAACAGGTTCACCGGTGAAAAAGTTGAAAATAGCACATTTTTCAACTGTGATTTTTCGGGTGCCGACCTTAGCGGCACTGAATTTATTGGCTGCCAGTTTTATGATCGAGAAAGTCAGAAAGGATGTAATTTTAGTCGCGCTAACCTGAAAGATGCCATTTTCAAAAGTTGTGATCTCTCCATGGCTGATTTCAGGAATATCAATGCGCTGGGAATCGAAATTCGCCACTGCCGGGCACAAGGGTCAGATTTTCGCGGCGCAAGTTTTATGAATATGATCACCACCCGCACCTGGTTTTGTAGCGCCTATATCACCAATACCAACTTAAGCTACGCCAACTTTTCAAAAGTCGTACTGGAAAAGTGCGAGCTGTGGGAAAACCGCTGGATGGGTACTCAGGTGCTGGGCGCAACGTTCAGTGGATCAGACCTCTCTGGCGGCGAGTTTTCATCCTTCGACTGGCGAGCAGCAAACGTTACGCACTGTGATTTGACCAATTCGGAACTGGGCGATTTAGATATCCGCGGGGTTGATTTGCAAGGCGTCAAACTGGACAGCTACCAGGCATCGTTGCTCCTGGAACGTCTTGGTATCGCTGTCATGGGTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002718","ARO_id":"39152","ARO_name":"QnrB4","ARO_description":"QnrB4 is a plasmid-mediated quinolone resistance protein found in Escherichia coli","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1708":{"model_id":"1708","model_name":"tet36","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1200"}},"model_sequences":{"sequence":{"374":{"protein_sequence":{"accession":"CAD55718.1","sequence":"MRTINIGILAHIDAGKTSITENLLFASGATIVRGSVDKGNTTTDSMDIEKRRGITVRASTTSIQWNDTKINIIDTPGHMDFLAEVERTFRMLDGAILVVSAKEGIQAQTRLLFNVLQQLEIPTILFVNKIDREGVNLNQLYLEIQNSLSKDIIFMQSVEGKELTSSCTIHYISEKNRETILEKDDLLLEKYLSDTQLSNLDYWNSMVRLVQAAKLHPIYHGSAMYGIGIEDLLNSITTFIETSLPQENALSAYVYKIEHNKKEQKRAYLKIIGGTLKSRKLYSLNGSDENLKIRGLKTFYSGDEIDVDEVFTNDIAIADHADNLMVGDYLGIMPNLFDKLNIPSPALKSSIHPAKVENRSKLISAMNVLSVEDPSLAFSINADNNELEVSLYGATQREVILTLLEERFSVDAYFEEVKTIYKERLKTKSEYTIHIEVPPNPYWASIGLIIEPLPIGAGLVMESEISLGYLNRSFQNAVFDGVKKACESGLYGWEVTDLKVTFSHGIYYSPVSTPADFRSLAPYVFRLALQQADVELLEPILDFKLQIPLAVNARAITDINKMQGEISTITSDGDWTTILGNIPLDTSKEYSAEVSSYTQGLGVFVTRFSGYRPTNKKVSRSVELNEKDKLMYMFEKESIK"},"dna_sequence":{"accession":"AJ514254","fmin":"0","fmax":"1923","strand":"+","sequence":"ATGAGAACTATAAATATAGGTATTCTTGCACATATTGATGCAGGAAAGACCTCCATTACAGAGAACTTGCTATTTGCGAGTGGAGCAACCATAGTACGTGGAAGTGTGGACAAAGGAAACACTACAACCGATTCGATGGATATCGAAAAACGAAGAGGTATCACAGTTAGAGCGTCTACAACATCTATTCAATGGAATGATACAAAGATTAATATCATCGACACTCCTGGACACATGGACTTTCTGGCAGAGGTAGAACGCACTTTTAGGATGCTAGATGGTGCTATACTTGTGGTGTCTGCCAAAGAGGGCATTCAAGCTCAAACAAGGTTGTTGTTCAATGTCCTGCAACAACTAGAAATACCTACAATTCTATTCGTCAACAAAATAGACAGAGAGGGAGTCAATCTAAATCAGCTTTATTTAGAGATACAAAATAGCCTTTCTAAAGATATTATCTTTATGCAATCCGTTGAAGGCAAGGAATTAACATCTAGCTGTACAATACACTACATATCAGAAAAGAACAGAGAAACAATTTTAGAGAAAGATGATCTCTTGCTTGAAAAATACTTGAGTGATACACAGCTTTCTAATTTAGATTATTGGAATTCAATGGTTCGTCTTGTTCAAGCTGCTAAATTACATCCTATCTATCATGGTTCAGCAATGTATGGCATTGGTATTGAAGATTTGCTAAACTCAATCACTACTTTTATCGAAACATCTCTACCTCAAGAGAACGCTTTGTCTGCCTATGTTTATAAAATTGAGCATAATAAGAAGGAACAGAAACGAGCCTATCTAAAGATTATAGGTGGAACCCTTAAATCTCGAAAATTATATAGCCTCAATGGCTCAGATGAGAATCTGAAGATAAGAGGTTTAAAGACCTTTTACTCAGGAGACGAAATAGATGTAGACGAAGTTTTTACAAATGATATTGCAATTGCAGATCATGCTGATAACTTAATGGTAGGAGATTATCTAGGAATAATGCCAAACTTATTCGACAAATTGAATATTCCTAGTCCTGCTCTCAAATCGTCTATACATCCTGCAAAAGTAGAGAATAGGAGTAAATTGATTTCTGCTATGAATGTATTATCAGTAGAAGATCCATCTTTGGCCTTTAGCATTAATGCTGATAATAATGAATTGGAGGTTTCGCTTTATGGAGCAACTCAACGGGAGGTGATTTTGACTTTATTGGAAGAGAGATTTTCGGTAGATGCTTACTTTGAAGAGGTGAAAACTATCTATAAAGAACGTCTTAAAACAAAATCGGAATACACCATTCATATCGAAGTGCCACCTAATCCGTATTGGGCATCTATTGGCTTGATTATAGAGCCTTTGCCAATTGGGGCGGGACTTGTAATGGAGAGTGAAATATCATTGGGATATTTGAATCGATCCTTTCAGAATGCAGTATTCGATGGAGTCAAGAAAGCCTGTGAATCGGGTTTGTACGGTTGGGAAGTAACTGACCTTAAAGTCACTTTTTCTCACGGAATCTATTATAGCCCAGTGAGTACACCTGCCGACTTTAGAAGTTTAGCACCTTATGTTTTTCGATTAGCTTTGCAACAAGCTGATGTTGAGTTATTGGAGCCAATCTTAGATTTTAAATTGCAAATTCCACTAGCTGTGAATGCTAGAGCTATTACAGACATCAACAAGATGCAAGGCGAAATATCTACTATTACTTCAGATGGTGATTGGACTACTATTTTGGGTAATATTCCTTTAGATACTAGTAAAGAATACTCAGCAGAGGTCAGTTCCTACACACAAGGCTTGGGCGTTTTTGTTACTCGATTTTCGGGTTATCGACCTACCAACAAAAAGGTAAGCAGAAGTGTAGAACTGAATGAAAAAGATAAGCTGATGTATATGTTTGAGAAGGAAAGTATCAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36798","NCBI_taxonomy_name":"Bacteroides coprosuis DSM 18011","NCBI_taxonomy_id":"679937"}}}},"ARO_accession":"3000197","ARO_id":"36336","ARO_name":"tet36","ARO_description":"Tet36 is a tetracycline resistance gene found in Bacteroides similar to Tet(Q), and binds to the ribosome to confer antibiotic resistance as a ribosomal protection protein.","ARO_category":{"35921":{"category_aro_accession":"0000002","category_aro_cvterm_id":"35921","category_aro_name":"tetracycline-resistant ribosomal protection protein","category_aro_description":"A family of proteins known to bind to the 30S ribosomal subunit. This interaction prevents tetracycline and tetracycline derivatives from inhibiting ribosomal function. Thus, these proteins confer elevated resistance to tetracycline derivatives as a ribosomal protection protein.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1709":{"model_id":"1709","model_name":"TEM-115","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1952":{"protein_sequence":{"accession":"AAN04881.1","sequence":"MSIQHFRVALIPFFAAFCFPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDHWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AF535127","fmin":"208","fmax":"1069","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCTTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCATTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000978","ARO_id":"37358","ARO_name":"TEM-115","ARO_description":"TEM-115 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1711":{"model_id":"1711","model_name":"AQU-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"725"}},"model_sequences":{"sequence":{"1113":{"protein_sequence":{"accession":"BAM76830.1","sequence":"MKQTSPLSSLALSALLLSPLTQAAPADPLVGVVDEVIRPLVKEHRIPGMAVAVFKEGQPHYFNYGVAELATGKKVSEQTLFEIGSVSKTYTATLGAYAVVKGSIGLDDKVSRHAPWLKGSAFDGITMAELATYSAGGLPLQFPDEVESLEQMQAYYRQWTPAYQPGSHRQYSNPSIGLFGYLAASSLQQPFAQLMEQTLLPGLGLHHTYINVPKQAMANYAYGYSKEDKPIRVTPGVLADEAYGIKTSSADLLAFVKANINGVDDKGLQQAIALTHQGRYSVGEMTQGLGWESYPYPVSEQTLLAGNSVQVIMKANPTTAAPKEMGSQRLFNKTGSTNGFGAYVAFVPAKGVGIVMLANRNYPIQERVKAAHSILSKLAP"},"dna_sequence":{"accession":"AB765395","fmin":"0","fmax":"1143","strand":"+","sequence":"ATGAAGCAAACCTCACCCTTGTCGTCGCTGGCGCTGAGCGCCCTGCTGCTGTCGCCCCTCACCCAGGCCGCTCCCGCCGATCCGCTGGTCGGGGTAGTGGATGAGGTCATTCGTCCGCTGGTGAAAGAGCACAGGATCCCGGGCATGGCGGTAGCCGTGTTCAAAGAGGGGCAACCCCACTACTTCAACTACGGGGTTGCCGAGCTGGCGACGGGGAAGAAGGTCAGCGAGCAGACCCTGTTCGAGATTGGCTCGGTCAGCAAAACCTATACCGCCACCCTGGGGGCCTACGCCGTGGTCAAGGGGAGCATTGGGCTGGATGACAAGGTGAGCCGGCACGCTCCCTGGCTCAAGGGCTCCGCCTTTGATGGCATCACCATGGCCGAGCTTGCCACTTACAGTGCCGGGGGTCTGCCGCTGCAATTCCCCGACGAGGTGGAATCGCTCGAGCAGATGCAGGCTTACTATCGCCAGTGGACGCCGGCCTATCAACCAGGCAGCCATCGCCAGTACTCCAACCCCAGTATCGGCCTGTTCGGCTATCTGGCGGCGAGCAGTCTGCAGCAGCCGTTTGCCCAGTTGATGGAGCAGACCCTGCTGCCCGGGCTCGGCCTGCATCACACCTATATCAATGTGCCGAAGCAGGCGATGGCGAACTACGCCTATGGCTATTCGAAAGAGGACAAGCCCATCAGGGTCACGCCAGGGGTGCTGGCGGACGAGGCCTACGGCATCAAGACCAGCTCGGCGGATCTGCTCGCCTTCGTGAAGGCCAACATCAACGGGGTGGATGACAAGGGATTGCAGCAGGCCATCGCTTTGACCCACCAGGGGCGCTACTCGGTAGGCGAGATGACCCAGGGGCTGGGCTGGGAGAGTTACCCCTATCCGGTCAGCGAGCAGACGCTGCTGGCGGGCAACTCGGTCCAGGTGATCATGAAGGCCAATCCGACGACGGCCGCGCCGAAGGAGATGGGGAGCCAGCGGCTCTTCAACAAGACCGGCTCGACCAACGGCTTTGGCGCCTATGTGGCCTTCGTGCCGGCCAAGGGAGTGGGCATCGTCATGCTGGCCAACCGCAACTACCCCATCCAGGAGAGGGTAAAGGCGGCCCACTCCATCCTGAGCAAGCTGGCTCCCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39651","NCBI_taxonomy_name":"Aeromonas dhakensis","NCBI_taxonomy_id":"196024"}}}},"ARO_accession":"3002993","ARO_id":"39427","ARO_name":"AQU-1","ARO_description":"AQU-1 is a chromosomal class C beta-lactamase found in clinical Aeromonas dhakensis isolates","ARO_category":{"39426":{"category_aro_accession":"3002992","category_aro_cvterm_id":"39426","category_aro_name":"AQU beta-lactamase","category_aro_description":"AQU beta-lactamases are chromosomal class C beta-lactamases that confer resistance to cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1712":{"model_id":"1712","model_name":"IMP-41","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1970":{"protein_sequence":{"accession":"BAM62795.1","sequence":"MKKLFVLCIFLFCSITAAGASLPDLKIEKLEEGVYVHTSFEEVNGWGVFSKHGLVVLVNTDAYLIDTPFTAKDTEKLVNWFVERGYKIKGSISSHFHSDSTGGIEWLNSQSIPTYASVLTNELLKKDGKVQAKNSFSGVSYWLVKNKIEVFYPGPGHTQDNVVVWLPKNKILFGGCFVKPYGLGNLDDANVEAWPHSAEKLISKYGNAKLVVPSHSDIGDASLLKLTWEQAVKGLNESKKSNTVH"},"dna_sequence":{"accession":"AB753458","fmin":"0","fmax":"738","strand":"+","sequence":"ATGAAAAAACTATTTGTTTTATGTATATTTTTGTTTTGTAGCATTACTGCCGCAGGAGCGTCTTTGCCTGATTTAAAAATTGAGAAGCTTGAAGAGGGTGTTTATGTTCATACATCGTTTGAAGAAGTTAACGGCTGGGGTGTTTTTTCTAAACACGGTTTGGTGGTTCTTGTAAATACTGACGCCTATCTGATTGACACTCCATTTACTGCTAAAGATACTGAAAAGTTAGTCAATTGGTTTGTGGAGCGCGGCTATAAAATCAAAGGCAGTATTTCCTCACATTTCCATAGCGACAGCACGGGTGGAATAGAGTGGCTTAATTCTCAATCTATTCCCACGTATGCATCTGTATTAACAAATGAACTTCTCAAAAAAGACGGTAAGGTGCAAGCTAAAAACTCATTTAGCGGAGTTAGCTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCAGGGCACACTCAAGATAACGTAGTGGTTTGGCTACCTAAAAATAAAATCTTATTTGGTGGTTGTTTTGTTAAACCATATGGTCTTGGTAATCTAGATGACGCAAATGTTGAAGCATGGCCACATTCGGCTGAAAAATTAATATCTAAGTATGGTAATGCAAAACTGGTTGTTCCAAGCCATAGTGACATAGGAGATGCGTCGCTCTTGAAGCTTACGTGGGAACAGGCGGTAAAAGGGCTTAATGAAAGCAAAAAAAGTAACACTGTTCATTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002232","ARO_id":"38632","ARO_name":"IMP-41","ARO_description":"IMP-41 is a beta-lactamase found in Pseudomonas and Acinetobacter spp.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1713":{"model_id":"1713","model_name":"vanYM","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"479":{"protein_sequence":{"accession":"ACL82959.1","sequence":"MVFQGNLLLVNNEYPVLEESIKTDVVNLFKHDELTKGYELLNREIYLSEKVAREFSEMVDAAEKEGVRHFSINSGFRNFDEQNALYQEMGSDYALPAGYSEHNLGLALDIGSTQMEMSEAPEGKWLEDNAWEYGFILRYPMDKTAITGIQYEPWHFRYVGLPHSAIIEEKNFALEEYLDFLKEQKSISGTIHGENYEISYYPITEKTDIEMPANLHYEISGNNMDGVIVTVYR"},"dna_sequence":{"accession":"FJ349556","fmin":"3056","fmax":"3758","strand":"+","sequence":"ATGGTCTTTCAAGGAAACTTACTCTTGGTTAATAACGAATATCCGGTTCTCGAAGAGAGTATAAAAACAGACGTTGTAAATTTATTTAAACATGATGAATTGACAAAAGGATATGAATTGCTCAATAGGGAAATTTATTTATCGGAGAAAGTTGCCCGTGAATTTTCAGAGATGGTAGATGCGGCTGAAAAAGAAGGAGTTCGCCATTTTTCAATCAATAGTGGGTTTCGAAACTTTGATGAGCAAAATGCCCTTTATCAAGAAATGGGGTCTGACTACGCCTTGCCTGCAGGTTATAGCGAACATAATTTAGGTTTAGCACTTGATATCGGATCTACTCAAATGGAAATGAGTGAGGCACCGGAAGGAAAGTGGCTAGAAGATAATGCGTGGGAATACGGCTTTATTTTACGCTATCCAATGGACAAAACGGCCATCACAGGTATTCAGTATGAACCTTGGCATTTTCGCTATGTGGGATTACCGCACAGTGCAATTATAGAGGAAAAGAATTTTGCTTTAGAAGAATATTTGGATTTCCTAAAAGAACAAAAATCCATTTCAGGTACTATACATGGCGAAAATTATGAGATTTCTTATTATCCTATTACCGAAAAAACAGACATTGAAATGCCTGCCAATCTTCATTATGAAATATCAGGAAACAATATGGATGGTGTGATTGTGACAGTGTATCGCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002961","ARO_id":"39395","ARO_name":"vanYM","ARO_description":"vanYM is a vanY variant found in the vanM gene cluster","ARO_category":{"36216":{"category_aro_accession":"3000077","category_aro_cvterm_id":"36216","category_aro_name":"vanY","category_aro_description":"VanY is a D,D-carboxypeptidase that cleaves removes the terminal D-Ala from peptidoglycan for the addition of D-Lactate. The D-Ala-D-Lac peptidoglycan subunits have reduced binding affinity with vancomycin compared to D-Ala-D-Ala.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1714":{"model_id":"1714","model_name":"ErmW","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"493":{"protein_sequence":{"accession":"BAA03402.1","sequence":"MSSIRRRHAAASLDTPAVGGRHELGQNFLVDRGVCTRIAEVVSSTTAHPVLELGAGDGAITRALVAANLPVTALELDPRRVRRLQRTFADGVTVVHGDMLRYDFGPYPHHVVSTVPFSITTPLLRRLIGQRFWHTAVLLVQWEVARKRAGVGGTTMLTAASWPWYEFTLVERVPKTSFDPVPSVDGGILVIERRSAPLLDDRCVGDYQNLVREVYTGPGRGLAAILRTRLPGREVDAWLRRERVDPAALPRDLKAGHWASLYRLYREVGTRPAPAGRSVRARPGSVGPDRSLPPRGLRSGPPRARRRGGGA"},"dna_sequence":{"accession":"D14532","fmin":"1038","fmax":"1974","strand":"+","sequence":"ATGTCATCAATCCGGCGCCGGCACGCCGCCGCTTCGCTCGACACCCCTGCCGTGGGCGGCAGGCACGAACTCGGTCAGAACTTCCTCGTCGACCGAGGTGTATGCACAAGGATCGCCGAGGTCGTCTCCTCGACGACGGCCCATCCGGTCCTCGAACTGGGCGCCGGTGACGGTGCCATCACCCGGGCCCTGGTCGCGGCGAATCTCCCGGTCACCGCGCTGGAACTCGACCCCCGGCGGGTCCGGCGGCTCCAGCGGACCTTCGCCGACGGGGTCACCGTCGTGCACGGGGACATGCTCCGGTACGACTTCGGGCCGTACCCGCACCACGTGGTGTCGACCGTGCCGTTCTCCATCACCACGCCGCTGCTCCGGCGCCTGATCGGCCAGCGGTTCTGGCACACCGCGGTGCTGTTGGTGCAGTGGGAGGTGGCCCGTAAGCGGGCCGGTGTGGGCGGCACCACGATGCTCACCGCAGCCAGTTGGCCGTGGTACGAGTTCACCCTGGTGGAGCGGGTGCCGAAGACCTCGTTCGACCCGGTGCCGAGCGTCGACGGCGGCATCCTCGTCATCGAGCGTCGATCCGCGCCGCTGCTCGACGACCGCTGCGTGGGTGACTACCAGAACCTGGTACGCGAGGTGTACACCGGTCCCGGTCGTGGTCTGGCCGCGATTCTCCGTACCCGTCTGCCCGGTCGTGAGGTGGACGCCTGGCTCCGCCGCGAGCGGGTGGACCCGGCGGCCCTGCCCCGCGACCTCAAGGCCGGGCACTGGGCATCCCTCTACCGGCTCTACCGGGAGGTGGGTACTCGGCCCGCCCCTGCCGGCCGGTCCGTCCGGGCCCGGCCCGGATCCGTCGGCCCCGACCGCTCGCTCCCTCCGCGCGGCCTGCGATCCGGTCCGCCGAGGGCTCGACGACGTGGTGGAGGCGCCTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39571","NCBI_taxonomy_name":"Micromonospora griseorubida","NCBI_taxonomy_id":"28040"}}}},"ARO_accession":"3001306","ARO_id":"37705","ARO_name":"ErmW","ARO_description":"ErmW is a methyltransferase found in the mycinamicin producer Micromonospora griseorubida. Like other Erm enzymes, it catalyzes the methylation of A2058 of the 23S ribosomal RNA. The gene is found within the mycinamicin biosynthetic cluster and is responsible for self-resistance.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1715":{"model_id":"1715","model_name":"OXA-73","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1218":{"protein_sequence":{"accession":"AAW22056.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETPSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKPQVGWLTGWVEQPDGKIVAFALKMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"AY762325","fmin":"115","fmax":"937","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGACCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCCCAATTAGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAAAATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001785","ARO_id":"38185","ARO_name":"OXA-73","ARO_description":"OXA-73 is a beta-lactamase found in Klebsiella pneumonia","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1716":{"model_id":"1716","model_name":"OXA-398","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1613":{"protein_sequence":{"accession":"AIT76095.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETPSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKQQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"KM087842","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGACCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCCCAATTAGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACAACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001584","ARO_id":"37984","ARO_name":"OXA-398","ARO_description":"OXA-398 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1717":{"model_id":"1717","model_name":"OXA-230","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"971":{"protein_sequence":{"accession":"AFM55002.1","sequence":"MKFKMKGLFCVILSSLAFSGCVYDSKLQRPVISERETEIPLLFNQAQTQAVFVTYDGIHLKSYGNDLSRAKTEYIPASTFKMLNALIGLQNGKATNTEVFQWNGEKRAFSAWEKDMTLAEAMQASAVPVYQELARRIGLELMREEVKRVGFGNAEIGQQVDNFWLVGPLKISPEQEVQFAYQLAMKQLPFDRNVQQQVKDMLYIERRGDSKLYAKSGWGMDVEPQVGWYTGWVEQPNGKVTAFALNMNMQAGNDPAERKQLTLSILDKLGLFFYLR"},"dna_sequence":{"accession":"JQ422054","fmin":"100","fmax":"931","strand":"+","sequence":"ATGAAGTTTAAAATGAAAGGTTTATTTTGTGTCATCCTCAGTAGTTTGGCATTTTCAGGTTGTGTTTATGATTCAAAACTACAACGCCCAGTCATATCAGAGCGAGAAACTGAGATTCCTTTATTATTTAATCAAGCACAGACTCAAGCTGTGTTTGTTACTTATGATGGGATTCATCTAAAAAGTTATGGTAATGATCTAAGCCGAGCAAAGACTGAATATATTCCTGCATCTACATTTAAGATGTTGAATGCTTTAATTGGCTTGCAAAATGGAAAAGCAACCAATACTGAAGTATTTCAGTGGAATGGTGAAAAGCGTGCTTTTTCAGCATGGGAAAAAGATATGACTTTGGCAGAAGCGATGCAGGCTTCAGCTGTTCCCGTATATCAAGAGCTTGCTCGACGTATTGGCTTGGAATTGATGCGTGAAGAAGTGAAGCGTGTAGGTTTTGGCAATGCGGAGATTGGTCAGCAAGTCGATAATTTTTGGTTGGTGGGTCCTTTAAAAATCTCCCCTGAACAAGAAGTTCAATTTGCCTATCAACTGGCGATGAAGCAATTACCTTTTGATCGAAATGTACAGCAACAAGTCAAAGATATGCTTTATATCGAGAGACGTGGTGACAGTAAACTGTATGCTAAAAGTGGTTGGGGAATGGATGTTGAACCTCAAGTGGGTTGGTATACGGGATGGGTTGAACAACCCAATGGCAAGGTGACTGCATTTGCGTTAAATATGAACATGCAAGCAGGTAATGATCCAGCTGAACGTAAACAATTAACCTTAAGTATTTTGGACAAATTGGGTCTATTTTTTTATTTAAGATAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39090","NCBI_taxonomy_name":"Acinetobacter bereziniae","NCBI_taxonomy_id":"106648"}}}},"ARO_accession":"3001693","ARO_id":"38093","ARO_name":"OXA-230","ARO_description":"OXA-230 is a beta-lactamase found in A. bereziniae","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1719":{"model_id":"1719","model_name":"ceoA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"730"}},"model_sequences":{"sequence":{"302":{"protein_sequence":{"accession":"AAB58160.1","sequence":"MAILRTSRSRIATAAIVTLAVVGLGTFGAMRVSANAPEKAAAPLPEVDVATVVPQTVTDWQSYSGRLEAVEKVDVRPQVSGTIVAVNFKDGALVKKGDVLFVIDPRPYQAEVDRAAAQLAAAQARNGYAQTDWQRAQRLIGDNAIAKRDYDEKQNAAREAKREPEGRRSRAGNGAHQSRLYAHHRAGVGPRVARGNHARQRRVGRRVGRAADDAGIGVADLRVVRRRRADLPAIHQRRAQRPQGAGRARPRERNRLLAQRRDRFGRQPARHVVRHDPRARPLRQRGRHPGPGPLRTREGGRQRAARGAARRRRGDQHRPGQEVRVRRRPAGPRVVSRSAARDAARQPARDRERAVGRRPRGRERHAARASGRAGEAAHGPDDGRRCAVRAVASTAKPAAPAKADS"},"dna_sequence":{"accession":"U97042","fmin":"0","fmax":"1218","strand":"+","sequence":"ATGGCCATCCTACGCACCTCCCGTTCCCGAATCGCGACCGCGGCGATCGTCACGCTCGCCGTCGTCGGCCTCGGCACGTTCGGCGCGATGCGCGTGAGCGCGAACGCCCCCGAGAAAGCGGCGGCGCCGCTGCCCGAAGTCGACGTCGCGACCGTCGTGCCGCAGACCGTGACCGACTGGCAAAGCTATTCGGGCCGCCTCGAGGCGGTCGAGAAAGTCGACGTGCGCCCGCAGGTGTCGGGCACGATCGTCGCGGTGAACTTCAAGGACGGCGCGCTCGTGAAGAAAGGCGACGTGCTGTTCGTGATCGACCCGCGCCCGTACCAGGCGGAAGTCGACCGCGCCGCCGCGCAGCTCGCGGCCGCGCAGGCCCGCAACGGCTACGCGCAGACCGACTGGCAGCGCGCGCAGCGGCTGATCGGCGACAACGCGATCGCGAAGCGCGACTACGACGAGAAGCAGAACGCGGCGCGCGAAGCGAAACGCGAACCTGAAGGCCGCCGAAGCCGCGCTGGAAACGGCGCGCATCAATCTCGGCTATACGCGCATCACCGCGCCGGTGTCGGGCCGCGTGTCGCGCGCGGAAATCACGCTCGGCAACGTCGTGTCGGCCGGCGCGTCGGCCGCGCCGCTGACGACGCTGGTATCGGTGTCGCCGATCTACGCGTCGTTCGACGCCGACGAGCAGACCTACCTGCAATACATCAACGGCGCGCGCAGCGGCCGCAAGGTGCCGGTCGAGCTCGGCCTCGCGAACGAAACCGGCTACTCGCGCAGCGGCGAGATCGATTCGGTCGACAACCGGCTCGACACGTCGTCCGGCACGATCCGCGTGCGCGCCCGCTTCGACAACGCGGACGGCACCCTGGTCCCGGGCCTCTACGCACGCGTGAAGGTGGGCGGCAGCGCGCCGCACGAGGCGCTGCTCGTCGACGACGCGGCGATCAACACCGACCAGGACAAGAAGTTCGTGTTCGTCGTCGACCAGCAGGGCCGCGTGTCGTATCGCGAAGTGCAGCAAGGGATGCAGCACGGCAACCGGCGCGTGATCGTGAGCGGGCTGTCGGCCGGCGACCGCGTGGTCGTGAACGGCACGCAGCGCGTGCGTCCGGGCGAGCAGGTGAAGCCGCACATGGTCCCGATGACGGGCGGCGATGCGCCGTCCGCGCCGTCGCGAGCACCGCGAAGCCGGCCGCACCGGCGAAGGCGGATTCGTAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36822","NCBI_taxonomy_name":"Burkholderia cepacia","NCBI_taxonomy_id":"292"}}}},"ARO_accession":"3003009","ARO_id":"39443","ARO_name":"ceoA","ARO_description":"ceoA is a periplasmic linker subunit of the CeoAB-OpcM efflux pump","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1720":{"model_id":"1720","model_name":"tap","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"75":{"protein_sequence":{"accession":"CAA03986.1","sequence":"MTNTKRGPLLLILFAALTAGAGNGITIVAFPWLVLQHNGSALDASIVAMAGTLPLLVATLIAGAAVDYLGRRRVSMISDLLSALSVAAVPVLALIFGVDAVNVAVLAVLAGLGAFFDPAGMTARETMLPEAAGRAGWTLDHANSVYEAVFNLGYIVGPGIGGLMIATLGGINTMWVTAGAFCCSILAISVLRLEGAGAPDRSVLTEAVLAGIVEGLRFVWYTPVLRTLAIVDLVATGLYMPMESVLFPKYFTDRNEPTELGWVLMALSIGGLLGALGYAVMSRYMSRRATMLTAVITLGVAMTVIAFLPPLPLILVLCAIVGFVYGPIAPIYNYVMQTTAPQHLRGRVVGVMGSLAYAAGPLGLILAGPLADAAGLHATFLALSLPMLLLGVVAVFLPRLRELDLASKP"},"dna_sequence":{"accession":"AJ000283","fmin":"619","fmax":"1849","strand":"+","sequence":"ATGACGAACACCAAGCGCGGCCCCTTGCTGCTGATCCTGTTCGCCGCGTTGACGGCCGGCGCCGGCAACGGAATCACCATCGTCGCGTTCCCGTGGCTGGTGTTGCAGCACAACGGATCCGCGCTCGACGCCTCGATCGTCGCGATGGCCGGCACCCTGCCGCTGCTGGTGGCCACACTGATCGCCGGGGCGGCGGTGGATTACCTGGGTCGCCGACGGGTTTCGATGATCTCGGATCTGCTCTCGGCGCTGTCGGTCGCTGCGGTACCCGTGCTGGCCCTGATTTTCGGGGTGGACGCGGTCAATGTCGCGGTGCTGGCGGTCCTGGCGGGGCTGGGAGCGTTCTTCGACCCGGCCGGCATGACAGCGCGCGAGACCATGCTGCCCGAGGCCGCGGGCCGGGCCGGTTGGACGCTGGACCATGCCAACTCGGTGTACGAGGCGGTCTTCAACCTGGGCTACATCGTCGGCCCCGGTATCGGCGGCCTGATGATCGCCACGCTCGGCGGGATCAACACCATGTGGGTGACGGCCGGGGCGTTCTGCTGCTCGATCCTGGCCATCTCGGTGCTGCGACTGGAGGGCGCGGGCGCGCCGGACCGCTCGGTGCTGACCGAGGCCGTTTTGGCGGGCATAGTCGAGGGACTGCGATTCGTCTGGTACACACCGGTATTGCGCACCCTGGCCATCGTCGACCTGGTGGCCACCGGCTTGTACATGCCGATGGAATCGGTCCTTTTTCCGAAGTACTTCACGGACCGGAACGAACCCACCGAACTGGGCTGGGTGCTGATGGCGTTGAGCATCGGCGGACTGTTGGGTGCGCTCGGTTACGCCGTGATGTCCAGGTACATGAGCCGACGGGCCACCATGCTGACCGCCGTGATCACCCTCGGGGTGGCGATGACGGTGATCGCCTTCCTGCCACCGCTGCCGCTGATCCTGGTGCTGTGCGCAATCGTCGGCTTCGTCTACGGACCGATCGCACCCATCTACAACTACGTCATGCAGACCACCGCTCCCCAACACCTGCGTGGCCGCGTGGTCGGGGTGATGGGCTCATTGGCCTACGCCGCGGGCCCGCTCGGGCTGATCCTGGCCGGGCCGCTGGCCGACGCCGCAGGCCTGCACGCGACGTTCCTGGCACTGTCCCTACCGATGCTGTTGCTCGGCGTCGTGGCGGTGTTCCTGCCGCGGCTGCGCGAGCTGGACCTAGCATCGAAACCGTGAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36886","NCBI_taxonomy_name":"Mycobacterium fortuitum","NCBI_taxonomy_id":"1766"}}}},"ARO_accession":"3000343","ARO_id":"36482","ARO_name":"tap","ARO_description":"Efflux pump proteins contained within Mycobacterial genomes which confer resistance to a number of different antibiotics including aminoglycosides, and tetracyclines.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1722":{"model_id":"1722","model_name":"TEM-184","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1723":{"protein_sequence":{"accession":"CCA61905.1","sequence":"MSIKHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAVTMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTTPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"FR848831","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTAAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCGTAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001375","ARO_id":"37775","ARO_name":"TEM-184","ARO_description":"From the Lahey list of beta-lactamases. Not yet released.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1723":{"model_id":"1723","model_name":"IMP-44","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"872":{"protein_sequence":{"accession":"BAM98942.1","sequence":"MKKLFVLCIFLFCSITAAGASLPDLKIEKLEEGVYVHTSFEEVNGWGVFSKHGLVVLVNTDAYLIDTPSTAKDTEKLVNWFVERGYKIKGSISSHFHSDSTGGIEWLNSQSIPTYASVLTNELLKKDGKVQAKNSFSGVSYWLVKNKIEVFYPGPGHTQDNVVVWLPKNKILFGGCFVKPYGLGNLDDANVEAWPHSAEKLISKYGNAKLVVPSHSDIGDASLLKLTWEQAVKGLNESKKSNTVH"},"dna_sequence":{"accession":"AB777501","fmin":"1398","fmax":"2136","strand":"+","sequence":"ATGAAAAAACTATTTGTTTTATGTATATTTTTGTTTTGTAGCATTACTGCCGCAGGAGCGTCTTTGCCTGATTTAAAAATTGAGAAGCTTGAAGAGGGTGTTTATGTTCATACATCGTTTGAAGAAGTTAACGGCTGGGGTGTTTTTTCTAAACACGGTTTGGTGGTTCTTGTAAATACTGACGCCTATCTGATTGACACTCCATCTACTGCTAAAGATACTGAAAAGTTAGTCAATTGGTTTGTGGAGCGCGGCTATAAAATCAAAGGCAGTATTTCCTCACATTTCCATAGCGACAGCACGGGTGGAATAGAGTGGCTTAATTCTCAATCTATTCCCACGTATGCATCTGTATTAACAAATGAACTTCTCAAAAAAGACGGTAAGGTGCAAGCTAAAAACTCATTTAGCGGAGTTAGCTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCAGGGCACACTCAAGATAACGTAGTGGTTTGGCTACCTAAAAATAAAATCTTATTTGGTGGTTGTTTTGTTAAACCATATGGTCTTGGTAATCTAGATGACGCAAATGTTGAAGCATGGCCACATTCGGCTGAAAAATTAATATCTAAGTATGGTAATGCAAAACTGGTTGTTCCAAGCCATAGTGACATAGGAGATGCGTCGCTCTTGAAGCTTACGTGGGAACAGGCGGTAAAAGGGCTTAATGAAAGCAAAAAAAGTAACACTGTTCATTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002235","ARO_id":"38635","ARO_name":"IMP-44","ARO_description":"IMP-44 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1724":{"model_id":"1724","model_name":"vanHM","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"534":{"protein_sequence":{"accession":"ACL82960.1","sequence":"MVLVMKDIGITIYGSEQDEADVFQEISSRFGVTPTIVSSPISETNVMLAPKNKCISVGHKSEIHKSILIALKESGVKYISTRSIGYNHIDMKAAEKMGIAVENVTYSPDSVADYTLMLILMAIRHTKSTLCSMEKHDFRLNSVRGKVLRDLTVGVLGTGHIGKAVIERLQGFGGHVLAYGNNKEATANYVSFNELLQKSDILTIHVPLSDDTYHMIGHEQIKAMKQGAFLINTARGGLIDTEVLVKALEDGKLGGAALDVLEGEEGLFYFDCTQKPINNQFLLKLQRMPNVTITPHTAYYSEKTLRDTVEKTVKNCLEFERRETHE"},"dna_sequence":{"accession":"FJ349556","fmin":"3883","fmax":"4864","strand":"+","sequence":"ATGGTCTTAGTAATGAAAGATATCGGCATTACCATTTATGGATCTGAGCAGGATGAGGCTGATGTGTTCCAGGAAATTTCATCTCGATTTGGCGTTACACCTACCATTGTAAGCTCTCCTATATCAGAAACCAACGTAATGTTAGCCCCTAAAAATAAGTGTATCAGCGTGGGGCACAAGTCTGAGATTCACAAATCTATCCTTATTGCATTGAAGGAATCCGGCGTCAAATATATCTCTACTCGAAGTATTGGTTACAATCATATAGATATGAAGGCAGCGGAAAAAATGGGTATTGCTGTCGAGAACGTCACTTATTCACCAGATAGTGTTGCCGATTATACATTGATGCTGATACTTATGGCAATACGCCATACGAAATCTACTTTGTGCTCTATGGAAAAACATGATTTCAGACTGAACAGCGTCCGTGGTAAAGTACTGCGTGACCTGACAGTAGGTGTACTGGGAACCGGTCATATAGGCAAAGCGGTTATTGAGCGACTACAGGGGTTTGGAGGTCACGTGTTGGCGTACGGCAACAACAAAGAGGCGACGGCAAATTATGTATCCTTCAATGAATTACTGCAAAAAAGTGACATTCTAACCATTCATGTACCCCTTAGCGATGACACATACCATATGATCGGTCACGAACAGATTAAAGCAATGAAACAGGGCGCCTTTCTTATTAATACTGCTCGAGGTGGACTTATAGATACCGAAGTTCTGGTTAAAGCACTGGAGGACGGAAAACTGGGGGGCGCCGCATTAGATGTATTAGAGGGAGAAGAAGGGCTTTTCTACTTTGATTGCACCCAAAAGCCAATTAACAATCAATTTTTGCTGAAACTTCAAAGGATGCCAAATGTGACAATCACACCGCATACGGCTTACTATAGCGAAAAAACGTTACGTGATACTGTTGAAAAAACAGTCAAGAACTGTTTGGAATTTGAGAGGAGAGAGACACATGAATAGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002947","ARO_id":"39381","ARO_name":"vanHM","ARO_description":"vanHM is a vanH variant in the vanM gene cluster","ARO_category":{"36015":{"category_aro_accession":"3000006","category_aro_cvterm_id":"36015","category_aro_name":"vanH","category_aro_description":"VanH is a D-specific alpha-ketoacid dehydrogenase that synthesizes D-lactate. D-lactate is incorporated into the end of the peptidoglycan subunits, decreasing vancomycin binding affinity.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1725":{"model_id":"1725","model_name":"TEM-101","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"842":{"protein_sequence":{"accession":"AAM18924.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASKRGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIVEIGASLIKHW"},"dna_sequence":{"accession":"AF495873","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTAAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGTCGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000964","ARO_id":"37344","ARO_name":"TEM-101","ARO_description":"TEM-101 is an extended-spectrum beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1726":{"model_id":"1726","model_name":"FOX-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1189":{"protein_sequence":{"accession":"CAB89086.1","sequence":"MQQRRALALLMLGSLLLAPCTYASGEAPLTATVDGIIQPMLKAYRIPGMAVAVLKDGKAHYFNYGVANRESGQRVSEQTLFEIGSVSKTLTATLGAYAAVKGGFELDDKVSQHAPWLKGSAFDGVTMAELATYSAGGLPLQFPDEVDSNDKMQTYYRSWSPVYPAGTHRQYSNPSIGLFGHLAANSLGQPFEQLMSQTLLPKLGLHHTYIQVPESAMANYAYGYSKEDKPIRATPGVLAAEAYGIKTGSADLLKFVEANMGYQGDAALKSAIALTHTGFHSVGEMTQGLGWESYDYPVTEQVLLAGNSPAVSFQANPVTRFAVPKAMGEQRLYNKTGSTGGFGAYVAFVPARGIAIVMLANRNYPIEARVKAAHAILSQLAE"},"dna_sequence":{"accession":"AJ277535","fmin":"0","fmax":"1149","strand":"+","sequence":"ATGCAACAACGACGTGCGCTCGCGCTACTGATGCTGGGTAGCCTGCTGTTAGCCCCTTGCACTTATGCCAGCGGGGAGGCCCCGCTGACCGCCACTGTGGACGGCATTATCCAGCCGATGCTCAAGGCGTATCGGATCCCGGGGATGGCGGTCGCTGTACTGAAAGATGGCAAGGCCCACTATTTCAACTATGGGGTTGCCAACCGCGAGAGCGGCCAGCGCGTCAGCGAGCAGACCCTGTTCGAGATTGGCTCGGTCAGCAAGACCCTGACCGCGACCCTTGGCGCCTATGCCGCAGTCAAGGGGGGCTTTGAGCTGGATGACAAGGTGAGCCAGCACGCCCCCTGGCTCAAAGGTTCCGCCTTTGATGGTGTGACCATGGCCGAGCTTGCCACCTACAGTGCGGGTGGTTTGCCGCTGCAGTTCCCCGATGAGGTAGATTCGAATGACAAGATGCAAACTTACTATCGGAGCTGGTCACCGGTTTATCCGGCGGGGACTCATCGCCAGTATTCCAACCCCAGCATAGGCCTGTTTGGTCACCTGGCCGCAAATAGTCTGGGCCAGCCATTTGAGCAACTGATGAGCCAGACCCTGCTGCCCAAACTGGGTTTGCACCACACCTATATCCAGGTGCCGGAGTCGGCCATGGCGAACTATGCCTACGGCTATTCGAAGGAAGATAAGCCTATCCGGGCCACTCCGGGCGTGCTGGCTGCCGAGGCTTACGGGATCAAGACCGGTTCGGCGGATCTGCTGAAGTTTGTCGAGGCCAACATGGGGTATCAGGGAGATGCCGCGCTAAAAAGCGCGATCGCGCTGACCCACACCGGCTTCCATTCGGTGGGGGAAATGACCCAGGGGCTGGGCTGGGAGAGTTACGACTATCCCGTCACCGAGCAGGTGCTGCTGGCGGGCAACTCACCAGCGGTGAGCTTCCAGGCCAATCCGGTTACGCGCTTTGCGGTGCCCAAAGCGATGGGCGAGCAGCGGCTCTATAACAAGACGGGCTCGACTGGTGGCTTTGGCGCCTATGTGGCGTTCGTGCCTGCCAGAGGGATAGCCATCGTCATGCTGGCCAATCGCAACTATCCCATCGAGGCCAGGGTGAAGGCGGCTCACGCCATCCTGAGTCAGTTGGCCGAGTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002158","ARO_id":"38558","ARO_name":"FOX-4","ARO_description":"FOX-4 is a beta-lactamase found in Escherichia coli","ARO_category":{"36206":{"category_aro_accession":"3000067","category_aro_cvterm_id":"36206","category_aro_name":"FOX beta-lactamase","category_aro_description":"FOX beta-lactamases are plasmid-encoded AmpC-type beta-lactamase which conferred resistance to broad-spectrum cephalosporins and cephamycins","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1727":{"model_id":"1727","model_name":"SHV-73","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1716":{"protein_sequence":{"accession":"CAJ47128.2","sequence":"MRIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPVGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADRTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM176548","fmin":"16","fmax":"874","strand":"+","sequence":"ATGCGTATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAATTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGTAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAGGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGGATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001127","ARO_id":"37507","ARO_name":"SHV-73","ARO_description":"SHV-73 is a broad-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1728":{"model_id":"1728","model_name":"OXA-42","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1934":{"protein_sequence":{"accession":"CAD32564.1","sequence":"MKFRHALSSAFVLLGCIAASAHAKTICTAIADAGTGKLLVQDGDCGRRASPASTFKIAISLMGYDAGFLRNEHDPVLPYRDSYIAWGGEAWKQPTDPTRWLKYSVVWYSQQVAHHLGAQRFAQYAKAFGYGNADVSGDPGQNNGLDRAWIGSSLQISPLEQLEFLGKMLNRKLPVSPTAVDMTERIVESTTLADGTVVHGKTGVSYPLLADGTRDWARGSGWFVGWIVRGNQTLVFARLTQDERKQPVSAGIRTREAFLRDLPRLLAAR"},"dna_sequence":{"accession":"AJ488302","fmin":"0","fmax":"810","strand":"+","sequence":"ATGAAATTCCGACACGCGCTGTCGAGCGCATTCGTTTTGCTGGGTTGCATCGCCGCGTCGGCGCATGCGAAGACGATCTGCACGGCGATCGCCGATGCGGGCACGGGCAAGCTGCTGGTGCAGGACGGCGATTGCGGCCGCCGCGCATCGCCCGCGTCGACGTTCAAGATCGCGATCAGCCTGATGGGCTACGACGCAGGCTTCCTGCGCAACGAGCATGACCCGGTGCTGCCGTATCGCGACAGTTACATCGCGTGGGGTGGCGAAGCATGGAAGCAGCCGACCGATCCGACGCGCTGGCTCAAGTATTCGGTCGTGTGGTATTCGCAGCAGGTGGCGCACCATCTCGGCGCGCAGCGCTTCGCGCAGTATGCGAAGGCGTTCGGCTACGGCAATGCGGACGTGTCCGGCGATCCCGGCCAGAACAACGGCCTCGATCGCGCGTGGATCGGCTCGTCGCTGCAGATCTCGCCGCTCGAACAATTGGAATTCCTCGGCAAGATGCTCAATCGCAAGCTGCCCGTGTCGCCCACAGCCGTCGACATGACGGAGCGGATCGTCGAATCGACGACGCTTGCCGACGGAACGGTGGTGCACGGCAAGACCGGCGTGTCCTATCCGCTGCTGGCCGACGGCACACGCGACTGGGCGCGTGGATCCGGCTGGTTCGTCGGCTGGATCGTGCGTGGCAATCAGACGCTGGTGTTCGCGCGCCTCACGCAGGACGAGCGCAAGCAGCCCGTTTCAGCCGGCATACGGACGCGCGAGGCCTTCCTGCGCGACTTGCCCCGGCTTCTCGCCGCGCGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36923","NCBI_taxonomy_name":"Burkholderia pseudomallei","NCBI_taxonomy_id":"28450"}}}},"ARO_accession":"3001769","ARO_id":"38169","ARO_name":"OXA-42","ARO_description":"OXA-42 is a beta-lactamase found in Burkholderia pseudomallei","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1729":{"model_id":"1729","model_name":"CTX-M-66","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1107":{"protein_sequence":{"accession":"ABQ45409.1","sequence":"MVKKSLRQFTLMATATVTLLLGNVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"EF576988","fmin":"239","fmax":"1115","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAATGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3001927","ARO_id":"38327","ARO_name":"CTX-M-66","ARO_description":"CTX-M-66 is a beta-lactamase found in Proteus mirabilis","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1730":{"model_id":"1730","model_name":"OXA-235","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1296":{"protein_sequence":{"accession":"AFH36330.1","sequence":"MKTLILLPLLSCLSLTACSLPVSNSSSQITSTQSIQTIAKLFDQAQSSGVLVIQRGPHLQVYGNDLSRAHTEYIPASTFKILNALIGLQHGKATTNEIFKWDGKKRSFAAWEKDMTLGQAMQASAVPVYQELARRIGLELMQQEVQRIRFGNQQIGQHIDNFWLVGPLKITPEQEVEFASALAQEQLAFDPQVQQQVKAMLLLQERQDYRLYAKSGWGMDVEPQVGWLTGWIETPQDEIVAFSLNMQMQSNMDPAIRLKILQQALAELALYPKAEG"},"dna_sequence":{"accession":"JQ820240","fmin":"590","fmax":"1421","strand":"+","sequence":"ATGAAAACTCTTATTTTGTTGCCTTTACTTAGTTGCTTGAGCCTGACAGCCTGTAGCTTGCCTGTTTCAAATTCGTCCTCTCAAATCACTTCAACTCAATCTATTCAAACCATTGCCAAATTATTTGATCAGGCACAAAGCTCTGGCGTTTTAGTAATTCAACGGGGCCCACATCTACAGGTCTATGGCAATGATTTGAGTCGTGCACATACCGAATATATTCCTGCTTCAACCTTTAAAATACTCAATGCCCTGATTGGCCTGCAACATGGTAAAGCCACGACCAATGAAATCTTTAAATGGGATGGCAAGAAGCGCAGTTTTGCAGCCTGGGAAAAAGACATGACTCTCGGCCAAGCCATGCAAGCTTCTGCTGTACCCGTCTATCAGGAACTGGCACGTCGCATTGGTCTGGAACTAATGCAACAGGAAGTGCAACGCATTCGATTTGGTAATCAGCAGATTGGTCAGCATATCGACAACTTCTGGTTAGTCGGACCTTTGAAAATCACCCCGGAACAAGAAGTCGAATTTGCCTCTGCGCTTGCTCAAGAGCAACTTGCCTTTGATCCTCAAGTCCAGCAACAAGTCAAAGCCATGTTACTGTTACAGGAGCGACAAGATTATCGACTATATGCCAAATCTGGTTGGGGTATGGATGTGGAGCCGCAAGTCGGCTGGCTCACCGGCTGGATCGAAACACCTCAGGACGAAATCGTGGCATTTTCACTGAATATGCAGATGCAAAGTAATATGGATCCGGCGATCCGTCTTAAAATTTTGCAGCAGGCCTTGGCCGAATTAGCGCTTTATCCGAAAGCTGAAGGGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001676","ARO_id":"38076","ARO_name":"OXA-235","ARO_description":"OXA-235 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1731":{"model_id":"1731","model_name":"mphB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"637":{"protein_sequence":{"accession":"BAA12910.1","sequence":"MSKDIKQVIEIAKKHNLFLKEETIQFNESGLDFQAVFAQDNNGIDWVLRLPRREDVMPRTKVEKQALDLVNKYAISFQAPNWIIYTEELIAYKKLDGVPAGTIDHNIGNYIWEIDINNVPELFHKSLGRVLAELHSIPSNKAAALDLVVHTPEEARMSMKQRMDAVRAKFGVGENLWNRWQAWLNDDDMWPKKTGLIHGDVHAGHTMIDKDANVTGLIDWTEAKVTDVSHDFIFNYRAFGEEGLEALILAYKEIGGYYWPKMKEHIIELNAAYPVSIAEFALVSGIEEYEQMAKEALEVQGS"},"dna_sequence":{"accession":"D85892","fmin":"1158","fmax":"2067","strand":"+","sequence":"ATGAGTAAAGATATTAAACAAGTAATCGAGATAGCAAAAAAACACAATCTTTTTCTAAAAGAAGAAACGATACAGTTTAATGAATCAGGGCTTGATTTTCAAGCTGTTTTTGCACAAGATAATAATGGAATTGATTGGGTTCTAAGATTGCCTAGACGGGAAGATGTGATGCCTAGAACAAAGGTAGAAAAACAAGCTTTGGATTTGGTAAATAAGTACGCTATATCCTTTCAGGCACCAAACTGGATCATTTACACAGAGGAACTAATAGCTTATAAAAAGTTAGATGGTGTGCCAGCAGGTACGATAGATCATAACATAGGTAACTATATTTGGGAGATAGACATAAATAATGTTCCAGAATTATTTCACAAGTCGCTAGGCAGGGTGTTAGCAGAGCTTCATAGCATACCTAGTAATAAAGCCGCAGCGCTTGATCTTGTAGTACACACACCAGAAGAAGCAAGAATGTCAATGAAGCAGCGTATGGATGCAGTAAGAGCAAAGTTCGGAGTAGGTGAGAATCTATGGAACAGATGGCAAGCGTGGTTGAATGATGATGATATGTGGCCTAAGAAAACTGGACTGATTCATGGAGATGTACATGCCGGACATACTATGATTGATAAGGATGCCAATGTGACTGGATTAATCGATTGGACTGAAGCGAAGGTTACAGATGTTTCGCATGACTTTATTTTCAACTATAGAGCTTTTGGGGAAGAAGGGTTAGAAGCTTTAATTCTCGCTTATAAGGAAATTGGTGGATATTACTGGCCTAAAATGAAAGAGCATATTATCGAACTTAATGCAGCATACCCAGTTTCAATCGCTGAGTTTGCATTAGTGTCTGGAATTGAGGAATATGAGCAGATGGCAAAGGAAGCATTGGAAGTACAAGGTTCGTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000318","ARO_id":"36457","ARO_name":"mphB","ARO_description":"The mphB gene encodes for MPH(2')-II. This enzymes phosphorylates 14-membered and 16-membered macrolides.  It phosphorylates macrolides in GTP- dependent manner at 2'-OH hydroxyl of desosamine sugar of macrolides.","ARO_category":{"36472":{"category_aro_accession":"3000333","category_aro_cvterm_id":"36472","category_aro_name":"macrolide phosphotransferase (MPH)","category_aro_description":"Macrolide phosphotransferases (MPH) are enzymes encoded by macrolide phosphotransferase genes (mph genes). These enzymes phosphorylate macrolides in GTP dependent manner at 2'-OH of desosamine sugar thereby inactivating them. Characterized MPH's are differentiated based on their substrate specificity.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35946":{"category_aro_accession":"0000027","category_aro_cvterm_id":"35946","category_aro_name":"roxithromycin","category_aro_description":"Roxithromycin is a semi-synthetic, 14-carbon ring macrolide antibiotic derived from erythromycin. It is used to treat respiratory tract, urinary and soft tissue infections. Roxithromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35974":{"category_aro_accession":"0000057","category_aro_cvterm_id":"35974","category_aro_name":"telithromycin","category_aro_description":"Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36315":{"category_aro_accession":"3000176","category_aro_cvterm_id":"36315","category_aro_name":"dirithromycin","category_aro_description":"Dirithromycin is an oxazine derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome to inhibit bacterial protein synthesis.","category_aro_class_name":"Antibiotic"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1732":{"model_id":"1732","model_name":"SHV-151","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1145":{"protein_sequence":{"accession":"AFQ23957.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQPSGSVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"JX121118","fmin":"0","fmax":"858","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCCGTCGGGCAGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001190","ARO_id":"37570","ARO_name":"SHV-151","ARO_description":"SHV-151 is a beta-lactamase.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1733":{"model_id":"1733","model_name":"OXA-415","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1765":{"protein_sequence":{"accession":"AIG94927.1","sequence":"MAIRIFAILFSIFSLATFAHAQEGTLERSDWRKFFSEFQAKGTIVVADERQADRAMLVFDPVRSKKRYSPASTFKIPHTLFALDAGAVRDEFQIFRWDGVNRGFAGHNQDQDLRSAMRNSTVWVYELFAKEIGDDKARRYLKKIDYGNADPSTSNGDYWIEDSLAISAQEQIAFLRKLYRNELPFRVEHQRLVKDLMIVEAGRNWILRAKTGWEGRMGWWVGWVEWPTGSVFFALNIDTPNRMDDLFKREAIVRAILRSIEALPPNPAVNSDAAR"},"dna_sequence":{"accession":"KJ865754","fmin":"0","fmax":"828","strand":"+","sequence":"ATGGCAATCCGAATCTTCGCGATACTTTTCTCCATTTTTTCTCTTGCCACTTTCGCGCATGCGCAAGAAGGCACGCTAGAACGTTCTGACTGGAGGAAGTTTTTCAGCGAATTTCAAGCCAAAGGCACGATAGTTGTGGCAGACGAACGCCAAGCGGATCGTGCCATGTTGGTTTTTGATCCTGTGCGATCGAAGAAACGCTACTCGCCTGCATCGACATTCAAGATACCTCATACACTTTTTGCACTTGATGCAGGCGCTGTTCGTGATGAGTTCCAGATTTTTCGATGGGACGGCGTTAACAGGGGCTTTGCAGGCCACAATCAAGACCAAGATTTGCGATCAGCAATGCGGAATTCTACTGTTTGGGTGTATGAGCTATTTGCAAAGGAAATTGGTGATGACAAAGCTCGGCGCTATTTGAAGAAAATCGACTATGGCAACGCCGATCCTTCGACAAGTAATGGCGATTACTGGATAGAAGACAGCCTTGCAATCTCGGCGCAGGAGCAAATTGCATTTCTCAGGAAGCTCTATCGTAACGAGCTGCCCTTTCGGGTAGAACATCAGCGCTTGGTCAAGGATCTCATGATTGTGGAAGCCGGTCGCAACTGGATACTGCGTGCAAAGACGGGCTGGGAAGGCCGTATGGGTTGGTGGGTAGGATGGGTTGAGTGGCCGACTGGCTCCGTATTCTTCGCACTGAATATTGATACGCCAAACAGAATGGATGATCTTTTCAAGAGGGAGGCAATCGTGCGGGCAATCCTTCGCTCTATTGAAGCGTTACCGCCCAACCCGGCAGTCAACTCGGACGCTGCGCGATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001606","ARO_id":"38006","ARO_name":"OXA-415","ARO_description":"OXA-415 is a beta-lactamase. From the Lahey list of OXA beta-lactamases","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1734":{"model_id":"1734","model_name":"IND-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1016":{"protein_sequence":{"accession":"AAG29765.2","sequence":"MRKNVRIFTVLSLFLINFFNAQARDFVIEQPFGKQLYLYKTFGVFDGKEYSTNALYLVTKKGVVLFDVPWQKTQYQSLMDTIKKRHNLPVIAVFATHSHSDRAGDLSFYNKKGIPTYATAKTNELLKKEGKATSSKLTKIGKKYKIGGEEFTVDFLGEGHTADNVVVWFPKYNVLDGGCLVKSSAAVDLGYTGEANVEQWPATMKKLQAKYPSTAKVIPGHDEWKGNDHVKHTLELLDQQKQ"},"dna_sequence":{"accession":"AF219135","fmin":"0","fmax":"729","strand":"+","sequence":"ATGAGGAAAAATGTTAGGATTTTTACTGTGTTGTCTCTGTTCTTAATTAATTTTTTTAATGCGCAGGCCCGTGACTTTGTAATTGAGCAGCCTTTTGGCAAACAACTTTATCTGTATAAAACCTTCGGAGTTTTTGACGGCAAAGAATATTCAACCAATGCGCTTTATCTGGTCACTAAAAAAGGAGTAGTCCTTTTTGATGTCCCATGGCAGAAAACCCAGTATCAAAGTCTTATGGATACGATAAAGAAACGTCATAACTTACCGGTGATCGCTGTATTTGCAACACATTCACACTCAGACAGAGCCGGAGACCTGAGTTTTTACAATAAAAAAGGCATCCCGACCTATGCCACGGCCAAAACCAATGAACTGCTGAAGAAAGAAGGAAAAGCAACTTCCAGTAAATTAACAAAGATTGGAAAGAAATATAAAATAGGCGGTGAAGAATTCACTGTAGACTTCTTAGGTGAAGGTCACACAGCAGATAACGTGGTGGTTTGGTTTCCAAAATATAACGTCCTGGACGGTGGCTGCTTAGTGAAAAGCAGTGCAGCAGTTGATCTTGGATATACAGGAGAAGCTAATGTAGAACAATGGCCGGCAACCATGAAAAAGCTGCAGGCTAAATACCCCTCCACTGCAAAGGTAATTCCGGGACACGACGAGTGGAAAGGCAACGACCATGTAAAACATACACTGGAGCTTTTAGATCAACAAAAACAGTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36916","NCBI_taxonomy_name":"Chryseobacterium indologenes","NCBI_taxonomy_id":"253"}}}},"ARO_accession":"3002260","ARO_id":"38660","ARO_name":"IND-4","ARO_description":"IND-4 is a beta-lactamase found in Chryseobacterium indologenes","ARO_category":{"36199":{"category_aro_accession":"3000060","category_aro_cvterm_id":"36199","category_aro_name":"IND beta-lactamase","category_aro_description":"IND beta-lactamases are class B carbapenem-hydrolyzing beta-lactamases","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1735":{"model_id":"1735","model_name":"vatA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"144":{"protein_sequence":{"accession":"AAA26683.1","sequence":"MNLNNDHGPDPENILPIKGNRNLQFIKPTITNENILVGEYSYYDSKRGESFEDQVLYHYEVIGDKLIIGRFCSIGPGTTFIMNGANHRMDGSTYPFHLFRMGWEKYMPSLKDLPLKGDIEIGNDVWIGRDVTIMPGVKIGDGAIIAAEAVVTKNVAPYSIVGGNPLKFIRKRFSDGVIEEWLALQWWNLDMKIINENLPFIINGDIEMLKRKRKLLDDT"},"dna_sequence":{"accession":"L07778","fmin":"0","fmax":"660","strand":"+","sequence":"TTGAATTTAAACAATGACCATGGACCTGATCCCGAAAATATTTTACCGATAAAAGGGAATCGGAATCTTCAATTTATAAAACCTACTATAACGAACGAAAACATTTTGGTGGGGGAATATTCTTATTATGATAGTAAGCGAGGAGAATCCTTTGAAGATCAAGTCTTATATCATTATGAAGTGATTGGAGATAAGTTGATTATAGGAAGATTTTGTTCAATTGGTCCCGGAACAACATTTATTATGAATGGTGCAAACCATCGGATGGATGGATCAACATATCCTTTTCATCTATTCAGGATGGGTTGGGAGAAGTATATGCCTTCCTTAAAAGATCTTCCCTTGAAAGGGGACATTGAAATTGGAAATGATGTATGGATAGGTAGAGATGTAACCATTATGCCTGGGGTGAAAATTGGGGACGGGGCAATCATTGCTGCAGAAGCTGTTGTCACAAAGAATGTTGCTCCCTATTCTATTGTCGGTGGAAATCCCTTAAAATTTATAAGAAAAAGGTTTTCTGATGGAGTTATCGAAGAATGGTTAGCTTTACAATGGTGGAATTTAGATATGAAAATTATTAATGAAAATCTTCCCTTCATAATAAATGGAGATATCGAAATGCTGAAGAGAAAAAGAAAACTTCTAGATGACACTTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3002840","ARO_id":"39274","ARO_name":"vatA","ARO_description":"vatA is a plasmid-mediated acetyltransferase found in Staphylococcus aureus","ARO_category":{"36592":{"category_aro_accession":"3000453","category_aro_cvterm_id":"36592","category_aro_name":"streptogramin vat acetyltransferase","category_aro_description":"vat (Virginiamycin acetyltransferases) enzymes catalyze the transfer of an acetyl group from acetyl-CoA to the secondary alcohol of streptogramin A compounds, thus inactivating virginiamycin-like antibiotics and conferring resistance to these compounds.","category_aro_class_name":"AMR Gene Family"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1736":{"model_id":"1736","model_name":"GES-24","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1555":{"protein_sequence":{"accession":"BAP75641.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRTAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMSDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"AB901141","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAACGGCGCAGCGCTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGAGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3002353","ARO_id":"38753","ARO_name":"GES-24","ARO_description":"GES-24 is a beta-lactamase. From the Lahey list of GES beta-lactamases.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1737":{"model_id":"1737","model_name":"ANT(4')-Ia","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"185":{"protein_sequence":{"accession":"AAO83986.1","sequence":"MNMNGPASMAQKERLQTCQEIAKRLHEVYGNDVLAIGVYGSVSRGTDGPFSDIEMFCVLRDSAETVDKSYEWSAGPWKAEVNVCSASILLKDAATVEDRWPLTHGPYFSPLRLYDPEGFFQRLRLAAESPTKEDFRQAIHEILVGEMYEYVGKLRNVNRNGPSTYLPSLALRFAHYGAMLIGLHNQTLFSTGAMVLPEALKLPHRPKGFDHVAELAMSGDLAQPAKIVSACEDFWKGLVAWAAEHDYVIHSKRIPF"},"dna_sequence":{"accession":"EF540343","fmin":"214","fmax":"985","strand":"+","sequence":"ATGAATATGAATGGACCTGCATCAATGGCGCAAAAAGAAAGACTTCAAACTTGCCAAGAAATTGCCAAGAGATTACACGAGGTTTATGGCAACGACGTTCTCGCCATTGGCGTCTACGGTTCTGTGTCCAGAGGCACAGATGGCCCTTTCTCAGATATTGAGATGTTTTGCGTACTCCGTGACTCGGCTGAAACGGTAGATAAAAGTTATGAATGGTCAGCTGGACCGTGGAAAGCGGAAGTTAACGTTTGCAGTGCGAGTATACTGTTAAAAGACGCTGCAACCGTTGAAGACCGATGGCCGCTGACACATGGGCCTTACTTCTCTCCGCTTCGTCTCTATGATCCTGAAGGCTTCTTTCAACGCTTGCGGCTCGCAGCGGAATCGCCGACAAAAGAAGATTTCCGCCAAGCTATTCATGAAATTCTTGTAGGGGAAATGTATGAATATGTTGGCAAGCTTCGAAATGTAAATCGAAATGGCCCTTCTACCTACTTGCCATCCTTGGCATTGCGCTTTGCCCACTATGGCGCAATGTTGATCGGCCTCCACAATCAGACACTCTTTTCTACGGGCGCTATGGTTTTGCCTGAAGCGCTGAAACTGCCGCATCGGCCAAAAGGGTTCGACCATGTTGCTGAGTTAGCGATGTCTGGAGACTTAGCACAACCAGCGAAGATCGTGTCAGCGTGCGAAGATTTCTGGAAAGGCCTAGTCGCGTGGGCAGCGGAGCATGATTACGTCATTCACTCAAAACGAATCCCGTTTTGAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36882","NCBI_taxonomy_name":"Bacillus clausii","NCBI_taxonomy_id":"79880"}}}},"ARO_accession":"3002623","ARO_id":"39023","ARO_name":"ANT(4')-Ia","ARO_description":"ANT(4')-Ia is a plasmid-encoded aminoglycoside nucleotidyltransferase in S. epidermidis, S. aureus, Enterococcus spp. and Bacillus spp.","ARO_category":{"36368":{"category_aro_accession":"3000229","category_aro_cvterm_id":"36368","category_aro_name":"ANT(4')","category_aro_description":"Nucleotidylylation of 2-deoxystreptamine aminoglycosides at the hydroxyl group at position 4'","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1738":{"model_id":"1738","model_name":"CTX-M-45","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1981":{"protein_sequence":{"accession":"BAA28282.1","sequence":"MVTKRVQRMMSAAAACIPLLLGSPTLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTARAGADVASLRWVMRWAKPSGAVGDVAQRQYDRAAGIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"D89862","fmin":"111","fmax":"981","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTCCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCCCAACGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCTTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGGCGCGGGCTGGCGCAGACGTTGCGTCATTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGCGCAGCCGGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001907","ARO_id":"38307","ARO_name":"CTX-M-45","ARO_description":"CTX-M-45 is a beta-lactamase found in Escherichia coli","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1739":{"model_id":"1739","model_name":"SHV-16","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1872":{"protein_sequence":{"accession":"AAC98092.2","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKITHRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AF072684","fmin":"117","fmax":"993","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCACTCATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001075","ARO_id":"37455","ARO_name":"SHV-16","ARO_description":"SHV-16 is an extended-spectrum beta-lactamase that has been found in clinical isolates. It differs from SHV-1 by a 163DRWET167 insertion.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1740":{"model_id":"1740","model_name":"TEM-53","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1886":{"protein_sequence":{"accession":"AAD22538.1","sequence":"MSIQHFRVALIPFFAAFCFPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AF104441","fmin":"193","fmax":"1054","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCTTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000922","ARO_id":"37302","ARO_name":"TEM-53","ARO_description":"TEM-53 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1741":{"model_id":"1741","model_name":"OXA-359","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1763":{"protein_sequence":{"accession":"AGZ83155.1","sequence":"MYKKAFIVATSLLFLSACSSNTVEQHQIYSISANKNSEEIKSLFDQAQTTGVLVIKRGQTEEIYGNDLKRASTEYVPASIFKMLNALIGLEHHKATATEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNANIGSKVDNFWLVGPLKITPQQEAQFAYQLAHKTLPFSKDVQEQVQSMVFIEEKNGRKIYAKSGWGWDVEPQVGWLTGWVIQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"KF421162","fmin":"0","fmax":"822","strand":"+","sequence":"ATGTATAAAAAAGCCTTTATCGTTGCAACAAGCCTCCTATTTTTATCTGCCTGTTCTTCTAATACGGTGGAACAACATCAAATATATTCTATTTCTGCCAATAAAAATTCAGAAGAAATTAAATCGCTGTTTGATCAAGCACAGACCACGGGTGTTTTGGTTATTAAGCGAGGGCAAACAGAAGAAATTTATGGCAATGATCTTAAAAGAGCATCAACTGAATATGTTCCAGCTTCTATTTTTAAAATGTTAAATGCTTTAATTGGACTTGAACACCATAAGGCAACTGCAACTGAAGTGTTTAAATGGGATGGGCAAAAACGTTTATTTCCTGATTGGGAAAAAGATATGACGCTGGGCGATGCCATGAAAGCTTCTGCTATTCCGGTCTATCAAGAATTAGCCCGACGAATTGGTCTGGATCTTATGTCTAAAGAGGTGAAACGAATTGGTTTCGGTAATGCCAATATTGGCTCAAAAGTAGATAATTTTTGGCTTGTTGGTCCACTAAAAATCACACCTCAACAAGAAGCCCAGTTTGCTTATCAATTGGCCCATAAAACACTTCCATTTAGCAAAGATGTACAAGAACAAGTTCAATCAATGGTGTTCATAGAGGAAAAGAATGGACGTAAAATTTATGCTAAAAGTGGTTGGGGATGGGATGTTGAACCGCAAGTTGGTTGGTTAACAGGCTGGGTCATTCAACCACAAGGAGAAATTGTCGCATTCTCACTGAATTTAGAAATGAAAAAAGGAACTCCTAGCTCTATTCGCAAAGAAATTGCTTATAAAGGCTTAGAACAACTGGGTATCTTATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3001546","ARO_id":"37946","ARO_name":"OXA-359","ARO_description":"OXA-359 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1742":{"model_id":"1742","model_name":"SHV-28","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1946":{"protein_sequence":{"accession":"AAG15384.1","sequence":"MRFIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AF299299","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTTTATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGAGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATCGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001086","ARO_id":"37466","ARO_name":"SHV-28","ARO_description":"SHV-28 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1743":{"model_id":"1743","model_name":"OXA-338","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1841":{"protein_sequence":{"accession":"AHN07454.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KF048909","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAATATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAACGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001526","ARO_id":"37926","ARO_name":"OXA-338","ARO_description":"OXA-338 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1744":{"model_id":"1744","model_name":"cmrA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"699":{"protein_sequence":{"accession":"AAC45805.1","sequence":"MPFAIYVLGLAVFAQGTSEFMLSGLIPDMARDLGVSVPAAGLLTSAFAVGMIIGAPLMAIASMRWPRRRALLTFLITFMLVHVIGALTSSFEVLLVTRIVGALANAGFLAVALGAAMAMVPADMKGRATSVLLGGVTIACVAGVPGGAFLGEIWGWRAAFWAVVVISAPAVVAIMFATPAEPPAESTPNAKRELSSLRSRKLQLMLVLGALINGATFCSFTYMAPTLTDISGFDSRWIPLLLGLFGLGSFIGVSVGGRLADTRPFQLLAVGSAALLTGWIVFALTASHPAVTLVMLFVQGALSFAVGSTLISQVLYAADAAPTLGGSFATAAFNVGAALGPALGGLAIGMGLSYRAPLWTSAALVTLAIVIGAATLSLWRRPASVQETVPA"},"dna_sequence":{"accession":"AF015087","fmin":"435","fmax":"1611","strand":"+","sequence":"GTGCCTTTCGCTATCTACGTCCTCGGGCTTGCCGTCTTTGCCCAGGGCACATCCGAATTCATGTTGTCCGGGCTCATACCGGATATGGCCCGCGACCTCGGCGTCTCGGTCCCCGCCGCCGGACTCCTCACCTCCGCCTTCGCGGTCGGGATGATCATCGGCGCTCCGCTGATGGCCATCGCCAGCATGCGGTGGCCCCGGCGACGCGCCCTTTTGACATTCCTCATCACGTTCATGCTGGTCCACGTCATCGGCGCGCTCACCAGCAGCTTCGAGGTCTTGCTGGTCACACGCATCGTCGGCGCCCTCGCCAACGCCGGATTCTTGGCGGTGGCCCTGGGCGCGGCGATGGCGATGGTGCCCGCCGACATGAAAGGGCGCGCAACGTCCGTCCTCCTCGGTGGTGTCACGATCGCATGTGTAGCCGGAGTTCCCGGGGGCGCCTTCCTCGGTGAAATATGGGGCTGGCGTGCAGCGTTCTGGGCTGTCGTCGTCATCTCCGCCCCTGCGGTGGTGGCGATCATGTTCGCCACCCCGGCCGAGCCGCCAGCAGAGTCCACACCGAACGCCAAGCGTGAACTGTCCTCGCTGCGCTCACGCAAGCTCCAGCTGATGCTTGTCCTCGGTGCCCTGATCAACGGCGCAACATTCTGTTCGTTCACCTACATGGCGCCCACTCTCACCGACATCTCCGGTTTCGACTCCCGTTGGATTCCGTTGCTGCTGGGGTTGTTCGGGCTCGGATCGTTCATCGGCGTCAGCGTCGGAGGCAGGCTCGCCGATACCCGGCCGTTCCAACTTCTCGCCGTGGGATCCGCAGCACTGTTGACGGGATGGATCGTCTTCGCTCTCACGGCATCCCACCCTGCGGTGACATTGGTGATGCTGTTCGTGCAGGGCGCTCTGTCCTTCGCGGTCGGCTCGACCTTGATCTCCCAGGTGCTCTACGCCGCCGACGCGGCGCCGACCTTGGGTGGATCGTTCGCGACGGCCGCGTTCAACGTCGGCGCTGCACTGGGCCCGGCCCTCGGCGGGCTGGCGATCGGTATGGGCCTGAGCTACCGCGCCCCGCTCTGGACGAGCGCCGCGCTGGTGACTCTCGCGATCGTCATCGGCGCAGCCACCTTGTCGCTCTGGCGGCGTCCAGCGTCCGTCCAGGAAACCGTCCCAGCCTGAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39553","NCBI_taxonomy_name":"Rhodococcus rhodochrous","NCBI_taxonomy_id":"1829"}}}},"ARO_accession":"3002702","ARO_id":"39136","ARO_name":"cmrA","ARO_description":"cmrA is a transposon-encoded chloramphenicol exporter that is found in Rhodococcus rhodochrous","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1746":{"model_id":"1746","model_name":"IMP-24","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1907":{"protein_sequence":{"accession":"ABM68358.1","sequence":"MKKLFVLCVCFLCSITAAGAALPDLKIEKLEEGVYVHTSFEEVNGWGVVSKHGLVVLVNTDAYLIDTPFTATDTEKLVNWFVERGYKIKGTISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKDGKVQAKNSFSGVSYWLVKNKIEVFYPGPGHTQDNVVVWLPEKKILFGGCFVKPDGLGNLGDANLEAWPKSAKILMSKYGKAKLVVSSHSEIGDASLLKRTWEQAVKGLNESRKPSQPSN"},"dna_sequence":{"accession":"EF192154","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAAGAAATTATTTGTTTTATGTGTATGCTTCCTTTGTAGCATTACTGCCGCAGGAGCGGCTTTGCCTGATTTAAAAATCGAGAAGCTTGAAGAAGGTGTTTATGTTCATACATCGTTCGAAGAAGTTAACGGTTGGGGTGTTGTTTCTAAACACGGTTTGGTGGTTCTTGTAAACACTGACGCCTATCTGATTGACACTCCATTTACTGCTACAGATACTGAAAAGTTAGTCAATTGGTTTGTGGAGCGCGGCTATAAAATCAAAGGCACTATTTCCTCACATTTCCATAGCGACAGCACAGGGGGAATAGAGTGGCTTAATTCTCAATCTATTCCCACGTATGCATCTGAATTAACAAATGAACTTCTTAAAAAAGACGGTAAGGTGCAAGCTAAAAACTCATTTAGCGGAGTTAGTTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCCGGCCCGGGGCACACTCAAGATAACGTAGTGGTTTGGTTACCTGAAAAGAAAATTTTATTCGGTGGTTGTTTTGTTAAACCGGACGGTCTTGGTAATTTGGGTGACGCAAATTTAGAAGCTTGGCCAAAGTCCGCCAAAATATTAATGTCTAAATATGGTAAAGCAAAACTGGTTGTTTCAAGTCATAGTGAAATTGGGGACGCATCACTCTTGAAACGTACATGGGAACAGGCTGTTAAAGGGCTAAATGAAAGTAGAAAACCATCACAGCCAAGTAACTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36783","NCBI_taxonomy_name":"Serratia marcescens","NCBI_taxonomy_id":"615"}}}},"ARO_accession":"3002215","ARO_id":"38615","ARO_name":"IMP-24","ARO_description":"IMP-24 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1747":{"model_id":"1747","model_name":"CMY-103","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1441":{"protein_sequence":{"accession":"AHA80104.1","sequence":"MMKKSICCALLLTASFSTFAATKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEEKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDEVTDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQGKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"KF526116","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCGCTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCACAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACGAGGAGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAATTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTACCGCTGCAGATCCCCGATGAAGTTACGGATAAAGCCGCATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGCGGTGAAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAAGGGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGTTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACAGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATAGTGATGCTGGCAAACAAAAGCTACCCCAACCCGGCTCGCGTCGAGGCGGCCTGGCGCATTCTTGAAAAACTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002115","ARO_id":"38515","ARO_name":"CMY-103","ARO_description":"CMY-103 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1748":{"model_id":"1748","model_name":"lsaC","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"960"}},"model_sequences":{"sequence":{"76":{"protein_sequence":{"accession":"AEA37904.1","sequence":"MSTIKIENLTFSYYGYVKPVFENVSFSFDTNWKTGLIGRNGIGKSTLFKLLLNQEVYKGKISKSVDFIKFPPNLSDTSKLGIELYRELISDEEEWKLFRELHLLKVDESLIYRKFETLSKGEQTKILLAILFTREDGFLLIDEPTNHLDMDGRKIVSEYLKNKKGFLLISHDRDFLDGCINHIISINRNSIDVQSGNFTSWYENKLMKDQFEISQNEKLRKDIKRLKEAARQSQIWSDKVENTKNGVKVSGVKPDKGHIGHQSAKMMKKSKNLENRQNKAIEEKQNLLKDIETKESLLLHPLHHHKNPLISVCDLSSYYGKKQILSNISFDIKQGDIVAIYGGNGSGKSTLIKILLGLNHEYSGDVKLASNLKISYVPQDTSNLTGSLNEYIHKQGVDETLCKTILRKLDFARELFEIDMKNYSDGQKKKVLIAVSLSKSAHIFIWDEPLNYLDVISRIQIEEIIKEANPTLIFVEHDKSFVEDIANKIIRL"},"dna_sequence":{"accession":"HM990671","fmin":"5192","fmax":"6671","strand":"+","sequence":"ATGTCAACAATTAAAATTGAAAACCTTACTTTCTCATATTATGGCTATGTAAAACCTGTATTTGAAAATGTATCATTTTCATTTGATACGAACTGGAAAACAGGACTAATAGGAAGAAACGGAATTGGGAAATCAACACTATTTAAGCTGCTTCTAAACCAAGAAGTTTATAAGGGGAAAATCAGCAAAAGTGTTGACTTTATTAAATTCCCACCCAATTTAAGTGATACTTCAAAATTAGGGATTGAGTTATATAGAGAACTAATATCAGATGAGGAAGAATGGAAATTATTTAGAGAACTTCATTTGCTAAAGGTAGATGAGAGTCTTATTTACAGAAAGTTTGAAACGCTTTCTAAAGGAGAACAAACAAAAATCCTTTTAGCTATTTTGTTTACAAGAGAAGATGGTTTTTTACTTATAGATGAACCAACAAACCATTTAGATATGGACGGAAGAAAAATTGTCAGTGAATATCTGAAAAATAAAAAAGGTTTTTTGCTTATATCACATGATAGAGATTTTTTAGATGGTTGTATCAATCATATTATTTCTATTAACAGGAATTCTATTGATGTCCAATCAGGAAATTTTACATCGTGGTATGAAAATAAATTGATGAAAGACCAATTTGAGATTAGTCAAAATGAGAAATTAAGAAAAGATATTAAACGATTAAAAGAAGCTGCAAGACAAAGTCAAATTTGGTCTGATAAAGTTGAAAATACTAAAAACGGCGTGAAAGTATCAGGTGTAAAACCAGACAAGGGGCATATAGGTCATCAGTCAGCTAAGATGATGAAAAAATCTAAGAATTTGGAGAATAGACAAAATAAGGCAATAGAAGAAAAACAGAATTTACTAAAAGATATTGAAACAAAGGAAAGTCTATTATTGCATCCGTTACATCACCACAAAAATCCTCTAATATCAGTTTGCGATTTATCATCATATTATGGAAAAAAGCAGATATTAAGTAATATAAGTTTTGATATAAAGCAAGGTGATATAGTGGCTATATATGGGGGTAATGGTAGCGGAAAATCAACCTTGATTAAAATTTTATTAGGTCTAAATCACGAGTATTCAGGTGATGTAAAATTAGCAAGTAATTTAAAAATATCATATGTTCCTCAAGATACATCCAATTTAACAGGTAGCCTAAACGAGTATATTCATAAGCAAGGTGTTGATGAAACATTGTGCAAAACAATTCTTAGAAAATTAGATTTTGCAAGAGAATTATTTGAAATAGATATGAAGAACTATAGCGATGGACAAAAAAAGAAAGTTTTAATTGCTGTAAGTTTGTCAAAGTCAGCTCATATATTTATTTGGGACGAACCACTGAATTATTTAGATGTAATATCAAGAATACAGATTGAGGAAATTATAAAAGAAGCAAATCCTACACTCATATTTGTGGAACACGATAAGAGTTTTGTAGAAGATATAGCGAATAAAATAATACGATTATAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36847","NCBI_taxonomy_name":"Streptococcus agalactiae","NCBI_taxonomy_id":"1311"}}}},"ARO_accession":"3003112","ARO_id":"39688","ARO_name":"lsaC","ARO_description":"LsaC is an ABC efflux pump expressed in Streptococcus agalactiae. It confers resistance to lincomycin, clindamycin, dalfopristin, and tiamulin","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"37716":{"category_aro_accession":"3001317","category_aro_cvterm_id":"37716","category_aro_name":"pleuromutilin","category_aro_description":"Pleuromutilin is a natural product antibiotic produced by Clitopilus passeckerianus. Related antibiotics of clinical significance, such as tiamulin and retapamulin, are semi-synthetic derivatives of this compound.","category_aro_class_name":"Antibiotic"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1749":{"model_id":"1749","model_name":"IMP-18","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"912":{"protein_sequence":{"accession":"AEQ73520.1","sequence":"MKKLFVLCVFFLCNIAAADDSLPDLKIEKLEKGVYVHTSFEEVKGWGVVTKHGLVVLVKNDAYLIDTPITAKDTEKLVNWFIEHGYRIKGSISTHFHGDSTAGIEWLNSQSISTYASELTNELLKKDNKVQATNSFSGVSYSLIKNKIEVFYPGPGHTQDNVVVWLPEKKILFGGCFVKPDGLGNLGDANLEAWPKSAKILMSKYGKAKLVVSSHSEIGNASLLQRTWEQAVKGLNESKKPLQPSS"},"dna_sequence":{"accession":"JN596991","fmin":"482","fmax":"1223","strand":"+","sequence":"ATGAAAAAATTATTTGTTTTATGTGTATTCTTCCTTTGCAACATTGCTGCTGCAGATGATTCTTTGCCTGATTTAAAAATTGAGAAGCTTGAAAAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAAAGGTTGGGGTGTAGTCACAAAACACGGTTTAGTGGTTCTTGTAAAGAATGATGCTTATCTGATAGATACTCCAATTACCGCTAAAGATACTGAAAAATTAGTTAATTGGTTTATTGAGCACGGCTATAGAATCAAAGGCAGTATTTCCACACATTTCCATGGCGACAGTACGGCTGGAATAGAGTGGCTTAATTCTCAATCTATCTCCACGTATGCCTCTGAATTAACAAATGAACTTCTAAAAAAAGACAATAAGGTGCAAGCTACAAATTCTTTTAGTGGAGTTAGTTATTCACTTATCAAAAACAAAATTGAAGTTTTCTATCCAGGTCCAGGACACACTCAAGATAACGTAGTGGTTTGGTTACCTGAAAAGAAAATTTTATTCGGTGGTTGCTTTGTTAAACCGGACGGTCTTGGAAATTTAGGGGATGCAAATTTAGAAGCTTGGCCAAAGTCCGCTAAAATATTAATGTCTAAATATGGTAAAGCAAAACTGGTTGTTTCAAGTCATAGTGAAATTGGAAACGCATCACTCTTGCAACGCACATGGGAGCAGGCTGTTAAAGGGTTAAATGAAAGTAAAAAACCGTTACAGCCAAGTAGCTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002209","ARO_id":"38609","ARO_name":"IMP-18","ARO_description":"IMP-18 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1750":{"model_id":"1750","model_name":"OXA-254","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1530":{"protein_sequence":{"accession":"BAN10684.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAITVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"AB781687","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTACAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001682","ARO_id":"38082","ARO_name":"OXA-254","ARO_description":"OXA-254 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1751":{"model_id":"1751","model_name":"Erm(33)","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"511":{"protein_sequence":{"accession":"NP_899170.1","sequence":"MNKKNIKDSQNFITSKRNIDKIMTNISLNEHDNIFEIGSGKGHFTLELVQRCNFVTAIEIDHKLCKTTENKLVDHDNFQVLNKDILQFKFPKNQSYNIFGNIPYNISTDIVKRITFESQAKYSYLIVEKGFAKRLQNLQRALGLLLMVEMDIKMLKKVPPLYFHPKPSVDSVLIVLERHQPLISKKDYKKYRSFVYKWVNREYRVLFTKNQFRQALKHANVTNINKLSKEQFLSIFNSYKLFH"},"dna_sequence":{"accession":"NC_005076","fmin":"9897","fmax":"10629","strand":"+","sequence":"ATGAACAAAAAAAATATAAAAGACAGTCAAAACTTTATTACTTCGAAACGTAATATAGATAAAATAATGACAAATATAAGCTTAAATGAACATGATAATATCTTTGAAATTGGCTCAGGAAAAGGGCATTTTACCCTTGAATTAGTACAAAGGTGTAATTTCGTAACTGCTATTGAAATAGACCATAAATTATGCAAGACTACAGAAAATAAACTTGTTGATCACGATAATTTTCAAGTTTTAAACAAGGATATATTGCAGTTTAAATTTCCTAAAAACCAATCCTATAATATATTTGGTAATATTCCTTATAACATCAGTACGGATATTGTCAAAAGAATTACCTTTGAAAGTCAGGCTAAATATAGCTATCTTATCGTTGAGAAGGGATTTGCGAAAAGATTGCAAAATCTGCAACGAGCTTTGGGTTTACTATTAATGGTGGAGATGGATATAAAAATGCTCAAAAAAGTACCACCACTATATTTTCATCCTAAGCCAAGTGTAGACTCTGTATTGATTGTTCTTGAACGACATCAACCATTGATTTCAAAGAAGGACTACAAAAAGTATCGATCTTTTGTTTATAAGTGGGTAAACCGTGAATATCGTGTTCTTTTCACTAAAAACCAATTCCGACAGGCTTTGAAGCATGCAAATGTCACTAATATTAATAAACTATCGAAGGAACAATTTCTTTCTATTTTCAATAGTTACAAATTGTTTCACTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36794","NCBI_taxonomy_name":"Staphylococcus sciuri","NCBI_taxonomy_id":"1296"}}}},"ARO_accession":"3000599","ARO_id":"36738","ARO_name":"Erm(33)","ARO_description":"ErmD confers MLSb phenotype.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35946":{"category_aro_accession":"0000027","category_aro_cvterm_id":"35946","category_aro_name":"roxithromycin","category_aro_description":"Roxithromycin is a semi-synthetic, 14-carbon ring macrolide antibiotic derived from erythromycin. It is used to treat respiratory tract, urinary and soft tissue infections. Roxithromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35974":{"category_aro_accession":"0000057","category_aro_cvterm_id":"35974","category_aro_name":"telithromycin","category_aro_description":"Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36315":{"category_aro_accession":"3000176","category_aro_cvterm_id":"36315","category_aro_name":"dirithromycin","category_aro_description":"Dirithromycin is an oxazine derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome to inhibit bacterial protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin 1A is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"vernamycin B-gamma","category_aro_description":"Vernamycin B-gamma is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1752":{"model_id":"1752","model_name":"mdtK","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"900"}},"model_sequences":{"sequence":{"3624":{"protein_sequence":{"accession":"AML99881.1","sequence":"MNVSTALRQAVVRTPWYAKRKSYKVLFWREITPLAIPIFLENTCVLLMGVLSTFLVSWLGKEAMAGVGLADSFNMVIMAFFAAIDLGTTVVVAFSLGKRDRRRARAAARQSLVIMTLFAVVLAVVIHYFGSEIINIVAGEATPEVKGLALTYLELTVLSYPAAAIALIGSGALRGAGNTKIPLMINGGMNILNIIISSILIYGAFSWQGLGFAGAGLGLTISRYIGAVAIIWVLMIGFNPALRIPLKSYLKPLNFGIIWEVMGIGIPASIESVLFNGSKLLTQMFVAGMGTNVIAGNFIAFSVAALINLPGNALGSASTIITGKRLGTGQIGQAERQLRHVFWMSTIVLTAIAWGTAPFAGLFASFYTQEQDVKEVVKVLLWLNAAFMPIWAAAWVLPSGFKGARDVRFAMWVSMLGMWGCRVVAGYTLGIVLGMGVVGVWLGMFLDWAVRGALFYWRLISGRWLWRYPRVKRE"},"dna_sequence":{"accession":"CP014358.1","fmin":"2161325","fmax":"2162750","strand":"-","sequence":"TTACTCCCTCTTTACGCGCGGGTATCTCCACAGCCAGCGCCCGCTTATCAGACGCCAGTAAAACAGTGCGCCACGCACGGCCCAGTCAAGAAACATCCCCAGCCAAACCCCTACAACCCCCATACCCAGCACAATACCAAGCGTATACCCTGCCACAACGCGACAGCCCCACATCCCCAGCATCGATACCCACATCGCAAATCGCACATCGCGCGCGCCTTTAAAACCCGACGGCAACACCCACGCGGCCGCCCAAATTGGCATAAAGGCAGCATTAAGCCAGAGCAGAACTTTCACTACCTCTTTTACGTCCTGCTCCTGGGTATAAAATGAGGCAAACAGACCCGCAAACGGCGCCGTCCCCCAGGCAATTGCCGTAAGTACGATAGTCGACATCCAGAATACATGGCGCAGTTGACGCTCTGCCTGACCAATTTGCCCGGTACCAAGACGCTTACCGGTGATAATAGTCGACGCCGAACCAAGGGCGTTACCCGGCAGGTTGATAAGCGCCGCCACGGAAAAGGCAATAAAGTTACCCGCAATAACGTTAGTGCCCATTCCGGCGACAAACATTTGCGTCAGTAGCTTGCTACCGTTGAACAGCACTGATTCAATGCTCGCCGGAATACCGATACCCATCACTTCCCAGATAATGCCGAAATTCAGCGGCTTCAGATAGCTTTTCAGCGGAATGCGCAGCGCCGGATTAAAACCAATCATCAGCACCCAAATAATCGCTACCGCGCCGATGTAGCGCGAAATGGTTAATCCCAGCCCCGCGCCGGCAAAACCCAGCCCTTGCCAGGAGAAAGCCCCGTAAATCAGGATGCTGCTGATAATAATATTGAGAATGTTCATCCCGCCGTTAATCATCAACGGGATTTTCGTATTCCCTGCCCCACGCAGCGCGCCGCTACCGATTAGCGCAATTGCCGCAGCCGGATAACTCAGCACCGTCAGTTCAAGGTACGTTAACGCCAGCCCCTTTACTTCTGGCGTCGCCTCGCCTGCGACAATATTAATAATTTCACTGCCGAAATAATGAATGACCACTGCCAGCACAACGGCAAATAGCGTCATAATCACCAGCGACTGGCGCGCCGCCGCCCTTGCGCGTCGCCTGTCGCGCTTGCCGAGGCTAAAGGCGACCACCACCGTAGTACCAAGATCGATAGCCGCAAAAAAAGCCATAATTACCATATTAAAACTGTCGGCAAGCCCCACGCCCGCCATTGCTTCCTTGCCCAGCCAACTGACGAGAAAAGTACTGAGCACGCCCATTAGCAAAACACAGGTATTTTCCAGAAAAATAGGGATAGCAAGTGGGGTGATTTCACGCCAGAACAACACTTTGTAGCTCTTGCGTTTGGCATACCAGGGCGTACGGACGACAGCCTGGCGTAAGGCAGTGGAGACGTTCAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35732","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium","NCBI_taxonomy_id":"90371"}}}},"ARO_accession":"3001327","ARO_id":"37726","ARO_name":"MdtK","ARO_description":"A multidrug and toxic compound extrusions (MATE) transporter conferring resistance to norfloxacin, doxorubicin and acriflavine.","ARO_category":{"36251":{"category_aro_accession":"3000112","category_aro_cvterm_id":"36251","category_aro_name":"multidrug and toxic compound extrusion (MATE) transporter","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Multidrug and toxic compound extrusion (MATE) transporters utilize the cationic gradient across the membrane as an energy source. Although there is a diverse substrate specificity, almost all MATE transporters recognize fluoroquinolones. Arciflavine, ethidium and aminoglycosides are also good substrates.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1753":{"model_id":"1753","model_name":"SHV-148","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"829":{"protein_sequence":{"accession":"AFQ23954.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQQ"},"dna_sequence":{"accession":"JX121115","fmin":"0","fmax":"858","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001187","ARO_id":"37567","ARO_name":"SHV-148","ARO_description":"SHV-148 is a beta-lactamase.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1754":{"model_id":"1754","model_name":"vanO","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"650"}},"model_sequences":{"sequence":{"675":{"protein_sequence":{"accession":"AHA41500.1","sequence":"MSRLKVGVIFGGASEEHPVSIKSAREVARSLDTEKYEPFWIGITTGGEWKLCDGPDADWENRSARPAVLSPDRSVHGLLVMEQGGYETVRLDLVFPVLHGKLGEDGAIQGLLELAGIPYVGCDIQGSAVCMDKALAYIVAKSAGIATPSFWVVAENEKVDADHLRYPVFVKPARSGSSFGVSKVTREDELPNALSAARQYDSKVLIEEAVAGSEIGCAVMGELFGLITGEVDRVDLSHGFFRIHQEDSPETGSENSTFIVPADISDESRRLVQETAKAIYRTLGCKGLARVDMFLTDDGRVVLNEVNTMPGMTSYSRYPRMMAAAGLPISDMIDRLISMTMHGKKR"},"dna_sequence":{"accession":"KF478993","fmin":"1539","fmax":"2580","strand":"+","sequence":"ATGAGCAGATTGAAGGTCGGGGTCATCTTCGGAGGGGCTTCCGAAGAACATCCCGTCTCCATCAAGTCGGCGCGAGAGGTGGCAAGAAGTCTCGACACGGAGAAGTACGAACCGTTCTGGATCGGCATCACGACCGGCGGCGAGTGGAAGCTCTGTGACGGCCCCGACGCGGATTGGGAGAATCGCAGCGCCCGTCCCGCCGTGCTGTCACCCGATCGAAGTGTGCACGGCCTGCTGGTCATGGAGCAGGGGGGCTACGAAACCGTGCGCCTCGACCTCGTCTTCCCCGTACTTCACGGCAAGCTCGGCGAAGACGGCGCGATCCAAGGCCTGTTGGAGCTCGCCGGCATCCCCTACGTCGGCTGCGACATCCAGGGCTCGGCTGTGTGCATGGACAAGGCCCTGGCCTACATCGTGGCCAAGAGCGCGGGAATCGCCACGCCGAGCTTTTGGGTTGTCGCGGAGAACGAGAAGGTCGACGCCGATCACCTTCGCTATCCGGTCTTCGTGAAGCCGGCCCGTTCGGGTTCATCTTTCGGCGTCAGCAAGGTCACCCGAGAAGACGAGCTGCCGAACGCGCTGAGCGCGGCGCGACAGTACGACTCGAAGGTCCTGATCGAAGAAGCCGTGGCCGGCAGCGAGATCGGCTGCGCGGTCATGGGTGAACTATTCGGCCTGATCACTGGGGAGGTGGACCGCGTCGACCTCTCGCACGGATTCTTCAGGATCCACCAGGAGGACTCACCCGAAACCGGATCGGAGAACTCGACGTTCATCGTTCCCGCCGACATCTCCGACGAATCGCGCCGGCTCGTCCAAGAGACCGCCAAGGCCATCTACCGCACCCTGGGCTGCAAGGGACTTGCCCGCGTTGACATGTTCCTCACCGACGACGGACGGGTGGTCCTCAACGAGGTCAACACCATGCCCGGCATGACGTCGTACAGCCGGTACCCGCGGATGATGGCCGCCGCGGGACTGCCGATCTCCGACATGATCGACCGGCTCATCTCGATGACAATGCACGGGAAGAAGCGATGAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36897","NCBI_taxonomy_name":"Rhodococcus equi","NCBI_taxonomy_id":"43767"}}}},"ARO_accession":"3002913","ARO_id":"39347","ARO_name":"vanO","ARO_description":"VanO is a D-Ala-D-Ala ligase homolog that can synthesize D-Ala-D-Lac, an alternative substrate for peptidoglycan synthesis that reduces vancomycin binding affinity. It is associated with both vancomycin and teicoplanin resistance.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"39340":{"category_aro_accession":"3002906","category_aro_cvterm_id":"39340","category_aro_name":"van ligase","category_aro_description":"van ligases synthesize alternative substrates for peptidoglycan synthesis that reduce vancomycin binding affinity.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1755":{"model_id":"1755","model_name":"CTX-M-23","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1411":{"protein_sequence":{"accession":"AAL99990.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAVAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTETTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTNGL"},"dna_sequence":{"accession":"AF488377","fmin":"62","fmax":"938","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGTCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGACGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGTGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACTTGGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGACGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGGGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCAACGGTTTGTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001885","ARO_id":"38285","ARO_name":"CTX-M-23","ARO_description":"CTX-M-23 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1756":{"model_id":"1756","model_name":"CMY-93","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1549":{"protein_sequence":{"accession":"AHM76768.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYQGKPYYFTWGKADIANNRPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKFSDPVTHYWPELTGKQWQGISLLHLATYTAGGLPLQVPDDVTDKAALLRFYQNWQPQWAPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTKRVLRPLKLAHTWITVPQSEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMTRWVQANMDASQVQEKTLQQGIELAQSRYWRVGDMYQGLGWEMLNWPVKADSIISGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"KF992025","fmin":"1026","fmax":"2172","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCGCTGCTGCTGACAGCTTCGTTCTCCACGTTTGCCGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCGCTGATGCAGGAGCAGGCAATTCCGGGCATGGCCGTTGCGATTATCTATCAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCGTCCAGTCACTCAACAAACGCTGTTTGAACTCGGATCGGTCAGTAAAACGTTCAACGGTGTGCTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGTTCAGCGATCCGGTCACGCATTACTGGCCTGAACTGACTGGTAAGCAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTACACGGCAGGCGGCCTGCCGCTTCAGGTTCCGGACGACGTTACGGATAAAGCCGCGTTACTACGCTTTTATCAAAACTGGCAGCCGCAATGGGCCCCAGGCGCTAAACGTCTTTATGCTAACTCCAGCATTGGTCTGTTTGGTGCCCTGGCGGTCAAACCCTCAGGCATGAGCTACGAAGAGGCGATGACCAAACGCGTCCTGCGCCCCTTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAGCGAACAAAAAGATTATGCCTGGGGTTATCGCGAAGGAAAGCCAGTGCATGTATCCCCTGGCCAACTTGATGCCGAAGCCTACGGGGTGAAATCGAGCGTTATCGATATGACCCGTTGGGTTCAGGCCAACATGGACGCCAGCCAGGTTCAGGAGAAAACGCTCCAGCAGGGCATCGAGCTTGCGCAGTCACGTTACTGGCGTGTTGGCGATATGTACCAGGGCCTGGGCTGGGAGATGCTGAACTGGCCGGTGAAAGCCGACTCGATAATTAGCGGTAGCGACAGCAAAGTGGCACTGGCAGCGCTTCCTGCCGTTGAGGTAAACCCGCCCGCGCCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGCGGATTCGGCAGCTACGTTGCTTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAGAGCTACCCAAACCCTGTTCGCGTCGAGGCCGCCTGGCGCATTCTTGAAAAACTGCAGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002106","ARO_id":"38506","ARO_name":"CMY-93","ARO_description":"CMY-93 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1757":{"model_id":"1757","model_name":"emrA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"675"}},"model_sequences":{"sequence":{"411":{"protein_sequence":{"accession":"BAA16547.1","sequence":"MSANAETQTPQQPVKKSGKRKRLLLLLTLLFIIIAVAIGIYWFLVLRHFEETDDAYVAGNQIQIMSQVSGSVTKVWADNTDFVKEGDVLVTLDPTDARQAFEKAKTALASSVRQTHQLMINSKQLQANIEVQKIALAKAQSDYNRRVPLGNANLIGREELQHARDAVTSAQAQLDVAIQQYNANQAMILGTKLEDQPAVQQAATEVRNAWLALERTRIISPMTGYVSRRAVQPGAQISPTTPLMAVVPATNMWVDANFKETQIANMRIGQPVTITTDIYGDDVKYTGKVVGLDMGTGSAFSLLPAQNATGNWIKVVQRLPVRIELDQKQLEQYPLRIGLSTLVSVNTTNRDGQVLANKVRSTPVAVSTAREISLAPVNKLIDDIVKANAG"},"dna_sequence":{"accession":"AP009048","fmin":"2810082","fmax":"2811255","strand":"+","sequence":"ATGAGCGCAAATGCGGAGACTCAAACCCCGCAGCAACCGGTAAAGAAGAGCGGCAAACGTAAGCGTCTGCTCCTCCTTCTCACCTTGCTCTTTATAATTATTGCCGTAGCGATAGGGATTTATTGGTTTTTGGTACTGCGTCACTTCGAAGAAACCGATGACGCATACGTGGCAGGGAATCAAATTCAAATTATGTCTCAGGTGTCTGGCAGCGTGACGAAAGTCTGGGCCGATAACACCGATTTTGTAAAAGAAGGCGACGTGCTGGTCACTCTCGACCCGACAGATGCTCGCCAGGCGTTTGAAAAAGCCAAAACTGCACTGGCTTCCAGCGTTCGCCAAACCCACCAGCTGATGATTAACAGCAAGCAGTTGCAGGCGAATATTGAGGTGCAGAAAATCGCCCTCGCGAAAGCACAAAGCGACTACAACCGCCGTGTGCCGCTGGGCAATGCCAACCTGATTGGTCGCGAAGAGCTGCAACACGCCCGCGACGCCGTCACCAGTGCCCAGGCGCAACTGGACGTCGCGATTCAACAATACAATGCCAATCAGGCGATGATTCTGGGGACTAAACTGGAAGATCAGCCAGCCGTGCAACAGGCTGCCACCGAAGTACGTAACGCCTGGCTGGCGCTGGAGCGTACTCGTATTATCAGTCCGATGACCGGTTATGTCTCCCGCCGCGCGGTACAGCCTGGGGCGCAAATTAGCCCAACGACGCCGCTGATGGCGGTCGTTCCAGCCACCAATATGTGGGTGGATGCCAACTTTAAAGAGACGCAGATTGCCAATATGCGTATCGGTCAGCCGGTCACTATCACCACGGATATTTACGGCGATGATGTGAAATACACCGGTAAAGTGGTTGGTCTGGATATGGGCACAGGTAGCGCGTTCTCACTGCTTCCAGCGCAAAATGCGACCGGTAACTGGATCAAAGTCGTTCAGCGTCTGCCTGTGCGTATCGAACTGGACCAGAAACAGCTGGAGCAATATCCGCTGCGTATCGGTTTGTCCACGCTGGTGAGCGTCAATACCACTAACCGTGACGGTCAGGTACTGGCAAATAAAGTACGTTCCACTCCGGTAGCGGTAAGCACCGCGCGTGAAATCAGCCTGGCACCTGTCAATAAACTGATCGACGATATCGTAAAAGCTAACGCTGGCTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36839","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. W3110","NCBI_taxonomy_id":"316407"}}}},"ARO_accession":"3000027","ARO_id":"36036","ARO_name":"emrA","ARO_description":"EmrA is a membrane fusion protein, providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli, a Gram-negative bacterium.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1758":{"model_id":"1758","model_name":"OXA-326","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"974":{"protein_sequence":{"accession":"AGW16408.1","sequence":"MYKKAFIVATSILFLSACSSNTVKQHQIHSISANKNSEAIKSLFDQAQTTGVLVIKRGQTEEIYGNDLKRASTDYVPASTFKMLNALIGLEHHKVTTTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNANIGSKVDDFWLVGPLKITPQQETQFAYQLAHKTLPFSKNVQEQVQSMVFIEEKNGSKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"KF203100","fmin":"0","fmax":"822","strand":"+","sequence":"ATGTATAAAAAAGCCTTTATCGTTGCAACAAGTATTCTATTTTTATCCGCCTGTTCTTCCAATACGGTAAAACAACATCAAATACACTCTATTTCTGCCAATAAAAATTCAGAAGCAATTAAATCACTGTTTGATCAGGCACAGACCACGGGTGTTTTGGTGATTAAGCGAGGGCAAACAGAAGAAATTTATGGCAATGATCTTAAAAGAGCATCAACAGACTATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTAATTGGACTTGAACATCATAAGGTAACTACAACTGAAGTATTTAAATGGGATGGGCAAAAACGTTTATTTCCTGATTGGGAAAAGGACATGACACTGGGTGATGCCATGAAAGCTTCTGCAATTCCAGTTTACCAAGAATTAGCCCGACGAATTGGTCTGGATCTTATGTCCAAAGAGGTGAAACGAATTGGTTTCGGTAATGCTAACATTGGCTCAAAAGTAGATGATTTCTGGCTTGTTGGCCCTCTAAAAATTACACCTCAACAAGAAACCCAATTTGCTTATCAATTAGCCCATAAAACTCTTCCATTTAGCAAAAATGTACAAGAACAAGTTCAATCAATGGTGTTCATAGAAGAAAAAAATGGAAGTAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTGGAACCACAAGTTGGTTGGTTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTCGCATTCTCACTTAATTTAGAAATGAAAAAAGGAACTCCTAGCTCTATTCGCAAAGAAATTGCTTATAAAGGCTTAGAACAACTGGGTATCTTATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3001514","ARO_id":"37914","ARO_name":"OXA-326","ARO_description":"OXA-326 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1759":{"model_id":"1759","model_name":"vanF","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"650"}},"model_sequences":{"sequence":{"258":{"protein_sequence":{"accession":"AAF36803.1","sequence":"MNRLKIAILFGGCSEEHDVSVKSAKEIANNIDTEKYEPIYIGITRSGVWKMCEKPCMDWDNENCRSAVLSPDKKMHGLLVMRNKGYQIQRIDAVFSVLHGKSGEDGAIQGLFELSSIPYVGCDVQSSAVCMDKSLTYIVAQNAGFGTPEFLILNHGDIPDSNTLTYPVFVKPARSGSSFGVNKVNNEDELDAAIETARQYDSKVLIEQAVPGLEVGCAVLGNGTDLIVGEVDQISLSHGIFRIHQEDQPEKGSENAVVLVPANLSAEKRIKIQETAKAIYKALGCKGLSRVDMFLQENGRIILNEVNTLPGFTAYSRYPRMMAAAGMTLSGLIDHCITLALKG"},"dna_sequence":{"accession":"AF155139","fmin":"5939","fmax":"6971","strand":"+","sequence":"TTGAATAGATTAAAAATAGCCATCCTGTTTGGGGGCTGTTCAGAGGAACACGATGTGTCGGTAAAATCGGCGAAAGAGATTGCCAATAACATTGACACGGAAAAATATGAGCCGATATACATCGGAATCACCCGATCCGGCGTCTGGAAAATGTGCGAAAAGCCATGCATGGATTGGGACAACGAAAACTGCCGTTCGGCAGTGCTTTCTCCGGACAAAAAAATGCACGGGCTGCTTGTTATGCGGAATAAAGGATATCAAATCCAACGTATAGACGCGGTATTTTCGGTTTTGCACGGCAAATCGGGTGAAGACGGCGCCATACAAGGTTTATTTGAATTGTCCAGCATCCCCTATGTAGGCTGTGATGTTCAAAGTTCGGCGGTGTGTATGGACAAATCCCTGACATACATTGTGGCCCAAAATGCTGGTTTTGGCACTCCTGAATTTTTGATTTTGAATCATGGCGATATACCGGATTCAAATACCTTAACATATCCTGTTTTTGTTAAACCGGCGCGTTCCGGCTCATCTTTCGGCGTGAATAAAGTCAATAACGAGGACGAATTAGACGCCGCCATTGAAACAGCAAGGCAGTATGACAGTAAAGTCCTGATTGAACAAGCTGTTCCAGGCCTTGAAGTTGGCTGTGCCGTGTTGGGAAACGGTACCGACTTAATCGTTGGCGAAGTGGACCAAATTTCACTTTCGCATGGTATCTTTCGTATTCATCAAGAAGATCAACCAGAAAAAGGCTCCGAAAACGCAGTTGTTTTGGTTCCCGCAAACCTGTCGGCAGAGAAACGCATAAAGATACAAGAGACGGCGAAAGCAATTTATAAGGCGCTCGGCTGTAAAGGTCTTTCTCGTGTTGATATGTTTTTGCAGGAAAACGGACGTATTATACTGAATGAAGTCAATACGTTGCCGGGATTCACGGCATACAGCCGTTATCCCCGTATGATGGCTGCCGCGGGGATGACACTGTCCGGGTTAATTGATCATTGCATCACACTGGCACTCAAAGGATGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39542","NCBI_taxonomy_name":"Paenibacillus popilliae ATCC 14706","NCBI_taxonomy_id":"1212764"}}}},"ARO_accession":"3002908","ARO_id":"39342","ARO_name":"vanF","ARO_description":"VanF is a D-Ala-D-Ala ligase homolog that can synthesize D-Ala-D-Lac, an alternative substrate for peptidoglycan synthesis that reduces vancomycin binding affinity. It is associated with both vancomycin and teicoplanin resistance in Paenibacillus popilliae","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"39340":{"category_aro_accession":"3002906","category_aro_cvterm_id":"39340","category_aro_name":"van ligase","category_aro_description":"van ligases synthesize alternative substrates for peptidoglycan synthesis that reduce vancomycin binding affinity.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1760":{"model_id":"1760","model_name":"QnrB35","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"555":{"protein_sequence":{"accession":"AEL00456.1","sequence":"MALALIGEKIDRNRFTGAKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAILKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKAVLEKCELWENRWMGTQMLGATLSGSDLSGGEFSSFDWRTANFTHCDLTNSELGDLDIRGVDLQGVKLDSYQAALLMERLGIAVIG"},"dna_sequence":{"accession":"JN173057","fmin":"2306","fmax":"2951","strand":"+","sequence":"ATGGCTCTGGCATTAATTGGCGAAAAAATTGACAGAAACCGCTTCACCGGTGCAAAAGTTGAAAATAGCACTTTTTTTAACTGTGATTTTTCGGGCGCCGACCTTAGCGGTACTGAATTTATCGGCTGTCAGTTCTATGATCGAGAAAGCCAGAAAGGGTGCAATTTCAGTCGCGCAATACTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAACGTCAGTGCGTTGGGCATAGAAATTCGCCACTGCCGAGCACAGGGTGCAGATTTTCGCGGCGCAAGTTTCATGAATATGATCACCACGCGCACCTGGTTTTGCAGCGCATATATCACTAATACCAATCTAAGCTATGCCAACTTTTCGAAGGCCGTGCTTGAAAAGTGCGAATTGTGGGAAAATCGCTGGATGGGAACTCAGATGCTGGGTGCGACGTTGAGTGGTTCCGATCTCTCCGGTGGCGAGTTTTCGTCGTTCGACTGGCGGACGGCAAATTTCACGCACTGTGATTTGACCAATTCAGAACTGGGTGATTTAGATATTCGGGGCGTCGATTTACAAGGTGTCAAATTGGACAGCTATCAGGCCGCGTTGCTCATGGAACGTCTTGGCATCGCTGTCATTGGCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002750","ARO_id":"39184","ARO_name":"QnrB35","ARO_description":"QnrB35 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1761":{"model_id":"1761","model_name":"OXA-351","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1133":{"protein_sequence":{"accession":"AGW83449.1","sequence":"MYKKALIVAISILFLSACSSNMVKQHQIHSISANKNSEEIKSLFDQAQTTGVLVIKRGQTEEIYGNDLKRASTDYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPDWEKDMTLSDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNANIGSKVDDFWLVGPLKITPQQETQFAYQLAHKTLPFSKNVQEQVQSMVFIEEKNGSKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"KF297580","fmin":"0","fmax":"822","strand":"+","sequence":"ATGTATAAAAAAGCCCTTATCGTTGCAATAAGTATCCTATTTTTATCCGCCTGTTCTTCCAATATGGTCAAACAACATCAAATACACTCTATTTCTGCCAATAAAAATTCAGAAGAAATTAAATCACTGTTTGATCAAGCACAGACCACTGGAGTTTTGGTGATTAAGCGAGGGCAAACAGAAGAAATTTATGGCAATGATCTTAAAAGAGCATCAACCGACTATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTAATTGGACTTGAACATCATAAGGCAACTACAACTGAAGTATTTAAATGGAATGGGCAAAAACGTTTATTTCCTGATTGGGAAAAGGACATGACACTGAGCGATGCCATGAAAGCTTCTGCAATTCCAGTTTACCAAGAATTAGCCCGACGGATTGGTCTGGATCTTATGTCCAAAGAGGTGAAACGAATTGGTTTCGGTAATGCTAACATTGGCTCAAAAGTAGATGATTTTTGGCTTGTTGGCCCTCTAAAAATTACACCTCAACAAGAAACCCAATTTGCTTATCAATTAGCCCATAAAACTCTTCCATTTAGCAAAAATGTACAAGAACAAGTTCAATCGATGGTGTTCATAGAGGAAAAAAATGGAAGTAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTTGAACCGCAAGTTGGTTGGTTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTGGCATTTTCACTTAATTTAGAAATGAAAAAAGGAACTCCTAGCTCTATTCGCAAAGAAATTGCTTATAAAGGCTTAGAACAACTGGGTATTTTATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3001538","ARO_id":"37938","ARO_name":"OXA-351","ARO_description":"OXA-351 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1762":{"model_id":"1762","model_name":"aadA16","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"373":{"protein_sequence":{"accession":"ACF17980.1","sequence":"MSNAVPAEISVQLSQALNVIERHLGSTLLAVHLYGSALDGGLKPCSDIDLLVTVTAQLDETVRQALFVDFLEVSASPGQSEALRALEVTIVVYGDVAPWRYLARRELQFGEWQRKDILAGIFEPATTDVDLAILLTKARQHSLALAGSAAEDFFNSVPESDLFKALADTLKLWNSQPDWAGDERNVVLTLSRIWYSAATGKIAPKDVAANWVMERLPVQHQPVLLEAQQAYLGQGMDCLASRADQLTAFIYFVKHEAASLLGSTPMMSNSSFKPTPLRGAA"},"dna_sequence":{"accession":"EU675686","fmin":"3196","fmax":"4042","strand":"+","sequence":"ATGAGCAACGCAGTGCCCGCCGAGATTTCGGTACAGCTATCACAGGCACTCAACGTCATCGAGCGTCATCTGGGATCGACGTTGCTGGCCGTGCATTTGTACGGCTCTGCACTCGACGGTGGCCTGAAGCCATGCAGTGATATTGATTTGCTGGTTACTGTGACTGCACAGCTCGATGAGACTGTGCGGCAGGCTCTGTTCGTAGATTTCCTGGAAGTTTCCGCTTCTCCCGGCCAAAGTGAAGCTCTCCGTGCCTTGGAAGTTACCATCGTCGTGTACGGCGATGTTGCTCCTTGGCGTTATCTAGCCAGACGGGAACTGCAATTCGGGGAGTGGCAGCGCAAGGACATTCTTGCGGGCATCTTCGAGCCCGCGACAACCGATGTTGATCTGGCTATTCTGCTAACTAAAGCAAGGCAACACAGCCTTGCCTTGGCAGGTTCGGCCGCGGAAGATTTCTTCAACTCAGTCCCGGAAAGCGATCTATTCAAAGCACTGGCCGACACCTTGAAACTATGGAACTCACAACCGGATTGGGCAGGCGACGAGCGGAATGTAGTGCTTACTTTGTCTCGCATTTGGTACAGCGCAGCAACCGGCAAGATCGCGCCGAAGGATGTAGCTGCCAACTGGGTAATGGAACGCCTGCCCGTCCAACATCAGCCCGTGCTGCTTGAAGCCCAGCAGGCTTACCTTGGACAAGGGATGGATTGCTTGGCCTCACGCGCTGATCAGTTGACTGCGTTCATTTACTTTGTGAAGCACGAAGCCGCCAGTCTGCTCGGCTCCACGCCAATGATGTCTAACAGTTCATTCAAGCCGACGCCGCTTCGCGGCGCAGCTTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002616","ARO_id":"39016","ARO_name":"aadA16","ARO_description":"aadA16 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids and integrons in E. coli, V. cholerae and K. pneumoniae","ARO_category":{"41439":{"category_aro_accession":"3004275","category_aro_cvterm_id":"41439","category_aro_name":"ANT(3'')","category_aro_description":"Nucleotidylylation of streptomycin at the hydroxyl group at position 3''","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1763":{"model_id":"1763","model_name":"NDM-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"777":{"protein_sequence":{"accession":"AEA41876.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMAGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"JF703135","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGGCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGATGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3000590","ARO_id":"36729","ARO_name":"NDM-2","ARO_description":"NDM-2 was isolated from a strain of Acinetobacter baumannii in Germany from a patient hospitalized in Cairo.  A single amino acid substitution (P28R) differentiates this gene from NDM-1 and the two enzymes appear to have an identical spectrum of hydrolysis.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1764":{"model_id":"1764","model_name":"OXA-97","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4347":{"protein_sequence":{"accession":"ABO33299.1","sequence":"MKLLKILSLVCLSISIGACAEHSMSRAKTSTIPQVNNSIIDQNVQALFNEISGDAVFVTYDGQNIKKYGTHLDRAKTAYIPASTFKIANALIGLENHKATSTEIFKWDGKPRFFKAWDKDFTLGEAMQASTVPVYQELARRIGPSLMQSELQRIGYGNMQIGTEVDQFWLKGPLTITPIQEVKFVYDLAQGQLPFKPEVQQQVKEMLYVERRGENRLYAKSGWGMAVDPQVGWYVGFVEKADGQVVAFALNMQMKAGDDIALRKQLSLDVLDKLGVFHYL"},"dna_sequence":{"accession":"EF102240.1","fmin":"11722","fmax":"12565","strand":"-","sequence":"TTATAAATAATGAAAAACACCCAACTTATCTAGCACATCTAAAGACAATTGTTTACGTAGAGCAATATCATCACCAGCTTTCATTTGCATATTTAAAGCAAATGCCACCACTTGCCCATCTGCCTTTTCAACAAAACCCACATACCAACCCACTTGCGGGTCTACAGCCATTCCCCAGCCACTTTTAGCATATAGACGATTCTCCCCTCTGCGCTCTACATACAACATCTCTTTCACTTGTTGCTGAACTTCAGGTTTAAAAGGCAATTGCCCTTGGGCTAAATCATACACAAACTTTACTTCTTGTATAGGTGTAATTGTCAAAGGCCCTTTCAACCAAAATTGATCAACTTCCGTGCCTATTTGCATATTGCCATAACCAATACGTTGCAATTCACTTTGCATTAAGCTTGGACCAATACGACGTGCCAATTCTTGATATACAGGCACTGTAGATGCTTGCATGGCTTCGCCCAAAGTAAAATCTTTGTCCCATGCTTTAAAAAAACGTGGCTTTCCATCCCACTTAAATATTTCTGTAGATGTTGCTTTATGATTTTCTAAACCAATTAGTGCATTGGCAATTTTAAATGTAGATGCAGGAATATAAGCTGTTTTTGCTCGGTCTAAATGCGTGCCATATTTTTTAATATTTTGACCATCATATGTGACAAACACAGCATCACCTGAGATTTCATTAAAAAGCGCTTGAACATTCTGATCGATGATTGAGTTATTCACTTGTGGAATTGTACTTGTTTTTGCTCGACTCATACTATGCTCAGCACAAGCCCCAATACTTATGCTTAAGCAAACTAAACTCAATATTTTTAATAATTTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001647","ARO_id":"38047","ARO_name":"OXA-97","ARO_description":"OXA-97 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1765":{"model_id":"1765","model_name":"OXA-56","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1056":{"protein_sequence":{"accession":"AAR32651.1","sequence":"MKTFAAYVITACLSSTALASSITENTFWNKEFSAEAVNGVFVLCKSSSKSCATNNLARASKEYLPASTFKIPNAIIGLETGVIKNEHQIFKWDGKPRAMKQWERDLSLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLFLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKGAEVYFFAFNMDIDNENKLPLRKSIPTKIMASEGIIGG"},"dna_sequence":{"accession":"AY445080","fmin":"0","fmax":"801","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTACTGCGTGTCTTTCAAGTACGGCATTAGCTAGTTCAATTACAGAAAATACGTTTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTTTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATAACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGATTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAACAATGGGAAAGAGACTTGAGCTTAAGAGGGGCAATACAAGTTTCAGCGGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATATCTTAAAAAATTTTCATATGGTAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAGGGTCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATTTTTAAATAAATTGTCAGCATCAAAAGAAAATCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCTGCGCCTGAATATCTTGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGTTGGGTTGAGAAGGGAGCAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAATAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGCAAGTGAGGGCATCATTGGTGGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001795","ARO_id":"38195","ARO_name":"OXA-56","ARO_description":"OXA-56 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1766":{"model_id":"1766","model_name":"VIM-14","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1082":{"protein_sequence":{"accession":"AAT48653.1","sequence":"MLKVISSLLVYMTASVMAVASPLAHSGEPSSEYPTVNEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEAEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSANVLYGGCAVHELSRTSAGNVADADLAEWPTSVERIQKHYPEAEVVIPGHGLPGGLDLLQHTANVVKAHKNRSVAE"},"dna_sequence":{"accession":"AY635904","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTACATGACCGCGTCTGTCATGGCTGTCGCAAGTCCGTTAGCCCATTCCGGGGAGCCGAGTAGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGAGAGGTCCGACTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCGGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAAAAGCAAATTGGACTTCCCGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGCAGAGGGGAACGAGATTCCCACGCATTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGCTCTTCTATCCTGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAACGTGCTATACGGTGGTTGTGCCGTTCATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCGTTGAGCGGATTCAAAAACACTACCCGGAAGCAGAGGTCGTCATTCCCGGGCACGGTCTACCGGGCGGTCTAGACTTGCTCCAGCACACAGCGAACGTTGTCAAAGCACACAAAAATCGCTCAGTCGCCGAGTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002284","ARO_id":"38684","ARO_name":"VIM-14","ARO_description":"VIM-14 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1767":{"model_id":"1767","model_name":"OKP-A-16","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1287":{"protein_sequence":{"accession":"ACN65418.1","sequence":"MRYVRLCLISLIAALPLVAFASPQPLEQVTRSESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIRYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKSVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMAATLRKLLTSHALSARSQQQLLQWMVDDQVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPNGKAERIVVIYLRDTPATMAERNQQIARIGAALIEHWQR"},"dna_sequence":{"accession":"FJ755840","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGTGGCATTCGCCAGCCCTCAGCCGCTCGAGCAAGTTACACGCAGCGAAAGTCAGCTGGCGGGCCGCGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGAGACGAACAGCTGGATCGGCGGATCCGCTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGTGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGAGCGTTGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGACTTGACCGCTGGGAAACGGAGCTCAATGAGGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCAGCCAGCATGGCCGCCACCCTGCGCAAGCTGCTAACCAGCCACGCGCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGACCAGGTAGCCGGTCCGCTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGCGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGAACGGCAAAGCGGAGCGCATCGTGGTGATCTATCTGCGGGATACGCCGGCGACCATGGCCGAGCGTAACCAGCAGATCGCCAGAATAGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002433","ARO_id":"38833","ARO_name":"OKP-A-16","ARO_description":"OKP-A-16 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1768":{"model_id":"1768","model_name":"CTX-M-144","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1185":{"protein_sequence":{"accession":"AHX39588.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAVAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDLRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"KJ020573","fmin":"274","fmax":"1150","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGTGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCTGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002002","ARO_id":"38402","ARO_name":"CTX-M-144","ARO_description":"CTX-M-144 is a beta-lactamase. From the Lahey list of CTX-M beta-lactamases.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1769":{"model_id":"1769","model_name":"CTX-M-115","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"766":{"protein_sequence":{"accession":"AIL54055.1","sequence":"MMTQSIRRSMLTVMATLPLLFSSATLHAQANSVQQQLEALEKSSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKQSESDKHLLNQRVEIKKSDLVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSASIRAGLPKSWVVGDKTGSGDYGTTNDIAIIWPENHAPLVLVTYFTQPEQKAESRRDVLAAAAKIVTHSF"},"dna_sequence":{"accession":"KJ911020","fmin":"111","fmax":"987","strand":"+","sequence":"ATGATGACTCAGAGCATTCGCCGCTCAATGTTAACGGTGATGGCGACGCTACCCCTGCTATTTAGCAGCGCAACGCTGCATGCGCAGGCGAACAGCGTGCAACAGCAGCTGGAAGCCCTGGAGAAAAGTTCGGGAGGTCGGCTTGGCGTTGCGCTGATTAACACCGCCGATAATTCGCAGATTCTCTACCGTGCCGATGAACGTTTTGCGATGTGCAGTACCAGTAAGGTGATGGCGGCCGCGGCGGTGCTTAAACAGAGCGAGAGCGATAAGCACCTGCTAAATCAGCGCGTTGAAATCAAGAAGAGCGACCTGGTTAACTACAATCCCATTGCTGAGAAACACGTTAACGGCACTATGACGCTGGCTGAGCTTGGCGCAGCGGCGCTGCAGTATAGCGACAATACTGCCATGAATAAGCTGATTGCCCATCTGGGTGGGCCCGATAAAGTGACGGCGTTTGCTCGCTCGTTGGGTGATGAGACCTTCCGTCTGGACAGAACCGAGCCCACGCTCAATACCGCCATTCCAGGCGACCCGCGTGATACCACCACGCCGCTCGCGATGGCGCAGACCCTGAAAAATCTGACGCTGGGTAAAGCGCTGGCGGAAACTCAGCGGGCACAGTTGGTGACGTGGCTTAAGGGCAATACTACCGGTAGCGCGAGCATTCGGGCGGGTCTGCCGAAATCATGGGTAGTGGGCGATAAAACCGGCAGCGGAGATTATGGCACCACCAACGATATCGCGATTATCTGGCCGGAAAACCACGCACCGCTGGTTCTGGTGACCTACTTTACCCAACCGGAGCAGAAGGCGGAAAGCCGTCGGGATGTTCTGGCTGCGGCGGCGAAAATCGTAACCCACAGTTTCTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001975","ARO_id":"38375","ARO_name":"CTX-M-115","ARO_description":"CTX-M-115 is a beta-lactamase found in Acinetobacter baumannii","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1770":{"model_id":"1770","model_name":"TEM-127","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1644":{"protein_sequence":{"accession":"AAR89358.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDNVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AY368236","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATAATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000989","ARO_id":"37369","ARO_name":"TEM-127","ARO_description":"TEM-127 is a broad-spectrum beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1771":{"model_id":"1771","model_name":"TEM-19","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"928":{"protein_sequence":{"accession":"AFN21551.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"JX042489","fmin":"141","fmax":"1002","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3000890","ARO_id":"37270","ARO_name":"TEM-19","ARO_description":"TEM-19 is an extended-spectrum beta-lactamase that has been found in clinical isolates.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1772":{"model_id":"1772","model_name":"aadA11","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"13":{"protein_sequence":{"accession":"AAV32840.1","sequence":"MSNAVPAEISVQLSLALNAIERHLESTLLAVHLYGSALDGGLKPYSDIDLLVTVAAQLDETVRQALVVDLLEISASPGQSEALRALEVTIVVHGDVVPWRYPARRELQFGEWQRKDILAGIFEPATTDVDLAILLTKVRQHSLALAGSAAEDFFNPVPEGDLFKALSDTLKLWNSQPDWEGDERNVVLTLSRIWYSAATGKIAPKDIVANWAIERLPDQHKPVLLEARQAYLGQGEDCLASRADQLAAFVHFVKHEATKLLGAMPVMSNNSFKPNPLRGSA"},"dna_sequence":{"accession":"AY758206","fmin":"2743","fmax":"3589","strand":"+","sequence":"ATGAGTAACGCAGTACCCGCCGAGATTTCGGTACAGCTATCACTGGCTCTCAACGCCATCGAGCGTCATCTGGAATCAACGTTGCTGGCCGTGCATTTGTACGGCTCTGCACTGGACGGTGGCCTGAAGCCATACAGTGATATTGATTTGCTGGTTACTGTGGCTGCACAGCTCGATGAGACTGTCCGACAAGCCCTGGTCGTAGATCTCTTGGAAATTTCTGCCTCCCCTGGCCAAAGTGAGGCTCTCCGCGCCTTGGAAGTTACCATCGTCGTGCATGGTGATGTTGTCCCTTGGCGTTATCCGGCCAGACGGGAACTGCAATTCGGGGAGTGGCAGCGTAAGGACATTCTTGCGGGCATCTTCGAGCCCGCCACAACCGATGTTGATCTGGCTATTCTGCTAACTAAAGTAAGGCAGCATAGCCTTGCATTGGCAGGTTCGGCCGCAGAGGATTTCTTTAACCCAGTTCCGGAAGGCGATCTATTCAAGGCATTGAGCGACACTCTGAAACTATGGAATTCGCAGCCGGATTGGGAAGGCGATGAGCGGAATGTAGTGCTTACCTTGTCTCGCATTTGGTACAGCGCAGCAACCGGCAAGATCGCACCGAAGGATATCGTTGCCAACTGGGCAATTGAGCGTCTGCCAGATCAACATAAGCCCGTACTGCTTGAAGCCCGGCAGGCTTATCTTGGACAAGGAGAAGATTGCTTGGCCTCACGCGCGGATCAGTTGGCGGCGTTCGTTCACTTCGTGAAACATGAAGCCACTAAATTGCTTGGTGCCATGCCAGTGATGTCTAACAATTCATTCAAGCCGAACCCGCTTCGCGGGTCGGCTTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002611","ARO_id":"39011","ARO_name":"aadA11","ARO_description":"aadA11 is an integron-encoded aminoglycoside nucleotidyltransferase gene in E. coli and P. aeruginosa","ARO_category":{"41439":{"category_aro_accession":"3004275","category_aro_cvterm_id":"41439","category_aro_name":"ANT(3'')","category_aro_description":"Nucleotidylylation of streptomycin at the hydroxyl group at position 3''","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1774":{"model_id":"1774","model_name":"CTX-M-106","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1271":{"protein_sequence":{"accession":"ADZ31262.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDRTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRHDVLASAARIIAEG"},"dna_sequence":{"accession":"HQ913565","fmin":"0","fmax":"870","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAGGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCACGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001966","ARO_id":"38366","ARO_name":"CTX-M-106","ARO_description":"CTX-M-106 is a beta-lactamase. From the Lahey list of CTX-M beta-lactamases.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1775":{"model_id":"1775","model_name":"QnrS7","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"348":{"protein_sequence":{"accession":"AHE41344.1","sequence":"METYNHTYRHHNFSHKDLSDLTFTACTFIRSDFRRANLRDTTFVNCKFIEQGDIEGCHFDVADLHDASFQQCQLAMANFSNANCYGIEFRACDLKGANFSRTNFAHQVSNRMYFCSAFISGCNLSYANMERVCLEKCELFENRWIGTNLAGASLKESDLSRGVFSEDVWGQFSLQGANLCHAELDGLDPRKVDTSGIKIAAWQQELILEALGIVVYPD"},"dna_sequence":{"accession":"KF730651","fmin":"0","fmax":"657","strand":"+","sequence":"ATGGAAACCTACAATCATACATATCGGCACCACAACTTTTCACATAAAGACTTAAGTGATCTCACCTTCACCGCTTGCACATTCATTCGCAGCGACTTTCGACGTGCTAACTTGCGTGATACGACATTCGTCAACTGCAAGTTCATTGAACAGGGTGATATCGAAGGCTGCCACTTTGATGTCGCAGATCTTCATGATGCAAGTTTCCAACAATGCCAACTTGCGATGGCAAACTTCAGTAATGCCAATTGCTACGGTATAGAGTTCCGTGCGTGTGATTTAAAAGGTGCCAACTTTTCCCGAACAAACTTTGCCCATCAAGTGAGTAATCGTATGTACTTTTGCTCAGCATTTATTTCTGGATGTAATCTTTCCTATGCCAATATGGAGAGGGTTTGTTTAGAAAAATGTGAGTTGTTTGAAAATCGCTGGATAGGAACGAACCTAGCGGGTGCATCACTGAAAGAGTCAGACTTAAGTCGAGGTGTTTTTTCCGAAGATGTCTGGGGGCAATTTAGCCTACAGGGTGCCAATTTATGCCACGCCGAACTCGACGGTTTAGATCCCCGCAAAGTCGATACATCAGGTATCAAAATTGCAGCCTGGCAGCAAGAACTGATTCTCGAAGCACTGGGTATTGTTGTTTATCCTGACTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002796","ARO_id":"39230","ARO_name":"QnrS7","ARO_description":"QnrS7 is a plasmid-mediated quinolone resistance protein found in Escherichia coli","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1776":{"model_id":"1776","model_name":"SHV-159","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1788":{"protein_sequence":{"accession":"AFQ23965.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVGDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"JX121126","fmin":"0","fmax":"858","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGGCGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGTATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001198","ARO_id":"37578","ARO_name":"SHV-159","ARO_description":"SHV-159 is a beta-lactamase.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1777":{"model_id":"1777","model_name":"OXA-177","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"968":{"protein_sequence":{"accession":"ADI58621.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWVVGPLKITPQQEAQFAYKLANKTLPFSQKVQDGVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"HM113563","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGGTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGGAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001661","ARO_id":"38061","ARO_name":"OXA-177","ARO_description":"OXA-177 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1778":{"model_id":"1778","model_name":"OKP-A-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1598":{"protein_sequence":{"accession":"CAJ19602.1","sequence":"MRYVRLCLISLIAALPLAVFASPQPLEQITLSESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDERLDRRIRYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKSVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMAATLRKLLTSHALSDRSQQQLLQWMVDDQVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPNGKAERIVVIYLRDTPATMAERNQQIARIGAALIEHWQR"},"dna_sequence":{"accession":"AM051143","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCAGCCGCTCGAACAAATTACACTCAGCGAAAGTCAGCTGGCGGGCCGCGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGAGACGAACGGCTGGATCGGCGGATCCGCTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGAGCGTTGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAGCTCAATGAAGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCAGCCAGCATGGCCGCCACCCTGCGCAAGCTGCTAACCAGCCACGCGCTGAGCGACCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGACCAGGTGGCCGGTCCGCTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGCGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGAACGGCAAAGCGGAGCGCATCGTGGTGATCTATCTGCGGGATACGCCGGCGACCATGGCCGAGCGTAACCAGCAGATCGCCAGAATAGGCGCGGCGCTGATCGAGCACTGGCAGCGCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002422","ARO_id":"38822","ARO_name":"OKP-A-5","ARO_description":"OKP-A-5 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1779":{"model_id":"1779","model_name":"CTX-M-12","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1008":{"protein_sequence":{"accession":"AAG34108.1","sequence":"MVKKSLRQFTLMATAAVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPSLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDILASAAKIVTDGL"},"dna_sequence":{"accession":"AF305837","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAGCCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCGGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTCGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAGTCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTGGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCAGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATTTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATATATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001875","ARO_id":"38275","ARO_name":"CTX-M-12","ARO_description":"CTX-M-12 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1780":{"model_id":"1780","model_name":"OXA-146","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1524":{"protein_sequence":{"accession":"ACI28281.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETPSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAAMDIKPQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"FJ194494","fmin":"171","fmax":"996","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGACCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCCCAATTAGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001779","ARO_id":"38179","ARO_name":"OXA-146","ARO_description":"OXA-146 is a beta-lactamase found in Enterobacteriaceae","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1718":{"model_id":"1718","model_name":"DIM-1 beta-lactamase","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1968":{"protein_sequence":{"accession":"AGC92784.1","sequence":"MRTHFTALLLLFSLSSLANDEVPELRIEKVKENIFLHTSYSRVNGFGLVSSNGLVVIDKGNAFIVDTPWSDRDTETLVHWIRKNGYELLGSVSTHWHEDRTAGIKWLNDQSISTYATTSTNHLLKENKKEPAKYTLKGNESTLVDGLIEVFYPGGGHTIDNVVVWLPKSKILFGGCFVRSLDSEGLGYTGEAHIDQWSRSAQNALSRYSEAQIVIPGHGKIGDIALLKHTKSLAETASNKSIQPNANASAD"},"dna_sequence":{"accession":"KC004136","fmin":"40","fmax":"796","strand":"+","sequence":"ATGAGAACACATTTTACAGCGTTATTACTTCTATTCAGCTTGTCTTCGCTTGCTAACGACGAGGTACCTGAGCTAAGAATCGAGAAAGTAAAAGAGAACATCTTTTTGCACACATCATACAGTCGTGTGAATGGGTTTGGTTTGGTCAGTTCAAACGGCCTTGTTGTCATAGATAAGGGTAATGCTTTCATTGTTGATACACCTTGGTCAGACCGAGATACAGAAACGCTCGTACATTGGATTCGTAAAAATGGTTATGAGCTACTGGGGAGTGTTTCTACTCATTGGCATGAGGATAGAACCGCAGGAATTAAATGGCTTAATGACCAATCAATTTCTACGTATGCCACGACTTCAACCAACCATCTCTTGAAAGAAAATAAAAAAGAGCCAGCGAAATACACCTTGAAAGGAAATGAGTCCACATTGGTTGACGGCCTTATCGAAGTATTTTATCCAGGAGGTGGTCATACAATAGACAACGTAGTGGTGTGGTTGCCAAAGTCGAAAATCTTATTTGGCGGCTGTTTTGTGCGTAGCCTTGATTCCGAGGGGTTAGGCTACACTGGTGAAGCCCATATTGATCAATGGTCCCGATCAGCTCAGAATGCTCTGTCTAGGTACTCAGAAGCCCAGATAGTAATTCCTGGCCATGGGAAAATCGGGGATATAGCGCTGTTAAAACACACCAAAAGTCTGGCTGAGACAGCCTCTAACAAATCAATCCAGCCGAACGCTAACGCGTCGGCTGATTGAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39662","NCBI_taxonomy_name":"Enterobacter sp. SL1","NCBI_taxonomy_id":"1284354"}}}},"ARO_accession":"3000848","ARO_id":"37228","ARO_name":"DIM-1","ARO_description":"Dutch imipenemase or DIM-1 is an integron-encoded metallo-beta-lactamase from Pseudomonas stutzeri","ARO_category":{"41372":{"category_aro_accession":"3004208","category_aro_cvterm_id":"41372","category_aro_name":"DIM beta-lactamase","category_aro_description":"DIM type beta-lactamases were first identified from a carbapenem-resistant Pseudomonas stutzeri strain isolated from a Dutch patient. Encoded in mobile elements, these MBLs significantly hydrolyze broad-spectrum cephalosporins and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1607":{"model_id":"1607","model_name":"Streptococcus pneumoniae PBP1a conferring resistance to amoxicillin","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"4483":"S575T","4484":"N609D"},"clinical":{"4483":"S575T","4484":"N609D"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1350"}},"model_sequences":{"sequence":{"692":{"protein_sequence":{"accession":"AFC91828.1","sequence":"MNKPTILHLIKYLSISFLSLVIAAIVLGGGVFFYYVSKAPSLSESKLVATTSSKIYDNKNQLIADLGSERRVNAQANDIPTDLVKAIVSIEDHRFFDHRGIDTIRILGAFLRNLQSNSLQGGSTLTQQLIKLTYFSTSTSDQTISRKTQEAWLAIQLEQKATKQEILTYYINKVYMSNGNYGMQTAAQNYYGKDLNNLSLPQLALLAGMPQAPNQYDPYSHPEAAQDRRNLVLSEMKNQGYISAEQYEKAVNTPITDGLQSLKSASNYPAYMDNYLKEVINQVEKETGYNLLTTGMDVYTNVDQEAQKHLWDIYNTDEYVAYPDDELQVASTIVDVSNGKVIAQLGARHQSSNVSFGINQAVETNRDWGSTMKPITDYAPALEYGVYDSTATIVHDEPYNYPGTNTPVYNWDRGYFGNITLQYALQQSRNVPAVETLNKVGLNRAKTFLNGLGIDYPSIHYSNAISSNTTESDKKYGASSEKMAAAYAAFANGGTYYKPMYIHKVVFSDGSEKEFSNVGTRAMKETTAYMMTDMMKTVLSYGTGRNAYLAWLPQAGKTGTSNYTDEEIENHIKTSQFVAPDELFAGYTRKYSMAVWTGYSNRLTPLVGNGLTVAAKVYRSMMTYLSEGSNPEDWNIPEGLYRNGEFVFKNGARSTWTQPAPQQPPSTESSSSSSDSSTSQSSSTTPSTNNSTTTDPNNNTQQSNTTPDQQNQNPQPAQP"},"dna_sequence":{"accession":"JN645776","fmin":"0","fmax":"2160","strand":"+","sequence":"ATGAACAAACCAACGATTCTGCACCTAATCAAGTATCTGAGCATTAGCTTCTTAAGCTTGGTTATCGCAGCCATTGTCTTAGGCGGAGGAGTTTTTTTCTACTACGTTAGCAAGGCTCCTAGCCTATCCGAGAGTAAACTAGTTGCAACAACTTCTAGTAAAATCTACGACAATAAAAATCAACTCATTGCTGACTTGGGTTCTGAACGCCGCGTCAATGCCCAAGCTAATGATATTCCCACAGATTTGGTTAAGGCAATCGTTTCTATCGAAGACCATCGCTTCTTCGACCACAGGGGGATTGATACCATCCGTATCCTGGGAGCTTTCTTGCGCAATCTGCAAAGCAATTCCCTCCAAGGTGGATCAACTCTCACCCAACAGTTGATTAAGTTGACTTACTTTTCAACTTCGACTTCCGACCAGACTATTTCTCGTAAGACTCAGGAAGCTTGGTTAGCGATTCAGTTAGAACAAAAAGCAACCAAGCAAGAAATCTTGACCTACTATATAAATAAGGTCTACATGTCTAATGGCAACTATGGAATGCAGACAGCAGCTCAAAACTACTATGGTAAAGACCTCAATAATTTAAGTTTACCTCAGTTAGCCTTGCTGGCTGGAATGCCTCAGGCACCAAACCAATATGACCCCTATTCACATCCAGAAGCAGCCCAAGACCGCCGAAACTTGGTCTTATCTGAAATGAAAAATCAAGGCTACATCTCTGCTGAACAGTATGAGAAAGCAGTCAATACACCAATTACTGATGGACTACAAAGTCTCAAATCAGCAAGTAATTACCCTGCTTACATGGATAATTACCTCAAGGAAGTCATCAATCAAGTTGAAAAAGAAACAGGCTATAACCTGCTCACAACTGGGATGGATGTCTACACAAATGTAGACCAAGAAGCTCAAAAACATCTGTGGGATATTTACAATACAGACGAATACGTTGCCTATCCAGACGATGAATTGCAAGTCGCTTCTACCATTGTTGATGTTTCTAACGGTAAAGTCATTGCCCAGCTAGGAGCACGCCATCAGTCAAGTAATGTTTCCTTCGGAATTAACCAAGCAGTAGAAACAAACCGCGACTGGGGATCAACTATGAAACCGATCACAGACTATGCTCCTGCCTTGGAGTACGGTGTCTACGATTCAACTGCTACTATCGTTCACGATGAGCCCTATAACTACCCTGGGACAAATACTCCTGTTTATAACTGGGATAGGGGCTACTTTGGCAACATCACCTTGCAATACGCCCTGCAACAATCGCGAAACGTCCCAGCCGTGGAAACTCTAAACAAGGTCGGACTCAACCGCGCCAAGACTTTCCTAAATGGTCTCGGAATCGACTACCCAAGTATTCACTACTCAAATGCCATTTCAAGTAACACAACCGAATCAGACAAAAAATATGGAGCAAGTAGTGAAAAGATGGCTGCTGCTTACGCTGCCTTTGCAAATGGTGGAACTTACTATAAACCAATGTATATCCATAAAGTCGTCTTTAGTGATGGGAGTGAAAAAGAGTTCTCTAATGTCGGAACTCGTGCCATGAAGGAAACAACAGCCTATATGATGACCGACATGATGAAAACAGTCTTGAGTTATGGAACTGGACGAAATGCCTATCTTGCTTGGCTCCCTCAGGCTGGTAAAACAGGAACCTCTAACTATACAGACGAGGAAATTGAAAACCACATCAAGACCTCTCAATTTGTAGCACCTGACGAACTATTTGCTGGCTATACGCGTAAATATTCAATGGCTGTATGGACAGGCTATTCTAACCGTCTGACACCACTTGTAGGCAATGGCCTTACGGTCGCTGCCAAAGTTTACCGCTCTATGATGACCTACCTGTCTGAAGGAAGCAATCCAGAGGATTGGAATATACCAGAGGGGCTCTACAGAAATGGAGAATTCGTATTTAAAAATGGTGCTCGTTCTACGTGGACTCAACCTGCTCCACAACAACCCCCATCAACTGAAAGTTCAAGCTCATCATCAGATAGTTCAACTTCACAGTCTAGCTCAACCACTCCAAGCACAAATAATAGTACGACTACCGATCCTAACAATAATACGCAACAATCAAATACAACCCCTGATCAACAAAATCAGAATCCTCAACCAGCACAACCATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35917","NCBI_taxonomy_name":"Streptococcus pneumoniae","NCBI_taxonomy_id":"1313"}}}},"ARO_accession":"3003041","ARO_id":"39475","ARO_name":"Streptococcus pneumoniae PBP1a conferring resistance to amoxicillin","ARO_description":"PBP1a is a penicillin-binding protein found in Streptococcus pneumoniae","ARO_category":{"40661":{"category_aro_accession":"3003938","category_aro_cvterm_id":"40661","category_aro_name":"Penicillin-binding protein mutations conferring resistance to beta-lactam antibiotics","category_aro_description":"Mutations in PBP transpeptidases that change the affinity for penicillin thereby conferring resistance to penicillin antibiotics","category_aro_class_name":"AMR Gene Family"},"35927":{"category_aro_accession":"0000008","category_aro_cvterm_id":"35927","category_aro_name":"cefoxitin","category_aro_description":"Cefoxitin is a cephamycin antibiotic often grouped with the second generation cephalosporins. Cefoxitin is bactericidal and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. Cefoxitin's 7-alpha-methoxy group and 3' leaving group make it a poor substrate for most beta-lactamases.","category_aro_class_name":"Antibiotic"},"35930":{"category_aro_accession":"0000011","category_aro_cvterm_id":"35930","category_aro_name":"cloxacillin","category_aro_description":"Cloxacillin is a semisynthetic, isoxazolyl penicillin derivative in the beta-lactam class of antibiotics. It interferes with peptidogylcan synthesis and is commonly used for treating penicillin-resistant Staphylococcus aureus infections.","category_aro_class_name":"Antibiotic"},"35934":{"category_aro_accession":"0000015","category_aro_cvterm_id":"35934","category_aro_name":"methicillin","category_aro_description":"Derived from penicillin to combat penicillin-resistance, methicillin is insensitive to beta-lactamases (also known as penicillinases) secreted by many penicillin-resistant bacteria. Methicillin is bactericidal, and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Antibiotic"},"35961":{"category_aro_accession":"0000043","category_aro_cvterm_id":"35961","category_aro_name":"carbenicillin","category_aro_description":"Carbenicillin is a semi-synthetic antibiotic belonging to the carboxypenicillin subgroup of the penicillins. It has gram-negative coverage which includes Pseudomonas aeruginosa but limited gram-positive coverage. The carboxypenicillins are susceptible to degradation by beta-lactamase enzymes. Carbenicillin antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Antibiotic"},"35971":{"category_aro_accession":"0000054","category_aro_cvterm_id":"35971","category_aro_name":"penicillin","category_aro_description":"Penicillin (sometimes abbreviated PCN) is a beta-lactam antibiotic used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms. It works by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Antibiotic"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35975":{"category_aro_accession":"0000058","category_aro_cvterm_id":"35975","category_aro_name":"cefazolin","category_aro_description":"Cefazolin (INN), also known as cefazoline or cephazolin, is a first generation cephalosporin antibiotic. It is administered parenterally, and is active against a broad spectrum of bacteria.","category_aro_class_name":"Antibiotic"},"35976":{"category_aro_accession":"0000059","category_aro_cvterm_id":"35976","category_aro_name":"cefepime","category_aro_description":"Cefepime (INN) is a fourth-generation cephalosporin antibiotic developed in 1994. It contains an aminothiazolyl group that decreases its affinity with beta-lactamases. Cefepime shows high binding affinity with penicillin-binding proteins and has an extended spectrum of activity against Gram-positive and Gram-negative bacteria, with greater activity against both Gram-negative and Gram-positive organisms than third-generation agents.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35978":{"category_aro_accession":"0000061","category_aro_cvterm_id":"35978","category_aro_name":"ceftobiprole","category_aro_description":"Ceftobiprole (Zeftera\/Zevtera) is a next generation (5th generation) cephalosporin antibiotic with activity against methicillin-resistant Staphylococcus aureus, penicillin-resistant Streptococcus pneumoniae, Pseudomonas aeruginosa, and Enterococci. Ceftobiprole inhibits transpeptidases essential to building cell walls, and is a poor substrate for most beta-lactamases.","category_aro_class_name":"Antibiotic"},"35979":{"category_aro_accession":"0000062","category_aro_cvterm_id":"35979","category_aro_name":"ceftriaxone","category_aro_description":"Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"35980":{"category_aro_accession":"0000063","category_aro_cvterm_id":"35980","category_aro_name":"cefuroxime","category_aro_description":"Cefuroxime is a second-generation cephalosporin antibiotic with increased stability with beta-lactamases than first-generation cephalosporins. Cefuroxime is active against Gram-positive organisms but less active against methicillin-resistant strains.","category_aro_class_name":"Antibiotic"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"35987":{"category_aro_accession":"0000070","category_aro_cvterm_id":"35987","category_aro_name":"ertapenem","category_aro_description":"Ertapenem is a carbapenem antibiotic and is highly resistant to beta-lactamases like other carbapenems. It inhibits bacterial cell wall synthesis.","category_aro_class_name":"Antibiotic"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"35995":{"category_aro_accession":"0000078","category_aro_cvterm_id":"35995","category_aro_name":"piperacillin","category_aro_description":"Piperacillin is an acetylureidopenicillin and has an extended spectrum of targets relative to other beta-lactam antibiotics. It inhibits cell wall synthesis in bacteria, and is usually taken with the beta-lactamase inhibitor tazobactam to overcome penicillin-resistant bacteria.","category_aro_class_name":"Antibiotic"},"36309":{"category_aro_accession":"3000170","category_aro_cvterm_id":"36309","category_aro_name":"imipenem","category_aro_description":"Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.","category_aro_class_name":"Antibiotic"},"36689":{"category_aro_accession":"3000550","category_aro_cvterm_id":"36689","category_aro_name":"aztreonam","category_aro_description":"Aztreonam was the first monobactam discovered, and is greatly effective against Gram-negative bacteria while inactive against Gram-positive bacteria. Artreonam is a poor substrate for beta-lactamases, and may even act as an inhibitor. In Gram-negative bacteria, Aztreonam interferes with filamentation, inhibiting cell division and leading to cell death.","category_aro_class_name":"Antibiotic"},"36976":{"category_aro_accession":"3000632","category_aro_cvterm_id":"36976","category_aro_name":"benzylpenicillin","category_aro_description":"Benzylpenicillin, commonly referred to as penicillin G, is effective against both Gram-positive and Gram-negative bacteria. It is unstable in acid.","category_aro_class_name":"Antibiotic"},"36977":{"category_aro_accession":"3000633","category_aro_cvterm_id":"36977","category_aro_name":"phenoxymethylpenicillin","category_aro_description":"Phenoxymethylpenicillin, or penicillin V, is a penicillin derivative that is acid stable but less active than benzylpenicillin (penicillin G).","category_aro_class_name":"Antibiotic"},"36978":{"category_aro_accession":"3000634","category_aro_cvterm_id":"36978","category_aro_name":"propicillin","category_aro_description":"Propicillin is an orally taken penicillin derivative that has high absorption but poor activity.","category_aro_class_name":"Antibiotic"},"36979":{"category_aro_accession":"3000635","category_aro_cvterm_id":"36979","category_aro_name":"dicloxacillin","category_aro_description":"Dicloxacillin is a penicillin derivative that has an extra chlorine atom in comparison to cloxacillin. While more active than cloxacillin, its high affinity for serum protein reduces its activity in human serum in vitro.","category_aro_class_name":"Antibiotic"},"36980":{"category_aro_accession":"3000636","category_aro_cvterm_id":"36980","category_aro_name":"flucloxacillin","category_aro_description":"Flucloxacillin is similar to cloxacillin, with an extra additional fluorine atom.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"36982":{"category_aro_accession":"3000638","category_aro_cvterm_id":"36982","category_aro_name":"azlocillin","category_aro_description":"Azlocillin is a semisynthetic derivative of penicillin that is notably active against Ps. aeruginosa and other Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36983":{"category_aro_accession":"3000639","category_aro_cvterm_id":"36983","category_aro_name":"mezlocillin","category_aro_description":"Mezlocillin is a penicillin derivative taken parenterally.","category_aro_class_name":"Antibiotic"},"36984":{"category_aro_accession":"3000640","category_aro_cvterm_id":"36984","category_aro_name":"doripenem","category_aro_description":"Doripenem is a carbapenem with a broad range of activity against Gram-positive and Gram-negative bacteria, and along with meropenem, it is the most active beta-lactam antibiotic against Pseudomonas aeruginosa. It inhibits bacterial cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36985":{"category_aro_accession":"3000641","category_aro_cvterm_id":"36985","category_aro_name":"cefalexin","category_aro_description":"Cefalexin is a cephalosporin antibiotic that causes filamentation. It is resistant to staphylococcal beta-lactamase, but degraded by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"36986":{"category_aro_accession":"3000642","category_aro_cvterm_id":"36986","category_aro_name":"cefadroxil","category_aro_description":"Cefadroxil, or p-hydroxycephalexin, is an cephalosporin antibiotic similar to cefalexin.","category_aro_class_name":"Antibiotic"},"36987":{"category_aro_accession":"3000643","category_aro_cvterm_id":"36987","category_aro_name":"cefotiam","category_aro_description":"Cefotiam is a cephalosporin antibiotic with similar activity to cefuroxime but more active against enterobacteria. It is consumed orally as the prodrug cefotiam hexetil.","category_aro_class_name":"Antibiotic"},"36988":{"category_aro_accession":"3000644","category_aro_cvterm_id":"36988","category_aro_name":"cefaclor","category_aro_description":"Cefaclor is a semisynthetic cephalosporin derived from cephalexin. It has broad-spectrum antibiotic activity.","category_aro_class_name":"Antibiotic"},"36989":{"category_aro_accession":"3000645","category_aro_cvterm_id":"36989","category_aro_name":"cefotaxime","category_aro_description":"Cefotaxime is a semisynthetic cephalosporin taken parenterally. It is resistant to most beta-lactamases and active against Gram-negative rods and cocci due to its aminothiazoyl and methoximino functional groups.","category_aro_class_name":"Antibiotic"},"36990":{"category_aro_accession":"3000646","category_aro_cvterm_id":"36990","category_aro_name":"cefixime","category_aro_description":"Cefixime is a cephalosporin resistant to most beta-lactamases. It is active against many enterobacteria, but activity against staphylococci is poor.","category_aro_class_name":"Antibiotic"},"36991":{"category_aro_accession":"3000647","category_aro_cvterm_id":"36991","category_aro_name":"cefpodoxime","category_aro_description":"Cefpodoxime is a semisynthetic cephalosporin that acts similarly to cefotaxime with broad-spectrum activity. It is stable to many plasmid-mediated beta-lactamses. Cefpodoxime is consumed as the prodrug cefpodoxime proxetil.","category_aro_class_name":"Antibiotic"},"36992":{"category_aro_accession":"3000648","category_aro_cvterm_id":"36992","category_aro_name":"ceftibuten","category_aro_description":"Ceftibuten is a semisynthetic cephalosporin active against Gram-negative bacilli. It is resistant against many plasmid-mediated beta-lactamases.","category_aro_class_name":"Antibiotic"},"36993":{"category_aro_accession":"3000649","category_aro_cvterm_id":"36993","category_aro_name":"cefditoren","category_aro_description":"Cefditoren is a semisynthetic cephalosporin active against staphylococci, streptococci, and and most enterobacteria. It is resistant to staphylococcal and most enterobacterial beta-lactamases, and is usually taken as the prodrug cefditoren pivoxil.","category_aro_class_name":"Antibiotic"},"36994":{"category_aro_accession":"3000650","category_aro_cvterm_id":"36994","category_aro_name":"cefdinir","category_aro_description":"Cefdinir is similar to cefixime with a modified side-chain at its 7-amino position. It also shares similar activity with cefixime but is more active against staphylococci. It has also be shown to enhance phagocytosis.","category_aro_class_name":"Antibiotic"},"36995":{"category_aro_accession":"3000651","category_aro_cvterm_id":"36995","category_aro_name":"ceftaroline","category_aro_description":"Ceftaroline is a novel cephalosporin active against methicillin resistant Staphylococcus aureus. Like other cephalosporins it binds penicillin-binding proteins to inhibit cell wall synthesis. It strongly binds with PBP2a, associated with methicillin resistance. It is taken orally as the prodrug ceftaroline fosamil.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"37085":{"category_aro_accession":"3000705","category_aro_cvterm_id":"37085","category_aro_name":"isopenicillin N","category_aro_description":"Isopenicillin N is a natural penicillin derivative produced by Penicillium chrysogenum with activity similar to penicillin N.","category_aro_class_name":"Antibiotic"},"37086":{"category_aro_accession":"3000706","category_aro_cvterm_id":"37086","category_aro_name":"penicillin N","category_aro_description":"Penicillin N is a penicillin derivative produced by Cephalosporium acremonium.","category_aro_class_name":"Antibiotic"},"37141":{"category_aro_accession":"3000761","category_aro_cvterm_id":"37141","category_aro_name":"mecillinam","category_aro_description":"Mecillinam is a broad-spectrum beta-lactam antibiotic that was semi-synthetically derived to have a different drug centre, being a 6-alpha-amidinopenicillanate instead of a 6-alpha-acylaminopenicillanate. Contrasting most beta-lactam drugs, mecillinam is most active against Gram-negative bacteria. It binds specifically to penicillin binding protein 2 (PBP2).","category_aro_class_name":"Antibiotic"},"40928":{"category_aro_accession":"3004001","category_aro_cvterm_id":"40928","category_aro_name":"cefmetazole","category_aro_description":"Cefmetazole is a semi-synthetic cephamycin antibiotic with broad spectrum antibiotic activity against both gram-positive and gram-negative bacteria, that disrupt cell wall synthesis through binding to PBPs causing cell lysis.","category_aro_class_name":"Antibiotic"},"40929":{"category_aro_accession":"3004002","category_aro_cvterm_id":"40929","category_aro_name":"cefonicid","category_aro_description":"Cefonicid is a second-generation cephalosporin-class beta-lactam antibiotic with broad spectrum activity. Particularly used against urinary tract infections and lower respiratory infections. Causes cell lysis by inactivation of PBPs through binding, inhibiting peptidoglycan synthesis.","category_aro_class_name":"Antibiotic"},"40932":{"category_aro_accession":"3004005","category_aro_cvterm_id":"40932","category_aro_name":"cefprozil","category_aro_description":"Cefprozil is a cephalosporin and beta-lactam antibiotic with bactericidal activity. It selectively binds to PBPs and inhibits peptidoglycan synthesis, a major cell wall component, resulting in cell lysis.","category_aro_class_name":"Antibiotic"},"40933":{"category_aro_accession":"3004006","category_aro_cvterm_id":"40933","category_aro_name":"ceftiofur","category_aro_description":"Ceftiofur is a third-generation broad spectrum cephalosporin and beta-lactam antibiotic. It causes cell lysis by disrupting peptidoglycan cross-linkage and cell wall formation by binding to PBPs.","category_aro_class_name":"Antibiotic"},"40934":{"category_aro_accession":"3004007","category_aro_cvterm_id":"40934","category_aro_name":"ceftizoxime","category_aro_description":"Ceftizoxime is a third-generation cephalosporin and broad spectrum beta-lactam antibiotic. Ceftizoxime causes bacterial cell lysis through peptidoglycan cross-linking inhibition by binding to PBPs.","category_aro_class_name":"Antibiotic"},"40935":{"category_aro_accession":"3004008","category_aro_cvterm_id":"40935","category_aro_name":"cephapirin","category_aro_description":"Cephapirin is a first-generation cephalosporin and broad spectrum beta-lactam antibiotic. Inactivation of penicillin-binding proteins through cephapirin binding disrupts peptidoglycan cross-linking, resulting in cell lysis.","category_aro_class_name":"Antibiotic"},"40936":{"category_aro_accession":"3004009","category_aro_cvterm_id":"40936","category_aro_name":"cefradine","category_aro_description":"Cefradine is a first-generation cephalosporin and broad spectrum beta-lactam antibiotic. Cefradine binding to penicillin-binding proteins disrupts cell wall peptidoglycan cross-linkage, resulting in cell lysis.","category_aro_class_name":"Antibiotic"},"40943":{"category_aro_accession":"3004016","category_aro_cvterm_id":"40943","category_aro_name":"loracarbef","category_aro_description":"Loracarbef is a second-generation cephalosporin (carbacephem) and broad spectrum beta-lactam antibiotic. Loracarbef inhibits PBPs through binding, disrupting peptidoglycan cell wall cross-linkage and resulting in cell death.","category_aro_class_name":"Antibiotic"},"40944":{"category_aro_accession":"3004017","category_aro_cvterm_id":"40944","category_aro_name":"moxalactam","category_aro_description":"Moxalactam (Latamoxef) is a broad spectrum cephalosporin (oxacephem) and beta-lactam antibiotic. Moxalactam binding to PBPs inhibits peptidoglycan cross-linkage in the cell wall, resulting in cell death. Moxalactam is proposed to be effective against meningitides as it passes the blood-brain barrier.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1773":{"model_id":"1773","model_name":"tet(43)","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"4346":{"protein_sequence":{"accession":"ACS83748.1","sequence":"MPPSHHMLRPIEQCSILWNDVRYSNSVRLKEAGMTATTQASAPAARTYLSLRAAWIPLFALCLAFFVEMVDNTLLTIALPTIGRDLGASVTSLQWVTGAYSLTFGGLLLTAGSLADRFGRRRVLQIGLLAFGLISLTVIAVATAGQLIAVRAALGLAAAAMAPITNSLVFRLFEGEDLRRRAMTLMIVVGMSGFILGPLLGGTVLAHASWQWLLLINAPIALIALIGVRLGVPADDAEGLTKDRLDVKGSALSIAAIGLACYTLTSGVEHGWMSAVTWACGIGAAAALMGFVWHERRTDHPMLDLDVFRNRTVRGASIAQVGTSIAMASLMFGLILHFQGAYGWSPMRAGLANLPLILTMILATPVSEGLAKRFGHRIAMLIGAGLLAGSLAGLAWGVGHGYLVIAVFMVTFTLGLRTVMTIAAVGLVGAMPENRTSLGAALNDTAQEVGTSLGMAVIGTLIAVLXTTTLPNGDXSLDLATSYFAGERIAYLFLAVVVGVIAGWGALTLSNSKEMEDVH"},"dna_sequence":{"accession":"GQ244501.1","fmin":"59","fmax":"1619","strand":"-","sequence":"CTAGTGGACGTCTTCCATCTCCTTGGAGTTGGACAACGTGAGCGCGCCCCATCCCGCGATCACTCCGACTACGACGGCAAGGAACAGATAAGCGATGCGCTCCCCGGCGAAGTATGAAGTCGCGAGGTCGAGGCTCCMGTCGCCGTTGGGAAGCGTCGTGGTGRCGAGCACCGCGATGAGCGTGCCGATCACTGCCATGCCGAGGCTTGTTCCTACTTCTTGGGCGGTGTCGTTGAGTGCCGCGCCGAGCGAGGTGCGGTTCTCCGGCATCGCACCAACGAGGCCCACCGCCGCGATCGTCATAACGGTGCGGAGACCGAGGGTGAAGGTCACCATGAATACCGCGATGACGAGGTASCCATGCCCCACGCCCCACGCGAGGCCAGCGAGCGATCCGGCGAGGAGACCCGCGCCGATGAGCATGGCAATGCGGTGGCCGAACCTCTTCGCGAGGCCCTCAGAGACCGGTGTCGCAAGAATCATCGTGAGGATGAGCGGCAGGTTGGCGAGGCCGGCGCGCATGGGGCTCCAGCCGTACGCGCCCTGGAAGTGAAGGATCAGGCCGAACATCAGCGAAGCCATCGCGATTGAGGTGCCTACCTGGGCGATCGATGCGCCGCGAACGGTGCGGTTCCTGAAGACGTCGAGGTCCAGCATGGGGTGATCGGTGCGGCGCTCGTGCCACACGAATCCCATCAGCGCGGCAGCCGCGCCGATCCCGCAGGCCCAGGTGACGGCAGACATCCAGCCGTGCTCCACTCCGCTCGTGAGTGTGTAGCAAGCGAGGCCGATCGCGGCGATGCTGAGTGCCGAGCCCTTCACGTCAAGGCGGTCCTTTGTGAGTCCCTCGGCGTCGTCCGCAGGCACGCCAAGGCGAACGCCGATGAGCGCAATGAGCGCGATGGGTGCGTTGATAAGCAGCAACCACTGCCAGCTGGCGTGAGCGAGAACCGTTCCGCCGAGTAGCGGGCCAAGGATGAATCCGCTCATGCCGACGACGATCATGAGGGTCATTGCCCGCCGACGGAGGTCCTCGCCCTCGAACAGCCTGAACACGAGGGAGTTGGTGATTGGGGCCATCGCGGCGGCGGCGAGGCCGAGCGCAGCGCGCACCGCGATCAGCTGGCCCGCGGTTGCCACGGCAATCACCGTGAGGCTGATGAGCCCAAAGGCGAGAAGGCCAATCTGCAGCACGCGGCGCCGGCCAAAGCGGTCGGCGAGCGAGCCCGCTGTCAGCAACAGGCCGCCAAAGGTCAGCGAATAGGCGCCGGTCACCCACTGCAAGGAGGTGACGCTCGCGCCGAGGTCGCGCCCGATCGTCGGCAGCGCGATCGTGAGCAGGGTGTTGTCAACCATCTCCACGAAGAACGCGAGGCAGAGCGCGAAGAGCGGAATCCACGCGGCGCGCAGCGACAGATAGGTACGTGCCGCGGGTGCCGAGGCTTGAGTTGTGGCGGTCATACCGGCCTCCTTCAGTCGAACGCTGTTCGAGTATCGAACGTCGTTCCATAGAATAGAACATTGTTCGATTGGGCGCAACATGTGGTGAGATGGGGGCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37082","NCBI_taxonomy_name":"uncultured bacterium AOTet43","NCBI_taxonomy_id":"654983"}}}},"ARO_accession":"3000573","ARO_id":"36712","ARO_name":"tet(43)","ARO_description":"Tet(43) is a tetracycline resistance gene with unknown origins, isolated from metagenomic DNA.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1781":{"model_id":"1781","model_name":"AAC(2')-Ia","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"53":{"protein_sequence":{"accession":"AAA03550.1","sequence":"MGIEYRSLHTSQLTLSEKEALYDLLIEGFEGDFSHDDFAHTLGGMHVMAFDQQKLVGHVAIIQRHMALDNTPISVGYVEAMVVEQSYRRQGIGRQLMLQTNKIIASCYQLGLLSASDDGQKLYHSVGWQIWKGKLFELKQGSYIRSIEEEGGVMGWKADGEVDFTASLYCDFRGGDQW"},"dna_sequence":{"accession":"L06156","fmin":"263","fmax":"800","strand":"+","sequence":"ATGGGCATAGAATACCGCAGTCTGCATACCAGCCAATTGACACTGAGTGAAAAAGAAGCGCTTTACGATTTATTAATTGAAGGTTTTGAAGGCGATTTTTCGCATGACGATTTCGCGCACACTTTAGGTGGAATGCACGTCATGGCTTTTGATCAACAAAAATTGGTTGGTCATGTTGCAATTATTCAACGCCATATGGCCCTAGATAATACGCCTATCTCTGTAGGGTATGTTGAAGCGATGGTAGTTGAACAAAGTTATCGTCGCCAAGGTATTGGGCGGCAATTGATGCTGCAAACCAATAAAATTATAGCTTCGTGTTATCAATTAGGGCTGCTGTCGGCTTCAGATGATGGACAAAAATTGTATCATTCGGTTGGATGGCAAATCTGGAAAGGTAAGTTGTTTGAATTGAAACAAGGGAGCTATATCCGTTCTATTGAAGAAGAAGGCGGAGTCATGGGCTGGAAAGCGGATGGTGAGGTTGATTTTACCGCTTCGCTTTACTGTGATTTTCGTGGCGGTGATCAGTGGTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36946","NCBI_taxonomy_name":"Providencia stuartii","NCBI_taxonomy_id":"588"}}}},"ARO_accession":"3002523","ARO_id":"38923","ARO_name":"AAC(2')-Ia","ARO_description":"AAC(2')-Ia is a chromosomal-encoded aminoglycoside acetyltransferase in P. stuartii","ARO_category":{"36480":{"category_aro_accession":"3000341","category_aro_cvterm_id":"36480","category_aro_name":"AAC(2')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 2'.","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1782":{"model_id":"1782","model_name":"TEM-12","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"996":{"protein_sequence":{"accession":"AAA25053.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"M88143","fmin":"367","fmax":"1228","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3000884","ARO_id":"37264","ARO_name":"TEM-12","ARO_description":"TEM-12 is an extended-spectrum beta-lactamase found in Klebsiella oxytoca.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1783":{"model_id":"1783","model_name":"VIM-36","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1578":{"protein_sequence":{"accession":"AGC50806.1","sequence":"MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATRSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"JX982635","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCGGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002306","ARO_id":"38706","ARO_name":"VIM-36","ARO_description":"VIM-36 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1784":{"model_id":"1784","model_name":"OXA-334","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1687":{"protein_sequence":{"accession":"AGW16416.1","sequence":"MKTVQLCLIVLITTFGSACTTISPSVETAKNQHQQSTQQQIQQAFNQLQTTGVIVIKDKHGLHSYGNDLSRAQTPYVPASTFKMLNALIGLEHGKATRTEVFKWDGQKRSFTAWEKDMTLGQAMQASAVPVYQELARRIGVDLMQKEVQRIGYGNQQIGTVVDNFWLVGPLQITPVQEVLFVEKLANTQLAFKPDVQHTVQDMLLIEQKPNYKLYAKSGWGMDLEPQVGWWAGWVETSTGEKAYFALNMQMKTGISASVREQLVKQSLTALGII"},"dna_sequence":{"accession":"KF203108","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAAAACTGTACAGTTGTGCCTCATCGTCCTCATTACTACCTTCGGTTCCGCATGTACCACAATAAGCCCCTCCGTAGAAACAGCTAAAAACCAACATCAGCAAAGCACGCAGCAGCAGATCCAACAAGCCTTCAATCAACTCCAAACCACGGGGGTGATTGTCATTAAGGATAAACATGGCTTACACAGCTACGGCAATGACTTGAGCCGTGCTCAGACACCCTATGTACCGGCCTCTACCTTTAAAATGCTGAATGCCTTAATCGGACTAGAACATGGTAAAGCAACCAGAACCGAGGTGTTTAAATGGGATGGTCAAAAGCGCAGCTTCACTGCCTGGGAAAAAGACATGACTTTAGGGCAAGCCATGCAAGCATCTGCCGTTCCCGTTTATCAGGAGCTTGCACGGCGCATTGGTGTAGATCTAATGCAAAAAGAAGTACAGCGCATTGGATATGGCAATCAACAGATTGGCACCGTTGTCGATAATTTTTGGTTAGTCGGTCCACTGCAAATTACGCCTGTTCAAGAAGTCCTTTTTGTAGAGAAGCTGGCCAATACGCAACTCGCTTTTAAGCCAGATGTGCAACATACCGTACAAGACATGCTACTGATTGAACAAAAACCGAATTATAAACTCTACGCCAAATCAGGCTGGGGTATGGACCTAGAACCACAAGTGGGCTGGTGGGCAGGCTGGGTCGAAACTTCAACAGGTGAAAAAGCGTATTTTGCTTTGAATATGCAGATGAAAACGGGAATTTCAGCCAGCGTGCGTGAGCAACTGGTCAAACAAAGTCTGACAGCACTGGGGATAATTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39092","NCBI_taxonomy_name":"Acinetobacter johnsonii","NCBI_taxonomy_id":"40214"}}}},"ARO_accession":"3001522","ARO_id":"37922","ARO_name":"OXA-334","ARO_description":"OXA-334 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1785":{"model_id":"1785","model_name":"TEM-48","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1650":{"protein_sequence":{"accession":"CAA71323.1","sequence":"MSIQHFRVALIPFFAAFCFPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASKRGSRGIIAALGPDGKPSRIVVIYMTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"Y10280","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCTTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTAAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACATGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000917","ARO_id":"37297","ARO_name":"TEM-48","ARO_description":"TEM-48 is an extended-spectrum beta-lactamase found Klebsiella pneumoniae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1786":{"model_id":"1786","model_name":"mexY","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1800"}},"model_sequences":{"sequence":{"414":{"protein_sequence":{"accession":"BAA34300.1","sequence":"MARFFIDRPVFAWVISLLIVLAGVLAIRFLPVAQYPDIAPPVVNVSATYPGASAKVVEEAVTAIIEREMNGAPGLLYTKATSSTGQASLTLTFRQGVNANLAAVEVQNRLKIVESRLPESVRRDGIYVEKAADSIQLIVTLTSSSGRYDAMELGEIASSNVLQALRRVEGVGKVETWGAEYAMRIWPDPAKLTSMNLSASDLVNAVRRHNARLTVGDIGNLGVPDSAPISATVKVDDTLVTPEQFGEIPLAHPRDGGAIRLRDVARVEFGQSEYGFVSRVNQMTATGLAVKMAPGSNAVATAKRIRATLDELSRYFPEGVSYNIPYDTSAFVEISIRKVVSTLLEAMLLVFAVMYLFMQNFRATLIPTLVVPVALLGTFTVMLGLGFSINVLTMFGMVLAIGILVDDAIIVVENVERLMAEEGLSPHDATVKAMRQISGAIVGITVVLVSVFVPMAFFSGAVGNIYRQFAVTLAVSIGFSAFLALSLTPALCATLLRPIDADHHEKRGFFGWFNRAFLRLTGRYRNAVAGILARPIRWMLVYTLVIGVVALLFVRLPQAFLPEEDQGDFMIMVMQPEGTPMAETMANVGDVERYLAEHEPVAYAYAVGGFSLYGDGTSSAMIFATLKDWSERREASQHVGAIVERINQRFAGLPNRTVYAMNSPPLPDLGSTSGFDFRLQDRGGVGYEALVKARDQLLARAAEDPRLANVMFAGQGEAPQIRLDIDRRKAETLGVSMDEINTTLAVMFGSDYIGDFMHGSQVRKVVVQADRRKRLGIDDIGRLHVRNEQGEMGAAGDVRQGRLDPRPAATDPLQRLSLVQPRGPGRAGLQQREAMQAMEQLMQGTARGIRPRVVRPVLRRTPVAGAQAPALFALSVLIVFLALAALYESWSIPLAVILVVPLGVLGALLGVSLRGLPNDIYFKVGLITIIGLSAKNAILIIEVAKDHYQEGMSLLQATLEAARLRLRPIVMTSLAFGFGVVPLALSSGAGIRAQVAIGTGVLGGIVTATVLAVFLVPLFFLVVGRLFRLRKAPRTGNSPQIPTEQA"},"dna_sequence":{"accession":"AB015853","fmin":"1330","fmax":"4471","strand":"+","sequence":"ATGGCTCGTTTCTTCATTGACCGGCCGGTCTTCGCCTGGGTGATCTCCCTGCTGATCGTGCTCGCCGGGGTCCTGGCGATCCGCTTCCTGCCGGTCGCCCAGTACCCGGACATCGCGCCGCCGGTGGTCAACGTCAGCGCCACGTATCCCGGCGCCTCGGCCAAGGTGGTCGAGGAAGCGGTGACCGCGATCATCGAGCGCGAGATGAACGGCGCGCCCGGCCTGCTCTACACCAAGGCCACCAGCAGCACCGGCCAGGCCTCGCTGACCCTGACCTTCCGCCAGGGCGTGAACGCGAACCTCGCCGCGGTGGAAGTGCAGAACCGCCTGAAGATCGTCGAGTCGCGCCTGCCCGAATCGGTGCGGCGCGACGGCATCTACGTGGAGAAGGCGGCGGACAGCATCCAGCTGATCGTTACCCTTACCTCCTCCAGCGGCCGCTACGACGCCATGGAGCTGGGCGAGATCGCCTCGTCCAACGTGTTGCAGGCGCTGCGCCGGGTGGAGGGCGTGGGCAAGGTCGAGACCTGGGGCGCCGAGTACGCCATGCGCATCTGGCCCGACCCGGCCAAGCTGACCTCGATGAACCTCAGCGCCAGCGACCTGGTCAACGCCGTGCGCCGGCACAACGCCCGCCTCACCGTGGGCGACATCGGCAACCTCGGGGTCCCCGACTCGGCGCCGATCAGCGCCACGGTGAAGGTCGACGACACCCTGGTGACGCCCGAGCAGTTCGGCGAAATTCCGCTGGCGCATCCGCGCGACGGCGGCGCGATCCGCCTGCGCGACGTGGCCCGCGTCGAGTTCGGCCAGAGCGAGTACGGCTTCGTCTCGCGGGTCAACCAAATGACCGCCACCGGCCTGGCGGTGAAGATGGCGCCCGGCTCCAACGCGGTGGCCACCGCCAAGCGCATCCGCGCCACCCTCGACGAGCTGTCGCGCTACTTCCCGGAGGGCGTGAGCTACAACATCCCCTATGACACCTCGGCGTTCGTCGAGATCTCGATCAGGAAGGTGGTCAGCACCCTGCTCGAGGCGATGCTGCTGGTGTTCGCCGTGATGTACCTGTTCATGCAGAACTTCCGCGCCACCCTGATCCCGACACTGGTGGTGCCGGTGGCCCTGCTGGGCACCTTCACGGTGATGCTCGGCCTGGGCTTCTCGATCAACGTGCTGACCATGTTCGGCATGGTCCTGGCGATCGGCATCCTGGTGGACGACGCGATCATCGTGGTGGAGAACGTCGAGCGGCTGATGGCCGAGGAAGGCCTGTCGCCGCACGACGCCACGGTCAAGGCGATGCGCCAGATCAGCGGGGCCATCGTCGGCATCACCGTAGTGCTGGTCTCGGTGTTCGTGCCGATGGCGTTCTTCAGCGGCGCGGTGGGCAACATCTACCGCCAGTTCGCGGTGACCCTGGCGGTCTCCATCGGCTTCTCGGCGTTCCTCGCGCTGTCGCTGACCCCGGCCCTGTGCGCCACCCTGCTGCGCCCGATCGACGCCGACCACCACGAGAAGCGCGGCTTCTTCGGCTGGTTCAACCGCGCCTTCCTGCGCCTGACCGGACGCTACCGCAACGCGGTGGCCGGCATCCTCGCCCGGCCGATCCGCTGGATGCTGGTCTACACCCTGGTCATCGGCGTGGTCGCCCTGCTCTTCGTGCGCCTGCCGCAGGCGTTCCTGCCGGAAGAGGACCAGGGCGACTTCATGATCATGGTGATGCAGCCCGAAGGCACGCCGATGGCGGAGACCATGGCCAACGTCGGCGACGTCGAGCGCTACCTGGCGGAGCACGAACCGGTGGCCTACGCCTATGCGGTCGGCGGCTTCAGCCTGTACGGCGACGGCACCAGCTCGGCGATGATCTTCGCCACCCTGAAGGACTGGTCGGAACGCCGGGAGGCCAGCCAGCACGTCGGCGCCATCGTCGAGCGCATCAACCAGCGCTTCGCCGGCCTGCCCAACCGTACGGTGTATGCGATGAACTCGCCGCCGCTGCCGGACCTGGGTTCCACCAGCGGCTTCGACTTCCGCCTGCAGGACCGTGGCGGGGTTGGCTACGAGGCCCTGGTCAAGGCCCGCGACCAGTTGCTGGCGCGCGCCGCCGAGGACCCGCGCCTGGCCAACGTGATGTTCGCCGGCCAGGGCGAGGCGCCGCAGATCCGCCTGGACATCGACCGGCGCAAGGCGGAGACCCTTGGCGTGAGCATGGACGAGATCAACACCACCCTGGCGGTGATGTTCGGCTCGGACTACATCGGCGACTTCATGCACGGCAGCCAGGTGCGCAAGGTGGTGGTCCAGGCCGACCGGCGCAAGCGCCTGGGCATCGACGACATCGGCCGGCTTCACGTGCGCAACGAGCAGGGCGAGATGGGTGCCGCTGGCGACGTTCGCCAAGGCCGCCTGGACCCTCGGCCCGCCGCAACTGACCCGCTACAACGGCTATCCCTCGTTCAACCTCGAGGGCCAGGCCGCGCCGGGCTACAGCAGCGCGAAGCCATGCAGGCGATGGAGCAATTGATGCAGGGAACTGCCCGAGGCATTCGCCCACGAGTGGTCCGGCCAGTCCTTCGAAGAACGCCTGTTGCCGGCGCCCAGGCGCCGGCGCTGTTCGCCCTCTCGGTGTTGATCGTGTTCCTCGCCCTGGCCGCCCTCTACGAAAGCTGGTCGATCCCGCTGGCGGTGATCCTGGTGGTGCCGCTGGGCGTACTCGGCGCACTGCTCGGGGTGAGCCTGCGCGGTCTGCCCAACGACATCTACTTCAAGGTCGGCCTGATCACCATCATCGGCCTCTCGGCGAAGAACGCCATCCTCATCATCGAGGTGGCCAAGGACCATTACCAGGAAGGCATGAGCCTGCTGCAGGCGACCCTGGAGGCCGCGCGCCTGCGCCTGCGACCGATCGTCATGACCTCGCTGGCGTTCGGTTTCGGCGTGGTCCCGCTGGCGCTCTCCAGCGGCGCCGGTATCCGCGCCCAGGTCGCCATCGGCACCGGGGTGCTCGGCGGGATCGTCACCGCCACGGTACTCGCGGTGTTCCTGGTACCGCTGTTCTTCCTGGTGGTCGGGCGCCTGTTCCGGTTGCGCAAGGCGCCGCGCACCGGCAACTCGCCCCAGATCCCCACGGAGCAAGCCTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3003033","ARO_id":"39467","ARO_name":"mexY","ARO_description":"MexY is the RND-type membrane protein of the efflux complex MexXY-OprM.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavin","category_aro_description":"Acriflavin is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36193":{"category_aro_accession":"3000054","category_aro_cvterm_id":"36193","category_aro_name":"acridine dye","category_aro_description":"Acridine dyes are cell permeable, basic molecules with an acridine chromophore. These compounds intercalate DNA. The image shown represents the core structure of the acridine family, with specific dyes containing varying substituents.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1787":{"model_id":"1787","model_name":"VIM-42","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"2128":{"protein_sequence":{"accession":"AJP08641.1","sequence":"MLKVISSLLVYMTASVMAVASPLAHSGEPSGEYPTVNEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEAEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSANVLYGGCAVHELSSTSAGNVADADLAEWPTSIERIQKHYPEAEVVIPGHGLPGGLDLLQHTANVVKAHKNRSVAE"},"dna_sequence":{"accession":"KP071470","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTACATGACCGCGTCTGTCATGGCTGTCGCAAGTCCGTTAGCCCATTCCGGGGAGCCGAGTGGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGAGAGGTCCGACTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCGGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAAAAGCAAATTGGACTTCCCGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGCAGAGGGGAACGAGATTCCCACGCATTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGCTCTTCTATCCTGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAACGTGCTATACGGTGGTTGTGCCGTTCATGAGTTGTCAAGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAAAAACACTACCCGGAAGCAGAGGTCGTCATTCCCGGGCACGGTCTACCGGGCGGTCTAGACTTGCTCCAGCACACAGCGAACGTTGTCAAAGCACACAAAAATCGCTCAGTCGCCGAGTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3003178","ARO_id":"39755","ARO_name":"VIM-42","ARO_description":"From the Lahey list of beta-lactamases.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1788":{"model_id":"1788","model_name":"ACT-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1972":{"protein_sequence":{"accession":"ACJ05686.1","sequence":"MMTKSLCCALLLSTSCSVLAAPMSEKQLAEVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAITTRVFKPLKLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVKDMANWVMVNMKPDSLQDSSLKEGITLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVEGSDNKVALAPLPAREVNPPAPPVNASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"FJ237366","fmin":"40","fmax":"1186","strand":"+","sequence":"ATGATGACTAAATCCCTTTGCTGCGCCCTGCTGCTCAGCACCTCCTGCTCGGTATTGGCTGCCCCGATGTCAGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAAAGCTCAGGCCATTCCGGGTATGGCGGTGGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGTAAAGCCGATGTCGCGGCGAATAAACCCGTCACCCCACAAACCTTATTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTCGGCGGCGATGCCATTGCTCGCGGTGAAATATCGCTGGGCGATCCGGTGACAAAATACTGGCCTGAGCTGACAGGCAAGCAGTGGCAGGGGATCCGCATGCTGGATCTGGCAACCTATACCGCAGGTGGTTTGCCGTTACAGGTACCGGATGAGGTCACGGATAACGCCTCACTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATAACGACGCGGGTCTTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGCGACGGTAAGGCGGTACACGTTTCGCCAGGAATGCTGGACGCTGAAGCCTATGGCGTAAAAACCAACGTGAAGGATATGGCAAACTGGGTGATGGTCAACATGAAGCCGGACTCGCTTCAGGATAGTTCACTCAAGGAAGGCATTACCCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGATTAGGCTGGGAAATGCTTAACTGGCCGGTCGATGCCAAAACCGTGGTTGAAGGTAGCGACAATAAGGTGGCGCTGGCACCGCTGCCTGCGAGAGAAGTGAATCCACCGGCGCCCCCGGTCAATGCGTCATGGGTCCATAAAACAGGCTCTACCGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001825","ARO_id":"38225","ARO_name":"ACT-6","ARO_description":"ACT-6 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1789":{"model_id":"1789","model_name":"QnrB44","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"634":{"protein_sequence":{"accession":"AFA52645.1","sequence":"MTPLLYKKTGTNMALALVGEKIDRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNASALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFTTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"JQ349153","fmin":"0","fmax":"680","strand":"+","sequence":"ATGACGCCATTACTGTATAAAAAAACAGGTACAAATATGGCTCTGGCACTCGTTGGCGAAAAAATTGACAGAAACCGTTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTAAGTGGTACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCAATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATGCCAGTGCGCTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGTGCAGATTTCCGCGGCGCAAGCTTTATGAATATGATCACTACACGCACCTGGTTTTGCAGCGCATATATCACTAACACAAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGCTGGAAAAGTGTGAGCTGTGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTACGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTGACTTAGATATTCGGGGCGTTGATTTACAAGGCGTTAAGTTGGACAACTACCAGGCATCGTTGCTCATGGAACGTCTTGGCATCGCGGTCATTGGTTA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002759","ARO_id":"39193","ARO_name":"QnrB44","ARO_description":"QnrB44 is a plasmid-mediated quinolone resistance protein found in Escherichia coli","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1790":{"model_id":"1790","model_name":"vanHF","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"487":{"protein_sequence":{"accession":"AAF36802.1","sequence":"MKNIGITIYGCERDEAEVFNELSPRFGVIPAITSSAVSETNAMLAPGNQCISVGHKSEISESILLALKESGVKYISTRSIGCNHIDVKAAESMGIAVGNVAYSPDSVADYTLMLMLMAIRNAKSIVSRAEKYDFRLDTVPGKELREMTVGVLGTGQIGKAVIERLRGFGCHVLAYGHSKEAAANYVSLNELLQKSDILTIHVPLGTDTYHMIGHEQIEAVKQGAFLINTARGGLVDTGALIKALENGRLGGAALDVLEGEEGLFYFDCTQKPIDNQLLLKLHKMPNVIITPHTAYYTGRALYDTVEKTILNCLEFERRETLE"},"dna_sequence":{"accession":"AF155139","fmin":"4978","fmax":"5947","strand":"+","sequence":"ATGAAAAATATCGGCATTACCATTTATGGATGTGAGAGGGACGAGGCTGAAGTGTTCAATGAACTTTCGCCACGCTTTGGTGTCATACCTGCCATTACAAGCTCTGCCGTATCGGAAACCAACGCAATGTTAGCTCCCGGCAATCAATGTATCAGCGTGGGGCACAAATCTGAGATTTCCGAATCCATTCTTCTTGCTCTGAAGGAATCCGGCGTCAAATATATCTCTACCCGAAGTATTGGCTGCAATCACATAGACGTGAAGGCCGCGGAAAGTATGGGTATCGCTGTTGGAAACGTGGCATATTCACCGGATAGCGTTGCCGATTATACATTGATGCTGATGCTGATGGCGATACGAAACGCAAAATCCATTGTGAGCCGTGCGGAAAAATATGATTTCAGATTGGATACTGTCCCTGGAAAAGAATTGCGTGAGATGACGGTTGGCGTGCTGGGAACCGGTCAAATAGGCAAGGCGGTTATTGAGCGACTGCGGGGATTTGGATGTCATGTGCTGGCGTATGGTCACAGCAAAGAGGCGGCGGCCAATTATGTATCCCTCAATGAATTGCTGCAGAAAAGCGACATTCTCACCATTCATGTGCCGCTCGGCACGGACACATATCATATGATTGGTCACGAACAGATTGAAGCAGTGAAACAGGGCGCGTTTCTTATCAATACAGCGCGCGGCGGGCTTGTGGATACCGGCGCGCTGATCAAAGCGTTGGAAAATGGAAGGTTAGGCGGCGCGGCGTTGGATGTGTTGGAAGGAGAAGAAGGGCTTTTCTATTTTGATTGCACACAGAAACCGATTGACAACCAACTATTGCTTAAGCTCCACAAGATGCCAAATGTGATCATCACGCCGCATACGGCGTACTATACCGGACGGGCACTGTATGATACCGTTGAAAAGACAATATTGAACTGTCTGGAATTTGAGAGGAGAGAGACACTTGAATAGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39542","NCBI_taxonomy_name":"Paenibacillus popilliae ATCC 14706","NCBI_taxonomy_id":"1212764"}}}},"ARO_accession":"3002945","ARO_id":"39379","ARO_name":"vanHF","ARO_description":"vanHF is a vanH variant in the vanF gene cluster","ARO_category":{"36015":{"category_aro_accession":"3000006","category_aro_cvterm_id":"36015","category_aro_name":"vanH","category_aro_description":"VanH is a D-specific alpha-ketoacid dehydrogenase that synthesizes D-lactate. D-lactate is incorporated into the end of the peptidoglycan subunits, decreasing vancomycin binding affinity.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1791":{"model_id":"1791","model_name":"TEM-164","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2033":{"protein_sequence":{"accession":"ABX71157.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQVGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQTAEIGASLIKHW"},"dna_sequence":{"accession":"EU274580","fmin":"214","fmax":"1075","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGGTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGACCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001030","ARO_id":"37410","ARO_name":"TEM-164","ARO_description":"TEM-164 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1792":{"model_id":"1792","model_name":"DHA-20","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1414":{"protein_sequence":{"accession":"AIT76101.1","sequence":"MKKSLSATLISALLAFSAPGFSAADNVAAVVDSTIKPLMAQQDIPGMAVAVSVKGKPYYFNYGFADVQAKQPVTENTLFELGSVSKTFTGVLGAVSVAKKEMTLNDPAEKYQPELALPQWKGITLLDLATYTAGGLPLQVPDAVKSRADLLNFYQQWQPSRKPGDMRLYANSSIGLFGALTANAAGMPYEQLLTARILAPLGLSHTFITVPESAQSQYAYGYKNKKPVRVSPGQLDAESYGVKSASKDMLRWAEMNMEPSRAGNADLEMAMYLAQTRYYKTAAINQGLGWEMYDWPQQKDMIINGVTNEVALQPHPVTDNQVQPYNRASWVHKTGATTGFGAYVAFIPEKQVAIVILANKNYPNTERVKAAQAILSALE"},"dna_sequence":{"accession":"KM087848","fmin":"0","fmax":"1140","strand":"+","sequence":"ATGAAAAAATCGTTATCTGCAACACTGATTTCCGCCCTGCTGGCATTTTCCGCCCCGGGGTTTTCTGCCGCTGATAATGTCGCGGCGGTGGTGGACAGCACCATTAAACCGCTGATGGCACAGCAGGATATTCCCGGGATGGCGGTTGCCGTCTCCGTAAAGGGTAAGCCCTATTATTTCAATTACGGTTTTGCCGATGTTCAGGCAAAACAGCCTGTCACTGAAAATACACTATTTGAGCTCGGATCTGTAAGTAAAACTTTCACAGGTGTGCTGGGTGCGGTTTCCGTGGCGAAAAAAGAGATGACGCTGAATGACCCGGCAGAAAAATACCAGCCGGAGCTGGCTCTGCCGCAGTGGAAGGGGATCACACTGTTGGATCTGGCCACCTACACCGCAGGCGGGCTGCCGTTACAGGTACCGGATGCGGTGAAAAGCCGTGCGGATCTGCTGAATTTCTATCAGCAGTGGCAGCCGTCCCGGAAACCGGGCGATATGCGTCTGTATGCAAACAGCAGTATCGGCCTGTTTGGTGCTCTGACCGCCAACGCAGCGGGGATGCCGTATGAGCAGTTGCTGACTGCACGGATCCTGGCACCGCTGGGGTTATCTCACACCTTTATTACTGTGCCGGAAAGCGCGCAAAGCCAGTATGCGTACGGTTATAAAAACAAAAAACCGGTCCGCGTGTCGCCGGGACAGCTTGATGCGGAATCTTACGGCGTGAAATCCGCCTCAAAAGATATGCTGCGCTGGGCGGAAATGAATATGGAGCCGTCACGGGCCGGTAATGCGGATCTGGAAATGGCAATGTATCTTGCACAGACCCGCTACTATAAAACCGCCGCGATTAACCAGGGGCTGGGCTGGGAAATGTATGACTGGCCGCAGCAGAAAGATATGATCATTAACGGCGTGACCAACGAGGTCGCATTGCAGCCGCACCCGGTAACAGACAACCAGGTTCAGCCGTATAACCGTGCTTCCTGGGTGCATAAAACGGGGGCAACAACCGGTTTCGGCGCCTATGTGGCCTTTATTCCGGAAAAACAGGTGGCGATTGTGATTCTGGCGAATAAAAACTACCCGAATACCGAAAGAGTCAAAGCCGCACAGGCTATTTTGAGTGCACTGGAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36934","NCBI_taxonomy_name":"Citrobacter koseri","NCBI_taxonomy_id":"545"}}}},"ARO_accession":"3002151","ARO_id":"38551","ARO_name":"DHA-20","ARO_description":"DHA-20 is a beta-lactamase. From the Lahey list of DHA beta-lactamases.","ARO_category":{"36207":{"category_aro_accession":"3000068","category_aro_cvterm_id":"36207","category_aro_name":"DHA beta-lactamase","category_aro_description":"DHA beta-lactamases are plasmid-mediated AmpC \u03b2-lactamases that confer resistance to cephamycins and oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1793":{"model_id":"1793","model_name":"DHA-14","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"827":{"protein_sequence":{"accession":"AIT76107.1","sequence":"MKKSLSATLISALLAFSAPGFSAADNVAAVVDSTIKPLMAQQDIPGMAVAVSVKGKPYYFNYGFADIQAKQPVTENTLFELGSVSKTFTGVLGAVSVAKKEMALNDPAAKYQPELALPQWKGITLLDLATYTAGGLPLQVPDAVKSRADLLHFYQQWQPSRKPGDMRLYANSSIGLFGALTANAAGMPYEQLLTARILAPLGLSHTFITVPESAQSQYAYGYKNKKPVRVSPGQLDAESYGVKSASKDMLRWAEMNMEPSRAGNADLEMAMYLAQTRYYKTAAINQGLGWEMYDWPQQKDMIINGVTNEVALQPHPVTDNQVQPYNRASWVHKTGATTGFGAYVAFIPEKQVAIVILANKNYPNTERVKAAQAILSALE"},"dna_sequence":{"accession":"KM087854","fmin":"0","fmax":"1140","strand":"+","sequence":"ATGAAAAAATCGTTATCTGCAACACTGATTTCCGCTCTGCTGGCGTTTTCCGCCCCGGGGTTTTCTGCCGCTGATAATGTCGCGGCGGTGGTGGACAGCACCATTAAACCGCTGATGGCACAGCAGGATATTCCCGGGATGGCGGTTGCCGTCTCCGTAAAGGGTAAGCCCTATTATTTCAATTATGGTTTTGCCGATATTCAGGCAAAACAGCCGGTCACTGAAAATACACTATTTGAGCTCGGATCTGTAAGTAAAACTTTCACAGGTGTGCTGGGTGCGGTTTCTGTGGCGAAAAAAGAGATGGCGCTGAATGATCCGGCGGCAAAATACCAGCCGGAGCTGGCTCTGCCGCAGTGGAAGGGGATCACATTGCTGGATCTGGCTACCTATACCGCAGGCGGACTGCCGTTACAGGTGCCGGATGCGGTAAAAAGCCGTGCGGATCTGCTGCACTTCTATCAGCAGTGGCAGCCGTCCCGGAAACCGGGCGATATGCGTCTGTATGCAAACAGCAGTATCGGCCTGTTTGGTGCTCTGACCGCAAACGCGGCGGGGATGCCGTATGAGCAGTTGCTGACTGCACGGATCCTGGCACCGCTGGGGTTATCTCACACCTTTATTACTGTGCCGGAAAGTGCGCAAAGCCAGTATGCGTACGGTTATAAAAACAAAAAACCGGTCCGCGTGTCGCCGGGACAGCTTGATGCGGAATCTTACGGCGTGAAATCCGCCTCAAAAGATATGCTGCGCTGGGCGGAAATGAATATGGAGCCGTCACGGGCCGGTAATGCGGATCTGGAAATGGCAATGTATCTTGCACAGACCCGCTACTATAAAACCGCCGCGATTAACCAGGGGCTGGGCTGGGAAATGTATGACTGGCCGCAGCAGAAAGATATGATCATTAACGGCGTGACCAACGAGGTCGCATTGCAGCCGCACCCGGTAACAGACAACCAGGTTCAGCCGTATAACCGTGCTTCCTGGGTGCATAAAACGGGGGCAACAACTGGTTTCGGCGCCTATGTGGCCTTTATTCCGGAAAAACAGGTGGCGATTGTGATTCTGGCGAATAAAAACTACCCGAATACCGAAAGAGTCAAAGCCGCACAGGCTATTTTGAGTGCACTGGAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36917","NCBI_taxonomy_name":"Morganella morganii","NCBI_taxonomy_id":"582"}}}},"ARO_accession":"3002145","ARO_id":"38545","ARO_name":"DHA-14","ARO_description":"DHA-14 is a beta-lactamase. From the Lahey list of DHA beta-lactamases.","ARO_category":{"36207":{"category_aro_accession":"3000068","category_aro_cvterm_id":"36207","category_aro_name":"DHA beta-lactamase","category_aro_description":"DHA beta-lactamases are plasmid-mediated AmpC \u03b2-lactamases that confer resistance to cephamycins and oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1794":{"model_id":"1794","model_name":"tmrB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"375"}},"model_sequences":{"sequence":{"4345":{"protein_sequence":{"accession":"CAB12108.2","sequence":"MIIWINGAFGSGKTQTAFELHRRLNPSYVYDPEKMGFALRSMVPQEIAKDDFQSYPLWRAFNYSLLASLTDTYRGILIVPMTIVHPEYFNEIIGRLRQEGRIVHHFTLMASKETLLKRLRTRAEGKNSWAAKQIDRCVEGLSSPIFEDHIQTDNLSIQDVAENIAARAELPLDPDTRGSLRRFADRLMVKLNHIRIK"},"dna_sequence":{"accession":"AL009126.3","fmin":"339155","fmax":"339749","strand":"-","sequence":"TTATTTGATGCGGATATGATTCAGCTTTACCATTAATCTGTCGGCGAACCTTCGGAGGCTGCCTCTTGTATCAGGATCTAATGGGAGTTCGGCTCTCGCGGCAATGTTCTCTGCCACATCCTGAATCGACAGGTTGTCTGTTTGAATGTGGTCCTCAAAAATGGGTGATGATAATCCTTCAACACAGCGGTCAATTTGTTTGGCGGCCCATGAGTTTTTTCCTTCTGCTCTGGTGCGCAGCCTTTTTAACAAGGTTTCCTTTGAAGCCATTAGTGTAAAGTGGTGAACGATCCTGCCTTCCTGTCTGAGCCTGCCGATGATCTCATTGAAGTATTCAGGGTGTACAATCGTCATAGGCACAATAAGGATGCCGCGGTATGTATCTGTCAGAGAAGCTAGCAAACTGTAATTGAACGCCCGCCATAAAGGATAGCTTTGAAAATCGTCCTTTGCGATCTCCTGCGGCACCATGGAGCGCAGCGCAAAACCCATTTTCTCGGGATCATACACGTAAGATGGGTTCAGCCTTCTGTGCAGTTCGAAGGCTGTTTGTGTTTTTCCCGAACCGAATGCCCCGTTTATCCAAATGATCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39579","NCBI_taxonomy_name":"Bacillus subtilis subsp. subtilis str. 168","NCBI_taxonomy_id":"224308"}}}},"ARO_accession":"3003059","ARO_id":"39493","ARO_name":"tmrB","ARO_description":"tmrB is an ATP-binding tunicamycin resistance protein found in Bacillus subtilis","ARO_category":{"41449":{"category_aro_accession":"3004285","category_aro_cvterm_id":"41449","category_aro_name":"tunicamycin resistance protein","category_aro_description":"A grouping of tunicamycin resistance proteins that are homologous to tmrB found in Bacillus subtilis.","category_aro_class_name":"AMR Gene Family"},"35928":{"category_aro_accession":"0000009","category_aro_cvterm_id":"35928","category_aro_name":"tunicamycin","category_aro_description":"Tunicamycin is mixture of homologous nucleoside antibiotics that block the reaction of UDP-N-acetylglucosamine and dolichyl phosphate in the first step of glycoprotein synthesis.","category_aro_class_name":"Antibiotic"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36383":{"category_aro_accession":"3000244","category_aro_cvterm_id":"36383","category_aro_name":"reduced permeability to antibiotic","category_aro_description":"Reduction in permeability to antibiotic, generally through reduced production of porins, can provide resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1795":{"model_id":"1795","model_name":"VEB-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1329":{"protein_sequence":{"accession":"AAK29174.1","sequence":"MKIVKRILLVLLSLFFTIVYSNAQADNLTLKIENVLKAKNARIGVAIFNSNEKDTLKINNDFHFPMQSVMKFPIALAVLSEIDKGNLSFEQKIEITPQDLLPKTWSPIKEEFPNGTTLTIEQILNYTVSESDNIGCDILLKLIGGTDSVQKFLNANHFTDISIKANEEQMHKDWNTQYQNWATPTAMNKLLIDTYNNKNQLLSKKSYDFIWKIMRETTTGSNRLKGQLPKNTIVAHKTGTSGINNGIAAATNDVGVITLPNGQLIFISVFVAESKETSEINEKIISDIAKITWNYYLNK"},"dna_sequence":{"accession":"AY027870","fmin":"46","fmax":"946","strand":"+","sequence":"ATGAAAATCGTAAAAAGGATATTATTAGTATTGTTAAGTTTATTTTTTACAATTGTGTATTCAAATGCTCAAGCTGACAACTTAACTTTGAAAATTGAGAATGTTTTAAAGGCAAAAAATGCCAGAATAGGAGTAGCAATATTCAACAGCAATGAGAAGGATACTTTGAAGATTAATAACGACTTCCATTTCCCGATGCAAAGCGTTATGAAATTTCCGATTGCTTTAGCCGTTTTGTCTGAGATAGATAAAGGGAATCTTTCTTTTGAACAAAAAATAGAGATTACCCCTCAAGACCTTTTGCCTAAAACGTGGAGTCCGATTAAAGAGGAATTCCCTAATGGAACAACTTTGACGATTGAACAAATACTAAATTATACAGTATCAGAGAGCGACAATATTGGTTGTGATATTTTGCTAAAATTAATCGGAGGAACTGATTCTGTTCAAAAATTCTTGAATGCTAATCATTTCACTGATATTTCAATCAAAGCAAACGAAGAACAAATGCACAAGGATTGGAATACCCAATATCAAAATTGGGCAACCCCAACAGCGATGAACAAACTGTTAATAGATACTTATAATAATAAGAACCAATTACTTTCTAAAAAAAGTTATGATTTTATTTGGAAAATTATGAGAGAAACAACAACAGGAAGTAACCGATTAAAAGGACAATTACCAAAGAATACAATTGTTGCTCATAAAACAGGGACTTCCGGAATAAATAATGGAATTGCAGCAGCCACTAATGATGTTGGGGTAATTACTTTACCGAATGGACAATTAATTTTTATAAGCGTATTTGTTGCAGAGTCCAAAGAAACTTCGGAAATTAATGAAAAGATTATTTCAGACATTGCAAAAATAACGTGGAATTACTATTTGAATAAATAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002371","ARO_id":"38771","ARO_name":"VEB-2","ARO_description":"VEB-2 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36182":{"category_aro_accession":"3000043","category_aro_cvterm_id":"36182","category_aro_name":"VEB beta-lactamase","category_aro_description":"VEB beta-lactamases or Vietnamese extended-spectrum beta-lactamases are class A beta-lactamases that confer high-level resistance to oxyimino cephalosporins and to aztreonam","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1796":{"model_id":"1796","model_name":"CMY-119","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1344":{"protein_sequence":{"accession":"AIT76098.1","sequence":"MMKKSLCCALLLTASFSTFASAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWIQVNMDASRVQEKMLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAAEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"KM087845","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACGTTTGCCTCCGCCAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAACTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCGTTTTTATCAAAACTGGCAGCCGCAATGGACCCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACAGTTCCGCAAAGCGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAACCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGTTGGATTCAGGTCAACATGGATGCCAGCCGCGTTCAGGAGAAAATGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGTGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGCTGAGGTAAACCCGCCCGCCCCGGCAGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACTGGAGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002130","ARO_id":"38530","ARO_name":"CMY-119","ARO_description":"CMY-119 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1797":{"model_id":"1797","model_name":"ErmY","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"630":{"protein_sequence":{"accession":"BAB20748.1","sequence":"MNKKDIKFSQNFITSKRHINKIMSNLELNRNDNVFEIGSGKGHFTLELVQKCNYVTVIEIDSNLCIQTQNKVTNYDNFRIINKDILQFKFPNNKAYKIYGNIPYYISTDIVRKIVFESEATVSYLIVEEGFAKRLLNTNRSLALLLMTEVDISILSKIPKEYFHPKPKINSSLIILKRHPSKISYKDKKMYNNFVMKWVNQEYSKLFTKNQFNKALNYAKIKDLKNINFEQFLSVFNSYKLFNN"},"dna_sequence":{"accession":"AB014481","fmin":"0","fmax":"735","strand":"+","sequence":"ATGAACAAAAAAGATATAAAATTTAGTCAAAATTTTATTACTTCGAAACGACATATAAATAAAATAATGAGTAATTTAGAATTAAATAGAAATGATAATGTTTTTGAAATTGGTTCAGGAAAAGGGCATTTCACACTAGAACTGGTTCAAAAATGTAATTATGTAACAGTTATCGAGATAGATTCAAATTTATGTATTCAAACACAAAATAAAGTTACAAATTACGATAACTTTCGAATTATAAATAAGGATATATTACAGTTTAAGTTCCCAAACAACAAAGCATATAAAATCTACGGTAATATACCTTATTATATAAGTACGGATATAGTACGAAAAATTGTCTTTGAAAGTGAAGCAACAGTTAGTTACTTAATAGTTGAAGAAGGATTTGCTAAAAGGCTACTCAATACAAATCGTTCTCTAGCGTTACTTTTAATGACTGAAGTAGATATATCCATATTAAGTAAAATCCCTAAAGAATACTTTCATCCAAAGCCTAAAATTAATAGCTCTTTAATTATATTAAAAAGACACCCGTCAAAAATATCATACAAAGATAAAAAAATGTATAATAATTTTGTTATGAAATGGGTTAACCAAGAATACAGCAAACTATTTACCAAAAATCAGTTTAATAAAGCCTTAAATTATGCAAAAATAAAGGATTTAAAGAACATTAACTTCGAACAATTTTTATCAGTATTTAATAGCTATAAATTGTTTAATAACTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3002825","ARO_id":"39259","ARO_name":"ErmY","ARO_description":"ErmY is a plasmid-mediated methyltransferase found in Staphylococcus aureus","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1798":{"model_id":"1798","model_name":"SHV-183","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1945":{"protein_sequence":{"accession":"CDN33427.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASKRGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"HG934764","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCAAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001351","ARO_id":"37751","ARO_name":"SHV-183","ARO_description":"From the Lahey list of beta-lactamases. Not yet released.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1799":{"model_id":"1799","model_name":"TEM-147","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1881":{"protein_sequence":{"accession":"ABB84515.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDHWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSVLPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"DQ279850","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCATTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGTCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001014","ARO_id":"37394","ARO_name":"TEM-147","ARO_description":"TEM-147 is an extended-spectrum beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1800":{"model_id":"1800","model_name":"SHV-120","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1543":{"protein_sequence":{"accession":"AEG79634.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGKRGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"JF812965","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCAAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001167","ARO_id":"37547","ARO_name":"SHV-120","ARO_description":"SHV-120 is a beta-lactamase that has been found in clinical isolates.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1801":{"model_id":"1801","model_name":"AAC(6')-Ib11","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"366":{"protein_sequence":{"accession":"AAN41403.1","sequence":"MKNTIHINSNDSVTLRLMTEHDLAMLYEWLNRSHIVEWWGGEEARPTLADVQEQYLPSVLAQESVTPYIAMLNGEPIGYAQSYVALGSGDGWWEEETDPGVRGIDLSLANASQLGKGLGTKLVRALVELLFNDPEVTKIQTDPSPSNLRAIRCYEKAGFERQGTVTTPDGPAVYMVQTRQAFERTRSDA"},"dna_sequence":{"accession":"AY136758","fmin":"377","fmax":"947","strand":"+","sequence":"ATGAAAAACACAATACATATCAACAGCAACGATTCCGTCACACTGCGCCTCATGACTGAGCATGACCTTGCGATGCTCTATGAGTGGCTAAATCGATCTCATATCGTCGAGTGGTGGGGCGGAGAAGAAGCACGCCCGACACTTGCTGACGTACAGGAACAGTACTTGCCAAGCGTTTTAGCGCAAGAGTCCGTCACTCCATACATTGCAATGCTGAATGGAGAGCCGATTGGGTATGCCCAGTCGTACGTTGCTCTTGGAAGCGGGGACGGATGGTGGGAAGAAGAAACCGATCCAGGAGTACGCGGAATAGACCTGTCACTGGCGAATGCATCACAACTGGGCAAAGGCTTGGGAACCAAGCTGGTTCGAGCTCTGGTTGAGTTGCTGTTCAATGATCCCGAGGTCACCAAGATCCAAACGGACCCGTCGCCGAGCAACTTGCGAGCGATCCGATGCTACGAGAAAGCGGGGTTTGAGAGGCAAGGTACCGTAACCACCCCAGATGGTCCAGCCGTGTACATGGTTCAAACACGCCAGGCATTCGAGCGAACACGCAGTGATGCCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35732","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium","NCBI_taxonomy_id":"90371"}}}},"ARO_accession":"3002582","ARO_id":"38982","ARO_name":"AAC(6')-Ib11","ARO_description":"AAC(6')-Ib11 is an integron-encoded aminoglycoside acetyltransferase in S. enterica","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1802":{"model_id":"1802","model_name":"OXA-168","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1452":{"protein_sequence":{"accession":"ADK35872.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETPSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKPQVGWLAGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"HM488989","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGACCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCCCAATTAGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGGCCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001468","ARO_id":"37868","ARO_name":"OXA-168","ARO_description":"OXA-168 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1803":{"model_id":"1803","model_name":"QnrVC3","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"483":{"protein_sequence":{"accession":"ADI81040.1","sequence":"MEKSKQLYNQVNFSHQDLQEHIFSNCTFIHCNFKRSNLRDTQFINCTFIEQGALEGCDFSYADLRDASFKNCQLSMSHFKGANCFGIELRDCDLKGANFTQVSFVNQVSNKMYFCSAYITGCNLSYANFEQQLIEKCDLFENRWIGANLRGASFTESYLSRGDFSEDCWEQFRVQGCDLSHSELYGLDPRKIDLTGVKICSWQQEQLLEQLGVIIVPD"},"dna_sequence":{"accession":"HM015626","fmin":"883","fmax":"1540","strand":"+","sequence":"ATGGAAAAATCAAAGCAATTATATAATCAAGTGAACTTCTCACATCAGGACTTGCAAGAACATATCTTTAGCAATTGTACTTTTATACATTGTAATTTTAAGCGCTCAAACCTCCGAGATACACAGTTCATTAACTGTACTTTCATAGAGCAGGGGGCATTGGAAGGGTGCGATTTTTCTTATGCTGATCTTCGAGATGCTTCATTTAAAAACTGTCAGCTTTCAATGTCCCATTTTAAGGGGGCAAATTGCTTTGGTATTGAACTGAGAGATTGTGATCTTAAAGGAGCAAATTTTACTCAAGTTAGTTTTGTAAATCAGGTTTCGAATAAAATGTACTTTTGTTCTGCATACATAACAGGTTGTAACTTATCCTATGCCAATTTTGAGCAGCAGCTTATTGAAAAATGTGACCTGTTCGAAAATAGATGGATTGGTGCAAATCTTCGAGGCGCTTCATTTACAGAATCATATTTAAGCCGTGGTGATTTTTCGGAAGACTGCTGGGAACAGTTTAGAGTACAAGGCTGTGATTTAAGCCATTCAGAGCTTTATGGTTTAGATCCTCGAAAGATTGATCTTACGGGTGTAAAAATATGCTCGTGGCAACAGGAACAGTTACTGGAGCAATTAGGGGTAATCATTGTTCCTGACTAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36920","NCBI_taxonomy_name":"Vibrio cholerae non-O1\/non-O139","NCBI_taxonomy_id":"156539"}}}},"ARO_accession":"3002800","ARO_id":"39234","ARO_name":"QnrVC3","ARO_description":"QnrVC3 is an integron-mediated quinolone resistance protein found in Vibrio cholerae","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1804":{"model_id":"1804","model_name":"OXA-107","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1289":{"protein_sequence":{"accession":"ABV31687.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGEKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWVVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"EF650033","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAATGGGATGGGGAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGGTGGTGGGTCCTCTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36939","NCBI_taxonomy_name":"Acinetobacter baumannii A424","NCBI_taxonomy_id":"1082934"}}}},"ARO_accession":"3001638","ARO_id":"38038","ARO_name":"OXA-107","ARO_description":"OXA-107 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1805":{"model_id":"1805","model_name":"TEM-131","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1953":{"protein_sequence":{"accession":"AAR10958.1","sequence":"MSIQHFRVALIPFFAAFCFPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTTPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGTGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AY436361","fmin":"131","fmax":"992","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCTTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAARGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAACCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35732","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium","NCBI_taxonomy_id":"90371"}}}},"ARO_accession":"3000995","ARO_id":"37375","ARO_name":"TEM-131","ARO_description":"TEM-131 is an extended-spectrum beta-lactamase found in Salmonella enterica.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1806":{"model_id":"1806","model_name":"OXA-14","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1044":{"protein_sequence":{"accession":"AAA93528.1","sequence":"IACLSSTALAGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEDQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG"},"dna_sequence":{"accession":"L38523","fmin":"0","fmax":"774","strand":"+","sequence":"TATCGCGTGTCTTTCGAGTACGGCATTAGCTGGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTCTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATGACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAGCAATGGGAAAGAGACTTGACCTTAAGAGGGGCAATACAAGTTTCAGCTGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCCTATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAAGACCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATATTTAAATAAATTGTCAGCATCTAAAGAAAACCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCGGCACCTGAATATCTAGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGGTGGGTTGAGAAGGAGACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAGTAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGAAAGTGAGGGCATCATTGGTGGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001409","ARO_id":"37809","ARO_name":"OXA-14","ARO_description":"OXA-14 is a beta-lactamase found in P. aeruginosa.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1807":{"model_id":"1807","model_name":"OXA-70","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"980":{"protein_sequence":{"accession":"AAW81341.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDKKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQHEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"AY750912","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATAAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAACATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001618","ARO_id":"38018","ARO_name":"OXA-70","ARO_description":"OXA-70 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1809":{"model_id":"1809","model_name":"QnrB5","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"256":{"protein_sequence":{"accession":"ABC17628.1","sequence":"MTPLLYKNTGIDMTLALVGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDSYQASLLMERLGIAIIG"},"dna_sequence":{"accession":"DQ303919","fmin":"0","fmax":"681","strand":"+","sequence":"ATGACGCCATTACTGTATAAAAACACAGGCATAGATATGACTCTGGCATTAGTTGGCGAAAAAATTGACAGAAATCGCTTCACCGGTGAGAAAGTTGAAAATAGTACATTTTTTAACTGCGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGCCAGTTCTATGATCGCGAAAGTCAGAAAGGGTGCAATTTTAGTCGCGCAATGCTGAAAGATGCCATTTTCAAAAGCTGTGATTTATCAATGGCAGATTTCCGCAACGTCAGTGCCTTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGTGCAAGCTTTATGAATATGATCACCACGCGCACCTGGTTTTGCAGCGCATATATCACTAATACTAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAGCTGTGGGAAAACCGCTGGATGGGGACTCAGGTACTGGGTGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTAGGTGACTTAGATATTCGGGGTGTTGATTTACAAGGCGTTAAGTTAGACAGCTACCAGGCATCGTTGCTCATGGAGCGGCTTGGCATCGCGATTATTGGCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35665","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Berta","NCBI_taxonomy_id":"28142"}}}},"ARO_accession":"3002719","ARO_id":"39153","ARO_name":"QnrB5","ARO_description":"QnrB5 is a plasmid-mediated quinolone resistance protein found in Salmonella enterica","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1810":{"model_id":"1810","model_name":"VIM-15","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1164":{"protein_sequence":{"accession":"ACB54702.1","sequence":"MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLFGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"EU419745","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTTTGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002285","ARO_id":"38685","ARO_name":"VIM-15","ARO_description":"VIM-15 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1811":{"model_id":"1811","model_name":"CARB-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1096":{"protein_sequence":{"accession":"AAZ91704.1","sequence":"MKFLLAFSLLIPSVVFASSSKFQQVEQDVKAIEVSLSARIGVSVLDTQNGEYWDYNGNQRFPLTSTFKTIACAKLLYDAEQGKVNPNSTVEIKKTDLVTYSPVIEKQVGQAITLDDACFATMTTSDNTAANIILSAVGGPKGVTDFLRQIGDKETRLDRIEPDLNEGKLGDLRDTTTPKAIASTLNKFLFGSALSEMNQKKLESWMVNNQVTGNLLRSVLPAGRNIADRSGAGGFGARSITAVVWSEHQAPIIVSIYLAQTQASMAERNDAIVKIGHSIFDVYTSQSR"},"dna_sequence":{"accession":"DQ157752","fmin":"797","fmax":"1664","strand":"+","sequence":"ATGAAGTTTTTATTGGCATTTTCGCTTTTAATACCATCCGTGGTTTTTGCAAGTAGTTCAAAGTTTCAGCAAGTTGAACAAGACGTTAAGGCAATTGAAGTTTCTCTTTCTGCTCGTATAGGTGTTTCCGTTCTTGATACTCAAAATGGAGAATATTGGGATTACAATGGCAATCAGCGCTTCCCGTTAACAAGTACTTTTAAAACAATAGCTTGCGCTAAATTACTATATGATGCTGAGCAAGGAAAAGTTAATCCCAATAGTACAGTCGAGATTAAGAAAACAGATCTTGTGACCTATTCCCCTGTAATAGAAAAGCAAGTAGGGCAGGCAATCACACTCGATGATGCGTGCTTCGCAACTATGACTACAAGTGATAATACTGCGGCAAATATCATCCTAAGTGCTGTAGGTGGCCCCAAAGGCGTTACTGATTTTTTAAGACAAATTGGGGACAAAGAGACTCGTCTAGACCGTATTGAGCCTGATTTAAATGAAGGTAAGCTCGGTGATTTGAGGGATACGACAACTCCTAAGGCAATAGCCAGTACTTTGAATAAATTTTTATTTGGTTCCGCGCTATCTGAAATGAACCAGAAAAAATTAGAGTCTTGGATGGTGAACAATCAAGTCACTGGTAATTTACTACGTTCAGTATTGCCGGCGGGACGGAACATTGCGGATCGCTCAGGTGCTGGCGGATTTGGTGCTCGGAGTATTACAGCAGTTGTGTGGAGTGAGCATCAAGCCCCAATTATTGTGAGCATCTATCTAGCTCAAACACAGGCTTCAATGGCAGAGCGAAATGATGCGATTGTTAAAATTGGTCATTCAATTTTTGACGTTTATACATCACAGTCGCGCTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002241","ARO_id":"38641","ARO_name":"CARB-2","ARO_description":"CARB-2 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1812":{"model_id":"1812","model_name":"KHM-1 beta-lactamase","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1557":{"protein_sequence":{"accession":"BAF91108.1","sequence":"MKIALVISFGLLLFTNMVCADDSLPELDIQKIEDGVYLYTAYEKIEGWGLVGSNGLVVLDNKNAYLIDTPISATDTEKLVKWIDAQGFTAKASISTHFHTDSTGGIAFLNSKSIPTYASKLTNQLLKNKGEEQATHSFGKNPYWLLKNKIEAFYPGAGHTPDNLVVWLPKQKILFGGCFVKPEGLGNLSHAVIAEWPASAEKLIARYSNATMVVPGHGKVGDASLLEKTRQRAVEALAAKK"},"dna_sequence":{"accession":"AB364006","fmin":"61","fmax":"787","strand":"+","sequence":"ATGAAAATAGCTCTTGTTATATCGTTTGGTCTGCTGTTGTTTACCAATATGGTATGCGCTGACGATTCATTACCAGAACTAGATATCCAAAAAATAGAAGACGGCGTTTATCTGTACACCGCTTACGAAAAAATCGAAGGCTGGGGGCTTGTTGGCTCTAACGGATTAGTCGTGCTTGATAACAAAAATGCTTATCTGATTGATACGCCCATTTCAGCCACAGATACTGAAAAATTAGTGAAGTGGATTGACGCGCAGGGCTTTACGGCCAAGGCAAGTATTTCTACCCATTTCCACACCGACAGTACAGGCGGTATTGCATTTCTCAACTCCAAGTCCATTCCAACCTATGCCTCCAAGCTAACTAACCAGCTGCTTAAAAATAAAGGCGAAGAGCAGGCTACGCATTCGTTCGGTAAGAATCCTTATTGGCTATTAAAAAATAAAATCGAAGCCTTTTATCCGGGTGCGGGTCACACACCTGATAATTTAGTAGTGTGGCTGCCGAAACAGAAAATTTTATTTGGTGGCTGTTTTGTCAAACCCGAAGGCCTTGGCAATCTTAGCCATGCGGTAATTGCAGAATGGCCAGCTTCCGCCGAAAAACTTATCGCCCGTTATAGCAATGCAACAATGGTAGTTCCCGGTCACGGAAAAGTTGGCGACGCATCGCTGCTGGAAAAAACCAGGCAGCGCGCAGTTGAAGCGCTTGCAGCTAAAAAGTGAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3000847","ARO_id":"37227","ARO_name":"KHM-1","ARO_description":"KHM-1 is a plasmid-mediated metallo-beta-lactamase found in Citrobacter freundii that confers resistance to all broad-spectrum beta-lactams, execpt for monobactams.","ARO_category":{"41371":{"category_aro_accession":"3004207","category_aro_cvterm_id":"41371","category_aro_name":"KHM beta-latamase","category_aro_description":"KHM beta-lactmases are Class B beta-lactamases that can confer resistance to all classes of beta-lactams, except the monobactams.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1813":{"model_id":"1813","model_name":"MOX-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1199":{"protein_sequence":{"accession":"ACI89425.1","sequence":"MQQRQSILWGALATLMWAGLAHAGDTSAVDPLRPVVDASIRPLLKEHRIPGMAVAVLKDGKAHYFNYGVADRERAVGVSEQTLFEIGSVSKPLTATLGAYAVVKGAMQLDDKASRHAPWLKGSAFDSITMGELATYSAGGLPLQFPEEVDSLEKMQAYYRQWTPAYSPGSHRQYSNPSIGLFGHLAASSMKQPFAQLMEQTLLPGLGLHHTYVNVPKQAMASYAYGYSKEDKPIRVSPGMLADEAYGIKTSSADLLRFVKANISGVDDKALQQAISLTHKGHYSVGGMTQGLGWESYAYPVSEQTLLAGNSAEVILEANPTAAPRESGNLMLFNKTGSTSGFGAYVAFVPAKGIGIVMLANRNYPIPARVKAAHAILTQLAR"},"dna_sequence":{"accession":"FJ262599","fmin":"0","fmax":"1149","strand":"+","sequence":"ATGCAACAACGACAATCCATCCTGTGGGGCGCTTTGGCCACCCTGATGTGGGCCGGTCTGGCTCATGCCGGTGACACTTCAGCGGTCGATCCCCTGCGCCCCGTGGTGGATGCCAGCATCCGGCCGCTGCTCAAGGAGCACAGGATCCCGGGCATGGCGGTGGCCGTGCTCAAGGATGGCAAGGCCCACTATTTCAACTACGGTGTGGCCGATCGGGAGCGCGCGGTCGGTGTCAGCGAGCAGACCCTGTTCGAGATAGGCTCCGTGAGCAAGCCCCTGACCGCGACCCTAGGAGCCTATGCGGTGGTCAAGGGAGCGATGCAACTGGATGACAAGGCGAGCCGGCACGCCCCCTGGCTCAAGGGATCCGCCTTTGACAGCATCACCATGGGGGAGCTGGCTACCTACAGCGCGGGCGGCTTGCCGCTGCAATTCCCCGAGGAGGTGGATTCGCTCGAGAAGATGCAGGCCTACTACCGCCAGTGGACCCCAGCCTACTCGCCGGGTTCCCATCGCCAGTACTCTAACCCCAGCATAGGGCTGTTCGGCCACCTGGCGGCGAGCAGCATGAAGCAGCCGTTTGCCCAGTTGATGGAGCAGACGCTCCTGCCGGGGCTTGGCCTGCACCACACCTATGTCAATGTGCCGAAGCAGGCCATGGCGAGTTATGCCTATGGCTATTCGAAAGAGGACAAGCCCATCAGGGTCAGCCCCGGCATGCTGGCGGACGAGGCCTACGGCATCAAGACCAGCTCGGCGGATCTGCTGCGCTTTGTGAAGGCCAACATCAGCGGGGTTGATGACAAGGCGTTGCAGCAGGCCATCTCCCTGACCCACAAAGGGCACTACTCGGTAGGCGGGATGACCCAGGGACTGGGTTGGGAGAGTTACGCCTATCCCGTCAGCGAGCAGACATTGCTGGCGGGCAATTCGGCCGAGGTGATTCTCGAAGCCAATCCGACGGCGGCGCCCCGGGAGTCGGGGAACCTGATGCTCTTCAACAAGACCGGCTCGACCAGCGGCTTCGGCGCCTATGTGGCCTTCGTGCCGGCCAAAGGGATCGGCATCGTCATGCTGGCCAACCGCAACTATCCTATCCCGGCCAGGGTGAAAGCGGCCCACGCCATCCTGACGCAACTGGCCAGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36936","NCBI_taxonomy_name":"Aeromonas caviae","NCBI_taxonomy_id":"648"}}}},"ARO_accession":"3002184","ARO_id":"38584","ARO_name":"MOX-4","ARO_description":"MOX-4 is a beta-lactamase found in Aeromonas caviae","ARO_category":{"36222":{"category_aro_accession":"3000083","category_aro_cvterm_id":"36222","category_aro_name":"MOX beta-lactamase","category_aro_description":"MOX beta-lactamases are plasmid-mediated AmpC-type beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1814":{"model_id":"1814","model_name":"AAC(6')-Ie-APH(2'')-Ia","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"305":{"protein_sequence":{"accession":"NP_863643.1","sequence":"MNIVENEICIRTLIDDDFPLMLKWLTDERVLEFYGGRDKKYTLESLKKHYTEPWEDEVFRVIIEYNNVPIGYGQIYKMYDELYTDYHYPKTDEIVYGMDQFIGEPNYWSKGIGTRYIKLIFEFLKKERNANAVILDPHKNNPRAIRAYQKSGFRIIEDLPEHELHEGKKEDCYLMEYRYDDNATNVKAMKYLIEHYFDNFKVDSIEIIGSGYDSVAYLVNNEYIFKTKFSTNKKKGYAKEKAIYNFLNTNLETNVKIPNIEYSYISDELSILGYKEIKGTFLTPEIYSTMSEEEQNLLKRDIASFLRQMHGLDYTDISECTIDNKQNVLEEYILLRETIYNDLTDIEKDYIESFMERLNATTVFEGKKCLCHNDFSCNHLLLDGNNRLTGIIDFGDSGIIDEYCDFIYLLEDSEEEIGTNFGEDILRMYGNIDIEKAKEYQDIVEEYYPIETIVYGIKNIKQEFIENGRKEIYKRTYKD"},"dna_sequence":{"accession":"NC_005024","fmin":"42504","fmax":"43944","strand":"+","sequence":"ATGAATATAGTTGAAAATGAAATATGTATAAGAACTTTAATAGATGATGATTTTCCTTTGATGTTAAAATGGTTAACTGATGAAAGAGTATTAGAATTTTATGGTGGTAGAGATAAAAAATATACATTAGAATCATTAAAAAAACATTATACAGAGCCTTGGGAAGATGAAGTTTTTAGAGTAATTATTGAATATAACAATGTTCCTATTGGATATGGACAAATATATAAAATGTATGATGAGTTATATACTGATTATCATTATCCAAAAACTGATGAGATAGTCTATGGTATGGATCAATTTATAGGAGAGCCAAATTATTGGAGTAAAGGAATTGGTACAAGATATATTAAATTGATTTTTGAATTTTTGAAAAAAGAAAGAAATGCTAATGCAGTTATTTTAGACCCTCATAAAAATAATCCAAGAGCAATAAGGGCATACCAAAAATCTGGTTTTAGAATTATTGAAGATTTGCCAGAACATGAATTACACGAGGGCAAAAAAGAAGATTGTTATTTAATGGAATATAGATATGATGATAATGCCACAAATGTTAAGGCAATGAAATATTTAATTGAGCATTACTTTGATAATTTCAAAGTAGATAGTATTGAAATAATCGGTAGTGGTTATGATAGTGTGGCATATTTAGTTAATAATGAATACATTTTTAAAACAAAATTTAGTACTAATAAGAAAAAAGGTTATGCAAAAGAAAAAGCAATATATAATTTTTTAAATACAAATTTAGAAACTAATGTAAAAATTCCTAATATTGAATATTCGTATATTAGTGATGAATTATCTATACTAGGTTATAAAGAAATTAAAGGAACTTTTTTAACACCAGAAATTTATTCTACTATGTCAGAAGAAGAACAAAATTTGTTAAAACGAGATATTGCCAGTTTTTTAAGACAAATGCACGGTTTAGATTATACAGATATTAGTGAATGTACTATTGATAATAAACAAAATGTATTAGAAGAGTATATATTGTTGCGTGAAACTATTTATAATGATTTAACTGATATAGAAAAAGATTATATAGAAAGTTTTATGGAAAGACTAAATGCAACAACAGTTTTTGAGGGTAAAAAGTGTTTATGCCATAATGATTTTAGTTGTAATCATCTATTGTTAGATGGCAATAATAGATTAACTGGAATAATTGATTTTGGAGATTCTGGAATTATAGATGAATATTGTGATTTTATATACTTACTTGAAGATAGTGAAGAAGAAATAGGAACAAATTTTGGAGAAGATATATTAAGAATGTATGGAAATATAGATATTGAGAAAGCAAAAGAATATCAAGATATAGTTGAAGAATATTATCCTATTGAAACTATTGTTTATGGAATTAAAAATATTAAACAGGAATTTATCGAAAATGGTAGAAAAGAAATTTATAAAAGGACTTATAAAGATTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3002597","ARO_id":"38997","ARO_name":"AAC(6')-Ie-APH(2'')-Ia","ARO_description":"AAC(6')-Ie-APH(2'')-Ia is an aminoglycoside acetyltransferase encoded by plasmids and transposons in S. aureus, E. faecalis, E. faecium and Staphylococcus warneri","ARO_category":{"36267":{"category_aro_accession":"3000128","category_aro_cvterm_id":"36267","category_aro_name":"APH(2'')","category_aro_description":"Phosphorylation of 2-deoxystreptamine aminoglycosides on the hydroxyl group at position 2''","category_aro_class_name":"AMR Gene Family"},"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1815":{"model_id":"1815","model_name":"CTX-M-134","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1964":{"protein_sequence":{"accession":"AFX60298.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGSYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"JX896165","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCAGCTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001992","ARO_id":"38392","ARO_name":"CTX-M-134","ARO_description":"CTX-M-134 is a beta-lactamase. From the Lahey list of CTX-M beta-lactamases.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1816":{"model_id":"1816","model_name":"TEM-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"932":{"protein_sequence":{"accession":"CAA46344.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"X65252","fmin":"175","fmax":"1036","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000880","ARO_id":"37260","ARO_name":"TEM-8","ARO_description":"TEM-8 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1817":{"model_id":"1817","model_name":"vgaB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1080"}},"model_sequences":{"sequence":{"475":{"protein_sequence":{"accession":"AAB95639.1","sequence":"MLKIDMKNVKKYYADKLILNIKELKIYSGDKIGIVGKNGVGKTTLLKIIKGLIEIDEGNIIISEKTTIKYISQLEEPHSKIIDGKYASIFQVENKWNDNMSGGEKTRFKLAEGFQDQCSLMLVDEPTSNLDIEGIELITNTFKEYRDTFLVVSHDRIFLDQVCTKIFEIENGYIREFIGNYTNYIEQKEMLLRKQQEEYEKYNSKRKQLEQAIKLKENKAQGMIKPPSKTMGTSESRIWKMQHATKQKKMHRNTKSLETRIDKLNHVEKIKELPSIKMDLPNREQFHGRNVISLKNLSIKFNNQFLWRDASFVIKGGEKVAIIGNNGVGKTTLLKLILEKVESVIISPSVKIGYVSQNLDVLQSHKSILENVMSTSIQDETIARIVLARLHFYRNDVHKEINVLSGGEQIKVAFAKLFVSDCNTLILDEPTNYLDIDAVEALEELLITYEGVVLFASHDKKFIQNLAEQLLIIENNKVKKFEGTYIEYLKIKDKPKLNTNEKELKEKKMILEMQISSLLSKISMEENEEKNKELDEKYKLKLKELKSLNKNI"},"dna_sequence":{"accession":"U82085","fmin":"0","fmax":"1659","strand":"+","sequence":"ATGCTTAAAATCGACATGAAGAATGTAAAAAAATATTATGCAGATAAATTAATTTTAAATATAAAAGAACTAAAGATTTATAGTGGGGATAAAATAGGTATTGTAGGTAAGAATGGAGTTGGCAAAACAACACTTTTAAAAATAATAAAAGGACTAATAGAGATTGACGAAGGAAATATAATTATAAGTGAAAAAACAACTATTAAATATATCTCTCAATTAGAAGAACCACATAGTAAGATAATTGATGGAAAATATGCTTCAATATTTCAAGTTGAAAATAAGTGGAATGACAATATGAGTGGTGGTGAAAAAACTAGATTTAAACTAGCAGAGGGATTTCAAGATCAATGTTCTTTAATGCTCGTAGATGAACCTACAAGTAATTTAGATATCGAAGGAATAGAGTTGATAACAAATACTTTTAAAGAGTACCGTGATACTTTTTTGGTAGTATCTCATGATAGAATTTTTTTAGATCAAGTTTGTACAAAAATTTTTGAAATTGAAAATGGATATATTAGAGAATTCATCGGTAATTATACAAACTATATAGAGCAAAAAGAAATGCTTCTACGAAAGCAACAAGAAGAATACGAAAAGTATAATTCTAAAAGAAAGCAATTGGAGCAAGCTATAAAGCTAAAAGAGAATAAGGCGCAAGGAATGATTAAGCCCCCTTCAAAAACAATGGGAACATCTGAATCTAGAATATGGAAAATGCAACATGCTACTAAACAAAAAAAGATGCATAGAAATACGAAATCGTTGGAAACACGAATAGATAAATTAAATCATGTAGAAAAAATAAAAGAGCTTCCTTCTATTAAAATGGATTTACCTAATAGAGAGCAATTTCATGGTCGCAATGTAATTAGTTTAAAAAACTTATCTATAAAATTTAATAATCAATTTCTTTGGAGAGATGCTTCATTTGTCATTAAAGGTGGAGAAAAGGTTGCTATAATTGGTAACAATGGTGTAGGAAAAACAACATTGTTGAAGCTGATTCTAGAAAAAGTAGAATCAGTAATAATATCACCATCAGTTAAAATTGGATACGTCAGTCAAAACTTAGATGTTCTACAATCTCATAAATCTATCTTAGAAAATGTTATGTCTACCTCCATTCAAGATGAAACAATAGCAAGAATTGTTCTAGCAAGATTACATTTTTATCGCAATGATGTTCATAAAGAAATAAATGTTTTGAGTGGTGGAGAACAAATAAAGGTTGCTTTTGCCAAGCTATTTGTTAGCGATTGTAATACATTAATTCTTGATGAACCAACAAACTATTTGGATATCGATGCTGTTGAGGCATTAGAAGAATTGTTAATTACCTATGAAGGTGTTGTGTTATTTGCTTCCCATGATAAAAAATTTATACAAAACCTAGCTGAACAATTGTTAATAATAGAAAATAATAAAGTGAAAAAATTCGAAGGAACATATATAGAATATTTAAAAATTAAAGATAAACCAAAATTAAATACAAATGAAAAAGAACTCAAAGAAAAAAAGATGATACTAGAAATGCAAATTTCATCATTATTAAGTAAAATCTCAATGGAAGAAAATGAAGAAAAAAACAAAGAATTAGATGAAAAGTACAAATTGAAATTAAAAGAATTGAAAAGCCTAAATAAAAATATTTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3000118","ARO_id":"36257","ARO_name":"vgaB","ARO_description":"Vga(B) is an efflux protein expressed in staphylococci that confers resistance to streptogramin A antibiotics and related compounds. It is associated with plasmid DNA.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37716":{"category_aro_accession":"3001317","category_aro_cvterm_id":"37716","category_aro_name":"pleuromutilin","category_aro_description":"Pleuromutilin is a natural product antibiotic produced by Clitopilus passeckerianus. Related antibiotics of clinical significance, such as tiamulin and retapamulin, are semi-synthetic derivatives of this compound.","category_aro_class_name":"Antibiotic"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1818":{"model_id":"1818","model_name":"GES-26","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"2105":{"protein_sequence":{"accession":"AJP67510.1","sequence":"MRFIHALLLAAIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMGDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"KP096411","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGCGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGGGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3003181","ARO_id":"39758","ARO_name":"GES-26","ARO_description":"From the Lahey list of beta-lactamases.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1819":{"model_id":"1819","model_name":"TEM-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4344":{"protein_sequence":{"accession":"CAA45828.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"X64523.1","fmin":"476","fmax":"1337","strand":"-","sequence":"TTACCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCTGACTCCCCGTCGTGTAGATAACTACGATACGGGAGGGCTTACCATCTGGCCCCAGTGCTGCAATGATACCGCGAGATCCACGCTCACTGGCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGTTTGCGCAACGTTGTTGCCATTGCTGCAGGCATCGTGGTGTCACGCTCGTCGTTTGGTATGGCTTCATTCAGCTCCGGTTCCCAACGATCAAGGCGGGTTACATGATCCCCCATGTTGTGCAAAAAAGCGGTTAGCTCCTTCGGTCCTCCGATCGTTGTCAGAAGTAAGTTGGCCGCAGTGTTATCACTCATGGTTATGGCAGCACTGCATAATTCTCTTACTGTCATGCCATCCGTAAGATGCTTTTCTGTGACTGGTGAGTACTTAACCAAGTCATTCTGAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGCCCGGCGTCAACACGGGATAATACCGCACCACATAGCAGAACTTTAAAAGTGCTCATCATTGGAAAACGTTCTTCGGGGCGAAAACTCTCAAGGATCTTACCGCTGTTGAGATCCAGCTCGATGTAACCCACTCGTGCACCCAACTTATCTTCAGCATCTTTTACTTTCACCAGCGTTTCTGGGTGAGCAAAAACAGGAAGGCAAAATGCCGCAAAAAAGGGAATAAGGGCGACACGGAAATGTTGAATACTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000875","ARO_id":"37255","ARO_name":"TEM-3","ARO_description":"TEM-3 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1820":{"model_id":"1820","model_name":"bacA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4343":{"protein_sequence":{"accession":"AAC76093.1","sequence":"MSDMHSLLIAAILGVVEGLTEFLPVSSTGHMIIVGHLLGFEGDTAKTFEVVIQLGSILAVVVMFWRRLFGLIGIHFGRPLQHEGESKGRLTLIHILLGMIPAVVLGLLFHDTIKSLFNPINVMYALVVGGLLLIAAECLKPKEPRAPGLDDMTYRQAFMIGCFQCLALWPGFSRSGATISGGMLMGVSRYAASEFSFLLAVPMMMGATALDLYKSWGFLTSGDIPMFAVGFITAFVVALIAIKTFLQLIKRISFIPFAIYRFIVAAAVYVVFF"},"dna_sequence":{"accession":"U00096.3","fmin":"3203309","fmax":"3204131","strand":"-","sequence":"TTAAAAGAACACGACATACACCGCAGCCGCCACAATAAAGCGATAAATGGCGAACGGGATAAACGAAATGCGCTTAATCAATTGCAGGAAGGTTTTAATCGCTATCAGCGCCACCACAAAAGCGGTGATAAACCCAACGGCAAACATCGGGATATCGCCGCTTGTCAGGAAGCCCCAGCTTTTGTAGAGATCGAGCGCCGTTGCGCCCATCATCATCGGCACCGCCAGCAGGAACGAAAACTCGGAAGCAGCGTAACGGCTCACCCCCATCAGCATCCCACCTGAAATGGTCGCCCCGGAACGGGAGAAACCCGGCCACAGCGCCAGACACTGGAAACAGCCAATCATAAATGCCTGACGATAGGTCATATCATCAAGACCCGGCGCACGCGGCTCTTTCGGCTTCAGGCATTCGGCGGCAATCAGCAACAAACCGCCAACGACCAGCGCATACATCACATTTATCGGGTTAAACAATGACTTAATCGTGTCGTGGAACAACAGCCCCAATACCACCGCCGGAATCATCCCCAGCAAAATGTGGATCAGCGTTAAACGACCTTTGCTTTCACCTTCGTGCTGCAACGGGCGGCCAAAGTGGATGCCAATCAGGCCAAACAGACGCCGCCAGAACATCACTACTACCGCCAGAATTGATCCTAACTGGATCACAACTTCAAAGGTTTTCGCCGTGTCGCCCTCAAACCCCAACAAGTGACCGACAATAATCATATGGCCCGTGCTGGATACCGGCAGAAATTCTGTCAATCCTTCGACCACACCCAATATTGCCGCTATCAGCAGCGAGTGCATATCGCTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3002986","ARO_id":"39420","ARO_name":"bacA","ARO_description":"bacA is a gene that recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin","ARO_category":{"39982":{"category_aro_accession":"3003398","category_aro_cvterm_id":"39982","category_aro_name":"undecaprenyl pyrophosphate related proteins","category_aro_description":"Undecaprenyl phosphate is a universal lipid carrier of glycan biosynthetic intermediates for carbohydrate polymers that are exported to the bacterial cell envelope. Antibiotics that targets this compound or proteins associated with the production of this compound leads to cell death.","category_aro_class_name":"AMR Gene Family"},"36973":{"category_aro_accession":"3000629","category_aro_cvterm_id":"36973","category_aro_name":"bacitracin A","category_aro_description":"Bacitracin A is the primary component of bacitracin. It contains many uncommon amino acids and interferes with bacterial cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36974":{"category_aro_accession":"3000630","category_aro_cvterm_id":"36974","category_aro_name":"bacitracin B","category_aro_description":"Bacitracin B is a component of bacitracin, an antibiotic mixture that interferes with bacterial cell wall synthesis. It differs from Bacitracin A with a valine instead of an isoleucine in its peptide.","category_aro_class_name":"Antibiotic"},"36975":{"category_aro_accession":"3000631","category_aro_cvterm_id":"36975","category_aro_name":"bacitracin F","category_aro_description":"Bacitracin F is a component of bacitracin, an antibiotic mixture that interferes with bacterial cell wall synthesis. It is formed when the thiazoline ring of bacitracin A is oxidatively deaminated.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1821":{"model_id":"1821","model_name":"AAC(6')-Ir","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"581":{"protein_sequence":{"accession":"AAD03490.1","sequence":"MKIMPVSEPFLADWLQLRILLWPDHEDAHLLEMRQLLEQPHTLQLLSYNDQQQAVAMLEASIRYEYVNGQQSSPVAFLEGIYVLPEYRRLGVASTLVQQVEHWAKQFACTEFASDAALDNTISHAMHRALGFQETECVVYFKKNIS"},"dna_sequence":{"accession":"AF031326","fmin":"0","fmax":"441","strand":"+","sequence":"ATGAAAATCATGCCTGTAAGCGAGCCGTTCTTGGCCGACTGGCTGCAATTAAGAATATTACTCTGGCCTGATCATGAAGACGCGCATTTACTGGAAATGCGGCAGTTACTCGAACAACCACATACCCTGCAATTATTAAGCTATAACGATCAGCAGCAAGCAGTTGCGATGCTGGAAGCGTCGATTCGATATGAATATGTGAATGGCCAGCAAAGCTCACCGGTGGCTTTTCTGGAAGGTATTTATGTGTTGCCAGAATATCGACGTTTAGGTGTTGCTAGCACGTTGGTACAGCAGGTAGAACACTGGGCCAAGCAGTTTGCATGTACCGAATTTGCTTCAGATGCTGCGCTGGATAATACGATCAGTCATGCCATGCATCGCGCACTGGGCTTTCAGGAAACCGAGTGTGTGGTTTATTTTAAGAAAAACATCAGTTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39512","NCBI_taxonomy_name":"Acinetobacter genomosp. 14","NCBI_taxonomy_id":"70345"}}}},"ARO_accession":"3002561","ARO_id":"38961","ARO_name":"AAC(6')-Ir","ARO_description":"AAC(6')-Ir is a chromosomal-encoded aminoglycoside acetyltransferase in Acinetobacter genomosp. 14","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1823":{"model_id":"1823","model_name":"OXY-1-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"815":{"protein_sequence":{"accession":"AAL78275.1","sequence":"MLKSSWRKTALMAAAAVPLLLASGSLWASADAIQQKLADLEKRSGGRLGVALINTADDSQTLYRGDERFAMCSTGKVMAAAAVLKQSESNPEVVNKRLEIKKSDLVVWSPITEKHLQSGMTLAELSAAALQYSDNTAMNKMISYLGGPEKVTAFAQSIGDVTFRLDRTEPALNSAIPGDKRDTTTPLAMAESLRKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPASWAVGDKTGGGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKSRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"AY077482","fmin":"161","fmax":"1037","strand":"+","sequence":"ATGTTGAAAAGTTCGTGGCGTAAAACCGCCCTGATGGCCGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGTTCATTATGGGCCAGTGCCGATGCTATCCAGCAAAAGCTGGCTGATTTAGAAAAACGTTCCGGCGGTCGGCTGGGCGTAGCGCTGATTAACACGGCAGATGATTCGCAAACCCTCTATCGCGGCGATGAACGTTTTGCCATGTGCAGCACCGGTAAAGTGATGGCCGCCGCCGCGGTGTTAAAACAGAGCGAAAGCAATCCAGAGGTGGTGAATAAAAGGCTGGAGATTAAAAAATCGGATTTAGTGGTCTGGAGCCCGATCACCGAAAAACATCTGCAAAGCGGAATGACCCTGGCGGAACTCAGCGCGGCGGCGCTGCAGTACAGCGACAATACCGCGATGAATAAGATGATTAGCTACCTTGGCGGACCGGAAAAGGTGACCGCATTCGCCCAGAGTATCGGGGATGTCACTTTTCGTCTCGATCGTACGGAGCCGGCGCTGAACAGCGCGATTCCCGGCGATAAGCGCGATACCACCACCCCGTTGGCGATGGCCGAAAGCCTGCGCAAGCTGACGCTGGGCAATGCGCTGGGCGAACAGCAGCGCGCCCAGTTAGTGACGTGGCTAAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCAGGCCTGCCCGCAAGCTGGGCGGTCGGGGATAAAACCGGCGGCGGAGATTACGGCACCACCAACGATATCGCGGTGATCTGGCCGGAAAATCATGCCCCGCTGGTGCTGGTGACCTATTTTACCCAGCCGCAGCAGGATGCGAAAAGCCGCAAAGAGGTGTTAGCCGCGGCGGCAAAAATCGTCACCGAAGGGCTTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002391","ARO_id":"38791","ARO_name":"OXY-1-3","ARO_description":"OXY-1-3 is a beta-lactamase found in Klebsiella oxytoca","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1824":{"model_id":"1824","model_name":"oleI","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"498":{"protein_sequence":{"accession":"ABA42118.2","sequence":"MTSEHRSASVTPRHISFFNIPGHGHVNPSLGIVQELVARGHRVSYAITDEFAAQVKAAGATPVVYDSILPKESNPEESWPEDQESAMGLFLDEAVRVLPQLEDAYADDRPDLIVYDIASWPAPVLGRKWDIPFVQLSPTFVAYEGFEEDVPAVQDPTADRGEEAAAPAGTGDAEEGAEAEDGLVRFFTRLSAFLEEHGVDTPATEFLIAPNRCIVALPRTFQIKGDTVGDNYTFVGPTYGDRSHQGTWEGPGDGRPVLLIALGSAFTDHLDFYRTCLSAVDGLDWHVVLSVGRFVDPADLGEVPPNVEVHQWVPQLDILTKASAFITHAGMGSTMEALSNAVPMVAVPQIAEQTMNAERIVELGLGRHIPRDQVTAEKLREAVLAVASDPGVAERLAAVRQEIREAGGARAAADILEGILAEAG"},"dna_sequence":{"accession":"DQ195535","fmin":"0","fmax":"1275","strand":"+","sequence":"ATGACGAGCGAGCACCGCTCTGCCTCCGTGACACCCCGTCACATCTCCTTCTTCAACATCCCCGGCCACGGCCACGTGAACCCGTCACTCGGCATCGTCCAGGAACTGGTCGCGCGCGGCCACCGGGTCAGCTACGCCATCACCGACGAGTTCGCCGCACAGGTCAAGGCGGCCGGCGCGACGCCCGTGGTGTACGACTCCATCCTGCCGAAGGAGTCCAACCCCGAGGAGTCGTGGCCGGAGGACCAGGAGTCCGCGATGGGCCTGTTCCTCGACGAAGCCGTCCGGGTCCTGCCGCAGCTGGAGGACGCCTACGCCGACGACCGGCCGGACCTGATCGTCTACGACATCGCCTCCTGGCCCGCCCCGGTGCTCGGCCGGAAGTGGGACATCCCCTTCGTCCAGCTCTCCCCGACCTTCGTCGCCTACGAGGGCTTCGAGGAGGACGTACCCGCGGTGCAGGACCCCACGGCCGACCGCGGCGAGGAGGCCGCCGCCCCCGCGGGGACCGGGGACGCCGAGGAGGGTGCCGAGGCCGAGGACGGCCTGGTGCGCTTCTTCACCCGGCTCTCGGCCTTCCTGGAGGAGCACGGGGTGGACACCCCGGCCACCGAGTTCCTCATCGCGCCCAACCGCTGCATCGTCGCGCTGCCGCGCACCTTCCAGATCAAGGGCGACACGGTCGGCGACAACTACACCTTCGTCGGTCCCACCTACGGCGACCGGTCCCACCAGGGCACCTGGGAAGGCCCCGGGGACGGGCGTCCGGTGCTGCTGATCGCCCTGGGCTCGGCGTTCACCGACCACCTCGACTTCTACCGCACCTGCCTGTCCGCCGTCGACGGCCTGGACTGGCACGTGGTGCTCTCCGTGGGCCGCTTCGTCGACCCCGCGGACCTCGGCGAGGTCCCGCCGAACGTCGAGGTGCACCAGTGGGTGCCGCAGCTCGACATCCTGACCAAAGCCTCCGCGTTCATCACGCACGCGGGCATGGGCAGCACCATGGAGGCCCTGTCGAACGCGGTGCCCATGGTCGCGGTGCCGCAGATCGCGGAGCAGACGATGAACGCCGAGCGGATCGTCGAGCTGGGCCTCGGCCGGCACATCCCGCGGGACCAGGTCACGGCCGAGAAGCTGCGCGAGGCCGTGCTCGCCGTCGCCTCCGACCCCGGTGTCGCCGAACGGCTCGCGGCCGTCCGGCAGGAGATCCGTGAGGCGGGCGGCGCCCGGGCGGCCGCCGACATCCTGGAGGGCATCCTCGCCGAAGCAGGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36823","NCBI_taxonomy_name":"Streptomyces antibioticus","NCBI_taxonomy_id":"1890"}}}},"ARO_accession":"3000866","ARO_id":"37246","ARO_name":"oleI","ARO_description":"OleI is a glycosyltransferase found in Streptomyces antibioticus, specifically the oleandomycin biosynthetic cluster. OleI glycosylates oleandomycin to confer self-resistance.","ARO_category":{"36604":{"category_aro_accession":"3000465","category_aro_cvterm_id":"36604","category_aro_name":"ole glycosyltransferase","category_aro_description":"OleI and OleD are glycosyltransferases found in Streptomyces antibioticus which is a natural producer of antibiotic oleandomycin. OleI glycosylates antibiotic oleandomycin whereas OleD can glycosylate a wide variety of macrolides.","category_aro_class_name":"AMR Gene Family"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1825":{"model_id":"1825","model_name":"CTX-M-27","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1704":{"protein_sequence":{"accession":"AAO61597.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGGYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"AY156923","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGGCTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001889","ARO_id":"38289","ARO_name":"CTX-M-27","ARO_description":"CTX-M-27 is a beta-lactamase found in Escherichia coli","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1826":{"model_id":"1826","model_name":"ykkC","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"180"}},"model_sequences":{"sequence":{"489":{"protein_sequence":{"accession":"CAB13166.1","sequence":"MKWGLVVLAAVFEVVWVIGLKHADSALTWSGTAIGIIFSFYLLMKATHSLPVGTVYAVFTGLGTAGTVLSEIVLFHEPVGWPKLLLIGVLLIGVIGLKLVTQDETEEKGGEA"},"dna_sequence":{"accession":"AL009126","fmin":"1376516","fmax":"1376855","strand":"+","sequence":"ATGAAATGGGGATTGGTCGTGCTTGCCGCTGTTTTCGAGGTTGTTTGGGTGATAGGCTTAAAGCACGCTGACTCAGCCTTAACATGGAGCGGCACTGCCATCGGCATCATATTCAGCTTTTACCTTCTAATGAAGGCGACTCACAGTCTGCCTGTTGGTACCGTGTATGCCGTCTTTACCGGGCTCGGCACAGCGGGAACAGTACTTAGTGAAATCGTTCTTTTTCATGAACCGGTTGGATGGCCGAAGCTATTGTTAATTGGCGTGCTCTTAATCGGTGTAATCGGGTTGAAGCTTGTGACACAGGATGAGACAGAGGAAAAAGGAGGCGAGGCATAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39579","NCBI_taxonomy_name":"Bacillus subtilis subsp. subtilis str. 168","NCBI_taxonomy_id":"224308"}}}},"ARO_accession":"3003063","ARO_id":"39497","ARO_name":"ykkC","ARO_description":"ykkC is an SMR-type protein that is a subunit of the ykkCD efflux pump","ARO_category":{"36004":{"category_aro_accession":"0010003","category_aro_cvterm_id":"36004","category_aro_name":"small multidrug resistance (SMR) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Small multidrug resistance (SMR) proteins are a relatively small family of transporters, restricted to prokaryotic cells. They are also the smallest multidrug transporters, with only four transmembrane alpha-helices and no significant extramembrane domain.","category_aro_class_name":"AMR Gene Family"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1827":{"model_id":"1827","model_name":"SHV-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1149":{"protein_sequence":{"accession":"CAA39164.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASKRGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"X55640","fmin":"111","fmax":"972","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCAAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001064","ARO_id":"37444","ARO_name":"SHV-5","ARO_description":"SHV-5 is an extended-spectrum beta-lactamase found in Acinetobacter baumannii, Enterobacter cloacae, E. coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Salmonella enterica.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1828":{"model_id":"1828","model_name":"GES-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1969":{"protein_sequence":{"accession":"AAR97271.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVKWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMSDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"AY494718","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCATCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCAAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGAGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002335","ARO_id":"38735","ARO_name":"GES-6","ARO_description":"GES-6 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1829":{"model_id":"1829","model_name":"CMY-87","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1284":{"protein_sequence":{"accession":"BAL63057.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLNDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVQPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"AB699171","fmin":"0","fmax":"1143","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCGCTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGCATGGCCGTGGCAATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGTTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAACGACCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTACACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGCGGTGCAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACAGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATAGTGATGCTGGCAAACAAAAGCTATCCTAACCCGGCTCGCGTAGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002100","ARO_id":"38500","ARO_name":"CMY-87","ARO_description":"CMY-87 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1830":{"model_id":"1830","model_name":"APH(3'')-Ib","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"545":{"protein_sequence":{"accession":"ABK33456.1","sequence":"MNRTNIFFGESHSDWLPVRGGESGDFVFRRGDGHAFAKIAPASRRGELAGERDRLIWLKGRGVACPEVINWQEEQEGACLVITAIPGVPAADLSGADLLKAWPSMGQQLGAVHSLLVDQCPFERRLSRMFGRAVDVVSRNAVNPDFLPDEDKSTPQLDLLARVERELPVRLDQERTDMVVCHGDPCMPNFMVDPKTLQCTGLIDLGRLGTADRYADLALMIANAEENWAAPDEAERAFAVLFNVLGIEAPDRERLAFYLRLDPLTWG"},"dna_sequence":{"accession":"AF313472","fmin":"15593","fmax":"16397","strand":"+","sequence":"TTGAATCGAACTAATATTTTTTTTGGTGAATCGCATTCTGACTGGTTGCCTGTCAGAGGCGGAGAATCTGGTGATTTTGTTTTTCGACGTGGTGACGGGCATGCCTTCGCGAAAATCGCACCTGCTTCCCGCCGCGGTGAGCTCGCTGGAGAGCGTGACCGCCTCATTTGGCTCAAAGGTCGAGGTGTGGCTTGCCCCGAGGTGATCAACTGGCAGGAGGAACAGGAGGGTGCATGCTTGGTGATAACGGCAATTCCGGGAGTACCGGCGGCTGATCTGTCTGGAGCGGATTTGCTCAAAGCGTGGCCGTCAATGGGGCAGCAACTTGGCGCTGTTCACAGCCTATTGGTTGATCAATGTCCGTTTGAGCGCAGGCTGTCGCGAATGTTCGGACGCGCCGTTGATGTGGTGTCCCGCAATGCCGTCAATCCCGACTTCTTACCGGACGAGGACAAGAGTACGCCGCAGCTCGATCTTTTGGCTCGTGTCGAACGAGAGCTACCGGTGCGGCTCGACCAAGAGCGCACCGATATGGTTGTTTGCCATGGTGATCCCTGCATGCCGAACTTCATGGTGGACCCTAAAACTCTTCAATGCACGGGTCTGATCGACCTTGGGCGGCTCGGAACAGCAGATCGCTATGCCGATTTGGCACTCATGATTGCTAACGCCGAAGAGAACTGGGCAGCGCCAGATGAAGCAGAGCGCGCCTTCGCTGTCCTATTCAATGTATTGGGGATCGAAGCCCCCGACCGCGAACGCCTTGCCTTCTATCTGCGATTGGACCCTCTGACTTGGGGTTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002639","ARO_id":"39039","ARO_name":"APH(3'')-Ib","ARO_description":"APH(3'')-Ib is an aminoglycoside phosphotransferase encoded by plasmids, transposons, integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.","ARO_category":{"36266":{"category_aro_accession":"3000127","category_aro_cvterm_id":"36266","category_aro_name":"APH(3'')","category_aro_description":"Phosphorylation of streptomycin on the hydroxyl group at position 3''","category_aro_class_name":"AMR Gene Family"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1831":{"model_id":"1831","model_name":"AAC(6')-Iid","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"207":{"protein_sequence":{"accession":"CAE50925.1","sequence":"MIISEFDRENIVLRDQLADLLRLTWPDEYGTEPMKEVEQLMAPERIAVSAIEGEELVGFVGAIPQYGKTGWELHPLVVASTHRKQQIGTRLVSYLEKEVASYGGLVIYLGTDDVEGQTNLVETDLFEDTFAKLQEIKNINHHPYTFYEKLGYQIIGVIPDANGWNQPDIWLAKRVAKREPTE"},"dna_sequence":{"accession":"AJ584700","fmin":"33","fmax":"582","strand":"+","sequence":"ATGATTATCAGTGAGTTTGATCGTGAGAATATTGTCTTGCGAGATCAGCTTGCAGATCTTTTAAGATTGACTTGGCCTGATGAGTATGGAACAGAGCCGATGAAAGAAGTCGAACAGTTGATGGCTCCAGAACGGATTGCTGTATCGGCGATTGAAGGGGAGGAATTGGTCGGTTTTGTTGGAGCGATCCCTCAATATGGCAAAACAGGGTGGGAGTTACATCCTTTGGTAGTAGCAAGCACACATCGCAAACAACAAATCGGGACACGATTGGTTTCCTACCTGGAAAAAGAAGTCGCTTCATATGGTGGCCTGGTCATCTATCTAGGGACAGATGATGTTGAAGGACAAACAAATTTAGTTGAAACGGATTTATTTGAAGATACCTTTGCAAAGTTACAAGAAATCAAAAATATCAATCATCATCCCTATACATTTTATGAGAAACTTGGCTATCAGATCATCGGTGTGATCCCAGATGCGAATGGGTGGAACCAGCCTGATATTTGGTTAGCAAAACGAGTGGCCAAACGAGAGCCAACGGAATAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39521","NCBI_taxonomy_name":"Enterococcus hirae","NCBI_taxonomy_id":"1354"}}}},"ARO_accession":"3002589","ARO_id":"38989","ARO_name":"AAC(6')-Iid","ARO_description":"AAC(6')-Iid is a chromosomal-encoded aminoglycoside acetyltransferase in Enterococcus durans","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1832":{"model_id":"1832","model_name":"QnrS2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"145":{"protein_sequence":{"accession":"ABF47470.1","sequence":"METYRHTYRHHSFSHQDLSDITFTACTFIRCDFRRANLRDATFINCKFIEQGDIEGCHFDVADLRDASFQQCQLAMANFSNANCYGIELRECDLKGANFSRANFANQVSNRMYFCSAFITGCNLSYANMERVCLEKCELFENRWIGTHLAGASLKESDLSRGVFSEDVWGQFSLQGANLCHAELDGLDPRKVDTSGIKIASWQQEQLLEALGIVVFPD"},"dna_sequence":{"accession":"DQ485530","fmin":"0","fmax":"657","strand":"+","sequence":"ATGGAAACCTACCGTCACACATATCGACACCACAGTTTTTCACATCAAGATCTAAGTGATATTACTTTCACTGCTTGCACCTTTATCCGATGCGATTTTCGACGTGCTAACTTGCGTGATGCGACATTTATTAACTGCAAGTTCATTGAACAGGGTGATATCGAAGGTTGCCATTTTGATGTCGCAGACCTTCGCGATGCAAGTTTCCAACAATGCCAGCTTGCGATGGCAAACTTTAGTAACGCCAATTGCTACGGTATTGAGTTACGTGAGTGTGATTTAAAAGGGGCCAACTTTTCCCGAGCAAACTTTGCCAATCAAGTGAGTAATCGTATGTACTTTTGCTCAGCCTTTATTACTGGATGTAACCTGTCTTATGCCAATATGGAGCGGGTCTGTTTAGAAAAATGTGAGCTGTTTGAAAATCGCTGGATAGGGACTCACCTCGCGGGCGCATCACTGAAAGAGTCAGACTTAAGTCGAGGTGTTTTTTCTGAAGATGTCTGGGGACAGTTTAGCCTACAGGGTGCTAATTTATGTCACGCCGAACTCGACGGTTTAGATCCTCGAAAAGTCGATACATCAGGTATCAAAATTGCCAGCTGGCAACAAGAACAGCTTCTCGAAGCGTTGGGTATTGTTGTTTTTCCTGACTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35715","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Anatum","NCBI_taxonomy_id":"58712"}}}},"ARO_accession":"3002791","ARO_id":"39225","ARO_name":"QnrS2","ARO_description":"QnrS2 is a plasmid-mediated quinolone resistance protein found in Salmonella enterica","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1833":{"model_id":"1833","model_name":"OXA-374","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1379":{"protein_sequence":{"accession":"AHL30274.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKTTTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPKGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KF986255","fmin":"16","fmax":"841","strand":"+","sequence":"ATGAACATTAAAGCCCTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTCTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGACAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTAAAGGAAATATTGTAGCATTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001560","ARO_id":"37960","ARO_name":"OXA-374","ARO_description":"OXA-374 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1834":{"model_id":"1834","model_name":"TEM-94","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"852":{"protein_sequence":{"accession":"CAC85661.1","sequence":"MSIQHFRVALIPFFAAFCFPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTTPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASERGSRGIIAALGPDGKPSRIVVIYMTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AJ318094","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCTTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACATGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000961","ARO_id":"37341","ARO_name":"TEM-94","ARO_description":"TEM-94 is an extended-spectrum beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1836":{"model_id":"1836","model_name":"OXA-201","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1372":{"protein_sequence":{"accession":"ADX07746.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIQVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWVVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"HQ734812","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCAAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGGTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001666","ARO_id":"38066","ARO_name":"OXA-201","ARO_description":"OXA-201 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1837":{"model_id":"1837","model_name":"CTX-M-59","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1781":{"protein_sequence":{"accession":"ABD73290.1","sequence":"MMTQSIRRSMLTVMATLPLLFSSATLHAQANSVQQQLEALEKSSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKQSESDKLLLNQRVEIKKSDLVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSASIRAGLPKSWVVGDKTGSGDYGTTNDIAVIWPENHAPLVLVTYFTQPEQKAESRRDILAAAAKIVTHGF"},"dna_sequence":{"accession":"DQ408762","fmin":"0","fmax":"876","strand":"+","sequence":"ATGATGACTCAGAGCATTCGCCGCTCAATGTTAACGGTGATGGCGACGCTACCCCTGCTATTTAGCAGCGCAACGCTGCATGCGCAGGCGAACAGCGTGCAACAGCAGCTGGAAGCCCTGGAGAAAAGTTCGGGAGGTCGGCTTGGCGTTGCGCTGATTAACACCGCCGATAATTCGCAGATTCTCTACCGTGCCGATGAACGTTTTGCGATGTGCAGTACCAGTAAGGTGATGGCGGCCGCGGCGGTGCTTAAACAGAGCGAGAGCGATAAGCTCCTGCTAAATCAGCGCGTTGAAATCAAGAAGAGCGACCTGGTTAACTACAATCCCATTGCGGAGAAACACGTTAACGGCACGATGACGCTGGCTGAGCTTGGCGCAGCGGCGCTGCAGTATAGCGACAATACTGCCATGAATAAGCTGATTGCCCATCTGGGTGGTCCCGATAAAGTGACGGCGTTTGCTCGCTCGTTGGGTGATGAGACCTTCCGTCTGGACAGAACCGAGCCCACGCTCAATACCGCCATTCCAGGCGACCCGCGTGATACCACCACGCCGCTCGCGATGGCGCAGACCCTGAAAAATCTGACGCTGGGTAAAGCGCTGGCGGAAACTCAGCGGGCACAGTTGGTGACGTGGCTTAAGGGCAATACTACCGGTAGCGCGAGCATTCGGGCGGGTCTGCCGAAATCATGGGTAGTGGGCGATAAAACCGGCAGCGGAGATTATGGCACCACCAACGATATCGCGGTTATCTGGCCGGAAAACCACGCACCGCTGGTTCTGGTGACCTACTTTACCCAACCGGAGCAGAAGGCGGAAAGCCGTCGGGATATTCTGGCTGCGGCGGCGAAAATCGTAACCCACGGTTTCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001920","ARO_id":"38320","ARO_name":"CTX-M-59","ARO_description":"CTX-M-59 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1838":{"model_id":"1838","model_name":"ACT-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1893":{"protein_sequence":{"accession":"ACJ05689.1","sequence":"MMKKSLCCALLLGISCSALAAPVSEKQLAEVVANTVTPLMKAQSIPGMAVAVIYQGKPHYYTFGKADIAASKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNAALLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPFEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGMKTNVQDMANWVMANMAPENVADASLKQGISLAQSRYWRIGSMYQGLGWEMLNWPVEANTVIEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYPILDALQ"},"dna_sequence":{"accession":"FJ237369","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCTCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCGCGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCGATTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGTAAACCGCACTATTACACGTTTGGCAAAGCCGATATCGCGGCCAGCAAACCCGTTACGCCTCAGACTCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGGGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGGATTCGTATGCTGGATCTCGCAACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAATGCCGCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGTATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGCCCTTTGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCATGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAATATGGCGCCGGAGAACGTTGCTGATGCCTCACTTAAGCAGGGCATCTCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGATCGAGGGCAGCGACAGTAAGGTGGCGCTGGCACCGCTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCCTATCCTCGACGCGCTACAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001824","ARO_id":"38224","ARO_name":"ACT-5","ARO_description":"ACT-5 is a beta-lactamase found in Escherichia coli","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1839":{"model_id":"1839","model_name":"aadA14","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"4342":{"protein_sequence":{"accession":"CAI57696.1","sequence":"MTNKPPESIAEQVSEARSILENHLETIQAIHLFGSAVDGGLKPFSDIDLLVTVGTPLNESTRAALMSDLLAVSAFPGTDSKRRALEVTVLTQEDVVPWRYPAKRQMQFGEWLRDDINARIFEPALMDHDLAILLTKVRRHSVALYGPAAHEFFDEIPVVDVQRSLLETLTLWTTEADWKGDERNIVLALVRIWYTAMTGEITSKVAAADWALQRLPREIKSVVIAARDAYLGLEAADLAAYPKERADLRNHIHSSVTAKLQ"},"dna_sequence":{"accession":"AJ884726.1","fmin":"539","fmax":"1325","strand":"-","sequence":"CTATTGCAGTTTCGCCGTCACGCTAGAATGGATATGGTTCCGAAGGTCTGCCCGTTCTTTCGGATAAGCTGCCAGATCTGCGGCTTCCAGCCCCAGATACGCATCCCTTGCGGCAATAACAACGCTTTTGATCTCACGAGGCAGACGCTGAAGCGCCCAGTCTGCTGCAGCAACTTTAGAAGTAATCTCTCCGGTCATTGCGGTGTACCAGATACGCACCAAGGCGAGAACGATGTTTCTCTCATCCCCTTTCCAATCCGCCTCTGTAGTCCAGAGTGTCAATGTTTCCAGTAACGAACGCTGCACATCGACGACAGGAATTTCATCGAAAAATTCGTGAGCAGCTGGGCCGTACAAGGCAACGCTATGTCGCCGCACTTTCGTCAGCAAGATGGCGAGGTCATGATCCATCAGTGCGGGCTCGAAAATCCTCGCATTGATATCATCACGCAACCATTCACCAAATTGCATTTGCCGTTTCGCTGGATATCGCCACGGCACTACGTCTTCCTGAGTCAGCACCGTCACCTCAAGTGCACGGCGTTTTGAATCGGTGCCAGGGAAAGCGGATACCGCCAACAAATCGGACATCAATGCAGCTCTGGTTGACTCGTTTAAAGGAGTGCCCACCGTAACCAACAGGTCGATATCACTAAATGGCTTTAATCCACCATCTACTGCGGAACCAAACAAGTGAATCGCCTGAATAGTTTCAAGATGATTTTCTAAAATTGATCGAGCCTCGGATACTTGTTCTGCAATCGACTCAGGGGGCTTATTAGTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36867","NCBI_taxonomy_name":"Pasteurella multocida","NCBI_taxonomy_id":"747"}}}},"ARO_accession":"3002614","ARO_id":"39014","ARO_name":"aadA14","ARO_description":"aadA14 is a plasmid-encoded aminoglycoside nucleotidyltransferase gene in Pasteurella multocida","ARO_category":{"41439":{"category_aro_accession":"3004275","category_aro_cvterm_id":"41439","category_aro_name":"ANT(3'')","category_aro_description":"Nucleotidylylation of streptomycin at the hydroxyl group at position 3''","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1840":{"model_id":"1840","model_name":"CMY-59","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1443":{"protein_sequence":{"accession":"BAJ17544.1","sequence":"GPGHLFAFNYGTDFMMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHASPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"AB587082","fmin":"0","fmax":"1188","strand":"+","sequence":"GGGCCCGGACACCTTTTTGCTTTTAATTACGGAACTGATTTCATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGCTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002069","ARO_id":"38469","ARO_name":"CMY-59","ARO_description":"CMY-59 is a beta-lactamase found in Shigella spp.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1841":{"model_id":"1841","model_name":"OXA-76","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1465":{"protein_sequence":{"accession":"AAX51234.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEKLGIL"},"dna_sequence":{"accession":"AY949203","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAAAAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001621","ARO_id":"38021","ARO_name":"OXA-76","ARO_description":"OXA-76 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1842":{"model_id":"1842","model_name":"IMI-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1356":{"protein_sequence":{"accession":"ACX71212.1","sequence":"MSLNVKQSRIAILFISCLFSISFFSQANTKGIDEIKNLETDFNGRVGVYALDTGSGKSFSYKANERFPLCSSFKGFLAAAVLKGSQDNQLNLNQIVNYNTRSLEFHSPITTKYKDNGMSLGDMAAAALQYSDNGATNIILERYIGGPEGMTKFMRSIGDEDFRLDRWELDLNTAIPGDERDTSTPAAVAKSLKTLALGNILSEREKETYQTWLKGNTTGAARIRASVPSDWVVGDKTGSCGAYGTANDYAVVWPKNRAPLIISVYTTKNEKEAKHEDKVIAEASRIAIDNLK"},"dna_sequence":{"accession":"GU015024","fmin":"0","fmax":"879","strand":"+","sequence":"ATGTCACTTAATGTAAAACAAAGTAGAATAGCCATCTTGTTTATCTCTTGTTTATTTTCAATATCATTTTTCTCACAGGCCAATACAAAGGGTATCGATGAGATTAAAAACCTTGAAACAGATTTCAATGGTAGAGTTGGTGTCTACGCTTTAGACACTGGCTCAGGTAAATCATTTTCGTACAAAGCAAATGAACGATTTCCATTATGTAGTTCTTTCAAAGGCTTTTTAGCTGCTGCTGTATTAAAAGGCTCTCAAGATAATCAACTCAATCTTAATCAGATCGTGAATTACAATACAAGAAGTTTAGAGTTCCATTCACCCATCACAACTAAATATAAAGATAATGGAATGTCATTAGGTGATATGGCTGCTGCCGCTTTACAATATAGCGACAATGGTGCTACTAATATTATTCTTGAACGTTATATCGGTGGTCCTGAGGGTATGACTAAATTCATGCGGTCGATTGGAGATGAAGATTTTAGACTCGATCGTTGGGAGTTAGATCTAAACACAGCTATTCCAGGCGATGAACGTGACACATCTACACCTGCAGCAGTAGCTAAGAGCCTGAAAACTCTTGCTCTGGGTAACATACTTAGTGAGCGTGAAAAGGAAACCTATCAGACATGGTTAAAGGGTAACACAACCGGTGCAGCGCGTATTCGTGCTAGCGTACCAAGCGATTGGGTAGTTGGCGATAAAACTGGTAGTTGCGGAGCATACGGTACTGCAAATGATTATGCGGTAGTCTGGCCAAAGAACCGGGCTCCTCTTATAATTTCTGTATACACAACAAAAAACGAAAAAGAAGCCAAGCATGAGGATAAAGTAATCGCAGAAGCTTCAAGAATYGCAATTGATAACCTTAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001860","ARO_id":"38260","ARO_name":"IMI-3","ARO_description":"IMI-3 is a beta-lactamase found in Enterobacteriaceae","ARO_category":{"36027":{"category_aro_accession":"3000018","category_aro_cvterm_id":"36027","category_aro_name":"IMI beta-lactamase","category_aro_description":"IMI beta-lactamases are a group of TEM-1-like beta-lactamase that are known to hydrolyze imipenem. IMI beta-lactamases are inhibited by clavulanic acid and tazobactam.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1843":{"model_id":"1843","model_name":"rmtD","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"4340":{"protein_sequence":{"accession":"ABY64751.1","sequence":"MSELKEKLLASKKYRDVCPDTIERIWRECSAKFKKEKDVDKAAREALHGVTGAFMTEREYKRAMEMAAARDWEALLGMHASTRERLPVESMDRVFDQLFEASGTPARILDLACGLNPVYLAHRLPNAAITGVDISGQCVNVIRAFGGAEARLGDLLCEIPEDEANAALLFKVLPLLERQRAGAAMDALMRVNAEWIVASFPTRSLGGRNVGMEKHYSEWMEAHVPENRAIAARLTGENELFYVLKRK"},"dna_sequence":{"accession":"EU269034.2","fmin":"1479","fmax":"2223","strand":"-","sequence":"TCATTTTCGTTTCAGCACGTAAAACAGCTCGTTTTCGCCGGTCAGCCGCGCGGCAATCGCGCGATTTTCCGGCACGTGCGCCTCCATCCATTCGGAATAGTGCTTTTCCATGCCGACGTTGCGCCCGCCGAGCGAACGCGTCGGAAACGATGCGACGATCCATTCCGCATTCACGCGCATTAGCGCATCCATCGCCGCGCCCGCACGCTGGCGCTCCAAAAGCGGCAGCACCTTAAACAGCAGCGCCGCATTCGCCTCGTCTTCCGGGATTTCGCACAGCAAATCGCCCAAACGCGCTTCCGCGCCGCCAAACGCACGAATTACGTTTACGCACTGACCGCTGATATCCACGCCGGTAATCGCCGCATTTGGCAATCGATGCGCGAGGTAGACAGGATTCAGCCCGCACGCGAGATCGAGGATTCGCGCCGGCGTTCCGCTGGCTTCAAACAGCTGATCGAACACGCGATCCATCGATTCCACAGGCAGCCGTTCGCGCGTGGACGCGTGCATTCCAAGCAGCGCTTCCCAATCGCGTGCCGCCGCCATTTCCATTGCGCGTTTGTATTCGCGCTCGGTCATGAACGCGCCGGTCACGCCGTGAAGCGCTTCGCGCGCCGCCTTGTCCACGTCCTTTTCCTTTTTGAATTTCGCGCTGCATTCACGCCATATGCGCTCGATCGTGTCCGGGCAAACGTCGCGATATTTTTTCGAAGCGAGCAGTTTTTCCTTCAGTTCGCTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002667","ARO_id":"39067","ARO_name":"rmtD","ARO_description":"RmtD is a 16S rRNA methyltransferase found in Pseudomonas aeruginosa which methylates G1405 of the 16S rRNA. It confers high level resistance to many aminoglycosides.","ARO_category":{"41435":{"category_aro_accession":"3004271","category_aro_cvterm_id":"41435","category_aro_name":"16S rRNA methyltransferase (G1405)","category_aro_description":"Methyltransferases that methylate the G1405 position of 16S rRNA, which is part of an aminoglycoside binding site.","category_aro_class_name":"AMR Gene Family"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1844":{"model_id":"1844","model_name":"OXA-128","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1368":{"protein_sequence":{"accession":"ABY77907.1","sequence":"MNIKALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNVLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQEVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"EU375515","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGTTCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTAGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAGAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001648","ARO_id":"38048","ARO_name":"OXA-128","ARO_description":"OXA-128 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1845":{"model_id":"1845","model_name":"OXA-312","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1298":{"protein_sequence":{"accession":"AGU69250.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKTTTTEVFKWDGQKRLFPEWEKDMTLGDAMKASALPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KF057029","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCCCTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTCTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGACAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTCTTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCATTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001683","ARO_id":"38083","ARO_name":"OXA-312","ARO_description":"OXA-312 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1846":{"model_id":"1846","model_name":"CTX-M-91","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1864":{"protein_sequence":{"accession":"ACX34099.1","sequence":"MMRKSVRRAMLMTTACVSLLLASVPLCAQANDVQQKLAALEKSSGGRLGVALINTADNTQTLYRADERFAMCSTSKVMAVAAVLKQSETQKGLLSQRVEIKPSDLINYNPIAEKHVNGTMTFGELSAAALQYSDNTAMNKLIAHLGGPDKVTAFARTIGDDTFRLDRTEPTLNTAIPGDPRDTTTPLAMAQSLRNLTLGNALGDTQRAQLVMWLKGNTTGAASIQAGLPTSWVVGDKTGSGDYGTTNDIAVIWPEGRAPLVLVTYFTQSEPKAESRRDVLAAAARIVTDGY"},"dna_sequence":{"accession":"GQ870432","fmin":"30","fmax":"906","strand":"+","sequence":"ATGATGAGAAAAAGCGTAAGGCGGGCGATGTTAATGACGACAGCCTGTGTTTCGCTGCTGTTGGCCAGTGTGCCGCTGTGTGCCCAGGCGAACGATGTTCAACAGAAGCTCGCGGCGCTGGAGAAAAGCAGCGGGGGACGACTGGGTGTGGCGTTGATTAACACCGCCGATAACACGCAGACGCTCTACCGCGCCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCGGTAGCGGCGGTGCTTAAGCAAAGTGAAACGCAAAAGGGCTTGTTGAGTCAGCGGGTTGAAATTAAGCCCTCAGACTTGATTAACTACAACCCCATTGCGGAAAAACACGTCAATGGCACGATGACATTCGGGGAGTTGAGCGCGGCGGCGCTACAGTACAGCGATAATACTGCCATGAATAAGCTGATTGCCCATCTCGGGGGGCCGGATAAAGTGACGGCATTTGCCCGTACGATTGGCGATGACACGTTCCGGCTCGATCGTACCGAGCCGACGCTCAACACCGCGATCCCCGGCGACCCGCGCGATACCACCACGCCGTTAGCGATGGCGCAGTCTCTGCGCAATCTGACGTTGGGCAATGCCCTGGGTGACACTCAGCGTGCGCAGCTGGTGATGTGGCTGAAAGGCAACACCACCGGCGCTGCCAGCATTCAGGCAGGGCTACCCACATCGTGGGTTGTCGGGGATAAAACCGGCAGCGGCGATTATGGTACGACGAATGATATCGCGGTTATTTGGCCGGAAGGTCGCGCGCCGCTCGTTCTGGTGACTTACTTCACCCAGTCGGAGCCGAAGGCAGAGAGCCGTCGTGACGTGCTCGCTGCTGCCGCCAGAATTGTCACCGACGGTTATTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3001951","ARO_id":"38351","ARO_name":"CTX-M-91","ARO_description":"CTX-M-91 is a beta-lactamase found in Escherichia coli","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1847":{"model_id":"1847","model_name":"emrB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"900"}},"model_sequences":{"sequence":{"20":{"protein_sequence":{"accession":"AAC75733.1","sequence":"MQQQKPLEGAQLVIMTIALSLATFMQVLDSTIANVAIPTIAGNLGSSLSQGTWVITSFGVANAISIPLTGWLAKRVGEVKLFLWSTIAFAIASWACGVSSSLNMLIFFRVIQGIVAGPLIPLSQSLLLNNYPPAKRSIALALWSMTVIVAPICGPILGGYISDNYHWGWIFFINVPIGVAVVLMTLQTLRGRETRTERRRIDAVGLALLVIGIGSLQIMLDRGKELDWFSSQEIIILTVVAVVAICFLIVWELTDDNPIVDLSLFKSRNFTIGCLCISLAYMLYFGAIVLLPQLLQEVYGYTATWAGLASAPVGIIPVILSPIIGRFAHKLDMRRLVTFSFIMYAVCFYWRAYTFEPGMDFGASAWPQFIQGFAVACFFMPLTTITLSGLPPERLAAASSLSNFTRTLAGSIGTSITTTMWTNRESMHHAQLTESVNPFNPNAQAMYSQLEGLGMTQQQASGWIAQQITNQGLIISANEIFWMSAGIFLVLLGLVWFAKPPFGAGGGGGGAH"},"dna_sequence":{"accession":"U00096","fmin":"2812615","fmax":"2814154","strand":"+","sequence":"ATGCAACAGCAAAAACCGCTGGAAGGCGCGCAACTGGTCATTATGACGATTGCGCTGTCACTGGCGACATTCATGCAGGTGCTGGACTCCACCATTGCTAACGTGGCGATCCCCACTATCGCCGGGAATCTGGGCTCATCGCTCAGCCAGGGAACGTGGGTAATCACTTCTTTCGGGGTGGCGAATGCCATCTCGATCCCGCTTACCGGCTGGCTGGCAAAGCGCGTCGGGGAAGTGAAACTGTTCCTTTGGTCCACCATCGCCTTTGCTATTGCGTCGTGGGCGTGTGGTGTCTCCAGCAGCCTGAATATGCTGATCTTCTTCCGCGTGATTCAGGGGATTGTCGCCGGGCCGTTGATCCCGCTTTCGCAAAGTCTATTGCTGAATAACTACCCGCCAGCCAAACGCTCGATCGCGCTGGCGTTGTGGTCGATGACGGTGATTGTCGCGCCAATTTGCGGCCCGATCCTCGGCGGTTATATCAGCGATAATTACCACTGGGGCTGGATATTCTTCATCAACGTGCCGATTGGCGTGGCGGTGGTGTTGATGACACTGCAAACTCTGCGCGGACGTGAAACCCGCACCGAACGGCGGCGGATTGATGCCGTGGGGCTGGCACTGCTGGTTATTGGTATCGGCAGCCTGCAGATTATGCTCGACCGCGGTAAAGAGCTGGACTGGTTTTCATCACAGGAAATTATCATCCTTACCGTGGTGGCGGTGGTGGCTATCTGCTTCCTGATTGTCTGGGAGCTGACCGACGATAACCCGATAGTCGATCTGTCGTTGTTTAAGTCGCGCAACTTCACCATCGGCTGCTTGTGTATCAGCCTCGCGTATATGCTCTACTTCGGCGCTATTGTTCTGCTGCCGCAGTTGTTGCAGGAGGTCTACGGTTACACGGCGACCTGGGCAGGTTTGGCCTCTGCGCCGGTAGGGATTATTCCGGTGATCCTGTCGCCGATTATCGGCCGCTTCGCGCATAAACTGGATATGCGGCGGCTGGTAACCTTCAGCTTTATTATGTATGCCGTCTGCTTCTACTGGCGTGCCTATACCTTTGAACCAGGTATGGATTTTGGCGCGTCGGCCTGGCCGCAGTTTATCCAGGGGTTTGCGGTGGCCTGCTTCTTTATGCCGCTGACCACCATTACGCTGTCTGGTTTGCCACCGGAACGACTGGCGGCGGCATCGAGCCTCTCTAACTTTACGCGAACGCTGGCGGGGTCTATCGGCACGTCGATAACCACGACCATGTGGACCAACCGCGAGTCGATGCACCATGCGCAGTTGACTGAGTCGGTAAACCCGTTCAACCCGAATGCCCAGGCGATGTACAGTCAACTGGAAGGGCTTGGGATGACGCAACAGCAGGCATCAGGCTGGATTGCCCAGCAGATCACCAATCAGGGGCTGATTATTTCCGCCAATGAGATCTTCTGGATGTCAGCCGGGATATTCCTCGTCCTGCTGGGGCTGGTGTGGTTTGCTAAACCGCCATTTGGCGCAGGTGGCGGCGGAGGCGGTGCGCACTAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3000074","ARO_id":"36213","ARO_name":"emrB","ARO_description":"emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP), nalidixic acid, and thioloactomycin.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1848":{"model_id":"1848","model_name":"CTX-M-75","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1743":{"protein_sequence":{"accession":"ACS32294.1","sequence":"MMTQSIRRSMLTVMATLSLLFSSATLHAQANSVQQQLEALEKSSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKQSESDKHLLNQRVEIKKSDLVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSASIRAGLPKSWVVGDKTGSGDYGTTNDIAVIWPENHAPLVLVTYFTQPEQKAESRRDILAAAAKIVTHGF"},"dna_sequence":{"accession":"GQ149244","fmin":"0","fmax":"873","strand":"+","sequence":"ATGATGACCCAGAGCATTCGCCGCAGCATGCTGACCGTGATGGCGACCCTGAGCCTGCTGTTTAGCAGCGCGACCCTGCATGCGCAGGCGAACAGCGTGCAGCAGCAGCTGGAAGCGCTGGAAAAAAGCAGCGGCGGCCGCCTGGGCGTGGCGCTGATTAACACCGCGGATAACAGCCAGATTCTGTATCGCGCGGATGAACGCTTTGCGATGTGCAGCACCAGCAAAGTGATGGCGGCGGCGGCGGTGCTGAAACAGAGCGAAAGCGATAAACATCTGCTGAACCAGCGCGTGGAAATTAAAAAAAGCGATCTGGTGAACTATAACCCGATTGCGGAAAAACATGTGAACGGCACCATGACCCTGGCGGAACTGGGCGCGGCGGCGCTGCAGTATAGCGATAACACCGCGATGAACAAACTGATTGCGCATCTGGGCGGCCCGGATAAAGTGACCGCGTTTGCGCGCAGCCTGGGCGATGAAACCTTTCGCCTGGATCGCACCGAACCGACCCTGAACACCGCGATTCCGGGCGATCCGCGCGATACCACCACCCCGCTGGCGATGGCGCAGACCCTGAAAAACCTGACCCTGGGCAAAGCGCTGGCGGAAACCCAGCGCGCGCAGCTGGTGACCTGGCTGAAAGGCAACACCACCGGCAGCGCGAGCATTCGCGCGGGCCTGCCGAAAAGCTGGGTGGTGGGCGATAAAACCGGCAGCGGCGATTATGGCACCACCAACGATATTGCGGTGATTTGGCCGGAAAACCATGCGCCGCTGGTGCTGGTGACCTATTTTACCCAGCCGGAACAGAAAGCGGAAAGCCGCCGCGATATTCTGGCGGCGGCGGCGAAAATTGTGACCCATGGCTTT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36946","NCBI_taxonomy_name":"Providencia stuartii","NCBI_taxonomy_id":"588"}}}},"ARO_accession":"3001936","ARO_id":"38336","ARO_name":"CTX-M-75","ARO_description":"CTX-M-75 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1850":{"model_id":"1850","model_name":"FomB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"653":{"protein_sequence":{"accession":"BAA32494.1","sequence":"MLENLTIRSSRVVDLNLVKVRLSTNLEDFAAYSYFSAFAEDESAPADYEVVCVDLDRDDIPAELYADRTDRTFRGKRFKGGYYLVHYFGEPAHLITVGRTFYVFGRSLEKTVWPYFVKHILTVHSADHGFLHLKAAGFELPGAGATLLVGRNGAGKTVFLAQACLNGARFLSNTHTLVRDGVAHGVPSSIRVRRDQCFGELIDKHDLTAHMESGDYVTDSSTLFESPQISTARVRNVVIVDYDPARPQGLMPISPAAAGTFMEQFSFAVTTYGLKDDLLAHHGDFDTYVDSLARMRAQLTELVEGARCYRANADMLAKEVRDSTLKQLAE"},"dna_sequence":{"accession":"AB016934","fmin":"7388","fmax":"8381","strand":"+","sequence":"ATGCTGGAAAACCTCACGATCCGCAGCAGCCGCGTCGTCGACCTCAACCTGGTCAAGGTCAGGCTGTCCACCAACCTCGAGGACTTCGCGGCGTACTCCTACTTCTCGGCCTTCGCCGAGGACGAGTCCGCGCCCGCCGACTACGAGGTCGTCTGCGTCGACCTGGACCGGGACGACATCCCGGCCGAGCTGTACGCCGACCGGACCGACCGGACCTTCCGCGGCAAGCGGTTCAAGGGCGGCTACTACCTCGTCCACTACTTCGGGGAGCCCGCCCACCTCATCACGGTGGGCCGCACGTTCTACGTGTTCGGCAGGTCCCTCGAGAAGACCGTCTGGCCCTACTTCGTCAAGCACATCCTGACCGTCCACTCCGCGGACCACGGCTTCCTGCACCTGAAGGCGGCGGGCTTCGAACTGCCCGGCGCCGGAGCCACCCTGCTCGTCGGGCGCAACGGCGCGGGGAAGACCGTCTTCCTGGCCCAGGCGTGCCTCAACGGCGCCCGGTTCCTCAGCAACACCCACACGCTGGTCCGGGACGGGGTCGCGCACGGCGTCCCCTCCTCGATCCGGGTGCGCCGCGACCAGTGCTTCGGTGAACTCATCGACAAGCACGACCTGACGGCGCACATGGAGTCGGGCGACTACGTCACCGACTCCTCGACTCTCTTCGAGAGTCCGCAGATCAGCACGGCACGCGTCCGGAACGTCGTCATCGTCGACTACGACCCCGCACGCCCCCAGGGCCTCATGCCGATCTCGCCGGCCGCGGCCGGCACCTTCATGGAGCAGTTCTCCTTCGCGGTCACCACCTACGGCCTCAAGGACGATCTGCTCGCCCACCACGGGGACTTCGACACCTACGTCGACTCCCTGGCCCGGATGCGGGCGCAGCTGACCGAACTGGTCGAGGGCGCGCGCTGCTACCGGGCCAACGCAGACATGCTGGCCAAGGAAGTCCGGGATTCGACGCTCAAGCAGCTTGCCGAATGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39587","NCBI_taxonomy_name":"Streptomyces wedmorensis","NCBI_taxonomy_id":"43759"}}}},"ARO_accession":"3000449","ARO_id":"36588","ARO_name":"FomB","ARO_description":"An enzyme which on its own cannot provide fosfomycin resistance, however in conjunction with FomA, it leads to the formation of fosfomycin with three phosphates total, which makes it inactive.","ARO_category":{"41410":{"category_aro_accession":"3004246","category_aro_cvterm_id":"41410","category_aro_name":"Fom phosphotransferase family","category_aro_description":"Two members of the Fom family have been identified, FomA and FomB. FomB must interact with FomA confer resistance to fosfomycin, however FomA is capable of conferring resistance alone.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1851":{"model_id":"1851","model_name":"KPC-13","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1869":{"protein_sequence":{"accession":"AEA73284.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLGTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"HQ342889","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGGCACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCTATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3002323","ARO_id":"38723","ARO_name":"KPC-13","ARO_description":"KPC-13 is a beta-lactamase. From the Lahey list of KPC beta-lactamases.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1852":{"model_id":"1852","model_name":"rmtF","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"691":{"protein_sequence":{"accession":"AFJ11385.1","sequence":"MDERAQAALDALLSAKNLRDVCPETVRRVFMELLPRYRKPKDAEKAARTHLHQITGAFMTADAQKKARALLARWNEGDESALAAALSLHASTRERLPGADEWMRRVSPFLGADARVLDLACGLNPILLGSMGVTNALGMDIHLGCVRLVNETARARGWHTRARACDLLSEIPAEEADAALLMKLLPVLEAQKTGRAAELLASLRAPRLVVTFPTRTLGGRGVGMEKHYADWFERILPDTLSVRDRFTVSDELVYLVERT"},"dna_sequence":{"accession":"JQ808129","fmin":"1598","fmax":"2378","strand":"+","sequence":"ATGGATGAACGAGCGCAGGCGGCACTGGACGCGCTGCTTTCCGCGAAGAATCTGCGGGACGTATGTCCCGAGACGGTGCGGCGCGTGTTTATGGAGCTTTTGCCGCGATACAGAAAACCGAAGGACGCGGAGAAGGCGGCGCGCACGCATCTGCACCAGATCACCGGCGCGTTCATGACGGCGGACGCGCAGAAAAAGGCGCGGGCATTGCTTGCGCGCTGGAACGAGGGCGACGAATCGGCGCTCGCTGCCGCGCTGTCCCTGCACGCGTCCACGCGCGAGCGCCTGCCGGGCGCGGATGAATGGATGCGGCGCGTTTCGCCGTTTCTGGGCGCGGACGCGCGCGTGCTCGATCTGGCCTGCGGGCTGAACCCGATCCTACTGGGCTCCATGGGCGTGACGAACGCGCTGGGCATGGACATTCATCTGGGCTGCGTGCGACTTGTGAACGAAACGGCGCGGGCGCGCGGCTGGCATACGCGCGCGCGAGCCTGCGACCTGCTGAGCGAGATTCCCGCGGAGGAAGCCGACGCGGCGCTTCTGATGAAGCTCCTGCCCGTGCTGGAAGCCCAGAAAACCGGCCGCGCCGCCGAGCTGCTCGCAAGCCTCCGCGCCCCCAGGCTGGTCGTGACCTTCCCCACCCGCACCCTCGGCGGCCGCGGCGTGGGCATGGAAAAGCACTATGCCGACTGGTTCGAGCGCATCCTCCCCGATACCCTCTCCGTCCGCGACCGATTTACGGTGTCGGACGAGCTGGTGTATCTGGTGGAGCGGACGTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002666","ARO_id":"39066","ARO_name":"rmtF","ARO_description":"RmtF is a 16S rRNA methyltransferase found in Pseudomonas aeruginosa which methylates G1405 of the 16S rRNA. It confers high level resistance to many aminoglycosides.","ARO_category":{"41435":{"category_aro_accession":"3004271","category_aro_cvterm_id":"41435","category_aro_name":"16S rRNA methyltransferase (G1405)","category_aro_description":"Methyltransferases that methylate the G1405 position of 16S rRNA, which is part of an aminoglycoside binding site.","category_aro_class_name":"AMR Gene Family"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1853":{"model_id":"1853","model_name":"OXA-20","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1207":{"protein_sequence":{"accession":"YP_001844885.1","sequence":"MIIRFLALLFSAVVLVSLGHAQEKTHESSNWGKYFSDFNAKGTIVVVDERTNGNSTSVYNESRAQQRYSPASTFKIPHTLFALDAGAVRDEFHVFRWDGAKRSFAGHNQDQNLRSAMRNSTVWVYQLFAKEIGENKARSYLEKLNYGNADPSTKSGDYWIDGNLAISANEQISILKKLYRNELPFRVEHQRLVKDLMIVEAKRDWILRAKTGWDGQMGWWVGWVEWPTGPVFFALNIDTPNRMEDLHKREAIARAILQSVNALPPN"},"dna_sequence":{"accession":"NC_010611","fmin":"251961","fmax":"252762","strand":"+","sequence":"TTGATAATCCGATTTCTAGCACTGCTTTTCTCAGCTGTTGTACTTGTCTCTCTTGGTCATGCACAAGAAAAAACGCATGAGAGCTCTAATTGGGGGAAATACTTTAGTGATTTCAACGCTAAAGGTACAATAGTTGTAGTAGATGAACGCACAAACGGTAATTCCACATCGGTTTATAATGAATCCCGGGCTCAGCAGCGCTATTCGCCTGCGTCCACATTCAAGATTCCGCATACCCTTTTTGCGCTGGATGCAGGGGCGGTTCGCGATGAGTTTCATGTTTTTCGATGGGACGGCGCTAAAAGAAGCTTTGCAGGTCACAATCAAGACCAAAACCTACGATCGGCAATGCGCAATTCTACCGTTTGGGTCTATCAACTATTCGCAAAAGAAATAGGCGAAAACAAAGCACGAAGCTACCTAGAAAAATTAAACTACGGCAATGCAGACCCCTCGACCAAGAGCGGTGACTACTGGATAGATGGAAATCTTGCAATTTCAGCAAATGAACAAATTTCCATCCTAAAGAAGCTTTATCGAAATGAGCTTCCTTTTAGGGTAGAGCACCAACGCTTGGTTAAAGACTTGATGATTGTCGAAGCCAAACGTGATTGGATACTACGTGCCAAAACAGGCTGGGATGGTCAAATGGGTTGGTGGGTCGGTTGGGTAGAGTGGCCTACAGGCCCAGTATTTTTTGCGTTAAATATCGACACGCCAAACAGGATGGAAGACCTTCATAAACGAGAGGCAATTGCGCGTGCTATTCTTCAATCCGTCAATGCTTTGCCACCCAACTAGC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35523","NCBI_taxonomy_name":"Acinetobacter baumannii ACICU","NCBI_taxonomy_id":"405416"}}}},"ARO_accession":"3001415","ARO_id":"37815","ARO_name":"OXA-20","ARO_description":"OXA-20 is a beta-lactamase found in P. aeruginosa","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1854":{"model_id":"1854","model_name":"rmtA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"533":{"protein_sequence":{"accession":"BAC20579.1","sequence":"MSFDDALASILSSKKYRSLCPDTVRRILDQEWGRHKSPKLAVEATRTRLHGICGAYVTPESLKAAAAALSVGDVQKALSLHASTKERLAELDCLYDFIFSGGVPHRVLDIACGLNPLALFIRDITSVWACDIHQGLGDVITPFAHHQGLDFTFALQDVMCTPPTETGDLALVFKLLPLLEREQAGAAMALLQALATPRIAVSFPTRSLGGRGKGMEANYSAWFEGALPDEFEIEDTKTIGIELVYMIKRNK"},"dna_sequence":{"accession":"AB083212","fmin":"0","fmax":"756","strand":"+","sequence":"ATGAGCTTTGACGATGCCCTAGCGTCCATCCTTTCCTCAAAAAAATATCGTTCCCTCTGCCCGGATACCGTACGGCGGATTTTAGATCAGGAATGGGGGCGGCACAAATCGCCTAAGCTGGCAGTGGAGGCCACTCGCACCCGGCTGCACGGGATTTGCGGGGCCTATGTCACGCCGGAATCGCTCAAGGCTGCAGCAGCGGCATTATCGGTTGGCGATGTGCAAAAGGCACTGTCGCTGCACGCCTCTACCAAGGAGCGGTTGGCCGAATTGGACTGCCTCTACGATTTTATCTTTTCTGGCGGGGTGCCCCATCGTGTGTTGGATATCGCTTGCGGCCTAAACCCGCTGGCCCTCTTTATACGTGACATAACATCTGTATGGGCGTGCGACATCCATCAGGGGTTGGGCGATGTGATCACCCCCTTTGCCCATCATCAGGGATTGGACTTCACGTTCGCCCTGCAGGATGTGATGTGTACGCCGCCCACTGAGACGGGGGATTTGGCACTGGTATTTAAATTACTGCCTTTGCTGGAGCGAGAGCAAGCTGGCGCCGCCATGGCGCTACTGCAGGCACTAGCTACCCCTCGGATTGCCGTCAGCTTCCCCACCCGCAGTTTAGGCGGGCGCGGCAAGGGCATGGAAGCAAACTATTCCGCATGGTTCGAGGGGGCACTGCCTGATGAATTTGAAATTGAGGATACCAAGACCATTGGAATAGAGCTTGTGTACATGATAAAAAGGAATAAGTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3000859","ARO_id":"37239","ARO_name":"rmtA","ARO_description":"RmtA is a 16S rRNA methyltransferase found in Pseudomonas aeruginosa which methylates G1405 of the 16S rRNA. It confers high level resistance to many aminoglycosides.","ARO_category":{"41435":{"category_aro_accession":"3004271","category_aro_cvterm_id":"41435","category_aro_name":"16S rRNA methyltransferase (G1405)","category_aro_description":"Methyltransferases that methylate the G1405 position of 16S rRNA, which is part of an aminoglycoside binding site.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1855":{"model_id":"1855","model_name":"CTX-M-72","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1591":{"protein_sequence":{"accession":"AAV97957.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDGTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"AY847148","fmin":"8","fmax":"884","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACGGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001933","ARO_id":"38333","ARO_name":"CTX-M-72","ARO_description":"CTX-M-72 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1856":{"model_id":"1856","model_name":"QnrB20","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"573":{"protein_sequence":{"accession":"BAG55487.1","sequence":"MTPLLYKKTGTNMALALVGEKINRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNASALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRRVDLQGVKLDNYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"AB379831","fmin":"0","fmax":"681","strand":"+","sequence":"ATGACGCCATTACTGTATAAAAAAACAGGCACAAATATGGCTCTGGCACTCGTTGGCGAAAAAATTAACAGAAACCGCTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCGATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATGCCAGTGCGCTTGGCATTGAAATTCGCCACTGTCGTGCGCAAGGCGCAGATTTTCGCGGCGCAAGTTTTATGAATATGATCACTACTCGCACCTGGTTTTGCAGTGCATATATCACTAACACAAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAGCTGTGGGAAAACCGTTGGATGGGGGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTGACTTAGATATTCGGCGCGTTGATTTACAAGGCGTTAAGTTGGACAACTACCAGGCATCGTTGCTCATGGAACGTCTTGGCATCGCGGTGATTGGTTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002735","ARO_id":"39169","ARO_name":"QnrB20","ARO_description":"QnrB20 is a plasmid-mediated quinolone resistance protein found in Escherichia coli","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1857":{"model_id":"1857","model_name":"VIM-9","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1166":{"protein_sequence":{"accession":"AAS13760.1","sequence":"MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSIRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"AY524988","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGATACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002279","ARO_id":"38679","ARO_name":"VIM-9","ARO_description":"VIM-9 is a beta-lactamase found in Pseudomonas spp.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1858":{"model_id":"1858","model_name":"OXA-387","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1135":{"protein_sequence":{"accession":"AHK51384.1","sequence":"MNIKTLLLITSAIFISACSPYIMTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KJ173478","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAATGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTTGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001573","ARO_id":"37973","ARO_name":"OXA-387","ARO_description":"OXA-387 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1859":{"model_id":"1859","model_name":"QnrVC7","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"3307":{"protein_sequence":{"accession":"AJA36815.1","sequence":"MDKTDQLYVQADFSHQDLSGQYFKNCKFFCCSFKRANLRDTQFVDCSFIERGELEGCDFSYSDLRDASFKNCSLSMSYFKGANCFGIEFRECDLKGANFAQASFMNQVSNRMYFCSAYITGCNLSYANFERQCIEKCDLFENRWIGANLSGTSFKESDLSRGVFSEGCWSQCRLQGCDLSHSELYGLDPRKVDLTGVKICSWQQEQLLEQLGLIVVPD"},"dna_sequence":{"accession":"KM555152","fmin":"0","fmax":"657","strand":"+","sequence":"ATGGATAAAACAGACCAGTTATATGTACAAGCTGACTTTTCACATCAAGACTTGAGTGGTCAGTATTTTAAAAATTGCAAATTTTTCTGCTGTTCCTTTAAACGGGCAAACCTCCGCGATACACAATTTGTAGATTGTTCTTTCATTGAACGAGGAGAATTAGAGGGGTGTGATTTTTCTTACTCGGATCTTAGAGACGCATCTTTTAAAAACTGCAGTCTTTCAATGTCGTATTTCAAAGGTGCAAATTGTTTTGGTATCGAGTTCAGAGAGTGCGATTTAAAGGGGGCAAATTTTGCTCAAGCTAGCTTCATGAATCAGGTATCGAACAGAATGTATTTTTGTTCAGCCTATATAACAGGTTGTAATCTGTCATACGCAAATTTTGAAAGGCAGTGTATCGAAAAGTGTGATTTGTTTGAGAATAGATGGATTGGTGCAAATTTGAGTGGGACATCATTTAAAGAGTCTGATTTAAGTCGGGGAGTATTTTCTGAAGGGTGCTGGAGCCAGTGTAGGTTGCAAGGTTGTGATTTGAGCCACTCGGAGCTGTATGGTTTAGACCCCCGGAAAGTTGACCTTACAGGTGTAAAAATCTGTTCGTGGCAACAAGAACAACTTTTAGAGCAATTAGGTTTAATAGTAGTTCCTGACTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36789","NCBI_taxonomy_name":"Vibrio cholerae","NCBI_taxonomy_id":"666"}}}},"ARO_accession":"3003193","ARO_id":"39770","ARO_name":"QnrVC7","ARO_description":"QnrVC7 is a fluoroquinolone resistance gene in Lahey's list of qnr genes.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1860":{"model_id":"1860","model_name":"OXA-165","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1205":{"protein_sequence":{"accession":"ADK35869.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETPSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDVKPQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"HM488986","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGACCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCCCAATTAGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATGTAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001465","ARO_id":"37865","ARO_name":"OXA-165","ARO_description":"OXA-165 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1861":{"model_id":"1861","model_name":"LEN-15","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1268":{"protein_sequence":{"accession":"AAL50725.1","sequence":"MRYVRLCVISLLATLPLVVYAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGLEQLDRRIHYRQQDLVDYSPVSEKHLVDGMTIGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSPRSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGARGIVALLGPDGKPERIVVIYLRDTPASMAERNQHIAGIGQR"},"dna_sequence":{"accession":"AF452105","fmin":"0","fmax":"840","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCACCCTGCCACTGGTGGTATACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGTCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCCCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGACAAGACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCCAGCGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002478","ARO_id":"38878","ARO_name":"LEN-15","ARO_description":"LEN-15 is a beta-lactamase. From the Pasteur Institute list of LEN beta-lactamases.","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1862":{"model_id":"1862","model_name":"OXA-109","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1449":{"protein_sequence":{"accession":"ABV31689.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIQVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"EF650035","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCAAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001640","ARO_id":"38040","ARO_name":"OXA-109","ARO_description":"OXA-109 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1863":{"model_id":"1863","model_name":"VIM-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1006":{"protein_sequence":{"accession":"AAG27703.1","sequence":"MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATKSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGSEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"AF300454","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGAAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAGCGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002273","ARO_id":"38673","ARO_name":"VIM-3","ARO_description":"VIM-3 is a beta-lactamase found in Pseudomonas spp.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1864":{"model_id":"1864","model_name":"CMY-67","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"864":{"protein_sequence":{"accession":"AFK08541.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDEVTDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVQPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEVAWRILEKLQ"},"dna_sequence":{"accession":"JQ711185","fmin":"1027","fmax":"2173","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCGCTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGCATGGCCGTGGCAATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGTTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGACCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTACACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGAAGTTACGGATAAAGCCGCATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGCGGTGCAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACAGGATCCACAGGCGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTAATGTTGGCAAACAAAAGCTACCCCAACCCGGCTCGCGTCGAGGTGGCCTGGCGCATTCTTGAAAAACTGCAATAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002080","ARO_id":"38480","ARO_name":"CMY-67","ARO_description":"CMY-67 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1865":{"model_id":"1865","model_name":"ACC-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"778":{"protein_sequence":{"accession":"CCK86740.1","sequence":"MQNTLKLLSVITCLAATAQGALAANIDESKIKDTVDDLIQPLMQKNNIPGMSVAVTVNGKNYIYNYGLAAKQPQQPVTENTLFEVGSLSKTFAATLASYAQLSGKLSLDQSVSHYVPELRGSSFDHVSVLNVGTHTSGLQLFMPEDIKNTTQLMAYLKAWKPADAAGTHRVYSNIGTGLLGMIAAKSLGVSYEDAIEKTLLPQLGMHHSYLKVPADQMENYAWGYNKKDEPVHVNMEILGNEAYGIKTTSSDLLRYVQANMGQLKLDANAKMQQALTATHTGYFKSGEITQDLMWEQLPYPVSLPNLLTGNDMAMTKSVATPIVPPLPPQENVWINKTGSTNGFGAYIAFVPAKKMGIVMLANKNYSIDQRVTVAYKILSSLEGNK"},"dna_sequence":{"accession":"HE819401","fmin":"0","fmax":"1161","strand":"+","sequence":"ATGCAGAACACATTGAAGCTGTTATCCGTGATTACCTGTCTGGCAGCAACTGCCCAAGGTGCTCTGGCTGCTAATATCGATGAGAGCAAAATTAAAGACACCGTTGATGACCTGATCCAGCCGCTGATGCAGAAGAATAATATTCCCGGTATGTCGGTCGCAGTGACCGTCAACGGTAAAAACTACATTTATAACTATGGGTTAGCGGCAAAACAGCCTCAGCAGCCGGTTACGGAAAATACGTTATTTGAAGTGGGTTCGCTGAGTAAAACGTTTGCTGCCACCTTGGCGTCCTATGCGCAGTTGAGCGGTAAGCTGTCTTTGGATCAAAGCGTTAGCCATTACGTTCCAGAGTTGCGTGGCAGCAGCTTTGACCACGTTAGCGTACTCAATGTGGGCACGCATACCTCAGGCCTACAGCTATTTATGCCGGAAGATATTAAAAATACCACACAGCTGATGGCTTATCTAAAAGCATGGAAACCTGCCGATGCGGCTGGAACCCATCGCGTTTATTCCAATATCGGTACTGGTTTGCTAGGGATGATTGCGGCGAAAAGTCTGGGTGTGAGCTATGAAGATGCGATTGAGAAAACCCTCCTTCCTCAGTTAGGCATGCATCACAGCTACTTGAAGGTTCCGGCTGACCAGATGGAAAACTATGCGTGGGGCTACAACAAGAAAGATGAGCCAGTGCACGTGAATATGGAGATTTTGGGTAACGAAGCTTATGGTATCAAAACCACCTCCAGTGACTTGTTACGCTACGTGCAAGCCAATATGGGGCAGTTAAAGCTTGATGCTAATGCCAAGATGCAACAGGCTCTGACTGCCACCCACACCGGCTATTTCAAATCGGGTGAGATTACTCAGGATCTGATGTGGGAGCAGCTGCCATATCCGGTTTCTCTGCCGAATTTGCTCACCGGTAACGATATGGCGATGACGAAAAGCGTGGCTACGCCGATTGTTCCCCCGTTACCGCCACAGGAAAATGTGTGGATTAATAAGACCGGATCAACTAACGGCTTCGGTGCCTATATTGCGTTTGTTCCTGCTAAGAAGATGGGGATCGTGATGCTGGCTAACAAAAACTACTCAATCGATCAGCGAGTGACGGTGGCGTATAAAATCCTGAGCTCATTGGAAGGGAATAAGTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36784","NCBI_taxonomy_name":"Hafnia alvei","NCBI_taxonomy_id":"569"}}}},"ARO_accession":"3001819","ARO_id":"38219","ARO_name":"ACC-5","ARO_description":"ACC-5 is a beta-lactamase. From the Lahey list of ACC beta-lactamases. It is detected among Gram-negative bacteria isolates (Gamma- and Alpha-proteobacteria) from urban water sources.","ARO_category":{"36212":{"category_aro_accession":"3000073","category_aro_cvterm_id":"36212","category_aro_name":"ACC beta-lactamase","category_aro_description":"ACC beta-lactamases or Ambler class C beta-lactamases are AmpC beta-lactamases. They possess an interesting resistance phenotype due to their low activity against cephamycins.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1866":{"model_id":"1866","model_name":"KPC-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1517":{"protein_sequence":{"accession":"ACE62798.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAIDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"EU729727","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATAGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002317","ARO_id":"38717","ARO_name":"KPC-7","ARO_description":"KPC-7 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1867":{"model_id":"1867","model_name":"CTX-M-116","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"824":{"protein_sequence":{"accession":"AEI70324.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAVAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTNGL"},"dna_sequence":{"accession":"JF966749","fmin":"157","fmax":"1033","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGTCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGACGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGTGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCAACGGTTTGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3001976","ARO_id":"38376","ARO_name":"CTX-M-116","ARO_description":"CTX-M-116 is a beta-lactamase found in Proteus mirabilis","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1868":{"model_id":"1868","model_name":"TEM-82","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1162":{"protein_sequence":{"accession":"AAL29434.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMVSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDEQNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AF427128","fmin":"208","fmax":"1069","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGGTGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACAAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000949","ARO_id":"37329","ARO_name":"TEM-82","ARO_description":"TEM-82 is an inhibitor-resistant beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1869":{"model_id":"1869","model_name":"OXY-2-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1540":{"protein_sequence":{"accession":"AAL78278.2","sequence":"MIKSSWRKIAMLAAAVPLLLASSALWASTDAIHQKLTDLEKRSGGRLGVALINTADNSQILYRGDERFAMCSTSKVMAAAAVLKQSESNKEVVNKRLEINAADLVVWSPITEKHLQSGMTLAELSAATLQYSDNTAMNLIIGYLGGPEKVTAFARSIGDATFRLDRTEPTLNTAIPGDERDTSTPLAMAESLRKLTLGDALGEQQRAQLVTWLKGNTTGGQSIRAGLPESWVVGDKTGAGDYGTTNDIAVIWPEDHAPLVLVTYFTQPQQDAKNRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"AY077485","fmin":"183","fmax":"1056","strand":"+","sequence":"ATGATAAAAAGTTCGTGGCGTAAAATTGCAATGCTAGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCAGCGCACTGTGGGCCAGTACCGATGCTATCCATCAGAAGCTGACAGATCTCGAGAAGCGTTCAGGCGGCAGGTTGGGCGTGGCGCTAATCAACACGGCAGATAATTCTCAAATCTTATATCGCGGCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCCGCCGCCGCGGTATTAAAACAGAGCGAAAGCAATAAAGAGGTGGTAAATAAAAGGCTGGAGATTAACGCAGCCGATTTGGTGGTCTGGAGTCCGATTACCGAAAAACATCTCCAGAGCGGAATGACGCTGGCTGAGCTAAGCGCGGCGACGCTGCAATATAGCGACAATACGGCGATGAATCTGATCATCGGCTACCTTGGCGGGCCGGAAAAAGTCACCGCCTTCGCCCGCAGTATCGGCGATGCCACCTTTCGTCTCGATCGTACGGAGCCCACGCTGAATACCGCCATCCCGGGCGATGAGCGTGATACCAGCACGCCGCTGGCGATGGCTGAAAGCCTACGCAAGCTGACGCTTGGCGATGCGCTGGGCGAACAGCAACGCGCCCAGTTAGTCACCTGGCTGAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCGGGCCTGCCTGAAAGCTGGGTGGTCGGCGATAAAACCGGCGCCGGAGATTACGGCACCACCAATGATATTGCGGTTATCTGGCCGGAAGATCACGCTCCGCTGGTATTAGTCACCTACTTTACCCAGCCGCAGCAGGATGCGAAAAACCGCAAAGAGGTGTTAGCCGCAGCGGCAAAAATCGTGACCGAAGGGCTTTAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002401","ARO_id":"38801","ARO_name":"OXY-2-6","ARO_description":"OXY-2-6 is a beta-lactamase found in Klebsiella oxytoca","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1870":{"model_id":"1870","model_name":"OXA-66","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4337":{"protein_sequence":{"accession":"ABK34774.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"EF016356.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001615","ARO_id":"38015","ARO_name":"OXA-66","ARO_description":"OXA-66 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1871":{"model_id":"1871","model_name":"OXA-389","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1302":{"protein_sequence":{"accession":"AHL30287.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPKWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDKVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KJ135346","fmin":"14","fmax":"839","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTCAAGTGGGACGGGCAAAAAAGGCTATTCCCAAAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATAAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTGGGTTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAGC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001575","ARO_id":"37975","ARO_name":"OXA-389","ARO_description":"OXA-389 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1872":{"model_id":"1872","model_name":"vanXYL","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"168":{"protein_sequence":{"accession":"ABX54688.1","sequence":"MDNDYKYYLQLVNKQYPWQINNGSKKMVRVPYTDKEIYLDAVVVEHLIQLIETIQLQEKIEIVDGYRTIDEQKELWEFSLKDRGKRYTHDYVAYPGCSEHHTGLALDIGLKKTAHDIIAPKFNGEEAKKFLEHMKDYGFILRYPPNKKKVTGIAYEPWHFRYVGVPHSQIITQQAWTLEEYIAFLHTVGEKVS"},"dna_sequence":{"accession":"EU250284","fmin":"1996","fmax":"2578","strand":"+","sequence":"ATGGATAACGATTACAAGTATTATTTACAATTAGTCAATAAGCAATATCCTTGGCAGATAAACAATGGTTCTAAAAAAATGGTAAGGGTGCCTTATACAGATAAAGAAATTTATTTAGATGCAGTTGTTGTTGAACATTTGATTCAGTTGATCGAAACTATTCAATTACAAGAGAAAATAGAAATAGTTGATGGTTACCGTACGATAGACGAACAAAAAGAATTATGGGAATTTTCTTTAAAAGATAGAGGGAAACGATATACTCATGATTATGTTGCCTATCCTGGGTGTAGTGAGCATCATACTGGACTTGCATTAGATATTGGTCTTAAAAAAACAGCACATGATATCATAGCACCAAAATTTAATGGAGAAGAGGCAAAAAAATTTTTAGAGCATATGAAAGATTACGGATTTATTTTAAGGTACCCTCCAAACAAAAAAAAGGTAACAGGGATTGCGTATGAACCGTGGCATTTTAGGTATGTTGGAGTTCCTCACAGCCAAATCATTACTCAGCAAGCTTGGACGCTGGAAGAATATATCGCTTTTTTACACACAGTAGGAGAAAAAGTTTCATGAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3002968","ARO_id":"39402","ARO_name":"vanXYL","ARO_description":"vanXYL is a vanXY variant found in the vanL gene cluster","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36635":{"category_aro_accession":"3000496","category_aro_cvterm_id":"36635","category_aro_name":"vanXY","category_aro_description":"VanXY is a protein with both D,D-carboxypeptidase and D,D-dipeptidase activity, found in Enterococcus gallinarum. It cleaves and removes the terminal D-Ala of peptidoglycan subunits for the incorporation of D-Ser by VanC. D-Ala-D-Ser has low binding affinity with vancomycin.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1873":{"model_id":"1873","model_name":"linG","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4180":{"protein_sequence":{"accession":"ABG65740.1","sequence":"MLQLKMIELFKEGCHEDARIIAALMFGSFAIGEGDEFSDIEFAVFIQDDHFENFDQRSWLNAVSPVAAYFPDDFGHHTALFENGIRGEFHFMRKSDIPVISTWQGYGWFPSLEAAVLLDRSGELSRYASALVGGPPIREGAPLVEGLVLNLISLMLFGANLLNRGEYARAWALLSKAHENLLKLVRLHEGATDHWPTPSRALEKDISEDSYNRYLACTSSAEPRALCAAYHQTWTWSLELFKSVTEPLNIELPRTVIAQAKRLLNESATPHNK"},"dna_sequence":{"accession":"DQ836009.1","fmin":"1309","fmax":"2131","strand":"+","sequence":"ATGCTTCAGCTGAAAATGATCGAACTCTTCAAGGAAGGTTGTCATGAGGATGCACGAATAATCGCGGCATTGATGTTCGGCTCATTTGCTATCGGAGAGGGTGACGAGTTCTCTGATATCGAATTCGCAGTGTTCATCCAGGATGACCATTTTGAAAATTTCGATCAGCGCTCGTGGCTTAATGCCGTAAGTCCGGTTGCTGCTTACTTTCCGGACGACTTCGGCCACCACACCGCACTTTTTGAAAACGGCATTCGCGGTGAATTCCATTTCATGCGAAAATCGGACATACCGGTCATTTCCACTTGGCAAGGCTATGGGTGGTTTCCCTCGCTTGAGGCGGCTGTTTTGTTGGACCGATCAGGAGAGTTGTCAAGGTACGCAAGCGCTCTCGTGGGCGGTCCCCCGATACGTGAAGGCGCGCCGCTGGTGGAAGGGCTTGTGTTGAACCTCATCAGCCTGATGCTCTTTGGGGCCAATCTTTTAAATCGGGGAGAGTACGCTCGCGCCTGGGCTTTGCTCAGCAAAGCACATGAAAACCTACTCAAGCTGGTTCGACTCCACGAAGGGGCAACAGACCACTGGCCGACACCTTCACGCGCGCTCGAAAAGGATATCTCGGAGGACTCGTATAATCGCTATCTGGCATGCACAAGCAGTGCAGAACCAAGAGCACTATGTGCAGCCTATCATCAAACGTGGACGTGGAGTCTCGAATTGTTCAAGAGCGTGACAGAACCTCTGAATATCGAGCTTCCGAGAACTGTAATTGCGCAGGCAAAAAGGTTGCTCAATGAGTCTGCGACGCCGCACAACAAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35767","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Stanley","NCBI_taxonomy_id":"192953"}}}},"ARO_accession":"3002879","ARO_id":"39313","ARO_name":"linG","ARO_description":"linG is an integron-associated gene cassette, with aadA2, encoding a lincosomide nucleotidyltransferase found in Salmonella enterica. linG confers resistance to lincosomide antibiotics.","ARO_category":{"36360":{"category_aro_accession":"3000221","category_aro_cvterm_id":"36360","category_aro_name":"lincosamide nucleotidyltransferase (LNU)","category_aro_description":"Resistance to the lincosamide antibiotic by ATP-dependent modification of the 3' and\/or 4'-hydroxyl groups of the methylthiolincosamide sugar.","category_aro_class_name":"AMR Gene Family"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1874":{"model_id":"1874","model_name":"OXA-196","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"802":{"protein_sequence":{"accession":"AEB98922.1","sequence":"MNIQALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDHARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWVVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"HQ425494","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAACATTCAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCATGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGGTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36949","NCBI_taxonomy_name":"Acinetobacter nosocomialis","NCBI_taxonomy_id":"106654"}}}},"ARO_accession":"3001481","ARO_id":"37881","ARO_name":"OXA-196","ARO_description":"OXA-196 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1875":{"model_id":"1875","model_name":"MIR-11","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"1182":{"protein_sequence":{"accession":"AIT76112.1","sequence":"MMTKSLSCALLLSVTSSAFAAPMSEKQLAEVVERTVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEIALGDPVAKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDTASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEEAHYAWGYREGKAVHVSPGMLDAEAYGVKTNVKDMASWLIANMKPDSLQAPSLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"KM087859","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGACAAAATCCCTAAGCTGTGCCCTGCTGCTCAGCGTCACCAGCTCTGCATTCGCCGCACCGATGTCCGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTAATTTATCAGGGTCAGCCACACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGCGGCGATGCCATTGCCCGAGGTGAAATAGCGCTGGGCGATCCGGTAGCAAAATACTGGCCTGAGCTCACGGGCAAACAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTATACCGCAGGCGGTCTGCCGTTACAGGTGCCGGATGAGGTCACGGATACCGCTTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCTAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTTAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAACCCCTCAAGCTGGACCATACCTGGATTAACGTCCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGAGGGTAAAGCGGTCCACGTTTCGCCAGGGATGCTGGACGCGGAAGCCTATGGCGTAAAAACTAACGTGAAGGATATGGCGAGCTGGCTGATAGCCAACATGAAGCCGGATTCTCTTCAGGCTCCCTCACTCAAGCAAGGCATTGCTCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCCATGTATCAGGGGTTGGGCTGGGAGATGCTCAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCATTGCCCGTGGCAGAAGTGAATCCACCCGCGCCGCCGGTCAAGGCCTCCTGGGTCCATAAAACAGGCTCGACGGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3002176","ARO_id":"38576","ARO_name":"MIR-11","ARO_description":"MIR-11 is a beta-lactamase. From the Lahey list of MIR beta-lactamases.","ARO_category":{"36197":{"category_aro_accession":"3000058","category_aro_cvterm_id":"36197","category_aro_name":"MIR beta-lactamase","category_aro_description":"MIR beta-lactamases are plasmid-mediated beta-lactamases that confer resistance to oxyimino- and alpha-methoxy beta-lactams","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1876":{"model_id":"1876","model_name":"LEN-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1038":{"protein_sequence":{"accession":"CAG25836.1","sequence":"ATLPLAVDAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGVEQLDRRIHYRQQDLVDYSPVSEKHLTDGMTIGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPPGWFIADKTGAGERGARGIVALLGPDGKPERIVVIYLRDTPASMAERNQHIAG"},"dna_sequence":{"accession":"AJ635425","fmin":"0","fmax":"789","strand":"+","sequence":"GCCACCCTGCCACTGGCGGTAGACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCAGGGGTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTACCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCGCTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGCCGGGCTGGTTTATCGCCGACAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002457","ARO_id":"38857","ARO_name":"LEN-7","ARO_description":"LEN-7 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1877":{"model_id":"1877","model_name":"CMY-12","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1421":{"protein_sequence":{"accession":"CAA76382.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYSNSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYARGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKNYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"Y16785","fmin":"0","fmax":"1143","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACTCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCCGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAACTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTACAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3002023","ARO_id":"38423","ARO_name":"CMY-12","ARO_description":"CMY-12 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1878":{"model_id":"1878","model_name":"SRT-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"725"}},"model_sequences":{"sequence":{"1794":{"protein_sequence":{"accession":"AAS07017.3","sequence":"MTKMNRLAAALIAALILPTAQAAQQQDIDAVIQPLMKKYGVPGMAIAVSVDGKQQIYPYGVASKQTGKPITEETLFEVGSLSKTFTATLAVYAQQQGKLSFNDPASRYLPELRGSAFDGVSLLNLATHTSGLPLFVPDDVTNDAQLMAYYRAWQPKHPAGSYRVYSNLGIGMLGMIAAKSLDQPFIQAMEQGMLPALGMSHTYVQVPAAQMANYAQGYSKDDKPVRVNPGPLDAESYGIKSNARDLIRYLDANLQQVKVAQPWRDALAATHVGYYKAGAFTQDLMWENYPYPVKLSRLIEGNNAGMIMNGTPATAITPPQPELRAGWYNKTGSTGGFSTYAVFIPAKNIAVVMLANKWFPNDDRVEAAYHIVQALEKR"},"dna_sequence":{"accession":"AY524276","fmin":"0","fmax":"1137","strand":"+","sequence":"ATGACGAAAATGAACCGCCTGGCGGCCGCGCTGATCGCCGCACTGATCTTGCCGACCGCGCAGGCCGCGCAGCAGCAGGATATCGACGCCGTTATTCAGCCGCTGATGAAAAAATATGGCGTACCGGGCATGGCGATCGCCGTGTCGGTCGACGGCAAACAGCAGATTTACCCGTATGGCGTCGCCTCGAAGCAGACCGGCAAACCGATCACCGAGGAGACGCTGTTCGAAGTGGGCTCGCTGAGCAAAACCTTTACCGCGACGCTGGCGGTCTATGCGCAGCAGCAGGGCAAGCTGTCGTTCAACGATCCGGCCAGCCGCTATCTGCCCGAGCTGCGCGGCAGCGCCTTCGACGGCGTCAGCCTGCTGAATCTGGCGACGCATACCTCCGGCCTGCCGCTGTTCGTGCCGGACGACGTCACTAACGACGCCCAGCTGATGGCCTACTACCGGGCCTGGCAGCCGAAACACCCGGCGGGCAGCTACCGTGTCTATTCCAACCTCGGCATCGGCATGCTGGGCATGATCGCCGCCAAGAGCCTCGACCAGCCGTTTATCCAGGCGATGGAACAGGGGATGCTGCCGGCGCTGGGCATGAGCCACACCTACGTTCAGGTGCCGGCGGCGCAGATGGCTAACTATGCGCAGGGTTACAGCAAGGACGATAAGCCGGTGCGGGTCAACCCCGGCCCGCTGGATGCCGAGTCTTACGGCATCAAGTCCAACGCTCGCGATCTGATTCGCTATCTGGACGCCAACCTGCAGCAGGTGAAGGTGGCGCAGCCGTGGCGCGACGCGCTGGCCGCGACGCACGTCGGGTATTACAAGGCGGGCGCGTTCACGCAGGATCTGATGTGGGAGAACTACCCGTATCCGGTGAAACTGTCGCGTTTGATTGAAGGCAACAACGCCGGGATGATCATGAACGGCACGCCGGCCACCGCCATCACGCCGCCGCAGCCGGAATTGCGCGCCGGCTGGTATAACAAAACCGGCTCCACCGGCGGCTTCTCCACCTACGCGGTATTTATCCCGGCGAAAAATATCGCCGTGGTGATGCTGGCCAACAAGTGGTTCCCGAACGACGATCGCGTCGAGGCGGCTTACCACATCGTCCAGGCGCTGGAGAAGCGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36783","NCBI_taxonomy_name":"Serratia marcescens","NCBI_taxonomy_id":"615"}}}},"ARO_accession":"3002494","ARO_id":"38894","ARO_name":"SRT-2","ARO_description":"SRT-2, isolated from Serratia marcescens, is a chromosomal beta-lactamase that confers resistance to cefotaxime","ARO_category":{"36234":{"category_aro_accession":"3000095","category_aro_cvterm_id":"36234","category_aro_name":"SRT beta-lactamase","category_aro_description":"SRT beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1879":{"model_id":"1879","model_name":"AAC(3)-IIIa","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6":{"protein_sequence":{"accession":"CAA39184.1","sequence":"MTDLNIPHTHAHLVDAFQALGIRAGQALMLHASVKAVGAVMGGPNVILQALMDALTPDGTLMMYAGWQDIPDFIDSLPDALKAVYLEQHPPFDPATARAVRENSVLAEFLRTWPCVHRSANPEASMVAVGRQAALLTANHALDYGYGVESPLAKLVAIEGYVLMLGAPLDTITLLHHAEYLAKMRHKNVVRYPCPILRDGRKVWVTVEDYDTGDPHDDYSFEQIARDYVAQGGGTRGKVGDADAYLFAAQDLTRFAVQWLESRFGDSASYG"},"dna_sequence":{"accession":"X55652","fmin":"1123","fmax":"1939","strand":"+","sequence":"ATGACCGATTTGAATATCCCGCATACACACGCGCACCTTGTAGACGCATTTCAGGCGCTCGGCATCCGCGCGGGGCAGGCGCTCATGCTGCACGCATCCGTTAAAGCAGTGGGCGCGGTGATGGGCGGCCCCAATGTGATCTTGCAGGCGCTCATGGATGCGCTCACGCCCGACGGCACGCTGATGATGTATGCGGGATGGCAAGACATCCCCGACTTTATCGACTCGCTGCCGGACGCGCTCAAGGCCGTGTATCTTGAGCAGCACCCACCCTTTGACCCCGCCACCGCCCGCGCCGTGCGCGAAAACAGCGTGCTAGCGGAATTTTTGCGCACATGGCCGTGCGTGCATCGCAGCGCAAACCCCGAAGCCTCTATGGTGGCGGTAGGCAGGCAGGCCGCTTTGCTGACCGCTAATCACGCGCTGGATTATGGCTACGGAGTCGAGTCGCCGCTGGCTAAACTGGTGGCAATAGAAGGATACGTGCTGATGCTTGGCGCGCCGCTGGATACCATCACACTGCTGCACCACGCGGAATATCTGGCCAAGATGCGCCACAAGAACGTGGTCCGCTACCCGTGCCCGATTCTGCGGGACGGGCGCAAAGTGTGGGTGACCGTTGAGGACTATGACACCGGTGATCCGCACGACGATTATAGTTTTGAGCAAATCGCGCGCGATTATGTGGCGCAGGGCGGCGGCACACGCGGCAAAGTCGGTGATGCGGATGCTTACCTGTTCGCCGCGCAGGACCTCACACGGTTTGCGGTGCAGTGGCTTGAATCACGGTTCGGTGACTCAGCGTCATACGGATAGG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002536","ARO_id":"38936","ARO_name":"AAC(3)-IIIa","ARO_description":"AAC(3)-IIIa is a chromosomal-encoded aminoglycoside acetyltransferase in P. aeruginosa","ARO_category":{"36461":{"category_aro_accession":"3000322","category_aro_cvterm_id":"36461","category_aro_name":"AAC(3)","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 3.","category_aro_class_name":"AMR Gene Family"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1880":{"model_id":"1880","model_name":"adeN","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"420"}},"model_sequences":{"sequence":{"569":{"protein_sequence":{"accession":"AGV28567.1","sequence":"MHDPVLESHHLVCEKPQTRRGIERRLALLLSATELFLEKGYDAVSLDDIVNHAGGSKTSIYKYFGNKDGLFTAICDYRREMFFKDICIAFQPEQTSLKDYLIQTLIRFYKPFIQPEHIAFLRLVIEQTQCNATLSQYLYEKCALDVQNTIAQALLISHQSGEITCTSPDHSSLMYFGILRDIEWRMIMGMPLPPNETEVIDYINYCVDIFLKGHHKV"},"dna_sequence":{"accession":"KF147862","fmin":"0","fmax":"654","strand":"+","sequence":"ATGCATGATCCAGTCCTTGAGTCACATCATCTCGTATGTGAAAAACCCCAAACACGCCGCGGTATAGAACGTCGTTTAGCTCTATTGCTAAGCGCAACCGAGCTGTTTTTGGAAAAAGGATATGATGCTGTCTCTCTTGACGACATCGTTAATCATGCTGGTGGTTCAAAAACCTCTATTTATAAATACTTCGGTAATAAAGATGGCTTATTTACTGCAATCTGCGATTATCGCCGTGAAATGTTTTTTAAAGATATCTGCATTGCATTTCAACCAGAGCAAACTTCTTTAAAAGATTATTTAATCCAAACTCTCATCCGTTTTTATAAGCCCTTTATTCAACCTGAACACATTGCCTTTTTACGTTTGGTTATTGAACAAACTCAATGTAATGCAACTTTGAGCCAATACTTATATGAAAAATGTGCTCTGGATGTCCAAAATACAATTGCTCAAGCCTTACTCATATCTCATCAATCAGGTGAAATTACCTGTACATCTCCTGATCATTCCTCTCTTATGTATTTTGGAATTTTACGTGATATTGAATGGCGAATGATTATGGGAATGCCTCTCCCACCCAATGAGACAGAAGTTATTGATTATATTAATTATTGTGTTGATATTTTCTTAAAGGGGCATCATAAAGTCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3000559","ARO_id":"36698","ARO_name":"adeN","ARO_description":"AdeN is a repressor of AdeIJK, a RND-type efflux pump in Acinetobacter baumannii. Its inactivation increases expression of AdeJ.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36309":{"category_aro_accession":"3000170","category_aro_cvterm_id":"36309","category_aro_name":"imipenem","category_aro_description":"Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"40523":{"category_aro_accession":"3003832","category_aro_cvterm_id":"40523","category_aro_name":"ticarcillin","category_aro_description":"Ticarcillin is a carboxypenicillin used for the treatment of Gram-negative bacteria, particularly P. aeruginosa. Ticarcillin's antibiotic properties arise from its ability to prevent cross-linking of peptidoglycan during cell wall synthesis, when the bacteria try to divide, causing cell death.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1881":{"model_id":"1881","model_name":"OXA-72","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1138":{"protein_sequence":{"accession":"ABP87779.2","sequence":"MKKFILPIFSISILVSLSACSSIKTKSEDNFHISSQQHEKAIKSYFDEAQTQGVIIIKEGKNLSTYGNALARANKEYVPASTFKMLNALIGLENHKATTNEIFKWDGKKRTYPMWEKDMTLGEAMALSAVPVYQELARRTGLELMQKEVKRVNFGNTNIGTQVDNFWLVGPLKITPVQEVNFADDLAHNRLPFKLETQEEVKKMLLIKEVNGSKIYAKSGWGMDVTPQVGWLTGWVEQANGKKIPFSLNLEMKEGMSGSIRNEITYKSLENLGII"},"dna_sequence":{"accession":"EF534256","fmin":"0","fmax":"827","strand":"+","sequence":"ATGAAAAAATTTATACTTCCTATATTCAGCATTTCTATTCTAGTTTCTCTCAGTGCATGTTCATCTATTAAAACTAAATCTGAAGATAATTTTCATATTTCTTCTCAGCAACATGAAAAAGCTATTAAAAGCTATTTTGATGAAGCTCAAACACAGGGTGTAATTATTATTAAAGAGGGTAAAAATCTTAGCACCTATGGTAATGCTCTTGCACGAGCAAATAAAGAATATGTCCCTGCATCAACATTTAAGATGCTAAATGCTTTAATCGGGCTAGAAAATCATAAAGCAACAACAAATGAGATTTTCAAATGGGATGGTAAAAAAAGAACTTATCCTATGTGGGAGAAAGATATGACTTTAGGTGAGGCAATGGCATTGTCAGCAGTTCCAGTATATCAAGAGCTTGCAAGACGGACTGGCCTAGAGCTAATGCAGAAAGAAGTAAAGCGGGTTAATTTTGGAAATACAAATATTGGAACACAGGTCGATAATTTTTGGTTAGTTGGCCCCCTTAAAATTACACCAGTACAAGAAGTTAATTTTGCCGATGACCTTGCACATAACCGATTACCTTTTAAATTAGAAACTCAAGAAGAAGTTAAAAAAATGCTTCTAATTAAAGAAGTAAATGGTAGTAAGATTTATGCAAAAAGTGGATGGGGAATGGATGTTACTCCACAGGTAGGTTGGTTGACTGGTTGGGTGGAGCAAGCTAATGGAAAAAAAATCCCCTTTTCGCTCAACTTAGAAATGAAAGAAGGAATGTCTGGTTCTATTCGTAATGAAATTACTTATAAGTCGCTAGAAAATCTTGGAATCATTTA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001705","ARO_id":"38105","ARO_name":"OXA-72","ARO_description":"OXA-72 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1882":{"model_id":"1882","model_name":"OXA-80","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1768":{"protein_sequence":{"accession":"ABV71247.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAILVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"EU019535","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCTAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001634","ARO_id":"38034","ARO_name":"OXA-80","ARO_description":"OXA-80 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1883":{"model_id":"1883","model_name":"DHA-10","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"2110":{"protein_sequence":{"accession":"AJO16043.1","sequence":"MKKSLSATLISALLAFSAPGFSAADNVAAVVDSTIKPLMAQQDIPGMAVAVSVKGKPYYFNYGFADVQAKQPVTENTLFELGSVSKTFTGVLGAVSVAKKEMTLNDPAEKYQPELALPQWKGITLLDLATYTAGGLPLQVPDEVKSRADLLHFYQQWQPSRKPGDMRLYANSSIGLFGALTANAAGMPYEQLLTARILAPLGLSHTFITVPESAQSQYAYGYKNKKPVRVSPGQLDAESYGVKSASKDMLRWAEMNMEPSRAGNADLEMAMYLAQTRYYKTAAINQGLGWEMYDWPQQKDMIINGVTNEVALQPHPVTDNQVQPYNRASWVHKTGATTGFGAYVAFIPEKQVAIVILANKNYPNTERVKAAQAILSALE"},"dna_sequence":{"accession":"KP050490","fmin":"0","fmax":"1140","strand":"+","sequence":"ATGAAAAAATCGTTATCTGCAACACTGATTTCTGCCCTGCTGGCGTTTTCCGCCCCGGGGTTTTCTGCCGCTGATAATGTCGCGGCGGTGGTGGACAGCACCATTAAACCGCTGATGGCACAGCAGGATATTCCCGGGATGGCGGTTGCTGTCTCTGTAAAGGGTAAGCCCTATTATTTCAATTACGGTTTTGCCGATGTTCAGGCAAAACAGCCGGTCACTGAAAATACACTATTTGAGCTCGGATCTGTAAGTAAAACTTTCACAGGTGTGCTGGGTGCGGTTTCTGTGGCGAAAAAAGAGATGACGCTGAATGACCCGGCGGAAAAATACCAGCCGGAGCTGGCTCTGCCGCAGTGGAAAGGGATCACGCTGCTGGATCTGGCCACCTACACCGCAGGCGGGCTGCCGTTACAGGTACCGGATGAGGTGAAAAGCCGTGCGGATCTGCTGCATTTCTATCAGCAGTGGCAGCCGTCCCGGAAACCGGGCGATATGCGTCTGTATGCAAACAGCAGTATCGGCCTGTTTGGTGCTCTGACCGCCAACGCAGCGGGGATGCCGTATGAGCAGTTGCTGACCGCGCGGATCCTGGCACCGCTGGGGTTATCTCACACCTTTATTACCGTGCCGGAAAGTGCGCAAAGCCAGTATGCGTACGGTTATAAAAACAAAAAACCGGTCCGCGTGTCGCCGGGACAGCTTGATGCGGAATCTTACGGCGTGAAATCCGCCTCAAAAGATATGCTGCGCTGGGCAGAAATGAATATGGAGCCGTCACGGGCCGGTAATGCGGATCTGGAAATGGCAATGTATCTCGCCCAGACCCGCTACTATAAAACTGCCGCGATTAATCAGGGGCTGGGCTGGGAAATGTATGACTGGCCGCAGCAGAAAGATATGATCATTAACGGCGTGACCAACGAGGTCGCATTGCAGCCGCACCCGGTAACAGACAACCAGGTTCAGCCGTATAACCGCGCTTCCTGGGTGCATAAAACGGGGGCAACAACTGGTTTCGGCGCCTATGTGGCCTTTATTCCGGAAAAACAGGTGGCGATTGTGATTCTGGCGAATAAAAACTACCCGAATACCGAAAGAGTCAAAGCCGCACAGGCTATTTTGAGTGCACTGGAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36917","NCBI_taxonomy_name":"Morganella morganii","NCBI_taxonomy_id":"582"}}}},"ARO_accession":"3002141","ARO_id":"38541","ARO_name":"DHA-10","ARO_description":"DHA-10 is a beta-lactamase. From the Lahey list of DHA beta-lactamases.","ARO_category":{"36207":{"category_aro_accession":"3000068","category_aro_cvterm_id":"36207","category_aro_name":"DHA beta-lactamase","category_aro_description":"DHA beta-lactamases are plasmid-mediated AmpC \u03b2-lactamases that confer resistance to cephamycins and oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1884":{"model_id":"1884","model_name":"CTX-M-111","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1740":{"protein_sequence":{"accession":"AEM44649.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGQGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"JF274243","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCAGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36953","NCBI_taxonomy_name":"Shigella sp. SH202","NCBI_taxonomy_id":"1074432"}}}},"ARO_accession":"3001971","ARO_id":"38371","ARO_name":"CTX-M-111","ARO_description":"CTX-M-111 is a beta-lactamase found in Shigella spp.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1886":{"model_id":"1886","model_name":"LEN-24","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1977":{"protein_sequence":{"accession":"CAP12352.2","sequence":"MRYVRLCVISLLANLPLAVDAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGLEQLDRRIHYRQQDLVDYSPVSEKHLVDGMTIGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPPGWFIADKTGAGERGARGIVALLGPDGKPERIVVIYLRDTPASMAERNQHIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM850914","fmin":"30","fmax":"891","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCAACCTGCCACTGGCGGTAGACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGTCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGCCGGGCTGGTTTATCGCCGACAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002471","ARO_id":"38871","ARO_name":"LEN-24","ARO_description":"LEN-24 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1887":{"model_id":"1887","model_name":"TEM-70","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1496":{"protein_sequence":{"accession":"AAF01046.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASQQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AF188199","fmin":"214","fmax":"1075","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCAGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000936","ARO_id":"37316","ARO_name":"TEM-70","ARO_description":"TEM-70 is a beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1888":{"model_id":"1888","model_name":"MIR-10","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"1102":{"protein_sequence":{"accession":"AIT76111.1","sequence":"MMTKSLSCALLLSVASSAFAAPMSEKQLAEVVERTVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEIALGDPVAKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDTASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEEAHYAWGYREGKAVHVSPGMLDAEAYGVKTNVKDMASWVIANMKPDSLQAPSLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"KM087858","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGACAAAATCCCTAAGCTGTGCCCTGCTGCTCAGCGTCGCCAGCTCTGCATTCGCCGCACCGATGTCCGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTAATTTATCAGGGTCAGCCACACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGCGGCGATGCCATTGCCCGGGGTGAAATAGCGCTGGGCGATCCGGTAGCAAAATACTGGCCTGAGCTCACGGGCAAGCAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTATACCGCAGGCGGTCTGCCGTTACAGGTGCCGGATGAGGTCACGGATACCGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGTACCACGCGTCTTTACGCTAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAACCCCTCAAGCTGGACCATACCTGGATTAACGTCCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGAGGGTAAAGCGGTCCACGTTTCGCCAGGGATGCTGGACGCGGAAGCCTATGGCGTAAAAACTAACGTGAAGGATATGGCGAGCTGGGTGATAGCCAACATGAAGCCGGATTCTCTTCAGGCTCCCTCACTCAAGCAAGGCATTGCTCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCTATGTATCAGGGGTTAGGCTGGGAGATGCTCAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCATTGCCCGTGGCAGAAGTGAATCCACCCGCGCCGCCGGTCAAGGCCTCCTGGGTCCATAAAACAGGCTCGACGGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36926","NCBI_taxonomy_name":"Enterobacter asburiae","NCBI_taxonomy_id":"61645"}}}},"ARO_accession":"3002175","ARO_id":"38575","ARO_name":"MIR-10","ARO_description":"MIR-10 is a beta-lactamase. From the Lahey list of MIR beta-lactamases.","ARO_category":{"36197":{"category_aro_accession":"3000058","category_aro_cvterm_id":"36197","category_aro_name":"MIR beta-lactamase","category_aro_description":"MIR beta-lactamases are plasmid-mediated beta-lactamases that confer resistance to oxyimino- and alpha-methoxy beta-lactams","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1889":{"model_id":"1889","model_name":"NDM-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"939":{"protein_sequence":{"accession":"AFB82585.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGLVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"JQ348841","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGCTGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002355","ARO_id":"38755","ARO_name":"NDM-4","ARO_description":"NDM-4 is a beta-lactamase found in Escherichia coli","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"40523":{"category_aro_accession":"3003832","category_aro_cvterm_id":"40523","category_aro_name":"ticarcillin","category_aro_description":"Ticarcillin is a carboxypenicillin used for the treatment of Gram-negative bacteria, particularly P. aeruginosa. Ticarcillin's antibiotic properties arise from its ability to prevent cross-linking of peptidoglycan during cell wall synthesis, when the bacteria try to divide, causing cell death.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1890":{"model_id":"1890","model_name":"TEM-86","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1497":{"protein_sequence":{"accession":"CAC43230.1","sequence":"MSIQHFRVALIPFFAAFCFPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGTGKRGSRGIIAALGPDGKPSRIVVIYMTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AJ277415","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCTTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAACCGGTAAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACATGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000953","ARO_id":"37333","ARO_name":"TEM-86","ARO_description":"TEM-86 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1891":{"model_id":"1891","model_name":"AAC(6')-Iih","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"250":{"protein_sequence":{"accession":"CAE50926.1","sequence":"MIISEFDRDNLVLRDQLADLLRLTWPDEYGEQPMKEVERLLEDERIAVSAIEGDELIGFVGAIPQYGQTGWELHPLVVESMYRKQQVGTRLVSYLEKEIASQGGIVVYLGTDDVEGQTSLAIEEDLFEDTFDKLETIQNRKDHPYEFYEKLGYQIVGVIPDANGWNKPDIWMAKRIARKHGSE"},"dna_sequence":{"accession":"AJ584701","fmin":"10","fmax":"562","strand":"+","sequence":"ATGATTATCAGTGAGTTTGATCGTGATAATTTGGTTTTACGTGACCAATTAGCCGATCTTTTGAGATTGACTTGGCCAGATGAATACGGTGAACAGCCGATGAAAGAAGTAGAGCGACTGCTGGAAGATGAAAGGATCGCCGTCTCTGCAATCGAAGGAGATGAGCTGATTGGTTTTGTCGGTGCGATTCCACAATATGGTCAAACTGGTTGGGAACTGCATCCCTTAGTCGTCGAAAGTATGTACCGTAAGCAACAAGTTGGTACACGCCTAGTGAGTTATCTAGAAAAAGAGATTGCCTCACAAGGAGGAATCGTTGTCTATTTAGGAACTGATGATGTGGAAGGGCAAACAAGCTTGGCGATTGAAGAAGACCTGTTTGAAGATACCTTTGACAAGCTTGAAACGATTCAAAACAGGAAAGATCATCCTTATGAATTCTATGAGAAACTTGGCTATCAGATCGTTGGGGTAATTCCGGATGCGAATGGCTGGAACAAGCCAGATATTTGGATGGCCAAACGAATTGCTAGAAAACATGGAAGTGAATGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39522","NCBI_taxonomy_name":"Enterococcus durans","NCBI_taxonomy_id":"53345"}}}},"ARO_accession":"3002590","ARO_id":"38990","ARO_name":"AAC(6')-Iih","ARO_description":"AAC(6')-Iih is a chromosomal-encoded aminoglycoside acetyltransferase in Enterococcus hirae","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1892":{"model_id":"1892","model_name":"OXA-114a","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1921":{"protein_sequence":{"accession":"ABX38721.1","sequence":"MTVRRLSCALGAALSLSALGGGPVQAAVLCTVVADAADGRILFQQGTQQACAERYTPASTFKLAIALMGADAGILQGPHEPVWNYQPAYPDWGGDAWRQPTDPARWIKYSVVWYSQLTAKALGQDRFQRYTSAFGYGNADVSGEPGKHNGTDGAWIISSLRISPLEQLAFLRKLVNRQLPVKAAAYELAENLFEAGQADGWRLYGKTGTGSPGSNGVYTAANAYGWFVGWARKDGRQLVYARLLQDERATRPNAGLRARDELVRDWPAMAGAWRP"},"dna_sequence":{"accession":"EU188842","fmin":"0","fmax":"828","strand":"+","sequence":"ATGACCGTTCGACGCCTTTCGTGCGCCCTTGGCGCAGCCCTTTCCCTGTCCGCGCTGGGCGGCGGCCCCGTCCAGGCCGCCGTCCTGTGCACCGTGGTGGCCGACGCCGCCGACGGCCGCATCCTGTTCCAGCAAGGCACGCAGCAGGCCTGCGCCGAGCGCTACACGCCGGCCTCGACCTTCAAGCTGGCCATCGCCCTGATGGGCGCCGACGCCGGCATCCTGCAAGGCCCGCACGAGCCGGTCTGGAACTACCAGCCCGCCTATCCCGACTGGGGCGGCGACGCCTGGCGCCAGCCCACCGATCCGGCGCGCTGGATCAAGTATTCGGTGGTCTGGTATTCACAGCTGACGGCCAAGGCGCTGGGACAGGACCGCTTCCAGCGCTACACCAGCGCGTTCGGCTACGGCAATGCGGACGTCTCGGGCGAGCCCGGCAAGCACAACGGCACCGACGGCGCGTGGATCATCTCGTCGCTGCGCATTTCGCCGCTGGAACAACTGGCTTTCCTGCGCAAGCTGGTGAATCGGCAATTGCCGGTCAAGGCCGCCGCCTATGAGCTTGCCGAAAACCTCTTCGAGGCGGGCCAGGCCGATGGCTGGCGCCTGTATGGCAAGACCGGCACCGGGTCGCCCGGCAGCAACGGCGTCTACACGGCGGCCAATGCCTACGGTTGGTTCGTCGGCTGGGCGCGCAAGGATGGCCGCCAGCTGGTGTACGCCCGCCTGCTGCAGGATGAGCGCGCCACCCGACCCAACGCCGGCCTGCGCGCCCGCGACGAGCTGGTGCGCGACTGGCCGGCCATGGCCGGCGCGTGGCGCCCGTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36941","NCBI_taxonomy_name":"Achromobacter xylosoxidans","NCBI_taxonomy_id":"85698"}}}},"ARO_accession":"3001609","ARO_id":"38009","ARO_name":"OXA-114a","ARO_description":"OXA-114a is a beta-lactamase found in Achromobacter xylosoxidans.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1893":{"model_id":"1893","model_name":"SHV-127","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"828":{"protein_sequence":{"accession":"ACV32637.1","sequence":"MRFIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNNAERMVVIYLRDTPASMAERNQ"},"dna_sequence":{"accession":"GQ390809","fmin":"0","fmax":"813","strand":"+","sequence":"ATGCGTTTTATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAATGCAGAGCGCATGGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001174","ARO_id":"37554","ARO_name":"SHV-127","ARO_description":"SHV-127 is a beta-lactamase that has been found in clinical isolates.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1895":{"model_id":"1895","model_name":"CfxA3","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"1514":{"protein_sequence":{"accession":"AAL79549.2","sequence":"MEKNRKKQIVVLSIALVCIFILVFSLFHKSATKDSANPPLTNVLTDSISQIVSACPGEIGVAVIVNNRDTVKVNNKSVYPMMSVFKVHQALALCNDFDNKGISLDTLVNINRDKLDPKTWSPMLKDYSGPVISLTVRDLLRYTLTQSDNNASNLMFKDMVNVAQTDSFIATLIPRSSFQIAYTEEEMSADHNKAYSNYTSPLGAAMLMNRLFTEGLIDDEKQSFIKNTLKECKTGVDRIAAPLLDKEGVVIAHKTGSGDVNENGVLAAHNDVAYICLPNNISYTLAVFVKDFKGNESQASQYVAHISAVVYSLLMQTSVKS"},"dna_sequence":{"accession":"AF472622","fmin":"52","fmax":"1018","strand":"+","sequence":"ATGGAAAAAAACAGAAAAAAACAAATCGTAGTTTTGAGTATAGCTTTAGTTTGCATTTTCATCTTGGTATTTTCATTGTTCCATAAATCAGCGACAAAAGATAGCGCAAATCCTCCTTTAACAAATGTTTTGACTGATAGCATTTCTCAAATTGTCTCAGCTTGTCCTGGCGAAATTGGTGTGGCGGTTATTGTTAATAACAGAGATACGGTTAAGGTCAATAATAAGAGTGTTTATCCTATGATGAGTGTGTTTAAGGTTCATCAGGCATTAGCTCTTTGTAATGACTTTGACAATAAAGGAATTTCACTTGATACCTTAGTAAATATAAATAGGGATAAACTTGACCCAAAGACTTGGAGTCCTATGCTGAAAGATTATTCAGGGCCAGTCATATCATTGACAGTGAGAGATTTGCTGCGTTATACTCTTACTCAGAGTGACAACAATGCAAGCAACCTTATGTTTAAGGATATGGTTAATGTCGCTCAAACAGATAGTTTTATAGCCACACTCATTCCTCGTTCAAGTTTTCAGATAGCTTATACGGAAGAGGAAATGTCGGCTGACCATAACAAGGCTTACTCTAACTATACATCTCCTCTTGGTGCTGCAATGTTGATGAATCGTTTGTTTACTGAAGGTCTTATCGATGATGAGAAACAAAGTTTCATTAAGAATACGTTAAAAGAATGCAAAACAGGTGTAGATAGGATAGCAGCTCCACTTCTTGATAAAGAAGGGGTTGTTATAGCGCATAAGACAGGTTCAGGTGATGTTAATGAAAATGGTGTTCTTGCAGCTCACAATGATGTTGCCTATATATGTCTGCCTAATAATATCAGTTATACCTTAGCGGTATTTGTTAAGGATTTCAAGGGAAATGAATCACAAGCGTCACAATATGTTGCGCATATATCAGCTGTAGTATATTCTTTATTAATGCAAACTTCAGTAAAATCTTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36958","NCBI_taxonomy_name":"Capnocytophaga ochracea","NCBI_taxonomy_id":"1018"}}}},"ARO_accession":"3003003","ARO_id":"39437","ARO_name":"CfxA3","ARO_description":"cfxA3 beta-lactamase is a class A beta-lactamase found in Capnocytophaga ochracea","ARO_category":{"39434":{"category_aro_accession":"3003000","category_aro_cvterm_id":"39434","category_aro_name":"CfxA beta-lactamase","category_aro_description":"cfxA beta-lactamases are class A beta-lactamases","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1896":{"model_id":"1896","model_name":"NDM-12","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1829":{"protein_sequence":{"accession":"BAO79439.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGLVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLDDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"AB926431","fmin":"510","fmax":"1323","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGCTGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGATGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002362","ARO_id":"38762","ARO_name":"NDM-12","ARO_description":"NDM-12 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1898":{"model_id":"1898","model_name":"OXA-379","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1764":{"protein_sequence":{"accession":"AHL30279.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSTSKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRIGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWEWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KF986260","fmin":"20","fmax":"845","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGTTCACCTTATATAGTGACTGCTAATCCAAATCACAGCACTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTATTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGAATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001565","ARO_id":"37965","ARO_name":"OXA-379","ARO_description":"OXA-379 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1899":{"model_id":"1899","model_name":"vanYF","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"380":{"protein_sequence":{"accession":"AAF36805.1","sequence":"MKKWGLLLVFALFLVFIFNILPISQDKVEDRIYEQNDKDTSDDKMTAENMQKIELTEEQIYQGNLLLVNNEHPVHQKSIKSDIINLFTHKELTKGYGLLDNEIKLSEEIAGKFSEMIAAAEEDGVSNFLISSGYRDLDEQSRLYEEMGSDFALPAGHSEHNLGLSLDVGSTQMKMDKAPEGKWIEKNCWEYGFILRYPLDKTDVTGIQYEPWHIRYVGLPHSAIMQEMNLALEEYLDYLKEEKSISVRVDGKKYTISYDPISQNETIEVEVPADEQYEISGNNIDGVIVTTFS"},"dna_sequence":{"accession":"AF155139","fmin":"3396","fmax":"4278","strand":"+","sequence":"ATGAAAAAGTGGGGACTTTTATTGGTTTTTGCATTATTTCTAGTATTTATTTTTAATATATTACCGATATCCCAAGATAAAGTAGAGGATCGAATATATGAACAAAATGACAAAGATACATCGGATGATAAAATGACAGCTGAAAATATGCAAAAGATTGAGCTTACGGAAGAGCAGATCTATCAAGGGAATCTACTCTTGGTCAACAATGAACATCCTGTTCACCAAAAGAGTATAAAATCGGATATTATAAATTTATTTACGCACAAAGAATTGACAAAGGGGTATGGGTTACTTGATAACGAAATTAAATTGTCAGAGGAAATAGCTGGGAAATTTTCAGAGATGATAGCTGCGGCTGAAGAGGATGGCGTTAGTAATTTTTTAATTAGCAGTGGTTATCGAGACTTGGATGAGCAAAGCAGACTTTATGAGGAAATGGGTTCTGATTTTGCTTTGCCAGCAGGTCATAGTGAACACAACTTGGGGTTATCGCTTGATGTAGGATCTACTCAAATGAAGATGGATAAAGCGCCTGAAGGAAAGTGGATAGAAAAAAATTGTTGGGAATACGGCTTTATATTACGCTATCCCTTGGATAAAACGGATGTTACAGGAATTCAATATGAACCTTGGCATATTCGCTATGTCGGTTTGCCTCACAGTGCGATTATGCAGGAAATGAATTTAGCTTTGGAAGAATATTTAGATTATTTAAAAGAAGAAAAGAGCATTTCTGTTCGTGTTGATGGGAAAAAATATACAATTTCATATGATCCCATTTCTCAAAACGAGACAATTGAAGTTGAAGTACCAGCGGATGAACAGTATGAAATATCTGGTAATAATATTGATGGAGTAATTGTGACCACATTTTCTTGAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39542","NCBI_taxonomy_name":"Paenibacillus popilliae ATCC 14706","NCBI_taxonomy_id":"1212764"}}}},"ARO_accession":"3002958","ARO_id":"39392","ARO_name":"vanYF","ARO_description":"vanYF is a vanY variant found in the vanF gene cluster","ARO_category":{"36216":{"category_aro_accession":"3000077","category_aro_cvterm_id":"36216","category_aro_name":"vanY","category_aro_description":"VanY is a D,D-carboxypeptidase that cleaves removes the terminal D-Ala from peptidoglycan for the addition of D-Lactate. The D-Ala-D-Lac peptidoglycan subunits have reduced binding affinity with vancomycin compared to D-Ala-D-Ala.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1900":{"model_id":"1900","model_name":"ACT-13","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1094":{"protein_sequence":{"accession":"CCK86741.1","sequence":"MMMTKSLCCALLLSTSCSVLAAPMSEKQLAEVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAITTRVFKPLKLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVKDMASWVMVNMKPDSLEESSLRKGLTLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVEGSDNKVALAPLPAREVNPPAPPVNASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILSAL"},"dna_sequence":{"accession":"HE819402","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGATGACTAAATCCCTTTGCTGCGCCCTGCTGCTCAGCACCTCCTGCTCGGTATTGGCTGCACCGATGTCAGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAAAGCGCAGGCCATTCCGGGTATGGCAGTGGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCTGTCACCCCACAAACCTTATTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTACTCGGCGGCGATGCCATTGCTCGGGGTGAAATATCGCTGGGCGATCCGGTGACCAAATACTGGCCTGAGCTGACAGGCAAGCAGTGGCAGGGGATCCGCATGCTGGATCTGGCAACCTATACCGCAGGAGGTCTGCCGTTACAGGTACCGGATGAGGTCACGGATAACGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATAACGACGCGGGTCTTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGCGACGGTAAGGCGGTACACGTTTCGCCAGGAATGCTGGACGCTGAAGCCTATGGCGTAAAAACCAACGTGAAGGATATGGCAAGCTGGGTGATGGTCAACATGAAGCCGGACTCGCTTGAGGAAAGTTCACTCAGGAAAGGCCTTACCCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGGTTGGGCTGGGAAATGCTTAACTGGCCGGTCGATGCAAAAACCGTGGTTGAAGGTAGCGACAATAAGGTGGCGCTGGCACCGCTGCCTGCGAGAGAAGTGAATCCACCGGCGCCCCCGGTCAACGCATCCTGGGTCCATAAAACCGGCTCTACCGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATTTTGAGCGCGCTGTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36926","NCBI_taxonomy_name":"Enterobacter asburiae","NCBI_taxonomy_id":"61645"}}}},"ARO_accession":"3001835","ARO_id":"38235","ARO_name":"ACT-13","ARO_description":"ACT-13 is a beta-lactamase. From the Lahey list of ACT beta-lactamases.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1901":{"model_id":"1901","model_name":"CTX-M-51","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1256":{"protein_sequence":{"accession":"ABA62022.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAVAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTAGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"DQ211987","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGTCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAGCTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCACAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGCAGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001913","ARO_id":"38313","ARO_name":"CTX-M-51","ARO_description":"CTX-M-51 is a beta-lactamase. From the Lahey list of CTX-M beta-lactamases.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1902":{"model_id":"1902","model_name":"OXA-246","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"886":{"protein_sequence":{"accession":"AHC31001.1","sequence":"MKTFAAYVIIACLSSTALAGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKNFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG"},"dna_sequence":{"accession":"KF711993","fmin":"0","fmax":"801","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTATCGCGTGTCTTTCGAGTACGGCATTAGCTGGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTCTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATGACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAGCAATGGGAAAGAGACTTGACCTTAAGAGGGGCAATACAAGTTTCAGCTGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAACTTTTCCTATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAAGGCCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATATTTAAATAAATTGTCAGCATCTAAAGAAAACCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCGGCACCTGAATATCTAGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGGTGGGTTGAGAAGGAGACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAGTAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGAAAGTGAGGGCATCATTGGTGGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001807","ARO_id":"38207","ARO_name":"OXA-246","ARO_description":"OXA-246 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1903":{"model_id":"1903","model_name":"mdtE","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"675"}},"model_sequences":{"sequence":{"4330":{"protein_sequence":{"accession":"BAE77781.1","sequence":"MNRRRKLLIPLLFCGAMLTACDDKSAENAAAMTPEVGVVTLSPGSVNVLSELPGRTVPYEVAEIRPQVGGIIIKRNFIEGDKVNQGDSLYQIDPAPLQAELNSAKGSLAKALSTASNARITFNRQASLLKTNYVSRQDYDTARTQLNEAEANVTVAKAAVEQATINLQYANVTSPITGVSGKSSVTVGALVTANQADSLVTVQRLDPIYVDLTQSVQDFLRMKEEVASGQIKQVQGSTPVQLNLENGKRYSQTGTLKFSDPTVDETTGSVTLRAIFPNPNGDLLPGMYVTALVDEGSRQNVLLVPQEGVTHNAQGKATALILDKDDVVQLREIEASKAIGDQWVVTSGLQAGDRVIVSGLQRIRPGIKARAISSSQENASTESKQ"},"dna_sequence":{"accession":"AP009048.1","fmin":"3980025","fmax":"3981183","strand":"-","sequence":"TTATTGTTTCGATTCGGTGCTGGCGTTTTCCTGGCTGGAGGAAATTGCTCGTGCTTTGATACCCGGACGAATGCGTTGCAAACCGGAAACGATCACCCGATCGCCAGCCTGCAAGCCAGAGGTGACGACCCACTGGTCGCCGATGGCTTTGCTGGCTTCAATTTCGCGTAGCTGCACGACATCGTCTTTATCCAGAATGAGCGCCGTTGCTTTACCCTGGGCGTTGTGGGTGACGCCTTCCTGCGGCACCAGTAATACATTCTGGCGGCTACCTTCATCCACTAATGCCGTGACGTACATGCCAGGCAGCAAGTCACCATTTGGGTTGGGGAAAATCGCCCGTAACGTCACGGAGCCCGTGGTTTCATCCACTGTCGGGTCGGAGAATTTCAGCGTGCCGGTCTGGCTGTAGCGTTTACCATTTTCCAGATTGAGCTGTACTGGCGTACTGCCCTGAACCTGTTTGATTTGCCCACTGGCGACCTCTTCTTTCATGCGTAAGAAATCTTGCACCGACTGCGTGAGATCGACATAAATCGGGTCCAGACGTTGTACGGTAACCAGCGAATCTGCCTGATTAGCGGTAACGAGTGCGCCGACGGTCACCGACGATTTCCCGCTGACGCCCGTAATCGGCGAGGTGACATTCGCGTATTGCAGATTGATCGTCGCCTGTTCAACAGCCGCTTTGGCGACGGTGACATTGGCTTCTGCTTCATTCAACTGGGTGCGCGCGGTGTCGTAATCCTGACGGCTAACGTAGTTGGTCTTCAGCAACGATGCCTGGCGGTTAAAGGTGATGCGGGCATTGCTGGCGGTAGAGAGCGCTTTCGCCAGCGAGCCTTTGGCGGAGTTTAGCTCGGCCTGTAAAGGTGCAGGATCAATCTGATACAGCGAATCGCCCTGGTTCACTTTATCGCCTTCGATAAAGTTGCGTTTAATGATAATACCGCCCACCTGGGGACGTATCTCGGCAACTTCATAAGGAACGGTTCTACCGGGCAATTCGCTCAACACATTGACCGAACCGGGGGAGAGTGTGACGACACCGACCTCAGGCGTCATGGCGGCGGCGTTTTCCGCCGATTTGTCATCGCAGGCGGTGAGCATCGCGCCGCAGAATAACAACGGTATTAACAGCTTTCTTCTTCTGTTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36839","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. W3110","NCBI_taxonomy_id":"316407"}}}},"ARO_accession":"3000795","ARO_id":"37175","ARO_name":"mdtE","ARO_description":"MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35930":{"category_aro_accession":"0000011","category_aro_cvterm_id":"35930","category_aro_name":"cloxacillin","category_aro_description":"Cloxacillin is a semisynthetic, isoxazolyl penicillin derivative in the beta-lactam class of antibiotics. It interferes with peptidogylcan synthesis and is commonly used for treating penicillin-resistant Staphylococcus aureus infections.","category_aro_class_name":"Antibiotic"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1904":{"model_id":"1904","model_name":"ACT-32","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1419":{"protein_sequence":{"accession":"AIT76088.1","sequence":"MMKKSLCCALLLGISCSALATPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVVEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILDALQ"},"dna_sequence":{"accession":"KM087835","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCTCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCACGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAACGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAGGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTGCCCGTGGTAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGACGCGCTACAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001852","ARO_id":"38252","ARO_name":"ACT-32","ARO_description":"ACT-32 is a beta-lactamase. From the Lahey list of ACT beta-lactamases.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1905":{"model_id":"1905","model_name":"ACT-21","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1854":{"protein_sequence":{"accession":"AHA80106.1","sequence":"MMKKSLCCALLLGISCSALAAPVSEKQLAEVVANTVTPLMKAQSIPGMAVAVIYQGKPHYYTFGKADVAASKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNAALLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPFEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGMKTNVQDMANWVMANMAPENVADASLKQGISLAQSRYWRIGSMYQGLGWEMLNWPVEANTVIEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYPILDALQ"},"dna_sequence":{"accession":"KF526118","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCTCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCGCGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCGATTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGTAAACCGCACTATTACACGTTCGGTAAAGCCGATGTTGCGGCCAGCAAACCCGTTACGCCTCAGACTCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGGGTTTTAGGAGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGGATTCGTATGCTGGATCTCGCAACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAATGCCGCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGTATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGCCCTTTGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCATGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAATATGGCGCCGGAGAACGTTGCTGATGCCTCACTTAAGCAGGGCATCTCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGATCGAGGGCAGCGACAGTAAGGTGGCGCTGGCACCGCTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCCTATCCTCGACGCGCTACAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39098","NCBI_taxonomy_name":"Enterobacter hormaechei","NCBI_taxonomy_id":"158836"}}}},"ARO_accession":"3001842","ARO_id":"38242","ARO_name":"ACT-21","ARO_description":"ACT-21 is a beta-lactamase. From the Lahey list of ACT beta-lactamases.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1906":{"model_id":"1906","model_name":"CTX-M-17","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"907":{"protein_sequence":{"accession":"AAK71471.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAKGL"},"dna_sequence":{"accession":"AY033516","fmin":"2835","fmax":"3711","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCAAGGGGCTGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001880","ARO_id":"38280","ARO_name":"CTX-M-17","ARO_description":"CTX-M-17 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1907":{"model_id":"1907","model_name":"vanSA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3276":{"protein_sequence":{"accession":"AAA65954.1","sequence":"MVIKLKNKKNDYSKLERKLYMYIVAIVVVAIVFVLYIRSMIRGKLGDWILSILENKYDLNHLDAMKLYQYSIRNNIDIFIYVAIVISILILCRVMLSKFAKYFDEINTGIDVLIQNEDKQIELSAEMDVMEQKLNTLKRTLEKREQDAKLAEQRKNDVVMYLAHDIKTPLTSIIGYLSLLDEAPDMPVDQKAKYVHITLDKAYRLEQLIDEFFEITRYNLQTITLTKTHIDLYYMLVQMTDEFYPQLSAHGKQAVIHAPEDLTVSGDPDKLARVFNNILKNAAAYSEDNSIIDITAGLSGDVVSIEFKNTGSIPKDKLAAIFEKFYRLDNARSSDTGGAGLGLAIAKEIIVQHGGQIYAESNDNYTTFRVELPAMPDLVDKRRS"},"dna_sequence":{"accession":"M97297","fmin":"4649","fmax":"5803","strand":"+","sequence":"TTGGTTATAAAATTGAAAAATAAAAAAAACGACTATTCCAAACTAGAACGAAAACTTTACATGTATATCGTTGCAATTGTTGTGGTAGCAATTGTATTCGTGTTGTATATTCGTTCAATGATCCGAGGGAAACTTGGGGATTGGATCTTAAGTATTTTGGAAAACAAATATGACTTAAATCACCTGGACGCGATGAAATTATATCAATATTCCATACGGAACAATATAGATATCTTTATTTATGTGGCGATTGTCATTAGTATTCTTATTCTATGTCGCGTCATGCTTTCAAAATTCGCAAAATACTTTGACGAGATAAATACCGGCATTGATGTACTTATTCAGAACGAAGATAAACAAATTGAGCTTTCTGCGGAAATGGATGTTATGGAACAAAAGCTCAACACATTAAAACGGACTCTGGAAAAGCGAGAGCAGGATGCAAAGCTGGCCGAACAAAGAAAAAATGACGTTGTTATGTACTTGGCGCACGATATTAAAACGCCCCTTACATCCATTATCGGTTATTTGAGCCTGCTTGACGAGGCTCCAGACATGCCGGTAGATCAAAAGGCAAAGTATGTGCATATCACGTTGGACAAAGCGTATCGACTCGAACAGCTAATCGACGAGTTTTTTGAGATTACACGGTATAACCTACAAACGATAACGCTAACAAAAACGCACATAGACCTATACTATATGCTGGTGCAGATGACCGATGAATTTTATCCTCAGCTTTCCGCACATGGAAAACAGGCGGTTATTCACGCCCCCGAGGATCTGACCGTGTCCGGCGACCCTGATAAACTCGCGAGAGTCTTTAACAACATTTTGAAAAACGCCGCTGCATACAGTGAGGATAACAGCATCATTGACATTACCGCGGGCCTCTCCGGGGATGTGGTGTCAATCGAATTCAAGAACACTGGAAGCATCCCAAAAGATAAGCTAGCTGCCATATTTGAAAAGTTCTATAGGCTGGACAATGCTCGTTCTTCCGATACGGGTGGCGCGGGACTTGGATTGGCGATTGCAAAAGAAATTATTGTTCAGCATGGAGGGCAGATTTACGCGGAAAGCAATGATAACTATACGACGTTTAGGGTAGAGCTTCCAGCGATGCCAGACTTGGTTGATAAAAGGAGGTCCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002931","ARO_id":"39365","ARO_name":"vanSA","ARO_description":"vanSA, also known as vanS, is a vanS variant found in the vanA gene cluster","ARO_category":{"36210":{"category_aro_accession":"3000071","category_aro_cvterm_id":"36210","category_aro_name":"vanS","category_aro_description":"VanS is similar to histidine protein kinases like EnvZ and acts as a response regulator by activating VanR. VanS is required for high level transcription of other van glycopeptide resistance genes.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"35948":{"category_aro_accession":"0000029","category_aro_cvterm_id":"35948","category_aro_name":"teicoplanin","category_aro_description":"Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation  and transpeptidation.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1908":{"model_id":"1908","model_name":"OKP-A-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1675":{"protein_sequence":{"accession":"CAJ19603.1","sequence":"MRYVRLCLISLIAALPLAAFASPQPLEQVTRSESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDERLDRRIRYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKRVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMAATLRKLLTSHALSDRSQQQLLQWMVDDQVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPNGKAERIVVIYLRDTPATMAERNQQIAKIGAALIEHWQR"},"dna_sequence":{"accession":"AM051144","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGCATTCGCCAGCCCTCAGCCGCTCGAGCAAGTTACACGCAGCGAAAGTCAGCTGGCGGGCCGCGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCACGGGTGGATGCCGGAGACGAACGGCTGGATCGGCGGATCCGCTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGCGCGTTGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAGCTCAATGAAGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCAGCCAGCATGGCCGCCACCCTGCGCAAGCTGCTAACCAGCCACGCGCTGAGCGACCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGACCAGGTGGCCGGTCCGCTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGCGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGAACGGCAAAGCGGAGCGCATCGTGGTGATCTATCTGCGGGATACGCCGGCGACCATGGCCGAGCGTAACCAGCAGATCGCCAAAATAGGCGCGGCGCTGATCGAGCACTGGCAGCGCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002423","ARO_id":"38823","ARO_name":"OKP-A-6","ARO_description":"OKP-A-6 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1909":{"model_id":"1909","model_name":"AAC(6')-Iak","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"3283":{"protein_sequence":{"accession":"BAO21229.1","sequence":"MTGSAATIRPAKAADAVAWAQLRLGLWPDADDPLETLVAALAEDAGAVFLACAAGGQAIGFAEVRLRHDYVNGTDSSPVGFLEGWYVQPQWQGRGVGRALLAAVRAWTRDAGCRELASDSRVEDVQAHAAHRACGFEETERVVYFRMPLEPSA"},"dna_sequence":{"accession":"AB894482","fmin":"35038","fmax":"35500","strand":"-","sequence":"TCACGCCGATGGCTCCAGTGGCATGCGGAAATAGACCACCCGTTCGGTCTCTTCGAAGCCGCAGGCCCGATGCGCGGCGTGAGCCTGCACGTCCTCCACGCGACTGTCCGAAGCCAGTTCGCGGCAGCCCGCGTCGCGCGTCCATGCCCGCACCGCCGCCAGCAGGGCGCGGCCCACGCCGCGGCCTTGCCACTGCGGCTGCACGTACCAGCCCTCCAGGAAGCCCACCGGCGAGGAATCGGTGCCGTTCACGTAGTCATGGCGCAGGCGCACTTCGGCGAAGCCGATCGCCTGGCCACCCGCTGCACACGCCAGGAAAACCGCACCTGCGTCCTCGGCCAGCGCCGCCACCAGCGTCTCCAGCGGATCATCGGCATCGGGCCACAGGCCCAGACGCAGCTGCGCCCACGCGACCGCATCGGCCGCCTTGGCCGGGCGGATCGTGGCCGCGCTGCCGGTCAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37076","NCBI_taxonomy_name":"Stenotrophomonas maltophilia","NCBI_taxonomy_id":"40324"}}}},"ARO_accession":"3003199","ARO_id":"39782","ARO_name":"AAC(6')-Iak","ARO_description":"AAC(6')-Iak is a 6'-N-aminoglycoside acetyltransferase-encoding gene isolated from a multidrug-resistant clinical isolate of Stenotrophomonas maltophilia","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1910":{"model_id":"1910","model_name":"CTX-M-136","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2042":{"protein_sequence":{"accession":"AGG08693.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAVAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"KC351754","fmin":"157","fmax":"1033","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGTACCAGTAAAGTGATGGCCGTGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGTTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3001995","ARO_id":"38395","ARO_name":"CTX-M-136","ARO_description":"CTX-M-136 is a beta-lactamase. From the Lahey list of CTX-M beta-lactamases.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1911":{"model_id":"1911","model_name":"AAC(6')-Iad","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"264":{"protein_sequence":{"accession":"BAD12078.1","sequence":"MIRKATVQDPPLLARLAMNVWKESSLKELVAEFEQMTKSNDAVAFILFIEDQAVGFAQCQLRHDYVEGTNTSPVGYLEGIFVEKEFRHRGYASELLLKCEDWVKTKGCLQFASDCELDNIDSLAFHLKVGFTEANRMICFTKQL"},"dna_sequence":{"accession":"AB119105","fmin":"0","fmax":"435","strand":"+","sequence":"ATGATTAGAAAAGCAACTGTCCAAGATCCACCATTATTAGCTCGTCTAGCAATGAATGTATGGAAAGAAAGCAGTTTAAAAGAATTAGTAGCAGAATTCGAGCAGATGACTAAAAGTAATGATGCTGTGGCATTTATACTATTTATAGAGGATCAAGCTGTCGGGTTTGCTCAATGTCAATTGCGTCATGATTATGTTGAAGGGACGAATACGAGTCCTGTAGGCTATTTAGAAGGTATATTTGTCGAGAAAGAATTTCGTCACAGAGGATACGCGAGCGAACTATTGTTAAAATGCGAAGATTGGGTGAAAACAAAAGGCTGCCTTCAATTTGCTAGTGATTGTGAATTAGATAATATTGATAGCTTGGCTTTTCATCTCAAAGTAGGTTTTACTGAAGCAAATCGAATGATTTGTTTTACAAAGCAACTTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3002572","ARO_id":"38972","ARO_name":"AAC(6')-Iad","ARO_description":"AAC(6')-Iad is a plasmid-encoded aminoglycoside acetyltransferase in Acinetobacter genomosp. 3","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1912":{"model_id":"1912","model_name":"LRA-13","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1200"}},"model_sequences":{"sequence":{"4328":{"protein_sequence":{"accession":"ACH58991.1","sequence":"MNFRHIVMAALCGLAWTPAIHATEVCIAIAEAGTGAVLVQRGDCQRQVTPASTFKIAISLMGYDSGFLKDAHAPKLPFRPGYVDWRPSWREPTDPAKWMSDSVVWYSQQVTKSLGMQRFADYTRNFKYGNADVSGDAENDGLSMSWISSSLRISPLEQLAFLDKIVNRRLGVSAHAYDMTAQLTKFDQPPAGWRINGKTGAASGYGWYVGWASKGSRTFVFAHLMQRDATQPQDVSAGVLARDEFLKELPGLMIKDMVDRAVQPLMKKYDIPGMAVAVTDNGKNYFFNYGLASRETGQAVTSHTLFEIGSLSKTMAATLTSYAQVNGQLALTDTVSRHMPKLRGGGFDKISLLNLGTHTAGDFPMQVPDHIETYEQLMEYYKNWKPGVAAGGARTYSNLTVGLLGIITAQSMGMPFAEAMENRLFPQLGMHHSYINVPAAEMKNYAQGYNQANAPVRINPAVLATEAYGVKTDAADLIRFVDANMGLVKLDEKLQRAVTGTHTAYFKTGELTQDLIWEQYPAASKLDRMLAGVSEKMVFESNPATRLAPPMPPQADVLINKTGSTGGFGAYALFNPGKKTGIVMLANKSYPGAERVTAAWHILDQLDQR"},"dna_sequence":{"accession":"EU408352.1","fmin":"35394","fmax":"37224","strand":"-","sequence":"CTAACGCTGGTCCAGTTGATCCAGTATGTGCCAGGCCGCCGTCACCCTTTCTGCGCCAGGATAGCTCTTGTTCGCCAGCATCACGATGCCGGTCTTCTTGCCCGGGTTGAACAGCGCATAGGCGCCAAAGCCGCCGGTTGATCCGGTCTTGTTGATCAGCACATCCGCTTGCGGCGGCATCGGCGGCGCCAGCCTGGTCGCGGGATTGCTTTCAAAGACCATTTTTTCGGAAACGCCCGCCAGCATGCGATCGAGTTTCGATGCGGCGGGATATTGTTCCCAGATCAGATCCTGCGTCAGCTCACCCGTCTTGAAGTAGGCGGTGTGCGTGCCGGTGACCGCGCGCTGCAGTTTTTCGTCCAGCTTGACCAACCCCATGTTGGCGTCGACAAACCGGATCAAGTCGGCGGCATCGGTCTTTACCCCGTATGCCTCGGTTGCCAGCACCGCCGGATTGATCCTGACCGGTGCGTTGGCCTGGTTGTAGCCTTGCGCGTAGTTCTTCATCTCCGCCGCCGGCACATTGATATAGCTGTGATGCATGCCAAGCTGGGGGAACAACCTGTTTTCCATCGCCTCCGCAAACGGCATGCCCATGCTTTGCGCCGTGATGATGCCCAGCAGGCCGACGGTCAGGTTGGAGTAGGTCCTGGCGCCGCCCGCAGCAACCCCGGGCTTCCAGTTTTTGTAGTACTCCATCAGCTGCTCGTAGGTCTCGATATGGTCGGGAACCTGCATCGGAAAATCGCCGGCCGTGTGGGTGCCCAGATTGAGCAGGCTGATCTTGTCGAAGCCGCCGCCGCGCAGCTTGGGCATATGCCGGCTGACCGTGTCGGTCAACGCAAGCTGGCCGTTGACCTGCGCGTAGGAAGTCAGCGTTGCCGCCATGGTCTTGCTCAGCGAACCGATCTCGAACAGGGTGTGGCTGGTAACGGCTTGCCCGGTTTCCCTCGACGCCAGCCCGTAGTTGAAGAAGTAGTTCTTGCCGTTGTCGGTGACGGCCACCGCCATCCCCGGGATATCGTATTTCTTCATCAACGGCTGGACGGCGCGGTCCACCATATCCTTGATCATCAAGCCGGGGAGTTCCTTGAGGAATTCGTCACGCGCCAGCACGCCCGCCGACACGTCTTGCGGCTGCGTCGCGTCCCTCTGCATCAGGTGCGCAAAGACGAAGGTTCGCGAACCTTTCGACGCCCATCCCACGTACCAGCCATAACCGGAGGCGGCGCCGGTCTTGCCGTTGATGCGCCATCCCGCCGGAGGCTGATCGAATTTCGTCAATTGCGCGGTCATGTCGTAGGCATGGGCGCTCACGCCCAGCCGACGGTTGACGATCTTGTCCAGGAACGCGAGTTGTTCCAGCGGCGAGATCCGCAGCGAGGAACTTATCCACGACATGCTCAGGCCGTCATTTTCCGCGTCCCCCGAAACGTCGGCATTGCCATACTTGAAGTTCCGCGTGTAGTCGGCGAAACGCTGCATGCCCAGGGATTTTGTCACCTGCTGCGAATACCATACGACCGAATCGCTCATCCACTTGGCCGGATCCGTCGGTTCGCGCCAGCTGGGCCGCCAATCGACATAGCCTGGACGGAACGGCAGTTTCGGCGCGTGCGCGTCCTTCAGAAAACCCGAGTCGTAGCCCATCAGGCTGATGGCGATCTTGAAGGTCGACGCCGGCGTCACCTGGCGCTGGCAATCGCCGCGCTGGACCAGCACAGCGCCGGTGCCGGCCTCGGCGATGGCGATACACACTTCGGTGGCGTGGATGGCTGGCGTCCAGGCGAGACCGCACAGCGCCGCCATGACTATGTGGCGAAAATTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39085","NCBI_taxonomy_name":"uncultured bacterium BLR13","NCBI_taxonomy_id":"506515"}}}},"ARO_accession":"3002484","ARO_id":"38884","ARO_name":"LRA-13","ARO_description":"LRA-13 is a class D\/class C fusion bifunctional beta-lactamase isolated from soil samples in Alaska.","ARO_category":{"41395":{"category_aro_accession":"3004231","category_aro_cvterm_id":"41395","category_aro_name":"class C LRA beta-lactamase","category_aro_description":"Beta-lactamases that are part of the LRA gene family and are classified as Class C beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"41405":{"category_aro_accession":"3004241","category_aro_cvterm_id":"41405","category_aro_name":"class D LRA beta-lactamase","category_aro_description":"Beta-lactamases that are part of the LRA gene family and are classified as Class D beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1913":{"model_id":"1913","model_name":"dfrK","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"50":{"protein_sequence":{"accession":"CBL80435.1","sequence":"MKVSLIAAMDKNRVLGKENDIPWRIPKDWEYVKNTTKGYPIILGRKNLESIGRALPGRRNIILTRDKGFSFNGCEIVHSIEDVFEICNNEEEIFIFGGEQIYNLFLPYVEKMYITKIHYEFEGDTFFPEVNYEEWSEVSVTQGITDEKNPYTYYFHIYERKAS"},"dna_sequence":{"accession":"FN812951","fmin":"0","fmax":"492","strand":"+","sequence":"ATGAAAGTTTCTTTAATTGCTGCGATGGATAAGAATAGGGTATTAGGTAAAGAGAATGACATACCTTGGAGAATCCCAAAGGATTGGGAGTATGTTAAAAATACTACAAAGGGATATCCAATTATATTAGGAAGGAAGAATCTTGAATCAATCGGAAGAGCATTACCTGGAAGAAGAAATATTATTCTGACAAGAGATAAGGGTTTCAGCTTTAATGGTTGTGAAATTGTCCATTCAATAGAAGATGTTTTTGAGATATGTAATAACGAAGAGGAAATTTTCATTTTCGGGGGAGAACAAATTTATAATTTGTTTCTACCATATGTTGAGAAAATGTACATTACAAAAATTCATTACGAATTTGAAGGAGATACATTCTTTCCAGAAGTGAATTATGAAGAGTGGAGCGAAGTATCTGTTACACAAGGAATAACAGATGAAAAAAATCCTTATACATACTATTTTCATATTTATGAGCGAAAAGCTTCTTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3002869","ARO_id":"39303","ARO_name":"dfrK","ARO_description":"dfrK is a plasmid-encoded dihydrofolate reductase found in Staphylococcus aureus","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36408":{"category_aro_accession":"3000269","category_aro_cvterm_id":"36408","category_aro_name":"brodimoprim","category_aro_description":"Brodimoprim is a structural derivative of trimethoprim and an inhibitor of bacterial dihydrofolate reductase. The 4-methoxy group of trimethoprim is replaced with a bromine atom.","category_aro_class_name":"Antibiotic"},"36423":{"category_aro_accession":"3000284","category_aro_cvterm_id":"36423","category_aro_name":"tetroxoprim","category_aro_description":"Tetroxoprim is a trimethoprim derivative that inhibits bacterial dihydrofolate reductase.","category_aro_class_name":"Antibiotic"},"36476":{"category_aro_accession":"3000337","category_aro_cvterm_id":"36476","category_aro_name":"iclaprim","category_aro_description":"Iclaprim is a bactericidal compound that inhibits dihydrofolate reductase. It is used against clinically important Gram-positive pathogens, including methicillin-sensitive Staphylococcus aureus and methicillin-resistant S. aureus.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1914":{"model_id":"1914","model_name":"BEL-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1359":{"protein_sequence":{"accession":"ACT09140.1","sequence":"MKLLLYPLLLFLVIPAFAQADFEHAISDLEAHNQAKIGVALVSENGNLIQGYRANERFAMCSTFKLPLAALVLSRIDAGEENPERKLHYDSAFLEEYAPAAKRYVATGYMTVTEAIQSALQLSDNAAANLLLKEVGGPPLLTKYFRSLGDKVSRLDRIESTLNTNTPGDERDTTTPMSMAQTVSKLIFGDTLTYKSKGQLRRLLIGNQTGDKTIRAGLPDSWVTGDKTGSCANGGRNDVAFFITTAGKKYVLSVYTNAPELQGEERALLIASVAKLARQYVVH"},"dna_sequence":{"accession":"GQ202694","fmin":"0","fmax":"852","strand":"+","sequence":"ATGAAACTGCTGCTCTACCCGTTATTGCTGTTCCTTGTCATTCCAGCCTTTGCCCAGGCGGACTTTGAACATGCCATTTCAGATCTTGAGGCGCACAATCAAGCCAAGATCGGAGTGGCCCTAGTTAGTGAAAATGGCAACCTGATTCAAGGGTATCGTGCGAATGAAAGGTTCGCGATGTGCTCAACTTTCAAGTTGCCGTTGGCCGCTCTTGTTCTGAGTCGCATTGACGCTGGGGAAGAGAATCCTGAGCGCAAGCTTCATTACGATTCCGCGTTCCTTGAAGAGTACGCCCCAGCCGCAAAACGGTATGTGGCAACTGGATATATGACTGTAACTGAGGCAATTCAATCCGCCCTCCAACTCAGCGACAATGCCGCAGCTAACCTGCTGTTAAAAGAGGTTGGCGGCCCACCTTTATTGACAAAGTATTTCCGTAGCCTGGGTGATAAAGTAAGTCGCCTTGATCGTATTGAATCGACTTTGAACACCAATACGCCCGGCGATGAAAGAGATACAACAACGCCCATGTCCATGGCACAGACTGTGTCAAAGCTGATTTTTGGAGACACGTTGACATATAAATCCAAGGGGCAGCTAAGGCGATTACTCATCGGCAATCAGACCGGGGACAAAACCATTCGAGCTGGCTTGCCTGATTCATGGGTAACGGGTGACAAGACAGGCTCGTGTGCGAATGGCGGCCGTAACGATGTGGCGTTTTTTATAACCACTGCCGGAAAAAAATATGTTCTTTCTGTATATACCAATGCACCTGAATTGCAAGGCGAGGAAAGGGCGTTATTAATTGCTTCTGTAGCAAAGTTAGCACGTCAATATGTTGTTCACTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002387","ARO_id":"38787","ARO_name":"BEL-3","ARO_description":"BEL-3 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"38784":{"category_aro_accession":"3002384","category_aro_cvterm_id":"38784","category_aro_name":"BEL beta-lactamase","category_aro_description":"BEL beta-lactamases are class A expanded-spectrum beta-lactamases that are inhibited by clavulanic acid. They are chromosomally encoded and hydrolyze most cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1915":{"model_id":"1915","model_name":"CMY-47","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1816":{"protein_sequence":{"accession":"ADH82410.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDEVTDKAELLRFYQNWQPQWTPGAKRLYANSSIGLFGALVVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"HM046998","fmin":"1039","fmax":"2185","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCGCTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAATTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGAGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGAAGTTACGGATAAAGCCGAATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGTTGGTGGTAAAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACAGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATAGTGATGCTGGCAAACAAAAGCTATCCTAACCCGGCTCGCGTAGAGGCGGCCTGGCGCATTCTTGAAAAACTGCAATAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002058","ARO_id":"38458","ARO_name":"CMY-47","ARO_description":"CMY-47 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1916":{"model_id":"1916","model_name":"TEM-208","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"929":{"protein_sequence":{"accession":"AGL39384.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDFVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"KC865667","fmin":"183","fmax":"1044","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTTGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001385","ARO_id":"37785","ARO_name":"TEM-208","ARO_description":"From the Lahey list of beta-lactamases. Not yet released.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1918":{"model_id":"1918","model_name":"spd","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"758":{"protein_sequence":{"accession":"AGW81558.1","sequence":"MEEPNKQIDNVLIELKRLFSKDLLGVYLYGSYVKGGLKKDSDVDFLVIINRDMTKEEKRILISKIMPISKEIGEDTSLKYIELTVLNYHENENWSYPPIEEFIYGEWLREDYLNYFIPEKNNNIDLTILLYQAKLSSISIYGENNINNLIPDVPFIDLQKAIKESSKELIKDFYGDETNVILTLCRMIVTYETGKFYSKDLAGSMIIENLSENLSIEENNLISLAISSYKNGNSVDWELFPVKSVIKKLYAYLNYKL"},"dna_sequence":{"accession":"KC895984","fmin":"1081","fmax":"1855","strand":"+","sequence":"ATGGAGGAACCAAATAAGCAAATTGATAATGTTTTAATAGAATTGAAACGATTGTTTTCAAAAGATTTATTAGGAGTCTATTTATATGGTTCTTATGTTAAAGGGGGTTTAAAAAAAGATAGTGATGTTGATTTTCTAGTGATAATAAATAGAGATATGACTAAAGAAGAAAAAAGAATATTAATTTCGAAAATTATGCCTATCTCTAAAGAAATTGGTGAAGATACAAGTTTAAAATATATAGAATTAACTGTGCTTAATTATCATGAAAATGAAAATTGGTCTTATCCACCTATTGAAGAGTTTATCTATGGGGAATGGCTTAGAGAAGATTATTTAAATTATTTTATTCCAGAAAAGAATAACAACATTGATTTAACAATATTATTATATCAAGCCAAGCTTTCTTCAATATCAATTTATGGCGAAAATAATATTAATAACTTAATTCCTGATGTTCCATTTATTGATTTACAAAAAGCTATAAAGGAAAGTTCTAAAGAATTGATAAAAGATTTTTATGGTGATGAAACAAATGTTATTTTAACCCTTTGTCGTATGATCGTAACTTATGAAACAGGTAAGTTTTATTCAAAAGATTTAGCTGGCAGTATGATAATAGAAAATTTATCAGAAAATTTATCAATTGAAGAAAATAATTTAATAAGTTTAGCTATTTCTAGTTATAAAAATGGTAATAGCGTTGATTGGGAACTTTTTCCTGTTAAGAGTGTCATTAAAAAACTTTATGCTTATTTGAATTATAAATTATGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3002631","ARO_id":"39031","ARO_name":"spd","ARO_description":"spd is a plasmid-encoded aminoglycoside nucleotidyltransferase gene in S. aureus","ARO_category":{"36367":{"category_aro_accession":"3000228","category_aro_cvterm_id":"36367","category_aro_name":"ANT(9)","category_aro_description":"Nucleotidylylation of spectinomycin at the hydroxyl group at position 9","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1919":{"model_id":"1919","model_name":"SHV-27","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1873":{"protein_sequence":{"accession":"AAG01039.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIDDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AF293345","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGACGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001085","ARO_id":"37465","ARO_name":"SHV-27","ARO_description":"SHV-27 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1920":{"model_id":"1920","model_name":"vanSF","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"680":{"protein_sequence":{"accession":"AAR84673.1","sequence":"MGKILRGFRSKMIILLGLSMLLSSAITYLLFKVLQLYYYTSVDYGDTLAYFRKIIQNIGDFNVFLLLFILLSILFFFLLTKPYSAYFNEISKGIHYLAQGDFKHRVQILSNDEFSDIAQSINLASEKLEQAIERGDFSESSKEQLVVNLAHDLRTPLTSVLGYLDLILKDDNLTENQIRHYLTIAFTKSQRLERLIDELFEITRMNYGMLPIKKKQIDLSELLIQLKEELYPVFEKNDLIARMNITSPLSIMGDGELLARVFENLLINANRYGYEGQYVDINGFIDSEEVVIQVINYGDAIPPDELPHIFDMLFTGDKARTHQENSTGLGLFIAENIVEQHNGTITAESDLIRTIFEVRLPMADS"},"dna_sequence":{"accession":"AF155139","fmin":"2199","fmax":"3297","strand":"+","sequence":"ATGGGTAAAATACTACGAGGCTTTCGTTCAAAAATGATAATATTGTTAGGTTTAAGCATGTTGTTGTCTAGCGCCATAACATACCTACTCTTTAAAGTACTCCAATTGTATTATTATACAAGTGTTGATTATGGAGATACACTAGCTTATTTTCGCAAAATCATACAAAATATTGGAGACTTTAACGTCTTTTTACTGTTATTTATCTTGCTTTCGATATTATTTTTCTTTTTACTTACAAAACCCTATTCTGCCTATTTCAATGAAATTTCAAAAGGAATTCATTATCTCGCTCAGGGTGACTTTAAGCATCGAGTTCAAATATTGTCAAATGATGAATTTAGTGATATTGCACAAAGCATTAATCTGGCAAGTGAAAAATTGGAACAAGCCATAGAAAGGGGTGACTTTTCGGAAAGTAGTAAAGAGCAGTTAGTAGTAAATTTGGCTCATGATTTGCGCACACCTCTTACCTCTGTTTTAGGTTATTTAGATTTAATCCTTAAGGATGATAACTTGACTGAAAATCAGATCAGACATTATTTAACGATTGCCTTTACCAAATCTCAACGCTTAGAAAGGTTAATTGATGAATTATTTGAAATAACTAGGATGAATTATGGCATGTTACCAATTAAAAAGAAACAAATCGATTTAAGTGAGCTACTTATTCAATTGAAAGAAGAGTTGTATCCTGTCTTCGAGAAAAACGATTTGATAGCAAGAATGAATATTACTTCCCCTTTATCTATTATGGGTGATGGAGAGTTATTGGCACGTGTGTTTGAAAATCTTCTGATTAATGCAAATCGCTATGGGTATGAGGGGCAGTATGTAGATATCAACGGTTTTATTGATTCAGAGGAAGTCGTTATTCAAGTTATCAATTATGGGGATGCTATTCCTCCAGATGAACTGCCTCATATTTTTGATATGCTTTTTACTGGTGACAAAGCACGAACTCATCAAGAAAATAGTACAGGTCTCGGTTTATTCATTGCGGAGAATATTGTAGAGCAACACAATGGGACAATAACTGCCGAAAGTGATTTAATACGCACGATATTTGAAGTCCGATTACCAATGGCGGATTCCTAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39542","NCBI_taxonomy_name":"Paenibacillus popilliae ATCC 14706","NCBI_taxonomy_id":"1212764"}}}},"ARO_accession":"3002936","ARO_id":"39370","ARO_name":"vanSF","ARO_description":"vanSF is a vanS variant found in the vanF gene cluster","ARO_category":{"36210":{"category_aro_accession":"3000071","category_aro_cvterm_id":"36210","category_aro_name":"vanS","category_aro_description":"VanS is similar to histidine protein kinases like EnvZ and acts as a response regulator by activating VanR. VanS is required for high level transcription of other van glycopeptide resistance genes.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1921":{"model_id":"1921","model_name":"EreB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3349":{"protein_sequence":{"accession":"CAA01212.1","sequence":"MRFEEWVKDKHIPXKXNHPDDNYDDFKPLRXIIGDTRVVALGENSHFIKEFFLLRHTLLRFFIEDLGFTTFAFEFGFAEGQIINNWIHGQGTDDEIGRFLKHFYYPEELKTTFLWLREYNKAAKEKITFLGIDIPRNGGSYLPNMEIVHDFFRTADKEALHIIDDAFNIAKKIDYFSTSQAALNLHELTDSEKCRLTSQLARVKVRLEAMAPIHIEKYGIDKYETILHYANGMIYLDYNIQAMSGFISGGGMQGDMGAKDKYMADSVLWHLKNPQSEQKVIVVAHNAHIQKTPILYDGFLSCLPMGQRLKNAIGDDYMSLGITSYSGHTAALYPEVDTKYGFRVDNFQLQEPNEGSVEKAISGCGVTNSFVFFRNIPEDLQSIPNMIRFXSIYMKAELEKAFDGIFQIEKSSVSEVVYE"},"dna_sequence":{"accession":"A15097","fmin":"382","fmax":"1642","strand":"+","sequence":"ATGAGGTTCGAAGAATGGGTCAAAGATAAGCATATTCCTTNCAAACNGAATCACCCTGATGATAATTACGATGATTTTAAGCCATTAAGAAANATAATTGGAGATACCCGAGTTGTAGCATTAGGTGAAAATTCTCATTTCATAAAAGAATTCTTTTTGTTACGACATACGCTTTTGCGTTTTTTTATCGAAGATCTAGGTTTTACTACGTTTGCTTTTGAATTTGGTTTTGCTGAGGGTCAAATCATCAATAACTGGATACATGGACAAGGAACTGACGATGAAATAGGCAGATTCTTAAAACACTTCTATTATCCAGAAGAGCTCAAAACCACATTTCTATGGCTAAGGGAGTACAATAAAGCAGCAAAAGAAAAAATCACATTTCTTGGCATTGATATACCCAGAAATGGAGGTTCATACTTACCAAATATGGAGATAGTGCATGACTTTTTTAGAACAGCGGATAAAGAAGCACTACACATTATCGATGATGCATTTAATATTGCAAAAAAGATTGATTACTTCTCCACATCACAGGCAGCCTTAAATTTACATGAGCTAACAGATTCTGAGAAATGCCGTTTAACTAGCCAATTAGCTCGAGTAAAAGTTCGCCTTGAAGCTATGGCTCCAATTCACATTGAAAAATATGGGATTGATAAATATGAGACAATTCTGCATTATGCCAACGGTATGATATACTTGGACTATAACATTCAAGCTATGTCGGGCTTTATTTCAGGAGGCGGAATGCAGGGCGATATGGGTGCAAAAGACAAATACATGGCAGATTCTGTGCTGTGGCATTTAAAAAACCCACAAAGTGAGCAGAAAGTGATAGTAGTAGCACATAATGCACATATTCAAAAAACACCCATTCTGTATGATGGATTTCTAAGTTGCCTACCAATGGGCCAAAGACTTAAAAATGCCATTGGTGATGATTATATGTCTTTAGGTATTACTTCTTATAGTGGGCATACTGCAGCCCTCTATCCGGAAGTTGATACAAAATATGGTTTTCGAGTTGATAACTTCCAACTGCAGGAACCAAATGAAGGTTCTGTCGAGAAAGCTATTTCTGGTTGTGGAGTTACTAATTCTTTTGTCTTTTTTAGAAATATTCCTGAAGATTTACAATCCATCCCGAACATGATTCGATTTGANTCTATTTACATGAAAGCAGAACTCGAGAAAGCTTTCGATGGAATATTTCAAATTGAAAAGTCATCTGTATCTGAGGTCGTTTATGAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000363","ARO_id":"36502","ARO_name":"EreB","ARO_description":"EreB is an erythromycin esterase-like protein that hydrolyses the drug's lactone ring.","ARO_category":{"36459":{"category_aro_accession":"3000320","category_aro_cvterm_id":"36459","category_aro_name":"macrolide esterase","category_aro_description":"Hydrolytic enzymes that cleave the macrocycle lactone ring of macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35946":{"category_aro_accession":"0000027","category_aro_cvterm_id":"35946","category_aro_name":"roxithromycin","category_aro_description":"Roxithromycin is a semi-synthetic, 14-carbon ring macrolide antibiotic derived from erythromycin. It is used to treat respiratory tract, urinary and soft tissue infections. Roxithromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1922":{"model_id":"1922","model_name":"marA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"230"}},"model_sequences":{"sequence":{"579":{"protein_sequence":{"accession":"YP_489794.1","sequence":"MSRRNTDAITIHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKETGHSLGQYIRSRKMTEIAQKLKESNEPILYLAERYGFESQQTLTRTFKNYFDVPPHKYRMTNMQGESRFLHPLNHYNS"},"dna_sequence":{"accession":"NC_007779","fmin":"1621287","fmax":"1621671","strand":"+","sequence":"ATGTCCAGACGCAATACTGACGCTATTACCATTCATAGCATTTTGGACTGGATCGAGGACAACCTGGAATCGCCACTGTCACTGGAGAAAGTGTCAGAGCGTTCGGGTTACTCCAAATGGCACCTGCAACGGATGTTTAAAAAAGAAACCGGTCATTCATTAGGCCAATACATCCGCAGCCGTAAGATGACGGAAATCGCGCAAAAGCTGAAGGAAAGTAACGAGCCGATACTCTATCTGGCAGAACGATATGGCTTCGAGTCGCAACAAACTCTGACCCGAACCTTCAAAAATTACTTTGATGTTCCGCCGCATAAATACCGGATGACCAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAGT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36839","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. W3110","NCBI_taxonomy_id":"316407"}}}},"ARO_accession":"3000263","ARO_id":"36402","ARO_name":"marA","ARO_description":"In the presence of antibiotic stress, E. coli overexpresses the global activator protein MarA, which besides inducing MDR efflux pump AcrAB, also down- regulates synthesis of the porin OmpF.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"41445":{"category_aro_accession":"3004281","category_aro_cvterm_id":"41445","category_aro_name":"General Bacterial Porin with reduced permeability to beta-lactams","category_aro_description":"These are GBPs that are associated with decreased susceptibility to beta-lactams either through mutations in the porin protein, absence of the porin protein, or expression of the porin protein.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"},"36383":{"category_aro_accession":"3000244","category_aro_cvterm_id":"36383","category_aro_name":"reduced permeability to antibiotic","category_aro_description":"Reduction in permeability to antibiotic, generally through reduced production of porins, can provide resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1923":{"model_id":"1923","model_name":"APH(3'')-Ia","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"91":{"protein_sequence":{"accession":"CAA37605.1","sequence":"MSDHPGPGAVTPELFGVGGDWLAVTAGESGASVFRAADATRYAKCVPAADAAGLEAERDRIAWLSGQGVPGPRVLDWYAGDAGACLVTRAVPGVPADRVGADDLRTAWGAVADAVRRLHEVPVASCPFRRGLDSVVDAARDVVARGAVHPEFLPVEQRLVPPAELLARLTGELARRRDQEAADTVVCHGDLCLPNIVLHPETLEVSGFIDLGRLGAADRHADLALLLANARETWVDEERARFADAAFAERYGIAPDPERLRFYLHLDPLTWG"},"dna_sequence":{"accession":"X53527","fmin":"0","fmax":"819","strand":"+","sequence":"ATGAGTGATCACCCCGGGCCGGGGGCCGTCACGCCGGAGCTGTTCGGCGTGGGCGGCGACTGGCTGGCCGTCACCGCGGGCGAATCGGGCGCCTCCGTCTTTCGCGCCGCGGACGCCACCCGGTACGCCAAGTGCGTGCCCGCCGCGGACGCGGCCGGTCTTGAGGCGGAACGCGACCGGATCGCCTGGCTGAGCGGGCAGGGCGTACCGGGCCCCCGCGTCCTCGACTGGTACGCCGGTGACGCGGGCGCCTGCCTGGTCACCCGTGCCGTCCCCGGCGTACCCGCTGATCGGGTGGGCGCCGATGACCTTCGCACTGCCTGGGGGGCCGTCGCGGACGCGGTCCGTCGGCTGCACGAGGTGCCCGTGGCCTCGTGTCCGTTCCGCCGGGGGCTGGACTCCGTGGTCGACGCCGCCCGTGACGTGGTGGCCCGTGGCGCGGTGCATCCGGAGTTCCTGCCGGTGGAGCAGCGGCTCGTTCCCCCGGCGGAGCTGCTGGCCCGGCTCACCGGGGAGCTCGCCCGTCGGCGCGATCAGGAGGCCGCCGACACGGTCGTCTGCCACGGTGATCTCTGCCTGCCCAACATCGTCCTCCATCCGGAGACCCTGGAGGTGTCGGGCTTCATCGACCTGGGACGGCTCGGGGCGGCCGACCGCCACGCCGACCTGGCGCTGCTGCTGGCCAACGCGCGCGAGACCTGGGTGGACGAGGAGCGGGCGCGGTTCGCCGACGCGGCGTTCGCCGAGCGTTACGGCATCGCCCCGGACCCGGAACGGCTGCGCTTCTACCTCCATCTCGATCCGCTCACCTGGGGCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36903","NCBI_taxonomy_name":"Streptomyces griseus","NCBI_taxonomy_id":"1911"}}}},"ARO_accession":"3002638","ARO_id":"39038","ARO_name":"APH(3'')-Ia","ARO_description":"APH(3'')-Ia is a chromosomal-encoded aminoglycoside phosphotransferase in S. griseus","ARO_category":{"36266":{"category_aro_accession":"3000127","category_aro_cvterm_id":"36266","category_aro_name":"APH(3'')","category_aro_description":"Phosphorylation of streptomycin on the hydroxyl group at position 3''","category_aro_class_name":"AMR Gene Family"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1924":{"model_id":"1924","model_name":"vanM","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"650"}},"model_sequences":{"sequence":{"651":{"protein_sequence":{"accession":"ACL82961.1","sequence":"MNRLKIAILFGGCSEEHNVSVKSAAEIANNIDIGKYEPIYIGITQSGVWKTCEKPCIDWDNEHCRSAVLSPDKKMHGLLIMQDKGYQIQRIDVVFSVLHGKSGEDGAIQGLFELSGIPYVGCDIQSSAVCMDKSLAYIIAKNAGIATPEFQVIYKDDKPAADSFTYPVFVKPARSGSSYGVNKVNSADELDSAIDLARQYDSKILIEQGVLGYEVGCAVLGNSFDLIVGEVDQIRLQHGIFRIHQEAEPEKGSENATITVPAELSAEERERIKEAAKNIYKALGCRGLSRVDMFLQDNGRIVLNEVNTMPGFTSYSRYPRMMVSAGITIPELIDHLIVLAVKE"},"dna_sequence":{"accession":"FJ349556","fmin":"4856","fmax":"5888","strand":"+","sequence":"ATGAATAGATTGAAAATAGCCATCCTGTTTGGGGGTTGCTCAGAAGAGCATAATGTATCGGTAAAATCAGCGGCAGAGATTGCCAACAACATTGATATAGGAAAATATGAACCAATATACATCGGAATAACCCAATCTGGCGTTTGGAAAACATGCGAAAAACCATGTATAGATTGGGATAATGAACACTGTCGCTCGGCAGTACTTTCTCCGGATAAAAAAATGCATGGGTTGCTTATTATGCAAGATAAAGGATATCAAATACAGCGTATAGATGTAGTCTTTTCAGTGTTGCACGGAAAATCGGGTGAAGACGGCGCCATACAAGGATTATTTGAATTGTCTGGTATACCTTATGTAGGCTGTGATATTCAAAGTTCGGCGGTTTGTATGGACAAATCACTGGCATATATTATTGCGAAAAACGCTGGCATAGCTACTCCTGAATTTCAGGTCATTTATAAAGACGATAAGCCAGCGGCAGATTCGTTTACCTATCCCGTTTTTGTTAAGCCAGCACGTTCAGGTTCCTCCTATGGTGTGAATAAAGTTAATAGTGCGGATGAATTGGACTCCGCAATTGACTTGGCAAGACAATATGACAGCAAAATCCTAATTGAGCAGGGTGTTTTAGGTTATGAGGTCGGTTGTGCCGTATTGGGAAACAGTTTCGACTTGATTGTTGGTGAAGTGGATCAAATCAGACTGCAACACGGTATTTTTCGTATTCATCAGGAAGCCGAGCCGGAAAAAGGTTCTGAAAACGCAACTATAACCGTTCCCGCAGAACTATCGGCAGAGGAGCGAGAACGGATAAAAGAAGCGGCAAAAAATATATATAAGGCGCTCGGGTGTAGAGGTCTTTCTCGTGTTGATATGTTTTTACAAGATAACGGCCGCATTGTACTAAATGAAGTCAATACCATGCCTGGTTTCACGTCATACAGCCGTTATCCACGTATGATGGTCTCAGCAGGTATAACAATTCCCGAACTGATTGACCATCTGATTGTATTAGCTGTAAAGGAGTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002911","ARO_id":"39345","ARO_name":"vanM","ARO_description":"VanM is a D-Ala-D-Ala ligase homolog that can synthesize D-Ala-D-Lac, an alternative substrate for peptidoglycan synthesis that reduces vancomycin binding affinity. It is associated with both vancomycin and teicoplanin resistance.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"39340":{"category_aro_accession":"3002906","category_aro_cvterm_id":"39340","category_aro_name":"van ligase","category_aro_description":"van ligases synthesize alternative substrates for peptidoglycan synthesis that reduce vancomycin binding affinity.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1926":{"model_id":"1926","model_name":"CMY-34","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1993":{"protein_sequence":{"accession":"ABN51006.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGISLLHLATYTAGGLPLQIPDDVTDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"EF394370","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTAGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002045","ARO_id":"38445","ARO_name":"CMY-34","ARO_description":"CMY-34 is a beta-lactamase found in Escherichia coli","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1927":{"model_id":"1927","model_name":"SHV-29","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"2024":{"protein_sequence":{"accession":"AAG49894.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGSVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAAERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AF301532","fmin":"7","fmax":"868","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCAGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGTTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGCCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGGATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001087","ARO_id":"37467","ARO_name":"SHV-29","ARO_description":"SHV-29 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1928":{"model_id":"1928","model_name":"OXA-50","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"1935":{"protein_sequence":{"accession":"AAQ76277.1","sequence":"MRPLLFSALLLLSGHTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLRDAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"AY306130","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGTGCCCTTCTCCTGCTTTCCGGGCATACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTTGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001796","ARO_id":"38196","ARO_name":"OXA-50","ARO_description":"OXA-50 is a beta-lactamase found in Pseudomonas aeruginosa. It confers decreased susceptibility to ampicillin and ticarcillin and, interestingly, to moxalactam and meropenem in P. aeruginosa but not in E. coli. Also confers resistance to piperacillin-tazobactam and cephalotin.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1929":{"model_id":"1929","model_name":"ACT-24","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"779":{"protein_sequence":{"accession":"AHL39336.1","sequence":"MMKKSLCCALLLGISCSALAAPVSEKQLAEVVANTITPLMKAQSIPGMAVAVIYQGKPHYYTFGKADIAASKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNAALLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMGYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGISLAQSRYWRIGSMYQGLGWEMLNWPVEANTVIDGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYHILDALQ"},"dna_sequence":{"accession":"KJ207207","fmin":"479","fmax":"1625","strand":"+","sequence":"ATGATGAAAAAATCTCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCGCGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGATTACCCCGCTGATGAAAGCCCAGTCGATTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGTAAACCGCACTATTATACGTTTGGCAAAGCCGATATCGCGGCCAGCAAACCCGTTACGCCTCAGACTCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGGGTTTTAGGAGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGGATTCGTATGCTGGATCTCGCAACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAATGCCGCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGTATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGGGCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAACGTTGCTGATGCCTCACTTAAGCAGGGCATCTCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGATCGACGGCAGCGACAGTAAGGTGGCGCTGGCACCGCTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGACGCGCTACAGTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001844","ARO_id":"38244","ARO_name":"ACT-24","ARO_description":"ACT-24 is a beta-lactamase. From the Lahey list of ACT beta-lactamases.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1930":{"model_id":"1930","model_name":"CTX-M-29","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1862":{"protein_sequence":{"accession":"AAP22736.1","sequence":"MVKKSLRQFTLMATAAVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVDGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTNGL"},"dna_sequence":{"accession":"AY267213","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAGCCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGGGTGGCATTGATTAACACTGCGGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTGGTTAACTATAATCCGATTGCGGAAAAGCACGTCGATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCAACGGTTTGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001891","ARO_id":"38291","ARO_name":"CTX-M-29","ARO_description":"CTX-M-29 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1931":{"model_id":"1931","model_name":"TEM-150","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"926":{"protein_sequence":{"accession":"CAJ66089.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPDTLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AM183304","fmin":"208","fmax":"1069","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGATACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001017","ARO_id":"37397","ARO_name":"TEM-150","ARO_description":"TEM-150 is a beta-lactamase found in Enterobacter spp., E. coli, and Klebsiella pneumoniae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1932":{"model_id":"1932","model_name":"IMP-32","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1339":{"protein_sequence":{"accession":"AFR33816.1","sequence":"MKKLFVLCVFFFCNIAVAEESLPDLKIEKLEEGVYVHTSFEEVKGWSVVTKHGLVVLVKNDAYLIDTPITAKDTEKLVNWFVERGYKIKGSISTHFHGDSTAGIEWLNSQSIPTYASELTNELLKKDNKVQAKHSFYGVSYSLIKNKIEVFYPGPGHTQDNVVVWLPEKKILFGGCFVKPDGLGYLGDANLEAWPKSAKILMSKYGKAKLVVSSHSDIGDVSLLKRTWEQAVKGLNESKKSSQPSD"},"dna_sequence":{"accession":"JQ002629","fmin":"113","fmax":"854","strand":"+","sequence":"ATGAAAAAATTATTTGTTTTATGTGTATTCTTCTTCTGCAACATTGCAGTTGCAGAAGAATCTTTGCCTGATTTAAAAATTGAGAAGCTTGAAGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAAAGGTTGGAGTGTGGTCACTAAACACGGTTTGGTGGTTCTTGTGAAAAATGACGCCTATCTGATTGATACTCCAATTACTGCTAAAGATACTGAAAAATTAGTCAATTGGTTTGTTGAGCGGGGCTATAAAATCAAAGGCAGTATTTCCACACATTTCCATGGTGACAGTACGGCTGGAATAGAGTGGCTTAATTCTCAATCTATCCCCACATATGCTTCTGAATTAACAAATGAACTTCTTAAAAAAGACAATAAGGTACAAGCTAAACACTCTTTTTATGGGGTTAGTTATTCACTAATAAAAAACAAAATTGAAGTTTTTTATCCAGGCCCAGGGCACACTCAAGATAACGTAGTGGTTTGGTTACCTGAAAAGAAAATTTTATTCGGTGGTTGCTTTGTTAAACCGGACGGTCTTGGCTATTTGGGGGACGCAAATTTAGAAGCTTGGCCAAAGTCCGCTAAAATATTAATGTCTAAATATGGTAAAGCAAAACTAGTTGTGTCGAGTCATAGTGATATTGGAGATGTATCACTCTTGAAACGTACATGGGAGCAGGCTGTTAAAGGGCTGAATGAAAGTAAAAAATCATCACAGCCAAGCGACTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002223","ARO_id":"38623","ARO_name":"IMP-32","ARO_description":"IMP-32 is a beta-lactamase. From the Lahey list of IMP beta-lactamases.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1933":{"model_id":"1933","model_name":"SHV-160","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1944":{"protein_sequence":{"accession":"AFQ23966.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSEGQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASKRGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"JX121127","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAGGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCAAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001199","ARO_id":"37579","ARO_name":"SHV-160","ARO_description":"SHV-160 is a beta-lactamase.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1934":{"model_id":"1934","model_name":"lnuD","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"153":{"protein_sequence":{"accession":"ABR14060.1","sequence":"MVNKADAIEIILYAEENEIDIWLDGGWGVDALLGEETRSHNDIDLFVEEKNGKTFIEILKEKGFTEVIEAYTTTDHTVWKDDKDRIIDLHVFEFNEQGDLVFEGESYPSNVFSGIGKIGNKVVKCIDAENQVLFHLGYEHDENDVHDVRLLCERYNIPVPSEYK"},"dna_sequence":{"accession":"EF452177","fmin":"0","fmax":"495","strand":"+","sequence":"ATGGTAAATAAAGCAGATGCTATTGAGATAATTTTATATGCCGAAGAAAATGAGATTGACATTTGGCTAGATGGTGGTTGGGGGGTTGATGCTCTATTAGGAGAAGAAACAAGGTCCCACAACGATATTGATTTATTTGTAGAAGAAAAAAACGGCAAAACGTTTATTGAAATATTGAAAGAAAAAGGCTTTACCGAAGTTATTGAAGCTTATACCACTACAGATCACACGGTTTGGAAGGACGATAAAGACAGGATAATCGATCTTCATGTATTTGAATTCAACGAACAAGGAGACCTTGTTTTTGAAGGAGAATCGTATCCATCAAACGTGTTTAGTGGAATTGGGAAAATAGGTAACAAAGTTGTAAAATGTATAGATGCTGAAAATCAGGTTTTATTTCACCTGGGATATGAGCATGATGAAAATGATGTTCATGACGTAAGGTTATTATGCGAGAGATATAATATTCCTGTTCCTAGTGAATACAAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36887","NCBI_taxonomy_name":"Streptococcus uberis","NCBI_taxonomy_id":"1349"}}}},"ARO_accession":"3002838","ARO_id":"39272","ARO_name":"lnuD","ARO_description":"lnuD is a plasmid-mediated nucleotidyltransferase found in Streptococcus uberis","ARO_category":{"36360":{"category_aro_accession":"3000221","category_aro_cvterm_id":"36360","category_aro_name":"lincosamide nucleotidyltransferase (LNU)","category_aro_description":"Resistance to the lincosamide antibiotic by ATP-dependent modification of the 3' and\/or 4'-hydroxyl groups of the methylthiolincosamide sugar.","category_aro_class_name":"AMR Gene Family"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1936":{"model_id":"1936","model_name":"CTX-M-43","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1820":{"protein_sequence":{"accession":"AAZ14955.1","sequence":"MMTQSIRRSMLTVMATLPLLFSSATLHAQANSVQQQLEALEKSSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKQSESDKHLLNQRVEIKKSDLVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSASIRAGLPKSWVVGDKTGSGGYGTTNDIAVIWPENHAPLVLVTYFTQPEQKAERRRDILAAAAKIVTHGF"},"dna_sequence":{"accession":"DQ102702","fmin":"0","fmax":"876","strand":"+","sequence":"ATGATGACTCAGAGCATTCGCCGCTCAATGTTAACGGTGATGGCGACGCTACCCCTGCTATTTAGCAGCGCAACGCTGCATGCGCAGGCGAACAGCGTGCAACAGCAGCTGGAAGCCCTGGAGAAAAGTTCGGGAGGTCGGCTTGGCGTTGCGCTGATTAACACCGCCGATAATTCGCAGATTCTCTACCGTGCCGATGAACGTTTTGCGATGTGCAGTACCAGTAAGGTGATGGCGGCCGCGGCGGTGCTTAAACAGAGCGAGAGCGATAAGCACCTGCTAAATCAGCGCGTTGAAATCAAGAAGAGCGACCTGGTTAACTACAATCCCATTGCGGAGAAACACGTTAACGGCACGATGACGCTGGCTGAGCTTGGCGCAGCGGCGCTGCAGTATAGCGACAATACTGCCATGAATAAGCTGATTGCCCATCTGGGTGGTCCCGATAAAGTGACGGCGTTTGCTCGCTCGTTGGGTGATGAGACCTTCCGTCTGGACAGAACCGAGCCCACGCTCAATACCGCCATTCCAGGCGACCCGCGTGATACCACCACGCCGCTCGCGATGGCGCAGACCCTGAAAAATCTGACGCTGGGTAAAGCGCTGGCGGAAACTCAGCGGGCACAGTTGGTGACGTGGCTTAAGGGCAATACTACCGGTAGCGCGAGCATTCGGGCGGGTCTGCCGAAATCATGGGTAGTGGGCGATAAAACCGGCAGCGGAGGTTATGGCACCACCAACGATATCGCGGTTATCTGGCCGGAAAACCACGCACCGCTGGTTCTGGTGACCTACTTTACCCAACCGGAGCAGAAGGCGGAAAGGCGTCGGGATATTCTGGCTGCGGCGGCGAAAATCGTAACCCACGGTTTCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001905","ARO_id":"38305","ARO_name":"CTX-M-43","ARO_description":"CTX-M-43 is a beta-lactamase found in Pseudomonas aeruginosa and Acinetobacter spp.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1937":{"model_id":"1937","model_name":"OXA-118","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"965":{"protein_sequence":{"accession":"AAK55330.1","sequence":"MAIRFLTILLSTFFLTSFVHAQEHVLERSDWKKFFSDLRAEGAIVISDERQAEHALLVFGQERAAKRYSPASTFKLPHTLFALDADAVRDEFQVFRWDGVKRSFAGHNQDQDLRSAMRNSAVWVYELFAKEIGKDKARHYLKQIDYGNADPSTIKGDYWIDGNLEISAHEQISFLRKLYRNQLPFQVEHQRLVKDLMITEAGRNWILRAKTGWEGRFGWWVGWVEWPTGPVFFALNIDTPNRTDDLFKREAIARAILRSIDALPPN"},"dna_sequence":{"accession":"AF371964","fmin":"118","fmax":"919","strand":"+","sequence":"ATGGCAATCCGATTCCTCACCATACTGCTATCTACTTTTTTTCTTACCTCATTCGTGCATGCGCAAGAACACGTGCTAGAGCGTTCTGACTGGAAGAAGTTCTTCAGCGACCTCCGGGCCGAAGGTGCAATCGTTATTTCAGACGAACGTCAAGCGGAGCATGCTTTATTGGTTTTTGGTCAAGAGCGAGCAGCAAAGCGTTACTCGCCTGCTTCAACCTTCAAGCTTCCACACACACTTTTTGCACTCGATGCAGACGCCGTTCGTGATGAGTTCCAGGTTTTTCGATGGGACGGCGTTAAACGGAGCTTTGCGGGCCATAATCAAGACCAAGACTTGCGATCAGCGATGCGAAATTCTGCGGTCTGGGTTTATGAGCTATTTGCAAAAGAGATCGGAAAGGACAAAGCAAGACACTATTTAAAGCAAATTGATTATGGCAACGCCGACCCTTCGACAATCAAGGGCGATTACTGGATAGATGGCAATCTTGAAATCTCAGCGCACGAACAGATTTCGTTTCTCAGAAAACTCTATCGAAATCAGCTGCCATTTCAGGTGGAACATCAGCGCTTGGTCAAAGATCTCATGATTACGGAAGCCGGGCGCAACTGGATACTACGCGCAAAGACCGGCTGGGAAGGCAGGTTTGGCTGGTGGGTAGGGTGGGTGGAGTGGCCAACCGGTCCCGTATTCTTCGCGCTGAATATTGATACGCCAAACAGAACGGATGATCTTTTCAAAAGAGAGGCAATCGCGCGGGCAATCCTTCGCTCTATCGACGCATTGCCGCCCAACTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36822","NCBI_taxonomy_name":"Burkholderia cepacia","NCBI_taxonomy_id":"292"}}}},"ARO_accession":"3001768","ARO_id":"38168","ARO_name":"OXA-118","ARO_description":"OXA-118 is a beta-lactamase found in Burkholderia cepacia","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1938":{"model_id":"1938","model_name":"mtrD","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"2130"}},"model_sequences":{"sequence":{"4318":{"protein_sequence":{"accession":"NP_274718.1","sequence":"MAKFFIDRPIFAWVISIFIIAAGIFGIKSLPVSQYPSVAAPTITLRATYPGASAQVMEDSVLSVIERNMNGVEGLDYMSTSADSSGSGSVSLTFTPDTDENLAQVEVQNKLSEVLSTLPATVQQYGVTVSKARSNFLMIVMLSSDVQSTEEMNDYAQRNIVPELQRIEGVGQVRLFGAQRAMRIWVDPKKLQNYNLSFADVGSALSAQNVQISAGSIGSLPAVRGQTVTATVTAQGQLGTAEEFGNVILRANTDGSNVYLKDVARVGLGMEDYSSSTRLNGVNTTGMAVMLSNSGNAMATAKAVKERMATLEKYFPQGMSWKTPYDTSKFVEISIEKVIHTLIEAMVLVFVVMYLFLQNIRYTLIPTIVVPISLLGGFAFISYMGMSINVLTMFAMVLVIGIVVDDAIVVVENVERIMAGEGLPPKEATKKAMGQISGAVIGITAVLISVFVPLAMFSGATGNIYKQFALTMASSIAFSAFLALTLTPALCATMLKTIPKGHHEEKKGFFGWFNKKFNSWTHGYEGRVAKVLRKTFRMMVVYIGLAVVGVFLFMRLPTSFLPTEDQGFVMVSVQLPAGATQERTNATLAQVTQLAKSIPEIENIITVSGFSFSGSGQNMAMGFAILKDWNERTAPGSDAVAIAGKLTGMMMGTLKDGFGIAVVPPPILELGNGSGLSINLQDRNNTGHTALLAKRNELIQKMRASGLFDPSTVRAGGLEDSPQLKIDINRAAAAAQGISFADIRTALASALSSSYVSDFPNQGRLQRVMVQADEDARMQPADILNLTVPNKSGVAVPLSTIATVSWENGTEQSVRFNGYPSMKLSASPATGVSTGQAMAAVQKMVDELGGGYSLEWGGQSREEAKGGSQTLILYGLAVAAVFLVLAALYESWSIPLAVILVIPLGLIGAAAGVTGRNLFEGLLGSVPSFANDIYFQVGFVTVMGLSAKNAILIIEFAKDLQAQGKSAVEAALEAARLRFRPIIMTSFAFILGVVPLYIAGGASSASQRAIGTTVFWGMLIGTLLSVFLVPLFYVVVRKFFKETAHEHEMAVKHAAEAGITGSDDSQH"},"dna_sequence":{"accession":"NC_003112","fmin":"1791966","fmax":"1795170","strand":"-","sequence":"TTAATGTTGGCTGTCGTCCGAACCGGTGATGCCCGCTTCGGCGGCGTGTTTTACTGCCATTTCGTGTTCGTGCGCGGTTTCTTTGAAGAATTTGCGCACCACCACATAGAAAAGCGGAACAAGGAACACGGACAAGAGCGTGCCGATGAGCATCCCCCAGAATACGGTTGTACCGATGGCGCGCTGGCTGGCAGAACTTGCACCGCCGGCAATATACAGGGGAACCACGCCCAAAATAAAGGCGAACGAGGTCATGATAATCGGACGGAAACGCAGGCGGGCGGCTTCCAAAGCGGCTTCAACCGCGCTTTTCCCTTGCGCTTGAAGGTCTTTGGCAAATTCGATAATCAAAATCGCATTTTTCGCACTCAAACCCATCACGGTAACGAAACCGACTTGAAAGTAGATGTCGTTGGCGAACGAGGGAACGCTGCCCAACAGTCCTTCAAACAGGTTGCGCCCGGTTACGCCCGCAGCCGCACCGATCAAACCCAACGGAATCACAAGGATGACCGCCAGCGGAATCGACCAGCTTTCATAAAGCGCGGCAAGTACCAAAAATACGGCTGCAACCGCCAAACCGTACAAAATCAGGGTTTGCGAGCCGCCTTTTGCCTCTTCGCGCGACTGTCCGCCCCACTCCAGGCTGTAACCGCCGCCCAATTCGTCAACCATTTTTTGAACCGCCGCCATAGCCTGCCCGGTGGAAACGCCGGTTGCAGGCGAAGCGGACAGCTTCATCGAAGGATAACCGTTGAAGCGTACGCTCTGTTCCGTACCGTTTTCCCAAGAAACAGTAGCAATGGTGGAAAGCGGTACGGCGACGCCGGATTTGTTCGGCACGGTCAGGTTCAAAATATCGGCAGGCTGCATACGGGCATCCTCGTCGGCCTGCACCATCACGCGTTGCAGACGGCCTTGGTTCGGGAAGTCGCTGACATAAGACGAACTCAGCGCGCTTGCCAATGCGGTGCGGATGTCGGCAAACGAAATGCCTTGCGCCGCCGCCGCGGCACGGTTGATGTCGATTTTCAACTGCGGCGAGTCTTCCAAACCGCCAGCACGGACGGTGCTGGGGTCAAACAAACCGCTGGCACGCATTTTCTGAATCAACTCGTTGCGCTTCGCCAGCAATGCGGTATGGCCGGTATTGTTGCGGTCTTGCAGGTTGATGCTCAGACCCGAACCGTTGCCCAACTCCAGAATCGGAGGCGGGACGACGGCGATGCCAAAACCGTCTTTAAGCGTCCCCATCATCATACCCGTCAGCTTGCCGGCAATCGCAACGGCATCGCTGCCGGGCGCGGTACGCTCGTTCCAATCTTTCAATATGGCAAAACCCATCGCCATATTCTGACCGCTGCCCGAAAAGCTGAAGCCGGAAACGGTAATGATGTTTTCTATTTCAGGAATGCTTTTCGCCAGTTGGGTAACTTGCGCCAAAGTCGCATTGGTGCGCTCTTGGGTCGCTCCTGCAGGCAGTTGCACGCTGACCATGACGAAGCCTTGGTCTTCGGTCGGCAGGAATGAAGTCGGCAGGCGCATAAACAGGAACACGCCCACAACCGCCAAGCCGATATAGACAACCATCATGCGGAAAGTCTTACGCAGCACTTTGGCAACCCGGCCTTCGTAACCGTGCGTCCAACTGTTGAATTTCTTGTTAAACCAGCCGAAGAAACCTTTTTTCTCTTCGTGATGCCCTTTCGGGATTGTCTTCAACATTGTGGCACACAAAGCAGGGGTAAGGGTCAGCGCAAGGAAGGCGGAGAATGCGATTGATGACGCCATCGTCAGGGCAAACTGTTTGTAAATATTGCCCGTCGCCCCGCTGAACATCGCCAACGGTACGAACACGGAAATCAGAACGGCGGTAATACCGATGACCGCGCCCGAAATCTGACCCATCGCTTTTTTGGTCGCTTCTTTGGGCGGCAAGCCTTCACCCGCCATAATGCGCTCGACGTTTTCAACCACCACAATCGCGTCATCGACCACGATGCCGATGACCAAAACCATCGCAAACATGGTCAGTACGTTAATCGACATGCCCATATAAGAGATGAAGGCGAAACCGCCCAACAGCGAAATCGGTACGACGATGGTCGGAATCAGCGTATAACGGATGTTTTGCAGGAAGAGATACATTACGACAAACACCAGCACCATCGCTTCGATTAAAGTGTGAATCACTTTTTCAATCGAAATTTCGACGAATTTGGAAGTATCGTAAGGGGTTTTCCAGCTCATACCCTGAGGAAAGTATTTTTCCAACGTCGCCATGCGTTCTTTAACCGCCTTTGCCGTCGCCATCGCATTGCCGCTGTTGGACAGCATCACCGCCATACCGGTGGTATTTACACCGTTCAGACGGGTTGAGGAAGAATAGTCTTCCATACCCAGTCCGACCCTTGCCACATCCTTCAGGTAAACATTAGAACCGTCGGTATTGGCGCGGAGGATGACGTTGCCGAATTCTTCTGCCGTACCCAACTGCCCTTGCGCCGTTACGGTAGCCGTAACCGTCTGTCCGCGAACGGCGGGAAGCGAACCGATAGAACCCGCTGAAATCTGGACGTTCTGGGCGGACAGCGCGCTGCCAACATCGGCAAACGACAAATTGTAGTTTTGCAGTTTCTTAGGATCAACCCAAATCCGCATCGCGCGTTGCGCGCCGAACAGGCGTACCTGCCCCACGCCTTCGATACGCTGCAACTCGGGAACGATATTACGCTGCGCGTAGTCGTTCATCTCTTCGGTTGACTGCACATCCGACGAAAGCATCACAATCATCAGGAAATTGGAACGCGCCTTGGATACGGTTACGCCGTATTGCTGGACAGTTGCCGGCAGCGTGCTCAATACTTCGGAAAGCTTGTTCTGCACTTCCACCTGCGCCAGATTCTCGTCGGTATCGGGCGTAAAGGTCAGGCTCACGCTGCCGCTGCCGCTCGAATCGGCGGAAGTGGACATATAATCCAAACCTTCCACGCCGTTCATATTCCGCTCGATCACGGAAAGCACGCTGTCTTCCATTACCTGCGCGGACGCGCCCGGATAAGTGGCCCTCAGGGTGATGGTCGGGGCGGCGACGGACGGATATTGCGAAACCGGCAGGCTTTTGATGCCGAAAATACCCGCCGCAATAATGAAAATCGAAATAACCCACGCAAAAATGGGGCGGTCGATAAAAAATTTAGCCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39597","NCBI_taxonomy_name":"Neisseria meningitidis MC58","NCBI_taxonomy_id":"122586"}}}},"ARO_accession":"3000811","ARO_id":"37191","ARO_name":"mtrD","ARO_description":"MtrD is the inner membrane multidrug transporter of the MtrCDE efflux complex.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35971":{"category_aro_accession":"0000054","category_aro_cvterm_id":"35971","category_aro_name":"penicillin","category_aro_description":"Penicillin (sometimes abbreviated PCN) is a beta-lactam antibiotic used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms. It works by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1939":{"model_id":"1939","model_name":"AAC(6')-Ix","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"170":{"protein_sequence":{"accession":"AAD03496.1","sequence":"MNIMPISESQLSDWLALRSLLWPDHDDAHLLEMHQLLKQTDTLQLLAYTDSQQAVAMLEASIRHEYVNGTQTSPVAFLEGIYILPEYRRSGIATQLVQYVEEWAKQFACTEFASDAAIDNTISHAMHRALGFHETERVVYFKKNIG"},"dna_sequence":{"accession":"AF031332","fmin":"0","fmax":"441","strand":"+","sequence":"ATGAATATTATGCCGATATCTGAATCACAATTATCAGATTGGCTAGCATTAAGAAGCTTACTCTGGCCTGATCATGACGATGCGCATTTATTGGAAATGCATCAGCTACTTAAACAAACAGATACTTTACAATTATTGGCTTATACCGATAGCCAACAAGCAGTTGCAATGTTAGAAGCATCGATTCGGCATGAATATGTGAATGGTACGCAAACCTCACCTGTGGCTTTTCTGGAAGGGATTTATATCTTACCTGAATATCGACGTTCAGGCATTGCGACCCAGTTAGTTCAGTACGTAGAGGAGTGGGCGAAACAATTTGCATGTACTGAGTTCGCTTCAGATGCAGCGATTGACAATACGATTAGCCATGCAATGCATCGAGCACTGGGTTTTCATGAAACTGAACGTGTGGTGTATTTTAAGAAAAATATCGGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39519","NCBI_taxonomy_name":"Acinetobacter sp. BM2722","NCBI_taxonomy_id":"70351"}}}},"ARO_accession":"3002568","ARO_id":"38968","ARO_name":"AAC(6')-Ix","ARO_description":"AAC(6')-Ix is a chromosomal-encoded aminoglycoside acetyltransferase in Acinetobacter sp.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1940":{"model_id":"1940","model_name":"QnrB30","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"327":{"protein_sequence":{"accession":"ADM52194.1","sequence":"MTPLLYKKTGTNMALALVGEKIDRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSSDLSMADFRNASALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"HM439650","fmin":"0","fmax":"681","strand":"+","sequence":"ATGACGCCATTACTGTATAAAAAAACAGGTACAAATATGGCACTGGCACTCGTTGGCGAAAAAATTGACAGAAACCGCTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCGATGCTAAAAGATGCCATTTTTAAAAGCAGTGATTTATCCATGGCGGATTTTCGCAATGCCAGTGCGCTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGCGCAAGTTTTATGAATATGATCACTACTCGCACCTGGTTTTGTAGTGCATATATCACTAACACAAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGCTGGAAAAGTGTGAGCTGTGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGGGACTTAGATATTCGGGGCGTTGATTTACAAGGCGTTAAGTTGGACAACTACCAGGCATCGTTGCTCATGGAACGTCTTGGCATCGCGGTGATTGGTTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39584","NCBI_taxonomy_name":"Citrobacter braakii","NCBI_taxonomy_id":"57706"}}}},"ARO_accession":"3002745","ARO_id":"39179","ARO_name":"QnrB30","ARO_description":"QnrB30 is a plasmid-mediated quinolone resistance protein found in Citrobacter braakii","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1925":{"model_id":"1925","model_name":"MexB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1950"}},"model_sequences":{"sequence":{"113":{"protein_sequence":{"accession":"AAA74437.1","sequence":"MSKFFIDRPIFAWVIALVIMLAGGLSILSLPVNQYPAIAPPAIAVQVSYPGASAETVQDTVVQVIEQQMNGIDNLRYISSESNSDGSMTTTVTFEQGTDPDIAQVQVQNKLQLATPLLPQEVQRQGIRVTKAVKNFLMVVGVVSTDGSMTKEDLSNYIVSNIQDPLSRTKGVGDFQVFGSQYSMRIWLDPAKLNSYQLTPGDVSSAIQAQNVQISSGQLGGLPAVKGQQLNATIIGKTRLQTAEQFENILLKVNPDGSQVRLKDVADVGLGGQDYSINAQFNGSPASGIAIKLATGANALDTAKAIRQTIANLEPFMPQGMKVVYPYDTTPVVSASIHEVVKTLGEAILLVFLVMYLFLQNFRATLIPTIAVPVVLLGTFGVLAAFGFSINTLTMFGMVLAIGLLVDDAIVVVENVERVMAEEGLSPREAARKSMGQIQGALVGIAMVLSAVFLPMAFFGGSTGVIYRQFSITIVSAMALSVIVALILTPALCATMLKPIEKGDHGEHKGGFFGWFNRMFLSTTHGYERGVASILKHRAPYLLIYVVIVAGMIWMFTRIPTAFLPDEDQGVLFAQVQTPPGSSAERTQVVVDSMREYLLEKESSSVSSVFTVTGFNFAGRGQSSGMAFIMLKPWEERPGGENSVFELAKRAQMHFFSFKDAMVFAFAPPSVLELGNATGFDLFLQDQAGVGHEVLLQARNKFLMLAAQNPALQRVRPNGMSDEPQYKLEIDDEKASALGVSLADINSTVSIAWGSSYVNDFIDRGRVKRVYLQGRPDARMNPDDLSKWYVRNDKGEMVPFNAFATGKWEYGSPKLERYNGVPAMEILGEPAPGLSSGDAMAAVEEIVKQLPKGVGYSWTGLSYEERLSGSQAPALYALSLLVVFLCLAALYESWSIPFSVMLVVPLGVIGALLATSMRGLSNDVFFQVGLLTTIGLSAKNAILIVEFAKELHEQGKGIVEAAIEACRMRLRPIVMTSLAFILGVVPLAISTGAGSGSQHAIGTGVIGGMVTATVLAIFWVPLFYVAVSTLFKDEASKQQASVEKGQ"},"dna_sequence":{"accession":"L11616","fmin":"1569","fmax":"4710","strand":"+","sequence":"ATGTCGAAGTTTTTCATTGATAGGCCCATTTTCGCGTGGGTGATCGCCTTGGTGATCATGCTCGCGGGCGGCCTGTCGATCCTCAGTCTGCCGGTCAACCAGTACCCGGCCATCGCCCCGCCGGCCATCGCCGTGCAGGTGAGCTACCCGGGCGCCTCGGCCGAGACGGTGCAGGACACCGTGGTCCAGGTGATCGAGCAGCAGATGAACGGGATCGACAATCTGCGCTACATCTCCTCGGAGAGTAACTCCGACGGCAGCATGACCACCACCGTGACCTTCGAACAGGGCACCGACCCCGACATCGCCCAGGTCCAGGTGCAGAACAAGCTGCAACTGGCCACCCCGCTACTGCCGCAGGAAGTGCAGCGCCAGGGGATCCGGGTGACCAAGGCGGTGAAGAACTTCCTCATGGTGGTCGGTGTGGTTTCCACCGACGGCAGCATGACCAAGGAAGACCTGTCGAACTACATCGTTTCCAACATCCAGGACCCACTCTCGCGGACCAAGGGCGTCGGTGACTTCCAGGTGTTCGGCTCGCAGTACTCGATGCGCATCTGGCTCGACCCGGCCAAGCTGAACAGCTACCAGCTGACCCCCGGCGACGTGAGCAGCGCGATCCAGGCGCAGAACGTGCAGATTTCCTCCGGCCAGCTCGGCGGCTTGCCGGCGGTCAAGGGCCAGCAGCTCAACGCCACCATCATCGGCAAGACCCGCCTGCAGACCGCGGAGCAATTCGAGAACATCCTGCTCAAGGTCAATCCCGACGGTTCCCAGGTGCGCCTGAAGGACGTCGCCGATGTAGGCCTGGGCGGCCAGGACTACAGCATCAACGCGCAGTTCAACGGCAGCCCGGCGTCCGGTATCGCGATCAAGCTGGCCACCGGCGCCAACGCGCTGGATACCGCCAAGGCGATCCGCCAGACCATCGCCAACCTGGAACCGTTCATGCCGCAGGGCATGAAGGTGGTCTACCCGTACGACACCACCCCGGTGGTCTCGGCCTCGATCCATGAGGTAGTGAAGACCCTCGGCGAGGCGATCCTCCTCGTGTTCCTGGTGATGTACCTGTTCCTGCAGAACTTCCGCGCCACGCTGATCCCGACCATCGCCGTACCGGTGGTGCTGCTGGGGACCTTCGGCGTGCTCGCCGCGTTCGGCTTCTCGATCAACACCCTGACCATGTTCGGCATGGTGCTGGCCATCGGCTTGCTGGTGGACGACGCCATCGTGGTGGTGGAGAACGTCGAGCGGGTGATGGCCGAGGAAGGCCTGTCGCCAAGGGAGGCGGCGCGCAAGTCCATGGGCCAGATCCAGGGCGCGCTGGTCGGTATCGCCATGGTGCTCTCGGCGGTATTCCTGCCGATGGCGTTCTTCGGCGGCTCCACCGGGGTGATCTACCGGCAGTTCTCCATCACCATCGTGTCGGCCATGGCCCTCTCGGTGATCGTGGCGCTGATCCTCACCCCGGCGCTCTGCGCGACCATGCTCAAGCCGATCGAGAAAGGCGACCATGGCGAGCACAAGGGCGGCTTCTTCGGCTGGTTCAACCGGATGTTCCTTTCCACCACCCACGGCTACGAGCGGGGCGTGGCGTCGATCCTCAAGCATCGCGCGCCGTACCTGCTGATCTACGTGGTGATCGTGGCCGGGATGATCTGGATGTTCACCCGCATTCCCACCGCGTTCCTCCCCGACGAGGACCAGGGCGTACTGTTCGCCCAGGTACAGACCCCGCCGGGCTCCAGTGCCGAGCGTACCCAGGTGGTGGTGGACTCGATGCGCGAATACCTGCTGGAGAAGGAAAGCTCTTCGGTCAGCTCGGTGTTCACCGTGACCGGCTTCAACTTCGCCGGCCGCGGCCAGAGTTCGGGCATGGCGTTCATCATGCTCAAGCCCTGGGAAGAGCGTCCCGGTGGCGAGAACAGCGTGTTCGAACTGGCCAAGCGCGCGCAGATGCACTTCTTCAGCTTCAAGGACGCGATGGTGTTCGCCTTCGCGCCGCCGTCGGTACTGGAACTGGGTAACGCCACCGGCTTCGACCTGTTCCTCCAGGACCAGGCGGGTGTCGGCCACGAAGTCCTGCTCCAGGCGCGCAACAAGTTCCTCATGCTCGCCGCGCAGAACCCGGCGCTGCAACGCGTGCGCCCCAACGGCATGAGCGACGAACCGCAGTACAAGCTGGAGATCGACGACGAGAAGGCCAGCGCCCTCGGCGTGTCCCTTGCCGACATCAACAGCACCGTGTCCATCGCCTGGGGTTCCAGCTACGTCAACGATTTCATCGACCGTGGCCGGGTCAAGCGGGTCTACCTGCAGGGCAGGCCGGACGCGCGGATGAACCCGGACGACCTGAGCAAGTGGTACGTGCGCAACGACAAGGGCGAGATGGTGCCGTTCAACGCCTTCGCCACCGGCAAGTGGGAATACGGTTCGCCGAAGCTGGAGCGCTACAATGGCGTGCCGGCGATGGAGATCCTCGGCGAGCCGGCGCCCGGCCTGAGTTCCGGTGACGCCATGGCGGCGGTCGAGGAGATCGTCAAGCAATTGCCGAAAGGCGTTGGCTACTCCTGGACCGGCCTGTCCTACGAGGAGCGCTTGTCCGGCTCGCAGGCGCCGGCGCTGTATGCGCTGTCGCTGCTGGTGGTGTTCCTCTGCCTGGCGGCCCTGTACGAAAGCTGGTCGATTCCGTTCTCGGTGATGCTGGTGGTGCCGTTGGGCGTGATCGGTGCGCTGCTGGCGACGTCCATGCGCGGCCTGTCCAACGACGTGTTCTTCCAGGTGGGCCTGTTGACGACCATCGGCCTGTCGGCGAAGAACGCCATTCTCATCGTGGAGTTCGCCAAGGAGCTGCACGAGCAGGGCAAGGGCATCGTCGAGGCGGCCATCGAAGCCTGCCGCATGCGTCTGCGGCCGATCGTGATGACCTCCCTGGCGTTCATCCTCGGCGTGGTCCCGCTGGCGATCTCCACCGGCGCCGGCTCGGGCAGCCAGCATGCGATCGGTACCGGCGTGATCGGCGGCATGGTCACTGCGACCGTCCTGGCGATCTTCTGGGTACCGCTGTTCTACGTGGCGGTCAGCACGCTGTTCAAGGACGAGGCGTCCAAGCAGCAGGCGTCCGTCGAAAAGGGGCAATGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3000378","ARO_id":"36517","ARO_name":"MexB","ARO_description":"MexB is the inner membrane multidrug exporter of the efflux complex MexAB-OprM.","ARO_category":{"35996":{"category_aro_accession":"0000079","category_aro_cvterm_id":"35996","category_aro_name":"clavulanate","category_aro_description":"Clavulanic acid is a beta-lactamase inhibitor (marketed by GlaxoSmithKline, formerly Beecham) combined with penicillin group antibiotics to overcome certain types of antibiotic resistance. It is used to overcome resistance in bacteria that secrete beta-lactamase, which otherwise inactivates most penicillins.","category_aro_class_name":"Adjuvant"},"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35979":{"category_aro_accession":"0000062","category_aro_cvterm_id":"35979","category_aro_name":"ceftriaxone","category_aro_description":"Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36468":{"category_aro_accession":"3000329","category_aro_cvterm_id":"36468","category_aro_name":"sulfamethoxazole","category_aro_description":"Sulfamethoxazole is a sulfonamide antibiotic usually taken with trimethoprim, a diaminopyrimidine antibiotic. Sulfamethoxazole inhibits dihydropteroate synthase, essential to tetrahydrofolic acid biosynthesis. This pathway generates compounds used in the synthesis of many amino acids and nucleotides.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36689":{"category_aro_accession":"3000550","category_aro_cvterm_id":"36689","category_aro_name":"aztreonam","category_aro_description":"Aztreonam was the first monobactam discovered, and is greatly effective against Gram-negative bacteria while inactive against Gram-positive bacteria. Artreonam is a poor substrate for beta-lactamases, and may even act as an inhibitor. In Gram-negative bacteria, Aztreonam interferes with filamentation, inhibiting cell division and leading to cell death.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"40362":{"category_aro_accession":"3003708","category_aro_cvterm_id":"40362","category_aro_name":"panipenem","category_aro_description":"Panipenem is a carbapenem antibacterial agent with a broad spectrum of in vitro activity covering a wide range of Gram-negative and Gram-positive aerobic and anaerobic bacterial.  It is used in combination with betamipron to inhibit panipenem uptake into the renal tubule and prevent nephrotoxicity.","category_aro_class_name":"Antibiotic"},"40523":{"category_aro_accession":"3003832","category_aro_cvterm_id":"40523","category_aro_name":"ticarcillin","category_aro_description":"Ticarcillin is a carboxypenicillin used for the treatment of Gram-negative bacteria, particularly P. aeruginosa. Ticarcillin's antibiotic properties arise from its ability to prevent cross-linking of peptidoglycan during cell wall synthesis, when the bacteria try to divide, causing cell death.","category_aro_class_name":"Antibiotic"},"40957":{"category_aro_accession":"3004024","category_aro_cvterm_id":"40957","category_aro_name":"trimethoprim-sulfamethoxazole","category_aro_description":"An antibiotic cocktail containing the diaminopyrimidine antibiotic Trimethoprim and the sulfonamide antibiotic sulfamethoxazole (1 TMP:5 SMX).","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36421":{"category_aro_accession":"3000282","category_aro_cvterm_id":"36421","category_aro_name":"sulfonamide antibiotic","category_aro_description":"Sulfonamides are broad spectrum, synthetic antibiotics that contain the sulfonamide group. Sulfonamides inhibit dihydropteroate synthase, which catalyzes the conversion of p-aminobenzoic acid to dihydropteroic acid as part of the tetrahydrofolic acid biosynthetic pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor of many nucleotides and amino acids. Many sulfamides are taken with trimethoprim, an inhibitor of dihydrofolate reductase, also disturbing the trihydrofolic acid synthesis pathway.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1917":{"model_id":"1917","model_name":"tet(30)","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"740"}},"model_sequences":{"sequence":{"606":{"protein_sequence":{"accession":"AAD09860.1","sequence":"MNKALIVILSTVALDAIGAGLIFPILPDILVEVTGGGDIGFLYGVMLGVFAVMQFVFSPILGALSDRFGRRPVLLLSLAGTLLDYLVMAFSPLGWVLVVGRAMAGITSANMAVASAYITDITPAEQRAQRFGTVGAVMSLGFIIGPVIGGVIGAWWLRAPFLVAALFNGLNLFVALFVLPESRKAGPGKFAFKELNPLAPLVWLWNFKPLLPLVTVSVVFGLVAAIPGTIWVLYGAERFGWDSVHMGLSLSVFGVSGALAQAFLVGPLSRRFGDLGTLMIGVGFDMLAYMLMAFANQSWMGYAVAPLFALGGVAMPALQSLVTSRVSDDQQGQLQGVLASLMSLAGIIGPVLTTAVFFSTKSIWIGTIWLVGAALYLLALPLFATVKTPKAVAA"},"dna_sequence":{"accession":"AF090987","fmin":"0","fmax":"1185","strand":"+","sequence":"ATGAACAAGGCCCTTATCGTTATTCTCTCAACCGTTGCCCTCGACGCCATTGGCGCAGGCCTGATCTTCCCGATCCTGCCGGACATCTTGGTCGAGGTGACTGGCGGCGGCGACATCGGGTTCCTCTATGGGGTCATGCTGGGGGTATTCGCCGTCATGCAATTTGTGTTCTCGCCGATCCTTGGTGCGCTCAGCGACCGGTTCGGTCGGCGCCCGGTCTTGTTGCTTTCTTTGGCCGGTACCCTGCTTGATTACCTTGTTATGGCATTTTCCCCGCTCGGCTGGGTGCTCGTCGTCGGGCGGGCCATGGCGGGGATCACCAGCGCAAATATGGCGGTGGCAAGCGCCTACATCACTGACATCACCCCAGCCGAGCAGCGCGCGCAGCGGTTTGGCACGGTTGGTGCCGTGATGAGCCTGGGCTTTATCATCGGTCCCGTCATTGGTGGCGTCATTGGCGCCTGGTGGCTTCGGGCACCATTTCTTGTGGCAGCCCTGTTCAATGGCCTCAACCTGTTCGTCGCGCTGTTTGTTCTGCCGGAAAGCCGAAAGGCCGGTCCGGGCAAGTTTGCGTTCAAGGAACTTAACCCGTTGGCGCCATTGGTGTGGCTTTGGAATTTCAAGCCGCTCCTGCCACTTGTAACCGTCTCTGTCGTCTTCGGTCTGGTGGCCGCCATCCCGGGAACGATCTGGGTGCTCTATGGCGCCGAGCGGTTCGGATGGGATTCGGTGCATATGGGCCTGTCGCTATCGGTTTTCGGCGTCAGTGGCGCCCTGGCGCAGGCCTTTCTCGTCGGGCCGCTCTCGCGCCGCTTTGGTGATTTGGGCACGTTGATGATCGGCGTTGGCTTTGACATGCTGGCTTATATGCTGATGGCCTTCGCCAACCAGAGCTGGATGGGCTACGCGGTAGCGCCCCTGTTTGCATTGGGCGGCGTTGCCATGCCGGCGCTGCAATCTCTGGTAACCAGCCGCGTGAGCGATGATCAGCAGGGCCAGTTGCAGGGCGTGCTCGCCAGCCTCATGAGCCTGGCGGGTATAATAGGGCCGGTGCTGACCACCGCAGTGTTCTTTTCCACCAAAAGCATCTGGATCGGGACGATCTGGCTGGTGGGTGCCGCACTTTATCTTCTCGCCTTGCCGCTGTTCGCAACGGTGAAAACCCCGAAGGCTGTGGCGGCTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36775","NCBI_taxonomy_name":"Agrobacterium tumefaciens str. C58","NCBI_taxonomy_id":"176299"}}}},"ARO_accession":"3000561","ARO_id":"36700","ARO_name":"tet(30)","ARO_description":"Tet30 is a tetracycline efflux pump found in agrobacterium, a Gram-negative bacterium.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1835":{"model_id":"1835","model_name":"tet(38)","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"850"}},"model_sequences":{"sequence":{"537":{"protein_sequence":{"accession":"AAV80464.1","sequence":"MNVEYSKIKKAVPILLFLFVFSLVIDNSFKLISVAIADDLNISVTTVSWQATLAGLVIGIGAVVYASLSDAISIRTLFIYGVILIIIGSIIGYIFQHQFPLLLVGRIIQTAGLAAAETLYVIYVAKYLSKEDQKTYLGLSTSSYSLSLVIGTLSGGFISTYLHWTNMFLIALIVVFTLPFLFKLLPKENNTNKAHLDFVGLILVATIATTVMLFITNFNWLYMIGALIAIIVFALYIKNAQRPLVNKSFFQNKRYASFLFIVFVMYAIQLGYIFTFPFIMEQIYHLQLDTTSLLLVPGYIVAVIVGALSGKIGEYLNSKQAIITAIILIALSLILPAFAVGNHISIFVISMIFFAGSFALMYAPLLNEAIKTIDLNMTGVAIGFYNLIINVAVSVGIAIAAALIDFKALNFPGNDALSSHFGIILIILGLMSIVGLVLFVILNRWTQSEK"},"dna_sequence":{"accession":"AY825285","fmin":"0","fmax":"1353","strand":"+","sequence":"ATGAATGTTGAATATTCTAAAATAAAGAAAGCAGTACCTATTTTATTATTCTTATTTGTATTCAGTTTGGTTATAGACAACTCATTTAAATTGATTTCTGTAGCCATTGCTGATGACTTAAACATATCTGTAACGACAGTAAGTTGGCAAGCGACATTAGCCGGTTTAGTAATTGGTATTGGCGCTGTAGTATACGCTTCATTATCTGATGCCATTAGTATACGCACACTATTTATTTATGGCGTGATATTAATCATTATCGGATCAATTATTGGTTACATTTTCCAACATCAATTCCCATTACTTTTAGTTGGACGTATTATTCAAACTGCCGGTTTAGCTGCTGCAGAGACATTATATGTGATATATGTTGCAAAGTATCTTTCTAAAGAGGACCAGAAGACTTACCTTGGCTTAAGTACGAGCAGTTATTCCTTGTCATTAGTTATCGGTACATTATCAGGTGGATTTATTTCTACGTATTTACACTGGACAAATATGTTTTTAATTGCATTAATCGTAGTATTTACGTTGCCATTCCTATTTAAATTATTACCAAAAGAAAATAATACGAATAAAGCTCATTTAGATTTTGTTGGCTTAATTCTAGTGGCAACTATTGCTACAACAGTCATGCTGTTTATTACGAACTTTAATTGGTTATATATGATTGGTGCCTTAATTGCGATTATCGTTTTTGCGCTATATATTAAAAATGCGCAACGTCCATTAGTAAATAAATCATTTTTCCAAAATAAACGTTATGCTTCATTTTTATTTATAGTATTTGTAATGTATGCTATCCAATTGGGTTATATTTTTACGTTCCCATTCATAATGGAGCAAATTTATCATCTGCAACTAGACACAACATCACTGTTATTAGTACCGGGTTATATAGTAGCAGTCATTGTTGGTGCATTAAGTGGTAAAATCGGCGAATATCTGAATTCAAAACAAGCGATTATCACAGCAATTATTTTAATAGCACTGAGCTTGATTTTACCTGCATTTGCAGTAGGTAATCACATTTCAATCTTCGTCATTTCTATGATATTCTTTGCAGGTAGCTTTGCTTTAATGTATGCACCTTTACTTAACGAAGCCATTAAAACAATAGATCTTAATATGACAGGTGTGGCTATTGGTTTTTATAATTTAATTATTAATGTGGCGGTATCTGTAGGTATTGCGATTGCTGCGGCTCTAATCGATTTTAAAGCATTAAATTTCCCAGGCAATGATGCATTAAGTTCACATTTCGGTATTATTTTAATTATTTTAGGTTTAATGAGTATTGTCGGATTAGTTTTATTCGTCATCTTAAATCGTTGGACACAATCTGAAAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3000565","ARO_id":"36704","ARO_name":"tet(38)","ARO_description":"Tet38 is a tetracycline efflux pump found in the Gram-positive Staphylococcus aureus. It is regulated by mgrA, which also regulates NorB.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1808":{"model_id":"1808","model_name":"tet(A)","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"275":{"protein_sequence":{"accession":"YP_007503840.1","sequence":"MNSSTKIALVITLLDAMGIGLIMPVLPTLLREFIASEDIANHFGVLLALYALMQVIFAPWLGKMSDRFGRRPVLLLSLIGASLDYLLLAFSSALWMLYLGRLLSGITGATGAVAASVIADTTSASQRVKWFGWLGASFGLGLIAGPIIGGFAGEISPHSPFFIAALLNIVTFLVVMFWFRETKNTRDNTDTEVGVETQSNSVYITLFKTMPILLIIYFSAQLIGQIPATVWVLFTENRFGWNSMMVGFSLAGLGLLHSVFQAFVAGRIATKWGEKTAVLLGFIADSSAFAFLAFISEGWLVFPVLILLAGGGIALPALQGVMSIQTKSHQQGALQGLLVSLTNATGVIGPLLFAVIYNHSLPIWDGWIWIIGLAFYCIIILLSMTFMLTPQAQGSKQETSA"},"dna_sequence":{"accession":"NC_020418","fmin":"458865","fmax":"460071","strand":"+","sequence":"ATGAATAGTTCGACAAAGATCGCATTGGTAATTACGTTACTCGATGCCATGGGGATTGGCCTTATCATGCCAGTCTTGCCAACGTTATTACGTGAATTTATTGCTTCGGAAGATATCGCTAACCACTTTGGCGTATTGCTTGCACTTTATGCGTTAATGCAGGTTATCTTTGCTCCTTGGCTTGGAAAAATGTCTGACCGATTTGGTCGGCGCCCAGTGCTGTTGTTGTCATTAATAGGCGCATCGCTGGATTACTTATTGCTGGCTTTTTCAAGTGCGCTTTGGATGCTGTATTTAGGCCGTTTGCTTTCAGGGATCACAGGAGCTACTGGGGCTGTCGCGGCATCGGTCATTGCCGATACCACCTCAGCTTCTCAACGCGTGAAGTGGTTCGGTTGGTTAGGGGCAAGTTTTGGGCTTGGTTTAATAGCGGGGCCTATTATTGGTGGTTTTGCAGGAGAGATTTCACCGCATAGTCCCTTTTTTATCGCTGCGTTGCTAAATATTGTCACTTTCCTTGTGGTTATGTTTTGGTTCCGTGAAACCAAAAATACACGTGATAATACAGATACCGAAGTAGGGGTTGAGACGCAATCGAATTCGGTATACATCACTTTATTTAAAACGATGCCCATTTTGTTGATTATTTATTTTTCAGCGCAATTGATAGGCCAAATTCCCGCAACGGTGTGGGTGCTATTTACCGAAAATCGTTTTGGATGGAATAGCATGATGGTTGGCTTTTCATTAGCGGGTCTTGGTCTTTTACACTCAGTATTCCAAGCCTTTGTGGCAGGAAGAATAGCCACTAAATGGGGCGAAAAAACGGCAGTACTGCTCGGATTTATTGCAGATAGTAGTGCATTTGCCTTTTTAGCGTTTATATCTGAAGGTTGGTTAGTTTTCCCTGTTTTAATTTTATTGGCTGGTGGTGGGATCGCTTTACCTGCATTACAGGGAGTGATGTCTATCCAAACAAAGAGTCATCAGCAAGGTGCTTTACAGGGATTATTGGTGAGCCTTACCAATGCAACCGGTGTTATTGGCCCATTACTGTTTGCTGTTATTTATAATCATTCACTACCAATTTGGGATGGCTGGATTTGGATTATTGGTTTAGCGTTTTACTGTATTATTATCCTGCTATCGATGACCTTCATGTTAACCCCTCAAGCTCAGGGGAGTAAACAGGAGACAAGTGCTTAGT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40075","NCBI_taxonomy_name":"Morganella morganii subsp. morganii KT","NCBI_taxonomy_id":"1124991"}}}},"ARO_accession":"3000165","ARO_id":"36304","ARO_name":"tet(A)","ARO_description":"TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1885":{"model_id":"1885","model_name":"tet(Z)","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"281":{"protein_sequence":{"accession":"AAD25063.1","sequence":"MLITATLDAAGLGLVMPILPTLLDQVGAPDDMIPLHVGLLTALYAIMQFLCAPILGRLSDRFGRRRVLVASLAGATIDYLVLALTDTLWVFYLARAVAGITGATNAVTATVIADITPPDQRAKRYGWLGACYGGGMIAGPAIGGLFGGVSPHLPFLVAAALAGITLVLSASLLRETRPPGSNGSHAQQPGTAKRTAVPGMLILLAVFGIVQFIGQAPGSTWVLFTQQRLDWNPVEVGVSLSIFGMVQVFVQAALTGRIVSRIGETRAILVGIAADAIGLIGLALIASTWAMLPILAALGLGSITLPALQTLLSRRAPEQQQGRLQGTLASLNSLTSIIGPVTFTGIFALTRTNADGTLWICAAALYVLCALLMIRETCASRRSR"},"dna_sequence":{"accession":"AF121000","fmin":"0","fmax":"1155","strand":"-","sequence":"TTATCGAGATCGCCGTGAGGCGCATGTCTCACGGATCATCAGGAGGGCGCAGAGAACGTAGAGCGCTGCGGCGCAGATCCAGAGGGTGCCGTCTGCATTCGTTCGGGTGAGTGCGAAAATGCCGGTGAAGGTGACCGGGCCGATGATCGAGGTGAGGCTGTTCAGGCTTGCAAGTGTTCCCTGCAGGCGTCCCTGCTGCTGCTCGGGCGCGCGTCTCGAGAGCAGCGTCTGCAGTGCGGGCAACGTGATGCTGCCGAGTCCGAGCGCTGCGAGGATCGGTAGCATCGCCCATGTGCTGGCGATGAGGGCAAGGCCGATGAGCCCAATGGCGTCTGCGGCGATACCGACGAGGATCGCCCGGGTCTCGCCGATCCGGGACACGATGCGTCCGGTCAGTGCCGCCTGCACGAATACTTGCACCATTCCGAAGATGGATAGCGAAACGCCGACTTCGACGGGGTTCCAGTCGAGGCGCTGCTGCGTGAAGAGCACCCAGGTGGAGCCTGGTGCTTGGCCGATGAACTGCACGATGCCGAAGACTGCGAGAAGGATAAGCATCCCCGGCACTGCGGTTCGCTTCGCCGTACCGGGTTGCTGTGCGTGCGAGCCGTTGCTGCCCGGTGGCCGCGTCTCACGCAGAAGACTCGCGCTGAGTACGAGGGTGATTCCGGCGAGCGCGGCGGCGACGAGGAATGGCAGATGCGGTGAGACCCCGCCGAAAAGACCGCCAATGGCGGGACCCGCGATCATGCCACCGCCGTAGCATGCGCCGAGCCACCCGTAGCGTTTTGCGCGCTGATCCGGCGGAGTAATGTCGGCGATCACCGTCGCGGTGACGGCGTTCGTGGCGCCGGTAATGCCTGCAACCGCGCGGGCGAGGTAAAAGACCCACAGCGTGTCCGTCAGTGCGAGCACGAGGTAGTCGATCGTCGCGCCTGCGAGGGAGGCGACAAGCACGCGGCGGCGTCCGAAACGGTCAGAGAGTCGGCCAAGGATCGGGGCGCAAAGAAACTGCATGATCGCATAGAGCGCTGTCAGTAGTCCGACGTGCAGTGGGATCATGTCGTCGGGGGCACCGACCTGGTCGAGAAGGGTAGGCAAGATCGGCATCACGAGGCCCAGCCCTGCAGCATCGAGGGTCGCCGTGATGAGCAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36777","NCBI_taxonomy_name":"Corynebacterium glutamicum","NCBI_taxonomy_id":"1718"}}}},"ARO_accession":"3000183","ARO_id":"36322","ARO_name":"tet(Z)","ARO_description":"TetZ is a tetracycline efflux protein found in Gram-positive bacteria (Corynebacterium and Lactobacillus). It is associated with plasmid DNA.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1941":{"model_id":"1941","model_name":"SHV-98","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"994":{"protein_sequence":{"accession":"CAQ03503.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPAIMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM941844","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGATCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001336","ARO_id":"37736","ARO_name":"SHV-98","ARO_description":"SHV-98 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1944":{"model_id":"1944","model_name":"CTX-M-148","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1351":{"protein_sequence":{"accession":"AHX39589.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVIAVAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAERRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"KJ020574","fmin":"244","fmax":"1120","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATAGCGGTCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGCGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002006","ARO_id":"38406","ARO_name":"CTX-M-148","ARO_description":"CTX-M-148 is a beta-lactamase. From the Lahey list of CTX-M beta-lactamases.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1945":{"model_id":"1945","model_name":"SHV-50","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1236":{"protein_sequence":{"accession":"AAP41108.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMTATLRKLLTSQRLSARSQRHLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AY288915","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGACCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCATCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001107","ARO_id":"37487","ARO_name":"SHV-50","ARO_description":"SHV-50 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1946":{"model_id":"1946","model_name":"CTX-M-10","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1995":{"protein_sequence":{"accession":"AAT68658.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTVDVQQKLAELEQQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"AY598759","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGTGGACGTACAGCAAAAACTTGCCGAATTAGAGCAGCAGTCGGGAGGAAGGCTGGGTGTGGCATTGATTAACACGGCGGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTCGAGATCAAAAAATCTGACCTGGTTAACTATAATCCGATTGCGGAAAAACACGTCAATGGGACGATGTCACTGGCTGAGCTCAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTTACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCTGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACGCTGCGTAATCTGACGCTGGGTAAAGCATTGGGTGACAGCCAACGGGCGCAGCTGGTGACGTGGATGAAAGGCAATACTACCGGTGCAGCGAGTATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGTACCACCAACGATATCGCGGTGATTTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCCCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001873","ARO_id":"38273","ARO_name":"CTX-M-10","ARO_description":"CTX-M-10 is a beta-lactamase found in Escherichia coli","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1947":{"model_id":"1947","model_name":"CTX-M-160","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2091":{"protein_sequence":{"accession":"AJU57235.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPEGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"KP128034","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTYGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGAAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3003168","ARO_id":"39745","ARO_name":"CTX-M-160","ARO_description":"From the Lahey list of beta-lactamases.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1948":{"model_id":"1948","model_name":"TEM-167","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"927":{"protein_sequence":{"accession":"ACJ04051.1","sequence":"MSIQHFRVALIPFFAAFCFPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSVLPAGWFIADKSGASERGSRGIIAALGPDGKPSRIVVIYMTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"FJ360884","fmin":"213","fmax":"1074","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCTTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGTCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACATGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001033","ARO_id":"37413","ARO_name":"TEM-167","ARO_description":"TEM-167 is an extended-spectrum beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1949":{"model_id":"1949","model_name":"cphA6","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"1579":{"protein_sequence":{"accession":"AAP69914.1","sequence":"MMKSWMKCTLAGAVVLMASFWGGSVRAAGISLKQVSGPVYVVEDNYYVKENSMVYFGAKGVTVVGATWTPDTARELHKLIKRVSSKPVLEVINTNYHTDRAGGNAYWKSIGAKVVSTRQTRDLMKSDWAEIVAFTRKGLPEYPDLPLVLPNVVHDGDFTLQEGKVRAFYAGPAHTPDGIFVYFPDEQVLYGNCILKEKLGNLSFANVKAYPQTIERLKAMKLPIKTVIGGHDSPLHGPELIDHYEELIKAAAHS"},"dna_sequence":{"accession":"AY227052","fmin":"0","fmax":"765","strand":"+","sequence":"ATGATGAAAAGTTGGATGAAGTGCACATTGGCCGGGGCCGTGGTGCTGATGGCGAGTTTCTGGGGCGGCAGCGTGCGGGCGGCGGGGATCTCCCTCAAGCAGGTAAGCGGCCCGGTGTATGTGGTGGAGGATAACTACTACGTAAAGGAAAACTCCATGGTCTATTTCGGGGCCAAGGGGGTGACTGTGGTGGGTGCGACCTGGACGCCGGATACCGCCCGCGAGCTGCACAAGCTGATCAAGCGGGTCAGCAGCAAGCCGGTGCTGGAGGTGATCAACACCAACTACCACACCGATCGGGCGGGTGGTAACGCCTACTGGAAGTCCATTGGCGCCAAGGTGGTCTCGACCCGCCAGACCCGGGATCTGATGAAGAGCGACTGGGCCGAGATTGTCGCCTTTACCCGCAAGGGGCTGCCGGAGTACCCAGATCTGCCGCTGGTGCTGCCCAACGTGGTGCACGATGGCGACTTCACCCTGCAAGAGGGCAAGGTGCGCGCCTTCTATGCGGGCCCGGCCCATACGCCGGACGGCATCTTTGTCTACTTCCCCGACGAGCAGGTGCTCTATGGCAACTGCATCCTCAAGGAGAAGCTGGGTAACCTGAGCTTTGCAAATGTGAAGGCCTATCCGCAGACCATCGAGCGACTCAAGGCGATGAAGCTGCCGATCAAGACGGTGATCGGCGGTCACGACTCGCCGCTGCACGGCCCCGAGTTGATTGATCACTATGAAGAGTTGATCAAGGCCGCTGCTCATTCATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39671","NCBI_taxonomy_name":"Aeromonas veronii bv. veronii","NCBI_taxonomy_id":"197701"}}}},"ARO_accession":"3003102","ARO_id":"39668","ARO_name":"cphA6","ARO_description":"cphA6 is an Ambler Class B MBL; subclass B2 originally isolated from Aeromonas veronii. This enzyme has specific activity against carbapenems and is active as a mono-zinc protein.","ARO_category":{"36720":{"category_aro_accession":"3000581","category_aro_cvterm_id":"36720","category_aro_name":"CphA beta-lactamase","category_aro_description":"CphA is an Ambler Class B MBL; subclass B2 originally isolated from Aeromonas hydrophilia.  This enzyme has specific activity against carbapenems and is active as a mono-zinc protein.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1950":{"model_id":"1950","model_name":"arr-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"250"}},"model_sequences":{"sequence":{"393":{"protein_sequence":{"accession":"AAC05822.1","sequence":"MVANPPKPFEVHESGAYLHGTKADLKVGDRLVPGRESNFEAGRIMKHVYITQTLDAAVWGAELAVGEGRGRIYIVEPEGEIEDDPNVTDKKLPGNPTRSYRTREPVRIVGELTDWEGHSPEQIAAMREGLEDLRRKGLAVIYD"},"dna_sequence":{"accession":"AF001493","fmin":"0","fmax":"432","strand":"+","sequence":"GTGGTGGCGAATCCGCCGAAACCGTTCGAAGTGCACGAGTCCGGGGCCTATCTGCACGGCACCAAGGCCGACCTCAAGGTGGGGGACCGACTGGTGCCCGGCCGCGAGTCCAACTTCGAGGCCGGGCGCATCATGAAGCACGTCTACATCACCCAGACGCTGGACGCCGCGGTGTGGGGCGCCGAGCTTGCTGTCGGTGAGGGTCGCGGGCGGATTTACATCGTCGAACCCGAGGGCGAGATCGAAGACGACCCGAACGTCACCGACAAGAAGCTCCCCGGCAACCCGACCCGCTCCTACCGCACCCGTGAGCCCGTGCGGATCGTCGGGGAGCTCACCGACTGGGAGGGGCATTCGCCGGAGCAGATCGCTGCCATGCGGGAGGGGCTCGAGGATCTACGGCGCAAGGGGCTCGCGGTCATCTATGACTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36871","NCBI_taxonomy_name":"Mycobacterium smegmatis","NCBI_taxonomy_id":"1772"}}}},"ARO_accession":"3002846","ARO_id":"39280","ARO_name":"arr-1","ARO_description":"arr-1 is a chromosome-encoded ribosyltransferase found in Mycobacterium smegmatis","ARO_category":{"36529":{"category_aro_accession":"3000390","category_aro_cvterm_id":"36529","category_aro_name":"rifampin ADP-ribosyltransferase (Arr)","category_aro_description":"Enzyme responsible for the ADP-ribosylative inactivation of rifampin at the 23-OH position using NAD+.","category_aro_class_name":"AMR Gene Family"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36656":{"category_aro_accession":"3000517","category_aro_cvterm_id":"36656","category_aro_name":"rifaximin","category_aro_description":"Rifaximin is a semi-synthetic rifamycin used to treat traveller's diarrhea. Rifaximin inhibits RNA synthesis by binding to the beta subunit of bacterial RNA polymerase.","category_aro_class_name":"Antibiotic"},"36669":{"category_aro_accession":"3000530","category_aro_cvterm_id":"36669","category_aro_name":"rifabutin","category_aro_description":"Rifabutin is a semisynthetic rifamycin used in tuberculosis therapy. It inhibits DNA-dependent RNA synthesis.","category_aro_class_name":"Antibiotic"},"36673":{"category_aro_accession":"3000534","category_aro_cvterm_id":"36673","category_aro_name":"rifapentine","category_aro_description":"Rifapentine is a semisynthetic rifamycin that inhibits DNA-dependent RNA synthesis. It is often used in the treatment of tuberculosis and leprosy.","category_aro_class_name":"Antibiotic"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1951":{"model_id":"1951","model_name":"TEM-76","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1887":{"protein_sequence":{"accession":"AAF05613.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMGDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AF190694","fmin":"208","fmax":"1069","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGGGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000942","ARO_id":"37322","ARO_name":"TEM-76","ARO_description":"TEM-76 is an inhibitor-resistant beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1952":{"model_id":"1952","model_name":"OXA-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"796":{"protein_sequence":{"accession":"AIA58911.1","sequence":"MLAVKIKPFTKPILIMKNTIHINFAIFLIIANIIYSSASASTDISTVASPLFEGTEGCFLLYDASTNAEIAQFNKAKCATQMAPDSTFKIALSLMAFDAEIIDQKTIFKWDKTPKGMEIWNSNHTPKTWMQFSVVWVSQEITQKIGLNKIKNYLKDFDYGNQDFSGDKERNNGLTEAWLESSLKISPEEQIQFLRKIINHNLPVKNSAIENTIENMYLQDLDNSTKLYGKTGAGFTANRTLQNGWFEGFIISKSGHKYVFVSALTGNLGSNLTSSIKAKKNAITILNTLNL"},"dna_sequence":{"accession":"KJ510410","fmin":"6950","fmax":"7826","strand":"+","sequence":"TTGTTAGCCGTTAAAATTAAGCCCTTTACCAAACCAATACTTATTATGAAAAACACAATACATATCAACTTCGCTATTTTTTTAATAATTGCAAATATTATCTACAGCAGCGCCAGTGCATCAACAGATATCTCTACTGTTGCATCTCCATTATTTGAAGGAACTGAAGGTTGTTTTTTACTTTACGATGCATCCACAAACGCTGAAATTGCTCAATTCAATAAAGCAAAGTGTGCAACGCAAATGGCACCAGATTCAACTTTCAAGATCGCATTATCACTTATGGCATTTGATGCGGAAATAATAGATCAGAAAACCATATTCAAATGGGATAAAACCCCCAAAGGAATGGAGATCTGGAACAGCAATCATACACCAAAGACGTGGATGCAATTTTCTGTTGTTTGGGTTTCGCAAGAAATAACCCAAAAAATTGGATTAAATAAAATCAAGAATTATCTCAAAGATTTTGATTATGGAAATCAAGACTTCTCTGGAGATAAAGAAAGAAACAACGGATTAACAGAAGCATGGCTCGAAAGTAGCTTAAAAATTTCACCAGAAGAACAAATTCAATTCCTGCGTAAAATTATTAATCACAATCTCCCAGTTAAAAACTCAGCCATAGAAAACACCATAGAGAACATGTATCTACAAGATCTGGATAATAGTACAAAACTGTATGGGAAAACTGGTGCAGGATTCACAGCAAATAGAACCTTACAAAACGGATGGTTTGAAGGGTTTATTATAAGCAAATCAGGACATAAATATGTTTTTGTGTCCGCACTTACAGGAAACTTGGGGTCGAATTTAACATCAAGCATAAAAGCCAAGAAAAATGCGATCACCATTCTAAACACACTAAATTTATAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001396","ARO_id":"37796","ARO_name":"OXA-1","ARO_description":"OXA-1 is a beta-lactamase found in E. coli","ARO_category":{"35994":{"category_aro_accession":"0000077","category_aro_cvterm_id":"35994","category_aro_name":"tazobactam","category_aro_description":"Tazobactam is a compound which inhibits the action of bacterial beta-lactamases.","category_aro_class_name":"Adjuvant"},"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"35995":{"category_aro_accession":"0000078","category_aro_cvterm_id":"35995","category_aro_name":"piperacillin","category_aro_description":"Piperacillin is an acetylureidopenicillin and has an extended spectrum of targets relative to other beta-lactam antibiotics. It inhibits cell wall synthesis in bacteria, and is usually taken with the beta-lactamase inhibitor tazobactam to overcome penicillin-resistant bacteria.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1953":{"model_id":"1953","model_name":"SHV-155","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1472":{"protein_sequence":{"accession":"AFQ23961.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQQ"},"dna_sequence":{"accession":"JX121122","fmin":"0","fmax":"858","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGTATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001194","ARO_id":"37574","ARO_name":"SHV-155","ARO_description":"SHV-155 is a beta-lactamase.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1954":{"model_id":"1954","model_name":"TEM-154","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1243":{"protein_sequence":{"accession":"ACO07310.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMLSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"FJ807656","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGCTGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001020","ARO_id":"37400","ARO_name":"TEM-154","ARO_description":"TEM-154 is a CMT-type, inhibitor-resistant, extended-spectrum beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1955":{"model_id":"1955","model_name":"OXA-29","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"973":{"protein_sequence":{"accession":"CAC35728.1","sequence":"MKKLSVLLWLTLFYCGTIWAQSTCFLVQENQTVLKHEGKDCNKRFAPESTFKIALSLMGFDSGILKDTLNPEWPYKKEYELYLNVWKYPHNPRTWIRDSCVWYSQVLTQQLGMTRFKNYVDAFHYGNQDISGDKGQNNGLTHSWLSSSLAISPSEQIQFLQKIVNKKLSVNPKAFTMTKDILYIQELAGGWKLYGKTGNGRQLTKDKSQKLSLQHGWFIGWIEKDGRVITFTKHIADSKKHVTFASFRAKNETLNQLFYLINELEK"},"dna_sequence":{"accession":"AJ400619","fmin":"33","fmax":"834","strand":"+","sequence":"ATGAAGAAACTAAGCGTACTTCTATGGTTGACACTATTTTATTGCGGAACTATTTGGGCCCAAAGTACTTGCTTTTTGGTACAGGAAAATCAAACTGTGCTAAAGCACGAGGGTAAAGATTGCAATAAGCGTTTTGCGCCAGAATCAACCTTTAAAATTGCTTTGAGTCTTATGGGTTTTGATTCAGGAATATTAAAAGACACACTCAATCCGGAATGGCCGTACAAAAAAGAATATGAACTTTATCTTAATGTTTGGAAATATCCTCATAATCCACGTACCTGGATAAGAGATTCCTGTGTTTGGTATTCACAAGTTCTAACACAACAATTAGGTATGACTCGATTTAAGAATTATGTTGATGCATTTCACTATGGCAATCAGGATATTTCCGGCGACAAAGGTCAGAATAATGGATTAACCCATTCCTGGCTATCAAGCTCGCTTGCCATCTCACCAAGTGAGCAAATTCAGTTTCTGCAAAAAATAGTCAATAAAAAACTATCCGTGAATCCCAAAGCTTTCACTATGACTAAAGACATTCTATATATTCAAGAATTAGCGGGTGGTTGGAAACTGTATGGAAAAACAGGGAATGGTCGACAGTTAACAAAAGACAAAAGCCAAAAACTATCACTACAACACGGATGGTTCATCGGCTGGATTGAGAAAGATGGTCGTGTGATTACCTTTACGAAACACATTGCAGATAGTAAAAAACATGTAACCTTCGCCAGTTTCAGAGCGAAAAATGAGACCCTGAATCAATTATTTTACTTAATTAATGAATTGGAAAAATAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36922","NCBI_taxonomy_name":"Fluoribacter gormanii","NCBI_taxonomy_id":"464"}}}},"ARO_accession":"3001424","ARO_id":"37824","ARO_name":"OXA-29","ARO_description":"OXA-29 is a beta-lactamase found in Legionella gormanii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1956":{"model_id":"1956","model_name":"IMI-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1190":{"protein_sequence":{"accession":"AAA93461.1","sequence":"MSLNVKPSRIAILFSSCLVSISFFSQANTKGIDEIKDLETDFNGRIGVYALDTGSGKSFSYKANERFPLCSSFKGFLAAAVLKGSQDNQLNLNQIVNYNTRSLEFHSPITTKYKDNGMSLGDMAAAALQYSDNGATNIILERYIGGPEGMTKFMRSIGDKDFRLDRWELDLNTAIPGDERDTSTPAAVAKSLKTLALGNILNEREKETYQTWLKGNTTGAARIRASVPSDWVVGDKTGSCGAYGTANDYAVVWPKNRAPLIISVYTTKNEKEAKHEDKVIAEASRIAIDNLK"},"dna_sequence":{"accession":"U50278","fmin":"1263","fmax":"2142","strand":"+","sequence":"ATGTCACTTAATGTAAAACCAAGTAGAATAGCCATCTTGTTTAGCTCTTGTTTAGTTTCAATATCATTTTTCTCACAGGCCAATACAAAGGGCATCGATGAGATTAAAGACCTTGAAACAGATTTCAATGGTAGAATTGGTGTCTACGCTTTAGACACTGGCTCAGGCAAATCATTTTCATACAAAGCAAATGAACGATTTCCATTATGTAGTTCTTTCAAAGGTTTTTTAGCTGCTGCTGTATTAAAAGGCTCTCAAGATAATCAACTAAATCTTAATCAGATCGTGAATTATAATACAAGAAGTTTAGAGTTCCATTCACCCATCACAACTAAATATAAAGATAATGGAATGTCATTAGGTGATATGGCTGCTGCAGCTTTACAATATAGCGACAATGGTGCTACTAATATTATCCTTGAACGATATATCGGTGGTCCTGAGGGTATGACTAAATTCATGCGGTCGATTGGAGATAAAGATTTTAGACTCGATCGTTGGGAGTTAGATCTAAACACAGCTATTCCTGGCGATGAACGTGACACATCTACACCTGCAGCAGTAGCTAAGAGCCTGAAAACCCTTGCACTGGGTAACATACTCAATGAGCGTGAAAAGGAAACCTATCAGACATGGTTAAAGGGTAACACAACCGGTGCAGCGCGTATTCGTGCTAGCGTACCAAGCGATTGGGTAGTTGGCGATAAAACTGGTAGTTGCGGTGCATACGGTACGGCAAATGATTATGCGGTAGTCTGGCCAAAGAACCGAGCTCCTCTTATAATTTCTGTATACACTACAAAAAACGAAAAAGAAGCCAAGCATGAGGATAAAGTAATCGCAGAAGCTTCAAGAATCGCAATTGATAACCTTAAATAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001858","ARO_id":"38258","ARO_name":"IMI-1","ARO_description":"IMI-1 is a beta-lactamase found in Enterobacter cloacae","ARO_category":{"36027":{"category_aro_accession":"3000018","category_aro_cvterm_id":"36027","category_aro_name":"IMI beta-lactamase","category_aro_description":"IMI beta-lactamases are a group of TEM-1-like beta-lactamase that are known to hydrolyze imipenem. IMI beta-lactamases are inhibited by clavulanic acid and tazobactam.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1957":{"model_id":"1957","model_name":"VIM-18","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1407":{"protein_sequence":{"accession":"CAO83029.1","sequence":"MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATRSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLANEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"AM778091","fmin":"26","fmax":"815","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCGGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAGC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002288","ARO_id":"38688","ARO_name":"VIM-18","ARO_description":"VIM-18 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1958":{"model_id":"1958","model_name":"VIM-33","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1331":{"protein_sequence":{"accession":"AFP99175.1","sequence":"MLKVISSLLVYMTASVMAVASPLAHSGEPSGEYPTVNEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEAEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSANVLFGGCAVHELSSTSAGNVADADLAEWPTSVERIQKHYPEAEVVIPGHGLPGGLDLLQHTANVVKAHKNRSVAE"},"dna_sequence":{"accession":"JX258134","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTACATGACCGCGTCTGTCATGGCTGTCGCAAGTCCGTTAGCCCATTCCGGGGAGCCGAGTGGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGAGAGGTCCGACTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCGGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAAAAGCAAATTGGACTTCCCGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGCAGAGGGGAACGAGATTCCCACGCATTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGCTCTTCTATCCTGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAACGTGCTATTCGGTGGTTGTGCCGTTCATGAGTTGTCAAGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCGTTGAGCGGATTCAAAAACACTACCCGGAAGCAGAGGTCGTCATTCCCGGGCACGGTCTACCGGGCGGTCTAGACTTGCTCCAGCACACAGCGAACGTTGTCAAAGCACACAAAAATCGCTCAGTCGCCGAGTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002303","ARO_id":"38703","ARO_name":"VIM-33","ARO_description":"VIM-33 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1959":{"model_id":"1959","model_name":"ACT-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"759":{"protein_sequence":{"accession":"ACJ05688.1","sequence":"MMRKSLCCALLLGISCSALATPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEALQ"},"dna_sequence":{"accession":"FJ237368","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAGAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCACGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTAGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCACATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAACGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAGGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001830","ARO_id":"38230","ARO_name":"ACT-7","ARO_description":"ACT-7 is a beta-lactamase. From the Lahey list of ACT beta-lactamases.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1960":{"model_id":"1960","model_name":"smeB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"2090"}},"model_sequences":{"sequence":{"521":{"protein_sequence":{"accession":"AAD51345.1","sequence":"MVRFFIDRPIFAWVIAIAVSLLGLLAILILPVDRYPQIAPPTITIRATYTGASSQTVENAVTQVIEQSQQSLDHLMYMTSTSASDGSAQVNLVFATGTNPDTAQVQVQNQLQAAMATLPQAVQQNGLTITKSSGSIFEVLSFTSEDGSMDNFDVANFMEARIDDQISRVSGVGNIQPIGQEYAMRIWLDPEKMRQYALMPWDIETALQAQNTDVSAGELGGQPALKGQQLDATVTARSRLHTPEQFAQVVLKADANGSVVRLGDVAKIGLGPESYDSISTFNGKPSASLGIELNAGANAIAVSKAIDARLQQLQKYWPHGYTAHVAFTTTPFVTISLKEVVITLIEAIILVVLVMYLFLQNWRATLIPTIAVPVVLLGTFGVLAAFGYSINTLTMFALVLAIGLLVDDAIVVVENVERVMTFEGLAPKPATLKAMGQITGALVGIVLVLTAVFLPMAFFSGVTGVIYRQFSVTIAAAMILSVLVAMTITPALCGSILHQIPKGGHPHGDHGGEPSLLGKFFIWFNHRFERTSNGLRHRVDRFLGRRTLGVLFYLVLSVATGLLLWHLPGAFLPDEDQGMLNALVKLPAGSTLEQTRAVMDRLSAVAVKDDGVLSIQATAGFSVTGSGQNVGQAFIRLKDWDDRKDDADTIAARLTRAMASVPDAQVFITSPPAILGLGDAGGFTLELQDEGGAGHAAAVAARNTLLKEAAKDPKLVNVRYASLEDAPVYAVKVDDAKAQAMGVNPQDVNDTLNAALGGDFVNNFIYKGRIKKVFIQGTAEARMQPQDIERWSVRNQAGQMVPLSSLISTHWTSAPAAVQRYNGISAMEITGQPAPGVSSGEAMAEIARLADTLPEGFSHAWSDMAYQEQLSGNQAPMLYAISLLFVFLCLAALYESWAVPFAVMLAVPVGMFGAVLMMNLRGLNNDVYFQVGLLTTIGLAAKNGILIVEFARILEQQGKSTREAILQAVYLRLRPIVMTSLAFLMGVLPLVFATGAGSAARRSLGTGVAGGTVASMVLGMFFVPLFYLLVRRLFPGRAPADATVPETSP"},"dna_sequence":{"accession":"AF173226","fmin":"3767","fmax":"6917","strand":"+","sequence":"ATGGTTCGTTTCTTCATCGACCGGCCGATCTTCGCCTGGGTGATCGCCATCGCGGTCAGCCTGCTCGGCCTGCTCGCGATCCTGATCCTGCCGGTGGACCGCTACCCGCAGATCGCCCCGCCCACCATCACCATCCGCGCCACCTACACCGGCGCCTCGTCGCAGACCGTGGAAAACGCGGTCACCCAGGTCATCGAGCAGTCCCAGCAAAGCCTCGATCACCTGATGTACATGACCTCGACCAGTGCCTCCGACGGCTCGGCGCAGGTCAACCTGGTGTTCGCCACCGGTACCAATCCGGATACCGCGCAGGTGCAGGTGCAGAACCAGCTGCAGGCCGCCATGGCCACGCTGCCGCAGGCGGTGCAGCAGAACGGCCTGACCATCACCAAGTCCAGTGGTTCGATCTTCGAGGTGCTGTCGTTCACCAGCGAAGACGGCAGCATGGACAACTTCGATGTCGCCAACTTCATGGAAGCGCGCATCGATGACCAGATCAGCCGCGTCAGCGGTGTCGGCAACATCCAGCCGATCGGCCAGGAATACGCCATGCGCATCTGGCTGGATCCGGAGAAGATGCGCCAGTACGCGCTGATGCCCTGGGACATCGAGACCGCATTGCAGGCACAGAACACCGATGTCTCCGCCGGTGAGCTGGGTGGCCAGCCGGCGCTGAAGGGCCAGCAGCTCGACGCCACGGTAACCGCGCGCAGCCGCCTGCACACGCCCGAGCAGTTCGCGCAGGTGGTGCTCAAGGCCGATGCCAACGGCAGCGTGGTGCGTCTGGGCGACGTGGCAAAGATCGGCCTCGGGCCGGAAAGCTACGACAGCATCAGCACCTTCAATGGCAAGCCGTCGGCGTCGCTGGGCATTGAACTCAATGCCGGTGCCAACGCGATCGCCGTCTCCAAGGCCATCGATGCACGGCTTCAGCAGCTGCAGAAGTACTGGCCGCATGGCTACACCGCCCACGTGGCCTTCACCACCACCCCATTCGTGACCATTTCGCTGAAGGAAGTGGTGATCACCCTGATCGAAGCGATCATCCTGGTGGTGCTGGTGATGTACCTGTTCCTGCAGAACTGGCGCGCCACGCTGATCCCGACCATCGCGGTGCCGGTGGTGCTGCTGGGCACGTTCGGCGTGCTGGCTGCATTCGGGTATTCGATCAACACCCTGACCATGTTCGCACTGGTGCTGGCCATCGGCCTGCTGGTGGACGATGCCATCGTGGTGGTGGAGAACGTAGAGCGGGTGATGACCTTCGAAGGGCTGGCGCCGAAGCCGGCCACGCTGAAGGCGATGGGCCAGATCACCGGCGCGCTGGTCGGCATCGTGCTGGTGCTGACCGCGGTGTTCCTGCCGATGGCGTTCTTCAGCGGTGTAACCGGGGTGATCTATCGCCAGTTCTCGGTGACGATCGCCGCCGCGATGATCCTGTCGGTGCTGGTGGCGATGACCATCACCCCGGCACTGTGTGGCAGCATCCTGCACCAGATTCCCAAGGGCGGCCATCCGCATGGCGACCACGGTGGCGAGCCGAGCCTGCTGGGCAAGTTCTTCATCTGGTTCAACCACCGCTTCGAGCGCACCTCCAACGGCCTGCGCCATCGCGTGGATCGTTTCCTCGGCCGCCGCACGCTCGGCGTGCTGTTCTACCTGGTGCTGAGCGTGGCCACCGGCCTGTTGCTGTGGCACCTGCCGGGCGCGTTCCTGCCCGATGAAGACCAGGGCATGCTCAACGCGCTGGTGAAGCTGCCGGCCGGTTCCACGCTGGAGCAGACGCGGGCGGTGATGGATCGTCTGAGTGCCGTCGCGGTGAAGGACGACGGCGTGCTCTCGATCCAGGCCACCGCCGGTTTCAGTGTTACCGGCAGCGGCCAGAACGTCGGCCAGGCCTTCATCCGGCTGAAGGACTGGGATGACCGCAAGGACGACGCCGATACCATCGCCGCACGCTTGACGCGGGCGATGGCCAGCGTGCCCGATGCGCAGGTGTTCATCACCTCGCCACCGGCCATCCTGGGCCTCGGCGATGCGGGTGGCTTCACCCTGGAACTGCAGGACGAAGGCGGTGCAGGCCATGCCGCCGCCGTGGCCGCGCGCAACACGCTGCTGAAGGAAGCCGCCAAGGACCCGAAGCTGGTCAACGTGCGCTACGCCAGCCTGGAAGACGCGCCGGTATACGCGGTGAAGGTGGACGACGCCAAGGCGCAGGCGATGGGCGTGAACCCGCAGGACGTCAATGACACCTTGAACGCGGCGTTGGGCGGCGACTTCGTCAACAACTTCATCTACAAGGGGCGCATCAAGAAGGTGTTCATCCAGGGCACCGCCGAAGCACGCATGCAGCCGCAGGACATCGAGCGCTGGAGCGTGCGCAACCAGGCCGGGCAGATGGTGCCGCTGTCGTCGTTGATCAGCACGCATTGGACCAGCGCGCCGGCCGCAGTGCAGCGCTACAACGGCATCTCGGCGATGGAAATCACCGGCCAGCCGGCACCGGGCGTCAGCTCCGGCGAGGCGATGGCCGAGATCGCGCGCCTGGCCGACACGCTGCCGGAAGGCTTCAGCCATGCCTGGTCGGACATGGCCTACCAGGAACAGCTGTCGGGCAACCAGGCGCCGATGCTGTACGCCATCTCGCTGCTGTTCGTGTTCCTGTGCCTGGCCGCGCTGTATGAAAGCTGGGCGGTGCCGTTCGCGGTGATGCTGGCGGTGCCGGTGGGCATGTTCGGCGCCGTGCTGATGATGAACCTGCGTGGCCTCAACAACGACGTGTACTTCCAGGTCGGCCTGCTGACCACGATTGGTCTGGCAGCGAAGAACGGCATCCTGATCGTCGAGTTCGCGCGCATCCTCGAACAGCAGGGCAAGAGCACCCGCGAAGCGATCCTGCAGGCGGTCTACCTGCGGCTGCGGCCGATCGTAATGACCTCGCTGGCGTTCCTGATGGGCGTACTGCCGCTGGTGTTCGCCACCGGCGCCGGTTCGGCTGCGCGCCGTTCGCTGGGTACCGGCGTGGCCGGTGGTACGGTTGCCTCGATGGTGCTGGGCATGTTCTTCGTGCCGTTGTTCTACCTGCTGGTGCGCCGCCTGTTCCCGGGCCGCGCGCCGGCCGACGCCACTGTCCCGGAGACAAGCCCATGAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37076","NCBI_taxonomy_name":"Stenotrophomonas maltophilia","NCBI_taxonomy_id":"40324"}}}},"ARO_accession":"3003052","ARO_id":"39486","ARO_name":"smeB","ARO_description":"smeB is the inner membrane multidrug exporter of the efflux complex smeABC in Stenotrophomonas maltophilia","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1961":{"model_id":"1961","model_name":"TEM-105","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1071":{"protein_sequence":{"accession":"AAM61953.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCNAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AF516720","fmin":"214","fmax":"1075","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAATGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000968","ARO_id":"37348","ARO_name":"TEM-105","ARO_description":"TEM-105 is a beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1962":{"model_id":"1962","model_name":"OXA-47","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1614":{"protein_sequence":{"accession":"AAP69225.1","sequence":"MKNTIHINFAIFLIIANIIYSSASASTDISTVASQLFEGTEGCFLLYDASTNAEIAQFNKAKCAAQMAPDSTFKIALSLMAFDAEIIDQKTIFKWDKIPKGMEIWNSNHTPKTWMQFSVVWVSQEITQKIGLNKIKNYLKDFDYGNQDFSGDKERNNGLTEAWLESSLKISPEEQIQFLRKIINHNLPVRNSAIENTIDNMYLQDLENSTKLYGKTGAGFTANRTLQNGWFEGFIISKSGHKYVFVSALTGSLGSNLTSSIKAKKNAITILNTLNL"},"dna_sequence":{"accession":"AY237830","fmin":"0","fmax":"831","strand":"+","sequence":"ATGAAAAACACAATACATATCAACTTCGCTATTTTTTTAATAATTGCAAATATTATCTACAGCAGCGCCAGTGCATCAACAGATATCTCTACTGTTGCATCTCAATTATTTGAAGGAACTGAAGGTTGTTTTTTACTTTACGATGCATCCACAAACGCTGAAATTGCTCAATTCAATAAAGCAAAGTGCGCAGCGCAAATGGCACCAGATTCAACTTTCAAGATCGCATTATCACTTATGGCATTTGATGCGGAAATAATAGATCAGAAAACCATATTCAAATGGGATAAAATCCCAAAAGGAATGGAAATTTGGAACAGCAATCATACACCAAAGACGTGGATGCAATTTTCTGTTGTTTGGGTTTCGCAAGAAATAACCCAAAAAATTGGATTAAATAAAATCAAAAATTATCTCAAAGATTTTGATTATGGAAATCAAGACTTCTCTGGAGATAAAGAAAGAAACAACGGATTAACAGAAGCATGGCTCGAAAGTAGCTTAAAAATTTCACCGGAAGAACAAATTCAATTCCTGCGTAAAATTATTAATCACAATCTTCCAGTTAGAAATTCAGCCATAGAAAACACCATAGATAACATGTATCTACAAGATCTGGAGAATAGTACAAAACTGTATGGGAAAACTGGTGCAGGATTTACAGCAAATAGAACCCTACAAAACGGATGGTTTGAAGGGTTTATTATAAGCAAATCAGGACATAAATATGTTTTTGTGTCCGCACTTACAGGAAGCTTGGGGTCGAATTTAACATCAAGCATAAAAGCCAAGAAAAATGCAATCACCATTCTAAACACACTAAATTTATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001781","ARO_id":"38181","ARO_name":"OXA-47","ARO_description":"OXA-47 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1963":{"model_id":"1963","model_name":"TEM-190","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1000":{"protein_sequence":{"accession":"AEL88240.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMLSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRGEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERDRQIAEIGASLIKHW"},"dna_sequence":{"accession":"JN416112","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGCTGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTGGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAGATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001050","ARO_id":"37430","ARO_name":"TEM-190","ARO_description":"TEM-190 is a beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1964":{"model_id":"1964","model_name":"IMP-45","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"953":{"protein_sequence":{"accession":"AIA58910.1","sequence":"MSKLFVFFMFLFCSITAAGESLPDLKIEKLDEGVYVHTSFEEVNGWGVIPKHGLVVLVNTDAYLIDTPFTAKDTENLVNWFVERGYRIKGSISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKDGKVQAKYSFSGVSYWLVKKKIEVFYPGPGHAPDNVVVWLPENRVLFGGCFVKPYGLGNLGDANLEAWPKSAKLLMSKYSKAKLVVPGHSDIGDSSLLKLTWEQTVKGFNESKKSTTAH"},"dna_sequence":{"accession":"KJ510410","fmin":"5740","fmax":"6478","strand":"+","sequence":"ATGAGCAAGTTATTTGTATTCTTTATGTTTTTGTTTTGTAGCATTACTGCCGCAGGAGAGTCTTTGCCAGATTTAAAAATTGAGAAGCTTGACGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGTTGGGGTGTTATTCCTAAACACGGCTTGGTGGTTCTTGTAAATACTGATGCCTATCTGATAGACACTCCATTTACTGCTAAAGATACTGAAAATTTAGTTAATTGGTTTGTTGAGCGCGGCTATAGAATAAAAGGCAGTATTTCCTCACATTTCCATAGCGACAGCACGGGTGGAATAGAGTGGCTTAATTCTCAATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTTCTTAAAAAAGACGGTAAGGTACAAGCTAAATATTCATTTAGCGGAGTTAGCTATTGGCTAGTTAAGAAAAAGATTGAAGTTTTTTATCCTGGTCCAGGGCACGCTCCAGATAACGTAGTGGTTTGGCTGCCTGAAAATAGAGTTTTGTTCGGTGGTTGTTTTGTTAAACCCTACGGTCTAGGTAATTTGGGTGACGCAAATTTAGAAGCTTGGCCAAAATCCGCCAAATTATTAATGTCAAAATATAGTAAGGCAAAACTGGTTGTACCAGGTCATAGTGACATAGGAGATTCGTCGCTCTTGAAGCTTACATGGGAGCAGACGGTAAAAGGATTCAATGAAAGCAAAAAAAGTACCACTGCACATTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002236","ARO_id":"38636","ARO_name":"IMP-45","ARO_description":"IMP-45 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1965":{"model_id":"1965","model_name":"LEN-11","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"937":{"protein_sequence":{"accession":"CAG25828.1","sequence":"ATLPLAVDAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGLEQLDRRIHYRQQDLVDYSPVSEKHLVDGMTIGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGARGIVALLGPDGKPERIVVIYLRDTPASMAERNQHIAG"},"dna_sequence":{"accession":"AJ635417","fmin":"0","fmax":"789","strand":"+","sequence":"GCCACCCTGCCACTGGCGGTAGACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGTCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGACAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002461","ARO_id":"38861","ARO_name":"LEN-11","ARO_description":"LEN-11 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1967":{"model_id":"1967","model_name":"OXA-116","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"798":{"protein_sequence":{"accession":"ABW95047.1","sequence":"LLITSAIFISACSPYIVSANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSL"},"dna_sequence":{"accession":"EU220744","fmin":"0","fmax":"786","strand":"+","sequence":"TTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTGGGTTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001441","ARO_id":"37841","ARO_name":"OXA-116","ARO_description":"OXA-116 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1968":{"model_id":"1968","model_name":"SHV-189","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"2125":{"protein_sequence":{"accession":"AJO16047.1","sequence":"MRYFRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGSVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGKRGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"KP050494","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATTTTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCAGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCAAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGGATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3003156","ARO_id":"39733","ARO_name":"SHV-189","ARO_description":"From the Lahey list of beta-lactamases.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1970":{"model_id":"1970","model_name":"SHV-44","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"2025":{"protein_sequence":{"accession":"AAP82228.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQLQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AY259119","fmin":"116","fmax":"977","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACTGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATCGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001102","ARO_id":"37482","ARO_name":"SHV-44","ARO_description":"SHV-44 is a broad-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1971":{"model_id":"1971","model_name":"dfrB2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"354":{"protein_sequence":{"accession":"FAA00064.1","sequence":"MGQSSDEANAPVAGQFALPLSATFGLGDRVRKKSGAAWQGQVVGWYCTKLTPEGYAVESESHPGSVQIYPVAALERVA"},"dna_sequence":{"accession":"BR000038","fmin":"0","fmax":"237","strand":"+","sequence":"ATGGGTCAAAGTAGCGATGAAGCCAACGCTCCCGTTGCAGGGCAGTTTGCGCTTCCCCTGAGTGCCACCTTTGGCTTAGGGGATCGCGTACGCAAGAAATCTGGTGCCGCTTGGCAGGGTCAAGTCGTCGGTTGGTATTGCACAAAACTCACTCCTGAAGGCTATGCGGTCGAGTCCGAATCCCACCCAGGCTCAGTGCAAATTTATCCTGTGGCTGCACTTGAACGTGTGGCCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3003021","ARO_id":"39455","ARO_name":"dfrB2","ARO_description":"dfrB2 is an integron-encoded dihydrofolate reductase found in an uncultured bacterium from a wastewater treatment plant","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36408":{"category_aro_accession":"3000269","category_aro_cvterm_id":"36408","category_aro_name":"brodimoprim","category_aro_description":"Brodimoprim is a structural derivative of trimethoprim and an inhibitor of bacterial dihydrofolate reductase. The 4-methoxy group of trimethoprim is replaced with a bromine atom.","category_aro_class_name":"Antibiotic"},"36423":{"category_aro_accession":"3000284","category_aro_cvterm_id":"36423","category_aro_name":"tetroxoprim","category_aro_description":"Tetroxoprim is a trimethoprim derivative that inhibits bacterial dihydrofolate reductase.","category_aro_class_name":"Antibiotic"},"36476":{"category_aro_accession":"3000337","category_aro_cvterm_id":"36476","category_aro_name":"iclaprim","category_aro_description":"Iclaprim is a bactericidal compound that inhibits dihydrofolate reductase. It is used against clinically important Gram-positive pathogens, including methicillin-sensitive Staphylococcus aureus and methicillin-resistant S. aureus.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1972":{"model_id":"1972","model_name":"OXA-149","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1754":{"protein_sequence":{"accession":"ACX31141.1","sequence":"MNIKALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKHVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"GQ853680","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCCCTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATTCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCATGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001454","ARO_id":"37854","ARO_name":"OXA-149","ARO_description":"OXA-149 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1973":{"model_id":"1973","model_name":"TEM-111","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1643":{"protein_sequence":{"accession":"AAL77062.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGADERGSRGIIAALGPDGKPSRIVVIYMTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AF468003","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGATGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACATGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000974","ARO_id":"37354","ARO_name":"TEM-111","ARO_description":"TEM-111 is a beta-lactamase found in E. coli and P. mirabilis","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1974":{"model_id":"1974","model_name":"emrD","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3622":{"protein_sequence":{"accession":"EFF04178.1","sequence":"MIMKRHRNVNLLLMLVLLVAVGQMAQTIYIPAIADMARDLNVREGAVQSVMGAYLLTYGVSQLFYGPISDRVGRRPVILVGMSIFMLATLVAVTTSSLTVLIAASAMQGMGTGVGGVMARTLPRDLYERTQLRHANSLLNMGILVSPLLAPLIGGLLDTMWNWRACYLFLLVLCAGVTFSMARWMPETRPVDAPRTRLLTSYKTLFGNGGFNCYLLMLIGGLAGIAAFEACSGVLMGAVLGLSSMTVSILFILPIPAAFFGAWFAGRPNKRFSTLMWQSVICCLLAGLLMWIPDWFGVMNVWTLLVPAALFFFGAGMLFPLATSGAMEPFPFLAGTAGALVGGLQNIGSGVLASLSAMLPQTGQGSLGLLMTLMGLLIVLCWLPLATRMSHQGQPV"},"dna_sequence":{"accession":"GG749185.1","fmin":"116812","fmax":"118003","strand":"+","sequence":"GTGATAATGAAAAGGCATAGAAACGTCAATTTGTTATTGATGTTGGTATTACTCGTGGCCGTCGGTCAGATGGCGCAAACCATTTATATTCCAGCTATTGCCGATATGGCGCGCGATCTCAACGTCCGTGAAGGGGCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGGTGTCTCACAGCTGTTTTATGGCCCGATTTCCGACCGTGTGGGTCGCCGACCGGTGATCCTCGTCGGAATGTCCATTTTTATGCTGGCAACGCTGGTCGCGGTCACGACCTCCAGTTTGACGGTATTGATTGCCGCCAGCGCGATGCAGGGGATGGGCACCGGCGTTGGCGGCGTAATGGCGCGTACTTTGCCGCGTGATTTATATGAACGGACACAGTTGCGCCATGCTAACAGCCTGTTAAACATGGGGATTCTTGTTAGTCCGTTGCTCGCACCGCTAATCGGCGGTCTGCTGGATACGATGTGGAACTGGCGCGCCTGTTATCTCTTTTTGTTGGTTCTTTGTGCTGGCGTGACCTTCAGTATGGCCCGCTGGATGCCGGAAACGCGTCCGGTCGATGCACCGCGCACGCGCCTGCTTACCAGTTATAAAACGCTTTTCGGTAACGGCGGTTTTAACTGTTATTTGCTGATGCTGATTGGCGGTCTGGCCGGGATTGCCGCCTTTGAAGCCTGCTCCGGCGTGCTGATGGGCGCGGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCGGCATTTTTTGGGGCATGGTTTGCCGGGCGTCCTAATAAACGCTTCTCAACGTTGATGTGGCAGTCGGTTATCTGCTGCCTGCTGGCTGGCTTGCTGATGTGGATCCCCGACTGGTTTGGCGTGATGAATGTCTGGACGCTGCTTGTTCCCGCCGCGCTATTCTTTTTCGGTGCCGGGATGCTGTTTCCGCTGGCGACCAGCGGCGCGATGGAGCCGTTCCCCTTCCTGGCGGGCACGGCTGGCGCGCTGGTCGGTGGTCTGCAAAACATTGGTTCCGGCGTGCTGGCGTCGCTCTCAGCGATGTTGCCGCAAACCGGTCAGGGCAGCCTGGGGTTGTTGATGACCTTAATGGGATTGTTGATCGTGCTGTGCTGGCTACCGCTGGCGACGCGGATGTCGCATCAGGGGCAGCCCGTTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40541","NCBI_taxonomy_name":"Escherichia coli B185","NCBI_taxonomy_id":"550676"}}}},"ARO_accession":"3000309","ARO_id":"36448","ARO_name":"emrD","ARO_description":"EmrD is a multidrug transporter from the Major Facilitator Superfamily (MFS) primarily found in Escherichia coli. EmrD couples efflux of amphipathic compounds with proton import across the plasma membrane.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1975":{"model_id":"1975","model_name":"blt","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"710":{"protein_sequence":{"accession":"AAC36944.1","sequence":"MKKSINEQKTIFIILLSNIFVAFLGIGLIIPVMPSFMKIMHLSGSTMGYLVAAFAISQLITSPFAGRWVDRFGRKKMIILGLLIFSLSELIFGLGTHVSIFYFSRILGGVSAAFIMPAVTAYVADITTLKERSKAMGYVSAAISTGFIIGPGAGGFIAGFGIRMPFFFASAIALIAAVTSVFILKESLSIEERHQLSSHTKESNFIKDLKRSIHPVYFIAFIIVFVMAFGLSAYETVFSLFSDHKFGFTPKDIAAIITISSIVAVVIQVLLFGKLVNKLGEKRMIQLCLITGAILAFVSTVMSGFLTVLLVTCFIFLAFDLLRPALTAHLSNMAGNQQGFVAGMNSTYTSLGNIFGPALGGILFDLNIHYPFLFAGFVMIVGLGLTMVWKEKKNDAAALN"},"dna_sequence":{"accession":"L32599","fmin":"1236","fmax":"2439","strand":"+","sequence":"ATGAAAAAATCAATAAATGAGCAAAAAACGATATTCATTATACTATTAAGCAACATCTTCGTAGCATTTCTTGGTATCGGTTTAATCATTCCAGTTATGCCTTCTTTTATGAAAATCATGCATTTATCCGGCAGCACAATGGGTTATCTTGTTGCGGCTTTTGCCATTTCTCAGTTAATTACTTCACCTTTTGCAGGTAGGTGGGTTGACCGTTTCGGGAGAAAAAAAATGATTATTCTCGGGTTGCTTATATTCAGTTTATCTGAGTTGATTTTCGGATTAGGGACCCATGTTTCAATATTTTATTTCTCGAGGATATTGGGTGGTGTAAGTGCGGCTTTTATCATGCCCGCGGTAACAGCATATGTAGCTGATATTACAACCCTAAAGGAAAGGTCAAAGGCTATGGGGTATGTTTCTGCTGCAATTAGCACCGGCTTTATTATTGGACCTGGTGCGGGAGGATTTATTGCCGGCTTTGGTATCCGCATGCCGTTTTTCTTCGCCTCCGCCATCGCGTTAATAGCAGCTGTCACTTCCGTTTTTATACTAAAAGAGTCATTGTCGATAGAAGAACGCCATCAACTCTCATCTCATACAAAGGAATCAAATTTCATTAAAGACTTGAAGAGATCCATTCATCCTGTCTATTTCATTGCATTTATTATCGTCTTTGTAATGGCTTTTGGTTTATCAGCTTATGAAACGGTATTCAGCTTGTTTTCTGATCATAAATTTGGCTTCACACCAAAAGATATTGCAGCCATTATTACGATTAGTTCCATTGTTGCGGTAGTTATTCAAGTTTTACTATTCGGGAAATTGGTCAACAAACTTGGAGAGAAAAGAATGATTCAGCTGTGCTTAATAACCGGTGCGATCTTGGCTTTCGTGTCTACTGTTATGTCAGGATTTTTAACTGTTTTGCTTGTAACTTGTTTTATTTTTCTGGCGTTCGATTTGCTACGTCCGGCCTTAACCGCTCATTTATCCAATATGGCCGGTAACCAGCAGGGTTTCGTAGCAGGCATGAACTCCACATACACCAGCCTGGGAAATATATTTGGACCTGCTCTAGGCGGTATACTATTTGATCTTAACATTCATTATCCTTTCCTTTTTGCAGGTTTCGTTATGATTGTCGGCCTTGGTCTTACAATGGTTTGGAAAGAAAAAAAGAATGATGCTGCAGCTTTGAATTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39579","NCBI_taxonomy_name":"Bacillus subtilis subsp. subtilis str. 168","NCBI_taxonomy_id":"224308"}}}},"ARO_accession":"3003006","ARO_id":"39440","ARO_name":"blt","ARO_description":"blt is an MFS efflux pump that confers resistance to multiple drugs such as rhodamine and acridine dyes, and fluoroquinolone antibiotics","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavin","category_aro_description":"Acriflavin is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36193":{"category_aro_accession":"3000054","category_aro_cvterm_id":"36193","category_aro_name":"acridine dye","category_aro_description":"Acridine dyes are cell permeable, basic molecules with an acridine chromophore. These compounds intercalate DNA. The image shown represents the core structure of the acridine family, with specific dyes containing varying substituents.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1976":{"model_id":"1976","model_name":"mefA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"4300":{"protein_sequence":{"accession":"YP_008997285.1","sequence":"MEKYNNWKLKFYTIWAGQAVSLITSAILQMAIIFYLTEKTGSAMVLSMASLVGFLPYAVFGPAIGVLVDRHDRKKIMIGADLIIAAAGAVLAIVAFYMELPVWMVMIVLFIRSIGTAFHTPALNSVTPLLVPEEQLTKCAGYSQSLQSISYIVSPAVAALLYSVWDLNAIIAIDVLGAVIASITVAIVRIPKLGNQVQSLEPNFIREMKEGIVVLRQNKGLFALLLLGTLYTFVYMPINALFPLISMEYFNGTPVHISITEISFAFGMLAGGLLLGRLGSFEKRVLLITSSFFIMGASLAVSGILPPNGFVIFVVCCAIMGLSVPFYSGVQTALFQEKIKPEYLGRVFSLTGSIMSLAMPIGLILSGFFADRIGVNHWFLLSGILIIGIAIVCPMITEVRKLDLK"},"dna_sequence":{"accession":"NC_023287","fmin":"65291","fmax":"66509","strand":"-","sequence":"TTATTTTAAATCTAATTTTCTAACCTCTGTTATCATTGGGCAAACTATAGCAATGCCAATAATTAAAATACCTGATAGTAAAAACCAATGATTTACACCAATTCTATCAGCAAAGAATCCAGAAAGAATTAATCCAATTGGCATAGCAAGTGACATGATACTTCCGGTCAAAGAAAATACACGTCCTAAATATTCAGGCTTAATTTTCTCCTGAAAAAGAGCTGTTTGCACACCGCTATAAAATGGCACCGAAAGCCCCATTATTGCACAGCAAACTACAAATATTACAAATCCATTTGGAGGAAGTATTCCCGAAACGGCTAAACTGGCCCCCATTATAAAAAATGAACTAGTTATTAGTAATACACGCTTTTCGAAGCTCCCTAATCTTCCTAACAATAAGCCTCCTGCTAGCATTCCAAAGGCAAAGGAAATTTCCGTAATAGAAATATGCACAGGTGTTCCATTAAAGTATTCCATGCTTATTAAAGGAAATAGTGCATTAATTGGCATATAAACAAAAGTATATAGTGTTCCTAAGAGTAATAAGGCAAACAATCCTTTGTTTTGTCTCAGAACGACAATTCCTTCTTTCATTTCTCTTATGAAATTTGGTTCCAAACTTTGCACTTGATTACCCAGCTTAGGTATACGTACAATTGCTACCGTAATAGATGCAATCACAGCACCCAATACGTCGATGGCAATAATAGCATTTAAATCCCAAACGGAGTATAAGAGTGCTGCAACTGCCGGACTAACAATATAGCTTATAGACTGCAAAGACTGACTATAGCCTGCGCATTTCGTTAGCTGCTCTTCTGGTACTAAAAGTGGTGTAACCGAATTGAGTGCTGGGGTATGAAAAGCTGTTCCAATGCTACGGATAAACAATACTATCATAACCATCCAGACAGGTAGCTCCATATAGAATGCAACAATAGCAAGCACTGCACCAGCTGCTGCGATAATTAAATCAGCACCAATCATTATCTTCTTCCTATCATGACGATCCACTAGCACACCAATTGCAGGTCCAAAGACCGCATAGGGTAAAAAACCTACTAGTGAAGCCATAGACAAGACCATCGCAGATCCAGTTTTTTCTGTAAGGTAAAAAATAATCGCCATTTGCAGGATGGCACTAGTGATTAATGATACTGCTTGCCCTGCCCATATTGTATAAAACTTAAGTTTCCAATTGTTGTATTTTTCCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39580","NCBI_taxonomy_name":"Exiguobacterium sp. S3-2","NCBI_taxonomy_id":"1389960"}}}},"ARO_accession":"3000615","ARO_id":"36909","ARO_name":"mefA","ARO_description":"mefA is a motive efflux pump in Streptococcus pneumoniae that confers resistance to macrolides. It is found on the same operon as mefE and the ABC-efflux pump mel.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1977":{"model_id":"1977","model_name":"AAC(6')-Ik","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"541":{"protein_sequence":{"accession":"AAA87229.1","sequence":"MNIKPASEASLKDWLKLRIKLWNDLEESHLQEMHQLLAEKHALQLLVYSDDHAVGMLEASIRYEYVNGTETSPVAFLEGIYVLPEYRRLGVATLLVRQVEAWAKQFSCTEFASDAALDNVISHAMHRALGFQETERVVYFSKKID"},"dna_sequence":{"accession":"L29510","fmin":"368","fmax":"806","strand":"+","sequence":"ATGAATATTAAACCAGCATCAGAAGCTTCACTCAAAGATTGGTTAAAACTAAGAATAAAGCTTTGGAATGATCTTGAAGAATCACATTTGCAAGAGATGCATCAGTTATTGGCTGAAAAGCATGCATTACAATTATTAGTCTATTCGGATGATCACGCGGTTGGCATGCTAGAAGCATCTATTCGGTATGAATATGTAAACGGGACAGAGACTTCTCCCGTGGCATTTCTAGAAGGCATTTATGTACTTCCAGAATATCGTCGCTTAGGTGTAGCAACTTTACTTGTTCGTCAGGTTGAGGCGTGGGCAAAACAATTTTCTTGTACTGAGTTTGCATCTGATGCGGCATTGGACAATGTCATTAGTCATGCAATGCATCGTGCATTGGGTTTTCAAGAAACTGAAAGAGTTGTTTATTTTAGTAAAAAAATAGATTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39511","NCBI_taxonomy_name":"Acinetobacter sp. CIP-A165","NCBI_taxonomy_id":"40373"}}}},"ARO_accession":"3002558","ARO_id":"38958","ARO_name":"AAC(6')-Ik","ARO_description":"AAC(6')-Ik is a chromosomal-encoded aminoglycoside acetyltransferase in Acinetobacter sp.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1978":{"model_id":"1978","model_name":"OXA-200","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1294":{"protein_sequence":{"accession":"ADX07745.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAILVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGLDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"HQ734811","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCCCTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCTAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTAGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATTGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001665","ARO_id":"38065","ARO_name":"OXA-200","ARO_description":"OXA-200 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1979":{"model_id":"1979","model_name":"FosA4","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"1439":{"protein_sequence":{"accession":"BAP18892.1","sequence":"MLQGLNHLTLAVSDLASSLAFYQRLPGMRLHARWDSGAYLSCGALWLCLSLDAQRRKTPAQESDYTHYAFSVAEEHFAEVVAQLAHAGAEVWKDNRSEGASYYFLDPDGHKLELHVGHLAQRLAACRERPYKGMVFFD"},"dna_sequence":{"accession":"AB908992","fmin":"0","fmax":"417","strand":"+","sequence":"ATGCTGCAGGGATTGAATCATCTGACGCTGGCGGTCAGCGATCTGGCGTCAAGCCTGGCGTTTTATCAGCGGTTACCTGGAATGCGTCTGCACGCCCGTTGGGATAGCGGAGCATATCTTTCCTGCGGGGCGTTGTGGCTATGCTTGTCGCTGGATGCGCAGCGGCGTAAAACGCCCGCTCAGGAAAGCGACTATACCCATTATGCTTTCAGCGTGGCGGAAGAGCACTTTGCCGAGGTGGTCGCCCAGCTGGCGCACGCGGGGGCCGAAGTATGGAAAGACAACCGCAGCGAAGGGGCGTCGTACTATTTTCTCGACCCTGACGGCCATAAGCTGGAACTGCATGTGGGTCATTTGGCACAGCGGCTGGCCGCCTGTCGGGAACGCCCGTACAAGGGGATGGTCTTTTTTGACTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3003210","ARO_id":"39794","ARO_name":"FosA4","ARO_description":"fosA4 is an enzyme that confers resistance to fosfomycin in Escherichia coli by breaking the epoxide ring of the molecule.","ARO_category":{"36272":{"category_aro_accession":"3000133","category_aro_cvterm_id":"36272","category_aro_name":"fosfomycin thiol transferase","category_aro_description":"Catalyzes the addition of a thiol group from a nucleophilic molecule to fosfomycin.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1980":{"model_id":"1980","model_name":"OXA-247","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"972":{"protein_sequence":{"accession":"AGC70814.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGSNTKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"JX893517","fmin":"0","fmax":"786","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGACAGTTTCTGGCTCGACGGTGGTATTCGAATTTCGGCCACGGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATGCTGACCGAAGCCAATGGCGACTATATTATTCGGGCTAAAACTGGATCCAATACTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001791","ARO_id":"38191","ARO_name":"OXA-247","ARO_description":"OXA-247 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1981":{"model_id":"1981","model_name":"vanA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"3277":{"protein_sequence":{"accession":"AAA65956.1","sequence":"MNRIKVAILFGGCSEEHDVSVKSAIEIAANINKEKYEPLYIGITKSGVWKMCEKPCAEWENDNCYSAVLSPDKKMHGLLVKKNHEYEINHVDVAFSALHGKSGEDGSIQGLFELSGIPFVGCDIQSSAICMDKSLTYIVAKNAGIATPAFWVINKDDRPVAATFTYPVFVKPARSGSSFGVKKVNSADELDYAIESARQYDSKILIEQAVSGCEVGCAVLGNSAALVVGEVDQIRLQYGIFRIHQEVEPEKGSENAVITVPADLSAEERGRIQETAKKIYKALGCRGLARVDMFLQDNGRIVLNEVNTLPGFTSYSRYPRMMAAAGIALPELIDRLIVLALKG"},"dna_sequence":{"accession":"M97297","fmin":"6979","fmax":"8010","strand":"+","sequence":"ATGAATAGAATAAAAGTTGCAATACTGTTTGGGGGTTGCTCAGAGGAGCATGACGTATCGGTAAAATCTGCAATAGAGATAGCCGCTAACATTAATAAAGAAAAATACGAGCCGTTATACATTGGAATTACGAAATCTGGTGTATGGAAAATGTGCGAAAAACCTTGCGCGGAATGGGAAAACGACAATTGCTATTCAGCTGTACTCTCGCCGGATAAAAAAATGCACGGATTACTTGTTAAAAAGAACCATGAATATGAAATCAACCATGTTGATGTAGCATTTTCAGCTTTGCATGGCAAGTCAGGTGAAGATGGATCCATACAAGGTCTGTTTGAATTGTCCGGTATCCCTTTTGTAGGCTGCGATATTCAAAGCTCAGCAATTTGTATGGACAAATCGTTGACATACATCGTTGCGAAAAATGCTGGGATAGCTACTCCCGCCTTTTGGGTTATTAATAAAGATGATAGGCCGGTGGCAGCTACGTTTACCTATCCTGTTTTTGTTAAGCCGGCGCGTTCAGGCTCATCCTTCGGTGTGAAAAAAGTCAATAGCGCGGACGAATTGGACTACGCAATTGAATCGGCAAGACAATATGACAGCAAAATCTTAATTGAGCAGGCTGTTTCGGGCTGTGAGGTCGGTTGTGCGGTATTGGGAAACAGTGCCGCGTTAGTTGTTGGCGAGGTGGACCAAATCAGGCTGCAGTACGGAATCTTTCGTATTCATCAGGAAGTCGAGCCGGAAAAAGGCTCTGAAAACGCAGTTATAACCGTTCCCGCAGACCTTTCAGCAGAGGAGCGAGGACGGATACAGGAAACGGCAAAAAAAATATATAAAGCGCTCGGCTGTAGAGGTCTAGCCCGTGTGGATATGTTTTTACAAGATAACGGCCGCATTGTACTGAACGAAGTCAATACTCTGCCCGGTTTCACGTCATACAGTCGTTATCCCCGTATGATGGCCGCTGCAGGTATTGCACTTCCCGAACTGATTGACCGCTTGATCGTATTAGCGTTAAAGGGGTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3000010","ARO_id":"36019","ARO_name":"vanA","ARO_description":"VanA is a D-Ala-D-Ala ligase homolog that synthesizes D-Ala-D-Lac, an alternative substrate for peptidoglycan synthesis that reduces vancomycin binding affinity. It has been isolated from VREs. It is associated with both vancomycin and teicoplanin resistance.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"39340":{"category_aro_accession":"3002906","category_aro_cvterm_id":"39340","category_aro_name":"van ligase","category_aro_description":"van ligases synthesize alternative substrates for peptidoglycan synthesis that reduce vancomycin binding affinity.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"35948":{"category_aro_accession":"0000029","category_aro_cvterm_id":"35948","category_aro_name":"teicoplanin","category_aro_description":"Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation  and transpeptidation.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1982":{"model_id":"1982","model_name":"IMP-9","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1516":{"protein_sequence":{"accession":"AAK59385.1","sequence":"MSKLFVFFMFLFCSITAAGESLPDLKIEKLDEGVYVHTSFEEVNGWGVIPKHGLVVLVNTDAYLIDTPFTAKDTENLVNWFVERGYRIKGSISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKDGKVQAKYSFSGVSYWLVKKKIEVFYPGPGHAPDNVVVWLPENRVLFGGCFVKPYGLGNLGDANLEAWPKSAKLLMSKYSKAKLVVPSHSDIGDSSLLKLTWEQTVKGFNESKKSTTAH"},"dna_sequence":{"accession":"AY033653","fmin":"2787","fmax":"3525","strand":"+","sequence":"ATGAGCAAGTTATTTGTATTCTTTATGTTTTTGTTTTGTAGCATTACTGCCGCAGGAGAGTCTTTGCCAGATTTAAAAATTGAGAAGCTTGACGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGTTGGGGTGTTATTCCTAAACACGGCTTGGTGGTTCTTGTAAATACTGATGCCTATCTGATAGACACTCCATTTACTGCTAAAGATACTGAAAATTTAGTTAATTGGTTTGTTGAGCGCGGCTATAGAATAAAAGGCAGTATTTCCTCACATTTCCATAGCGACAGCACGGGTGGAATAGAGTGGCTTAATTCTCAATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTTCTTAAAAAAGACGGTAAGGTACAAGCTAAATATTCATTTAGCGGAGTTAGCTATTGGCTAGTTAAGAAAAAGATTGAAGTTTTTTATCCTGGTCCAGGGCACGCTCCAGATAACGTAGTGGTTTGGCTGCCTGAAAATAGAGTTTTGTTCGGTGGTTGTTTTGTTAAACCCTACGGTCTAGGTAATTTGGGTGACGCAAATTTAGAAGCTTGGCCAAAATCCGCCAAATTATTAATGTCAAAATATAGTAAGGCAAAACTGGTTGTACCAAGTCATAGTGACATAGGAGATTCGTCGCTCTTGAAGCTTACATGGGAGCAGACGGTAAAAGGATTCAATGAAAGCAAAAAAAGTACCACTGCACATTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002200","ARO_id":"38600","ARO_name":"IMP-9","ARO_description":"IMP-9 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1983":{"model_id":"1983","model_name":"vanTN","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1300"}},"model_sequences":{"sequence":{"259":{"protein_sequence":{"accession":"AEP40502.2","sequence":"MKNVNTGINQFRLIAAFMVVAIHCFPFQSFSKTLDILITLTLFRTAVPFFLMVTGFYLIGPIATKRGYPAYLKIKKFLKKQVKLYVLATLIYLPLAFYSGVITFKTSVIQFFQLIFFEGVLYHLWYFPALILGVLIVYCLLQRFTLRQVLLVTFLFYLLCLGGDSWWGLARQIPVLEKSYQGIFTLMIHTRNGLFFAPFFLTLGASFHQSEWNMRTSKAKYFLLIASLGMLVESYLLHSFSSPKHDSAYLFLPVVMFFLFPLILNWQPTRVIADASTISLGIYVLHPYVIAVVHTLAKKITILNNSLIYYLCVSLLTSLIILYVHSKKKKTTKNQATFVPRTKKVLSKQAVIHNLAQINQVIPKTTKIMAVIKANAYGTDDTEFARILEQQGVDFFAVATIDEGIRLRENGIKSKILILGYTPSIRIKELAHYTLIQTIVSKEHAYSLNQQKIPISCHLKIDTGMHRLGVEPVVQEVSSLYRLPYLNIQGIYSHLGSADDRSDKGMKRTRKQISIFDYLLHELELQKIDVGVTHLQSSYGILNYPELVYDYVRPGILLYGYLSEHNGDSKINLNLQPILDVQALLVSKKWVAAGEYLGYSLDTKLVSPKLIGIVSIGYADGVPRELSHNEFYLAYQGQNLPQIGRICMDMLLVDLTDSPEIKVESQISIFPELEQTANQTNTLTNEIISRLGNRFYTEWS"},"dna_sequence":{"accession":"JF802084","fmin":"2161","fmax":"4264","strand":"+","sequence":"ATGAAAAACGTAAATACCGGGATCAATCAATTTCGATTGATCGCTGCTTTCATGGTCGTTGCGATTCACTGTTTTCCTTTTCAGTCGTTTAGTAAAACTCTTGATATATTGATTACTTTGACACTCTTTCGAACTGCCGTACCTTTTTTCTTAATGGTCACAGGTTTTTATTTAATTGGACCGATTGCCACTAAGAGAGGCTATCCAGCCTATTTAAAGATAAAAAAATTTTTAAAAAAGCAAGTGAAGCTATATGTGCTTGCTACGCTCATTTATCTTCCACTAGCTTTTTATAGTGGTGTGATCACTTTCAAGACGAGTGTCATTCAATTTTTTCAACTCATCTTTTTCGAAGGAGTTCTTTACCACTTGTGGTATTTTCCAGCATTGATTTTAGGTGTTCTCATCGTTTACTGCTTATTACAGCGGTTCACGCTTCGACAAGTTTTATTAGTGACTTTTCTATTCTATTTACTATGTTTGGGCGGCGATAGCTGGTGGGGGTTAGCTAGACAAATTCCTGTGTTAGAAAAAAGTTATCAAGGGATATTTACGCTCATGATCCATACTCGAAATGGACTATTTTTTGCCCCTTTCTTTTTAACACTCGGTGCTTCGTTCCATCAATCAGAGTGGAACATGCGTACATCTAAAGCCAAGTATTTTTTGTTGATTGCTAGTTTAGGCATGCTAGTGGAAAGCTATTTGCTACACTCCTTTAGTTCACCAAAACATGATAGTGCATACCTATTCTTGCCTGTGGTGATGTTTTTTCTTTTTCCACTTATTTTGAACTGGCAGCCTACACGTGTCATTGCCGACGCTTCGACAATCAGTTTAGGTATTTATGTCCTTCATCCTTATGTCATTGCTGTTGTCCATACTTTAGCCAAAAAAATAACGATACTAAACAATAGTTTAATTTATTATCTCTGCGTTTCCCTTTTAACTAGTTTGATTATTCTTTATGTACACTCTAAGAAAAAGAAAACGACAAAAAATCAGGCTACGTTTGTCCCTAGAACAAAAAAAGTACTCTCTAAGCAAGCAGTTATCCATAATTTGGCACAAATCAATCAAGTGATTCCGAAAACAACGAAAATAATGGCTGTCATAAAAGCCAACGCTTATGGAACTGATGATACAGAATTTGCTCGAATCTTAGAACAACAAGGAGTTGATTTTTTTGCTGTCGCTACCATTGATGAAGGCATTCGTTTGCGAGAAAATGGAATTAAAAGCAAAATCTTAATTCTAGGCTATACACCATCGATACGAATAAAAGAATTAGCTCACTACACATTAATACAAACAATCGTTAGCAAAGAACATGCTTATTCATTAAATCAACAAAAGATACCTATTTCGTGCCATCTAAAAATTGATACTGGCATGCATCGTTTAGGTGTTGAGCCTGTGGTTCAGGAGGTTTCATCCTTATATCGATTACCCTACTTAAATATTCAAGGTATTTATTCTCATCTCGGTTCAGCTGATGATCGAAGTGACAAAGGAATGAAACGCACGAGAAAACAAATTTCGATTTTTGATTATTTATTACATGAACTAGAACTTCAAAAAATCGATGTCGGTGTTACGCATCTGCAAAGTAGCTATGGTATTTTGAATTATCCTGAACTGGTCTATGATTATGTTCGTCCTGGTATTCTTTTATACGGTTATTTAAGTGAACATAATGGAGATTCAAAAATCAACTTAAATTTGCAACCAATTTTAGATGTCCAAGCACTGCTCGTATCAAAAAAATGGGTTGCTGCTGGTGAATATCTTGGCTATAGCCTTGATACTAAACTAGTTTCTCCAAAGCTGATTGGTATCGTCAGCATCGGCTATGCAGACGGTGTTCCTAGAGAGTTATCTCACAATGAGTTTTATCTTGCTTATCAGGGACAAAATCTACCACAAATCGGACGAATTTGTATGGATATGCTATTAGTGGATTTGACTGATTCTCCAGAAATCAAAGTAGAGTCACAAATTAGTATCTTCCCAGAACTAGAACAAACTGCTAATCAAACGAATACATTGACTAACGAAATCATCAGTCGCTTAGGTAATCGTTTCTACACCGAATGGTCCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002975","ARO_id":"39409","ARO_name":"vanTN","ARO_description":"vanTN is a vanT variant found in the vanN gene cluster","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36511":{"category_aro_accession":"3000372","category_aro_cvterm_id":"36511","category_aro_name":"vanT","category_aro_description":"VanT is a membrane bound serine racemase, converting L-serine to D-serine. It is associated with VanC, which incorporated D-serine into D-Ala-D-Ser terminal end of peptidoglycan subunits that have a decreased binding affinity with vancomycin. It was isolated from Enterococcus gallinarum.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1984":{"model_id":"1984","model_name":"SHV-144","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1871":{"protein_sequence":{"accession":"AFK93491.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPVGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"JQ926986","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGTAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGGATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001345","ARO_id":"37745","ARO_name":"SHV-144","ARO_description":"SHV-144 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1985":{"model_id":"1985","model_name":"SHV-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1394":{"protein_sequence":{"accession":"AAA87176.1","sequence":"MRYFRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGSVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASKRGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"U20270","fmin":"124","fmax":"985","strand":"+","sequence":"ATGCGTTATTTTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCAGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCAAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001066","ARO_id":"37446","ARO_name":"SHV-7","ARO_description":"SHV-7 is an extended-spectrum beta-lactamase found in E. coli.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1986":{"model_id":"1986","model_name":"OXA-309","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1131":{"protein_sequence":{"accession":"CCW28916.1","sequence":"MKTLQLALIALITTFGSACTTISPSVETAKNHQQQSAQQQIQQAFDQLQTTGVIVIKDKHGLHSYGNDLSRAQTPYVPASTFKMLNALIGLEHGKATRTEVFKWDGQKRSFPAWEKDMTLGQAMQASAVPVYQELARRIGVDLMQKEVQRIGYGNQQIGTVVDNFWLVGPLQITPVQEVLFVEKLANTQLAFKPDVQHTVQDMLLIEQKPNYKLYAKSGWGMDLEPQVGWWAGWVETSTGEKAYFALNMQMKTGISASVREQLVKQSLTALGII"},"dna_sequence":{"accession":"HF947514","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAAAACTTTACAGTTGGCTCTCATCGCCCTCATTACAACCTTCGGTTCTGCATGTACCACAATAAGCCCCTCAGTAGAAACAGCTAAAAATCACCAGCAACAAAGCGCGCAGCAGCAGATCCAACAGGCCTTCGATCAACTCCAAACCACTGGGGTGATTGTCATTAAGGATAAGCATGGCTTACACAGCTACGGCAATGACTTGAGCCGTGCTCAGACACCCTATGTACCCGCCTCTACCTTTAAAATGCTGAATGCCTTAATCGGACTAGAACATGGTAAAGCAACCAGAACCGAGGTGTTTAAATGGGATGGTCAAAAGCGCAGCTTCCCTGCCTGGGAAAAAGACATGACTTTAGGGCAAGCCATGCAAGCATCTGCCGTTCCCGTTTATCAGGAGCTTGCACGGCGTATTGGTGTAGATCTAATGCAAAAAGAAGTACAGCGCATTGGATATGGCAATCAACAGATTGGCACCGTTGTCGATAATTTTTGGTTAGTCGGTCCACTGCAAATTACGCCTGTTCAAGAAGTCCTTTTTGTAGAGAAGCTGGCCAATACGCAACTCGCTTTTAAGCCAGATGTGCAACATACCGTACAAGACATGCTACTGATTGAACAAAAACCGAATTATAAACTCTACGCCAAATCAGGCTGGGGTATGGACCTAGAACCACAAGTGGGCTGGTGGGCAGGCTGGGTCGAAACTTCAACAGGTGAAAAAGCGTATTTTGCTTTGAATATGCAGATGAAAACGGGAATTTCAGCCAGCGTGCGTGAGCAACTGGTCAAACAAAGTCTGACAGCACTGGGGATAATTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39092","NCBI_taxonomy_name":"Acinetobacter johnsonii","NCBI_taxonomy_id":"40214"}}}},"ARO_accession":"3001504","ARO_id":"37904","ARO_name":"OXA-309","ARO_description":"OXA-309 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1987":{"model_id":"1987","model_name":"QnrA1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"403":{"protein_sequence":{"accession":"ABI50486.1","sequence":"MDIIDKVFQQEDFSRQDLSDSRFRRCRFYQCDFSHCQLQDASFEDCSFIESGAVEGCHFSYADLRDASFKACRLSLANFSGANCFGIEFRECDLKGANFSRARFYNQVSHKMYFCSAYISGCNLAYTNLSGQCLEKCELFENNWSNANLSGASLMGSDLSRGTFSRDCWQQVNLRGCDLTFADLDGLDPRRVNLEGVKICAWQQEQLLEPLGVIVLPD"},"dna_sequence":{"accession":"DQ831141","fmin":"8921","fmax":"9578","strand":"+","sequence":"ATGGATATTATTGATAAAGTTTTTCAGCAAGAGGATTTCTCACGCCAGGATTTGAGTGACAGCCGTTTTCGCCGCTGCCGCTTTTATCAGTGTGACTTCAGCCACTGTCAGCTGCAGGATGCCAGTTTCGAGGATTGCAGTTTCATTGAAAGCGGCGCCGTTGAAGGGTGTCACTTCAGCTATGCCGATCTGCGCGATGCCAGTTTCAAGGCCTGCCGTCTGTCTTTGGCCAACTTCAGCGGTGCCAACTGCTTTGGCATAGAGTTCAGGGAGTGCGATCTCAAGGGCGCCAACTTTTCCCGGGCCCGCTTCTACAATCAAGTCAGCCATAAGATGTACTTCTGCTCGGCTTATATCTCAGGTTGCAACCTGGCCTATACCAACTTGAGTGGCCAATGCCTGGAAAAATGCGAGCTGTTTGAAAACAACTGGAGCAATGCCAATCTCAGCGGCGCTTCCTTGATGGGCTCAGATCTCAGCCGCGGCACCTTCTCCCGCGACTGTTGGCAACAGGTCAATCTGCGGGGCTGTGACCTAACCTTTGCCGATCTGGATGGGCTCGACCCCAGACGGGTCAACCTCGAAGGAGTCAAGATCTGTGCCTGGCAACAGGAGCAACTGCTGGAACCCTTGGGAGTAATAGTGCTGCCGGATTAGC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002707","ARO_id":"39141","ARO_name":"QnrA1","ARO_description":"QnrA1 is a plasmid-mediated quinolone resistance protein found in Klebsiella pneumoniae","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1988":{"model_id":"1988","model_name":"CMY-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1100":{"protein_sequence":{"accession":"CAB36900.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGELAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"AJ011291","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGAGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002018","ARO_id":"38418","ARO_name":"CMY-7","ARO_description":"CMY-7 is a beta-lactamase found in Salmonella typhimurium","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1990":{"model_id":"1990","model_name":"CMY-82","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"905":{"protein_sequence":{"accession":"AHL39324.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYQGKPYYFTWGKADIANNRPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTHYWPELTGKQWQGISLLHLATYTAGGLPLQVPDDVTDKAALLRFYQNWQPQWAPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTKRVLRPLKLAHTWITVPQSEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMTRWVQANMDASQVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPVKADSIISGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"KJ207203","fmin":"5","fmax":"1151","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCGCTGCTGCTGACAGCTTCGTTCTCCACGTTTGCCGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCGCTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCGATTATCTATCAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCGTCCAGTCACTCAACAAACGCTGTTTGAACTCGGATCGGTCAGTAAAACGTTCAACGGCGTGCTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGCATTACTGGCCTGAACTGACTGGTAAGCAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTACACGGCAGGCGGCCTGCCGCTTCAGGTTCCGGACGACGTTACGGATAAAGCCGCGTTACTACGCTTTTATCAAAACTGGCAGCCGCAATGGGCCCCAGGCGCTAAACGTCTTTATGCTAACTCCAGCATTGGTCTGTTTGGTGCCCTGGCGGTCAAACCCTCAGGCATGAGCTACGAAGAGGCGATGACCAAACGCGTCCTGCGCCCCTTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAGCGAACAAAAAGATTATGCCTGGGGTTATCGCGAAGGAAAGCCAGTGCATGTATCCCCTGGCCAACTTGATGCCGAAGCCTACGGGGTGAAATCGAGCGTTATCGATATGACCCGTTGGGTTCAGGCCAACATGGACGCCAGCCAGGTTCAGGAGAAAACGCTCCAGCAGGGCATCGAGCTTGCGCAGTCACGTTACTGGCGTATTGGCGATATGTACCAGGGCCTGGGCTGGGAGATGCTGAACTGGCCGGTGAAGGCCGACTCGATAATTAGCGGTAGCGACAGCAAAGTGGCACTGGCAGCGCTTCCTGCCGTTGAGGTAAACCCGCCCGCGCCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGCGGATTCGGCAGCTACGTTGCGTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAGAGCTACCCAAACCCTGTTCGCGTCGAGGCCGCCTGGCGCATTCTTGAAAAACTGCAGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002095","ARO_id":"38495","ARO_name":"CMY-82","ARO_description":"CMY-82 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1991":{"model_id":"1991","model_name":"otrC","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"650"}},"model_sequences":{"sequence":{"421":{"protein_sequence":{"accession":"AAR96051.1","sequence":"MTRKTISNGARNAVEVRGLVKHFGEVKAVDGVDLDVREGTVLGVLGPXGAAXXRGALPAHVXGPDAGRRPWRFXTWCANRRALRRTIGXHRPVRXGRRESFSGRENLYMIGRXLDLSRKDARARADELLERFSLTEAAGRAAAKYSGGMRRRLDLAASMIGRPAVLYLDEPTTGLDPRTRNEVWDEVRSMVRDGATVLLTTQYMEEAEQLAHELTVIDRGRVIADGKVDELKTKVGGRTLQIRPAHAAELDRMVGAIAQAGLDGIAGATADHEDGVVNVPIVSDEQLSAVVGMLGERGFTISGHQHPSAQLXEVFLAITGQKTSEAADGGPQDGPQDQQGVQDKQYEEVPA"},"dna_sequence":{"accession":"AY509111","fmin":"0","fmax":"1056","strand":"+","sequence":"ATGACGCGAAAGACGATATCCAACGGCGCGAGGAACGCCGTCGAAGTGCGGGGACTGGTCAAGCACTTCGGCGAGGTGAAGGCCGTGGACGGGGTGGATCTCGATGTGAGGGAAGGCACCGTGCTCGGTGTGCTCGGGCCGANCGGCGCGGCAANANAACGTGGTGCGCTGCCTGCCCACGTTGNTGGTCCGGACGCCGGCAGGCGACCGTGGCGGTTTNAAACGTGGTGCGCCAACCGGCGCGCGTTGCGCCGCACGATCGGCCNTCACCGGCCAGTACGCNTCGGTCGACGAGAAAGCTTCTCCGGCCGNGAGAACCTGTACATGATCGGCCGCNTGCTGGACCTCTCCCGCAAGGACGCCCGCGCGCGGGCCGACGAGCTGCTGGAGCGGTTCTCCCTCACCGAGGCCGCCGGCCGGGCCGCCGCCAAGTACTCCGGCGGTATGCGCCGCCGCCTCGACCTGGCCGCCTCCATGATCGGCAGGCCCGCGGTGCTGTATCTGGACGAGCCGACGACGGGCCTCGACCCCCGCACCCGCAACGAGGTGTGGGACGAGGTCCGCAGCATGGTGCGCGACGGCGCCACGGTCCTGCTCACCACCCAGTACATGGAAGAGGCCGAGCAGCTGGCCCACGAGCTGACGGTCATCGACCGCGGCCGGGTCATCGCCGACGGCAAGGTGGACGAGCTGAAGACCAAGGTCGGCGGCCGTACGCTCCAGATACGCCCGGCGCACGCCGCCGAGCTGGACCGGATGGTCGGCGCCATCGCGCAGGCCGGCCTGGACGGCATCGCGGGCGCCACCGCCGACCACGAGGACGGCGTGGTCAACGTCCCGATCGTCAGCGACGAGCAGCTGTCCGCCGTGGTCGGCATGCTCGGCGAGCGGGGCTTCACGATCTCCGGGCATCAACACCCATCTGCCCAGCTGNACGAGGTGTTCCTGGCCATCACCGGCCAGAAGACCTCGGAGGCCGCCGACGGCGGCCCGCAGGACGGACCGCAGGACCAGCAGGGCGTTCAGGACAAGCAGTACGAGGAGGTTCCGGCATGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36773","NCBI_taxonomy_name":"Streptomyces rimosus","NCBI_taxonomy_id":"1927"}}}},"ARO_accession":"3002894","ARO_id":"39328","ARO_name":"otrC","ARO_description":"otrC is a tetracycline resistance efflux pump found in Streptomyces rimosus","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1992":{"model_id":"1992","model_name":"dfrA1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"3594":{"protein_sequence":{"accession":"CAC19929.1","sequence":"MKLSLMVAISKNGVIGNGPDIPWSAKGEQLLFKAITYNQWLLVGRKTFESMGALPNRKYAVVTRSSFTSDNENVLIFPSIKDALPNRKYAVVTRSSFTSDNENVLIFPSIKDALTNLKKITDHVIVSGGGEIYKSLIDQVDTLHISTIDIEPEGDVYFPEIPSNFRPVFTQDFASNINYSYQIWQKG"},"dna_sequence":{"accession":"AJ400733.1","fmin":"21","fmax":"585","strand":"+","sequence":"GTGAAACTATCACTAATGGTAGCTATATCGAAGAATGGAGTTATCGGGAATGGCCCTGATATTCCATGGAGTGCCAAAGGTGAACAGCTCCTGTTTAAAGCTATTACCTATAACCAATGGCTGTTGGTTGGACGCAAGACTTTTGAATCAATGGGAGCATTACCCAACCGAAAGTATGCGGTCGTAACACGTTCAAGCTTTACATCTGACAATGAGAACGTATTGATCTTTCCATCAATTAAAGATGCTTTACCCAACCGAAAGTATGCGGTCGTAACACGTTCAAGCTTTACATCTGACAATGAGAACGTATTGATCTTTCCATCAATTAAAGATGCTTTAACCAACCTAAAGAAAATAACGGATCATGTCATTGTTTCAGGTGGTGGGGAGATATACAAAAGCCTGATCGATCAAGTAGATACACTACATATATCTACAATAGACATCGAGCCGGAAGGTGATGTTTACTTTCCTGAAATCCCCAGCAATTTTAGGCCAGTTTTTACCCAAGACTTCGCCTCTAACATAAATTATAGTTACCAAATCTGGCAAAAGGGTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3002854","ARO_id":"39288","ARO_name":"dfrA1","ARO_description":"dfrA1 is an integron-encoded dihydrofolate reductase found in Escherichia coli","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36408":{"category_aro_accession":"3000269","category_aro_cvterm_id":"36408","category_aro_name":"brodimoprim","category_aro_description":"Brodimoprim is a structural derivative of trimethoprim and an inhibitor of bacterial dihydrofolate reductase. The 4-methoxy group of trimethoprim is replaced with a bromine atom.","category_aro_class_name":"Antibiotic"},"36423":{"category_aro_accession":"3000284","category_aro_cvterm_id":"36423","category_aro_name":"tetroxoprim","category_aro_description":"Tetroxoprim is a trimethoprim derivative that inhibits bacterial dihydrofolate reductase.","category_aro_class_name":"Antibiotic"},"36476":{"category_aro_accession":"3000337","category_aro_cvterm_id":"36476","category_aro_name":"iclaprim","category_aro_description":"Iclaprim is a bactericidal compound that inhibits dihydrofolate reductase. It is used against clinically important Gram-positive pathogens, including methicillin-sensitive Staphylococcus aureus and methicillin-resistant S. aureus.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1993":{"model_id":"1993","model_name":"QnrB74","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"556":{"protein_sequence":{"accession":"AHX97725.1","sequence":"MALALVGEKIDRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNSSALGIEIRHCRAQGADFRGASFMNMIITRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWIGAQVLGATFSGSDFFGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"KJ415247","fmin":"0","fmax":"645","strand":"+","sequence":"ATGGCTCTGGCACTCGTTGGCGAAAAAATTGACAGAAACCGTTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACTTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCGATGCTGAAAGATGCCATTTTTAAAAGTTGTGATTTATCCATGGCGGATTTTCGCAATTCCAGTGCGCTGGGTATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGCGCAAGCTTTATGAATATGATTATCACGCGCACCTGGTTTTGTAGCGCATATATCACGAATACCAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAGCTGTGGGAAAACCGTTGGATAGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATTTCTTCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACTAATTCGGAGTTGGGTGACTTAGATATTCGGGGCGTTGATTTACAAGGCGTTAAGTTGGACAACTACCAGGCGTCGTTGCTCATGGAGCGGCTTGGCATCGCGGTGATTGGTTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002786","ARO_id":"39220","ARO_name":"QnrB74","ARO_description":"QnrB74 is a plasmid-mediated quinolone resistance protein found in Escherichia coli","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1995":{"model_id":"1995","model_name":"AAC(6')-Iz","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"205":{"protein_sequence":{"accession":"AAD52985.1","sequence":"MIASAPTIRQATPADAAAWAQLRLGLWPDADDPLEELTQSLADAEGAVFLACAADGETVGFAEVRLRHDYVNGTESSPVGFLEGWYVQPQWQGSGVGRALLAAVQAWTRDAGCRELASDSRVEDVQAHAAHRACGFEETERVVYFRMPLEPSA"},"dna_sequence":{"accession":"AF140221","fmin":"389","fmax":"851","strand":"+","sequence":"GTGATCGCCAGCGCGCCCACGATCCGCCAGGCCACGCCGGCCGATGCGGCTGCATGGGCGCAGTTGCGTCTCGGCCTGTGGCCTGATGCCGATGATCCGCTGGAGGAGCTGACGCAGTCGCTGGCAGATGCCGAAGGTGCTGTGTTCTTGGCCTGTGCCGCGGATGGCGAGACGGTTGGTTTCGCTGAAGTGCGCCTGCGCCATGACTACGTGAACGGTACCGAGTCTTCGCCGGTGGGGTTCCTGGAGGGCTGGTACGTGCAGCCGCAGTGGCAAGGCAGCGGCGTCGGCCGCGCCCTGCTGGCGGCGGTGCAGGCGTGGACGCGCGATGCGGGCTGCCGCGAACTGGCTTCGGACAGTCGCGTGGAAGACGTGCAGGCTCACGCCGCGCATCGGGCCTGCGGCTTCGAAGAGACCGAACGGGTCGTCTATTTCCGCATGCCGCTGGAGCCATCGGCGTGAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37076","NCBI_taxonomy_name":"Stenotrophomonas maltophilia","NCBI_taxonomy_id":"40324"}}}},"ARO_accession":"3002570","ARO_id":"38970","ARO_name":"AAC(6')-Iz","ARO_description":"AAC(6')-Iz is a chromosomal-encoded aminoglycoside acetyltransferase in S. maltophilia","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1996":{"model_id":"1996","model_name":"vanXM","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"375"}},"model_sequences":{"sequence":{"717":{"protein_sequence":{"accession":"ACL82962.1","sequence":"MEKGFTFLDEILNDVRWDAKYATWDNFTGKPIDGYEVNRIIGTYELADALLKVQELAFNQGYGLLLWDGYRPQQAVNCFLQWAAQPEDNRTKAKYYPNIDRTEMVSKGYVASKSSHSRGSAIDLTLYRLDTDELVPMGSGFDFMDERSHHEAKGITSNEAQNRRFLRSIMENSGFEAYSFEWWHYVLINEPYPYSCFDFPVK"},"dna_sequence":{"accession":"FJ349556","fmin":"5893","fmax":"6502","strand":"+","sequence":"ATGGAAAAAGGATTTACCTTTTTAGATGAAATATTAAACGATGTTCGTTGGGACGCTAAATATGCTACGTGGGACAACTTCACTGGAAAACCAATTGATGGATATGAAGTAAATCGAATTATAGGAACATATGAGTTAGCCGATGCGCTATTGAAGGTTCAAGAATTAGCTTTTAACCAAGGTTATGGATTGCTTTTATGGGACGGTTACCGTCCCCAACAAGCTGTAAATTGTTTTTTGCAATGGGCGGCACAGCCGGAAGATAATCGAACAAAGGCAAAATATTATCCCAATATTGACCGAACTGAGATGGTTTCAAAAGGATACGTGGCTTCAAAATCAAGTCATAGCCGCGGAAGTGCAATTGATCTTACACTTTATCGATTAGACACGGACGAACTTGTTCCGATGGGGAGCGGATTTGATTTTATGGATGAGCGCTCTCATCATGAGGCAAAAGGAATTACGAGCAATGAAGCGCAAAACCGTAGATTTTTGCGTTCCATTATGGAAAACAGTGGGTTTGAAGCGTATAGTTTCGAATGGTGGCACTATGTATTGATAAACGAACCTTATCCCTATAGCTGCTTTGATTTTCCTGTCAAATAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002953","ARO_id":"39387","ARO_name":"vanXM","ARO_description":"vanXM is a vanX variant found in the vanM gene cluster","ARO_category":{"36020":{"category_aro_accession":"3000011","category_aro_cvterm_id":"36020","category_aro_name":"vanX","category_aro_description":"VanX is a D,D-dipeptidase that cleaves D-Ala-D-Ala but not D-Ala-D-Lac, ensuring that the latter dipeptide that has reduced binding affinity with vancomycin is used to synthesize peptidoglycan substrate.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1997":{"model_id":"1997","model_name":"tlrC","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1020"}},"model_sequences":{"sequence":{"158":{"protein_sequence":{"accession":"AAA26832.1","sequence":"MRTSPSSQLSLHGVTKRYDDRVVLSQVSLAISPGEKAGIIGDNGAGKSTLLRLLAGEERPDAGEVTVIAPGGVGYLPQTLGLPPRATVQDAIDLAMTELRVLEAELRRTEAALAEAATDEALQDALTAYARLTEQYEVRDGYGADARVDAALHGLGLPGLPRDRRLGTLSGGERSRLALAATLASQPELLLLDEPTNDLDDRAVHWLEEHLSGHRGTVVTVTHDRVFLDRLTATVLEVDGRGVSRHGDGYAGYLAAKAAERRRRQQQYDEWRAELDRNRRLAEANVARLDGIPRKMGKAAFGHGAFRARGRDHGAMSRVRNAKERVERLTANPVAPPADRLSLTARIATADGPGEAPAAELDGVVVGSRLRVPKLRLGAAERLLITGPNGAGKSTLLSVLAGELSPDAGAVSVPGRVGHLRQEETPWPAKLTVLEAFAHNRPGDRDEQADRRLSLGLFEPEALRLRVGELSYGQRRRIELARLVSEPVGLLLLDEPTNHLSPALVEELEEALTGYGGALVLVTHDRRMRSRFTGSHLELREGVVSGAR"},"dna_sequence":{"accession":"M57437","fmin":"0","fmax":"1647","strand":"+","sequence":"ATGCGTACATCACCTTCCTCCCAGCTTTCCCTGCACGGTGTCACCAAGCGCTACGACGACCGTGTCGTGCTCAGTCAGGTCTCCCTCGCCATCTCCCCGGGGGAGAAGGCCGGCATCATCGGCGACAACGGGGCCGGGAAGTCCACCCTGCTCCGTCTGCTCGCCGGTGAGGAACGGCCCGACGCGGGGGAGGTGACCGTGATCGCGCCCGGCGGTGTCGGCTACCTCCCGCAGACCCTCGGCCTGCCGCCGCGGGCCACGGTGCAGGACGCCATCGATCTGGCCATGACCGAGCTGCGCGTCCTGGAGGCCGAACTGCGCCGTACCGAGGCCGCGTTGGCCGAGGCCGCCACGGACGAGGCCCTGCAGGACGCCCTCACCGCGTACGCCCGTCTGACCGAGCAGTACGAGGTCCGTGACGGCTACGGCGCCGATGCCCGCGTGGACGCCGCGCTGCACGGTCTCGGGCTGCCCGGACTGCCACGTGACCGGCGGCTGGGCACCCTCTCCGGTGGAGAGCGATCGCGGCTGGCGCTGGCGGCCACCCTGGCGTCCCAGCCGGAACTGCTGCTGCTCGACGAGCCGACCAACGACCTGGACGACCGGGCCGTCCACTGGCTGGAGGAACATCTGAGCGGCCACCGCGGCACCGTCGTCACGGTGACCCACGACCGGGTGTTCCTGGACCGGCTCACCGCCACGGTCCTGGAGGTCGACGGCCGCGGCGTCTCCCGCCACGGCGACGGCTACGCGGGGTATCTCGCCGCCAAGGCCGCCGAGCGCCGCCGGCGGCAGCAGCAGTACGACGAGTGGCGCGCCGAACTCGACCGCAACCGCCGGCTGGCCGAGGCCAACGTCGCCCGGCTGGACGGCATCCCGCGCAAGATGGGGAAGGCCGCCTTCGGGCACGGCGCGTTCCGCGCGCGCGGGCGCGACCACGGCGCGATGAGCCGGGTCCGCAACGCCAAGGAGCGGGTCGAGCGGCTCACCGCGAATCCGGTGGCGCCACCGGCGGACCGGCTCTCCCTCACCGCGCGCATCGCCACGGCGGACGGCCCGGGGGAGGCGCCGGCCGCGGAACTCGACGGCGTGGTCGTCGGCAGCCGGCTGCGCGTGCCGAAGCTGCGCCTGGGCGCGGCCGAACGGCTGCTGATCACCGGCCCCAATGGCGCGGGCAAGAGCACCCTGCTGTCCGTGCTGGCCGGGGAACTGAGCCCGGACGCGGGCGCGGTGAGCGTCCCCGGGCGCGTGGGGCATCTGCGCCAGGAGGAGACGCCCTGGCCCGCGAAGCTGACCGTGCTGGAGGCCTTCGCCCACAACCGGCCCGGCGACCGGGACGAACAGGCCGACCGGCGGCTGTCCCTCGGCCTGTTCGAGCCGGAGGCGCTGCGGCTGCGGGTCGGGGAGCTGTCGTACGGTCAGCGCCGCCGCATCGAACTGGCCCGGCTGGTCAGCGAGCCGGTGGGTCTGCTCCTGCTGGACGAGCCCACCAACCACCTCTCACCGGCGCTGGTGGAGGAGTTGGAGGAGGCGCTGACGGGCTACGGGGGCGCGCTGGTGCTGGTCACCCACGACCGGCGGATGCGAAGCCGGTTCACCGGCTCGCATCTGGAGCTGCGCGAGGGCGTCGTCTCCGGCGCACGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36838","NCBI_taxonomy_name":"Streptomyces fradiae","NCBI_taxonomy_id":"1906"}}}},"ARO_accession":"3002827","ARO_id":"39261","ARO_name":"tlrC","ARO_description":"tlrC is an efflux pump found in Streptomyces fradiae and confers resistance to mycinamicin, tylosin and lincosamides. tlrC is found in the tylosin biosynthetic cluster and is one mechanism by which S. fradiae protects itself from self-destruction when producing this macrolide.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1998":{"model_id":"1998","model_name":"CTX-M-83","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1170":{"protein_sequence":{"accession":"ACI29345.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTHVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"FJ214366","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCACGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35667","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Derby","NCBI_taxonomy_id":"28144"}}}},"ARO_accession":"3001944","ARO_id":"38344","ARO_name":"CTX-M-83","ARO_description":"CTX-M-83 is a beta-lactamase found in Salmonella enterica","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1999":{"model_id":"1999","model_name":"TEM-215","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2127":{"protein_sequence":{"accession":"AJO16045.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLRNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"KP050492","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCGCAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001392","ARO_id":"37792","ARO_name":"TEM-215","ARO_description":"From the Lahey list of beta-lactamases. Not yet released.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2000":{"model_id":"2000","model_name":"TEM-24","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1801":{"protein_sequence":{"accession":"CAA46345.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGTGKRGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"X65253","fmin":"175","fmax":"1036","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAACCGGTAAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000894","ARO_id":"37274","ARO_name":"TEM-24","ARO_description":"TEM-24 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2001":{"model_id":"2001","model_name":"OXA-250","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1297":{"protein_sequence":{"accession":"CCJ32598.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGEKRLFPEWEKNMTLGDAMKASAILVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGLDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"HE963771","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAATGGGATGGGGAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCTGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTCTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATTGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001675","ARO_id":"38075","ARO_name":"OXA-250","ARO_description":"OXA-250 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2004":{"model_id":"2004","model_name":"TEM-189","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"847":{"protein_sequence":{"accession":"AEL79515.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMLSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGKRGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"JN254627","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGCTGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTAAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001049","ARO_id":"37429","ARO_name":"TEM-189","ARO_description":"TEM-189 is a beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2005":{"model_id":"2005","model_name":"CTX-M-89","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1630":{"protein_sequence":{"accession":"ACR56321.1","sequence":"MMRKSVRRAMLMTTACVSLLLASVPLCAQANDVQQKLAALEKSSGGRLGVALINTADNTQTLYRADERFAMCSTSKVMAVAAVLKQSETQKGLLSQRVEIKPSDLINYNPIAEKHVNGTMTFGELSAAALQYSDNTAMNKLIAHLGGPDKVTAFARTIGDDTFRLDRTEPTLNTAIPGDPRDTTTPLAMAQALRNLTLGNALGDTQRAQLVMWLKGNTTGAASIQAGLPTSWVVGDKTGSGDYGTTNDIAVIWPEGRAPLVLVTYFTQSEPKAESRRDVLAAAARIVTDGY"},"dna_sequence":{"accession":"FJ971899","fmin":"30","fmax":"906","strand":"+","sequence":"ATGATGAGAAAAAGCGTAAGGCGGGCGATGTTAATGACGACAGCCTGTGTTTCGCTGCTGTTGGCCAGTGTGCCGCTGTGTGCCCAGGCGAACGATGTTCAACAAAAGCTCGCGGCGCTGGAGAAAAGCAGCGGGGGACGACTGGGTGTGGCGTTGATTAACACCGCCGATAACACGCAGACGCTCTACCGCGCCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCGGTAGCGGCGGTGCTTAAGCAAAGTGAAACGCAAAAGGGCTTGTTGAGTCAGCGGGTTGAAATTAAGCCCTCAGACTTGATTAACTACAACCCCATTGCGGAAAAACACGTCAATGGCACGATGACATTCGGGGAGTTGAGCGCGGCGGCGCTACAGTACAGCGATAATACTGCCATGAATAAGCTGATTGCCCATCTCGGGGGGCCGGATAAAGTGACGGCATTTGCCCGTACGATTGGCGATGACACGTTCCGGCTCGATCGTACCGAGCCGACGCTCAACACCGCGATCCCCGGCGACCCGCGCGATACCACCACGCCGTTAGCGATGGCGCAGGCTCTGCGCAATCTGACGTTGGGCAATGCCCTGGGTGACACTCAGCGTGCGCAGCTGGTGATGTGGCTGAAAGGCAACACCACCGGCGCTGCCAGCATTCAGGCAGGGCTACCCACATCGTGGGTTGTCGGGGATAAAACCGGCAGCGGCGATTATGGTACGACGAATGATATCGCGGTTATTTGGCCGGAAGGTCGCGCGCCGCTCGTTCTGGTGACTTACTTCACCCAGTCGGAGCCGAAGGCAGAGAGCCGTCGTGACGTGCTCGCTGCTGCCGCCAGAATTGTCACCGACGGTTATTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3001949","ARO_id":"38349","ARO_name":"CTX-M-89","ARO_description":"CTX-M-89 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2006":{"model_id":"2006","model_name":"IMP-27","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"837":{"protein_sequence":{"accession":"AEH41427.1","sequence":"MKKLFVLCVFVFCSITVAGETLPNLRVEKLEEGVYVHTSYEEVKGWGVVTKHGLVVLIGADAYLIDTPFTAKDTEKLVNWFVERGYKIKGTVSSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKDGKVQAKNSFDGVSYWLAKDKIEVFYPGPGHTQDNVVVWLPEKEILFGGCFVKPHGLGNLGDANLEAWPESAKILMEKYGKAKLVVSGHSETGDATHLKRTWEQAVKGLKESKKTLQPSN"},"dna_sequence":{"accession":"JF894248","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAAAAAATTATTTGTTTTATGTGTCTTTGTCTTTTGTAGTATTACTGTCGCAGGTGAGACTTTGCCTAATTTGAGAGTTGAAAAGCTTGAAGAAGGTGTTTATGTTCATACATCGTATGAAGAAGTTAAAGGTTGGGGTGTTGTTACTAAACACGGTTTGGTGGTTCTCATAGGCGCTGACGCCTATCTGATTGATACTCCATTTACTGCTAAAGATACTGAAAAGTTAGTCAATTGGTTTGTGGAGCGCGGCTATAAAATAAAAGGCACTGTTTCCTCACATTTCCATAGCGACAGTACGGGGGGAATAGAGTGGCTTAACTCTCAGTCTATCCCCACGTATGCGTCTGAATTAACGAATGAACTTCTGAAAAAAGACGGTAAGGTTCAAGCCAAAAACTCATTTGACGGGGTTAGTTATTGGCTGGCGAAAGATAAAATAGAAGTGTTTTATCCTGGCCCTGGCCACACTCAAGACAACGTAGTAGTTTGGCTGCCTGAAAAGGAAATATTATTTGGCGGTTGCTTTGTTAAGCCTCACGGCCTTGGTAATTTGGGTGACGCAAATTTAGAGGCTTGGCCAGAGTCCGCCAAAATATTGATGGAAAAATATGGTAAAGCAAAGCTGGTTGTTTCAGGTCATAGCGAAACCGGAGACGCGACACACTTGAAGCGTACCTGGGAGCAGGCTGTTAAAGGACTTAAAGAAAGTAAAAAGACATTGCAGCCAAGCAACTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3002218","ARO_id":"38618","ARO_name":"IMP-27","ARO_description":"IMP-27 is a beta-lactamase. From the Lahey list of IMP beta-lactamases.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2007":{"model_id":"2007","model_name":"OXA-335","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1762":{"protein_sequence":{"accession":"AGW16417.1","sequence":"MKILILLPLLSCLGLTACSLPVSSLPSQSTSTQAIASLFDQAQSSGVLVIQRDQQVQVYGNDLNRANTEYVPASTFKMPNALIGLQHGKATTNEIFKWDGKKRSFTAWEKDMTLGQAMQASAVPVYQELARRIGLELMQQEVQRIQFGNQQIGQQVDNFWLVGPLKVTPKQEVQFVSALAREQLAFDPQVQQQVKAMLFLQERKAYRLYVKSGWGMDVEPQVGWLTGWVETPQAEIVAFSLNMQMQNGIDPAIRLEILQQALAELGLYPKAEG"},"dna_sequence":{"accession":"KF203109","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAAAATTTTGATTTTGCTGCCTTTACTTAGTTGCTTGGGCCTGACAGCATGTAGCCTACCCGTTTCATCTCTCCCATCTCAAAGCACTTCGACTCAAGCGATTGCCAGCTTATTTGATCAGGCGCAAAGCTCTGGTGTTTTAGTGATTCAGCGTGATCAACAAGTACAGGTCTATGGCAATGATTTAAATCGTGCAAATACCGAATATGTTCCCGCCTCTACTTTTAAAATGCCCAATGCTCTGATTGGCCTGCAACATGGCAAAGCCACAACCAATGAAATTTTTAAATGGGATGGCAAGAAACGCAGCTTTACCGCCTGGGAAAAAGACATGACTCTCGGCCAAGCCATGCAAGCTTCTGCGGTACCGGTCTATCAAGAACTGGCGCGTCGTATTGGTCTGGAATTAATGCAACAGGAAGTACAACGCATCCAATTTGGTAATCAGCAGATTGGTCAACAGGTCGATAACTTCTGGTTGGTAGGCCCTTTGAAAGTTACTCCAAAACAGGAAGTCCAATTTGTTTCTGCGTTGGCCCGAGAGCAACTGGCCTTTGATCCTCAAGTCCAGCAACAAGTCAAAGCCATGTTATTTTTACAGGAGCGGAAAGCTTATCGACTATATGTCAAATCCGGTTGGGGCATGGATGTGGAACCGCAAGTCGGCTGGCTCACCGGCTGGGTTGAAACACCGCAGGCTGAAATCGTGGCATTTTCGCTGAATATGCAGATGCAAAATGGTATAGATCCGGCGATCCGCCTTGAAATTTTGCAGCAGGCTTTGGCCGAATTAGGGCTTTATCCAAAAGCTGAAGGATGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36948","NCBI_taxonomy_name":"Acinetobacter lwoffii","NCBI_taxonomy_id":"28090"}}}},"ARO_accession":"3001523","ARO_id":"37923","ARO_name":"OXA-335","ARO_description":"OXA-335 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2008":{"model_id":"2008","model_name":"SHV-145","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1943":{"protein_sequence":{"accession":"AFN88952.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGERCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"JX013655","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACGCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001185","ARO_id":"37565","ARO_name":"SHV-145","ARO_description":"SHV-145 is a beta-lactamase.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2009":{"model_id":"2009","model_name":"aadA6","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"199":{"protein_sequence":{"accession":"CAJ32504.1","sequence":"MSNAVPAEISVQLSLALNAIERHLESTLLAVHLYGSALDGGLKPYSDIDLLVTVAARLDETVRQALVVDLLEISASPGQSEALRALEVTIVVHGDVVPWRYPARRELQFGEWQRKDILAGIFEPATTDVDLAILLTKVRQHSLALAGSAAEDFFNPVPEGDLFKALSDTLKLWNSQPDWEGDERNVVLTLSRIWYSAATGKIAPKDIVANWAMERLPDQHKPVLLEARQAYLGQGEDCLASRADQLAAFVHFVKHEATKLLSAMPVMSNNSFKPTPLRGAA"},"dna_sequence":{"accession":"AM087411","fmin":"1611","fmax":"2457","strand":"+","sequence":"ATGAGTAACGCAGTACCCGCCGAGATTTCGGTACAGCTATCACTGGCTCTCAACGCCATCGAGCGTCATCTGGAATCAACGTTGCTGGCCGTGCATTTGTACGGCTCTGCACTGGACGGTGGCCTGAAGCCATACAGTGATATTGATTTGCTGGTTACTGTGGCTGCACGGCTCGATGAGACTGTCCGACAAGCCCTGGTCGTAGATCTCTTGGAAATTTCTGCCTCCCCTGGCCAAAGTGAAGCTCTCCGCGCCTTGGAAGTTACCATCGTCGTGCATGGTGATGTTGTCCCTTGGCGTTATCCGGCCAGACGGGAACTGCAATTCGGGGAGTGGCAGCGTAAGGACATTCTTGCGGGCATCTTCGAGCCCGCCACAACCGATGTTGATCTGGCTATTCTGCTAACTAAAGTAAGGCAGCATAGCCTTGCATTGGCAGGTTCGGCCGCAGAGGATTTCTTTAACCCAGTTCCGGAAGGCGATCTATTCAAGGCATTGAGCGACACTCTGAAACTATGGAATTCGCAGCCGGATTGGGAAGGCGATGAGCGGAATGTAGTGCTTACCTTGTCTCGCATTTGGTACAGCGCAGCAACCGGCAAGATCGCACCGAAGGATATCGTTGCCAACTGGGCAATGGAGCGTCTGCCAGATCAACATAAGCCCGTACTGCTTGAAGCCCGGCAGGCTTATCTTGGACAAGGAGAAGATTGCTTGGCCTCACGCGCGGATCAGTTGGCGGCGTTCGTTCACTTCGTGAAACATGAAGCCACTAAATTGCTTAGTGCCATGCCAGTGATGTCTAACAATTCATTCAAGCCGACGCCGCTTCGCGGCGCGGCTTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002606","ARO_id":"39006","ARO_name":"aadA6","ARO_description":"aadA6 is an integron-encoded aminoglycoside nucleotidyltransferase gene in P. aeruginosa","ARO_category":{"41439":{"category_aro_accession":"3004275","category_aro_cvterm_id":"41439","category_aro_name":"ANT(3'')","category_aro_description":"Nucleotidylylation of streptomycin at the hydroxyl group at position 3''","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2010":{"model_id":"2010","model_name":"CTX-M-129","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1550":{"protein_sequence":{"accession":"AFJ59956.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLRGNTTGAASIRAGLPTSWTVGDKTGSGGYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"JX017364","fmin":"238","fmax":"1114","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAGAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGGCTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001988","ARO_id":"38388","ARO_name":"CTX-M-129","ARO_description":"CTX-M-129 is a beta-lactamase. From the Lahey list of CTX-M beta-lactamases.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2011":{"model_id":"2011","model_name":"QnrB60","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"690":{"protein_sequence":{"accession":"BAN04743.1","sequence":"MALALIGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAILKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKAVLEKCELWENRWMGTQVLGATLSGSDLSGGEFSSFDWRTANFTHCDLTNSELGDLDIRGVDLQGVKLDSYQAVLLMERLGIAVIG"},"dna_sequence":{"accession":"AB734055","fmin":"376","fmax":"1021","strand":"+","sequence":"ATGGCTCTGGCATTAATTGGCGAAAAAATTGACAGAAACCGCTTCACCGGTGAAAAAGTTGAAAATAGCACTTTTTTTAACTGTGATTTTTCGGGTGCCGACCTTAGCGGTACTGAATTTATCGGCTGTCAGTTCTATGATCGAGAAAGCCAGAAAGGGTGCAATTTCAGTCGCGCAATACTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAACGTCAGTGCGTTGGGCATAGAAATTCGCCACTGCCGCGCACAGGGTGCAGATTTTCGCGGCGCAAGTTTCATGAATATGATCACCACGCGCACCTGGTTTTGCAGCGCATATATCACTAATACCAATCTAAGCTACGCCAACTTTTCGAAGGCCGTGCTTGAAAAGTGCGAATTGTGGGAAAATCGCTGGATGGGAACTCAGGTGCTGGGTGCGACGTTGAGTGGTTCCGATCTCTCCGGTGGCGAGTTTTCGTCGTTCGACTGGCGGACGGCAAATTTCACGCACTGTGATTTGACCAATTCAGAACTGGGTGATTTAGATATTCGGGGCGTCGATTTACAAGGTGTCAAATTGGACAGCTATCAGGCCGTATTGCTCATGGAACGTCTTGGCATCGCTGTCATTGGCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002773","ARO_id":"39207","ARO_name":"QnrB60","ARO_description":"QnrB60 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2012":{"model_id":"2012","model_name":"SHV-178","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1473":{"protein_sequence":{"accession":"AHA80963.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWVVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"KF705209","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGGTGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001361","ARO_id":"37761","ARO_name":"SHV-178","ARO_description":"From the Lahey list of beta-lactamases.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2013":{"model_id":"2013","model_name":"Erm(41)","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"225"}},"model_sequences":{"sequence":{"357":{"protein_sequence":{"accession":"ABW06859.1","sequence":"MDLGAGHGALTAHLVAAGARVLAVELHPGRARHLRSRFAEEDVRVAEADLLAFRWPRRPFRVVASPPYQVTSALIRSLLTPESRLLAADLVLQRGAVHKHAKRAPVRHWTLRAGITLPRSAFHHPPQVDSSVLVIRRR"},"dna_sequence":{"accession":"EU177504","fmin":"0","fmax":"417","strand":"+","sequence":"GTGGATCTGGGCGCAGGACACGGCGCGCTGACGGCACATCTGGTTGCCGCTGGCGCCAGGGTGCTAGCCGTCGAGCTGCATCCGGGGCGGGCTCGACACCTTCGTTCACGGTTTGCCGAGGAAGATGTCCGGGTAGCGGAAGCGGACCTACTCGCCTTCCGGTGGCCGCGACGGCCATTTCGGGTGGTGGCGAGCCCGCCCTACCAAGTCACCAGCGCACTGATCCGGAGTCTCTTGACGCCGGAATCCCGGCTGCTGGCTGCCGACCTGGTGCTGCAGCGCGGGGCTGTGCACAAACATGCGAAGCGAGCACCTGTTCGCCATTGGACGCTACGGGCCGGAATCACATTGCCGCGAAGCGCTTTCCATCATCCACCGCAGGTGGATTCGTCGGTGCTGGTGATCAGGCGGCGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36888","NCBI_taxonomy_name":"Mycobacterium abscessus","NCBI_taxonomy_id":"36809"}}}},"ARO_accession":"3000603","ARO_id":"36742","ARO_name":"Erm(41)","ARO_description":"Erm41 confers MLSb phenotype.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35946":{"category_aro_accession":"0000027","category_aro_cvterm_id":"35946","category_aro_name":"roxithromycin","category_aro_description":"Roxithromycin is a semi-synthetic, 14-carbon ring macrolide antibiotic derived from erythromycin. It is used to treat respiratory tract, urinary and soft tissue infections. Roxithromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35974":{"category_aro_accession":"0000057","category_aro_cvterm_id":"35974","category_aro_name":"telithromycin","category_aro_description":"Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36315":{"category_aro_accession":"3000176","category_aro_cvterm_id":"36315","category_aro_name":"dirithromycin","category_aro_description":"Dirithromycin is an oxazine derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome to inhibit bacterial protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin 1A is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"vernamycin B-gamma","category_aro_description":"Vernamycin B-gamma is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2015":{"model_id":"2015","model_name":"DHA-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1631":{"protein_sequence":{"accession":"AAR87489.1","sequence":"MKKSLSATLISALLAFSAPGFSAADNVAAVVDSTIKPLMAQQDIPGMAVAVSVKGKPYYFNYGFADIQAKQPVTENTLFELGSVSKTFTGVLGAVSVAKKEMALNDPAAKYQPELALPQWKGITLLDLATYTAGGLPLQVPDAVKSRADLLNFYQQWQPSRKPGDMRLYANSSIGLFGALTANAAGMPYEQLLTARILAPLGLSHTFITVPDSAQSQYAYGYKNKKPVRVSPGQLDAESYGVKSASKDMLRWAEMNIEPSRAGNADLEMAMYLAQTRYYKTAAINQGLGWEMYDWPQQKDMIINGVTNEVALQPHPVTDNQVQPYNRASWVHKTGATTGFGAYVAFIPEKQVAIVILANKNYPNTERVKAAQAILSALE"},"dna_sequence":{"accession":"AY494945","fmin":"1309","fmax":"2449","strand":"+","sequence":"ATGAAAAAATCGTTATCTGCAACACTGATTTCCGCTCTGCTGGCGTTTTCCGCCCCGGGGTTTTCTGCCGCTGATAATGTCGCGGCGGTGGTGGACAGCACCATTAAACCGCTGATGGCACAGCAGGATATTCCCGGGATGGCGGTTGCCGTCTCCGTAAAGGGTAAGCCCTATTATTTCAATTATGGTTTTGCCGATATTCAGGCAAAACAGCCGGTCACTGAAAATACACTATTTGAGCTCGGATCTGTAAGTAAAACTTTCACAGGTGTGCTGGGTGCGGTTTCTGTGGCGAAAAAAGAGATGGCGCTGAATGATCCGGCGGCAAAATACCAGCCGGAGCTGGCTCTGCCGCAGTGGAAGGGGATCACATTGCTGGATCTGGCTACCTATACCGCAGGCGGACTGCCGTTACAGGTGCCGGATGCGGTAAAAAGCCGTGCGGATCTGCTGAATTTCTATCAGCAGTGGCAGCCGTCCCGGAAACCGGGCGATATGCGTCTGTATGCAAACAGCAGTATCGGCCTGTTTGGTGCTCTGACCGCAAACGCGGCGGGGATGCCGTATGAGCAGTTGCTGACTGCACGGATCCTGGCACCGCTGGGGTTATCTCACACCTTTATTACTGTGCCGGATAGTGCGCAAAGCCAGTATGCGTACGGTTATAAAAACAAAAAACCGGTCCGCGTGTCGCCAGGACAGCTTGATGCGGAATCTTACGGCGTGAAATCCGCCTCAAAAGATATGCTGCGCTGGGCGGAAATGAATATTGAGCCGTCACGGGCCGGTAATGCGGATCTGGAAATGGCAATGTATCTCGCCCAGACCCGCTACTATAAAACCGCCGCGATTAACCAGGGGCTGGGCTGGGAAATGTATGACTGGCCGCAGCAGAAAGATATGATCATTAACGGCGTGACCAACGAGGTCGCATTGCAGCCGCATCCGGTAACAGACAACCAGGTTCAGCCGTATAACCGTGCTTCCTGGGTGCATAAAACGGGCGCAACAACTGGTTTCGGCGCCTATGTGGCCTTTATTCCGGAAAAACAGGTGGCGATTGTGATTCTGGCGAATAAAAACTACCCGAATACCGAAAGAGTCAAAGCTGCACAGGCTATTTTGAGTGCACTGGAATAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002134","ARO_id":"38534","ARO_name":"DHA-3","ARO_description":"DHA-3 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36207":{"category_aro_accession":"3000068","category_aro_cvterm_id":"36207","category_aro_name":"DHA beta-lactamase","category_aro_description":"DHA beta-lactamases are plasmid-mediated AmpC \u03b2-lactamases that confer resistance to cephamycins and oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2016":{"model_id":"2016","model_name":"OXA-370","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1214":{"protein_sequence":{"accession":"AHF71363.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYETRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"KF900153","fmin":"0","fmax":"798","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGACAGTTTCTGGCTCGACGGTGGTATTCGAATTTCGGCCACGGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATGCTGACCGAAGCCAATGGCGACTATATTATTCGGGCTAAAACTGGATACGAGACTAGAATCGAACCTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39099","NCBI_taxonomy_name":"Enterobacter sp. 87F-2","NCBI_taxonomy_id":"1445416"}}}},"ARO_accession":"3001774","ARO_id":"38174","ARO_name":"OXA-370","ARO_description":"OXA-370 is a beta-lactamase found in Enterobacter hormaechei","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2017":{"model_id":"2017","model_name":"CTX-M-37","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1273":{"protein_sequence":{"accession":"AAT70415.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLHAQTADVQQKLAELEQQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVDGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"AY649755","fmin":"17","fmax":"893","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGCATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCAGCAGTCGGGAGGAAGGCTGGGTGTGGCATTGATTAACACAGCGGATAATTCGCAAATACTTTATCGTGCAGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTGGTTAACTATAATCCGATTGCGGAAAAGCACGTCGATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGCACCGAGCCGACGTTAAACACAGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACGCTGCGTAATCTGACGCTGGGTAAAGCATTGGGTGACAGCCAACGGGCGCAGCTGGTGACGTGGATGAAAGGCAATACTACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGTACCACCAACGATATCGCGGTGATTTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCCCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001899","ARO_id":"38299","ARO_name":"CTX-M-37","ARO_description":"CTX-M-37 is a beta-lactamase found in Salmonella enterica","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2018":{"model_id":"2018","model_name":"CMY-76","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1664":{"protein_sequence":{"accession":"AFK73437.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEEKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVQPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"JQ733573","fmin":"1027","fmax":"2173","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCGCTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACGAGGAGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAATTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGCGGTGCAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACAGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATAGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGCGTCGAGGCGGCCTGGCGCATTCTTGAAAAACTGCAATAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002089","ARO_id":"38489","ARO_name":"CMY-76","ARO_description":"CMY-76 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2019":{"model_id":"2019","model_name":"OXA-213","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1128":{"protein_sequence":{"accession":"AEV91552.1","sequence":"MYKKALIVATSILFLSACSSNMVKQHQIHSISANKNSEEIKSLFDQAQTTGVLVIKRGQTEEIYGNDFKRASTDYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRVGFGNANIGSKVDNFWLVGPLKITPQQETQFAYQLAHKTLPFSKDVQEQVQSMVFIEEKNGSKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"JN861781","fmin":"0","fmax":"822","strand":"+","sequence":"ATGTACAAAAAAGCCCTTATCGTTGCAACAAGTATCCTATTTTTATCCGCCTGTTCTTCCAATATGGTAAAACAACATCAAATACACTCTATTTCTGCCAATAAAAATTCAGAAGAAATTAAATCACTGTTTGATCAAGCACAGACCACGGGAGTTTTGGTGATTAAGCGAGGGCAAACAGAAGAAATTTATGGCAATGATTTTAAAAGAGCATCAACCGACTATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTAATTGGACTTGAACATCATAAGGCAACTACAACTGAAGTATTTAAATGGAATGGGCAAAAACGTTTATTTCCTGATTGGGAAAAGGACATGACACTGGGCGATGCCATGAAAGCGTCTGCAATTCCAGTTTACCAAGAATTAGCCCGACGAATTGGTCTAGATCTTATGTCCAAAGAGGTGAAACGAGTTGGTTTTGGTAATGCTAACATTGGTTCAAAAGTAGATAATTTTTGGCTCGTTGGCCCTCTAAAAATTACACCTCAACAAGAAACCCAATTTGCTTATCAATTAGCCCATAAAACGCTTCCATTTAGTAAAGATGTACAAGAACAAGTTCAATCAATGGTGTTCATAGAAGAAAAAAATGGAAGTAAGATTTATGCCAAAAGTGGGTGGGGATGGGATGTTGAACCACAAGTTGGTTGGTTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTCGCATTCTCACTTAATTTAGAAATGAAAAAAGGAACTCCCAGCTCTATTCGCAAAGAAATTGCTTATAAAGGCTTAGAACAACTGGGTATCTTATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3001712","ARO_id":"38112","ARO_name":"OXA-213","ARO_description":"OXA-213 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2020":{"model_id":"2020","model_name":"tetO","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1200"}},"model_sequences":{"sequence":{"4234":{"protein_sequence":{"accession":"AAA23033.2","sequence":"MKIINLGILAHVDAGKTTLTESLLYTSGAIAELGSVDEGTTRTDTMNLERQRGITIQTAVTSFQWEDVKVNIIDTPGHMDFLAEVYRSLSVLDGAVLLVSAKDGIQAQTRILFHALQIMKIPTIFFINKIDQEGIDLPMVYREMKAKLSSEIIVKQKVGQHPHINVTDNDDMEQWDAVIMGNDELLEKYMSGKPFKMSELEQEENRRFQNGTLFPVYHGSAKNNLGTRQLIEVIASKFYSSTPEGQSELCGQVFKIEYSEKRRRFVYVRIYSGTLHLRDVIRISEKEKIKITEMYVPTNGELYSSDTACSGDIVILPNDVLQLNSILGNEILLPQRKFIENPLPMIQTTIAVKKSEQREILLGALTEISDCDPLLKYYVDTTTHEIILSFLGNVQMEVICAILEEKYHVEAEIKEPTVIYMERPLRKAEYTIHIEVPPNPFWASVGLSIEPLPIGSGVQYESRVSLGYLNQSFQNAVMEGVLYGCEQGLYGWKVTDCKICFEYGLYYSPVSTPADFRLLSPIVLEQALKKAGTELLEPYLHFEIYAPQEYLSRAYHDAPRYCADIVSTQIKNDEVILKGEIPARCIQEYRNDLTYFTNGQGVCLTELKGYQPAIGKFICQPRRPNSRIDKVRHMFHKLA"},"dna_sequence":{"accession":"M18896.2","fmin":"206","fmax":"2126","strand":"+","sequence":"ATGAAAATAATTAACTTAGGCATTCTGGCTCACGTTGACGCAGGAAAGACAACATTAACGGAAAGTTTATTGTATACCAGTGGTGCAATTGCAGAACTAGGGAGCGTAGATGAAGGCACAACAAGGACAGATACAATGAATTTGGAGCGTCAAAGGGGAATCACTATCCAGACAGCAGTGACATCTTTTCAGTGGGAGGATGTAAAAGTCAACATTATAGATACGCCAGGCCATATGGATTTTTTGGCGGAAGTATACCGTTCTTTATCCGTATTAGACGGAGCAGTATTATTAGTTTCTGCAAAGGATGGCATACAGGCACAGACCCGTATACTGTTTCATGCACTACAGATAATGAAGATTCCGACAATTTTTTTCATCAATAAAATTGACCAAGAGGGGATTGATTTGCCAATGGTATATCGGGAAATGAAAGCAAAGCTTTCTTCGGAAATTATAGTGAAGCAAAAGGTTGGGCAGCATCCCCATATAAATGTAACGGACAATGACGATATGGAACAGTGGGATGCGGTAATTATGGGAAACGATGAACTATTAGAGAAATATATGTCAGGGAAACCGTTTAAAATGTCAGAACTGGAACAGGAAGAAAACAGGAGATTCCAAAACGGAACGTTATTTCCCGTTTATCACGGAAGCGCTAAAAACAATCTGGGGACTCGGCAGCTTATAGAAGTAATTGCCAGTAAATTTTATTCATCAACGCCTGAAGGTCAATCTGAACTATGCGGGCAGGTTTTTAAGATTGAATATTCAGAGAAAAGGCGGCGTTTTGTTTATGTGCGTATATATAGCGGAACATTGCATTTGAGGGATGTTATTAGAATATCTGAAAAAGAGAAAATAAAAATCACAGAGATGTATGTTCCGACAAACGGTGAATTATATTCATCCGATACAGCCTGCTCTGGTGATATTGTAATTTTACCAAATGATGTTTTGCAGCTAAACAGTATTTTGGGGAACGAAATACTGTTGCCGCAGAGAAAATTTATTGAAAATCCTCTCCCTATGATCCAAACAACGATTGCAGTAAAGAAATCTGAACAGCGGGAAATATTGCTTGGGGCACTTACAGAAATTTCAGATTGCGACCCTCTTTTAAAATATTATGTGGATACTACAACGCATGAGATTATACTTTCTTTTTTGGGGAATGTGCAGATGGAAGTCATTTGTGCCATCCTTGAGGAAAAATATCATGTGGAGGCAGAAATAAAAGAGCCTACTGTTATATATATGGAAAGACCGCTTAGAAAAGCAGAATATACCATCCACATAGAAGTCCCGCCAAATCCTTTCTGGGCTTCTGTCGGGTTGTCCATAGAGCCGCTCCCTATTGGAAGCGGAGTGCAGTATGAAAGCAGAGTTTCACTTGGATATTTAAATCAATCGTTCCAAAATGCGGTTATGGAGGGGGTTCTTTATGGCTGCGAGCAGGGGCTGTATGGATGGAAAGTGACAGACTGTAAAATCTGTTTTGAATATGGATTGTATTATAGTCCTGTAAGTACCCCCGCAGACTTTCGGCTGCTTTCCCCTATCGTATTGGAGCAGGCTTTAAAAAAAGCAGGGACAGAACTATTAGAGCCATATCTCCACTTTGAAATTTATGCACCGCAGGAATATCTCTCACGGGCGTATCATGATGCTCCAAGGTATTGTGCAGATATTGTAAGTACTCAGATAAAGAATGACGAGGTCATTCTGAAAGGAGAAATCCCTGCTAGATGTATTCAAGAATACAGGAACGATTTAACTTATTTCACAAATGGGCAGGGAGTCTGCTTGACAGAGTTAAAAGGATACCAGCCAGCTATTGGTAAATTTATTTGCCAACCCCGCCGCCCGAATAGCCGTATAGATAAGGTTCGGCATATGTTCCACAAGTTAGCTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3000190","ARO_id":"36329","ARO_name":"tetO","ARO_description":"TetO is a ribosomal protection protein. It is associated with conjugative plasmids.","ARO_category":{"35921":{"category_aro_accession":"0000002","category_aro_cvterm_id":"35921","category_aro_name":"tetracycline-resistant ribosomal protection protein","category_aro_description":"A family of proteins known to bind to the 30S ribosomal subunit. This interaction prevents tetracycline and tetracycline derivatives from inhibiting ribosomal function. Thus, these proteins confer elevated resistance to tetracycline derivatives as a ribosomal protection protein.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2021":{"model_id":"2021","model_name":"SHV-165","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1065":{"protein_sequence":{"accession":"AFQ23970.1","sequence":"MRYIRLCIISLLAPLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASKRGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"JX121131","fmin":"0","fmax":"858","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCCCCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCAAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001203","ARO_id":"37583","ARO_name":"SHV-165","ARO_description":"SHV-165 is a beta-lactamase.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2022":{"model_id":"2022","model_name":"CTX-M-104","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1104":{"protein_sequence":{"accession":"ADY02555.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAENRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"HQ833652","fmin":"235","fmax":"1111","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAACCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001963","ARO_id":"38363","ARO_name":"CTX-M-104","ARO_description":"CTX-M-104 is a beta-lactamase found in Escherichia coli","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2023":{"model_id":"2023","model_name":"OXA-132","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1753":{"protein_sequence":{"accession":"ACD84990.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEMTYKSLEQLGIL"},"dna_sequence":{"accession":"EU547447","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATGACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001653","ARO_id":"38053","ARO_name":"OXA-132","ARO_description":"OXA-132 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2024":{"model_id":"2024","model_name":"ACC-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1852":{"protein_sequence":{"accession":"AAF86691.1","sequence":"MRKKMQNTLKLLSVITCLAATAQGAMAANIDESKIKDTVDGLIQPLMQKNNIPGMSVAVTIRGRNYIYNYGLAAKQPQQPVTENTLFEVGSLSKTFAAILASYAQASGKLSLEQSVSHYVPELRGSSFDHVSVLNVGTHTSGLQLFMPEDIKNTTQLMTYLKAWKPADAAGTHRVYSNIGTGLLGMIAAKSLGVSYEDAIEQTILPLLGMNQTYLKVPADQMENYAWGYNKKDEPVHVNMEILGNEAYGIKTTSSDLLRYVQANMGQLKLDGNAKIQHALTATHTGYFKSGEITQDLMWEQLPYPVSLPNLLTGNDMAMTKSVATPIVPPLPPQENVWINKTGSTNGFGAYIAFVPAKKMGIVMLANKNYSIDQRVTVAYKILSSLEVNK"},"dna_sequence":{"accession":"AF180952","fmin":"1564","fmax":"2737","strand":"+","sequence":"ATGCGTAAAAAAATGCAGAACACCTTGAAGCTGTTATCCGTGATTACCTGTCTGGCAGCAACTGCCCAAGGTGCTATGGCTGCCAATATCGATGAGAGCAAAATTAAAGACACCGTCGATGGCCTAATCCAGCCGCTGATGCAGAAGAATAATATTCCCGGTATGTCGGTCGCAGTGACCATCAGAGGTAGGAACTATATTTATAACTACGGGTTAGCGGCAAAACAGCCTCAGCAGCCGGTGACGGAAAATACGTTATTTGAAGTGGGTTCGCTGAGTAAAACGTTTGCTGCCATCTTGGCGTCCTATGCGCAGGCGAGCGGTAAGCTGTCTTTGGAGCAAAGCGTTAGCCACTATGTTCCAGAACTACGTGGCAGCAGCTTTGACCACGTTAGCGTACTCAATGTGGGTACGCATACCTCAGGTCTACAGCTGTTTATGCCGGAAGATATCAAGAACACCACACAGCTGATGACTTATCTAAAAGCATGGAAACCTGCTGATGCGGCTGGAACCCATCGCGTTTATTCCAATATCGGTACCGGTTTGCTAGGGATGATTGCGGCGAAAAGTCTGGGTGTGAGCTATGAAGATGCGATTGAGCAAACCATCCTTCCTCTATTAGGCATGAATCAAACCTACCTGAAGGTTCCGGCTGACCAGATGGAAAACTATGCGTGGGGCTACAACAAGAAAGATGAGCCAGTGCACGTCAATATGGAGATTTTGGGTAACGAAGCTTATGGTATCAAAACCACCTCCAGCGACTTGTTACGCTACGTGCAAGCCAATATGGGGCAGTTAAAGCTTGATGGTAATGCCAAGATCCAACATGCACTGACAGCCACCCACACCGGCTATTTCAAATCGGGTGAGATTACTCAGGATCTGATGTGGGAGCAGCTGCCATATCCAGTTTCTCTGCCGAATTTGCTCACCGGTAACGATATGGCGATGACGAAAAGCGTGGCTACGCCGATTGTTCCCCCGTTACCGCCACAGGAAAATGTGTGGATTAATAAGACCGGATCAACTAACGGCTTCGGTGCCTATATTGCGTTTGTTCCTGCTAAGAAGATGGGGATCGTGATGCTGGCTAACAAAAACTACTCAATCGATCAACGAGTGACGGTGGCGTATAAAATCCTGAGCTCGTTGGAAGTGAATAAGTAGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36784","NCBI_taxonomy_name":"Hafnia alvei","NCBI_taxonomy_id":"569"}}}},"ARO_accession":"3001816","ARO_id":"38216","ARO_name":"ACC-2","ARO_description":"ACC-2 is a beta-lactamase found in Hafnia alvei","ARO_category":{"36212":{"category_aro_accession":"3000073","category_aro_cvterm_id":"36212","category_aro_name":"ACC beta-lactamase","category_aro_description":"ACC beta-lactamases or Ambler class C beta-lactamases are AmpC beta-lactamases. They possess an interesting resistance phenotype due to their low activity against cephamycins.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2025":{"model_id":"2025","model_name":"TEM-57","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"850":{"protein_sequence":{"accession":"ACJ43254.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLDRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"FJ405211","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGATCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000926","ARO_id":"37306","ARO_name":"TEM-57","ARO_description":"TEM-57 is a broad-spectrum beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2026":{"model_id":"2026","model_name":"OXA-84","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2015":{"protein_sequence":{"accession":"ABC26006.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAISVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLAGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"DQ309276","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTTCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGCGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001624","ARO_id":"38024","ARO_name":"OXA-84","ARO_description":"OXA-84 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2027":{"model_id":"2027","model_name":"CMY-84","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1037":{"protein_sequence":{"accession":"AFK73455.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPALTGKQWRGISLLHLATYTAGGLPLQIPDDITDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"JQ733579","fmin":"1027","fmax":"2173","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCACTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGCACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGACATTACGGATAAAGCCGCATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGCGGTGAAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAACTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTGCACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACAGGATCCACAGGCGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTAATGTTGGCAAACAAAAGCTATCCCAACCCGGCTCGCGTCGAGGCGGCCTGGCGCATTCTTGAAAAACTGCAATAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002097","ARO_id":"38497","ARO_name":"CMY-84","ARO_description":"CMY-84 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2028":{"model_id":"2028","model_name":"QnrB43","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"633":{"protein_sequence":{"accession":"AFA52643.1","sequence":"MTPLLYKKTGTNMALALVGEKIDRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNASALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLAGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"JQ349151","fmin":"0","fmax":"680","strand":"+","sequence":"ATGACGCCATTACTGTATAAAAAAACAGGTACAAATATGGCTCTGGCACTCGTTGGCGAAAAAATTGACAGAAACCGCTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCGATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATGCCAGTGCGCTTGGCATTGAAATTCGCCACTGTCGTGCGCAAGGCGCAGATTTCCGCGGCGCAAGCTTTATGAATATGATCACTACTCGCACCTGGTTTTGCAGCGCATATATCACTAACACAAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAATGTGAGCTGTGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTTGCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTGACTTAGATATTCGGGGCGTTGATTTACAAGGCGTTAAGTTGGACAACTACCAGGCATCGCTGCTCATGGAACGTCTTGGCATCGCGGTAATTGGTTA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002758","ARO_id":"39192","ARO_name":"QnrB43","ARO_description":"QnrB43 is a plasmid-mediated quinolone resistance protein found in Escherichia coli","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2029":{"model_id":"2029","model_name":"TEM-123","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1321":{"protein_sequence":{"accession":"AAQ93490.1","sequence":"MSIKHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASERGSRGIIALGPDGKPSRIVVIYTTGSQATMDEANRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AY327539","fmin":"0","fmax":"858","strand":"+","sequence":"ATGAGTATTAAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTGAGCGTGGATCTCGCGGTATCATTGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAAGCAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3000985","ARO_id":"37365","ARO_name":"TEM-123","ARO_description":"TEM-123 is an extended-spectrum beta-lactamase found in Proteus mirabilis.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2030":{"model_id":"2030","model_name":"AAC(3)-IXa","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"655":{"protein_sequence":{"accession":"AAA25334.1","sequence":"MEEMSLLNHSGGPVTRSRIKHDLADLGLKDGDVVIFHTRMSAIGYVAGGTQTIIGALLDVVGARGTLMVPCGWNNAPPYDFLDWPRDWQDALRAEHPAYDPDLSEADYNNGRLPEALPRWPGAIRSRHPDASFAALGPAAAELMAEHPWDHPHGPDTPLARLIAHSGRVLLLGAPLDTMTLLHHAEALADVRSKRFVTYEQPILVNGQRVWRQFRDIDSEEGAFDYSTVRRGVEPFEAIARDMLSAGIGRQGRVGAADSYLFDAGPVFNFAINWIEAKLKR"},"dna_sequence":{"accession":"M55427","fmin":"273","fmax":"1119","strand":"+","sequence":"ATGGAAGAGATGAGCTTACTCAATCACTCCGGCGGTCCCGTTACCCGAAGCCGGATCAAGCATGACCTTGCTGATCTCGGTCTCAAAGACGGAGACGTGGTGATTTTCCACACCCGCATGTCTGCCATCGGGTACGTGGCTGGCGGAACGCAGACAATCATCGGCGCACTCCTCGACGTTGTGGGAGCCCGTGGAACCCTTATGGTGCCCTGTGGCTGGAACAACGCGCCTCCATATGACTTCCTCGATTGGCCACGGGACTGGCAGGACGCCCTGCGAGCAGAGCATCCCGCGTACGACCCGGACCTCAGTGAGGCGGACTACAATAATGGTCGTCTCCCAGAAGCGCTGCCGCGCTGGCCTGGCGCGATCCGAAGTCGGCACCCCGACGCCAGTTTCGCAGCCCTGGGGCCGGCTGCAGCCGAACTGATGGCAGAGCATCCGTGGGACCATCCTCACGGACCCGACACCCCGCTAGCACGGCTGATCGCCCATAGCGGCCGAGTCTTGTTACTTGGCGCTCCATTGGACACCATGACGCTGTTGCATCACGCTGAGGCGTTGGCCGACGTCCGCAGCAAACGGTTCGTGACCTACGAACAACCGATCCTCGTTAACGGCCAGCGGGTGTGGCGACAATTCCGCGATATCGACTCTGAGGAAGGAGCGTTTGACTACTCGACGGTGCGCCGAGGGGTGGAGCCGTTCGAGGCCATTGCACGGGACATGCTCTCGGCAGGAATCGGTCGTCAGGGCAGGGTCGGCGCCGCGGATAGCTACCTGTTTGACGCCGGGCCTGTCTTCAATTTTGCGATCAACTGGATCGAGGCCAAGCTGAAGAGATAGC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39506","NCBI_taxonomy_name":"Micromonospora chalcea","NCBI_taxonomy_id":"1874"}}}},"ARO_accession":"3002543","ARO_id":"38943","ARO_name":"AAC(3)-IXa","ARO_description":"AAC(3)-IXa is a chromosomal-encoded aminoglycoside acetyltransferase in Micromonospora chalcea","ARO_category":{"36461":{"category_aro_accession":"3000322","category_aro_cvterm_id":"36461","category_aro_name":"AAC(3)","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 3.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2031":{"model_id":"2031","model_name":"OXA-173","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1924":{"protein_sequence":{"accession":"ADI58617.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAVPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGLDVNLQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"HM113559","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTGTTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATTGGATGTAAACCTACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001657","ARO_id":"38057","ARO_name":"OXA-173","ARO_description":"OXA-173 is a beta-lactamase found in A. baumannii","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2032":{"model_id":"2032","model_name":"CTX-M-62","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"787":{"protein_sequence":{"accession":"ABP04245.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTESTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"EF219134","fmin":"2125","fmax":"3001","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGTCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGAAGACTGGGGGTGGCATTGATTAACACAGCGGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTCGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTGGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGTCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCAGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATTTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001923","ARO_id":"38323","ARO_name":"CTX-M-62","ARO_description":"CTX-M-62 is a beta-lactamase found in Escherichia coli","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2033":{"model_id":"2033","model_name":"mtrR","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"410"}},"model_sequences":{"sequence":{"4254":{"protein_sequence":{"accession":"ACF30254.1","sequence":"MRKTKTEALKTKEHLMLAALETFYRKGIARTSLNEIAQAAGVTRGALYWHFKNKEDLFDALFQRICDDIENCIAQDAADAEGGSWTVFRHTLLHFFERLQSNDIYYKFHNILFLKCEHTEQNAAVIAIARKHQAIWREKITAVLTEAVENQDLADDLDKETAVIFIKSTLDGLIWRWFSSGESFDLGKTAPRIIGIMMDNLENHPCLRRK"},"dna_sequence":{"accession":"CP001050.1","fmin":"1332866","fmax":"1333499","strand":"+","sequence":"ATGAGAAAAACCAAAACCGAAGCCTTGAAAACCAAAGAACACCTGATGCTTGCCGCCTTGGAAACCTTTTACCGCAAAGGGATTGCCCGCACCTCGCTCAACGAAATCGCCCAAGCCGCCGGCGTAACGCGCGGCGCGCTCTATTGGCATTTCAAAAATAAGGAAGACTTGTTTGACGCGTTGTTCCAACGTATCTGCGACGACATCGAAAACTGCATCGCGCAAGATGCCGCAGATGCCGAAGGAGGTTCTTGGACGGTATTCCGCCACACGCTGCTGCACTTTTTCGAGCGGCTGCAAAGCAACGACATCTACTACAAATTCCACAACATCCTGTTTTTAAAATGCGAACACACGGAGCAAAACGCCGCCGTTATCGCCATTGCCCGCAAGCATCAGGCAATCTGGCGCGAGAAAATTACCGCCGTTTTGACCGAAGCGGTGGAAAATCAGGATTTGGCTGACGATTTGGACAAGGAAACGGCGGTCATCTTCATCAAATCGACGTTGGACGGGCTGATTTGGCGTTGGTTCTCTTCCGGCGAAAGTTTCGATTTGGGCAAAACCGCCCCGCGCATCATCGGGATAATGATGGACAACTTGGAAAACCATCCCTGCCTGCGCCGGAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37080","NCBI_taxonomy_name":"Neisseria gonorrhoeae NCCP11945","NCBI_taxonomy_id":"521006"}}}},"ARO_accession":"3000817","ARO_id":"37197","ARO_name":"mtrR","ARO_description":"MtrR is a repressor of mtrCDE expression. Mutations in mtrR increase multidrug resistance.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35971":{"category_aro_accession":"0000054","category_aro_cvterm_id":"35971","category_aro_name":"penicillin","category_aro_description":"Penicillin (sometimes abbreviated PCN) is a beta-lactam antibiotic used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms. It works by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"40728":{"category_aro_accession":"3003957","category_aro_cvterm_id":"40728","category_aro_name":"palmitic acid","category_aro_description":"Palmitic acid is the most common saturated fatty acid found in animals, plants, and microorganisms. Palmitic acid is found to have antibacterial properties.","category_aro_class_name":"Antibiotic"},"40729":{"category_aro_accession":"3003958","category_aro_cvterm_id":"40729","category_aro_name":"oleic acid","category_aro_description":"Oleic acid is a fatty acid that occurs naturally in various animal and vegetable fats and oils. Oleic acid is found to have antibacterial activity, particularly in inhibiting the growth of several Gram-positive bacterial species.","category_aro_class_name":"Antibiotic"},"40730":{"category_aro_accession":"3003959","category_aro_cvterm_id":"40730","category_aro_name":"linoleic acid","category_aro_description":"Linoleic acid is a polyunsaturated omega-6 fatty acid. Linoleic acid has been found to have antibacterial activity, particularly in inhibiting the growth of Gram-positive bacterial species.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40727":{"category_aro_accession":"3003956","category_aro_cvterm_id":"40727","category_aro_name":"antibacterial free fatty acids","category_aro_description":"Amongst the diverse and potent biological activities of free fatty acids (FFAs) is the ability to kill or inhibit the growth of bacteria. The antibacterial properties of FFAs are used by many organisms to defend against parasitic or pathogenic bacteria. The prime target of FFA action is the cell membrane, where FFAs disrupt the electron transport chain and oxidative phosphorylation. Besides interfering with cellular energy production, FFA action may also result from the inhibition of enzyme activity, impairment of nutrient uptake, generation of peroxidation and auto-oxidation degradation products or direct lysis of bacterial cells.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2034":{"model_id":"2034","model_name":"TEM-108","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1320":{"protein_sequence":{"accession":"AAM28884.1","sequence":"MDPQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAELSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTSELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERSRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AF506748","fmin":"38","fmax":"899","strand":"+","sequence":"ATGGATCCTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGAATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTAGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCAGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAGTAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35732","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium","NCBI_taxonomy_id":"90371"}}}},"ARO_accession":"3000971","ARO_id":"37351","ARO_name":"TEM-108","ARO_description":"TEM-108 is a beta-lactamase that has been found in clinical isolates.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2035":{"model_id":"2035","model_name":"CTX-M-15","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1430":{"protein_sequence":{"accession":"AAL02127.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"AY044436","fmin":"1435","fmax":"2311","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001878","ARO_id":"38278","ARO_name":"CTX-M-15","ARO_description":"CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35979":{"category_aro_accession":"0000062","category_aro_cvterm_id":"35979","category_aro_name":"ceftriaxone","category_aro_description":"Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2036":{"model_id":"2036","model_name":"SHV-163","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"916":{"protein_sequence":{"accession":"AFQ23969.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGSVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQQ"},"dna_sequence":{"accession":"JX121130","fmin":"0","fmax":"858","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCAGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGGATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001202","ARO_id":"37582","ARO_name":"SHV-163","ARO_description":"SHV-163 is a beta-lactamase.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2037":{"model_id":"2037","model_name":"tetT","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1200"}},"model_sequences":{"sequence":{"520":{"protein_sequence":{"accession":"AAF01499.1","sequence":"MKIINIGILAHVDAGKTTVTEGLLYKSGAINKIGRVDNATTTTDSMELERDRGITIRASTVSFNYNDTKVNIIDTPGHMDFIAEVERTLKVLDGAILVISAKEGIQVQTKVIFNTLVKLNIPTLIFVNKIDRKGVCLDEIYTQIQEKLTSNLAIMQSVKIKDKGDFELTNVRDDKVIQSQIIEKLLDINDYLAEKYINGDVIAEKEYNDVFLDEINNCNLYPVFHGSALKNIGIDELLFAITKYLPTKSYNTEDLLSAYVYKIDRDEKSRKMTFLRVFSGNIRTRQDVYINGTEETFKIKSLESIMNGEIVKVGQVNSGDIAIISNANSLKIGDYIGKKYDGILDIKIAQPALRASIKPCDLSKRSKLIEALFELTEEDPFLDCEINGDTGEIILRLFGNIQMEVIESLLKSRYKIDARFGELKTIYKERPKRNSKAVIHIEVPPNPYWASIGLSIEPLPIGSGLLYKTEVSYGYLNNSFQNAVKDAVEKACKEGLYGWEVTDLKVTFDYGLYYSPVSTPSDFRNLTPYVFWEALRKAGTEILEPYLKYTVQVPNDFCGRVMSDLRKMRASIEDIIAKGEETTLSGKIPVDTSKSYQSELLSYSNGKGIFITEPYGYDIYNDKPIINDIGNDNNDSNKEGLRYLFQKQDEN"},"dna_sequence":{"accession":"L42544","fmin":"0","fmax":"1956","strand":"+","sequence":"ATGAAAATTATTAATATAGGAATATTAGCACATGTTGATGCAGGTAAAACAACTGTTACAGAAGGTTTATTATATAAAAGTGGGGCGATTAATAAAATTGGAAGAGTTGATAATGCTACAACGACAACGGATTCGATGGAACTTGAAAGAGATAGGGGAATAACTATACGGGCGTCTACAGTTTCATTTAATTACAATGATACAAAGGTAAATATCATAGATACACCTGGGCACATGGATTTCATAGCCGAAGTTGAGCGAACTCTGAAAGTGTTAGATGGAGCTATTTTAGTAATTTCAGCAAAAGAAGGAATTCAAGTCCAAACTAAAGTGATTTTTAATACTTTAGTGAAATTAAATATACCAACACTTATATTTGTGAATAAAATAGATCGAAAGGGAGTATGTTTGGATGAGATATACACTCAAATACAGGAGAAATTAACTTCTAATCTTGCAATAATGCAATCAGTTAAAATAAAAGATAAAGGTGATTTTGAATTGACAAATGTAAGGGATGATAAAGTAATTCAAAGTCAAATAATAGAGAAGTTACTGGATATAAATGATTATCTAGCAGAAAAATATATAAATGGCGATGTCATTGCAGAAAAAGAATATAATGATGTATTTTTGGATGAGATTAATAACTGCAATCTTTATCCTGTATTTCATGGTTCGGCTTTAAAAAATATTGGAATTGACGAGCTATTATTTGCCATTACTAAATATCTTCCTACCAAGAGCTATAATACTGAAGACCTTTTATCAGCGTATGTTTATAAGATTGATAGGGATGAAAAATCTAGAAAGATGACTTTCTTAAGAGTATTCAGTGGGAATATAAGGACACGTCAAGATGTTTATATAAATGGCACAGAAGAAACTTTCAAGATAAAAAGTCTGGAATCAATTATGAATGGTGAAATTGTGAAGGTAGGTCAGGTTAATAGTGGGGATATTGCTATTATTTCTAATGCTAATTCTCTGAAGATAGGTGATTATATTGGTAAGAAATATGACGGGATTTTAGATATAAAGATAGCCCAACCGGCATTGAGAGCATCAATTAAACCTTGTGATTTAAGCAAAAGAAGCAAACTGATAGAAGCACTATTTGAATTAACTGAAGAAGACCCATTTCTCGATTGTGAAATTAACGGAGATACTGGAGAAATCATATTGAGGCTATTTGGAAATATTCAAATGGAAGTAATAGAATCACTACTTAAAAGCCGATACAAAATAGATGCTAGATTTGGTGAATTGAAAACAATATATAAAGAACGACCTAAGAGAAACTCTAAAGCAGTAATCCATATAGAGGTTCCACCAAATCCTTATTGGGCATCTATTGGACTGTCAATAGAACCACTACCAATAGGGTCAGGATTATTATATAAGACAGAGGTGTCCTATGGATATTTAAATAATTCATTTCAAAATGCAGTAAAAGATGCTGTAGAGAAGGCTTGTAAAGAAGGGCTTTATGGATGGGAAGTTACAGACTTAAAGGTAACTTTTGACTACGGATTATACTATAGCCCGGTAAGTACCCCCTCTGACTTTAGGAATTTAACACCATATGTATTTTGGGAAGCTCTTCGAAAAGCAGGAACTGAAATATTAGAACCTTATTTAAAATATACAGTTCAAGTTCCAAATGATTTCTGCGGAAGGGTTATGAGTGATCTTAGAAAGATGAGGGCTTCTATTGAAGATATAATAGCCAAGGGAGAGGAGACAACTTTAAGTGGAAAGATACCTGTTGATACATCGAAGTCCTATCAGTCAGAATTACTTTCTTATTCAAATGGAAAGGGTATATTTATTACTGAGCCTTATGGGTATGATATATATAATGATAAGCCTATAATTAATGATATTGGGAACGACAATAATGATAGCAACAAGGAAGGGTTAAGATATTTATTTCAAAAACAGGATGAAAATTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36764","NCBI_taxonomy_name":"Streptococcus pyogenes","NCBI_taxonomy_id":"1314"}}}},"ARO_accession":"3000193","ARO_id":"36332","ARO_name":"tetT","ARO_description":"Tet(T) is a ribosomal protection protein of streptococci. It is similar to Tet(Q).","ARO_category":{"35921":{"category_aro_accession":"0000002","category_aro_cvterm_id":"35921","category_aro_name":"tetracycline-resistant ribosomal protection protein","category_aro_description":"A family of proteins known to bind to the 30S ribosomal subunit. This interaction prevents tetracycline and tetracycline derivatives from inhibiting ribosomal function. Thus, these proteins confer elevated resistance to tetracycline derivatives as a ribosomal protection protein.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2038":{"model_id":"2038","model_name":"KPC-17","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"873":{"protein_sequence":{"accession":"AGJ01154.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQLVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"KC465200","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGCTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002327","ARO_id":"38727","ARO_name":"KPC-17","ARO_description":"KPC-17 is a beta-lactamase. From the Lahey list of KPC beta-lactamases.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2039":{"model_id":"2039","model_name":"CARB-18","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"942":{"protein_sequence":{"accession":"AIL92327.1","sequence":"MKKLFLLVGLMVCSTVSYASKLNEDISLIEKQTSGRIGVSVWDTQTDERWDYRGDERFPLMSTFKTLACATMLSDMDSGKLNKNATAKIDERNIVVWSPVMDKLAGQSTRIEHACEAAMLMSDNTAANLVLNEIGGPKAVTLFLRSIGDKATRLDRLEPRLNEAKPGDKRDTTTPNAMVNTLHTLMEDNALSYESRTQLKIWMQDNKVSDSLMRSVLPKGWSIADRSGAGNYGSRGISAMIWKDNYKPVYISIYVTDTDLSLQARDQLIAQISQLILEHYKES"},"dna_sequence":{"accession":"KJ934266","fmin":"0","fmax":"852","strand":"+","sequence":"ATGAAAAAGTTATTCCTGTTGGTTGGGCTGATGGTTTGCTCAACTGTTAGTTACGCCTCCAAATTAAACGAAGACATCTCCCTCATCGAGAAACAAACATCTGGGCGAATTGGAGTGTCAGTCTGGGATACACAAACGGACGAGCGTTGGGATTATCGCGGAGACGAACGTTTCCCATTAATGAGCACATTCAAAACGTTAGCGTGTGCCACCATGCTAAGCGACATGGACAGCGGCAAACTCAACAAAAATGCCACAGCGAAAATCGATGAACGCAATATTGTGGTTTGGTCTCCGGTGATGGATAAACTGGCTGGACAAAGCACACGYATCGAACACGCTTGTGAAGCCGCCATGTTGATGAGCGACAACACCGCCGCGAACTTAGTGCTAAATGAAATTGGTGGTCCTAAAGCGGTCACGCTGTTTTTGCGATCTATTGGCGACAAAGCAACGCGACTTGACCGATTGGAACCCCGTTTGAATGAAGCAAAACCGGGCGACAAGCGAGACACCACAACGCCTAACGCCATGGTAAACACCCTACATACCTTGATGGAAGATAACGCCCTATCTTACGAGTCACGCACACAGCTGAAAATCTGGATGCAAGACAACAAAGTATCGGATTCKCTCATGCGCTCTGTTCTGCCAAAAGGCTGGTCGATTGCAGACCGCTCTGGCGCAGGTAACTACGGTTCACGCGGCATTAGCGCGATGATCTGGAAAGACAACTACAAGCCGGTTTACATCAGTATTTACGTCACAGACACTGACCTTTCGCTTCAAGCTCGCGATCAACTGATCGCGCAAATCAGCCAACTGATTTTAGAGCACTACAAAGAAAGTTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39615","NCBI_taxonomy_name":"Vibrio parahaemolyticus","NCBI_taxonomy_id":"670"}}}},"ARO_accession":"3003174","ARO_id":"39751","ARO_name":"CARB-18","ARO_description":"From the Lahey list of beta-lactamases.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2040":{"model_id":"2040","model_name":"TEM-60","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1079":{"protein_sequence":{"accession":"AAC05975.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDPNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTMPAAMRTTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRCALPAGWLIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AF047171","fmin":"135","fmax":"996","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCCTAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGCGAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTGCGCCCTTCCGGCTGGCTGGTTAATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36946","NCBI_taxonomy_name":"Providencia stuartii","NCBI_taxonomy_id":"588"}}}},"ARO_accession":"3000929","ARO_id":"37309","ARO_name":"TEM-60","ARO_description":"TEM-60 is an extended-spectrum beta-lactamase that has been found in clinical isolates.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2041":{"model_id":"2041","model_name":"OXA-424","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1055":{"protein_sequence":{"accession":"AJA32742.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGEKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KM588352","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCCCTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTCTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAATGGGATGGGGAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAGGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATAGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003147","ARO_id":"39724","ARO_name":"OXA-424","ARO_description":"OXA-424 is a \u00df-lactamase found in clinical isolates of Acinetobacter baumannii found in China. It is carbapenem resistant.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2042":{"model_id":"2042","model_name":"IND-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1340":{"protein_sequence":{"accession":"ACZ65152.1","sequence":"MKKSIQFFIVSMLLSPFANSQVKDFVIEPPIKSNLYIYKTFGVFGGKEYSANAAYLKTKKGVILFDVPWEKVQYQSLMDTIKKRHNLPVIAVFATHSHDDRAGDLSFFNNKGIKTYATLKTNEFLKKDGKATSTEIIQTGKPYHIGGEEFVVDFLGEGHTADNVVVWFPKYNVLDGGCLVKSNSATDLGYIKEANVEQWPKTMNKLKTKYSKATLIIPGHDEWKGGGHVEHTLELLNKK"},"dna_sequence":{"accession":"GU186044","fmin":"39","fmax":"759","strand":"+","sequence":"ATGAAAAAAAGCATTCAATTTTTTATTGTTTCCATGTTGTTGAGCCCTTTTGCCAATTCACAGGTAAAAGATTTTGTAATTGAGCCACCTATTAAATCCAATCTATATATTTACAAGACTTTTGGAGTATTCGGAGGTAAAGAATATTCTGCCAATGCAGCCTATCTTAAGACTAAAAAAGGTGTAATTCTGTTTGATGTACCCTGGGAAAAAGTACAGTATCAAAGCCTGATGGATACCATCAAAAAACGTCATAACTTACCGGTAATTGCCGTATTTGCTACGCATTCCCATGATGACCGTGCAGGAGACTTAAGCTTTTTCAATAATAAAGGCATTAAGACGTATGCTACCCTGAAAACCAATGAGTTTCTGAAGAAAGATGGAAAAGCAACATCCACAGAGATCATCCAAACCGGAAAACCTTATCACATTGGCGGAGAAGAATTTGTGGTCGATTTTCTTGGTGAAGGACATACTGCTGATAATGTAGTGGTATGGTTTCCAAAATATAATGTTTTGGATGGCGGATGTCTTGTAAAAAGTAATTCTGCTACTGACTTAGGATACATTAAAGAAGCCAATGTAGAACAATGGCCCAAGACGATGAATAAATTAAAAACCAAATATTCAAAAGCCACATTAATTATTCCCGGGCATGATGAATGGAAAGGGGGTGGACATGTTGAACACACTTTAGAGCTTTTGAACAAAAAATAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36916","NCBI_taxonomy_name":"Chryseobacterium indologenes","NCBI_taxonomy_id":"253"}}}},"ARO_accession":"3002264","ARO_id":"38664","ARO_name":"IND-8","ARO_description":"IND-8 is a beta-lactamase found in Escherichia coli","ARO_category":{"36199":{"category_aro_accession":"3000060","category_aro_cvterm_id":"36199","category_aro_name":"IND beta-lactamase","category_aro_description":"IND beta-lactamases are class B carbapenem-hydrolyzing beta-lactamases","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2043":{"model_id":"2043","model_name":"aadA8","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"558":{"protein_sequence":{"accession":"AAN41439.1","sequence":"MRVAVTIEISNQLSEVLSVIERHLESTLLAVHLYGSAVDGGLKPYSDIDLLVTVAVKLDETTRRALLNDLMEASAFPGESETLRAIEVTLVVHDDIIPWRYPAKRELQFGEWQRNDILAGIFEPAMIDIDLAILLTKAREHSVALVGPAAEEFFDPVPEQDLFEALRETLKLWNSQPDWAGDERNVVLTLSRIWYSAITGKIAPKDVAADWAMERLPAQYQPVILEARQAYLGQEEDRLASRADQLEEFVHYVKGEITKVVGK"},"dna_sequence":{"accession":"AY139603","fmin":"106","fmax":"898","strand":"+","sequence":"ATGAGGGTAGCGGTGACCATCGAAATTTCGAACCAACTATCAGAGGTGCTAAGCGTCATTGAGCGCCATCTGGAATCAACGTTGCTGGCCGTGCATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCATACAGCGATATTGATTTGTTGGTTACTGTGGCCGTAAAGCTTGATGAAACGACGCGGCGAGCATTGCTCAATGACCTTATGGAGGCTTCGGCTTTCCCTGGCGAGAGCGAGACGCTCCGCGCTATAGAAGTCACCCTTGTCGTGCATGACGACATCATCCCGTGGCGTTATCCGGCTAAGCGCGAGCTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCGGGTATCTTCGAGCCAGCCATGATCGACATTGATCTGGCTATCCTGCTTACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCGGCAGCGGAGGAATTCTTTGACCCGGTTCCTGAACAGGATCTATTCGAGGCGCTGAGGGAAACCTTGAAGCTATGGAACTCGCAGCCCGACTGGGCCGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAATAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATGGAGCGCCTGCCGGCCCAGTATCAGCCCGTCATACTTGAAGCTAGACAGGCTTATCTTGGACAAGAAGAAGATCGCTTGGCCTCGCGCGCAGATCAGTTGGAAGAATTTGTTCACTACGTGAAAGGCGAGATCACCAAGGTAGTCGGCAAATAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3002608","ARO_id":"39008","ARO_name":"aadA8","ARO_description":"aadA8 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids and integrons in V. cholerae, K. pneumoniae and Bacillus endophyticus","ARO_category":{"41439":{"category_aro_accession":"3004275","category_aro_cvterm_id":"41439","category_aro_name":"ANT(3'')","category_aro_description":"Nucleotidylylation of streptomycin at the hydroxyl group at position 3''","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2044":{"model_id":"2044","model_name":"QnrB31","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"369":{"protein_sequence":{"accession":"ADQ43424.1","sequence":"MTPLLYKKTGTNMALALVGEKIDRNRFTGEKIENSTFFLCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNASALGIEISHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRRVDLQGVKLDNYQASLLMERLGIAIIG"},"dna_sequence":{"accession":"HQ418999","fmin":"0","fmax":"681","strand":"+","sequence":"ATGACGCCATTACTGTATAAGAAAACAGGTACAAATATGGCTCTGGCGCTCGTGGGCGAAAAAATTGACAGAAACCGTTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTTTATGTGATTTTTCAGGAGCCGACCTGAGCGGCACTGAGTTTATCGGCTGTCAATTCTATGATCGTGAAAGCCAGAAAGGCTGCAATTTTAGTCGTGCGATGTTAAAGGATGCCATTTTTAAAAGCTGCGATTTATCCATGGCGGATTTTCGCAATGCAAGCGCCCTGGGTATTGAGATTTCTCATTGTAGGGCTCAGGGTGCAGATTTTCGCGGCGCAAGCTTTATGAACATGATTACCACGCGCACTTGGTTCTGCAGCGCGTATATCACGAATACGAATCTGTCTTATGCCAATTTTTCGAAAGTCGTGTTGGAGAAGTGTGAGTTATGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCAACTTTCGACTGGCGAGCAGCAAACTTTACACATTGCGATCTCACAAATTCGGAGTTGGGTGACTTAGATATTCGTCGGGTTGATTTACAAGGCGTTAAGTTGGACAACTACCAGGCTTCGTTGCTCATGGAGCGACTTGGCATCGCGATAATTGGTTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002746","ARO_id":"39180","ARO_name":"QnrB31","ARO_description":"QnrB31 is a plasmid-mediated quinolone resistance protein found in Klebsiella pneumoniae","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2045":{"model_id":"2045","model_name":"OXY-2-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1307":{"protein_sequence":{"accession":"AAL78281.2","sequence":"MIKSSWRKIAMLAAVPLLLASGALWASTDAIHQKLTDLEKRSGGRLGVALINTADNSQILYRGDERFAMCSTSKVMAAAAVLKQSESNKEVVNKRLEINAADLVVWSPITEKHLQSGMTLAELSAATLQYSDNTAMNLIIGYLGGPEKVTAFARSIGDATFRLDRTEPTLNTAIPGDERDTSTPLAMAESLRKLTLGDALGEQQRAQLVTWLKGNTTGGQSIRAGLPESWVVGDKTGGGDYGTTNDIAVIWPEDHAPLVLVTYFTQPQQDAKNRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"AY077488","fmin":"161","fmax":"1031","strand":"+","sequence":"ATGATAAAAAGTTCGTGGCGTAAAATTGCAATGCTAGCCGCCGTTCCGCTGCTGCTGGCGAGCGGCGCACTGTGGGCCAGTACCGATGCTATCCATCAGAAGCTGACAGATCTCGAGAAGCGTTCAGGCGGCAGGTTGGGCGTGGCGCTAATCAACACGGCAGATAATTCTCAAATCTTATATCGCGGCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCCGCCGCCGCGGTATTAAAACAGAGCGAAAGCAATAAAGAGGTGGTAAATAAAAGGCTGGAGATTAACGCAGCCGATTTGGTGGTCTGGAGTCCGATTACCGAAAAACATCTCCAGAGCGGAATGACGCTGGCTGAGCTAAGCGCGGCGACGCTGCAATATAGCGACAATACGGCGATGAATCTGATCATCGGCTACCTTGGCGGGCCGGAAAAAGTCACCGCCTTCGCCCGCAGTATCGGCGATGCCACCTTTCGTCTCGATCGTACGGAGCCCACGCTGAATACCGCCATCCCGGGCGATGAGCGTGATACCAGCACGCCGCTGGCGATGGCTGAAAGCCTACGCAAGCTGACGCTTGGCGATGCGCTGGGCGAACAGCAACGCGCCCAGTTAGTCACCTGGCTGAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCGGGCCTGCCTGAAAGCTGGGTGGTCGGCGATAAAACCGGCGGCGGAGATTACGGCACCACCAATGATATTGCGGTTATCTGGCCGGAAGATCACGCTCCGCTGGTATTAGTCACCTACTTTACCCAGCCGCAGCAGGATGCGAAAAACCGCAAAGAGGTGTTAGCCGCAGCGGCAAAAATCGTGACCGAAGGGCTTTAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002398","ARO_id":"38798","ARO_name":"OXY-2-3","ARO_description":"OXY-2-3 is a beta-lactamase found in Klebsiella oxytoca","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2047":{"model_id":"2047","model_name":"OXA-322","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1930":{"protein_sequence":{"accession":"AGW16404.1","sequence":"MYKKVLIVATSILFLSACSSNSVKQHQIHSISANKNSEEIKSLFDQAQTTGVLVIKRGQTEEIYGNDLKRASTNYIPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNANIGSKVDDFWLVGPLKITPQQETQFAYQLAHKTLPFSQDVQEQVQSMVFIEEKNGSKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"KF203096","fmin":"0","fmax":"822","strand":"+","sequence":"ATGTATAAAAAAGTCCTTATCGTTGCAACAAGTATTCTATTTTTATCCGCCTGTTCTTCTAACTCAGTAAAACAACATCAAATACATTCTATTTCTGCCAATAAAAATTCAGAAGAAATTAAATCACTTTTTGATCAAGCACAGACCACGGGAGTTTTGGTGATTAAGCGAGGGCAAACAGAAGAAATTTATGGCAATGATCTTAAAAGAGCATCAACCAACTATATTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTAATTGGACTTGAACATCATAAGGCAACTACAACTGAAGTATTTAAATGGGATGGGCAAAAACGTTTATTTCCTGATTGGGAAAAGGACATGACACTGGGTGATGCCATGAAAGCTTCTGCAATCCCAGTTTACCAAGAATTAGCCCGACGAATTGGTCTGGATCTTATGTCTAAAGAAGTAAAGCGAATTGGTTTCGGTAATGCTAACATTGGCTCAAAAGTAGATGATTTCTGGCTTGTTGGCCCTCTAAAAATTACACCTCAACAAGAAACCCAATTTGCTTATCAATTAGCCCATAAAACGCTTCCATTTAGCCAAGATGTACAAGAACAAGTTCAATCAATGGTGTTCATAGAGGAAAAAAATGGAAGTAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTTGAACCGCAAGTTGGTTGGTTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTGGCATTTTCACTTAATTTAGAAATGAAAAAAGGAACTCCTAGCTCTATTCGCAAAGAAATTGCTTATAAAGGCTTAGAACAACTGGGTATTTTATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3001510","ARO_id":"37910","ARO_name":"OXA-322","ARO_description":"OXA-322 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2048":{"model_id":"2048","model_name":"OXA-57","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1137":{"protein_sequence":{"accession":"CAF74882.1","sequence":"MKFRHALSSAFVLLGCIAASAHAKTICTAIADAGTGKLLVQDGDCGRRASPASTFKIAISLMGYDAGFLRNEHDPVLPYRDSYIAWGGEAWKQPTDPTRWLKYSVVWYSQQVAHHLGAQRFAQYAKAFGYGNADVSGDPGQNNGLDRAWIGSSLQISPLEQLEFLGKMLDRKLPVSPTAVDMTERIVESTTLADGTVVHGKTGVSYPLLADGTRDWARGSGWFVGWIVRGKQTLVFARLTQDERKQPVSAGIRTREAFLRDLPRLLAAR"},"dna_sequence":{"accession":"AJ631966","fmin":"0","fmax":"810","strand":"+","sequence":"ATGAAATTCCGACACGCGCTGTCGAGCGCATTCGTTTTGCTGGGTTGCATCGCCGCGTCGGCGCATGCGAAGACGATCTGCACGGCGATCGCCGATGCGGGCACGGGCAAGCTGCTGGTGCAGGACGGCGATTGCGGCCGCCGCGCATCGCCCGCGTCGACGTTCAAGATCGCGATCAGCCTGATGGGCTACGACGCAGGCTTCCTGCGCAACGAGCATGACCCGGTGCTGCCGTATCGCGACAGTTACATCGCGTGGGGTGGCGAAGCATGGAAGCAGCCGACCGATCCGACGCGCTGGCTCAAGTATTCGGTCGTGTGGTATTCGCAGCAGGTGGCGCACCATCTCGGCGCGCAGCGCTTCGCGCAGTATGCGAAGGCGTTCGGCTACGGCAATGCGGACGTGTCCGGCGATCCCGGCCAGAACAACGGCCTCGATCGCGCGTGGATCGGCTCGTCGCTGCAGATCTCGCCGCTCGAACAATTGGAATTCCTCGGCAAGATGCTCGATCGCAAGCTGCCCGTGTCGCCCACAGCCGTCGACATGACGGAGCGGATCGTCGAATCGACGACGCTTGCCGACGGAACGGTGGTGCACGGCAAGACCGGCGTGTCCTATCCGCTGCTGGCCGACGGCACACGCGACTGGGCGCGTGGATCCGGCTGGTTTGTCGGCTGGATCGTGCGTGGCAAGCAGACGCTGGTGTTCGCGCGCCTCACGCAGGACGAGCGCAAGCAGCCCGTTTCAGCCGGCATACGGACGCGCGAGGCCTTCCTGCGCGACTTGCCCCGGCTTCTCGCCGCGCGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36925","NCBI_taxonomy_name":"Burkholderia pseudomallei 576","NCBI_taxonomy_id":"557724"}}}},"ARO_accession":"3001771","ARO_id":"38171","ARO_name":"OXA-57","ARO_description":"OXA-57 is a beta-lactamase found in Burkholderia pseudomallei","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2049":{"model_id":"2049","model_name":"QnrB72","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"469":{"protein_sequence":{"accession":"AGN92479.1","sequence":"MTLALVCEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNMITMRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"KC741443","fmin":"0","fmax":"645","strand":"+","sequence":"ATGACTCTGGCATTAGTTTGCGAAAAAATTGACAGAAATCGCTTCACCGGTGAGAAAGTTGAAAATAGTACATTTTTTAACTGCGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGCCAGTTCTATGATCGCGAAAGTCAGAAAGGATGCAATTTTAGTCGCGCAATGCTGAAAGATGCCATTTTCAAAAGCTGTGATTTATCAATGGCAGATTTCCGCAACGTCAGCGCATTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGTGCAAGCTTTATGAATATGATCACCATGCGCACCTGGTTTTGCAGCGCATATATCACTAATACCAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAGCTATGGGAAAACCGCTGGATGGGGACTCAGGTACTGGGTGCGACGTTTAGTGGTTCAGATCTCTCCGGTGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTAGGTGACTTAGATATTCGGGGTGTTGATTTACAAGGCGTTAAGTTAGACAACTACCAGGCATCGTTGCTCATGGAGCGGCTTGGCATCGCTGTGATTGGTTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39586","NCBI_taxonomy_name":"Citrobacter sp. TR21_24","NCBI_taxonomy_id":"1344960"}}}},"ARO_accession":"3002784","ARO_id":"39218","ARO_name":"QnrB72","ARO_description":"QnrB72 is a plasmid-mediated quinolone resistance protein found in Citrobacter sp. TR21_24","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2050":{"model_id":"2050","model_name":"OXA-331","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1459":{"protein_sequence":{"accession":"AGW16413.1","sequence":"MYKKALIVATSILFLSACSSNTVKQNQIHSISANKNSEEIKSLFDQAQTTGVLVIKRGQTEEIYGNDLKRASTAYVPASTFKMLNALIGLEHHKATITEVFKWNGQKRLFPDWEKDMTLSDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNANIGSKVDDFWLVGPLKITPQQETQFAYQLAHKTLPFSKNVQEQVQSMVFIEEKNGSKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"KF203105","fmin":"0","fmax":"822","strand":"+","sequence":"ATGTATAAAAAAGCCCTTATCGTTGCAACAAGTATCCTATTTTTATCCGCCTGTTCTTCCAATACGGTAAAACAAAATCAAATACATTCTATTTCTGCCAATAAAAATTCAGAAGAAATTAAATCACTATTTGATCAAGCACAGACCACGGGTGTTTTGGTGATTAAGCGAGGACAAACAGAAGAAATTTATGGCAATGATCTTAAAAGAGCATCAACCGCCTATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTAATTGGACTTGAACATCATAAGGCAACTATAACTGAAGTGTTTAAATGGAATGGGCAAAAACGTTTATTTCCTGATTGGGAAAAGGATATGACACTGAGCGATGCCATGAAAGCTTCTGCAATTCCAGTTTACCAAGAATTAGCCCGACGGATTGGTCTGGATCTTATGTCCAAAGAGGTGAAACGAATTGGTTTCGGTAATGCTAACATTGGCTCAAAAGTAGATGATTTTTGGCTTGTTGGCCCTCTAAAAATTACACCTCAACAAGAAACCCAATTTGCTTATCAATTAGCCCATAAAACTCTTCCATTTAGCAAAAATGTACAAGAACAAGTTCAATCAATGGTGTTCATAGAGGAAAAAAATGGAAGTAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTTGAACCGCAAGTTGGTTGGTTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTGGCATTTTCACTTAATTTAGAAATGAAAAAAGGAACTCCTAGCTCTATTCGCAAAGAAATTGCTTATAAAGGCTTAGAACAACTGGGTATTTTATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3001519","ARO_id":"37919","ARO_name":"OXA-331","ARO_description":"OXA-331 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2051":{"model_id":"2051","model_name":"dfrA15","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"2102":{"protein_sequence":{"accession":"AHB39758.1","sequence":"MKLSLMAAISKNGVIGNGPDIPWSAKGEQLLFKAITYNQWLLVGRKTFESMGALPNRKYAVVTRSSFTSSDENVLVFPSIDEALNHLKTITDHVIVSGGGEIYKSLIDKVDTLHISTIDIEPEGDVYFPEIPSSFRPVFSQDFVSNINYSYQIWQKG"},"dna_sequence":{"accession":"KF534911","fmin":"39","fmax":"513","strand":"+","sequence":"GTGAAACTATCACTAATGGCAGCAATTTCGAAGAATGGAGTTATCGGAAATGGCCCAGATATTCCATGGAGTGCCAAAGGGGAACAATTACTCTTCAAAGCGATTACCTATAATCAGTGGCTTTTGGTAGGCCGAAAGACTTTCGAGTCAATGGGGGCTTTACCCAACCGAAAATATGCCGTTGTAACTCGTTCAAGCTTCACTTCCAGTGATGAGAATGTATTGGTATTTCCATCTATCGATGAAGCGCTAAATCATCTGAAGACGATAACGGATCATGTGATTGTGTCTGGTGGTGGTGAAATATACAAAAGCCTGATCGATAAAGTTGATACTTTACATATTTCAACAATCGACATTGAGCCAGAAGGTGATGTCTATTTTCCAGAAATCCCCAGTAGTTTTAGGCCAGTTTTTAGCCAAGACTTCGTGTCTAACATAAATTATAGTTACCAAATCTGGCAAAAGGGTTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3003013","ARO_id":"39447","ARO_name":"dfrA15","ARO_description":"dfrA15 is an integron-encoded dihydrofolate reductase found in Vibrio cholerae","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36408":{"category_aro_accession":"3000269","category_aro_cvterm_id":"36408","category_aro_name":"brodimoprim","category_aro_description":"Brodimoprim is a structural derivative of trimethoprim and an inhibitor of bacterial dihydrofolate reductase. The 4-methoxy group of trimethoprim is replaced with a bromine atom.","category_aro_class_name":"Antibiotic"},"36423":{"category_aro_accession":"3000284","category_aro_cvterm_id":"36423","category_aro_name":"tetroxoprim","category_aro_description":"Tetroxoprim is a trimethoprim derivative that inhibits bacterial dihydrofolate reductase.","category_aro_class_name":"Antibiotic"},"36476":{"category_aro_accession":"3000337","category_aro_cvterm_id":"36476","category_aro_name":"iclaprim","category_aro_description":"Iclaprim is a bactericidal compound that inhibits dihydrofolate reductase. It is used against clinically important Gram-positive pathogens, including methicillin-sensitive Staphylococcus aureus and methicillin-resistant S. aureus.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2052":{"model_id":"2052","model_name":"APH(3'')-Ic","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"276":{"protein_sequence":{"accession":"ABC68330.1","sequence":"MTEWLPVTRGESGAGVFRNSDGSSYAKVVDAAAVADLAAERDRVSWAHRHGVPGPAVIDWRVTEDGGACLITSTVRGVAADRLSESALRAAWPAIVEAVRTLHALPADGCPYRRDLDDMLARARAVVGAGAVNPEFLSDEDREVPAEALLDRVEREADLRRREEAADWVVCHGDLCLPNILVDPDRHTVEGFIDLGRLGLADRHADLALLLANTADTVPGFAEEATAGLAAGYPAQVDPERLRFYLALDPLTWG"},"dna_sequence":{"accession":"DQ336355","fmin":"602","fmax":"1367","strand":"+","sequence":"GTGACCGAGTGGCTGCCCGTCACACGCGGTGAATCCGGTGCCGGGGTCTTCAGGAACTCCGACGGTTCGAGCTACGCGAAGGTGGTCGACGCCGCGGCGGTGGCAGACCTGGCCGCGGAGCGTGACCGGGTGTCCTGGGCCCACAGGCACGGTGTCCCCGGGCCCGCGGTCATCGACTGGCGTGTCACCGAAGACGGCGGCGCGTGCTTGATCACGAGCACTGTGCGCGGTGTCGCTGCCGATCGGCTTTCCGAATCGGCGCTGCGGGCGGCCTGGCCGGCGATTGTGGAGGCGGTCCGGACACTGCACGCCCTTCCGGCCGACGGTTGTCCCTACCGGCGCGATCTCGACGACATGCTGGCCCGGGCCCGCGCGGTCGTCGGCGCCGGTGCCGTGAACCCGGAGTTCCTGTCCGACGAGGACCGCGAGGTACCGGCGGAGGCGCTGCTGGACCGAGTCGAACGGGAAGCCGATCTACGTCGTCGGGAGGAGGCCGCCGACTGGGTGGTGTGCCACGGCGATCTGTGCCTGCCGAACATTTTGGTCGACCCCGACCGTCACACCGTCGAGGGATTCATCGATCTGGGCAGGCTGGGGCTGGCCGACCGGCACGCCGACCTGGCACTGCTGCTGGCCAATACGGCTGATACCGTTCCGGGCTTCGCCGAGGAGGCCACGGCGGGGTTGGCCGCGGGGTATCCGGCGCAGGTGGATCCGGAGCGGCTGCGGTTCTATCTCGCGCTCGATCCGCTGACCTGGGGATGAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36886","NCBI_taxonomy_name":"Mycobacterium fortuitum","NCBI_taxonomy_id":"1766"}}}},"ARO_accession":"3002640","ARO_id":"39040","ARO_name":"APH(3'')-Ic","ARO_description":"APH(3'')-Ic is a chromosomal-encoded aminoglycoside phosphotransferase in M. fortuitum","ARO_category":{"36266":{"category_aro_accession":"3000127","category_aro_cvterm_id":"36266","category_aro_name":"APH(3'')","category_aro_description":"Phosphorylation of streptomycin on the hydroxyl group at position 3''","category_aro_class_name":"AMR Gene Family"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2053":{"model_id":"2053","model_name":"dfrA7","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"525":{"protein_sequence":{"accession":"ACS44716.1","sequence":"MKISLISATSENGVIGNGPDIPWSAKGEQLLFKALTYNQWLLVGRKTFDSMGVLPNRKYAVVSRKGISSSNENVLVFPSIEIALQELSKITDHLYVSGGGQIYNSLIEKADIIHLSTVHVEVEGDINFPKIPENFNLVFEQFFLSNINYTYQIWKKG"},"dna_sequence":{"accession":"FJ854362","fmin":"2338","fmax":"2812","strand":"+","sequence":"TTGAAAATTTCATTGATTTCTGCAACGTCAGAAAATGGCGTAATCGGTAATGGCCCTGATATCCCATGGTCAGCAAAAGGTGAGCAGTTACTCTTTAAAGCGCTCACATATAATCAGTGGCTCCTTGTTGGAAGGAAAACATTTGACTCTATGGGTGTTCTTCCAAATCGAAAATATGCAGTAGTGTCGAGGAAAGGAATTTCAAGCTCAAATGAAAATGTATTAGTCTTTCCTTCAATAGAAATCGCTTTGCAAGAACTATCGAAAATTACAGATCATTTATATGTCTCTGGTGGCGGTCAAATCTACAATAGTCTTATTGAAAAAGCAGATATAATTCATTTGTCTACTGTTCACGTTGAGGTTGAAGGTGATATCAATTTTCCTAAAATTCCAGAGAATTTCAATTTGGTTTTTGAGCAGTTTTTTTTGTCTAATATAAATTACACATATCAGATTTGGAAAAAAGGCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3002862","ARO_id":"39296","ARO_name":"dfrA7","ARO_description":"dfrA7 is an integron-encoded dihydrofolate reductase found in Escherichia coli","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36408":{"category_aro_accession":"3000269","category_aro_cvterm_id":"36408","category_aro_name":"brodimoprim","category_aro_description":"Brodimoprim is a structural derivative of trimethoprim and an inhibitor of bacterial dihydrofolate reductase. The 4-methoxy group of trimethoprim is replaced with a bromine atom.","category_aro_class_name":"Antibiotic"},"36423":{"category_aro_accession":"3000284","category_aro_cvterm_id":"36423","category_aro_name":"tetroxoprim","category_aro_description":"Tetroxoprim is a trimethoprim derivative that inhibits bacterial dihydrofolate reductase.","category_aro_class_name":"Antibiotic"},"36476":{"category_aro_accession":"3000337","category_aro_cvterm_id":"36476","category_aro_name":"iclaprim","category_aro_description":"Iclaprim is a bactericidal compound that inhibits dihydrofolate reductase. It is used against clinically important Gram-positive pathogens, including methicillin-sensitive Staphylococcus aureus and methicillin-resistant S. aureus.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2054":{"model_id":"2054","model_name":"msrC","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"950"}},"model_sequences":{"sequence":{"363":{"protein_sequence":{"accession":"AAK01167.1","sequence":"MENLAVNITNLQVRFGNQLELSIDSLRVYQQDRIGIIGENGVGKTTLLKLIVGELIPNQGKIQTEITFNYLPQLTYLAEAKDLNLELASHFQLKLEETSERKWSGGEERKIELIRLLSSYEQGMLLDEPTTHLDRKSMDRLIEELRYYYGTLIFVSHDRYFLDELATKVWEVKDGEIREFPENYSAYLTQRELEKKTQLREAESIMKEKKRLEKSIQEKKKQAEKLEKVSSKKKKQQIRPDRLSSSKQKDSVQKAIQKNTKTLERRLQKIGETTKPQQMKQIRFPVPKSLELHNRYPIMGQNIQLERSGRTLLINSDFQFSLGKKIAIVGENGSGKTTLLEHIRKQGEGILLSPKVSFQVYQQKDYQMTSEESVIRFVMRQTEFSESLVRSLLNHLGFAQETLTKPLCTLSGGEATRLTIALLFTKPSNVLLLDEPTNFIDVATIEALEQLMQVYPGTILFTSHDSYFVERTADEVYEIKGQKIKKVLTRNF"},"dna_sequence":{"accession":"AF313494","fmin":"0","fmax":"1479","strand":"+","sequence":"ATGGAAAATTTAGCAGTAAATATAACAAACCTGCAAGTTCGTTTTGGTAACCAGTTAGAATTATCTATTGATTCTCTTCGTGTCTATCAGCAAGATCGGATAGGAATCATAGGGGAAAATGGAGTCGGTAAAACAACGTTGCTGAAACTGATAGTCGGTGAACTTATCCCCAATCAAGGGAAAATCCAAACAGAGATCACTTTCAACTATCTGCCTCAATTAACCTATCTTGCTGAGGCAAAGGACCTAAATTTGGAATTAGCCAGTCATTTCCAGTTGAAACTGGAAGAAACTTCGGAACGGAAATGGAGTGGAGGGGAAGAACGAAAGATCGAGTTGATACGTCTTCTTTCTTCTTATGAACAAGGGATGCTTCTAGACGAGCCGACAACCCATCTAGATAGAAAAAGTATGGATCGACTAATTGAAGAGCTTCGTTATTATTATGGCACGCTGATTTTTGTTAGTCATGACCGCTATTTTCTAGATGAGTTGGCAACGAAAGTCTGGGAAGTAAAAGACGGAGAAATCCGAGAGTTTCCGGAGAATTATAGTGCCTATCTCACTCAAAGGGAATTGGAGAAAAAGACTCAGCTACGAGAAGCAGAGTCGATCATGAAAGAGAAAAAACGATTGGAAAAATCGATCCAAGAAAAGAAAAAACAAGCGGAAAAGTTAGAAAAAGTGTCCAGTAAAAAGAAAAAGCAACAAATCAGACCGGATCGGTTGTCTTCCTCTAAACAAAAAGACAGTGTACAAAAAGCCATCCAAAAGAATACGAAAACATTAGAGAGAAGACTCCAAAAAATAGGAGAAACAACCAAACCGCAACAGATGAAACAAATCCGTTTTCCAGTACCAAAATCTCTTGAACTCCACAATCGTTATCCAATCATGGGACAAAATATCCAATTGGAAAGAAGCGGAAGAACATTACTGATAAATAGCGATTTTCAATTTTCTTTAGGTAAAAAAATCGCGATTGTCGGCGAAAATGGATCAGGTAAGACAACTTTATTGGAACATATCCGCAAACAAGGAGAAGGAATCCTTCTCTCTCCGAAAGTAAGCTTTCAAGTATATCAGCAAAAGGATTATCAAATGACATCTGAAGAATCCGTCATTCGTTTTGTCATGAGACAAACAGAGTTTTCGGAATCACTTGTCCGCAGTTTGTTGAATCATTTAGGGTTTGCTCAGGAAACTCTGACGAAACCGTTGTGTACGTTAAGTGGGGGAGAAGCGACTCGTTTGACGATTGCTTTGCTTTTTACTAAGCCAAGTAATGTGTTGCTGTTAGATGAACCGACTAATTTCATTGATGTGGCAACGATCGAAGCTTTAGAGCAGCTGATGCAAGTATATCCGGGAACGATTTTGTTTACTTCACATGATTCCTACTTTGTCGAGCGTACGGCTGATGAAGTTTATGAAATAAAAGGGCAGAAAATAAAAAAAGTACTTACGAGAAATTTTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002819","ARO_id":"39253","ARO_name":"msrC","ARO_description":"msrC is a chromosomal-encoded ABC-efflux pump expressed in Enterococcus faecium that confers resistance to erythromycin and other macrolide and streptogramin B antibiotics.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2055":{"model_id":"2055","model_name":"LRA-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1917":{"protein_sequence":{"accession":"ACH58987.1","sequence":"MKSKLLLAAALAALAGTSMAAQAAELQYKPPPITNKEWETPFPGFKIVGNMYYVGTYDLGCYLIDTGAGLILINSGADGSYPLIKANIEKLGFKTSDIKIITSTHGHGDHVGDLAAFQKDAPAAKTYMNFRDAPTIESGGNIDYRRPEGRGFYPYHPVKVDVRTKPGDHIKLGNTDLTLHQAYGHTPGATSFTFTVQDGGRNYNVLIVNMNGINAGVKLLGSPGYPTIVEDFASTLKEQATYTPDLWVSSHAGQFNLHQVYKPGDPYNPARFGDLAAYKLKIANATKAYEKQLAEERAAKAK"},"dna_sequence":{"accession":"EU408348","fmin":"1243","fmax":"2152","strand":"+","sequence":"ATGAAATCGAAACTGCTTCTTGCCGCGGCCTTGGCCGCACTCGCCGGCACGTCGATGGCCGCCCAGGCGGCCGAACTGCAATATAAGCCGCCGCCGATCACCAACAAGGAATGGGAGACCCCGTTCCCCGGCTTCAAGATCGTCGGCAACATGTATTATGTCGGCACCTACGATCTGGGCTGCTATCTGATCGACACGGGGGCCGGGCTTATTCTGATCAATTCCGGCGCCGACGGTTCGTATCCGCTGATCAAGGCCAATATCGAGAAGCTCGGTTTCAAGACCAGCGACATCAAGATCATCACCTCGACGCACGGCCACGGCGATCATGTCGGCGACCTCGCCGCGTTCCAGAAAGATGCGCCCGCCGCCAAGACCTATATGAATTTTCGCGATGCGCCGACCATCGAATCGGGCGGCAACATCGATTACCGGCGCCCTGAGGGGCGCGGGTTTTATCCCTACCATCCGGTGAAGGTTGATGTGCGCACCAAGCCGGGCGACCATATCAAGCTCGGCAACACCGATCTGACGCTGCACCAGGCTTACGGCCATACGCCGGGGGCGACGAGCTTCACCTTCACGGTCCAGGATGGTGGGCGCAATTACAACGTGCTGATCGTCAACATGAACGGCATCAATGCGGGCGTGAAATTGCTCGGCTCGCCGGGGTATCCGACCATCGTCGAGGATTTTGCCAGCACGCTGAAGGAACAGGCGACCTATACGCCCGACCTCTGGGTCTCTTCGCATGCGGGCCAGTTCAACCTGCATCAGGTCTACAAGCCGGGCGATCCGTACAACCCGGCGCGCTTCGGCGATTTGGCGGCCTACAAATTGAAGATCGCCAACGCGACGAAGGCTTACGAAAAACAATTGGCTGAAGAGCGCGCCGCGAAGGCGAAGTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39081","NCBI_taxonomy_name":"uncultured bacterium BLR3","NCBI_taxonomy_id":"506521"}}}},"ARO_accession":"3002510","ARO_id":"38910","ARO_name":"LRA-3","ARO_description":"LRA-3 is a beta-lactamase isolated from soil samples in Alaska","ARO_category":{"41390":{"category_aro_accession":"3004226","category_aro_cvterm_id":"41390","category_aro_name":"subclass B3 LRA beta-lactamase","category_aro_description":"Beta-lactamases that are part of the LRA gene family and are classified as B3 (metallo-) beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2056":{"model_id":"2056","model_name":"mdtO","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1300"}},"model_sequences":{"sequence":{"3300":{"protein_sequence":{"accession":"BAE78083.1","sequence":"MSALNSLPLPVVRLLAFFHEELSERRPGRVPQTVQLWVGCLLVILISMTFEIPFVALSLAVLFYGIQSNAFYTKFVAILFVVATVLEIGSLFLIYKWSYGEPLIRLIIAGPILMGCMFLMRTHRLGLVFFAVAIVAIYGQTFPAMLDYPEVVVRLTLWCIVVGLYPTLLMTLIGVLWFPSRAISQMHQALNDRLDDAISHLTDSLAPLPETRIEREALALQKLNVFCLADDANWRTQNAWWQSCVATVTYIYSTLNRYDPTSFADSQAIIEFRQKLASEINKLQHAVAEGQCWQSDWRISESEAMAARECNLENICQTLLQLGQMDPNTPPTPAAKPPSMAADAFTNPDYMRYAVKTLLACLICYTFYSGVDWEGIHTCMLTCVIVANPNVGSSYQKMVLRFGGAFCGAILALLFTLLVMPWLDNIVELLFVLAPIFLLGAWIATSSERSSYIGTQMVVTFALATLENVFGPVYDLVEIRDRALGIIIGTVVSAVIYTFVWPESEARTLPQKLAGTLGMLSKVMRIPRQQEVTALRTYLQIRIGLHAAFNACEEMCQRVALERQLDSEERALLIERSQTVIRQGRDLLHAWDATWNSAQALDNALQPDRAGQFADALEKYAAGLATALSRSPQITLEETPASQAILPTLLKQEQHVCQLFARLPDWTAPALTPATEQAQGATQ"},"dna_sequence":{"accession":"AP009048","fmin":"4304505","fmax":"4306557","strand":"-","sequence":"TCATTGCGTGGCTCCTTGTGCCTGTTCCGTGGCGGGCGTTAATGCCGGGGCTGTCCAGTCTGGCAAGCGGGCGAAAAGCTGGCAGACGTGTTGCTCCTGTTTTAATAAGGTGGGCAGGATGGCCTGAGAGGCGGGTGTCTCTTCAAGCGTTATTTGAGGAGAACGGCTGAGTGCGGTTGCCAGACCGGCAGCGTATTTCTCCAGGGCGTCGGCAAACTGACCTGCTCTGTCCGGCTGTAGTGCGTTATCCAGCGCCTGCGCCGAGTTCCAGGTGGCATCCCAGGCGTGAAGAAGATCGCGGCCCTGACGAATAACCGTTTGCGAACGTTCAATCAGTAATGCGCGTTCTTCGCTGTCCAGTTGACGCTCCAGCGCCACGCGTTGGCACATCTCTTCACAGGCATTAAACGCCGCATGCAGACCGATACGAATTTGCAGATAAGTGCGCAGAGCCGTGACTTCCTGCTGGCGTGGGATCCGCATTACTTTACTTAACATACCCAGCGTGCCAGCCAGTTTTTGCGGCAGTGTGCGCGCTTCACTTTCAGGCCAGACAAAGGTGTAAATCACCGCGGACACCACGGTACCAATGATGATACCCAGGGCGCGATCGCGAATTTCCACCAGGTCGTACACTGGGCCAAAAACGTTTTCGAGCGTGGCGAGCGCGAAGGTGACCACCATCTGTGTGCCGATATAAGAAGAGCGTTCAGAGCTGGTGGCAATCCATGCGCCCAACAGGAAAATCGGTGCCAGCACAAACAGCAATTCGACAATATTGTCCAGCCAGGGCATGACCAGTAGCGTGAATAACAGCGCCAGAATCGCGCCGCAAAAGGCCCCGCCAAAACGCAGCACCATCTTCTGGTACGACGAACCGACATTTGGGTTAGCGACGATCACGCATGTCAGCATACAGGTGTGAATGCCTTCCCAGTCCACGCCGCTGTAAAAGGTGTAACAGATCAAACAGGCGAGCAGCGTTTTTACCGCGTAGCGCATATAGTCTGGATTGGTAAAAGCATCGGCGGCCATTGATGGCGGTTTGGCTGCGGGCGTTGGCGGCGTATTCGGGTCCATCTGACCCAGTTGTAACAACGTCTGGCAGATATTCTCCAGGTTACATTCCCGTGCCGCCATCGCTTCACTTTCACTGATCCGCCAGTCGCTTTGCCAGCACTGACCTTCAGCAACGGCATGCTGCAGCTTGTTGATTTCTGAAGCTAATTTTTGTCGGAATTCAATAATTGCCTGAGAATCAGCAAAAGAGGTGGGATCGTAGCGATTCAGCGTCGAGTAAATGTAGGTTACCGTTGCCACGCAGCTTTGCCACCATGCGTTTTGAGTTCGCCAGTTGGCATCGTCCGCGAGGCAAAAGACATTGAGTTTTTGTAGCGCCAGCGCCTCTCTTTCAATCCGCGTTTCGGGTAGCGGTGCGAGGCTGTCTGTCAGGTGACTAATGGCATCATCAAGCCGATCATTAAGCGCCTGATGCATTTGCGAAATGGCACGACTGGGAAACCACAGCACGCCGATTAACGTCATCAGCAAGGTTGGATAGAGGCCAACAACGATACACCACAGCGTTAAGCGCACGACCACTTCCGGATAGTCGAGCATGGCGGGGAAGGTTTGCCCGTAAATAGCGACAATGGCGACGGCGAAAAAGACCAGCCCCAAGCGATGGGTGCGCATCAAAAACATGCAGCCCATCAGGATCGGTCCGGCGATGATCAATCGGATCAACGGTTCGCCGTATGACCATTTGTAGATCAAAAACAGGCTGCCGATCTCCAGCACCGTGGCAACCACAAACAAGATCGCGACAAATTTGGTGTAAAACGCGTTCGACTGAATACCGTAAAACAGCACTGCCAGCGATAACGCCACAAAAGGGATCTCAAAGGTCATCGAGATCAGAATCACCAGCAGGCAGCCTACCCAGAGTTGCACGGTCTGCGGCACGCGACCTGGTCGCCGCTCGCTTAACTCTTCATGAAAGAACGCCAGCAGCCTGACCACCGGTAATGGCAGGGAGTTGAGCGCGCTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36839","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. W3110","NCBI_taxonomy_id":"316407"}}}},"ARO_accession":"3003549","ARO_id":"40151","ARO_name":"mdtO","ARO_description":"Multidrug resistance efflux pump. Could be involved in resistance to puromycin, acriflavine and tetraphenylarsonium chloride","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavin","category_aro_description":"Acriflavin is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35965":{"category_aro_accession":"0000047","category_aro_cvterm_id":"35965","category_aro_name":"puromycin","category_aro_description":"Puromycin is an aminonucleoside antibiotic, derived from Streptomyces alboniger, that causes premature chain termination during ribosomal protein translation.","category_aro_class_name":"Antibiotic"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36193":{"category_aro_accession":"3000054","category_aro_cvterm_id":"36193","category_aro_name":"acridine dye","category_aro_description":"Acridine dyes are cell permeable, basic molecules with an acridine chromophore. These compounds intercalate DNA. The image shown represents the core structure of the acridine family, with specific dyes containing varying substituents.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2057":{"model_id":"2057","model_name":"SHV-179","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1559":{"protein_sequence":{"accession":"AHA80962.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMNTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"KF705208","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAACACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001362","ARO_id":"37762","ARO_name":"SHV-179","ARO_description":"From the Lahey list of beta-lactamases.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2058":{"model_id":"2058","model_name":"pp-flo","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"285":{"protein_sequence":{"accession":"BAA07072.1","sequence":"MTTLHPAWAYTLPAALLLMAPFDILASLAMDIYLPVVPAMPGILNTTPAMIQLTLSLYMVMLGVGQVIFGPLSDRIGRRPILLAGATAFVIASLGAAWSSTAPAFVAFRLLQAVGASAMLVATFATVRDVYANRPEGVVIYGLFSSVLAFVPALGPIAGALIGEFLGWQAIFITLAILAMLALLNAGFRWHETRPLDQVKTRRSVLPIFASPAFWVYTVGFSAGMGTFFVFFSTAPRVLIGQAEYSEIGFSFAFATVALVMIVTTRFAKSFVARWGIAGCGRVGWRCLFAAVLLGIGELYGSLNSSPSSYRCGLSRSVLSSRCPLPRTALLAEFDDIAGSAVAFYFCVQSLIVSIVGTLAVALLNGDTAWPVIC"},"dna_sequence":{"accession":"D37826","fmin":"1070","fmax":"2195","strand":"+","sequence":"ATGACCACCCTACACCCCGCGTGGGCCTATACGCTGCCCGCAGCACTGCTGCTGATGGCTCCTTTCGACATCCTCGCTTCACTGGCGATGGATATTTATCTCCCTGTCGTTCCAGCGATGCCCGGCATCCTGAACACGACGCCCGCTATGATCCAACTCACGTTGAGCCTCTATATGGTGATGCTCGGCGTGGGCCAGGTGATTTTTGGTCCGCTCTCAGACAGAATCGGGCGACGGCCAATTCTACTTGCGGGCGCAACGGCTTTCGTCATTGCGTCTCTGGGAGCAGCTTGGTCTTCAACTGCACCGGCCTTTGTCGCTTTCCGTCTACTTCAAGCAGTGGGCGCGTCGGCCATGCTGGTGGCGACGTTCGCGACGGTTCGCGACGTTTATGCCAACCGTCCTGAGGGTGTCGTCATCTACGGCCTTTTCAGTTCGGTGCTGGCGTTCGTGCCTGCGCTCGGCCCTATCGCCGGAGCATTGATCGGCGAGTTCTTGGGATGGCAGGCGATATTCATTACTTTGGCTATACTGGCGATGCTCGCACTCCTAAATGCGGGTTTCAGGTGGCACGAAACCCGCCCTCTGGATCAAGTCAAGACGCGCCGATCTGTCTTGCCGATCTTCGCGAGTCCGGCTTTTTGGGTTTACACTGTCGGCTTTAGCGCCGGTATGGGCACCTTCTTCGTCTTCTTCTCGACGGCTCCCCGTGTGCTCATAGGCCAAGCGGAATATTCCGAGATCGGATTCAGCTTTGCCTTCGCCACTGTCGCGCTTGTAATGATCGTGACAACCCGTTTCGCGAAGTCCTTTGTCGCCAGATGGGGCATCGCAGGATGTGGGCGCGTGGGATGGCGTTGCTTGTTTGCGGCGGTCCTGTTGGGGATCGGCGAACTTTACGGCTCGCTCAATTCCTCACCTTCATCCTACCGATGTGGGTTGTCGCGGTCGGTATTGTCTTCACGGTGTCCGTTACCGCGAACGGCGCTTTTGGCAGAGTTCGACGACATCGCGGGATCAGCGGTCGCTTTCTACTTCTGCGTTCAAAGCCTGATAGTCAGCATTGTCGGGACATTGGCGGTGGCACTTTTAAACGGTGACACAGCGTGGCCCGTGATCTGTTAGC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39539","NCBI_taxonomy_name":"Photobacterium damselae subsp. piscicida","NCBI_taxonomy_id":"38294"}}}},"ARO_accession":"3002812","ARO_id":"39246","ARO_name":"pp-flo","ARO_description":"pp-flo is a plasmid chloramphenicol exporter that is found in Photobacterium damselae subsp. piscicida","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36600":{"category_aro_accession":"3000461","category_aro_cvterm_id":"36600","category_aro_name":"florfenicol","category_aro_description":"Florfenicol is a fluorine derivative of chloramphenicol, where the nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3) and the hydroxyl group (-OH), by a fluorine group (-F). The action mechanism is the same as chloramphenicol's, where the antibiotic binds to the 23S RNA of the 50S subunit of bacterial ribosomes to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2059":{"model_id":"2059","model_name":"OKP-A-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"765":{"protein_sequence":{"accession":"CAG25812.2","sequence":"MRYVRLCLISLIAALPLAVFASPPPLEQITRSESQLAGRVGYVEMDLVSGRTLAAWRANERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIRYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKSVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMAATLRKLLTSHTLSARSQQQLLQWMVDDQVAGPLIRAVLPAGWFIAEKTGAGERGSRGIVALLGPNGKAERIVVIYLRDTPASMAERNQQIARIGAALIEHWQR"},"dna_sequence":{"accession":"AJ635401","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCCGCCGCTTGAGCAAATTACACGCAGCGAAAGTCAGCTGGCGGGCCGCGTGGGCTATGTTGAAATGGATCTGGTCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAATGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGAGACGAACAGCTGGATCGGCGGATCCGCTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGAGCGTTGGCGGCCCCGCTGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAGCTCAATGAAGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCAGCCAGCATGGCCGCCACCCTGCGCAAGCTGCTAACCAGCCACACTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGACCAGGTAGCCGGTCCGCTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGAAAAAACCGGGGCCGGCGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGAACGGCAAAGCGGAGCGCATCGTGGTGATCTATCTGCGGGATACGCCGGCGTCCATGGCCGAGCGTAACCAGCAGATCGCCAGAATAGGCGCGGCGCTGATCGAGCACTGGCAGCGCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002418","ARO_id":"38818","ARO_name":"OKP-A-1","ARO_description":"OKP-A-1 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2060":{"model_id":"2060","model_name":"FosC2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"580":{"protein_sequence":{"accession":"BAJ10053.1","sequence":"MLRGLNHITIAVSDLERSVEFYTRLLGMKAHVRWDSGAYLSLEATWICLSCDEVHPSQDYCHIAFDVSEENFEPVTKKLREAHVVEWKQNRSEGLSLYLLDPDGHKLEIHSGSLQSRLESLKSKPYQGLVWL"},"dna_sequence":{"accession":"AB522969","fmin":"0","fmax":"399","strand":"+","sequence":"GTGTTACGAGGATTGAATCATATTACTATTGCAGTAAGTGACCTTGAACGTTCCGTGGAGTTCTATACGCGTCTATTAGGAATGAAGGCACATGTCCGCTGGGATAGTGGGGCATATCTGAGCTTGGAGGCTACTTGGATTTGCTTGTCTTGTGACGAAGTGCATCCGAGCCAAGATTACTGTCACATCGCGTTTGATGTTTCCGAAGAGAATTTCGAACCAGTTACTAAAAAGCTTCGCGAAGCACATGTCGTTGAATGGAAACAAAATAGAAGCGAAGGACTTTCTTTATACTTGCTCGATCCTGACGGCCATAAATTGGAAATCCATAGCGGTAGCCTACAAAGTCGTTTGGAATCGTTGAAGTCTAAACCCTATCAAGGGTTAGTATGGCTATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002874","ARO_id":"39308","ARO_name":"FosC2","ARO_description":"FosC2 is an enzyme that phosphorylates fosfomycin to confer resistance in Escherichia coli","ARO_category":{"41409":{"category_aro_accession":"3004245","category_aro_cvterm_id":"41409","category_aro_name":"fosC phosphotransferase family","category_aro_description":"The fosC family of phosphotransferases phosphorylate fosfomycin to confer resistance and have been found in various bacterial isolates.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2061":{"model_id":"2061","model_name":"VIM-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1007":{"protein_sequence":{"accession":"CAD61201.1","sequence":"MFQIRSFLVGISAFVMAVLGSAAYSAQPGGEYPTVDDIPVGEVRLYKIGDGVWSHIATQKLGDTVYSSNGLIVRDADELLLIDTAWGAKNTVALLAEIEKQIGLPVTRSISTHFHDDRVGGVDVLRAAGVATYTSPLTRQLAEAAGNEVPAHSLKALSSSGDVVRFGPVEVFYPGAAHSGDNLVVYVPAVRVLFGGCAVHEASRESAGNVADANLAEWPATIKRIQQRYPEAEVVIPGHGLPGGLELLQHTTNVVKTHKVRPVAE"},"dna_sequence":{"accession":"AJ536835","fmin":"149","fmax":"947","strand":"+","sequence":"ATGTTTCAAATTCGCAGCTTTCTGGTTGGTATCAGTGCATTCGTCATGGCCGTACTTGGATCAGCAGCATATTCCGCACAGCCTGGCGGTGAATATCCGACAGTAGATGACATACCGGTAGGGGAAGTTCGGCTGTACAAGATTGGCGATGGCGTTTGGTCGCATATCGCAACTCAGAAACTCGGTGACACGGTGTACTCGTCTAATGGACTTATCGTCCGCGATGCTGATGAGTTGCTTCTTATTGATACAGCGTGGGGGGCGAAGAACACGGTAGCCCTTCTCGCGGAGATTGAAAAGCAAATTGGACTTCCAGTAACGCGCTCAATTTCTACGCACTTCCATGACGATCGAGTCGGTGGAGTTGATGTCCTCCGGGCGGCTGGAGTGGCAACGTACACCTCACCCTTGACACGCCAGCTGGCCGAAGCGGCGGGAAACGAGGTGCCTGCGCACTCTCTAAAAGCGCTCTCCTCTAGTGGAGATGTGGTGCGCTTCGGTCCCGTAGAGGTTTTCTATCCTGGTGCTGCGCATTCGGGCGACAATCTTGTGGTATACGTGCCGGCCGTGCGCGTACTGTTTGGTGGCTGTGCAGTTCATGAGGCGTCACGCGAATCCGCGGGTAATGTTGCCGATGCCAATTTGGCAGAATGGCCTGCTACCATTAAACGAATTCAACAGCGGTATCCGGAAGCAGAGGTCGTCATCCCCGGCCACGGTCTACCGGGCGGTCTGGAATTGCTCCAACACACAACTAACGTTGTCAAAACGCACAAAGTACGCCCGGTGGCCGAGTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002277","ARO_id":"38677","ARO_name":"VIM-7","ARO_description":"VIM-7 is a beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2062":{"model_id":"2062","model_name":"mphC","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"648":{"protein_sequence":{"accession":"CAJ51085.1","sequence":"MTQHNEIIKIAEKHQLHIKPQTISLNESGLDFQVAFGEDEHGIEWVLRLPRRPDVYKRTKPEKQMVDFLQKNVSFEVPNWKVHTKDLIAYPKLTGKPAATIDPEIQNYVWEIEHKPVTKNFINTLAETLVDLHNIPEENITAHHINIKTIQEIKNDFQRRMNKVRETYGVADGLWNRWKQWLENDELWPRRATMIHGDLHPGHIMVDNQANVTGLIDWTEATYSDPSMDFMGYHRVFDDEGLEQLITAYDKAGGETWPRMKEHIIELNAVFPMFIAEFAMESGEPAYEKMALQELGMKE"},"dna_sequence":{"accession":"AM180066","fmin":"788","fmax":"1688","strand":"+","sequence":"ATGACTCAACATAATGAAATTATTAAAATTGCAGAAAAACATCAATTACACATCAAACCTCAAACAATATCATTGAATGAATCAGGGCTAGATTTCCAAGTTGCATTTGGAGAAGATGAACACGGAATAGAGTGGGTTTTAAGACTACCAAGAAGACCTGACGTTTATAAACGAACAAAACCCGAAAAACAAATGGTAGACTTCTTACAAAAAAATGTTTCGTTTGAAGTACCGAATTGGAAAGTACATACAAAAGACCTTATTGCTTATCCAAAACTTACAGGCAAACCCGCAGCCACAATAGATCCAGAAATACAAAATTACGTATGGGAAATTGAACACAAACCAGTAACAAAAAATTTTATTAACACATTAGCTGAAACACTCGTAGATTTACACAACATACCAGAGGAAAATATTACCGCACACCATATAAATATCAAAACTATACAAGAAATAAAAAATGATTTTCAAAGAAGAATGAATAAAGTTAGAGAAACTTATGGCGTGGCAGATGGATTATGGAACAGATGGAAACAATGGTTAGAAAACGACGAACTGTGGCCTCGACGTGCAACCATGATACATGGAGACTTACATCCAGGACATATAATGGTAGATAACCAAGCAAATGTCACAGGACTCATAGACTGGACTGAAGCAACCTATTCCGATCCATCAATGGACTTTATGGGATACCATCGTGTATTCGACGACGAAGGCTTAGAGCAACTCATAACAGCATACGATAAAGCTGGAGGAGAAACATGGCCACGAATGAAAGAGCATATAATAGAACTCAATGCAGTATTCCCAATGTTTATCGCTGAGTTTGCTATGGAATCAGGAGAACCAGCGTATGAAAAAATGGCATTGCAAGAGTTAGGTATGAAAGAGTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39576","NCBI_taxonomy_name":"Staphylococcus equorum","NCBI_taxonomy_id":"246432"}}}},"ARO_accession":"3000319","ARO_id":"36458","ARO_name":"mphC","ARO_description":"The mphC gene was identified from Staphylococcus aureus.  This gene shows similarity to mphB gene from Escherchia coli.","ARO_category":{"36472":{"category_aro_accession":"3000333","category_aro_cvterm_id":"36472","category_aro_name":"macrolide phosphotransferase (MPH)","category_aro_description":"Macrolide phosphotransferases (MPH) are enzymes encoded by macrolide phosphotransferase genes (mph genes). These enzymes phosphorylate macrolides in GTP dependent manner at 2'-OH of desosamine sugar thereby inactivating them. Characterized MPH's are differentiated based on their substrate specificity.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35946":{"category_aro_accession":"0000027","category_aro_cvterm_id":"35946","category_aro_name":"roxithromycin","category_aro_description":"Roxithromycin is a semi-synthetic, 14-carbon ring macrolide antibiotic derived from erythromycin. It is used to treat respiratory tract, urinary and soft tissue infections. Roxithromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35974":{"category_aro_accession":"0000057","category_aro_cvterm_id":"35974","category_aro_name":"telithromycin","category_aro_description":"Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36315":{"category_aro_accession":"3000176","category_aro_cvterm_id":"36315","category_aro_name":"dirithromycin","category_aro_description":"Dirithromycin is an oxazine derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome to inhibit bacterial protein synthesis.","category_aro_class_name":"Antibiotic"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2063":{"model_id":"2063","model_name":"blaR1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1150"}},"model_sequences":{"sequence":{"4299":{"protein_sequence":{"accession":"ABU39979.1","sequence":"MTLPHILLSLVLITATILVIFFVRAVFYKQLSAKWRYHLWFLLITVLTLPFIPIHLLTGLSFFDQGRQQITPSAQKRFGFADQNEQWMVDFGTSVSRFDDTFIHAVFVSIWIGGMIFFLLLTLYHYAKLQRLVKAASRIQNQKVENAFSDCMAELQITNKLTNLESPAIQTPMTFGWLKTYILLPKNIELYLSDDEIRHVLLHELHHYKSKHIKVNYIFVVYQIVYWFHPLVWKAFKEMRLDRELACDTEVLLTLGQREYKAYGQTIMRFLERNSRFLYLTNPLHSSKKAFKNTKSYNIAFFYWRVKSGAQLKKPWVVFAGLTRFCIAQFPFLTATAVSTERYQFDESQAVVEDYSTYFAGNEGSFVLYSLTSDQFEIYNKEKSVRRVSPNSSYKIYTALMALELGVIGRDDSWLEWDGVEYEDEAWNSGQDLKSAMSQSVTWYFQELDERIKQRNIQSFVNQLDYGNKDLSGGLNHYWLESSLKISPVEQVELLHSFYTNQLDFKEEHVQFVKEVMKLEENQKGTLYGKTGTGIVNGHAINGWFIGFVETETDTYFFATNIQQKIMHMEARLLKSLYPFCQAKEFID"},"dna_sequence":{"accession":"EF540343.1","fmin":"1463","fmax":"3230","strand":"-","sequence":"CTAATCAATAAATTCCTTTGCTTGACAGAATGGATAAAGTGATTTCAGCAGCCGTGCTTCCATATGCATGATCTTCTGTTGAATGTTTGTCGCAAAAAAGTACGTATCCGTTTCAGTTTCGACAAATCCAATAAACCAACCATTTATTGCATGGCCGTTCACAATGCCAGTCCCGGTTTTTCCATAAAGCGTTCCCTTTTGATTTTCTTCAAGTTTCATAACCTCTTTAACGAATTGCACATGCTCTTCTTTAAAGTCCAGTTGGTTTGTATAGAAGGAATGGAGAAGCTCCACTTGTTCTACCGGTGATATTTTCAAGGAAGATTCCAGCCAATAGTGATTTAATCCACCGGAAAGATCTTTATTCCCATAGTCTAATTGGTTTACAAAAGATTGGATGTTCCTTTGTTTGATCCGCTCGTCTAACTCTTGAAAGTACCAAGTGACTGACTGGCTCATCGCCGATTTCAAATCTTGCCCGCTATTCCAGGCTTCATCCTCGTATTCGACTCCATCCCACTCTAACCATGAATCATCTCGCCCAATCACGCCTAGTTCCAATGCCATGAGCGCGGTGTAAATTTTATAGGAAGAATTGGGGGAGACTCTTCTTACACTTTTTTCTTTATTATAGATTTCGAACTGGTCGCTGGTTAAGCTATATAATACAAAACTACCCTCATTTCCTGCAAAATAAGTGCTGTAATCTTCAACAACCGCCTGGCTTTCATCAAATTGGTAGCGCTCTGTAGAAACAGCGGTTGCCGTTAAAAAAGGAAATTGAGCAATGCAAAAACGGGTGAGACCAGCAAAAACCACCCATGGCTTTTTTAATTGGGCGCCGCTTTTGACTCGCCAGTAAAAGAAAGCAATGTTATAAGATTTCGTATTTTTAAAAGCTTTTTTCGAACTATGCAGTGGGTTCGTTAAGTATAAAAATCGAGAATTTCTTTCCAGAAAACGCATGATCGTCTGGCCATACGCTTTATACTCCCGCTGTCCCAATGTAAGCAAGACCTCCGTATCACAAGCTAATTCCCGATCAAGACGCATCTCTTTAAAGGCTTTCCATACTAAAGGATGAAACCAATAAACAATTTGGTAAACGACAAATATATAGTTCACTTTAATATGTTTGCTTTTATAATGGTGCAACTCATGCAACAACACATGTCTGATTTCATCATCAGATAGATACAATTCGATATTTTTGGGCAACAAGATGTACGTCTTTAACCATCCAAAGGTCATTGGCGTTTGAATGGCAGGGGATTCTAAATTGGTTAATTTATTCGTTATTTGCAATTCTGCCATACAATCGCTAAACGCGTTTTCGACTTTTTGATTTTGTATACGACTTGCCGCTTTTACTAGTCGTTGTAGCTTTGCATAATGGTATAAAGTCAATAAAAGGAAAAAAATCATTCCACCAATCCAGATGGAAACAAACACTGCATGAATGAATGTATCGTCAAAGCGACTAACAGACGTGCCAAAATCAACCATCCATTGCTCATTTTGATCCGCAAAACCGAAACGCTTCTGTGCTGAAGGGGTAATCTGTTGACGCCCCTGGTCAAAAAAAGACAAGCCCGTCAATAGATGAATCGGTATAAACGGAAGCGTCAACACAGTAATGAGTAAAAACCATAAATGATAACGCCATTTTGCTGATAATTGTTTATAAAAAACCGCTCTTACAAAAAAGATCACTAGAATCGTTGCCGTTATTAATACAAGAGAAAGTAAAATATGCGGTAACGTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36882","NCBI_taxonomy_name":"Bacillus clausii","NCBI_taxonomy_id":"79880"}}}},"ARO_accession":"3000217","ARO_id":"36356","ARO_name":"blaR1","ARO_description":"blaR1 is a transmembrane spanning and signal transducing protein which in response to interaction with beta-lactam antibiotics results in upregulation of the blaZ\/blaR1\/blaI operon.","ARO_category":{"41361":{"category_aro_accession":"3004197","category_aro_cvterm_id":"41361","category_aro_name":"blaZ beta-lactamase","category_aro_description":"blaZ beta-lactamases are Class A beta-lactamases. These beta-lactamases are responsible for penicillin resistance in Staphylococcus aures.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2064":{"model_id":"2064","model_name":"TEM-196","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"3690":{"protein_sequence":{"accession":"AFE48832.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKIFESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"JQ034306","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCTTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTCGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36790","NCBI_taxonomy_name":"Shigella sonnei","NCBI_taxonomy_id":"624"}}}},"ARO_accession":"3001376","ARO_id":"37776","ARO_name":"TEM-196","ARO_description":"From the Lahey list of beta-lactamases. Not yet released.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2065":{"model_id":"2065","model_name":"CMY-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3360":{"protein_sequence":{"accession":"YP_009075895.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKFSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"NG_035159","fmin":"2373","fmax":"3519","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGTTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACTTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002016","ARO_id":"38416","ARO_name":"CMY-5","ARO_description":"CMY-5 is a beta-lactamase found in Klebsiella oxytoca","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1966":{"model_id":"1966","model_name":"lmrA","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2887":"Q52P"},"clinical":{"2887":"Q52P"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"4312":{"protein_sequence":{"accession":"CAB12062.1","sequence":"MSYGDSREKILSAATRLFQLQGYYGTGLNQIIKESGAPKGSLYYHFPGGKEQLAIEAVNEMKEYIRQKIADCMEACTDPAEGIQAFLKELSCQFSCTEDIEGLPVGLLAAETSLKSEPLREACHEAYKEWASVYEEKLRQTGCSESRAKEASTVVNAMIEGGILLSLTAKNSTPLLHISSCIPDLLKR"},"dna_sequence":{"accession":"AL009126","fmin":"290131","fmax":"290698","strand":"-","sequence":"TTATCTCTTCAGCAGGTCAGGAATGCAGCTGGAGATATGAAGGAGCGGCGTACTGTTTTTTGCCGTCAAAGATAAAAGGATGCCGCCTTCAATCATCGCGTTAACCACAGTGCTGGCTTCTTTTGCACGGCTCTCGCTGCAGCCAGTCTGCCGCAGTTTTTCCTCATACACAGAGGCCCATTCTTTGTAGGCTTCATGACAGGCTTCGCGCAACGGTTCGCTTTTCAATGACGTCTCAGCCGCTAGCAAGCCCACAGGCAAGCCTTCAATGTCTTCCGTACATGAAAACTGGCAGGAGAGCTCCTTCAAAAAGGCTTGAATGCCTTCCGCTGGATCGGTGCAGGCTTCCATGCAGTCCGCGATTTTCTGACGGATATACTCCTTCATCTCATTCACGGCTTCGATCGCAAGCTGTTCTTTACCCCCGGGAAAGTGGTAGTAAAGAGAGCCTTTAGGCGCGCCGCTTTCCTTTATAATCTGGTTCAGCCCCGTGCCGTAATACCCTTGCAGCTGAAAAAGCCGGGTAGCTGCCGAAAGGATTTTCTCACGGGAATCTCCATAACTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39579","NCBI_taxonomy_name":"Bacillus subtilis subsp. subtilis str. 168","NCBI_taxonomy_id":"224308"}}}},"ARO_accession":"3003028","ARO_id":"39462","ARO_name":"lmrA","ARO_description":"lmrA is the repressor to the lmrAB operon in Bacillus subtilis. lmrA mutations result in lincomycin resistance.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2071":{"model_id":"2071","model_name":"AAC(6')-Ib8","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"3719":{"protein_sequence":{"accession":"YP_009062819.1","sequence":"MSLKPGPKRIAESTGQPDQRQRDNKKTPGNTDKLGITKYSIVTNSTDSVTLRLMTEHDLAMLYEWLNRSHIVEWWGGEEARPTLADVQEQYLPSVLAQESVTPYIAMLNGEPIGYAQSYVALGSGDGWWEEETDPGVRGIDQSLANASQLGKGLGTKLVRALVELLFNDPEVTKIQTDPSPSNLRAIRCYEKAGFERQGTVTTPDGPAVYMVQTRQAFERTRSDA"},"dna_sequence":{"accession":"NC_025003.1","fmin":"4171","fmax":"4849","strand":"+","sequence":"ATGAGCCTTAAACCCGGACCAAAAAGAATTGCCGAATCGACGGGGCAACCTGATCAACGCCAACGCGACAATAAAAAGACGCCTGGAAATACTGACAAGTTAGGCATCACAAAGTACAGCATCGTGACCAACAGCACCGATTCCGTCACACTGCGCCTCATGACTGAGCATGACCTTGCGATGCTCTATGAGTGGCTAAATCGATCTCATATCGTCGAGTGGTGGGGCGGAGAAGAAGCACGCCCGACACTTGCTGACGTACAGGAACAGTACTTGCCAAGCGTTTTAGCGCAAGAGTCCGTCACTCCATACATTGCAATGCTGAATGGAGAGCCGATTGGGTATGCCCAGTCGTACGTTGCTCTTGGAAGCGGGGACGGATGGTGGGAAGAAGAAACCGATCCAGGAGTACGCGGAATAGACCAGTCACTGGCGAATGCATCACAACTGGGCAAAGGCTTGGGAACCAAGCTGGTTCGAGCTCTGGTTGAGTTGCTGTTCAATGATCCCGAGGTCACCAAGATCCAAACGGACCCGTCGCCGAGCAACTTGCGAGCGATCCGATGCTACGAGAAAGCGGGGTTTGAGAGGCAAGGTACCGTAACCACCCCAGATGGTCCAGCCGTGTACATGGTTCAAACACGCCAGGCATTCGAGCGAACACGCAGTGATGCCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3002579","ARO_id":"38979","ARO_name":"AAC(6')-Ib8","ARO_description":"AAC(6')-Ib8 is a plasmid-encoded aminoglycoside acetyltransferase in E. cloacae","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2072":{"model_id":"2072","model_name":"NmcR","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"3361":{"protein_sequence":{"accession":"CAA79966.1","sequence":"MRARLPLNALRAFEASARYLNFTKAGLELHVSQAAVSQQVRTLEQMLGVALFTRVPRGLQLTDEGMHLLPSITEALQMMSSAMDKFHEGKIKEVLTIAVVGTFAIGWLLPRITAFLNENPWIDIRILTHNNVVNLAAEGIDASIRFGTGGWINTENILLFQAPHTVLCSPETSKKLYIPSDLKKVCLLRSYRKEEWNNWFKAAGIDPWTITGPIFDSTRLMIDAVKLGDYAALVPYHMFQKELNERSVAKPFEIYATLGGYWLTLQKSRVNHNSEALNVFKEWIIEHSREFVLKS"},"dna_sequence":{"accession":"Z21956","fmin":"191","fmax":"1079","strand":"-","sequence":"CTAGGATTTTAATACAAACTCTCTGCTATGCTCGATAATCCATTCCTTGAAAACATTAAGTGCTTCACTATTATGATTAACCCGAGATTTCTGCAAAGTAAGCCAATAACCGCCAAGCGTGGCATAAATTTCAAAAGGTTTTGCCACGGATCGCTCATTTAATTCTTTTTGAAACATATGATAAGGAACTAGTGCTGCATAATCACCTAACTTTACAGCATCTATCATAAGTCTGGTAGAATCAAAGATAGGCCCTGTAATAGTCCAAGGGTCGATCCCAGCAGCTTTAAACCAATTATTCCATTCCTCCTTTCGATAGGAACGCAGTAAGCAAACTTTTTTTAAGTCTGATGGAATGTACAATTTCTTGGATGTTTCCGGGGAACACAATACTGTATGCGGCGCCTGAAAGAGTAAAATATTTTCCGTATTAATCCAGCCGCCTGTTCCAAATCTAATAGATGCATCAATACCTTCTGCAGCAAGATTGACAACGTTATTATGCGTTAAAATTCTAATATCAATCCATGGATTTTCATTAAGAAACGCAGTAATCCGAGGAAGGAGCCATCCTATTGCAAAAGTCCCTACGACAGCAATAGTAAGCACCTCTTTAATCTTACCTTCATGGAATTTATCCATCGCAGAACTCATCATCTGCAAAGCTTCTGTAATCGAAGGCAAAAGATGCATGCCTTCGTCTGTCAACTGTAACCCACGCGGTACTCTTGTAAAAAGAGCCACACCAAGCATTTGTTCAAGTGTTCTGACCTGCTGGCTTACGGCGGCCTGGCTTACATGAAGTTCTAGTCCGGCTTTAGTAAAATTTAGATATCTTGCTGAGGCTTCAAAAGCTCGTAATGCATTTAAAGGTAATCTGGCACGCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3003665","ARO_id":"40275","ARO_name":"NmcR","ARO_description":"NmcR is a homolog of the LysR regulator found in Enterobacter cloacae that contribute to the regulation of NmcA beta-lactamase","ARO_category":{"35996":{"category_aro_accession":"0000079","category_aro_cvterm_id":"35996","category_aro_name":"clavulanate","category_aro_description":"Clavulanic acid is a beta-lactamase inhibitor (marketed by GlaxoSmithKline, formerly Beecham) combined with penicillin group antibiotics to overcome certain types of antibiotic resistance. It is used to overcome resistance in bacteria that secrete beta-lactamase, which otherwise inactivates most penicillins.","category_aro_class_name":"Adjuvant"},"41359":{"category_aro_accession":"3004195","category_aro_cvterm_id":"41359","category_aro_name":"NmcA beta-lactamase","category_aro_description":"nmcA beta-lactamases are chromosomal-encoded Class A beta-lactamases first isolated from Enterobacter cloacae, specifically a clinical strain known as NOR-1. nmcA beta-lactamases have been shown to hydrolyze carbapenems.","category_aro_class_name":"AMR Gene Family"},"35927":{"category_aro_accession":"0000008","category_aro_cvterm_id":"35927","category_aro_name":"cefoxitin","category_aro_description":"Cefoxitin is a cephamycin antibiotic often grouped with the second generation cephalosporins. Cefoxitin is bactericidal and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. Cefoxitin's 7-alpha-methoxy group and 3' leaving group make it a poor substrate for most beta-lactamases.","category_aro_class_name":"Antibiotic"},"35975":{"category_aro_accession":"0000058","category_aro_cvterm_id":"35975","category_aro_name":"cefazolin","category_aro_description":"Cefazolin (INN), also known as cefazoline or cephazolin, is a first generation cephalosporin antibiotic. It is administered parenterally, and is active against a broad spectrum of bacteria.","category_aro_class_name":"Antibiotic"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2079":{"model_id":"2079","model_name":"sgm","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"3696":{"protein_sequence":{"accession":"WP_063978071.1","sequence":"MTAPAADDRIDEIERAITKSRRYQTVAPATVRRLARAALVAARGDVPDAVKRTKRGLHEIYGAFLPPSPPNYAALLRHLDSAVDAGDDEAVRAALLRAMSVHISTRERLPHLDEFYRELFRHLPRPNTLRDLACGLNPLAAPWMGLPAETVYIASDIDARLVGFVDEALTRLNVPHRTNVADLLEDRLDEPADVTLLLKTLPCLETQQRGSGWEVIDIVNSPNIVVTFPTKSLGQRSKGMFQNYSQSFESQARERSCRIQRLEIGNELIYVIQK"},"dna_sequence":{"accession":"NG_050600","fmin":"100","fmax":"925","strand":"+","sequence":"ATGACGGCACCTGCGGCCGACGACCGTATCGACGAGATTGAGCGGGCCATCACCAAGAGCAGGCGTTACCAGACGGTGGCGCCGGCCACCGTGCGCCGCCTGGCCCGCGCTGCTCTCGTCGCCGCGCGGGGTGACGTGCCCGACGCGGTGAAGCGCACCAAGCGGGGTCTGCACGAGATCTACGGCGCCTTCCTGCCGCCCAGCCCTCCCAACTACGCAGCGTTGCTGCGGCACCTGGACTCGGCAGTGGACGCCGGTGACGACGAGGCGGTTCGAGCGGCCCTACTTCGCGCTATGTCCGTACATATCTCCACCCGCGAGCGATTGCCGCACCTCGACGAGTTCTACCGGGAACTCTTCCGGCACCTCCCCCGACCGAACACGCTGCGTGACCTCGCCTGTGGTCTCAACCCCCTGGCCGCGCCCTGGATGGGCCTGCCCGCCGAGACCGTCTACATCGCCTCGGACATCGACGCCCGCCTGGTCGGCTTCGTGGACGAGGCCCTGACCCGACTCAATGTTCCACATCGGACGAACGTGGCCGACCTGCTCGAGGACCGTCTTGACGAGCCGGCCGACGTCACGCTATTGCTGAAGACGCTGCCCTGTCTGGAGACTCAGCAACGAGGATCGGGCTGGGAAGTGATTGACATTGTCAACTCGCCGAATATCGTGGTAACCTTCCCGACCAAGTCTCTCGGTCAGCGATCGAAGGGGATGTTTCAGAACTATTCACAGAGTTTTGAGTCCCAGGCCAGAGAGCGGTCATGCCGTATTCAGCGACTGGAGATTGGCAACGAGCTGATTTACGTCATTCAGAAATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40607","NCBI_taxonomy_name":"Micromonospora zionensis","NCBI_taxonomy_id":"1879"}}}},"ARO_accession":"3000862","ARO_id":"37242","ARO_name":"sgm","ARO_description":"Sgm, or sisomicin-gentamicin methyltransferase, methylates G1405 of 16S rRNA to confer resistance to various aminoglycosides.","ARO_category":{"41435":{"category_aro_accession":"3004271","category_aro_cvterm_id":"41435","category_aro_name":"16S rRNA methyltransferase (G1405)","category_aro_description":"Methyltransferases that methylate the G1405 position of 16S rRNA, which is part of an aminoglycoside binding site.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2081":{"model_id":"2081","model_name":"patA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"3692":{"protein_sequence":{"accession":"NP_417544.5","sequence":"MNRLPSSASALACSAHALNLIEKRTLDHEEMKALNREVIEYFKEHVNPGFLEYRKSVTAGGDYGAVEWQAGSLNTLVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAMLAKTLAALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRGKFTFIATSGAFHGKSLGALSATAKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLNNAKTIRIEPPLTLTIEQCELVIKAARKALAAMRVSVEEA"},"dna_sequence":{"accession":"NC_000913.3","fmin":"3219493","fmax":"3220873","strand":"+","sequence":"TTGAACAGGTTACCTTCGAGCGCATCGGCTTTAGCGTGCAGCGCCCACGCCCTGAATCTCATTGAGAAGCGAACGCTGGATCATGAGGAGATGAAAGCACTTAACCGAGAGGTGATTGAATACTTCAAAGAGCATGTCAATCCGGGGTTTTTAGAGTATCGCAAATCTGTTACCGCCGGCGGGGATTACGGAGCCGTAGAGTGGCAAGCGGGAAGTTTAAATACGCTTGTCGACACCCAGGGCCAGGAGTTTATCGACTGCCTGGGAGGTTTTGGAATTTTCAACGTGGGGCACCGTAATCCAGTTGTGGTTTCCGCCGTACAGAATCAACTTGCGAAACAACCGCTGCACAGCCAGGAGCTGCTCGATCCGTTACGGGCGATGTTGGCGAAAACCCTTGCTGCGCTAACGCCCGGTAAACTGAAATACAGCTTCTTCTGTAATAGCGGCACCGAGTCCGTTGAAGCAGCGCTGAAGCTGGCGAAAGCTTACCAGTCACCGCGCGGCAAGTTTACTTTTATTGCCACCAGCGGCGCGTTCCACGGTAAATCACTTGGCGCGCTGTCGGCCACGGCGAAATCGACCTTCCGCAAACCGTTTATGCCGTTACTGCCGGGCTTCCGTCATGTGCCGTTTGGCAATATCGAAGCCATGCGCACGGCTCTTAACGAGTGCAAAAAAACCGGTGATGATGTGGCTGCGGTGATCCTCGAACCGATTCAGGGTGAAGGTGGCGTAATTCTGCCGCCGCCGGGCTATCTCACCGCCGTACGTAAGCTATGCGATGAGTTCGGCGCACTGATGATCCTCGATGAAGTACAAACGGGCATGGGGCGCACGGGCAAGATGTTCGCCTGCGAGCATGAGAACGTACAGCCGGATATCCTCTGCCTTGCCAAAGCGCTCGGCGGCGGCGTGATGCCGATTGGCGCGACCATCGCCACTGAAGAGGTGTTTTCAGTTCTGTTCGACAACCCATTCCTGCATACCACCACCTTTGGCGGCAACCCGCTGGCCTGTGCGGCGGCGCTGGCGACCATCAATGTGTTGCTGGAGCAGAACTTACCGGCTCAGGCTGAGCAAAAAGGCGATATGTTGCTGGACGGTTTCCGTCAACTGGCGCGGGAATATCCCGATCTGGTACAGGAAGCGCGTGGTAAAGGGATGTTGATGGCGATTGAGTTTGTTGATAACGAAATCGGCTATAACTTTGCCAGCGAGATGTTCCGCCAGCGCGTACTGGTGGCCGGAACGCTCAATAACGCCAAAACGATCCGCATTGAACCGCCACTGACACTGACCATTGAACAGTGTGAACTGGTGATCAAAGCGGCGCGTAAGGCGCTGGCGGCCATGCGAGTAAGTGTCGAAGAAGCGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3000024","ARO_id":"36033","ARO_name":"patA","ARO_description":"PatA is an ABC transporter of Streptococcus pneumoniae that interacts with PatB to confer fluoroquinolone resistance.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2087":{"model_id":"2087","model_name":"aadA13","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"3363":{"protein_sequence":{"accession":"YP_009081591.1","sequence":"MRDSVTAEISTQLSKVLSVIEHHLEPTLLAVHLYGSAVDGGLKPYSDIDLLVTVTARLDDTTRRALFNDLLEVSAFPGESEILRAIEVTIVVHEDIMPWRYPAKRELQFGEWQRNDILAGIFEPATIDIDLAILLTKAREHSVALVGPAAEELFDPVPEQDLIKALNETLKLWNSQPDWAGDERNVVLTLSRIWYSAATGKIAPKDVAANWAMEHLPAQHQSVLLEARQAYLGQEEDRSVLRADKLEEFIHFMKSEITKVLGNDV"},"dna_sequence":{"accession":"NG_036525","fmin":"633","fmax":"1431","strand":"+","sequence":"ATGAGGGACTCAGTGACCGCCGAAATTTCGACGCAACTATCCAAGGTGCTTAGTGTTATCGAGCACCATCTGGAACCGACGTTGCTTGCCGTACATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCATACAGTGATATTGATTTGCTGGTTACTGTGACCGCAAGGCTTGATGACACAACGCGGCGAGCTTTGTTCAACGATCTTTTGGAGGTTTCGGCTTTCCCAGGCGAGAGTGAGATTCTCCGCGCTATAGAAGTCACCATTGTCGTGCACGAAGACATTATGCCGTGGCGTTATCCAGCCAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCGGGTATCTTCGAGCCAGCCACGATCGACATCGATCTGGCTATCTTGCTAACGAAAGCGAGAGAACATAGCGTGGCTTTGGTAGGTCCGGCGGCGGAGGAACTCTTTGATCCAGTTCCTGAACAAGATCTAATCAAGGCGCTGAATGAAACCTTGAAGCTATGGAACTCGCAGCCCGACTGGGCCGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAGCAACTGGTAAAATCGCGCCGAAGGATGTCGCTGCCAACTGGGCAATGGAACATCTACCTGCCCAGCATCAGTCTGTCTTGCTTGAAGCTAGACAGGCTTATCTTGGGCAAGAGGAAGATCGCTCGGTCTTGCGCGCAGATAAGTTGGAAGAATTTATTCACTTCATGAAAAGCGAGATCACCAAGGTGCTCGGCAATGATGTCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002613","ARO_id":"39013","ARO_name":"aadA13","ARO_description":"aadA13 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids and integrons in Pseudomonas rettgeri, P. aeruginosa, Y. enterocolitica and E. coli","ARO_category":{"41439":{"category_aro_accession":"3004275","category_aro_cvterm_id":"41439","category_aro_name":"ANT(3'')","category_aro_description":"Nucleotidylylation of streptomycin at the hydroxyl group at position 3''","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2103":{"model_id":"2103","model_name":"SHV-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"3691":{"protein_sequence":{"accession":"WP_063864673.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQLQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"NG_050068","fmin":"100","fmax":"961","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACTGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGGATCGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001062","ARO_id":"37442","ARO_name":"SHV-3","ARO_description":"SHV-3 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2110":{"model_id":"2110","model_name":"CARB-20","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"3694":{"protein_sequence":{"accession":"WP_020835015.1","sequence":"MKKLFLLVGLMVCSTVSYASKLNEDISLIEKQTSGRIGVSVWDTQTDERWDYRGDERFPLMSTFKTLACATMLSDMDSGKLNKNATARIDERNIVVWSPVMDKLAGQSTRIEHACEAAMLMSDNTAANLVLNEIGGPKAVTLFLRSIGDKATRLDRLEPRLNEAKPGDKRDTTTPNAMVNTLHTLMEDNALSYESRTQLKIWMQDNKVSDSLMRSVLPKGWSIADRSGAGNYGSRGISAMIWKDNYKPVYISIYVTDTDLSLQARDQLIAQISQLILEHYKES"},"dna_sequence":{"accession":"NG_048723.1","fmin":"0","fmax":"1052","strand":"+","sequence":"ATCGACAGGGATTTAACAGTGGTTAGAGTATTCACTCGTTATAGTTTGCTTAACATCGCCAAAGTGCGAATCAAAACCAAAAGAATGAAGAACACCACGCATGAAAAAGTTATTCCTGTTGGTTGGGCTGATGGTTTGCTCAACTGTTAGTTACGCCTCCAAATTAAACGAAGACATCTCCCTCATCGAGAAACAAACATCTGGGCGAATTGGAGTGTCAGTCTGGGATACACAAACGGACGAGCGTTGGGATTATCGCGGAGACGAACGTTTCCCATTAATGAGCACATTCAAAACGTTAGCGTGTGCCACCATGCTAAGCGACATGGACAGCGGCAAACTCAACAAAAATGCCACAGCGAGAATCGATGAACGCAATATTGTGGTTTGGTCTCCGGTGATGGATAAACTGGCTGGACAAAGCACGCGTATCGAACACGCTTGTGAAGCCGCCATGTTGATGAGCGACAACACCGCCGCAAACTTAGTGCTAAATGAAATTGGTGGTCCTAAAGCGGTCACGCTGTTTTTGCGCTCTATTGGCGACAAAGCAACGCGACTTGACCGATTGGAGCCCCGTTTGAACGAAGCAAAACCGGGCGACAAGCGAGACACCACAACGCCTAACGCCATGGTAAACACCCTACACACCTTGATGGAAGATAACGCCCTATCTTACGAGTCACGCACACAGCTGAAAATCTGGATGCAAGACAACAAAGTATCGGATTCTCTCATGCGCTCTGTTCTACCAAAAGGCTGGTCGATTGCAGACCGCTCTGGCGCAGGTAACTACGGTTCACGCGGCATTAGCGCGATGATTTGGAAAGACAACTACAAGCCGGTTTACATCAGTATTTACGTCACAGATACTGACCTTTCGCTTCAAGCTCGCGATCAACTGATCGCGCAAATCAGCCAACTGATTTTAGAGCACTACAAAGAAAGTTAAGCTCGAACTCGAGCAACCAAGCCCTTCTCATTCAGAGGGGCTTTTTCTTACCTGCTCTCTCAAATTCTTAACAAATCTCTCTTATTCTTGCTGTCTTCAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37072","NCBI_taxonomy_name":"Vibrio","NCBI_taxonomy_id":"662"}}}},"ARO_accession":"3003150","ARO_id":"39727","ARO_name":"CARB-20","ARO_description":"CARB-20 is a beta-lactamase found worldwide in Vibrio parahaemolyticus","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2112":{"model_id":"2112","model_name":"patB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"770"}},"model_sequences":{"sequence":{"3693":{"protein_sequence":{"accession":"NP_358969.1","sequence":"MGKYDFTSLPNRLGHHTYKWKETETDSEVLPAWIADMDFVVLPEIHQAVQTYADQLVYGYTYASEDLIKEVQKWEATQYGYNFDKEALVFIEGVVPAISTAIQTFTKEGEAVLINTPVYPPFARSVKLNNRRLITNSLVEKDSLFEIDFDQLEKDLVEEEVKLYVLCNPHNPGGRVWEKEVLEKIGQLCQKHGVLLVSDEIHQDLTLFGHKHQSFNTINPAFKNFAIVLSSATKTFNIAGTKNSYAVIENPKLRLAFQKRLLANNQHEISGLGYLATEAAYRYGKDWLEELKQVFEDHINYVVDLFGKETKIKVMKPQGTYLIWLDFSAYDLTDETLQELLRNEAKVILNRGLDFGEEGSLHARINIAMPKSLLQEVCQRIVATFAKC"},"dna_sequence":{"accession":"NC_003098.1","fmin":"1359228","fmax":"1360395","strand":"-","sequence":"TTAACATTTGGCAAAAGTAGCCACAATCCGCTGACAGACTTCTTGCAACAGAGATTTGGGCATAGCTATATTGATGCGGGCATGGAGACTTCCTTCCTCTCCAAAATCCAAACCACGGTTGAGGATAACCTTGGCTTCATTTCTCAACAACTCTTGCAATGTTTCATCAGTCAGGTCATAAGCTGAAAAGTCAAGCCAAATCAAGTAGGTACCTTGCGGTTTCATGACCTTGATTTTAGTCTCTTTTCCAAATAGATCCACCACATAATTGATGTGGTCTTCAAAGACTTGCTTGAGTTCCTCTAGCCAATCTTTACCGTATCGATAGGCAGCTTCTGTCGCCAAATAACCCAAGCCTGAAATTTCATGCTGATTATTGGCCAACAGGCGTTTCTGGAAAGCCAGTCTCAACTTAGGATTTTCAATGACTGCATAGGAATTTTTTGTTCCAGCAATATTAAATGTTTTAGTGGCACTGCTCAAGACGATAGCAAAATTTTTGAAGGCAGGATTGATGGTATTGAAAGACTGGTGTTTGTGACCAAAGAGGGTCAAATCTTGGTGAATCTCATCCGAAACTAACAAAACACCGTGTTTTTGGCAGAGTTGGCCAATCTTCTCCAACACTTCTTTTTCCCAAACACGTCCACCAGGATTGTGAGGGTTGCAAAGAACATAGAGTTTAACCTCCTCTTCCACCAAATCCTTTTCAAGTTGGTCAAAGTCAATCTCAAACAGACTATCCTTTTCCACTAAGGAATTAGTAATCAATCTACGATTATTCAACTTGACACTGCGAGCAAAGGGTGGGTAGACAGGCGTGTTAATTAAAACCGCCTCGCCTTCTTTTGTAAAGGTTTGAATAGCTGTTGAGATGGCTGGTACCACACCCTCGATAAAGACAAGAGCCTCTTTGTCAAAGTTGTAACCGTATTGTGTAGCTTCCCACTTTTGAACTTCCTTAATTAAGTCTTCACTGGCATAGGTATAACCATAAACCAGTTGGTCTGCGTAAGTTTGCACGGCTTGGTGGATTTCAGGCAAGACTACAAAGTCCATATCCGCTATCCAAGCTGGTAGAACTTCACTATCCGTTTCTGTTTCTTTCCATTTATAGGTATGGTGCCCTAAACGGTTGGGCAGGCTTGTAAAATCATATTTTCCCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39596","NCBI_taxonomy_name":"Streptococcus pneumoniae R6","NCBI_taxonomy_id":"171101"}}}},"ARO_accession":"3000025","ARO_id":"36034","ARO_name":"patB","ARO_description":"PatB is an ABC transporter of Streptococcus pneumoniae that interacts with PatA to confer fluoroquinolone resistance..","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2114":{"model_id":"2114","model_name":"APH(3')-IIa","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4436":{"protein_sequence":{"accession":"WP_000572405.1","sequence":"MIEQDGLHAGSPAAWVERLFGYDWAQQTIGCSDAAVFRLSAQGRPVLFVKTDLSGALNELQDEAARLSWLATTGVPCAAVLDVVTEAGRDWLLLGEVPGQDLLSSHLAPAEKVSIMADAMRRLHTLDPATCPFDHQAKHRIERARTRMEAGLVDQDDLDEEHQGLAPAELFARLKARMPDGEDLVVTHGDACLPNIMVENGRFSGFIDCGRLGVADRYQDIALATRDIAEELGGEWADRFLVLYGIAAPDSQRIAFYRLLDEFF"},"dna_sequence":{"accession":"V00618.1","fmin":"150","fmax":"945","strand":"+","sequence":"ATGATTGAACAAGATGGATTGCACGCAGGTTCTCCGGCCGCTTGGGTGGAGAGGCTATTCGGCTATGACTGGGCACAACAGACAATCGGCTGCTCTGATGCCGCCGTGTTCCGGCTGTCAGCGCAGGGGCGCCCGGTTCTTTTTGTCAAGACCGACCTGTCCGGTGCCCTGAATGAACTGCAGGACGAGGCAGCGCGGCTATCGTGGCTGGCCACGACGGGCGTTCCTTGCGCAGCTGTGCTCGACGTTGTCACTGAAGCGGGAAGGGACTGGCTGCTATTGGGCGAAGTGCCGGGGCAGGATCTCCTGTCATCTCACCTTGCTCCTGCCGAGAAAGTATCCATCATGGCTGATGCAATGCGGCGGCTGCATACGCTTGATCCGGCTACCTGCCCATTCGACCACCAAGCGAAACATCGCATCGAGCGAGCACGTACTCGGATGGAAGCCGGTCTTGTCGATCAGGATGATCTGGACGAAGAGCATCAGGGGCTCGCGCCAGCCGAACTGTTCGCCAGGCTCAAGGCGCGCATGCCCGACGGCGAGGATCTCGTCGTGACCCATGGCGATGCCTGCTTGCCGAATATCATGGTGGAAAATGGCCGCTTTTCTGGATTCATCGACTGTGGCCGGCTGGGTGTGGCGGACCGCTATCAGGACATAGCGTTGGCTACCCGTGATATTGCTGAAGAGCTTGGCGGCGAATGGGCTGACCGCTTCCTCGTGCTTTACGGTATCGCCGCTCCCGATTCGCAGCGCATCGCCTTCTATCGCCTTCTTGACGAGTTCTTCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3002644","ARO_id":"39044","ARO_name":"APH(3')-IIa","ARO_description":"APH(3')-IIa is a transposon-encoded aminoglycoside phosphotransferase in E. coli","ARO_category":{"36265":{"category_aro_accession":"3000126","category_aro_cvterm_id":"36265","category_aro_name":"APH(3')","category_aro_description":"Phosphorylation of 2-deoxystreptamine aminoglycosides on the hydroxyl group at position 3'","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2115":{"model_id":"2115","model_name":"TEM-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4276":{"protein_sequence":{"accession":"WP_063864911.1","sequence":"MSIQHFRVALIPFFAAFCFPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASERGSRGIIAALGPDGKPSRIVVIYMTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"NG_050265","fmin":"100","fmax":"961","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCTTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACATGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000876","ARO_id":"37256","ARO_name":"TEM-4","ARO_description":"TEM-4 is an extended-spectrum beta-lactamase that has been found in clinical isolates.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2117":{"model_id":"2117","model_name":"AAC(6')-Ib7","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"3683":{"protein_sequence":{"accession":"AKN19287.1","sequence":"MRSRNWSRTLTERSGGNGAVAVFMACYDCFFVQSMPRASKQQARYAVGRCLMLWSSNDVTQQGSRPKTKLGITKYSIVTNSNDSVTLRLMTEHDLAMLYEWLNRSHIVEWWGGEEARPTLADVQEQYLPSVLAQESVTPYIAMLNGEPIGYAQSYVALGSGDGWWEEETDPGVRGIDQLLANASQLGKGLGTKLVRALVELLFNDPEVTKIQTDPSPSNLRAIRCYEKAGFERQGTVTTPDGPAVYMVQTRQAFERTRSDA"},"dna_sequence":{"accession":"Y11946.1","fmin":"0","fmax":"980","strand":"+","sequence":"CTGTTCGGTTCGTAAACTGTAATGCAAGTAGCGTATGCGCTCACGCAACTGGTCCAGAACCTTGACCGAACGCAGCGGTGGTAACGGCGCAGTGGCGGTTTTCATGGCTTGTTATGACTGTTTTTTTGTACAGTCTATGCCTCGGGCATCCAAGCAGCAAGCGCGTTACGCCGTGGGTCGATGTTTGATGTTATGGAGCAGCAACGATGTTACGCAGCAGGGCAGTCGCCCTAAAACAAAGTTAGGCATCACAAAGTACAGCATCGTGACCAACAGCAACGATTCCGTCACACTGCGCCTCATGACTGAGCATGACCTTGCGATGCTCTATGAGTGGCTAAATCGATCTCATATCGTCGAGTGGTGGGGCGGAGAAGAAGCACGCCCGACACTTGCTGACGTACAGGAACAGTACTTGCCAAGCGTTTTAGCGCAAGAGTCCGTCACTCCATACATTGCAATGCTGAATGGAGAGCCGATTGGGTATGCCCAGTCGTACGTTGCTCTTGGAAGCGGGGACGGATGGTGGGAAGAAGAAACCGATCCAGGAGTACGCGGAATAGACCAGTCACTGGCGAATGCATCACAACTGGGCAAAGGCTTGGGAACCAAGCTGGTTCGAGCTCTGGTTGAGTTGCTGTTCAATGATCCCGAGGTCACCAAGATCCAAACGGACCCGTCGCCGAGCAACTTGCGAGCGATCCGATGCTACGAGAAAGCGGGGTTTGAGAGGCAAGGTACCGTAACCACCCCAGATGGTCCAGCCGTGTACATGGTTCAAACACGCCAGGCATTCGAGCGAACACGCAGTGATGCCTAACCCTTCCATCGAGGACGTCCACGGGCTGGCGCCTTGGCCGCCCCTCATGTCAAACGTTAGACATCATGAGGGTAGCGGTGACCATCGAAATTTCGAACCAACTATCAGAGGTGCTAAGCGTCATTGAGCGCCATCTGGAATCAACGTTGCTGGCCGTGCA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35906","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Corvallis","NCBI_taxonomy_id":"593905"}}}},"ARO_accession":"3002578","ARO_id":"38978","ARO_name":"AAC(6')-Ib7","ARO_description":"AAC(6')-Ib7 is a plasmid-encoded aminoglycoside acetyltransferase in E. cloacae and C. freundii","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2119":{"model_id":"2119","model_name":"LRA-10","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"3697":{"protein_sequence":{"accession":"ACH58999.1","sequence":"MAIAILSSCFAPLASRAADDSARIRAIVDQAIRPVMAEHDVPGMAVAVTVDGQPFVFNYGVASRESNTPVSDATLFELGSISKTFAATLASYAQVTGKLSLDDHPGKYMPQLKGSAIDKATLLNLGTYTAGGLPLQFPDDVSDQQMASYFQHWKPKAAPGVQRTYSNPSLGLFGHLTSLALKSRFTDALETNVLTQMGMKSTYVHVPQSAMANYAWGYDQANKPGRMNPGVLADGIYGIRSTAADMIRYVQANIAPGKLETPLRRAVEGTHVGYFKVGGMVQGLGWEQYPYPVSLQQLQAGNSTTMAWEANPAQKLTPPSVPSGATLFNKTGSTSRFGAYVAFVPEKKIGIVILANKNIPGPDRIKAAHAILEQL"},"dna_sequence":{"accession":"EU408357.1","fmin":"52","fmax":"1180","strand":"-","sequence":"TTACAGTTGTTCCAGGATCGCATGGGCCGCCTTGATACGGTCCGGACCCGGGATGTTCTTGTTCGCGAGGATGACGATGCCGATTTTCTTCTCCGGCACGAACGCCACGTAGGCGCCGAAGCGGCTGGTGGAGCCGGTCTTGTTGAACAGGGTCGCGCCGGACGGTACGCTCGGCGGCGTGAGTTTCTGCGCGGGGTTGGCTTCCCATGCCATGGTGGTGGAGTTGCCGGCCTGTAGCTGCTGCAGGGAGACCGGGTAAGGGTATTGCTCCCAGCCGAGTCCCTGCACCATGCCGCCCACCTTGAAGTAGCCGACATGGGTGCCTTCCACCGCGCGCCGCAACGGCGTTTCCAGCTTGCCCGGGGCGATGTTGGCTTGCACATAGCGGATCATGTCGGCGGCTGTCGACCGGATGCCATAGATTCCGTCGGCGAGGACGCCGGGGTTCATGCGGCCAGGCTTGTTTGCTTGATCGTATCCCCAGGCGTAATTGGCCATGGCGCTTTGTGGCACGTGGACATAGGTGCTCTTCATGCCCATCTGCGTGAGGACATTCGTTTCCAGCGCGTCGGTAAAACGGCTCTTCAGCGCAAGGCTGGTCAGGTGTCCGAACAGCCCGAGGCTGGGATTGGAATAGGTCCGTTGTACGCCGGGCGCGGCCTTCGGTTTCCAGTGCTGGAAGTAGCTGGCCATCTGCTGGTCCGAGACGTCGTCCGGGAATTGCAGCGGCAGTCCGCCCGCCGTGTAGGTGCCCAGATTGAGCAGGGTGGCCTTGTCGATCGCGCTGCCCTTCAGCTGCGGCATGTACTTGCCGGGATGGTCGTCCAGCGACAGCTTGCCGGTCACCTGCGCATACGAGGCCAGCGTGGCGGCAAAAGTCTTGCTGATGGAGCCGAGCTCGAACAGCGTCGCGTCGCTGACGGGCGTGTTGCTCTCGCGCGAGGCGACGCCATAGTTGAAGACGAACGGTTGGCCGTCGACCGTCACGGCGACCGCCATGCCCGGCACGTCGTGTTCGGCCATGACGGGGCGTATCGCCTGGTCGACGATGGCGCGGATCCTGGCGCTGTCGTCGGCGGCCCGGCTGGCGAGCGGCGCGAAACAGGAAGACAGGATGGCGATTGCCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39682","NCBI_taxonomy_name":"uncultured bacterium BLR10","NCBI_taxonomy_id":"506513"}}}},"ARO_accession":"3002489","ARO_id":"38889","ARO_name":"LRA-10","ARO_description":"LRA-10 is a beta-lactamase isolated from soil samples in Alaska","ARO_category":{"41395":{"category_aro_accession":"3004231","category_aro_cvterm_id":"41395","category_aro_name":"class C LRA beta-lactamase","category_aro_description":"Beta-lactamases that are part of the LRA gene family and are classified as Class C beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2121":{"model_id":"2121","model_name":"LRA-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"3698":{"protein_sequence":{"accession":"ACH58998.1","sequence":"MRSKFLLATALVLSTAFTADAADAPKRLPVNITNQDWLKPFPGFKIVGNMYYVGTYDLGCYLIDTGAGLILVNTGIMGSYPLMKASIESLGFKTSDIKIITATHGHSDHVADMASFKKDAPSAVVYMSERDVESLESGGNFDYRRPAPEGRGGLVYDPIHVDVKTKPGDHIKLGNVDMTVLQAYGHTPGATSFQFQQTDAGKTYNVMIVNMNGINAGVKLLGSPKYPTIVEDFKNTIDMQATYKPDIWVSSHAGQFNLHQVYKPGDAYNPARFGDQAAYQQKIATAKANYEKQLAEERAAAK"},"dna_sequence":{"accession":"EU408356.1","fmin":"7570","fmax":"8479","strand":"+","sequence":"ATGCGGTCGAAATTCCTGCTTGCTACTGCGCTCGTTCTGTCGACGGCCTTCACCGCCGATGCAGCAGACGCGCCGAAGCGCCTTCCCGTCAACATCACCAACCAGGATTGGCTGAAGCCGTTTCCGGGATTCAAGATCGTCGGCAACATGTATTATGTCGGCACCTACGATCTCGGCTGCTACCTGATCGATACCGGCGCAGGGCTGATCCTCGTCAACACCGGCATCATGGGTTCCTACCCGCTGATGAAGGCGAGCATCGAATCCCTCGGCTTCAAGACCAGCGACATCAAGATTATCACCGCGACGCATGGCCATTCCGACCATGTCGCCGATATGGCGTCGTTCAAGAAGGACGCGCCGAGCGCCGTCGTCTATATGAGCGAGCGCGATGTGGAGAGCCTCGAAAGCGGCGGTAATTTCGATTACCGCCGCCCCGCACCGGAAGGCCGTGGCGGTCTCGTCTATGATCCCATCCATGTCGATGTGAAGACGAAGCCCGGCGATCACATCAAGCTCGGCAATGTCGATATGACCGTGCTGCAGGCCTATGGCCACACGCCGGGCGCGACGAGCTTCCAATTCCAGCAGACGGATGCGGGCAAGACCTACAATGTGATGATCGTGAACATGAACGGCATCAACGCCGGCGTTAAGCTGCTGGGTTCGCCGAAATATCCGACCATCGTCGAGGACTTCAAGAACACCATCGACATGCAGGCGACGTACAAGCCCGACATCTGGGTGTCGTCGCATGCGGGGCAGTTCAACCTGCATCAGGTCTATAAGCCGGGCGATGCGTACAATCCGGCCCGCTTCGGCGATCAGGCCGCCTATCAGCAGAAGATCGCGACCGCGAAGGCGAATTACGAGAAGCAGCTCGCCGAGGAACGCGCGGCGGCGAAATGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39087","NCBI_taxonomy_name":"uncultured bacterium BLR7","NCBI_taxonomy_id":"506523"}}}},"ARO_accession":"3002486","ARO_id":"38886","ARO_name":"LRA-7","ARO_description":"LRA-7 is a beta-lactamase isolated from soil samples in Alaska","ARO_category":{"41390":{"category_aro_accession":"3004226","category_aro_cvterm_id":"41390","category_aro_name":"subclass B3 LRA beta-lactamase","category_aro_description":"Beta-lactamases that are part of the LRA gene family and are classified as B3 (metallo-) beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2123":{"model_id":"2123","model_name":"vgaC","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"110"}},"model_sequences":{"sequence":{"3686":{"protein_sequence":{"accession":"AMP35312.1","sequence":"MRTVSIFKNGNNRAIRLPRDLDFDGVSELEIVREGDSIILRPVRPTWGSFAQLDRADPDFMAEREDVVSDEGRFEP"},"dna_sequence":{"accession":"KU302801","fmin":"102199","fmax":"102430","strand":"+","sequence":"ATGCGCACAGTTTCGATATTTAAAAACGGCAATAACCGCGCCATCCGTCTGCCCCGGGACCTGGATTTTGATGGCGTCAGCGAGCTGGAGATCGTCCGGGAAGGGGACAGCATCATTCTGCGTCCCGTCCGGCCGACCTGGGGCTCGTTCGCGCAGCTGGACAGGGCCGATCCGGACTTTATGGCGGAGCGTGAGGATGTGGTCAGCGATGAAGGACGCTTTGAGCCATGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3002831","ARO_id":"39265","ARO_name":"vgaC","ARO_description":"vgaC is an efflux protein expressed in staphylococci that confers resistance to streptogramin A antibiotics and related compounds. It is associated with plasmid DNA.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37716":{"category_aro_accession":"3001317","category_aro_cvterm_id":"37716","category_aro_name":"pleuromutilin","category_aro_description":"Pleuromutilin is a natural product antibiotic produced by Clitopilus passeckerianus. Related antibiotics of clinical significance, such as tiamulin and retapamulin, are semi-synthetic derivatives of this compound.","category_aro_class_name":"Antibiotic"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2130":{"model_id":"2130","model_name":"opcM","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"980"}},"model_sequences":{"sequence":{"3687":{"protein_sequence":{"accession":"AAC43969.1","sequence":"MDNMHNTNGLMRFAKVAAASTLLATLLAACAVGPDYQRPDAVVPAAFKEAPTLAAGEQAGTWKTAEPSDGRTPRRMVKVFGDPVLDSLETQALAANQNLKAAAARVEEARAATRSARSQWFPQVGAGFGPTREGLSSASQFQPQGTGPTNATLWRAQGTVSYEADLFGRVGRNVEASRADQAQSEALFRSVQLALQADVAQNYFELRQLDSDQDLYHRTVELREQALKLVQRRFNEGDISELDVSRAKNELASAQADAVDVARRRAASEHALAILLGKAPADFAFKETPIVPVAVKIPPGLPSALLERRPDVSAAERAMAAANARIGLAKSAYFRSSISPGRSAISVDARQPVPVVEPYFLLGPFAGTALTLPLFDGGRRAAGVQQARAQYDEQGANYRQQVLVAFREVEDNLADLRLLDDQIRAQEAAVNASRRAATLSRSEYQEGEVAYLDVIDSERSVLQSQLQANQLTGAQAVSTVNLIRALGGGWGNAPAPTAVGDAASGKADVAAR"},"dna_sequence":{"accession":"U38944.1","fmin":"0","fmax":"1536","strand":"+","sequence":"ATGGACAACATGCACAACACGAACGGCCTGATGCGCTTCGCGAAGGTGGCGGCCGCGAGCACCCTGCTCGCGACGCTGCTCGCCGCGTGTGCGGTCGGCCCCGACTACCAGCGTCCCGACGCGGTGGTGCCCGCCGCGTTCAAGGAAGCGCCGACCCTCGCCGCCGGCGAGCAGGCCGGCACGTGGAAGACGGCCGAGCCGTCGGATGGCCGAACACCGCGGCGAATGGTGAAGGTGTTCGGCGACCCGGTGCTCGATTCGCTCGAGACGCAGGCGCTTGCCGCGAACCAGAACCTGAAGGCCGCGGCCGCGCGGGTCGAGGAAGCGCGGGCGGCGACGCGTTCGGCGCGCTCGCAATGGTTCCCGCAGGTCGGCGCCGGTTTCGGGCCGACGCGCGAGGGGCTGTCGTCGGCGTCGCAGTTCCAGCCGCAGGGCACCGGCCCGACCAACGCGACGCTGTGGCGCGCGCAGGGCACGGTGTCGTACGAAGCCGATCTGTTCGGCCGCGTCGGCCGCAACGTCGAGGCGTCGCGTGCCGATCAGGCGCAGAGCGAAGCGCTGTTCCGTTCGGTGCAGCTCGCGCTGCAGGCCGACGTCGCGCAGAACTACTTCGAACTGCGTCAGCTCGATTCGGACCAGGACCTGTACCACCGCACGGTCGAGTTGCGCGAGCAGGCACTGAAGCTCGTGCAGCGCCGCTTCAACGAAGGCGACATCAGCGAGCTCGACGTGTCGCGCGCGAAGAACGAACTGGCGAGCGCGCAGGCCGATGCGGTCGACGTCGCGCGCCGGCGCGCGGCGTCCGAGCATGCGCTCGCCATCCTGCTCGGCAAGGCGCCCGCGGATTTCGCGTTCAAGGAAACGCCGATCGTGCCGGTCGCGGTGAAGATTCCGCCGGGCCTGCCGTCCGCGCTGCTCGAACGCCGCCCGGACGTGTCGGCGGCCGAACGCGCGATGGCGGCCGCGAACGCGCGGATCGGGCTCGCGAAGTCGGCGTACTTCCGAAGCTCGATATCACCGGGTCGTTCGGCTATAAGCGTCGACGCTCGGCAACCTGTTCCTGTGGTCGAGCCGTACTTCCTGCTCGGGCCGTTCGCCGGTACCGCGCTGACGTTGCCGCTGTTCGACGGCGGACGGCGGGCGGCCGGCGTGCAGCAGGCGCGCGCGCAGTACGACGAGCAGGGCGCGAACTACCGGCAGCAGGTGCTCGTCGCGTTCCGCGAGGTCGAGGACAATCTCGCCGATCTGCGTTTGCTCGATGATCAGATCCGCGCGCAGGAGGCGGCCGTCAATGCGTCGCGCCGGGCGGCGACGTTGTCGCGCAGCGAATATCAGGAAGGCGAGGTCGCATATCTCGACGTGATCGACAGCGAGCGCTCGGTGCTGCAGTCGCAGTTGCAGGCGAACCAGTTGACGGGTGCGCAGGCGGTGTCGACCGTCAATCTGATCCGTGCGCTGGGCGGCGGGTGGGGGAATGCGCCGGCGCCGACGGCGGTGGGTGATGCGGCGTCTGGCAAGGCTGACGTAGCTGCGCGG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36822","NCBI_taxonomy_name":"Burkholderia cepacia","NCBI_taxonomy_id":"292"}}}},"ARO_accession":"3003037","ARO_id":"39471","ARO_name":"opcM","ARO_description":"OpcM is an outer membrane factor protein found in Burkholderia cepacia. It is part of the CeoAB-OpcM complex.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2134":{"model_id":"2134","model_name":"CMY-36","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3695":{"protein_sequence":{"accession":"ABY58049.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDCIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPENEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"EU331426.1","fmin":"2374","fmax":"3520","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACTGTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCTTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCAGAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCACAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002047","ARO_id":"38447","ARO_name":"CMY-36","ARO_description":"CMY-36 is a beta-lactamase found in Klebsiella pneumoniae","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2135":{"model_id":"2135","model_name":"ACT-33","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3684":{"protein_sequence":{"accession":"AIT76087.1","sequence":"MMKKSLCCALLLGISCSALATPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILDALQ"},"dna_sequence":{"accession":"KM087834.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCTCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCACGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTAGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCACATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAACGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAGGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGACGCGCTACAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001853","ARO_id":"38253","ARO_name":"ACT-33","ARO_description":"ACT-33 is a beta-lactamase. From the Lahey list of ACT beta-lactamases.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2138":{"model_id":"2138","model_name":"NmcA beta-lactamase","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"3362":{"protein_sequence":{"accession":"CAA79967.1","sequence":"MSLNVKQSRIAILFSSCLISISFFSQANTKGIDEIKNLETDFNGRIGVYALDTGSGKSFSYRANERFPLCSSFKGFLAAAVLKGSQDNRLNLNQIVNYNTRSLEFHSPITTKYKDNGMSLGDMAAAALQYSDNGATNIILERYIGGPEGMTKFMRSIGDEDFRLDRWELDLNTAIPGDERDTSTPAAVAKSLKTLALGNILSEHEKETYQTWLKGNTTGAARIRASVPSDWVVGDKTGSCGAYGTANDYAVVWPKNRAPLIISVYTTKNEKEAKHEDKVIAEASRIAIDNLK"},"dna_sequence":{"accession":"Z21956","fmin":"1220","fmax":"2099","strand":"+","sequence":"ATGTCACTTAATGTAAAGCAAAGTAGAATAGCCATCTTGTTTAGCTCTTGTTTAATTTCAATATCATTTTTCTCACAGGCCAATACGAAGGGCATTGATGAGATTAAAAACCTTGAAACAGATTTCAATGGCAGGATTGGTGTCTACGCTTTAGACACTGGCTCGGGTAAATCATTTTCGTACAGAGCAAATGAACGATTTCCATTATGTAGTTCTTTTAAAGGTTTTTTAGCTGCTGCTGTATTAAAAGGCTCTCAAGATAATCGACTTAATCTTAATCAGATTGTGAATTATAATACAAGAAGTTTAGAGTTCCATTCACCCATCACAACTAAATATAAAGATAATGGAATGTCATTAGGTGATATGGCTGCTGCTGCTTTACAATATAGCGACAATGGTGCTACTAATATTATTCTTGAACGTTATATCGGTGGTCCAGAGGGTATGACTAAATTCATGCGGTCGATTGGAGATGAAGATTTTAGACTCGATCGTTGGGAGTTAGATCTAAACACAGCTATTCCAGGCGATGAGCGTGACACATCTACACCTGCAGCAGTAGCCAAGAGTCTGAAAACCCTTGCTCTGGGTAACATACTTAGTGAACATGAAAAGGAAACCTATCAGACATGGTTAAAGGGTAACACAACCGGTGCAGCGCGTATTCGTGCTAGCGTACCAAGCGATTGGGTAGTTGGCGATAAAACTGGTAGTTGCGGAGCATACGGTACGGCAAATGATTATGCGGTAGTCTGGCCAAAGAACCGGGCTCCTCTTATAATTTCTGTATACACAACAAAAAACGAAAAAGAAGCCAAGCATGAGGATAAAGTAATCGCAGAAGCTTCAAGAATTGCAATTGATAACCTTAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3003589","ARO_id":"40199","ARO_name":"NmcA","ARO_description":"NmcA is a class A serine beta-lactamase isolated from Enterobacter cloacae.","ARO_category":{"35996":{"category_aro_accession":"0000079","category_aro_cvterm_id":"35996","category_aro_name":"clavulanate","category_aro_description":"Clavulanic acid is a beta-lactamase inhibitor (marketed by GlaxoSmithKline, formerly Beecham) combined with penicillin group antibiotics to overcome certain types of antibiotic resistance. It is used to overcome resistance in bacteria that secrete beta-lactamase, which otherwise inactivates most penicillins.","category_aro_class_name":"Adjuvant"},"41359":{"category_aro_accession":"3004195","category_aro_cvterm_id":"41359","category_aro_name":"NmcA beta-lactamase","category_aro_description":"nmcA beta-lactamases are chromosomal-encoded Class A beta-lactamases first isolated from Enterobacter cloacae, specifically a clinical strain known as NOR-1. nmcA beta-lactamases have been shown to hydrolyze carbapenems.","category_aro_class_name":"AMR Gene Family"},"35927":{"category_aro_accession":"0000008","category_aro_cvterm_id":"35927","category_aro_name":"cefoxitin","category_aro_description":"Cefoxitin is a cephamycin antibiotic often grouped with the second generation cephalosporins. Cefoxitin is bactericidal and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. Cefoxitin's 7-alpha-methoxy group and 3' leaving group make it a poor substrate for most beta-lactamases.","category_aro_class_name":"Antibiotic"},"35975":{"category_aro_accession":"0000058","category_aro_cvterm_id":"35975","category_aro_name":"cefazolin","category_aro_description":"Cefazolin (INN), also known as cefazoline or cephazolin, is a first generation cephalosporin antibiotic. It is administered parenterally, and is active against a broad spectrum of bacteria.","category_aro_class_name":"Antibiotic"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2156":{"model_id":"2156","model_name":"NDM-14","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"3685":{"protein_sequence":{"accession":"AJP18054.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMGALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"KM210086.1","fmin":"9067","fmax":"9880","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGGCGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGATGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36948","NCBI_taxonomy_name":"Acinetobacter lwoffii","NCBI_taxonomy_id":"28090"}}}},"ARO_accession":"3003183","ARO_id":"39760","ARO_name":"NDM-14","ARO_description":"NDM-14 is a beta-lactamase found in Acinetobacter lwoffii.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1942":{"model_id":"1942","model_name":"BJP-1 beta-lactamase","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4315":{"protein_sequence":{"accession":"BAL75272.1","sequence":"MKKLTAALCALAFFATGAQAQTVKDFIAAVTKKWTTPFEPFQLIDNIYYVGTDGIAVYVIKTSQGLILMDTALPQSTGMIKDNITKLGLKVADIKIILNTHAHFDHTGGFAEVKKETGAQLIAGERDKPLLEGGYYPGDEKNEDLAFPAVKVDRTVKEGDKVTLGETTLTAHATPGHSPGCTSWEMTVKDGGQDRQVLFFCSGTVALNRLVGQPTHAGIVDDYRATYAKVKAMKIDVLLGPHPEVYGMQAKRAAMKDGAPNPFVKPGELATYATSLSEDFDKQLAKQTAALEKK"},"dna_sequence":{"accession":"AP012279","fmin":"2172316","fmax":"2173201","strand":"-","sequence":"CTATTTCTTCTCTAGCGCCGCTGTCTGCTTGGCGAGCTGCTTGTCGAAGTCCTCCGACAGGCTGGTCGCGTAGGTCGCGAGCTCGCCGGGCTTGACGAACGGGTTCGGTGCGCCGTCCTTCATTGCCGCGCGCTTGGCCTGCATGCCGTAGACTTCGGGATGCGGTCCGAGCAGGACGTCGATCTTCATCGCCTTCACCTTGGCATAGGTCGCGCGATAGTCGTCGACGATGCCGGCGTGGGTTGGCTGGCCGACCAGCCGGTTTAGCGCCACCGTGCCGCTGCAGAAGAACAGCACCTGGCGGTCCTGGCCGCCGTCCTTGACGGTCATCTCCCAGCTCGTGCAGCCCGGCGAGTGGCCGGGAGTGGCGTGCGCCGTCAGCGTGGTCTCACCAAGCGTGACCTTATCGCCTTCCTTCACGGTGCGATCGACCTTGACCGCGGGGAAGGCGAGATCCTCGTTCTTCTCGTCGCCGGGATAGTAGCCGCCTTCGAGCAGCGGCTTGTCGCGCTCGCCGGCGATGAGCTGCGCGCCGGTCTCCTTCTTGACCTCGGCGAAGCCGCCGGTGTGATCGAAATGCGCGTGCGTGTTGAGGATGATCTTGATGTCGGCGACCTTCAGGCCGAGCTTCGTGATGTTGTCCTTGATCATGCCGGTAGACTGTGGAAGCGCCGTGTCCATCAGGATCAGGCCTTGCGAGGTCTTGATGACGTAGACGGCGATGCCGTCGGTGCCGACATAATAGATGTTGTCGATCAGCTGGAACGGCTCGAACGGCGTGGTCCATTTCTTGGTGACCGCCGCAATGAAATCCTTGACCGTCTGCGCCTGCGCGCCCGTTGCGAAAAACGCCAGCGCACACAGCGCGGCCGTGAGCTTCTTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39673","NCBI_taxonomy_name":"Bradyrhizobium sp. S23321","NCBI_taxonomy_id":"335659"}}}},"ARO_accession":"3000856","ARO_id":"37236","ARO_name":"BJP-1","ARO_description":"BJP-1 is a subclass B3 ortholog found in Bradyrhizobium japonicum that hydrolyzes most beta-lactams except aztreonam, ticarcillin, and temocillin.","ARO_category":{"41383":{"category_aro_accession":"3004219","category_aro_cvterm_id":"41383","category_aro_name":"BJP beta-lactamase","category_aro_description":"BJP beta-lactamases are a subclass B3 family.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2092":{"model_id":"2092","model_name":"Enterobacter aerogenes acrR with mutation conferring multidrug antibiotic resistance","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2992":"R45C"},"clinical":{"2992":"R45C"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"410"},"40494":{"param_type":"frameshift mutation","param_description":"A frameshift is a type of genetic mutation caused by a nucleotide insertion or deletion \u2260 3 bases. This changes the grouping of codons and thus the reading frame during translation, resulting in a incomplete or inactive protein product. Many frameshift mutations generate downstream STOP codons, resulting in premature peptide translation termination. Frameshifts may also confer antibiotic resistance through partial or total protein loss-of-function. Frameshift mutations are included with relevant models when applicable, with the following notation: [wild-type AA][position]fs;[[wild-type AA][position]STOP], where AA is an amino acid. If the premature STOP codon position is unknown or does not exist, [wild-type AA][position]fs is sufficient. This parameter is currently not included in detection algorithms.","param_type_id":"40494","param_value":{"7538":"A47fs"}},"41343":{"param_type":"deletion mutation from nucleotide sequence","param_description":"A subtype of the deletion mutation detection model parameter. This parameter is used when a set of deletion mutations is reported in a nucleotide sequence format. Such mutations may be of variable length - possibly causing a frameshift, but not premature termination of functional knockout. Mutation parameters of this type are reported in the CARD with the notation: [-]nt[position]:[nucleotides].","param_type_id":"41343","param_value":{"8024":"-nt139:1"}}},"model_sequences":{"sequence":{"3573":{"protein_sequence":{"accession":"CAC35723.1","sequence":"MARKTKQQALETRQLILDVALRLFSQQGVSSTSLAAIAKAAGVTRGAIYWHFKNKSDLFNEIWSLSDASISDLEVEYRAKFPNDPLSVVREILVYILEATVVEERRRLMMEIIFHKCEFVGEMAVVQQAQRSLWLESYDRIEQTLKDCITAQQLPANLLTRRAAILMRSYLSGLMENWLFAPESFNLHAEARAYVDALIEMYQTCPSLRSSSEVMA"},"dna_sequence":{"accession":"AJ306389.1","fmin":"636","fmax":"1287","strand":"-","sequence":"TCAGGCCATGACCTCAGACGAACTTCGTAGCGACGGGCAGGTCTGATACATCTCAATCAGCGCATCGACATAAGCACGGGCTTCCGCATGAAGGTTAAAACTCTCTGGTGCAAAGAGCCAGTTTTCCATTAATCCGGAAAGATAACTGCGCATCAGAATTGCCGCACGGCGAGTGAGTAAATTCGCAGGTAATTGTTGAGCAGTGATACAATCTTTTAATGTTTGCTCAATACGATCGTAGCTTTCAAGCCATAAACTGCGCTGCGCTTGTTGGACAACGGCCATTTCTCCGACAAATTCGCATTTATGGAAGATGATTTCCATCATCAGGCGCCTACGCTCCTCTACTACCGTCGCTTCGAGGATATAAACCAGTATTTCGCGAACAACTGACAGTGGATCGTTAGGGAATTTTGCCCGATACTCAACTTCGAGATCGCTAATGCTGGCGTCAGAAAGACTCCATATTTCATTAAACAGATCGGATTTGTTTTTGAAATGCCAGTATATAGCGCCCCTGGTCACTCCAGCAGCTTTTGCAATCGCGGCCAACGAGGTAGATGATACCCCTTGCTGCGAAAACAATCGCAGGGCGACGTCAAGAATCAGTTGCCGGGTTTCAAGTGCCTGTTGTTTGGTTTTTCGTGCCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36770","NCBI_taxonomy_name":"Enterobacter aerogenes","NCBI_taxonomy_id":"548"}}}},"ARO_accession":"3003374","ARO_id":"39958","ARO_name":"Enterobacter aerogenes acrR with mutation conferring multidrug antibiotic resistance","ARO_description":"AcrR is a repressor of the AcrAB-TolC multidrug efflux complex. AcrR mutations result in high level antibiotic resistance.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"29":{"model_id":"29","model_name":"Escherichia coli folP with mutation conferring resistance to sulfonamides","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2114":"P64R","2115":"P64L","2281":"P64S","2282":"P64A","2283":"P64H"},"experimental":{"2114":"P64R","2115":"P64L","2281":"P64S","2282":"P64A","2283":"P64H"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4281":{"protein_sequence":{"accession":"YP_491362.1","sequence":"MKLFAQGTSLDLSHPHVMGILNVTPDSFSDGGTHNSLIDAVKHANLMINAGATIIDVGGESTRPGAAEVSVEEELQRVIPVVEAIAQRFEVWISVDTSKPEVIRESAKVGAHIINDIRSLSEPGALEAAAETGLPVCLMHMQGNPKTMQEAPKYDDVFAEVNRYFIEQIARCEQAGIAKEKLLLDPGFGFGKNLSHNYSLLARLAEFHHFNLPLLVGMSRKSMIGQLLNVGPSERLSGSLACAVIAAMQGAHIIRVHDVKETVEAMRVVEATLSAKENKRYE"},"dna_sequence":{"accession":"NC_007779","fmin":"3323917","fmax":"3324766","strand":"-","sequence":"TTACTCATAGCGTTTGTTTTCCTTTGCAGACAGAGTGGCTTCCACCACCCGCATCGCTTCTACGGTTTCTTTGACGTCATGAACACGAATGATGTGCGCGCCTTGCATTGCGGCAATGACCGCACAGGCCAGACTACCGCTCAGGCGCTCGGACGGCCCCACGTTCAGCAGCTGCCCAATCATCGATTTTCGTGACATACCCACCAACAGCGGCAGGTTGAAATGGTGAAATTCAGCCAGGCGCGCCAGTAATGAATAGTTATGGGAGAGATTTTTACCGAAACCGAATCCGGGGTCGAGCAACAATTTCTCTTTTGCGATACCCGCCTGCTCGCAACGTGCTATTTGCTCAATAAAGTAGCGATTCACTTCTGCAAAGACATCGTCATACTTCGGAGCTTCCTGCATGGTTTTTGGATTTCCCTGCATATGCATCAGACAAACCGGTAAACCGGTTTCTGCAGCCGCCTCCAGAGCGCCAGGTTCGGAAAGGGAGCGGATATCATTAATAATGTGAGCGCCAACTTTCGCTGACTCACGGATGACTTCTGGTTTGGATGTATCGACTGAGATCCAGACTTCGAAGCGTTGAGCAATTGCCTCAACCACAGGAATAACACGTTGCAACTCTTCTTCAACGCTAACTTCCGCCGCCCCTGGGCGCGTGGACTCGCCACCAACGTCAATGATCGTCGCGCCAGCGTTGATCATCAGATTCGCATGTTTCACCGCATCTATCAGCGAGTTATGCGTGCCACCATCCGAAAAGGAATCAGGCGTGACGTTGAGGATCCCCATTACGTGAGGATGGCTAAGGTCCAGTGAAGTACCCTGGGCAAAGAGTTTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36839","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. W3110","NCBI_taxonomy_id":"316407"}}}},"ARO_accession":"3003386","ARO_id":"39970","ARO_name":"Escherichia coli folP with mutation conferring resistance to sulfonamides","ARO_description":"Point mutations in Escherichia coli dihydropteroate synthase folP prevent sulfonamide antibiotics from inhibiting its role in folate synthesis, thus conferring sulfonamide resistance.","ARO_category":{"39999":{"category_aro_accession":"3003415","category_aro_cvterm_id":"39999","category_aro_name":"sulfonamide resistant dihydropteroate synthase folP","category_aro_description":"Point mutations in dihydropteroate synthase folP prevent sulfonamide antibiotics from inhibiting its role in folate synthesis, thus conferring sulfonamide resistance","category_aro_class_name":"AMR Gene Family"},"36463":{"category_aro_accession":"3000324","category_aro_cvterm_id":"36463","category_aro_name":"sulfadiazine","category_aro_description":"Sulfadiazine is a potent inhibitor of dihydropteroate synthase, interfering with the tetrahydrofolic biosynthesis pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor to many nucleotides and amino acids.","category_aro_class_name":"Antibiotic"},"36464":{"category_aro_accession":"3000325","category_aro_cvterm_id":"36464","category_aro_name":"sulfadimidine","category_aro_description":"Sulfadimidine is an alkaline sulfonamide antibiotic that inhibits dihydropteroate synthase, and enzyme in the tetrahydrofolic acid biosynthesis pathway. This interferes with the production of folate, which is a precursor to many amino acids and nucleotides.","category_aro_class_name":"Antibiotic"},"36466":{"category_aro_accession":"3000327","category_aro_cvterm_id":"36466","category_aro_name":"sulfadoxine","category_aro_description":"Sulfadoxine is an inhibitor of dihydropteroate synthase, interfering with the tetrahydrofolic biosynthesis pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor to many nucleotides and amino acids.","category_aro_class_name":"Antibiotic"},"36468":{"category_aro_accession":"3000329","category_aro_cvterm_id":"36468","category_aro_name":"sulfamethoxazole","category_aro_description":"Sulfamethoxazole is a sulfonamide antibiotic usually taken with trimethoprim, a diaminopyrimidine antibiotic. Sulfamethoxazole inhibits dihydropteroate synthase, essential to tetrahydrofolic acid biosynthesis. This pathway generates compounds used in the synthesis of many amino acids and nucleotides.","category_aro_class_name":"Antibiotic"},"36469":{"category_aro_accession":"3000330","category_aro_cvterm_id":"36469","category_aro_name":"sulfisoxazole","category_aro_description":"Sulfisoxazole is an inhibitor of dihydropteroate synthase, interfering with the tetrahydrofolic biosynthesis pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor to many nucleotides and amino acids.","category_aro_class_name":"Antibiotic"},"37027":{"category_aro_accession":"3000683","category_aro_cvterm_id":"37027","category_aro_name":"sulfacetamide","category_aro_description":"Sulfacetamide is a very soluable sulfonamide antibiotic previously used to treat urinary tract infections. Its relatively low activity and toxicity to those with Stevens-Johnson syndrome have reduced its use and availability.","category_aro_class_name":"Antibiotic"},"37028":{"category_aro_accession":"3000684","category_aro_cvterm_id":"37028","category_aro_name":"mafenide","category_aro_description":"Mafenide is a sulfonamide used topically for treating burns.","category_aro_class_name":"Antibiotic"},"37042":{"category_aro_accession":"3000698","category_aro_cvterm_id":"37042","category_aro_name":"sulfasalazine","category_aro_description":"Sulfasalazine is a derivative of the early sulfonamide sulfapyridine (salicylazosulfapyridine). It was developed to increase water solubility and is taken orally for ulcerative colitis.","category_aro_class_name":"Antibiotic"},"37043":{"category_aro_accession":"3000699","category_aro_cvterm_id":"37043","category_aro_name":"sulfamethizole","category_aro_description":"Sulfamethizole is a short-acting sulfonamide that inhibits dihydropteroate synthetase.","category_aro_class_name":"Antibiotic"},"39996":{"category_aro_accession":"3003412","category_aro_cvterm_id":"39996","category_aro_name":"dapsone","category_aro_description":"Dapsone is a sulfone in which it inhibits folic acid synthesis, such as the dihydropteroate synthase.","category_aro_class_name":"Antibiotic"},"36421":{"category_aro_accession":"3000282","category_aro_cvterm_id":"36421","category_aro_name":"sulfonamide antibiotic","category_aro_description":"Sulfonamides are broad spectrum, synthetic antibiotics that contain the sulfonamide group. Sulfonamides inhibit dihydropteroate synthase, which catalyzes the conversion of p-aminobenzoic acid to dihydropteroic acid as part of the tetrahydrofolic acid biosynthetic pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor of many nucleotides and amino acids. Many sulfamides are taken with trimethoprim, an inhibitor of dihydrofolate reductase, also disturbing the trihydrofolic acid synthesis pathway.","category_aro_class_name":"Drug Class"},"39985":{"category_aro_accession":"3003401","category_aro_cvterm_id":"39985","category_aro_name":"sulfone antibiotic","category_aro_description":"A sulfone active against a wide range of bacteria but mainly employed for its actions against mycobacterium laprae. Its mechanism of action  involves inhibition of folic acid synthesis in susceptible organisms.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1994":{"model_id":"1994","model_name":"gimA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"626":{"protein_sequence":{"accession":"CAA11707.1","sequence":"MRRGDLHETYRLDYAPHMHDPAHIAMFSIAAHGHVNPSLEVIRELVARGHRVTYAIPPLFAEKVAETGAEPKLWNSTLPGPDADPDAWGTTPLDNVEPFLDDAIQALPQLIAAYEGDEPDLVLHDITSYPARVLAHRWGVPAVSLSPNLVAWEGYEEEVGRPTWEEPLKTERGRAYDARFRGWLKENGITEDPDPFVGRPDRSLVLIPKALQPHADRVDEKTHTFVGACQGDRAAEGDWRRPEGAEKVVLVSLGSSFTKRPAFYRACVEAFGALPGWHVVLQVGRHVDPAELGDVPENVEVRSWVPQLAILKQADLFVTHAGAGGSQEGLATATPIVAVPQAVDQFGNADMLQGLGVGRHLPTEEATAEALRAAGLALVEDPEVARRLKEIQAGMAREGGTRRAADLIEAELAAART"},"dna_sequence":{"accession":"AJ223970","fmin":"796","fmax":"2050","strand":"+","sequence":"GTGAGAAGAGGTGATTTGCACGAGACGTATCGTCTTGATTACGCTCCGCACATGCACGATCCCGCTCATATCGCGATGTTCTCCATCGCCGCGCACGGTCACGTGAACCCCAGCCTGGAAGTGATCCGGGAACTCGTCGCGCGAGGGCACCGGGTGACCTACGCGATCCCGCCGCTCTTCGCCGAGAAGGTCGCCGAGACGGGCGCCGAACCCAAGCTGTGGAACAGCACGCTGCCCGGCCCCGACGCCGACCCGGACGCGTGGGGGACCACACCGCTGGACAACGTCGAGCCGTTCCTCGACGACGCGATCCAGGCGCTCCCGCAGCTCATCGCGGCGTACGAGGGCGACGAGCCGGACCTGGTCCTGCACGACATCACCTCCTACCCGGCCCGCGTCCTCGCCCATCGCTGGGGCGTTCCCGCCGTCTCGCTCTCGCCGAACCTGGTCGCCTGGGAGGGGTACGAGGAGGAGGTCGGCCGGCCGACGTGGGAGGAGCCGCTGAAGACCGAGCGCGGCCGGGCGTACGACGCCCGCTTCCGTGGCTGGCTGAAGGAGAACGGGATCACCGAGGACCCCGACCCCTTCGTCGGCCGTCCCGACCGGTCGCTGGTCCTCATCCCGAAGGCGCTCCAGCCGCACGCCGACCGGGTCGACGAGAAGACGCACACCTTCGTCGGTGCCTGCCAGGGCGACCGCGCCGCCGAGGGCGACTGGCGGCGTCCGGAGGGCGCGGAGAAGGTCGTCCTCGTCTCGCTCGGGTCCTCGTTCACCAAGCGGCCGGCGTTCTACCGGGCGTGCGTCGAGGCGTTCGGCGCGCTGCCCGGCTGGCACGTGGTGCTCCAGGTCGGCCGGCACGTCGACCCCGCCGAGCTGGGCGACGTACCGGAGAACGTGGAGGTCCGCTCCTGGGTGCCGCAGCTGGCGATCCTGAAGCAGGCTGACCTGTTCGTCACGCACGCGGGCGCGGGCGGCAGCCAGGAGGGCCTCGCCACCGCCACGCCGATAGTGGCGGTACCGCAGGCGGTGGACCAGTTCGGCAACGCGGACATGCTCCAGGGGCTCGGCGTGGGCCGCCACCTGCCCACCGAGGAAGCCACCGCCGAGGCGCTGCGCGCCGCCGGGCTCGCCCTGGTCGAGGACCCGGAGGTGGCCCGGCGGCTGAAGGAGATCCAGGCCGGGATGGCCCGGGAGGGCGGCACCCGGCGGGCCGCCGACCTGATCGAGGCGGAGCTGGCGGCGGCGAGGACCTGAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36864","NCBI_taxonomy_name":"Streptomyces ambofaciens","NCBI_taxonomy_id":"1889"}}}},"ARO_accession":"3000463","ARO_id":"36602","ARO_name":"gimA","ARO_description":"A macrolide glycosyltransferase encoded by the gimA gene in Streptomyces ambofaciens, a natural producer of the macrolide antibiotic spiramycin. Chalcomycin, methymycin, tylosin, pikromycin, rosaramicin, oleandomycin, josamycin, and carbomycin are preferred substrates of gimA glycosyltransferase, while erythromycin and spiramycin have notably low binding affinities. GimA may be able to inactivate spiramycin precursors. Described by Gourmelen et al. 1998.","ARO_category":{"41400":{"category_aro_accession":"3004236","category_aro_cvterm_id":"41400","category_aro_name":"gimA family macrolide glycosyltransferase","category_aro_description":"This family of macrolide glycosyltransferases derive from gimA, which was discovered in Streptomyces ambofaciens.","category_aro_class_name":"AMR Gene Family"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"37621":{"category_aro_accession":"3001222","category_aro_cvterm_id":"37621","category_aro_name":"chalcomycin","category_aro_description":"Produced by Streptomyces bikiniensis","category_aro_class_name":"Antibiotic"},"37631":{"category_aro_accession":"3001232","category_aro_cvterm_id":"37631","category_aro_name":"methymycin","category_aro_description":"Produced by Streptomyces venezuelae ATCC 15439.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2003":{"model_id":"2003","model_name":"pmrA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"3674":{"protein_sequence":{"accession":"NP_358469.1","sequence":"MTEINWKDNLRIAWFGNFLTGASISLVVPFMPIFVENLGVGSQQVAFYAGLAISVSAISAALFSPIWGILADKYGRKPMMIRAGLAMTITMGGLAFVPNIYWLIFLRLLNGVFAGFVPNATALIASQVPKEKSGSALGTLSTGVVAGTLTGPFIGGFIAELFGIRTVFLLVGSFLFLAAILTICFIKEDFQPVAKEKAIPTKELFTSVKYPYLLLNLFLTSFVIQFSAQSIGPILALYVRDLGQTENLLFVSGLIVSSMGFSSMMSAGVMGKLGDKVGNHRLLVVAQFYSVIIYLLCANASSPLQLGLYRFLFGLGTGALIPGVNALLSKMTPKAGISRVFAFNQVFFYLGGVVGPMAGSAVAGQFGYHAVFYATSLCVAFSCLFNLIQFRTLLKVKEI"},"dna_sequence":{"accession":"NC_003098.1","fmin":"866210","fmax":"867410","strand":"+","sequence":"ATGACAGAGATTAACTGGAAGGATAATCTGCGTATTGCCTGGTTTGGTAATTTTCTGACAGGAGCCAGTATTTCTTTGGTTGTACCTTTTATGCCCATCTTCGTGGAAAATCTAGGTGTAGGGAGTCAGCAAGTCGCTTTTTATGCAGGCTTAGCAATTTCTGTCTCTGCTATTTCCGCGGCGCTCTTTTCTCCTATTTGGGGTATTCTTGCTGACAAATACGGCCGAAAACCCATGATGATTCGGGCAGGTCTTGCTATGACTATCACTATGGGAGGCTTGGCCTTTGTCCCAAATATCTATTGGTTAATCTTTCTTCGTTTACTAAACGGTGTATTTGCAGGTTTTGTTCCTAATGCAACGGCACTGATAGCCAGTCAGGTTCCAAAGGAGAAATCAGGCTCTGCCTTAGGTACTTTGTCTACAGGCGTAGTTGCAGGTACTCTAACCGGTCCCTTTATTGGTGGCTTTATCGCAGAATTATTTGGCATTCGTACAGTTTTCTTACTGGTTGGTAGTTTTCTATTTTTAGCTGCTATTTTGACTATTTGCTTTATCAAGGAAGATTTTCAACCAGTAGCCAAGGAAAAGGCTATTCCAACAAAGGAATTATTTACCTCGGTTAAATATCCCTATCTTTTGCTCAATCTCTTTTTAACCAGTTTTGTCATCCAATTTTCAGCTCAATCGATCGGCCCTATTTTGGCTCTTTATGTACGCGACTTAGGGCAGACAGAGAATCTTCTTTTTGTCTCTGGTTTGATTGTGTCCAGTATGGGCTTTTCCAGTATGATGAGTGCAGGAGTCATGGGCAAGCTAGGTGACAAGGTGGGCAATCATCGTCTCTTGGTTGTCGCCCAGTTTTATTCAGTCATCATCTATCTCCTCTGTGCCAATGCCTCTAGCCCCCTTCAACTAGGACTCTATCGTTTCCTCTTTGGCTTGGGAACCGGTGCCTTGATTCCAGGGGTTAATGCCCTACTCAGCAAAATGACTCCCAAAGCCGGCATTTCGAGGGTCTTTGCCTTCAATCAGGTATTCTTTTATCTGGGAGGTGTTGTTGGTCCCATGGCAGGTTCTGCAGTAGCAGGTCAATTTGGCTACCATGCTGTCTTTTATGCGACAAGCCTTTGTGTTGCCTTTAGTTGTCTCTTTAACCTGATTCAATTTCGAACATTATTAAAAGTAAAGGAAATCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39596","NCBI_taxonomy_name":"Streptococcus pneumoniae R6","NCBI_taxonomy_id":"171101"}}}},"ARO_accession":"3000822","ARO_id":"37202","ARO_name":"pmrA","ARO_description":"PmrA is a MFS-type efflux pump expressed in Streptococcus pneumoniae that confers low-level resistance to norfloxacin, ciprofloxacin, and acriflavine.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2046":{"model_id":"2046","model_name":"tet(33)","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"4246":{"protein_sequence":{"accession":"CAD12227.2","sequence":"MSSLTSARGSLATVLITASLDAAGMGLVMPILPALLHEAGVTADAVPLNVGVLIALYAVMQFIFAPVLGTLSDRFGRRRVLLVSLAGATVDYLVLATTSALSVFYIARAVAGITGATNAVTATVIADITPPHQRAKRFGLLSACYGGGMIAGPAMGGLFGAISPHLPFLLAALLSASNLALTFILLRETRPDSPARSASLAQHRGRPGLSAVPGITFLLIAFGLVQFIGQAPGATWVLFTEHRLDWSPVEVGISLSVFGIVQVLVQALLTGRIVEWIGEAKTVIIGCITDALGLVGLAIVTDAFSMAPILAALGIGGIGLPALQTLLSQRVDEQHQGRLQGVLASINSVTSIFGPVAFTTIFALTYINADGFLWLCAAALYVPCVILIMRGTAASPKFGSWASGDSM"},"dna_sequence":{"accession":"AJ420072.1","fmin":"22939","fmax":"24163","strand":"+","sequence":"GTGTCATCTCTCACTTCCGCTCGTGGCTCGTTGGCCACGGTCCTCATCACGGCTAGCCTCGACGCCGCCGGCATGGGCCTGGTGATGCCGATTCTTCCCGCACTGCTACACGAGGCAGGGGTCACCGCTGATGCGGTTCCGCTGAACGTCGGAGTGCTGATCGCGCTCTACGCGGTAATGCAGTTCATCTTTGCCCCCGTACTGGGAACGCTGTCGGACCGATTCGGCCGCCGCCGGGTGCTGCTTGTTTCCCTGGCCGGTGCGACCGTCGACTATCTCGTGCTCGCCACGACGTCCGCTCTGTCGGTGTTCTATATCGCCCGCGCAGTGGCTGGGATAACCGGAGCGACCAATGCGGTCACCGCCACCGTGATCGCCGACATCACGCCACCCCACCAGCGCGCCAAGCGTTTCGGTTTACTCAGTGCCTGCTATGGCGGCGGAATGATCGCGGGGCCAGCCATGGGTGGACTGTTCGGTGCCATCTCGCCACATCTGCCGTTTTTGCTCGCTGCTCTTCTCTCAGCGAGCAATCTGGCACTCACCTTTATCCTGTTACGCGAGACCCGTCCTGATTCCCCTGCGCGCTCTGCGTCGCTCGCTCAGCATCGTGGTCGCCCCGGCCTCAGCGCGGTGCCTGGGATTACCTTCCTATTAATCGCATTCGGCCTTGTTCAATTCATTGGGCAGGCTCCAGGTGCGACCTGGGTGCTGTTTACTGAACACCGCCTCGACTGGAGTCCCGTCGAAGTTGGAATCTCCCTGTCCGTTTTCGGGATCGTACAGGTTCTCGTGCAGGCCCTCCTTACTGGCCGCATCGTGGAGTGGATCGGTGAGGCAAAAACAGTCATCATCGGGTGTATTACCGACGCCTTGGGTCTCGTAGGCCTGGCGATTGTCACTGACGCATTTTCCATGGCACCTATCTTGGCGGCACTGGGGATCGGTGGCATCGGCCTCCCCGCTCTGCAAACCCTTCTCTCCCAGCGCGTCGATGAACAGCACCAAGGGCGCCTCCAGGGTGTGCTCGCCAGCATCAACAGCGTCACATCGATCTTCGGACCGGTCGCTTTCACAACGATCTTCGCGCTCACTTACATCAACGCCGACGGCTTCCTCTGGCTCTGCGCCGCAGCACTCTACGTGCCCTGCGTGATTCTCATCATGCGTGGTACAGCAGCGTCCCCGAAGTTCGGCTCTTGGGCGAGCGGCGACTCGATGTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36777","NCBI_taxonomy_name":"Corynebacterium glutamicum","NCBI_taxonomy_id":"1718"}}}},"ARO_accession":"3000478","ARO_id":"36617","ARO_name":"tet(33)","ARO_description":"Tet33 is a tetracycline efflux pump found in Gram-positive bacteria, including Arthrobacter and Corynebacterium.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1969":{"model_id":"1969","model_name":"tet(35)","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"710"}},"model_sequences":{"sequence":{"64":{"protein_sequence":{"accession":"AAK37619.1","sequence":"MCVIMPASSWGAYIITIIGGILVSHGITEYSALGAYVRLIPMNFYAVFALLMVFAVAWFGLDIGKMREHEIAASQGRGFDKDKENDSQEAHDLNEELDIRESEKGKVSDLILPIVTLIVATIASMLYTGGQALAADGKEFVLLGAFENTDVGTSLIYGSLLGLAVALFTVIKQGLPMVEIARTLWIGAKSMFGAILILVFAWTIGSVIGDMKTGSYLSTMAQGNINPHWLPVILFLLSGLMAFSTGTSWGTFGIMLPIAGDMAGATDVALMLPMLSAVLAGAVFGDHCSPISDTTILSSTGARCNHIDHVSTQLPYALSVAFVSCIGFITLGMTASIAFSFIAASITFVIVCAILSWLSKSKMASCQNA"},"dna_sequence":{"accession":"AF353562","fmin":"0","fmax":"1110","strand":"-","sequence":"CTACGCGTTCTGGCAGGATGCCATTTTAGACTTCGACAGCCACGACAGAATCGCACAAACGATAACGAAAGTGATCGATGCTGCGATGAAAGAGAACGCGATCGATGCAGTCATACCCAGCGTGATAAAGCCAATACATGACACAAACGCCACTGATAATGCATAAGGTAGCTGCGTCGATACGTGATCGATGTGGTTACAGCGTGCACCTGTTGACGACAGAATCGTTGTATCTGAAATTGGTGAACAGTGGTCACCAAATACTGCACCAGCTAGAACCGCACTTAGCATTGGTAGCATTAGTGCCACGTCTGTTGCGCCAGCCATGTCACCCGCGATTGGAAGCATGATACCGAACGTACCCCATGACGTACCTGTAGAGAACGCCATTAGGCCAGACAGCAAGAACAGGATAACTGGTAGCCAGTGTGGGTTGATGTTGCCTTGCGCCATTGTAGATAGGTAAGAACCCGTCTTCATGTCACCGATAACTGAACCAATAGTCCAAGCGAAAACAAGGATAAGGATTGCACCAAACATTGACTTAGCACCAATCCAAAGCGTGCGTGCAATCTCAACCATTGGTAGACCTTGCTTAATAACAGTGAACAATGCAACTGCTAGACCAAGTAAACTACCGTAGATTAGAGAAGTACCAACATCCGTGTTTTCAAACGCACCCAACAGCACAAATTCTTTACCATCTGCTGCTAGCGCTTGACCACCGGTGTAAAGCATTGAAGCAATAGTCGCCACAATAAGCGTTACGATAGGAAGAATTAGGTCAGAAACCTTACCCTTCTCGCTTTCACGAATATCTAGCTCTTCGTTTAGGTCGTGTGCTTCTTGTGAGTCGTTCTCTTTATCTTTATCAAAACCACGGCCTTGAGATGCTGCGATTTCATGTTCACGCATCTTACCGATATCTAGACCAAACCACGCCACTGCAAATACCATTAGTAGAGCAAATACTGCGTAGAAGTTCATAGGAATAAGACGAACGTAAGCACCAAGCGCCGAGTATTCAGTGATGCCGTGTGACACCAAGATACCACCGATGATGGTAATGATGTACGCACCCCAACTAGAAGCTGGCATGATCACACACAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36785","NCBI_taxonomy_name":"Vibrio harveyi","NCBI_taxonomy_id":"669"}}}},"ARO_accession":"3000481","ARO_id":"36620","ARO_name":"tet(35)","ARO_description":"Tet35 is a tetracycline efflux pump found in the Gram-negative Vibrio and Stenotrophomonas. It is unrelated to other tet resistance genes.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2014":{"model_id":"2014","model_name":"pmrF","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"2115":{"protein_sequence":{"accession":"AAC75314.1","sequence":"MFEIHPVKKVSVVIPVYNEQESLPELIRRTTTACESLGKEYEILLIDDGSSDNSAHMLVEASQAENSHIVSILLNRNYGQHSAIMAGFSHVTGDLIITLDADLQNPPEEIPRLVAKADEGYDVVGTVRQNRQDSWFRKTASKMINRLIQRTTGKAMGDYGCMLRAYRRHIVDAMLHCHERSTFIPILANIFARRAIEIPVHHAEREFGESKYSFMRLINLMYDLVTCLTTTPLRMLSLLGSIIAIGGFSIAVLLVILRLTFGPQWAAEGVFMLFAVLFTFIGAQFIGMGLLGEYIGRIYTDVRARPRYFVQQVIRPSSKENE"},"dna_sequence":{"accession":"U00096","fmin":"2367070","fmax":"2368039","strand":"+","sequence":"ATGTTTGAAATCCACCCTGTTAAGAAAGTCTCGGTGGTTATTCCCGTTTATAACGAGCAGGAAAGCTTACCGGAATTAATCAGGCGCACCACCACAGCCTGTGAATCGTTGGGGAAAGAGTATGAGATCCTGCTGATTGATGACGGCAGTAGCGATAATTCCGCGCATATGCTGGTCGAAGCCTCACAAGCGGAGAACAGCCATATTGTGTCTATTTTGCTTAACCGCAATTACGGGCAACATTCAGCGATTATGGCGGGATTCAGTCACGTTACTGGCGACTTAATTATTACCCTTGATGCCGATCTCCAGAATCCGCCAGAAGAAATCCCCCGCCTGGTGGCAAAAGCCGATGAAGGTTACGACGTGGTAGGGACTGTACGCCAGAACCGCCAGGACAGCTGGTTTCGTAAAACCGCTTCGAAGATGATTAACCGGCTTATTCAGCGCACCACTGGCAAAGCGATGGGTGATTACGGTTGTATGCTGCGCGCCTATCGCCGTCATATTGTCGATGCGATGTTGCACTGCCATGAACGCAGCACCTTTATCCCGATTCTGGCGAATATCTTCGCCCGCCGTGCCATTGAAATTCCAGTACATCATGCCGAGCGTGAGTTTGGTGAATCCAAATACAGTTTTATGCGCCTGATTAATTTGATGTACGACCTGGTGACCTGCCTTACCACAACGCCGCTACGTATGCTGAGTCTGCTCGGCAGCATTATTGCGATTGGAGGTTTTAGCATTGCGGTGCTGCTGGTGATTTTACGCCTGACCTTCGGACCACAATGGGCGGCAGAAGGCGTCTTTATGCTATTTGCCGTGCTGTTTACTTTTATTGGCGCTCAGTTTATCGGCATGGGATTACTCGGTGAATATATCGGCAGGATCTACACCGATGTCCGCGCCCGCCCCCGCTATTTTGTTCAGCAAGTTATCCGTCCATCCAGCAAGGAAAATGAATAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3003578","ARO_id":"40188","ARO_name":"PmrF","ARO_description":"PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A, which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.","ARO_category":{"41433":{"category_aro_accession":"3004269","category_aro_cvterm_id":"41433","category_aro_name":"pmr phosphoethanolamine transferase","category_aro_description":"This family of phosphoethanolamine transferase catalyze the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine to lipid A, which impedes the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3":{"model_id":"3","model_name":"Pseudomonas aeruginosa ompF with mutation","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2253":"G141D","2254":"G141E","2255":"R154A","2256":"R154D"},"clinical":{"2253":"G141D","2254":"G141E","2255":"R154A","2256":"R154D"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"650"}},"model_sequences":{"sequence":{"4201":{"protein_sequence":{"accession":"NP_415449.1","sequence":"MMKRNILAVIVPALLVAGTANAAEIYNKDGNKVDLYGKAVGLHYFSKGNGENSYGGNGDMTYARLGFKGETQINSDLTGYGQWEYNFQGNNSEGADAQTGNKTRLAFAGLKYADVGSFDYGRNYGVVYDALGYTDMLPEFGGDTAYSDDFFVGRVGGVATYRNSNFFGLVDGLNFAVQYLGKNERDTARRSNGDGVGGSISYEYEGFGIVGAYGAADRTNLQEAQPLGNGKKAEQWATGLKYDANNIYLAANYGETRNATPITNKFTNTSGFANKTQDVLLVAQYQFDFGLRPSIAYTKSKAKDVEGIGDVDLVNYFEVGATYYFNKNMSTYVDYIINQIDSDNKLGVGSDDTVAVGIVYQF"},"dna_sequence":{"accession":"NC_000913.3","fmin":"985893","fmax":"986982","strand":"-","sequence":"TTAGAACTGGTAAACGATACCCACAGCAACGGTGTCGTCTGAACCTACGCCCAGTTTGTTGTCAGAATCGATCTGGTTGATGATGTAGTCAACATAGGTGGACATGTTTTTGTTGAAGTAGTAGGTTGCGCCCACTTCAAAGTAGTTCACCAGATCAACATCACCGATACCTTCTACGTCTTTCGCTTTAGATTTGGTGTAAGCGATGGACGGACGCAGACCGAAATCGAACTGGTATTGCGCAACTAACAGAACGTCTTGCGTTTTGTTGGCGAAGCCGCTGGTGTTTGTAAATTTATTAGTGATCGGCGTAGCGTTACGGGTTTCACCGTAGTTCGCTGCCAGGTAGATGTTGTTCGCGTCGTACTTCAGACCAGTAGCCCACTGTTCAGCTTTTTTACCGTTGCCAAGAGGTTGAGCTTCTTGCAGGTTGGTACGGTCAGCTGCACCATAAGCACCAACGATACCAAAGCCTTCGTATTCGTAGCTGATAGAACCGCCAACACCGTCGCCGTTAGAACGGCGTGCAGTGTCACGCTCGTTTTTACCCAGGTACTGAACAGCGAAGTTCAGGCCATCAACCAGACCAAAGAAGTTGGAGTTACGATAGGTAGCAACGCCGCCAACACGACCAACGAAGAAGTCATCGCTGTATGCAGTATCACCACCAAATTCTGGCAGCATATCGGTGTAACCCAGTGCATCATAAACCACACCGTAGTTACGGCCGTAATCGAAAGAACCAACGTCAGCGTATTTAAGACCCGCGAATGCCAGACGCGTTTTGTTACCAGTTTGAGCGTCAGCGCCTTCAGAGTTGTTACCCTGGAAGTTATATTCCCACTGACCATAACCGGTCAGATCGGAATTGATTTGAGTTTCCCCTTTAAAACCAAGACGGGCATAGGTCATGTCGCCATTGCCACCGTAACTGTTTTCACCGTTACCCTTGGAAAAATAATGCAGACCAACAGCTTTACCGTACAGATCTACTTTGTTGCCATCTTTGTTATAGATTTCTGCAGCGTTTGCAGTACCTGCTACTAACAGAGCAGGGACGATCACTGCCAGAATATTGCGCTTCATCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3003390","ARO_id":"39974","ARO_name":"Escherichia coli ompF with mutation conferring resistance to beta-lactam antibiotics","ARO_description":"The Escherichia coli ompF (oprF) is a nonspecific porin channel involved in the membrane translocation of small hydrophilic molecules, including and especially beta-lactam antibiotics. Mutations in ompF can decrease diffusion of antibiotics across the cellular membrane, thereby decreasing overall susceptibility through absence of porin function.","ARO_category":{"41445":{"category_aro_accession":"3004281","category_aro_cvterm_id":"41445","category_aro_name":"General Bacterial Porin with reduced permeability to beta-lactams","category_aro_description":"These are GBPs that are associated with decreased susceptibility to beta-lactams either through mutations in the porin protein, absence of the porin protein, or expression of the porin protein.","category_aro_class_name":"AMR Gene Family"},"35976":{"category_aro_accession":"0000059","category_aro_cvterm_id":"35976","category_aro_name":"cefepime","category_aro_description":"Cefepime (INN) is a fourth-generation cephalosporin antibiotic developed in 1994. It contains an aminothiazolyl group that decreases its affinity with beta-lactamases. Cefepime shows high binding affinity with penicillin-binding proteins and has an extended spectrum of activity against Gram-positive and Gram-negative bacteria, with greater activity against both Gram-negative and Gram-positive organisms than third-generation agents.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36383":{"category_aro_accession":"3000244","category_aro_cvterm_id":"36383","category_aro_name":"reduced permeability to antibiotic","category_aro_description":"Reduction in permeability to antibiotic, generally through reduced production of porins, can provide resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2002":{"model_id":"2002","model_name":"Bacillus pumilus cat86","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"143":{"protein_sequence":{"accession":"AAA22289.1","sequence":"MFKQIDENYLRKEHFHHYMTLTRCSYSLVINLDITKLHAILKEKKLKVYPVQIYLLARAVQKIPEFRMDQVNDELGYWEILHPSYTILNKETKTFSSIWTPFDENFAQFYKSCVADIETFSKSSNLFPKPHMPENMFNISSLPWIDFTSFNLNVSTDEAYLLPIFTIGKFKVEEGKIILPVAIQVHHAVCDGYHAGQYVEYLRWLIEHCDEWLNDSLHIT"},"dna_sequence":{"accession":"K00544","fmin":"0","fmax":"663","strand":"+","sequence":"TTGTTTAAACAAATAGACGAAAATTATCTGCGAAAAGAGCACTTTCACCATTATATGACGTTAACCCGATGCTCATATAGCTTGGTGATCAATCTAGACATCACGAAATTGCATGCAATATTAAAAGAAAAAAAGCTGAAAGTATATCCTGTGCAAATTTATTTGTTAGCAAGAGCTGTGCAAAAAATTCCTGAGTTTCGGATGGATCAAGTGAACGATGAACTTGGTTACTGGGAGATTCTCCATCCTAGTTATACGATTCTAAATAAAGAAACAAAGACGTTTTCAAGTATTTGGACGCCTTTTGATGAAAACTTTGCTCAGTTTTATAAAAGCTGTGTAGCCGATATTGAAACATTTAGCAAAAGCAGCAACCTATTTCCGAAACCTCATATGCCAGAAAACATGTTCAATATTTCAAGTCTACCGTGGATTGATTTTACTTCTTTTAACCTTAATGTATCTACAGATGAAGCTTATTTACTGCCTATATTTACGATAGGCAAATTTAAGGTGGAAGAAGGAAAAATCATTTTGCCCGTTGCCATACAAGTACATCATGCTGTTTGTGATGGCTATCATGCCGGTCAATATGTTGAATATTTGAGGTGGCTTATTGAACATTGTGACGAGTGGTTAAATGATTCATTGCATATTACCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36821","NCBI_taxonomy_name":"Bacillus pumilus","NCBI_taxonomy_id":"1408"}}}},"ARO_accession":"3002672","ARO_id":"39106","ARO_name":"Bacillus pumilus cat86","ARO_description":"cat86 is a chromosome-encoded variant of the cat gene found in Bacillus pumilus","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. cat is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Bacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini","category_aro_class_name":"AMR Gene Family"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"90":{"model_id":"90","model_name":"Staphylococcus aureus rpoB mutants conferring resistance to rifampicin","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2054":"H481N","2055":"A473T","2056":"Q465R","2057":"L466S","2083":"A477T","2862":"Q468K"},"clinical":{"2054":"H481N","2055":"A473T","2056":"Q465R","2057":"L466S","2083":"A477T","2862":"Q468K"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"2300"}},"model_sequences":{"sequence":{"2113":{"protein_sequence":{"accession":"YP_039996.1","sequence":"MAGQVVQYGRHRKRRNYARISEVLELPNLIEIQTKSYEWFLREGLIEMFRDISPIEDFTGNLSLEFVDYRLGEPKYDLEESKNRDATYAAPLRVKVRLIIKETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDKNGRENYDATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFSSDQEIVDLLGDNEYLRNTLEKDGTENTEQALLEIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGRYKTNKKLHLKHRLFNQKLAEPIVNTETGEIVVEEGTVLDRRKIDEIMDVLESNANSEVFELHGSVIDEPVEIQSIKVYVPNDDEGRTTTVIGNAFPDSEVKCITPADIIASMSYFFNLLSGIGYTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQDTESITPQQLINIRPVIASIKEFFGSSQLSQFMDQANPLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVDLDTHAITDQIDYLTADEEDSYVVAQANSKLDENGRFMDDEVVCRFRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEAPFVGTGMEHVAARDSGAAITAKHRGRVEHVESNEILVRRLVEENGVEHEGELDRYPLAKFKRSNSGTCYNQRPIVAVGDVVEFNEILADGPSMELGEMALGRNVVVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSESALKNLDDRGIVYIGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNREEGDDTLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGRPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWSTIEEAGMARDGKTVLYDGRTGEPFDNRISVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDTVGRVKTYEAIVKGENISRPSVPESFRVLMKELQSLGLDVKVMDEQDNEIEMTDVDDDDVVERKVDLQQNDAPETQKEVTD"},"dna_sequence":{"accession":"NC_002952","fmin":"590830","fmax":"594382","strand":"+","sequence":"TTGGCAGGTCAAGTTGTCCAATATGGAAGACATCGTAAACGTAGAAACTACGCGAGAATTTCAGAAGTATTAGAATTACCAAACTTAATAGAAATTCAAACTAAATCTTACGAGTGGTTCCTAAGAGAAGGTTTAATCGAAATGTTTAGAGACATTTCTCCAATTGAAGATTTTACTGGTAATTTGTCATTAGAGTTTGTGGATTACCGTTTAGGAGAACCAAAATATGATTTAGAAGAATCTAAAAACCGTGACGCTACTTATGCTGCACCTCTTCGTGTAAAAGTGCGTCTAATCATTAAAGAAACAGGAGAAGTTAAAGAACAAGAAGTCTTTATGGGTGATTTCCCATTAATGACTGATACAGGTACGTTCGTTATCAATGGTGCAGAACGTGTAATCGTATCTCAATTAGTTCGTTCACCATCCGTTTATTTCAATGAAAAAATCGACAAAAATGGTCGTGAAAACTATGATGCAACAATTATTCCAAACCGAGGTGCATGGTTAGAATATGAAACAGATGCTAAAGATGTTGTATACGTGCGTATTGATAGAACACGTAAACTACCATTAACAGTATTGTTACGTGCATTAGGTTTCTCAAGTGACCAAGAAATTGTTGACCTTTTAGGTGACAATGAATATTTACGTAATACTTTAGAGAAAGACGGCACTGAAAACACTGAACAAGCGTTATTAGAAATCTATGAACGTTTACGTCCAGGTGAACCACCAACTGTTGAAAATGCTAAAAGTCTATTGTATTCACGTTTCTTTGATCCAAAACGCTATGACTTAGCAAGCGTGGGTCGTTATAAAACAAACAAAAAATTACATTTAAAACATCGTTTATTCAATCAAAAATTAGCTGAGCCAATTGTGAATACTGAAACTGGTGAAATTGTAGTTGAAGAAGGTACAGTGCTTGATCGTCGTAAAATCGACGAAATCATGGATGTACTTGAATCAAACGCAAACAGCGAAGTGTTTGAATTGCATGGTAGCGTTATAGACGAGCCAGTAGAAATTCAATCAATTAAAGTATATGTTCCTAACGATGATGAAGGTCGTACGACAACTGTAATTGGTAATGCTTTCCCTGACTCAGAAGTTAAATGTATTACACCGGCAGATATCATCGCTTCAATGAGTTACTTCTTTAACTTATTAAGTGGTATTGGATATACAGATGATATTGACCATTTAGGTAACCGTCGTTTACGTTCTGTAGGTGAATTACTACAAAACCAATTCCGTATCGGTTTATCAAGAATGGAAAGAGTTGTACGTGAAAGAATGTCAATTCAAGATACTGAGTCTATCACACCTCAACAATTAATTAATATTCGACCTGTTATTGCATCTATTAAAGAATTCTTTGGTAGCTCTCAATTATCACAATTCATGGACCAAGCAAATCCATTAGCTGAGTTAACGCATAAACGTCGTCTATCAGCATTAGGACCTGGTGGTTTAACACGTGAACGTGCTCAAATGGAAGTGCGTGACGTTCACTACTCTCACTATGGCCGTATGTGTCCAATTGAAACGCCTGAGGGACCAAACATTGGATTGATTAACTCATTATCAAGTTATGCACGTGTAAATGAATTCGGCTTTATTGAAACACCATATCGTAAAGTTGATTTAGATACACATGCTATCACTGATCAAATTGACTATTTAACAGCTGACGAAGAAGATAGCTATGTTGTAGCACAAGCAAACTCTAAATTAGATGAAAATGGTCGTTTCATGGATGATGAAGTTGTATGTCGTTTCCGTGGTAACAATACAGTTATGGCTAAAGAAAAAATGGATTATATGGATGTATCGCCGAAGCAAGTTGTTTCAGCAGCGACAGCATGTATTCCATTCTTAGAAAATGATGACTCAAACCGTGCATTGATGGGTGCGAACATGCAACGTCAAGCAGTGCCTTTGATGAATCCAGAAGCACCATTTGTTGGTACAGGTATGGAACACGTTGCAGCACGTGATTCTGGTGCAGCTATTACAGCTAAGCACAGAGGTCGTGTTGAACATGTTGAATCTAATGAAATTCTTGTACGTCGTCTAGTTGAAGAGAACGGCGTTGAGCATGAAGGTGAATTAGATCGCTATCCATTAGCTAAATTTAAACGTTCAAACTCAGGTACATGTTACAACCAACGTCCAATCGTTGCAGTTGGAGATGTTGTTGAGTTTAACGAGATTTTAGCAGATGGACCATCTATGGAATTAGGAGAAATGGCATTAGGTAGAAACGTAGTAGTTGGTTTCATGACTTGGGACGGTTACAACTATGAGGATGCCGTTATCATGAGTGAAAGACTTGTGAAAGATGACGTGTATACTTCTATTCATATTGAAGAGTATGAATCAGAAGCACGTGATACTAAGTTAGGACCTGAAGAAATCACAAGAGATATTCCTAATGTTTCTGAAAGTGCACTTAAGAACTTAGACGATCGTGGTATCGTTTATATTGGTGCAGAAGTAAAAGATGGAGATATTTTAGTTGGTAAAGTAACGCCTAAAGGTGTAACTGAGTTAACTGCCGAAGAAAGATTGTTACATGCAATCTTTGGTGAAAAAGCACGTGAAGTTAGAGATACTTCATTACGTGTACCTCACGGCGCTGGCGGTATCGTTCTTGATGTAAAAGTATTCAATCGTGAAGAAGGCGACGACACATTATCACCTGGTGTAAACCAATTAGTACGTGTATATATCGTTCAAAAACGTAAAATTCATGTTGGTGATAAGATGTGTGGTCGACATGGTAACAAAGGTGTCATTTCTAAGATTGTTCCTGAAGAAGATATGCCTTACTTACCAGATGGACGTCCGATTGATATCATGTTAAATCCTCTTGGTGTACCATCTCGTATGAACATCGGACAAGTATTAGAGCTACACTTAGGTATGGCTGCTAAAAATCTTGGTATTCACGTTGCATCACCAGTATTTGACGGTGCAAACGATGACGATGTATGGTCAACAATTGAAGAAGCTGGTATGGCTCGTGATGGTAAAACTGTACTTTATGATGGACGTACAGGTGAACCATTCGATAACCGTATTTCAGTAGGTGTAATGTACATGTTGAAACTTGCGCACATGGTTGATGATAAATTACATGCGCGTTCAACAGGACCATATTCACTTGTTACACAACAACCACTTGGCGGTAAAGCGCAATTCGGTGGACAACGTTTCGGTGAGATGGAGGTATGGGCACTTGAAGCATATGGTGCTGCATACACATTACAAGAAATCTTAACTTACAAATCCGATGATACAGTAGGACGTGTGAAAACATACGAGGCTATTGTTAAAGGTGAAAACATCTCTAGACCAAGTGTTCCAGAATCATTCCGAGTATTGATGAAAGAATTACAAAGTTTAGGTTTAGATGTAAAAGTTATGGATGAGCAAGATAATGAAATCGAAATGACAGACGTTGATGACGATGATGTTGTAGAACGCAAAGTAGATTTACAACAAAATGATGCTCCTGAAACACAAAAAGAAGTTACTGATTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35517","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus MRSA252","NCBI_taxonomy_id":"282458"}}}},"ARO_accession":"3003285","ARO_id":"39869","ARO_name":"Staphylococcus aureus rpoB mutants conferring resistance to rifampicin","ARO_description":"Point mutations that occurs in Staphylococcus aureus rpoB resulting in resistance to rifampicin","ARO_category":{"36349":{"category_aro_accession":"3000210","category_aro_cvterm_id":"36349","category_aro_name":"rifamycin-resistant beta-subunit of RNA polymerase (rpoB)","category_aro_description":"Rifampin resistant RNA polymerases include amino acids substitutions which disrupt the affinity of rifampin for its binding site. These mutations are frequently concentrated in the rif I region of the beta-subunit and most often involve amino acids which make direct interactions with rifampin. However, mutations which also confer resistance can occur outside this region and may involve amino acids which do not directly make contact with rifampin.","category_aro_class_name":"AMR Gene Family"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36656":{"category_aro_accession":"3000517","category_aro_cvterm_id":"36656","category_aro_name":"rifaximin","category_aro_description":"Rifaximin is a semi-synthetic rifamycin used to treat traveller's diarrhea. Rifaximin inhibits RNA synthesis by binding to the beta subunit of bacterial RNA polymerase.","category_aro_class_name":"Antibiotic"},"36669":{"category_aro_accession":"3000530","category_aro_cvterm_id":"36669","category_aro_name":"rifabutin","category_aro_description":"Rifabutin is a semisynthetic rifamycin used in tuberculosis therapy. It inhibits DNA-dependent RNA synthesis.","category_aro_class_name":"Antibiotic"},"36673":{"category_aro_accession":"3000534","category_aro_cvterm_id":"36673","category_aro_name":"rifapentine","category_aro_description":"Rifapentine is a semisynthetic rifamycin that inhibits DNA-dependent RNA synthesis. It is often used in the treatment of tuberculosis and leprosy.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"111":{"model_id":"111","model_name":"Escherichia coli gyrB conferring resistance to aminocoumarin","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2156":"R136L","2157":"R136C","2158":"R136H","2159":"R136S","2160":"R136G","2161":"R136I","2162":"R136E"},"clinical":{"2156":"R136L","2157":"R136C","2158":"R136H","2159":"R136S","2160":"R136G","2161":"R136I","2162":"R136E"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1600"}},"model_sequences":{"sequence":{"2063":{"protein_sequence":{"accession":"BAE77595.1","sequence":"MSNSYDSSSIKVLKGLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDDGRGIPTGIHPEEGVSAAEVIMTVLHAGGKFDDNSYKVSGGLHGVGVSVVNALSQKLELVIQREGKIHRQIYEHGVPQAPLAVTGETEKTGTMVRFWPSLETFTNVTEFEYEILAKRLRELSFLNSGVSIRLRDKRDGKEDHFHYEGGIKAFVEYLNKNKTPIHPNIFYFSTEKDGIGVEVALQWNDGFQENIYCFTNNIPQRDGGTHLAGFRAAMTRTLNAYMDKEGYSKKAKVSATGDDAREGLIAVVSVKVPDPKFSSQTKDKLVSSEVKSAVEQQMNELLAEYLLENPTDAKIVVGKIIDAARAREAARRAREMTRRKGALDLAGLPGKLADCQERDPALSELYLVEGDSAGGSAKQGRNRKNQAILPLKGKILNVEKARFDKMLSSQEVATLITALGCGIGRDEYNPDKLRYHSIIIMTDADVDGSHIRTLLLTFFYRQMPEIVERGHVYIAQPPLYKVKKGKQEQYIKDDEAMDQYQISIALDGATLHTNASAPALAGEALEKLVSEYNATQKMINRMERRYPKAMLKELIYQPTLTEADLSDEQTVTRWVNALVSELNDKEQHGSQWKFDVHTNAEQNLFEPIVRVRTHGVDTDYPLDHEFITGGEYRRICTLGEKLRGLLEEDAFIERGERRQPVASFEQALDWLVKESRRGLSIQRYKGLGEMNPEQLWETTMDPESRRMLRVTVKDAIAADQLFTTLMGDAVEPRRAFIEENALKAANIDI"},"dna_sequence":{"accession":"AP009048","fmin":"3760295","fmax":"3762710","strand":"+","sequence":"ATGTCGAATTCTTATGACTCCTCCAGTATCAAAGTCCTGAAAGGGCTGGATGCGGTGCGTAAGCGCCCGGGTATGTATATCGGCGACACGGATGACGGCACCGGTCTGCACCACATGGTATTCGAGGTGGTAGATAACGCTATCGACGAAGCGCTCGCGGGTCACTGTAAAGAAATTATCGTCACCATTCACGCCGATAACTCTGTCTCTGTACAGGATGACGGGCGCGGCATTCCGACCGGTATTCACCCGGAAGAGGGCGTATCGGCGGCGGAAGTGATCATGACCGTTCTGCACGCAGGCGGTAAATTTGACGATAACTCCTATAAAGTGTCCGGCGGTCTGCACGGCGTTGGTGTTTCGGTAGTAAACGCCCTGTCGCAAAAACTGGAGCTGGTTATCCAGCGCGAGGGTAAAATTCACCGTCAGATCTACGAACACGGTGTACCGCAGGCCCCGCTGGCGGTTACCGGCGAGACTGAAAAAACCGGCACCATGGTGCGTTTCTGGCCCAGCCTCGAAACCTTCACCAATGTGACCGAGTTCGAATATGAAATTCTGGCGAAACGTCTGCGTGAGTTGTCGTTCCTCAACTCCGGCGTTTCCATTCGTCTGCGCGACAAGCGCGACGGCAAAGAAGACCACTTCCACTATGAAGGCGGCATCAAGGCGTTCGTTGAATATCTGAACAAGAACAAAACGCCGATCCACCCGAATATCTTCTACTTCTCCACTGAAAAAGACGGTATTGGCGTCGAAGTGGCGTTGCAGTGGAACGATGGCTTCCAGGAAAACATCTACTGCTTTACCAACAACATTCCGCAGCGTGACGGCGGTACTCACCTGGCAGGCTTCCGTGCGGCGATGACCCGTACCCTGAACGCCTACATGGACAAAGAAGGCTACAGCAAAAAAGCCAAAGTCAGCGCCACCGGTGACGATGCGCGTGAAGGCCTGATTGCGGTCGTTTCCGTGAAAGTGCCGGACCCGAAATTCTCCTCCCAGACCAAAGACAAACTGGTTTCTTCTGAGGTGAAATCGGCGGTTGAACAGCAGATGAACGAACTGCTGGCAGAATACCTGCTGGAAAACCCAACCGACGCGAAAATCGTGGTTGGCAAAATTATCGATGCTGCCCGTGCCCGTGAAGCGGCGCGTCGCGCGCGTGAAATGACCCGCCGTAAAGGTGCGCTCGACTTAGCGGGCCTGCCGGGCAAACTGGCAGACTGCCAGGAACGCGATCCGGCGCTTTCCGAACTGTACCTGGTGGAAGGGGACTCCGCGGGCGGCTCTGCGAAGCAGGGGCGTAACCGCAAGAACCAGGCGATTCTGCCGCTGAAGGGTAAAATCCTCAACGTCGAGAAAGCGCGCTTCGATAAGATGCTCTCTTCTCAGGAAGTGGCGACGCTTATCACCGCGCTTGGCTGTGGTATCGGTCGTGACGAGTACAACCCGGACAAACTGCGTTATCACAGCATCATCATCATGACCGATGCGGACGTCGACGGCTCGCACATTCGTACGCTGCTGTTGACCTTCTTCTATCGTCAGATGCCGGAAATCGTTGAACGCGGTCACGTCTACATCGCTCAGCCGCCGCTGTACAAAGTGAAGAAAGGCAAGCAGGAACAGTACATTAAAGACGACGAAGCGATGGATCAGTACCAGATCTCTATCGCGCTGGACGGCGCAACGCTGCACACCAACGCCAGTGCACCGGCATTGGCTGGCGAAGCGTTAGAGAAACTGGTATCTGAGTACAACGCGACGCAGAAAATGATCAATCGTATGGAGCGTCGTTATCCGAAAGCAATGCTGAAAGAGCTTATCTATCAGCCGACGTTGACGGAAGCTGACCTTTCTGATGAGCAGACCGTTACCCGCTGGGTGAACGCGCTGGTCAGCGAACTGAACGACAAAGAACAGCACGGCAGCCAGTGGAAGTTTGATGTTCACACCAATGCTGAGCAAAACCTGTTCGAGCCGATTGTTCGCGTGCGTACCCACGGTGTGGATACTGACTATCCGCTGGATCACGAGTTTATCACCGGTGGCGAATATCGTCGTATCTGCACGCTGGGTGAGAAACTGCGTGGCTTGCTGGAAGAAGATGCGTTTATCGAACGTGGCGAGCGTCGTCAGCCGGTAGCCAGCTTCGAGCAGGCGCTGGACTGGCTGGTGAAAGAGTCCCGTCGCGGCCTCTCCATCCAGCGTTATAAAGGTCTGGGCGAGATGAACCCGGAACAGCTGTGGGAAACCACTATGGACCCGGAAAGTCGTCGTATGCTGCGCGTTACCGTTAAAGATGCGATTGCTGCCGACCAGTTGTTCACCACGCTGATGGGCGACGCCGTTGAACCGCGCCGTGCGTTTATTGAAGAGAACGCCCTGAAAGCGGCGAATATCGATATTTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36839","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. W3110","NCBI_taxonomy_id":"316407"}}}},"ARO_accession":"3003303","ARO_id":"39887","ARO_name":"Escherichia coli gyrB conferring resistance to aminocoumarin","ARO_description":"Point mutation in Escherichia coli resulting in aminocoumarin resistance","ARO_category":{"36618":{"category_aro_accession":"3000479","category_aro_cvterm_id":"36618","category_aro_name":"aminocoumarin resistant gyrB","category_aro_description":"Point mutations in DNA gyrase subunit B (gyrB) can result in resistance to aminocoumarins. These mutations usually involve arginine residues in organisms.","category_aro_class_name":"AMR Gene Family"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36271":{"category_aro_accession":"3000132","category_aro_cvterm_id":"36271","category_aro_name":"clorobiocin","category_aro_description":"Clorobiocin is an aminocoumarin antibiotic produced by Streptomyces roseochromogenes, and binds DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36289":{"category_aro_accession":"3000150","category_aro_cvterm_id":"36289","category_aro_name":"coumermycin A1","category_aro_description":"Coumermycin A1 is an antibiotic produced by Streptomyces rishiriensis, and binds DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"196":{"model_id":"196","model_name":"Mycobacterium tuberculosis embB mutations conferring resistance to ethambutol","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2238":"D328Y","2239":"D328G","2240":"F330V","2242":"G406A","2243":"L413P","2296":"S297A","2297":"D299E","2298":"M306L","2299":"M306V","2300":"M306I","2301":"M306T","2345":"D311H","2413":"L239P","2414":"D240H","2426":"Y334H","2430":"A356V","2431":"A357S","2440":"E368A","2446":"P375A","2450":"E378A","2453":"S380R","2460":"P397Q","2464":"N399H","2470":"G406S","2471":"G406C","2472":"G406D","2478":"P446H","2482":"R460C","2485":"I465D","2486":"R469P","2487":"R471P","2488":"Q497R","2489":"Q497K","2490":"G745D","2491":"D959A","2492":"M1000R","2493":"D1024N","3588":"E504Q","3589":"R507G","3590":"D331Y","3593":"Y319C","3594":"Y333C","3595":"Y319N","3596":"T630I"},"clinical":{"2238":"D328Y","2239":"D328G","2240":"F330V","2242":"G406A","2243":"L413P","2296":"S297A","2297":"D299E","2298":"M306L","2299":"M306V","2300":"M306I","2301":"M306T","2345":"D311H","2413":"L239P","2414":"D240H","2426":"Y334H","2430":"A356V","2431":"A357S","2440":"E368A","2446":"P375A","2450":"E378A","2453":"S380R","2460":"P397Q","2464":"N399H","2470":"G406S","2471":"G406C","2472":"G406D","2478":"P446H","2482":"R460C","2485":"I465D","2486":"R469P","2487":"R471P","2488":"Q497R","2489":"Q497K","2490":"G745D","2491":"D959A","2492":"M1000R","2493":"D1024N","3588":"E504Q","3589":"R507G","3590":"D331Y","3593":"Y319C","3594":"Y333C","3595":"Y319N","3596":"T630I"}},"40330":{"param_type":"multiple resistance variants","param_description":"A set of nucleotide or amino acid substitutions that are each required to confer resistance to an antibiotic drug or drug class by co-mutation. Compare to single resistance variant, where only one substitution is required. Multiple resistance variants parameters are indicated on appropriate models using the following notation: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2],...,[wild-type n][position n][mutation n]. When each included substitution is detected in a protein sequence, resistance is conferred. This parameter is not currently included in any detection algorithms.","param_type_id":"40330","param_value":{"3592":"A314G,Y322C"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"2000"}},"model_sequences":{"sequence":{"2078":{"protein_sequence":{"accession":"CCP46624.1","sequence":"MTQCASRRKSTPNRAILGAFASARGTRWVATIAGLIGFVLSVATPLLPVVQTTAMLDWPQRGQLGSVTAPLISLTPVDFTATVPCDVVRAMPPAGGVVLGTAPKQGKDANLQALFVVVSAQRVDVTDRNVVILSVPREQVTSPQCQRIEVTSTHAGTFANFVGLKDPSGAPLRSGFPDPNLRPQIVGVFTDLTGPAPPGLAVSATIDTRFSTRPTTLKLLAIIGAIVATVVALIALWRLDQLDGRGSIAQLLLRPFRPASSPGGMRRLIPASWRTFTLTDAVVIFGFLLWHVIGANSSDDGYILGMARVADHAGYMSNYFRWFGSPEDPFGWYYNLLALMTHVSDASLWMRLPDLAAGLVCWLLLSREVLPRLGPAVEASKPAYWAAAMVLLTAWMPFNNGLRPEGIIALGSLVTYVLIERSMRYSRLTPAALAVVTAAFTLGVQPTGLIAVAALVAGGRPMLRILVRRHRLVGTLPLVSPMLAAGTVILTVVFADQTLSTVLEATRVRAKIGPSQAWYTENLRYYYLILPTVDGSLSRRFGFLITALCLFTAVFIMLRRKRIPSVARGPAWRLMGVIFGTMFFLMFTPTKWVHHFGLFAAVGAAMAALTTVLVSPSVLRWSRNRMAFLAALFFLLALCWATTNGWWYVSSYGVPFNSAMPKIDGITVSTIFFALFAIAAGYAAWLHFAPRGAGEGRLIRALTTAPVPIVAGFMAAVFVASMVAGIVRQYPTYSNGWSNVRAFVGGCGLADDVLVEPDTNAGFMKPLDGDSGSWGPLGPLGGVNPVGFTPNGVPEHTVAEAIVMKPNQPGTDYDWDAPTKLTSPGINGSTVPLPYGLDPARVPLAGTYTTGAQQQSTLVSAWYLLPKPDDGHPLVVVTAAGKIAGNSVLHGYTPGQTVVLEYAMPGPGALVPAGRMVPDDLYGEQPKAWRNLRFARAKMPADAVAVRVVAEDLSLTPEDWIAVTPPRVPDLRSLQEYVGSTQPVLLDWAVGLAFPCQQPMLHANGIAEIPKFRITPDYSAKKLDTDTWEDGTNGGLLGITDLLLRAHVMATYLSRDWARDWGSLRKFDTLVDAPPAQLELGTATRSGLWSPGKIRIGP"},"dna_sequence":{"accession":"AL123456","fmin":"4246513","fmax":"4249810","strand":"+","sequence":"ATGACACAGTGCGCGAGCAGACGCAAAAGCACCCCAAATCGGGCGATTTTGGGGGCTTTTGCGTCTGCTCGCGGGACGCGCTGGGTGGCCACCATCGCCGGGCTGATTGGCTTTGTGTTGTCGGTGGCGACGCCGCTGCTGCCCGTCGTGCAGACCACCGCGATGCTCGACTGGCCACAGCGGGGGCAACTGGGCAGCGTGACCGCCCCGCTGATCTCGCTGACGCCGGTCGACTTTACCGCCACCGTGCCGTGCGACGTGGTGCGCGCCATGCCACCCGCGGGCGGGGTGGTGCTGGGCACCGCACCCAAGCAAGGCAAGGACGCCAATTTGCAGGCGTTGTTCGTCGTCGTCAGCGCCCAGCGCGTGGACGTCACCGACCGCAACGTGGTGATCTTGTCCGTGCCGCGCGAGCAGGTGACGTCCCCGCAGTGTCAACGCATCGAGGTCACCTCTACCCACGCCGGCACCTTCGCCAACTTCGTCGGGCTCAAGGACCCGTCGGGCGCGCCGCTGCGCAGCGGCTTCCCCGACCCCAACCTGCGCCCGCAGATTGTCGGGGTGTTCACCGACCTGACCGGGCCCGCGCCGCCCGGGCTGGCGGTCTCGGCGACCATCGACACCCGGTTCTCCACCCGGCCGACCACGCTGAAACTGCTGGCGATCATCGGGGCGATCGTGGCCACCGTCGTCGCACTGATCGCGTTGTGGCGCCTGGACCAGTTGGACGGGCGGGGCTCAATTGCCCAGCTCCTCCTCAGGCCGTTCCGGCCTGCATCGTCGCCGGGCGGCATGCGCCGGCTGATTCCGGCAAGCTGGCGCACCTTCACCCTGACCGACGCCGTGGTGATATTCGGCTTCCTGCTCTGGCATGTCATCGGCGCGAATTCGTCGGACGACGGCTACATCCTGGGCATGGCCCGAGTCGCCGACCACGCCGGCTACATGTCCAACTATTTCCGCTGGTTCGGCAGCCCGGAGGATCCCTTCGGCTGGTATTACAACCTGCTGGCGCTGATGACCCATGTCAGCGACGCCAGTCTGTGGATGCGCCTGCCAGACCTGGCCGCCGGGCTAGTGTGCTGGCTGCTGCTGTCGCGTGAGGTGCTGCCCCGCCTCGGGCCGGCGGTGGAGGCCAGCAAACCCGCCTACTGGGCGGCGGCCATGGTCTTGCTGACCGCGTGGATGCCGTTCAACAACGGCCTGCGGCCGGAGGGCATCATCGCGCTCGGCTCGCTGGTCACCTATGTGCTGATCGAGCGGTCCATGCGGTACAGCCGGCTCACACCGGCGGCGCTGGCCGTCGTTACCGCCGCATTCACACTGGGTGTGCAGCCCACCGGCCTGATCGCGGTGGCCGCGCTGGTGGCCGGCGGCCGCCCGATGCTGCGGATCTTGGTGCGCCGTCATCGCCTGGTCGGCACGTTGCCGTTGGTGTCGCCGATGCTGGCCGCCGGCACCGTCATCCTGACCGTGGTGTTCGCCGACCAGACCCTGTCAACGGTGTTGGAAGCCACCAGGGTTCGCGCCAAAATCGGGCCGAGCCAGGCGTGGTATACCGAGAACCTGCGTTACTACTACCTCATCCTGCCCACCGTCGACGGTTCGCTGTCGCGGCGCTTCGGCTTTTTGATCACCGCGCTATGCCTGTTCACCGCGGTGTTCATCATGTTGCGGCGCAAGCGAATTCCCAGCGTGGCCCGCGGACCGGCGTGGCGGCTGATGGGCGTCATCTTCGGCACCATGTTCTTCCTGATGTTCACGCCCACCAAGTGGGTGCACCACTTCGGGCTGTTCGCCGCCGTAGGGGCGGCGATGGCCGCGCTGACGACGGTGTTGGTATCCCCATCGGTGCTGCGCTGGTCGCGCAACCGGATGGCGTTCCTGGCGGCGTTATTCTTCCTGCTGGCGTTGTGTTGGGCCACCACCAACGGCTGGTGGTATGTCTCCAGCTACGGTGTGCCGTTCAACAGCGCGATGCCGAAGATCGACGGGATCACAGTCAGCACAATCTTTTTCGCCCTGTTTGCGATCGCCGCCGGCTATGCGGCCTGGCTGCACTTCGCGCCCCGCGGCGCCGGCGAAGGGCGGCTGATCCGCGCGCTGACGACAGCCCCGGTACCGATCGTGGCCGGTTTCATGGCGGCGGTGTTCGTCGCGTCCATGGTGGCCGGGATCGTGCGACAGTACCCGACCTACTCCAACGGCTGGTCCAACGTGCGGGCGTTTGTCGGCGGCTGCGGACTGGCCGACGACGTACTCGTCGAGCCTGATACCAATGCGGGTTTCATGAAGCCGCTGGACGGCGATTCGGGTTCTTGGGGCCCCTTGGGCCCGCTGGGTGGAGTCAACCCGGTCGGCTTCACGCCCAACGGCGTACCGGAACACACGGTGGCCGAGGCGATCGTGATGAAACCCAACCAGCCCGGCACCGACTACGACTGGGATGCGCCGACCAAGCTGACGAGTCCTGGCATCAATGGTTCTACGGTGCCGCTGCCCTATGGGCTCGATCCCGCCCGGGTACCGTTGGCAGGCACCTACACCACCGGCGCACAGCAACAGAGCACACTCGTCTCGGCGTGGTATCTCCTGCCTAAGCCGGACGACGGGCATCCGCTGGTCGTGGTGACCGCCGCGGGCAAGATCGCCGGCAACAGCGTGCTGCACGGGTACACCCCCGGGCAGACTGTGGTGCTCGAATACGCCATGCCGGGACCCGGAGCGCTGGTACCCGCCGGGCGGATGGTGCCCGACGACCTATACGGAGAGCAGCCCAAGGCGTGGCGCAACCTGCGCTTCGCCCGAGCAAAGATGCCCGCCGATGCCGTCGCGGTCCGGGTGGTGGCCGAGGATCTGTCGCTGACACCGGAGGACTGGATCGCGGTGACCCCGCCGCGGGTACCGGACCTGCGCTCACTGCAGGAATATGTGGGCTCGACGCAGCCGGTGCTGCTGGACTGGGCGGTCGGTTTGGCCTTCCCGTGCCAGCAGCCGATGCTGCACGCCAATGGCATCGCCGAAATCCCGAAGTTCCGCATCACACCGGACTACTCGGCTAAGAAGCTGGACACCGACACGTGGGAAGACGGCACTAACGGCGGCCTGCTCGGGATCACCGACCTGTTGCTGCGGGCCCACGTCATGGCCACCTACCTGTCCCGCGACTGGGCCCGCGATTGGGGTTCCCTGCGCAAGTTCGACACCCTGGTCGATGCCCCTCCCGCCCAGCTCGAGTTGGGCACCGCGACCCGCAGCGGCCTGTGGTCACCGGGCAAGATCCGAATTGGTCCATAGC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3003326","ARO_id":"39910","ARO_name":"Mycobacterium tuberculosis embB mutations conferring resistance to ethambutol","ARO_description":"Point mutations that occur within Mycobacterium tuberculosis embB gene resulting in resistance to ethambutol","ARO_category":{"39310":{"category_aro_accession":"3002876","category_aro_cvterm_id":"39310","category_aro_name":"ethambutol resistant arabinosyltransferase","category_aro_description":"Arabinosyl transferases allow for the polymerization of arabinose to form arabinan. Arabinan is required for formation of mycobacterial cell walls and arabinosyltransferases are targets of the drug ethambutol. Mutations in these genes can confer resistance to ethambutol.","category_aro_class_name":"AMR Gene Family"},"36636":{"category_aro_accession":"3000497","category_aro_cvterm_id":"36636","category_aro_name":"ethambutol","category_aro_description":"Ethambutol is an antimycobacterial drug prescribed to treat tuberculosis. It is usually given in combination with other tuberculosis drugs, such as isoniazid, rifampicin, and pyrazinamide. Ethambutol inhibits arabinosyl biosynthesis, disrupting mycobacterial cell wall formation.","category_aro_class_name":"Antibiotic"},"36666":{"category_aro_accession":"3000527","category_aro_cvterm_id":"36666","category_aro_name":"polyamine antibiotic","category_aro_description":"Polyamine antibiotics are organic compounds having two or more primary amino groups.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"335":{"model_id":"335","model_name":"Staphylococcus aureus parE conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2827":"P587S","2828":"D434H","2829":"D434N"},"clinical":{"2827":"P587S","2828":"D434H","2829":"D434N"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"2101":{"protein_sequence":{"accession":"YP_040771.1","sequence":"MAMNKQNNYSDDSIQVLEGLEAVRKRPGMYIGSTDKRGLHHLVYEIVDNSVDEVLNGYGNEIDVTINKDGSISIEDNGRGMPTGIHKSGKPTVEVIFTVLHAGGKFGQGGYKTSGGLHGVGASVVNALSEWLEVEIHRDGNIYHQSFKNGGSPSSGLVKKGKTKKTGTKVTFKPDDTIFKASTSFNFDVLSERLQESAFLLKNLKITLNDLRSGKERQEHYHYEEGIKEFVSYVNEGKEVLHDVATFSGEANGIEVDVAFQYNDQYSESILSFVNNVRTKDGGTHEVGFKTAMTRVFNDYARRINELKTKDKNLDGNDIREGLTAVVSVRIPEELLQFEGQTKSKLGTSEARSAVDSVVADKLPFYLEEKGQLSKSLVKKAIKAQQAREAARKAREDARSGKKNKRKDTLLSGKLTPAQSKNTDKNELYLVEGDSAGGSAKLGRDRKFQAILPLRGKVINTEKARLEDIFKNEEINTIIHTIGAGVGTDFKIEDSNYNRVIIMTDADTDGAHIQVLLLTFFFKYMKPLVQAGRVFIALPPLYKLEKGKGKTKRVEYAWTDEELNKLQKELGKGFTLQRYKGLGEMNPEQLWETTMNPETRTLIRVQVEDEVRSSKRVTTLMGDKVQPRREWIEKHFEFGMQEDQSILDNSEVQVLENDQFDEEEI"},"dna_sequence":{"accession":"NC_002952","fmin":"1417762","fmax":"1419760","strand":"+","sequence":"TTGGCAATGAATAAACAAAATAATTATTCAGATGATTCAATACAGGTTTTAGAGGGGTTAGAAGCAGTTCGTAAAAGACCTGGTATGTATATTGGATCAACTGATAAACGGGGATTACATCATCTAGTATATGAAATTGTCGATAACTCCGTCGATGAAGTATTGAATGGTTACGGTAACGAAATAGATGTAACAATTAATAAAGATGGTAGTATTTCTATAGAAGATAATGGACGTGGTATGCCAACAGGTATACATAAATCAGGTAAACCGACAGTCGAAGTTATCTTTACTGTTTTACATGCAGGAGGTAAATTTGGACAAGGCGGCTATAAAACTTCAGGTGGTCTTCACGGCGTTGGTGCTTCAGTTGTAAATGCATTGAGTGAATGGCTTGAAGTTGAAATCCATCGAGATGGTAATATATATCATCAAAGTTTTAAAAACGGTGGTTCGCCATCTTCTGGTTTAGTGAAAAAAGGTAAAACTAAGAAAACAGGTACCAAAGTAACATTTAAACCTGATGACACAATTTTTAAAGCATCTACATCATTTAATTTTGATGTTTTAAGTGAACGACTACAAGAGTCTGCGTTCTTATTGAAAAATTTAAAAATAACGCTTAATGATTTACGCAGTGGTAAAGAGCGTCAAGAGCATTACCATTATGAAGAAGGAATCAAAGAATTTGTTAGTTATGTCAATGAAGGAAAAGAAGTTTTGCATGACGTGGCTACATTTTCAGGTGAAGCAAATGGTATAGAGGTAGACGTAGCTTTCCAATATAATGATCAATATTCAGAAAGTATTTTAAGTTTTGTAAATAATGTACGTACTAAAGATGGTGGTACACATGAAGTTGGTTTTAAAACAGCAATGACACGTGTATTTAATGATTATGCACGTCGTATTAATGAACTTAAAACAAAAGATAAAAACTTAGACGGTAATGATATTCGTGAAGGTTTAACAGCTGTTGTGTCTGTACGTATTCCAGAAGAATTACTACAATTTGAAGGACAAACGAAATCTAAATTGGGTACTTCTGAAGCAAGAAGTGCTGTTGATTCAGTAGTTGCAGACAAATTACCATTCTATTTAGAAGAAAAAGGACAATTGTCTAAATCACTTGTAAAAAAAGCAATTAAAGCACAACAAGCAAGGGAAGCTGCACGTAAAGCTCGTGAAGATGCTCGTTCAGGTAAGAAAAACAAGCGTAAAGACACTTTGCTATCTGGTAAATTAACACCTGCACAAAGTAAAAATACAGATAAAAATGAATTGTATTTAGTCGAAGGTGATTCTGCGGGAGGTTCAGCAAAACTTGGACGAGACCGCAAATTCCAAGCGATATTACCATTACGTGGTAAGGTAATTAATACAGAGAAAGCACGTCTGGAAGATATTTTTAAAAATGAAGAAATTAATACAATTATCCACACAATCGGGGCAGGCGTTGGTACTGACTTTAAAATTGAAGATAGTAACTATAATCGTGTAATTATTATGACTGATGCTGATACTGATGGTGCGCATATTCAAGTGCTATTGTTAACATTCTTCTTCAAATATATGAAACCGCTTGTTCAAGCAGGTCGTGTATTTATTGCTTTACCTCCACTTTATAAATTGGAAAAAGGTAAAGGCAAAACAAAGCGAGTTGAATACGCTTGGACAGACGAAGAGCTTAATAAATTACAAAAAGAACTTGGTAAGGGCTTCACGTTACAACGTTACAAAGGTTTGGGTGAGATGAACCCTGAACAATTATGGGAAACGACGATGAACCCAGAAACACGAACTTTAATTCGTGTACAAGTTGAAGATGAAGTGCGTTCATCTAAACGTGTAACAACATTAATGGGTGACAAAGTACAACCTAGACGTGAATGGATTGAAAAGCATTTTGAGTTTGGTATGCAAGAGGACCAAAGTATTTTAGATAATTCTGAAGTACAAGTGCTTGAAAATGATCAATTTGATGAGGAGGAAATCTAGT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35517","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus MRSA252","NCBI_taxonomy_id":"282458"}}}},"ARO_accession":"3003315","ARO_id":"39899","ARO_name":"Staphylococcus aureus parE conferring resistance to fluoroquinolones","ARO_description":"Point mutation in Staphylococcus aureus parE resulting in fluoroquinolones resistance","ARO_category":{"39897":{"category_aro_accession":"3003313","category_aro_cvterm_id":"39897","category_aro_name":"fluoroquinolone resistant parE","category_aro_description":"ParE is a subunit of topoisomerase IV, necessary for cell survival. Point mutations in ParE prevent fluoroquinolones from inhibiting DNA synthesis, thus conferring resistance.","category_aro_class_name":"AMR Gene Family"},"35942":{"category_aro_accession":"0000023","category_aro_cvterm_id":"35942","category_aro_name":"enoxacin","category_aro_description":"Enoxacin belongs to a group called fluoroquinolones. Its mode of action depends upon blocking bacterial DNA replication by binding itself to DNA gyrase and causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37004":{"category_aro_accession":"3000660","category_aro_cvterm_id":"37004","category_aro_name":"lomefloxacin","category_aro_description":"Lomefloxacin is a difluoropiperazinyl quinolone, sharing similar activities with other fluoroquinolones. It is used to treat urinary tract infections. Relative to other fluoroquinolones, it has a longer half life and has higher serum concentrations.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"37008":{"category_aro_accession":"3000664","category_aro_cvterm_id":"37008","category_aro_name":"trovafloxacin","category_aro_description":"Trovafloxacin is a trifluoroquinalone with a broad spectrum of activity that acts by inhibiting the uncoiling of supercoiled DNA. While potent against many Gram-positive and Gram-negative bacteria, it is less active against pseudomonads and Cl. difficile. It is usually taken as the prodrug trovafloxacin mesylate or alatrofloxacin mesylate for oral or intravenous administration, respectively.","category_aro_class_name":"Antibiotic"},"37009":{"category_aro_accession":"3000665","category_aro_cvterm_id":"37009","category_aro_name":"grepafloxacin","category_aro_description":"Grepafloxacin is a broad-spectrum antibacterial quinoline. It is no longer taken due to its high toxicity.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"37142":{"category_aro_accession":"3000762","category_aro_cvterm_id":"37142","category_aro_name":"pefloxacin","category_aro_description":"Pefloxacin is structurally and functionally similar to norfloxacin. It is poorly active against mycobacteria, while anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"366":{"model_id":"366","model_name":"Mycobacterium tuberculosis iniA mutant conferring resistance to Ethambutol","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3333":"S501W","3334":"G308R","3856":"P3A","3857":"R537H"},"experimental":{"3333":"S501W","3334":"G308R"},"clinical":{"3856":"P3A","3857":"R537H"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1240"},"41343":{"param_type":"deletion mutation from nucleotide sequence","param_description":"A subtype of the deletion mutation detection model parameter. This parameter is used when a set of deletion mutations is reported in a nucleotide sequence format. Such mutations may be of variable length - possibly causing a frameshift, but not premature termination of functional knockout. Mutation parameters of this type are reported in the CARD with the notation: [-]nt[position]:[nucleotides].","param_type_id":"41343","param_value":{"8026":"-nt93:5"}}},"model_sequences":{"sequence":{"2099":{"protein_sequence":{"accession":"CCP43072.1","sequence":"MVPAGLCAYRDLRRKRARKWGDTVTQPDDPRRVGVIVELIDHTIAIAKLNERGDLVQRLTRARQRITDPQVRVVIAGLLKQGKSQLLNSLLNLPAARVGDDEATVVITVVSYSAQPSARLVLAAGPDGTTAAVDIPVDDISTDVRRAPHAGGREVLRVEVGAPSPLLRGGLAFIDTPGVGGLGQPHLSATLGLLPEADAVLVVSDTSQEFTEPEMWFVRQAHQICPVGAVVATKTDLYPRWREIVNANAAHLQRARVPMPIIAVSSLLRSHAVTLNDKELNEESNFPAIVKFLSEQVLSRATERVRAGVLGEIRSATEQLAVSLGSELSVVNDPNLRDRLASDLERRKREAQQAVQQTALWQQVLGDGFNDLTADVDHDLRTRFRTVTEDAERQIDSCDPTAHWAEIGNDVENAIATAVGDNFVWAYQRSEALADDVARSFADAGLDSVLSAELSPHVMGTDFGRLKALGRMESKPLRRGHKMIIGMRGSYGGVVMIGMLSSVVGLGLFNPLSVGAGLILGRMAYKEDKQNRLLRVRSEAKANVRRFVDDISFVVSKQSRDRLKMIQRLLRDHYREIAEEITRSLTESLQATIAAAQVAETERDNRIRELQRQLGILSQVNDNLAGLEPTLTPRASLGRA"},"dna_sequence":{"accession":"AL123456","fmin":"410837","fmax":"412760","strand":"+","sequence":"ATGGTCCCCGCCGGTTTGTGCGCATACCGTGATCTGAGGCGTAAACGAGCGAGAAAGTGGGGCGACACGGTGACCCAGCCCGATGACCCACGTCGGGTCGGTGTGATCGTCGAACTGATCGATCACACTATCGCCATCGCCAAACTGAACGAGCGTGGTGATCTAGTACAGCGGTTGACGCGGGCTCGCCAGCGGATCACCGACCCGCAGGTCCGTGTGGTGATCGCCGGGCTGCTCAAACAGGGCAAGAGTCAATTGCTCAATTCGTTGCTCAACCTGCCCGCGGCGCGAGTAGGCGATGACGAGGCCACCGTGGTGATCACCGTCGTAAGCTACAGCGCCCAACCGTCGGCCCGGCTTGTGCTGGCCGCCGGGCCCGACGGGACAACCGCAGCGGTTGACATTCCCGTCGATGACATCAGCACCGATGTGCGTCGGGCTCCGCACGCCGGTGGCCGCGAGGTGTTGCGGGTCGAGGTCGGCGCGCCCAGCCCGCTGCTGCGGGGCGGGCTGGCGTTTATCGATACTCCGGGTGTGGGCGGCCTCGGACAGCCCCACCTGTCGGCGACGCTGGGGCTGCTACCCGAGGCCGATGCCGTCTTGGTGGTCAGCGACACCAGCCAGGAATTCACCGAACCCGAGATGTGGTTCGTGCGGCAGGCCCACCAGATCTGTCCGGTCGGGGCGGTCGTGGCCACCAAGACCGACCTGTATCCGCGCTGGCGGGAGATCGTCAATGCCAATGCAGCACATCTGCAGCGGGCCCGGGTTCCGATGCCGATCATCGCAGTCTCATCACTGTTGCGCAGCCACGCGGTCACGCTTAACGACAAAGAGCTCAACGAAGAGTCCAACTTTCCGGCGATCGTCAAGTTTCTCAGCGAGCAGGTGCTTTCCCGCGCGACGGAGCGAGTGCGTGCTGGGGTACTCGGCGAAATACGTTCGGCAACAGAGCAATTGGCGGTGTCTCTAGGTTCCGAACTATCGGTGGTCAACGACCCGAACCTCCGTGACCGACTTGCTTCGGATTTGGAGCGGCGCAAACGGGAAGCCCAGCAGGCGGTGCAACAGACAGCGCTGTGGCAGCAGGTGCTGGGCGACGGGTTCAACGACCTGACTGCTGACGTGGACCACGACCTACGAACCCGCTTCCGCACCGTCACCGAAGACGCCGAGCGCCAGATCGACTCCTGTGACCCGACTGCGCATTGGGCCGAGATTGGCAACGACGTCGAGAATGCGATCGCCACAGCGGTCGGCGACAACTTCGTGTGGGCATACCAGCGTTCCGAAGCGTTGGCCGACGACGTCGCTCGCTCCTTTGCCGACGCGGGGTTGGACTCGGTCCTGTCAGCAGAGCTGAGCCCCCACGTCATGGGCACCGACTTCGGCCGGCTCAAAGCGCTGGGCCGGATGGAATCGAAACCGCTGCGCCGGGGCCATAAAATGATTATCGGCATGCGGGGTTCCTATGGCGGCGTGGTCATGATTGGCATGCTGTCGTCGGTGGTCGGACTTGGGTTGTTCAACCCGCTATCGGTGGGGGCCGGGTTGATCCTCGGCCGGATGGCATATAAAGAGGACAAACAAAACCGGTTGCTGCGGGTGCGCAGCGAGGCCAAGGCCAATGTGCGGCGCTTCGTCGACGACATTTCGTTCGTCGTCAGCAAACAATCACGGGATCGGCTCAAGATGATCCAGCGTCTGCTGCGCGACCACTACCGCGAGATCGCCGAAGAGATCACCCGGTCGCTCACCGAGTCCCTGCAGGCGACCATCGCGGCGGCGCAGGTGGCGGAAACCGAGCGGGACAATCGAATTCGGGAACTTCAGCGGCAATTGGGTATCCTGAGCCAGGTCAACGACAACCTTGCCGGCTTGGAGCCAACCTTGACGCCCCGGGCGAGCTTGGGACGAGCGTGAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3003448","ARO_id":"40041","ARO_name":"Mycobacterium tuberculosis iniA mutant conferring resistance to Ethambutol","ARO_description":"Specific mutations in Mycobacterium tuberculosis iniA resulting in resistance to ethambutol","ARO_category":{"40040":{"category_aro_accession":"3003447","category_aro_cvterm_id":"40040","category_aro_name":"Ethambutol resistant iniA","category_aro_description":"Mutations that occurs on the iniA genes resulting in the resistance to ethambutol","category_aro_class_name":"AMR Gene Family"},"36636":{"category_aro_accession":"3000497","category_aro_cvterm_id":"36636","category_aro_name":"ethambutol","category_aro_description":"Ethambutol is an antimycobacterial drug prescribed to treat tuberculosis. It is usually given in combination with other tuberculosis drugs, such as isoniazid, rifampicin, and pyrazinamide. Ethambutol inhibits arabinosyl biosynthesis, disrupting mycobacterial cell wall formation.","category_aro_class_name":"Antibiotic"},"36666":{"category_aro_accession":"3000527","category_aro_cvterm_id":"36666","category_aro_name":"polyamine antibiotic","category_aro_description":"Polyamine antibiotics are organic compounds having two or more primary amino groups.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"462":{"model_id":"462","model_name":"Staphylococcus aureus pgsA mutations conferring resistance to daptomycin","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2213":"A64V","2214":"S177F","2215":"K66R","2229":"V59N"},"experimental":{"2213":"A64V","2214":"S177F","2215":"K66R","2229":"V59N"}},"41344":{"param_type":"insertion mutation from peptide sequence","param_description":"A subtype of the insertion mutation detection model parameter. This parameter is used when a set of insertion mutations is reported in a peptide sequence format. These are specific to codon insertions, where a multiple of three nucleotides are inserted. This does not cause a frameshift mutation. Mutation parameters of this type are reported in CARD with the notation: [+][AAs][position range].","param_type_id":"41344","param_value":{"3863":"+G76","3864":"+E77"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"3553":{"protein_sequence":{"accession":"WP_001025093","sequence":"MNIPNQITVFRVVLIPVFILFALVDFGFGNVSFLGGYEIRIELLISGFIFILASLSDFVDGYLARKWNLVTNMGKFLDPLADKLLVASALIVLVQLGLTNSVVAIIIIAREFAVTGLRLLQIEQGFVSAAGQLGKIKTAVTMVAITWLLLGDPLATLIGLSLGQILLYIGVIFTILSGIEYFYKGRDVFKQK"},"dna_sequence":{"accession":"NC_003923","fmin":"1278585","fmax":"1279164","strand":"+","sequence":"ATGAATATTCCGAACCAGATTACGGTTTTTAGAGTAGTGTTAATACCAGTTTTTATATTGTTTGCGTTAGTTGATTTTGGATTTGGCAATGTGTCATTTCTAGGAGGATATGAAATAAGAATTGAGTTATTAATCAGTGGTTTTATTTTTATATTGGCTTCCCTTAGCGATTTTGTTGATGGTTATTTAGCTAGAAAATGGAATTTAGTTACAAATATGGGGAAATTTTTGGATCCATTAGCGGATAAATTATTAGTTGCAAGTGCTTTAATTGTACTTGTGCAACTAGGACTAACAAATTCTGTAGTAGCAATCATTATTATTGCCAGAGAATTTGCCGTAACTGGTTTACGTTTACTACAAATTGAACAAGGATTCGTAAGTGCAGCTGGTCAATTAGGTAAAATTAAAACAGCAGTTACTATGGTAGCAATTACTTGGTTGTTATTAGGTGATCCATTGGCAACATTGATTGGTTTGTCATTAGGACAAATTTTATTATACATTGGCGTTATTTTTACTATCTTATCTGGTATTGAATACTTTTATAAAGGTAGAGATGTTTTTAAACAAAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3003323","ARO_id":"39907","ARO_name":"Staphylococcus aureus pgsA mutations conferring resistance to daptomycin","ARO_description":"Point mutations that occur within Staphylococcus aureus pgsA gene resulting in resistance to daptomycin","ARO_category":{"39627":{"category_aro_accession":"3003080","category_aro_cvterm_id":"39627","category_aro_name":"daptomycin resistant pgsA","category_aro_description":"pgsA or phosphatidylglycerophosphate synthetase is an integral membrane protein involved in phospholipid biosynthesis. It is a CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase. Laboratory experiments have detected mutations conferring daptomycin resistance in Entercoccus.","category_aro_class_name":"AMR Gene Family"},"35985":{"category_aro_accession":"0000068","category_aro_cvterm_id":"35985","category_aro_name":"daptomycin","category_aro_description":"Daptomycin is a novel lipopeptide antibiotic used in the treatment of certain infections caused by Gram-positive organisms. Daptomycin interferes with the bacterial cell membrane, reducing membrane potential and inhibiting cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"489":{"model_id":"489","model_name":"Mycobacterium tuberculosis gidB mutation conferring resistance to streptomycin","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2663":"W45C","2664":"R47Q","2665":"I55S","2666":"D67H","2667":"S70R","2668":"G71V","2670":"Q127P","2671":"A134E","2672":"A138E","2673":"W148R","2674":"A183E","2675":"V188G","2676":"A200E","3235":"P75S","3670":"A183T","3672":"W45S","3673":"P84L","3675":"H48Y","3676":"G30R","3678":"N52T","3679":"G117E","3681":"L79F","3682":"L49F","3683":"G164C","3688":"P84C","3689":"V188M"},"clinical":{"2663":"W45C","2664":"R47Q","2665":"I55S","2666":"D67H","2667":"S70R","2668":"G71V","2670":"Q127P","2671":"A134E","2672":"A138E","2673":"W148R","2674":"A183E","2675":"V188G","2676":"A200E","3235":"P75S","3670":"A183T","3672":"W45S","3673":"P84L","3675":"H48Y","3676":"G30R","3678":"N52T","3679":"G117E","3681":"L79F","3682":"L49F","3683":"G164C","3688":"P84C","3689":"V188M"}},"40394":{"param_type":"nonsense mutation","param_description":"A nucleotide substitution resulting in a change from an amino acid codon to a STOP codon. Nonsense mutations truncate protein translation prematurely, resulting in a defective or completely inactive protein. In CARD, nonsense mutations may be attached to models using the notation: [wild type amino acid][position][STOP] (e.g. Q42STOP). This parameter is not currently used in detection algorithms.","param_type_id":"40394","param_value":{"3677":"C52STOP"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"},"41345":{"param_type":"insertion mutation from nucleotide sequence","param_description":"A subtype of the insertion mutation detection model parameter. This parameter is used when a set of insertion mutations is reported in a nucleotide sequence format. Such mutations may be of variable length - possibly causing a frameshift, but not causing premature termination or a functional knockout. Mutation parameters of this type are reported in CARD with the notation: [+]nt[position]:[nucleotides].","param_type_id":"41345","param_value":{"8037":"+nt350:G","8038":"+nt351:G"}},"41343":{"param_type":"deletion mutation from nucleotide sequence","param_description":"A subtype of the deletion mutation detection model parameter. This parameter is used when a set of deletion mutations is reported in a nucleotide sequence format. Such mutations may be of variable length - possibly causing a frameshift, but not premature termination of functional knockout. Mutation parameters of this type are reported in the CARD with the notation: [-]nt[position]:[nucleotides].","param_type_id":"41343","param_value":{"8039":"-nt115:C"}}},"model_sequences":{"sequence":{"4316":{"protein_sequence":{"accession":"CCP46748.1","sequence":"MSPIEPAASAIFGPRLGLARRYAEALAGPGVERGLVGPREVGRLWDRHLLNCAVIGELLERGDRVVDIGSGAGLPGVPLAIARPDLQVVLLEPLLRRTEFLREMVTDLGVAVEIVRGRAEESWVQDQLGGSDAAVSRAVAALDKLTKWSMPLIRPNGRMLAIKGERAHDEVREHRRVMIASGAVDVRVVTCGANYLRPPATVVFARRGKQIARGSARMASGGTA"},"dna_sequence":{"accession":"AL123456","fmin":"4407527","fmax":"4408202","strand":"-","sequence":"TCACGCCGTCCCTCCACTCGCCATCCGTGCCGACCCTCGGGCGATCTGCTTTCCACGTCGTGCGAACACCACGGTCGCGGGCGGACGCAAATAGTTCGCGCCACATGTCACCACCCTGACATCAACCGCGCCCGATGCGATCATCACACGCCGGTGCTCCCGTACTTCGTCGTGAGCCCGCTCGCCTTTGATGGCGAGCATTCGCCCGTTCGGCCGTATCAACGGCATGCTCCATTTCGTCAACTTGTCCAACGCGGCCACCGCCCGTGACACCGCAGCGTCGCTGCCGCCCAATTGGTCCTGCACCCAGGACTCCTCGGCGCGCCCCCGCACGATCTCAACGGCCACGCCCAGATCTGTCACCATCTCTCGAAGAAACTCGGTGCGGCGCAGTAGCGGTTCTAGGAGAACTACCTGGAGGTCCGGCCGCGCTATCGCCAATGGCACGCCCGGCAACCCGGCTCCGCTACCGATATCCACGACCCGGTCACCGCGTTCGAGGAGCTCACCGATCACGGCGCAGTTCAGTAGATGCCGGTCCCATAGCCTACCGACTTCGCGGGGTCCCACCAGCCCCCGCTCCACACCGGGTCCCGCCAACGCTTCGGCGTACCGCCGAGCAAGGCCAAGCCGCGGTCCGAAGATCGCAGACGCCGCGGGCTCGATCGGAGACAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3003470","ARO_id":"40063","ARO_name":"Mycobacterium tuberculosis gidB mutation conferring resistance to streptomycin","ARO_description":"Specific mutations that occurs on Mycobacterium tuberculosis gidB causing it to be streptomycin resistant","ARO_category":{"40059":{"category_aro_accession":"3003466","category_aro_cvterm_id":"40059","category_aro_name":"antibiotic resistant gidB","category_aro_description":"GidB is a m7G methyltransferase specific for 16S rRNA. Mutations within the gidB gene causes changes in the structure or 16s rRNA, leading to resistance to aminoglycosides","category_aro_class_name":"AMR Gene Family"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"505":{"model_id":"505","model_name":"Mycobacterium tuberculosis iniC mutant conferring resistance to ethambutol","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2346":"P248A","3352":"W83G"},"clinical":{"2346":"P248A"},"experimental":{"3352":"W83G"}},"40394":{"param_type":"nonsense mutation","param_description":"A nucleotide substitution resulting in a change from an amino acid codon to a STOP codon. Nonsense mutations truncate protein translation prematurely, resulting in a defective or completely inactive protein. In CARD, nonsense mutations may be attached to models using the notation: [wild type amino acid][position][STOP] (e.g. Q42STOP). This parameter is not currently used in detection algorithms.","param_type_id":"40394","param_value":{"3530":"Q351STOP"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"900"},"41345":{"param_type":"insertion mutation from nucleotide sequence","param_description":"A subtype of the insertion mutation detection model parameter. This parameter is used when a set of insertion mutations is reported in a nucleotide sequence format. Such mutations may be of variable length - possibly causing a frameshift, but not causing premature termination or a functional knockout. Mutation parameters of this type are reported in CARD with the notation: [+]nt[position]:[nucleotides].","param_type_id":"41345","param_value":{"8017":"+nt98:A","8018":"+nt79:T"}}},"model_sequences":{"sequence":{"2100":{"protein_sequence":{"accession":"CCP43073.1","sequence":"MSTSDRVRAILHATIQAYRGAPAYRQRGDVFCQLDRIGARLAEPLRIALAGTLKAGKSTLVNALVGDDIAPTDATEATRIVTWFRHGPTPRVTANHRGGRRANVPITRRGGLSFDLRRINPAELIDLEVEWPAEELIDATIVDTPGTSSLACDASERTLRLLVPADGVPRVDAVVFLLRTLNAADVALLKQIGGLVGGSVGALGIIGVASRADEIGAGRIDAMLSANDVAKRFTRELNQMGICQAVVPVSGLLALTARTLRQTEFIALRKLAGAERTELNRALLSVDRFVRRDSPLPVDAGIRAQLLERFGMFGIRMSIAVLAAGVTDSTGLAAELLERSGLVALRNVIDQQFAQRSDMLKAHTALVSLRRFVQTHPVPATPYVIADIDPLLADTHAFEELRMLSLLPSRATTLNDDEIASLRRIIGGSGTSAAARLGLDPANSREAPRAALAAAQHWRRRAAHPLNDPFTTRACRAAVRSAEAMVAEFSARR"},"dna_sequence":{"accession":"AL123456","fmin":"412756","fmax":"414238","strand":"+","sequence":"GTGAGCACCAGCGACCGGGTCCGCGCGATTCTGCACGCAACCATCCAGGCCTACCGGGGTGCGCCGGCCTATCGTCAGCGTGGCGACGTTTTTTGCCAGCTGGACCGCATCGGTGCGCGCCTAGCCGAACCGCTGCGCATCGCGTTGGCTGGCACACTCAAGGCCGGAAAATCCACTCTCGTCAACGCCCTTGTCGGCGACGACATCGCTCCGACCGATGCCACCGAGGCCACCCGGATTGTGACCTGGTTCCGGCACGGTCCGACACCGCGGGTCACCGCCAACCATCGCGGCGGTCGACGCGCCAACGTGCCGATCACCCGTCGGGGCGGGCTGAGTTTCGACCTGCGCAGGATCAACCCGGCCGAGCTGATCGACCTGGAAGTCGAGTGGCCAGCCGAGGAACTCATCGACGCCACCATTGTTGACACCCCGGGAACGTCGTCGTTGGCATGCGATGCCTCCGAGCGCACGTTGCGGCTGCTGGTCCCCGCCGACGGGGTGCCTCGGGTGGATGCGGTGGTGTTCCTGTTGCGCACCCTGAACGCCGCTGACGTCGCGCTGCTCAAACAGATCGGTGGGCTGGTCGGCGGGTCGGTGGGAGCCCTGGGCATCATCGGGGTGGCGTCTCGCGCGGATGAGATCGGCGCGGGCCGCATCGACGCGATGCTCTCGGCCAACGACGTGGCCAAGCGGTTCACCCGCGAACTGAACCAGATGGGCATTTGCCAGGCGGTGGTGCCGGTATCCGGACTTCTTGCGCTGACCGCGCGCACACTGCGCCAGACCGAGTTCATCGCGCTGCGCAAGCTGGCCGGTGCCGAGCGCACCGAGCTCAATAGGGCCCTGCTGAGCGTGGACCGTTTTGTGCGCCGGGACAGTCCGCTACCGGTGGACGCGGGCATCCGTGCGCAATTGCTCGAGCGGTTCGGCATGTTCGGCATCCGGATGTCGATTGCCGTGCTGGCGGCCGGCGTGACCGATTCGACCGGGCTGGCCGCCGAACTGCTGGAGCGCAGCGGGCTGGTGGCGCTGCGCAATGTGATAGACCAGCAGTTCGCGCAGCGCTCCGACATGCTTAAGGCGCATACCGCCTTGGTCTCCTTGCGCCGATTCGTGCAGACGCATCCGGTGCCGGCGACCCCGTACGTCATTGCCGACATCGACCCGTTGCTAGCCGACACCCACGCCTTCGAAGAACTCCGAATGCTAAGCCTTTTGCCTTCGCGGGCAACGACATTGAACGACGACGAAATCGCGTCGCTGCGCCGCATCATCGGCGGGTCGGGCACCAGTGCCGCCGCTCGGCTGGGCCTGGATCCCGCGAATTCTCGCGAGGCCCCGCGCGCCGCGCTGGCCGCAGCGCAACACTGGCGTCGCCGTGCGGCGCATCCACTCAACGATCCGTTCACTACCAGGGCCTGTCGCGCGGCGGTGCGCAGCGCCGAGGCGATGGTGGCGGAGTTCTCTGCTCGCCGCTGAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3003451","ARO_id":"40044","ARO_name":"Mycobacterium tuberculosis iniC mutant conferring resistance to ethambutol","ARO_description":"Specific mutations that occurs on Mycobacterium tuberculosis iniC causing it to be ethambutol resistant.","ARO_category":{"40043":{"category_aro_accession":"3003450","category_aro_cvterm_id":"40043","category_aro_name":"Ethambutol resistant iniC","category_aro_description":"Mutations that occurs on the iniC genes resulting in the resistance to ethambutol","category_aro_class_name":"AMR Gene Family"},"36636":{"category_aro_accession":"3000497","category_aro_cvterm_id":"36636","category_aro_name":"ethambutol","category_aro_description":"Ethambutol is an antimycobacterial drug prescribed to treat tuberculosis. It is usually given in combination with other tuberculosis drugs, such as isoniazid, rifampicin, and pyrazinamide. Ethambutol inhibits arabinosyl biosynthesis, disrupting mycobacterial cell wall formation.","category_aro_class_name":"Antibiotic"},"36666":{"category_aro_accession":"3000527","category_aro_cvterm_id":"36666","category_aro_name":"polyamine antibiotic","category_aro_description":"Polyamine antibiotics are organic compounds having two or more primary amino groups.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"597":{"model_id":"597","model_name":"Klebsiella pneumoniae ramR mutants","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2110":"K5E","2111":"T43M","2112":"T162I","2113":"A19V","2134":"A16D","2135":"I88N","2863":"G96D"},"clinical":{"2110":"K5E","2111":"T43M","2112":"T162I","2113":"A19V","2134":"A16D","2135":"I88N","2863":"G96D"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"360"}},"model_sequences":{"sequence":{"4332":{"protein_sequence":{"accession":"ABR76005.1","sequence":"MARPKSEDKKQALLEAATAAFAQSGIAASTSAIARSAGVAEGTLFRYFATKDELLNELYLAIKLRLVRTMIAGLDPDEKRPKENARNIWNSYIDWGVRNPMEHKAIRRMALSERITDETRRQVKESFPELNEMCQLSVKEIFLSEAYRAFGDALFLSLAETTIEFASHDPQRAREIIALGFEAMWHALHEADA"},"dna_sequence":{"accession":"CP000647","fmin":"622039","fmax":"622621","strand":"-","sequence":"TTAGGCGTCCGCCTCATGCAGGGCGTGCCACATGGCTTCAAAGCCGAGGGCGATAATCTCCCGGGCGCGCTGCGGATCGTGGCTGGCGAATTCGATGGTGGTTTCCGCCAGCGACAGAAACAGGGCGTCGCCAAAGGCGCGGTACGCCTCGCTGAGGAATATCTCTTTCACCGACAGCTGGCACATTTCGTTGAGCTCCGGAAAGCTCTCTTTTACCTGGCGGCGGGTTTCGTCGGTGATGCGCTCGCTGAGCGCCATCCGGCGGATCGCTTTGTGCTCCATCGGGTTGCGCACGCCCCAGTCGATATAGCTGTTCCAGATATTGCGCGCGTTCTCTTTCGGGCGCTTCTCGTCCGGATCCAGCCCGGCGATCATTGTGCGCACCAGGCGCAGCTTAATCGCGAGGTACAGCTCGTTGAGCAACTCATCCTTGGTGGCGAAATAGCGAAACAGCGTTCCCTCGGCCACACCGGCGCTGCGGGCGATGGCCGACGTCGAGGCGGCTATGCCGGACTGGGCGAAAGCCGCGGTGGCAGCTTCCAGTAACGCTTGCTTTTTATCTTCACTCTTTGGACGAGCCAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37607","NCBI_taxonomy_name":"Klebsiella pneumoniae subsp. pneumoniae MGH 78578","NCBI_taxonomy_id":"272620"}}}},"ARO_accession":"3003380","ARO_id":"39964","ARO_name":"Klebsiella pneumoniae ramR mutants","ARO_description":"RamR is a repressor that regulates RamA expression. Mutations lead to the upregulation of AcrAB, which is positively regulated by RamA.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"627":{"model_id":"627","model_name":"Escherichia coli rpoB mutants conferring resistance to rifampicin","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2024":"Q513L","2025":"Q513P","2026":"H526Y","2027":"R529C","2028":"R529S","2029":"S531F","2030":"L533P","2031":"T563P","2032":"P564L","2033":"V146F","2034":"R687H"},"clinical":{"2024":"Q513L","2025":"Q513P","2026":"H526Y","2027":"R529C","2028":"R529S","2029":"S531F","2030":"L533P","2031":"T563P","2032":"P564L","2033":"V146F","2034":"R687H"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"2500"}},"model_sequences":{"sequence":{"2096":{"protein_sequence":{"accession":"NP_312937.1","sequence":"MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQDPEGQYGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEGTVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRDNKLQMELVPERLRGETASFDIEANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEYIAGKVVAKDYIDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETLRVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLREEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGGVVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEMQLKQAKKDLSEELQILEAGLFSRIRAVLVAGGVEAEKLDKLPRDRWLELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDEEVMRLAENLRKGMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE"},"dna_sequence":{"accession":"NC_002695","fmin":"4990140","fmax":"4994169","strand":"+","sequence":"ATGGTTTACTCCTATACCGAGAAAAAACGTATTCGTAAGGATTTTGGTAAACGTCCACAAGTTCTGGATGTACCTTATCTCCTTTCTATCCAGCTTGACTCGTTTCAGAAATTTATCGAGCAAGATCCTGAAGGGCAGTATGGTCTGGAAGCTGCTTTCCGTTCCGTATTCCCGATTCAGAGCTACAGCGGTAATTCCGAGCTGCAATACGTCAGCTACCGCCTTGGCGAACCGGTGTTTGACGTCCAGGAATGTCAAATCCGTGGCGTGACCTATTCCGCACCGCTGCGCGTTAAACTGCGTCTGGTGATCTATGAGCGCGAAGCGCCGGAAGGCACCGTAAAAGACATTAAAGAACAAGAAGTCTACATGGGCGAAATTCCGCTCATGACAGACAACGGTACCTTTGTTATCAACGGTACTGAGCGTGTTATCGTTTCCCAGCTGCACCGTAGTCCGGGCGTCTTCTTTGACTCCGACAAAGGTAAAACCCACTCTTCGGGTAAAGTGCTGTATAACGCGCGCATCATCCCTTACCGTGGTTCCTGGCTGGACTTCGAATTCGATCCGAAGGACAACCTGTTCGTACGTATCGACCGTCGCCGTAAACTGCCTGCGACCATCATTCTGCGTGCCCTGAACTACACCACAGAGCAGATCCTCGACCTGTTCTTTGAAAAAGTTATCTTTGAAATCCGTGATAACAAGCTGCAGATGGAACTGGTGCCGGAACGCCTGCGTGGTGAAACCGCATCCTTTGACATCGAAGCTAACGGTAAAGTGTACGTAGAAAAAGGCCGCCGTATCACTGCGCGCCACATTCGCCAGCTGGAAAAAGACGACGTCAAACTGATCGAAGTCCCGGTTGAGTACATCGCAGGTAAAGTGGTTGCTAAAGACTATATTGATGAGTCTACCGGCGAGCTGATCTGCGCAGCGAACATGGAGCTGAGCCTGGATCTGCTGGCTAAGCTGAGCCAGTCTGGTCACAAGCGTATCGAAACGCTGTTCACCAATGATCTGGATCACGGCCCGTATATCTCTGAAACCTTACGTGTCGACCCAACTAACGACCGTCTGAGCGCACTGGTAGAAATCTACCGCATGATGCGCCCTGGCGAGCCGCCGACTCGTGAAGCAGCGGAAAGCCTGTTCGAGAACCTGTTCTTCTCCGAAGACCGTTATGACCTGTCTGCGGTTGGTCGTATGAAGTTCAACCGTTCTCTGCTGCGCGAAGAAATCGAAGGTTCTGGTATCCTGAGCAAAGACGACATCATTGATGTTATGAAAAAGCTCATCGATATCCGTAACGGTAAAGGCGAAGTCGATGATATCGACCACCTCGGCAACCGTCGTATCCGTTCCGTTGGCGAAATGGCGGAAAACCAGTTCCGCGTTGGCCTGGTACGTGTAGAGCGTGCGGTGAAAGAGCGTCTGTCTCTGGGCGATCTGGATACCCTGATGCCTCAGGATATGATCAACGCCAAGCCGATTTCCGCAGCAGTGAAAGAGTTCTTCGGTTCCAGCCAGCTGTCTCAGTTTATGGACCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCAACTCTCTGTCCGTGTACGCACAGACTAACGAATACGGCTTCCTTGAGACTCCGTATCGTAAAGTGACTGACGGTGTTGTAACTGACGAAATTCACTACCTGTCTGCTATCGAAGAAGGCAACTACGTTATCGCCCAGGCGAACTCCAACCTGGATGAAGAAGGCCACTTCGTAGAAGACCTGGTAACCTGCCGTAGCAAAGGCGAATCCAGCTTGTTCAGCCGTGACCAGGTTGACTACATGGACGTATCCACCCAGCAGGTGGTATCCGTCGGTGCGTCCCTGATCCCGTTCCTGGAACACGATGACGCCAACCGTGCATTGATGGGTGCGAACATGCAACGTCAGGCCGTTCCGACTCTGCGTGCTGATAAGCCGCTGGTTGGTACTGGTATGGAACGTGCTGTTGCCGTTGACTCCGGTGTAACTGCGGTTGCTAAACGTGGTGGTGTCGTTCAGTACGTGGATGCTTCCCGTATCGTTATCAAAGTTAACGAAGACGAGATGTATCCGGGTGAAGCAGGTATCGACATCTACAACCTGACCAAATACACCCGTTCTAACCAGAACACCTGTATTAACCAGATGCCGTGTGTGTCTCTGGGTGAACCGGTTGAACGTGGCGACGTGCTGGCAGACGGTCCGTCCACCGACCTCGGTGAACTGGCGCTTGGTCAGAACATGCGCGTAGCGTTCATGCCGTGGAATGGTTACAACTTCGAAGACTCCATCCTCGTATCCGAGCGTGTTGTTCAGGAAGACCGTTTCACCACCATCCACATTCAGGAACTGGCGTGTGTGTCCCGTGACACCAAGCTGGGGCCAGAAGAGATCACCGCTGACATCCCGAACGTGGGTGAAGCTGCGCTCTCCAAACTGGATGAATCCGGTATCGTTTATATTGGTGCGGAAGTGACCGGTGGCGACATTCTGGTTGGTAAGGTTACGCCGAAAGGTGAAACTCAGCTGACCCCAGAAGAAAAACTGCTGCGTGCGATCTTCGGTGAGAAAGCGTCTGACGTTAAAGACTCTTCTCTGCGCGTACCAAACGGTGTATCCGGTACGGTTATCGACGTTCAGGTCTTTACTCGCGATGGCGTAGAAAAAGACAAACGTGCGCTGGAAATCGAAGAAATGCAGCTCAAACAGGCGAAGAAAGACCTGTCTGAAGAACTGCAGATCCTCGAAGCGGGTCTGTTCAGCCGTATCCGTGCTGTGCTGGTAGCCGGTGGCGTTGAAGCTGAGAAGCTCGACAAATTGCCGCGCGATCGCTGGCTGGAGCTGGGCCTGACCGACGAAGAGAAACAAAATCAGCTGGAACAGCTGGCTGAGCAGTATGACGAACTGAAACACGAGTTCGAGAAGAAACTCGAAGCGAAACGCCGCAAAATCACCCAGGGCGACGATCTGGCACCGGGCGTGCTGAAGATTGTTAAGGTATATCTGGCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACTTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAGGAAGTCGCGAAACTGCGTGAATTCATCCAGCGTGCGTACGATCTGGGCGCTGACGTTCGTCAGAAAGTTGACCTGAGTACCTTCAGCGATGAAGAAGTTATGCGTCTGGCTGAAAACCTGCGCAAAGGTATGCCAATCGCAACGCCGGTGTTCGACGGTGCGAAAGAAGCAGAAATTAAAGAGCTGCTGAAACTTGGCGACCTGCCGACTTCTGGTCAGATCCGCCTGTACGACGGCCGCACTGGTGAACAGTTCGAACGTCCGGTAACCGTTGGTTACATGTACATGCTGAAACTGAACCACCTGGTCGACGACAAGATGCACGCGCGTTCCACCGGTTCTTACAGCCTGGTTACTCAGCAGCCGCTGGGTGGTAAGGCACAGTTCGGTGGTCAGCGTTTCGGGGAGATGGAAGTGTGGGCGCTGGAAGCATACGGCGCAGCATACACCCTGCAGGAAATGCTCACCGTTAAGTCTGATGACGTGAACGGTCGTACTAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCGAACTGGAAGACGAGTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36747","NCBI_taxonomy_name":"Escherichia coli O157:H7 str. Sakai","NCBI_taxonomy_id":"386585"}}}},"ARO_accession":"3003288","ARO_id":"39872","ARO_name":"Escherichia coli rpoB mutants conferring resistance to rifampicin","ARO_description":"Point mutations that occurs in Escherichia coli rpoB resulting in resistance to rifampicin","ARO_category":{"36349":{"category_aro_accession":"3000210","category_aro_cvterm_id":"36349","category_aro_name":"rifamycin-resistant beta-subunit of RNA polymerase (rpoB)","category_aro_description":"Rifampin resistant RNA polymerases include amino acids substitutions which disrupt the affinity of rifampin for its binding site. These mutations are frequently concentrated in the rif I region of the beta-subunit and most often involve amino acids which make direct interactions with rifampin. However, mutations which also confer resistance can occur outside this region and may involve amino acids which do not directly make contact with rifampin.","category_aro_class_name":"AMR Gene Family"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36656":{"category_aro_accession":"3000517","category_aro_cvterm_id":"36656","category_aro_name":"rifaximin","category_aro_description":"Rifaximin is a semi-synthetic rifamycin used to treat traveller's diarrhea. Rifaximin inhibits RNA synthesis by binding to the beta subunit of bacterial RNA polymerase.","category_aro_class_name":"Antibiotic"},"36669":{"category_aro_accession":"3000530","category_aro_cvterm_id":"36669","category_aro_name":"rifabutin","category_aro_description":"Rifabutin is a semisynthetic rifamycin used in tuberculosis therapy. It inhibits DNA-dependent RNA synthesis.","category_aro_class_name":"Antibiotic"},"36673":{"category_aro_accession":"3000534","category_aro_cvterm_id":"36673","category_aro_name":"rifapentine","category_aro_description":"Rifapentine is a semisynthetic rifamycin that inhibits DNA-dependent RNA synthesis. It is often used in the treatment of tuberculosis and leprosy.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"756":{"model_id":"756","model_name":"Enterococcus faecium liaR mutant conferring daptomycin resistance","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"22":"W73C"},"clinical":{"22":"W73C"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"40":{"protein_sequence":{"accession":"AFK58562.1","sequence":"MIKVLLVDDHEMVRLGVSSYLSIQEDIEVIGEAENGRQGYEKAMTLRPDVILMDLVMEEMDGIESTKAILKDWPEAKIIIVTSFIDDEKVYPAIEAGAAGYLLKTSTAHEIADAIRATQRGERVLEPEVTTKMMEKMSRRNEPVLHEELTNRENEILMLISEGKSNQEIADELFITLKTVKTHVSNILAKLEVEDRTQAAIYAFKHGLVK"},"dna_sequence":{"accession":"CP003583","fmin":"914819","fmax":"915452","strand":"+","sequence":"ATGATAAAAGTTTTATTAGTAGATGACCATGAAATGGTGCGCTTAGGCGTCTCTTCTTATTTATCTATTCAAGAAGACATTGAAGTAATTGGAGAAGCTGAAAATGGACGACAAGGCTATGAGAAGGCGATGACACTTCGACCGGACGTCATTTTAATGGACTTAGTCATGGAAGAAATGGATGGTATCGAATCAACAAAAGCAATCTTAAAAGATTGGCCAGAAGCTAAAATCATTATCGTAACCAGTTTTATTGATGACGAAAAAGTTTATCCTGCCATTGAAGCAGGTGCAGCAGGGTATTTGTTGAAGACCTCTACCGCACATGAAATTGCTGATGCTATAAGGGCAACGCAACGTGGCGAGCGAGTATTAGAACCAGAAGTGACAACAAAAATGATGGAAAAAATGAGTCGGCGAAATGAGCCTGTATTACATGAAGAACTAACGAATCGGGAAAATGAAATTTTAATGCTGATTTCTGAAGGAAAAAGTAATCAGGAAATAGCGGACGAATTGTTTATTACACTGAAAACAGTAAAAACACATGTTTCCAATATATTGGCTAAGCTAGAAGTGGAAGACCGTACACAAGCCGCTATCTATGCATTCAAACATGGTTTGGTGAAATAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37599","NCBI_taxonomy_name":"Enterococcus faecium DO","NCBI_taxonomy_id":"333849"}}}},"ARO_accession":"3003078","ARO_id":"39625","ARO_name":"Enterococcus faecium liaR mutant conferring daptomycin resistance","ARO_description":"liaR is a response regulator found in the liaFSR signal transduction pathway. Mutations confer daptomycin resistance.","ARO_category":{"41427":{"category_aro_accession":"3004263","category_aro_cvterm_id":"41427","category_aro_name":"daptomycin resistant liaR","category_aro_description":"Mutations to the liaR response regulator that confer resistance to daptomycin.","category_aro_class_name":"AMR Gene Family"},"35985":{"category_aro_accession":"0000068","category_aro_cvterm_id":"35985","category_aro_name":"daptomycin","category_aro_description":"Daptomycin is a novel lipopeptide antibiotic used in the treatment of certain infections caused by Gram-positive organisms. Daptomycin interferes with the bacterial cell membrane, reducing membrane potential and inhibiting cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"794":{"model_id":"794","model_name":"Staphylococcus aureus rpoC conferring resistance to daptomycin","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2071":"Q961K","2070":"F632S"},"experimental":{"2071":"Q961K","2070":"F632S"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"2400"}},"model_sequences":{"sequence":{"2053":{"protein_sequence":{"accession":"YP_039997.1","sequence":"MIDVNNFHYMKIGLASPEKIRSWSFGEVKKPETINYRTLKPEKDGLFCERIFGPTKDWECSCGKYKRVRYKGMVCDRCGVEVTKSKVRRERMGHIELAAPVSHIWYFKGIPSRMGLLLDMSPRALEEVIYFASYVVVDPGPTGLEKKTLLSEAEFRDYYDKYPGQFVAKMGAEGIKDLLEEIDLDEELKLLRDELESATGQRLTRAIKRLEVVESFRNSGNKPSWMILDVLPIIPPEIRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPGIIVQNEKRMLQEAVDALIDNGRRGRPVTGPGNRPLKSLSHMLKGKQGRFRQNLLGKRVDYSGRSVIAVGPSLKMYQCGLPKEMALELFKPFVMKELVQREIATNIKNAKSKIERMDDEVWDVLEEVIREHPVLLNRAPTLHRLGIQAFEPTLVEGRAIRLHPLVTTAYNADFDGDQMAVHVPLSKEAQAEARMLMLAAQNILNPKDGKPVVTPSQDMVLGNYYLTLERKDAVNTGAIFNNTNEVLKAYANGFVHLHTRIGVHASSFNNPTFTEEQNKKILATSVGKIIFNEIIPDSFAYINEPTQENLERKTPNRYFIDPTTLGEGGLKEYFENEELIEPFNKKFLGNIIAEVFNRFSITDTSMMLDRMKDLGFKFSSKAGITVGVADIVVLPDKQQILDEHEKLVDRITKQFNRGLITEEERYNAVVEIWTDAKDQIQGELMQSLDKTNPIFMMSDSGARGNASNFTQLAGMRGLMAAPSGKIIELPITSSFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIVREEDCGTDRGLLVSDIKEGTEMIEPFIERIEGRYSKETIRHPETDEVIIRPDELITPEIAKKITDAGIEQMYIRSAFTCNARHGVCEKCYGKNLATGEKVEVGEAVGTIAAQSIGEPGTQLTMRTFHTGGVAGSDITQGLPRIQEIFEARNPKGQAVITEIEGVVEDIKLAKDRQQEIVVKGANETRSYLASGTSRIIVEIGQPVQRGEVLTEGSIEPKNYLSVAGLNATESYLLKEVQKVYRMQGVEIDDKHVEVMVRQMLRKVRIIEAGDTKLLPGSLVDIHNFTDANREAFKHRKRPATAKPVLLGITKASLETESFLSAASFQETTRVLTDAAIKGKRDDLLGLKENVIIGKLIPAGTGMRRYSDVKYEKTAKPVAEVESQTEVTE"},"dna_sequence":{"accession":"NC_002952","fmin":"594518","fmax":"598142","strand":"+","sequence":"TTGATTGATGTAAATAATTTCCATTATATGAAAATAGGATTGGCTTCACCTGAAAAAATCCGTTCTTGGTCTTTTGGTGAAGTTAAAAAACCTGAAACAATCAACTACCGTACATTAAAACCTGAAAAAGATGGTCTATTCTGTGAAAGAATTTTCGGACCTACAAAAGACTGGGAATGTAGTTGTGGTAAATACAAACGTGTTCGCTACAAAGGCATGGTCTGTGACAGATGTGGAGTTGAAGTAACTAAATCTAAAGTACGTCGTGAAAGAATGGGTCACATTGAACTTGCTGCTCCAGTTTCTCACATTTGGTATTTCAAAGGTATACCAAGTCGTATGGGATTATTACTTGACATGTCACCAAGAGCATTAGAAGAAGTTATTTACTTTGCTTCTTATGTTGTTGTAGATCCAGGTCCAACTGGTTTAGAAAAGAAAACTTTATTATCTGAAGCTGAATTCAGAGATTATTATGATAAATACCCAGGTCAATTCGTTGCAAAAATGGGTGCAGAAGGTATTAAAGATTTACTTGAAGAGATTGATCTTGACGAAGAACTTAAATTGTTACGCGATGAGTTGGAATCAGCTACTGGTCAAAGACTTACTCGTGCAATTAAACGTTTAGAAGTTGTTGAATCATTCCGTAATTCAGGTAACAAACCTTCATGGATGATTTTAGATGTACTTCCAATCATCCCACCAGAAATTCGTCCAATGGTTCAATTAGATGGTGGACGATTTGCAACAAGTGACTTAAACGACTTATACCGTCGTGTAATTAATCGAAATAATCGTTTGAAACGTTTATTAGATTTAGGTGCACCTGGTATCATCGTTCAAAACGAAAAACGTATGTTACAAGAAGCCGTTGACGCTTTAATTGATAATGGTCGTCGTGGTCGTCCAGTTACTGGCCCAGGTAACCGTCCATTAAAATCTTTATCTCATATGTTAAAAGGTAAACAAGGTCGTTTCCGTCAAAACCTACTTGGTAAACGTGTTGACTATTCAGGACGTTCAGTTATCGCGGTAGGTCCAAGCTTGAAAATGTACCAATGTGGTTTACCGAAAGAAATGGCACTTGAACTATTTAAACCATTTGTAATGAAAGAATTAGTTCAACGTGAAATTGCAACTAACATTAAAAATGCGAAGAGTAAAATCGAACGCATGGATGATGAAGTTTGGGACGTATTGGAAGAAGTAATTAGAGAACATCCTGTATTACTTAACCGTGCACCAACACTTCATAGACTTGGTATTCAAGCATTTGAACCAACTTTAGTTGAAGGTCGTGCGATTCGTCTACATCCACTTGTAACAACAGCTTATAACGCTGACTTTGATGGTGACCAAATGGCGGTTCACGTTCCTTTATCAAAAGAGGCACAAGCTGAAGCAAGAATGTTGATGTTAGCAGCACAAAACATCTTGAACCCTAAAGATGGTAAACCAGTAGTTACACCATCACAAGATATGGTACTTGGTAACTATTACCTTACTTTAGAAAGAAAAGATGCAGTAAATACAGGCGCAATCTTTAATAATACAAATGAAGTGTTAAAAGCATATGCAAATGGCTTTGTACATTTACACACAAGAATTGGTGTACATGCAAGTTCATTCAACAACCCAACATTTACTGAAGAACAAAACAAAAAGATTCTTGCTACGTCAGTAGGTAAAATTATATTCAATGAAATCATTCCGGATTCATTTGCTTATATTAATGAACCTACGCAAGAAAACTTAGAAAGAAAGACACCAAACAGATACTTCATCGATCCTACAACTTTAGGTGAAGGTGGATTAAAAGAATACTTTGAAAATGAAGAATTAATTGAACCTTTCAACAAAAAATTCTTAGGTAATATTATTGCAGAAGTATTCAACAGATTTAGCATCACTGATACATCAATGATGTTAGACCGTATGAAAGACTTAGGATTCAAATTCTCATCTAAAGCTGGTATTACAGTAGGTGTTGCTGATATCGTAGTATTACCTGATAAGCAACAAATACTTGATGAGCATGAAAAATTAGTCGACAGAATTACAAAACAATTCAATCGTGGTTTAATCACTGAAGAAGAAAGATATAATGCAGTTGTTGAAATTTGGACAGATGCAAAAGATCAAATTCAAGGTGAATTGATGCAATCACTTGATAAAACTAACCCAATCTTCATGATGAGTGATTCAGGTGCCCGTGGTAACGCATCTAACTTTACACAGTTAGCAGGTATGCGTGGATTGATGGCCGCACCATCTGGTAAGATTATCGAATTACCAATCACATCTTCATTCCGTGAAGGTTTAACAGTACTTGAATACTTCATCTCAACTCACGGTGCGCGTAAAGGTCTTGCCGATACAGCACTTAAGACAGCTGACTCAGGATATCTTACTCGTCGTCTTGTTGACGTGGCACAAGATGTTATTGTTCGTGAAGAAGACTGTGGTACAGATAGAGGTTTATTAGTTTCTGATATTAAAGAAGGTACAGAAATGATTGAACCATTTATCGAACGTATTGAAGGTCGTTATTCTAAAGAAACAATTCGTCATCCTGAAACTGATGAAGTTATCATTCGTCCTGATGAATTAATTACACCTGAAATTGCTAAGAAAATTACAGATGCTGGTATTGAACAAATGTATATTCGCTCAGCATTTACTTGTAACGCAAGACACGGTGTTTGTGAAAAATGTTACGGTAAAAACCTTGCTACTGGTGAAAAAGTTGAAGTTGGTGAAGCAGTTGGTACAATTGCAGCCCAATCTATCGGTGAACCAGGTACACAGCTTACAATGCGTACATTCCATACAGGTGGGGTAGCAGGTAGCGATATCACACAAGGTCTTCCTCGTATTCAAGAGATTTTCGAAGCACGTAACCCTAAAGGTCAAGCGGTAATTACGGAAATCGAAGGTGTCGTAGAAGATATTAAATTAGCAAAAGATAGACAACAAGAAATTGTTGTTAAAGGTGCTAATGAAACAAGATCATATCTTGCTTCAGGTACTTCAAGAATTATTGTAGAAATCGGTCAACCAGTACAACGTGGTGAAGTATTAACTGAAGGTTCTATTGAACCTAAGAATTACTTATCTGTTGCTGGATTAAACGCGACTGAAAGCTACTTATTAAAAGAAGTACAAAAAGTTTACCGTATGCAAGGGGTAGAAATCGACGATAAACACGTTGAGGTTATGGTTCGACAAATGTTACGTAAAGTTAGAATTATCGAAGCAGGTGATACGAAGTTATTACCAGGTTCATTAGTTGATATTCACAACTTTACAGATGCAAATAGAGAAGCATTTAAACACCGCAAGCGCCCTGCAACAGCTAAACCAGTATTACTTGGTATTACTAAAGCATCACTTGAAACAGAAAGTTTCTTATCTGCAGCATCATTCCAAGAAACAACAAGAGTTCTAACAGATGCAGCAATTAAAGGTAAGCGTGATGACTTATTAGGTCTTAAAGAAAACGTAATTATCGGTAAGCTAATTCCAGCTGGTACTGGTATGAGACGTTATAGCGACGTAAAATACGAAAAAACAGCTAAACCAGTTGCAGAAGTTGAATCTCAAACTGAAGTAACGGAATAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35517","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus MRSA252","NCBI_taxonomy_id":"282458"}}}},"ARO_accession":"3003291","ARO_id":"39875","ARO_name":"Staphylococcus aureus rpoC conferring resistance to daptomycin","ARO_description":"Point mutations that occurs in Staphylococcus aureus rpoC resulting in resistance to daptomycin","ARO_category":{"39874":{"category_aro_accession":"3003290","category_aro_cvterm_id":"39874","category_aro_name":"daptomycin resistant beta prime subunit of RNA polymerase (rpoC)","category_aro_description":"Daptomycin resistant RNA polymerases include amino acids substitutions which alter the binding affinity of daptomycin to the protein, resulting in antibiotic resistance.","category_aro_class_name":"AMR Gene Family"},"35985":{"category_aro_accession":"0000068","category_aro_cvterm_id":"35985","category_aro_name":"daptomycin","category_aro_description":"Daptomycin is a novel lipopeptide antibiotic used in the treatment of certain infections caused by Gram-positive organisms. Daptomycin interferes with the bacterial cell membrane, reducing membrane potential and inhibiting cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"821":{"model_id":"821","model_name":"Mycobacterium tuberculosis embB mutants conferring resistance to rifampicin","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2649":"Y319D","2650":"Y333H"},"clinical":{"2649":"Y319D","2650":"Y333H"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"2000"}},"model_sequences":{"sequence":{"3327":{"protein_sequence":{"accession":"AAK48268.1","sequence":"MTQCASRRKSTPNRAILGAFASARGTRWVATIAGLIGFVLSVATPLLPVVQTTAMLDWPQRGQLGSVTAPLISLTPVDFTATVPCDVVRAMPPAGGVVLGTAPKQGKDANLQALFVVVSAQRVDVTDRNVVILSVPREQVTSPQCQRIEVTSTHAGTFANFVGLKDPSGAPLRSGFPDPNLRPQIVGVFTDLTGPAPPGLAVSATIDTRFSTRPTTLKLLAIIGAIVATVVALIALWRLDQLDGRGSIAQLLLRPFRPASSPGGMRRLIPASWRTFTLTDAVVIFGFLLWHVIGANSSDDGYILGMARVADHAGYMSNYFRWFGSPEDPFGWYYNLLALMTHVSDASLWMRLPDLAAGLVCWLLLSREVLPRLGPAVEASKPAYWAAAMVLLTAWMPFNNGLRPEGIIALGSLVTYVLIERSMRYSRLTPAALAVVTAAFTLGVQPTGLIAVAALVAGGRPMLRILVRRHRLVGTLPLVSPMLAAGTVILTVVFADQTLSTVLEATRVRAKIGPSQAWYTENLRYYYLILPTVDGSLSRRFGFLITALCLFTAVFIMLRRKRIPSVARGPAWRLMGVIFGTMFFLMFTPTKWVHHFGLFAAVGAAMAALTTVLVSPSVLRWSRNRMAFLAALFFLLALCWATTNGWWYVSSYGVPFNSAMPKIDGITVSTIFFALFAIAAGYAAWLHFAPRGAGEGRLIRALTTAPVPIVAGFMAAVFVASMVAGIVRQYPTYSNGWSNVRAFVGGCGLADDVLVEPDTNAGFMKPLDGDSGSWGPLGPLGGVNPVGFTPNGVPEHTVAEAIVMKPNQPGTDYDWDAPTKLTSPGINGSTVPLPYGLDPARVPLAGTYTTGAQQQSTLVSAWYLLPKPDDGHPLVVVTAAGKIAGNSVLHGYTPGQTVVLEYAMPGPGALVPAGRMVPDDLYGEQPKAWRNLRFARAKMPADAVAVRVVAEDLSLTPEDWIAVTPPRVPDLRSLQEYVGSTQPVLLDWAVGLAFPCQQPMLHANGIAEIPKFRITPDYSAKKLDTDTWEDGTNGGLLGITDLLLRAHVMATYLSRDWARDWGSLRKFDTLVDAPPAQLELGTATRSGLWSPGKIRIGP"},"dna_sequence":{"accession":"AE000516","fmin":"4238826","fmax":"4242123","strand":"+","sequence":"ATGACACAGTGCGCGAGCAGACGCAAAAGCACCCCAAATCGGGCGATTTTGGGGGCTTTTGCGTCTGCTCGCGGGACGCGCTGGGTGGCCACCATCGCCGGGCTGATTGGCTTTGTGTTGTCGGTGGCGACGCCGCTGCTGCCCGTCGTGCAGACCACCGCGATGCTCGACTGGCCACAGCGGGGGCAACTGGGCAGCGTGACCGCCCCGCTGATCTCGCTGACGCCGGTCGACTTTACCGCCACCGTGCCGTGCGACGTGGTGCGCGCCATGCCACCCGCGGGCGGGGTGGTGCTGGGCACCGCACCCAAGCAAGGCAAGGACGCCAATTTGCAGGCGTTGTTCGTCGTCGTCAGCGCCCAGCGCGTGGACGTCACCGACCGCAACGTGGTGATCTTGTCCGTGCCGCGCGAGCAGGTGACGTCCCCGCAGTGTCAACGCATCGAGGTCACCTCTACCCACGCCGGCACCTTCGCCAACTTCGTCGGGCTCAAGGACCCGTCGGGCGCGCCGCTGCGCAGCGGCTTCCCCGACCCCAACCTGCGCCCGCAGATTGTCGGGGTGTTCACCGACCTGACCGGGCCCGCGCCGCCCGGGCTGGCGGTCTCGGCGACCATCGACACCCGGTTCTCCACCCGGCCGACCACGCTGAAACTGCTGGCGATCATCGGGGCGATCGTGGCCACCGTCGTCGCACTGATCGCGTTGTGGCGCCTGGACCAGTTGGACGGGCGGGGCTCAATTGCCCAGCTCCTCCTCAGGCCGTTCCGGCCTGCATCGTCGCCGGGCGGCATGCGCCGGCTGATTCCGGCAAGCTGGCGCACCTTCACCCTGACCGACGCCGTGGTGATATTCGGCTTCCTGCTCTGGCATGTCATCGGCGCGAATTCGTCGGACGACGGCTACATCCTGGGCATGGCCCGAGTCGCCGACCACGCCGGCTACATGTCCAACTATTTCCGCTGGTTCGGCAGCCCGGAGGATCCCTTCGGCTGGTATTACAACCTGCTGGCGCTGATGACCCATGTCAGCGACGCCAGTCTGTGGATGCGCCTGCCAGACCTGGCCGCCGGGCTAGTGTGCTGGCTGCTGCTGTCGCGTGAGGTGCTGCCCCGCCTCGGGCCGGCGGTGGAGGCCAGCAAACCCGCCTACTGGGCGGCGGCCATGGTCTTGCTGACCGCGTGGATGCCGTTCAACAACGGCCTGCGGCCGGAGGGCATCATCGCGCTCGGCTCGCTGGTCACCTATGTGCTGATCGAGCGGTCCATGCGGTACAGCCGGCTCACACCGGCGGCGCTGGCCGTCGTTACCGCCGCATTCACACTGGGTGTGCAGCCCACCGGCCTGATCGCGGTGGCCGCGCTGGTGGCCGGCGGCCGCCCGATGCTGCGGATCTTGGTGCGCCGTCATCGCCTGGTCGGCACGTTGCCGTTGGTGTCGCCGATGCTGGCCGCCGGCACCGTCATCCTGACCGTGGTGTTCGCCGACCAGACCCTGTCAACGGTGTTGGAAGCCACCAGGGTTCGCGCCAAAATCGGGCCGAGCCAGGCGTGGTATACCGAGAACCTGCGTTACTACTACCTCATCCTGCCCACCGTCGACGGTTCGCTGTCGCGGCGCTTCGGCTTTTTGATCACCGCGCTATGCCTGTTCACCGCGGTGTTCATCATGTTGCGGCGCAAGCGAATTCCCAGCGTGGCCCGCGGACCGGCGTGGCGGCTGATGGGCGTCATCTTCGGCACCATGTTCTTCCTGATGTTCACGCCCACCAAGTGGGTGCACCACTTCGGGCTGTTCGCCGCCGTAGGGGCGGCGATGGCCGCGCTGACGACGGTGTTGGTATCCCCATCGGTGCTGCGCTGGTCGCGCAACCGGATGGCGTTCCTGGCGGCGTTATTCTTCCTGCTGGCGTTGTGTTGGGCCACCACCAACGGCTGGTGGTATGTCTCCAGCTACGGTGTGCCGTTCAACAGCGCGATGCCGAAGATCGACGGGATCACAGTCAGCACAATCTTTTTCGCCCTGTTTGCGATCGCCGCCGGCTATGCGGCCTGGCTGCACTTCGCGCCCCGCGGCGCCGGCGAAGGGCGGCTGATCCGCGCGCTGACGACAGCCCCGGTACCGATCGTGGCCGGTTTCATGGCGGCGGTGTTCGTCGCGTCCATGGTGGCCGGGATCGTGCGACAGTACCCGACCTACTCCAACGGCTGGTCCAACGTGCGGGCGTTTGTCGGCGGCTGCGGACTGGCCGACGACGTACTCGTCGAGCCTGATACCAATGCGGGTTTCATGAAGCCGCTGGACGGCGATTCGGGTTCTTGGGGCCCCTTGGGCCCGCTGGGTGGAGTCAACCCGGTCGGCTTCACGCCCAACGGCGTACCGGAACACACGGTGGCCGAGGCGATCGTGATGAAACCCAACCAGCCCGGCACCGACTACGACTGGGATGCGCCGACCAAGCTGACGAGTCCTGGCATCAATGGTTCTACGGTGCCGCTGCCCTATGGGCTCGATCCCGCCCGGGTACCGTTGGCAGGCACCTACACCACCGGCGCACAGCAACAGAGCACACTCGTCTCGGCGTGGTATCTCCTGCCTAAGCCGGACGACGGGCATCCGCTGGTCGTGGTGACCGCCGCGGGCAAGATCGCCGGCAACAGCGTGCTGCACGGGTACACCCCCGGGCAGACTGTGGTGCTCGAATACGCCATGCCGGGACCCGGAGCGCTGGTACCCGCCGGGCGGATGGTGCCCGACGACCTATACGGAGAGCAGCCCAAGGCGTGGCGCAACCTGCGCTTCGCCCGAGCAAAGATGCCCGCCGATGCCGTCGCGGTCCGGGTGGTGGCCGAGGATCTGTCGCTGACACCGGAGGACTGGATCGCGGTGACCCCACCGCGGGTACCGGACCTGCGCTCACTGCAGGAATATGTGGGCTCGACGCAGCCGGTGCTGCTGGACTGGGCGGTCGGTTTGGCCTTCCCGTGCCAGCAGCCGATGCTGCACGCCAATGGCATCGCCGAAATCCCGAAGTTCCGCATCACACCGGACTACTCGGCTAAGAAGCTGGACACCGACACGTGGGAAGACGGCACTAACGGCGGCCTGCTCGGGATCACCGACCTGTTGCTGCGGGCCCACGTCATGGCCACCTACCTGTCCCGCGACTGGGCCCGCGATTGGGGTTCCCTGCGCAAGTTCGACACCCTGGTCGATGCCCCTCCCGCCCAGCTCGAGTTGGGCACCGCGACCCGCAGCGGCCTGTGGTCACCGGGCAAGATCCGAATTGGTCCATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37081","NCBI_taxonomy_name":"Mycobacterium tuberculosis CDC1551","NCBI_taxonomy_id":"83331"}}}},"ARO_accession":"3003465","ARO_id":"40058","ARO_name":"Mycobacterium tuberculosis embB mutants conferring resistance to rifampicin","ARO_description":"Specific mutations that occurs on Mycobacterium tuberculosis embB causing it to be rifampicin resistant","ARO_category":{"40057":{"category_aro_accession":"3003464","category_aro_cvterm_id":"40057","category_aro_name":"rifamycin-resistant arabinosyltransferase","category_aro_description":"Arabinosyl transferases allow for the polymerization of arabinose to form arabinan. Arabanan is required for formation of mycobacterial cell walls and arabinosyltransferases are targets of the drug ethambutol. Mutations in these genes can confer resistance to rifampicin.","category_aro_class_name":"AMR Gene Family"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36636":{"category_aro_accession":"3000497","category_aro_cvterm_id":"36636","category_aro_name":"ethambutol","category_aro_description":"Ethambutol is an antimycobacterial drug prescribed to treat tuberculosis. It is usually given in combination with other tuberculosis drugs, such as isoniazid, rifampicin, and pyrazinamide. Ethambutol inhibits arabinosyl biosynthesis, disrupting mycobacterial cell wall formation.","category_aro_class_name":"Antibiotic"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36666":{"category_aro_accession":"3000527","category_aro_cvterm_id":"36666","category_aro_name":"polyamine antibiotic","category_aro_description":"Polyamine antibiotics are organic compounds having two or more primary amino groups.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"851":{"model_id":"851","model_name":"Mycobacterium tuberculosis pncA mutations conferring resistance to pyrazinamide","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2572":"I5S","2573":"V7G","2575":"Q10R","2576":"Q10P","2582":"A26G","2584":"Y41H","2598":"P69R","2602":"C72R","2605":"L85P","2608":"K96N","2614":"N118T","2618":"G132S","2621":"H137P","2623":"C138Y","2625":"V139L","2629":"T142K","2630":"T142M","3424":"D12E","3425":"T47A","3426":"A140S","3427":"P54T","3434":"G17D","3435":"Y34S","4158":"D8Y","4159":"Q10K","4162":"T47S","4163":"D49V","4164":"S66P","4165":"K96E","4166":"A102T","4167":"A102V","4169":"L116R","4170":"V125D","4172":"I133T","4173":"Q141P","4174":"R154G","4175":"T160P","4176":"A161P","4177":"D12A","4178":"D12N","4179":"H51Q","4180":"A171P","4192":"H57D","4193":"W68L","4195":"V139A","4196":"R121P","4199":"H137R","4201":"W119R","4202":"F94P","4204":"T76P","4205":"L19P","4207":"S104C","4208":"I90S","4209":"M1S","4210":"L4W","4211":"V7D","4212":"V7F","4213":"A8G","4214":"V9G","4217":"C14R","4218":"C14Y","4219":"G23V","4221":"V45G","4222":"A46E","4223":"D49A","4224":"F58L","4225":"Y68D","4226":"S67P","4227":"W68R","4228":"W68G","4229":"W68S","4232":"T76I","4233":"G78D","4234":"L85R","4235":"K96Q","4236":"Y103H","4237":"Y103S","4239":"T135P","4240":"D136N","4241":"D136Y","4242":"V139M","4245":"A146T","4246":"V155G","4247":"L159R","4248":"L172P","4249":"V180F","4272":"L172A","4274":"A171T","4280":"H51Y","4276":"P62H","4281":"A171V","4282":"D136H","4283":"A3E","4284":"L27P","4286":"P54L","4287":"C72W","4291":"M175V","4292":"H59D","4293":"A46V","4294":"D53A","4296":"H71E","4297":"H82R","4298":"G97S","4299":"A134V","4300":"C138S","4301":"T168N","4307":"T47P","4308":"A121P"},"clinical":{"2572":"I5S","2573":"V7G","2575":"Q10R","2576":"Q10P","2582":"A26G","2584":"Y41H","2598":"P69R","2602":"C72R","2605":"L85P","2608":"K96N","2614":"N118T","2618":"G132S","2621":"H137P","2623":"C138Y","2625":"V139L","2629":"T142K","2630":"T142M","3424":"D12E","3425":"T47A","3426":"A140S","3427":"P54T","3434":"G17D","3435":"Y34S","4158":"D8Y","4159":"Q10K","4162":"T47S","4163":"D49V","4164":"S66P","4165":"K96E","4166":"A102T","4167":"A102V","4169":"L116R","4170":"V125D","4172":"I133T","4173":"Q141P","4174":"R154G","4175":"T160P","4176":"A161P","4177":"D12A","4178":"D12N","4179":"H51Q","4180":"A171P","4192":"H57D","4193":"W68L","4195":"V139A","4196":"R121P","4199":"H137R","4201":"W119R","4202":"F94P","4204":"T76P","4205":"L19P","4207":"S104C","4208":"I90S","4209":"M1S","4210":"L4W","4211":"V7D","4212":"V7F","4213":"A8G","4214":"V9G","4217":"C14R","4218":"C14Y","4219":"G23V","4221":"V45G","4222":"A46E","4223":"D49A","4224":"F58L","4225":"Y68D","4226":"S67P","4227":"W68R","4228":"W68G","4229":"W68S","4232":"T76I","4233":"G78D","4234":"L85R","4235":"K96Q","4236":"Y103H","4237":"Y103S","4239":"T135P","4240":"D136N","4241":"D136Y","4242":"V139M","4245":"A146T","4246":"V155G","4247":"L159R","4248":"L172P","4249":"V180F","4272":"L172A","4274":"A171T","4280":"H51Y","4276":"P62H","4281":"A171V","4282":"D136H","4283":"A3E","4284":"L27P","4286":"P54L","4287":"C72W","4291":"M175V","4292":"H59D","4293":"A46V","4294":"D53A","4296":"H71E","4297":"H82R","4298":"G97S","4299":"A134V","4300":"C138S","4301":"T168N","4307":"T47P","4308":"A121P"}},"40394":{"param_type":"nonsense mutation","param_description":"A nucleotide substitution resulting in a change from an amino acid codon to a STOP codon. Nonsense mutations truncate protein translation prematurely, resulting in a defective or completely inactive protein. In CARD, nonsense mutations may be attached to models using the notation: [wild type amino acid][position][STOP] (e.g. Q42STOP). This parameter is not currently used in detection algorithms.","param_type_id":"40394","param_value":{"3433":"Y99STOP","3436":"Y41STOP","4160":"Q10STOP","4168":"Y103STOP","4230":"W68STOP","4238":"W119STOP","4243":"Q141STOP","4309":"S88STOP"}},"40330":{"param_type":"multiple resistance variants","param_description":"A set of nucleotide or amino acid substitutions that are each required to confer resistance to an antibiotic drug or drug class by co-mutation. Compare to single resistance variant, where only one substitution is required. Multiple resistance variants parameters are indicated on appropriate models using the following notation: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2],...,[wild-type n][position n][mutation n]. When each included substitution is detected in a protein sequence, resistance is conferred. This parameter is not currently included in any detection algorithms.","param_type_id":"40330","param_value":{"4215":"Q10P,Y99D","4220":"A25E,A26G,A28D","8095":"V130G,+nt420:GG","8103":"D53N,+nt349:CACTG"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"},"41345":{"param_type":"insertion mutation from nucleotide sequence","param_description":"A subtype of the insertion mutation detection model parameter. This parameter is used when a set of insertion mutations is reported in a nucleotide sequence format. Such mutations may be of variable length - possibly causing a frameshift, but not causing premature termination or a functional knockout. Mutation parameters of this type are reported in CARD with the notation: [+]nt[position]:[nucleotides].","param_type_id":"41345","param_value":{"8096":"+nt420:G","8098":"+nt193:A","8099":"+nt52:G","8100":"+nt493:C","8102":"+nt218:CGCATTGCCG","8104":"+nt221:G","8105":"+nt407:C","8108":"+nt392:G","8109":"+nt532:C","8110":"+nt480:TGAC","8111":"+nt465:T","8112":"+nt414:G","8113":"+nt391:GG","8114":"+nt382:AG","8115":"+nt368:18","8116":"+nt287:T","8128":"+nt388:AGGTCGATG","8129":"+nt403:C","8130":"+nt397:T","8131":"+nt475:C"}},"41343":{"param_type":"deletion mutation from nucleotide sequence","param_description":"A subtype of the deletion mutation detection model parameter. This parameter is used when a set of deletion mutations is reported in a nucleotide sequence format. Such mutations may be of variable length - possibly causing a frameshift, but not premature termination of functional knockout. Mutation parameters of this type are reported in the CARD with the notation: [-]nt[position]:[nucleotides].","param_type_id":"41343","param_value":{"8097":"-nt301:G","8101":"-nt386:ATG","8106":"-nt195:68","8107":"-nt512:C","8117":"-nt452:T","8118":"-nt406:G","8119":"-nt386:ATGT","8120":"-nt381:GG","8121":"-nt341:C","8122":"-nt307:TACAG","8123":"-nt161:C","8124":"-nt158:A","8125":"-nt151:80","8126":"-nt77:G","8127":"-nt267:24","8132":"-nt70:G","8133":"-nt518:5","8134":"-nt446:8","8135":"-nt443:G","8136":"-nt1:11","8137":"-nt416:TG","8138":"-nt391:G","8139":"-nt104:C","8140":"-nt71:G","8141":"-nt28:C","8142":"-nt379:11","8143":"-nt84:C"}}},"model_sequences":{"sequence":{"4349":{"protein_sequence":{"accession":"CCP44816.1","sequence":"MRALIIVDVQNDFCEGGSLAVTGGAALARAISDYLAEAADYHHVVATKDFHIDPGDHFSGTPDYSSSWPPHCVSGTPGADFHPSLDTSAIEAVFYKGAYTGAYSGFEGVDENGTPLLNWLRQRGVDEVDVVGIATDHCVRQTAEDAVRNGLATRVLVDLTAGVSADTTVAALEEMRTASVELVCSS"},"dna_sequence":{"accession":"AL123456","fmin":"2288680","fmax":"2289241","strand":"-","sequence":"TCAGGAGCTGCAAACCAACTCGACGCTGGCGGTGCGCATCTCCTCCAGCGCGGCGACGGTGGTATCGGCCGACACACCCGCTGTCAGGTCCACCAGCACCCTGGTGGCCAAGCCATTGCGTACCGCGTCCTCGGCCGTCTGGCGCACACAATGATCGGTGGCAATACCGACCACATCGACCTCATCGACGCCGCGTTGCCGCAGCCAATTCAGCAGTGGCGTGCCGTTCTCGTCGACTCCTTCGAAGCCGCTGTACGCTCCGGTGTAGGCACCCTTGTAGAACACCGCCTCGATTGCCGACGTGTCCAGACTGGGATGGAAGTCCGCGCCGGGAGTACCGCTGACGCAATGCGGTGGCCACGACGAGGAATAGTCCGGTGTGCCGGAGAAGTGGTCACCCGGGTCGATGTGGAAGTCCTTGGTTGCCACGACGTGATGGTAGTCCGCCGCTTCGGCCAGGTAGTCGCTGATGGCGCGGGCCAGCGCGGCGCCACCGGTTACCGCCAGCGAGCCACCCTCGCAGAAGTCGTTCTGCACGTCGACGATGATCAACGCCCGCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3003394","ARO_id":"39978","ARO_name":"Mycobacterium tuberculosis pncA mutations conferring resistance to pyrazinamide","ARO_description":"pncA is a pyrazinamidase\/nicotinamidase. It catalyzes the activation of pyrazinamide. Some mutation within pncA are associated with loss of enzyme activity, resulting in pyrazinamide resistance.","ARO_category":{"40002":{"category_aro_accession":"3003418","category_aro_cvterm_id":"40002","category_aro_name":"pyrazinamide resistant pncA","category_aro_description":"pncA is a pyrazinamidase\/nicotinamidase. It catalyzes the activation of pyrazinamide to pyrazinoic acid. Mutations arise within the pncA gene that caused the loss of pyrazinamidase activity is the major mechanism of antibiotic resistance","category_aro_class_name":"AMR Gene Family"},"39997":{"category_aro_accession":"3003413","category_aro_cvterm_id":"39997","category_aro_name":"pyrazinamide","category_aro_description":"Pyrazinamide is an Antimycobacterial. It is highly specific and active only against Mycobacterium tuberculosis. This compound is a prodrug and needs to be activated inside the cell. It interferes with the bacterium's ability to synthesize new fatty acids, causing cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"984":{"model_id":"984","model_name":"Bartonella bacilliformis gyrA conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2121":"D90G","2122":"D95N"},"clinical":{"2121":"D90G","2122":"D95N"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1500"}},"model_sequences":{"sequence":{"2058":{"protein_sequence":{"accession":"AAL82403.1","sequence":"MTDLTRLPEHDVSTGIEPVSIIEEMQCSYLDYAMSVIVSRALPDVRDGLKPVHRRILHAMNEMGLLFNKPYRKSAGVVGEVMGKFHPHGDASIYDALVRMAQDFSLRNPLIDGQGNFGSVDGDPPAAMRYTECRLEKVAEELLADIDKDTVDFQDNYDGREHEPIVLPARFPNLLVNGSGGIAVGMATNIPPHNLGEVIDGCVALIDNPNITIDEMLAIIPGPDFPTGGIILGHSGVRSAYETGRGSIIMRAKVEIEEIRNQRQAIIVSEIPYQVNKATMVEKMAELVRDKRIEGISDLRDESDRDGYRVVIELKREAVADVVLNQLYRYTPLQASFGCNMVALNGGKPEQMTLLDMLRAFVSFREEVVSRRTKYLLRKARERAHVLVGLAIAVANIDEIIELIRKAHDPQTARTQLMERRWPASEVAALIKLIDDPRHIIHEDNTYNLSEEQARAILELRLQRLTALGRNEIADELNAIGEDIADYLGILASRSRIMDIVKSELSALRETFATPRRTVFGFGSAEMDCEDLIVPEDMVVTVSHSGYIKRVPLNTYRAQRRGGKGRSGMATKDQDFVTRLFVANTHTPVLFFSSRGIVYKEKVWRLPVGTPQSRGRALINMLPLQQGERITTIMPLPEDEASWGKLDIMFATTRGTVRRNKLSDFIQVNRNGKIAMKLDEEGDEILSVETCTEHDDVVLITANGQCIRFPVTDIRVFSGRNSMGVRGINMVEGDKVISMTILEHVEATSVERSAYIKRAINERRVAGSDDEDILTVDEDGEETEVELTDERYAELSAHEQMLLTVSEFGYGKRSSSYDFRISGRGGKGIRATDLSKAAEIGKLVAAFPVGERDQIMLVSDGGQLIRVPVNCIRIAGRSTKGVTVFNTAKGEKVVSVERISESENDTNQLDIESEEHSGTVSMSEEKKL"},"dna_sequence":{"accession":"AF469609","fmin":"566","fmax":"3353","strand":"+","sequence":"GTGACCGATCTTACTCGACTACCAGAACATGATGTGTCGACCGGTATTGAACCAGTCAGTATCATTGAAGAAATGCAGTGCTCTTATCTAGATTATGCGATGAGCGTAATTGTGTCGCGCGCACTGCCTGATGTCCGTGATGGGCTTAAGCCTGTCCATCGGCGCATTCTTCATGCGATGAATGAAATGGGACTTTTGTTCAATAAGCCTTATCGTAAGTCAGCGGGTGTTGTTGGTGAAGTGATGGGAAAGTTTCATCCTCATGGTGATGCTTCAATTTATGATGCCTTGGTGCGTATGGCACAGGATTTTTCTTTACGAAATCCTCTGATTGATGGACAGGGAAATTTTGGCTCTGTTGACGGTGATCCACCCGCAGCGATGCGTTACACGGAATGTCGTTTAGAAAAAGTTGCAGAAGAACTTTTAGCTGATATTGATAAAGATACTGTTGATTTTCAAGATAATTATGATGGGCGTGAGCATGAACCTATAGTTTTGCCTGCACGTTTCCCTAACCTGTTAGTAAATGGATCGGGTGGTATTGCTGTAGGTATGGCAACCAATATTCCTCCACATAATCTAGGTGAGGTTATTGATGGATGTGTTGCTTTGATCGATAATCCTAACATAACTATAGATGAGATGTTAGCAATTATTCCGGGGCCTGATTTTCCTACAGGTGGTATTATTCTTGGCCATTCTGGTGTCCGTTCTGCTTATGAAACAGGGCGTGGTTCAATTATTATGCGTGCTAAGGTTGAGATCGAGGAAATTCGCAATCAGCGGCAGGCAATTATCGTAAGCGAAATACCTTATCAAGTTAATAAAGCAACAATGGTTGAGAAGATGGCCGAATTGGTGCGTGATAAACGTATCGAAGGAATCTCCGATTTGCGTGATGAATCTGATCGTGATGGGTATCGAGTTGTCATTGAGCTAAAAAGAGAAGCTGTTGCAGACGTTGTTTTGAATCAGCTTTATCGTTATACACCGTTGCAAGCCTCATTTGGTTGCAATATGGTTGCGTTGAATGGAGGAAAGCCTGAACAAATGACGTTGCTTGACATGCTTCGTGCATTTGTTTCCTTCCGCGAAGAAGTGGTAAGCCGGCGCACAAAATATCTTTTGCGTAAAGCACGTGAGCGTGCGCATGTTTTAGTTGGTCTTGCTATCGCTGTTGCTAATATTGATGAGATTATAGAATTAATTCGCAAAGCTCATGATCCACAGACAGCGCGTACACAGTTAATGGAACGGCGTTGGCCGGCTTCTGAGGTAGCAGCTTTGATTAAGCTTATAGATGATCCTCGTCATATTATTCATGAGGATAATACGTACAATTTGTCTGAAGAACAAGCGCGTGCTATTTTAGAATTGCGTTTGCAAAGATTAACAGCGCTTGGTCGTAATGAAATTGCTGATGAACTCAATGCAATTGGAGAAGATATTGCTGACTATCTTGGTATTTTAGCATCACGCTCACGGATCATGGACATTGTTAAAAGTGAGCTCAGCGCTTTGCGTGAAACATTTGCAACACCACGGCGTACTGTATTTGGTTTTGGTAGTGCCGAGATGGACTGCGAAGATCTGATTGTTCCAGAAGATATGGTGGTGACAGTGAGCCATAGTGGCTATATTAAGCGTGTGCCTCTAAATACATACCGTGCGCAGCGTCGTGGTGGTAAGGGACGTTCTGGTATGGCAACAAAGGATCAGGATTTTGTTACTCGCTTATTCGTGGCCAATACACATACACCAGTTCTTTTCTTTTCATCACGTGGGATTGTTTATAAAGAGAAGGTTTGGCGTTTACCTGTTGGTACGCCGCAATCACGCGGTAGAGCTTTAATTAATATGTTGCCTTTGCAACAAGGCGAGCGCATTACAACAATTATGCCATTGCCGGAGGATGAGGCAAGTTGGGGTAAACTGGATATTATGTTTGCAACAACGCGTGGAACTGTGCGCCGTAATAAATTATCAGACTTTATTCAAGTTAATCGCAATGGTAAAATAGCAATGAAACTTGATGAAGAGGGAGATGAGATCCTTTCTGTAGAGACCTGTACAGAACATGATGACGTTGTTCTTATTACAGCAAACGGGCAGTGTATTCGTTTTCCAGTTACTGATATTCGTGTATTTTCTGGTCGTAATTCGATGGGGGTACGCGGTATCAATATGGTTGAGGGTGATAAGGTCATTTCAATGACTATTTTAGAGCATGTTGAAGCGACATCAGTCGAACGTTCTGCTTATATTAAACGTGCAATCAATGAGCGTCGTGTTGCAGGTTCAGATGATGAAGATATTTTAACTGTTGATGAAGATGGAGAGGAAACTGAGGTTGAATTAACAGATGAACGTTATGCAGAACTTAGCGCTCATGAGCAAATGCTTTTAACAGTTAGTGAATTTGGTTATGGAAAACGCTCTTCTTCTTATGATTTCCGTATTTCAGGACGCGGTGGAAAAGGGATACGCGCAACTGATCTATCAAAGGCGGCTGAAATTGGTAAGTTAGTAGCAGCCTTTCCAGTAGGAGAACGAGATCAAATTATGTTAGTTTCGGATGGAGGACAGCTTATTCGTGTTCCCGTCAACTGTATTCGTATAGCGGGTCGTTCAACTAAAGGGGTCACAGTCTTTAATACAGCAAAAGGTGAAAAAGTTGTATCGGTTGAGCGTATTTCTGAATCTGAAAATGATACTAATCAGTTAGATATTGAAAGTGAGGAACATTCCGGAACAGTTAGCATGAGTGAAGAGAAAAAACTCTGAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40073","NCBI_taxonomy_name":"Bartonella bacilliformis","NCBI_taxonomy_id":"774"}}}},"ARO_accession":"3003297","ARO_id":"39881","ARO_name":"Bartonella bacilliformis gyrA conferring resistance to fluoroquinolones","ARO_description":"Point mutation of Bartonella bacilliformis gyrA resulted in the lowered affinity between fluoroquinolones and gyrA. Thus, conferring resistance.","ARO_category":{"39876":{"category_aro_accession":"3003292","category_aro_cvterm_id":"39876","category_aro_name":"fluoroquinolone resistant gyrA","category_aro_description":"DNA gyrase is responsible for DNA supercoiling and consists of two alpha and two beta subunits. GyrA point mutations confer resistance by preventing fluoroquinolone antibiotics from binding the alpha-subunit.","category_aro_class_name":"AMR Gene Family"},"35942":{"category_aro_accession":"0000023","category_aro_cvterm_id":"35942","category_aro_name":"enoxacin","category_aro_description":"Enoxacin belongs to a group called fluoroquinolones. Its mode of action depends upon blocking bacterial DNA replication by binding itself to DNA gyrase and causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37004":{"category_aro_accession":"3000660","category_aro_cvterm_id":"37004","category_aro_name":"lomefloxacin","category_aro_description":"Lomefloxacin is a difluoropiperazinyl quinolone, sharing similar activities with other fluoroquinolones. It is used to treat urinary tract infections. Relative to other fluoroquinolones, it has a longer half life and has higher serum concentrations.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"37008":{"category_aro_accession":"3000664","category_aro_cvterm_id":"37008","category_aro_name":"trovafloxacin","category_aro_description":"Trovafloxacin is a trifluoroquinalone with a broad spectrum of activity that acts by inhibiting the uncoiling of supercoiled DNA. While potent against many Gram-positive and Gram-negative bacteria, it is less active against pseudomonads and Cl. difficile. It is usually taken as the prodrug trovafloxacin mesylate or alatrofloxacin mesylate for oral or intravenous administration, respectively.","category_aro_class_name":"Antibiotic"},"37009":{"category_aro_accession":"3000665","category_aro_cvterm_id":"37009","category_aro_name":"grepafloxacin","category_aro_description":"Grepafloxacin is a broad-spectrum antibacterial quinoline. It is no longer taken due to its high toxicity.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"37142":{"category_aro_accession":"3000762","category_aro_cvterm_id":"37142","category_aro_name":"pefloxacin","category_aro_description":"Pefloxacin is structurally and functionally similar to norfloxacin. It is poorly active against mycobacteria, while anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"40463":{"category_aro_accession":"3003780","category_aro_cvterm_id":"40463","category_aro_name":"nybomycin","category_aro_description":"A  heterocyclic antibiotic that targets mutant gyrA (type II topoisomerase) containing an S84L substitution, counteracting acquired quinolone resistance. It is effective against quinolone-resistant Gram-positive bacteria including S. aureus and E. faecalis. Due to its ability to counteract quinolone resistance by targeting the mutant form of the gyrA protein, it is classified as a reverse antibiotic (RA).","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1001":{"model_id":"1001","model_name":"Staphylococcus aureus mprF mutations conferring resistance to daptomycin","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2204":"F57S","2205":"I418N","2206":"S295L","2207":"G61V","2208":"S337L","2209":"L826F","2210":"P314L","2211":"T345I","2212":"T345A","3609":"I420N","3613":"T345K","3614":"T472K","3615":"M347R","3616":"L341S","3617":"V351E"},"clinical":{"2204":"F57S","2205":"I418N","2206":"S295L","2207":"G61V","2208":"S337L","2209":"L826F","2210":"P314L","2211":"T345I","2212":"T345A","3609":"I420N","3613":"T345K","3614":"T472K","3615":"M347R","3616":"L341S","3617":"V351E"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1600"}},"model_sequences":{"sequence":{"3542":{"protein_sequence":{"accession":"ADJ67256","sequence":"MNQEVKNKIFSILKITFATALFIFVAITLYRELSGINFKDTLVEFSKINRMSLVLLFIGGGASLVILSMYDVILSRALKMDISLGKVLRVSYIINALNAIVGFGGFIGAGVRAMVYKNYTHDKKKLVHFISLILISMLTGLSLLSLLIVFHVFDASLILDKITWVRWVLYVVSFFLPLFIIYSMVRPPDKNNRFVGLYCTLVSCVEWLAAAVVLYFCGVIVDAHVSFMSFIAIFIIAALSGLVSFIPGGFGAFDLVVLLGFKTLGVPEEKVLLMLLLYRFAYYFVPVIIALILSSFEFGTSAKKYIEGSKYFIPAKDVTSFLMSYQKDIIAKIPSLSLAILVFFTSMINLTIVYDALYDGNHLTYYILLAIHTSACLLLLLNVVGIYKQSRRAIIFAMISILLITVATFFTYASYILITWLAIIFVLLIVAFRRARRLKRPVRMRNIVAMLLFSLFILYVNHIFIAGTLYALDIYTIEMHTSVLRYYFWLTILIIAIIIGMIAWLFDYQFSKVRISSKIEDCEEIINQYGGNYLSHLIYSGDKQFFTNENKTAFLMYRYKASSLVVLGDPLGDENAFDELLEAFYNYAEYLGYDVIFYQVTDQHMPLYHNFGNQFFKLGEEAIIDLTQFSTSGKKRRGFRATLNKFDELNISFEIIEPPFSTEFINELQHVSDLWLDNRQEMHFSVGEFNEEYLSKAPIGVMRNEENEVIAFCSLMPTYFNDAISVDLIRWLPELDLPLMDGLYLHMLLWSKEQGYTKFNMGMATLSNVGQLHYSYLRERLAGRVFEHFNGLYRFQGLRRYKSKYNPNWEPRFLVYRKDNSLWESLSKVMRVIRHK"},"dna_sequence":{"accession":"HM140977","fmin":"0","fmax":"2511","strand":"+","sequence":"ATGAATCAGGAAGTTAAAAACAAAATATTTTCAATCTTAAAAATTACGTTTGCTACAGCTTTATTTATTTTTGTAGCAATCACATTGTATCGGGAGTTATCTGGTATTAACTTTAAAGATACGTTGGTTGAATTTAGTAAGATTAACCGTATGTCCTTAGTGTTACTATTTATTGGTGGTGGGGCATCGCTTGTTATTCTATCAATGTATGATGTGATTTTATCTAGAGCTTTAAAAATGGATATATCCTTAGGCAAAGTTTTAAGAGTAAGTTATATCATCAATGCATTGAATGCGATTGTAGGTTTCGGTGGCTTTATTGGTGCAGGCGTTAGAGCAATGGTTTATAAAAACTATACGCATGATAAAAAGAAATTAGTTCACTTTATATCCTTAATACTTATTTCAATGTTGACAGGTTTAAGCTTATTATCATTGCTAATTGTATTCCATGTTTTCGATGCATCTTTAATCTTAGATAAGATTACATGGGTAAGATGGGTATTATATGTAGTGTCATTTTTCTTACCATTATTCATTATTTATTCAATGGTTAGACCACCCGATAAAAACAATCGTTTTGTAGGATTGTACTGCACTTTAGTGTCGTGTGTTGAATGGTTAGCAGCTGCAGTTGTATTATATTTCTGTGGTGTAATTGTTGACGCTCATGTATCATTCATGTCCTTTATTGCAATATTTATCATTGCTGCATTATCAGGTTTAGTCAGCTTTATTCCTGGTGGTTTCGGCGCTTTCGATTTAGTTGTATTACTAGGATTTAAAACTTTAGGTGTCCCTGAGGAAAAAGTATTATTAATGCTACTTCTATATCGTTTTGCGTACTATTTTGTACCGGTAATTATTGCATTAATTTTATCATCATTTGAATTTGGTACATCAGCTAAGAAGTACATTGAGGGATCTAAATACTTTATTCCTGCTAAAGATGTTACGTCATTTTTAATGTCTTATCAAAAGGATATTATTGCTAAAATTCCATCATTATCATTAGCAATTTTAGTATTCTTTACAAGTATGATCAACTTAACGATTGTTTACGATGCTTTATATGATGGAAATCACTTAACGTATTATATTCTATTGGCAATTCATACTAGTGCTTGTTTATTACTTTTACTGAATGTAGTTGGTATTTATAAGCAAAGTAGACGTGCCATTATCTTTGCTATGATTTCAATTTTATTAATCACAGTGGCGACATTCTTCACTTACGCTTCATATATTTTAATAACATGGTTAGCTATTATTTTTGTTCTGCTTATTGTAGCTTTCCGTAGAGCACGTAGGTTGAAACGCCCAGTAAGAATGAGAAATATAGTTGCAATGCTTTTATTCAGTTTATTTATTTTATATGTTAACCATATATTTATTGCTGGAACGTTATATGCATTAGATATTTATACGATTGAAATGCATACATCTGTATTGCGCTATTACTTCTGGCTTACGATTTTAATCATCGCTATCATCATAGGTATGATTGCATGGTTGTTTGATTATCAATTTAGCAAAGTACGTATTTCTTCTAAAATTGAAGATTGCGAGGAGATTATTAATCAGTACGGCGGTAATTATTTGAGTCACTTGATATATAGTGGTGACAAGCAGTTTTTCACTAATGAAAATAAAACAGCATTTTTAATGTATCGTTATAAAGCAAGTTCATTAGTGGTTCTTGGAGATCCGTTAGGTGATGAAAATGCCTTTGATGAATTGTTAGAAGCATTCTATAATTACGCTGAGTATTTAGGCTATGATGTTATATTCTATCAAGTTACAGATCAACACATGCCTTTATATCATAATTTCGGTAACCAATTTTTCAAATTAGGTGAAGAAGCAATTATTGATTTAACGCAATTTTCAACTTCAGGTAAAAAACGCCGTGGATTTAGAGCGACTTTAAATAAATTCGATGAACTTAATATTTCGTTCGAAATTATTGAACCACCGTTTTCAACTGAATTTATAAATGAACTTCAACATGTAAGTGATTTATGGCTAGATAATCGTCAGGAAATGCATTTCTCTGTTGGTGAATTTAATGAAGAATACTTATCTAAAGCGCCAATTGGTGTAATGCGAAATGAAGAAAATGAAGTAATTGCATTTTGTAGTTTAATGCCAACATACTTTAATGATGCCATTTCAGTCGATTTAATTAGATGGTTGCCAGAGTTAGATTTACCATTAATGGATGGTCTATACTTGCATATGTTACTTTGGAGTAAAGAACAAGGTTATACAAAATTTAATATGGGTATGGCAACGTTATCGAACGTTGGTCAATTGCATTATTCATATTTAAGAGAACGACTTGCAGGCCGTGTCTTTGAACATTTCAACGGTCTATATCGTTTCCAAGGATTACGTCGTTATAAATCTAAATATAATCCGAATTGGGAACCACGCTTTTTAGTTTATCGTAAAGATAATTCGCTTTGGGAATCACTTTCTAAAGTAATGCGTGTAATACGTCACAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3003319","ARO_id":"39903","ARO_name":"Staphylococcus aureus mprF with mutation conferring resistance to daptomycin","ARO_description":"Point mutations that occur within Staphylococcus aureus mprF gene resulting in resistance to daptomycin","ARO_category":{"39638":{"category_aro_accession":"3003091","category_aro_cvterm_id":"39638","category_aro_name":"daptomycin resistant mprF","category_aro_description":"MprF is a integral membrane protein that modifies the negatively-charged phosphatidylglycerol on the membrane surface of both Gram-positive and Gram-negative bacteria. This confers resistance to cationic peptides that disrupt the cell membrane, including defensins. Mutations in mprF can additionally confer resistance to daptomycin in S. aureus.","category_aro_class_name":"AMR Gene Family"},"35985":{"category_aro_accession":"0000068","category_aro_cvterm_id":"35985","category_aro_name":"daptomycin","category_aro_description":"Daptomycin is a novel lipopeptide antibiotic used in the treatment of certain infections caused by Gram-positive organisms. Daptomycin interferes with the bacterial cell membrane, reducing membrane potential and inhibiting cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1088":{"model_id":"1088","model_name":"Staphylococcus aureus rpoB mutants conferring resistance to daptomycin","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2047":"I953S","2048":"A1085V","2049":"A621E"},"clinical":{"2047":"I953S","2048":"A1085V","2049":"A621E"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"2300"}},"model_sequences":{"sequence":{"3332":{"protein_sequence":{"accession":"YP_039996.1","sequence":"MAGQVVQYGRHRKRRNYARISEVLELPNLIEIQTKSYEWFLREGLIEMFRDISPIEDFTGNLSLEFVDYRLGEPKYDLEESKNRDATYAAPLRVKVRLIIKETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDKNGRENYDATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFSSDQEIVDLLGDNEYLRNTLEKDGTENTEQALLEIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGRYKTNKKLHLKHRLFNQKLAEPIVNTETGEIVVEEGTVLDRRKIDEIMDVLESNANSEVFELHGSVIDEPVEIQSIKVYVPNDDEGRTTTVIGNAFPDSEVKCITPADIIASMSYFFNLLSGIGYTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQDTESITPQQLINIRPVIASIKEFFGSSQLSQFMDQANPLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVDLDTHAITDQIDYLTADEEDSYVVAQANSKLDENGRFMDDEVVCRFRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEAPFVGTGMEHVAARDSGAAITAKHRGRVEHVESNEILVRRLVEENGVEHEGELDRYPLAKFKRSNSGTCYNQRPIVAVGDVVEFNEILADGPSMELGEMALGRNVVVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSESALKNLDDRGIVYIGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNREEGDDTLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGRPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWSTIEEAGMARDGKTVLYDGRTGEPFDNRISVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDTVGRVKTYEAIVKGENISRPSVPESFRVLMKELQSLGLDVKVMDEQDNEIEMTDVDDDDVVERKVDLQQNDAPETQKEVTD"},"dna_sequence":{"accession":"NC_002952","fmin":"590830","fmax":"594382","strand":"+","sequence":"TTGGCAGGTCAAGTTGTCCAATATGGAAGACATCGTAAACGTAGAAACTACGCGAGAATTTCAGAAGTATTAGAATTACCAAACTTAATAGAAATTCAAACTAAATCTTACGAGTGGTTCCTAAGAGAAGGTTTAATCGAAATGTTTAGAGACATTTCTCCAATTGAAGATTTTACTGGTAATTTGTCATTAGAGTTTGTGGATTACCGTTTAGGAGAACCAAAATATGATTTAGAAGAATCTAAAAACCGTGACGCTACTTATGCTGCACCTCTTCGTGTAAAAGTGCGTCTAATCATTAAAGAAACAGGAGAAGTTAAAGAACAAGAAGTCTTTATGGGTGATTTCCCATTAATGACTGATACAGGTACGTTCGTTATCAATGGTGCAGAACGTGTAATCGTATCTCAATTAGTTCGTTCACCATCCGTTTATTTCAATGAAAAAATCGACAAAAATGGTCGTGAAAACTATGATGCAACAATTATTCCAAACCGAGGTGCATGGTTAGAATATGAAACAGATGCTAAAGATGTTGTATACGTGCGTATTGATAGAACACGTAAACTACCATTAACAGTATTGTTACGTGCATTAGGTTTCTCAAGTGACCAAGAAATTGTTGACCTTTTAGGTGACAATGAATATTTACGTAATACTTTAGAGAAAGACGGCACTGAAAACACTGAACAAGCGTTATTAGAAATCTATGAACGTTTACGTCCAGGTGAACCACCAACTGTTGAAAATGCTAAAAGTCTATTGTATTCACGTTTCTTTGATCCAAAACGCTATGACTTAGCAAGCGTGGGTCGTTATAAAACAAACAAAAAATTACATTTAAAACATCGTTTATTCAATCAAAAATTAGCTGAGCCAATTGTGAATACTGAAACTGGTGAAATTGTAGTTGAAGAAGGTACAGTGCTTGATCGTCGTAAAATCGACGAAATCATGGATGTACTTGAATCAAACGCAAACAGCGAAGTGTTTGAATTGCATGGTAGCGTTATAGACGAGCCAGTAGAAATTCAATCAATTAAAGTATATGTTCCTAACGATGATGAAGGTCGTACGACAACTGTAATTGGTAATGCTTTCCCTGACTCAGAAGTTAAATGTATTACACCGGCAGATATCATCGCTTCAATGAGTTACTTCTTTAACTTATTAAGTGGTATTGGATATACAGATGATATTGACCATTTAGGTAACCGTCGTTTACGTTCTGTAGGTGAATTACTACAAAACCAATTCCGTATCGGTTTATCAAGAATGGAAAGAGTTGTACGTGAAAGAATGTCAATTCAAGATACTGAGTCTATCACACCTCAACAATTAATTAATATTCGACCTGTTATTGCATCTATTAAAGAATTCTTTGGTAGCTCTCAATTATCACAATTCATGGACCAAGCAAATCCATTAGCTGAGTTAACGCATAAACGTCGTCTATCAGCATTAGGACCTGGTGGTTTAACACGTGAACGTGCTCAAATGGAAGTGCGTGACGTTCACTACTCTCACTATGGCCGTATGTGTCCAATTGAAACGCCTGAGGGACCAAACATTGGATTGATTAACTCATTATCAAGTTATGCACGTGTAAATGAATTCGGCTTTATTGAAACACCATATCGTAAAGTTGATTTAGATACACATGCTATCACTGATCAAATTGACTATTTAACAGCTGACGAAGAAGATAGCTATGTTGTAGCACAAGCAAACTCTAAATTAGATGAAAATGGTCGTTTCATGGATGATGAAGTTGTATGTCGTTTCCGTGGTAACAATACAGTTATGGCTAAAGAAAAAATGGATTATATGGATGTATCGCCGAAGCAAGTTGTTTCAGCAGCGACAGCATGTATTCCATTCTTAGAAAATGATGACTCAAACCGTGCATTGATGGGTGCGAACATGCAACGTCAAGCAGTGCCTTTGATGAATCCAGAAGCACCATTTGTTGGTACAGGTATGGAACACGTTGCAGCACGTGATTCTGGTGCAGCTATTACAGCTAAGCACAGAGGTCGTGTTGAACATGTTGAATCTAATGAAATTCTTGTACGTCGTCTAGTTGAAGAGAACGGCGTTGAGCATGAAGGTGAATTAGATCGCTATCCATTAGCTAAATTTAAACGTTCAAACTCAGGTACATGTTACAACCAACGTCCAATCGTTGCAGTTGGAGATGTTGTTGAGTTTAACGAGATTTTAGCAGATGGACCATCTATGGAATTAGGAGAAATGGCATTAGGTAGAAACGTAGTAGTTGGTTTCATGACTTGGGACGGTTACAACTATGAGGATGCCGTTATCATGAGTGAAAGACTTGTGAAAGATGACGTGTATACTTCTATTCATATTGAAGAGTATGAATCAGAAGCACGTGATACTAAGTTAGGACCTGAAGAAATCACAAGAGATATTCCTAATGTTTCTGAAAGTGCACTTAAGAACTTAGACGATCGTGGTATCGTTTATATTGGTGCAGAAGTAAAAGATGGAGATATTTTAGTTGGTAAAGTAACGCCTAAAGGTGTAACTGAGTTAACTGCCGAAGAAAGATTGTTACATGCAATCTTTGGTGAAAAAGCACGTGAAGTTAGAGATACTTCATTACGTGTACCTCACGGCGCTGGCGGTATCGTTCTTGATGTAAAAGTATTCAATCGTGAAGAAGGCGACGACACATTATCACCTGGTGTAAACCAATTAGTACGTGTATATATCGTTCAAAAACGTAAAATTCATGTTGGTGATAAGATGTGTGGTCGACATGGTAACAAAGGTGTCATTTCTAAGATTGTTCCTGAAGAAGATATGCCTTACTTACCAGATGGACGTCCGATTGATATCATGTTAAATCCTCTTGGTGTACCATCTCGTATGAACATCGGACAAGTATTAGAGCTACACTTAGGTATGGCTGCTAAAAATCTTGGTATTCACGTTGCATCACCAGTATTTGACGGTGCAAACGATGACGATGTATGGTCAACAATTGAAGAAGCTGGTATGGCTCGTGATGGTAAAACTGTACTTTATGATGGACGTACAGGTGAACCATTCGATAACCGTATTTCAGTAGGTGTAATGTACATGTTGAAACTTGCGCACATGGTTGATGATAAATTACATGCGCGTTCAACAGGACCATATTCACTTGTTACACAACAACCACTTGGCGGTAAAGCGCAATTCGGTGGACAACGTTTCGGTGAGATGGAGGTATGGGCACTTGAAGCATATGGTGCTGCATACACATTACAAGAAATCTTAACTTACAAATCCGATGATACAGTAGGACGTGTGAAAACATACGAGGCTATTGTTAAAGGTGAAAACATCTCTAGACCAAGTGTTCCAGAATCATTCCGAGTATTGATGAAAGAATTACAAAGTTTAGGTTTAGATGTAAAAGTTATGGATGAGCAAGATAATGAAATCGAAATGACAGACGTTGATGACGATGATGTTGTAGAACGCAAAGTAGATTTACAACAAAATGATGCTCCTGAAACACAAAAAGAAGTTACTGATTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35517","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus MRSA252","NCBI_taxonomy_id":"282458"}}}},"ARO_accession":"3003287","ARO_id":"39871","ARO_name":"Staphylococcus aureus rpoB mutants conferring resistance to daptomycin","ARO_description":"Point mutations that occurs in Staphylococcus aureus rpoB resulting in resistance to daptomycin","ARO_category":{"39637":{"category_aro_accession":"3003090","category_aro_cvterm_id":"39637","category_aro_name":"daptomycin resistant beta-subunit of RNA polymerase (rpoB)","category_aro_description":"Daptomycin resistant RNA polymerases include amino acids substitutions which alter expression of the dlt operon, which increases the cell surface positive charge. Known from S. aureus.","category_aro_class_name":"AMR Gene Family"},"35985":{"category_aro_accession":"0000068","category_aro_cvterm_id":"35985","category_aro_name":"daptomycin","category_aro_description":"Daptomycin is a novel lipopeptide antibiotic used in the treatment of certain infections caused by Gram-positive organisms. Daptomycin interferes with the bacterial cell membrane, reducing membrane potential and inhibiting cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1108":{"model_id":"1108","model_name":"Enterococcus faecium liaS mutant conferring daptomycin resistance","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"39":"A180T","44":"T120A","2203":"E192G","2252":"H264Q"},"clinical":{"39":"A180T","44":"T120A","2203":"E192G","2252":"H264Q"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"650"}},"model_sequences":{"sequence":{"37":{"protein_sequence":{"accession":"AFK58561.1","sequence":"MMGKISRAMLAVYSGIAAFLIILFSLFTYFYASNQSHWWGELLRARLLYVPLIFHLLAISLGVGLIVFLLLSLIQKTKYGKIEEKLRALSSGNYESKLLLLPIPSASDDLYIKDIDKEITKIKEKMIEVSSELQIVTSRPQYVDGQTKEEILELERHRLARELHDSVSQQLFAAMMMMSALTEQAEKSETPEMFRKQLKMVAEIINASQSEMRALLLHLRPVNLEEKSLKQGIEQLLKELQNKIQISLKWDVEDVKLSSSIEDHLFRIVQELLSNTLRHAKANELEVYLHKIDNNLLLRIIDDGTGFNMNETKTGSYGLNNIKERVAGIGGTVKIISFKGQGTSVEIKVPLMKEA"},"dna_sequence":{"accession":"CP003583","fmin":"913745","fmax":"914813","strand":"+","sequence":"ATGATGGGAAAAATATCCAGAGCGATGCTAGCTGTTTATTCGGGGATTGCGGCTTTCCTTATTATTCTATTTTCACTTTTCACTTATTTTTATGCCAGCAATCAAAGTCATTGGTGGGGAGAATTACTGCGTGCACGTTTATTATATGTTCCGCTTATCTTCCATTTGTTAGCCATTTCCTTAGGTGTAGGATTAATTGTCTTTCTATTATTATCACTTATTCAAAAGACAAAATACGGGAAAATCGAAGAAAAGCTGCGTGCACTTTCTTCTGGCAATTATGAATCCAAATTGTTGCTTCTTCCGATCCCAAGTGCATCGGACGATTTATACATCAAAGATATTGATAAGGAAATCACTAAGATAAAAGAAAAAATGATTGAAGTATCTAGTGAATTACAAATTGTAACGAGCCGTCCCCAATATGTAGATGGACAAACCAAAGAAGAAATTTTAGAATTAGAAAGACATCGATTAGCCCGTGAGCTGCATGATTCAGTTTCGCAACAATTGTTTGCAGCAATGATGATGATGTCGGCATTGACGGAGCAAGCAGAAAAAAGCGAGACACCAGAAATGTTTCGCAAGCAGTTGAAAATGGTAGCAGAGATCATCAACGCTTCCCAGTCTGAGATGCGTGCGCTGCTTCTTCATCTACGTCCAGTCAATTTAGAAGAGAAAAGTTTAAAGCAAGGTATCGAGCAGTTATTGAAGGAATTGCAAAATAAAATCCAGATTTCGCTGAAATGGGATGTAGAAGATGTAAAACTATCTAGTTCCATTGAGGATCACTTGTTCCGAATCGTTCAAGAATTGTTATCAAATACATTAAGACATGCTAAAGCCAATGAATTAGAGGTATATTTGCACAAAATAGACAATAATCTTTTGTTACGTATTATTGACGACGGAACAGGGTTTAATATGAATGAAACGAAAACGGGAAGTTATGGATTGAACAATATCAAAGAACGAGTAGCTGGTATTGGTGGAACAGTAAAAATCATTAGTTTTAAAGGTCAAGGTACAAGTGTAGAAATCAAGGTCCCTTTGATGAAGGAGGCATAGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37599","NCBI_taxonomy_name":"Enterococcus faecium DO","NCBI_taxonomy_id":"333849"}}}},"ARO_accession":"3003079","ARO_id":"39626","ARO_name":"Enterococcus faecium liaS mutant conferring daptomycin resistance","ARO_description":"liaS is a histidine kinase found in the liaFSR signal transduction pathway. Mutations confer daptomycin resistance.","ARO_category":{"41428":{"category_aro_accession":"3004264","category_aro_cvterm_id":"41428","category_aro_name":"daptomycin resistant liaS","category_aro_description":"Mutations in the liaS histidine kinase that confer daptomycin resistance.","category_aro_class_name":"AMR Gene Family"},"35985":{"category_aro_accession":"0000068","category_aro_cvterm_id":"35985","category_aro_name":"daptomycin","category_aro_description":"Daptomycin is a novel lipopeptide antibiotic used in the treatment of certain infections caused by Gram-positive organisms. Daptomycin interferes with the bacterial cell membrane, reducing membrane potential and inhibiting cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1166":{"model_id":"1166","model_name":"Staphylococcus aureus gyrA conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2117":"S84L","2118":"S85P","2119":"E88K","2120":"E88A"},"clinical":{"2117":"S84L","2118":"S85P","2119":"E88K","2120":"E88A"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1500"}},"model_sequences":{"sequence":{"2057":{"protein_sequence":{"accession":"YP_039483.1","sequence":"MAELPQSRINERNITSEMRESFLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKSARIVGDVMGKYHPHGDLSIYEAMVRMAQDFSYRYPLVDGQGNFGSMDGDGAAAMRYTEARMTKITLELLRDINKDTIDFIDNYDGNEREPSVLPARFPNLLANGASGIAVGMATNIPPHNLTELINGVLSLSKNPDISIAELMEDIEGPDFPTAGLILGKSGIRRAYETGRGSIQMRSRAVIEERGGGRQRIVVTEIPFQVNKARMIEKIAELVRDKKIDGITDLRDETSLRTGVRVVIDVRKDANASVILNNLYKQTPLQTSFGVNMIALVNGRPKLINLKEALVHYLEHQKTVVRRRTQYNLRKAKDRAHILEGLRIALDHIDEIISTIRESETDKVAMESLQQRFKLSEKQAQAILDMRLRRLTGLERDKIEAEYNELLNYISELEAILADEEVLLQLVRDELTEIRDRFGDDRRTEIQLGGFEDLEDEDLIPEEQIVITLSHNNYIKRLPVSTYRAQNRGGRGVQGMNTLEEDFVSQLVTLSTHDHVLFFTNKGRVYKLKGYEVPELSRQSKGIPVVNAIELENDEIISTMIAVKDLESEDNFLVFATKRGVVKRSALSNFSRINRNGKIAISFREDDELIAVRLTSGQEDILIGTSHASLIRFPESTLRPLGRTATGVKGITLREGDEVVGLDVAHANSVDEVLVVTENGYGKRTPVNDYRLSNRGGKGIKTATITERNGNVVCITTVTGEEDLMIVTNAGVIIRLDVADISQNGRAAQGVRLIRLGDDQFVSTVAKVKEDADEENEDEQSTVSEDGTEQQREAVVNDETPGNAIHTEVIDSEVNDEDGRIEVRQDFMDRVEEDIQQSSDDDEE"},"dna_sequence":{"accession":"NC_002952","fmin":"7004","fmax":"9665","strand":"+","sequence":"ATGGCTGAATTACCTCAATCAAGAATAAATGAACGAAATATTACCAGTGAAATGCGTGAATCATTTTTAGATTATGCGATGAGTGTTATCGTTGCTCGTGCATTGCCAGATGTTCGTGACGGTTTAAAACCAGTACATCGTCGTATACTATATGGATTAAATGAACAAGGTATGACACCGGATAAATCATATAAAAAATCAGCACGTATCGTTGGTGACGTAATGGGTAAATATCACCCTCATGGTGACTTATCTATCTATGAAGCAATGGTACGTATGGCTCAAGATTTCAGTTATCGTTATCCGCTTGTTGATGGCCAAGGTAACTTTGGTTCAATGGATGGAGATGGCGCAGCAGCAATGCGTTATACTGAAGCACGTATGACTAAAATCACACTTGAACTGTTACGTGATATTAATAAAGATACAATAGATTTTATCGATAACTATGATGGTAATGAAAGAGAGCCGTCAGTCTTACCTGCTCGATTCCCTAACTTGTTAGCCAATGGTGCATCAGGTATCGCGGTAGGTATGGCAACGAATATTCCACCACATAACTTAACAGAATTGATCAATGGTGTACTTAGCTTAAGTAAGAATCCTGATATTTCAATTGCTGAGTTAATGGAAGATATTGAAGGTCCTGATTTCCCAACTGCTGGACTTATTTTAGGTAAGAGTGGTATTAGACGCGCATATGAAACAGGTCGTGGTTCAATTCAAATGCGTTCTCGTGCAGTTATTGAAGAACGTGGAGGCGGACGTCAACGTATTGTTGTCACTGAAATTCCTTTCCAAGTGAATAAGGCTCGTATGATTGAAAAAATTGCAGAGCTTGTTCGTGACAAGAAAATTGACGGTATTACTGATTTACGTGATGAAACAAGTTTACGTACTGGTGTGCGTGTCGTTATTGATGTGCGTAAGGATGCCAATGCTAGTGTCATTTTAAATAACTTATACAAACAAACACCTCTTCAAACATCATTTGGTGTGAATATGATTGCTCTAGTGAATGGTAGACCGAAGCTGATTAATTTAAAAGAAGCGTTAGTACATTATTTAGAGCATCAAAAGACAGTTGTTAGAAGACGTACGCAATACAACTTACGTAAAGCTAAAGATCGTGCCCACATTTTAGAAGGGTTACGTATTGCGTTAGATCATATCGATGAAATTATTTCAACGATTCGTGAATCAGAAACAGATAAAGTCGCAATGGAAAGTTTGCAACAACGCTTCAAACTTTCTGAAAAACAAGCTCAAGCTATTTTAGACATGCGTTTAAGACGTCTAACAGGTTTAGAGAGAGACAAAATTGAAGCTGAATATAATGAGTTATTAAATTATATTAGTGAATTAGAAGCAATCTTAGCTGATGAAGAAGTGTTATTACAGTTAGTTAGAGATGAATTGACTGAAATTAGAGATCGCTTCGGTGATGATCGTCGTACTGAAATTCAATTAGGTGGATTTGAAGACTTAGAGGACGAGGACTTAATTCCAGAAGAACAAATTGTAATTACTTTGAGCCATAATAACTATATTAAACGTTTGCCGGTATCTACATATCGTGCTCAAAACCGTGGTGGTCGTGGTGTTCAAGGTATGAATACATTGGAAGAAGATTTTGTCAGTCAATTGGTAACTTTAAGTACACATGACCATGTATTGTTCTTTACTAACAAAGGTCGTGTATACAAACTAAAAGGTTATGAAGTGCCTGAGTTATCAAGACAGTCTAAAGGTATTCCTGTAGTGAATGCTATTGAACTTGAAAATGATGAAATCATTAGTACAATGATTGCTGTTAAAGACCTTGAAAGTGAAGATAACTTCTTAGTGTTTGCAACTAAACGTGGTGTCGTTAAACGTTCAGCATTAAGTAACTTCTCAAGAATAAATAGAAATGGTAAGATTGCGATTTCGTTCAGAGAAGATGATGAGTTAATTGCAGTTCGCTTAACAAGTGGTCAAGAAGATATCTTGATTGGTACATCACATGCATCATTAATTCGATTCCCTGAATCAACATTACGTCCTTTAGGCCGTACAGCAACGGGTGTGAAAGGTATTACACTTCGTGAAGGTGACGAAGTTGTAGGGCTTGATGTAGCTCATGCAAACAGTGTTGATGAAGTATTAGTAGTTACTGAAAATGGTTATGGTAAACGTACGCCAGTTAATGACTATCGTTTATCAAATCGTGGTGGTAAAGGTATTAAAACAGCTACGATTACTGAGCGTAATGGTAATGTTGTATGTATCACTACAGTAACTGGTGAAGAAGATTTAATGATTGTTACTAATGCAGGTGTCATTATTCGACTAGATGTTGCAGATATTTCTCAAAATGGTCGTGCAGCACAAGGTGTTCGCTTAATTCGCTTAGGCGATGATCAATTTGTTTCAACGGTTGCTAAAGTAAAAGAGGATGCAGACGAAGAAAATGAAGATGAACAATCTACTGTATCTGAAGATGGTACTGAACAACAACGTGAAGCGGTTGTAAATGATGAAACACCAGGAAATGCAATTCATACTGAAGTGATTGATTCAGAAGTAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGACCGTGTTGAAGAAGACATACAACAATCATCAGATGATGATGAAGAATAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35517","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus MRSA252","NCBI_taxonomy_id":"282458"}}}},"ARO_accession":"3003296","ARO_id":"39880","ARO_name":"Staphylococcus aureus gyrA conferring resistance to fluoroquinolones","ARO_description":"Point mutation of Staphylococcus aureus gyrA resulted in the lowered affinity between fluoroquinolones and gyrA. Thus, conferring resistance.","ARO_category":{"39876":{"category_aro_accession":"3003292","category_aro_cvterm_id":"39876","category_aro_name":"fluoroquinolone resistant gyrA","category_aro_description":"DNA gyrase is responsible for DNA supercoiling and consists of two alpha and two beta subunits. GyrA point mutations confer resistance by preventing fluoroquinolone antibiotics from binding the alpha-subunit.","category_aro_class_name":"AMR Gene Family"},"35942":{"category_aro_accession":"0000023","category_aro_cvterm_id":"35942","category_aro_name":"enoxacin","category_aro_description":"Enoxacin belongs to a group called fluoroquinolones. Its mode of action depends upon blocking bacterial DNA replication by binding itself to DNA gyrase and causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37004":{"category_aro_accession":"3000660","category_aro_cvterm_id":"37004","category_aro_name":"lomefloxacin","category_aro_description":"Lomefloxacin is a difluoropiperazinyl quinolone, sharing similar activities with other fluoroquinolones. It is used to treat urinary tract infections. Relative to other fluoroquinolones, it has a longer half life and has higher serum concentrations.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"37008":{"category_aro_accession":"3000664","category_aro_cvterm_id":"37008","category_aro_name":"trovafloxacin","category_aro_description":"Trovafloxacin is a trifluoroquinalone with a broad spectrum of activity that acts by inhibiting the uncoiling of supercoiled DNA. While potent against many Gram-positive and Gram-negative bacteria, it is less active against pseudomonads and Cl. difficile. It is usually taken as the prodrug trovafloxacin mesylate or alatrofloxacin mesylate for oral or intravenous administration, respectively.","category_aro_class_name":"Antibiotic"},"37009":{"category_aro_accession":"3000665","category_aro_cvterm_id":"37009","category_aro_name":"grepafloxacin","category_aro_description":"Grepafloxacin is a broad-spectrum antibacterial quinoline. It is no longer taken due to its high toxicity.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"37142":{"category_aro_accession":"3000762","category_aro_cvterm_id":"37142","category_aro_name":"pefloxacin","category_aro_description":"Pefloxacin is structurally and functionally similar to norfloxacin. It is poorly active against mycobacteria, while anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"40463":{"category_aro_accession":"3003780","category_aro_cvterm_id":"40463","category_aro_name":"nybomycin","category_aro_description":"A  heterocyclic antibiotic that targets mutant gyrA (type II topoisomerase) containing an S84L substitution, counteracting acquired quinolone resistance. It is effective against quinolone-resistant Gram-positive bacteria including S. aureus and E. faecalis. Due to its ability to counteract quinolone resistance by targeting the mutant form of the gyrA protein, it is classified as a reverse antibiotic (RA).","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1175":{"model_id":"1175","model_name":"Enterococcus faecium cls conferring resistance to daptomycin","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2072":"H215R","2073":"R218Q","2074":"G178T","2075":"K59T","3574":"N13I","3578":"N13T","3584":"A20D","3585":"R267H","3586":"D27N"},"clinical":{"2072":"H215R","2073":"R218Q","2074":"G178T","2075":"K59T","3574":"N13I","3578":"N13T","3584":"A20D","3585":"R267H","3586":"D27N"}},"41344":{"param_type":"insertion mutation from peptide sequence","param_description":"A subtype of the insertion mutation detection model parameter. This parameter is used when a set of insertion mutations is reported in a peptide sequence format. These are specific to codon insertions, where a multiple of three nucleotides are inserted. This does not cause a frameshift mutation. Mutation parameters of this type are reported in CARD with the notation: [+][AAs][position range].","param_type_id":"41344","param_value":{"3851":"+MPL110-112"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"900"}},"model_sequences":{"sequence":{"3560":{"protein_sequence":{"accession":"ALL09868","sequence":"MVSSIITALYLLNALIALVAILIKPRDVAAIWAWLLVLFALPGVGFVLYLFFGRGLTDKKKFYLRQSDLKELENFQSFRGDTIEHYDPDMGDKDKQQFVDFFSSLNRMPLTRMNSVTLLTDGQEKLDSLLQDLKKAKHSIHIEYYAFVTDNIGQQVLHVLEEKAAEGVEVRILYDAFGSHGTKAKDFNRLIKNGGHVHTFVTSQRALLRFRLNYHDHRKIVVIDGKISYTGGFNIANQYVNTTKKFGYWRDTHIRIFGAASSLLQLRFLTDWNVSVPEEKKVGYHLNYFFKKADRDESKLADTSIQLVSSGPNNEREQIKLSFIKLITSAKKRVWIQTPYLVPDESVIAALKIATASGVDVKIMIPNKPDHPFIYRATQYYARQLIKENVQILVYENGFLHAKTLIMDDEICMVGSANQDIRSYRLNFETSAVIYDPEFLEELATQFKEDETHCSSMTTETVKEMSNWLLFKQQISRLFSPIL"},"dna_sequence":{"accession":"CP013009","fmin":"1008840","fmax":"1010292","strand":"-","sequence":"TTATAGGATTGGAGAAAATAATCGAGAAATTTGTTGCTTGAATAATAGCCAGTTAGACATTTCCTTGACTGTTTCAGTTGTCATGGATGAACAATGTGTCTCATCTTCTTTGAACTGAGTAGCAAGTTCTTCTAAAAACTCAGGATCGTAAATGACAGCACTTGTTTCAAAATTCAATCGGTAGCTACGAATATCTTGATTTGCTGAACCTACCATGCAGATTTCATCATCCATTATCAATGTTTTTGCATGGAGGAAGCCGTTCTCATAGACAAGGATTTGTACATTTTCCTTGATCAGCTGCCGAGCATAATATTGTGTTGCTCGATAAATAAAAGGATGATCCGGTTTGTTGGGAATCATGATTTTCACATCTACACCAGAGGCAGTTGCGATTTTTAAAGCAGCAATGACACTTTCATCAGGAACAAGGTAAGGTGTCTGTATCCAAACACGTTTTTTAGCAGAAGTAATCAATTTGATAAATGAAAGCTTGATTTGTTCCCTTTCGTTATTCGGTCCGCTTGAAACAAGCTGGATGGATGTATCAGCAAGCTTAGATTCATCTCGATCTGCTTTTTTAAAGAAATAATTCAAATGATAGCCGACCTTTTTTTCTTCAGGTACCGAGACGTTCCAGTCTGTTAAGAAGCGAAGCTGGAGCAAAGAAGAAGCGGCACCGAAAATCCGTATATGCGTATCGCGCCAATAGCCGAATTTTTTTGTTGTATTTACATATTGATTGGCAATATTGAAACCACCGGTATAACTAATCTTTCCATCGATCACAACGATTTTTCGGTGATCATGGTAATTCAATCGGAAACGAAGTAATGCCCTTTGTGAGGTAACAAATGTATGGACATGTCCACCATTTTTGATTAGACGATTGAAATCTTTTGCTTTTGTGCCATGAGAGCCAAATGCATCATATAATATTCGAACTTCCACGCCTTCTGCGGCTTTTTCTTCTAAAACATGTAAGACTTGCTGGCCGATATTATCTGTCACAAATGCGTAATATTCGATATGGATCGAATGTTTGGCTTTTTTTAGATCTTGAAGCAGTGAATCCAATTTCTCTTGTCCGTCTGTGAGAAGAGTGACAGAATTCATTCTTGTCAGCGGCATACGATTTAATGAAGAGAAGAAGTCAACAAATTGCTGTTTGTCTTTATCGCCCATGTCAGGATCGTAATGTTCAATGGTATCTCCTCTAAAAGACTGAAAGTTTTCTAATTCTTTCAAGTCACTTTGTCGGAGATAGAATTTTTTCTTATCCGTTAATCCACGTCCGAAAAATAAATATAATACAAAGCCCACCCCAGGAAGGGCAAATAATACTAAGAGCCATGCCCAAATGGCTGCTACATCTCGGGGTTTGATCAAAATAGCCACCAAAGCAATAAGTGCATTTAATAGATAAAGGGCGGTTATAATACTAGATACCAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3003092","ARO_id":"39639","ARO_name":"Enterococcus faecium cls conferring resistance to daptomycin","ARO_description":"cls or cardiolipin synthetase is an inner membrane protein that is involved in membrane synthesis. Specific mutations in Enterococcus can confer resistance to daptomycin.","ARO_category":{"39856":{"category_aro_accession":"3003272","category_aro_cvterm_id":"39856","category_aro_name":"daptomycin resistant cls","category_aro_description":"Cardiolipin synthetase catalyzes the formation of cardiolipin from two phosphatidylglycerol molecules. Cardiolipin is important in membrane translocation and permeabilization. Current known mutations on the enzyme confer resistance to daptomycin.","category_aro_class_name":"AMR Gene Family"},"35985":{"category_aro_accession":"0000068","category_aro_cvterm_id":"35985","category_aro_name":"daptomycin","category_aro_description":"Daptomycin is a novel lipopeptide antibiotic used in the treatment of certain infections caused by Gram-positive organisms. Daptomycin interferes with the bacterial cell membrane, reducing membrane potential and inhibiting cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1176":{"model_id":"1176","model_name":"Mycobacterium tuberculosis katG mutations conferring resistance to isoniazid","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2284":"S315T","3236":"P131R","3238":"W91R","3239":"R463L","3240":"L101P","3241":"R128Q","3242":"P131Q","3243":"V68G","3244":"A234G","3245":"S315N","3246":"M126I","3247":"S315I","3693":"D194Y","3696":"D63E","3697":"R104L","3698":"W107R","3699":"H108E","3700":"H108Q","3701":"N138D","3702":"N138S","3703":"Y229F","3704":"W300G","3705":"T262R","3706":"T275P","3707":"W328G","3708":"Y337C","3709":"A350S","3710":"S315G","3711":"S315R","3712":"L587M","3713":"G629S","3714":"D735N","3723":"Q127E","3724":"P232S","3725":"N133T","3726":"S383P","3727":"H97R","3728":"R489S","3729":"M420T","3730":"D387H","3731":"G123E","3732":"G299S","3733":"D419H","3734":"M176T","3735":"R632C","3737":"D542H","3740":"Y64S","3741":"Y95C","3742":"P131T","3743":"A139P","3744":"D142G","3745":"A162V","3746":"G269D","3747":"T306P","3748":"R385W","3749":"D387G","3750":"T394M","3751":"Q439P","3752":"F483L","3753":"A541D","3754":"G32D","3755":"V47E","3756":"D194G","3757":"A256T","3759":"T667P","3760":"M624V","3761":"A717P","3762":"I335T","3764":"Q127P","3766":"Q352E","3767":"Y98C","3768":"A379T","3769":"G269R","3770":"A431V","3777":"S17T","3786":"A93T","3793":"D36E","3794":"A110V","3795":"A139V","3796":"G300W","3797":"H276M","3798":"Q295H","3802":"S17N","3803":"G19D","3804":"Q224E","3805":"A243S","3806":"A550D","3807":"P2S","3808":"S140N","3810":"G279D","3811":"G285D","3812":"G316D","3813":"S457I","3814":"G593D","8239":"S303L","8240":"S303C","8242":"D311N","8243":"D311S","8244":"L427I","8246":"L430V","8247":"T435R","8248":"L436G","8249":"Q471Y","8250":"Q471H","8251":"L472K","8252":"L472Q","8253":"L472I","8254":"V473D","8255":"V473I","8256":"V473K","8257":"V473R","8258":"V473M","8259":"V473S","8260":"V473F","8261":"V473W","8262":"V473Y","8263":"V473G","8264":"V473N","3715":"W107F","3716":"M255C","3717":"M255I","3718":"M255Y","3719":"T275V","3720":"W321F","3721":"W328F","3722":"R418L"},"clinical":{"2284":"S315T","3236":"P131R","3238":"W91R","3239":"R463L","3240":"L101P","3241":"R128Q","3242":"P131Q","3243":"V68G","3244":"A234G","3245":"S315N","3246":"M126I","3247":"S315I","3693":"D194Y","3696":"D63E","3697":"R104L","3698":"W107R","3699":"H108E","3700":"H108Q","3701":"N138D","3702":"N138S","3703":"Y229F","3704":"W300G","3705":"T262R","3706":"T275P","3707":"W328G","3708":"Y337C","3709":"A350S","3710":"S315G","3711":"S315R","3712":"L587M","3713":"G629S","3714":"D735N","3723":"Q127E","3724":"P232S","3725":"N133T","3726":"S383P","3727":"H97R","3728":"R489S","3729":"M420T","3730":"D387H","3731":"G123E","3732":"G299S","3733":"D419H","3734":"M176T","3735":"R632C","3737":"D542H","3740":"Y64S","3741":"Y95C","3742":"P131T","3743":"A139P","3744":"D142G","3745":"A162V","3746":"G269D","3747":"T306P","3748":"R385W","3749":"D387G","3750":"T394M","3751":"Q439P","3752":"F483L","3753":"A541D","3754":"G32D","3755":"V47E","3756":"D194G","3757":"A256T","3759":"T667P","3760":"M624V","3761":"A717P","3762":"I335T","3764":"Q127P","3766":"Q352E","3767":"Y98C","3768":"A379T","3769":"G269R","3770":"A431V","3777":"S17T","3786":"A93T","3793":"D36E","3794":"A110V","3795":"A139V","3796":"G300W","3797":"H276M","3798":"Q295H","3802":"S17N","3803":"G19D","3804":"Q224E","3805":"A243S","3806":"A550D","3807":"P2S","3808":"S140N","3810":"G279D","3811":"G285D","3812":"G316D","3813":"S457I","3814":"G593D","8239":"S303L","8240":"S303C","8242":"D311N","8243":"D311S","8244":"L427I","8246":"L430V","8247":"T435R","8248":"L436G","8249":"Q471Y","8250":"Q471H","8251":"L472K","8252":"L472Q","8253":"L472I","8254":"V473D","8255":"V473I","8256":"V473K","8257":"V473R","8258":"V473M","8259":"V473S","8260":"V473F","8261":"V473W","8262":"V473Y","8263":"V473G","8264":"V473N"},"experimental":{"3715":"W107F","3716":"M255C","3717":"M255I","3718":"M255Y","3719":"T275V","3720":"W321F","3721":"W328F","3722":"R418L"}},"40394":{"param_type":"nonsense mutation","param_description":"A nucleotide substitution resulting in a change from an amino acid codon to a STOP codon. Nonsense mutations truncate protein translation prematurely, resulting in a defective or completely inactive protein. In CARD, nonsense mutations may be attached to models using the notation: [wild type amino acid][position][STOP] (e.g. Q42STOP). This parameter is not currently used in detection algorithms.","param_type_id":"40394","param_value":{"3694":"E454STOP","3763":"E506STOP","8241":"Y304STOP"}},"40330":{"param_type":"multiple resistance variants","param_description":"A set of nucleotide or amino acid substitutions that are each required to confer resistance to an antibiotic drug or drug class by co-mutation. Compare to single resistance variant, where only one substitution is required. Multiple resistance variants parameters are indicated on appropriate models using the following notation: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2],...,[wild-type n][position n][mutation n]. When each included substitution is detected in a protein sequence, resistance is conferred. This parameter is not currently included in any detection algorithms.","param_type_id":"40330","param_value":{"3758":"N596S, Y597H"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1400"},"41343":{"param_type":"deletion mutation from nucleotide sequence","param_description":"A subtype of the deletion mutation detection model parameter. This parameter is used when a set of deletion mutations is reported in a nucleotide sequence format. Such mutations may be of variable length - possibly causing a frameshift, but not premature termination of functional knockout. Mutation parameters of this type are reported in the CARD with the notation: [-]nt[position]:[nucleotides].","param_type_id":"41343","param_value":{"8040":"-nt571:GGCGGC","8041":"-nt1501:G","8043":"-nt1525:A","8045":"-nt1293:G","8053":"-nt249:G","8054":"-nt368:G","8055":"-nt126:G","8056":"-nt81:C","8065":"-nt54:C","8069":"-nt241:G","8070":"-nt60:A"}},"41345":{"param_type":"insertion mutation from nucleotide sequence","param_description":"A subtype of the insertion mutation detection model parameter. This parameter is used when a set of insertion mutations is reported in a nucleotide sequence format. Such mutations may be of variable length - possibly causing a frameshift, but not causing premature termination or a functional knockout. Mutation parameters of this type are reported in CARD with the notation: [+]nt[position]:[nucleotides].","param_type_id":"41345","param_value":{"8048":"+nt1365:G","8051":"+nt392:T","8066":"+nt325:T","8067":"+nt518:GGTC","8068":"+nt135:T"}}},"model_sequences":{"sequence":{"3465":{"protein_sequence":{"accession":"NP_216424.1","sequence":"MPEQHPPITETTTGAASNGCPVVGHMKYPVEGGGNQDWWPNRLNLKVLHQNPAVADPMGAAFDYAAEVATIDVDALTRDIEEVMTTSQPWWPADYGHYGPLFIRMAWHAAGTYRIHDGRGGAGGGMQRFAPLNSWPDNASLDKARRLLWPVKKKYGKKLSWADLIVFAGNCALESMGFKTFGFGFGRVDQWEPDEVYWGKEATWLGDERYSGKRDLENPLAAVQMGLIYVNPEGPNGNPDPMAAAVDIRETFRRMAMNDVETAALIVGGHTFGKTHGAGPADLVGPEPEAAPLEQMGLGWKSSYGTGTGKDAITSGIEVVWTNTPTKWDNSFLEILYGYEWELTKSPAGAWQYTAKDGAGAGTIPDPFGGPGRSPTMLATDLSLRVDPIYERITRRWLEHPEELADEFAKAWYKLIHRDMGPVARYLGPLVPKQTLLWQDPVPAVSHDLVGEAEIASLKSQIRASGLTVSQLVSTAWAAASSFRGSDKRGGANGGRIRLQPQVGWEVNDPDGDLRKVIRTLEEIQESFNSAAPGNIKVSFADLVVLGGCAAIEKAAKAAGHNITVPFTPGRTDASQEQTDVESFAVLEPKADGFRNYLGKGNPLPAEYMLLDKANLLTLSAPEMTVLVGGLRVLGANYKRLPLGVFTEASESLTNDFFVNLLDMGITWEPSPADDGTYQGKDGSGKVKWTGSRVDLVFGSNSELRALVEVYGADDAQPKFVQDFVAAWDKVMNLDRFDVR"},"dna_sequence":{"accession":"NC_000962.3","fmin":"2153888","fmax":"2156111","strand":"-","sequence":"TCAGCGCACGTCGAACCTGTCGAGGTTCATCACCTTGTCCCAGGCAGCGACGAAGTCCTGCACGAACTTCGGCTGCGCGTCATCGGCGCCATAGACCTCGACAAGCGCCCGCAACTCCGAGTTGGACCCGAAGACCAGGTCCACGCGGCTGCCGGTCCACTTCACCTTGCCACTGCCATCCTTGCCCTGGTAGGTCCCGTCATCTGCTGGCGAGGGCTCCCAGGTGATACCCATGTCGAGCAGGTTCACGAAGAAGTCGTTGGTCAGTGACTCGGAGGCCTCGGTGAACACGCCCAGCGGTAAGCGCTTGTAGTTTGCGCCGAGGACGCGCAGGCCACCTACCAGCACCGTCATCTCAGGGGCACTGAGCGTAAGCAGGTTCGCCTTGTCGAGCAGCATGTACTCGGCCGGCAACGGGTTGCCCTTTCCGAGGTAGTTTCGGAAGCCATCTGCCTTGGGCTCCAGCACGGCAAAGGATTCCACGTCGGTTTGTTCCTGCGACGCATCCGTGCGGCCCGGGGTGAAGGGCACCGTGATGTTGTGGCCAGCCGCCTTTGCTGCTTTCTCTATGGCGGCACAGCCACCGAGCACGACGAGGTCGGCGAAGGACACTTTGATGTTCCCCGGCGCCGCGGAGTTGAATGACTCCTGGATCTCTTCCAGGGTGCGAATGACCTTGCGCAGATCCCCGTCGGGGTCGTTGACCTCCCACCCGACTTGTGGCTGCAGGCGGATGCGACCACCGTTGGCGCCGCCGCGCTTGTCGCTACCACGGAACGACGACGCCGCCGCCCATGCGGTCGAAACTAGCTGTGAGACAGTCAATCCCGATGCCCGGATCTGGCTCTTAAGGCTGGCAATCTCGGCTTCGCCGACGAGGTCGTGGCTGACCGCAGGGACCGGATCCTGCCACAGCAGGGTCTGCTTGGGGACCAGCGGCCCAAGGTATCTCGCAACGGGACCCATGTCTCGGTGGATCAGCTTGTACCAGGCCTTGGCGAACTCGTCGGCCAATTCCTCGGGGTGTTCCAGCCAGCGACGCGTGATCCGCTCATAGATCGGATCCACCCGCAGCGAGAGGTCAGTGGCCAGCATCGTCGGGGAGCGCCCTGGCCCGCCGAACGGGTCCGGGATGGTGCCGGCACCGGCGCCGTCCTTGGCGGTGTATTGCCAAGCGCCAGCAGGGCTCTTCGTCAGCTCCCACTCGTAGCCGTACAGGATCTCGAGGAAACTGTTGTCCCATTTCGTCGGGGTGTTCGTCCATACGACCTCGATGCCGCTGGTGATCGCGTCCTTACCGGTTCCGGTGCCATACGAGCTCTTCCAGCCCAAGCCCATCTGCTCCAGCGGAGCAGCCTCGGGTTCGGGGCCGACCAGATCGGCCGGGCCGGCGCCATGGGTCTTACCGAAAGTGTGACCGCCGACGATCAGCGCCGCTGTTTCGACGTCGTTCATGGCCATGCGCCGAAACGTCTCGCGAATGTCGACCGCCGCGGCCATGGGGTCCGGGTTGCCGTTCGGCCCCTCCGGGTTCACGTAGATCAGCCCCATCTGCACCGCGGCCAGCGGGTTCTCCAGATCCCGCTTACCGCTGTAACGCTCATCGCCGAGCCAGGTGGCTTCCTTGCCCCAATAGACCTCATCGGGCTCCCACTGGTCGACCCGGCCGAAGCCGAACCCGAACGTCTTGAAGCCCATCGATTCCAGCGCGCAGTTGCCGGCGAAAACAATCAGGTCCGCCCATGAGAGCTTCTTGCCGTACTTCTTCTTGACCGGCCACAGCAGCCGGCGCGCCTTGTCCAAGCTGGCGTTGTCGGGCCAGCTGTTAAGCGGCGCGAACCGCTGCATGCCGCCCCCGGCGCCGCCGCGGCCGTCGTGGATGCGGTAGGTGCCGGCAGCGTGCCACGCCATCCGGATAAACAGCGGCCCGTAGTGGCCGTAGTCGGCGGGCCACCACGGCTGCGAGGTGGTCATCACTTCCTCGATGTCCCGCGTCAGGGCGTCAACGTCGATGGTCGCGACCTCCGCGGCATAGTCGAACGCCGCACCCATCGGGTCAGCGACGGCCGGGTTTTGGTGCAGTACCTTCAGATTGAGCCGGTTGGGCCACCAGTCCTGGTTTCCGCCGCCCTCGACGGGGTATTTCATATGACCCACGACGGGACAGCCGTTGCTAGCGGCTCCGGTGGTGGTTTCTGTAATGGGTGGGTGTTGCTCGGGCAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3003392","ARO_id":"39976","ARO_name":"Mycobacterium tuberculosis katG mutations conferring resistance to isoniazid","ARO_description":"katG is a catalase-peroxidase that catalyzes the activation of isoniazid. Isoniazid inhibits mycolic acid synthesis, which prevents cell wall synthesis in mycobacteria. Mutations in katG results in inability to activate isoniazid. Over 280 different mutations have been documented in PubMed for katG, with mutations to Ser315 being the most prevalent.","ARO_category":{"40000":{"category_aro_accession":"3003416","category_aro_cvterm_id":"40000","category_aro_name":"isoniazid resistant katG","category_aro_description":"Bifunctional enzyme with both catalase and broad-spectrum peroxidase activity. It is a catalase-peroxidases that catalyzes the activation of isoniazid. Mutations that arises within this protein cause changes that results in the inability for katG to activate antibiotics, conferring resistance","category_aro_class_name":"AMR Gene Family"},"36659":{"category_aro_accession":"3000520","category_aro_cvterm_id":"36659","category_aro_name":"isoniazid","category_aro_description":"Isoniazid is an organic compound that is the first-line anti tuberculosis medication in prevention and treatment. As a prodrug, it is activated by mycobacterial catalase-peroxidases such as M. tuberculosis KatG. Isoniazid inhibits mycolic acid synthesis, which prevents cell wall synthesis in mycobacteria.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1197":{"model_id":"1197","model_name":"Mycobacterium tuberculosis rpsL mutations conferring resistance to Streptomycin","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2045":"K88Q","2651":"T40I","2653":"K43R","2661":"K88R"},"clinical":{"2045":"K88Q","2651":"T40I","2653":"K43R","2661":"K88R"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"2087":{"protein_sequence":{"accession":"AAK44936.1","sequence":"MPTIQQLVRKGRRDKISKVKTAALKGSPQRRGVCTRVYTTTPKKPNSALRKVARVKLTSQVEVTAYIPGEGHNLQEHSMVLVRGGRVKDLPGVRYKIIRGSLDTQGVKNRKQARSRYGAKKEKG"},"dna_sequence":{"accession":"AE000516","fmin":"783533","fmax":"783908","strand":"+","sequence":"ATGCCAACCATCCAGCAGCTGGTCCGCAAGGGTCGTCGGGACAAGATCAGTAAGGTCAAGACCGCGGCTCTGAAGGGCAGCCCGCAGCGTCGTGGTGTATGCACCCGCGTGTACACCACCACTCCGAAGAAGCCGAACTCGGCGCTTCGGAAGGTTGCCCGCGTGAAGTTGACGAGTCAGGTCGAGGTCACGGCGTACATTCCCGGCGAGGGCCACAACCTGCAGGAGCACTCGATGGTGCTGGTGCGCGGCGGCCGGGTGAAGGACCTGCCTGGTGTGCGCTACAAGATCATCCGCGGTTCGCTGGATACGCAGGGTGTCAAGAACCGCAAACAGGCACGCAGCCGTTACGGCGCTAAGAAGGAGAAGGGCTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37081","NCBI_taxonomy_name":"Mycobacterium tuberculosis CDC1551","NCBI_taxonomy_id":"83331"}}}},"ARO_accession":"3003395","ARO_id":"39979","ARO_name":"Mycobacterium tuberculosis rpsL mutations conferring resistance to Streptomycin","ARO_description":"Ribosomal protein S12 stabilizes the highly conservedpseudoknot structure formed by 16S rRNA. Amino acidsubstitutions in RpsL affect the higher-order structure of 16SrRNA and confer streptomycin resistance by disrupting interactions between 16S rRNA and streptomycin.","ARO_category":{"40003":{"category_aro_accession":"3003419","category_aro_cvterm_id":"40003","category_aro_name":"antibiotic resistant rpsL","category_aro_description":"Ribosomal protein S12 stabilizes the highly conserved pseudoknot structure formed by 16S rRNA. Amino acid substitutions in RpsL affect the higher-order structure of 16S rRNA and confer antibiotic resistance","category_aro_class_name":"AMR Gene Family"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1203":{"model_id":"1203","model_name":"Mycobacterium tuberculosis ndh mutant conferring resistance to isoniazid","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2310":"V18A","2402":"R13C","3641":"A300P","3642":"R268H","3643":"T110A","3644":"G313R","3646":"L50V"},"clinical":{"2310":"V18A","2402":"R13C","3641":"A300P","3642":"R268H","3643":"T110A","3644":"G313R","3646":"L50V"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"4385":{"protein_sequence":{"accession":"CCP44620.1","sequence":"MSPQQEPTAQPPRRHRVVIIGSGFGGLNAAKKLKRADVDIKLIARTTHHLFQPLLYQVATGIISEGEIAPPTRVVLRKQRNVQVLLGNVTHIDLAGQCVVSELLGHTYQTPYDSLIVAAGAGQSYFGNDHFAEFAPGMKSIDDALELRGRILSAFEQAERSSDPERRAKLLTFTVVGAGPTGVEMAGQIAELAEHTLKGAFRHIDSTKARVILLDAAPAVLPPMGAKLGQRAAARLQKLGVEIQLGAMVTDVDRNGITVKDSDGTVRRIESACKVWSAGVSASRLGRDLAEQSRVELDRAGRVQVLPDLSIPGYPNVFVVGDMAAVEGVPGVAQGAIQGAKYVASTIKAELAGANPAEREPFQYFDKGSMATVSRFSAVAKIGPVEFSGFIAWLIWLVLHLAYLIGFKTKITTLLSWTVTFLSTRRGQLTITDQQAFARTRLEQLAELAAEAQGSAASAKVAS"},"dna_sequence":{"accession":"AL123456","fmin":"2101650","fmax":"2103042","strand":"-","sequence":"CTAGCTGGCCACCTTAGCGCTTGCCGCTGAGCCCTGCGCCTCGGCGGCCAGCTCGGCCAGCTGTTCGAGCCGCGTTCGCGCAAATGCCTGCTGGTCGGTGATGGTCAGCTGGCCGCGGCGAGTACTGAGGAAAGTCACCGTCCACGACAGCAGAGTGGTGATCTTGGTCTTGAACCCGATCAGGTACGCCAGGTGCAGCACCAGCCAAATCAGCCAGGCGATAAAGCCGCTGAACTCAACGGGACCGATCTTGGCCACCGCCGAAAACCTCGAAACCGTGGCCATCGATCCCTTGTCGAAGTACTGGAATGGCTCACGCTCCGCCGGGTTGGCGCCGGCCAGTTCGGCCTTGATCGTGCTGGCGACGTATTTCGCCCCCTGGATGGCGCCCTGCGCCACACCCGGCACACCCTCCACAGCGGCCATATCGCCCACCACGAACACGTTCGGGTACCCGGGAATGGACAGGTCGGGCAGCACTTGGACCCGGCCGGCCCGGTCGAGCTCAACCCGTGATTGCTCGGCAAGGTCCCTGCCCAACCGACTGGCCGAAACCCCGGCCGACCAGACCTTGCAGGCCGACTCGATGCGCCGGACGGTGCCGTCGGAGTCCTTGACGGTGATGCCGTTGCGGTCGACGTCGGTGACCATCGCACCCAGCTGGATTTCCACGCCCAGCTTCTGCAACCGGGCAGCCGCCCGCTGACCGAGCTTTGCGCCCATCGGTGGCAGCACCGCCGGGGCGGCGTCAAGCAGAATCACCCGCGCCTTGGTCGAGTCGATGTGCCGGAATGCGCCCTTCAACGTGTGCTCGGCCAGCTCGGCGATCTGTCCGGCCATTTCAACACCGGTGGGGCCAGCCCCGACAACGGTGAATGTCAGTAGCTTGGCCCGCCGTTCCGGATCGCTGGACCGTTCGGCTTGCTCGAAAGCGCTCAATATGCGGCCACGCAACTCCAACGCGTCGTCGATGGACTTCATGCCGGGTGCGAATTCGGCGAAATGGTCGTTGCCGAAATAAGACTGGCCAGCACCCGCGGCGACGATCAGGCTGTCGTAGGGGGTTTGGTAGGTGTGACCGAGCAATTCCGAGACGACGCACTGCCCGGCCAGGTCGATGTGGGTGACGTTGCCCAACAGTACCTGGACATTGCGCTGCTTACGCAGCACGACCCGGGTCGGCGGAGCGATTTCTCCCTCGGAGATAATCCCGGTGGCCACTTGGTACAGCAGCGGCTGGAACAGGTGATGGGTGGTGCGCGCGATCAGCTTGATGTCAACGTCGGCCCGCTTGAGCTTCTTTGCCGCGTTTAGCCCGCCGAACCCAGATCCGATGATCACAACTCGATGCCTACGAGGTGGTTGCGCTGTGGGTTCTTGCTGGGGACTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3003461","ARO_id":"40054","ARO_name":"Mycobacterium tuberculosis ndh with mutation conferring resistance to isoniazid","ARO_description":"Point mutations in the Mycobacterium tuberculosis ndh gene shown clinically to confer resistance to isoniazid.","ARO_category":{"40053":{"category_aro_accession":"3003460","category_aro_cvterm_id":"40053","category_aro_name":"antibiotic resistant ndh","category_aro_description":"ndh is a NADH oxidase. It participates in antibiotic resistance by diminishing NADH oxidation and consequently causes an increase in NADH concentration and depletion of NAD+. This alteration of the NADH\/NAD+ ratio prevents the peroxidation reactions required for the activation of INH, as well as the displacement of the NADH-isonicotinic acyl complex from InhA enzyme binding site.","category_aro_class_name":"AMR Gene Family"},"36659":{"category_aro_accession":"3000520","category_aro_cvterm_id":"36659","category_aro_name":"isoniazid","category_aro_description":"Isoniazid is an organic compound that is the first-line anti tuberculosis medication in prevention and treatment. As a prodrug, it is activated by mycobacterial catalase-peroxidases such as M. tuberculosis KatG. Isoniazid inhibits mycolic acid synthesis, which prevents cell wall synthesis in mycobacteria.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1237":{"model_id":"1237","model_name":"Mycobacterium tuberculosis rpoB mutants conferring resistance to rifampicin","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3251":"S531L","3252":"H526C","3253":"L533R","3254":"L538R","3255":"H526Y","3256":"D516V","3257":"L533P","3258":"S531W","3259":"S531G","3260":"H526D","3261":"H526S","3262":"K527Q","3263":"D516T","3264":"D516Y","3265":"M515I","3266":"M515V","3267":"L511P","3268":"I572F","3269":"S522L","3270":"V176F","3271":"Q438K","3272":"D441V","3273":"D441Y","3274":"S447Q","3275":"H451Y","3276":"H451C","3277":"H451D","3278":"H451R","3279":"S456L","3280":"S456W","3993":"V146F","3994":"A381V","3995":"L521P","3996":"H526R","3997":"S522W","3998":"Q513P","4000":"Q490H","4001":"E504A","4002":"Q513L","4003":"Q513K","4004":"D516N","4005":"D516G","4007":"H526L","4008":"S450L","4011":"S509R","4012":"S509Q","4013":"Q517L","4014":"L524S","4015":"R528P","4016":"H526T","4019":"R529Q","4020":"H526N","4021":"S512I","4022":"L511R","4023":"S512T","4024":"S531C","4025":"H526E","4028":"L511V","4030":"N518T","4031":"S522Q","4032":"K527N","4033":"R528H","4035":"S512R","4036":"L521M","4037":"H526G","4038":"F505L","4039":"S574L","4040":"G507S","4041":"G507D","4042":"T508P","4043":"T508A","4044":"T508H","4046":"Q513D","4047":"Q513E","4048":"D516H","4049":"N519K","4051":"G523A","4052":"H526F","4053":"H526Q","4055":"S531F","4063":"D518H","4073":"Q513R","4075":"H526P","4076":"Q517H","4077":"T508S","4078":"L511M","4080":"D516K","4082":"N518H","4083":"N518I","4106":"L538P","4107":"L545M","4109":"L571V","4110":"R633C","4111":"E672D","8229":"T508N","8230":"S512N","8237":"P520T"},"clinical":{"3251":"S531L","3252":"H526C","3253":"L533R","3254":"L538R","3255":"H526Y","3256":"D516V","3257":"L533P","3258":"S531W","3259":"S531G","3260":"H526D","3261":"H526S","3262":"K527Q","3263":"D516T","3264":"D516Y","3265":"M515I","3266":"M515V","3267":"L511P","3268":"I572F","3269":"S522L","3270":"V176F","3271":"Q438K","3272":"D441V","3273":"D441Y","3274":"S447Q","3275":"H451Y","3276":"H451C","3277":"H451D","3278":"H451R","3279":"S456L","3280":"S456W","3993":"V146F","3994":"A381V","3995":"L521P","3996":"H526R","3997":"S522W","3998":"Q513P","4000":"Q490H","4001":"E504A","4002":"Q513L","4003":"Q513K","4004":"D516N","4005":"D516G","4007":"H526L","4008":"S450L","4011":"S509R","4012":"S509Q","4013":"Q517L","4014":"L524S","4015":"R528P","4016":"H526T","4019":"R529Q","4020":"H526N","4021":"S512I","4022":"L511R","4023":"S512T","4024":"S531C","4025":"H526E","4028":"L511V","4030":"N518T","4031":"S522Q","4032":"K527N","4033":"R528H","4035":"S512R","4036":"L521M","4037":"H526G","4038":"F505L","4039":"S574L","4040":"G507S","4041":"G507D","4042":"T508P","4043":"T508A","4044":"T508H","4046":"Q513D","4047":"Q513E","4048":"D516H","4049":"N519K","4051":"G523A","4052":"H526F","4053":"H526Q","4055":"S531F","4063":"D518H","4073":"Q513R","4075":"H526P","4076":"Q517H","4077":"T508S","4078":"L511M","4080":"D516K","4082":"N518H","4083":"N518I","4106":"L538P","4107":"L545M","4109":"L571V","4110":"R633C","4111":"E672D","8229":"T508N","8230":"S512N","8237":"P520T"}},"40394":{"param_type":"nonsense mutation","param_description":"A nucleotide substitution resulting in a change from an amino acid codon to a STOP codon. Nonsense mutations truncate protein translation prematurely, resulting in a defective or completely inactive protein. In CARD, nonsense mutations may be attached to models using the notation: [wild type amino acid][position][STOP] (e.g. Q42STOP). This parameter is not currently used in detection algorithms.","param_type_id":"40394","param_value":{"4045":"Q513STOP","4074":"S522STOP"}},"41342":{"param_type":"deletion mutation from peptide sequence","param_description":"A subtype of the deletion mutation detection model parameter. This parameter is used when a set of deletion mutations is reported in a peptide sequence format. These are specific to codon deletions, where a multiple of 3 nucleotides are deleted. Mutations of this type are reported in the CARD with the notation: [-][AAs][position range].","param_type_id":"41342","param_value":{"4026":"-DQ516-517","4027":"-QN517-518","4006":"-N516","8083":"-K527","8084":"-P520","8085":"-Q517","8086":"-N519","8231":"-Q513","8232":"-F514","8233":"-M515","8234":"-D516","8235":"-N518","8238":"-H526"}},"41344":{"param_type":"insertion mutation from peptide sequence","param_description":"A subtype of the insertion mutation detection model parameter. This parameter is used when a set of insertion mutations is reported in a peptide sequence format. These are specific to codon insertions, where a multiple of three nucleotides are inserted. This does not cause a frameshift mutation. Mutation parameters of this type are reported in CARD with the notation: [+][AAs][position range].","param_type_id":"41344","param_value":{"3999":"+R514","4017":"+F514"}},"40330":{"param_type":"multiple resistance variants","param_description":"A set of nucleotide or amino acid substitutions that are each required to confer resistance to an antibiotic drug or drug class by co-mutation. Compare to single resistance variant, where only one substitution is required. Multiple resistance variants parameters are indicated on appropriate models using the following notation: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2],...,[wild-type n][position n][mutation n]. When each included substitution is detected in a protein sequence, resistance is conferred. This parameter is not currently included in any detection algorithms.","param_type_id":"40330","param_value":{"4057":"S531L,S622A","4058":"H526S,M515V","4059":"H526S,P535H","4060":"H526Y,E541G","4061":"D516Y,L511R","4062":"D516E,S522L","4065":"S531L,F514V","4066":"S531L,H526C","4067":"L511R,D516V","4068":"L511P,M515I","4069":"L524W,T525P,H526Q,-527K","4070":"Q513H,-514F,-515M,-516D","4084":"-519N,S522L,S531L","4086":"H526D,S531","4087":"L511P,S512T,D516V","4103":"T516I,G523W,D525Y","4104":"H526D,E541G,S553A","4105":"H526P,K527Q","4108":"E562G,P564L","4072":"-515M,-516D,-517Q,-518N"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"2300"}},"model_sequences":{"sequence":{"4199":{"protein_sequence":{"accession":"CCP43410.1","sequence":"MADSRQSKTAASPSPSRPQSSSNNSVPGAPNRVSFAKLREPLEVPGLLDVQTDSFEWLIGSPRWRESAAERGDVNPVGGLEEVLYELSPIEDFSGSMSLSFSDPRFDDVKAPVDECKDKDMTYAAPLFVTAEFINNNTGEIKSQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDETIDKSTDKTLHSVKVIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTSEQIVERFGFSEIMRSTLEKDNTVGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLHVGEPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVETDDIDHFGNRRLRTVGELIQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVSDEIVYLTADEEDRHVVAQANSPIDADGRFVEPRVLVRRKAGEVEYVPSSEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVVVAEESGVIEEVSADYITVMHDNGTRRTYRMRKFARSNHGTCANQCPIVDAGDRVEAGQVIADGPCTDDGEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNISDEVLADLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDEDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLADGTPVDIILNTHGVPRRMNIGQILETHLGWCAHSGWKVDAAKGVPDWAARLPDELLEAQPNAIVSTPVFDGAQEAELQGLLSCTLPNRDGDVLVDADGKAMLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLCLNVEVLSSDGAAIELREGEDEDLERAAANLGINLSRNESASVEDLA"},"dna_sequence":{"accession":"AL123456.3","fmin":"759806","fmax":"763325","strand":"+","sequence":"TTGGCAGATTCCCGCCAGAGCAAAACAGCCGCTAGTCCTAGTCCGAGTCGCCCGCAAAGTTCCTCGAATAACTCCGTACCCGGAGCGCCAAACCGGGTCTCCTTCGCTAAGCTGCGCGAACCACTTGAGGTTCCGGGACTCCTTGACGTCCAGACCGATTCGTTCGAGTGGCTGATCGGTTCGCCGCGCTGGCGCGAATCCGCCGCCGAGCGGGGTGATGTCAACCCAGTGGGTGGCCTGGAAGAGGTGCTCTACGAGCTGTCTCCGATCGAGGACTTCTCCGGGTCGATGTCGTTGTCGTTCTCTGACCCTCGTTTCGACGATGTCAAGGCACCCGTCGACGAGTGCAAAGACAAGGACATGACGTACGCGGCTCCACTGTTCGTCACCGCCGAGTTCATCAACAACAACACCGGTGAGATCAAGAGTCAGACGGTGTTCATGGGTGACTTCCCGATGATGACCGAGAAGGGCACGTTCATCATCAACGGGACCGAGCGTGTGGTGGTCAGCCAGCTGGTGCGGTCGCCCGGGGTGTACTTCGACGAGACCATTGACAAGTCCACCGACAAGACGCTGCACAGCGTCAAGGTGATCCCGAGCCGCGGCGCGTGGCTCGAGTTTGACGTCGACAAGCGCGACACCGTCGGCGTGCGCATCGACCGCAAACGCCGGCAACCGGTCACCGTGCTGCTCAAGGCGCTGGGCTGGACCAGCGAGCAGATTGTCGAGCGGTTCGGGTTCTCCGAGATCATGCGATCGACGCTGGAGAAGGACAACACCGTCGGCACCGACGAGGCGCTGTTGGACATCTACCGCAAGCTGCGTCCGGGCGAGCCCCCGACCAAAGAGTCAGCGCAGACGCTGTTGGAAAACTTGTTCTTCAAGGAGAAGCGCTACGACCTGGCCCGCGTCGGTCGCTATAAGGTCAACAAGAAGCTCGGGCTGCATGTCGGCGAGCCCATCACGTCGTCGACGCTGACCGAAGAAGACGTCGTGGCCACCATCGAATATCTGGTCCGCTTGCACGAGGGTCAGACCACGATGACCGTTCCGGGCGGCGTCGAGGTGCCGGTGGAAACCGACGACATCGACCACTTCGGCAACCGCCGCCTGCGTACGGTCGGCGAGCTGATCCAAAACCAGATCCGGGTCGGCATGTCGCGGATGGAGCGGGTGGTCCGGGAGCGGATGACCACCCAGGACGTGGAGGCGATCACACCGCAGACGTTGATCAACATCCGGCCGGTGGTCGCCGCGATCAAGGAGTTCTTCGGCACCAGCCAGCTGAGCCAATTCATGGACCAGAACAACCCGCTGTCGGGGTTGACCCACAAGCGCCGACTGTCGGCGCTGGGGCCCGGCGGTCTGTCACGTGAGCGTGCCGGGCTGGAGGTCCGCGACGTGCACCCGTCGCACTACGGCCGGATGTGCCCGATCGAAACCCCTGAGGGGCCCAACATCGGTCTGATCGGCTCGCTGTCGGTGTACGCGCGGGTCAACCCGTTCGGGTTCATCGAAACGCCGTACCGCAAGGTGGTCGACGGCGTGGTTAGCGACGAGATCGTGTACCTGACCGCCGACGAGGAGGACCGCCACGTGGTGGCACAGGCCAATTCGCCGATCGATGCGGACGGTCGCTTCGTCGAGCCGCGCGTGCTGGTCCGCCGCAAGGCGGGCGAGGTGGAGTACGTGCCCTCGTCTGAGGTGGACTACATGGACGTCTCGCCCCGCCAGATGGTGTCGGTGGCCACCGCGATGATTCCCTTCCTGGAGCACGACGACGCCAACCGTGCCCTCATGGGGGCAAACATGCAGCGCCAGGCGGTGCCGCTGGTCCGTAGCGAGGCCCCGCTGGTGGGCACCGGGATGGAGCTGCGCGCGGCGATCGACGCCGGCGACGTCGTCGTCGCCGAAGAAAGCGGCGTCATCGAGGAGGTGTCGGCCGACTACATCACTGTGATGCACGACAACGGCACCCGGCGTACCTACCGGATGCGCAAGTTTGCCCGGTCCAACCACGGCACTTGCGCCAACCAGTGCCCCATCGTGGACGCGGGCGACCGAGTCGAGGCCGGTCAGGTGATCGCCGACGGTCCCTGTACTGACGACGGCGAGATGGCGCTGGGCAAGAACCTGCTGGTGGCCATCATGCCGTGGGAGGGCCACAACTACGAGGACGCGATCATCCTGTCCAACCGCCTGGTCGAAGAGGACGTGCTCACCTCGATCCACATCGAGGAGCATGAGATCGATGCTCGCGACACCAAGCTGGGTGCGGAGGAGATCACCCGCGACATCCCGAACATCTCCGACGAGGTGCTCGCCGACCTGGATGAGCGGGGCATCGTGCGCATCGGTGCCGAGGTTCGCGACGGGGACATCCTGGTCGGCAAGGTCACCCCGAAGGGTGAGACCGAGCTGACGCCGGAGGAGCGGCTGCTGCGTGCCATCTTCGGTGAGAAGGCCCGCGAGGTGCGCGACACTTCGCTGAAGGTGCCGCACGGCGAATCCGGCAAGGTGATCGGCATTCGGGTGTTTTCCCGCGAGGACGAGGACGAGTTGCCGGCCGGTGTCAACGAGCTGGTGCGTGTGTATGTGGCTCAGAAACGCAAGATCTCCGACGGTGACAAGCTGGCCGGCCGGCACGGCAACAAGGGCGTGATCGGCAAGATCCTGCCGGTTGAGGACATGCCGTTCCTTGCCGACGGCACCCCGGTGGACATTATTTTGAACACCCACGGCGTGCCGCGACGGATGAACATCGGCCAGATTTTGGAGACCCACCTGGGTTGGTGTGCCCACAGCGGCTGGAAGGTCGACGCCGCCAAGGGGGTTCCGGACTGGGCCGCCAGGCTGCCCGACGAACTGCTCGAGGCGCAGCCGAACGCCATTGTGTCGACGCCGGTGTTCGACGGCGCCCAGGAGGCCGAGCTGCAGGGCCTGTTGTCGTGCACGCTGCCCAACCGCGACGGTGACGTGCTGGTCGACGCCGACGGCAAGGCCATGCTCTTCGACGGGCGCAGCGGCGAGCCGTTCCCGTACCCGGTCACGGTTGGCTACATGTACATCATGAAGCTGCACCACCTGGTGGACGACAAGATCCACGCCCGCTCCACCGGGCCGTACTCGATGATCACCCAGCAGCCGCTGGGCGGTAAGGCGCAGTTCGGTGGCCAGCGGTTCGGGGAGATGGAGTGCTGGGCCATGCAGGCCTACGGTGCTGCCTACACCCTGCAGGAGCTGTTGACCATCAAGTCCGATGACACCGTCGGCCGCGTCAAGGTGTACGAGGCGATCGTCAAGGGTGAGAACATCCCGGAGCCGGGCATCCCCGAGTCGTTCAAGGTGCTGCTCAAAGAACTGCAGTCGCTGTGCCTCAACGTCGAGGTGCTATCGAGTGACGGTGCGGCGATCGAACTGCGCGAAGGTGAGGACGAGGACCTGGAGCGGGCCGCGGCCAACCTGGGAATCAATCTGTCCCGCAACGAATCCGCAAGTGTCGAGGATCTTGCGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3003283","ARO_id":"39867","ARO_name":"Mycobacterium tuberculosis rpoB mutants conferring resistance to rifampicin","ARO_description":"Point mutations that occurs in Mycobacterium tuberculosis rpoB resulting in resistance to rifampicin.","ARO_category":{"36349":{"category_aro_accession":"3000210","category_aro_cvterm_id":"36349","category_aro_name":"rifamycin-resistant beta-subunit of RNA polymerase (rpoB)","category_aro_description":"Rifampin resistant RNA polymerases include amino acids substitutions which disrupt the affinity of rifampin for its binding site. These mutations are frequently concentrated in the rif I region of the beta-subunit and most often involve amino acids which make direct interactions with rifampin. However, mutations which also confer resistance can occur outside this region and may involve amino acids which do not directly make contact with rifampin.","category_aro_class_name":"AMR Gene Family"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36656":{"category_aro_accession":"3000517","category_aro_cvterm_id":"36656","category_aro_name":"rifaximin","category_aro_description":"Rifaximin is a semi-synthetic rifamycin used to treat traveller's diarrhea. Rifaximin inhibits RNA synthesis by binding to the beta subunit of bacterial RNA polymerase.","category_aro_class_name":"Antibiotic"},"36669":{"category_aro_accession":"3000530","category_aro_cvterm_id":"36669","category_aro_name":"rifabutin","category_aro_description":"Rifabutin is a semisynthetic rifamycin used in tuberculosis therapy. It inhibits DNA-dependent RNA synthesis.","category_aro_class_name":"Antibiotic"},"36673":{"category_aro_accession":"3000534","category_aro_cvterm_id":"36673","category_aro_name":"rifapentine","category_aro_description":"Rifapentine is a semisynthetic rifamycin that inhibits DNA-dependent RNA synthesis. It is often used in the treatment of tuberculosis and leprosy.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1301":{"model_id":"1301","model_name":"Staphylococcus aureus cls conferring resistance to daptomycin","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"622":"A23V","653":"F60S","687":"L52F","3440":"T33N"},"clinical":{"622":"A23V","653":"F60S","687":"L52F"},"experimental":{"3440":"T33N"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"900"}},"model_sequences":{"sequence":{"740":{"protein_sequence":{"accession":"YP_500802.1","sequence":"MIELLSIALKHSNIILNSIFIGAFILNLLFAFTIIFMERRSANSIWAWLLVLVFLPLFGFILYLLLGRQIQRDQIFKIDKEDKKGLELIVDEQLAALKNENFSNSNYQIVKFKEMIQMLLYNNAAFLTTDNDLKIYTDGQEKFDDLIQDIRNATDYIHFQYYIIQNDELGRTILNELGKKAEQGVEVKILYDDMGSRGLRKKGLRPFRNKGGHAEAFFPSKLPLINLRMNNRNHRKIVVIDGQIGYVGGFNVGDEYLGKSKKFGYWRDTHLRIVGDAVNALQLRFILDWNSQATRDHISYDDRYFPDVNSGGTIGVQIASSGPDEEWEQIKYGYLKMISSAKKSIYIQSPYFIPDQAFLDSIKIAALGGVDVNIMIPNKPDHPFVFWATLKNAASLLDAGVKVFHYDNGFLHSKTLVIDDEIASVGTANMDHRSFTLNFEVNAFIYDQQIAKKLKQAFIDDLAVSSELTKARYAKRSLWIKFKEGISQLLSPIL"},"dna_sequence":{"accession":"NC_007795","fmin":"2155375","fmax":"2156860","strand":"+","sequence":"ATGATAGAGTTATTATCCATTGCACTCAAGCATTCTAATATTATTTTAAATTCAATATTTATTGGTGCATTTATTTTAAACTTATTATTCGCCTTTACCATTATTTTCATGGAAAGACGTTCTGCCAATTCTATCTGGGCTTGGTTACTAGTCTTAGTTTTCTTGCCTTTATTCGGCTTCATTTTATACTTACTATTAGGACGACAAATTCAACGTGACCAAATTTTCAAAATTGATAAGGAAGATAAAAAAGGATTAGAGTTAATCGTTGATGAGCAATTAGCTGCTTTAAAAAATGAAAACTTTTCAAATTCCAATTATCAAATTGTAAAATTTAAAGAAATGATTCAAATGTTGTTATATAATAACGCAGCATTTTTAACAACAGACAACGATTTAAAAATATACACAGACGGCCAAGAAAAATTTGATGACCTAATACAAGACATCCGTAATGCTACTGATTATATTCATTTTCAGTACTATATTATTCAAAATGATGAATTAGGTCGTACCATTTTAAATGAACTTGGTAAAAAAGCGGAACAAGGTGTAGAAGTTAAAATTCTTTATGATGACATGGGTTCTCGTGGACTGCGTAAAAAAGGCTTACGCCCGTTTCGCAATAAAGGTGGACATGCTGAAGCATTTTTCCCATCAAAATTACCTTTAATTAACTTGCGTATGAACAATCGAAACCATCGAAAAATTGTTGTAATAGATGGGCAAATTGGATATGTTGGTGGTTTTAATGTTGGTGATGAGTACTTAGGTAAATCAAAAAAATTCGGCTATTGGCGAGATACGCATTTACGAATTGTCGGGGATGCAGTGAATGCATTGCAATTACGATTTATTCTAGATTGGAATTCACAAGCCACACGTGACCACATCTCCTATGATGATCGTTATTTCCCAGATGTAAATTCTGGTGGAACAATTGGCGTTCAAATAGCTTCTAGTGGTCCTGACGAAGAATGGGAACAGATTAAATACGGCTATTTGAAAATGATTTCATCTGCTAAAAAATCGATTTATATTCAATCTCCCTATTTCATACCTGATCAAGCCTTTTTAGATTCTATTAAAATTGCGGCATTAGGTGGTGTTGATGTCAATATCATGATTCCTAATAAACCTGACCATCCGTTTGTTTTTTGGGCTACTTTAAAAAATGCAGCATCCTTATTAGATGCCGGTGTTAAAGTATTTCACTACGACAATGGCTTTTTACACTCAAAAACACTTGTTATAGATGATGAAATTGCAAGTGTGGGAACAGCTAATATGGACCATCGCAGTTTCACATTGAATTTCGAAGTCAACGCTTTTATTTATGACCAACAAATTGCCAAAAAATTAAAACAAGCTTTTATAGATGATTTAGCAGTATCTTCTGAATTAACAAAAGCACGTTATGCTAAGCGAAGTCTTTGGATTAAATTTAAAGAAGGTATTTCACAATTATTGTCACCTATCTTATAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35511","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus NCTC 8325","NCBI_taxonomy_id":"93061"}}}},"ARO_accession":"3003074","ARO_id":"39621","ARO_name":"Staphylococcus aureus cls conferring resistance to daptomycin","ARO_description":"cls or cardiolipin synthetase is an inner membrane protein that is involved in membrane synthesis. Specific mutations in S. aureus can confer resistance to daptomycin.","ARO_category":{"39856":{"category_aro_accession":"3003272","category_aro_cvterm_id":"39856","category_aro_name":"daptomycin resistant cls","category_aro_description":"Cardiolipin synthetase catalyzes the formation of cardiolipin from two phosphatidylglycerol molecules. Cardiolipin is important in membrane translocation and permeabilization. Current known mutations on the enzyme confer resistance to daptomycin.","category_aro_class_name":"AMR Gene Family"},"35985":{"category_aro_accession":"0000068","category_aro_cvterm_id":"35985","category_aro_name":"daptomycin","category_aro_description":"Daptomycin is a novel lipopeptide antibiotic used in the treatment of certain infections caused by Gram-positive organisms. Daptomycin interferes with the bacterial cell membrane, reducing membrane potential and inhibiting cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1320":{"model_id":"1320","model_name":"Klebsiella mutant PhoP conferring antibiotic resistance to colistin","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2871":"D191Y"},"clinical":{"2871":"D191Y"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"3527":{"protein_sequence":{"accession":"CDO13981.1","sequence":"MRVLVVEDNALLRHHLKVQLQELGHQVDAAEDAREADYYLGEHLPDIAIVDLGLPDEDGLSLIRRWRSHDVSLPVLVLTAREGWQDKVEVLSAGADDYVTKPFHIEEVAARMQALLRRNSGLASQVISLPPFQVDLSRRELSVNDQPIKLTAFEYTIMETLIRNRGKVVSKDSLMLQLYPDAELRESHTIDVLMGRLRKKIQAEYPQDVITTVRGQGYLFELR"},"dna_sequence":{"accession":"FO834906.1","fmin":"2325636","fmax":"2326308","strand":"-","sequence":"TCAGCGCAATTCGAACAGATAGCCCTGGCCGCGCACCGTGGTGATGACGTCCTGTGGGTATTCAGCCTGAATTTTCTTGCGCAGCCGACCCATCAGCACGTCGATGGTGTGGCTTTCTCGCAGTTCGGCATCCGGGTAAAGCTGGAGCATCAGCGAATCTTTGCTGACCACTTTGCCGCGGTTACGGATCAGGGTTTCCATAATGGTGTATTCAAAGGCGGTCAGCTTGATCGGCTGGTCATTCACCGACAGCTCGCGCCGGGAGAGGTCGACCTGGAACGGCGGCAGGGAGATCACCTGCGAGGCCAGACCGCTGTTACGGCGCAGCAGCGCCTGCATGCGGGCGGCAACCTCTTCAATATGGAAAGGCTTGGTGACGTAATCATCCGCCCCGGCGCTCAGCACTTCCACTTTATCCTGCCATCCTTCGCGGGCGGTCAGCACCAGCACCGGCAGCGACACGTCGTGGCTGCGCCAGCGGCGGATCAGTGATAAACCGTCTTCATCCGGCAGGCCGAGATCGACGATGGCGATATCCGGGAGATGTTCGCCCAGATAGTAGTCCGCTTCCCTGGCATCTTCCGCCGCATCGACCTGATGGCCCAGCTCCTGCAGCTGAACTTTGAGGTGGTGACGCAGCAGGGCATTATCCTCAACCACGAGTACGCGCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3003585","ARO_id":"40195","ARO_name":"Klebsiella mutant PhoP conferring antibiotic resistance to colistin","ARO_description":"A mutant phoP activates pmrHFIJKLM expression responsible for L-aminoarabinose synthesis and polymyxin resistance, by way of alteration of negative charge","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"41433":{"category_aro_accession":"3004269","category_aro_cvterm_id":"41433","category_aro_name":"pmr phosphoethanolamine transferase","category_aro_description":"This family of phosphoethanolamine transferase catalyze the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine to lipid A, which impedes the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1339":{"model_id":"1339","model_name":"Mycobacterium tuberculosis embR mutant conferring resistance to ethambutol","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2350":"C110Y","2369":"Q379R"},"clinical":{"2350":"C110Y","2369":"Q379R"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"4395":{"protein_sequence":{"accession":"CCP44023.1","sequence":"MAGSATVEKRLDFGLLGPLQMTIDGTPVPSGTPKQRAVLAMLVINRNRPVGVDALITALWEEWPPSGARASIHSYVSNLRKLLGGAGIDPRVVLAAAPPGYRLSIPDNTCDLGRFVAEKTAGVHAAAAGRFEQASRHLSAALREWRGPVLDDLRDFQFVEPFATALVEDKVLAHTAKAEAEIACGRASAVIAELEALTFEHPYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTLRALNERILRQQPLDAKKSAKTTAAGTVTVLDQRTMASGQQAVAYLHDIASGRGYPLQAAATRIGRLHDNDIVLDSANVSRHHAVIVDTGTNYVINDLRSSNGVHVQHERIRSAVTLNDGDHIRICDHEFTFQISAGTHGGT"},"dna_sequence":{"accession":"AL123456","fmin":"1416180","fmax":"1417347","strand":"-","sequence":"CTACGTGCCGCCATGCGTCCCCGCGCTGATCTGGAACGTGAATTCATGGTCACAGATGCGAATGTGGTCGCCGTCGTTCAGCGTGACCGCGGAGCGGATTCGCTCGTGCTGCACATGCACGCCGTTGGACGATCGGAGGTCGTTGATGACGTAGTTGGTGCCCGTGTCGACGATGACGGCGTGGTGGCGGCTGACGTTGGCGCTGTCTAGGACGATGTCGTTGTCATGCAGACGCCCGATCCGGGTCGCCGCGGCTTGCAGTGGGTAGCCGCGACCCGAGGCGATGTCGTGCAGGTAGGCCACCGCCTGCTGGCCCGACGCCATGGTGCGCTGATCGAGCACCGTGACGGTGCCGGCAGCGGTGGTTTTGGCGGACTTCTTGGCATCCAGCGGTTGCTGACGCAGAATCCGCTCGTTGAGAGCGCGCAACGTCGGACCGGGGTCGATGCCGAGGTCGTCGGCCAGTGTTGTCTTCACCCGGCGATAGGCGCCCAGCGCATCGGATTGCCGGTCGGAGAGGTAGTAGGCGGTGATCAGCTGTGTCCACAGCGGCTCCCGGTAGGGGTGTTCGAATGTCAGAGCCTCGAGCTCGGCGATCACTGCGCTGGCCCGCCCACACGCGATTTCGGCCTCCGCCTTGGCGGTATGGGCAAGAACCTTGTCTTCTACCAGCGCCGTGGCAAAGGGTTCGACGAACTGGAAGTCGCGCAGGTCATCGAGCACCGGCCCACGCCATTCTCTCAATGCGGCCGACAGGTGGCGGCTGGCTTGTTCGAACCGGCCGGCGGCGGCCGCGTGCACGCCCGCGGTTTTTTCGGCAACAAACCGCCCCAGATCGCAAGTGTTGTCGGGGATGCTGAGCCGATAACCCGGCGGCGCTGCGGCCAACACCACCCGTGGGTCGATCCCGGCGCCACCGAGGAGCTTACGCAGATTAGACACGTAGGAGTGGATACTCGCGCGTGCGCCCGAGGGTGGCCACTCCTCCCAGAGGGCGGTGATTAGGGCGTCGACTCCTACGGGCCTGTTGCGGTTGATGACCAACATGGCTAGCACAGCCCGTTGCTTGGGGGTGCCCGATGGCACCGGGGTGCCGTCGATAGTCATCTGCAATGGTCCAAGCAGGCCGAAGTCGAGCCGCTTCTCCACTGTCGCGCTACCAGCCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3003455","ARO_id":"40048","ARO_name":"Mycobacterium tuberculosis embR mutant conferring resistance to ethambutol","ARO_description":"Point mutation in the M.tuberculosis embR results in increased resistance to ethambutol","ARO_category":{"39310":{"category_aro_accession":"3002876","category_aro_cvterm_id":"39310","category_aro_name":"ethambutol resistant arabinosyltransferase","category_aro_description":"Arabinosyl transferases allow for the polymerization of arabinose to form arabinan. Arabinan is required for formation of mycobacterial cell walls and arabinosyltransferases are targets of the drug ethambutol. Mutations in these genes can confer resistance to ethambutol.","category_aro_class_name":"AMR Gene Family"},"36636":{"category_aro_accession":"3000497","category_aro_cvterm_id":"36636","category_aro_name":"ethambutol","category_aro_description":"Ethambutol is an antimycobacterial drug prescribed to treat tuberculosis. It is usually given in combination with other tuberculosis drugs, such as isoniazid, rifampicin, and pyrazinamide. Ethambutol inhibits arabinosyl biosynthesis, disrupting mycobacterial cell wall formation.","category_aro_class_name":"Antibiotic"},"36666":{"category_aro_accession":"3000527","category_aro_cvterm_id":"36666","category_aro_name":"polyamine antibiotic","category_aro_description":"Polyamine antibiotics are organic compounds having two or more primary amino groups.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1354":{"model_id":"1354","model_name":"Mycobacterium tuberculosis embA mutant conferring resistance to ethambutol","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2395":"D4N","2396":"A201T","2397":"G321S","2398":"G350D","2399":"A462V","2400":"D833A","2401":"P913S","3583":"G5S"},"clinical":{"2395":"D4N","2396":"A201T","2397":"G321S","2398":"G350D","2399":"A462V","2400":"D833A","2401":"P913S","3583":"G5S"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"2000"}},"model_sequences":{"sequence":{"2081":{"protein_sequence":{"accession":"AFN51820.1","sequence":"MPHDGNERSHRIARLAAVVSGIAGLLLCGIVPLLPVNQTTATIFWPQGSTADGNITQITAPLVSGAPRALDISIPCSAIATLPANGGLVLSTLPAGGVDTGKAGLFVRANQDTVVVAFRDSVAAVAARSTIAAGGCSALHIWADTGGAGADFMGIPGGAGTLPPEKKPQVGGIFTDLKVGAQPGLSARVDIDTRFITTPGALKKAVMLLGVLAVLVAMVGLAALDRLSRGRTLRDWLTRYRPRVRVGFASRLADAAVIATLLLWHVIGATSSDDGYLLTVARVAPKAGYVANYYRYFGTTEAPFDWYTSVLAQLAAVSTAGVWMRLPATLAGIACWLIVSRFVLRRLGPGPGGLASNRVAVFTAGAVFLSAWLPFNNGLRPEPLIALGVLVTWVLVERSIALGRLAPAAVAIIVATLTATLAPQGLIALAPLLTGARAIAQRIRRRRATDGLLAPLAVLAAALSLITVVVFRDQTLATVAESARIKYKVGPTIAWYQDFLRYYFLTVESNVEGSMSRRFAVLVLLFCLFGVLFVLLRRGRVAGLASGPAWRLIGTTAVGLLLLTFTPTKWAVQFGAFAGLAGVLGAVTAFTFARIGLHSRRNLTLYVTALLFVLAWATSGINGWFYVGNYGVPWYDIQPVIASHPVTSMFLTLSILTGLLAAWYHFRMDYAGHTEVKDNRRNRILASTPLLVVAVIMVAGEVGSMAKAAVFRYPLYTTAKANLTALSTGLSSCAMADDVLAEPDPNAGMLQPVPGQAFGPDGPLGGISPVGFKPEGVGEDLKSDPVVSKPGLVNSDASPNKPNAAITDSAGTAGGKGPVGINGSHAALPFGLDPARTPVMGSYGENNLAATATSAWYQLPPRSPDRPLVVVSAAGAIWSYKEDGDFIYGQSLKLQWGVTGPDGRIQPLGQVFPIDIGPQPAWRNLRFPLAWAPPEADVARIVAYDPNLSPEQWFAFTPPRVPVLESLQRLIGSATPVLMDIATAANFPCQRPFSEHLGIAELPQYRILPDHKQTAASSNLWQSSSTGGPFLFTQALLRTSTIATYLRGDWYRDWGSVEQYHRLVPADQAPDAVVEEGVITVPGWGRPGPIRALP"},"dna_sequence":{"accession":"CP003248","fmin":"4243410","fmax":"4246695","strand":"+","sequence":"GTGCCCCACGACGGTAATGAGCGATCTCACCGGATCGCACGCCTAGCAGCCGTCGTCTCGGGAATCGCGGGTCTGCTGCTGTGCGGCATCGTTCCGCTGCTTCCGGTGAACCAAACCACCGCGACCATCTTCTGGCCGCAGGGCAGCACCGCCGACGGCAACATCACCCAGATCACCGCCCCTCTGGTATCCGGGGCGCCACGCGCGCTGGACATCTCGATCCCCTGCTCGGCCATCGCCACGCTGCCCGCCAACGGCGGCCTGGTGCTGTCCACACTGCCGGCCGGTGGCGTGGATACCGGTAAGGCCGGGCTGTTCGTCCGCGCCAACCAGGACACGGTCGTCGTGGCGTTCCGCGACTCGGTGGCCGCGGTGGCGGCCCGCTCCACGATCGCAGCGGGAGGCTGTAGCGCGCTGCATATCTGGGCCGATACCGGCGGCGCGGGCGCTGATTTTATGGGTATACCCGGCGGCGCCGGGACCCTGCCGCCGGAGAAGAAGCCACAGGTTGGCGGCATCTTCACCGACCTGAAGGTCGGAGCGCAGCCCGGGCTGTCGGCCCGCGTCGACATCGACACTCGGTTTATCACGACGCCCGGCGCGCTCAAGAAGGCCGTGATGCTCCTCGGCGTGCTGGCGGTCCTGGTAGCCATGGTGGGGCTGGCCGCGCTGGACCGGCTCAGCAGGGGCCGCACCCTGCGCGACTGGCTGACCCGATATCGCCCGCGGGTGCGGGTCGGATTCGCCAGCCGGCTCGCTGACGCAGCGGTGATCGCGACCTTGTTGCTCTGGCATGTCATCGGCGCCACCTCGTCCGATGACGGCTACCTTCTGACCGTCGCCCGGGTCGCCCCGAAGGCCGGCTATGTAGCCAACTACTACCGGTATTTCGGCACGACGGAGGCGCCGTTCGACTGGTATACATCGGTGCTTGCCCAGCTGGCGGCGGTGAGCACCGCCGGCGTCTGGATGCGCCTGCCCGCCACCCTGGCCGGAATCGCCTGCTGGCTGATCGTCAGCCGTTTCGTGCTGCGGCGGCTGGGACCGGGCCCGGGCGGGCTGGCGTCCAACCGGGTCGCTGTGTTCACCGCTGGTGCGGTGTTCCTGTCCGCCTGGCTGCCGTTCAACAACGGCCTGCGTCCCGAGCCGCTGATCGCGCTGGGTGTGCTGGTCACGTGGGTGTTGGTGGAACGGTCGATCGCGCTCGGACGGCTGGCCCCGGCCGCGGTAGCCATCATCGTGGCGACGCTTACCGCGACGCTGGCACCGCAGGGGTTGATCGCGCTGGCCCCGCTGCTGACTGGTGCGCGCGCCATCGCCCAGAGGATCCGGCGCCGCCGGGCGACCGATGGACTGCTGGCGCCGCTGGCGGTGCTGGCCGCGGCGTTGTCGCTGATCACCGTGGTGGTGTTTCGGGACCAGACGCTGGCCACGGTGGCCGAATCGGCACGCATCAAGTACAAGGTCGGCCCGACCATCGCCTGGTACCAGGACTTCCTGCGCTACTACTTCCTTACCGTGGAGAGCAACGTTGAGGGGTCGATGTCCCGCCGGTTCGCGGTGCTGGTGTTGCTGTTCTGCCTGTTCGGGGTGCTGTTCGTGCTGCTGCGGCGCGGCCGGGTGGCGGGGCTGGCCAGCGGCCCGGCCTGGCGACTGATCGGCACTACGGCGGTCGGCCTGCTGCTGCTCACGTTCACGCCAACCAAGTGGGCCGTGCAGTTCGGCGCATTCGCCGGGCTGGCCGGGGTGTTGGGTGCGGTCACCGCGTTCACCTTTGCCCGCATCGGTCTACATAGTCGACGCAACCTCACGCTGTACGTGACCGCGTTGCTGTTCGTGCTGGCGTGGGCAACCTCGGGCATCAACGGGTGGTTCTACGTCGGCAACTACGGGGTGCCGTGGTATGACATCCAGCCCGTCATCGCCAGCCACCCGGTGACGTCGATGTTTCTGACGCTGTCGATCCTCACCGGATTGCTGGCAGCCTGGTATCACTTCCGGATGGACTACGCCGGGCACACCGAAGTCAAAGACAACCGGCGCAACCGCATCTTGGCCTCTACGCCACTGCTGGTGGTCGCGGTGATCATGGTCGCAGGCGAAGTCGGCTCGATGGCCAAGGCCGCGGTGTTCCGTTACCCGCTTTACACCACCGCCAAGGCCAACCTGACCGCGCTCAGCACCGGGCTGTCCAGCTGTGCGATGGCCGACGACGTGCTGGCCGAGCCCGACCCCAATGCCGGCATGCTGCAACCGGTTCCGGGCCAGGCGTTCGGACCGGACGGACCGCTGGGCGGTATCAGTCCCGTCGGCTTCAAACCCGAGGGCGTGGGCGAGGACCTCAAGTCCGACCCGGTGGTCTCCAAACCCGGGCTGGTCAACTCCGATGCGTCGCCCAACAAACCCAACGCCGCCATCACCGACTCCGCGGGCACCGCCGGAGGGAAGGGCCCGGTCGGGATCAACGGGTCGCACGCGGCGCTGCCGTTCGGATTGGACCCGGCACGTACCCCGGTGATGGGCAGCTACGGGGAGAACAACCTGGCCGCCACGGCCACCTCGGCCTGGTACCAGTTACCGCCCCGCAGCCCGGACCGGCCGCTGGTGGTGGTTTCCGCGGCCGGCGCCATCTGGTCCTACAAGGAGGACGGCGATTTCATCTACGGCCAGTCCCTGAAACTGCAGTGGGGCGTCACCGGCCCGGACGGCCGCATCCAGCCACTGGGGCAGGTATTTCCGATCGACATCGGACCGCAACCCGCGTGGCGCAATCTGCGGTTTCCGCTGGCCTGGGCGCCGCCGGAGGCCGACGTGGCGCGCATTGTCGCCTATGACCCGAACCTGAGCCCTGAGCAATGGTTCGCCTTCACCCCGCCCCGGGTTCCGGTGCTGGAATCTCTGCAGCGGTTGATCGGGTCAGCGACACCGGTGTTGATGGACATCGCGACCGCAGCCAACTTCCCCTGCCAGCGACCGTTTTCCGAGCATCTCGGCATTGCCGAGCTTCCGCAGTACCGGATCCTGCCGGACCACAAGCAGACGGCGGCGTCGTCGAACCTATGGCAGTCCAGCTCGACCGGCGGTCCGTTCCTGTTCACCCAGGCGCTGCTGCGCACCTCGACGATCGCCACGTACCTGCGTGGGGACTGGTATCGCGACTGGGGATCGGTGGAGCAGTACCACCGGCTGGTGCCGGCCGATCAGGCTCCAGACGCCGTTGTCGAGGAGGGCGTGATCACTGTGCCCGGCTGGGGTCGGCCAGGACCGATCAGGGCGCTGCCATGAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3003453","ARO_id":"40046","ARO_name":"Mycobacterium tuberculosis embA mutant conferring resistance to ethambutol","ARO_description":"Specific mutations that occurs on Mycobacterium tuberculosis embA leading to the lowered affinity of ethambutol to embA","ARO_category":{"39310":{"category_aro_accession":"3002876","category_aro_cvterm_id":"39310","category_aro_name":"ethambutol resistant arabinosyltransferase","category_aro_description":"Arabinosyl transferases allow for the polymerization of arabinose to form arabinan. Arabinan is required for formation of mycobacterial cell walls and arabinosyltransferases are targets of the drug ethambutol. Mutations in these genes can confer resistance to ethambutol.","category_aro_class_name":"AMR Gene Family"},"36636":{"category_aro_accession":"3000497","category_aro_cvterm_id":"36636","category_aro_name":"ethambutol","category_aro_description":"Ethambutol is an antimycobacterial drug prescribed to treat tuberculosis. It is usually given in combination with other tuberculosis drugs, such as isoniazid, rifampicin, and pyrazinamide. Ethambutol inhibits arabinosyl biosynthesis, disrupting mycobacterial cell wall formation.","category_aro_class_name":"Antibiotic"},"36666":{"category_aro_accession":"3000527","category_aro_cvterm_id":"36666","category_aro_name":"polyamine antibiotic","category_aro_description":"Polyamine antibiotics are organic compounds having two or more primary amino groups.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1360":{"model_id":"1360","model_name":"Bartonella bacilliformis gyrB conferring resistance to aminocoumarin","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3428":"G124S","3429":"R184Q","3430":"T214A","3431":"T214I"},"experimental":{"3428":"G124S","3429":"R184Q","3430":"T214A","3431":"T214I"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1500"}},"model_sequences":{"sequence":{"2062":{"protein_sequence":{"accession":"WP_005768149.1","sequence":"MSDETTSPTSGDYGAASIKVLKGLDAVRKRPGMYIGDTDDGSGLHHMVYEVVDNAIDEALAGYATLVNVTLHADGSCSVCDNGRGIPTDIHPTEHVSAAEVIMTQLHAGGKFDQNSYKVSGGLHGVGVSVVNALSVWLRLRIKRDGKIHEMSFTHGVADAPLKVVGQCGTESGTEISFLPSPETFTMVKFDFETLERRLRELAFLNSGVHILLVNQHHADVRSVELYYEGGLIEFIKYIDQSKKPLIDAPIYITSEKDGISVDVALWWNDSYHEKVLCFTNNIPQRDGGTHLAGFRSALTRQINGYAESSGIAKKEKVNLTGDDCREGLTAILSVKVPDPKFSSQTKDKLVSSEVRPIVENLVNEGLSAWLEEHPNEAKILISKVVEAAAAREAARKARELTRRKGALDITSLPGKLADCQERDPTKSEIFIVEGDSAGGSAKSGRSRQNQAILPLRGKILNVERARFDRMLSSEMIGTLITALGTSIGKDEFSPDKLRYHKIIIMTDADVDGAHIRTLLLTFFFRQMPELIERGHLYIAQPPLYKVSRGKSSQYIKNEAAFEDFLIDSGLEETTLELSSGEVCAGIDLRQFVQDARLLRQLLNGLHTRYDRNIVEQAAIAGAFNFEAFATPETAQKIADTIAKRLDLIADDMERGWSGQYTSDGSLCFERVLRGVKDVITLDAGFINSADARQIGHIAKNLKDIYRDPPLLRRKDKSERIFGPTSLLESIFINGKKGITLQRYKGLGEMNADQLWETTLDPDARSLLQVKINDATDADSLFSQLMGDEVEPRRIFIQKNALNVANLDI"},"dna_sequence":{"accession":"NC_008783","fmin":"1406995","fmax":"1409425","strand":"+","sequence":"ATGAGTGATGAAACAACCTCACCGACATCTGGTGACTATGGTGCCGCTTCTATCAAGGTTCTCAAAGGTCTTGATGCTGTCCGTAAACGTCCTGGTATGTACATCGGTGATACCGACGACGGTTCAGGCTTACACCATATGGTTTATGAAGTCGTCGACAACGCTATTGATGAAGCATTAGCTGGCTACGCAACTCTTGTAAATGTTACGCTCCATGCCGATGGATCCTGTTCTGTTTGTGATAATGGACGTGGAATTCCAACTGATATTCACCCAACAGAACATGTATCAGCTGCTGAAGTGATCATGACGCAACTTCATGCTGGTGGAAAATTTGATCAAAATTCTTATAAAGTTTCAGGGGGATTACACGGCGTTGGTGTCTCTGTTGTTAATGCACTATCGGTTTGGTTGCGCCTTCGAATCAAGCGTGATGGTAAAATCCATGAAATGTCGTTTACTCATGGAGTGGCTGATGCTCCGCTCAAAGTCGTTGGTCAATGCGGTACAGAAAGTGGCACAGAAATCAGCTTTTTACCAAGCCCCGAAACCTTCACCATGGTTAAATTTGATTTCGAAACATTAGAGCGTCGTCTTAGAGAATTAGCTTTTTTGAATTCTGGTGTACACATTCTTCTTGTTAACCAACACCATGCTGATGTTCGATCAGTAGAATTATATTACGAAGGTGGATTAATTGAATTTATCAAATATATTGACCAATCAAAAAAACCCTTAATTGATGCACCGATTTACATCACAAGCGAAAAAGATGGGATCAGTGTAGATGTTGCTTTATGGTGGAACGATTCTTATCATGAGAAAGTATTGTGTTTCACCAATAATATTCCTCAACGCGATGGAGGAACCCATTTAGCGGGATTCCGCAGCGCCTTAACACGTCAAATTAACGGTTATGCTGAATCCTCAGGCATTGCAAAAAAAGAAAAAGTTAATTTAACTGGCGATGATTGCCGTGAAGGACTCACAGCCATTCTTTCCGTTAAAGTTCCCGATCCAAAATTTTCTTCACAGACAAAGGATAAATTGGTTTCTTCTGAAGTCCGTCCAATTGTTGAAAATTTGGTAAATGAAGGACTTTCAGCATGGCTAGAAGAACACCCTAATGAAGCAAAAATTCTCATTAGCAAAGTTGTAGAAGCTGCTGCAGCGCGCGAAGCAGCACGCAAAGCGCGTGAACTTACACGGCGAAAAGGAGCTCTCGATATCACTTCTTTACCAGGTAAACTTGCTGATTGTCAGGAACGTGATCCTACAAAATCAGAAATTTTTATCGTCGAGGGGGATTCAGCTGGTGGTTCAGCTAAAAGCGGACGTTCACGCCAAAATCAAGCAATTTTGCCTTTACGCGGTAAAATTCTTAATGTCGAACGAGCACGTTTCGACCGAATGCTTTCATCCGAAATGATTGGTACGCTTATTACTGCCCTTGGAACCTCTATTGGTAAGGATGAATTTTCACCTGATAAATTGCGTTATCACAAAATCATCATTATGACAGATGCAGATGTTGATGGCGCTCATATTCGCACCTTGCTTCTCACTTTCTTTTTCAGACAAATGCCTGAATTAATTGAACGTGGTCATCTTTATATCGCGCAACCACCTCTTTATAAAGTATCACGTGGTAAATCCTCTCAGTACATTAAAAATGAAGCAGCATTTGAAGATTTCTTAATTGATAGTGGTTTGGAAGAAACAACATTAGAATTATCAAGTGGTGAGGTTTGTGCAGGCATTGATTTACGCCAATTCGTCCAAGATGCCCGTTTGTTGCGCCAACTCTTAAACGGTCTCCATACCCGCTATGACCGCAATATTGTTGAGCAAGCAGCAATCGCTGGTGCTTTCAATTTTGAGGCTTTTGCAACACCAGAAACAGCACAAAAAATAGCGGATACGATAGCAAAACGTCTTGATTTAATTGCTGATGATATGGAACGTGGTTGGAGCGGTCAATATACATCAGATGGAAGTTTATGCTTTGAACGCGTTTTGCGCGGAGTTAAAGATGTTATTACTCTTGATGCAGGGTTTATAAATTCAGCAGATGCACGCCAAATTGGTCATATTGCCAAAAATCTCAAAGACATCTATCGTGATCCTCCTCTTTTGCGTCGCAAAGATAAGTCAGAACGCATTTTTGGTCCTACGAGTTTATTGGAAAGTATTTTTATAAACGGTAAAAAAGGTATTACTTTACAGCGTTACAAAGGCCTTGGAGAAATGAATGCTGATCAGCTTTGGGAAACAACTCTTGATCCTGATGCGCGTTCTCTTTTACAAGTTAAAATCAATGACGCAACTGATGCAGATTCTCTCTTCTCCCAGTTAATGGGTGATGAAGTTGAACCACGGCGAATTTTTATTCAAAAAAATGCCCTAAACGTTGCTAATCTTGATATCTAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40079","NCBI_taxonomy_name":"Bartonella bacilliformis KC583","NCBI_taxonomy_id":"360095"}}}},"ARO_accession":"3003302","ARO_id":"39886","ARO_name":"Bartonella bacilliformis gyrB conferring resistance to aminocoumarin","ARO_description":"Point mutation in Bartonella bacilliformis resulting in aminocoumarin resistance","ARO_category":{"36618":{"category_aro_accession":"3000479","category_aro_cvterm_id":"36618","category_aro_name":"aminocoumarin resistant gyrB","category_aro_description":"Point mutations in DNA gyrase subunit B (gyrB) can result in resistance to aminocoumarins. These mutations usually involve arginine residues in organisms.","category_aro_class_name":"AMR Gene Family"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36271":{"category_aro_accession":"3000132","category_aro_cvterm_id":"36271","category_aro_name":"clorobiocin","category_aro_description":"Clorobiocin is an aminocoumarin antibiotic produced by Streptomyces roseochromogenes, and binds DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36289":{"category_aro_accession":"3000150","category_aro_cvterm_id":"36289","category_aro_name":"coumermycin A1","category_aro_description":"Coumermycin A1 is an antibiotic produced by Streptomyces rishiriensis, and binds DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1395":{"model_id":"1395","model_name":"Neisseria gonorrhoeae mutant porin PIB (por) with reduced permeability to antibiotic","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"60":"G120K","61":"G120D","64":"A121D"},"clinical":{"60":"G120K","61":"G120D","64":"A121D"}},"40330":{"param_type":"multiple resistance variants","param_description":"A set of nucleotide or amino acid substitutions that are each required to confer resistance to an antibiotic drug or drug class by co-mutation. Compare to single resistance variant, where only one substitution is required. Multiple resistance variants parameters are indicated on appropriate models using the following notation: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2],...,[wild-type n][position n][mutation n]. When each included substitution is detected in a protein sequence, resistance is conferred. This parameter is not currently included in any detection algorithms.","param_type_id":"40330","param_value":{"3288":"G120R,A121H","3289":"G120P,A121P"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"54":{"protein_sequence":{"accession":"AAB57788.1","sequence":"MKKSLIALTLAALPVAATADVTLYGAIKAGVQTYRSVEHTKGKVSKVETGSEIADFGSKIGFKGQEDLGNGLKAVWQLEQGASVAGTNTGWGNKQSFVGLKGGFGTIRAGSLNSPLKNTGANVNAWESGKFTGNVLEISGMAQREHRYLSVRYDSPEFAGFSGSVQYAPKDNSGSNGESYHVGLNYRNNGFFAQYAGLFQRYGEGTKKIEYEHQVYSIPSLFVEKLQVHRLVGGYDNNALYVSVAAQQQDAKLYGARRANSHNSQTEVAATAAYRFGNVTPRVSYAHGFKGTVDSADHDNTYDQVVVGAEYDFSKRTSALVSAGWLQEGKGADKIVSTASAVVLRHKF"},"dna_sequence":{"accession":"U75641","fmin":"19","fmax":"1066","strand":"+","sequence":"ATGAAAAAATCCCTGATTGCCCTGACTTTGGCAGCCCTTCCTGTTGCGGCAACGGCCGATGTCACCCTGTACGGCGCCATCAAAGCCGGCGTACAAACTTACCGTTCTGTAGAACATACAAAAGGCAAGGTAAGTAAAGTGGAAACCGGCAGCGAAATCGCCGACTTCGGTTCAAAAATCGGCTTCAAAGGCCAAGAAGACCTCGGCAACGGCCTGAAGGCCGTTTGGCAGTTGGAACAAGGTGCCTCCGTCGCCGGCACTAACACCGGCTGGGGCAACAAACAATCCTTCGTCGGCTTGAAGGGCGGCTTCGGTACCATCCGCGCCGGTAGCCTGAACAGCCCCCTGAAAAACACCGGCGCCAACGTCAATGCTTGGGAATCCGGCAAATTTACCGGCAATGTGCTGGAAATCAGCGGAATGGCCCAACGGGAACACCGCTACCTGTCCGTACGCTACGATTCTCCCGAATTTGCCGGCTTCAGCGGCAGCGTACAATACGCACCTAAAGACAATTCAGGCTCAAACGGCGAATCTTACCACGTTGGTTTGAACTACCGAAACAACGGCTTCTTCGCACAATACGCCGGCTTGTTCCAAAGATACGGCGAAGGCACTAAAAAAATCGAATACGAACATCAAGTTTATAGTATCCCCAGCCTGTTTGTTGAAAAACTGCAAGTTCACCGTTTGGTAGGCGGTTACGACAATAATGCCCTGTACGTTTCCGTAGCCGCGCAACAACAAGATGCCAAATTGTATGGAGCAAGGAGGGCTAATTCGCACAACTCTCAAACCGAAGTTGCCGCTACCGCGGCATACCGTTTCGGCAATGTAACGCCCCGCGTTTCTTACGCCCACGGCTTCAAAGGCACTGTTGATAGTGCAGACCACGACAATACTTATGACCAAGTGGTTGTCGGTGCGGAATACGACTTCTCCAAACGCACTTCTGCCTTGGTTTCTGCCGGCTGGTTGCAAGAAGGCAAAGGCGCAGACAAAATCGTATCGACTGCCAGCGCCGTCGTTCTGCGCCACAAATTCTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36806","NCBI_taxonomy_name":"Neisseria gonorrhoeae","NCBI_taxonomy_id":"485"}}}},"ARO_accession":"3000464","ARO_id":"36603","ARO_name":"Neisseria gonorrhoeae porin PIB (por)","ARO_description":"Mutant forms of the porin Por result in reduced permeability to antibiotics, particularly tetracyclines and beta-lactams.","ARO_category":{"41445":{"category_aro_accession":"3004281","category_aro_cvterm_id":"41445","category_aro_name":"General Bacterial Porin with reduced permeability to beta-lactams","category_aro_description":"These are GBPs that are associated with decreased susceptibility to beta-lactams either through mutations in the porin protein, absence of the porin protein, or expression of the porin protein.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36383":{"category_aro_accession":"3000244","category_aro_cvterm_id":"36383","category_aro_name":"reduced permeability to antibiotic","category_aro_description":"Reduction in permeability to antibiotic, generally through reduced production of porins, can provide resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1432":{"model_id":"1432","model_name":"Mycobacterium tuberculosis mutant embC conferring resistance to ethambutol","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2261":"T270I","2262":"P398S","2263":"Q491R","2264":"L502P","2371":"A247P","2372":"L251R","2373":"A254G","2375":"H285Y","2376":"V287F","2377":"G288W","2378":"G288V","2379":"Y296H","2380":"Y296S","2381":"I297L","2382":"I297T","2383":"M300R","2384":"R302G","2385":"V303G","2386":"A307T","2387":"G308D","2388":"Y309N","2389":"M310K","2390":"G325S","2391":"W326R","2392":"Y327N","2393":"N394D","2394":"V981L","3290":"S244T","3612":"R738Q"},"clinical":{"2261":"T270I","2262":"P398S","2263":"Q491R","2264":"L502P","2371":"A247P","2372":"L251R","2373":"A254G","2375":"H285Y","2376":"V287F","2377":"G288W","2378":"G288V","2379":"Y296H","2380":"Y296S","2381":"I297L","2382":"I297T","2383":"M300R","2384":"R302G","2385":"V303G","2386":"A307T","2387":"G308D","2388":"Y309N","2389":"M310K","2390":"G325S","2391":"W326R","2392":"Y327N","2393":"N394D","2394":"V981L","3290":"S244T","3612":"R738Q"}},"40330":{"param_type":"multiple resistance variants","param_description":"A set of nucleotide or amino acid substitutions that are each required to confer resistance to an antibiotic drug or drug class by co-mutation. Compare to single resistance variant, where only one substitution is required. Multiple resistance variants parameters are indicated on appropriate models using the following notation: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2],...,[wild-type n][position n][mutation n]. When each included substitution is detected in a protein sequence, resistance is conferred. This parameter is not currently included in any detection algorithms.","param_type_id":"40330","param_value":{"4128":"I297L,W326R","4129":"A244T,G288W,V303G","4130":"T270I,I297T","4131":"V287F,T309N","4132":"L251R,A254G,T270I","4133":"G288V,M310K,Y327N","4134":"T270I,G288W,V303G","4135":"G288W,V303G","4136":"G272S,H285Y,M300R,A307T","4137":"A247P,T270I,I297T","4138":"Y296S,R302G","4139":"V287F,Y309N","4140":"A247P,I297L,W326R","4141":"T270I,Y296H,G308D,G325S"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"2000"}},"model_sequences":{"sequence":{"2080":{"protein_sequence":{"accession":"AFN51819.1","sequence":"MATEAAPPRIAVRLPSTSVRDAGANYRIARYVAVVAGLLGAVLAIATPLLPVNQTTAQLNWPQNGTFASVEAPLIGYVATDLNITVPCQAAAGLAGSQNTGKTVLLSTVPKQAPKAVDRGLLLQRANDDLVLVVRNVPLVTAPLSQVLGPTCQRLTFTAHADRVAAEFVGLVQGPNAEHPGAPLRGERSGYDFRPQIVGVFTDLAGPAPPGLSFSASVDTRYSSSPTPLKMAAMILGVALTGAALVALHILDTADGMRHRRFLPARWWSTGGLDTLVIAVLVWWHFVGANTSDDGYILTMARVSEHAGYMANYYRWFGTPEAPFGWYYDLLALWAHVSTASIWMRLPTLAMALTCWWVISREVIPRLGHAVKTSRAAAWTAAGMFLAVWLPLDNGLRPEPIIALGILLTWCSVERAVATSRLLPVAIACIIGALTLFSGPTGIASIGALLVAIGPLRTILHRRSRRFGVLPLVAPILAAATVTAIPIFRDQTFAGEIQANLLKRAVGPSLKWFDEHIRYERLFMASPDGSIARRFAVLALVLALAVSVAMSLRKGRIPGTAAGPSRRIIGITIISFLAMMFTPTKWTHHFGVFAGLAGSLGALAAVAVTGAAMRSRRNRTVFAAVVVFVLALSFASVNGWWYVSNFGVPWSNSFPKWRWSLTTALLELTVLVLLLAAWFHFVANGDGRRTARPTRFRARLAGIVQSPLAIATWLLVLFEVVSLTQAMISQYPAWSVGRSNLQALAGKTCGLAEDVLVELDPNAGMLAPVTAPLADALGAGLSEAFTPNGIPADVTADPVMERPGDRSFLNDDGLITGSEPGTEGGTTAAPGINGSRARLPYNLDPARTPVLGSWRAGVQVPAMLRSGWYRLPTNEQRDRAPLLVVTAAGRFDSREVRLQWATDEQAAAGHHGGSMEFADVGAAPAWRNLRAPLSAIPSTATQVRLVADDQDLAPQHWIALTPPRIPRVRTLQNVVGAADPVFLDWLVGLAFPCQRPFGHQYGVDETPKWRILPDRFGAEANSPVMDHNGGGPLGITELLMRATTVASYLKDDWFRDWGALQRLTPYYPDAQPADLNLGTVTRSGLWSPAPLRRG"},"dna_sequence":{"accession":"CP003248","fmin":"4240040","fmax":"4243325","strand":"+","sequence":"ATGGCTACCGAAGCCGCCCCACCCCGTATCGCCGTCCGGCTACCATCTACCTCCGTGCGCGACGCGGGAGCAAACTACCGGATCGCCCGGTACGTCGCTGTGGTGGCGGGTCTGCTAGGCGCTGTGCTGGCCATCGCCACCCCACTGCTGCCGGTCAACCAGACCACCGCGCAATTGAACTGGCCCCAAAACGGCACGTTCGCCAGTGTCGAGGCACCGCTGATTGGCTACGTGGCCACCGACTTGAACATCACCGTCCCCTGCCAGGCCGCCGCCGGACTGGCCGGATCGCAGAACACCGGCAAGACGGTGTTGTTGTCAACGGTGCCCAAGCAGGCGCCTAAGGCCGTCGATCGCGGGCTGCTGCTGCAACGGGCCAACGACGACCTGGTGCTTGTGGTGCGTAATGTCCCGTTGGTCACCGCCCCGCTGAGTCAGGTGCTCGGCCCGACCTGTCAGCGGTTGACATTCACCGCGCACGCCGATCGGGTCGCCGCCGAATTCGTCGGACTGGTGCAGGGACCCAATGCTGAGCACCCCGGTGCACCGCTGCGCGGTGAGCGCAGCGGCTACGACTTCCGCCCGCAGATCGTCGGGGTGTTCACCGACCTGGCCGGGCCGGCGCCACCGGGTCTGAGCTTCTCGGCGAGCGTGGATACCCGCTACAGCAGCAGCCCCACGCCGCTGAAGATGGCCGCCATGATCCTCGGGGTAGCGCTCACCGGCGCCGCCCTGGTGGCGCTGCACATCCTGGACACCGCCGACGGCATGCGGCACCGGCGGTTCCTGCCCGCGCGCTGGTGGTCGACCGGCGGTCTGGACACCCTGGTTATCGCCGTGCTGGTGTGGTGGCATTTCGTCGGGGCCAACACCTCCGACGACGGCTACATCCTGACCATGGCCCGGGTGTCCGAGCATGCGGGCTATATGGCCAACTACTACCGCTGGTTCGGCACACCCGAGGCGCCTTTCGGCTGGTACTACGACCTGCTGGCGCTGTGGGCTCATGTCAGCACGGCCAGTATCTGGATGCGCCTACCCACCCTGGCGATGGCGCTCACCTGCTGGTGGGTAATCAGCCGTGAGGTCATTCCCCGGCTGGGGCACGCCGTCAAGACGAGCCGGGCAGCGGCGTGGACGGCGGCGGGCATGTTTCTGGCTGTCTGGCTGCCGCTGGACAACGGCCTTCGGCCCGAGCCGATCATCGCCCTGGGCATCCTGCTGACCTGGTGCTCGGTGGAGCGGGCGGTGGCCACCAGCCGGCTGCTGCCGGTGGCAATCGCCTGCATCATCGGTGCCTTGACCCTGTTCTCCGGGCCGACGGGCATCGCCTCGATCGGTGCGCTGCTGGTCGCGATCGGGCCGCTACGGACCATCCTGCACCGGCGTTCCAGGCGGTTCGGCGTGCTACCACTGGTGGCGCCGATCCTGGCCGCGGCCACCGTCACCGCGATCCCGATCTTTCGTGATCAGACCTTCGCGGGCGAGATCCAGGCCAACCTCCTCAAGCGTGCCGTAGGGCCCAGCCTGAAGTGGTTCGACGAACACATCCGCTACGAGCGGCTGTTCATGGCCAGCCCCGACGGCTCGATCGCCCGCCGCTTCGCCGTGCTGGCCTTGGTGCTGGCGCTCGCGGTATCGGTGGCAATGTCGTTACGTAAGGGCCGCATTCCAGGTACCGCTGCTGGACCGAGCCGCCGCATCATCGGCATCACGATCATTTCCTTCCTCGCGATGATGTTCACCCCGACAAAGTGGACCCATCACTTCGGGGTGTTCGCGGGGTTGGCCGGGTCGCTGGGGGCGCTTGCCGCGGTCGCGGTGACGGGCGCTGCGATGCGCTCGCGGCGGAACCGGACCGTGTTCGCCGCCGTGGTGGTCTTCGTGTTGGCCCTGTCGTTCGCCAGTGTCAACGGCTGGTGGTACGTGTCCAACTTCGGTGTGCCATGGTCGAACTCGTTTCCGAAGTGGCGATGGTCGCTTACCACCGCACTCCTCGAGCTGACGGTGCTGGTGCTGCTGCTAGCGGCATGGTTCCACTTCGTCGCCAACGGTGACGGGCGCCGAACAGCCAGGCCAACCCGGTTTAGGGCACGACTAGCCGGAATTGTCCAGTCCCCGTTGGCAATTGCCACGTGGTTGCTGGTGCTTTTCGAGGTGGTATCGCTGACCCAGGCGATGATTTCCCAGTACCCGGCGTGGTCGGTTGGCCGGTCTAACCTACAGGCTTTGGCCGGCAAGACCTGCGGGCTGGCCGAAGACGTGCTGGTGGAGCTGGATCCCAACGCAGGCATGCTGGCGCCGGTGACCGCGCCGTTGGCCGACGCCCTGGGAGCCGGCCTGTCTGAAGCCTTCACACCCAACGGCATTCCCGCCGACGTCACCGCCGACCCGGTGATGGAACGTCCAGGGGATCGCAGTTTCCTCAACGACGACGGGCTGATCACCGGCAGCGAACCCGGCACCGAAGGGGGCACCACGGCCGCACCGGGAATCAACGGCTCCCGCGCCCGGCTGCCCTACAACCTGGACCCGGCCCGTACACCGGTGCTGGGCAGCTGGCGAGCCGGCGTGCAGGTGCCCGCCATGCTGCGGTCGGGCTGGTACCGGCTGCCCACCAACGAGCAGCGGGACAGGGCGCCGCTGCTGGTGGTGACGGCGGCCGGGCGATTCGACTCCCGCGAGGTCCGGTTGCAGTGGGCCACCGACGAGCAAGCGGCCGCCGGACACCACGGTGGGTCGATGGAATTCGCCGACGTCGGTGCCGCGCCGGCCTGGCGCAACCTGCGCGCACCACTGTCCGCCATCCCGAGCACCGCCACCCAGGTCCGGTTGGTCGCCGACGACCAGGATCTGGCGCCGCAGCACTGGATCGCCCTCACACCACCGCGGATTCCGCGGGTGCGCACGCTGCAGAACGTGGTGGGCGCAGCGGATCCGGTGTTCCTGGACTGGCTGGTGGGGCTGGCATTCCCCTGCCAACGCCCGTTCGGCCACCAATACGGCGTCGACGAGACACCCAAGTGGCGGATCCTGCCGGACCGGTTCGGCGCCGAAGCCAACTCACCGGTGATGGATCACAATGGCGGTGGCCCGCTGGGCATCACCGAGCTGCTGATGCGCGCAACCACGGTGGCCAGCTACCTCAAAGACGACTGGTTTAGGGACTGGGGCGCGTTACAGCGGTTGACGCCTTACTACCCCGACGCCCAGCCCGCTGATCTGAACCTAGGAACGGTGACTCGCAGCGGGCTGTGGAGTCCGGCGCCGTTGCGCCGCGGCTAGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3003327","ARO_id":"39911","ARO_name":"Mycobacterium tuberculosis mutant embC conferring resistance to ethambutol","ARO_description":"Point mutations in Mycobacterium tuberculosis embC that result in lower affinity between ethambutol and EmbC, resulting in resistance","ARO_category":{"39310":{"category_aro_accession":"3002876","category_aro_cvterm_id":"39310","category_aro_name":"ethambutol resistant arabinosyltransferase","category_aro_description":"Arabinosyl transferases allow for the polymerization of arabinose to form arabinan. Arabinan is required for formation of mycobacterial cell walls and arabinosyltransferases are targets of the drug ethambutol. Mutations in these genes can confer resistance to ethambutol.","category_aro_class_name":"AMR Gene Family"},"36636":{"category_aro_accession":"3000497","category_aro_cvterm_id":"36636","category_aro_name":"ethambutol","category_aro_description":"Ethambutol is an antimycobacterial drug prescribed to treat tuberculosis. It is usually given in combination with other tuberculosis drugs, such as isoniazid, rifampicin, and pyrazinamide. Ethambutol inhibits arabinosyl biosynthesis, disrupting mycobacterial cell wall formation.","category_aro_class_name":"Antibiotic"},"36666":{"category_aro_accession":"3000527","category_aro_cvterm_id":"36666","category_aro_name":"polyamine antibiotic","category_aro_description":"Polyamine antibiotics are organic compounds having two or more primary amino groups.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1574":{"model_id":"1574","model_name":"Mycobacterium tuberculosis inhA mutations conferring resistance to isoniazid","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2220":"I21V","2221":"I21T","2222":"I47T","2223":"V78A","2224":"S94A","2288":"I95P","2289":"I194T","2709":"I16T"},"clinical":{"2220":"I21V","2221":"I21T","2222":"I47T","2223":"V78A","2224":"S94A","2288":"I95P","2289":"I194T","2709":"I16T"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2085":{"protein_sequence":{"accession":"CCP44244.1","sequence":"MTGLLDGKRILVSGIITDSSIAFHIARVAQEQGAQLVLTGFDRLRLIQRITDRLPAKAPLLELDVQNEEHLASLAGRVTEAIGAGNKLDGVVHSIGFMPQTGMGINPFFDAPYADVSKGIHISAYSYASMAKALLPIMNPGGSIVGMDFDPSRAMPAYNWMTVAKSALESVNRFVAREAGKYGVRSNLVAAGPIRTLAMSAIVGGALGEEAGAQIQLLEEGWDQRAPIGWNMKDATPVAKTVCALLSDWLPATTGDIIYADGGAHTQLL"},"dna_sequence":{"accession":"AL123456","fmin":"1674201","fmax":"1675011","strand":"+","sequence":"ATGACAGGACTGCTGGACGGCAAACGGATTCTGGTTAGCGGAATCATCACCGACTCGTCGATCGCGTTTCACATCGCACGGGTAGCCCAGGAGCAGGGCGCCCAGCTGGTGCTCACCGGGTTCGACCGGCTGCGGCTGATTCAGCGCATCACCGACCGGCTGCCGGCAAAGGCCCCGCTGCTCGAACTCGACGTGCAAAACGAGGAGCACCTGGCCAGCTTGGCCGGCCGGGTGACCGAGGCGATCGGGGCGGGCAACAAGCTCGACGGGGTGGTGCATTCGATTGGGTTCATGCCGCAGACCGGGATGGGCATCAACCCGTTCTTCGACGCGCCCTACGCGGATGTGTCCAAGGGCATCCACATCTCGGCGTATTCGTATGCTTCGATGGCCAAGGCGCTGCTGCCGATCATGAACCCCGGAGGTTCCATCGTCGGCATGGACTTCGACCCGAGCCGGGCGATGCCGGCCTACAACTGGATGACGGTCGCCAAGAGCGCGTTGGAGTCGGTCAACAGGTTCGTGGCGCGCGAGGCCGGCAAGTACGGTGTGCGTTCGAATCTCGTTGCCGCAGGCCCTATCCGGACGCTGGCGATGAGTGCGATCGTCGGCGGTGCGCTCGGCGAGGAGGCCGGCGCCCAGATCCAGCTGCTCGAGGAGGGCTGGGATCAGCGCGCTCCGATCGGCTGGAACATGAAGGATGCGACGCCGGTCGCCAAGACGGTGTGCGCGCTGCTGTCTGACTGGCTGCCGGCGACCACGGGTGACATCATCTACGCCGACGGCGGCGCGCACACCCAATTGCTCTAGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3003393","ARO_id":"39977","ARO_name":"Mycobacterium tuberculosis inhA mutations conferring resistance to isoniazid","ARO_description":"inhA is a enoyl-acyl carrier reductase used in lipid metabolism and farry acid biosynthesis. It is inhibited by isoniazid. mutations in the promoter region or multiple copies of the inhA shows marked resistance to isoniazid mediated inhibition of mycolic acid biosynthesis.","ARO_category":{"40001":{"category_aro_accession":"3003417","category_aro_cvterm_id":"40001","category_aro_name":"antibiotic resistant inhA","category_aro_description":"inhA is a enoyl-acyl carrier reductase used in lipid metabolism and fatty acid biosynthesis. It is inhibited by isoniazid. Mutations in the promoter region or multiple copies of the inhA shows marked resistance to isoniazid mediated inhibition of mycolic acid biosynthesis.","category_aro_class_name":"AMR Gene Family"},"36659":{"category_aro_accession":"3000520","category_aro_cvterm_id":"36659","category_aro_name":"isoniazid","category_aro_description":"Isoniazid is an organic compound that is the first-line anti tuberculosis medication in prevention and treatment. As a prodrug, it is activated by mycobacterial catalase-peroxidases such as M. tuberculosis KatG. Isoniazid inhibits mycolic acid synthesis, which prevents cell wall synthesis in mycobacteria.","category_aro_class_name":"Drug Class"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1710":{"model_id":"1710","model_name":"Mycobacterium leprae gyrB conferring resistance to fluoroquinolone","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2165":"D464N","2169":"N502D","2172":"E504V"},"clinical":{"2165":"D464N","2169":"N502D","2172":"E504V"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1200"}},"model_sequences":{"sequence":{"2066":{"protein_sequence":{"accession":"CAC29513.1","sequence":"MAAQRKAQDEYGAASITILEGLEAVRKRPGMYVGSTGERGLHHLIWEVVDNSVDEAMAGYATQVDVRLFDDGSVEVADNGRGIPVAVHATGVPTVDVVMTQLHAGGKFGGKDSGYNVSGGLHGVGVSVVNALSTRVEVDIKRDGYEWSQFYDKAVPGILKQGEATEATGTTIRFWADPDIFETTKYDFGTVARRIQEVAFLNKGLTINLVDERVKQDEVVDDVVSDTAEAPVAMTVEEKSTESSAPHKVRHRTFHYPGGLVDFVKHINRTKTPIQQSIIDFDGKGAGHEVEVAMQWNGGYSESVHTFANTINTHEGGTHEEGFRSALTSVVNKYAKDKKLLKDKDPNLTGDDIREGLAAVISVKVSEPQFEGQTKTKLGNTEVKSFVQRVCNEQLIHWFEANPVDAKAVVNKAISSAQARIAARKARELVRRKSATDLGGLPGKLADCRSTDPRSSELYVVEGDSAGGSAKSGRDSMFQAILPLRGKIINVEKARIDRVLKNTEVQAIITALGTGIHDEFDISRLRYHKIVLMADADVDGQHISTLLLTLLFRFMRPLIEHGYVFLAQPPLYKLKWQRMDPEFAYSDSERDGLLETGLKLGKKINKEDGIQRYKGLGEMDAKELWETTMDPSVRVLRQVTLDDAAAADELFSILMGEDVDARRSFITRNAKDVRFLDV"},"dna_sequence":{"accession":"AL450380","fmin":"5228","fmax":"7265","strand":"+","sequence":"GTGGCTGCCCAGAGGAAGGCCCAAGACGAATATGGCGCTGCGTCCATCACTATTCTTGAAGGGCTGGAGGCCGTTCGCAAACGTCCCGGTATGTACGTCGGGTCAACTGGTGAGCGTGGTCTCCACCATCTGATATGGGAAGTGGTGGACAACTCAGTAGATGAGGCGATGGCCGGTTATGCTACGCAAGTTGATGTGCGGTTATTCGACGACGGTAGTGTCGAGGTCGCCGATAACGGTCGTGGTATTCCGGTGGCAGTGCATGCTACGGGGGTACCGACTGTTGACGTAGTTATGACCCAATTACATGCCGGCGGTAAATTCGGTGGTAAAGATAGCGGTTATAACGTCAGTGGTGGTTTGCATGGGGTAGGTGTGTCGGTGGTTAACGCATTGTCCACCAGGGTCGAGGTCGACATCAAACGTGACGGCTATGAATGGTCACAGTTTTACGACAAGGCTGTGCCGGGCATTCTTAAGCAAGGCGAAGCTACTGAGGCGACGGGAACGACGATTAGATTTTGGGCAGATCCTGACATTTTCGAAACCACAAAGTATGACTTTGGGACGGTGGCGCGCCGAATTCAAGAAGTGGCTTTCTTGAACAAGGGTTTGACGATCAATCTTGTTGACGAACGGGTGAAGCAGGACGAAGTTGTCGACGATGTCGTCAGCGATACAGCCGAGGCTCCTGTGGCTATGACCGTTGAAGAAAAGTCAACGGAGTCGAGTGCGCCGCACAAGGTTAGACACCGTACGTTCCACTACCCCGGAGGCCTGGTGGACTTCGTCAAGCACATCAACCGGACTAAGACTCCTATTCAACAGAGCATTATCGATTTTGATGGCAAAGGTGCCGGTCACGAGGTTGAAGTTGCGATGCAGTGGAACGGCGGCTATTCGGAATCAGTGCATACCTTTGCGAACACGATTAACACCCATGAAGGCGGCACCCACGAAGAAGGTTTCCGTAGCGCTTTGACATCAGTGGTGAACAAGTACGCTAAGGATAAAAAACTACTCAAAGACAAGGATCCCAACCTAACTGGCGACGATATCCGTGAAGGTCTGGCGGCGGTTATCTCGGTTAAGGTCAGTGAACCACAGTTTGAGGGTCAGACCAAAACAAAGCTGGGGAACACCGAAGTTAAGTCATTCGTGCAGAGGGTCTGTAATGAGCAACTTATTCACTGGTTTGAAGCCAATCCAGTAGATGCGAAAGCGGTTGTGAATAAGGCGATATCGTCGGCACAAGCCCGAATAGCTGCACGTAAAGCACGAGAGTTAGTGCGTCGAAAAAGTGCCACCGATCTTGGTGGACTTCCTGGAAAACTTGCCGATTGCCGCTCTACTGATCCTCGAAGTTCTGAACTGTATGTAGTGGAAGGTGATTCGGCTGGTGGTTCAGCAAAGAGTGGCCGTGATTCGATGTTTCAGGCAATCCTTCCGTTACGTGGCAAGATCATAAATGTTGAAAAGGCACGTATTGACCGAGTGCTAAAGAACACCGAAGTTCAAGCAATTATTACGGCATTGGGTACTGGAATCCATGATGAATTCGATATCTCCAGGCTGCGTTATCACAAAATTGTTTTGATGGCCGACGCTGACGTTGACGGCCAACATATCTCGACGCTGTTGTTGACTTTGTTATTTCGGTTCATGCGACCACTCATCGAGCATGGGTACGTGTTTTTAGCGCAGCCGCCACTTTACAAATTGAAGTGGCAACGTATGGATCCGGAATTTGCTTACTCCGATAGCGAGCGCGACGGCTTATTAGAGACCGGGCTTAAGCTTGGCAAGAAAATCAACAAAGAGGATGGTATCCAACGTTATAAAGGTTTAGGTGAAATGGATGCCAAGGAGTTGTGGGAAACCACCATGGACCCGTCGGTGCGAGTTTTGCGTCAAGTAACACTGGATGACGCGGCGGCTGCTGACGAGTTATTCTCTATTCTGATGGGTGAGGACGTCGATGCACGCCGTAGCTTTATCACCCGTAATGCCAAGGATGTTCGTTTCCTGGATGTCTAGT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40083","NCBI_taxonomy_name":"Mycobacterium leprae TN","NCBI_taxonomy_id":"272631"}}}},"ARO_accession":"3003304","ARO_id":"39888","ARO_name":"Mycobacterium leprae gyrB conferring resistance to fluoroquinolone","ARO_description":"Point mutation in Mycobacterium leprae gyrB resulting in fluoroquinolone resistance","ARO_category":{"37244":{"category_aro_accession":"3000864","category_aro_cvterm_id":"37244","category_aro_name":"fluoroquinolone resistant gyrB","category_aro_description":"Point mutations in DNA gyrase subunit B (gyrB) observed in Mycobacterium tuberculosis can result in resistance to fluoroquinolones.","category_aro_class_name":"AMR Gene Family"},"35942":{"category_aro_accession":"0000023","category_aro_cvterm_id":"35942","category_aro_name":"enoxacin","category_aro_description":"Enoxacin belongs to a group called fluoroquinolones. Its mode of action depends upon blocking bacterial DNA replication by binding itself to DNA gyrase and causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36271":{"category_aro_accession":"3000132","category_aro_cvterm_id":"36271","category_aro_name":"clorobiocin","category_aro_description":"Clorobiocin is an aminocoumarin antibiotic produced by Streptomyces roseochromogenes, and binds DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36289":{"category_aro_accession":"3000150","category_aro_cvterm_id":"36289","category_aro_name":"coumermycin A1","category_aro_description":"Coumermycin A1 is an antibiotic produced by Streptomyces rishiriensis, and binds DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37004":{"category_aro_accession":"3000660","category_aro_cvterm_id":"37004","category_aro_name":"lomefloxacin","category_aro_description":"Lomefloxacin is a difluoropiperazinyl quinolone, sharing similar activities with other fluoroquinolones. It is used to treat urinary tract infections. Relative to other fluoroquinolones, it has a longer half life and has higher serum concentrations.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"37008":{"category_aro_accession":"3000664","category_aro_cvterm_id":"37008","category_aro_name":"trovafloxacin","category_aro_description":"Trovafloxacin is a trifluoroquinalone with a broad spectrum of activity that acts by inhibiting the uncoiling of supercoiled DNA. While potent against many Gram-positive and Gram-negative bacteria, it is less active against pseudomonads and Cl. difficile. It is usually taken as the prodrug trovafloxacin mesylate or alatrofloxacin mesylate for oral or intravenous administration, respectively.","category_aro_class_name":"Antibiotic"},"37009":{"category_aro_accession":"3000665","category_aro_cvterm_id":"37009","category_aro_name":"grepafloxacin","category_aro_description":"Grepafloxacin is a broad-spectrum antibacterial quinoline. It is no longer taken due to its high toxicity.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"37142":{"category_aro_accession":"3000762","category_aro_cvterm_id":"37142","category_aro_name":"pefloxacin","category_aro_description":"Pefloxacin is structurally and functionally similar to norfloxacin. It is poorly active against mycobacteria, while anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"40937":{"category_aro_accession":"3004010","category_aro_cvterm_id":"40937","category_aro_name":"cinoxacin","category_aro_description":"Cinoxacin is a fluoroquinolone antibiotic primarily used for the treatment of urinary tract infections in adults. Cinoxacin binds to DNA gyrase, resulting in double-stranded DNA breaks and cell death.","category_aro_class_name":"Antibiotic"},"40938":{"category_aro_accession":"3004011","category_aro_cvterm_id":"40938","category_aro_name":"clinafloxacin","category_aro_description":"Clinafloxacin is a fluoroquinolone antibiotic and gyrase (DNA topoisomerase II) inhibitor. It binds to DNA gyrase and disrupts replication by causing double-stranded DNA breaks, resulting in cell death.","category_aro_class_name":"Antibiotic"},"40939":{"category_aro_accession":"3004012","category_aro_cvterm_id":"40939","category_aro_name":"Clofazimine","category_aro_description":"Clofazimine is a fluoroquinolone-class phenazine dye used for the treatment of leprosy. Clofazimine binds to DNA and disrupts bacterial DNA gyrase, thereby causing double-stranded DNA breaks, and subsequent cell death.","category_aro_class_name":"Antibiotic"},"40940":{"category_aro_accession":"3004013","category_aro_cvterm_id":"40940","category_aro_name":"fleroxacin","category_aro_description":"Fleroxacin is a broad spectrum fluoroquinolone antibiotic that inhibits the DNA supercoiling activity of bacterial DNA gyrase, resulting in double-stranded DNA breaks and subsequent cell death.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1822":{"model_id":"1822","model_name":"Staphylococcus aureus gyrB conferring resistance to aminocoumarin","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2142":"S128L","2143":"R144S","2144":"R144I","2145":"I56S","2146":"I102S","2147":"T173A","3442":"G85S"},"experimental":{"2142":"S128L","2143":"R144S","2144":"R144I","2145":"I56S","2146":"I102S","2147":"T173A","3442":"G85S"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1200"}},"model_sequences":{"sequence":{"2061":{"protein_sequence":{"accession":"YP_039482.1","sequence":"MVTALSDVNNTDNYGAGQIQVLEGLEAVRKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEVVIEKDNWIKVTDNGRGIPVDIQEKMGRPAVEVILTVLHAGGKFGGGGYKVSGGLHGVGSSVVNALSQDLEVYVHRNETIYHQAYKKGVPQFDLKEVGTTDKTGTVIRFKADGEIFTETTVYNYETLQQRIRELAFLNKGIQITLRDERDEENVREDSYHYEGGIKSYVELLNENKEPIHDEPIYIHQSKDDIEVEIAIQYNSGYATNLLTYANNIHTYEGGTHEDGFKRALTRVLNSYGLSSKIMKEDKDRLSGEDTREGMTAIISIKHGDPQFEGQTKTKLGNSEVRQVVDKLFSEHFERFLYENPQVARTVVEKGIMAARARVAAKKAREVTRRKSALDVASLPGKLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEKARLDRILNNNEIRQMITAFGTGIGGDFDLAKARYHKIVIMTDADVDGAHIRTLLLTFFYRFMRPLIEAGYVYIAQPPLYKLTQGKQKYYVYNDRELDKLKSELNPTPKWSIARYKGLGEMNADQLWETTMNPEHRALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNAVYANLDF"},"dna_sequence":{"accession":"NC_002952","fmin":"5036","fmax":"6968","strand":"+","sequence":"GTGACTGCATTGTCAGATGTAAACAACACGGATAATTATGGTGCTGGGCAAATACAAGTATTAGAAGGTTTAGAAGCAGTACGTAAAAGACCAGGTATGTATATAGGATCGACTTCAGAGAGAGGTTTGCACCATTTAGTGTGGGAAATTGTCGATAATAGTATCGATGAAGCATTAGCTGGTTATGCAAATCAAATTGAAGTTGTTATTGAAAAAGATAACTGGATTAAAGTAACGGATAACGGACGTGGTATCCCAGTTGATATTCAAGAAAAAATGGGACGTCCAGCTGTCGAAGTTATTTTAACTGTTTTACATGCTGGTGGTAAATTCGGCGGTGGCGGATACAAAGTATCTGGTGGTTTACATGGTGTTGGTTCATCAGTTGTAAACGCATTGTCACAAGACTTAGAAGTATATGTACACAGAAATGAGACTATATATCATCAAGCATATAAAAAAGGTGTACCTCAATTTGACTTAAAAGAAGTTGGCACAACTGATAAGACAGGTACTGTCATTCGTTTTAAAGCAGATGGAGAAATCTTCACAGAGACAACTGTATACAACTATGAAACATTACAGCAACGTATTAGAGAGCTTGCTTTCTTAAACAAAGGAATTCAAATCACATTAAGAGATGAACGTGATGAAGAAAACGTTAGAGAAGACTCCTATCACTATGAGGGCGGTATTAAATCTTATGTTGAGTTATTGAACGAAAATAAAGAACCTATTCATGATGAGCCGATTTATATTCATCAATCTAAAGATGATATTGAAGTAGAAATTGCGATTCAATATAACTCAGGATATGCCACAAATCTTTTAACTTACGCAAATAACATTCATACGTACGAAGGTGGTACGCATGAAGACGGATTCAAACGTGCATTAACGCGTGTCTTAAATAGTTATGGTTTAAGTAGCAAGATTATGAAAGAAGACAAAGATAGACTTTCTGGTGAAGATACACGTGAAGGTATGACAGCAATTATATCTATCAAACATGGTGATCCTCAATTCGAAGGTCAAACGAAGACAAAATTAGGTAATTCTGAAGTGCGTCAAGTTGTAGATAAATTATTCTCAGAGCACTTTGAACGATTTTTATATGAAAATCCACAAGTCGCACGTACAGTGGTTGAAAAAGGTATTATGGCGGCACGTGCACGTGTTGCTGCGAAAAAAGCGCGTGAAGTAACACGTCGTAAATCAGCGTTAGATGTAGCAAGTCTTCCAGGTAAATTAGCCGATTGCTCTAGTAAAAGTCCTGAAGAATGTGAGATTTTCTTAGTCGAAGGGGACTCTGCCGGGGGGTCTACAAAATCTGGTCGTGACTCTAGAACGCAGGCGATTTTACCATTACGAGGTAAGATATTAAATGTTGAAAAGGCACGATTAGATAGAATTTTGAATAACAATGAAATTCGTCAAATGATCACAGCATTTGGTACAGGAATCGGTGGCGACTTTGATCTAGCGAAAGCAAGATATCACAAAATCGTCATTATGACTGATGCCGATGTGGATGGAGCGCATATTAGAACATTGTTATTAACATTCTTCTATCGATTTATGAGACCGTTAATTGAAGCAGGCTATGTGTATATTGCACAGCCACCGTTGTATAAACTGACACAAGGTAAACAAAAGTATTATGTATACAATGATAGGGAACTTGATAAACTTAAATCTGAATTGAATCCAACACCAAAATGGTCTATTGCACGATACAAAGGTCTTGGAGAAATGAATGCAGATCAATTATGGGAAACAACAATGAACCCTGAGCACCGCGCTCTTTTACAAGTAAAACTTGAAGATGCGATTGAAGCGGACCAAACATTTGAAATGTTAATGGGTGACGTTGTAGAAAACCGTAGACAATTTATAGAAGATAATGCAGTTTATGCAAACTTAGACTTCTAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35517","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus MRSA252","NCBI_taxonomy_id":"282458"}}}},"ARO_accession":"3003301","ARO_id":"39885","ARO_name":"Staphylococcus aureus gyrB conferring resistance to aminocoumarin","ARO_description":"Point mutation in Staphylococcus aureus resulting in aminocoumarin resistance","ARO_category":{"36618":{"category_aro_accession":"3000479","category_aro_cvterm_id":"36618","category_aro_name":"aminocoumarin resistant gyrB","category_aro_description":"Point mutations in DNA gyrase subunit B (gyrB) can result in resistance to aminocoumarins. These mutations usually involve arginine residues in organisms.","category_aro_class_name":"AMR Gene Family"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36271":{"category_aro_accession":"3000132","category_aro_cvterm_id":"36271","category_aro_name":"clorobiocin","category_aro_description":"Clorobiocin is an aminocoumarin antibiotic produced by Streptomyces roseochromogenes, and binds DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36289":{"category_aro_accession":"3000150","category_aro_cvterm_id":"36289","category_aro_name":"coumermycin A1","category_aro_description":"Coumermycin A1 is an antibiotic produced by Streptomyces rishiriensis, and binds DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1849":{"model_id":"1849","model_name":"Mycobacterium tuberculosis tlyA mutations conferring resistance to aminoglycosides","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2189":"L150P","2188":"A91E","2235":"N236K","2257":"R14W","2259":"P183L","3831":"A67E","3832":"K69E","3833":"V128E","3836":"F185L","3840":"E238K","3401":"L118P"},"clinical":{"2189":"L150P","2235":"N236K","2257":"R14W"},"experimental":{"2188":"A91E","2259":"P183L","3831":"A67E","3832":"K69E","3833":"V128E","3836":"F185L","3840":"E238K","3401":"L118P"}},"40394":{"param_type":"nonsense mutation","param_description":"A nucleotide substitution resulting in a change from an amino acid codon to a STOP codon. Nonsense mutations truncate protein translation prematurely, resulting in a defective or completely inactive protein. In CARD, nonsense mutations may be attached to models using the notation: [wild type amino acid][position][STOP] (e.g. Q42STOP). This parameter is not currently used in detection algorithms.","param_type_id":"40394","param_value":{"3828":"R18STOP","3829":"Q22STOP","3835":"Q184STOP","3908":"R3STOP"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"},"41343":{"param_type":"deletion mutation from nucleotide sequence","param_description":"A subtype of the deletion mutation detection model parameter. This parameter is used when a set of deletion mutations is reported in a nucleotide sequence format. Such mutations may be of variable length - possibly causing a frameshift, but not premature termination of functional knockout. Mutation parameters of this type are reported in the CARD with the notation: [-]nt[position]:[nucleotides].","param_type_id":"41343","param_value":{"8027":"-nt758:G","8028":"-nt673:GT","8029":"-nt653:T","8030":"-nt586:G","8031":"-nt477:G","8032":"-nt400:A","8033":"-nt23:A","8034":"-nt26:C","8035":"-nt310:G"}},"41345":{"param_type":"insertion mutation from nucleotide sequence","param_description":"A subtype of the insertion mutation detection model parameter. This parameter is used when a set of insertion mutations is reported in a nucleotide sequence format. Such mutations may be of variable length - possibly causing a frameshift, but not causing premature termination or a functional knockout. Mutation parameters of this type are reported in CARD with the notation: [+]nt[position]:[nucleotides].","param_type_id":"41345","param_value":{"8036":"+nt397:C"}}},"model_sequences":{"sequence":{"2076":{"protein_sequence":{"accession":"AAK46002.1","sequence":"MARRARVDAELVRRGLARSRQQAAELIGAGKVRIDGLPAVKPATAVSDTTALTVVTDSERAWVSRGAHKLVGALEAFAIAVAGRRCLDAGASTGGFTEVLLDRGAAHVVAADVGYGQLAWSLRNDPRVVVLERTNARGLTPEAIGGRVDLVVADLSFISLATVLPALVGCASRDADIVPLVKPQFEVGKGQVGPGGVVHDPQLRARSVLAVARRAQELGWHSVGVKASPLPGPSGNVEYFLWLRTQTDRALSAKGLEDAVHRAISEGP"},"dna_sequence":{"accession":"AE000516","fmin":"1908741","fmax":"1909548","strand":"+","sequence":"GTGGCACGACGTGCCCGCGTTGACGCCGAGCTGGTCCGGCGGGGCCTGGCGCGATCACGTCAACAGGCCGCGGAGTTGATCGGCGCCGGCAAGGTGCGCATCGACGGGCTGCCGGCGGTCAAGCCGGCCACCGCCGTGTCCGACACCACCGCGCTGACCGTGGTGACCGACAGTGAACGCGCCTGGGTATCGCGCGGAGCGCACAAACTAGTCGGTGCGCTGGAGGCGTTCGCGATCGCGGTGGCGGGCCGGCGCTGTCTGGACGCGGGCGCATCGACCGGTGGGTTCACCGAAGTACTGCTGGACCGTGGTGCCGCCCACGTGGTGGCCGCCGATGTCGGATACGGCCAGCTGGCGTGGTCGCTGCGCAACGATCCTCGGGTGGTGGTCCTCGAGCGGACCAACGCACGTGGCCTCACACCGGAGGCGATCGGCGGTCGCGTCGACCTGGTAGTGGCCGACCTGTCGTTCATCTCGTTGGCTACCGTGTTGCCCGCGCTGGTTGGATGCGCTTCGCGCGACGCCGATATCGTTCCACTGGTGAAGCCGCAGTTTGAGGTGGGGAAAGGTCAGGTCGGCCCCGGTGGGGTGGTCCATGACCCGCAGTTGCGTGCGCGGTCGGTGCTCGCGGTCGCGCGGCGGGCACAGGAGCTGGGCTGGCACAGCGTCGGCGTCAAGGCCAGCCCGCTGCCGGGCCCATCGGGCAATGTCGAGTACTTCCTGTGGTTGCGCACGCAGACCGACCGGGCATTGTCGGCCAAGGGATTGGAGGATGCGGTGCACCGTGCGATTAGCGAGGGCCCGTAGT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37081","NCBI_taxonomy_name":"Mycobacterium tuberculosis CDC1551","NCBI_taxonomy_id":"83331"}}}},"ARO_accession":"3003445","ARO_id":"40038","ARO_name":"Mycobacterium tuberculosis tlyA mutations conferring resistance to aminoglycosides","ARO_description":"Specific mutations that arise in Mycobacterium tuberculosis tlyA resulting in aminoglycosides resistance","ARO_category":{"40036":{"category_aro_accession":"3003443","category_aro_cvterm_id":"40036","category_aro_name":"Antibiotic resistant tlyA","category_aro_description":"tlyA encodes for hemolysin. It Catalyzes the 2'-O-methylation at nucleotides C1409 in 16S rRNA and C1920 in 23S rRNA. Mutation that arise within this gene reduces the binding affinity of aminoglycosides to rRNA","category_aro_class_name":"AMR Gene Family"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1935":{"model_id":"1935","model_name":"Mycobacterium tuberculosis gyrA conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2091":"D94G","2092":"D89V","2093":"D94A","2094":"D89N","2095":"D89G","2096":"G88C","2180":"S91P","2181":"D94N","2216":"D94Y","2217":"D94V","2502":"G88A","2503":"A90V","2504":"A90G","3841":"A74S","3844":"T80A","3847":"S95T","3848":"L109V","3849":"P102H","4589":"D94T"},"clinical":{"2091":"D94G","2092":"D89V","2093":"D94A","2094":"D89N","2095":"D89G","2096":"G88C","2180":"S91P","2181":"D94N","2216":"D94Y","2217":"D94V","2502":"G88A","2503":"A90V","2504":"A90G","3841":"A74S","3844":"T80A","3847":"S95T","3848":"L109V","3849":"P102H","4589":"D94T"}},"40438":{"param_type":"co-dependent single resistance variant","param_description":"A model parameter to describe mutations in multiple genes or proteins where resistance is co-dependent on each. For example, the G247S SNP in M. tuberculosis gyrA does not confer resistance to fluoroquinolones. However, when the D500N SNP is also present in gyrB, resistance is conferred. In this case, gyrA G247S is co-dependent on gyrB D500N to confer resistance. This parameter is noted on relevant models with the following notation: [cvterm-id-gene-1],[gene-1-SNP]+[cvterm-id-gene-2],[gene-2-SNP]+ ... +[cvterm-id-gene-n],[gene-n-SNP] e.g. 39879,G247S+40052,D500N. This parameter is not currently included in any detection algorithms.","param_type_id":"40438","param_value":{"3611":"39879,G247S+40052,D500N","3843":"39879,A90V+40052,D472H"}},"40330":{"param_type":"multiple resistance variants","param_description":"A set of nucleotide or amino acid substitutions that are each required to confer resistance to an antibiotic drug or drug class by co-mutation. Compare to single resistance variant, where only one substitution is required. Multiple resistance variants parameters are indicated on appropriate models using the following notation: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2],...,[wild-type n][position n][mutation n]. When each included substitution is detected in a protein sequence, resistance is conferred. This parameter is not currently included in any detection algorithms.","param_type_id":"40330","param_value":{"3842":"A90V,D94G"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1500"}},"model_sequences":{"sequence":{"2055":{"protein_sequence":{"accession":"CCP42728.1","sequence":"MTDTTLPPDDSLDRIEPVDIEQEMQRSYIDYAMSVIVGRALPEVRDGLKPVHRRVLYAMFDSGFRPDRSHAKSARSVAETMGNYHPHGDASIYDSLVRMAQPWSLRYPLVDGQGNFGSPGNDPPAAMRYTEARLTPLAMEMLREIDEETVDFIPNYDGRVQEPTVLPSRFPNLLANGSGGIAVGMATNIPPHNLRELADAVFWALENHDADEEETLAAVMGRVKGPDFPTAGLIVGSQGTADAYKTGRGSIRMRGVVEVEEDSRGRTSLVITELPYQVNHDNFITSIAEQVRDGKLAGISNIEDQSSDRVGLRIVIEIKRDAVAKVVINNLYKHTQLQTSFGANMLAIVDGVPRTLRLDQLIRYYVDHQLDVIVRRTTYRLRKANERAHILRGLVKALDALDEVIALIRASETVDIARAGLIELLDIDEIQAQAILDMQLRRLAALERQRIIDDLAKIEAEIADLEDILAKPERQRGIVRDELAEIVDRHGDDRRTRIIAADGDVSDEDLIAREDVVVTITETGYAKRTKTDLYRSQKRGGKGVQGAGLKQDDIVAHFFVCSTHDLILFFTTQGRVYRAKAYDLPEASRTARGQHVANLLAFQPEERIAQVIQIRGYTDAPYLVLATRNGLVKKSKLTDFDSNRSGGIVAVNLRDNDELVGAVLCSAGDDLLLVSANGQSIRFSATDEALRPMGRATSGVQGMRFNIDDRLLSLNVVREGTYLLVATSGGYAKRTAIEEYPVQGRGGKGVLTVMYDRRRGRLVGALIVDDDSELYAVTSGGGVIRTAARQVRKAGRQTKGVRLMNLGEGDTLLAIARNAEESGDDNAVDANGADQTGN"},"dna_sequence":{"accession":"AL123456","fmin":"7301","fmax":"9818","strand":"+","sequence":"ATGACAGACACGACGTTGCCGCCTGACGACTCGCTCGACCGGATCGAACCGGTTGACATCGAGCAGGAGATGCAGCGCAGCTACATCGACTATGCGATGAGCGTGATCGTCGGCCGCGCGCTGCCGGAGGTGCGCGACGGGCTCAAGCCCGTGCATCGCCGGGTGCTCTATGCAATGTTCGATTCCGGCTTCCGCCCGGACCGCAGCCACGCCAAGTCGGCCCGGTCGGTTGCCGAGACCATGGGCAACTACCACCCGCACGGCGACGCGTCGATCTACGACAGCCTGGTGCGCATGGCCCAGCCCTGGTCGCTGCGCTACCCGCTGGTGGACGGCCAGGGCAACTTCGGCTCGCCAGGCAATGACCCACCGGCGGCGATGAGGTACACCGAAGCCCGGCTGACCCCGTTGGCGATGGAGATGCTGAGGGAAATCGACGAGGAGACAGTCGATTTCATCCCTAACTACGACGGCCGGGTGCAAGAGCCGACGGTGCTACCCAGCCGGTTCCCCAACCTGCTGGCCAACGGGTCAGGCGGCATCGCGGTCGGCATGGCAACCAATATCCCGCCGCACAACCTGCGTGAGCTGGCCGACGCGGTGTTCTGGGCGCTGGAGAATCACGACGCCGACGAAGAGGAGACCCTGGCCGCGGTCATGGGGCGGGTTAAAGGCCCGGACTTCCCGACCGCCGGACTGATCGTCGGATCCCAGGGCACCGCTGATGCCTACAAAACTGGCCGCGGCTCCATTCGAATGCGCGGAGTTGTTGAGGTAGAAGAGGATTCCCGCGGTCGTACCTCGCTGGTGATCACCGAGTTGCCGTATCAGGTCAACCACGACAACTTCATCACTTCGATCGCCGAACAGGTCCGAGACGGCAAGCTGGCCGGCATTTCCAACATTGAGGACCAGTCTAGCGATCGGGTCGGTTTACGCATCGTCATCGAGATCAAGCGCGATGCGGTGGCCAAGGTGGTGATCAATAACCTTTACAAGCACACCCAGCTGCAGACCAGCTTTGGCGCCAACATGCTAGCGATCGTCGACGGGGTGCCGCGCACGCTGCGGCTGGACCAGCTGATCCGCTATTACGTTGACCACCAACTCGACGTCATTGTGCGGCGCACCACCTACCGGCTGCGCAAGGCAAACGAGCGAGCCCACATTCTGCGCGGCCTGGTTAAAGCGCTCGACGCGCTGGACGAGGTCATTGCACTGATCCGGGCGTCGGAGACCGTCGATATCGCCCGGGCCGGACTGATCGAGCTGCTCGACATCGACGAGATCCAGGCCCAGGCAATCCTGGACATGCAGTTGCGGCGCCTGGCCGCACTGGAACGCCAGCGCATCATCGACGACCTGGCCAAAATCGAGGCCGAGATCGCCGATCTGGAAGACATCCTGGCAAAACCCGAGCGGCAGCGTGGGATCGTGCGCGACGAACTCGCCGAAATCGTGGACAGGCACGGCGACGACCGGCGTACCCGGATCATCGCGGCCGACGGAGACGTCAGCGACGAGGATTTGATCGCCCGCGAGGACGTCGTTGTCACTATCACCGAAACGGGATACGCCAAGCGCACCAAGACCGATCTGTATCGCAGCCAGAAACGCGGCGGCAAGGGCGTGCAGGGTGCGGGGTTGAAGCAGGACGACATCGTCGCGCACTTCTTCGTGTGCTCCACCCACGATTTGATCCTGTTCTTCACCACCCAGGGACGGGTTTATCGGGCCAAGGCCTACGACTTGCCCGAGGCCTCCCGGACGGCGCGCGGGCAGCACGTGGCCAACCTGTTAGCCTTCCAGCCCGAGGAACGCATCGCCCAGGTCATCCAGATTCGCGGCTACACCGACGCCCCGTACCTGGTGCTGGCCACTCGCAACGGGCTGGTGAAAAAGTCCAAGCTGACCGACTTCGACTCCAATCGCTCGGGCGGAATCGTGGCGGTCAACCTGCGCGACAACGACGAGCTGGTCGGTGCGGTGCTGTGTTCGGCCGGCGACGACCTGCTGCTGGTCTCGGCCAACGGGCAGTCCATCAGGTTCTCGGCGACCGACGAGGCGCTGCGGCCAATGGGTCGTGCCACCTCGGGTGTGCAGGGCATGCGGTTCAATATCGACGACCGGCTGCTGTCGCTGAACGTCGTGCGTGAAGGCACCTATCTGCTGGTGGCGACGTCAGGGGGCTATGCGAAACGTACCGCGATCGAGGAATACCCGGTACAGGGCCGCGGCGGTAAAGGTGTGCTGACGGTCATGTACGACCGCCGGCGCGGCAGGTTGGTTGGGGCGTTGATTGTCGACGACGACAGCGAGCTGTATGCCGTCACTTCCGGCGGTGGCGTGATCCGCACCGCGGCACGCCAGGTTCGCAAGGCGGGACGGCAGACCAAGGGTGTTCGGTTGATGAATCTGGGCGAGGGCGACACACTGTTGGCCATCGCGCGCAACGCCGAAGAAAGTGGCGACGATAATGCCGTGGACGCCAACGGCGCAGACCAGACGGGCAATTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3003295","ARO_id":"39879","ARO_name":"Mycobacterium tuberculosis gyrA conferring resistance to fluoroquinolones","ARO_description":"Point mutation of Mycobacterium tuberculosis gyrA resulted in the lowered affinity between fluoroquinolones and gyrA. Thus, conferring resistance.","ARO_category":{"39876":{"category_aro_accession":"3003292","category_aro_cvterm_id":"39876","category_aro_name":"fluoroquinolone resistant gyrA","category_aro_description":"DNA gyrase is responsible for DNA supercoiling and consists of two alpha and two beta subunits. GyrA point mutations confer resistance by preventing fluoroquinolone antibiotics from binding the alpha-subunit.","category_aro_class_name":"AMR Gene Family"},"35942":{"category_aro_accession":"0000023","category_aro_cvterm_id":"35942","category_aro_name":"enoxacin","category_aro_description":"Enoxacin belongs to a group called fluoroquinolones. Its mode of action depends upon blocking bacterial DNA replication by binding itself to DNA gyrase and causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37004":{"category_aro_accession":"3000660","category_aro_cvterm_id":"37004","category_aro_name":"lomefloxacin","category_aro_description":"Lomefloxacin is a difluoropiperazinyl quinolone, sharing similar activities with other fluoroquinolones. It is used to treat urinary tract infections. Relative to other fluoroquinolones, it has a longer half life and has higher serum concentrations.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"37008":{"category_aro_accession":"3000664","category_aro_cvterm_id":"37008","category_aro_name":"trovafloxacin","category_aro_description":"Trovafloxacin is a trifluoroquinalone with a broad spectrum of activity that acts by inhibiting the uncoiling of supercoiled DNA. While potent against many Gram-positive and Gram-negative bacteria, it is less active against pseudomonads and Cl. difficile. It is usually taken as the prodrug trovafloxacin mesylate or alatrofloxacin mesylate for oral or intravenous administration, respectively.","category_aro_class_name":"Antibiotic"},"37009":{"category_aro_accession":"3000665","category_aro_cvterm_id":"37009","category_aro_name":"grepafloxacin","category_aro_description":"Grepafloxacin is a broad-spectrum antibacterial quinoline. It is no longer taken due to its high toxicity.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"37142":{"category_aro_accession":"3000762","category_aro_cvterm_id":"37142","category_aro_name":"pefloxacin","category_aro_description":"Pefloxacin is structurally and functionally similar to norfloxacin. It is poorly active against mycobacteria, while anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"40463":{"category_aro_accession":"3003780","category_aro_cvterm_id":"40463","category_aro_name":"nybomycin","category_aro_description":"A  heterocyclic antibiotic that targets mutant gyrA (type II topoisomerase) containing an S84L substitution, counteracting acquired quinolone resistance. It is effective against quinolone-resistant Gram-positive bacteria including S. aureus and E. faecalis. Due to its ability to counteract quinolone resistance by targeting the mutant form of the gyrA protein, it is classified as a reverse antibiotic (RA).","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1943":{"model_id":"1943","model_name":"Mycobacterium tuberculosis kasA mutant conferring resistance to isoniazid","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2567":"R121K","2568":"G387D","2569":"F413L","3771":"G269S","3772":"G312S","3791":"D66N"},"clinical":{"2567":"R121K","2568":"G387D","2569":"F413L","3771":"G269S","3772":"G312S","3791":"D66N"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"2084":{"protein_sequence":{"accession":"CCP45025.1","sequence":"MSQPSTANGGFPSVVVTAVTATTSISPDIESTWKGLLAGESGIHALEDEFVTKWDLAVKIGGHLKDPVDSHMGRLDMRRMSYVQRMGKLLGGQLWESAGSPEVDPDRFAVVVGTGLGGAERIVESYDLMNAGGPRKVSPLAVQMIMPNGAAAVIGLQLGARAGVMTPVSACSSGSEAIAHAWRQIVMGDADVAVCGGVEGPIEALPIAAFSMMRAMSTRNDEPERASRPFDKDRDGFVFGEAGALMLIETEEHAKARGAKPLARLLGAGITSDAFHMVAPAADGVRAGRAMTRSLELAGLSPADIDHVNAHGTATPIGDAAEANAIRVAGCDQAAVYAPKSALGHSIGAVGALESVLTVLTLRDGVIPPTLNYETPDPEIDLDVVAGEPRYGDYRYAVNNSFGFGGHNVALAFGRY"},"dna_sequence":{"accession":"AL123456","fmin":"2518114","fmax":"2519365","strand":"+","sequence":"GTGAGTCAGCCTTCCACCGCTAATGGCGGTTTCCCCAGCGTTGTGGTGACCGCCGTCACAGCGACGACGTCGATCTCGCCGGACATCGAGAGCACGTGGAAGGGTCTGTTGGCCGGCGAGAGCGGCATCCACGCACTCGAAGACGAGTTCGTCACCAAGTGGGATCTAGCGGTCAAGATCGGCGGTCACCTCAAGGATCCGGTCGACAGCCACATGGGCCGACTCGACATGCGACGCATGTCGTACGTCCAGCGGATGGGCAAGTTGCTGGGCGGACAGCTATGGGAGTCCGCCGGCAGCCCGGAGGTCGATCCAGACCGGTTCGCCGTTGTTGTCGGCACCGGTCTAGGTGGAGCCGAGAGGATTGTCGAGAGCTACGACCTGATGAATGCGGGCGGCCCCCGGAAGGTGTCCCCGCTGGCCGTTCAGATGATCATGCCCAACGGTGCCGCGGCGGTGATCGGTCTGCAGCTTGGGGCCCGCGCCGGGGTGATGACCCCGGTGTCGGCCTGTTCGTCGGGCTCGGAAGCGATCGCCCACGCGTGGCGTCAGATCGTGATGGGCGACGCCGACGTCGCCGTCTGCGGCGGTGTCGAAGGACCCATCGAGGCGCTGCCCATCGCGGCGTTCTCCATGATGCGGGCCATGTCGACCCGCAACGACGAGCCTGAGCGGGCCTCCCGGCCGTTCGACAAGGACCGCGACGGCTTTGTGTTCGGCGAGGCCGGTGCGCTGATGCTCATCGAGACGGAGGAGCACGCCAAAGCCCGTGGCGCCAAGCCGTTGGCCCGATTGCTGGGTGCCGGTATCACCTCGGACGCCTTTCATATGGTGGCGCCCGCGGCCGATGGTGTTCGTGCCGGTAGGGCGATGACTCGCTCGCTGGAGCTGGCCGGGTTGTCGCCGGCGGACATCGACCACGTCAACGCGCACGGCACGGCGACGCCTATCGGCGACGCCGCGGAGGCCAACGCCATCCGCGTCGCCGGTTGTGATCAGGCCGCGGTGTACGCGCCGAAGTCTGCGCTGGGCCACTCGATCGGCGCGGTCGGTGCGCTCGAGTCGGTGCTCACGGTGCTGACGCTGCGCGACGGCGTCATCCCGCCGACCCTGAACTACGAGACACCCGATCCCGAGATCGACCTTGACGTCGTCGCCGGCGAACCGCGCTATGGCGATTACCGCTACGCAGTCAACAACTCGTTCGGGTTCGGCGGCCACAATGTGGCGCTTGCCTTCGGGCGTTACTGAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3003463","ARO_id":"40056","ARO_name":"Mycobacterium tuberculosis kasA mutant conferring resistance to isoniazid","ARO_description":"Specific mutations on the Mycobacterium tuberculosis kasA gene resulting in lowered affinity of isoniazid, resulting in resistance","ARO_category":{"40055":{"category_aro_accession":"3003462","category_aro_cvterm_id":"40055","category_aro_name":"antibiotic resistant kasA","category_aro_description":"kasA is a  ketoacyl acyl carrier protein synthase that catalyzes the condensation reaction of fatty acid synthesis by the addition to an acyl acceptor of two carbons from malonyl-ACP. It is involved in elongation of fatty acids intermediate in the biosynthetic pathway of mycolic acids.","category_aro_class_name":"AMR Gene Family"},"36659":{"category_aro_accession":"3000520","category_aro_cvterm_id":"36659","category_aro_name":"isoniazid","category_aro_description":"Isoniazid is an organic compound that is the first-line anti tuberculosis medication in prevention and treatment. As a prodrug, it is activated by mycobacterial catalase-peroxidases such as M. tuberculosis KatG. Isoniazid inhibits mycolic acid synthesis, which prevents cell wall synthesis in mycobacteria.","category_aro_class_name":"Drug Class"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2068":{"model_id":"2068","model_name":"Escherichia coli 16S rRNA mutation conferring resistance to edeine","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3073":"A1499G","4842":"U1506A"},"clinical":{"3073":"A1499G","4842":"U1506A"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"3234":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"U00096","fmin":"4166659","fmax":"4168200","strand":"+","sequence":"AAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAGAAGCTTGCTTCTTTGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCGACTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTGGTCTTGACATCCACGGAAGTTTTCAGAGATGAGAATGTGCCTTCGGGAACCGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGGTCCGGCCGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACGACCAGGGCTACACACGTGCTACAATGGCGCATACAAAGAGAAGCGACCTCGCGAGAGCAAGCGGACCTCATAAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTGGATCAGAATGCCACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGCAAAAGAAGTAGGTAGCTTAACCTTCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGATCACCTCCTTA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36905","NCBI_taxonomy_name":"Escherichia coli K-12","NCBI_taxonomy_id":"83333"}}}},"ARO_accession":"3003223","ARO_id":"39807","ARO_name":"Escherichia coli 16S rRNA mutation conferring resistance to edeine","ARO_description":"Point mutations in the 3' minor domain of the 16S rRNA in Escherichia coli can confer resistance to edeine","ARO_category":{"40278":{"category_aro_accession":"3003667","category_aro_cvterm_id":"40278","category_aro_name":"16s rRNA with mutation conferring resistance to peptide antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to peptide antibiotics.","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36269":{"category_aro_accession":"3000130","category_aro_cvterm_id":"36269","category_aro_name":"edeine A","category_aro_description":"Edeine A is a subtype of the peptide antibiotic edeine, composed of beta-tyr, beta-ser, diaminopropionic acid, diaminohydroxyazelaic acid, glycine, and spermidine. Edeine A is a mixture of edeine A1 and its inactive isomer, edeine A2. Edeines bind to the 30S subunit to block fMet-tRNA interaction at the P site, inhibiting protein synthesis and subsequent structure\/function processes critical for life or replication.","category_aro_class_name":"Antibiotic"},"36273":{"category_aro_accession":"3000134","category_aro_cvterm_id":"36273","category_aro_name":"edeine B","category_aro_description":"Edeine B is a subtype of the peptide antibiotic edeine, composed of beta-tyr, beta-ser, diaminopropionic acid, diaminohydroxyazelaic acid, glycine, and guanylspermidine. Edeine B is a mixture of edeine B1 and its inactive isomer, edeine B2.  Edeines bind to the 30S subunit to block fMet-tRNA interaction at the P site, inhibiting protein synthesis and subsequent structure\/function processes critical for life or replication. Edeine B has also been shown to inhibit septation and cause filamentous morphology, also leading to cell death.","category_aro_class_name":"Antibiotic"},"36274":{"category_aro_accession":"3000135","category_aro_cvterm_id":"36274","category_aro_name":"edeine D","category_aro_description":"Edeine D is a subtype of edeine similar to edeine A with the beta-tyr replaced by beta-phe-beta-ala. Edeines bind to the 30S subunit to block fMet-tRNA interaction at the P site, inhibiting protein synthesis and subsequent structure\/function processes critical for life or replication.","category_aro_class_name":"Antibiotic"},"36275":{"category_aro_accession":"3000136","category_aro_cvterm_id":"36275","category_aro_name":"edeine F","category_aro_description":"Edeine F is a subtype of edeine similar to edeine B with beta-tyr replaced by beta-phe-beta-ala. Edeines bind to the 30S subunit to block fMet-tRNA interaction at the P site, inhibiting protein synthesis and subsequent structure\/function processes critical for life or replication.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2070":{"model_id":"2070","model_name":"Mycobacterium tuberculosis 16S rRNA mutation conferring resistance to amikacin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2980":"A1401G"},"clinical":{"2980":"A1401G"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"3261":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"AL123456.3","fmin":"1471846","fmax":"1473382","strand":"+","sequence":"TTTTGTTTGGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGTCTCTTCGGAGATACTCGAGTGGCGAACGGGTGAGTAACACGTGGGTGATCTGCCCTGCACTTCGGGATAAGCCTGGGAAACTGGGTCTAATACCGGATAGGACCACGGGATGCATGTCTTGTGGTGGAAAGCGCTTTAGCGGTGTGGGATGAGCCCGCGGCCTATCAGCTTGTTGGTGGGGTGACGGCCTACCAAGGCGACGACGGGTAGCCGGCCTGAGAGGGTGTCCGGCCACACTGGGACTGAGATACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGGGGGATGACGGCCTTCGGGTTGTAAACCTCTTTCACCATCGACGAAGGTCCGGGTTCTCTCGGATTGACGGTAGGTGGAGAAGAAGCACCGGCCAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCGAGCGTTGTCCGGAATTACTGGGCGTAAAGAGCTCGTAGGTGGTTTGTCGCGTTGTTCGTGAAATCTCACGGCTTAACTGTGAGCGTGCGGGCGATACGGGCAGACTAGAGTACTGCAGGGGAGACTGGAATTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGGTGGCGAAGGCGGGTCTCTGGGCAGTAACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGGTGGGTACTAGGTGTGGGTTTCCTTCCTTGGGATCCGTGCCGTAGCTAACGCATTAAGTACCCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGTGGATTAATTCGATGCAACGCGAAGAACCTTACCTGGGTTTGACATGCACAGGACGCGTCTAGAGATAGGCGTTCCCTTGTGGCCTGTGTGCAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCTCATGTTGCCAGCACGTAATGGTGGGGACTCGTGAGAGACTGCCGGGGTCAACTCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGCCCCTTATGTCCAGGGCTTCACACATGCTACAATGGCCGGTACAAAGGGCTGCGATGCCGCGAGGTTAAGCGAATCCTTAAAAGCCGGTCTCAGTTCGGATCGGGGTCTGCAACTCGACCCCGTGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTCGGTAACACCCGAAGCCAGTGGCCTAACCCTCGGGAGGGAGCTGTCGAAGGTGGGATCGGCGATTGGGACGAAGTCGTAACAAGGTAGCCGTACCGGAAGGTGCGGCTGGATCACCTCCTTTCT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3003481","ARO_id":"40077","ARO_name":"Mycobacterium tuberculosis 16S rRNA mutation conferring resistance to amikacin","ARO_description":"Point mutations in the 3' domain of 16S rRNA of Mycobacterium tuberculosis can confer resistance to amikacin.","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2069":{"model_id":"2069","model_name":"Escherichia coli 16S rRNA mutation in the rrsB gene conferring resistance to neomycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3060":"A1408G"},"clinical":{"3060":"A1408G"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"3235":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"U00096","fmin":"4166659","fmax":"4168200","strand":"+","sequence":"AAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAGAAGCTTGCTTCTTTGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCGACTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTGGTCTTGACATCCACGGAAGTTTTCAGAGATGAGAATGTGCCTTCGGGAACCGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGGTCCGGCCGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACGACCAGGGCTACACACGTGCTACAATGGCGCATACAAAGAGAAGCGACCTCGCGAGAGCAAGCGGACCTCATAAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTGGATCAGAATGCCACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGCAAAAGAAGTAGGTAGCTTAACCTTCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGATCACCTCCTTA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36905","NCBI_taxonomy_name":"Escherichia coli K-12","NCBI_taxonomy_id":"83333"}}}},"ARO_accession":"3003402","ARO_id":"39986","ARO_name":"Escherichia coli 16S rRNA (rrsB) mutation conferring resistance to neomycin","ARO_description":"Point mutations in the 3' minor domain of helix 44, in the rrsB 16S rRNA gene of Escherichia coli can confer resistance to neomycin","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2073":{"model_id":"2073","model_name":"Escherichia coli 16S rRNA mutation in the rrsB gene conferring resistance to G418","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"4812":"U1406A"},"clinical":{"4812":"U1406A"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"3230":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"U00096","fmin":"4166659","fmax":"4168200","strand":"+","sequence":"AAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAGAAGCTTGCTTCTTTGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCGACTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTGGTCTTGACATCCACGGAAGTTTTCAGAGATGAGAATGTGCCTTCGGGAACCGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGGTCCGGCCGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACGACCAGGGCTACACACGTGCTACAATGGCGCATACAAAGAGAAGCGACCTCGCGAGAGCAAGCGGACCTCATAAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTGGATCAGAATGCCACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGCAAAAGAAGTAGGTAGCTTAACCTTCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGATCACCTCCTTA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36905","NCBI_taxonomy_name":"Escherichia coli K-12","NCBI_taxonomy_id":"83333"}}}},"ARO_accession":"3003397","ARO_id":"39981","ARO_name":"Escherichia coli 16S rRNA (rrsB) mutation conferring resistance to G418","ARO_description":"Point mutations in the 3' minor domain of helix 44, in the rrsB 16S rRNA gene of Escherichia coli can confer resistance to G418","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2074":{"model_id":"2074","model_name":"Salmonella enterica serovar Typhimurium 16S rRNA mutation in the rrsD gene conferring resistance to spectinomycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"4810":"C1192U","4811":"C1065U"},"clinical":{"4810":"C1192U","4811":"C1065U"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"3227":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"AE006468","fmin":"3570463","fmax":"3572006","strand":"+","sequence":"AGGTAAGGAGGTGATCCAACCGCAGGTTCCCCTACGGTTACCTTGTTACGACTTCACCCCAGTCATGAATCACAAAGTGGTAAGCGCCCTCCCGAAGGTTAAGCTACCTACTTCTTTTGCAACCCACTCCCATGGTGTGACGGGCGGTGTGTACAAGGCCCGGGAACGTATTCACCGTGGCATTCTGATCCACGATTACTAGCGATTCCGACTTCATGGAGTCGAGTTGCAGACTCCAATCCGGACTACGACGCACTTTATGAGGTCCGCTTGCTCTCGCGAGGTCGCTTCTCTTTGTATGCGCCATTGTAGCACGTGTGTAGCCCTGGTCGTAAGGGCCATGATGACTTGACGTCATCCCCACCTTCCTCCAGTTTATCACTGGCAGTCTCCTTTGAGTTCCCGACCTAATCGCTGGCAACAAAGGATAAGGGTTGCGCTCGTTGCGGGACTTAACCCAACATTTCACAACACGAGCTGACGACAGCCATGCAGCACCTGTCTCACAGTTCCCGAAGGCACCAATCCATCTCTGGAAAGTTCTGTGGATGTCAAGACCAGGTAAGGTTCTTCGCGTTGCATCGAATTAAACCACATGCTCCACCGCTTGTGCGGGCCCCCGTCAATTCATTTGAGTTTTAACCTTGCGGCCGTACTCCCCAGGCGGTCTACTTAACGCGTTAGCTCCGGAAGCCACGCCTCAAGGGCACAACCTCCAAGTAGACATCGTTTACGGCGTGGACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTGAGCGTCAGTCTTTGTCCAGGGGGCCGCCTTCGCCACCGGTATTCCTCCAGATCTCTACGCATTTCACCGCTACACCTGGAATTCTACCCCCCTCTACAAGACTCAAGCCTGCCAGTTTCGAATGCAGTTCCCAGGTTGAGCCCGGGGATTTCACATCCGACTTGACAGACCGCCTGCGTGCGCTTTACGCCCAGTAATTCCGATTAACGCTTGCACCCTCCGTATTACCGCGGCTGCTGGCACGGAGTTAGCCGGTGCTTCTTCTGCGGGTAACGTCAATTGCTGCGGTTATTAACCACAACACCTTCCTCCCCGCTGAAAGTACTTTACAACCCGAAGGCCTTCTTCATACACGCGGCATGGCTGCATCAGGCTTGCGCCCATTGTGCAATATTCCCCACTGCTGCCTCCCGTAGGAGTCTGGACCGTGTCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCTCACCAACAAGCTAATCCCATCTGGGCACATCTGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACGTTATGCGGTATTAGCCACCGTTTCCAGTAGTTATCCCCCTCCATCAGGCAGTTTCCCAGACATTACTCACCCGTCCGCCACTCGTCAGCGAAGCAGCAAGCTGCTTCCTGTTACCGTTCGACTTGCATGTGTTAGGCCTGCCGCCAGCGTTCAATCTGAGCCATGATCAAACTCTTCAATT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35717","NCBI_taxonomy_name":"Salmonella enterica subsp. salamae","NCBI_taxonomy_id":"59202"}}}},"ARO_accession":"3003512","ARO_id":"40114","ARO_name":"Salmonella enterica 16S rRNA (rrsD) mutation conferring resistance to spectinomycin","ARO_description":"Point mutations in the helix 34 region of the rrsD 16S rRNA gene of Salmonella enterica serovar Typhimurium can confer resistance to spectinomycin","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2076":{"model_id":"2076","model_name":"Neisseria gonorrhoeae 16S rRNA mutation conferring resistance to spectinomycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"2700"},"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"7828":"C1198U"},"clinical":{"7828":"C1198U"}}},"model_sequences":{"sequence":{"4136":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"CP020418","fmin":"383737","fmax":"385288","strand":"+","sequence":"AGAGATTGAACATAAGAGTTTGATCCTGGCTCAGATTGAACGCTGGCGGCATGCTTTACACATGCAAGTCGGACGGCAGCACAGGGAAGCTTGCTTCTCGGGTGGCGAGTGGCGAACGGGTGAGTAACATATCGGAACGTACCGGGTAGCGGGGGATAACTGATCGAAAGATCAGCTAATACCGCATACGTCTTGAGAGGGAAAGCAGGGGACCTTCGGGCCTTGCGCTATCCGAGCGGCCGATATCTGATTAGCTGGTTGGCGGGGTAAAGGCCCACCAAGGCGACGATCAGTAGCGGGTCTGAGAGGATGATCCGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTGGACAATGGGCGCAAGCCTGATCCAGCCATGCCGCGTGTCTGAAGAAGGCCTTCGGGTTGTAAAGGACTTTTGTCAGGGAAGAAAAGGCCGTTGCCAATATCGGCGGCCGATGACGGTACCTGAAGAATAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGGGCGCAGACGGTTACTTAAGCAGGATGTGAAATCCCCGGGCTCAACCCGGGAACTGCGTTCTGAACTGGGTGACTCGAGTGTGTCAGAGGGAGGTGGAATTCCACGTGTAGCAGTGAAATGCGTAGAGATGTGGAGGAATACCGATGGCGAAGGCAGCCTCCTGGGATAACACTGACGTTCATGTCCGAAAGCGTGGGTAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCCTAAACGATGTCAATTAGCTGTTGGGCAACTTGATTGCTTGGTAGCGTAGCTAACGCGTGAAATTGACCGCCTGGGGAGTACGGTCGCAAGATTAAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGATGATGTGGATTAATTCGATGCAACGCGAAGAACCTTACCTGGTTTTGACATGTGCGGAATCCTCCGGAGACGGAGGAGTGCCTTCGGGAGCCGTAACACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCATTAGTTGCCATCATTCGGTTGGGCACTCTAATGAGACTGCCGGTGACAAGCCGGAGGAAGGTGGGGATGACGTCAAGTCCTCATGGCCCTTATGACCAGGGCTTCACACGTCATACAATGGTCGGTACAGAGGGTAGCCAAGCCGCGAGGCGGAGCCAATCTCACAAAACCGATCGTAGTCCGGATTGCACTCTGCAACTCGAGTGCATGAAGTCGGAATCGCTAGTAATCGCAGGTCAGCATACTGCGGTGAATACGTTCCCGGGTCTTGTACACACCGCCCGTCACACCATGGGAGTGGGGGATACCAGAAGTAGGTAGGGTAACCGCAAGGAGTCCGCTTACCACGGTATGCTTCATGACTGGGGTGAAGTCGTAACAAGGTAGCCGTAGGGGAACCTGCGGCTGGATCACCTCCTTTCTA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36806","NCBI_taxonomy_name":"Neisseria gonorrhoeae","NCBI_taxonomy_id":"485"}}}},"ARO_accession":"3003495","ARO_id":"40097","ARO_name":"Neisseria gonorrhoeae 16S rRNA mutation conferring resistance to spectinomycin","ARO_description":"Point mutations in the helix 34 region of 16S rRNA of Neisseria gonorrhoeae can confer resistance against spectinomycin","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2077":{"model_id":"2077","model_name":"Mycobacterium smegmatis 16S rRNA mutation in the rrsA gene conferring resistance to neomycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"4839":"U1389A"},"clinical":{"4839":"U1389A"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"4145":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NC_008596.1","fmin":"3823614","fmax":"3825143","strand":"-","sequence":"AGAAAGGAGGTGATCCAGCCGCACCTTCCGGTACGGCTACCTTGTTACGACTTCGTCCCAATCGCCGATCCCACCTTCGACGGCTCCCTCCACAAGGGTTAGGCCACCGGCTTCGGGTGTTACCGACTTTCATGACGTGACGGGCGGTGTGTACAAGGCCCGGGAACGTATTCACCGCAGCGTTGCTGATCTGCGATTACTAGCGACTCCGACTTCACGGGGTCGAGTTGCAGACCCCGATCCGAACTGAGACCGGCTTTGAAAGGATTCGCTCCACCTCACGGCATCGCAGCCCTTTGTACCGGCCATTGTAGCATGTGTGAAGCCCTGGACATAAGGGGCATGATGACTTGACGTCATCCCCACCTTCCTCCGAGTTGACCCCGGCAGTCTCTCACGAGTCCCCACCATAACGTGCTGGCAACATGAGACAAGGGTTGCGCTCGTTGCGGGACTTAACCCAACATCTCACGACACGAGCTGACGACAGCCATGCACCACCTGCACACAGGCCACAAGGGAACCGACATCTCTGCCGGCGTCCTGTGCATGTCAAACCCAGGTAAGGTTCTTCGCGTTGCATCGAATTAATCCACATGCTCCGCCGCTTGTGCGGGCCCCCGTCAATTCCTTTGAGTTTTAGCCTTGCGGCCGTACTCCCCAGGCGGGGTACTTAATGCGTTAGCTACGGCACGGATCCCAAGGAAGGAAACCCACACCTAGTACCCACCGTTTACGGCGTGGACTACCAGGGTATCTAATCCTGTTCGCTCCCCACGCTTTCGCTCCTCAGCGTCAGTTACTGCCCAGAGACCCGCCTTCGCCACCGGTGTTCCTCCTGATATCTGCGCATTCCACCGCTACACCAGGAATTCCAGTCTCCCCTGCAGTACTCTAGTCTGCCCGTATCGCCCGCACGCCCACAGTTAAGCTGTGAGTTTTCACGAACAACGCGACAAACCACCTACGAGCTCTTTACGCCCAGTAATTCCGGACAACGCTCGGACCCTACGTATTACCGCGGCTGCTGGCACGTAGTTGGCCGGTCCTTCTTCTGCACATACCGTCACTTGCGCTTCGTCTGTGCTGAAAGAGGTTTACAACCCGAAGGCCGTCATCCCTCACGCGGCGTCGCTGCATCAGGCTTGCGCCCATTGTGCAATATTCCCCACTGCTGCCTCCCGTAGGAGTCTGGGCCGTATCTCAGTCCCAGTGTGGCCGGTCACCCTCTCAGGCCGGCTACCCGTCGTCGCCTTGGTAGGCCATCACCCCACCAACAAGCTGATAGGCCGCGGGCCCATCCCACACCGCAAAAGCTTTCCCCTACCAGGCCATGCGACCAGCAGGGTGTATTCGGTATTAGACCCAGTTTCCCAGGCTTATCCCAAAGTGCAGGGCAGATCACCCACGTGTTACTCACCCGTTCGCCACTCGAGTACCCCCGAAAGGGCCTTTCCGTTCGACTTGCATGTGTTAAGCACGCCGCCAGCGTTCGTCCTGAGCCAGGATCAAACTCTCCAAACAAAAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36769","NCBI_taxonomy_name":"Mycobacterium smegmatis str. MC2 155","NCBI_taxonomy_id":"246196"}}}},"ARO_accession":"3003544","ARO_id":"40146","ARO_name":"Mycobacterium smegmatis 16S rRNA (rrsA) mutation conferring resistance to neomycin","ARO_description":"Point mutations in the helix 44 region of the 16S rRNA rrsA gene of Mycobacterium smegmatis can confer resistance to neomycin","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2109":{"model_id":"2109","model_name":"Mycobacterium tuberculosis gyrB mutant conferring resistance to fluoroquinolone","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3460":"V340L","3461":"D500H","3462":"N538D","3504":"T539N","3505":"T539P","3507":"E540D","3508":"N538K","3513":"E540V","3845":"N510D"},"clinical":{"3460":"V340L","3461":"D500H","3462":"N538D","3845":"N510D"},"experimental":{"3504":"T539N","3505":"T539P","3507":"E540D","3508":"N538K","3513":"E540V"}},"40330":{"param_type":"multiple resistance variants","param_description":"A set of nucleotide or amino acid substitutions that are each required to confer resistance to an antibiotic drug or drug class by co-mutation. Compare to single resistance variant, where only one substitution is required. Multiple resistance variants parameters are indicated on appropriate models using the following notation: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2],...,[wild-type n][position n][mutation n]. When each included substitution is detected in a protein sequence, resistance is conferred. This parameter is not currently included in any detection algorithms.","param_type_id":"40330","param_value":{"3463":"N538D,T546M","3464":"R485C,T539N","3506":"N538T,T546M","3512":"R485C,T546M"}},"40438":{"param_type":"co-dependent single resistance variant","param_description":"A model parameter to describe mutations in multiple genes or proteins where resistance is co-dependent on each. For example, the G247S SNP in M. tuberculosis gyrA does not confer resistance to fluoroquinolones. However, when the D500N SNP is also present in gyrB, resistance is conferred. In this case, gyrA G247S is co-dependent on gyrB D500N to confer resistance. This parameter is noted on relevant models with the following notation: [cvterm-id-gene-1],[gene-1-SNP]+[cvterm-id-gene-2],[gene-2-SNP]+ ... +[cvterm-id-gene-n],[gene-n-SNP] e.g. 39879,G247S+40052,D500N. This parameter is not currently included in any detection algorithms.","param_type_id":"40438","param_value":{"3610":"39879,G247S+40052,D500N","3846":"39879,A90V+40052,D472H"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1200"}},"model_sequences":{"sequence":{"3530":{"protein_sequence":{"accession":"CAA55486.1","sequence":"MGKNEARRSALAPDHGTVVCDPLRRLNRMHATPEESIRIVAAQKKKAQDEYGAASITILEGLEAVRKRPGMYIGSTGERGLHHLIWEVVDNAVDEAMAGYATTVNVVLLEDGGVEVADDGRGIPVATHASGIPTVDVVMTQLHAGGKFDSDAYAISGGLHGVGVSVVNALSTRLEVEIKRDGYEWSQVYEKSEPLGLKQGAPTKKTGSTVRFWADPAVFETTEYDFETVARRLQEMAFLNKGLTINLTDERVTQDEVVDEVVSDVAEAPKSASERAAESTAPHKVKSRTFHYPGGLVDFVKHINRTKNAIHSSIVDFSGKGTGHEVEIAMQWNAGYSESVHTFANTINTHEGGTHEEGFRSALTSVVNKYAKDRKLLKDKDPNLTGDDIREGLAAVISVKVSEPQFEGQTKTKLGNTEVKSFVQKVCNEQLTHWFEANPTDAKVVVNKAVSSAQARIAARKARELVRRKSATDIGGLPGKLADCRSTDPRKSELYVVEGDSAGGSAKSGRDSMFQAILPLRGKIINVEKARIDRVLKNTEVQAIITALGTGIHDEFDIGKLRYHKIVLMADADVDGQHISTLLLTLLFRFMRPLIENGHVFLAQPPLYKLKWQRSDPEFAYSDRERDGLLEAGLKAGKKINKEDGIQRYKGLGEMDAKELWETTMDPSVRVLRQVTLDDAAAADELFSILMGEDVDARRSFITRNAKDVRFLDV"},"dna_sequence":{"accession":"NC_009525.1","fmin":"5239","fmax":"7267","strand":"+","sequence":"GTGGCTGCCCAGAAAAAGAAGGCCCAAGACGAATACGGCGCTGCGTCTATCACCATTCTCGAAGGGCTGGAGGCCGTCCGCAAACGTCCCGGCATGTACATTGGCTCGACCGGTGAGCGCGGTTTACACCATCTCATTTGGGAGGTGGTCGACAACGCGGTCGACGAGGCGATGGCCGGTTATGCAACCACAGTGAACGTAGTGCTGCTTGAGGATGGCGGTGTCGAGGTCGCCGACGACGGCCGCGGCATTCCGGTCGCCACCCACGCCTCCGGCATACCGACCGTCGACGTGGTGATGACACAACTACATGCCGGCGGCAAGTTCGACTCGGACGCGTATGCGATATCTGGTGGTCTGCACGGCGTCGGCGTGTCGGTGGTTAACGCGCTATCCACCCGGCTCGAAGTCGAGATCAAGCGCGACGGGTACGAGTGGTCTCAGGTTTATGAGAAGTCGGAACCCCTGGGCCTCAAGCAAGGGGCGCCGACCAAGAAGACGGGGTCAACGGTGCGGTTCTGGGCCGACCCCGCTGTTTTCGAAACCACGGAATACGACTTCGAAACCGTCGCCCGCCGGCTGCAAGAGATGGCGTTCCTCAACAAGGGGCTGACCATCAACCTGACCGACGAGAGGGTGACCCAAGACGAGGTCGTCGACGAAGTGGTCAGCGACGTCGCCGAGGCGCCGAAGTCGGCAAGTGAACGCGCAGCCGAATCCACTGCACCGCACAAAGTTAAGAGCCGCACCTTTCACTATCCGGGTGGCCTGGTGGACTTCGTGAAACACATCAACCGCACCAAGAACGCGATTCATAGCAGCATCGTGGACTTTTCCGGCAAGGGCACCGGGCACGAGGTGGAGATCGCGATGCAATGGAACGCCGGGTATTCGGAGTCGGTGCACACCTTCGCCAACACCATCAACACCCACGAGGGCGGCACCCACGAAGAGGGCTTCCGCAGCGCGCTGACGTCGGTGGTGAACAAGTACGCCAAGGACCGCAAGCTACTGAAGGACAAGGACCCCAACCTCACCGGTGACGATATCCGGGAAGGCCTGGCCGCTGTGATCTCGGTGAAGGTCAGCGAACCGCAGTTCGAGGGCCAGACCAAGACCAAGTTGGGCAACACCGAGGTCAAATCGTTTGTGCAGAAGGTCTGTAACGAACAGCTGACCCACTGGTTTGAAGCCAACCCCACCGACGCGAAAGTCGTTGTGAACAAGGCTGTGTCCTCGGCGCAAGCCCGTATCGCGGCACGTAAGGCACGAGAGTTGGTGCGGCGTAAGAGCGCCACCGACATCGGTGGATTGCCCGGCAAGCTGGCCGATTGCCGTTCCACGGATCCGCGCAAGTCCGAACTGTATGTCGTAGAAGGTGACTCGGCCGGCGGTTCTGCAAAAAGCGGTCGCGATTCGATGTTCCAGGCGATACTTCCGCTGCGCGGCAAGATCATCAATGTGGAGAAAGCGCGCATCGACCGGGTGCTAAAGAACACCGAAGTTCAGGCGATCATCACGGCGCTGGGCACCGGGATCCACGACGAGTTCGATATCGGCAAGCTGCGCTACCACAAGATCGTGCTGATGGCCGACGCCGATGTTGACGGCCAACATATTTCCACGCTGTTGTTGACGTTGTTGTTCCGGTTCATGCGGCCGCTCATCGAGAACGGGCATGTGTTTTTGGCACAACCGCCGCTGTACAAACTCAAGTGGCAGCGCAGTGACCCGGAATTCGCATACTCCGACCGCGAGCGCGACGGTCTGCTGGAGGCGGGGCTGAAGGCCGGGAAGAAGATCAACAAGGAAGACGGCATTCAGCGGTACAAGGGTCTAGGTGAAATGGACGCTAAGGAGTTGTGGGAGACCACCATGGATCCCTCGGTTCGTGTGTTGCGTCAAGTGACGCTGGACGACGCCGCCGCCGCCGACGAGTTGTTCTCCATCCTGATGGGCGAGGACGTCGACGCGCGGCGCAGCTTTATCACCCGCAACGCCAAGGATGTTCGGTTCCTGGATGTCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40415","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Ra","NCBI_taxonomy_id":"419947"}}}},"ARO_accession":"3003459","ARO_id":"40052","ARO_name":"Mycobacterium tuberculosis gyrB mutant conferring resistance to fluoroquinolone","ARO_description":"Point mutation in Mycobacterium tuberculosis gyrB resulting in fluoroquinolone resistance","ARO_category":{"37244":{"category_aro_accession":"3000864","category_aro_cvterm_id":"37244","category_aro_name":"fluoroquinolone resistant gyrB","category_aro_description":"Point mutations in DNA gyrase subunit B (gyrB) observed in Mycobacterium tuberculosis can result in resistance to fluoroquinolones.","category_aro_class_name":"AMR Gene Family"},"35942":{"category_aro_accession":"0000023","category_aro_cvterm_id":"35942","category_aro_name":"enoxacin","category_aro_description":"Enoxacin belongs to a group called fluoroquinolones. Its mode of action depends upon blocking bacterial DNA replication by binding itself to DNA gyrase and causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36271":{"category_aro_accession":"3000132","category_aro_cvterm_id":"36271","category_aro_name":"clorobiocin","category_aro_description":"Clorobiocin is an aminocoumarin antibiotic produced by Streptomyces roseochromogenes, and binds DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36289":{"category_aro_accession":"3000150","category_aro_cvterm_id":"36289","category_aro_name":"coumermycin A1","category_aro_description":"Coumermycin A1 is an antibiotic produced by Streptomyces rishiriensis, and binds DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37004":{"category_aro_accession":"3000660","category_aro_cvterm_id":"37004","category_aro_name":"lomefloxacin","category_aro_description":"Lomefloxacin is a difluoropiperazinyl quinolone, sharing similar activities with other fluoroquinolones. It is used to treat urinary tract infections. Relative to other fluoroquinolones, it has a longer half life and has higher serum concentrations.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"37008":{"category_aro_accession":"3000664","category_aro_cvterm_id":"37008","category_aro_name":"trovafloxacin","category_aro_description":"Trovafloxacin is a trifluoroquinalone with a broad spectrum of activity that acts by inhibiting the uncoiling of supercoiled DNA. While potent against many Gram-positive and Gram-negative bacteria, it is less active against pseudomonads and Cl. difficile. It is usually taken as the prodrug trovafloxacin mesylate or alatrofloxacin mesylate for oral or intravenous administration, respectively.","category_aro_class_name":"Antibiotic"},"37009":{"category_aro_accession":"3000665","category_aro_cvterm_id":"37009","category_aro_name":"grepafloxacin","category_aro_description":"Grepafloxacin is a broad-spectrum antibacterial quinoline. It is no longer taken due to its high toxicity.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"37142":{"category_aro_accession":"3000762","category_aro_cvterm_id":"37142","category_aro_name":"pefloxacin","category_aro_description":"Pefloxacin is structurally and functionally similar to norfloxacin. It is poorly active against mycobacteria, while anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"40937":{"category_aro_accession":"3004010","category_aro_cvterm_id":"40937","category_aro_name":"cinoxacin","category_aro_description":"Cinoxacin is a fluoroquinolone antibiotic primarily used for the treatment of urinary tract infections in adults. Cinoxacin binds to DNA gyrase, resulting in double-stranded DNA breaks and cell death.","category_aro_class_name":"Antibiotic"},"40938":{"category_aro_accession":"3004011","category_aro_cvterm_id":"40938","category_aro_name":"clinafloxacin","category_aro_description":"Clinafloxacin is a fluoroquinolone antibiotic and gyrase (DNA topoisomerase II) inhibitor. It binds to DNA gyrase and disrupts replication by causing double-stranded DNA breaks, resulting in cell death.","category_aro_class_name":"Antibiotic"},"40939":{"category_aro_accession":"3004012","category_aro_cvterm_id":"40939","category_aro_name":"Clofazimine","category_aro_description":"Clofazimine is a fluoroquinolone-class phenazine dye used for the treatment of leprosy. Clofazimine binds to DNA and disrupts bacterial DNA gyrase, thereby causing double-stranded DNA breaks, and subsequent cell death.","category_aro_class_name":"Antibiotic"},"40940":{"category_aro_accession":"3004013","category_aro_cvterm_id":"40940","category_aro_name":"fleroxacin","category_aro_description":"Fleroxacin is a broad spectrum fluoroquinolone antibiotic that inhibits the DNA supercoiling activity of bacterial DNA gyrase, resulting in double-stranded DNA breaks and subsequent cell death.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2124":{"model_id":"2124","model_name":"Clostridium difficile EF-Tu mutants conferring resistance to elfamycin","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3422":"G261E"},"clinical":{"3422":"G261E"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3358":{"protein_sequence":{"accession":"WP_009887863.1","sequence":"MAKAKYERTKPHVNIGTIGHVDHGKTTLTAAITKTLYDRYQLGEAVDFANIDKAPEERERGITISTAHVEYETPNRHYAHVDCPGHADYVKNMITGAAQMDGAILVCSATDGPMPQTREHILLSRQVGVPYIVVFLNKCDMVDDEELLELVEMEVRDLLTEYDFPGDDTPIVRGSALMALEDPKSEWGDKIVELFEQIDEYIPAPERDTDKPFLMPVEDVFSITGRGTVATGRVERGVLKVQDEVELVGLTEAPRKVVVTGVEMFRKLLDQAQAGDNIGALLRGVQRNEIERGQVLAKTGSVKAHTKFTAEVYVLKKEEGGRHTPFFDGYRPQFYFRTTDVTGACKLPEGIEMVMPGDNVTMEVDLINSIVVEEGLRFSIREGGRTVASGVVATIIE"},"dna_sequence":{"accession":"NC_017174","fmin":"109609","fmax":"110803","strand":"+","sequence":"ATGGCTAAAGCTAAATACGAAAGAACAAAACCTCATGTTAATATAGGGACAATAGGACACGTAGACCACGGTAAAACTACATTAACAGCAGCAATAACAAAAACATTATATGACAGATATCAATTAGGAGAAGCAGTAGATTTCGCAAACATAGATAAAGCTCCAGAAGAAAGAGAAAGAGGAATCACAATATCAACAGCACACGTTGAGTATGAAACACCAAATAGACACTATGCACACGTTGACTGCCCAGGGCATGCTGACTACGTTAAGAACATGATAACAGGAGCAGCACAAATGGACGGAGCAATATTAGTTTGTTCAGCAACAGATGGACCAATGCCACAAACAAGAGAGCATATACTATTATCAAGACAAGTTGGAGTACCATATATAGTAGTATTCTTAAATAAATGTGACATGGTAGATGATGAAGAGTTATTAGAGTTAGTAGAGATGGAAGTAAGAGATTTATTAACAGAGTATGATTTCCCAGGAGATGACACTCCAATAGTAAGAGGATCAGCGTTAATGGCATTAGAAGATCCAAAGAGTGAGTGGGGAGATAAGATAGTAGAATTATTCGAGCAAATAGATGAATATATACCAGCACCAGAGAGAGATACAGATAAGCCATTCTTAATGCCAGTAGAGGACGTATTCTCAATCACAGGAAGAGGAACAGTTGCAACAGGAAGAGTGGAAAGAGGAGTACTAAAAGTACAAGACGAAGTAGAATTAGTAGGATTAACAGAAGCACCAAGAAAAGTAGTAGTAACAGGAGTAGAGATGTTCAGAAAATTATTAGACCAAGCACAAGCAGGGGATAATATAGGAGCATTATTAAGAGGAGTACAAAGAAACGAGATAGAAAGAGGACAAGTACTAGCAAAGACTGGATCAGTAAAGGCACACACAAAGTTTACAGCAGAAGTATATGTACTTAAAAAAGAAGAAGGTGGAAGACATACACCATTCTTTGATGGATATAGACCACAATTTTACTTCAGAACAACAGACGTAACAGGAGCTTGTAAGTTACCAGAAGGAATAGAGATGGTAATGCCTGGAGATAACGTAACAATGGAAGTAGACTTAATAAACTCAATAGTTGTAGAAGAGGGATTAAGATTCTCAATAAGAGAAGGTGGAAGAACAGTAGCTTCAGGAGTTGTTGCTACAATAATAGAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36807","NCBI_taxonomy_name":"Clostridium difficile","NCBI_taxonomy_id":"1496"}}}},"ARO_accession":"3003357","ARO_id":"39941","ARO_name":"Clostridium difficile EF-Tu mutants conferring resistance to elfamycin","ARO_description":"Sequence variants of Clostridium difficile elongation factor Tu that confer resistance to elfamycin antibiotics.","ARO_category":{"37711":{"category_aro_accession":"3001312","category_aro_cvterm_id":"37711","category_aro_name":"elfamycin resistant EF-Tu","category_aro_description":"Sequence variants of elongation factor Tu that confer resistance to elfamycin antibiotics.","category_aro_class_name":"AMR Gene Family"},"36725":{"category_aro_accession":"3000586","category_aro_cvterm_id":"36725","category_aro_name":"pulvomycin","category_aro_description":"Pulvomycin is a polyketide antibiotic that binds elongation factor Tu (EF-Tu) to inhibit protein biosynthesis by preventing the formation of the ternary complex (EF-Tu*GTP*aa-tRNA). Phenotypically, it was shown that pulvomycin sensitivity is dominant over resistance.","category_aro_class_name":"Antibiotic"},"37636":{"category_aro_accession":"3001237","category_aro_cvterm_id":"37636","category_aro_name":"GE2270A","category_aro_description":"GE2270A is the model molecule of cyclic thiazolyl peptide elfamycins. GE2270A is produced by Planobispora rosea. Biosynthesis of the molecule has been shown to originate as a ribosomally synthesized peptide that undergoes significant post-translational modification. Clinical use of cyclic thiazolyl peptides is hindered by their low water solubility and bioavailability.","category_aro_class_name":"Antibiotic"},"37641":{"category_aro_accession":"3001242","category_aro_cvterm_id":"37641","category_aro_name":"enacyloxin IIa","category_aro_description":"Enacyloxin IIa is structurally distinct but acts in a similar mechanism to kirromycin-like elfamycins. It prohibits the transfer of the amino acid at the A site to the elongating peptide chain. It is most likely that the mechanism of action is that EF-Tu*GDP is locked in the EF-Tu*GTP form, and EF-Tu*GDP*aa-tRNA is immobilized on the ribosome. It is an open question whether enacyloxin IIa actually belongs to the kirromycin-like group of elfamycins due to their high similarity.","category_aro_class_name":"Antibiotic"},"39998":{"category_aro_accession":"3003414","category_aro_cvterm_id":"39998","category_aro_name":"LFF571","category_aro_description":"LFF571 is a novel semi-synthetic thiopeptide antibiotic derived from GE2270. It has been shown to possess potent in vitro and in vivo activity against Gram-positive bacteria. It is hypothesized that it a translation inhibitor leading to cell death.","category_aro_class_name":"Antibiotic"},"37618":{"category_aro_accession":"3001219","category_aro_cvterm_id":"37618","category_aro_name":"elfamycin antibiotic","category_aro_description":"Elfamycins are molecules that inhibit bacterial elongation factor Tu (EF-Tu), a key protein which brings aminoacyl-tRNA (aa-tRNA) to the ribosome during protein synthesis. Elfamycins defined by their target (EF-Tu), rather than a conserved chemical backbone. Elfamycins follow two mechanisms to disrupt protein synthesis: 1. kirromycins and enacyloxin fix EF-Tu in the GTP bound conformation and lock EF-Tu onto the ribosome, and 2. pulvomycin and GE2270 cover the binding site of aa-tRNA disallowing EF-Tu from being charged with aa-tRNA. All elfamycins cause increased the affinity of EF-Tu for GTP.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2137":{"model_id":"2137","model_name":"Escherichia coli EF-Tu mutants conferring resistance to kirromycin","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3313":"Y161C","2947":"Q125K","3302":"G317D","3303":"Q125R","3305":"A376V","3306":"Y161D","3307":"Y161N","3308":"L121Q","3310":"A376S","3311":"Q125E","3312":"E379K","3410":"Q330H","3411":"A376T"},"experimental":{"3313":"Y161C","3302":"G317D","3303":"Q125R","3305":"A376V","3306":"Y161D","3307":"Y161N","3308":"L121Q","3310":"A376S","3311":"Q125E","3312":"E379K","3410":"Q330H","3411":"A376T"},"clinical":{"2947":"Q125K"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3531":{"protein_sequence":{"accession":"AAA50993.1","sequence":"MSKEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDNAPEEKARGITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALEGDAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVGEEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIKPHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMVVTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLG"},"dna_sequence":{"accession":"AH002539.2","fmin":"1760","fmax":"2945","strand":"+","sequence":"GTGTCTAAAGAAAAATTTGAACGTACAAAACCGCACGTTAACGTTGGTACTATCGGCCACGTTGACCACGGTAAAACTACTCTGACCGCTGCAATCACCACCGTACTGGCTAAAACCTACGGCGGTGCTGCTCGTGCATTCGACCAGATCGATAACGCGCCGGAAGAAAAAGCTCGTGGTATCACCATCAACACTTCTCACGTTGAATACGACACCCCGACCCGTCACTACGCACACGTAGACTGCCCGGGGCACGCCGACTATGTTAAAAACATGATCACCGGTGCTGCTCAGATGGACGGCGCGATCCTGGTAGTTGCTGCGACTGACGGCCCGATGCCGCAGACTCGTGAGCACATCCTGCTGGGTCGTCAGGTAGGCGTTCCGTACATCATCGTGTTCCTGAACAAATGCGACATGGTTGATGACGAAGAGCTGCTGGAACTGGTTGAAATGGAAGTTCGTGAACTTCTGTCTCAGTACGACTTCCCGGGCGACGACACTCCGATCGTTCGTGGTTCTGCTCTGAAAGCGCTGGAAGGCGACGCAGAGTGGGAAGCGAAAATCCTGGAACTGGCTGGCTTCCTGGATTCTTATATTCCGGAACCAGAGCGTGCGATTGACAAGCCGTTCCTGCTGCCGATCGAAGACGTATTCTCCATCTCCGGTCGTGGTACCGTTGTTACCGGTCGTGTAGAACGCGGTATCATCAAAGTTGGTGAAGAAGTTGAAATCGTTGGTATCAAAGAGACTCAGAAGTCTACCTGTACTGGCGTTGAAATGTTCCGCAAACTGCTGGACGAAGGCCGTGCTGGTGAGAACGTAGGTGTTCTGCTGCGTGGTATCAAACGTGAAGAAATCGAACGTGGTCAGGTACTGGCTAAGCCGGGCACCATCAAGCCGCACACCAAGTTCGAATCTGAAGTGTACATTCTGTCCAAAGATGAAGGCGGCCGTCATACTCCGTTCTTCAAAGGCTACCGTCCGCAGTTCTACTTCCGTACTACTGACGTGACTGGTACCATCGAACTGCCGGAAGGCGTAGAGATGGTAATGCCGGGCGACAACATCAAAATGGTTGTTACCCTGATCCACCCGATCGCGATGGACGACGGTCTGCGTTTCGCAATCCGTGAAGGCGGCCGTACCGTTGGCGCGGGCGTTGTTGCTAAAGTTCTGGGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3003368","ARO_id":"39952","ARO_name":"Escherichia coli EF-Tu mutants conferring resistance to kirromycin","ARO_description":"Sequence variants of Escherichia coli elongation factor Tu that confer resistance to kirromycin","ARO_category":{"37711":{"category_aro_accession":"3001312","category_aro_cvterm_id":"37711","category_aro_name":"elfamycin resistant EF-Tu","category_aro_description":"Sequence variants of elongation factor Tu that confer resistance to elfamycin antibiotics.","category_aro_class_name":"AMR Gene Family"},"36725":{"category_aro_accession":"3000586","category_aro_cvterm_id":"36725","category_aro_name":"pulvomycin","category_aro_description":"Pulvomycin is a polyketide antibiotic that binds elongation factor Tu (EF-Tu) to inhibit protein biosynthesis by preventing the formation of the ternary complex (EF-Tu*GTP*aa-tRNA). Phenotypically, it was shown that pulvomycin sensitivity is dominant over resistance.","category_aro_class_name":"Antibiotic"},"37636":{"category_aro_accession":"3001237","category_aro_cvterm_id":"37636","category_aro_name":"GE2270A","category_aro_description":"GE2270A is the model molecule of cyclic thiazolyl peptide elfamycins. GE2270A is produced by Planobispora rosea. Biosynthesis of the molecule has been shown to originate as a ribosomally synthesized peptide that undergoes significant post-translational modification. Clinical use of cyclic thiazolyl peptides is hindered by their low water solubility and bioavailability.","category_aro_class_name":"Antibiotic"},"37641":{"category_aro_accession":"3001242","category_aro_cvterm_id":"37641","category_aro_name":"enacyloxin IIa","category_aro_description":"Enacyloxin IIa is structurally distinct but acts in a similar mechanism to kirromycin-like elfamycins. It prohibits the transfer of the amino acid at the A site to the elongating peptide chain. It is most likely that the mechanism of action is that EF-Tu*GDP is locked in the EF-Tu*GTP form, and EF-Tu*GDP*aa-tRNA is immobilized on the ribosome. It is an open question whether enacyloxin IIa actually belongs to the kirromycin-like group of elfamycins due to their high similarity.","category_aro_class_name":"Antibiotic"},"39998":{"category_aro_accession":"3003414","category_aro_cvterm_id":"39998","category_aro_name":"LFF571","category_aro_description":"LFF571 is a novel semi-synthetic thiopeptide antibiotic derived from GE2270. It has been shown to possess potent in vitro and in vivo activity against Gram-positive bacteria. It is hypothesized that it a translation inhibitor leading to cell death.","category_aro_class_name":"Antibiotic"},"37618":{"category_aro_accession":"3001219","category_aro_cvterm_id":"37618","category_aro_name":"elfamycin antibiotic","category_aro_description":"Elfamycins are molecules that inhibit bacterial elongation factor Tu (EF-Tu), a key protein which brings aminoacyl-tRNA (aa-tRNA) to the ribosome during protein synthesis. Elfamycins defined by their target (EF-Tu), rather than a conserved chemical backbone. Elfamycins follow two mechanisms to disrupt protein synthesis: 1. kirromycins and enacyloxin fix EF-Tu in the GTP bound conformation and lock EF-Tu onto the ribosome, and 2. pulvomycin and GE2270 cover the binding site of aa-tRNA disallowing EF-Tu from being charged with aa-tRNA. All elfamycins cause increased the affinity of EF-Tu for GTP.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2144":{"model_id":"2144","model_name":"Mycobacterium bovis embB mutations conferring resistance to ethambutol","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2917":"F1012S","2950":"T610K","2969":"Q998R"},"clinical":{"2917":"F1012S","2950":"T610K","2969":"Q998R"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"2000"}},"model_sequences":{"sequence":{"3355":{"protein_sequence":{"accession":"CDO45096.1","sequence":"MTQCASRRKSTPSRAILGAFASARGTRWVATIAGLIGFVLSVATPLLPVVQTTAMLDWPQRGQLGSVTAPLISLTPVDFTATVPCDVVRAMPPAGGVVLGTAPKQGKDANLQALFVVVSAQRVDVTDRNVVILSVPREQVTSPQCQRIEVTSTHAGTFANFVGLKDPSGAPLRSGFPDPNLRPQIVGVFTDLTGPAPPGLAVSATIDTRFSTRPTTLKLLAIIGAIVATVVALIALWRLDQLDGRGSIAQLLLRPFRPASSPGGMRRLIPASWRTFTLTDAVVIFGFLLWHVIGANSSDDGYILGMARVADHAGYMSNYFRWFGSPEDPFGWYYNLLALMTHVSDASLWMRLPDLAAGLVCWLLLSREVLPRLGPAVAASKPAYWAAAMVLLTAWMPFNNGLRPEGIIALGSLVTYVLIERSMRYSRLTPAALAVVTAAFTLGVQPTGLIAVAALVAGGRPMLRILVRRHRLVGTLPLVSPMLAAGTVILTVVFADQTLSTVLEATRVRAKIGPSQAWYTENLRYYYLILPTVDGSLSRRFGFLITALCLFTAVFIMLRRKRIPSVARGPAWRLMGVIFGTMFFLMFTPTKWVHHFGLFAAVGAAMAALTTVLVSPSVLRWSRNRMAFLAALFFLLALCWATTNGWWYVSSYGVPFNSAMPKIDGITVSTIFFALFAIAAGYAAWLHFAPRGAGEGRLIRALTTAPVPIVAGFMAAVFVASMVAGIVRQYPTYSNGWSNVRAFVGGCGLADDVLVEPDTNAGFMKPLDGDSGSWGPLGPLGGVNPVGFTPNGVPEHTVAEAIVMKPNQPGTDYDWDAPTKLTSPGINGSTVPLPYGLDPARVPLAGTYTTGAQQQSTLVSAWYLLPKPDDGHPLVVVTAAGKIAGNSVLHGYTPGQTVVLEYAMPGPGALVPAGRMVPDDLYGEQPKAWRNLRFARAKMPADAVAVRVVAEDLSLTPEDWIAVTPPRVPDLRSLQEYVGSTQPVLLDWAVGLAFPCQQPMLHANGIAEIPKFRITPDYSAKKLDTDTWEDGTNGGLLGITDLLLRAHVMATYLSRDWARDWGSLRKFDTLVDAPPAQLELGTATRSGLWSPGKIRIGP"},"dna_sequence":{"accession":"BX248333","fmin":"4182808","fmax":"4186105","strand":"+","sequence":"ATGACACAGTGCGCGAGCAGACGCAAAAGCACCCCAAGTCGGGCGATTTTGGGGGCTTTTGCGTCTGCTCGCGGGACGCGCTGGGTGGCCACCATCGCCGGGCTGATTGGCTTTGTGTTGTCGGTGGCGACGCCGCTGCTGCCCGTCGTGCAGACCACCGCGATGCTCGACTGGCCACAGCGGGGGCAACTGGGCAGCGTGACCGCCCCGCTGATCTCGCTGACGCCGGTCGACTTTACCGCCACCGTGCCGTGCGACGTGGTGCGCGCCATGCCACCCGCGGGCGGGGTGGTGCTGGGCACCGCACCCAAGCAAGGCAAGGACGCCAATTTGCAGGCGTTGTTCGTCGTTGTCAGCGCCCAGCGCGTGGACGTCACCGACCGCAACGTGGTGATCTTGTCCGTGCCGCGCGAGCAGGTGACGTCCCCGCAGTGTCAACGCATCGAGGTCACCTCTACCCACGCCGGCACCTTCGCCAACTTCGTCGGGCTCAAGGACCCGTCGGGCGCGCCGCTGCGCAGCGGCTTCCCCGACCCCAACCTGCGCCCGCAGATTGTCGGGGTGTTCACCGACCTGACCGGGCCCGCGCCGCCCGGGCTGGCGGTCTCGGCGACCATCGACACCCGGTTCTCCACCCGGCCGACCACGCTGAAACTGCTGGCGATCATCGGGGCGATCGTGGCCACCGTCGTCGCACTGATCGCGTTGTGGCGCCTGGACCAGTTGGACGGGCGGGGCTCAATTGCCCAGCTCCTCCTCAGGCCGTTCCGGCCTGCATCGTCGCCGGGCGGCATGCGCCGGCTGATTCCGGCAAGCTGGCGCACCTTCACCCTGACCGACGCCGTGGTGATATTCGGCTTCCTGCTCTGGCATGTCATCGGCGCGAATTCGTCGGACGACGGCTACATCCTGGGCATGGCCCGAGTCGCCGACCACGCCGGCTACATGTCCAACTATTTCCGCTGGTTCGGCAGCCCGGAGGATCCCTTCGGCTGGTATTACAACCTGCTGGCGCTGATGACCCATGTCAGCGACGCCAGTCTGTGGATGCGCCTGCCAGACCTGGCCGCCGGGCTAGTGTGCTGGCTGCTGCTGTCGCGTGAGGTGCTGCCCCGCCTCGGGCCGGCGGTGGCGGCCAGCAAACCCGCCTACTGGGCGGCGGCCATGGTCTTGCTGACCGCGTGGATGCCGTTCAACAACGGCCTGCGGCCGGAGGGCATCATCGCGCTCGGCTCGCTGGTCACCTATGTGCTGATCGAGCGGTCCATGCGGTACAGCCGGCTCACACCGGCGGCGCTGGCCGTCGTTACCGCCGCATTCACACTGGGTGTGCAGCCCACCGGCCTGATCGCGGTGGCCGCGCTGGTGGCCGGCGGCCGCCCGATGCTGCGGATCTTGGTGCGCCGTCATCGCCTGGTCGGCACGTTGCCGTTGGTGTCGCCGATGCTGGCCGCCGGCACCGTCATCCTGACCGTGGTGTTCGCCGACCAGACCCTGTCAACGGTGTTGGAAGCCACCAGGGTTCGCGCCAAAATCGGGCCGAGCCAGGCGTGGTATACCGAGAACCTGCGTTACTACTACCTCATCCTGCCCACCGTCGACGGTTCGCTGTCGCGGCGCTTCGGCTTTTTGATCACCGCGCTATGCCTGTTCACCGCGGTGTTCATCATGTTGCGGCGCAAGCGAATTCCCAGCGTGGCCCGCGGACCGGCGTGGCGGCTGATGGGCGTCATCTTCGGCACCATGTTCTTCCTGATGTTCACGCCCACCAAGTGGGTGCACCACTTCGGGCTGTTCGCCGCCGTAGGGGCGGCGATGGCCGCGCTGACGACGGTGTTGGTATCCCCATCGGTGCTGCGCTGGTCGCGCAACCGGATGGCGTTCCTGGCGGCGTTATTCTTCCTGCTGGCGTTGTGTTGGGCCACCACCAACGGCTGGTGGTATGTCTCCAGCTACGGTGTGCCGTTCAACAGCGCGATGCCGAAGATCGACGGGATCACAGTCAGCACAATCTTTTTCGCCCTGTTTGCGATCGCCGCCGGCTATGCGGCCTGGCTGCACTTCGCGCCCCGCGGCGCCGGCGAAGGGCGGCTGATCCGCGCGCTGACGACAGCCCCGGTACCGATCGTGGCCGGTTTCATGGCGGCGGTGTTCGTCGCGTCCATGGTGGCCGGGATCGTGCGACAGTACCCGACCTACTCCAACGGCTGGTCCAACGTGCGGGCGTTTGTCGGCGGCTGCGGACTGGCCGACGACGTACTCGTCGAGCCTGATACCAATGCGGGTTTCATGAAGCCGCTGGACGGCGATTCGGGTTCTTGGGGCCCCTTGGGCCCGCTGGGTGGAGTCAACCCGGTCGGCTTCACGCCCAACGGCGTACCGGAACACACGGTGGCCGAGGCGATCGTGATGAAACCCAACCAGCCCGGCACCGACTACGACTGGGATGCGCCGACCAAGCTGACGAGTCCTGGCATCAATGGTTCTACGGTGCCGCTGCCCTATGGGCTCGATCCCGCCCGGGTACCGTTGGCAGGCACCTACACCACCGGCGCACAGCAACAGAGCACACTCGTCTCGGCGTGGTATCTCCTGCCTAAGCCGGACGACGGGCATCCGCTGGTCGTGGTGACCGCCGCGGGCAAGATCGCCGGCAACAGCGTGCTGCACGGGTACACCCCCGGGCAGACTGTGGTGCTCGAATACGCCATGCCGGGACCCGGAGCGCTGGTACCCGCCGGGCGGATGGTGCCCGACGACCTATACGGAGAGCAGCCCAAGGCGTGGCGCAACCTGCGCTTCGCCCGAGCAAAGATGCCCGCCGATGCCGTCGCGGTCCGGGTGGTGGCCGAGGATCTGTCGCTGACACCGGAGGACTGGATCGCGGTGACCCCGCCGCGGGTACCGGACCTGCGCTCACTGCAGGAATATGTGGGCTCGACGCAGCCGGTGCTGCTGGACTGGGCGGTCGGTTTGGCCTTCCCGTGCCAGCAGCCGATGCTGCACGCCAATGGCATCGCCGAAATCCCGAAGTTCCGCATCACACCGGACTACTCGGCTAAGAAGCTGGACACCGACACGTGGGAAGACGGCACTAACGGCGGCCTGCTCGGGATCACCGACCTGTTGCTGCGGGCCCACGTCATGGCCACCTACCTGTCCCGCGACTGGGCCCGCGATTGGGGTTCCCTGCGCAAGTTCGACACCCTGGTCGATGCCCCTCCCGCCCAGCTCGAGTTGGGCACCGCGACCCGCAGCGGCCTGTGGTCACCGGGCAAGATCCGAATTGGTCCATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40081","NCBI_taxonomy_name":"Mycobacterium bovis AF2122\/97","NCBI_taxonomy_id":"233413"}}}},"ARO_accession":"3003325","ARO_id":"39909","ARO_name":"Mycobacterium bovis embB mutations conferring resistance to ethambutol","ARO_description":"Point mutations that occur within Mycobacterium bovis embB gene resulting in resistance to ethambutol","ARO_category":{"39310":{"category_aro_accession":"3002876","category_aro_cvterm_id":"39310","category_aro_name":"ethambutol resistant arabinosyltransferase","category_aro_description":"Arabinosyl transferases allow for the polymerization of arabinose to form arabinan. Arabinan is required for formation of mycobacterial cell walls and arabinosyltransferases are targets of the drug ethambutol. Mutations in these genes can confer resistance to ethambutol.","category_aro_class_name":"AMR Gene Family"},"36636":{"category_aro_accession":"3000497","category_aro_cvterm_id":"36636","category_aro_name":"ethambutol","category_aro_description":"Ethambutol is an antimycobacterial drug prescribed to treat tuberculosis. It is usually given in combination with other tuberculosis drugs, such as isoniazid, rifampicin, and pyrazinamide. Ethambutol inhibits arabinosyl biosynthesis, disrupting mycobacterial cell wall formation.","category_aro_class_name":"Antibiotic"},"36666":{"category_aro_accession":"3000527","category_aro_cvterm_id":"36666","category_aro_name":"polyamine antibiotic","category_aro_description":"Polyamine antibiotics are organic compounds having two or more primary amino groups.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2148":{"model_id":"2148","model_name":"Ureaplasma urealyticum  gyrB conferring resistance to fluoroquinolone","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3048":"P462S","4638":"E502Q"},"clinical":{"3048":"P462S","4638":"E502Q"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1200"}},"model_sequences":{"sequence":{"3354":{"protein_sequence":{"accession":"WP_004025678.1","sequence":"MNDSNKENKYTAESIKVLEGLEAVRKRPGMYIGSTQSEGLHHMIWEIVDNSIDEAMGGFATVVKVIIKKDGVIRVEDDGRGIPVGIHEKTGLSGVETVLTVLHAGGKFDNDSYKVSGGLHGVGASVVNALSKNFKVWVNKNYVQHYVEFINGGHAIEPLKIINDKDIKEKGTTIEFIPDFEIMEENEWDELKIMARLKQLAYLNKGVNIEFESEMTNRKEKWHYEGGLKEYIADLNAEKEPLFDAIVYGEEEKEVKVPGHNDQTYNIKCEVAFQYNNSYNNSTHSFCNNINTTEGGTHEEGFKLAITRLLNKYAIDKKYLKDTDDKITKEDVSEGLTAIISIKHPNPQYEGQTKKKLGNSEVRPYVNEITSIIFEKFLNENPEESKKIVAKVMQAAEARRRSHEAREATRRKSPFESNSLPGKLADCSNRDSSVTEIYIVEGDSAGGSAKTGREREFQAILPLRGKIINVEKAKIDKIFANEEIQNMITAFGAGIGPEFNIEKLRYSKIIIMTDADVDGSHIRILLLTFFYRYMLPLIQNGNVYIAQPPLYKVSYGKTIKYAYSDQELEKIKSTLLNTKYNIQRYKGLGEMNPDQLWETTMDPKNRLLLKVNIEDAAIADKTFSLLMGDDVTPRKEFIEKNAKYVKNIDA"},"dna_sequence":{"accession":"NC_011374","fmin":"104283","fmax":"106236","strand":"+","sequence":"ATGAACGATTCTAATAAAGAAAATAAATACACCGCTGAAAGTATTAAAGTACTTGAAGGATTAGAAGCGGTACGAAAACGTCCTGGTATGTATATTGGTTCAACTCAATCAGAAGGTTTGCACCATATGATTTGAGAAATTGTTGATAACTCAATCGATGAAGCAATGGGTGGTTTTGCAACAGTTGTTAAAGTTATTATAAAAAAAGATGGAGTAATACGAGTTGAAGATGATGGACGTGGAATTCCAGTTGGAATTCATGAAAAAACTGGTTTATCAGGTGTTGAAACTGTATTAACTGTGTTGCATGCTGGAGGTAAATTTGATAATGATAGTTACAAAGTCTCTGGTGGATTACATGGTGTTGGTGCATCTGTTGTTAATGCTTTAAGTAAAAACTTTAAAGTTTGAGTTAATAAAAATTATGTTCAACATTACGTTGAATTTATTAATGGTGGACATGCTATTGAACCATTAAAAATAATTAACGACAAAGATATCAAAGAAAAAGGAACAACAATTGAGTTTATTCCTGACTTTGAAATCATGGAAGAAAATGAATGAGATGAGCTAAAAATAATGGCTCGTTTAAAACAATTAGCTTACCTTAATAAAGGTGTTAATATCGAATTTGAATCAGAAATGACTAATCGTAAAGAAAAATGACATTACGAAGGTGGTTTAAAAGAGTATATAGCTGATTTAAACGCTGAAAAAGAACCATTATTTGATGCTATTGTTTACGGTGAAGAAGAAAAAGAAGTTAAAGTTCCAGGTCACAATGATCAAACTTATAACATTAAATGTGAAGTAGCATTTCAATACAATAATTCGTACAACAATTCAACACACTCATTCTGTAATAACATTAATACTACAGAAGGTGGAACACACGAAGAAGGTTTTAAATTAGCGATTACACGTTTATTAAACAAATATGCAATCGATAAAAAGTATTTAAAAGACACTGATGATAAAATCACTAAAGAAGACGTGAGCGAAGGGTTAACAGCGATTATTTCTATTAAGCACCCTAACCCTCAATATGAAGGTCAAACAAAGAAAAAATTAGGAAATAGTGAAGTTCGTCCTTATGTTAATGAAATTACTTCTATAATTTTCGAAAAATTCTTAAATGAAAATCCAGAAGAATCAAAAAAAATTGTTGCTAAAGTTATGCAAGCCGCTGAGGCACGTCGTCGTTCTCATGAAGCGCGTGAAGCTACAAGACGAAAATCACCATTTGAATCAAATTCATTACCAGGTAAATTAGCTGATTGTTCAAATCGTGATTCAAGTGTTACAGAAATTTATATTGTCGAAGGGGATTCAGCTGGTGGATCAGCAAAAACTGGTCGTGAACGTGAATTCCAAGCAATTTTACCATTGCGTGGAAAAATTATTAATGTTGAAAAAGCAAAAATTGACAAGATTTTCGCTAATGAAGAAATTCAAAACATGATTACTGCTTTTGGAGCAGGAATAGGGCCTGAATTTAATATTGAAAAATTAAGATATTCAAAAATTATTATTATGACCGATGCCGATGTCGATGGTAGCCATATTCGAATCTTGTTATTAACATTCTTTTATCGATACATGTTACCATTGATTCAAAATGGTAATGTTTATATTGCTCAACCACCACTTTATAAAGTGAGTTATGGTAAAACAATTAAATATGCATATTCTGATCAAGAATTAGAAAAAATTAAATCAACATTGTTGAATACAAAATATAACATTCAACGTTATAAAGGGTTAGGGGAGATGAATCCTGATCAATTATGAGAAACAACAATGGATCCTAAAAATCGTCTTTTATTAAAAGTTAATATTGAAGATGCGGCAATCGCTGATAAAACATTTTCTTTATTAATGGGTGATGATGTAACACCACGAAAAGAATTTATTGAAAAAAATGCAAAATATGTAAAGAATATTGATGCTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40302","NCBI_taxonomy_name":"Ureaplasma urealyticum","NCBI_taxonomy_id":"2130"}}}},"ARO_accession":"3003305","ARO_id":"39889","ARO_name":"Ureaplasma urealyticum  gyrB conferring resistance to fluoroquinolone","ARO_description":"Point mutation in Ureaplasma urealyticum resulting in fluoroquinolone resistance","ARO_category":{"37244":{"category_aro_accession":"3000864","category_aro_cvterm_id":"37244","category_aro_name":"fluoroquinolone resistant gyrB","category_aro_description":"Point mutations in DNA gyrase subunit B (gyrB) observed in Mycobacterium tuberculosis can result in resistance to fluoroquinolones.","category_aro_class_name":"AMR Gene Family"},"35942":{"category_aro_accession":"0000023","category_aro_cvterm_id":"35942","category_aro_name":"enoxacin","category_aro_description":"Enoxacin belongs to a group called fluoroquinolones. Its mode of action depends upon blocking bacterial DNA replication by binding itself to DNA gyrase and causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36271":{"category_aro_accession":"3000132","category_aro_cvterm_id":"36271","category_aro_name":"clorobiocin","category_aro_description":"Clorobiocin is an aminocoumarin antibiotic produced by Streptomyces roseochromogenes, and binds DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36289":{"category_aro_accession":"3000150","category_aro_cvterm_id":"36289","category_aro_name":"coumermycin A1","category_aro_description":"Coumermycin A1 is an antibiotic produced by Streptomyces rishiriensis, and binds DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37004":{"category_aro_accession":"3000660","category_aro_cvterm_id":"37004","category_aro_name":"lomefloxacin","category_aro_description":"Lomefloxacin is a difluoropiperazinyl quinolone, sharing similar activities with other fluoroquinolones. It is used to treat urinary tract infections. Relative to other fluoroquinolones, it has a longer half life and has higher serum concentrations.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"37008":{"category_aro_accession":"3000664","category_aro_cvterm_id":"37008","category_aro_name":"trovafloxacin","category_aro_description":"Trovafloxacin is a trifluoroquinalone with a broad spectrum of activity that acts by inhibiting the uncoiling of supercoiled DNA. While potent against many Gram-positive and Gram-negative bacteria, it is less active against pseudomonads and Cl. difficile. It is usually taken as the prodrug trovafloxacin mesylate or alatrofloxacin mesylate for oral or intravenous administration, respectively.","category_aro_class_name":"Antibiotic"},"37009":{"category_aro_accession":"3000665","category_aro_cvterm_id":"37009","category_aro_name":"grepafloxacin","category_aro_description":"Grepafloxacin is a broad-spectrum antibacterial quinoline. It is no longer taken due to its high toxicity.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"37142":{"category_aro_accession":"3000762","category_aro_cvterm_id":"37142","category_aro_name":"pefloxacin","category_aro_description":"Pefloxacin is structurally and functionally similar to norfloxacin. It is poorly active against mycobacteria, while anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"40937":{"category_aro_accession":"3004010","category_aro_cvterm_id":"40937","category_aro_name":"cinoxacin","category_aro_description":"Cinoxacin is a fluoroquinolone antibiotic primarily used for the treatment of urinary tract infections in adults. Cinoxacin binds to DNA gyrase, resulting in double-stranded DNA breaks and cell death.","category_aro_class_name":"Antibiotic"},"40938":{"category_aro_accession":"3004011","category_aro_cvterm_id":"40938","category_aro_name":"clinafloxacin","category_aro_description":"Clinafloxacin is a fluoroquinolone antibiotic and gyrase (DNA topoisomerase II) inhibitor. It binds to DNA gyrase and disrupts replication by causing double-stranded DNA breaks, resulting in cell death.","category_aro_class_name":"Antibiotic"},"40939":{"category_aro_accession":"3004012","category_aro_cvterm_id":"40939","category_aro_name":"Clofazimine","category_aro_description":"Clofazimine is a fluoroquinolone-class phenazine dye used for the treatment of leprosy. Clofazimine binds to DNA and disrupts bacterial DNA gyrase, thereby causing double-stranded DNA breaks, and subsequent cell death.","category_aro_class_name":"Antibiotic"},"40940":{"category_aro_accession":"3004013","category_aro_cvterm_id":"40940","category_aro_name":"fleroxacin","category_aro_description":"Fleroxacin is a broad spectrum fluoroquinolone antibiotic that inhibits the DNA supercoiling activity of bacterial DNA gyrase, resulting in double-stranded DNA breaks and subsequent cell death.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2158":{"model_id":"2158","model_name":"Escherichia coli EF-Tu mutants conferring resistance to Pulvomycin","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2934":"T335A","2965":"R334C","3019":"R234F","3020":"R234S","3030":"R231C","3044":"R231V"},"clinical":{"2934":"T335A","2965":"R334C","3019":"R234F","3020":"R234S","3030":"R231C","3044":"R231V"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3356":{"protein_sequence":{"accession":"AAN82549.1","sequence":"MLSPEGESTIVRNIAVSKEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDNAPEEKARGITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALEGDAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVGEEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIKPHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMVVTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLG"},"dna_sequence":{"accession":"AE014075","fmin":"3901532","fmax":"3902762","strand":"-","sequence":"TTAGCCCAGAACTTTAGCAACAACGCCCGCGCCAACGGTACGGCCGCCTTCACGGATTGCGAAACGCAGACCGTCGTCCATCGCGATCGGGTGGATCAGGGTAACAACCATTTTGATGTTGTCGCCCGGCATTACCATCTCTACGCCTTCCGGCAGTTCGATGGTACCAGTCACGTCAGTAGTACGGAAGTAGAACTGCGGACGGTAGCCTTTGAAGAACGGAGTATGACGACCGCCTTCATCTTTGGACAGAATGTACACTTCAGATTCGAACTTGGTGTGCGGCTTGATGGTGCCCGGCTTAGCCAGTACCTGACCACGTTCGATTTCTTCACGTTTGATACCACGCAGCAGAACACCTACGTTCTCACCAGCACGGCCTTCGTCCAGCAGTTTGCGGAACATTTCAACGCCAGTACAGGTAGACTTCTGAGTCTCTTTGATACCAACGATTTCAACTTCTTCACCAACTTTGATGATACCGCGTTCTACACGACCGGTAACAACGGTACCACGACCGGAGATGGAGAATACGTCTTCGATCGGCAGCAGGAACGGCTTGTCAATCGCACGCTCTGGTTCCGGAATGTAAGAATCCAGGAAGCCAGCCAGTTCCAGGATTTTCGCTTCCCACTCTGCGTCGCCTTCCAGCGCTTTCAGAGCAGAACCACGAACGATCGGAGTGTCGTCGCCCGGGAAGTCGTACTGAGACAGAAGTTCACGAACTTCCATTTCAACCAGTTCCAGCAGCTCTTCGTCATCAACCATGTCGCATTTGTTCAGGAACACGATGATGTACGGAACGCCTACCTGACGACCCAGCAGGATGTGCTCACGAGTCTGCGGCATCGGGCCGTCAGTCGCAGCAACTACCAGGATCGCGCCGTCCATCTGAGCAGCACCGGTGATCATGTTTTTAACATAGTCGGCGTGCCCCGGGCAGTCTACGTGCGCGTAGTGACGGGTCGGGGTGTCGTATTCAACGTGAGAAGTGTTGATGGTGATACCACGAGCTTTTTCTTCCGGCGCGTTATCGATCTGGTCGAATGCACGAGCAGCACCGCCGTAGGTTTTAGCCAGTACGGTGGTGATTGCAGCGGTCAGAGTAGTTTTACCGTGGTCAACGTGGCCGATAGTACCAACGTTAACGTGCGGTTTTGTACGTTCAAATTTTTCTTTAGACACGGCTATATTCCTTACTATAGTGCTCTCCCCTTCAGGAGAGAGCAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36763","NCBI_taxonomy_name":"Escherichia coli CFT073","NCBI_taxonomy_id":"199310"}}}},"ARO_accession":"3003369","ARO_id":"39953","ARO_name":"Escherichia coli EF-Tu mutants conferring resistance to Pulvomycin","ARO_description":"Sequence variants of Escherichia coli elongation factor Tu that confer resistance to Pulvomycin","ARO_category":{"37711":{"category_aro_accession":"3001312","category_aro_cvterm_id":"37711","category_aro_name":"elfamycin resistant EF-Tu","category_aro_description":"Sequence variants of elongation factor Tu that confer resistance to elfamycin antibiotics.","category_aro_class_name":"AMR Gene Family"},"36725":{"category_aro_accession":"3000586","category_aro_cvterm_id":"36725","category_aro_name":"pulvomycin","category_aro_description":"Pulvomycin is a polyketide antibiotic that binds elongation factor Tu (EF-Tu) to inhibit protein biosynthesis by preventing the formation of the ternary complex (EF-Tu*GTP*aa-tRNA). Phenotypically, it was shown that pulvomycin sensitivity is dominant over resistance.","category_aro_class_name":"Antibiotic"},"37636":{"category_aro_accession":"3001237","category_aro_cvterm_id":"37636","category_aro_name":"GE2270A","category_aro_description":"GE2270A is the model molecule of cyclic thiazolyl peptide elfamycins. GE2270A is produced by Planobispora rosea. Biosynthesis of the molecule has been shown to originate as a ribosomally synthesized peptide that undergoes significant post-translational modification. Clinical use of cyclic thiazolyl peptides is hindered by their low water solubility and bioavailability.","category_aro_class_name":"Antibiotic"},"37641":{"category_aro_accession":"3001242","category_aro_cvterm_id":"37641","category_aro_name":"enacyloxin IIa","category_aro_description":"Enacyloxin IIa is structurally distinct but acts in a similar mechanism to kirromycin-like elfamycins. It prohibits the transfer of the amino acid at the A site to the elongating peptide chain. It is most likely that the mechanism of action is that EF-Tu*GDP is locked in the EF-Tu*GTP form, and EF-Tu*GDP*aa-tRNA is immobilized on the ribosome. It is an open question whether enacyloxin IIa actually belongs to the kirromycin-like group of elfamycins due to their high similarity.","category_aro_class_name":"Antibiotic"},"39998":{"category_aro_accession":"3003414","category_aro_cvterm_id":"39998","category_aro_name":"LFF571","category_aro_description":"LFF571 is a novel semi-synthetic thiopeptide antibiotic derived from GE2270. It has been shown to possess potent in vitro and in vivo activity against Gram-positive bacteria. It is hypothesized that it a translation inhibitor leading to cell death.","category_aro_class_name":"Antibiotic"},"37618":{"category_aro_accession":"3001219","category_aro_cvterm_id":"37618","category_aro_name":"elfamycin antibiotic","category_aro_description":"Elfamycins are molecules that inhibit bacterial elongation factor Tu (EF-Tu), a key protein which brings aminoacyl-tRNA (aa-tRNA) to the ribosome during protein synthesis. Elfamycins defined by their target (EF-Tu), rather than a conserved chemical backbone. Elfamycins follow two mechanisms to disrupt protein synthesis: 1. kirromycins and enacyloxin fix EF-Tu in the GTP bound conformation and lock EF-Tu onto the ribosome, and 2. pulvomycin and GE2270 cover the binding site of aa-tRNA disallowing EF-Tu from being charged with aa-tRNA. All elfamycins cause increased the affinity of EF-Tu for GTP.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2078":{"model_id":"2078","model_name":"Mycobacterium chelonae 16S rRNA mutation conferring resistance to kanamycin A","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3074":"A1355G"},"clinical":{"3074":"A1355G"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"2500"}},"model_sequences":{"sequence":{"3269":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NR_114659.1","fmin":"1","fmax":"1441","strand":"+","sequence":"GACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGCCCTTCGGGGTACTCGAGTGGCGAACGGGTGAGTAACACGTGGGTGATCTGCCCTGCACTCTGGGATAAGCCTGGGAAACTGGGTCTAATACCGGATAGGACCACACACTTCATGGTGAGTGGTGCAAAGCTTTTGCGGTGTGGGATGAGCCCGCGGCCTATCAGCTTGTTGGTGGGGTAATGGCCCACCAAGGCGACGACGGGTAGCCGGCCTGAGAGGGTGACCGGCCACACTGGGACTGAGATACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGAGGGATGACGGCCTTCGGGTTGTAAACCTCTTTCAGTAGGGACGAAGCGAAAGTGACGGTACCTACAGAAGAAGGACCGGCCAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTCCGAGCGTTGTCCGGAATTACTGGGCGTAAAGAGCTCGTAGGTGGTTTGTCGCGTTGTTCGTGAAAACTCACAGCTTAACTGTGGGCGTGCGGGCGATACGGGCAGACTAGAGTACTGCAGGGGAGACTGGAATTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGGTGGCGAAGGCGGGTCTCTGGGCAGTAACTGACGCTGAGGAGCGAAAGCGTGGGTAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGGTGGGTACTAGGTGTGGGTTTCCTTCCTTGGGATCCGTGCCGTAGCTAACGCATTAAGTACCCCGCCTGGGGAGTACGGTCGCAAGACTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGTGGATTAATTCGATGCAACGCGAAGAACCTTACCTGGGTTTGACATGCGCAGGACGTATCTAGAGATAGGTATTCCCTTGTGGCCTGCGTGCAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCCTATGTTGCCAGCGGGTAATGCCGGGGACTCGTAGGAGACTGCCGGGGTCAACTCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGCCCCTTATGTCCAGGGCTTCACACATGCTACAATGGCCAGTACAGAGGGCTGCGAAGCCGCAAGGTGGAGCGAATCCCTTAAAGCTGGTCTCAGTTCGGATTGGGGTCTGCAACTCGACCCCATGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTCGGTAACACCCGAAGCCAGTGGCCTAACCTTTTGGAGGGAGCTGTCGAAGGTGGGATCGGCGATTGGGACGAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37061","NCBI_taxonomy_name":"Mycobacterium","NCBI_taxonomy_id":"1763"}}}},"ARO_accession":"3003515","ARO_id":"40117","ARO_name":"Mycobacterium chelonae 16S rRNA mutation conferring resistance to kanamycin A","ARO_description":"Point mutations in the 16S rRNA of Mycobacterium chelonae can cause resistance to kanamycin A.","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1441":{"model_id":"1441","model_name":"Enterobacter aerogenes omp36 with mutation","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2085":"G133D"},"clinical":{"2085":"G133D"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"2109":{"protein_sequence":{"accession":"AAK11270.1","sequence":"MKVKVLSLLVPALLVAGAANAAEIYNKDGNKLDLYGKIDGLHYFSSDDSVDGDQTYMRIGVKGETQINDQLTGYGQWEYNVQANNTESSSDQAWTRLAFAGLKFGDAGSFDYGRNYGVVYDVTSWTDVLPEFGGDTYGSDNFLQSRANGVATYRNSDFFGLVDGLNFALQYQGKNGSVSGEDQTNNGRDFQKQNGEGFGTSVTYDIWDGISAGFAYSSSKRTDEQNNSTFVSKTDGGRYGVLGEGDHAETYTGGLKYDANNIYLATQYTQTYNATRTGNIGFANKAQNFEVVAQYQFDFGLRPSVAYLQSKGKDMGRYGDQDILKYVDLGATYYFNKNMSTYVDYKINLLDDNKFTKDASISTDNVVALGLVYQF"},"dna_sequence":{"accession":"AF335467","fmin":"36","fmax":"1164","strand":"+","sequence":"ATGAAAGTTAAAGTACTGTCCCTCCTGGTACCAGCACTGCTGGTAGCGGGCGCAGCAAATGCGGCTGAAATTTATAACAAAGACGGCAACAAATTAGACCTGTACGGTAAAATCGACGGTCTGCACTACTTCTCTTCCGACGACAGCGTCGACGGCGACCAGACCTACATGCGTATCGGCGTGAAAGGCGAAACCCAGATCAACGACCAGCTGACCGGTTACGGCCAGTGGGAATACAACGTTCAGGCGAACAACACTGAAAGCTCCAGCGACCAGGCATGGACTCGTCTGGCCTTCGCGGGTCTGAAATTCGGCGACGCGGGTTCTTTCGACTACGGTCGTAACTACGGCGTTGTTTACGACGTAACTTCCTGGACCGACGTTCTGCCGGAATTCGGCGGCGACACCTACGGTTCCGACAACTTCCTGCAGTCCCGTGCTAACGGTGTTGCCACCTACCGTAACTCTGACTTCTTCGGTCTGGTTGACGGCCTGAACTTTGCTCTGCAGTACCAGGGTAAAAACGGCAGCGTGAGCGGCGAAGATCAGACCAACAACGGTCGTGACTTCCAGAAACAGAACGGCGAAGGCTTCGGCACCTCCGTAACTTATGATATCTGGGACGGCATCAGCGCTGGTTTCGCGTACTCCAGCTCTAAACGTACCGACGAGCAGAACAACTCTACCTTCGTGTCTAAGACCGATGGTGGTCGTTACGGTGTTCTGGGTGAAGGCGATCACGCTGAAACCTACACCGGTGGTCTGAAATACGACGCCAACAACATCTACCTGGCGACTCAGTACACCCAGACTTACAACGCAACCCGCACCGGTAACATCGGTTTTGCTAACAAAGCGCAGAACTTCGAAGTCGTTGCTCAGTACCAGTTCGACTTCGGTCTGCGTCCGTCCGTGGCTTACCTGCAGTCTAAAGGTAAAGACATGGGCCGTTACGGCGACCAGGACATCCTGAAATATGTTGACCTGGGTGCGACCTACTACTTCAACAAAAACATGTCCACCTACGTTGATTACAAAATCAACCTGCTGGACGACAACAAGTTCACTAAAGATGCAAGCATCTCTACTGACAACGTTGTGGCTCTGGGCCTGGTTTACCAGTTCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36770","NCBI_taxonomy_name":"Enterobacter aerogenes","NCBI_taxonomy_id":"548"}}}},"ARO_accession":"3003385","ARO_id":"39969","ARO_name":"Enterobacter aerogenes Omp36","ARO_description":"Mutant forms of the porin Omp36 result in reduced permeability to antibiotics.","ARO_category":{"41445":{"category_aro_accession":"3004281","category_aro_cvterm_id":"41445","category_aro_name":"General Bacterial Porin with reduced permeability to beta-lactams","category_aro_description":"These are GBPs that are associated with decreased susceptibility to beta-lactams either through mutations in the porin protein, absence of the porin protein, or expression of the porin protein.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36383":{"category_aro_accession":"3000244","category_aro_cvterm_id":"36383","category_aro_name":"reduced permeability to antibiotic","category_aro_description":"Reduction in permeability to antibiotic, generally through reduced production of porins, can provide resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1545":{"model_id":"1545","model_name":"Escherichia coli gyrA conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"40330":{"param_type":"multiple resistance variants","param_description":"A set of nucleotide or amino acid substitutions that are each required to confer resistance to an antibiotic drug or drug class by co-mutation. Compare to single resistance variant, where only one substitution is required. Multiple resistance variants parameters are indicated on appropriate models using the following notation: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2],...,[wild-type n][position n][mutation n]. When each included substitution is detected in a protein sequence, resistance is conferred. This parameter is not currently included in any detection algorithms.","param_type_id":"40330","param_value":{"3329":"S83L,D87N","3328":"S83L,D87Y"}},"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2050":"S83I","2051":"D87N","2052":"D87G","2053":"D87H","2084":"D87Y","3318":"S83W","3326":"S83L","3327":"D87V","3404":"A67S","3405":"A84P","3397":"Q106H","3398":"G81C"},"clinical":{"2050":"S83I","2051":"D87N","2052":"D87G","2053":"D87H","2084":"D87Y","3318":"S83W","3326":"S83L","3327":"D87V"},"experimental":{"3404":"A67S","3405":"A84P","3397":"Q106H","3398":"G81C"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1500"}},"model_sequences":{"sequence":{"4362":{"protein_sequence":{"accession":"AAC75291.1","sequence":"MSDLAREITPVNIEEELKSSYLDYAMSVIVGRALPDVRDGLKPVHRRVLYAMNVLGNDWNKAYKKSARVVGDVIGKYHPHGDSAVYDTIVRMAQPFSLRYMLVDGQGNFGSIDGDSAAAMRYTEIRLAKIAHELMADLEKETVDFVDNYDGTEKIPDVMPTKIPNLLVNGSSGIAVGMATNIPPHNLTEVINGCLAYIDDEDISIEGLMEHIPGPDFPTAAIINGRRGIEEAYRTGRGKVYIRARAEVEVDAKTGRETIIVHEIPYQVNKARLIEKIAELVKEKRVEGISALRDESDKDGMRIVIEVKRDAVGEVVLNNLYSQTQLQVSFGINMVALHHGQPKIMNLKDIIAAFVRHRREVVTRRTIFELRKARDRAHILEALAVALANIDPIIELIRHAPTPAEAKTALVANPWQLGNVAAMLERAGDDAARPEWLEPEFGVRDGLYYLTEQQAQAILDLRLQKLTGLEHEKLLDEYKELLDQIAELLRILGSADRLMEVIREELELVREQFGDKRRTEITANSADINLEDLITQEDVVVTLSHQGYVKYQPLSEYEAQRRGGKGKSAARIKEEDFIDRLLVANTHDHILCFSSRGRVYSMKVYQLPEATRGARGRPIVNLLPLEQDERITAILPVTEFEEGVKVFMATANGTVKKTVLTEFNRLRTAGKVAIKLVDGDELIGVDLTSGEDEVMLFSAEGKVVRFKESSVRAMGCNTTGVRGIRLGEGDKVVSLIVPRGDGAILTATQNGYGKRTAVAEYPTKSRATKGVISIKVTERNGLVVGAVQVDDCDQIMMITDAGTLVRTRVSEISIVGRNTQGVILIRTAEDENVVGLQRVAEPVDEEDLDTIDGSAAEGDDEIAPEVDVDDEPEEE"},"dna_sequence":{"accession":"U00096","fmin":"2336792","fmax":"2339420","strand":"-","sequence":"TTATTCTTCTTCTGGCTCGTCGTCAACGTCCACTTCCGGAGCGATTTCATCGTCCCCTTCCGCGGCACTGCCGTCGATGGTATCCAGATCTTCCTCGTCAACCGGTTCAGCAACACGTTGCAGACCCACTACGTTTTCATCTTCCGCAGTACGGATGAGGATCACGCCCTGGGTGTTACGGCCCACGATGCTGATTTCCGAAACGCGAGTACGTACCAGCGTACCGGCATCGGTGATCATCATGATCTGGTCGCAGTCATCTACCTGTACCGCGCCAACAACTAAACCGTTACGTTCGGTAACCTTGATGGAGATAACCCCTTTCGTCGCACGCGACTTGGTTGGGTATTCCGCCACTGCGGTACGTTTACCGTAACCGTTTTGCGTTGCGGTGAGGATTGCGCCATCGCCACGAGGCACGATCAGAGAGACGACTTTATCGCCTTCACCTAAGCGAATACCGCGAACACCGGTGGTGTTGCAGCCCATCGCACGGACAGAAGACTCTTTAAAGCGCACCACTTTACCTTCAGCGGAGAACAGCATTACTTCGTCTTCGCCGCTGGTCAGGTCAACGCCGATCAGCTCATCGCCGTCAACCAGTTTGATCGCCACTTTACCGGCGGTACGCAGACGGTTGAACTCGGTGAGGACAGTTTTCTTCACGGTACCGTTAGCGGTCGCCATGAAGACTTTCACGCCTTCTTCAAACTCGGTCACTGGCAGGATCGCAGTGATACGTTCGTCCTGCTCCAGCGGCAGCAGGTTGACGATCGGACGACCGCGCGCGCCACGAGTGGCTTCCGGCAACTGATAAACTTTCATCGAATAGACGCGACCACGGCTGGAGAAGCACAGAATATGGTCGTGAGTGTTCGCCACCAGCAGTCGGTCGATAAAGTCTTCTTCTTTAATACGTGCGGCAGATTTACCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTGAGAGAGCGTCACGACCACATCTTCCTGGGTGATCAGATCTTCCAGGTTGATGTCTGCGCTGTTGGCGGTGATTTCAGTACGACGTTTGTCACCGAACTGTTCACGAACCAGCTCCAGCTCTTCACGGATCACTTCCATCAGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCGATCTGATCCAGCAGCTCTTTGTATTCGTCGAGCAGTTTTTCGTGCTCAAGACCGGTCAGTTTCTGCAAACGCAGATCCAGAATCGCCTGAGCTTGCTGTTCGGTCAGGTAGTACAGACCATCACGCACGCCGAACTCTGGCTCCAGCCATTCCGGACGCGCAGCATCGTCGCCAGCACGTTCGAGCATCGCGGCAACGTTGCCCAGCTGCCACGGATTAGCAACCAGCGCAGTTTTCGCTTCTGCAGGCGTCGGCGCATGACGGATCAGTTCGATGATCGGGTCGATGTTCGCCAGCGCCACGGCTAATGCTTCAAGGATATGAGCACGATCGCGAGCTTTACGCAGTTCGAAAATAGTACGACGGGTCACCACTTCACGGCGGTGACGAACAAACGCCGCGATGATGTCTTTCAGGTTCATGATCTTCGGCTGACCATGGTGCAATGCCACCATGTTGATACCGAAAGAAACCTGCAACTGGGTCTGGGAGTAGAGGTTGTTGAGCACAACTTCACCGACCGCATCGCGTTTCACTTCAATCACGATGCGCATACCGTCTTTGTCAGACTCGTCACGCAGCGCGCTGATGCCTTCCACGCGTTTTTCTTTTACCAGTTCCGCAATCTTCTCGATCAGGCGCGCTTTGTTTACCTGATACGGAATTTCGTGGACGATAATGGTTTCACGACCGGTTTTGGCGTCAACTTCCACTTCTGCGCGAGCGCGGATATACACCTTGCCGCGACCGGTACGGTAAGCTTCTTCAATACCGCGACGACCGTTAATGATTGCCGCCGTCGGGAAGTCCGGCCCCGGGATGTGTTCCATCAGCCCTTCAATGCTGATGTCTTCATCATCAATATACGCCAGACAACCGTTGATGACTTCCGTCAGGTTGTGCGGCGGGATGTTGGTTGCCATACCTACGGCGATACCGGAAGAACCGTTCACCAGCAGGTTAGGAATTTTGGTTGGCATGACGTCCGGAATTTTTTCCGTGCCGTCATAGTTATCAACGAAATCGACCGTCTCTTTTTCGAGATCGGCCATCAGTTCATGGGCAATTTTCGCCAGACGGATTTCCGTATAACGCATTGCCGCCGCAGAGTCGCCGTCGATAGAACCGAAGTTACCCTGACCGTCTACCAGCATATAACGCAGCGAGAATGGCTGCGCCATGCGGACGATCGTGTCATAGACCGCCGAGTCACCATGGGGATGGTATTTACCGATTACGTCACCAACGACACGGGCAGATTTTTTATAGGCTTTGTTCCAGTCATTGCCTAGTACGTTCATGGCGTAAAGTACGCGACGGTGTACCGGCTTCAGGCCATCTCGGACATCTGGCAGCGCACGGCCAACAATGACCGACATCGCATAATCCAGATAGGAGCTCTTCAGCTCTTCCTCAATGTTGACCGGTGTAATTTCTCTCGCAAGGTCGCTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3003294","ARO_id":"39878","ARO_name":"Escherichia coli gyrA conferring resistance to fluoroquinolones","ARO_description":"Point mutation of Escherichia coli gyrA resulted in the lowered affinity between fluoroquinolones and gyrA. Thus, conferring resistance","ARO_category":{"39876":{"category_aro_accession":"3003292","category_aro_cvterm_id":"39876","category_aro_name":"fluoroquinolone resistant gyrA","category_aro_description":"DNA gyrase is responsible for DNA supercoiling and consists of two alpha and two beta subunits. GyrA point mutations confer resistance by preventing fluoroquinolone antibiotics from binding the alpha-subunit.","category_aro_class_name":"AMR Gene Family"},"35942":{"category_aro_accession":"0000023","category_aro_cvterm_id":"35942","category_aro_name":"enoxacin","category_aro_description":"Enoxacin belongs to a group called fluoroquinolones. Its mode of action depends upon blocking bacterial DNA replication by binding itself to DNA gyrase and causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37004":{"category_aro_accession":"3000660","category_aro_cvterm_id":"37004","category_aro_name":"lomefloxacin","category_aro_description":"Lomefloxacin is a difluoropiperazinyl quinolone, sharing similar activities with other fluoroquinolones. It is used to treat urinary tract infections. Relative to other fluoroquinolones, it has a longer half life and has higher serum concentrations.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"37008":{"category_aro_accession":"3000664","category_aro_cvterm_id":"37008","category_aro_name":"trovafloxacin","category_aro_description":"Trovafloxacin is a trifluoroquinalone with a broad spectrum of activity that acts by inhibiting the uncoiling of supercoiled DNA. While potent against many Gram-positive and Gram-negative bacteria, it is less active against pseudomonads and Cl. difficile. It is usually taken as the prodrug trovafloxacin mesylate or alatrofloxacin mesylate for oral or intravenous administration, respectively.","category_aro_class_name":"Antibiotic"},"37009":{"category_aro_accession":"3000665","category_aro_cvterm_id":"37009","category_aro_name":"grepafloxacin","category_aro_description":"Grepafloxacin is a broad-spectrum antibacterial quinoline. It is no longer taken due to its high toxicity.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"37142":{"category_aro_accession":"3000762","category_aro_cvterm_id":"37142","category_aro_name":"pefloxacin","category_aro_description":"Pefloxacin is structurally and functionally similar to norfloxacin. It is poorly active against mycobacteria, while anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"40463":{"category_aro_accession":"3003780","category_aro_cvterm_id":"40463","category_aro_name":"nybomycin","category_aro_description":"A  heterocyclic antibiotic that targets mutant gyrA (type II topoisomerase) containing an S84L substitution, counteracting acquired quinolone resistance. It is effective against quinolone-resistant Gram-positive bacteria including S. aureus and E. faecalis. Due to its ability to counteract quinolone resistance by targeting the mutant form of the gyrA protein, it is classified as a reverse antibiotic (RA).","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1005":{"model_id":"1005","model_name":"Escherichia coli soxR with mutation conferring antibiotic resistance","model_type":"protein overexpression model","model_type_id":"41091","model_description":"This model detects protein overexpression based on the presence of mutations.The detection of the protein without an associated mutation indicates that the protein is likely to be expressed at low or basal levels. The detection of the protein with the mutation indicates that the protein is likely overexpressed. This model reflects how certain proteins are functional with and without mutations. For example, efflux pump subunits and regulators are functional with mutations and without mutations. Without mutations, efflux pump subunits and regulators are usually expressed at a low level. When an efflux pump regulator has a mutation, it can cause the overexpression of the efflux pump it is responsible for regulating, leading to resistance to specific drugs. Protein overexpression models have two parameters: a curated BLASTP cutoff, and a curated set of mutations (single resistance variants, frameshift mutations, indels, etc.) shown clinically to confer resistance. This model type is a combination of the protein homolog and protein variant model. A detected hit can be categorized as Perfect, Strict, or Loose with no mutation(s) or as Strict or Loose with mutation(s).","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2230":"R20H","2233":"G121D","3895":"R90G","3896":"S31A","3897":"R71S"},"clinical":{"2230":"R20H","2233":"G121D","3895":"R90G","3896":"S31A","3897":"R71S"}},"41342":{"param_type":"deletion mutation from peptide sequence","param_description":"A subtype of the deletion mutation detection model parameter. This parameter is used when a set of deletion mutations is reported in a peptide sequence format. These are specific to codon deletions, where a multiple of 3 nucleotides are deleted. Mutations of this type are reported in the CARD with the notation: [-][AAs][position range].","param_type_id":"41342","param_value":{"3893":"-S128"}},"40330":{"param_type":"multiple resistance variants","param_description":"A set of nucleotide or amino acid substitutions that are each required to confer resistance to an antibiotic drug or drug class by co-mutation. Compare to single resistance variant, where only one substitution is required. Multiple resistance variants parameters are indicated on appropriate models using the following notation: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2],...,[wild-type n][position n][mutation n]. When each included substitution is detected in a protein sequence, resistance is conferred. This parameter is not currently included in any detection algorithms.","param_type_id":"40330","param_value":{"3894":"T38S, G74R"}},"40494":{"param_type":"frameshift mutation","param_description":"A frameshift is a type of genetic mutation caused by a nucleotide insertion or deletion \u2260 3 bases. This changes the grouping of codons and thus the reading frame during translation, resulting in a incomplete or inactive protein product. Many frameshift mutations generate downstream STOP codons, resulting in premature peptide translation termination. Frameshifts may also confer antibiotic resistance through partial or total protein loss-of-function. Frameshift mutations are included with relevant models when applicable, with the following notation: [wild-type AA][position]fs;[[wild-type AA][position]STOP], where AA is an amino acid. If the premature STOP codon position is unknown or does not exist, [wild-type AA][position]fs is sufficient. This parameter is currently not included in detection algorithms.","param_type_id":"40494","param_value":{"7541":"L148fs"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"},"41343":{"param_type":"deletion mutation from nucleotide sequence","param_description":"A subtype of the deletion mutation detection model parameter. This parameter is used when a set of deletion mutations is reported in a nucleotide sequence format. Such mutations may be of variable length - possibly causing a frameshift, but not premature termination of functional knockout. Mutation parameters of this type are reported in the CARD with the notation: [-]nt[position]:[nucleotides].","param_type_id":"41343","param_value":{"8025":"-nt1130:2"}}},"model_sequences":{"sequence":{"2074":{"protein_sequence":{"accession":"AAC77033.1","sequence":"MEKKLPRIKALLTPGEVAKRSGVAVSALHFYESKGLITSIRNSGNQRRYKRDVLRYVAIIKIAQRIGIPLATIGEAFGVLPEGHTLSAKEWKQLSSQWREELDRRIHTLVALRDELDGCIGCGCLSRSDCPLRNPGDRLGEEGTGARLLEDEQN"},"dna_sequence":{"accession":"U00096","fmin":"4277468","fmax":"4277933","strand":"+","sequence":"ATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAACGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGCAATCAGCGGCGATATAAACGTGATGTGTTGCGATATGTTGCAATTATCAAAATTGCTCAGCGTATTGGCATTCCGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCGAAGGGCATACGTTAAGTGCGAAAGAGTGGAAACAGCTTTCGTCCCAATGGCGAGAAGAGTTGGATCGGCGCATTCATACCTTAGTGGCGCTGCGTGACGAACTGGACGGATGTATTGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3003381","ARO_id":"39965","ARO_name":"Escherichia coli soxR with mutation conferring antibiotic resistance","ARO_description":"SoxR is a sensory protein that upregulates soxS expression in the presence of redox-cycling drugs. This stress response leads to the expression many multidrug efflux pumps.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1055":{"model_id":"1055","model_name":"Escherichia coli parE conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2226":"D476N"},"clinical":{"2226":"D476N"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"4376":{"protein_sequence":{"accession":"YP_491222.1","sequence":"MTQTYNADAIEVLTGLEPVRRRPGMYTDTTRPNHLGQEVIDNSVDEALAGHAKRVDVILHADQSLEVIDDGRGMPVDIHPEEGVPAVELILCRLHAGGKFSNKNYQFSGGLHGVGISVVNALSKRVEVNVRRDGQVYNIAFENGEKVQDLQVVGTCGKRNTGTSVHFWPDETFFDSPRFSVSRLTHVLKAKAVLCPGVEITFKDEINNTEQRWCYQDGLNDYLAEAVNGLPTLPEKPFIGNFAGDTEAVDWALLWLPEGGELLTESYVNLIPTMQGGTHVNGLRQGLLDAMREFCEYRNILPRGVKLSAEDIWDRCAYVLSVKMQDPQFAGQTKERLSSRQCAAFVSGVVKDAFILWLNQNVQAAELLAEMAISSAQRRMRAAKKVVRKKLTSGPALPGKLADCTAQDLNRTELFLVEGDSAGGSAKQARDREYQAIMPLKGKILNTWEVSSDEVLASQEVHDISVAIGIDPDSDDLSQLRYGKICILADADSDGLHIATLLCALFVKHFRALVKHGHVYVALPPLYRIDLGKEVYYALTEEEKEGVLEQLKRKKGKPNVQRFKGLGEMNPMQLRETTLDPNTRRLVQLTIDDEDDQRTDAMMDMLLAKKRSEDRRNWLQEKGDMAEIEV"},"dna_sequence":{"accession":"NC_007779","fmin":"3172159","fmax":"3174052","strand":"-","sequence":"TTAAACCTCAATCTCCGCCATGTCGCCTTTCTCTTGCAACCAGTTGCGGCGATCTTCCGAGCGTTTCTTCGCCAGCAGCATATCCATCATCGCGTCAGTACGCTGATCGTCTTCATCATCGATAGTCAACTGCACCAGACGGCGAGTGTTCGGATCAAGCGTGGTTTCGCGCAATTGCATCGGGTTCATTTCCCCCAGACCTTTAAAACGCTGGACGTTCGGCTTGCCTTTCTTGCGTTTTAATTGCTCAAGTACGCCCTCTTTCTCTTCTTCCGTCAGCGCGTAATAAACCTCTTTCCCGAGATCAATACGGTAGAGCGGTGGCAGTGCGACGTAAACGTGACCGTGTTTCACCAACGCGCGGAAATGTTTTACGAACAAAGCGCAGAGCAGCGTGGCAATGTGCAGACCATCAGAGTCCGCATCCGCGAGGATACAGATTTTGCCATAACGAAGCTGGCTCAGATCGTCGCTGTCAGGATCGATACCGATCGCTACCGAAATATCGTGCACTTCCTGCGAAGCCAGCACTTCGTCGGAAGAGACTTCCCAGGTGTTAAGGATCTTACCTTTCAGTGGCATGATCGCCTGATATTCGCGATCGCGCGCCTGCTTGGCAGATCCGCCTGCGGAGTCACCTTCCACAAGGAACAGCTCGGTACGGTTAAGGTCCTGCGCGGTACAATCAGCCAGTTTGCCAGGCAACGCCGGGCCGCTGGTCAGCTTTTTACGCACCACTTTTTTGGCCGCACGCATACGGCGCTGGGCGCTGGAAATCGCCATCTCCGCCAGCAGTTCAGCCGCCTGAACGTTCTGGTTCAGCCACAGGATAAAGGCATCTTTCACCACGCCAGAAACGAATGCCGCGCATTGACGCGAAGAGAGACGCTCTTTCGTCTGCCCGGCAAACTGCGGATCCTGCATTTTTACTGACAGCACATAGGCGCAGCGATCCCAGATATCTTCCGCCGACAGCTTTACACCGCGCGGCAGAATATTGCGGTATTCACAGAACTCACGCATCGCGTCCAACAGGCCCTGACGCAGACCATTAACATGGGTACCGCCCTGCATCGTTGGGATAAGGTTGACGTAGCTTTCGGTCAGCAGTTCACCGCCTTCCGGCAGCCACAGTAGCGCCCAGTCCACAGCTTCAGTATCACCAGCGAAATTACCGATAAACGGTTTTTCCGGCAGCGTCGGCAGACCATTTACCGCTTCCGCCAGGTAATCATTCAGACCGTCCTGATAGCACCAGCGTTGTTCGGTATTGTTGATCTCATCTTTAAAAGTGATCTCAACGCCAGGGCACAATACCGCTTTGGCTTTCAGCACATGCGTCAGGCGTGAAACAGAAAATCGCGGGCTGTCAAAGAAGGTTTCATCCGGCCAGAAGTGCACACTGGTACCAGTATTGCGTTTACCGCAAGTGCCGACAACCTGTAAATCCTGCACCTTTTCGCCATTTTCAAAGGCGATGTTATAAACCTGACCATCGCGGCGCACGTTAACTTCTACGCGCTTCGACAGGGCGTTAACCACCGAAATCCCCACGCCATGCAGGCCGCCAGAGAACTGGTAATTTTTGTTAGAGAATTTACCGCCTGCATGCAGACGGCAAAGAATCAGTTCAACCGCCGGTACACCCTCTTCCGGGTGAATATCCACCGGCATCCCGCGCCCATCGTCAATAACTTCTAACGACTGGTCAGCATGTAAAATAACGTCCACGCGTTTTGCGTGACCCGCCAGTGCTTCATCCACACTGTTATCAATGACTTCTTGCCCCAAATGGTTAGGGCGAGTGGTATCGGTATACATCCCCGGACGGCGGCGAACCGGCTCAAGCCCGGTGAGTACCTCAATGGCATCAGCGTTATAAGTTTGCGTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36839","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. W3110","NCBI_taxonomy_id":"316407"}}}},"ARO_accession":"3003316","ARO_id":"39900","ARO_name":"Escherichia coli parE conferring resistance to fluoroquinolones","ARO_description":"Point mutation in Escherichia coli parE resulting in fluoroquinolones resistance","ARO_category":{"39897":{"category_aro_accession":"3003313","category_aro_cvterm_id":"39897","category_aro_name":"fluoroquinolone resistant parE","category_aro_description":"ParE is a subunit of topoisomerase IV, necessary for cell survival. Point mutations in ParE prevent fluoroquinolones from inhibiting DNA synthesis, thus conferring resistance.","category_aro_class_name":"AMR Gene Family"},"35942":{"category_aro_accession":"0000023","category_aro_cvterm_id":"35942","category_aro_name":"enoxacin","category_aro_description":"Enoxacin belongs to a group called fluoroquinolones. Its mode of action depends upon blocking bacterial DNA replication by binding itself to DNA gyrase and causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37004":{"category_aro_accession":"3000660","category_aro_cvterm_id":"37004","category_aro_name":"lomefloxacin","category_aro_description":"Lomefloxacin is a difluoropiperazinyl quinolone, sharing similar activities with other fluoroquinolones. It is used to treat urinary tract infections. Relative to other fluoroquinolones, it has a longer half life and has higher serum concentrations.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"37008":{"category_aro_accession":"3000664","category_aro_cvterm_id":"37008","category_aro_name":"trovafloxacin","category_aro_description":"Trovafloxacin is a trifluoroquinalone with a broad spectrum of activity that acts by inhibiting the uncoiling of supercoiled DNA. While potent against many Gram-positive and Gram-negative bacteria, it is less active against pseudomonads and Cl. difficile. It is usually taken as the prodrug trovafloxacin mesylate or alatrofloxacin mesylate for oral or intravenous administration, respectively.","category_aro_class_name":"Antibiotic"},"37009":{"category_aro_accession":"3000665","category_aro_cvterm_id":"37009","category_aro_name":"grepafloxacin","category_aro_description":"Grepafloxacin is a broad-spectrum antibacterial quinoline. It is no longer taken due to its high toxicity.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"37142":{"category_aro_accession":"3000762","category_aro_cvterm_id":"37142","category_aro_name":"pefloxacin","category_aro_description":"Pefloxacin is structurally and functionally similar to norfloxacin. It is poorly active against mycobacteria, while anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"212":{"model_id":"212","model_name":"Staphylococcus aureus parC conferring resistance to fluoroquinolone","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3982":"S80F","3983":"S80Y","3984":"E84G"},"clinical":{"3982":"S80F","3983":"S80Y","3984":"E84G"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1400"}},"model_sequences":{"sequence":{"2067":{"protein_sequence":{"accession":"YP_040772.1","sequence":"MSEIIQDLSLEDVLGDRFGRYSKYIIQERALPDVRDGLKPVQRRILYAMYSSGNTHDKNFRKSAKTVGDVIGQYHPHGDFSVYEAMVRLSQDWKLRHVLIEMHGNNGSIDNDPPAAMRYTEAKLSLLAEELLRDINKETVSFISNYDDTTLEPMVLPSRFPNLLVNGSTGISAGYATDIPPHNLAEVIQATLKYIDNPDITVNQLMKYIKGPDFPTGGIIQGIDGIKKAYESGKGRIIVRSKVEEETLRNGRKQLIITEIPYEVNKSSLVKRIDELRADKKVDGIVEVRDETDRTGLRIAIELKKDVNSESIKNYLYKNSDLQISYNFNMVAISDGRPKLMGIRQIIDSYLNHQIEVVANRTKFELDNAEKRMHIVEGLIKALSILDKVIELIRSSKNKRDAKENLIEVYEFTEEQAEAIVMLQLYRLTNTDIVALEGEHKELEALIKQLRHILDNHDALLNVIKEELNEIKKKFKSERLSLIEAEIEEIKIDKEVMVPSEEVILSMTRHGYIKRTSIRSYNASGVEDIGLKDGDSLLKHQEVNTQDTVLVFTNKGRYLFIPVHKLADIRWKELGQHVSQIVPIEEDEVVINVFNEKDFNTDAFYVFATQNGMIKKSTVPLFKTTRFNKPLIATKVKENDDLISVMRFEKDQLITIITNKGMSLTYNTSELSDTGLRAAGVKSINLKAEDFVVMTEGVSENDTILMATQRGSLKRISFKILQVAKRAQRGITLLKELKKNPHRIVAAHVVTGEHSQYTLYSKSNEEHGLINDIHKSEQYTNGSFIVDTDDFGEVIDMYIS"},"dna_sequence":{"accession":"NC_002952","fmin":"1419759","fmax":"1422162","strand":"+","sequence":"GTGAGTGAAATAATTCAAGATTTATCACTTGAAGATGTTTTAGGTGATCGCTTTGGAAGATATAGTAAATATATTATTCAAGAGCGTGCATTGCCAGATGTTCGTGATGGTTTAAAACCAGTACAACGTCGTATTTTATATGCAATGTATTCAAGTGGTAATACACACGATAAAAATTTCCGTAAAAGTGCGAAAACAGTCGGTGATGTTATTGGTCAATATCATCCACATGGAGACTTCTCAGTGTACGAAGCAATGGTCCGTTTAAGTCAAGACTGGAAGTTACGACATGTCTTAATAGAAATGCATGGTAATAATGGTAGTATCGATAATGATCCACCAGCGGCAATGCGTTACACTGAAGCTAAGTTAAGCTTACTAGCTGAAGAGTTATTACGTGATATTAATAAAGAGACAGTTTCCTTCATTTCAAACTATGATGATACGACGCTCGAACCAATGGTATTGCCATCAAGATTTCCTAACTTACTAGTGAATGGTTCTACAGGTATATCTGCAGGTTACGCGACAGATATACCACCACATAATTTAGCTGAAGTGATTCAAGCAACACTTAAATATATTGATAATCCGGATATTACAGTCAATCAATTAATGAAATATATTAAAGGTCCTGATTTTCCAACTGGCGGTATTATTCAAGGTATTGATGGTATTAAAAAAGCTTATGAATCAGGTAAAGGTAGAATTATAGTTCGTTCTAAAGTTGAAGAAGAAACTTTACGCAATGGACGTAAACAGTTAATTATTACTGAAATTCCATATGAAGTGAACAAAAGTAGCTTAGTAAAACGTATCGATGAATTACGTGCTGACAAAAAAGTCGATGGTATCGTTGAAGTACGTGATGAAACTGATAGAACTGGTTTACGAATAGCAATTGAATTGAAAAAAGATGTGAACAGTGAATCAATCAAAAATTATCTTTATAAAAACTCTGATTTACAGATTTCATATAATTTCAACATGGTCGCTATTAGTGATGGTCGTCCAAAATTGATGGGTATTCGTCAAATTATAGATAGTTATTTAAATCATCAAATTGAGGTTGTTGCAAATAGAACGAAGTTTGAATTAGATAATGCTGAAAAACGCATGCATATCGTTGAAGGTTTGATTAAAGCGTTGTCAATTTTAGATAAAGTAATCGAATTGATTCGTAGCTCTAAAAACAAGCGTGACGCTAAAGAAAACCTTATCGAAGTATACGAGTTCACAGAAGAACAGGCTGAAGCAATTGTAATGTTACAGTTATATCGTTTAACAAACACTGACATAGTTGCGCTTGAAGGTGAACATAAAGAACTTGAAGCATTAATCAAACAATTACGTCATATTCTTGATAACCATGATGCATTATTGAATGTCATCAAAGAAGAATTGAATGAAATTAAAAAGAAATTCAAATCTGAACGACTGTCTTTAATTGAAGCAGAAATTGAAGAAATTAAAATTGACAAAGAAGTTATGGTGCCTAGTGAAGAAGTTATTTTAAGTATGACACGTCATGGATATATTAAACGTACTTCTATTCGTAGCTATAATGCTAGCGGTGTTGAAGATATTGGTTTAAAAGATGGTGACAGTTTACTTAAACATCAAGAAGTAAATACGCAAGATACCGTACTAGTATTTACAAATAAAGGTCGTTATCTATTTATACCGGTTCATAAATTAGCAGATATTCGTTGGAAAGAATTGGGGCAACATGTATCACAAATAGTTCCTATCGAAGAAGATGAAGTGGTTATTAATGTCTTTAATGAAAAGGACTTTAATACAGATGCATTTTATGTTTTTGCGACTCAAAATGGCATGATTAAGAAAAGTACAGTGCCTCTATTTAAAACAACGCGTTTTAATAAACCTTTAATTGCTACTAAAGTTAAAGAAAATGATGATTTGATTAGTGTTATGCGCTTTGAAAAAGATCAATTAATTACCATCATTACAAATAAAGGTATGTCTTTAACTTATAATACAAGTGAACTATCAGATACCGGATTAAGGGCAGCTGGTGTTAAATCAATAAATCTTAAAGCAGAAGATTTCGTTGTTATGACAGAAGGTGTTTCTGAAAATGATACTATATTGATGGCCACACAACGCGGCTCGTTAAAACGTATTAGTTTTAAAATCTTACAAGTTGCTAAAAGAGCACAACGTGGAATAACTTTATTAAAAGAATTAAAGAAAAATCCACATCGTATAGTAGCTGCACATGTAGTGACAGGTGAACATAGTCAATATACATTATATTCAAAATCAAACGAAGAACATGGTTTAATTAATGATATTCATAAATCTGAACAATATACAAATGGCTCATTCATTGTAGATACCGATGATTTTGGTGAAGTAATAGACATGTATATTAGCTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35517","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus MRSA252","NCBI_taxonomy_id":"282458"}}}},"ARO_accession":"3003312","ARO_id":"39896","ARO_name":"Staphylococcus aureus parC conferring resistance to fluoroquinolone","ARO_description":"Point mutation in Staphylococcus aureus parC resulting in fluoroquinolone resistance","ARO_category":{"36913":{"category_aro_accession":"3000619","category_aro_cvterm_id":"36913","category_aro_name":"fluoroquinolone resistant parC","category_aro_description":"ParC is a subunit of topoisomerase IV, which decatenates and relaxes DNA to allow access to genes for transcription or translation. Point mutations in ParC prevent fluoroquinolone antibiotics from inhibiting DNA synthesis, and confer low-level resistance. Higher-level resistance results from both gyrA and parC mutations.","category_aro_class_name":"AMR Gene Family"},"40471":{"category_aro_accession":"3003786","category_aro_cvterm_id":"40471","category_aro_name":"fluoroquinolone self resistant parC","category_aro_description":"Inherent parC resistance to fluoroquinolone from an antibiotic producer. The presence of these genes confers self-resistance to the antibiotic it produces.","category_aro_class_name":"AMR Gene Family"},"35942":{"category_aro_accession":"0000023","category_aro_cvterm_id":"35942","category_aro_name":"enoxacin","category_aro_description":"Enoxacin belongs to a group called fluoroquinolones. Its mode of action depends upon blocking bacterial DNA replication by binding itself to DNA gyrase and causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37004":{"category_aro_accession":"3000660","category_aro_cvterm_id":"37004","category_aro_name":"lomefloxacin","category_aro_description":"Lomefloxacin is a difluoropiperazinyl quinolone, sharing similar activities with other fluoroquinolones. It is used to treat urinary tract infections. Relative to other fluoroquinolones, it has a longer half life and has higher serum concentrations.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"37008":{"category_aro_accession":"3000664","category_aro_cvterm_id":"37008","category_aro_name":"trovafloxacin","category_aro_description":"Trovafloxacin is a trifluoroquinalone with a broad spectrum of activity that acts by inhibiting the uncoiling of supercoiled DNA. While potent against many Gram-positive and Gram-negative bacteria, it is less active against pseudomonads and Cl. difficile. It is usually taken as the prodrug trovafloxacin mesylate or alatrofloxacin mesylate for oral or intravenous administration, respectively.","category_aro_class_name":"Antibiotic"},"37009":{"category_aro_accession":"3000665","category_aro_cvterm_id":"37009","category_aro_name":"grepafloxacin","category_aro_description":"Grepafloxacin is a broad-spectrum antibacterial quinoline. It is no longer taken due to its high toxicity.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"37142":{"category_aro_accession":"3000762","category_aro_cvterm_id":"37142","category_aro_name":"pefloxacin","category_aro_description":"Pefloxacin is structurally and functionally similar to norfloxacin. It is poorly active against mycobacteria, while anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2066":{"model_id":"2066","model_name":"Escherichia coli soxS with mutation conferring antibiotic resistance","model_type":"protein overexpression model","model_type_id":"41091","model_description":"This model detects protein overexpression based on the presence of mutations.The detection of the protein without an associated mutation indicates that the protein is likely to be expressed at low or basal levels. The detection of the protein with the mutation indicates that the protein is likely overexpressed. This model reflects how certain proteins are functional with and without mutations. For example, efflux pump subunits and regulators are functional with mutations and without mutations. Without mutations, efflux pump subunits and regulators are usually expressed at a low level. When an efflux pump regulator has a mutation, it can cause the overexpression of the efflux pump it is responsible for regulating, leading to resistance to specific drugs. Protein overexpression models have two parameters: a curated BLASTP cutoff, and a curated set of mutations (single resistance variants, frameshift mutations, indels, etc.) shown clinically to confer resistance. This model type is a combination of the protein homolog and protein variant model. A detected hit can be categorized as Perfect, Strict, or Loose with no mutation(s) or as Strict or Loose with mutation(s).","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3562":"A12S"},"clinical":{"3562":"A12S"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"3528":{"protein_sequence":{"accession":"NP_418486.1","sequence":"MSHQKIIQDLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTVTHQTLGDYIRQRRLLLAAVELRTTERPIFDIAMDLGYVSQQTFSRVFRRQFDRTPSDYRHRL"},"dna_sequence":{"accession":"NC_000913","fmin":"4277059","fmax":"4277383","strand":"-","sequence":"TTACAGGCGGTGGCGATAATCGCTGGGAGTGCGATCAAACTGCCGACGGAAAACGCGGGAGAAGGTCTGCTGCGAGACATAACCCAGGTCCATTGCGATATCAAAAATCGGACGCTCGGTGGTGCGCAACTCAACGGCGGCCAGTAACAGGCGGCGTTGGCGAATGTAATCGCCAAGCGTCTGATGCGTCACCGTGCGGAACATTCGTTGCAAGTACCACTTTGAATAGCCTGATTTTTTTGCGACTACATCAATGTTAAGCGGCTGGTCAATATGCTCGTCAATCCATGCGATAAGATCCTGAATAATTTTCTGATGGGACAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3003511","ARO_id":"40113","ARO_name":"Escherichia coli soxS with mutation conferring antibiotic resistance","ARO_description":"SoxS is a global regulator that up-regulates the expression of AcrAB efflux genes. It also reduces OmpF expression to decrease cell membrane permeability.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"41445":{"category_aro_accession":"3004281","category_aro_cvterm_id":"41445","category_aro_name":"General Bacterial Porin with reduced permeability to beta-lactams","category_aro_description":"These are GBPs that are associated with decreased susceptibility to beta-lactams either through mutations in the porin protein, absence of the porin protein, or expression of the porin protein.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"},"36383":{"category_aro_accession":"3000244","category_aro_cvterm_id":"36383","category_aro_name":"reduced permeability to antibiotic","category_aro_description":"Reduction in permeability to antibiotic, generally through reduced production of porins, can provide resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1989":{"model_id":"1989","model_name":"Klebsiella pneumoniae acrR with mutation conferring multidrug antibiotic resistance","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2128":"Y114F","2185":"M109I","2867":"V165I"},"clinical":{"2128":"Y114F","2185":"M109I","2867":"V165I"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"410"}},"model_sequences":{"sequence":{"2069":{"protein_sequence":{"accession":"ABR75897.1","sequence":"MARKTKQQARETRQLILDVALRLFSQQGVSSTSLATIAKAAGVTRGAIYWHFKNKSDLFNEIWELSDASISDLEIEYRAKFPNDPLSVIREILVYVLEATVTEERRRLMMEIIYHKCEFVGEMTVVQQAQRQLSLASYERIEQTLKECIAAKLLPANLLTRRAAVLMRSYLSGLMENWLFAPDSFDLHAEARDYVAILLEMYQFCPTLRGPESLSA"},"dna_sequence":{"accession":"CP000647","fmin":"489264","fmax":"489915","strand":"+","sequence":"ATGGCACGAAAAACCAAACAACAGGCACGTGAAACCCGGCAACTGATTCTGGATGTTGCTCTGCGTCTGTTTTCGCAGCAAGGCGTATCATCTACCTCGTTGGCAACAATTGCAAAAGCTGCGGGTGTAACGAGGGGGGCTATCTACTGGCATTTCAAGAATAAATCAGATTTATTCAACGAAATTTGGGAGCTGTCAGACGCCAGTATTAGCGATCTCGAAATTGAGTATCGGGCAAAATTCCCCAACGATCCACTCTCAGTTATCAGGGAGATTCTAGTCTATGTTCTTGAAGCGACAGTGACAGAAGAACGTCGACGATTAATGATGGAGATTATCTATCATAAGTGTGAGTTCGTCGGTGAAATGACCGTGGTGCAGCAGGCCCAGCGGCAGCTCTCCCTGGCGAGTTATGAGCGTATCGAGCAGACCTTGAAAGAGTGCATCGCGGCGAAGCTGCTGCCCGCCAATTTACTCACCCGGCGGGCGGCCGTGTTAATGCGCAGCTACCTTTCCGGGCTGATGGAAAACTGGCTGTTTGCCCCCGATTCGTTCGACCTGCATGCGGAAGCGCGGGACTACGTCGCTATTCTGCTGGAGATGTATCAATTCTGCCCGACGCTACGCGGCCCGGAGAGCTTGTCAGCTTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37607","NCBI_taxonomy_name":"Klebsiella pneumoniae subsp. pneumoniae MGH 78578","NCBI_taxonomy_id":"272620"}}}},"ARO_accession":"3003373","ARO_id":"39957","ARO_name":"Klebsiella pneumoniae acrR with mutation conferring multidrug antibiotic resistance","ARO_description":"AcrR is a repressor of the AcrAB-TolC multidrug efflux complex. AcrR mutations result in high level antibiotic resistance.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"535":{"model_id":"535","model_name":"Morganella morganii gyrB conferring resistance to fluoroquinolone","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2164":"S464Y","3448":"S463A"},"clinical":{"2164":"S464Y","3448":"S463A"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1200"}},"model_sequences":{"sequence":{"4329":{"protein_sequence":{"accession":"YP_007503908.1","sequence":"MSNTYDSSSIKVLKGLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGYCKDIIVTIHNDNSVSVQDDGRGIPTGIHEEEGVSAAEVIMTVLHAGGKFDDNSYKVSGGLHGVGVSVVNALSEKLELVIRRDGKVHEQIYRHGEPQDRLTVVGETDKTGTRVRFWPSMDTFKGETEFQYDILAKRLRELSFLNSGVSIRLIDKRDGKEDHFHYEGGIKAFVEYLSRAKTSIHNNVFYFSTEKDDIGVEISMQWNDSFQENVYCFTNNIPQRDGGAHLAGFRAAMTRTLNSYIEKEGLNKKSKVSTTGDDAREGLVAVISVKVPDPKFSSQTKDKLVSSEVKTAVETLMNEKLSEYLDENPNDTKIIVGKIIDAARAREAARRAREMTRRKGALDLAGLPGKLADCQERDPAFSELYLVEGDSAGGSAKQGRNRKNQAILPLKGKILNVEKARFDKMLASQEVATLITALGCGIGRDEYNPDKLRYHSIIIMTDADVDGSHIRTLLLTFFYRQMPEIIERGYVYIAQPPLYKVKKGKQEQYIKDDEAMEQYQVSIALDGAALYVNENAAPIQGEHLEKLLHEYNGAHKIIRRLERLYPLALLNSLVYQPKLEESALLNKTEVEAWAQSLTERLTRHEEHGSTYSYRIAENKERQLFEPVLTIRTHGVDTDYNLDFDFVHGSEYARISKLGELIRGLIEEGAYVVRGERRQNVSNFEQALDWLMKESRRGLAVQRYKGLGEMNPEQLWETTMNPETRRMLQVTVKDAIATDQLFTTLMGDDVEPRRAFIEENALKAANIDV"},"dna_sequence":{"accession":"NC_020418","fmin":"545199","fmax":"547614","strand":"-","sequence":"TTATACGTCGATGTTTGCCGCTTTCAGGGCATTCTCTTCGATAAAGGCACGGCGCGGTTCAACATCATCACCCATCAGTGTGGTGAATAACTGATCCGTTGCAATCGCATCTTTTACCGTGACCTGCAACATACGGCGGGTTTCCGGGTTCATTGTGGTTTCCCACAGCTGTTCCGGGTTCATTTCACCCAGCCCTTTATAGCGCTGTACAGCCAGACCACGGCGTGATTCTTTCATCAGCCAGTCCAGTGCCTGCTCAAAGTTGCTGACGTTCTGACGGCGTTCACCACGGACAACATAAGCACCTTCTTCAATCAGACCACGGATAAGCTCACCCAGTTTGGAGATACGGGCATATTCGCTGCCGTGAACAAAATCGAAATCCAGATTGTAGTCAGTATCCACACCGTGGGTACGGATAGTCAGTACCGGCTCAAACAGCTGGCGCTCTTTGTTTTCCGCAATACGGTAGCTGTAGGTGCTGCCGTGCTCTTCATGACGGGTCAGGCGCTCTGTCAGGCTCTGTGCCCAGGCTTCCACCTCGGTTTTGTTCAGCAGCGCGGATTCTTCCAGTTTCGGCTGGTAGACCAGGCTGTTTAACAGTGCCAGCGGATAGAGACGCTCTAAACGGCGGATAATTTTGTGTGCGCCGTTGTATTCGTGCAGCAGTTTTTCCAGATGTTCGCCCTGAATCGGAGCTGCATTTTCGTTTACATACAGTGCCGCGCCATCCAGTGCGATAGAGACCTGATACTGCTCCATCGCTTCGTCATCTTTAATATACTGTTCCTGCTTGCCTTTTTTCACTTTATACAGCGGCGGCTGTGCGATATACACATAACCGCGCTCAATGATTTCCGGCATCTGACGGTAGAAGAAAGTCAGTAACAGGGTACGGATGTGTGAACCATCGACGTCGGCATCGGTCATGATGATGATGCTGTGATAGCGCAGTTTGTCCGGGTTGTATTCGTCGCGGCCGATACCGCAGCCGAGTGCGGTGATCAGGGTGGCAACTTCCTGAGAAGCCAGCATTTTATCAAAACGCGCCTTCTCAACGTTCAGGATTTTACCTTTCAGCGGCAGGATAGCCTGGTTCTTACGGTTACGCCCCTGTTTTGCAGAGCCGCCCGCAGAGTCCCCTTCCACTAAGTACAGTTCGGAGAAGGCCGGGTCGCGTTCCTGACAATCCGCCAGTTTACCCGGCAGACCGGCTAAATCCAGCGCGCCTTTACGGCGGGTCATTTCACGGGCACGGCGTGCAGCTTCACGGGCGCGTGCGGCATCAATAATTTTGCCGACAATGATTTTGGTGTCGTTCGGGTTTTCATCCAGATATTCAGACAGCTTTTCGTTCATCAGGGTTTCAACCGCCGTTTTCACTTCGGAAGAGACCAGCTTGTCTTTAGTCTGGGAGGAGAATTTCGGATCCGGCACTTTGACGGAAATGACCGCCACCAGTCCTTCACGGGCATCGTCCCCGGTGGTGCTGACTTTGGATTTTTTATTCAGCCCTTCTTTCTCAATATAGCTGTTGAGGGTACGGGTCATGGCGGCGCGGAAACCGGCGAGGTGAGCACCACCGTCGCGCTGCGGAATGTTGTTGGTGAAGCAGTATACGTTTTCCTGGAAGGAGTCATTCCACTGCATGGAGATTTCCACGCCGATATCGTCTTTCTCAGTGGAGAAATAGAAAACGTTGTTATGAATCGAAGTTTTGGCGCGGCTTAAATATTCCACGAATGCTTTGATACCGCCTTCGTAGTGAAAGTGATCTTCTTTGCCGTCGCGTTTATCGATCAGACGGATCGATACACCGGAGTTCAGGAAGGAGAGTTCGCGCAGGCGTTTTGCCAGAATGTCGTACTGGAATTCAGTCTCGCCTTTGAAGGTGTCCATGCTCGGCCAGAAACGCACGCGTGTCCCGGTTTTATCGGTTTCGCCGACAACAGTCAGGCGATCCTGCGGTTCACCGTGGCGGTAAATCTGCTCGTGAACTTTGCCGTCACGGCGGATAACCAGTTCCAGTTTTTCAGACAGGGCGTTAACAACAGAGACCCCGACGCCGTGCAGGCCGCCTGAGACTTTATAGGAGTTATCATCGAACTTCCCGCCGGCGTGCAGAACAGTCATGATAACTTCTGCGGCGGAGACGCCTTCTTCTTCATGGATCCCGGTCGGGATACCGCGACCGTCATCCTGTACGGAGACTGAATTATCATTGTGAATGGTCACAATGATGTCTTTACAGTAACCGGCGAGGGCTTCGTCGATAGCGTTGTCAACAACCTCGAAGACCATGTGGTGTAAACCGGTTCCGTCATCGGTATCACCAATGTACATTCCCGGGCGTTTACGCACCGCGTCCAGCCCTTTTAATACTTTGATACTTGAGGAGTCATAGGTATTCGACAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40075","NCBI_taxonomy_name":"Morganella morganii subsp. morganii KT","NCBI_taxonomy_id":"1124991"}}}},"ARO_accession":"3003306","ARO_id":"39890","ARO_name":"Morganella morganii gyrB conferring resistance to fluoroquinolone","ARO_description":"Point mutation in Morganella morganii resulting in fluoroquinolone resistance","ARO_category":{"37244":{"category_aro_accession":"3000864","category_aro_cvterm_id":"37244","category_aro_name":"fluoroquinolone resistant gyrB","category_aro_description":"Point mutations in DNA gyrase subunit B (gyrB) observed in Mycobacterium tuberculosis can result in resistance to fluoroquinolones.","category_aro_class_name":"AMR Gene Family"},"35942":{"category_aro_accession":"0000023","category_aro_cvterm_id":"35942","category_aro_name":"enoxacin","category_aro_description":"Enoxacin belongs to a group called fluoroquinolones. Its mode of action depends upon blocking bacterial DNA replication by binding itself to DNA gyrase and causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36271":{"category_aro_accession":"3000132","category_aro_cvterm_id":"36271","category_aro_name":"clorobiocin","category_aro_description":"Clorobiocin is an aminocoumarin antibiotic produced by Streptomyces roseochromogenes, and binds DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36289":{"category_aro_accession":"3000150","category_aro_cvterm_id":"36289","category_aro_name":"coumermycin A1","category_aro_description":"Coumermycin A1 is an antibiotic produced by Streptomyces rishiriensis, and binds DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37004":{"category_aro_accession":"3000660","category_aro_cvterm_id":"37004","category_aro_name":"lomefloxacin","category_aro_description":"Lomefloxacin is a difluoropiperazinyl quinolone, sharing similar activities with other fluoroquinolones. It is used to treat urinary tract infections. Relative to other fluoroquinolones, it has a longer half life and has higher serum concentrations.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"37008":{"category_aro_accession":"3000664","category_aro_cvterm_id":"37008","category_aro_name":"trovafloxacin","category_aro_description":"Trovafloxacin is a trifluoroquinalone with a broad spectrum of activity that acts by inhibiting the uncoiling of supercoiled DNA. While potent against many Gram-positive and Gram-negative bacteria, it is less active against pseudomonads and Cl. difficile. It is usually taken as the prodrug trovafloxacin mesylate or alatrofloxacin mesylate for oral or intravenous administration, respectively.","category_aro_class_name":"Antibiotic"},"37009":{"category_aro_accession":"3000665","category_aro_cvterm_id":"37009","category_aro_name":"grepafloxacin","category_aro_description":"Grepafloxacin is a broad-spectrum antibacterial quinoline. It is no longer taken due to its high toxicity.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"37142":{"category_aro_accession":"3000762","category_aro_cvterm_id":"37142","category_aro_name":"pefloxacin","category_aro_description":"Pefloxacin is structurally and functionally similar to norfloxacin. It is poorly active against mycobacteria, while anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"40937":{"category_aro_accession":"3004010","category_aro_cvterm_id":"40937","category_aro_name":"cinoxacin","category_aro_description":"Cinoxacin is a fluoroquinolone antibiotic primarily used for the treatment of urinary tract infections in adults. Cinoxacin binds to DNA gyrase, resulting in double-stranded DNA breaks and cell death.","category_aro_class_name":"Antibiotic"},"40938":{"category_aro_accession":"3004011","category_aro_cvterm_id":"40938","category_aro_name":"clinafloxacin","category_aro_description":"Clinafloxacin is a fluoroquinolone antibiotic and gyrase (DNA topoisomerase II) inhibitor. It binds to DNA gyrase and disrupts replication by causing double-stranded DNA breaks, resulting in cell death.","category_aro_class_name":"Antibiotic"},"40939":{"category_aro_accession":"3004012","category_aro_cvterm_id":"40939","category_aro_name":"Clofazimine","category_aro_description":"Clofazimine is a fluoroquinolone-class phenazine dye used for the treatment of leprosy. Clofazimine binds to DNA and disrupts bacterial DNA gyrase, thereby causing double-stranded DNA breaks, and subsequent cell death.","category_aro_class_name":"Antibiotic"},"40940":{"category_aro_accession":"3004013","category_aro_cvterm_id":"40940","category_aro_name":"fleroxacin","category_aro_description":"Fleroxacin is a broad spectrum fluoroquinolone antibiotic that inhibits the DNA supercoiling activity of bacterial DNA gyrase, resulting in double-stranded DNA breaks and subsequent cell death.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1721":{"model_id":"1721","model_name":"Mycobacterium leprae folP with mutation conferring resistance to dapsone","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2140":"T53A","2175":"T53I","2200":"P55R","2201":"P55L","2202":"P55S","3292":"T53P","3293":"T53N","3294":"P55T","3295":"P55A","3296":"P55H","3406":"R54G","3407":"V48G","3408":"V48A","3409":"V48F"},"clinical":{"2140":"T53A","2175":"T53I","2200":"P55R","2201":"P55L","2202":"P55S"},"experimental":{"3292":"T53P","3293":"T53N","3294":"P55T","3295":"P55A","3296":"P55H","3406":"R54G","3407":"V48G","3408":"V48A","3409":"V48F"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2070":{"protein_sequence":{"accession":"CAC29732.1","sequence":"MSLAPVQVIGVLNVTDNSFSDGGRYLDPDDAVQHGLAMVAEGAAIVDVGGESTRPGAIRTDPRVELSRIVPVVKELAAQGITVSIDTTRADVARAALQSGARIVNDVSGGRADPAMAPLVAEAGVAWVLMHWRLMSAERPYEAPNYRDVVAEVRADLLAGVDQAVAAGVDPGSLVIDPGLGFAKTGQHNWALLNALPELVATGVPILLGASRKRFLGRLLAGADGAVRPPDGRETATAVISALAALHGAWGVRVHDVRASVDALKVVGAWLHAGPQIEKVRCDG"},"dna_sequence":{"accession":"AL450380","fmin":"296695","fmax":"297550","strand":"+","sequence":"GTGAGTTTGGCGCCAGTGCAGGTTATTGGGGTTTTGAACGTCACTGACAATTCGTTCTCAGATGGCGGACGTTACCTTGATCCTGACGATGCTGTCCAGCACGGCCTGGCAATGGTCGCGGAAGGCGCGGCGATTGTCGACGTCGGTGGCGAATCGACCCGGCCCGGTGCCATTAGGACCGATCCTCGAGTTGAACTCTCTCGTATCGTTCCTGTCGTAAAAGAACTTGCAGCACAGGGGATTACAGTAAGTATCGATACTACGCGCGCTGATGTTGCACGGGCGGCGCTGCAAAGCGGCGCACGGATCGTCAACGATGTGTCTGGTGGGCGAGCAGATCCCGCGATGGCTCCTCTGGTGGCTGAAGCCGGTGTTGCGTGGGTGTTGATGCACTGGCGACTGATGTCGGCTGAACGGCCGTATGAGGCTCCGAATTACCGCGACGTGGTGGCTGAAGTGCGTGCCGACCTACTGGCTGGTGTCGATCAGGCTGTGGCCGCAGGTGTTGATCCTGGGAGTCTAGTGATCGATCCCGGGCTTGGATTCGCCAAGACGGGACAGCACAATTGGGCGCTGCTGAATGCGTTACCGGAGTTGGTGGCTACTGGGGTCCCGATTCTACTTGGCGCCTCGCGTAAACGGTTCCTGGGTAGGTTATTAGCTGGGGCTGATGGCGCGGTACGACCGCCGGACGGACGTGAGACGGCGACCGCGGTGATTTCCGCACTTGCTGCCCTACACGGGGCTTGGGGTGTTCGGGTGCACGATGTGCGTGCCTCGGTCGACGCACTCAAGGTCGTCGGGGCTTGGCTGCATGCTGGGCCGCAGATTGAAAAGGTTAGATGTGATGGCTGAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40083","NCBI_taxonomy_name":"Mycobacterium leprae TN","NCBI_taxonomy_id":"272631"}}}},"ARO_accession":"3003389","ARO_id":"39973","ARO_name":"Mycobacterium leprae folP with mutation conferring resistance to dapsone","ARO_description":"Dapsone inhibits bacterial synthesis of dihydrofolic acid by competing with with para-aminobenzoate for the active site of dihydropteroate synthetase. Point mutation within the Mycobacterium leprae folP gene results in lowered affinity of dapsone for folP.","ARO_category":{"39972":{"category_aro_accession":"3003388","category_aro_cvterm_id":"39972","category_aro_name":"dapsone resistant dihydropteroate synthase folP","category_aro_description":"Dapsone inhibits bacterial synthesis of dihydrofolic acid by competing with with para-aminobenzoate for the active site of dihydropteroate synthetase. Thus acts as a competitive inhibitor of folP. Point mutation within the folP gene results in lowered affinity of dapsone for folP","category_aro_class_name":"AMR Gene Family"},"36463":{"category_aro_accession":"3000324","category_aro_cvterm_id":"36463","category_aro_name":"sulfadiazine","category_aro_description":"Sulfadiazine is a potent inhibitor of dihydropteroate synthase, interfering with the tetrahydrofolic biosynthesis pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor to many nucleotides and amino acids.","category_aro_class_name":"Antibiotic"},"36464":{"category_aro_accession":"3000325","category_aro_cvterm_id":"36464","category_aro_name":"sulfadimidine","category_aro_description":"Sulfadimidine is an alkaline sulfonamide antibiotic that inhibits dihydropteroate synthase, and enzyme in the tetrahydrofolic acid biosynthesis pathway. This interferes with the production of folate, which is a precursor to many amino acids and nucleotides.","category_aro_class_name":"Antibiotic"},"36466":{"category_aro_accession":"3000327","category_aro_cvterm_id":"36466","category_aro_name":"sulfadoxine","category_aro_description":"Sulfadoxine is an inhibitor of dihydropteroate synthase, interfering with the tetrahydrofolic biosynthesis pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor to many nucleotides and amino acids.","category_aro_class_name":"Antibiotic"},"36468":{"category_aro_accession":"3000329","category_aro_cvterm_id":"36468","category_aro_name":"sulfamethoxazole","category_aro_description":"Sulfamethoxazole is a sulfonamide antibiotic usually taken with trimethoprim, a diaminopyrimidine antibiotic. Sulfamethoxazole inhibits dihydropteroate synthase, essential to tetrahydrofolic acid biosynthesis. This pathway generates compounds used in the synthesis of many amino acids and nucleotides.","category_aro_class_name":"Antibiotic"},"36469":{"category_aro_accession":"3000330","category_aro_cvterm_id":"36469","category_aro_name":"sulfisoxazole","category_aro_description":"Sulfisoxazole is an inhibitor of dihydropteroate synthase, interfering with the tetrahydrofolic biosynthesis pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor to many nucleotides and amino acids.","category_aro_class_name":"Antibiotic"},"37027":{"category_aro_accession":"3000683","category_aro_cvterm_id":"37027","category_aro_name":"sulfacetamide","category_aro_description":"Sulfacetamide is a very soluable sulfonamide antibiotic previously used to treat urinary tract infections. Its relatively low activity and toxicity to those with Stevens-Johnson syndrome have reduced its use and availability.","category_aro_class_name":"Antibiotic"},"37028":{"category_aro_accession":"3000684","category_aro_cvterm_id":"37028","category_aro_name":"mafenide","category_aro_description":"Mafenide is a sulfonamide used topically for treating burns.","category_aro_class_name":"Antibiotic"},"37042":{"category_aro_accession":"3000698","category_aro_cvterm_id":"37042","category_aro_name":"sulfasalazine","category_aro_description":"Sulfasalazine is a derivative of the early sulfonamide sulfapyridine (salicylazosulfapyridine). It was developed to increase water solubility and is taken orally for ulcerative colitis.","category_aro_class_name":"Antibiotic"},"37043":{"category_aro_accession":"3000699","category_aro_cvterm_id":"37043","category_aro_name":"sulfamethizole","category_aro_description":"Sulfamethizole is a short-acting sulfonamide that inhibits dihydropteroate synthetase.","category_aro_class_name":"Antibiotic"},"39996":{"category_aro_accession":"3003412","category_aro_cvterm_id":"39996","category_aro_name":"dapsone","category_aro_description":"Dapsone is a sulfone in which it inhibits folic acid synthesis, such as the dihydropteroate synthase.","category_aro_class_name":"Antibiotic"},"36421":{"category_aro_accession":"3000282","category_aro_cvterm_id":"36421","category_aro_name":"sulfonamide antibiotic","category_aro_description":"Sulfonamides are broad spectrum, synthetic antibiotics that contain the sulfonamide group. Sulfonamides inhibit dihydropteroate synthase, which catalyzes the conversion of p-aminobenzoic acid to dihydropteroic acid as part of the tetrahydrofolic acid biosynthetic pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor of many nucleotides and amino acids. Many sulfamides are taken with trimethoprim, an inhibitor of dihydrofolate reductase, also disturbing the trihydrofolic acid synthesis pathway.","category_aro_class_name":"Drug Class"},"39985":{"category_aro_accession":"3003401","category_aro_cvterm_id":"39985","category_aro_name":"sulfone antibiotic","category_aro_description":"A sulfone active against a wide range of bacteria but mainly employed for its actions against mycobacterium laprae. Its mechanism of action  involves inhibition of folic acid synthesis in susceptible organisms.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"100":{"model_id":"100","model_name":"Mycobacterium tuberculosis ethA with mutation conferring resistance to ethionamide","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2494":"G43S","2495":"E223K","2496":"I338S","2497":"G385D","2498":"T392A","2499":"G413D","2500":"R463S","4143":"G43C","4144":"P51L","4145":"D58A","4146":"T84D","4149":"T342K","4150":"A381P","4151":"T186K","4157":"D55A"},"clinical":{"2494":"G43S","2495":"E223K","2496":"I338S","2497":"G385D","2498":"T392A","2499":"G413D","2500":"R463S","4143":"G43C","4144":"P51L","4145":"D58A","4146":"T84D","4149":"T342K","4150":"A381P","4151":"T186K","4157":"D55A"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"900"},"41343":{"param_type":"deletion mutation from nucleotide sequence","param_description":"A subtype of the deletion mutation detection model parameter. This parameter is used when a set of deletion mutations is reported in a nucleotide sequence format. Such mutations may be of variable length - possibly causing a frameshift, but not premature termination of functional knockout. Mutation parameters of this type are reported in the CARD with the notation: [-]nt[position]:[nucleotides].","param_type_id":"41343","param_value":{"8087":"-nt1290:C","8088":"-nt768:G","8089":"-nt110:A","8093":"-nt703:T","8094":"-nt65:1"}},"41345":{"param_type":"insertion mutation from nucleotide sequence","param_description":"A subtype of the insertion mutation detection model parameter. This parameter is used when a set of insertion mutations is reported in a nucleotide sequence format. Such mutations may be of variable length - possibly causing a frameshift, but not causing premature termination or a functional knockout. Mutation parameters of this type are reported in CARD with the notation: [+]nt[position]:[nucleotides].","param_type_id":"41345","param_value":{"8090":"+nt338:A","8091":"+nt811:1"}},"41339":{"param_type":"mutation in regulatory element","param_description":"An AMR detection model parameter to describe mutations in regulatory elements upstream of a coding DNA region shown to confer resistance to an antibiotic drug or drug class. Regulatory element mutations in CARD use the following notation: nt[wild-type][-][position][mutation].","param_type_id":"41339","param_value":{"8312":"ntT-11C"}}},"model_sequences":{"sequence":{"4283":{"protein_sequence":{"accession":"AAK48336.1","sequence":"MTEHLDVVIVGAGISGVSAAWHLQDRCPTKSYAILEKRESMGGTWDLFRYPGIRSDSDMYTLGFRFRPWTGRQAIADGKPILEYVKSTAAMYGIDRHIRFHHKVISADWSTAENRWTVHIQSHGTLSALTCEFLFLCSGYYNYDEGYSPRFAGSEDFVGPIIHPQHWPEDLDYDAKNIVVIGSGATAVTLVPALADSGAKHVTMLQRSPTYIVSQPDRDGIAEKLNRWLPETMAYTAVRWKNVLRQAAVYSACQKWPRRMRKMFLSLIQRQLPEGYDVRKHFGPHYNPWDQRLCLVPNGDLFRAIRHGKVEVVTDTIERFTATGIRLNSGRELPADIIITATGLNLQLFGGATATIDGQQVDITTTMAYKGMMLSGIPNMAYTVGYTNASWTLKADLVSEFVCRLLNYMDDNGFDTVVVERPGSDVEERPFMEFTPGYVLRSLDELPKQGSRTPWRLNQNYLRDIRLIRRGKIDDEGLRFAKRPAPVGV"},"dna_sequence":{"accession":"AE000516","fmin":"4318327","fmax":"4319797","strand":"-","sequence":"CTAAACCCCCACCGGGGCAGGCCTTTTGGCGAACCGCAGACCCTCGTCGTCGATCTTGCCGCGCCGGATGAGCCGGATGTCACGTAGGTAGTTCTGATTCAGGCGCCACGGTGTACGCGAACCCTGCTTGGGCAGCTCGTCCAGCGAGCGCAGCACGTAACCTGGGGTGAACTCCATGAAGGGCCGCTCTTCGACATCTGAGCCCGGTCGCTCGACGACCACGGTGTCAAAACCGTTGTCGTCCATGTAATTCAACAAGCGACAGACAAACTCCGACACCAGGTCGGCCTTCAGCGTCCAGGAGGCATTGGTGTAGCCAACCGTGTAGGCCATGTTGGGGATGCCGGAAAGCATCATGCCCTTGTAGGCCATCGTCGTGGTGATGTCCACTTGTTGTCCGTCGATAGTCGCCGTCGCCCCACCAAAAAGCTGCAGGTTCAACCCCGTTGCGGTAATGATGATGTCAGCCGGCAGTTCGCGACCTGAGTTCAGCCGGATTCCGGTCGCGGTGAACCGTTCAATGGTGTCGGTCACCACCTCGACCTTCCCGTGACGAATGGCCCGGAACAGGTCGCCGTTGGGCACCAAGCACAATCGCTGGTCCCAGGGGTTGTAGTGCGGGCCGAAGTGCTTTCGCACGTCGTACCCCTCGGGTAGCTGGCGCTGGATCAGGCTCAGGAACATCTTCCGCATGCGCCGTGGCCACTTCTGGCAGGCGCTGTACACGGCCGCCTGGCGCAGCACGTTCTTCCACCGTACCGCGGTGTAGGCCATGGTCTCCGGCAGCCAGCGGTTGAGCTTCTCGGCGATGCCGTCCCGGTCTGGCTGCGACACGATGTAGGTGGGTGAGCGCTGCAGCATCGTGACGTGCTTGGCGCCCGAGTCCGCCAGCGCCGGCACGAGCGTGACCGCCGTTGCGCCACTGCCGATCACGACGATGTTCTTAGCGTCGTAGTCGAGGTCCTCGGGCCAGTGCTGCGGATGGATGATCGGCCCGACGAAATCCTCCGAGCCGGCGAATCTCGGCGAGTAGCCCTCGTCGTAGTTGTAGTAGCCGCTGCACAGAAAGAGGAATTCGCAGGTGAGGGCGCTGAGCGTGCCGTGGCTTTGGATGTGAACGGTCCAGCGGTTTTCCGCGGTCGACCAATCGGCACTGATCACCTTGTGGTGGAACCGGATATGCCTGTCGATTCCATACATGGCCGCGGTGCTCTTGACGTACTCGAGGATGGGCTTGCCGTCGGCGATCGCCTGCCGTCCGGTCCAGGGACGGAATCGGAAACCTAGCGTGTACATGTCGGAGTCGGAGCGAATTCCGGGATAACGGAACAAATCCCAGGTGCCGCCCATGGATTCCCGCTTTTCCAGGATGGCGTAGCTCTTGGTCGGGCAACGGTCCTGCAGGTGCCAGGCCGCGCTGACACCGGAGATTCCAGCGCCCACGATGACAACGTCGAGGTGCTCGGTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37081","NCBI_taxonomy_name":"Mycobacterium tuberculosis CDC1551","NCBI_taxonomy_id":"83331"}}}},"ARO_accession":"3003458","ARO_id":"40051","ARO_name":"Mycobacterium tuberculosis ethA with mutation conferring resistance to ethionamide","ARO_description":"Specific mutations that occurs on Mycobacterium tuberculosis ethA causing it to be ethionamide resistant","ARO_category":{"40050":{"category_aro_accession":"3003457","category_aro_cvterm_id":"40050","category_aro_name":"ethionamide resistant ethA","category_aro_description":"Mutations that occurs on the ethA genes resulting in the inability to catalyzes the oxidation of ethionamide (ETH) to the corresponding sulfoxide (the active drug)","category_aro_class_name":"AMR Gene Family"},"36659":{"category_aro_accession":"3000520","category_aro_cvterm_id":"36659","category_aro_name":"isoniazid","category_aro_description":"Isoniazid is an organic compound that is the first-line anti tuberculosis medication in prevention and treatment. As a prodrug, it is activated by mycobacterial catalase-peroxidases such as M. tuberculosis KatG. Isoniazid inhibits mycolic acid synthesis, which prevents cell wall synthesis in mycobacteria.","category_aro_class_name":"Drug Class"},"40067":{"category_aro_accession":"3003474","category_aro_cvterm_id":"40067","category_aro_name":"ethionamide","category_aro_description":"ethionamide is a second-line antitubercular agent that inhibits mycolic acid synthesis","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"36":{"model_id":"36","model_name":"Mycobaterium leprae gyrA conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2127":"A91T"},"clinical":{"2127":"A91T"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1500"}},"model_sequences":{"sequence":{"2059":{"protein_sequence":{"accession":"CAC29514.1","sequence":"MTDITLPPGDGSIQRVEPVDIQQEMQRSYIDYAMSVIVGRALPEVRDGLKPVHRRVLYAMLDSGFRPDRSHAKSARSVAETMGNYHPHGDASIYDTLVRMAQPWSLRYPLVDGQGNFGSPGNDPPAAMRYCVSGNSLVRLLFGKSIRIGDIVTGAQFNSDNPIDLKVLDRHGNPVVADYLFHSGEHQTYTVRTTEGYEITGTSNHPLLCLVNVGGIPTLLWKLIGEIRSGDYVVLQRIPPVEFGPADWYSTMEALLFGAFISGGFVFQDHAGFNSLDRDYFTMVVNAYDTVVGGLRCISSRITVSGSTLLELDVYNLIEFKKTRLSGLCGQRSADKLVPDWLWHSPSTVKRAFLQALFEGEGFSSILSRNIIEISYSTLSERLAADVQQMLLEFGVVSERYCHTVNEYKVVIANRAQVEMFFTQVGFGVTKQAKLIRDVVSMSPCVGMDINCVPGLATFIRKHCDNRWVEEDSFNQHNVDCVQHWHHHSAEIVGHIADPDIRAIVTDLTDGRFYYARVASVTDTGIQPVFSLHVDTEDHSFLTNGFISHNTEARLTPLAMEMLREIDEETVDFISNYDGRVQEPMVLPSRFPNLLANGSGGIAVGMATNIPPHNLYELADAVFWCLENHDADEETMLVAVMERVKGPDFPTAGLIVGSQGIADAYKTGRGSIRIRGVVEVEEDSRGRTSLVITELPYQVNHDNFITSIAEQVRTGRLAGISNVEDQGSDRVGVRIVIEIKRDAVAKVVLNNLYKHTQLQTSFGANMLSIVDGVPRTLRLDQMICYYVEHQLDVIVRRTTYRLRKANERAHILRGLVKALDALDEVITLIRASQTVDIARVGVVELLDIDDIQAQAILDMQLRRLAALERQRIIDDLAKIEVEIADLGDILAKPERRRGIIRNELTEIAEKYGDDRRTRIIAVDGDVNDEDLIAREEVVVTITETGYAKRTKTDLYRSQKRGGKGVQGAGLKQDDIVRHFFVCSTHDWILFFTTQGRVYRAKAYELPEASRTARGQHVANLLAFQPEERIAQVIQIRSYEDAPYLVLATRAGLVKKSKLTDFDSNRSGGIVAINLRDNDELVGAVLCAADGDLLLVSANGQSIRFSATDEALRPMGRATSGVQGMRFNADDRLLSLNVVREDTYLLVATSGGYAKRTSIEEYPMQGRGGKGVLTVMYDRRRGSLVGAIVVDEDSELYAITSGGGVIRTTARQVRQAGRQTKGVRLMNLGEGDTLLAIARNAEESADGGVG"},"dna_sequence":{"accession":"AL450380","fmin":"7317","fmax":"11067","strand":"+","sequence":"ATGACTGATATCACGCTGCCACCAGGTGACGGTTCTATACAGCGGGTTGAGCCGGTCGACATTCAGCAGGAAATGCAGCGCAGCTATATTGATTACGCGATGAGTGTGATTGTGGGCCGGGCGTTGCCTGAAGTCCGCGATGGTCTCAAACCGGTACATCGTCGGGTCTTGTACGCGATGTTAGACTCCGGTTTCCGCCCGGACCGTAGCCACGCTAAGTCAGCACGGTCAGTCGCTGAGACGATGGGCAATTACCATCCGCACGGCGACGCATCGATTTATGACACGTTAGTGCGCATGGCGCAGCCGTGGTCGCTGCGGTATCCCTTGGTTGATGGGCAAGGCAATTTCGGTTCGCCGGGTAATGACCCACCGGCAGCGATGCGTTATTGTGTGTCAGGAAATTCCTTGGTGAGGTTGCTATTTGGGAAATCAATACGAATCGGTGATATCGTTACTGGAGCTCAGTTCAATTCGGACAATCCGATCGACTTGAAGGTTCTTGATCGGCATGGTAATCCGGTTGTAGCCGATTATTTATTCCATTCAGGAGAGCACCAAACCTATACAGTGCGCACCACTGAAGGCTATGAGATCACCGGGACGTCGAACCATCCCTTGTTGTGTTTAGTGAATGTCGGCGGTATACCCACCTTGTTGTGGAAGCTGATTGGAGAAATTCGATCAGGAGACTACGTTGTTTTACAGCGGATCCCACCAGTGGAATTTGGTCCGGCGGACTGGTATTCTACGATGGAAGCATTGTTATTCGGAGCCTTTATTAGTGGGGGCTTCGTTTTTCAGGACCATGCTGGATTTAACAGCCTTGACCGTGACTATTTCACCATGGTTGTTAATGCTTATGATACGGTTGTGGGTGGCCTGCGTTGCATATCTTCTCGAATCACCGTATCGGGGTCGACGCTACTCGAACTTGATGTTTATAACCTCATCGAGTTTAAGAAGACAAGACTTAGCGGTTTATGCGGGCAACGGTCTGCGGACAAGTTGGTACCTGACTGGTTGTGGCACTCACCTTCCACCGTCAAACGAGCATTCCTTCAGGCATTGTTTGAAGGTGAAGGATTTTCTTCGATATTGTCGCGAAATATAATTGAGATTTCCTACTCGACACTTAGTGAGCGACTGGCCGCCGACGTCCAGCAGATGCTGCTTGAATTCGGAGTCGTGTCTGAGCGCTATTGCCATACTGTCAATGAGTACAAGGTTGTCATAGCTAACCGCGCTCAAGTAGAAATGTTTTTCACCCAAGTCGGTTTCGGTGTTACTAAACAAGCTAAGCTTATCCGGGACGTGGTATCTATGTCTCCATGCGTTGGCATGGATATCAACTGCGTACCAGGTTTGGCCACTTTCATTCGTAAGCATTGTGATAACCGCTGGGTCGAGGAAGACTCATTTAATCAGCATAATGTTGATTGCGTCCAACATTGGCACCATCATAGCGCGGAAATCGTCGGCCACATCGCCGATCCCGATATTCGTGCCATCGTGACTGACCTTACTGATGGCCGGTTCTACTACGCGCGCGTCGCGTCCGTGACTGATACCGGTATTCAACCTGTGTTCAGTCTACATGTGGACACCGAGGATCATTCGTTTTTGACTAATGGATTCATCAGCCATAACACCGAGGCTCGGCTTACTCCATTGGCGATGGAAATGTTGCGCGAGATCGACGAGGAGACAGTTGATTTCATATCTAACTACGATGGCCGGGTGCAGGAACCGATGGTGTTGCCTAGCCGTTTTCCCAACCTGTTGGCTAATGGTTCTGGCGGTATCGCGGTCGGCATGGCTACCAATATCCCGCCGCACAACCTGTATGAGCTCGCCGACGCTGTGTTTTGGTGCCTAGAGAACCATGACGCTGACGAAGAGACGATGCTGGTCGCTGTTATGGAACGGGTCAAAGGTCCTGATTTCCCTACCGCCGGGTTGATTGTCGGTTCGCAAGGCATTGCCGATGCTTACAAGACTGGCCGTGGTTCCATTCGGATACGCGGAGTTGTTGAGGTTGAAGAAGATTCACGCGGAAGGACGTCATTGGTCATCACTGAGCTACCGTATCAGGTCAACCACGACAACTTCATCACTTCTATCGCTGAGCAAGTCCGCACTGGCCGGCTAGCCGGCATCTCCAATGTAGAAGACCAAGGCAGCGACCGGGTTGGTGTACGTATCGTCATCGAGATCAAGCGTGACGCGGTGGCCAAAGTGGTGCTCAATAACCTGTACAAGCATACTCAGCTGCAAACTAGTTTCGGAGCCAACATGTTGTCAATCGTTGACGGCGTGCCGCGCACTTTGCGGTTGGATCAGATGATTTGTTATTATGTCGAACATCAACTGGACGTCATTGTCCGGCGCACTACCTACCGATTGCGTAAAGCCAACGAGCGGGCTCATATTTTGCGTGGATTGGTCAAAGCGCTCGATGCGTTAGATGAGGTTATTACGTTGATTCGGGCATCGCAGACCGTGGATATTGCTCGTGTTGGGGTGGTCGAGTTACTCGATATCGACGACATTCAGGCTCAAGCTATCCTGGACATGCAGCTGCGGCGTTTGGCGGCTTTGGAGCGTCAACGCATTATTGATGATCTCGCTAAGATTGAGGTCGAGATCGCTGATCTGGGAGATATTCTGGCTAAGCCGGAGCGTCGGCGTGGTATCATTCGTAATGAACTGACTGAGATCGCAGAGAAGTACGGTGATGACCGTCGTACTCGGATAATAGCGGTTGATGGTGATGTCAACGACGAGGATTTGATTGCTCGTGAAGAGGTCGTTGTCACGATAACTGAAACTGGATATGCTAAACGTACTAAAACTGACCTGTATCGCAGCCAGAAACGCGGCGGGAAAGGTGTTCAAGGCGCCGGTTTGAAGCAGGACGACATCGTCCGGCATTTCTTCGTGTGTTCAACTCACGATTGGATCCTGTTTTTCACCACCCAAGGCCGCGTATACCGGGCCAAGGCCTATGAATTGCCAGAGGCTTCTCGAACGGCACGCGGGCAACACGTGGCCAATTTGCTTGCATTCCAGCCTGAAGAGCGCATCGCTCAGGTAATTCAGATCCGTAGCTATGAAGACGCTCCATACTTGGTCCTTGCCACGCGCGCCGGTCTGGTTAAGAAGTCAAAGTTGACCGATTTTGACTCTAATCGTTCGGGTGGGATCGTGGCAATTAATTTACGTGACAACGATGAGTTGGTCGGTGCAGTGTTGTGCGCGGCCGACGGCGACTTGCTTCTGGTATCGGCTAACGGCCAGTCTATCCGGTTCTCAGCGACTGACGAGGCCTTGCGTCCGATGGGGCGGGCTACCTCTGGTGTGCAGGGCATGCGGTTTAACGCCGATGATCGACTGTTGTCGTTGAATGTGGTTCGCGAAGATACTTACCTGCTTGTCGCAACGTCTGGGGGTTACGCTAAACGCACCTCGATTGAGGAGTACCCGATGCAGGGCCGTGGCGGAAAGGGTGTTCTAACGGTCATGTACGATCGTCGGCGCGGTAGCTTGGTTGGGGCCATCGTGGTTGATGAAGACAGCGAGTTGTACGCGATCACCTCAGGGGGTGGGGTAATTCGTACAACGGCACGCCAGGTTCGCCAGGCAGGACGCCAGACCAAGGGTGTTCGGTTGATGAACTTAGGTGAGGGCGACACGCTGTTAGCCATCGCACGTAATGCCGAAGAAAGCGCCGACGGCGGTGTCGGTTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40083","NCBI_taxonomy_name":"Mycobacterium leprae TN","NCBI_taxonomy_id":"272631"}}}},"ARO_accession":"3003298","ARO_id":"39882","ARO_name":"Mycobaterium leprae gyrA conferring resistance to fluoroquinolones","ARO_description":"Point mutation of Mycobaterium leprae gyrA resulted in the lowered affinity between fluoroquinolones and gyrA. Thus, conferring resistance.","ARO_category":{"39876":{"category_aro_accession":"3003292","category_aro_cvterm_id":"39876","category_aro_name":"fluoroquinolone resistant gyrA","category_aro_description":"DNA gyrase is responsible for DNA supercoiling and consists of two alpha and two beta subunits. GyrA point mutations confer resistance by preventing fluoroquinolone antibiotics from binding the alpha-subunit.","category_aro_class_name":"AMR Gene Family"},"35942":{"category_aro_accession":"0000023","category_aro_cvterm_id":"35942","category_aro_name":"enoxacin","category_aro_description":"Enoxacin belongs to a group called fluoroquinolones. Its mode of action depends upon blocking bacterial DNA replication by binding itself to DNA gyrase and causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37004":{"category_aro_accession":"3000660","category_aro_cvterm_id":"37004","category_aro_name":"lomefloxacin","category_aro_description":"Lomefloxacin is a difluoropiperazinyl quinolone, sharing similar activities with other fluoroquinolones. It is used to treat urinary tract infections. Relative to other fluoroquinolones, it has a longer half life and has higher serum concentrations.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"37008":{"category_aro_accession":"3000664","category_aro_cvterm_id":"37008","category_aro_name":"trovafloxacin","category_aro_description":"Trovafloxacin is a trifluoroquinalone with a broad spectrum of activity that acts by inhibiting the uncoiling of supercoiled DNA. While potent against many Gram-positive and Gram-negative bacteria, it is less active against pseudomonads and Cl. difficile. It is usually taken as the prodrug trovafloxacin mesylate or alatrofloxacin mesylate for oral or intravenous administration, respectively.","category_aro_class_name":"Antibiotic"},"37009":{"category_aro_accession":"3000665","category_aro_cvterm_id":"37009","category_aro_name":"grepafloxacin","category_aro_description":"Grepafloxacin is a broad-spectrum antibacterial quinoline. It is no longer taken due to its high toxicity.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"37142":{"category_aro_accession":"3000762","category_aro_cvterm_id":"37142","category_aro_name":"pefloxacin","category_aro_description":"Pefloxacin is structurally and functionally similar to norfloxacin. It is poorly active against mycobacteria, while anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"40463":{"category_aro_accession":"3003780","category_aro_cvterm_id":"40463","category_aro_name":"nybomycin","category_aro_description":"A  heterocyclic antibiotic that targets mutant gyrA (type II topoisomerase) containing an S84L substitution, counteracting acquired quinolone resistance. It is effective against quinolone-resistant Gram-positive bacteria including S. aureus and E. faecalis. Due to its ability to counteract quinolone resistance by targeting the mutant form of the gyrA protein, it is classified as a reverse antibiotic (RA).","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1696":{"model_id":"1696","model_name":"Salmonella serovars gyrB conferring resistance to fluoroquinolone","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2174":"E466D"},"experimental":{"2174":"E466D"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1200"}},"model_sequences":{"sequence":{"4348":{"protein_sequence":{"accession":"NP_462735.1","sequence":"MSNSYDSSSIKVLKGLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKDIVVTIHADNSVSVTDDGRGIPTGIHPEEGVSAAEVIMTVLHAGGKFDDNSYKVSGGLHGVGVSVVNALSQKLELVIQRDGKIHRQIYEHGVPQAPLAVTGDTDKTGTMVRFWPSHETFTNVTEFEYEILAKRLRELSFLNSGVSIRLRDKRDGKEDHFHYEGGIKAFVEYLNKNKTPIHPNIFYFSTEKDGIGVEVALQWNDGFQENIYCFTNNIPQRDGGTHLAGFRAAMTRTLNAYMDKEGYSKKAKVSATGDDAREGLIAVVSVKVPDPKFSSQTKDKLVSSEVKSAVEQQMNELLSEYLLENPSDAKIVVGKIIDAARAREAARRAREMTRRKGALDLAGLPGKLADCQERDPALSELYLVEGDSAGGSAKQGRNRKNQAILPLKGKILNVEKARFDKMLSSQEVATLITALGCGIGRDEYNPDKLRYHSIIIMTDADVDGSHIRTLLLTFFYRQMPEIVERGHVYIAQPPLYKVKKGKQEQYIKDDEAMDQYQISIALDGATLHANAHAPALSGEALEKLVSEYNATQKMIGRMERRFPKALLKELVYQPTLTEADLSDEQTVTRWVNALITELNEKEQHGSQWKFDVHTNTEQNLFEPIVRVRTHGVDTDYPLDHEFVTGAEYRRICTLGEKLRGLIEEDAFIERGERRQPVTSFEQALEWLVKESRRGLAIQRYKGLGEMNPDQLWETTMDPESRRMLRVTVKDAIAADQLFTTLMGDAVEPRRAFIEENALKAANIDI"},"dna_sequence":{"accession":"NC_003197.2","fmin":"4038867","fmax":"4041282","strand":"-","sequence":"TTAAATATCGATATTCGCTGCTTTCAGGGCGTTCTCCTCGATAAAGGCACGACGCGGCTCAACGGCATCACCCATCAGCGTAGTGAACAGCTGGTCGGCAGCAATTGCATCTTTGACGGTCACGCGCAGCATACGGCGGCTTTCCGGGTCCATGGTGGTTTCCCACAGCTGATCCGGGTTCATTTCACCCAGACCTTTATAACGCTGGATAGCCAGACCGCGACGTGATTCTTTCACCAGCCACTCCAGCGCCTGCTCGAAGCTGGTTACCGGCTGGCGACGCTCGCCGCGTTCGATAAACGCGTCCTCTTCAATCAGACCACGCAGCTTCTCGCCCAGCGTGCAGATACGACGATATTCCGCGCCGGTCACAAACTCGTGATCCAACGGATAATCGGTATCCACGCCATGCGTACGCACGCGAACGATCGGCTCGAACAGATTCTGTTCCGTATTAGTATGAACATCGAACTTCCACTGACTGCCGTGCTGCTCTTTCTCGTTCAGCTCGGTAATCAGCGCATTCACCCAGCGCGTTACAGTCTGCTCATCAGAAAGATCGGCTTCGGTCAGAGTTGGCTGATACACCAGCTCTTTGAGCAGCGCTTTCGGGAAGCGACGCTCCATACGACCAATCATTTTCTGCGTGGCGTTATATTCAGAGACCAGTTTTTCTAACGCTTCGCCGGATAGCGCCGGCGCATGAGCGTTCGCGTGCAGAGTCGCACCGTCAAGCGCGATGGAAATCTGGTACTGATCCATCGCTTCGTCGTCTTTAATGTACTGTTCCTGCTTACCTTTCTTCACTTTGTACAGCGGCGGCTGCGCAATGTAGACGTGGCCACGCTCGACAATTTCCGGCATCTGACGATAGAAGAAGGTCAACAGCAGCGTACGGATGTGCGAGCCGTCGACGTCCGCATCGGTCATGATGATGATGCTGTGATAGCGCAGCTTGTCCGGGTTGTACTCGTCGCGACCGATACCGCAGCCCAGCGCGGTGATCAGCGTCGCCACTTCCTGGGAGGAAAGCATCTTGTCGAAGCGCGCTTTCTCGACGTTAAGGATTTTACCTTTCAGCGGCAGAATCGCCTGGTTCTTGCGGTTACGCCCCTGCTTCGCAGAGCCGCCCGCGGAGTCCCCTTCCACCAGGTACAGTTCGGACAGCGCCGGGTCGCGTTCCTGACAGTCCGCCAGTTTGCCCGGCAGACCGGCTAAATCGAGCGCGCCTTTACGACGGGTCATTTCACGGGCGCGACGCGCCGCTTCACGCGCACGCGCGGCGTCGATAATTTTGCCGACGACGATTTTCGCGTCAGATGGGTTTTCCAGCAGGTATTCGCTCAGCAGTTCGTTCATCTGCTGTTCTACCGCCGATTTCACCTCGGAAGAGACCAGCTTATCTTTGGTCTGTGAGGAGAATTTCGGATCCGGTACTTTTACGGAAACCACCGCAATCAGACCTTCACGGGCATCGTCGCCGGTGGCGCTGACTTTGGCTTTTTTGCTGTAGCCTTCTTTGTCCATGTAGGCGTTCAGCGTACGGGTCATCGCCGCACGGAAGCCTGCAAGGTGAGTACCGCCGTCGCGCTGCGGAATGTTGTTGGTAAAGCAGTAGATGTTTTCCTGGAAACCATCGTTCCACTGCAGCGCTACTTCCACGCCGATACCGTCTTTTTCGGTGGAGAAATAGAAGATATTCGGGTGGATCGGCGTTTTATTCTTGTTCAGATATTCAACAAACGCCTTGATGCCGCCTTCGTAGTGGAAATGATCTTCTTTGCCATCGCGCTTGTCGCGCAGGCGGATGGAGACGCCTGAGTTCAGGAATGACAGTTCACGCAGGCGTTTCGCCAGGATCTCATATTCAAATTCAGTGACGTTGGTGAAGGTTTCGTGGCTCGGCCAGAAACGTACCATCGTGCCGGTTTTATCGGTATCGCCAGTGACGGCCAGGGGTGCCTGCGGCACGCCGTGCTCGTAGATCTGACGGTGAATTTTGCCATCTCGCTGGATAACCAGTTCCAGTTTTTGCGACAGAGCGTTGACTACCGAGACGCCCACGCCGTGCAGACCGCCGGAGACTTTATAGGAGTTATCGTCAAATTTACCGCCCGCGTGCAGAACGGTCATGATCACTTCCGCCGCCGAGACGCCTTCTTCCGGGTGAATCCCGGTCGGAATGCCACGGCCATCATCCGTTACGGACACGGAGTTATCGGCGTGAATAGTCACGACGATATCTTTACAGTGACCTGCGAGCGCTTCGTCGATAGCGTTATCTACCACCTCGAATACCATGTGGTGCAGACCGGTGCCGTCATCCGTGTCGCCGATATACATACCCGGGCGCTTACGCACCGCATCCAGCCCTTTCAGGACTTTGATACTGGAGGAGTCATAAGAATTCGACAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35734","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium str. LT2","NCBI_taxonomy_id":"99287"}}}},"ARO_accession":"3003307","ARO_id":"39891","ARO_name":"Salmonella serovars gyrB conferring resistance to fluoroquinolone","ARO_description":"Point mutation in Salmonella serovars resulting in fluoroquinolone resistance","ARO_category":{"37244":{"category_aro_accession":"3000864","category_aro_cvterm_id":"37244","category_aro_name":"fluoroquinolone resistant gyrB","category_aro_description":"Point mutations in DNA gyrase subunit B (gyrB) observed in Mycobacterium tuberculosis can result in resistance to fluoroquinolones.","category_aro_class_name":"AMR Gene Family"},"35942":{"category_aro_accession":"0000023","category_aro_cvterm_id":"35942","category_aro_name":"enoxacin","category_aro_description":"Enoxacin belongs to a group called fluoroquinolones. Its mode of action depends upon blocking bacterial DNA replication by binding itself to DNA gyrase and causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36271":{"category_aro_accession":"3000132","category_aro_cvterm_id":"36271","category_aro_name":"clorobiocin","category_aro_description":"Clorobiocin is an aminocoumarin antibiotic produced by Streptomyces roseochromogenes, and binds DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36289":{"category_aro_accession":"3000150","category_aro_cvterm_id":"36289","category_aro_name":"coumermycin A1","category_aro_description":"Coumermycin A1 is an antibiotic produced by Streptomyces rishiriensis, and binds DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37004":{"category_aro_accession":"3000660","category_aro_cvterm_id":"37004","category_aro_name":"lomefloxacin","category_aro_description":"Lomefloxacin is a difluoropiperazinyl quinolone, sharing similar activities with other fluoroquinolones. It is used to treat urinary tract infections. Relative to other fluoroquinolones, it has a longer half life and has higher serum concentrations.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"37008":{"category_aro_accession":"3000664","category_aro_cvterm_id":"37008","category_aro_name":"trovafloxacin","category_aro_description":"Trovafloxacin is a trifluoroquinalone with a broad spectrum of activity that acts by inhibiting the uncoiling of supercoiled DNA. While potent against many Gram-positive and Gram-negative bacteria, it is less active against pseudomonads and Cl. difficile. It is usually taken as the prodrug trovafloxacin mesylate or alatrofloxacin mesylate for oral or intravenous administration, respectively.","category_aro_class_name":"Antibiotic"},"37009":{"category_aro_accession":"3000665","category_aro_cvterm_id":"37009","category_aro_name":"grepafloxacin","category_aro_description":"Grepafloxacin is a broad-spectrum antibacterial quinoline. It is no longer taken due to its high toxicity.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"37142":{"category_aro_accession":"3000762","category_aro_cvterm_id":"37142","category_aro_name":"pefloxacin","category_aro_description":"Pefloxacin is structurally and functionally similar to norfloxacin. It is poorly active against mycobacteria, while anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"40937":{"category_aro_accession":"3004010","category_aro_cvterm_id":"40937","category_aro_name":"cinoxacin","category_aro_description":"Cinoxacin is a fluoroquinolone antibiotic primarily used for the treatment of urinary tract infections in adults. Cinoxacin binds to DNA gyrase, resulting in double-stranded DNA breaks and cell death.","category_aro_class_name":"Antibiotic"},"40938":{"category_aro_accession":"3004011","category_aro_cvterm_id":"40938","category_aro_name":"clinafloxacin","category_aro_description":"Clinafloxacin is a fluoroquinolone antibiotic and gyrase (DNA topoisomerase II) inhibitor. It binds to DNA gyrase and disrupts replication by causing double-stranded DNA breaks, resulting in cell death.","category_aro_class_name":"Antibiotic"},"40939":{"category_aro_accession":"3004012","category_aro_cvterm_id":"40939","category_aro_name":"Clofazimine","category_aro_description":"Clofazimine is a fluoroquinolone-class phenazine dye used for the treatment of leprosy. Clofazimine binds to DNA and disrupts bacterial DNA gyrase, thereby causing double-stranded DNA breaks, and subsequent cell death.","category_aro_class_name":"Antibiotic"},"40940":{"category_aro_accession":"3004013","category_aro_cvterm_id":"40940","category_aro_name":"fleroxacin","category_aro_description":"Fleroxacin is a broad spectrum fluoroquinolone antibiotic that inhibits the DNA supercoiling activity of bacterial DNA gyrase, resulting in double-stranded DNA breaks and subsequent cell death.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1323":{"model_id":"1323","model_name":"Salmonella serovars parE conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2227":"V461G"},"experimental":{"2227":"V461G"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"4403":{"protein_sequence":{"accession":"NP_462096.1","sequence":"MTQTYNADAIEVLTGLEPVRRRPGMYTDTTRPNHLGQEVIDNSVDEALAGHAKRVDVILHADQSLEVIDDGRGMPVDIHPEEGVPAVELILCRLHAGGKFSNKNYQFSGGLHGVGISVVNALSKRVEVTVRRDGQVYNIAFENGEKVQDLQVVGTCGKRNTGTSVHFWPDESFFDSPRFSVSRLMHVLKAKAVLCPGVEITFKDEVNNSEQRWCYQDGLNDYLGEAVNGLPTLPEKPFIGNFNGETEAVDWALLWLPEGGELLTESYVNLIPTMQGGTHVNGLRQGLLDAMREFCEYRNILPRGVKLSAEDIWDRCAYVLSVKMQDPQFAGQTKERLSSRQCAAFVSGVVKDAFSLWLNQNVQAAEQLAEMAIASAQRRLRAAKKVVRKKLTSGPALPGKLADCTAQDLNRTELFLVEGDSAGGSAKQARDREYQAIMPLKGKILNTWEVSSDEVLASQEVHDISVAIGIDPDSDDLSQLRYGKICILADADSDGLHIATLLCALFVRHFRALVKNGHVYVALPPLYRIDLGKEVYYALTEEEKAGVLEQLKRKKGKPNVQRFKGLGEMNPMQLRETTLDPNTRRLVQLTISDEDDQRTNAMMDMLLAKKRSEDRRNWLQEKGDLADLDV"},"dna_sequence":{"accession":"NC_003197.2","fmin":"3343968","fmax":"3345861","strand":"-","sequence":"TTACACGTCGAGATCCGCGAGATCGCCTTTTTCCTGTAGCCAGTTGCGTCGATCTTCAGAACGTTTCTTCGCCAGCAGCATATCCATCATCGCATTAGTACGCTGATCGTCTTCATCGCTAATGGTGAGCTGCACCAGGCGGCGAGTATTCGGATCAAGCGTGGTTTCGCGTAACTGCATCGGGTTCATTTCTCCCAGGCCTTTGAAACGCTGTACGTTCGGCTTGCCTTTCTTACGCTTCAGTTGTTCCAGTACGCCCGCCTTCTCTTCTTCCGTCAGCGCGTAATAGACCTCTTTACCCAAATCGATACGGTATAGCGGCGGTAGCGCGACGTAGACATGACCATTCTTCACCAGCGCGCGGAAGTGTCTGACAAACAGCGCGCAAAGCAGAGTAGCGATATGCAAACCATCGGAGTCCGCATCCGCCAGGATACAGATCTTGCCGTAGCGCAGCTGACTCAGATCGTCGCTGTCCGGATCGATACCGATCGCCACGGAAATATCATGCACTTCTTGCGAGGCCAGCACTTCATCGGAAGAGACCTCCCAGGTGTTAAGGATCTTACCTTTGAGCGGCATGATCGCCTGATATTCGCGATCGCGCGCCTGCTTGGCGGAACCGCCCGCCGAATCCCCTTCCACAAGGAACAGCTCGGTCCGATTAAGATCCTGCGCGGTACAGTCCGCCAGTTTCCCCGGCAACGCCGGGCCGCTGGTGAGCTTTTTGCGCACCACTTTTTTTGCGGCGCGCAGTCGCCGCTGCGCGCTGGCAATCGCCATCTCTGCCAGTTGTTCCGCCGCCTGCACGTTCTGGTTCAGCCACAGGCTGAAGGCATCTTTCACCACGCCGGAAACAAATGCCGCACATTGACGCGACGACAGACGCTCTTTGGTCTGCCCGGCAAATTGCGGGTCCTGCATTTTCACGGAAAGCACATAAGCGCAGCGATCCCAGATATCTTCCGCCGACAGTTTGACGCCGCGCGGCAGAATATTGCGGTATTCGCAAAATTCGCGCATCGCGTCGAGCAGGCCCTGGCGCAGACCGTTGACGTGCGTCCCCCCCTGCATGGTCGGGATCAGGTTGACGTAGCTTTCCGTCAGTAATTCGCCGCCTTCCGGCAGCCACAATAGCGCCCAGTCAACCGCTTCCGTTTCACCGTTAAAATTACCGATAAACGGCTTTTCCGGCAGCGTCGGCAGGCCGTTTACCGCTTCGCCCAGATAGTCGTTCAGACCATCCTGGTAGCACCAGCGCTGCTCGCTGTTATTCACTTCATCTTTAAAAGTGATTTCCACGCCGGGACACAGCACCGCTTTTGCTTTCAGAACGTGCATTAAGCGAGAGACAGAAAAACGCGGGCTGTCGAAGAAACTTTCGTCCGGCCAGAAATGGACGCTGGTTCCAGTATTACGTTTACCGCAGGTGCCGACAACCTGCAAATCCTGCACTTTTTCGCCGTTTTCAAACGCGATGTTATAGACCTGACCGTCGCGGCGCACGGTCACTTCCACGCGCTTTGACAGGGCATTTACTACCGAAATCCCCACCCCATGCAGACCACCAGAGAACTGATAGTTCTTATTGGAGAATTTACCGCCGGCATGAAGCCGACAGAGGATCAGTTCTACCGCCGGAACCCCCTCTTCCGGATGGATATCCACCGGCATCCCGCGTCCGTCGTCAATCACTTCCAGCGATTGATCGGCATGTAAAATGACATCCACGCGTTTGGCGTGACCTGCCAGTGCTTCATCCACACTATTATCAATCACTTCCTGACCCAAATGGTTGGGGCGGGTCGTATCGGTGTACATCCCCGGGCGGCGGCGTACCGGCTCAAGCCCAGTGAGTACCTCAATGGCATCAGCGTTATAAGTTTGCGTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35734","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium str. LT2","NCBI_taxonomy_id":"99287"}}}},"ARO_accession":"3003317","ARO_id":"39901","ARO_name":"Salmonella serovars parE conferring resistance to fluoroquinolones","ARO_description":"Point mutation in Salmonella serovars parE resulting in fluoroquinolones resistance","ARO_category":{"39897":{"category_aro_accession":"3003313","category_aro_cvterm_id":"39897","category_aro_name":"fluoroquinolone resistant parE","category_aro_description":"ParE is a subunit of topoisomerase IV, necessary for cell survival. Point mutations in ParE prevent fluoroquinolones from inhibiting DNA synthesis, thus conferring resistance.","category_aro_class_name":"AMR Gene Family"},"35942":{"category_aro_accession":"0000023","category_aro_cvterm_id":"35942","category_aro_name":"enoxacin","category_aro_description":"Enoxacin belongs to a group called fluoroquinolones. Its mode of action depends upon blocking bacterial DNA replication by binding itself to DNA gyrase and causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37004":{"category_aro_accession":"3000660","category_aro_cvterm_id":"37004","category_aro_name":"lomefloxacin","category_aro_description":"Lomefloxacin is a difluoropiperazinyl quinolone, sharing similar activities with other fluoroquinolones. It is used to treat urinary tract infections. Relative to other fluoroquinolones, it has a longer half life and has higher serum concentrations.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"37008":{"category_aro_accession":"3000664","category_aro_cvterm_id":"37008","category_aro_name":"trovafloxacin","category_aro_description":"Trovafloxacin is a trifluoroquinalone with a broad spectrum of activity that acts by inhibiting the uncoiling of supercoiled DNA. While potent against many Gram-positive and Gram-negative bacteria, it is less active against pseudomonads and Cl. difficile. It is usually taken as the prodrug trovafloxacin mesylate or alatrofloxacin mesylate for oral or intravenous administration, respectively.","category_aro_class_name":"Antibiotic"},"37009":{"category_aro_accession":"3000665","category_aro_cvterm_id":"37009","category_aro_name":"grepafloxacin","category_aro_description":"Grepafloxacin is a broad-spectrum antibacterial quinoline. It is no longer taken due to its high toxicity.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"37142":{"category_aro_accession":"3000762","category_aro_cvterm_id":"37142","category_aro_name":"pefloxacin","category_aro_description":"Pefloxacin is structurally and functionally similar to norfloxacin. It is poorly active against mycobacteria, while anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1671":{"model_id":"1671","model_name":"Salmonella serovars soxS with mutation conferring antibiotic resistance","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2234":"E52K"},"clinical":{"2234":"E52K"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"215"}},"model_sequences":{"sequence":{"4353":{"protein_sequence":{"accession":"NP_463130.1","sequence":"MSHQQIIQTLIEWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTVTHQTLGEYIRQRRLLLAAVELRTTERPIFDIAMDLGYVSQQTFSRVFRREFDRTPSDYRHRL"},"dna_sequence":{"accession":"NC_003197.2","fmin":"4503985","fmax":"4504309","strand":"-","sequence":"CTACAGGCGGTGACGGTAATCGCTGGGAGTGCGATCGAACTCGCGGCGGAATACACGCGAGAAGGTTTGCTGCGATACATAGCCCAGGTCCATCGCGATATCAAAAATCGGGCGCTCGGTCGTTCGTAGCTCAACGGCCGCCAACAGGAGACGGCGCTGGCGAATATACTCGCCTAATGTTTGATGCGTTACCGTACGAAACATCCGCTGCAAATACCACTTGGAGTAGCCCGATTTTTTTGCCACCACATCAATGTTTAGCGGTTGGTCGATATGTTCATCAATCCATTCGATAAGGGTCTGAATTATCTGCTGATGCGACAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35734","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium str. LT2","NCBI_taxonomy_id":"99287"}}}},"ARO_accession":"3003383","ARO_id":"39967","ARO_name":"Salmonella serovars soxS with mutation conferring antibiotic resistance","ARO_description":"SoxS is a global regulator that up-regulates the expression of AcrAB efflux genes. It also reduces OmpF expression to decrease cell membrane permeability.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"41445":{"category_aro_accession":"3004281","category_aro_cvterm_id":"41445","category_aro_name":"General Bacterial Porin with reduced permeability to beta-lactams","category_aro_description":"These are GBPs that are associated with decreased susceptibility to beta-lactams either through mutations in the porin protein, absence of the porin protein, or expression of the porin protein.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"},"36383":{"category_aro_accession":"3000244","category_aro_cvterm_id":"36383","category_aro_name":"reduced permeability to antibiotic","category_aro_description":"Reduction in permeability to antibiotic, generally through reduced production of porins, can provide resistance.","category_aro_class_name":"Resistance Mechanism"}}},"953":{"model_id":"953","model_name":"Enterococcus faecalis liaF mutant conferring daptomycin resistance","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"41342":{"param_type":"deletion mutation from peptide sequence","param_description":"A subtype of the deletion mutation detection model parameter. This parameter is used when a set of deletion mutations is reported in a peptide sequence format. These are specific to codon deletions, where a multiple of 3 nucleotides are deleted. Mutations of this type are reported in the CARD with the notation: [-][AAs][position range].","param_type_id":"41342","param_value":{"3861":"-I177"}},"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3862":"T194I"},"experimental":{"3862":"T194I"}},"41344":{"param_type":"insertion mutation from peptide sequence","param_description":"A subtype of the insertion mutation detection model parameter. This parameter is used when a set of insertion mutations is reported in a peptide sequence format. These are specific to codon insertions, where a multiple of three nucleotides are inserted. This does not cause a frameshift mutation. Mutation parameters of this type are reported in CARD with the notation: [+][AAs][position range].","param_type_id":"41344","param_value":{"3868":"+I177"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"4372":{"protein_sequence":{"accession":"AAO82601.1","sequence":"MNNPWRFFIVAEALLFILALWQIVHNPGLAVLLTIGVLLVAYVSRKASKTHFNNFQFVLGVVFIVIGAMNSTAVWFMLIFGVLFIGLKGFEISGVDIAERAPWRKKQMIMVETAAKEPKNGKRFKRRWFANERIGNNIYEWDDINIDLISGDTIIDLGNTLLPKEDNIIIIRKGFGRTRILVPLGVAILLEHSTFYGTVRFEEEKYQLKNESLKIYSNDYDTNLRRLKIMTNTLVGDVEVIRV"},"dna_sequence":{"accession":"AE016830","fmin":"2790820","fmax":"2791552","strand":"-","sequence":"TCATACACGGATCACCTCAACATCTCCTACTAAAGTGTTCGTCATAATTTTCAAACGACGAAGATTGGTATCATAATCATTGCTGTAAATTTTTAATGATTCGTTTTTCAATTGATATTTTTCTTCTTCAAAACGTACCGTTCCGTAAAAAGTTGAATGTTCTAACAAAATAGCTACACCTAACGGCACTAGAATTCGCGTGCGGCCAAAACCTTTACGAATAATAATAATATTGTCTTCTTTCGGTAGTAGCGTATTACCTAAATCAATAATGGTGTCCCCAGAGATTAAATCAATATTGATATCGTCCCATTCATAGATATTGTTACCAATGCGTTCGTTGGCAAACCAGCGGCGTTTAAACCGTTTGCCATTTTTAGGTTCTTTTGCCGCCGTCTCCACCATAATCATTTGTTTTTTTCGCCAAGGTGCTCGCTCAGCTATATCCACGCCTGAAATCTCAAAGCCTTTTAAGCCGATAAAGAGTACGCCAAAAATCAACATAAACCAAACAGCCGTGCTATTCATTGCACCAATGACAATAAAAACAACGCCGAGGACGAATTGAAAGTTGTTAAAATGTGTTTTAGATGCTTTCCTGGAAACGTAGGCCACAAGTAAAACGCCAATTGTTAATAAAACAGCTAATCCAGGATTATGTACAATTTGCCATAACGCCAGAATAAAAAGTAATGCTTCTGCGACGATAAAAAAGCGCCAAGGGTTATTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37592","NCBI_taxonomy_name":"Enterococcus faecalis V583","NCBI_taxonomy_id":"226185"}}}},"ARO_accession":"3003077","ARO_id":"39624","ARO_name":"Enterococcus faecalis liaF mutant conferring daptomycin resistance","ARO_description":"liaF is an accessory protein that acts as a negative regulator of liaRS signal transduction pathway. Mutations confer daptomycin resistance.","ARO_category":{"41426":{"category_aro_accession":"3004262","category_aro_cvterm_id":"41426","category_aro_name":"daptomycin resistant liaF","category_aro_description":"Mutations to the liaF accessory protein that confer resistance to daptomycin.","category_aro_class_name":"AMR Gene Family"},"35985":{"category_aro_accession":"0000068","category_aro_cvterm_id":"35985","category_aro_name":"daptomycin","category_aro_description":"Daptomycin is a novel lipopeptide antibiotic used in the treatment of certain infections caused by Gram-positive organisms. Daptomycin interferes with the bacterial cell membrane, reducing membrane potential and inhibiting cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1135":{"model_id":"1135","model_name":"Staphylococcus aureus parE conferring resistance to aminocoumarin","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2193":"R136G","4410":"G78S"},"clinical":{"2193":"R136G","4410":"G78S"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1250"}},"model_sequences":{"sequence":{"3681":{"protein_sequence":{"accession":"BAA11086.1","sequence":"MNKQNNYSDDSIQVLEGLEAVRKRPGMYIGSTDKRGLHHLVYEIVDNSVDEVLNGYGNEIDVTINKDGSISIEDNGRGMPTGIHKSGKPTVEVIFTVLHAGGKFGQGGYKTSGGLHGVGASVVNALSEWLEVEIHRDGNIYHQSFKNGGSPSSGLVKKGKTKKTGTKVTFKPDDTIFKASTSFNFDVLSERLQESAFLLKNLKITLNDLRSGKERQEHYHYEEGIKEFVSYVNEGKEVLHDVATFSGEANGIEVDVAFQYNDQYSESILSFVNNVRTKDGGTHEVGFKTAMTRVFNDYARRINELKTKDKNLDGNDIREGLTAVVSVRIPEELLQFEGQTKSKLGTSEARSAVDSVVADKLPFYLEEKGQLSKSLVKKAIKAQQAREAARKAREDARSGKKNKRKDTLLSGKLTPAQSKNTEKNELYLVEGDSAGGSAKLGRDRKFQAILPLRGKVINTEKARLEDIFKNEEINTIIHTIGAGVGTDFKIEDSNYNRVIIMTDADTDGAHIQVLLLTFFFKYMKPLVQAGRVFIALPPLYKLEKGKGKTKRVEYAWTDEELNKLQKELGKGFTLQRYKGLGEMNPEQLWETTMNPETRTLIRVQVEDEVRSSKRVTTLMGDKVQPRREWIEKHVEFGMQEDQSILDNSEVQVLENDQFDEEEI"},"dna_sequence":{"accession":"D67075.1","fmin":"384","fmax":"2376","strand":"+","sequence":"ATGAATAAACAAAATAATTATTCAGATGATTCAATACAGGTTTTAGAGGGGTTAGAAGCAGTTCGTAAAAGACCTGGTATGTATATTGGATCAACTGATAAACGGGGATTACATCATCTAGTATATGAAATTGTCGATAACTCCGTCGATGAAGTATTGAATGGTTACGGTAACGAAATAGATGTAACAATTAATAAAGATGGTAGTATTTCTATAGAAGATAATGGACGTGGTATGCCAACAGGTATACATAAATCAGGTAAACCGACAGTCGAAGTTATCTTTACTGTTTTACATGCAGGAGGTAAATTTGGACAAGGCGGCTATAAAACTTCAGGTGGTCTTCACGGTGTTGGTGCTTCAGTTGTAAATGCATTGAGTGAATGGCTTGAAGTTGAAATCCATCGAGATGGTAATATATATCATCAAAGTTTTAAAAACGGTGGTTCGCCATCTTCTGGTTTAGTGAAAAAAGGTAAAACTAAGAAAACAGGTACCAAAGTAACATTTAAACCTGATGACACAATTTTTAAAGCATCTACATCATTTAATTTTGATGTTTTAAGTGAACGACTACAAGAGTCTGCGTTCTTATTGAAAAATTTAAAAATAACGCTTAATGATTTACGCAGTGGTAAAGAGCGTCAAGAGCATTACCATTATGAAGAAGGAATCAAAGAGTTTGTTAGTTATGTCAATGAAGGAAAAGAAGTTTTGCATGACGTGGCTACATTTTCAGGTGAAGCAAATGGTATAGAGGTAGACGTAGCTTTCCAATATAATGATCAATATTCAGAAAGTATTTTAAGTTTTGTAAATAATGTACGTACTAAAGATGGTGGTACACATGAAGTTGGTTTTAAAACAGCAATGACACGTGTATTTAATGATTATGCACGTCGTATTAATGAACTTAAAACAAAAGATAAAAACTTAGATGGTAATGATATTCGTGAAGGTTTAACAGCTGTTGTGTCTGTTCGTATTCCAGAAGAATTATTGCAATTTGAAGGACAAACGAAATCTAAATTGGGTACTTCTGAAGCTAGAAGTGCTGTTGATTCAGTTGTTGCAGACAAATTGCCATTCTATTTAGAAGAAAAAGGACAATTGTCTAAATCACTTGTGAAAAAAGCGATTAAAGCACAACAAGCAAGGGAAGCTGCACGTAAAGCTCGTGAAGATGCTCGTTCAGGTAAGAAAAACAAGCGTAAAGACACTTTGCTATCTGGTAAATTAACACCTGCACAAAGTAAAAACACTGAAAAAAATGAATTGTATTTAGTCGAAGGTGATTCTGCGGGAGGTTCAGCAAAACTTGGACGAGACCGCAAATTCCAAGCGATATTACCATTACGTGGTAAGGTAATTAATACAGAGAAAGCACGTCTAGAAGATATTTTTAAAAATGAAGAAATTAATACAATTATCCACACAATCGGGGCAGGCGTTGGTACTGACTTTAAAATTGAAGATAGTAATTATAATCGTGTAATTATTATGACTGATGCTGATACTGATGGTGCGCATATTCAAGTGCTATTGTTAACATTCTTCTTCAAATATATGAAACCGCTTGTTCAAGCAGGTCGTGTATTTATTGCTTTACCTCCACTTTATAAATTGGAAAAAGGTAAAGGCAAAACAAAGCGAGTTGAATACGCTTGGACAGACGAAGAGCTTAATAAATTGCAAAAAGAACTTGGTAAAGGCTTCACGTTACAACGTTACAAAGGTTTGGGTGAAATGAACCCTGAGCAATTATGGGAAACGACGATGAACCCAGAAACACGAACTTTAATTCGTGTACAAGTTGAAGATGAAGTGCGTTCATCTAAACGTGTAACAACATTAATGGGTGACAAAGTACAACCTAGACGTGAATGGATTGAAAAGCATGTTGAGTTTGGTATGCAAGAGGACCAAAGTATTTTAGATAATTCTGAAGTACAAGTGCTTGAAAATGATCAATTTGATGAGGAGGAAATCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35597","NCBI_taxonomy_name":"Staphylococcus aureus RN4220","NCBI_taxonomy_id":"561307"}}}},"ARO_accession":"3003314","ARO_id":"39898","ARO_name":"Staphylococcus aureus parE conferring resistance to aminocoumarin","ARO_description":"Point mutation in Staphylococcus aureus parE resulting in aminocoumarin resistance. Please note: the reference sequence associated with this model corresponds to Staphylococcus aureus MRSA parE, while the SNPs correspond to Staphylococcus aureus RN4220 (for which a complete annotated genome does not exist in genbank at present).","ARO_category":{"36596":{"category_aro_accession":"3000457","category_aro_cvterm_id":"36596","category_aro_name":"aminocoumarin resistant parE","category_aro_description":"ParE is a subunit of topoisomerase IV, which decatenates and relaxes DNA to allow access to genes for transcription or translation. Point mutations in ParE prevent anticoumarin antibiotics from inhibiting DNA synthesis, thus conferring resistance.","category_aro_class_name":"AMR Gene Family"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36271":{"category_aro_accession":"3000132","category_aro_cvterm_id":"36271","category_aro_name":"clorobiocin","category_aro_description":"Clorobiocin is an aminocoumarin antibiotic produced by Streptomyces roseochromogenes, and binds DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36289":{"category_aro_accession":"3000150","category_aro_cvterm_id":"36289","category_aro_name":"coumermycin A1","category_aro_description":"Coumermycin A1 is an antibiotic produced by Streptomyces rishiriensis, and binds DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"570":{"model_id":"570","model_name":"Streptococcus pyogenes folP with mutation conferring resistance to sulfonamides","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2116":"F25I"},"clinical":{"2116":"F25I"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2095":{"protein_sequence":{"accession":"AAL97684.1","sequence":"MKIGRFVIEGNAAIMGILNVTPDSFSDGGSYTTVQKALDHVEQMIADGAKIIDVGGESTRPGCQFVSATDEIDRVVPVIKAIKENYDILISIDTYKTETARAALEAGADILNDVWAGLYDGQMFALAAEYDAPIILMHNQDEEVYQEVTQDVCDFLGNRAQAALDAGVPKNNIWIDPGFGFAKSVQQNTELLKGLDRVCQLGYPVLFGISRKRVVDALLGGNTKAKERDGATAALSAYALGKGCQIVRVHDVKANQDIVAVLSQLM"},"dna_sequence":{"accession":"AE009949","fmin":"878481","fmax":"879282","strand":"+","sequence":"ATGAAAATTGGAAGGTTTGTGATTGAGGGCAATGCGGCTATCATGGGGATTTTAAATGTGACTCCAGATTCTTTTTCAGATGGGGGGTCTTACACTACTGTGCAAAAAGCATTAGATCACGTTGAGCAAATGATTGCTGATGGTGCTAAAATCATCGACGTTGGTGGAGAATCAACACGTCCAGGTTGCCAATTTGTAAGCGCTACCGATGAAATTGACAGGGTGGTTCCTGTGATCAAGGCCATCAAAGAAAACTATGATATTCTAATCAGCATTGATACCTATAAAACCGAAACAGCTAGAGCAGCTTTAGAGGCGGGTGCCGATATTCTCAATGATGTTTGGGCAGGTTTGTACGACGGTCAAATGTTTGCCTTAGCAGCCGAGTACGATGCGCCTATCATCTTGATGCATAACCAAGACGAAGAAGTTTATCAAGAGGTAACACAAGACGTTTGTGATTTTCTAGGCAATAGAGCACAAGCAGCTCTTGATGCTGGCGTGCCAAAAAACAATATTTGGATTGATCCAGGATTTGGATTTGCCAAATCTGTTCAACAGAATACGGAGTTATTAAAAGGATTGGACCGCGTCTGTCAGTTGGGCTATCCTGTCTTGTTTGGTATTTCGAGAAAGCGTGTCGTAGATGCCTTGTTAGGCGGCAATACCAAAGCTAAAGAGCGAGACGGAGCGACAGCAGCCTTGTCTGCTTATGCCCTTGGAAAAGGCTGTCAGATTGTACGCGTACACGATGTCAAGGCTAATCAAGACATTGTGGCTGTGTTGAGCCAGTTGATGTGAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40082","NCBI_taxonomy_name":"Streptococcus pyogenes MGAS8232","NCBI_taxonomy_id":"186103"}}}},"ARO_accession":"3003387","ARO_id":"39971","ARO_name":"Streptococcus pyogenes folP with mutation conferring resistance to sulfonamides","ARO_description":"Point mutations in Streptococcus pyogenes dihydropteroate synthase folP prevent sulfonamide antibiotics from inhibiting its role in folate synthesis, thus conferring sulfonamide resistance.","ARO_category":{"39999":{"category_aro_accession":"3003415","category_aro_cvterm_id":"39999","category_aro_name":"sulfonamide resistant dihydropteroate synthase folP","category_aro_description":"Point mutations in dihydropteroate synthase folP prevent sulfonamide antibiotics from inhibiting its role in folate synthesis, thus conferring sulfonamide resistance","category_aro_class_name":"AMR Gene Family"},"36463":{"category_aro_accession":"3000324","category_aro_cvterm_id":"36463","category_aro_name":"sulfadiazine","category_aro_description":"Sulfadiazine is a potent inhibitor of dihydropteroate synthase, interfering with the tetrahydrofolic biosynthesis pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor to many nucleotides and amino acids.","category_aro_class_name":"Antibiotic"},"36464":{"category_aro_accession":"3000325","category_aro_cvterm_id":"36464","category_aro_name":"sulfadimidine","category_aro_description":"Sulfadimidine is an alkaline sulfonamide antibiotic that inhibits dihydropteroate synthase, and enzyme in the tetrahydrofolic acid biosynthesis pathway. This interferes with the production of folate, which is a precursor to many amino acids and nucleotides.","category_aro_class_name":"Antibiotic"},"36466":{"category_aro_accession":"3000327","category_aro_cvterm_id":"36466","category_aro_name":"sulfadoxine","category_aro_description":"Sulfadoxine is an inhibitor of dihydropteroate synthase, interfering with the tetrahydrofolic biosynthesis pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor to many nucleotides and amino acids.","category_aro_class_name":"Antibiotic"},"36468":{"category_aro_accession":"3000329","category_aro_cvterm_id":"36468","category_aro_name":"sulfamethoxazole","category_aro_description":"Sulfamethoxazole is a sulfonamide antibiotic usually taken with trimethoprim, a diaminopyrimidine antibiotic. Sulfamethoxazole inhibits dihydropteroate synthase, essential to tetrahydrofolic acid biosynthesis. This pathway generates compounds used in the synthesis of many amino acids and nucleotides.","category_aro_class_name":"Antibiotic"},"36469":{"category_aro_accession":"3000330","category_aro_cvterm_id":"36469","category_aro_name":"sulfisoxazole","category_aro_description":"Sulfisoxazole is an inhibitor of dihydropteroate synthase, interfering with the tetrahydrofolic biosynthesis pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor to many nucleotides and amino acids.","category_aro_class_name":"Antibiotic"},"37027":{"category_aro_accession":"3000683","category_aro_cvterm_id":"37027","category_aro_name":"sulfacetamide","category_aro_description":"Sulfacetamide is a very soluable sulfonamide antibiotic previously used to treat urinary tract infections. Its relatively low activity and toxicity to those with Stevens-Johnson syndrome have reduced its use and availability.","category_aro_class_name":"Antibiotic"},"37028":{"category_aro_accession":"3000684","category_aro_cvterm_id":"37028","category_aro_name":"mafenide","category_aro_description":"Mafenide is a sulfonamide used topically for treating burns.","category_aro_class_name":"Antibiotic"},"37042":{"category_aro_accession":"3000698","category_aro_cvterm_id":"37042","category_aro_name":"sulfasalazine","category_aro_description":"Sulfasalazine is a derivative of the early sulfonamide sulfapyridine (salicylazosulfapyridine). It was developed to increase water solubility and is taken orally for ulcerative colitis.","category_aro_class_name":"Antibiotic"},"37043":{"category_aro_accession":"3000699","category_aro_cvterm_id":"37043","category_aro_name":"sulfamethizole","category_aro_description":"Sulfamethizole is a short-acting sulfonamide that inhibits dihydropteroate synthetase.","category_aro_class_name":"Antibiotic"},"39996":{"category_aro_accession":"3003412","category_aro_cvterm_id":"39996","category_aro_name":"dapsone","category_aro_description":"Dapsone is a sulfone in which it inhibits folic acid synthesis, such as the dihydropteroate synthase.","category_aro_class_name":"Antibiotic"},"36421":{"category_aro_accession":"3000282","category_aro_cvterm_id":"36421","category_aro_name":"sulfonamide antibiotic","category_aro_description":"Sulfonamides are broad spectrum, synthetic antibiotics that contain the sulfonamide group. Sulfonamides inhibit dihydropteroate synthase, which catalyzes the conversion of p-aminobenzoic acid to dihydropteroic acid as part of the tetrahydrofolic acid biosynthetic pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor of many nucleotides and amino acids. Many sulfamides are taken with trimethoprim, an inhibitor of dihydrofolate reductase, also disturbing the trihydrofolic acid synthesis pathway.","category_aro_class_name":"Drug Class"},"39985":{"category_aro_accession":"3003401","category_aro_cvterm_id":"39985","category_aro_name":"sulfone antibiotic","category_aro_description":"A sulfone active against a wide range of bacteria but mainly employed for its actions against mycobacterium laprae. Its mechanism of action  involves inhibition of folic acid synthesis in susceptible organisms.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"431":{"model_id":"431","model_name":"Escherichia coli marR mutant conferring antibiotic resistance","model_type":"protein overexpression model","model_type_id":"41091","model_description":"This model detects protein overexpression based on the presence of mutations.The detection of the protein without an associated mutation indicates that the protein is likely to be expressed at low or basal levels. The detection of the protein with the mutation indicates that the protein is likely overexpressed. This model reflects how certain proteins are functional with and without mutations. For example, efflux pump subunits and regulators are functional with mutations and without mutations. Without mutations, efflux pump subunits and regulators are usually expressed at a low level. When an efflux pump regulator has a mutation, it can cause the overexpression of the efflux pump it is responsible for regulating, leading to resistance to specific drugs. Protein overexpression models have two parameters: a curated BLASTP cutoff, and a curated set of mutations (single resistance variants, frameshift mutations, indels, etc.) shown clinically to confer resistance. This model type is a combination of the protein homolog and protein variant model. A detected hit can be categorized as Perfect, Strict, or Loose with no mutation(s) or as Strict or Loose with mutation(s).","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2102":"Y137H","2103":"R94S","2104":"L78M","2105":"V45E","2106":"R73C","2107":"R73S","2108":"R77C","2109":"G103S","2130":"I49S","2131":"A70T","2132":"R77L","2133":"V96E","2852":"R94H","7640":"S3N","8206":"R58L"},"clinical":{"2102":"Y137H","2103":"R94S","2104":"L78M","2105":"V45E","2106":"R73C","2107":"R73S","2108":"R77C","2109":"G103S","2130":"I49S","2131":"A70T","2132":"R77L","2133":"V96E","2852":"R94H","7640":"S3N","8206":"R58L"}},"40394":{"param_type":"nonsense mutation","param_description":"A nucleotide substitution resulting in a change from an amino acid codon to a STOP codon. Nonsense mutations truncate protein translation prematurely, resulting in a defective or completely inactive protein. In CARD, nonsense mutations may be attached to models using the notation: [wild type amino acid][position][STOP] (e.g. Q42STOP). This parameter is not currently used in detection algorithms.","param_type_id":"40394","param_value":{"3898":"E31STOP"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"210"}},"model_sequences":{"sequence":{"2097":{"protein_sequence":{"accession":"AAC74603.2","sequence":"MKSTSDLFNEIIPLGRLIHMVNQKKDRLLNEYLSPLDITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTGGAAICEQCHQLVGQDLHQELTKNLTADEVATLEYLLKKVLP"},"dna_sequence":{"accession":"U00096","fmin":"1619119","fmax":"1619554","strand":"+","sequence":"GTGAAAAGTACCAGCGATCTGTTCAATGAAATTATTCCATTGGGTCGCTTAATCCATATGGTTAATCAGAAGAAAGATCGCCTGCTTAACGAGTATCTGTCTCCGCTGGATATTACCGCGGCACAGTTTAAGGTGCTCTGCTCTATCCGCTGCGCGGCGTGTATTACTCCGGTTGAACTGAAAAAGGTATTGTCGGTCGACCTGGGAGCACTGACCCGTATGCTGGATCGCCTGGTCTGTAAAGGCTGGGTGGAAAGGTTGCCGAACCCGAATGACAAGCGCGGCGTACTGGTAAAACTTACCACCGGCGGCGCGGCAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAACAAAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3003378","ARO_id":"39962","ARO_name":"Escherichia coli marR mutant conferring antibiotic resistance","ARO_description":"MarR is a repressor of the mar operon marRAB, thus regulating the expression of marA, the activator of multidrug efflux pump AcrAB.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2080":{"model_id":"2080","model_name":"Escherichia coli 16S rRNA mutation in the rrsH gene conferring resistance to spectinomycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"4818":"C1192U"},"clinical":{"4818":"C1192U"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"3228":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"U00096","fmin":"223771","fmax":"225312","strand":"+","sequence":"AAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAGAAGCTTGCTTCTTTGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCGACTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTGGTCTTGACATCCACAGAACTTTCCAGAGATGGATTGGTGCCTTCGGGAACTGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCTTTTGTTGCCAGCGGTCCGGCCGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACGACCAGGGCTACACACGTGCTACAATGGCGCATACAAAGAGAAGCGACCTCGCGAGAGCAAGCGGACCTCATAAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTGGATCAGAATGCCACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGCAAAAGAAGTAGGTAGCTTAACCTTCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGATCACCTCCTTA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36905","NCBI_taxonomy_name":"Escherichia coli K-12","NCBI_taxonomy_id":"83333"}}}},"ARO_accession":"3003372","ARO_id":"39956","ARO_name":"Escherichia coli 16S rRNA (rrsH) mutation conferring resistance to spectinomycin","ARO_description":"Point mutations in the 3' major domain of the rrsH 16S rRNA gene of Escherichia coli can confer resistance to spectinomycin","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2085":{"model_id":"2085","model_name":"Escherichia coli 16S rRNA mutation in the rrnB gene conferring resistance to spectinomycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2925":"G1068A"},"clinical":{"2925":"G1068A"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"3239":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"U00096","fmin":"4166659","fmax":"4168200","strand":"+","sequence":"AAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAGAAGCTTGCTTCTTTGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCGACTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTGGTCTTGACATCCACGGAAGTTTTCAGAGATGAGAATGTGCCTTCGGGAACCGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGGTCCGGCCGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACGACCAGGGCTACACACGTGCTACAATGGCGCATACAAAGAGAAGCGACCTCGCGAGAGCAAGCGGACCTCATAAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTGGATCAGAATGCCACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGCAAAAGAAGTAGGTAGCTTAACCTTCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGATCACCTCCTTA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36905","NCBI_taxonomy_name":"Escherichia coli K-12","NCBI_taxonomy_id":"83333"}}}},"ARO_accession":"3003377","ARO_id":"39961","ARO_name":"Escherichia coli 16S rRNA (rrnB) mutation conferring resistance to spectinomycin","ARO_description":"Point mutations in the 3' major domain of helix 35, in the rrnB gene operon for 16S rRNA of Escherichia coli can confer resistance to spectinomycin","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2086":{"model_id":"2086","model_name":"Escherichia coli 16S rRNA mutation in the rrnB gene conferring resistance to tetracycline","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2900":"A964G","2988":"A1055G","3071":"G1053A","4845":"C1054U"},"clinical":{"2900":"A964G","2988":"A1055G","3071":"G1053A","4845":"C1054U"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"3236":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"U00096","fmin":"4166659","fmax":"4168200","strand":"+","sequence":"AAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAGAAGCTTGCTTCTTTGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCGACTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTGGTCTTGACATCCACGGAAGTTTTCAGAGATGAGAATGTGCCTTCGGGAACCGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGGTCCGGCCGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACGACCAGGGCTACACACGTGCTACAATGGCGCATACAAAGAGAAGCGACCTCGCGAGAGCAAGCGGACCTCATAAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTGGATCAGAATGCCACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGCAAAAGAAGTAGGTAGCTTAACCTTCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGATCACCTCCTTA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36905","NCBI_taxonomy_name":"Escherichia coli K-12","NCBI_taxonomy_id":"83333"}}}},"ARO_accession":"3003411","ARO_id":"39995","ARO_name":"Escherichia coli 16S rRNA (rrnB) mutation conferring resistance to tetracycline","ARO_description":"Point mutations in the 3' major domain of the rrnB 16S rRNA gene of Escherichia coli can confer resistance to tetracycline","ARO_category":{"40280":{"category_aro_accession":"3003669","category_aro_cvterm_id":"40280","category_aro_name":"16S rRNA with mutation conferring resistance to tetracycline derivatives","category_aro_description":"Point mutations in the bacterial 16S rRNA region shown clinically to confer resistance to tetracycline and tetracycline derivatives (polyketide antibiotics).","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2088":{"model_id":"2088","model_name":"Mycobacterium smegmatis 16S rRNA mutation in the rrsB gene conferring resistance to streptomycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2948":"A503C","3056":"G504C","4828":"C502U","4829":"C506U"},"clinical":{"2948":"A503C","3056":"G504C","4828":"C502U","4829":"C506U"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"3250":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NC_008596.1","fmin":"5027948","fmax":"5029475","strand":"+","sequence":"TTTTTGTTTGGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGCCCTTTCGGGGGTACTCGAGTGGCGAACGGGTGAGTAACACGTGGGTGATCTGCCCTGCACTTTGGGATAAGCCTGGGAAACTGGGTCTAATACCGAATACACCCTGCTGGTCGCATGGCCTGGTAGGGGAAAGCTTTTGCGGTGTGGGATGGGCCCGCGGCCTATCAGCTTGTTGGTGGGGTGATGGCCTACCAAGGCGACGACGGGTAGCCGGCCTGAGAGGGTGACCGGCCACACTGGGACTGAGATACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGAGGGATGACGGCCTTCGGGTTGTAAACCTCTTTCAGCACAGACGAAGCGCAAGTGACGGTATGTGCAGAAGAAGGACCGGCCAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTCCGAGCGTTGTCCGGAATTACTGGGCGTAAAGAGCTCGTAGGTGGTTTGTCGCGTTGTTCGTGAAAACTCACAGCTTAACTGTGGGCGTGCGGGCGATACGGGCAGACTAGAGTACTGCAGGGGAGACTGGAATTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGGTGGCGAAGGCGGGTCTCTGGGCAGTAACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGGTGGGTACTAGGTGTGGGTTTCCTTCCTTGGGATCCGTGCCGTAGCTAACGCATTAAGTACCCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGTGGATTAATTCGATGCAACGCGAAGAACCTTACCTGGGTTTGACATGCACAGGACGCCGGCAGAGATGTCGGTTCCCTTGTGGCCTGTGTGCAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCTCATGTTGCCAGCACGTTATGGTGGGGACTCGTGAGAGACTGCCGGGGTCAACTCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGCCCCTTATGTCCAGGGCTTCACACATGCTACAATGGCCGGTACAAAGGGCTGCGATGCCGTGAGGTGGAGCGAATCCTTTCAAAGCCGGTCTCAGTTCGGATCGGGGTCTGCAACTCGACCCCGTGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTCGGTAACACCCGAAGCCGGTGGCCTAACCCTTGTGGAGGGAGCCGTCGAAGGTGGGATCGGCGATTGGGACGAAGTCGTAACAAGGTAGCCGTACCGGAAGGTGCGGCTGGATCACCTCCTTTCT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36769","NCBI_taxonomy_name":"Mycobacterium smegmatis str. MC2 155","NCBI_taxonomy_id":"246196"}}}},"ARO_accession":"3003541","ARO_id":"40143","ARO_name":"Mycobacterium smegmatis 16S rRNA (rrsB) mutation conferring resistance to streptomycin","ARO_description":"Point mutations in the helix 44 region of the 16S rRNA rrsB gene of Mycobacterium smegmatis can confer resistance to streptomycin","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2126":{"model_id":"2126","model_name":"Mycobacterium abscessus 16S rRNA mutation conferring resistance to tobramycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3049":"A1375G","4790":"C1376U","4791":"G1458U","4792":"U1373A"},"clinical":{"3049":"A1375G","4790":"C1376U","4791":"G1458U","4792":"U1373A"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"2600"}},"model_sequences":{"sequence":{"3253":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"CU458896.1","fmin":"1462398","fmax":"1463901","strand":"+","sequence":"AGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGCCCTTCGGGGTACTCGAGTGGCGAACGGGTGAGTAACACGTGGGTGATCTGCCCTGCACTCTGGGATAAGCCTGGGAAACTGGGTCTAATACCGGATAGGACCACACACTTCATGGTGAGTGGTGCAAAGCTTTTGCGGTGTGGGATGAGCCCGCGGCCTATCAGCTTGTTGGTGGGGTAATGGCCCACCAAGGCGACGACGGGTAGCCGGCCTGAGAGGGTGACCGGCCACACTGGGACTGAGATACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGAGGGATGACGGCCTTCGGGTTGTAAACCTCTTTCAGTAGGGACGAAGCGAAAGTGACGGTACCTACAGAAGAAGGACCGGCCAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTCCGAGCGTTGTCCGGAATTACTGGGCGTAAAGAGCTCGTAGGTGGTTTGTCGCGTTGTTCGTGAAAACTCACAGCTTAACTGTGGGCGTGCGGGCGATACGGGCAGACTAGAGTACTGCAGGGGAGACTGGAATTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGGTGGCGAAGGCGGGTCTCTGGGCAGTAACTGACGCTGAGGAGCGAAAGCGTGGGTAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGGTGGGTACTAGGTGTGGGTTTCCTTCCTTGGGATCCGTGCCGTAGCTAACGCATTAAGTACCCCGCCTGGGGAGTACGGTCGCAAGACTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGTGGATTAATTCGATGCAACGCGAAGAACCTTACCTGGGTTTGACATGCACAGGACGTACCTAGAGATAGGTATTCCCTTGTGGCCTGTGTGCAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCCTATGTTGCCAGCGGGTAATGCCGGGGACTCGTAGGAGACTGCCGGGGTCAACTCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGCCCCTTATGTCCAGGGCTTCACACATGCTACAATGGCCAGTACAGAGGGCTGCGAAGCCGTAAGGTGGAGCGAATCCCTTAAAGCTGGTCTCAGTTCGGATTGGGGTCTGCAACTCGACCCCATGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTCGGTAACACCCGAAGCCAGTGGCCTAACCTTTTGGAGGGAGCTGTCGAAGGTGGGATCGGCGATTGGGACGAAGTCGTAACAAGGTAGCCGTACCGGAAGGTGCGGCTGGATCACCT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36888","NCBI_taxonomy_name":"Mycobacterium abscessus","NCBI_taxonomy_id":"36809"}}}},"ARO_accession":"3003237","ARO_id":"39821","ARO_name":"Mycobacterium abscessus 16S rRNA mutation conferring resistance to tobramycin","ARO_description":"Point mutations in the 16S rRNA of Mycobacterium abscessus conferring resistance to tobramycin","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2091":{"model_id":"2091","model_name":"Mycobacterium chelonae 16S rRNA mutation conferring resistance to gentamicin C","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3008":"A1355G"},"clinical":{"3008":"A1355G"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"2500"}},"model_sequences":{"sequence":{"3273":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NR_114659.1","fmin":"1","fmax":"1441","strand":"+","sequence":"GACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGCCCTTCGGGGTACTCGAGTGGCGAACGGGTGAGTAACACGTGGGTGATCTGCCCTGCACTCTGGGATAAGCCTGGGAAACTGGGTCTAATACCGGATAGGACCACACACTTCATGGTGAGTGGTGCAAAGCTTTTGCGGTGTGGGATGAGCCCGCGGCCTATCAGCTTGTTGGTGGGGTAATGGCCCACCAAGGCGACGACGGGTAGCCGGCCTGAGAGGGTGACCGGCCACACTGGGACTGAGATACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGAGGGATGACGGCCTTCGGGTTGTAAACCTCTTTCAGTAGGGACGAAGCGAAAGTGACGGTACCTACAGAAGAAGGACCGGCCAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTCCGAGCGTTGTCCGGAATTACTGGGCGTAAAGAGCTCGTAGGTGGTTTGTCGCGTTGTTCGTGAAAACTCACAGCTTAACTGTGGGCGTGCGGGCGATACGGGCAGACTAGAGTACTGCAGGGGAGACTGGAATTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGGTGGCGAAGGCGGGTCTCTGGGCAGTAACTGACGCTGAGGAGCGAAAGCGTGGGTAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGGTGGGTACTAGGTGTGGGTTTCCTTCCTTGGGATCCGTGCCGTAGCTAACGCATTAAGTACCCCGCCTGGGGAGTACGGTCGCAAGACTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGTGGATTAATTCGATGCAACGCGAAGAACCTTACCTGGGTTTGACATGCGCAGGACGTATCTAGAGATAGGTATTCCCTTGTGGCCTGCGTGCAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCCTATGTTGCCAGCGGGTAATGCCGGGGACTCGTAGGAGACTGCCGGGGTCAACTCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGCCCCTTATGTCCAGGGCTTCACACATGCTACAATGGCCAGTACAGAGGGCTGCGAAGCCGCAAGGTGGAGCGAATCCCTTAAAGCTGGTCTCAGTTCGGATTGGGGTCTGCAACTCGACCCCATGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTCGGTAACACCCGAAGCCAGTGGCCTAACCTTTTGGAGGGAGCTGTCGAAGGTGGGATCGGCGATTGGGACGAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37061","NCBI_taxonomy_name":"Mycobacterium","NCBI_taxonomy_id":"1763"}}}},"ARO_accession":"3003517","ARO_id":"40119","ARO_name":"Mycobacterium chelonae 16S rRNA mutation conferring resistance to gentamicin C","ARO_description":"Point mutations in the 16S rRNA of Mycobacterium chelonae can confer resistance to gentamicin C","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2093":{"model_id":"2093","model_name":"Chlamydophila psittaci 16S rRNA mutation conferring resistance to spectinomycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2932":"G1194C","3010":"A1192G","3027":"C1193G","4808":"C1193U"},"clinical":{"2932":"G1194C","3010":"A1192G","3027":"C1193G","4808":"C1193U"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"2600"}},"model_sequences":{"sequence":{"3780":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"AB001778.1","fmin":"0","fmax":"1507","strand":"+","sequence":"AGAATTTGATCTTGGTTCAGATTGAACGCTGGCGGCGTGGATGAGGCATGCAAGTCGAACGGAATAATGACTTCGGTTGTTATTTAGTGGCGGAAGGGTTAGTAATACATAGATAATCTGTCCTCAACTTGGGAATAACGGTTGGAAACGACCGCTAATACCGAATGTGGTATGTTTAGGCATCTAAAACATATTAAAGAAGGGGATCTTCGGACCTTTCGGTTGAGGGAGAGTCTATGGGATATCAGCTTGTTGGTGGGGTAATGGCCTACCAAGGCTTTGACGTCTAGGCGGATTGAGAGATTGACCGCCAACACTGGGACTGAGACACTGCCCAGACTTCTACGGAAGGCTGCAGTCGAGAATCTTTCGCAATGGACGAAAGTCTGACGAAGCGACGCCGCGTGTGTGATGAAGGCTCTAGGGTTGTAAAGCACTTTCGCTTGGGAATAAGAGAGATTGGCTAATATCCAATCGATTTGAGCGTACCAGGTAAAGAAGCACCGGCTAACTCCGTGCCAGCAGCTGCGGTAATACGGAGGGTGCTAGCGTTAATCGGATTTATTGGGCGTAAAGGGCGTGTAGGCGGAAAGGAAAGTTAGATGTTAAATCTTGGGGCTCAACCCCAAGCCAGCATCTAATACTATCTTTCTAGAGGGTAGATGGAGAAAAGGGAATTCCACGTGTAGCGGTGAAATGCGTAGATATGTGGAAGAACACCAGTGGCGAAGGCGCTTTTCTAATTTACACCTGACGCTAAGGCGCGAAAGCAAGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCTTGCCGTAAACGATGCATACTTGATGTGGATAGTCTCAACCCTATCCGTGTCGTAGCTAACGCGTTAAGTATGCCGCCTGAGGAGTACACTCGCAAGGGTGAAACTCAAAAGAATTGACGGGGGCCCGCACAAGCAGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTGGGCTTGACATGTATTTGACCGCGGCAGAAATGTCGTTTTCCGCAAGGACAGATACACAGGTGCTGCATGGCTGTCGTCAGCTCGTGCCGTGAGGTGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCGTTAGTTGCCAACACTTAGGGTGGGAACTCTAACGAGACTGCCTGGGTTAACCAGGAGGAAGGCGAGGATGACGTCAAGTCAGCATGGCCCTTATGCCCAGGGCTACACACGTGCTACAATGGCCAGTACAGAAGGTAGCAATATCGTGAGATGGAGCAAATCCTCAAAGCTGGCCCCAGTTCGGATTGTAGTCTGCAACTCGACTACATGAAGTCGGAATTGCTAGTAATGGCGTGTCAGCTATAACGCCGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACATCATGGGAGTTGGTTTTGCCTTAAGTCGTTGACTCAACCTGCAAAGGAGAGAGGCGCCCAAGGTGAGGCTGATGACTGGGATGAAGTCGTAACAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40343","NCBI_taxonomy_name":"Chlamydia psittaci 6BC","NCBI_taxonomy_id":"331636"}}}},"ARO_accession":"3003485","ARO_id":"40087","ARO_name":"Chlamydophila psittaci 16S rRNA mutation conferring resistance to spectinomycin","ARO_description":"Point mutation in the 16S rRNA helix 34 region of Chlamydophila psittaci can confer resistance against spectinomycin","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2096":{"model_id":"2096","model_name":"Escherichia coli 16S rRNA mutation in the rrsC gene conferring resistance to kasugamicin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2941":"G926C","2951":"A1519C","2979":"A794G","2998":"A1519G","3050":"G926A","4822":"A794U","4823":"A1519U","4824":"G926U"},"clinical":{"2941":"G926C","2951":"A1519C","2979":"A794G","2998":"A1519G","3050":"G926A","4822":"A794U","4823":"A1519U","4824":"G926U"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"3229":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"U00096","fmin":"3941808","fmax":"3943349","strand":"+","sequence":"AAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCGACTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTGGTCTTGACATCCACGGAAGTTTTCAGAGATGAGAATGTGCCTTCGGGAACCGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGGTCCGGCCGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACGACCAGGGCTACACACGTGCTACAATGGCGCATACAAAGAGAAGCGACCTCGCGAGAGCAAGCGGACCTCATAAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTGGATCAGAATGCCACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGCAAAAGAAGTAGGTAGCTTAACCTTCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGATCACCTCCTTA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36905","NCBI_taxonomy_name":"Escherichia coli K-12","NCBI_taxonomy_id":"83333"}}}},"ARO_accession":"3003333","ARO_id":"39917","ARO_name":"Escherichia coli 16S rRNA (rrsC) mutation conferring resistance to kasugamicin","ARO_description":"Point mutations in the 3' minor, 3' major, and central domains in the rrsC 16S rRNA gene of Escherichia coli can confer resistance to kasugamicin","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37695":{"category_aro_accession":"3001296","category_aro_cvterm_id":"37695","category_aro_name":"kasugamycin","category_aro_description":"An unusual aminoglycoside because the cyclitol ring is not amino substituted; it was discovered as a fermentation product of Streptomyces kasugaensis.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2097":{"model_id":"2097","model_name":"Escherichia coli 16S rRNA mutation in the rrsB gene conferring resistance to paromomycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2995":"A1408G"},"clinical":{"2995":"A1408G"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"3238":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"U00096","fmin":"4166659","fmax":"4168200","strand":"+","sequence":"AAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAGAAGCTTGCTTCTTTGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCGACTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTGGTCTTGACATCCACGGAAGTTTTCAGAGATGAGAATGTGCCTTCGGGAACCGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGGTCCGGCCGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACGACCAGGGCTACACACGTGCTACAATGGCGCATACAAAGAGAAGCGACCTCGCGAGAGCAAGCGGACCTCATAAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTGGATCAGAATGCCACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGCAAAAGAAGTAGGTAGCTTAACCTTCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGATCACCTCCTTA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36905","NCBI_taxonomy_name":"Escherichia coli K-12","NCBI_taxonomy_id":"83333"}}}},"ARO_accession":"3003403","ARO_id":"39987","ARO_name":"Escherichia coli 16S rRNA (rrsB) mutation conferring resistance to paromomycin","ARO_description":"Point mutations in the 3' minor domain of helix 44, in the rrsB 16S rRNA gene of Escherichia coli can confer resistance to paromomycin","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2098":{"model_id":"2098","model_name":"Mycobacterium smegmatis 16S rRNA mutation in the rrsB gene conferring resistance to viomycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2985":"G1475A","4844":"G1475U"},"clinical":{"2985":"G1475A","4844":"G1475U"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"3248":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NC_008596.1","fmin":"5027948","fmax":"5029475","strand":"+","sequence":"TTTTTGTTTGGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGCCCTTTCGGGGGTACTCGAGTGGCGAACGGGTGAGTAACACGTGGGTGATCTGCCCTGCACTTTGGGATAAGCCTGGGAAACTGGGTCTAATACCGAATACACCCTGCTGGTCGCATGGCCTGGTAGGGGAAAGCTTTTGCGGTGTGGGATGGGCCCGCGGCCTATCAGCTTGTTGGTGGGGTGATGGCCTACCAAGGCGACGACGGGTAGCCGGCCTGAGAGGGTGACCGGCCACACTGGGACTGAGATACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGAGGGATGACGGCCTTCGGGTTGTAAACCTCTTTCAGCACAGACGAAGCGCAAGTGACGGTATGTGCAGAAGAAGGACCGGCCAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTCCGAGCGTTGTCCGGAATTACTGGGCGTAAAGAGCTCGTAGGTGGTTTGTCGCGTTGTTCGTGAAAACTCACAGCTTAACTGTGGGCGTGCGGGCGATACGGGCAGACTAGAGTACTGCAGGGGAGACTGGAATTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGGTGGCGAAGGCGGGTCTCTGGGCAGTAACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGGTGGGTACTAGGTGTGGGTTTCCTTCCTTGGGATCCGTGCCGTAGCTAACGCATTAAGTACCCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGTGGATTAATTCGATGCAACGCGAAGAACCTTACCTGGGTTTGACATGCACAGGACGCCGGCAGAGATGTCGGTTCCCTTGTGGCCTGTGTGCAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCTCATGTTGCCAGCACGTTATGGTGGGGACTCGTGAGAGACTGCCGGGGTCAACTCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGCCCCTTATGTCCAGGGCTTCACACATGCTACAATGGCCGGTACAAAGGGCTGCGATGCCGTGAGGTGGAGCGAATCCTTTCAAAGCCGGTCTCAGTTCGGATCGGGGTCTGCAACTCGACCCCGTGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTCGGTAACACCCGAAGCCGGTGGCCTAACCCTTGTGGAGGGAGCCGTCGAAGGTGGGATCGGCGATTGGGACGAAGTCGTAACAAGGTAGCCGTACCGGAAGGTGCGGCTGGATCACCTCCTTTCT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36769","NCBI_taxonomy_name":"Mycobacterium smegmatis str. MC2 155","NCBI_taxonomy_id":"246196"}}}},"ARO_accession":"3003547","ARO_id":"40149","ARO_name":"Mycobacterium smegmatis 16S rRNA (rrsB) mutation conferring resistance to viomycin","ARO_description":"Point mutations in the helix 44 region of the 16S rRNA rrsB gene of Mycobacterium smegmatis can confer resistance to viomycin.","ARO_category":{"40278":{"category_aro_accession":"3003667","category_aro_cvterm_id":"40278","category_aro_name":"16s rRNA with mutation conferring resistance to peptide antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to peptide antibiotics.","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35937":{"category_aro_accession":"0000018","category_aro_cvterm_id":"35937","category_aro_name":"viomycin","category_aro_description":"Viomycin sulfate (Viocin) is an polypeptide antibiotic used in the treatment of tuberculosis. It is produced by the actinomycete Streptomyces puniceus and binds to the bacterial ribosome, inhibiting prokaryotic protein synthesis and certain forms of RNA splicing.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"36629":{"category_aro_accession":"3000490","category_aro_cvterm_id":"36629","category_aro_name":"tuberactinomycin","category_aro_description":"Tuberactinomycins are a family of cyclic peptide antibiotics that are important in the treatment of tuberculosis. Tuberactinomycins contain nonproteinogenic amino acids and inhibit group I self-splicing RNA to disrupt prokaryotic protein synthesis.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2099":{"model_id":"2099","model_name":"Mycobacterium smegmatis 16S rRNA mutation in the rrsB gene conferring resistance to kanamycin A","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3029":"A1391G","4837":"U1389A"},"clinical":{"3029":"A1391G","4837":"U1389A"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"3251":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NC_008596.1","fmin":"5027948","fmax":"5029475","strand":"+","sequence":"TTTTTGTTTGGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGCCCTTTCGGGGGTACTCGAGTGGCGAACGGGTGAGTAACACGTGGGTGATCTGCCCTGCACTTTGGGATAAGCCTGGGAAACTGGGTCTAATACCGAATACACCCTGCTGGTCGCATGGCCTGGTAGGGGAAAGCTTTTGCGGTGTGGGATGGGCCCGCGGCCTATCAGCTTGTTGGTGGGGTGATGGCCTACCAAGGCGACGACGGGTAGCCGGCCTGAGAGGGTGACCGGCCACACTGGGACTGAGATACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGAGGGATGACGGCCTTCGGGTTGTAAACCTCTTTCAGCACAGACGAAGCGCAAGTGACGGTATGTGCAGAAGAAGGACCGGCCAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTCCGAGCGTTGTCCGGAATTACTGGGCGTAAAGAGCTCGTAGGTGGTTTGTCGCGTTGTTCGTGAAAACTCACAGCTTAACTGTGGGCGTGCGGGCGATACGGGCAGACTAGAGTACTGCAGGGGAGACTGGAATTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGGTGGCGAAGGCGGGTCTCTGGGCAGTAACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGGTGGGTACTAGGTGTGGGTTTCCTTCCTTGGGATCCGTGCCGTAGCTAACGCATTAAGTACCCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGTGGATTAATTCGATGCAACGCGAAGAACCTTACCTGGGTTTGACATGCACAGGACGCCGGCAGAGATGTCGGTTCCCTTGTGGCCTGTGTGCAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCTCATGTTGCCAGCACGTTATGGTGGGGACTCGTGAGAGACTGCCGGGGTCAACTCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGCCCCTTATGTCCAGGGCTTCACACATGCTACAATGGCCGGTACAAAGGGCTGCGATGCCGTGAGGTGGAGCGAATCCTTTCAAAGCCGGTCTCAGTTCGGATCGGGGTCTGCAACTCGACCCCGTGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTCGGTAACACCCGAAGCCGGTGGCCTAACCCTTGTGGAGGGAGCCGTCGAAGGTGGGATCGGCGATTGGGACGAAGTCGTAACAAGGTAGCCGTACCGGAAGGTGCGGCTGGATCACCTCCTTTCT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36769","NCBI_taxonomy_name":"Mycobacterium smegmatis str. MC2 155","NCBI_taxonomy_id":"246196"}}}},"ARO_accession":"3003542","ARO_id":"40144","ARO_name":"Mycobacterium smegmatis 16S rRNA (rrsB) mutation conferring resistance to kanamycin A","ARO_description":"Point mutations in the helix 44 region of the 16S rRNA rrsB gene of Mycobacterium smegmatis can confer resistance to kanamycin A","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2100":{"model_id":"2100","model_name":"Mycobacterium chelonae 16S rRNA mutation conferring resistance to amikacin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2981":"A1355G"},"clinical":{"2981":"A1355G"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"2500"}},"model_sequences":{"sequence":{"3272":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NR_114659.1","fmin":"1","fmax":"1441","strand":"+","sequence":"GACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGCCCTTCGGGGTACTCGAGTGGCGAACGGGTGAGTAACACGTGGGTGATCTGCCCTGCACTCTGGGATAAGCCTGGGAAACTGGGTCTAATACCGGATAGGACCACACACTTCATGGTGAGTGGTGCAAAGCTTTTGCGGTGTGGGATGAGCCCGCGGCCTATCAGCTTGTTGGTGGGGTAATGGCCCACCAAGGCGACGACGGGTAGCCGGCCTGAGAGGGTGACCGGCCACACTGGGACTGAGATACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGAGGGATGACGGCCTTCGGGTTGTAAACCTCTTTCAGTAGGGACGAAGCGAAAGTGACGGTACCTACAGAAGAAGGACCGGCCAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTCCGAGCGTTGTCCGGAATTACTGGGCGTAAAGAGCTCGTAGGTGGTTTGTCGCGTTGTTCGTGAAAACTCACAGCTTAACTGTGGGCGTGCGGGCGATACGGGCAGACTAGAGTACTGCAGGGGAGACTGGAATTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGGTGGCGAAGGCGGGTCTCTGGGCAGTAACTGACGCTGAGGAGCGAAAGCGTGGGTAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGGTGGGTACTAGGTGTGGGTTTCCTTCCTTGGGATCCGTGCCGTAGCTAACGCATTAAGTACCCCGCCTGGGGAGTACGGTCGCAAGACTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGTGGATTAATTCGATGCAACGCGAAGAACCTTACCTGGGTTTGACATGCGCAGGACGTATCTAGAGATAGGTATTCCCTTGTGGCCTGCGTGCAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCCTATGTTGCCAGCGGGTAATGCCGGGGACTCGTAGGAGACTGCCGGGGTCAACTCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGCCCCTTATGTCCAGGGCTTCACACATGCTACAATGGCCAGTACAGAGGGCTGCGAAGCCGCAAGGTGGAGCGAATCCCTTAAAGCTGGTCTCAGTTCGGATTGGGGTCTGCAACTCGACCCCATGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTCGGTAACACCCGAAGCCAGTGGCCTAACCTTTTGGAGGGAGCTGTCGAAGGTGGGATCGGCGATTGGGACGAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37061","NCBI_taxonomy_name":"Mycobacterium","NCBI_taxonomy_id":"1763"}}}},"ARO_accession":"3003514","ARO_id":"40116","ARO_name":"Mycobacterium chelonae 16S rRNA mutation conferring resistance to amikacin","ARO_description":"Point mutations in the 16S rRNA of Mycobacterium chelonae can cause resistance to amikacin.","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2102":{"model_id":"2102","model_name":"Mycobacterium smegmatis 16S rRNA mutation in the rrsB gene conferring resistance to hygromycin B","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"2700"},"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"7842":"U1348C","7843":"C1439U","7844":"U1441C"},"clinical":{"7842":"U1348C","7843":"C1439U","7844":"U1441C"}}},"model_sequences":{"sequence":{"4148":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"X52922.1","fmin":"0","fmax":"1454","strand":"+","sequence":"GGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGCCCTTTCGGGGGTACTCGAGTGGCGAACGGGTGAGTAACACGTGGGTGATCTGCCCTGCACTTTGGGATAAGCCTGGGAAACTGGGTCTAATACCGAATACACCCTGCTGGTCGCATGGCCTGGTAGGGGAAAGCTTTTGCGGTGTGGGATGGGCCCGCGGCCTATCAGCTTGTTGGTGGGGTGATGGCCTACCAAGGCGACGACGGGTAGCCGGCCTGAGAGGGTGACCGGCCACACTGGGACTGAGATACGGCCCAGACTNCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGAGGGATGACGGCCTTCGGGTTGTAAACCTCTTTCAGCACAGACGAAGCGCAAGTGACGGTATGTGCAGAAGAAGGACCGGCCAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTCCGAGCGTTGTCCGGAATTACTGGGCGTAAAGAGCTCGTAGGTGGTTTGTCGCGTTGTTCGTGAAAACTCACAGCTTAACTGTGGGCGTGCGGGCGATACGGGCAGACTAGAGTACTGCAGGGGAGACTGGAATTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGGTGGCGAAGGCGGGTCTCTGGGCAGTAACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCACGNCGTAAACGGTGGGTACTAGGTGTGGGTTTCCTTCCTTGGGATCCGTGCCGTAGCTAACGCATTAAGTANCCCGCCTGGGGAGTACGGNCGCAAGGCTAAAACTCAAAGGAATTGACGGGGGNCCGCACAAGCGGCGGAGCATGTGGATTAATTCGATGCAACGCGAAGAACCTTACCTGGGTTTGACATGCACAGGACGCCGGCAGAGATGTCGGTTCCCTTGTGGCCTGTGTGCAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCTCATGTTGCCAGCACGTTATGGTGGGGACTCGTGAGAGACTGCCGGGGTCAACTCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGCCCCTTATGTCCAGGGCTTCACACATGCTACAATGGCCGGTACAAAGGGCTGCGATGCCGTGAGGTGGAGCGAATCCTTTCAAAGCCGGTCTCAGTTCGGATCGGGGTCTGCAACTCGACCCCGTGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTCGGTAACACCCGAAGCCGGTGGCCTAACCCTTGTGGAGGGAGCCGTCGAAGGTGGGATCGGCGATTGGGACGAAGTCGTAACAAGGTAGCCG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36871","NCBI_taxonomy_name":"Mycobacterium smegmatis","NCBI_taxonomy_id":"1772"}}}},"ARO_accession":"3003540","ARO_id":"40142","ARO_name":"Mycobacterium smegmatis 16S rRNA (rrsB) mutation conferring resistance to hygromycin B","ARO_description":"Point mutations in the highly conserved helix 44 of the 16S rrsB rRNA gene of Mycobacterium smegmatis can confer resistance to hygromycin B. Resistance against hygromycin B is the result of conformational alterations that distorts a strong hydrogen bond leading to a change in the local geometry of the hygromycin B binding site.","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2105":{"model_id":"2105","model_name":"Mycobacterium abscessus 16S rRNA mutation conferring resistance to neomycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2896":"A1375G"},"clinical":{"2896":"A1375G"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"2600"}},"model_sequences":{"sequence":{"3255":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"CU458896.1","fmin":"1462398","fmax":"1463901","strand":"+","sequence":"AGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGCCCTTCGGGGTACTCGAGTGGCGAACGGGTGAGTAACACGTGGGTGATCTGCCCTGCACTCTGGGATAAGCCTGGGAAACTGGGTCTAATACCGGATAGGACCACACACTTCATGGTGAGTGGTGCAAAGCTTTTGCGGTGTGGGATGAGCCCGCGGCCTATCAGCTTGTTGGTGGGGTAATGGCCCACCAAGGCGACGACGGGTAGCCGGCCTGAGAGGGTGACCGGCCACACTGGGACTGAGATACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGAGGGATGACGGCCTTCGGGTTGTAAACCTCTTTCAGTAGGGACGAAGCGAAAGTGACGGTACCTACAGAAGAAGGACCGGCCAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTCCGAGCGTTGTCCGGAATTACTGGGCGTAAAGAGCTCGTAGGTGGTTTGTCGCGTTGTTCGTGAAAACTCACAGCTTAACTGTGGGCGTGCGGGCGATACGGGCAGACTAGAGTACTGCAGGGGAGACTGGAATTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGGTGGCGAAGGCGGGTCTCTGGGCAGTAACTGACGCTGAGGAGCGAAAGCGTGGGTAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGGTGGGTACTAGGTGTGGGTTTCCTTCCTTGGGATCCGTGCCGTAGCTAACGCATTAAGTACCCCGCCTGGGGAGTACGGTCGCAAGACTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGTGGATTAATTCGATGCAACGCGAAGAACCTTACCTGGGTTTGACATGCACAGGACGTACCTAGAGATAGGTATTCCCTTGTGGCCTGTGTGCAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCCTATGTTGCCAGCGGGTAATGCCGGGGACTCGTAGGAGACTGCCGGGGTCAACTCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGCCCCTTATGTCCAGGGCTTCACACATGCTACAATGGCCAGTACAGAGGGCTGCGAAGCCGTAAGGTGGAGCGAATCCCTTAAAGCTGGTCTCAGTTCGGATTGGGGTCTGCAACTCGACCCCATGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTCGGTAACACCCGAAGCCAGTGGCCTAACCTTTTGGAGGGAGCTGTCGAAGGTGGGATCGGCGATTGGGACGAAGTCGTAACAAGGTAGCCGTACCGGAAGGTGCGGCTGGATCACCT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36888","NCBI_taxonomy_name":"Mycobacterium abscessus","NCBI_taxonomy_id":"36809"}}}},"ARO_accession":"3003238","ARO_id":"39822","ARO_name":"Mycobacterium abscessus 16S rRNA mutation conferring resistance to neomycin","ARO_description":"Point mutations in the 16S rRNA of Mycobacterium abscessus conferring resistance to neomycin","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2106":{"model_id":"2106","model_name":"Mycobacterium smegmatis 16S rRNA mutation in the rrsA gene conferring resistance to kanamycin A","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2929":"A1391G","4838":"U1389A"},"clinical":{"2929":"A1391G","4838":"U1389A"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"4144":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NC_008596.1","fmin":"3823614","fmax":"3825143","strand":"-","sequence":"AGAAAGGAGGTGATCCAGCCGCACCTTCCGGTACGGCTACCTTGTTACGACTTCGTCCCAATCGCCGATCCCACCTTCGACGGCTCCCTCCACAAGGGTTAGGCCACCGGCTTCGGGTGTTACCGACTTTCATGACGTGACGGGCGGTGTGTACAAGGCCCGGGAACGTATTCACCGCAGCGTTGCTGATCTGCGATTACTAGCGACTCCGACTTCACGGGGTCGAGTTGCAGACCCCGATCCGAACTGAGACCGGCTTTGAAAGGATTCGCTCCACCTCACGGCATCGCAGCCCTTTGTACCGGCCATTGTAGCATGTGTGAAGCCCTGGACATAAGGGGCATGATGACTTGACGTCATCCCCACCTTCCTCCGAGTTGACCCCGGCAGTCTCTCACGAGTCCCCACCATAACGTGCTGGCAACATGAGACAAGGGTTGCGCTCGTTGCGGGACTTAACCCAACATCTCACGACACGAGCTGACGACAGCCATGCACCACCTGCACACAGGCCACAAGGGAACCGACATCTCTGCCGGCGTCCTGTGCATGTCAAACCCAGGTAAGGTTCTTCGCGTTGCATCGAATTAATCCACATGCTCCGCCGCTTGTGCGGGCCCCCGTCAATTCCTTTGAGTTTTAGCCTTGCGGCCGTACTCCCCAGGCGGGGTACTTAATGCGTTAGCTACGGCACGGATCCCAAGGAAGGAAACCCACACCTAGTACCCACCGTTTACGGCGTGGACTACCAGGGTATCTAATCCTGTTCGCTCCCCACGCTTTCGCTCCTCAGCGTCAGTTACTGCCCAGAGACCCGCCTTCGCCACCGGTGTTCCTCCTGATATCTGCGCATTCCACCGCTACACCAGGAATTCCAGTCTCCCCTGCAGTACTCTAGTCTGCCCGTATCGCCCGCACGCCCACAGTTAAGCTGTGAGTTTTCACGAACAACGCGACAAACCACCTACGAGCTCTTTACGCCCAGTAATTCCGGACAACGCTCGGACCCTACGTATTACCGCGGCTGCTGGCACGTAGTTGGCCGGTCCTTCTTCTGCACATACCGTCACTTGCGCTTCGTCTGTGCTGAAAGAGGTTTACAACCCGAAGGCCGTCATCCCTCACGCGGCGTCGCTGCATCAGGCTTGCGCCCATTGTGCAATATTCCCCACTGCTGCCTCCCGTAGGAGTCTGGGCCGTATCTCAGTCCCAGTGTGGCCGGTCACCCTCTCAGGCCGGCTACCCGTCGTCGCCTTGGTAGGCCATCACCCCACCAACAAGCTGATAGGCCGCGGGCCCATCCCACACCGCAAAAGCTTTCCCCTACCAGGCCATGCGACCAGCAGGGTGTATTCGGTATTAGACCCAGTTTCCCAGGCTTATCCCAAAGTGCAGGGCAGATCACCCACGTGTTACTCACCCGTTCGCCACTCGAGTACCCCCGAAAGGGCCTTTCCGTTCGACTTGCATGTGTTAAGCACGCCGCCAGCGTTCGTCCTGAGCCAGGATCAAACTCTCCAAACAAAAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36769","NCBI_taxonomy_name":"Mycobacterium smegmatis str. MC2 155","NCBI_taxonomy_id":"246196"}}}},"ARO_accession":"3003543","ARO_id":"40145","ARO_name":"Mycobacterium smegmatis 16S rRNA (rrsA) mutation conferring resistance to kanamycin A","ARO_description":"Point mutations in the helix 44 region of the 16S rRNA rrsA gene of Mycobacterium smegmastis can confer resistance to kanamycin A","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2111":{"model_id":"2111","model_name":"Mycobacterium chelonae 16S rRNA mutation conferring resistance to tobramycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2901":"A1355G"},"clinical":{"2901":"A1355G"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"2500"}},"model_sequences":{"sequence":{"3270":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NR_114659.1","fmin":"1","fmax":"1441","strand":"+","sequence":"GACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGCCCTTCGGGGTACTCGAGTGGCGAACGGGTGAGTAACACGTGGGTGATCTGCCCTGCACTCTGGGATAAGCCTGGGAAACTGGGTCTAATACCGGATAGGACCACACACTTCATGGTGAGTGGTGCAAAGCTTTTGCGGTGTGGGATGAGCCCGCGGCCTATCAGCTTGTTGGTGGGGTAATGGCCCACCAAGGCGACGACGGGTAGCCGGCCTGAGAGGGTGACCGGCCACACTGGGACTGAGATACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGAGGGATGACGGCCTTCGGGTTGTAAACCTCTTTCAGTAGGGACGAAGCGAAAGTGACGGTACCTACAGAAGAAGGACCGGCCAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTCCGAGCGTTGTCCGGAATTACTGGGCGTAAAGAGCTCGTAGGTGGTTTGTCGCGTTGTTCGTGAAAACTCACAGCTTAACTGTGGGCGTGCGGGCGATACGGGCAGACTAGAGTACTGCAGGGGAGACTGGAATTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGGTGGCGAAGGCGGGTCTCTGGGCAGTAACTGACGCTGAGGAGCGAAAGCGTGGGTAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGGTGGGTACTAGGTGTGGGTTTCCTTCCTTGGGATCCGTGCCGTAGCTAACGCATTAAGTACCCCGCCTGGGGAGTACGGTCGCAAGACTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGTGGATTAATTCGATGCAACGCGAAGAACCTTACCTGGGTTTGACATGCGCAGGACGTATCTAGAGATAGGTATTCCCTTGTGGCCTGCGTGCAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCCTATGTTGCCAGCGGGTAATGCCGGGGACTCGTAGGAGACTGCCGGGGTCAACTCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGCCCCTTATGTCCAGGGCTTCACACATGCTACAATGGCCAGTACAGAGGGCTGCGAAGCCGCAAGGTGGAGCGAATCCCTTAAAGCTGGTCTCAGTTCGGATTGGGGTCTGCAACTCGACCCCATGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTCGGTAACACCCGAAGCCAGTGGCCTAACCTTTTGGAGGGAGCTGTCGAAGGTGGGATCGGCGATTGGGACGAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37061","NCBI_taxonomy_name":"Mycobacterium","NCBI_taxonomy_id":"1763"}}}},"ARO_accession":"3003516","ARO_id":"40118","ARO_name":"Mycobacterium chelonae 16S rRNA mutation conferring resistance to tobramycin","ARO_description":"Point mutations in the 16S rRNA of Mycobacterium chelonae can cause resistance to tobramycin.","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2113":{"model_id":"2113","model_name":"Escherichia coli 16S rRNA mutation in the rrsB gene conferring resistance to tobramycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"4827":"U1406A"},"clinical":{"4827":"U1406A"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"3241":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"U00096","fmin":"4166659","fmax":"4168200","strand":"+","sequence":"AAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAGAAGCTTGCTTCTTTGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCGACTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTGGTCTTGACATCCACGGAAGTTTTCAGAGATGAGAATGTGCCTTCGGGAACCGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGGTCCGGCCGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACGACCAGGGCTACACACGTGCTACAATGGCGCATACAAAGAGAAGCGACCTCGCGAGAGCAAGCGGACCTCATAAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTGGATCAGAATGCCACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGCAAAAGAAGTAGGTAGCTTAACCTTCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGATCACCTCCTTA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36905","NCBI_taxonomy_name":"Escherichia coli K-12","NCBI_taxonomy_id":"83333"}}}},"ARO_accession":"3003408","ARO_id":"39992","ARO_name":"Escherichia coli 16S rRNA (rrsB) mutation conferring resistance to tobramycin","ARO_description":"Point mutations in the 3' minor domain of the rrnB 16S rRNA gene of Escherichia coli can confer resistance to tobramycin","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2116":{"model_id":"2116","model_name":"Pasteurella multocida 16S rRNA mutation conferring resistance to spectinomycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3059":"C1194G"},"clinical":{"3059":"C1194G"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"3252":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NC_002663.1","fmin":"341427","fmax":"342977","strand":"+","sequence":"TTGAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCTTAACACATGCAAGTCGAACGGTAGCAGGAAGAAAGCTTGCTTTCTTTGCTGACGAGTGGCGGACGGGTGAGTAATGCTTGGGAATCTGGCTTATGGAGGGGGATAACTGTGGGAAACTGCAGCTAATACCGCGTATTCTCTGAGGAGGAAAGGGTGGGACCTTAGGGCCACCTGCCATAAGATGAGCCCAAGTGGGATTAGGTAGTTGGTGGGGTAAAGGCCTACCAAGCCTGCGATCTCTAGCTGGTCTGAAAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCGCAATGGGGGGAACCCTGACGCAGCCATGCCGCGTGAATGAAGAAGGCCTTCGGGTTGTAAAGTTCTTTCGGTAATGAGGAAGGGATGTTGTTAAATAGATAGCATCATTGACGTTAATTACAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCGAGCGTTAATCGGAATAACTGGGCGTAAAGGGCACGCAGGCGGACTTTTAAGTGAGATGTGAAATCCCCGAGCTTAACTTGGGAACTGCATTTCAGACTGGGAGTCTAGAGTACTTTAGGGAGGGGTAGAATTCCACGTGTAGCGGTGAAATGCGTAGAGATGTGGAGGAATACCGAAGGCGAAGGCAGCCCCTTGGGAATGTACTGACGCTCATGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCTGTAAACGCTGTCGATTTGGGGATTGGGCTATATGCTTGGTGCCCGAAGCTAACGTGATAAATCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTACTCTTGACATCCTAAGAAGAGCTCAGAGATGAGCTTGTGCCTTCGGGAACTTAGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGATTCGGTCGGGAACTCAAAGGAGACTGCCAGTGACAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACGAGTAGGGCTACACACGTGCTACAATGGTGCATACAGAGGGCAGCGAGAGTGCGAGCTTGAGCGAATCTCAGAAAGTGCATCTAAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGCAAATCAGAATGTTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCCGTACACCATGGGAGTGGGTTGTACCAGAAGTAGATAGCTTAACCTTCGGGAGGGCGTTTACCACGGTATGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGATCACCTCCTTACCTAAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39783","NCBI_taxonomy_name":"Pasteurella multocida 36950","NCBI_taxonomy_id":"1075089"}}}},"ARO_accession":"3003493","ARO_id":"40095","ARO_name":"Pasteurella multocida 16S rRNA mutation conferring resistance to spectinomycin","ARO_description":"Point mutations in the helix 34 region of 16S rRNA of Pasteurella multocida can confer resistance to spectinomycin","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2122":{"model_id":"2122","model_name":"Mycobacterium chelonae 16S rRNA mutation conferring resistance to neomycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2953":"A1355G"},"clinical":{"2953":"A1355G"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"2500"}},"model_sequences":{"sequence":{"3271":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NR_114659.1","fmin":"1","fmax":"1441","strand":"+","sequence":"GACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGCCCTTCGGGGTACTCGAGTGGCGAACGGGTGAGTAACACGTGGGTGATCTGCCCTGCACTCTGGGATAAGCCTGGGAAACTGGGTCTAATACCGGATAGGACCACACACTTCATGGTGAGTGGTGCAAAGCTTTTGCGGTGTGGGATGAGCCCGCGGCCTATCAGCTTGTTGGTGGGGTAATGGCCCACCAAGGCGACGACGGGTAGCCGGCCTGAGAGGGTGACCGGCCACACTGGGACTGAGATACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGAGGGATGACGGCCTTCGGGTTGTAAACCTCTTTCAGTAGGGACGAAGCGAAAGTGACGGTACCTACAGAAGAAGGACCGGCCAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTCCGAGCGTTGTCCGGAATTACTGGGCGTAAAGAGCTCGTAGGTGGTTTGTCGCGTTGTTCGTGAAAACTCACAGCTTAACTGTGGGCGTGCGGGCGATACGGGCAGACTAGAGTACTGCAGGGGAGACTGGAATTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGGTGGCGAAGGCGGGTCTCTGGGCAGTAACTGACGCTGAGGAGCGAAAGCGTGGGTAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGGTGGGTACTAGGTGTGGGTTTCCTTCCTTGGGATCCGTGCCGTAGCTAACGCATTAAGTACCCCGCCTGGGGAGTACGGTCGCAAGACTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGTGGATTAATTCGATGCAACGCGAAGAACCTTACCTGGGTTTGACATGCGCAGGACGTATCTAGAGATAGGTATTCCCTTGTGGCCTGCGTGCAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCCTATGTTGCCAGCGGGTAATGCCGGGGACTCGTAGGAGACTGCCGGGGTCAACTCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGCCCCTTATGTCCAGGGCTTCACACATGCTACAATGGCCAGTACAGAGGGCTGCGAAGCCGCAAGGTGGAGCGAATCCCTTAAAGCTGGTCTCAGTTCGGATTGGGGTCTGCAACTCGACCCCATGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTCGGTAACACCCGAAGCCAGTGGCCTAACCTTTTGGAGGGAGCTGTCGAAGGTGGGATCGGCGATTGGGACGAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37061","NCBI_taxonomy_name":"Mycobacterium","NCBI_taxonomy_id":"1763"}}}},"ARO_accession":"3003518","ARO_id":"40120","ARO_name":"Mycobacterium chelonae 16S rRNA mutation conferring resistance to neomycin","ARO_description":"Point mutations in the 16S rRNA of Mycobacterium chelonae can cause resistance to neomycin.","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2147":{"model_id":"2147","model_name":"Escherichia coli EF-Tu mutants conferring resistance to Enacyloxin IIa","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3566":"A375T","3567":"G316D","3568":"Q124K","3569":"Q329H"},"clinical":{"3566":"A375T","3567":"G316D","3568":"Q124K","3569":"Q329H"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3532":{"protein_sequence":{"accession":"NP_417798.1","sequence":"MSKEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDNAPEEKARGITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALEGDAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVGEEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIKPHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMVVTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLG"},"dna_sequence":{"accession":"NC_000913.3","fmin":"3470144","fmax":"3471329","strand":"-","sequence":"TTAGCCCAGAACTTTAGCAACAACGCCCGCGCCAACGGTACGGCCGCCTTCACGGATTGCGAAACGCAGACCGTCGTCCATCGCGATCGGGTGGATCAGGGTAACAACCATTTTGATGTTGTCGCCCGGCATTACCATCTCTACGCCTTCCGGCAGTTCGATGGTACCAGTCACGTCAGTAGTACGGAAGTAGAACTGCGGACGGTAGCCTTTGAAGAACGGAGTATGACGGCCGCCTTCATCTTTGGACAGAATGTACACTTCAGATTCGAACTTGGTGTGCGGCTTGATGGTGCCCGGCTTAGCCAGTACCTGACCACGTTCGATTTCTTCACGTTTGATACCACGCAGCAGAACACCTACGTTCTCACCAGCACGGCCTTCGTCCAGCAGTTTGCGGAACATTTCAACGCCAGTACAGGTAGACTTCTGAGTCTCTTTGATACCAACGATTTCAACTTCTTCACCAACTTTGATGATACCGCGTTCTACACGACCGGTAACAACGGTACCACGACCGGAGATGGAGAATACGTCTTCGATCGGCAGCAGGAACGGCTTGTCAATCGCACGCTCTGGTTCCGGAATATAAGAATCCAGGAAGCCAGCCAGTTCCAGGATTTTCGCTTCCCACTCTGCGTCGCCTTCCAGCGCTTTCAGAGCAGAACCACGAACGATCGGAGTGTCGTCGCCCGGGAAGTCGTACTGAGACAGAAGTTCACGAACTTCCATTTCAACCAGTTCCAGCAGCTCTTCGTCATCAACCATGTCGCATTTGTTCAGGAACACGATGATGTACGGAACGCCTACCTGACGACCCAGCAGGATGTGCTCACGAGTCTGCGGCATCGGGCCGTCAGTCGCAGCAACTACCAGGATCGCGCCGTCCATCTGAGCAGCACCGGTGATCATGTTTTTAACATAGTCGGCGTGCCCCGGGCAGTCTACGTGTGCGTAGTGACGGGTCGGGGTGTCGTATTCAACGTGAGAAGTGTTGATGGTGATACCACGAGCTTTTTCTTCCGGCGCGTTATCGATCTGGTCGAATGCACGAGCAGCACCGCCGTAGGTTTTAGCCAGTACGGTGGTGATTGCAGCGGTCAGAGTAGTTTTACCGTGGTCAACGTGGCCGATAGTACCAACGTTAACGTGCGGTTTTGTACGTTCAAATTTTTCTTTAGACAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3003370","ARO_id":"39954","ARO_name":"Escherichia coli EF-Tu mutants conferring resistance to Enacyloxin IIa","ARO_description":"Sequence variants of Escherichia coli elongation factor Tu that confer resistance to Enacyloxin IIa","ARO_category":{"37711":{"category_aro_accession":"3001312","category_aro_cvterm_id":"37711","category_aro_name":"elfamycin resistant EF-Tu","category_aro_description":"Sequence variants of elongation factor Tu that confer resistance to elfamycin antibiotics.","category_aro_class_name":"AMR Gene Family"},"36725":{"category_aro_accession":"3000586","category_aro_cvterm_id":"36725","category_aro_name":"pulvomycin","category_aro_description":"Pulvomycin is a polyketide antibiotic that binds elongation factor Tu (EF-Tu) to inhibit protein biosynthesis by preventing the formation of the ternary complex (EF-Tu*GTP*aa-tRNA). Phenotypically, it was shown that pulvomycin sensitivity is dominant over resistance.","category_aro_class_name":"Antibiotic"},"37636":{"category_aro_accession":"3001237","category_aro_cvterm_id":"37636","category_aro_name":"GE2270A","category_aro_description":"GE2270A is the model molecule of cyclic thiazolyl peptide elfamycins. GE2270A is produced by Planobispora rosea. Biosynthesis of the molecule has been shown to originate as a ribosomally synthesized peptide that undergoes significant post-translational modification. Clinical use of cyclic thiazolyl peptides is hindered by their low water solubility and bioavailability.","category_aro_class_name":"Antibiotic"},"37641":{"category_aro_accession":"3001242","category_aro_cvterm_id":"37641","category_aro_name":"enacyloxin IIa","category_aro_description":"Enacyloxin IIa is structurally distinct but acts in a similar mechanism to kirromycin-like elfamycins. It prohibits the transfer of the amino acid at the A site to the elongating peptide chain. It is most likely that the mechanism of action is that EF-Tu*GDP is locked in the EF-Tu*GTP form, and EF-Tu*GDP*aa-tRNA is immobilized on the ribosome. It is an open question whether enacyloxin IIa actually belongs to the kirromycin-like group of elfamycins due to their high similarity.","category_aro_class_name":"Antibiotic"},"39998":{"category_aro_accession":"3003414","category_aro_cvterm_id":"39998","category_aro_name":"LFF571","category_aro_description":"LFF571 is a novel semi-synthetic thiopeptide antibiotic derived from GE2270. It has been shown to possess potent in vitro and in vivo activity against Gram-positive bacteria. It is hypothesized that it a translation inhibitor leading to cell death.","category_aro_class_name":"Antibiotic"},"37618":{"category_aro_accession":"3001219","category_aro_cvterm_id":"37618","category_aro_name":"elfamycin antibiotic","category_aro_description":"Elfamycins are molecules that inhibit bacterial elongation factor Tu (EF-Tu), a key protein which brings aminoacyl-tRNA (aa-tRNA) to the ribosome during protein synthesis. Elfamycins defined by their target (EF-Tu), rather than a conserved chemical backbone. Elfamycins follow two mechanisms to disrupt protein synthesis: 1. kirromycins and enacyloxin fix EF-Tu in the GTP bound conformation and lock EF-Tu onto the ribosome, and 2. pulvomycin and GE2270 cover the binding site of aa-tRNA disallowing EF-Tu from being charged with aa-tRNA. All elfamycins cause increased the affinity of EF-Tu for GTP.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2127":{"model_id":"2127","model_name":"Borrelia burgdorferi 16S rRNA mutation conferring resistance to kanamycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3012":"A1401G"},"clinical":{"3012":"A1401G"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"2500"}},"model_sequences":{"sequence":{"3266":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NR_044732.2","fmin":"0","fmax":"1477","strand":"+","sequence":"AATAACGAAGAGTTTGATCCTGGCTTAGAACTAACGCTGGCAGTGCGTCTTAAGCATGCAAGTCAAACGGGATGTAGCAATACATTCAGTGGCGAACGGGTGAGTAACGCGTGGATGATCTACCTATGAGATGGGGATAACTATTAGAAATAGTAGCTAATACCGAATAAGGTCAGTTAATTTGTTAATTGATGAAAGGAAGCCTTTAAACGTTCGCTTGTAGATGAGTCTGCGTCTTATTAGCTAGTTGGTAGGGTAAATGCCTACCAAGGCAATGATAAGTAACCGGCCTGAGAGGGTGAACGGTCACACTGGAACTGAGATACGGTCCAGNCTCCTACGGGAGGCAGCAGCTAAGAATCTTCCGCAATGGGCGAAAGCCTGACGGAGCGACACTGCGTGAATGAAGAAGGTCGAAAGATTGTAAAATTCTTTTATAAATGAGGAATAAGCTTTGTAGGAAATGACAAAGTGATGACGTTAATTTATGAATAAGCCCCGGCTAATTACGTGCCAGNAGCCGCGGTAATACGTAAGGGNNNAGCGTTGTTCGGGATTATTGGGCGTAAAGGGTGAGTAGGCGGATATATAAGTCTATGCATAAAATACCACAGCTCAACTGTGGACCTATGTTGGAAACTATATGTCTAGAGTCTGATAGAGGAAGTTAGAATTTCTGGTGTAAGGGTGGAATCTGTTGATATCAGAAAGAATACCGGAGGCGAAGGCGAACTTCTGGGTCAAGACTGACGCTGAGTCACGAAAGCGTAGGGAGCAAACAGGATTAGATACCCTGGTAGTCTACGCTGTAAACGATGCACACTTGGTGTTAACTAAAAGTTAGTACCGAAGCTAACGTGTTAAGTGTGCAGCCTGGGGAGTATGCTCGCAAGAGNGAAACTCAAAGGNATTNANNNGNGCCNGCACAAGNNGTGGAGCATGTGGTTTNNNNNNANNNTACGCGAGGAACCTTACCAGGGCTTGACATATATAGGATATAGTTAGAGATAATTATTCCCCGTTTGGGGTCTATATACAGGTGCTGCATGGTTGTCGTCAGCTCGTGCTGTGAGGTGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTTATCTGTTACCAGCATGTAATGGTGGGGACTCAGATAAGACTGCCGGTGATAAGTCGGAGGAAGGTGAGGATGACGTCAAATCATCATGGCCCTTATGTCCTGGGCTACACACGTGCTACAATGGCCTGTACAAAGCGAAGCGAAACAGTGATGTGAAGCAAAACGCATAAAGCAGGTCTCAGTCCGGATTGAAGTCTGAAACTCGACTTCATGAAGTTGGAATCGCTAGTAATCGTATATCAGAATGATACGGTGAATACGTTCTCGGGCNTTGTACACACCGCCCGTCACACCACCCGAGTTGAGGATACCCGAAGCTATTATTCTAACCCGTAAGGGAGGAAGGTATTTAAGGTATGTTTAGCA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40345","NCBI_taxonomy_name":"Borrelia burgdorferi","NCBI_taxonomy_id":"139"}}}},"ARO_accession":"3003503","ARO_id":"40105","ARO_name":"Borrelia burgdorferi 16S rRNA mutation conferring resistance to kanamycin","ARO_description":"Point mutations in the 3' minor domain of the 16S rRNA gene of Borrelia burgdorferi can confer resistance to kanamycin","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2084":{"model_id":"2084","model_name":"Mycobacterium abscessus 16S rRNA mutation conferring resistance to amikacin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3036":"A1375G","4793":"G1458U","4794":"U1373A","4795":"C1376U"},"clinical":{"3036":"A1375G","4793":"G1458U","4794":"U1373A","4795":"C1376U"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"2600"}},"model_sequences":{"sequence":{"3254":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"CU458896.1","fmin":"1462398","fmax":"1463901","strand":"+","sequence":"AGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGCCCTTCGGGGTACTCGAGTGGCGAACGGGTGAGTAACACGTGGGTGATCTGCCCTGCACTCTGGGATAAGCCTGGGAAACTGGGTCTAATACCGGATAGGACCACACACTTCATGGTGAGTGGTGCAAAGCTTTTGCGGTGTGGGATGAGCCCGCGGCCTATCAGCTTGTTGGTGGGGTAATGGCCCACCAAGGCGACGACGGGTAGCCGGCCTGAGAGGGTGACCGGCCACACTGGGACTGAGATACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGAGGGATGACGGCCTTCGGGTTGTAAACCTCTTTCAGTAGGGACGAAGCGAAAGTGACGGTACCTACAGAAGAAGGACCGGCCAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTCCGAGCGTTGTCCGGAATTACTGGGCGTAAAGAGCTCGTAGGTGGTTTGTCGCGTTGTTCGTGAAAACTCACAGCTTAACTGTGGGCGTGCGGGCGATACGGGCAGACTAGAGTACTGCAGGGGAGACTGGAATTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGGTGGCGAAGGCGGGTCTCTGGGCAGTAACTGACGCTGAGGAGCGAAAGCGTGGGTAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGGTGGGTACTAGGTGTGGGTTTCCTTCCTTGGGATCCGTGCCGTAGCTAACGCATTAAGTACCCCGCCTGGGGAGTACGGTCGCAAGACTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGTGGATTAATTCGATGCAACGCGAAGAACCTTACCTGGGTTTGACATGCACAGGACGTACCTAGAGATAGGTATTCCCTTGTGGCCTGTGTGCAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCCTATGTTGCCAGCGGGTAATGCCGGGGACTCGTAGGAGACTGCCGGGGTCAACTCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGCCCCTTATGTCCAGGGCTTCACACATGCTACAATGGCCAGTACAGAGGGCTGCGAAGCCGTAAGGTGGAGCGAATCCCTTAAAGCTGGTCTCAGTTCGGATTGGGGTCTGCAACTCGACCCCATGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTCGGTAACACCCGAAGCCAGTGGCCTAACCTTTTGGAGGGAGCTGTCGAAGGTGGGATCGGCGATTGGGACGAAGTCGTAACAAGGTAGCCGTACCGGAAGGTGCGGCTGGATCACCT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36888","NCBI_taxonomy_name":"Mycobacterium abscessus","NCBI_taxonomy_id":"36809"}}}},"ARO_accession":"3003239","ARO_id":"39823","ARO_name":"Mycobacterium abscessus 16S rRNA mutation conferring resistance to amikacin","ARO_description":"Point mutations in the 16S rRNA of Mycobacterium abscessus conferring resistance to amikacin","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2129":{"model_id":"2129","model_name":"Escherichia coli 16S rRNA mutation in the rrsB gene conferring resistance to spectinomycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2910":"C1192A","2919":"G1064A","2959":"G1064C","3070":"C1192G","4815":"G1064U","4816":"C1192U","4817":"C1066U"},"clinical":{"2910":"C1192A","2919":"G1064A","2959":"G1064C","3070":"C1192G","4815":"G1064U","4816":"C1192U","4817":"C1066U"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"3240":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"U00096","fmin":"4166659","fmax":"4168200","strand":"+","sequence":"AAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAGAAGCTTGCTTCTTTGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCGACTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTGGTCTTGACATCCACGGAAGTTTTCAGAGATGAGAATGTGCCTTCGGGAACCGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGGTCCGGCCGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACGACCAGGGCTACACACGTGCTACAATGGCGCATACAAAGAGAAGCGACCTCGCGAGAGCAAGCGGACCTCATAAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTGGATCAGAATGCCACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGCAAAAGAAGTAGGTAGCTTAACCTTCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGATCACCTCCTTA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36905","NCBI_taxonomy_name":"Escherichia coli K-12","NCBI_taxonomy_id":"83333"}}}},"ARO_accession":"3003376","ARO_id":"39960","ARO_name":"Escherichia coli 16S rRNA (rrsB) mutation conferring resistance to spectinomycin","ARO_description":"Point mutations in the 3' major domain of the rrsB 16S rRNA gene of Escherichia coli can confer resistance to spectinomycin","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2131":{"model_id":"2131","model_name":"Mycobacterium tuberculosis 16S rRNA mutation conferring resistance to streptomycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2911":"A1401G","2949":"G427C","3052":"A514C","3054":"A906G","4801":"C517U","4802":"C513U","4804":"C492U","4805":"A514U","7820":"C516U"},"clinical":{"2911":"A1401G","2949":"G427C","3052":"A514C","3054":"A906G","4801":"C517U","4802":"C513U","4804":"C492U","4805":"A514U","7820":"C516U"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"4123":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"AL123456.3","fmin":"1471845","fmax":"1473382","strand":"+","sequence":"TTTTGTTTGGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGTCTCTTCGGAGATACTCGAGTGGCGAACGGGTGAGTAACACGTGGGTGATCTGCCCTGCACTTCGGGATAAGCCTGGGAAACTGGGTCTAATACCGGATAGGACCACGGGATGCATGTCTTGTGGTGGAAAGCGCTTTAGCGGTGTGGGATGAGCCCGCGGCCTATCAGCTTGTTGGTGGGGTGACGGCCTACCAAGGCGACGACGGGTAGCCGGCCTGAGAGGGTGTCCGGCCACACTGGGACTGAGATACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGGGGGATGACGGCCTTCGGGTTGTAAACCTCTTTCACCATCGACGAAGGTCCGGGTTCTCTCGGATTGACGGTAGGTGGAGAAGAAGCACCGGCCAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCGAGCGTTGTCCGGAATTACTGGGCGTAAAGAGCTCGTAGGTGGTTTGTCGCGTTGTTCGTGAAATCTCACGGCTTAACTGTGAGCGTGCGGGCGATACGGGCAGACTAGAGTACTGCAGGGGAGACTGGAATTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGGTGGCGAAGGCGGGTCTCTGGGCAGTAACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGGTGGGTACTAGGTGTGGGTTTCCTTCCTTGGGATCCGTGCCGTAGCTAACGCATTAAGTACCCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGTGGATTAATTCGATGCAACGCGAAGAACCTTACCTGGGTTTGACATGCACAGGACGCGTCTAGAGATAGGCGTTCCCTTGTGGCCTGTGTGCAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCTCATGTTGCCAGCACGTAATGGTGGGGACTCGTGAGAGACTGCCGGGGTCAACTCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGCCCCTTATGTCCAGGGCTTCACACATGCTACAATGGCCGGTACAAAGGGCTGCGATGCCGCGAGGTTAAGCGAATCCTTAAAAGCCGGTCTCAGTTCGGATCGGGGTCTGCAACTCGACCCCGTGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTCGGTAACACCCGAAGCCAGTGGCCTAACCCTCGGGAGGGAGCTGTCGAAGGTGGGATCGGCGATTGGGACGAAGTCGTAACAAGGTAGCCGTACCGGAAGGTGCGGCTGGATCACCTCCTTTCT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3003480","ARO_id":"40076","ARO_name":"Mycobacterium tuberculosis 16S rRNA mutation conferring resistance to streptomycin","ARO_description":"Point mutations within the 530 loop of the 16S rRNA of Mycobacterium tuberculosis can result in resistance against streptomycin. These mutations do not directly inhibit the binding of streptomycin, but is hypothesized that they interfere with conformational perturbations that account for streptomycin's action on the ribosome.","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1558":{"model_id":"1558","model_name":"Bacillus subtilis mprF","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1650"}},"model_sequences":{"sequence":{"3342":{"protein_sequence":{"accession":"CAX52582.1","sequence":"MLIKKNALSILKIVFPIAVLLFVIYQSKKELTNLSFKRTLMVINGLERTDLFMLVLIGLLAVAAMSLYDYVLKYSLRLSITNGKVFRVSWIANSFNNVLGFGGLAGVGLRMMFYKEHTKDHKALVKGIAWLTSSMLLGLSVFSIFVAARVLPVDEVIHEKPWLWAVVIGFALILPLSLAVSKIKDRKAGDEENADKVKNPIFAYIGASVVEWLMAGTVIYFALFAMGIHADIRYVFGVFVIAAIGGMISLVPGGFGSFDLLFLLGMEQLGYHQEAIVTSIVLYRLAYSFIPFILGLFFAAGDLTENTMKRLETNPRIAPAIETTNVLLVVQRAVLVRILQGSLSLIVFVAGLIVLASVSLPIDRLTVIPHIPRPALLLFNGLSLSSALILLILPIELYKRTKRSYTMAITALVGGFVFSFLKGLNISAIFVLPMIIVLLVLLKKQFVREQASYTLGQLIFAVALFTVALFNYNLIAGFIWDRMKKVLRHEYFVHSTSHITHATIMAIIIVPLFFLIFTVVYHKRTKPIGEKADPERLAAFLNEKGGNALSHLGFLGDKRFYFSSDGNALLLFGKIARRLVVLGDPSGQRESFPLVLEEFLNEAHQKGFSVLFYQIEREDMALYHDFGYNFFKLGEEAYVDLNTFTLTGKKKAGLRAINNRFEREEYTFHVDHPPFSDAFLEELKQISDEWLGSKKEKGFSLGFFDPSYLQKAPIAYMKNAEGEIVAFANVMPMYQEGEISVDLMRYRGDAPNGIMDALFIRMFLWAKEEGCTSFNMGMAPLANVGTAFTSFWSERFAAVIFNNVRYMYSFSGLRAFKEKYKPEWRGKYLAYRKNRSLSVTMFLVTRLIGKSKKDSV"},"dna_sequence":{"accession":"AL009126","fmin":"916777","fmax":"919348","strand":"+","sequence":"TTGCTGATTAAAAAGAATGCTTTATCAATATTAAAAATCGTTTTTCCTATTGCTGTTTTGCTATTTGTTATTTATCAATCGAAAAAAGAACTGACAAATCTGTCATTCAAACGTACGCTCATGGTCATCAACGGACTGGAACGAACGGATTTATTCATGCTTGTGTTGATCGGCTTGCTGGCTGTTGCGGCTATGTCGCTGTATGATTACGTCCTGAAGTACTCACTGCGCCTATCGATCACAAACGGAAAAGTTTTCAGGGTTTCCTGGATCGCCAATTCATTTAATAATGTGTTGGGATTCGGCGGTTTAGCCGGAGTCGGGTTAAGAATGATGTTCTATAAGGAGCATACGAAAGACCATAAGGCACTCGTGAAAGGAATCGCCTGGCTCACATCATCTATGCTGCTCGGATTATCTGTTTTCAGCATTTTCGTTGCTGCGAGAGTGCTGCCAGTTGATGAAGTGATTCATGAGAAGCCTTGGCTGTGGGCGGTCGTTATCGGTTTTGCACTGATATTGCCGTTATCTTTAGCGGTGTCCAAAATAAAAGACCGCAAAGCTGGGGACGAAGAGAATGCGGATAAAGTGAAAAATCCGATTTTCGCATATATTGGAGCTTCAGTTGTTGAATGGCTCATGGCCGGGACCGTCATCTATTTTGCTTTGTTCGCTATGGGCATTCATGCAGATATCAGGTATGTGTTCGGGGTGTTCGTCATTGCGGCGATCGGAGGAATGATCAGCCTCGTGCCGGGCGGCTTCGGCTCGTTTGACCTTTTATTTTTGCTGGGGATGGAGCAGCTTGGCTATCATCAAGAGGCCATCGTTACTTCTATTGTGTTGTACAGGCTCGCCTACTCATTTATCCCATTTATCTTGGGACTGTTCTTTGCCGCCGGCGACCTGACGGAAAATACAATGAAGCGGCTCGAAACGAACCCGCGCATCGCACCGGCAATTGAGACGACAAACGTTCTGCTTGTTGTTCAGCGTGCGGTATTAGTGAGAATTTTGCAAGGCTCGCTTTCCCTTATTGTGTTCGTAGCAGGTCTGATTGTCTTGGCCTCAGTTTCCTTGCCGATTGACAGGCTGACGGTTATACCGCACATTCCGCGCCCGGCGCTTTTGCTGTTCAACGGCCTGTCCTTAAGCTCAGCGCTCATTCTGCTCATTTTGCCGATCGAGCTTTATAAACGGACAAAACGTTCCTACACGATGGCCATTACAGCGCTTGTCGGCGGCTTTGTGTTCAGCTTTTTAAAAGGGCTTAACATCAGCGCGATATTCGTACTGCCGATGATTATCGTATTGCTTGTGCTATTGAAAAAACAATTTGTCCGCGAACAGGCATCCTATACACTGGGACAATTGATATTCGCTGTGGCGCTGTTTACTGTGGCGCTCTTTAACTACAATCTGATCGCGGGCTTTATTTGGGACCGGATGAAGAAGGTGCTGCGTCACGAATATTTCGTCCACAGCACCTCGCATATTACACATGCAACCATCATGGCGATCATCATTGTGCCGCTGTTCTTCTTGATATTTACAGTGGTCTATCATAAGAGAACGAAACCGATCGGAGAGAAAGCTGACCCTGAGCGTCTTGCTGCGTTTCTCAATGAAAAAGGCGGCAACGCGCTGAGCCATCTTGGTTTTCTTGGAGATAAGCGGTTTTATTTTTCTAGCGATGGAAATGCACTGCTTCTGTTTGGGAAAATCGCCAGAAGGCTGGTCGTGCTCGGCGATCCATCTGGCCAAAGAGAATCATTCCCGCTCGTGCTGGAAGAATTTCTGAACGAAGCGCATCAGAAGGGATTCAGTGTTTTGTTCTATCAAATTGAACGAGAGGACATGGCGCTGTATCACGATTTTGGCTACAACTTCTTTAAATTGGGTGAGGAAGCATATGTAGATTTAAATACATTTACCTTGACTGGGAAGAAAAAAGCCGGCCTTCGGGCAATCAATAACCGCTTTGAGCGGGAGGAGTATACTTTCCATGTGGATCATCCCCCATTTTCTGATGCGTTTTTGGAGGAGCTGAAGCAAATCTCAGACGAATGGCTCGGCTCGAAAAAAGAGAAGGGATTCTCGCTCGGATTTTTTGATCCTTCCTATTTACAGAAAGCGCCGATCGCCTATATGAAAAATGCAGAAGGAGAGATCGTTGCATTCGCAAATGTCATGCCGATGTACCAGGAAGGAGAGATATCGGTCGATCTGATGCGCTATCGCGGCGACGCTCCAAATGGCATTATGGACGCATTGTTTATCCGTATGTTTTTATGGGCAAAGGAAGAGGGCTGTACGTCATTTAATATGGGGATGGCACCCTTGGCCAATGTCGGCACTGCCTTTACATCCTTCTGGTCCGAAAGGTTTGCCGCTGTCATTTTTAATAATGTCAGATACATGTACAGTTTCAGCGGCCTAAGAGCCTTTAAAGAAAAATATAAACCGGAGTGGCGAGGGAAATACTTAGCGTATCGGAAAAACAGATCTCTTTCTGTCACCATGTTCCTCGTTACACGTCTGATTGGCAAAAGCAAAAAAGACTCCGTCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39579","NCBI_taxonomy_name":"Bacillus subtilis subsp. subtilis str. 168","NCBI_taxonomy_id":"224308"}}}},"ARO_accession":"3003324","ARO_id":"39908","ARO_name":"Bacillus subtilis mprF","ARO_description":"MprF is a integral membrane protein that modifies the negatively-charged phosphatidylglycerol on the membrane surface. This confers resistance to cationic peptides that disrupt the cell membrane, including defensins. Additionally, large-scale mutations causing loss of function of the gene result in increased susceptibility to daptomycin.","ARO_category":{"37243":{"category_aro_accession":"3000863","category_aro_cvterm_id":"37243","category_aro_name":"defensin resistant mprF","category_aro_description":"MprF is a integral membrane protein that modifies the negatively-charged phosphatidylglycerol on the membrane surface of both Gram-positive and Gram-negative bacteria. This confers resistance to cationic peptides that disrupt the cell membrane, including defensins.","category_aro_class_name":"AMR Gene Family"},"37037":{"category_aro_accession":"3000693","category_aro_cvterm_id":"37037","category_aro_name":"defensin","category_aro_description":"Defensins are natural cationic peptides that have antibiotic properties. It is part of the innate immune system of plants and animals.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1894":{"model_id":"1894","model_name":"Salmonella enterica ramR mutants","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2136":"R46P","2137":"M84I","2138":"Y59H","2139":"T18P","2155":"G25A","2864":"E160D","3899":"T50P"},"clinical":{"2136":"R46P","2137":"M84I","2138":"Y59H","2139":"T18P","2155":"G25A","2864":"E160D","3899":"T50P"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"370"}},"model_sequences":{"sequence":{"4331":{"protein_sequence":{"accession":"ACH50230.1","sequence":"MARPKSEDKKQALLEAATQAIAQSGIAASTAVIARNAGVAEGTLFRYFATKDELINTLYLHLKQDLCQSMIMELDRSITDAKMMTRFIWNSYISWGLNHPARHRAIRQLAVSEKLTKETEQRADDMFPELRDLCHRSVLMVFMSDEYRAFGDGLFLALAETTMDFAARDPARAGEYIALGFEAMWRALTREEQ"},"dna_sequence":{"accession":"CP001138.1","fmin":"613435","fmax":"614017","strand":"-","sequence":"TTATTGCTCCTCGCGAGTCAGCGCGCGCCACATGGCTTCGAATCCCAGCGCAATATATTCGCCAGCGCGAGCGGGATCGCGCGCGGCGAAATCCATTGTTGTTTCAGCCAGCGCCAGAAAAAGGCCGTCGCCGAAGGCGCGGTACTCATCCGACATAAACACCATCAAAACGGAACGATGACATAAATCGCGCAATTCGGGGAACATATCGTCGGCCCGTTGTTCCGTCTCTTTGGTGAGCTTTTCGCTGACGGCCAGTTGACGGATCGCCCGATGGCGCGCGGGATGGTTCAGACCCCAACTGATGTAACTGTTCCAGATAAAACGGGTCATCATTTTGGCATCGGTAATGGATCGATCCAGCTCCATTATCATTGACTGGCAGAGATCCTGCTTTAAATGCAAATACAACGTGTTAATCAGCTCATCTTTGGTCGCGAAATAGCGAAACAATGTTCCTTCTGCAACACCTGCGTTACGCGCAATCACCGCCGTTGAGGCGGCGATACCGGATTGCGCTATCGCCTGGGTTGCCGCTTCCAGTAATGCTTGTTTTTTGTCTTCACTCTTCGGACGAGCCAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35834","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Agona str. SL483","NCBI_taxonomy_id":"454166"}}}},"ARO_accession":"3003379","ARO_id":"39963","ARO_name":"Salmonella enterica ramR mutants","ARO_description":"RamR is a repressor that regulates RamA expression. Mutations lead to the upregulation of AcrAB, which is positively regulated by RamA.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2132":{"model_id":"2132","model_name":"Mycobacterium tuberculosis 16S rRNA mutation conferring resistance to kanamycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2923":"C1402A","3014":"A1401G","4799":"C1402U","4800":"G1484U"},"clinical":{"2923":"C1402A","3014":"A1401G","4799":"C1402U","4800":"G1484U"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"3263":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"AL123456.3","fmin":"1471846","fmax":"1473382","strand":"+","sequence":"TTTTGTTTGGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGTCTCTTCGGAGATACTCGAGTGGCGAACGGGTGAGTAACACGTGGGTGATCTGCCCTGCACTTCGGGATAAGCCTGGGAAACTGGGTCTAATACCGGATAGGACCACGGGATGCATGTCTTGTGGTGGAAAGCGCTTTAGCGGTGTGGGATGAGCCCGCGGCCTATCAGCTTGTTGGTGGGGTGACGGCCTACCAAGGCGACGACGGGTAGCCGGCCTGAGAGGGTGTCCGGCCACACTGGGACTGAGATACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGGGGGATGACGGCCTTCGGGTTGTAAACCTCTTTCACCATCGACGAAGGTCCGGGTTCTCTCGGATTGACGGTAGGTGGAGAAGAAGCACCGGCCAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCGAGCGTTGTCCGGAATTACTGGGCGTAAAGAGCTCGTAGGTGGTTTGTCGCGTTGTTCGTGAAATCTCACGGCTTAACTGTGAGCGTGCGGGCGATACGGGCAGACTAGAGTACTGCAGGGGAGACTGGAATTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGGTGGCGAAGGCGGGTCTCTGGGCAGTAACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGGTGGGTACTAGGTGTGGGTTTCCTTCCTTGGGATCCGTGCCGTAGCTAACGCATTAAGTACCCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGTGGATTAATTCGATGCAACGCGAAGAACCTTACCTGGGTTTGACATGCACAGGACGCGTCTAGAGATAGGCGTTCCCTTGTGGCCTGTGTGCAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCTCATGTTGCCAGCACGTAATGGTGGGGACTCGTGAGAGACTGCCGGGGTCAACTCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGCCCCTTATGTCCAGGGCTTCACACATGCTACAATGGCCGGTACAAAGGGCTGCGATGCCGCGAGGTTAAGCGAATCCTTAAAAGCCGGTCTCAGTTCGGATCGGGGTCTGCAACTCGACCCCGTGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTCGGTAACACCCGAAGCCAGTGGCCTAACCCTCGGGAGGGAGCTGTCGAAGGTGGGATCGGCGATTGGGACGAAGTCGTAACAAGGTAGCCGTACCGGAAGGTGCGGCTGGATCACCTCCTTTCT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3003436","ARO_id":"40020","ARO_name":"Mycobacterium tuberculosis 16S rRNA mutation conferring resistance to kanamycin","ARO_description":"Point mutations in the 3' domain of 16S rRNA of Mycobacterium tuberculosis can confer resistance to kanamycin.","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2133":{"model_id":"2133","model_name":"Mycobacterium tuberculosis 16S rRNA mutation conferring resistance to viomycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2909":"A1401G"},"clinical":{"2909":"A1401G"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"3260":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"AL123456.3","fmin":"1471846","fmax":"1473382","strand":"+","sequence":"TTTTGTTTGGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGTCTCTTCGGAGATACTCGAGTGGCGAACGGGTGAGTAACACGTGGGTGATCTGCCCTGCACTTCGGGATAAGCCTGGGAAACTGGGTCTAATACCGGATAGGACCACGGGATGCATGTCTTGTGGTGGAAAGCGCTTTAGCGGTGTGGGATGAGCCCGCGGCCTATCAGCTTGTTGGTGGGGTGACGGCCTACCAAGGCGACGACGGGTAGCCGGCCTGAGAGGGTGTCCGGCCACACTGGGACTGAGATACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGGGGGATGACGGCCTTCGGGTTGTAAACCTCTTTCACCATCGACGAAGGTCCGGGTTCTCTCGGATTGACGGTAGGTGGAGAAGAAGCACCGGCCAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCGAGCGTTGTCCGGAATTACTGGGCGTAAAGAGCTCGTAGGTGGTTTGTCGCGTTGTTCGTGAAATCTCACGGCTTAACTGTGAGCGTGCGGGCGATACGGGCAGACTAGAGTACTGCAGGGGAGACTGGAATTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGGTGGCGAAGGCGGGTCTCTGGGCAGTAACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGGTGGGTACTAGGTGTGGGTTTCCTTCCTTGGGATCCGTGCCGTAGCTAACGCATTAAGTACCCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGTGGATTAATTCGATGCAACGCGAAGAACCTTACCTGGGTTTGACATGCACAGGACGCGTCTAGAGATAGGCGTTCCCTTGTGGCCTGTGTGCAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCTCATGTTGCCAGCACGTAATGGTGGGGACTCGTGAGAGACTGCCGGGGTCAACTCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGCCCCTTATGTCCAGGGCTTCACACATGCTACAATGGCCGGTACAAAGGGCTGCGATGCCGCGAGGTTAAGCGAATCCTTAAAAGCCGGTCTCAGTTCGGATCGGGGTCTGCAACTCGACCCCGTGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTCGGTAACACCCGAAGCCAGTGGCCTAACCCTCGGGAGGGAGCTGTCGAAGGTGGGATCGGCGATTGGGACGAAGTCGTAACAAGGTAGCCGTACCGGAAGGTGCGGCTGGATCACCTCCTTTCT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3003437","ARO_id":"40021","ARO_name":"Mycobacterium tuberculosis 16S rRNA mutation conferring resistance to viomycin","ARO_description":"Peptide antibiotics inhibit protein synthesis. Resistance to viomycin can be caused by an altered RNA molecule in the 16S ribosomal subunit.","ARO_category":{"40278":{"category_aro_accession":"3003667","category_aro_cvterm_id":"40278","category_aro_name":"16s rRNA with mutation conferring resistance to peptide antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to peptide antibiotics.","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35937":{"category_aro_accession":"0000018","category_aro_cvterm_id":"35937","category_aro_name":"viomycin","category_aro_description":"Viomycin sulfate (Viocin) is an polypeptide antibiotic used in the treatment of tuberculosis. It is produced by the actinomycete Streptomyces puniceus and binds to the bacterial ribosome, inhibiting prokaryotic protein synthesis and certain forms of RNA splicing.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"36629":{"category_aro_accession":"3000490","category_aro_cvterm_id":"36629","category_aro_name":"tuberactinomycin","category_aro_description":"Tuberactinomycins are a family of cyclic peptide antibiotics that are important in the treatment of tuberculosis. Tuberactinomycins contain nonproteinogenic amino acids and inhibit group I self-splicing RNA to disrupt prokaryotic protein synthesis.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2136":{"model_id":"2136","model_name":"Escherichia coli 16S rRNA mutation in the rrsB gene conferring resistance to kanamycin A","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2904":"A1408G","4813":"U1406A"},"clinical":{"2904":"A1408G","4813":"U1406A"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"3232":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"U00096","fmin":"4166659","fmax":"4168200","strand":"+","sequence":"AAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAGAAGCTTGCTTCTTTGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCGACTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTGGTCTTGACATCCACGGAAGTTTTCAGAGATGAGAATGTGCCTTCGGGAACCGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGGTCCGGCCGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACGACCAGGGCTACACACGTGCTACAATGGCGCATACAAAGAGAAGCGACCTCGCGAGAGCAAGCGGACCTCATAAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTGGATCAGAATGCCACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGCAAAAGAAGTAGGTAGCTTAACCTTCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGATCACCTCCTTA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36905","NCBI_taxonomy_name":"Escherichia coli K-12","NCBI_taxonomy_id":"83333"}}}},"ARO_accession":"3003399","ARO_id":"39983","ARO_name":"Escherichia coli 16S rRNA (rrsB) mutation conferring resistance to kanamycin A","ARO_description":"Point mutations in the 3' minor domain of helix 44, in the rrsB 16S rRNA gene of Escherichia coli can confer resistance to kanamycin A","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2140":{"model_id":"2140","model_name":"Escherichia coli 16S rRNA mutation in the rrsB gene conferring resistance to streptomycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2966":"A523C"},"clinical":{"2966":"A523C"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"3231":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"U00096","fmin":"4166659","fmax":"4168200","strand":"+","sequence":"AAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAGAAGCTTGCTTCTTTGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCGACTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTGGTCTTGACATCCACGGAAGTTTTCAGAGATGAGAATGTGCCTTCGGGAACCGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGGTCCGGCCGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACGACCAGGGCTACACACGTGCTACAATGGCGCATACAAAGAGAAGCGACCTCGCGAGAGCAAGCGGACCTCATAAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTGGATCAGAATGCCACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGCAAAAGAAGTAGGTAGCTTAACCTTCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGATCACCTCCTTA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36905","NCBI_taxonomy_name":"Escherichia coli K-12","NCBI_taxonomy_id":"83333"}}}},"ARO_accession":"3003405","ARO_id":"39989","ARO_name":"Escherichia coli 16S rRNA (rrsB) mutation conferring resistance to streptomycin","ARO_description":"Point mutations in the 5' domain of helix 18, in the rrsB 16S rRNA gene of Escherichia coli can confer resistance to streptomycin","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2141":{"model_id":"2141","model_name":"Mycobacterium smegmatis 16S rRNA mutation in the rrsB gene conferring resistance to neomycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"4840":"U1389A"},"clinical":{"4840":"U1389A"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"3249":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NC_008596.1","fmin":"5027948","fmax":"5029475","strand":"+","sequence":"TTTTTGTTTGGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGCCCTTTCGGGGGTACTCGAGTGGCGAACGGGTGAGTAACACGTGGGTGATCTGCCCTGCACTTTGGGATAAGCCTGGGAAACTGGGTCTAATACCGAATACACCCTGCTGGTCGCATGGCCTGGTAGGGGAAAGCTTTTGCGGTGTGGGATGGGCCCGCGGCCTATCAGCTTGTTGGTGGGGTGATGGCCTACCAAGGCGACGACGGGTAGCCGGCCTGAGAGGGTGACCGGCCACACTGGGACTGAGATACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGAGGGATGACGGCCTTCGGGTTGTAAACCTCTTTCAGCACAGACGAAGCGCAAGTGACGGTATGTGCAGAAGAAGGACCGGCCAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTCCGAGCGTTGTCCGGAATTACTGGGCGTAAAGAGCTCGTAGGTGGTTTGTCGCGTTGTTCGTGAAAACTCACAGCTTAACTGTGGGCGTGCGGGCGATACGGGCAGACTAGAGTACTGCAGGGGAGACTGGAATTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGGTGGCGAAGGCGGGTCTCTGGGCAGTAACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGGTGGGTACTAGGTGTGGGTTTCCTTCCTTGGGATCCGTGCCGTAGCTAACGCATTAAGTACCCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGTGGATTAATTCGATGCAACGCGAAGAACCTTACCTGGGTTTGACATGCACAGGACGCCGGCAGAGATGTCGGTTCCCTTGTGGCCTGTGTGCAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCTCATGTTGCCAGCACGTTATGGTGGGGACTCGTGAGAGACTGCCGGGGTCAACTCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGCCCCTTATGTCCAGGGCTTCACACATGCTACAATGGCCGGTACAAAGGGCTGCGATGCCGTGAGGTGGAGCGAATCCTTTCAAAGCCGGTCTCAGTTCGGATCGGGGTCTGCAACTCGACCCCGTGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTCGGTAACACCCGAAGCCGGTGGCCTAACCCTTGTGGAGGGAGCCGTCGAAGGTGGGATCGGCGATTGGGACGAAGTCGTAACAAGGTAGCCGTACCGGAAGGTGCGGCTGGATCACCTCCTTTCT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36769","NCBI_taxonomy_name":"Mycobacterium smegmatis str. MC2 155","NCBI_taxonomy_id":"246196"}}}},"ARO_accession":"3003545","ARO_id":"40147","ARO_name":"Mycobacterium smegmatis 16S rRNA (rrsB) mutation conferring resistance to neomycin","ARO_description":"Point mutations in the helix 44 region of the 16S rRNA rrsB gene of Mycobacterium smegmatis can confer resistance to neomycin","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2142":{"model_id":"2142","model_name":"Mycobacterium smegmatis 16S rRNA mutation  in the rrsA gene conferring resistance to viomycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3069":"G1475A","4843":"G1475U"},"clinical":{"3069":"G1475A","4843":"G1475U"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"4143":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NC_008596.1","fmin":"3823614","fmax":"3825143","strand":"-","sequence":"AGAAAGGAGGTGATCCAGCCGCACCTTCCGGTACGGCTACCTTGTTACGACTTCGTCCCAATCGCCGATCCCACCTTCGACGGCTCCCTCCACAAGGGTTAGGCCACCGGCTTCGGGTGTTACCGACTTTCATGACGTGACGGGCGGTGTGTACAAGGCCCGGGAACGTATTCACCGCAGCGTTGCTGATCTGCGATTACTAGCGACTCCGACTTCACGGGGTCGAGTTGCAGACCCCGATCCGAACTGAGACCGGCTTTGAAAGGATTCGCTCCACCTCACGGCATCGCAGCCCTTTGTACCGGCCATTGTAGCATGTGTGAAGCCCTGGACATAAGGGGCATGATGACTTGACGTCATCCCCACCTTCCTCCGAGTTGACCCCGGCAGTCTCTCACGAGTCCCCACCATAACGTGCTGGCAACATGAGACAAGGGTTGCGCTCGTTGCGGGACTTAACCCAACATCTCACGACACGAGCTGACGACAGCCATGCACCACCTGCACACAGGCCACAAGGGAACCGACATCTCTGCCGGCGTCCTGTGCATGTCAAACCCAGGTAAGGTTCTTCGCGTTGCATCGAATTAATCCACATGCTCCGCCGCTTGTGCGGGCCCCCGTCAATTCCTTTGAGTTTTAGCCTTGCGGCCGTACTCCCCAGGCGGGGTACTTAATGCGTTAGCTACGGCACGGATCCCAAGGAAGGAAACCCACACCTAGTACCCACCGTTTACGGCGTGGACTACCAGGGTATCTAATCCTGTTCGCTCCCCACGCTTTCGCTCCTCAGCGTCAGTTACTGCCCAGAGACCCGCCTTCGCCACCGGTGTTCCTCCTGATATCTGCGCATTCCACCGCTACACCAGGAATTCCAGTCTCCCCTGCAGTACTCTAGTCTGCCCGTATCGCCCGCACGCCCACAGTTAAGCTGTGAGTTTTCACGAACAACGCGACAAACCACCTACGAGCTCTTTACGCCCAGTAATTCCGGACAACGCTCGGACCCTACGTATTACCGCGGCTGCTGGCACGTAGTTGGCCGGTCCTTCTTCTGCACATACCGTCACTTGCGCTTCGTCTGTGCTGAAAGAGGTTTACAACCCGAAGGCCGTCATCCCTCACGCGGCGTCGCTGCATCAGGCTTGCGCCCATTGTGCAATATTCCCCACTGCTGCCTCCCGTAGGAGTCTGGGCCGTATCTCAGTCCCAGTGTGGCCGGTCACCCTCTCAGGCCGGCTACCCGTCGTCGCCTTGGTAGGCCATCACCCCACCAACAAGCTGATAGGCCGCGGGCCCATCCCACACCGCAAAAGCTTTCCCCTACCAGGCCATGCGACCAGCAGGGTGTATTCGGTATTAGACCCAGTTTCCCAGGCTTATCCCAAAGTGCAGGGCAGATCACCCACGTGTTACTCACCCGTTCGCCACTCGAGTACCCCCGAAAGGGCCTTTCCGTTCGACTTGCATGTGTTAAGCACGCCGCCAGCGTTCGTCCTGAGCCAGGATCAAACTCTCCAAACAAAAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36769","NCBI_taxonomy_name":"Mycobacterium smegmatis str. MC2 155","NCBI_taxonomy_id":"246196"}}}},"ARO_accession":"3003546","ARO_id":"40148","ARO_name":"Mycobacterium smegmatis 16S rRNA (rrsA) mutation conferring resistance to viomycin","ARO_description":"Point mutations in the helix 44 region of the 16S rRNA rrsA gene of Mycobacterium smegmatis can confer resistance to viomycin.","ARO_category":{"40278":{"category_aro_accession":"3003667","category_aro_cvterm_id":"40278","category_aro_name":"16s rRNA with mutation conferring resistance to peptide antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to peptide antibiotics.","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35937":{"category_aro_accession":"0000018","category_aro_cvterm_id":"35937","category_aro_name":"viomycin","category_aro_description":"Viomycin sulfate (Viocin) is an polypeptide antibiotic used in the treatment of tuberculosis. It is produced by the actinomycete Streptomyces puniceus and binds to the bacterial ribosome, inhibiting prokaryotic protein synthesis and certain forms of RNA splicing.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"36629":{"category_aro_accession":"3000490","category_aro_cvterm_id":"36629","category_aro_name":"tuberactinomycin","category_aro_description":"Tuberactinomycins are a family of cyclic peptide antibiotics that are important in the treatment of tuberculosis. Tuberactinomycins contain nonproteinogenic amino acids and inhibit group I self-splicing RNA to disrupt prokaryotic protein synthesis.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2143":{"model_id":"2143","model_name":"Borrelia burgdorferi 16S rRNA mutation conferring resistance to gentamicin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3038":"A1401G"},"clinical":{"3038":"A1401G"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"2500"}},"model_sequences":{"sequence":{"3268":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NR_044732.2","fmin":"0","fmax":"1477","strand":"+","sequence":"AATAACGAAGAGTTTGATCCTGGCTTAGAACTAACGCTGGCAGTGCGTCTTAAGCATGCAAGTCAAACGGGATGTAGCAATACATTCAGTGGCGAACGGGTGAGTAACGCGTGGATGATCTACCTATGAGATGGGGATAACTATTAGAAATAGTAGCTAATACCGAATAAGGTCAGTTAATTTGTTAATTGATGAAAGGAAGCCTTTAAACGTTCGCTTGTAGATGAGTCTGCGTCTTATTAGCTAGTTGGTAGGGTAAATGCCTACCAAGGCAATGATAAGTAACCGGCCTGAGAGGGTGAACGGTCACACTGGAACTGAGATACGGTCCAGNCTCCTACGGGAGGCAGCAGCTAAGAATCTTCCGCAATGGGCGAAAGCCTGACGGAGCGACACTGCGTGAATGAAGAAGGTCGAAAGATTGTAAAATTCTTTTATAAATGAGGAATAAGCTTTGTAGGAAATGACAAAGTGATGACGTTAATTTATGAATAAGCCCCGGCTAATTACGTGCCAGNAGCCGCGGTAATACGTAAGGGNNNAGCGTTGTTCGGGATTATTGGGCGTAAAGGGTGAGTAGGCGGATATATAAGTCTATGCATAAAATACCACAGCTCAACTGTGGACCTATGTTGGAAACTATATGTCTAGAGTCTGATAGAGGAAGTTAGAATTTCTGGTGTAAGGGTGGAATCTGTTGATATCAGAAAGAATACCGGAGGCGAAGGCGAACTTCTGGGTCAAGACTGACGCTGAGTCACGAAAGCGTAGGGAGCAAACAGGATTAGATACCCTGGTAGTCTACGCTGTAAACGATGCACACTTGGTGTTAACTAAAAGTTAGTACCGAAGCTAACGTGTTAAGTGTGCAGCCTGGGGAGTATGCTCGCAAGAGNGAAACTCAAAGGNATTNANNNGNGCCNGCACAAGNNGTGGAGCATGTGGTTTNNNNNNANNNTACGCGAGGAACCTTACCAGGGCTTGACATATATAGGATATAGTTAGAGATAATTATTCCCCGTTTGGGGTCTATATACAGGTGCTGCATGGTTGTCGTCAGCTCGTGCTGTGAGGTGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTTATCTGTTACCAGCATGTAATGGTGGGGACTCAGATAAGACTGCCGGTGATAAGTCGGAGGAAGGTGAGGATGACGTCAAATCATCATGGCCCTTATGTCCTGGGCTACACACGTGCTACAATGGCCTGTACAAAGCGAAGCGAAACAGTGATGTGAAGCAAAACGCATAAAGCAGGTCTCAGTCCGGATTGAAGTCTGAAACTCGACTTCATGAAGTTGGAATCGCTAGTAATCGTATATCAGAATGATACGGTGAATACGTTCTCGGGCNTTGTACACACCGCCCGTCACACCACCCGAGTTGAGGATACCCGAAGCTATTATTCTAACCCGTAAGGGAGGAAGGTATTTAAGGTATGTTTAGCA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40345","NCBI_taxonomy_name":"Borrelia burgdorferi","NCBI_taxonomy_id":"139"}}}},"ARO_accession":"3003504","ARO_id":"40106","ARO_name":"Borrelia burgdorferi 16S rRNA mutation conferring resistance to gentamicin","ARO_description":"Point mutations in the 3' minor domain of the 16S rRNA gene of Borrelia burgdorferi can confer resistance to gentamicin","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2145":{"model_id":"2145","model_name":"Escherichia coli 16S rRNA mutation in the rrsB gene conferring resistance to tetracycline","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3061":"G1058C"},"clinical":{"3061":"G1058C"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"3242":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"U00096","fmin":"4166659","fmax":"4168200","strand":"+","sequence":"AAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAGAAGCTTGCTTCTTTGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCGACTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTGGTCTTGACATCCACGGAAGTTTTCAGAGATGAGAATGTGCCTTCGGGAACCGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGGTCCGGCCGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACGACCAGGGCTACACACGTGCTACAATGGCGCATACAAAGAGAAGCGACCTCGCGAGAGCAAGCGGACCTCATAAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTGGATCAGAATGCCACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGCAAAAGAAGTAGGTAGCTTAACCTTCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGATCACCTCCTTA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36905","NCBI_taxonomy_name":"Escherichia coli K-12","NCBI_taxonomy_id":"83333"}}}},"ARO_accession":"3003410","ARO_id":"39994","ARO_name":"Escherichia coli 16S rRNA (rrsB) mutation conferring resistance to tetracycline","ARO_description":"Point mutations in the 3' major domain of the rrsB 16S rRNA gene of Escherichia coli can confer resistance to tetracycline","ARO_category":{"40280":{"category_aro_accession":"3003669","category_aro_cvterm_id":"40280","category_aro_name":"16S rRNA with mutation conferring resistance to tetracycline derivatives","category_aro_description":"Point mutations in the bacterial 16S rRNA region shown clinically to confer resistance to tetracycline and tetracycline derivatives (polyketide antibiotics).","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2146":{"model_id":"2146","model_name":"Escherichia coli 16S rRNA mutation in the rrnB gene conferring resistance to streptomycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"4825":"C528U","4826":"G527U"},"clinical":{"4825":"C528U","4826":"G527U"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"3237":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"U00096","fmin":"4166659","fmax":"4168200","strand":"+","sequence":"AAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAGAAGCTTGCTTCTTTGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCGACTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTGGTCTTGACATCCACGGAAGTTTTCAGAGATGAGAATGTGCCTTCGGGAACCGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGGTCCGGCCGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACGACCAGGGCTACACACGTGCTACAATGGCGCATACAAAGAGAAGCGACCTCGCGAGAGCAAGCGGACCTCATAAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTGGATCAGAATGCCACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGCAAAAGAAGTAGGTAGCTTAACCTTCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGATCACCTCCTTA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36905","NCBI_taxonomy_name":"Escherichia coli K-12","NCBI_taxonomy_id":"83333"}}}},"ARO_accession":"3003406","ARO_id":"39990","ARO_name":"Escherichia coli 16S rRNA (rrnB) mutation conferring resistance to streptomycin","ARO_description":"Point mutations in the 5' domain of helix 18, in the rrnB 16S rRNA gene of Escherichia coli can confer resistance to streptomycin","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2149":{"model_id":"2149","model_name":"Mycobacterium smegmatis 16S rRNA mutation in the rrsA gene conferring resistance to hygromycin B","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"4830":"U1482C","4831":"U1389C","4832":"C1480U"},"clinical":{"4830":"U1482C","4831":"U1389C","4832":"C1480U"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"4142":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NC_008596.1","fmin":"3823614","fmax":"3825143","strand":"-","sequence":"AGAAAGGAGGTGATCCAGCCGCACCTTCCGGTACGGCTACCTTGTTACGACTTCGTCCCAATCGCCGATCCCACCTTCGACGGCTCCCTCCACAAGGGTTAGGCCACCGGCTTCGGGTGTTACCGACTTTCATGACGTGACGGGCGGTGTGTACAAGGCCCGGGAACGTATTCACCGCAGCGTTGCTGATCTGCGATTACTAGCGACTCCGACTTCACGGGGTCGAGTTGCAGACCCCGATCCGAACTGAGACCGGCTTTGAAAGGATTCGCTCCACCTCACGGCATCGCAGCCCTTTGTACCGGCCATTGTAGCATGTGTGAAGCCCTGGACATAAGGGGCATGATGACTTGACGTCATCCCCACCTTCCTCCGAGTTGACCCCGGCAGTCTCTCACGAGTCCCCACCATAACGTGCTGGCAACATGAGACAAGGGTTGCGCTCGTTGCGGGACTTAACCCAACATCTCACGACACGAGCTGACGACAGCCATGCACCACCTGCACACAGGCCACAAGGGAACCGACATCTCTGCCGGCGTCCTGTGCATGTCAAACCCAGGTAAGGTTCTTCGCGTTGCATCGAATTAATCCACATGCTCCGCCGCTTGTGCGGGCCCCCGTCAATTCCTTTGAGTTTTAGCCTTGCGGCCGTACTCCCCAGGCGGGGTACTTAATGCGTTAGCTACGGCACGGATCCCAAGGAAGGAAACCCACACCTAGTACCCACCGTTTACGGCGTGGACTACCAGGGTATCTAATCCTGTTCGCTCCCCACGCTTTCGCTCCTCAGCGTCAGTTACTGCCCAGAGACCCGCCTTCGCCACCGGTGTTCCTCCTGATATCTGCGCATTCCACCGCTACACCAGGAATTCCAGTCTCCCCTGCAGTACTCTAGTCTGCCCGTATCGCCCGCACGCCCACAGTTAAGCTGTGAGTTTTCACGAACAACGCGACAAACCACCTACGAGCTCTTTACGCCCAGTAATTCCGGACAACGCTCGGACCCTACGTATTACCGCGGCTGCTGGCACGTAGTTGGCCGGTCCTTCTTCTGCACATACCGTCACTTGCGCTTCGTCTGTGCTGAAAGAGGTTTACAACCCGAAGGCCGTCATCCCTCACGCGGCGTCGCTGCATCAGGCTTGCGCCCATTGTGCAATATTCCCCACTGCTGCCTCCCGTAGGAGTCTGGGCCGTATCTCAGTCCCAGTGTGGCCGGTCACCCTCTCAGGCCGGCTACCCGTCGTCGCCTTGGTAGGCCATCACCCCACCAACAAGCTGATAGGCCGCGGGCCCATCCCACACCGCAAAAGCTTTCCCCTACCAGGCCATGCGACCAGCAGGGTGTATTCGGTATTAGACCCAGTTTCCCAGGCTTATCCCAAAGTGCAGGGCAGATCACCCACGTGTTACTCACCCGTTCGCCACTCGAGTACCCCCGAAAGGGCCTTTCCGTTCGACTTGCATGTGTTAAGCACGCCGCCAGCGTTCGTCCTGAGCCAGGATCAAACTCTCCAAACAAAAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36769","NCBI_taxonomy_name":"Mycobacterium smegmatis str. MC2 155","NCBI_taxonomy_id":"246196"}}}},"ARO_accession":"3003539","ARO_id":"40141","ARO_name":"Mycobacterium smegmatis 16S rRNA (rrsA) mutation conferring resistance to hygromycin B","ARO_description":"Point mutations in the highly conserved helix 44 of the 16S rrsA rRNA gene of Mycobacterium smegmatis can confer resistance to hygromycin B. Resistance against hygromycin B is the result of conformational alterations that distorts a strong hydrogen bond leading to a change in the local geometry of the hygromycin B binding site.","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2152":{"model_id":"2152","model_name":"Neisseria meningitidis 16S rRNA mutation conferring resistance to spectinomycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2897":"G1065C"},"clinical":{"2897":"G1065C"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"4137":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NC_003112","fmin":"60970","fmax":"62514","strand":"+","sequence":"TGAACATAAGAGTTTGATCCTGGCTCAGATTGAACGCTGGCGGCATGCTTTACACATGCAAGTCGGACGGCAGCACAGAGAAGCTTGCTTCTCGGGTGGCGAGTGGCGAACGGGTGAGTAACATATCGGAACGTACCGAGTAGTGGGGGATAACTGATCGAAAGATCAGCTAATACCGCATACGTCTTGAGAGAGAAAGCAGGGGACCTTCGGGCCTTGCGCTATTCGAGCGGCCGATATCTGATTAGCTAGTTGGTGGGGTAAAGGCCTACCAAGGCGACGATCAGTAGCGGGTCTGAGAGGATGATCCGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTGGACAATGGGCGCAAGCCTGATCCAGCCATGCCGCGTGTCTGAAGAAGGCCTTCGGGTTGTAAAGGACTTTTGTCAGGGAAGAAAAGGCTGTTGCTAATATCAGCGGCTGATGACGGTACCTGAAGAATAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGGGCGCAGACGGTTACTTAAGCAGGATGTGAAATCCCCGGGCTCAACCCGGGAACTGCGTTCTGAACTGGGTGACTCGAGTGTGTCAGAGGGAGGTAGAATTCCACGTGTAGCAGTGAAATGCGTAGAGATGTGGAGGAATACCGATGGCGAAGGCAGCCTCCTGGGACAACACTGACGTTCATGCCCGAAAGCGTGGGTAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCCTAAACGATGTCAATTAGCTGTTGGGCAACCTGATTGCTTGGTAGCGTAGCTAACGCGTGAAATTGACCGCCTGGGGAGTACGGTCGCAAGATTAAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGATGATGTGGATTAATTCGATGCAACGCGAAGAACCTTACCTGGTCTTGACATGTACGGAATCCTCCGGAGACGGAGGAGTGCCTTCGGGAGCCGTAACACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCATTAGTTGCCATCATTCAGTTGGGCACTCTAATGAGACTGCCGGTGACAAGCCGGAGGAAGGTGGGGATGACGTCAAGTCCTCATGGCCCTTATGACCAGGGCTTCACACGTCATACAATGGTCGGTACAGAGGGTAGCCAAGCCGCGAGGCGGAGCCAATCTCACAAAACCGATCGTAGTCCGGATTGCACTCTGCAACTCGAGTGCATGAAGTCGGAATCGCTAGTAATCGCAGGTCAGCATACTGCGGTGAATACGTTCCCGGGTCTTGTACACACCGCCCGTCACACCATGGGAGTGGGGGATACCAGAAGTAGGTAGGATAACCACAAGGAGTCCGCTTACCACGGTATGCTTCATGACTGGGGTGAAGTCGTAACAAGGTAGCCGTAGGGGAACCTGCGGCTGGATCACCTCCTTTCT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39597","NCBI_taxonomy_name":"Neisseria meningitidis MC58","NCBI_taxonomy_id":"122586"}}}},"ARO_accession":"3003497","ARO_id":"40099","ARO_name":"Neisseria meningitidis 16S rRNA mutation conferring resistance to spectinomycin","ARO_description":"Point mutations in the 16S rRNA of Neisseria meningitidis can confer resistance to spectinomycin","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2154":{"model_id":"2154","model_name":"Borrelia burgdorferi 16S rRNA mutation conferring resistance to spectinomycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2975":"A1184G","4806":"C1185U"},"clinical":{"2975":"A1184G","4806":"C1185U"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"2500"}},"model_sequences":{"sequence":{"3267":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NR_044732.2","fmin":"0","fmax":"1477","strand":"+","sequence":"AATAACGAAGAGTTTGATCCTGGCTTAGAACTAACGCTGGCAGTGCGTCTTAAGCATGCAAGTCAAACGGGATGTAGCAATACATTCAGTGGCGAACGGGTGAGTAACGCGTGGATGATCTACCTATGAGATGGGGATAACTATTAGAAATAGTAGCTAATACCGAATAAGGTCAGTTAATTTGTTAATTGATGAAAGGAAGCCTTTAAACGTTCGCTTGTAGATGAGTCTGCGTCTTATTAGCTAGTTGGTAGGGTAAATGCCTACCAAGGCAATGATAAGTAACCGGCCTGAGAGGGTGAACGGTCACACTGGAACTGAGATACGGTCCAGNCTCCTACGGGAGGCAGCAGCTAAGAATCTTCCGCAATGGGCGAAAGCCTGACGGAGCGACACTGCGTGAATGAAGAAGGTCGAAAGATTGTAAAATTCTTTTATAAATGAGGAATAAGCTTTGTAGGAAATGACAAAGTGATGACGTTAATTTATGAATAAGCCCCGGCTAATTACGTGCCAGNAGCCGCGGTAATACGTAAGGGNNNAGCGTTGTTCGGGATTATTGGGCGTAAAGGGTGAGTAGGCGGATATATAAGTCTATGCATAAAATACCACAGCTCAACTGTGGACCTATGTTGGAAACTATATGTCTAGAGTCTGATAGAGGAAGTTAGAATTTCTGGTGTAAGGGTGGAATCTGTTGATATCAGAAAGAATACCGGAGGCGAAGGCGAACTTCTGGGTCAAGACTGACGCTGAGTCACGAAAGCGTAGGGAGCAAACAGGATTAGATACCCTGGTAGTCTACGCTGTAAACGATGCACACTTGGTGTTAACTAAAAGTTAGTACCGAAGCTAACGTGTTAAGTGTGCAGCCTGGGGAGTATGCTCGCAAGAGNGAAACTCAAAGGNATTNANNNGNGCCNGCACAAGNNGTGGAGCATGTGGTTTNNNNNNANNNTACGCGAGGAACCTTACCAGGGCTTGACATATATAGGATATAGTTAGAGATAATTATTCCCCGTTTGGGGTCTATATACAGGTGCTGCATGGTTGTCGTCAGCTCGTGCTGTGAGGTGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTTATCTGTTACCAGCATGTAATGGTGGGGACTCAGATAAGACTGCCGGTGATAAGTCGGAGGAAGGTGAGGATGACGTCAAATCATCATGGCCCTTATGTCCTGGGCTACACACGTGCTACAATGGCCTGTACAAAGCGAAGCGAAACAGTGATGTGAAGCAAAACGCATAAAGCAGGTCTCAGTCCGGATTGAAGTCTGAAACTCGACTTCATGAAGTTGGAATCGCTAGTAATCGTATATCAGAATGATACGGTGAATACGTTCTCGGGCNTTGTACACACCGCCCGTCACACCACCCGAGTTGAGGATACCCGAAGCTATTATTCTAACCCGTAAGGGAGGAAGGTATTTAAGGTATGTTTAGCA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40345","NCBI_taxonomy_name":"Borrelia burgdorferi","NCBI_taxonomy_id":"139"}}}},"ARO_accession":"3003502","ARO_id":"40104","ARO_name":"Borrelia burgdorferi 16S rRNA mutation conferring resistance to spectinomycin","ARO_description":"Point mutations in the 3' major domain of the 16S rRNA gene of Borrelia burgdorferi can confer resistance to spectinomycin","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2155":{"model_id":"2155","model_name":"Propionibacterium acnes 16S rRNA mutation conferring resistance to tetracycline","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2931":"G1032C"},"clinical":{"2931":"G1032C"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"2600"}},"model_sequences":{"sequence":{"3259":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NR_040847.1","fmin":"0","fmax":"1486","strand":"+","sequence":"AGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGCCCTGCTTTTGTGGGGTGCTCGAGTGGCGAACGGGTGAGTAACACGTGAGTAACCTGCCCTTGACTTTGGGATAACTTCAGGAAACTGGGGCTAATACCGGATAGGAGCTCCTGCTGCATGGTGGGGGTTGGAAAGTTTCGGCGGTTGGGGATGGACTCGCGGCTTATCAGCTTGTTGGTGGGGTAGTGGCTTACCAAGGCTTTGACGGGTAGCCGGCCTGAGAGGGTGACCGGCCACATTGGGACTGAGATACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGGAAGCCTGATGCAGCAACGCCGCGTGCGGGATGACGGCCTTCGGGTTGTAAACCGCTTTCGCCTGTGACGAAGCGTGAGTGACGGTAATGGGTAAAGAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGTGATACGTAGGGTGCGAGCGTTGTCCGGATTTATTGGGCGTAAAGGGCTCGTAGGTGGTTGATCGCGTCGGAAGTGTAATCTTGGGGCTTAACCCTGAGCGTGCTTTCGATACGGGTTGACTTGAGGAAGGTAGGGGAGAATGGAATTCCTGGTGGAGCGGTGGAATGCGCAGATATCAGGAGGAACACCAGTGGCGAAGGCGGTTCTCTGGGCCTTTCCTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGCTTAGATACCCTGGTAGTCCACGCTGTAAACGGTGGGTACTAGGTGTGGGGTCCATTCCACGGGTTCCGTGCCGTAGCTAACGCTTTAAGTACCCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGCCCCGCACAAGCGGCGGAGCATGCGGATTAATTCGATGCAACGCGTAGAACCTTACCTGGGTTTGACATGGATCGGGAGTGCTCAGAGATGGGTGTGCCTCTTTTGGGGTCGGTTCACAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTTCACTGTTGCCAGCACGTTATGGTGGGGACTCAGTGGAGACCGCCGGGGTCAACTCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGCCCCTTATGTCCAGGGCTTCACGCATGCTACAATGGCTGGTACAGAGAGTGGCGAGCCTGTGAGGGTGAGCGAATCTCGGAAAGCCGGTCTCAGTTCGGATTGGGGTCTGCAACTCGACCTCATGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCCGGGGCTTGTACACACCGCCCGTCAAGTCATGAAAGTTGGTAACACCCGAAGCCGGTGGCCTAACCGTTGTGGGGGAGCCGTCGAAGGTGGGACTGGTGATTAGGACTAAGTCGTAACAAGGTAACC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40344","NCBI_taxonomy_name":"Propionibacterium acnes","NCBI_taxonomy_id":"1747"}}}},"ARO_accession":"3003499","ARO_id":"40101","ARO_name":"Propionibacterium acnes 16S rRNA mutation conferring resistance to tetracycline","ARO_description":"Tetracycline binds tightly to the helix 34 domain in 16S rRNA, where it interferes sterically with the binding of aminoacyl-tRNA to the ribosome A site to block protein synthesis. Mutations in the nucleotide sequence in this domain for Propionibacterium acnes can result in resistance against tetracycline.","ARO_category":{"40280":{"category_aro_accession":"3003669","category_aro_cvterm_id":"40280","category_aro_name":"16S rRNA with mutation conferring resistance to tetracycline derivatives","category_aro_description":"Point mutations in the bacterial 16S rRNA region shown clinically to confer resistance to tetracycline and tetracycline derivatives (polyketide antibiotics).","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2157":{"model_id":"2157","model_name":"Escherichia coli 16S rRNA mutation in the rrsB gene conferring resistance to gentamicin C","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3018":"A1408G"},"clinical":{"3018":"A1408G"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"3233":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"U00096","fmin":"4166659","fmax":"4168200","strand":"+","sequence":"AAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAGAAGCTTGCTTCTTTGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCGACTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTGGTCTTGACATCCACGGAAGTTTTCAGAGATGAGAATGTGCCTTCGGGAACCGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGGTCCGGCCGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACGACCAGGGCTACACACGTGCTACAATGGCGCATACAAAGAGAAGCGACCTCGCGAGAGCAAGCGGACCTCATAAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTGGATCAGAATGCCACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGCAAAAGAAGTAGGTAGCTTAACCTTCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGATCACCTCCTTA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36905","NCBI_taxonomy_name":"Escherichia coli K-12","NCBI_taxonomy_id":"83333"}}}},"ARO_accession":"3003396","ARO_id":"39980","ARO_name":"Escherichia coli 16S rRNA (rrsB) mutation conferring resistance to gentamicin C","ARO_description":"Point mutations in the 3' minor domain of helix 44, in the rrsB 16S rRNA gene of Escherichia coli can confer resistance to gentamicin C","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2176":{"model_id":"2176","model_name":"glycopeptide resistance gene cluster VanN","model_type":"gene cluster meta-model","model_type_id":"40298","model_description":"A meta-model to detect a defined gene cluster based on gene detection by other models.","model_param":{"40297":{"param_type":"gene order","param_description":"The gene order model parameter describes the relative order of a set of genes or other genetic elements on a chromosome, a plasmid or within an operon. Antibiotic resistance is only conferred when the detected set of genes appears in the indicated order; otherwise, no resistance phenotype is produced. This parameter is part of the gene cluster meta-model, and may be attached to detection models with the following notation: [[cvterm_id 1],[cvterm_id 2],...,[cvterm_id n]], where the cvterm_id denotes a gene-associated AMR term and an attached model id. This parameter currently (August 2017) lacks an algorithm for detection.","param_type_id":"40297","param_value":{"4681":"C:39346,C:39403,C:39409,R:39363,R:39374"}}},"ARO_accession":"3002917","ARO_id":"39351","ARO_name":"glycopeptide resistance gene cluster VanN","ARO_description":"Homologous to vanC, contains a D-Ala-D-Ser ligase. The plasmid-located vanM gene cluster is inducible and confers low resistance to vancomycin. vanN organisms remain susceptible to teicoplanin. Gene orientation: N(XY)TRS","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2177":{"model_id":"2177","model_name":"glycopeptide resistance gene cluster VanA","model_type":"gene cluster meta-model","model_type_id":"40298","model_description":"A meta-model to detect a defined gene cluster based on gene detection by other models.","model_param":{"40297":{"param_type":"gene order","param_description":"The gene order model parameter describes the relative order of a set of genes or other genetic elements on a chromosome, a plasmid or within an operon. Antibiotic resistance is only conferred when the detected set of genes appears in the indicated order; otherwise, no resistance phenotype is produced. This parameter is part of the gene cluster meta-model, and may be attached to detection models with the following notation: [[cvterm_id 1],[cvterm_id 2],...,[cvterm_id n]], where the cvterm_id denotes a gene-associated AMR term and an attached model id. This parameter currently (August 2017) lacks an algorithm for detection.","param_type_id":"40297","param_value":{"4671":"R:39353,R:39365,C:39376,C:36019,C:39383,A:39389,A:39396"}}},"ARO_accession":"3000236","ARO_id":"36375","ARO_name":"glycopeptide resistance gene cluster VanA","ARO_description":"This inducible cluster confers high resistance to both vancomycin and teicoplanin by allowing restructuring of peptidoglycan precursors to end in D-Ala-D-Lac. The vanA gene cluster can be located either on plasmids or on the chromosome.Gene orientation: vanRSHAXYZ","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"35948":{"category_aro_accession":"0000029","category_aro_cvterm_id":"35948","category_aro_name":"teicoplanin","category_aro_description":"Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation  and transpeptidation.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2178":{"model_id":"2178","model_name":"glycopeptide resistance gene cluster VanO","model_type":"gene cluster meta-model","model_type_id":"40298","model_description":"A meta-model to detect a defined gene cluster based on gene detection by other models.","model_param":{"40297":{"param_type":"gene order","param_description":"The gene order model parameter describes the relative order of a set of genes or other genetic elements on a chromosome, a plasmid or within an operon. Antibiotic resistance is only conferred when the detected set of genes appears in the indicated order; otherwise, no resistance phenotype is produced. This parameter is part of the gene cluster meta-model, and may be attached to detection models with the following notation: [[cvterm_id 1],[cvterm_id 2],...,[cvterm_id n]], where the cvterm_id denotes a gene-associated AMR term and an attached model id. This parameter currently (August 2017) lacks an algorithm for detection.","param_type_id":"40297","param_value":{"4682":"R:39364,R:39375,C:39382,C:39347,C:39388"}}},"ARO_accession":"3002918","ARO_id":"39352","ARO_name":"glycopeptide resistance gene cluster VanO","ARO_description":"Homologous to vanA, contains a D-Ala-D-Lac ligase. The chromosome-located vanO gene cluster is inducible. Not much is known about the biochemistry about the vanO gene cluster. Gene orientation: orf1 RS orf2 HOX","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2179":{"model_id":"2179","model_name":"glycopeptide resistance gene cluster VanE","model_type":"gene cluster meta-model","model_type_id":"40298","model_description":"A meta-model to detect a defined gene cluster based on gene detection by other models.","model_param":{"40297":{"param_type":"gene order","param_description":"The gene order model parameter describes the relative order of a set of genes or other genetic elements on a chromosome, a plasmid or within an operon. Antibiotic resistance is only conferred when the detected set of genes appears in the indicated order; otherwise, no resistance phenotype is produced. This parameter is part of the gene cluster meta-model, and may be attached to detection models with the following notation: [[cvterm_id 1],[cvterm_id 2],...,[cvterm_id n]], where the cvterm_id denotes a gene-associated AMR term and an attached model id. This parameter currently (August 2017) lacks an algorithm for detection.","param_type_id":"40297","param_value":{"4679":"C:39341,C:39401,C:39405,R:39358,R:39369"}}},"ARO_accession":"3000259","ARO_id":"36398","ARO_name":"glycopeptide resistance gene cluster VanE","ARO_description":"Homologous to VanC, contains a D-Ala-D-Ser ligase. The chromosome-located vanE gene cluster is inducible and confers low resistance to vancomycin. vanE organisms remain susceptible to teicoplanin. Gene orientation: E(XY)TRS","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2180":{"model_id":"2180","model_name":"glycopeptide resistance gene cluster VanL","model_type":"gene cluster meta-model","model_type_id":"40298","model_description":"A meta-model to detect a defined gene cluster based on gene detection by other models.","model_param":{"40297":{"param_type":"gene order","param_description":"The gene order model parameter describes the relative order of a set of genes or other genetic elements on a chromosome, a plasmid or within an operon. Antibiotic resistance is only conferred when the detected set of genes appears in the indicated order; otherwise, no resistance phenotype is produced. This parameter is part of the gene cluster meta-model, and may be attached to detection models with the following notation: [[cvterm_id 1],[cvterm_id 2],...,[cvterm_id n]], where the cvterm_id denotes a gene-associated AMR term and an attached model id. This parameter currently (August 2017) lacks an algorithm for detection.","param_type_id":"40297","param_value":{"4680":"C:39344,C:39402,C:39407,C:39408,R:39361,R:39372"}}},"ARO_accession":"3000260","ARO_id":"36399","ARO_name":"glycopeptide resistance gene cluster VanL","ARO_description":"Homologous to VanC, contains a D-Ala-D-Ser ligase. The chromosome-located vanL gene cluster is inducible and confers low resistance to vancomycin. vanL organisms remain susceptible to teicoplanin. It is the only van gene cluster with two vanT genes.Gene orientation: vanL(XY)TmTrRS","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2128":{"model_id":"2128","model_name":"Mycobacterium abscessus 16S rRNA mutation conferring resistance to gentamicin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2958":"A1375G","4796":"C1376U","4797":"G1458U","4798":"U1373A"},"clinical":{"2958":"A1375G","4796":"C1376U","4797":"G1458U","4798":"U1373A"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"2600"}},"model_sequences":{"sequence":{"3256":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"CU458896.1","fmin":"1462398","fmax":"1463901","strand":"+","sequence":"AGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGCCCTTCGGGGTACTCGAGTGGCGAACGGGTGAGTAACACGTGGGTGATCTGCCCTGCACTCTGGGATAAGCCTGGGAAACTGGGTCTAATACCGGATAGGACCACACACTTCATGGTGAGTGGTGCAAAGCTTTTGCGGTGTGGGATGAGCCCGCGGCCTATCAGCTTGTTGGTGGGGTAATGGCCCACCAAGGCGACGACGGGTAGCCGGCCTGAGAGGGTGACCGGCCACACTGGGACTGAGATACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGAGGGATGACGGCCTTCGGGTTGTAAACCTCTTTCAGTAGGGACGAAGCGAAAGTGACGGTACCTACAGAAGAAGGACCGGCCAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTCCGAGCGTTGTCCGGAATTACTGGGCGTAAAGAGCTCGTAGGTGGTTTGTCGCGTTGTTCGTGAAAACTCACAGCTTAACTGTGGGCGTGCGGGCGATACGGGCAGACTAGAGTACTGCAGGGGAGACTGGAATTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGGTGGCGAAGGCGGGTCTCTGGGCAGTAACTGACGCTGAGGAGCGAAAGCGTGGGTAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGGTGGGTACTAGGTGTGGGTTTCCTTCCTTGGGATCCGTGCCGTAGCTAACGCATTAAGTACCCCGCCTGGGGAGTACGGTCGCAAGACTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGTGGATTAATTCGATGCAACGCGAAGAACCTTACCTGGGTTTGACATGCACAGGACGTACCTAGAGATAGGTATTCCCTTGTGGCCTGTGTGCAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCCTATGTTGCCAGCGGGTAATGCCGGGGACTCGTAGGAGACTGCCGGGGTCAACTCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGCCCCTTATGTCCAGGGCTTCACACATGCTACAATGGCCAGTACAGAGGGCTGCGAAGCCGTAAGGTGGAGCGAATCCCTTAAAGCTGGTCTCAGTTCGGATTGGGGTCTGCAACTCGACCCCATGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTCGGTAACACCCGAAGCCAGTGGCCTAACCTTTTGGAGGGAGCTGTCGAAGGTGGGATCGGCGATTGGGACGAAGTCGTAACAAGGTAGCCGTACCGGAAGGTGCGGCTGGATCACCT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36888","NCBI_taxonomy_name":"Mycobacterium abscessus","NCBI_taxonomy_id":"36809"}}}},"ARO_accession":"3003240","ARO_id":"39824","ARO_name":"Mycobacterium abscessus 16S rRNA mutation conferring resistance to gentamicin","ARO_description":"Point mutations in the 16S rRNA of Mycobacterium abscessus conferring resistance to gentamicin","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2181":{"model_id":"2181","model_name":"glycopeptide resistance gene cluster VanF","model_type":"gene cluster meta-model","model_type_id":"40298","model_description":"A meta-model to detect a defined gene cluster based on gene detection by other models.","model_param":{"40297":{"param_type":"gene order","param_description":"The gene order model parameter describes the relative order of a set of genes or other genetic elements on a chromosome, a plasmid or within an operon. Antibiotic resistance is only conferred when the detected set of genes appears in the indicated order; otherwise, no resistance phenotype is produced. This parameter is part of the gene cluster meta-model, and may be attached to detection models with the following notation: [[cvterm_id 1],[cvterm_id 2],...,[cvterm_id n]], where the cvterm_id denotes a gene-associated AMR term and an attached model id. This parameter currently (August 2017) lacks an algorithm for detection.","param_type_id":"40297","param_value":{"4676":"R:39359,R:39370,A:39392,A:39397,C:39379,C:39342,C:39386"}}},"ARO_accession":"3000255","ARO_id":"36394","ARO_name":"glycopeptide resistance gene cluster VanF","ARO_description":"Homologous to vanA, contains a D-Ala-D-Lac ligase. The vanF gene cluster is inducible and confers high resistance to vancomycin in Paenibacillus popilliae. vanF organisms remain susceptible to teicoplanin. Gene orientation: RSYZHFX","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2182":{"model_id":"2182","model_name":"glycopeptide resistance gene cluster VanD","model_type":"gene cluster meta-model","model_type_id":"40298","model_description":"A meta-model to detect a defined gene cluster based on gene detection by other models.","model_param":{"40297":{"param_type":"gene order","param_description":"The gene order model parameter describes the relative order of a set of genes or other genetic elements on a chromosome, a plasmid or within an operon. Antibiotic resistance is only conferred when the detected set of genes appears in the indicated order; otherwise, no resistance phenotype is produced. This parameter is part of the gene cluster meta-model, and may be attached to detection models with the following notation: [[cvterm_id 1],[cvterm_id 2],...,[cvterm_id n]], where the cvterm_id denotes a gene-associated AMR term and an attached model id. This parameter currently (August 2017) lacks an algorithm for detection.","param_type_id":"40297","param_value":{"4674":"R:39357,R:39368,A:39391,C:39378,C:36014,C:39600"}}},"ARO_accession":"3000253","ARO_id":"36392","ARO_name":"glycopeptide resistance gene cluster VanD","ARO_description":"Homologous to vanA, contains a D-Ala-D-Lac ligase.  This cluster is constitutively expressed in the chromosome due to a dysfunctional D-ala-D-ala ligase and confers moderate resistance to both vancomycin and teicoplanin.Gene orientation: vanRSYHDX","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2183":{"model_id":"2183","model_name":"glycopeptide resistance gene cluster VanB","model_type":"gene cluster meta-model","model_type_id":"40298","model_description":"A meta-model to detect a defined gene cluster based on gene detection by other models.","model_param":{"40297":{"param_type":"gene order","param_description":"The gene order model parameter describes the relative order of a set of genes or other genetic elements on a chromosome, a plasmid or within an operon. Antibiotic resistance is only conferred when the detected set of genes appears in the indicated order; otherwise, no resistance phenotype is produced. This parameter is part of the gene cluster meta-model, and may be attached to detection models with the following notation: [[cvterm_id 1],[cvterm_id 2],...,[cvterm_id n]], where the cvterm_id denotes a gene-associated AMR term and an attached model id. This parameter currently (August 2017) lacks an algorithm for detection.","param_type_id":"40297","param_value":{"4672":"R:39355,R:39366,A:39390,A:39398,C:39377,C:36022,C:39384,A:39350"}}},"ARO_accession":"3000238","ARO_id":"36377","ARO_name":"glycopeptide resistance gene cluster VanB","ARO_description":"This inducible cluster confers resistance to vancomycin but organisms remain sensitive to teicoplanin by allowing restructuring of peptidoglycan precursors to end in D-Ala-D-Lac.  Sensitivity to teicoplanin is due to lack of binding to the sensor kinase VanS. The vanB gene cluster can be located either on plasmids or on the chromosome.Gene orientation: vanRSYWHBX","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2184":{"model_id":"2184","model_name":"glycopeptide resistance gene cluster VanC","model_type":"gene cluster meta-model","model_type_id":"40298","model_description":"A meta-model to detect a defined gene cluster based on gene detection by other models.","model_param":{"40297":{"param_type":"gene order","param_description":"The gene order model parameter describes the relative order of a set of genes or other genetic elements on a chromosome, a plasmid or within an operon. Antibiotic resistance is only conferred when the detected set of genes appears in the indicated order; otherwise, no resistance phenotype is produced. This parameter is part of the gene cluster meta-model, and may be attached to detection models with the following notation: [[cvterm_id 1],[cvterm_id 2],...,[cvterm_id n]], where the cvterm_id denotes a gene-associated AMR term and an attached model id. This parameter currently (August 2017) lacks an algorithm for detection.","param_type_id":"40297","param_value":{"4673":"C:36507,C:39400,C:39404,R:39356,R:39367"}}},"ARO_accession":"3000246","ARO_id":"36385","ARO_name":"glycopeptide resistance gene cluster VanC","ARO_description":"Confers low vancomycin resistance by engineering peptidoglycan precursors ending in D-Ala-D-Ser in an inducible or constitutive manner.  The vanC cluster is intrinsic to the Enterococcus gallinarum chromosome. vanC organisms remain susceptible to teicoplanin. Gene orientation: vanC(XY)TRS","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2185":{"model_id":"2185","model_name":"glycopeptide resistance gene cluster VanM","model_type":"gene cluster meta-model","model_type_id":"40298","model_description":"A meta-model to detect a defined gene cluster based on gene detection by other models.","model_param":{"40297":{"param_type":"gene order","param_description":"The gene order model parameter describes the relative order of a set of genes or other genetic elements on a chromosome, a plasmid or within an operon. Antibiotic resistance is only conferred when the detected set of genes appears in the indicated order; otherwise, no resistance phenotype is produced. This parameter is part of the gene cluster meta-model, and may be attached to detection models with the following notation: [[cvterm_id 1],[cvterm_id 2],...,[cvterm_id n]], where the cvterm_id denotes a gene-associated AMR term and an attached model id. This parameter currently (August 2017) lacks an algorithm for detection.","param_type_id":"40297","param_value":{"4677":"R:39362,R:39373,A:39395,C:39381,C:39345,C:39387"}}},"ARO_accession":"3000256","ARO_id":"36395","ARO_name":"glycopeptide resistance gene cluster VanM","ARO_description":"Homologous to vanA, contains a D-Ala-D-Lac ligase. The plasmid-located vanM gene cluster is inducible and confers high resistance to vancomycin and teicoplanin. Gene orientation: RSYHMX","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2186":{"model_id":"2186","model_name":"glycopeptide resistance gene cluster VanG","model_type":"gene cluster meta-model","model_type_id":"40298","model_description":"A meta-model to detect a defined gene cluster based on gene detection by other models.","model_param":{"40297":{"param_type":"gene order","param_description":"The gene order model parameter describes the relative order of a set of genes or other genetic elements on a chromosome, a plasmid or within an operon. Antibiotic resistance is only conferred when the detected set of genes appears in the indicated order; otherwise, no resistance phenotype is produced. This parameter is part of the gene cluster meta-model, and may be attached to detection models with the following notation: [[cvterm_id 1],[cvterm_id 2],...,[cvterm_id n]], where the cvterm_id denotes a gene-associated AMR term and an attached model id. This parameter currently (August 2017) lacks an algorithm for detection.","param_type_id":"40297","param_value":{"4678":"R:39360,R:39371,C:39549,A:39399,C:39343,A:39393,C:39406,R:36714"}}},"ARO_accession":"3000257","ARO_id":"36396","ARO_name":"glycopeptide resistance gene cluster VanG","ARO_description":"Contains a D-Ala-D-Ser ligase. The vanG gene cluster is inducible and confers low resistance to vancomycin. vanG organisms remain susceptible to teicoplanin. It is the only van gene cluster that contains two vanY genes.Gene orientation: vanRSYWGYT","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2090":{"model_id":"2090","model_name":"Mycobacterium abscessus 16S rRNA mutation conferring resistance to kanamycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3075":"A1375G","4786":"U1373A","4787":"G1458U","4788":"C1376U"},"clinical":{"3075":"A1375G","4786":"U1373A","4787":"G1458U","4788":"C1376U"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"2600"}},"model_sequences":{"sequence":{"3257":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"CU458896.1","fmin":"1462398","fmax":"1463901","strand":"+","sequence":"AGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGCCCTTCGGGGTACTCGAGTGGCGAACGGGTGAGTAACACGTGGGTGATCTGCCCTGCACTCTGGGATAAGCCTGGGAAACTGGGTCTAATACCGGATAGGACCACACACTTCATGGTGAGTGGTGCAAAGCTTTTGCGGTGTGGGATGAGCCCGCGGCCTATCAGCTTGTTGGTGGGGTAATGGCCCACCAAGGCGACGACGGGTAGCCGGCCTGAGAGGGTGACCGGCCACACTGGGACTGAGATACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGAGGGATGACGGCCTTCGGGTTGTAAACCTCTTTCAGTAGGGACGAAGCGAAAGTGACGGTACCTACAGAAGAAGGACCGGCCAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTCCGAGCGTTGTCCGGAATTACTGGGCGTAAAGAGCTCGTAGGTGGTTTGTCGCGTTGTTCGTGAAAACTCACAGCTTAACTGTGGGCGTGCGGGCGATACGGGCAGACTAGAGTACTGCAGGGGAGACTGGAATTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGGTGGCGAAGGCGGGTCTCTGGGCAGTAACTGACGCTGAGGAGCGAAAGCGTGGGTAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGGTGGGTACTAGGTGTGGGTTTCCTTCCTTGGGATCCGTGCCGTAGCTAACGCATTAAGTACCCCGCCTGGGGAGTACGGTCGCAAGACTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGTGGATTAATTCGATGCAACGCGAAGAACCTTACCTGGGTTTGACATGCACAGGACGTACCTAGAGATAGGTATTCCCTTGTGGCCTGTGTGCAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCCTATGTTGCCAGCGGGTAATGCCGGGGACTCGTAGGAGACTGCCGGGGTCAACTCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGCCCCTTATGTCCAGGGCTTCACACATGCTACAATGGCCAGTACAGAGGGCTGCGAAGCCGTAAGGTGGAGCGAATCCCTTAAAGCTGGTCTCAGTTCGGATTGGGGTCTGCAACTCGACCCCATGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTCGGTAACACCCGAAGCCAGTGGCCTAACCTTTTGGAGGGAGCTGTCGAAGGTGGGATCGGCGATTGGGACGAAGTCGTAACAAGGTAGCCGTACCGGAAGGTGCGGCTGGATCACCT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36888","NCBI_taxonomy_name":"Mycobacterium abscessus","NCBI_taxonomy_id":"36809"}}}},"ARO_accession":"3003236","ARO_id":"39820","ARO_name":"Mycobacterium abscessus 16S rRNA mutation conferring resistance to kanamycin","ARO_description":"Point mutations in the 16S rRNA of Mycobacterium abscessus conferring resistance to kanamycin","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"339":{"model_id":"339","model_name":"ANT(3'')-Ii-AAC(6')-IId fusion protein","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"900"}},"model_sequences":{"sequence":{"16":{"protein_sequence":{"accession":"AAL51021.2","sequence":"MSNAVPAEISVQLSLALNAIERHLESTLLAVHLYGSALDGGLKPYSDIDLLVTVAAQLDETVRQALVVDLLEISASPGQSEALRALEVTIVVHGDVVPWRYPARRELQFGEWQRKDILAGIFEPATTDVDLAILLTKVRQHSLALAGSAAEDFFNPVPEGDLFKALSDTLKLWNSQPDWEGDERNVVLTLSRIWYSAATGKIAPKDIVANWAIERLPDQHKPVLLEARQAYLGRGEDCLASRADQLAAFVHFVKHEATKLLGAMPVMSKTKLGITKYSIVTNSNDSVTLRLMTEHDLAMLYEWLNRSHIVEWWGGEEARPTLADVQEQYLPSVLAQESVTPYIAMLNGEPIGYAQSYVALGSGDGWWEEETDPGVRGIDQSLANASQLGKGLGTKLVRALVELLFNDPEVTKIQTDPSPSNLRAIRCYEKAGFERQGTVTTPDGPAVYMVQTRQAFERTRSDA"},"dna_sequence":{"accession":"AF453998","fmin":"3554","fmax":"4946","strand":"+","sequence":"ATGAGTAACGCAGTACCCGCCGAGATTTCGGTACAGCTATCACTGGCTCTCAACGCCATCGAGCGTCATCTGGAATCAACGTTGCTGGCCGTGCATTTGTACGGCTCTGCACTGGACGGTGGCCTGAAGCCATACAGTGATATTGATTTGCTGGTTACTGTGGCTGCACAGCTCGATGAGACTGTCCGACAAGCCCTGGTCGTAGATCTCTTGGAAATTTCTGCCTCCCCTGGCCAAAGTGAGGCTCTCCGCGCCTTGGAAGTTACCATCGTCGTGCATGGTGATGTTGTCCCTTGGCGTTATCCGGCCAGACGGGAACTGCAATTCGGGGAGTGGCAGCGTAAAGACATTCTTGCGGGCATCTTCGAGCCCGCCACAACCGATGTTGATCTGGCTATTCTGCTAACTAAAGTAAGGCAGCATAGCCTTGCATTGGCAGGTTCGGCCGCAGAGGATTTCTTTAACCCAGTTCCGGAAGGCGATCTATTCAAGGCATTGAGCGACACTCTGAAACTATGGAATTCGCAGCCGGATTGGGAAGGCGATGAGCGGAATGTAGTGCTTACCTTGTCTCGCATTTGGTACAGCGCAGCAACCGGCAAGATCGCACCGAAGGATATCGTTGCCAACTGGGCAATTGAGCGTCTGCCAGATCAACATAAGCCCGTACTGCTTGAAGCCCGGCAGGCTTATCTTGGACGAGGAGAAGATTGCTTGGCCTCACGCGCGGATCAGTTGGCGGCGTTCGTTCACTTCGTGAAACATGAAGCCACTAAATTGCTTGGTGCCATGCCAGTGATGTCTAAAACAAAGTTAGGCATCACAAAGTACAGCATCGTGACCAACAGCAACGATTCCGTCACACTGCGCCTCATGACTGAGCATGACCTTGCGATGCTCTATGAGTGGCTAAATCGATCTCATATCGTCGAGTGGTGGGGCGGAGAAGAAGCACGCCCGACACTTGCTGACGTACAGGAACAGTACTTGCCAAGCGTTTTAGCGCAAGAGTCCGTCACTCCATACATTGCAATGCTGAATGGAGAGCCGATTGGGTATGCCCAGTCGTACGTTGCTCTTGGAAGCGGGGACGGATGGTGGGAAGAAGAAACCGATCCAGGAGTACGCGGAATAGACCAGTCACTGGCGAATGCATCACAACTGGGCAAAGGCTTGGGAACCAAGCTGGTTCGAGCTCTGGTTGAGTTGCTGTTCAATGATCCCGAGGTCACCAAGATCCAAACGGACCCGTCGCCGAGCAACTTGCGAGCGATCCGATGCTACGAGAAAGCGGGGTTTGAGAGGCAAGGTACCGTAACCACCCCAGATGGTCCAGCCGTGTACATGGTTCAAACACGCCAGGCATTCGAGCGAACACGCAGTGATGCCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36783","NCBI_taxonomy_name":"Serratia marcescens","NCBI_taxonomy_id":"615"}}}},"ARO_accession":"3002598","ARO_id":"38998","ARO_name":"ANT(3'')-Ii-AAC(6')-IId fusion protein","ARO_description":"ANT(3'')-Ii-AAC(6')-Iid is an integron-encoded aminoglycoside acetyltransferase in S. marcescens.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"41439":{"category_aro_accession":"3004275","category_aro_cvterm_id":"41439","category_aro_name":"ANT(3'')","category_aro_description":"Nucleotidylylation of streptomycin at the hydroxyl group at position 3''","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1":{"model_id":"1","model_name":"PDC-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"1619":{"protein_sequence":{"accession":"ACQ82809.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDEMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"FJ666067","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACGAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTATGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002501","ARO_id":"38901","ARO_name":"PDC-4","ARO_description":"PDC-4 is a extended-spectrum beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2192":{"model_id":"2192","model_name":"TriA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"650"}},"model_sequences":{"sequence":{"3380":{"protein_sequence":{"accession":"NP_248846.1","sequence":"MSDARGAFHSKGRWSRMALPAILCAGLLVGCGAEPPAEEHVRVLAQTVKMAEFASATSITGDIQARVQADQSFRVGGKIVERLVDVGDHVAAGQVLARLDPQDQRSNVENAQAAVAAQQAQSKLADLNYQRQKALLPKGYTSQSEYDQALASVRSAQSSLKAAQAQLANARDLLSYTELRASDAGVITARQAEVGQVVQATVPIFTLARDGERDAVFNVYESLFSHDVDGQRITVSLLGKPEVTASGKVREITPTVDERSGTLKVKVGLDSVPAEMSLGSVVNASVAAPAEHSVVLPWSALSKVGEQPAVWLLDQQGKARLQPVRVARYASEKVVIDGGLEAGQTVVTVGGQLLHPGQVVEVAQPPQPTQSTASRDAVGGGQP"},"dna_sequence":{"accession":"NC_002516.2","fmin":"177306","fmax":"178458","strand":"+","sequence":"ATGTCAGACGCCAGAGGCGCTTTTCATTCCAAAGGTCGCTGGTCGCGGATGGCGCTGCCCGCCATCCTGTGCGCCGGCCTGCTTGTCGGTTGCGGCGCCGAGCCGCCCGCCGAGGAACACGTCCGTGTGCTGGCGCAGACGGTGAAGATGGCCGAGTTCGCCTCGGCCACCTCGATCACCGGCGACATCCAGGCACGGGTACAGGCCGACCAGTCGTTCCGTGTCGGCGGCAAGATCGTCGAGCGCCTGGTCGATGTCGGCGACCACGTCGCGGCTGGCCAGGTGCTGGCGCGGCTCGACCCGCAGGACCAGCGCAGCAACGTGGAGAACGCCCAGGCGGCGGTCGCCGCGCAGCAGGCGCAGTCGAAGCTCGCCGACCTCAACTACCAGCGGCAGAAGGCGCTGCTGCCCAAGGGCTACACCAGCCAGAGCGAGTACGACCAGGCGCTGGCCTCGGTGCGCAGCGCGCAGAGTTCGCTGAAGGCCGCCCAGGCGCAGTTGGCCAACGCCCGCGACCTGCTTTCCTATACCGAGCTGCGTGCCTCCGACGCCGGGGTCATCACCGCCCGCCAGGCCGAGGTCGGCCAGGTGGTGCAGGCCACCGTGCCGATCTTCACCCTGGCCCGCGACGGCGAGCGCGACGCGGTGTTCAACGTCTACGAGTCGTTGTTCAGCCACGATGTCGACGGCCAGCGGATCACCGTCAGCCTGCTCGGCAAGCCGGAAGTCACCGCCAGCGGCAAGGTCCGCGAGATCACCCCCACGGTGGACGAGCGCAGCGGTACGCTGAAGGTCAAGGTCGGCCTCGACTCGGTGCCGGCGGAAATGAGCCTCGGCAGCGTGGTCAACGCCAGCGTCGCCGCGCCGGCCGAGCACAGCGTGGTGCTGCCCTGGTCGGCGCTGTCCAAGGTCGGCGAGCAGCCGGCGGTCTGGTTGCTCGACCAGCAAGGCAAGGCGCGTCTGCAACCGGTGCGGGTGGCACGCTACGCCAGCGAGAAGGTGGTCATCGACGGTGGCCTGGAGGCGGGCCAGACGGTGGTCACGGTGGGCGGCCAACTGCTCCATCCGGGCCAGGTGGTCGAGGTGGCCCAGCCGCCGCAGCCGACCCAGAGCACCGCCAGCCGCGACGCCGTGGGCGGAGGCCAGCCATGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3003679","ARO_id":"40314","ARO_name":"TriA","ARO_description":"TriA is a membrane protein that is fused to TriB and both are required for the triclosan efflux pump function of TriABC-OpmH in P. aeruginosa.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2193":{"model_id":"2193","model_name":"TriB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"3381":{"protein_sequence":{"accession":"NP_248847.1","sequence":"MKPFSLAGLFGFALLLSGCGDEPPPAPPRPVLTVTVKTLKNDDLGRFAGSIQARYESVLGFRTNGRIASRLFDVGDFVGKGALLATLDPTDQQNQLRASQGDLASAEAQLIDAQANARRQEELFARSVTAQARLDDARTRLKTSQASFDQAKAAVQQARDQLSYTRLVTDFDGVITTWHAEAGQVVSAGQAVVTLARPEVREAVFDLPTEVAESLPADARFLVSAQLDPQARTTGSIRELGPQADASTRTRRVRLSLAQTPEAFRLGSTIQVQLSSAGSVRSVLPASVLLERDGKTQVWVVDGKQSSVALREVQVLSRDERQVVIGQGLADGDRVVRAGVNSLKPGQKIKLDEDAR"},"dna_sequence":{"accession":"NC_002516.2","fmin":"178454","fmax":"179525","strand":"+","sequence":"ATGAAGCCGTTTTCCCTCGCCGGCCTGTTCGGCTTCGCCCTGCTCCTCTCCGGCTGCGGCGACGAGCCGCCGCCGGCACCGCCGCGGCCGGTGCTGACGGTGACCGTGAAGACCCTGAAGAACGACGACCTCGGTCGCTTCGCCGGGAGCATCCAGGCGCGCTACGAGAGCGTGCTCGGCTTCCGCACCAACGGACGGATCGCCTCGCGCCTGTTCGACGTCGGTGACTTCGTCGGCAAGGGCGCGCTGCTGGCGACCCTCGACCCCACCGACCAGCAGAACCAGTTGCGCGCCAGCCAGGGCGACCTGGCCAGCGCCGAGGCACAGTTGATCGACGCCCAGGCCAATGCCCGGCGCCAGGAAGAACTGTTCGCCCGCAGCGTCACCGCCCAGGCGCGCCTGGACGATGCGCGGACCCGCCTGAAGACCAGCCAGGCCAGCTTCGACCAGGCCAAAGCGGCGGTGCAGCAGGCCAGGGACCAGCTTTCCTACACGCGCCTGGTGACCGATTTCGACGGCGTCATCACCACCTGGCACGCCGAGGCCGGGCAAGTGGTCAGCGCCGGCCAGGCGGTGGTCACCCTGGCCCGGCCCGAAGTGCGCGAGGCAGTCTTCGACCTGCCCACCGAGGTCGCCGAGAGCCTGCCGGCCGACGCGCGCTTCCTGGTCAGCGCCCAGCTCGACCCGCAGGCCAGGACCACCGGCAGCATCCGCGAGCTGGGTCCGCAGGCCGACGCCTCGACCCGCACCCGTCGCGTGCGCCTGAGCCTGGCGCAGACGCCGGAGGCGTTTCGCCTCGGTTCGACCATCCAGGTCCAGCTGAGCAGCGCCGGTAGCGTGCGCAGCGTGCTGCCGGCCAGCGTGCTGCTGGAGCGCGACGGCAAGACCCAGGTCTGGGTCGTCGATGGGAAACAGTCCAGCGTGGCCCTGCGCGAGGTACAGGTGCTCAGCCGCGACGAACGCCAGGTGGTGATCGGACAGGGCCTGGCCGACGGCGACCGGGTGGTCCGCGCCGGAGTCAACAGCCTCAAGCCCGGCCAGAAGATCAAACTCGACGAGGATGCGCGATGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3003680","ARO_id":"40315","ARO_name":"TriB","ARO_description":"TriB is a membrane protein that is fused to TriA and both are required for the triclosan efflux pump function of TriABC-OpmH in P. aeruginosa.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2194":{"model_id":"2194","model_name":"TriC","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1900"}},"model_sequences":{"sequence":{"3382":{"protein_sequence":{"accession":"NP_248848.1","sequence":"MKGGFNLSDWALRHQSLVWYLMAVSLVMGVFSYLNLGREEDPSFAIKTMVIQTRWPGATVDDTLEQVTDRIEKKLEELDSLDYVKSYTRPGESTVFVYLKDTTKAGDIPDIWYQVRKKISDIQGEFPQGIQGPGFNDEFGDVFGSVYAFTADGLDFRQLRDYVEKVRLDIRSVKDLGKVQMIGAQNEVIYLNFSTRKLAALGLDQRQVVQSLQAQNAVTPSGVVEAGPERISVRTSGNFRSEKDLQAVNLRVNDRFYRLSDLASISRDFVDPPTSLFRYKGEPAIGLAVAMKEGGNILEFGEALNARMQEITGELPVGVGVHQVSNQAQVVKKAVGGFTRALFEAVVIVLIVSFVSLGLRAGLVVACSIPLVLAMVFVFMEYTDITMQRVSLGALIIALGLLVDDAMITVEMMITRLELGDSLHDSATYAYTSTAFPMLTGTLVTVAGFVPIGLNASSAGEYTFTLFAVIAVALLLSWIVAVLFAPVIAVHILPKTLKHKSEQKKGRIAERFDSLLHLAMRRRWTTIFLTALLFGVSLFLMKFVQHQFFPSSDRPELLVDLNLPQNSSIHETRAVMDRLEATLKDDEDIDHWSAYVGEGAIRFYLPLDQQLQNNFYGQLVIVTKDLEARERVAARLRDRLRKDYVGISTYVQPLEMGPPVGRPIQYRVSGPQIDKVREYAMGLAGVLDGNPNIGDIVYDWNEPGKMLKIDIAQDKARQLGLSSEDVAQIMNSVVTGSAVTQVRDDIYLVNVIGRAEDSERGSLETLESLQIVTPSGTSIPLKAFAKVSYELEQPLVWRRDRKPTITVKASLRGEIQPTDLVARLAPEVKRFADGLPANYRIEVGGTVEESGKAEGPIAKVVPLMLFLMATFLMIQLQSVQKLFLVASVAPLGLIGVVAALLPTGTPMGFVAILGILALIGIIIRNSVILVTQIDAFEKDGKTPWEAVLEATHHRTRPILLTAAAASLGMIPIAREVFWGPMAYAMIGGIVAATLLTLIFLPALYVAWYRIPEPGR"},"dna_sequence":{"accession":"NC_002516.2","fmin":"179521","fmax":"182569","strand":"+","sequence":"ATGAAGGGCGGTTTCAACCTGTCGGACTGGGCCCTGCGCCACCAGTCCCTGGTCTGGTACCTGATGGCGGTATCGCTGGTGATGGGCGTGTTCTCCTACCTCAACCTGGGGCGCGAGGAGGATCCCTCGTTCGCCATCAAGACCATGGTCATCCAGACCCGCTGGCCGGGCGCCACGGTGGACGACACCCTGGAGCAGGTCACCGACCGCATCGAGAAGAAGCTCGAGGAGCTGGACTCGCTGGATTACGTGAAGAGCTACACGCGACCCGGCGAATCGACGGTCTTCGTCTACCTCAAGGACACCACCAAGGCCGGCGACATCCCGGATATCTGGTACCAGGTGCGCAAGAAGATATCCGACATCCAGGGCGAATTCCCCCAGGGCATCCAGGGACCGGGTTTCAACGACGAGTTCGGCGACGTGTTCGGCAGCGTCTACGCCTTCACCGCCGATGGCCTGGACTTCCGCCAGCTGCGCGACTACGTGGAGAAGGTGCGCCTGGACATCCGCTCGGTGAAAGACCTGGGCAAGGTGCAGATGATCGGTGCGCAGAACGAGGTCATCTACCTCAACTTCTCTACCCGCAAGCTGGCCGCCCTCGGTCTCGACCAGCGCCAGGTCGTGCAGAGCCTGCAGGCGCAGAACGCGGTGACCCCGTCCGGCGTGGTCGAGGCCGGCCCCGAGCGCATCTCGGTGCGCACCTCCGGCAACTTCCGTTCGGAAAAGGACCTGCAGGCGGTCAACCTGCGGGTCAACGATCGTTTCTACCGGCTGTCCGACCTGGCCAGCATCAGCCGCGATTTCGTCGACCCGCCGACCTCGCTGTTCCGCTACAAGGGCGAGCCGGCCATCGGCCTGGCGGTGGCGATGAAGGAGGGCGGCAATATCCTCGAGTTCGGCGAGGCGCTCAATGCGCGCATGCAGGAGATCACCGGCGAACTGCCGGTTGGCGTCGGCGTGCACCAGGTGTCGAACCAGGCCCAGGTGGTGAAGAAGGCGGTCGGCGGTTTCACCCGGGCGCTGTTCGAGGCGGTGGTGATCGTCCTCATCGTCAGCTTCGTCAGCCTCGGCCTGCGCGCCGGGCTGGTGGTGGCCTGCTCGATCCCGCTGGTGCTGGCGATGGTCTTCGTGTTCATGGAATACACCGACATCACCATGCAGCGGGTTTCCCTCGGCGCGCTGATCATCGCCCTCGGCCTGCTGGTGGACGATGCCATGATCACCGTGGAGATGATGATCACGCGCCTCGAACTGGGCGACTCGCTACACGACTCGGCGACCTACGCCTACACCTCGACGGCCTTCCCGATGCTCACCGGGACCCTGGTGACGGTGGCCGGCTTCGTACCCATCGGGCTCAACGCCAGCTCCGCCGGCGAGTACACCTTCACCCTGTTCGCAGTGATCGCCGTGGCGCTGCTGCTGTCGTGGATCGTCGCGGTGCTGTTCGCCCCGGTGATCGCCGTGCACATCCTGCCGAAGACTCTCAAGCACAAGTCGGAGCAGAAGAAGGGCCGCATTGCCGAGCGTTTCGACAGCCTGCTGCACCTGGCGATGCGCCGGCGCTGGACGACCATCTTCCTCACCGCGCTGCTGTTCGGCGTGTCGCTGTTCCTGATGAAGTTCGTCCAGCACCAGTTCTTCCCGTCTTCCGACCGTCCGGAACTGCTGGTCGACCTCAACCTGCCGCAGAACAGCAGCATCCACGAGACCAGGGCGGTGATGGACCGCCTGGAAGCGACGCTGAAGGACGACGAGGACATCGACCACTGGAGCGCCTACGTCGGCGAAGGCGCGATCCGCTTCTACCTGCCGCTGGACCAGCAGTTGCAGAACAACTTCTATGGCCAGCTGGTGATCGTCACCAAGGACCTGGAGGCCCGCGAGCGCGTCGCCGCACGCCTGCGCGATCGCTTGCGCAAGGACTACGTCGGCATCAGCACCTACGTGCAGCCGCTGGAGATGGGGCCGCCGGTGGGACGGCCGATCCAGTACCGGGTCAGCGGACCGCAGATCGACAAGGTCCGCGAGTACGCCATGGGCCTGGCCGGCGTGCTCGACGGCAACCCGAACATCGGCGATATCGTCTACGACTGGAACGAGCCCGGGAAGATGCTCAAGATCGACATCGCCCAGGACAAGGCGCGCCAGCTCGGGCTTTCCTCCGAGGACGTGGCGCAGATCATGAACAGCGTGGTGACCGGCAGCGCGGTGACCCAGGTGCGCGACGACATCTACCTGGTGAACGTCATCGGCCGCGCCGAGGATAGCGAGCGCGGCTCGCTGGAGACCCTGGAGAGCCTGCAGATCGTCACGCCCAGCGGCACCTCGATCCCGCTCAAGGCGTTCGCCAAGGTCAGCTACGAGCTGGAGCAGCCGCTGGTGTGGCGCCGCGACCGCAAGCCGACGATCACGGTGAAGGCGTCGCTGCGCGGCGAGATCCAGCCCACCGACCTGGTCGCCCGGCTGGCGCCGGAGGTCAAGCGCTTCGCCGACGGCCTGCCGGCGAACTACCGGATCGAAGTGGGCGGCACGGTGGAGGAGAGCGGCAAGGCCGAGGGCCCGATCGCCAAGGTGGTGCCGCTGATGCTGTTCCTCATGGCGACCTTCCTGATGATCCAGTTGCAGAGCGTGCAGAAGCTATTCCTGGTGGCCAGCGTCGCGCCGCTGGGGCTGATCGGGGTGGTCGCGGCGTTGCTGCCGACCGGCACGCCGATGGGCTTCGTGGCGATCCTCGGGATTCTCGCGCTGATCGGCATCATCATCCGCAACTCGGTGATCCTGGTGACCCAGATCGATGCCTTCGAGAAAGACGGCAAGACGCCCTGGGAAGCCGTGCTGGAAGCCACCCACCACCGCACCCGGCCGATCCTGCTGACGGCGGCGGCGGCCAGCCTGGGGATGATCCCCATCGCCCGCGAAGTGTTCTGGGGGCCGATGGCCTATGCGATGATCGGCGGCATCGTCGCCGCCACGCTGCTCACGCTGATCTTCCTGCCGGCGCTGTACGTCGCCTGGTACCGGATTCCGGAACCGGGACGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3003681","ARO_id":"40316","ARO_name":"TriC","ARO_description":"TriC is a resistance nodulation cell division (RND) transporter that is a part of TriABC-OpmH, a triclosan-specific efflux protein.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2195":{"model_id":"2195","model_name":"OpmH","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"850"}},"model_sequences":{"sequence":{"3383":{"protein_sequence":{"accession":"NP_253661.1","sequence":"MLRRLSLAAAVAAATGVAWAAQPTPLPTKTDLISVYKEAVDNNADLAAAQADYLARKEVVPQARAGLLPQLGAGARVGDTRIAFDERPATVKRNSQVVQATLSQPLFRADRWFQWQAAKETSDQARLEFSATQQDLILRSAETYFTVLRAQDNLATSKAEEAAFKRQLDQANERFDVGLSDKTDVLEAQASYDTARANRLIAEQRVDDAFQALVTLTNRDYSAIEGMRHTLPVVPPAPNDAKAWVDTAVQQNLRLLASNYAVNAAEETLRQRKAGHLPTLDAVAQYQKGDNDALGFANSAANPLVHYGKYVDERSIGLELNIPIYSGGLTSSQVRESYQRLNQSEQSREGQRRQVVQDTRNLHRAVNTDVEQVQARRQAIISNQSSLEATEIGYQVGTRNIVDVLNAQRQLYAAVRDYNNSRYDYILDTLRLKQAAGTLSPADLEALSAYLKQDYDPDKDFLPPDLAKAAAEQLQSKPRQQY"},"dna_sequence":{"accession":"NC_002516.2","fmin":"5584100","fmax":"5585549","strand":"+","sequence":"ATGCTGCGCAGACTCTCCCTGGCGGCCGCCGTGGCCGCTGCTACCGGTGTCGCCTGGGCCGCCCAGCCGACCCCGCTGCCGACCAAGACCGACCTGATCAGCGTCTACAAGGAAGCCGTCGACAACAACGCCGACCTCGCCGCCGCCCAGGCCGACTACCTGGCGCGCAAGGAAGTGGTGCCCCAGGCCCGCGCCGGCCTGCTGCCGCAACTCGGCGCCGGCGCCCGCGTCGGAGACACCCGGATCGCATTCGACGAGCGTCCGGCGACCGTCAAGCGCAACAGCCAGGTCGTCCAGGCCACCCTCAGCCAGCCGTTGTTCCGCGCCGACCGCTGGTTCCAGTGGCAGGCCGCCAAGGAAACCAGCGACCAGGCCCGGCTGGAATTCTCCGCGACCCAGCAGGACCTGATCCTGCGCAGCGCCGAGACCTACTTCACGGTGCTCCGCGCCCAGGACAACCTGGCCACCAGCAAGGCCGAGGAAGCCGCCTTCAAGCGCCAGCTGGACCAGGCCAACGAGCGCTTCGACGTGGGCCTTTCCGACAAGACCGACGTGCTCGAGGCCCAGGCCAGCTACGACACCGCCCGCGCCAACCGGTTGATCGCCGAACAGCGCGTGGACGATGCCTTCCAGGCCCTGGTGACCCTGACCAACCGCGACTACAGCGCCATCGAGGGCATGCGCCACACCCTGCCGGTGGTGCCGCCGGCGCCGAACGACGCCAAGGCCTGGGTCGACACCGCGGTGCAGCAGAACCTGCGCCTGCTGGCCAGCAACTACGCGGTCAACGCCGCCGAGGAAACCCTCCGCCAGCGCAAGGCCGGGCACCTGCCGACCCTCGATGCCGTGGCCCAGTACCAGAAGGGCGACAACGACGCCCTCGGCTTCGCCAACAGCGCCGCCAATCCGCTGGTGCACTATGGCAAGTATGTCGACGAGCGCAGCATTGGCCTGGAACTGAACATCCCGATCTACAGCGGCGGCCTGACCTCCTCCCAGGTCCGCGAGTCCTACCAGCGCCTCAACCAGAGCGAGCAATCCCGCGAAGGCCAGCGCCGCCAGGTGGTGCAGGATACCCGCAACCTGCACCGCGCGGTGAATACCGACGTCGAGCAGGTCCAGGCGCGGCGCCAGGCGATCATCTCCAACCAGAGTTCGCTGGAAGCCACCGAGATCGGCTACCAGGTCGGCACCCGCAACATCGTCGACGTGCTCAACGCCCAGCGCCAGCTGTACGCCGCCGTGCGCGACTACAACAACAGCCGCTACGACTACATCCTCGATACCCTGCGCCTGAAGCAGGCGGCCGGCACCCTCAGCCCGGCCGACCTGGAGGCGCTCAGCGCCTACCTGAAGCAGGACTACGATCCGGACAAGGACTTCCTCCCGCCGGACCTGGCCAAGGCCGCCGCCGAGCAGTTACAGAGCAAGCCGCGCCAGCAGTACTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3003682","ARO_id":"40317","ARO_name":"OpmH","ARO_description":"OpmH is an outer membrane efflux protein required for triclosan-specific efflux pump function.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2196":{"model_id":"2196","model_name":"Pseudomonas aeruginosa gyrA conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"40330":{"param_type":"multiple resistance variants","param_description":"A set of nucleotide or amino acid substitutions that are each required to confer resistance to an antibiotic drug or drug class by co-mutation. Compare to single resistance variant, where only one substitution is required. Multiple resistance variants parameters are indicated on appropriate models using the following notation: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2],...,[wild-type n][position n][mutation n]. When each included substitution is detected in a protein sequence, resistance is conferred. This parameter is not currently included in any detection algorithms.","param_type_id":"40330","param_value":{"3315":"T83I,D87G","3316":"T83I,D87N","3317":"T83I,D87H"}},"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3143":"T83I","3144":"H80R","3145":"D87N"},"clinical":{"3143":"T83I","3144":"H80R","3145":"D87N"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1500"}},"model_sequences":{"sequence":{"3384":{"protein_sequence":{"accession":"NP_251858.1","sequence":"MGELAKEILPVNIEDELKQSYLDYAMSVIVGRALPDARDGLKPVHRRVLYAMSELGNDWNKPYKKSARVVGDVIGKYHPHGDTAVYDTIVRMAQPFSLRYMLVDGQGNFGSVDGDNAAAMRYTEVRMAKLAHELLADLEKETVDWVPNYDGTEQIPAVMPTKIPNLLVNGSSGIAVGMATNIPPHNLGEVIDGCLALMDNPDLTVDELMQYIPGPDFPTAGIINGRAGIIEAYRTGRGRIYIRARAVVEEMEKGGGREQIIITELPYQLNKARLIEKIAELVKEKKIEGISELRDESDKDGMRVVIELRRGEVGEVVLNNLYAQTQLQSVFGINVVALVDGQPRTLNLKDMLEVFVRHRREVVTRRTVYELRKARERGHILEGQAVALSNIDPVIELIKSSPTPAEAKERLIATAWESSAVEAMVERAGADACRPEDLDPQYGLRDGKYYLSPEQAQAILELRLHRLTGLEHEKLLSEYQEILNLIGELIRILTNPARLMEVIREELEAVKAEFGDARRTEIVASQVDLTIADLITEEDRVVTISHGGYAKSQPLAAYQAQRRGGKGKSATGMKDEDYIEHLLVANSHATLLLFSSKGKVYWLRTFEIPEASRTARGRPLVNLLPLDEGERITAMLQIDLEALQQNGGADDDLDEAEGAVLEGEVVEAAEVEEVEGETAELVAEPTGAYIFMATAFGTVKKTPLVQFSRPRSSGLIALKLEEGDTLIAAAITDGAKEVMLFSSAGKVIRFAESVVRIMGRNARGVRGMRLGKGQQLISMLIPESGAQILTASERGFGKRTPLSKFPRRGRGGQGVIAMVTNERNGALIAAVQVQEGEEIMLISDQGTLVRTRVDEVSLSGRNTQGVTLIKLASDEVLVGLERVQEPSGGDDEDLPEGEEAAESLGESAESESEPAAEAEGNEE"},"dna_sequence":{"accession":"NC_002516.2","fmin":"3556426","fmax":"3559198","strand":"-","sequence":"TTACTCTTCGTTGCCTTCCGCTTCCGCCGCGGGCTCGGACTCGGACTCGGCCGACTCGCCCAGAGATTCGGCAGCTTCCTCGCCCTCGGGCAGGTCCTCGTCATCTCCGCCCGACGGCTCCTGGACACGCTCCAGACCGACCAGTACCTCGTCGCTGGCGAGCTTGATCAGGGTTACGCCCTGGGTATTGCGGCCGGACAGGGAGACTTCGTCGACACGCGTCCGCACCAGGGTGCCCTGGTCGGAAATCAGCATGATCTCCTCGCCTTCCTGGACCTGTACCGCGGCGATCAGCGCGCCGTTGCGCTCGTTGGTGACCATGGCGATCACCCCCTGGCCGCCGCGGCCGCGACGCGGGAACTTGCTCAGCGGGGTACGCTTGCCGAAGCCGCGCTCGGAGGCGGTGAGGATCTGCGCCCCGGACTCCGGAATCAGCATGGAGATCAGCTGCTGCCCCTTGCCCAGGCGCATGCCACGTACGCCGCGGGCGTTGCGGCCCATGATGCGCACCACGCTCTCGGCGAAGCGGATCACCTTGCCGGCGCTGGAGAACAGCATGACTTCCTTGGCGCCATCGGTGATCGCGGCGGCGATCAGGGTGTCGCCCTCTTCCAGCTTGAGCGCGATCAGGCCGCTGCTGCGCGGACGGCTGAACTGCACCAGCGGGGTCTTCTTCACGGTACCGAAGGCGGTGGCCATGAAGATGTAGGCGCCGGTCGGCTCGGCCACCAGCTCGGCGGTCTCGCCCTCGACTTCCTCGACCTCGGCGGCCTCGACCACCTCGCCCTCGAGCACCGCGCCTTCGGCTTCGTCGAGGTCGTCATCGGCGCCACCGTTCTGCTGCAGCGCCTCCAGGTCGATCTGCAACATCGCGGTGATCCGCTCGCCCTCATCCAGCGGCAGCAGGTTCACCAGCGGCCGGCCACGCGCGGTACGCGAGGCTTCCGGAATCTCGAAGGTACGCAGCCAGTAGACCTTGCCCTTGCTGGAGAACAGCAGGAGGGTCGCATGGCTGTTGGCCACCAGCAGGTGTTCGATGTAGTCCTCGTCCTTCATCCCGGTGGCGGACTTGCCTTTGCCGCCGCGACGCTGCGCCTGGTAGGCGGCCAGCGGCTGGGACTTGGCGTAGCCGCCGTGCGAGATGGTCACCACGCGGTCTTCCTCGGTGATCAGGTCGGCGATGGTCAGGTCGACCTGGGAAGCCACGATCTCGGTGCGGCGAGCATCGCCGAATTCGGCCTTGACCGCTTCCAGTTCCTCACGGATCACCTCCATCAGGCGCGCCGGGTTGGTCAGGATGCGGATCAGCTCGCCGATCAGGTTGAGGATTTCCTGGTATTCGGAGAGCAGCTTCTCGTGCTCCAGGCCGGTCAGGCGATGCAGGCGCAGCTCGAGGATCGCCTGGGCCTGCTCCGGCGACAGGTAGTACTTGCCGTCGCGCAGGCCGTACTGCGGATCCAGGTCTTCCGGACGACAGGCGTCGGCGCCGGCACGCTCGACCATCGCTTCCACCGCGCTGGACTCCCAGGCAGTGGCGATCAGGCGTTCCTTGGCCTCGGCCGGGGTCGGCGAACTCTTGATCAGCTCGATCACCGGGTCGATGTTCGACAGGGCGACCGCCTGGCCTTCCAGGATGTGCCCGCGCTCGCGGGCCTTGCGCAGCTCGTAGACGGTACGCCGGGTCACCACTTCGCGGCGGTGGCGGACGAACACCTCGAGCATGTCCTTCAGGTTCAGCGTGCGCGGCTGGCCGTCGACCAGGGCCACCACGTTGATGCCGAACACGCTCTGCAGCTGGGTCTGGGCATAGAGGTTGTTGAGGACCACCTCGCCCACCTCGCCGCGACGCAGCTCGATGACCACGCGCATGCCGTCCTTGTCAGACTCGTCGCGCAGCTCGGAAATACCCTCGATCTTCTTCTCTTTCACCAGCTCGGCGATCTTCTCGATCAACCGCGCCTTGTTCAACTGGTACGGCAGCTCGGTGATGATAATCTGCTCGCGACCGCCGCCCTTCTCCATCTCCTCGACGACGGCGCGGGCACGGATGTAGATGCGCCCGCGACCGGTGCGGTAGGCCTCGATGATCCCGGCGCGGCCGTTGATGATGCCGGCGGTGGGGAAGTCCGGACCGGGGATGTACTGCATCAGCTCATCGACGGTCAGGTCGGGGTTGTCCATCAGCGCCAGGCAGCCGTCGATCACTTCGCCGAGGTTGTGCGGCGGGATGTTGGTCGCCATGCCCACGGCGATACCGCTGGAACCGTTGACCAGCAGGTTGGGAATCTTGGTCGGCATGACCGCCGGGATCTGCTCGGTGCCATCGTAGTTGGGCACCCAGTCGACGGTTTCCTTTTCCAGGTCCGCCAGCAGTTCGTGGGCCAGCTTGGCCATGCGCACTTCGGTGTATCGCATGGCTGCGGCGTTGTCGCCGTCCACCGAACCGAAGTTGCCCTGGCCGTCTACCAGCATGTAGCGCAGCGAGAACGGCTGCGCCATGCGCACGATGGTGTCGTAGACCGCGGTGTCGCCGTGCGGGTGGTACTTACCGATCACGTCGCCGACCACACGGGCGGATTTCTTGTAGGGCTTGTTCCAGTCGTTGCCCAGCTCGCTCATGGCATAAAGCACACGGCGGTGCACCGGCTTCAGGCCGTCACGTGCATCCGGCAGGGCCCGCCCGACGATCACGCTCATCGCGTAGTCGAGATAGGACTGTTTCAGCTCGTCTTCGATATTGACCGGGAGAATTTCTTTGGCCAGTTCGCCCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3003684","ARO_id":"40319","ARO_name":"Pseudomonas aeruginosa gyrA conferring resistance to fluoroquinolones","ARO_description":"Point mutation of Pseudomonas aeruginosa gyrA resulted in the lowered affinity between fluoroquinolones and gyrA. Thus, conferring resistance.","ARO_category":{"39876":{"category_aro_accession":"3003292","category_aro_cvterm_id":"39876","category_aro_name":"fluoroquinolone resistant gyrA","category_aro_description":"DNA gyrase is responsible for DNA supercoiling and consists of two alpha and two beta subunits. GyrA point mutations confer resistance by preventing fluoroquinolone antibiotics from binding the alpha-subunit.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"37142":{"category_aro_accession":"3000762","category_aro_cvterm_id":"37142","category_aro_name":"pefloxacin","category_aro_description":"Pefloxacin is structurally and functionally similar to norfloxacin. It is poorly active against mycobacteria, while anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"40338":{"category_aro_accession":"3003690","category_aro_cvterm_id":"40338","category_aro_name":"sitafloxacin","category_aro_description":"Sitafloxacin is a fluoroquinolone active against multi-resistant Gram-positive and negative pathogens. Sitafloxacin shows inhibitory activity against DNA gyrase and topoisomerase IV, which blocks bacterial DNA replication, thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"40463":{"category_aro_accession":"3003780","category_aro_cvterm_id":"40463","category_aro_name":"nybomycin","category_aro_description":"A  heterocyclic antibiotic that targets mutant gyrA (type II topoisomerase) containing an S84L substitution, counteracting acquired quinolone resistance. It is effective against quinolone-resistant Gram-positive bacteria including S. aureus and E. faecalis. Due to its ability to counteract quinolone resistance by targeting the mutant form of the gyrA protein, it is classified as a reverse antibiotic (RA).","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2211":{"model_id":"2211","model_name":"mexP","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"650"}},"model_sequences":{"sequence":{"3405":{"protein_sequence":{"accession":"BAE06007.1","sequence":"MNLRHFIRITATLGVAALIAGCGESAPPGAASAPPSVPVAEVVVRPVTPYAEFTGSLTAVEQVELRPRVAGYIQDVTVPEGRLVEKGQQLFLIDPRVFKAAQDAARARLREAEAAALLARTEHERAELLYARKVVARERLDSAIASRNASKAQVDAARAALDAAQLDLGFTRVTAPIGGRVGHIQVTEGNYVTNGVTALTSIVSVDPLYVYFDVDERTYLQALAPTRGREGEQAPRVKVALLTDESYGRSSRLDFLANAADRGTGTVRVRAVVDNPDGQLTPGLFAKVRLETGKPRAQVLVADHSIGTDQGRRYVLVVDEGNKTQYRPVELGPMVDGLRVVRQGLQPGERIVVKGLVRPDMQITPRLAEIDGTPVDLSKTVGAAQ"},"dna_sequence":{"accession":"AB219524.1","fmin":"22","fmax":"1180","strand":"+","sequence":"ATGAATCTCAGACACTTCATCCGCATCACCGCGACGCTAGGTGTCGCGGCCCTTATCGCTGGCTGCGGGGAATCGGCGCCGCCGGGGGCGGCGAGCGCCCCGCCAAGCGTTCCCGTCGCCGAGGTGGTGGTTCGCCCGGTGACACCCTACGCCGAGTTCACCGGCTCGCTGACCGCTGTCGAGCAGGTAGAACTGCGGCCGCGCGTCGCCGGCTACATCCAGGACGTTACGGTGCCGGAAGGCCGCCTGGTAGAGAAGGGCCAGCAACTGTTCCTCATCGACCCGCGCGTGTTCAAGGCGGCGCAGGATGCCGCCAGGGCACGCCTGCGCGAGGCCGAGGCCGCGGCGTTGCTGGCGCGCACCGAACACGAGCGAGCCGAGCTGCTGTATGCGCGGAAGGTCGTCGCCCGGGAGCGGCTCGACAGCGCCATCGCCTCGCGCAATGCCAGCAAGGCCCAGGTCGATGCGGCCAGGGCCGCCCTCGACGCGGCGCAACTGGATCTCGGCTTCACGCGGGTGACGGCACCGATCGGCGGGCGTGTCGGGCATATCCAGGTCACCGAGGGCAACTACGTCACCAATGGCGTCACCGCGCTGACCAGCATCGTTTCGGTCGATCCGCTGTACGTGTACTTCGATGTCGACGAGCGCACCTACCTGCAGGCCCTGGCGCCGACCCGCGGCAGGGAAGGCGAGCAGGCCCCCAGGGTCAAGGTGGCGCTGCTCACCGACGAGTCCTATGGACGAAGCAGTCGCCTCGATTTCCTCGCCAACGCCGCCGACCGCGGGACCGGCACGGTCCGGGTTCGGGCGGTGGTGGACAACCCGGACGGGCAACTGACGCCGGGGCTGTTCGCCAAGGTCAGGCTGGAGACCGGCAAGCCTCGCGCGCAGGTGCTGGTCGCCGACCATTCCATCGGCACCGACCAGGGCAGGCGCTATGTGCTGGTCGTCGACGAAGGCAACAAGACCCAGTACCGGCCGGTGGAACTCGGCCCGATGGTCGACGGCCTGCGGGTCGTCCGCCAGGGCCTGCAGCCGGGCGAGCGCATCGTCGTCAAGGGCCTGGTCCGGCCGGACATGCAGATCACACCGCGCCTTGCGGAAATCGATGGCACGCCCGTCGACCTGTCGAAGACCGTGGGGGCCGCACAATGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3003698","ARO_id":"40350","ARO_name":"mexP","ARO_description":"MexP is the membrane fusion protein of the MexPQ-OpmE multidrug efflux complex","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavin","category_aro_description":"Acriflavin is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36309":{"category_aro_accession":"3000170","category_aro_cvterm_id":"36309","category_aro_name":"imipenem","category_aro_description":"Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"37626":{"category_aro_accession":"3001227","category_aro_cvterm_id":"37626","category_aro_name":"kitasamycin","category_aro_description":"Kitasamycin is a macrolide antibiotic and is produced by Streptoverticillium kitasatoense. The drug has antimicrobial activity against a wide spectrum of pathogens.","category_aro_class_name":"Antibiotic"},"40353":{"category_aro_accession":"3003701","category_aro_cvterm_id":"40353","category_aro_name":"rokitamycin","category_aro_description":"Rokitamycin is a macrolide antibiotic. Synthesized from strains of Streptomyces kitasatoensis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36193":{"category_aro_accession":"3000054","category_aro_cvterm_id":"36193","category_aro_name":"acridine dye","category_aro_description":"Acridine dyes are cell permeable, basic molecules with an acridine chromophore. These compounds intercalate DNA. The image shown represents the core structure of the acridine family, with specific dyes containing varying substituents.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2212":{"model_id":"2212","model_name":"mexQ","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1900"}},"model_sequences":{"sequence":{"3406":{"protein_sequence":{"accession":"BAE06008.1","sequence":"MTFPRFFIDRPIFAIVLSVLMMIGGIVSFFQLPLSEYPAVTPPTVQVTTAYPGANPDVIAQTVATPLEQAITGVEGMLYMSSQSATDGRMILTITFDQHIDPDMAQIQVQNRVSRVLSRLPDEVQRQGVVTQKTSPDILMVVHLLSPEQRYDPLYISNYAYLQVRDELLRLPGISDVVVWGAGEYSMRLWLDPDLIAARGLTAGEVIAAVREQNVQVAAGAVGQAPDSTAAFQVTVNTLGRLSDEEQFGDIIVRTGADGQVTRLRDVARIEMGGDAYALRSLLDGEPAVALQIIQSPGANALDTAEAVRATVARLEGNFPAGLSARIAYDPTVFVRASLQTVATTLLEAILLVVVVVVLFLRSWRASLIPLMAVPVSLVGTFAVMHLMGFSLNTLSLFGLVLSIGIVVDDAIVVVENVERHIENGEPPLQAARRAMDEVTGPIMAITSVLAAVFIPTAFLSGLQGEFYRQFALTIAISTILSALNSLTLSPALAGLLLRPRPAGGAVAGRFQRLLQVLGRPLRNAPEAYGNAVRKVVRVSGLALVVYGGLLGLTWVGFQAVPPGFVPMQDKYYLIGIAQLPNGASLERTDAVVRQMSRIGLDEPGVESVVAFPGLSVNGFVNVPNAAVMFFMLDPFESRTSADLGALAIAGRLQARFASIPDGFLGVFPPPPVPGLGTIGGFKMQVEDRGGAGLEALARQTQVLMMKATESGQLGGLMTSFDINAPQLEVVVDRTKVKSQGVRLADVFEALQVYLGSLYINDFNRFGRTYKVTAQADAPHRMQAEAIGRLQVRNAAGAMLPLSSFVTVTPSSGPDRVIHYNGYPSADISGGALPGVSSGQAVALMERLAGEVLPEGMTFEWTDLTYQQKLAGNSALFIFPLCVLLAYLILAAQYNSWLLPLAVLLIVPMCLLSAIAGVWLVGGDNNVFVQIGLVVLVGLAAKNAILIVEFARTLEAEGARALEAVVEACRLRLRPILMTSLAFIAGVVPLVMASGAGAEMRQAMGVAVFAGMLGVTLFGLFLTPVFYVLVRALAARLERRAGGSLAHLEGGRP"},"dna_sequence":{"accession":"AB219524.1","fmin":"1176","fmax":"4338","strand":"+","sequence":"ATGACATTCCCACGCTTCTTCATCGATAGGCCGATCTTCGCCATCGTTCTTTCGGTGCTGATGATGATCGGAGGCATCGTTTCGTTCTTCCAGTTGCCGCTGAGCGAATACCCGGCGGTGACGCCGCCGACCGTGCAGGTGACTACCGCCTATCCCGGCGCCAACCCCGACGTGATCGCGCAGACGGTGGCGACACCGCTGGAGCAGGCGATCACCGGGGTCGAGGGGATGCTGTACATGTCCTCGCAGTCGGCCACCGACGGGCGAATGATCCTGACCATCACCTTCGACCAGCACATCGATCCCGACATGGCCCAGATCCAGGTGCAGAACCGGGTCTCGCGGGTGCTCTCGCGCCTGCCCGACGAGGTGCAGCGGCAGGGCGTGGTCACCCAGAAGACCTCGCCGGACATCCTCATGGTGGTGCACCTGCTGTCGCCGGAGCAACGCTACGACCCGCTGTACATCTCGAACTACGCCTACCTCCAGGTGCGCGACGAACTGCTGCGCCTGCCGGGGATCAGCGATGTGGTGGTGTGGGGCGCCGGCGAGTACAGCATGCGCCTGTGGCTCGACCCCGACCTGATCGCCGCGCGCGGGCTGACGGCGGGCGAAGTGATCGCCGCGGTACGCGAACAGAACGTCCAGGTGGCGGCCGGCGCCGTCGGCCAGGCGCCGGACTCCACCGCGGCCTTCCAGGTCACGGTGAATACCCTCGGGCGGCTGAGCGACGAAGAGCAGTTCGGCGACATCATCGTCCGCACCGGCGCCGACGGCCAGGTGACGCGCCTGCGCGACGTCGCGCGGATCGAGATGGGCGGCGATGCCTATGCGCTGCGCAGCCTGCTGGACGGCGAGCCGGCGGTGGCCTTGCAGATCATCCAGAGCCCCGGAGCCAACGCGCTGGATACCGCCGAAGCGGTGCGTGCCACCGTGGCGAGGCTCGAAGGCAACTTCCCGGCCGGCCTGAGCGCGCGCATCGCCTACGACCCGACGGTGTTCGTCCGCGCTTCGTTGCAGACCGTGGCCACCACCCTGCTGGAGGCGATCCTGCTGGTCGTGGTGGTGGTGGTGCTGTTCCTGCGTAGCTGGCGTGCTTCGCTGATTCCGCTGATGGCCGTGCCGGTCTCGCTGGTCGGCACCTTCGCCGTCATGCACCTGATGGGTTTCTCGCTGAATACCCTGTCGTTGTTCGGCCTGGTGTTGTCGATCGGCATCGTCGTCGATGACGCCATCGTGGTGGTGGAAAACGTCGAGCGCCACATCGAGAACGGCGAGCCGCCGCTCCAGGCCGCGCGGCGTGCGATGGACGAGGTCACCGGGCCGATCATGGCGATCACCTCGGTGCTGGCGGCGGTGTTCATCCCCACGGCCTTTCTCAGTGGCCTGCAGGGCGAGTTCTATCGTCAGTTCGCCCTGACCATCGCCATCTCCACCATCCTGTCGGCGCTCAACTCGCTGACCCTCAGCCCGGCCCTGGCGGGCCTGCTGTTGCGTCCGCGGCCGGCCGGAGGTGCGGTGGCGGGGCGCTTCCAGCGACTGCTCCAGGTCCTCGGCCGACCGTTGCGAAATGCCCCCGAGGCCTACGGCAACGCGGTGCGCAAGGTGGTGCGGGTGAGCGGCCTGGCCCTGGTGGTGTATGGGGGCCTGCTTGGCCTGACCTGGGTCGGTTTCCAGGCGGTGCCGCCGGGCTTCGTGCCGATGCAGGACAAGTACTATCTGATCGGCATCGCCCAGTTGCCGAACGGAGCGTCGCTGGAGCGTACCGATGCGGTGGTCAGGCAGATGTCCCGGATCGGCCTCGACGAGCCGGGGGTGGAGAGCGTCGTGGCCTTCCCGGGCCTGTCGGTGAACGGTTTCGTCAACGTGCCGAACGCCGCGGTCATGTTCTTCATGCTCGATCCGTTCGAATCGCGCACCTCCGCCGATCTCGGCGCGCTGGCCATCGCCGGGCGCCTGCAAGCCAGGTTCGCCAGCATTCCCGACGGCTTCCTCGGGGTCTTCCCGCCGCCGCCGGTACCGGGGCTGGGAACCATCGGCGGCTTCAAGATGCAGGTCGAGGATCGCGGCGGCGCCGGGCTGGAAGCCCTGGCCAGGCAGACCCAGGTGCTGATGATGAAGGCCACTGAGTCCGGCCAGCTCGGGGGCTTGATGACCAGCTTCGATATCAATGCCCCGCAGCTCGAGGTGGTGGTCGACCGCACCAAGGTGAAGAGCCAGGGCGTTCGCCTGGCCGATGTGTTCGAGGCATTGCAGGTCTACCTCGGCTCGCTGTACATCAACGACTTCAACCGCTTCGGTCGCACCTACAAGGTCACTGCCCAGGCCGATGCGCCGCACCGCATGCAGGCCGAAGCCATCGGGCGCCTGCAGGTACGCAATGCCGCCGGGGCGATGTTGCCGCTGTCCTCGTTCGTCACCGTGACGCCCAGCTCCGGTCCCGACCGGGTGATCCACTACAACGGCTATCCGTCGGCGGATATCAGCGGCGGCGCGCTTCCCGGCGTCAGTTCGGGACAGGCGGTGGCGTTGATGGAGCGCCTGGCCGGCGAAGTGCTGCCCGAGGGCATGACCTTCGAATGGACCGACCTGACCTACCAGCAGAAGCTGGCCGGCAACAGCGCGCTGTTCATCTTCCCGCTGTGCGTGCTGCTGGCCTACCTGATCCTCGCCGCGCAGTACAACAGCTGGCTGTTGCCGCTGGCGGTCCTGCTGATCGTGCCGATGTGCCTGCTCAGCGCGATCGCCGGGGTGTGGCTGGTGGGCGGCGACAACAACGTGTTCGTCCAGATCGGGCTGGTGGTGCTGGTAGGCCTGGCGGCGAAGAACGCGATCCTGATCGTCGAGTTCGCCCGCACGCTGGAGGCCGAGGGCGCCCGTGCGCTGGAGGCGGTGGTCGAGGCTTGCCGCCTGCGCCTGCGGCCGATCCTGATGACCTCGCTGGCGTTCATCGCCGGCGTGGTGCCGTTGGTCATGGCCAGCGGCGCCGGAGCGGAAATGCGCCAGGCGATGGGCGTCGCGGTATTCGCCGGGATGCTCGGGGTGACGCTGTTCGGCCTGTTCCTCACGCCGGTGTTCTACGTACTGGTACGGGCACTGGCGGCGCGCCTGGAGCGACGCGCCGGCGGCAGCCTGGCGCATCTGGAGGGAGGCCGTCCATGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3003699","ARO_id":"40351","ARO_name":"mexQ","ARO_description":"MexQ is the inner membrane transporter of the multidrug efflux pump MexPQ-OpmE.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavin","category_aro_description":"Acriflavin is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36309":{"category_aro_accession":"3000170","category_aro_cvterm_id":"36309","category_aro_name":"imipenem","category_aro_description":"Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"37626":{"category_aro_accession":"3001227","category_aro_cvterm_id":"37626","category_aro_name":"kitasamycin","category_aro_description":"Kitasamycin is a macrolide antibiotic and is produced by Streptoverticillium kitasatoense. The drug has antimicrobial activity against a wide spectrum of pathogens.","category_aro_class_name":"Antibiotic"},"40353":{"category_aro_accession":"3003701","category_aro_cvterm_id":"40353","category_aro_name":"rokitamycin","category_aro_description":"Rokitamycin is a macrolide antibiotic. Synthesized from strains of Streptomyces kitasatoensis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36193":{"category_aro_accession":"3000054","category_aro_cvterm_id":"36193","category_aro_name":"acridine dye","category_aro_description":"Acridine dyes are cell permeable, basic molecules with an acridine chromophore. These compounds intercalate DNA. The image shown represents the core structure of the acridine family, with specific dyes containing varying substituents.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1450":{"model_id":"1450","model_name":"Escherichia coli parC conferring resistance to fluoroquinolone","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3972":"S80I","3973":"E84G"},"clinical":{"3972":"S80I","3973":"E84G"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1400"}},"model_sequences":{"sequence":{"4369":{"protein_sequence":{"accession":"AAC76055.1","sequence":"MSDMAERLALHEFTENAYLNYSMYVIMDRALPFIGDGLKPVQRRIVYAMSELGLNASAKFKKSARTVGDVLGKYHPHGDSACYEAMVLMAQPFSYRYPLVDGQGNWGAPDDPKSFAAMRYTESRLSKYSELLLSELGQGTADWVPNFDGTLQEPKMLPARLPNILLNGTTGIAVGMATDIPPHNLREVAQAAIALIDQPKTTLDQLLDIVQGPDYPTEAEIITSRAEIRKIYENGRGSVRMRAVWKKEDGAVVISALPHQVSGARVLEQIAAQMRNKKLPMVDDLRDESDHENPTRLVIVPRSNRVDMDQVMNHLFATTDLEKSYRINLNMIGLDGRPAVKNLLEILSEWLVFRRDTVRRRLNYRLEKVLKRLHILEGLLVAFLNIDEVIEIIRNEDEPKPALMSRFGLTETQAEAILELKLRHLAKLEEMKIRGEQSELEKERDQLQGILASERKMNNLLKKELQADAQAYGDDRRSPLQEREEAKAMSEHDMLPSEPVTIVLSQMGWVRSAKGHDIDAPGLNYKAGDSFKAAVKGKSNQPVVFVDSTGRSYAIDPITLPSARGQGEPLTGKLTLPPGATVDHMLMESDDQKLLMASDAGYGFVCTFNDLVARNRAGKALITLPENAHVMPPVVIEDASDMLLAITQAGRMLMFPVSDLPQLSKGKGNKIINIPSAEAARGEDGLAQLYVLPPQSTLTIHVGKRKIKLRPEELQKVTGERGRRGTLMRGLQRIDRVEIDSPRRASSGDSEE"},"dna_sequence":{"accession":"U00096","fmin":"3163714","fmax":"3165973","strand":"-","sequence":"TTACTCTTCGCTATCACCGCTGCTGGCACGGCGAGGAGAGTCGATCTCAACACGATCGATACGCTGCAAACCGCGCATCAACGTACCGCGGCGTCCACGTTCGCCAGTGACTTTCTGTAACTCTTCCGGGCGCAGTTTAATTTTGCGTTTCCCAACATGAATGGTCAGCGTGCTTTGCGGCGGCAGAACGTACAATTGCGCCAGACCATCTTCTCCACGCGCGGCTTCTGCCGATGGAATGTTGATAATCTTGTTGCCTTTGCCCTTCGACAGCTGCGGCAGATCACTTACCGGGAACATCAACATACGGCCTGCCTGAGTGATTGCCAGCAGCATATCGGAAGCATCTTCAATCACCACCGGCGGCATAACATGGGCATTTTCCGGTAAGGTGATCAAAGCCTTACCTGCACGGTTACGCGCCACCAGATCGTTAAAGGTGCAGACGAAACCGTAACCCGCATCGGAAGCCATCAGCAGTTTCTGATCGTCGCTTTCCATCAGCATATGGTCAACGGTCGCCCCAGGCGGCAACGTTAATTTGCCGGTGAGCGGCTCGCCCTGACCACGCGCCGACGGCAGCGTAATCGGGTCAATGGCATAGCTACGACCGGTGGAATCAACAAACACTACCGGTTGGTTGCTCTTACCTTTCACCGCCGCTTTGAAGCTATCACCCGCTTTATAATTCAGGCCCGGCGCGTCGATATCATGGCCTTTAGCGCTGCGTACCCAGCCCATCTGCGACAGCACAATGGTGACAGGTTCAGACGGCAGCATGTCGTGCTCGCTCATCGCTTTCGCTTCTTCGCGTTCCTGCAACGGCGAACGACGATCGTCACCGTAGGCTTGCGCGTCTGCCTGCAGTTCTTTCTTCAGCAGGTTATTCATTTTACGCTCGGAAGCCAAAATGCCCTGCAACTGGTCGCGCTCTTTTTCCAGTTCACTCTGCTCACCGCGAATCTTCATCTCTTCCAGTTTGGCAAGATGACGCAGTTTCAGTTCGAGGATCGCTTCCGCCTGGGTTTCCGTAAGGCCAAACCGCGACATCAGCGCCGGTTTCGGTTCATCTTCATTACGAATGATCTCAATCACTTCGTCGATATTGAGAAACGCCACCAGCAAACCTTCGAGGATATGCAGGCGCTTGAGGACTTTCTCCAGACGATAGTTCAGTCGGCGGCGCACGGTATCGCGGCGGAACACCAGCCATTCGGAGAGGATTTCCAGCAGGTTTTTCACCGCCGGACGACCATCCAGACCGATCATATTAAGGTTAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAAGAGGTGGTTCATCACCTGATCCATATCCACGCGGTTGGAACGCGGCACAATCACCAGGCGGGTCGGGTTCTCGTGGTCAGATTCATCGCGCAGATCGTCAACCATCGGCAGCTTTTTGTTGCGCATTTGCGCAGCAATTTGCTCCAGTACGCGCGCACCTGAAACCTGATGCGGCAATGCGCTGATAACCACCGCGCCATCTTCTTTCTTCCACACCGCGCGCATACGCACTGAACCACGTCCGTTCTCGTAGATTTTACGGATCTCGGCGCGCGAAGTGATAATTTCCGCTTCAGTCGGATAATCCGGCCCCTGCACGATATCCAGCAGCTGATCGAGCGTGGTTTTCGGCTGGTCGATTAATGCGATTGCCGCCTGAGCCACTTCACGCAGGTTATGCGGTGGAATATCGGTCGCCATGCCGACGGCAATACCGGTGGTGCCGTTAAGCAAAATGTTTGGCAGACGGGCAGGTAGCATTTTCGGCTCCTGCAAAGTGCCGTCGAAGTTTGGCACCCAGTCAGCCGTCCCCTGCCCCAGCTCGCTCAATAGCAGCTCGGAATATTTCGACAACCGGGATTCGGTGTAACGCATTGCCGCGAACGATTTCGGATCGTCCGGCGCGCCCCAGTTCCCCTGACCATCAACCAGCGGATAACGGTAAGAGAACGGTTGCGCCATCAGGACCATCGCTTCATAACAGGCGCTATCGCCGTGCGGATGGTATTTACCCAGTACGTCACCGACGGTACGGGCCGATTTTTTAAATTTGGCGCTGGCATTCAGGCCCAGTTCAGACATCGCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACATGGAGTAGTTTAAGTAGGCGTTTTCCGTAAATTCATGTAGCGCAAGGCGCTCTGCCATATCGCTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3003308","ARO_id":"39892","ARO_name":"Escherichia coli parC conferring resistance to fluoroquinolone","ARO_description":"Point mutation in Escherichia coli parC resulting in fluoroquinolone resistance","ARO_category":{"36913":{"category_aro_accession":"3000619","category_aro_cvterm_id":"36913","category_aro_name":"fluoroquinolone resistant parC","category_aro_description":"ParC is a subunit of topoisomerase IV, which decatenates and relaxes DNA to allow access to genes for transcription or translation. Point mutations in ParC prevent fluoroquinolone antibiotics from inhibiting DNA synthesis, and confer low-level resistance. Higher-level resistance results from both gyrA and parC mutations.","category_aro_class_name":"AMR Gene Family"},"40471":{"category_aro_accession":"3003786","category_aro_cvterm_id":"40471","category_aro_name":"fluoroquinolone self resistant parC","category_aro_description":"Inherent parC resistance to fluoroquinolone from an antibiotic producer. The presence of these genes confers self-resistance to the antibiotic it produces.","category_aro_class_name":"AMR Gene Family"},"35942":{"category_aro_accession":"0000023","category_aro_cvterm_id":"35942","category_aro_name":"enoxacin","category_aro_description":"Enoxacin belongs to a group called fluoroquinolones. Its mode of action depends upon blocking bacterial DNA replication by binding itself to DNA gyrase and causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37004":{"category_aro_accession":"3000660","category_aro_cvterm_id":"37004","category_aro_name":"lomefloxacin","category_aro_description":"Lomefloxacin is a difluoropiperazinyl quinolone, sharing similar activities with other fluoroquinolones. It is used to treat urinary tract infections. Relative to other fluoroquinolones, it has a longer half life and has higher serum concentrations.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"37008":{"category_aro_accession":"3000664","category_aro_cvterm_id":"37008","category_aro_name":"trovafloxacin","category_aro_description":"Trovafloxacin is a trifluoroquinalone with a broad spectrum of activity that acts by inhibiting the uncoiling of supercoiled DNA. While potent against many Gram-positive and Gram-negative bacteria, it is less active against pseudomonads and Cl. difficile. It is usually taken as the prodrug trovafloxacin mesylate or alatrofloxacin mesylate for oral or intravenous administration, respectively.","category_aro_class_name":"Antibiotic"},"37009":{"category_aro_accession":"3000665","category_aro_cvterm_id":"37009","category_aro_name":"grepafloxacin","category_aro_description":"Grepafloxacin is a broad-spectrum antibacterial quinoline. It is no longer taken due to its high toxicity.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"37142":{"category_aro_accession":"3000762","category_aro_cvterm_id":"37142","category_aro_name":"pefloxacin","category_aro_description":"Pefloxacin is structurally and functionally similar to norfloxacin. It is poorly active against mycobacteria, while anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2083":{"model_id":"2083","model_name":"Mycoplasma hominis parC conferring resistance to fluoroquinolone","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3977":"K134R","3978":"S80I"},"clinical":{"3977":"K134R","3978":"S80I"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1400"}},"model_sequences":{"sequence":{"3620":{"protein_sequence":{"accession":"AKJ52802.1","sequence":"MKKDRKEEIQEVTENIIEKNMADIMSDRFGRYSKYIIQQRAIPDARDGLKPVQRRILYSMWNLHLKNSEPFKKSARIVGDVIGRYHPHGDSSIYEALVRMAQDWKSNFPLIEMHGNKGSIDDDPAAAMRYTESRLEKISELMLRDLDRKVVKMAPNFDDSEYEPIVLPALFPNLLVNGAKGIAAGFATEIPPHNLGEVIDATIALIKNPTISIEELSEIVKGPDFPTGAIINGINEIKKALSSGQGRITISSKYHYVYDKKDESKIIGIEIIEIPFGVVKSKLVADIDAIAIDKKISGIKEVLDQTDRNGISIFIQLEDGANADAIIAYLMNKTELSISYSYNMVAIDNNRPVILNLYSALIAYLSHLKEVNINGINYDLKKFKLRLEIVEGFIKVAEISDEVIHLIKESDNSKKGVILALMNKFKFSELQATAIAELRLYKLSRMDQIEFQEEKKNLEIQIENCNKLLNDKWEFNQYLIKQLLEIKNQYSKPRLTEISDQKIDKEIDHKLLTKNEDFYLYITKDGYYKKISLKVYTSNELNTFKLKEEDNVFYFDKVNSLSKILFFTNLGNYFIIDCHLFKDCNWKDLGQHISSIVALESSEKIIRVIEITSFNSYANFILMSKLGYAKKVNLRDFENKSSLKTKTCMSFKDDNDELIDAQISNDEKMLFILLNNGMYHLVSENELKVGISLKARGIRLLLNLYKHPQLQVSGFITVSKYNNIIYLTQGGYIKCWDTSKLELTTRNTPKMLFTPLKNNILGLQSLAVTLSNLKMLYTDNNGNLAEYDWKFILKDKTKESKLLKLDYSFTNPGYFITPIKINELIEADEIEQEKIRQEYQGYIDKNIELTAEHALIKKSYDQDIQHLNNEEQEELFQISTEDIELPNVSNNVNDNQKDKKNIATKESVSQKIQEIEKIDLETIMQKIKQIKKK"},"dna_sequence":{"accession":"CP011538.1","fmin":"660262","fmax":"663064","strand":"-","sequence":"CTATTTTTTCTTAATTTGTTTAATTTTTTGCATTATTGTTTCAAGATCTATTTTTTCAATTTCTTGTATTTTCTGACTAACGCTTTCTTTTGTTGCTATATTTTTTTTATCTTTTTGGTTGTCATTAACATTATTTGAAACATTTGGTAATTCAATATCTTCTGTAGATATTTGAAATAGTTCTTCTTGTTCTTCATTATTTAAATGTTGAATATCTTGATCATAGGATTTTTTAATCAAAGCATGTTCAGCGGTCAATTCAATATTTTTATCAATATATCCTTGATATTCTTGTCTTATTTTTTCCTGCTCTATTTCATCAGCTTCAATTAATTCATTAATTTTTATTGGCGTAATAAAATACCCAGGGTTAGTAAATGAATAATCTAATTTAAGAAGTTTACTTTCCTTAGTCTTATCTTTTAATATAAATTTTCAATCATATTCTGCCAAATTACCATTATTATCAGTGTATAACATTTTTAAATTGCTCAATGTAACAGCAAGTGATTGAAGACCTAAAATATTATTTTTTAGTGGCGTAAACAACATTTTTGGAGTATTGCGTGTGGTCAATTCTAATTTGCTAGTATCCCAACATTTTATATAACCACCTTGCGTTAAATAAATTATATTGTTGTATTTTGAAACTGTTATAAAACCACTTACTTGAAGTTGAGGATGTTTATATAAGTTTAAAAGAAGTCTAATGCCTCTTGCTTTCAAAGAAATTCCAACCTTTAGTTCGTTTTCTGAAACTAAATGATACATACCATTATTTAGTAAAATAAATAGCATTTTTTCATCATTAGAAATTTGGGCATCTATTAATTCATCATTATCATCCTTAAACGACATGCAAGTTTTTGTTTTAAGAGAAGATTTATTTTCAAAATCTCTTAAATTAACTTTTTTGGCATATCCTAATTTTGACATTAAAATAAAGTTTGCATAACTATTGAATGACGTAATTTCTATAACTCTAATAATTTTTTCTGAGCTTTCTAGAGCTACTATTGATGAAATATGTTGACCAAGATCTTTTCAATTGCAATCTTTAAACAAATGGCAATCAATAATAAAATAATTCCCTAAATTTGTAAAGAATAATATCTTTGATAATGAGTTTACTTTATCAAAATAGAAAACATTATCTTCTTCTTTTAATTTGAATGTGTTTAATTCATTGCTAGTATAAACTTTTAAACTTATTTTTTTATAATATCCATCTTTGGTTATATATAAATAAAAATCTTCATTTTTTGTCAATAATTTATGATCAATTTCTTTATCGATTTTTTGATCTGAAATTTCCGTTAATCTTGGCTTTGAATATTGATTTTTTATTTCAAGCAATTGCTTTATTAAATATTGATTAAATTCTCATTTATCATTTAATAATTTATTGCAATTTTCAATTTGAATTTCAAGGTTTTTCTTTTCTTCTTGAAATTCGATTTGATCCATTCTTGAAAGCTTATACAATCTTAATTCAGCAATCGCTGTTGCTTGCAATTCACTAAATTTAAATTTATTCATCAATGCAAGGATAACACCTTTTTTTGAGTTATCGCTTTCTTTAATCAAATGTATAACTTCATCAGAAATTTCGGCTACTTTAATGAACCCTTCAACTATTTCTAGTCTCAATTTAAACTTCTTTAAATCATAATTAATACCATTTATATTAACTTCTTTTAAATGACTTAAATAAGCAATTAAGGCACTATAGAGATTCAAAATTACTGGACGGTTATTGTCAATTGCAACCATGTTATAACTATACGAGATGCTTAGTTCGGTTTTATTCATTAAGTATGCAATTATTGCGTCAGCATTTGCACCATCTTCTAATTGAATAAATATTGAAATTCCATTTCTATCTGTTTGGTCCAAAACTTCTTTAATACCAGAAATTTTTTTATCTATTGCAATTGCATCAATGTCGGCAACTAATTTTGATTTAACAACCCCAAAAGGAATTTCAATTATTTCAATACCAATAATTTTCGATTCATCTTTTTTATCATAAACGTAATGATATTTCGAAGAAATTGTAATTCTACCTTGCCCACTTGAAAGAGCTTTTTTTATTTCATTTATACCATTAATAATTGCTCCTGTTGGGAAATCTGGGCCTTTAACTATTTCACTTAATTCTTCAATTGATATTGTAGGATTTTTGATTAATGCAATTGTTGCATCAATAACTTCGCCTAGATTATGTGGTGGGATTTCTGTAGCAAAACCAGCAGCAATTCCTTTAGCACCGTTAACTAATAAATTAGGAAATAAGGCCGGCAAAACAATTGGTTCGTATTCAGAGTCATCAAAGTTTGGAGCCATTTTTACAACTTTTCTGTCTAAATCTCTCAACATCAGTTCACTAATTTTTTCAAGTCTTGATTCAGTGTAACGCATTGCAGCGGCAGGGTCATCATCAATTGAACCTTTATTACCATGCATTTCAATTAATGGGAAATTGCTTTTTCAATCTTGAGCCATTCTGACTAATGCCTCGTATATTGAACTATCTCCATGAGGGTGATAACGTCCGATAACATCCCCAACGATTCTAGCTGATTTTTTAAAAGGCTCGCTATTTTTTAAATGTAAATTTCACATTGAATATAAAATCCGACGTTGAACAGGTTTTAGTCCATCACGAGCATCAGGAATTGCTCTTTGTTGAATAATGTATTTTGAATAACGTCCGAATCTATCAGACATTATATCGGCCATATTTTTTTCAATAATGTTTTCAGTAACTTCTTGTATTTCTTCTTTTCTATCTTTTTTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40311","NCBI_taxonomy_name":"Mycoplasma hominis","NCBI_taxonomy_id":"2098"}}}},"ARO_accession":"3003310","ARO_id":"39894","ARO_name":"Mycoplasma hominis parC conferring resistance to fluoroquinolone","ARO_description":"Point mutation in Mycoplasma hominis parC resulting in fluoroquinolone resistance","ARO_category":{"36913":{"category_aro_accession":"3000619","category_aro_cvterm_id":"36913","category_aro_name":"fluoroquinolone resistant parC","category_aro_description":"ParC is a subunit of topoisomerase IV, which decatenates and relaxes DNA to allow access to genes for transcription or translation. Point mutations in ParC prevent fluoroquinolone antibiotics from inhibiting DNA synthesis, and confer low-level resistance. Higher-level resistance results from both gyrA and parC mutations.","category_aro_class_name":"AMR Gene Family"},"40471":{"category_aro_accession":"3003786","category_aro_cvterm_id":"40471","category_aro_name":"fluoroquinolone self resistant parC","category_aro_description":"Inherent parC resistance to fluoroquinolone from an antibiotic producer. The presence of these genes confers self-resistance to the antibiotic it produces.","category_aro_class_name":"AMR Gene Family"},"35942":{"category_aro_accession":"0000023","category_aro_cvterm_id":"35942","category_aro_name":"enoxacin","category_aro_description":"Enoxacin belongs to a group called fluoroquinolones. Its mode of action depends upon blocking bacterial DNA replication by binding itself to DNA gyrase and causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37004":{"category_aro_accession":"3000660","category_aro_cvterm_id":"37004","category_aro_name":"lomefloxacin","category_aro_description":"Lomefloxacin is a difluoropiperazinyl quinolone, sharing similar activities with other fluoroquinolones. It is used to treat urinary tract infections. Relative to other fluoroquinolones, it has a longer half life and has higher serum concentrations.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"37008":{"category_aro_accession":"3000664","category_aro_cvterm_id":"37008","category_aro_name":"trovafloxacin","category_aro_description":"Trovafloxacin is a trifluoroquinalone with a broad spectrum of activity that acts by inhibiting the uncoiling of supercoiled DNA. While potent against many Gram-positive and Gram-negative bacteria, it is less active against pseudomonads and Cl. difficile. It is usually taken as the prodrug trovafloxacin mesylate or alatrofloxacin mesylate for oral or intravenous administration, respectively.","category_aro_class_name":"Antibiotic"},"37009":{"category_aro_accession":"3000665","category_aro_cvterm_id":"37009","category_aro_name":"grepafloxacin","category_aro_description":"Grepafloxacin is a broad-spectrum antibacterial quinoline. It is no longer taken due to its high toxicity.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"37142":{"category_aro_accession":"3000762","category_aro_cvterm_id":"37142","category_aro_name":"pefloxacin","category_aro_description":"Pefloxacin is structurally and functionally similar to norfloxacin. It is poorly active against mycobacteria, while anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2075":{"model_id":"2075","model_name":"Salmonella enterica soxR with mutation conferring antibiotic resistance","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3900":"R20H","3901":"G121D"},"clinical":{"3900":"R20H","3901":"G121D"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"3574":{"protein_sequence":{"accession":"NP_458564.1","sequence":"MEKKSPRLKALLTPGEVAKRSGVAVSALHFYESKGLITSIRNSGNQRRYKRDVLRYVAIIKIAQRIGIPLATIGDAFGILPEGHTLSAKEWKQLSSQWREELDRRIHTLVALRDELDGCIGCGCLSRSDCPLRNPGDRLGEHGTGARLLEDD"},"dna_sequence":{"accession":"NC_003198.1","fmin":"4349504","fmax":"4349963","strand":"+","sequence":"ATGGAAAAAAAATCTCCCCGTTTAAAAGCCTTACTGACGCCGGGGGAAGTTGCGAAACGTAGCGGTGTTGCTGTGTCCGCCCTGCACTTCTATGAAAGCAAAGGGCTAATTACCAGTATCCGTAATAGCGGTAACCAACGGCGATACAAGCGTGACGTGTTGCGTTATGTCGCGATTATCAAGATTGCCCAGCGTATCGGCATCCCGCTGGCAACTATCGGCGACGCGTTTGGTATCTTGCCGGAAGGGCATACGTTAAGCGCGAAAGAGTGGAAGCAGCTCTCCTCGCAGTGGCGCGAAGAGTTAGACCGACGTATTCATACGCTGGTGGCGTTGCGCGATGAGCTGGACGGTTGTATCGGCTGCGGCTGTTTATCGCGTAGCGACTGTCCGCTGCGGAATCCAGGCGACAGGCTTGGCGAACACGGGACGGGCGCCCGGCTGCTTGAAGATGATTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35776","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhi str. CT18","NCBI_taxonomy_id":"220341"}}}},"ARO_accession":"3003382","ARO_id":"39966","ARO_name":"Salmonella enterica soxR with mutation conferring antibiotic resistance","ARO_description":"SoxR is a sensory protein that upregulates soxS expression in the presence of redox-cycling drugs. This stress response leads to the expression many multidrug efflux pumps.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2198":{"model_id":"2198","model_name":"Pseudomonas aeruginosa parE conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3149":"M437I","3150":"A473V"},"clinical":{"3149":"M437I","3150":"A473V"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"3386":{"protein_sequence":{"accession":"NP_253654.1","sequence":"MATYNADAIEVLSGLDPVRKRPGMYTDTTRPNHLAQEVIDNSVDEALAGHAKSVQVILHQDNSLEVIDDGRGMPVDIHPEEGVPGVELILTKLHAGGKFSNKNYQFSGGLHGVGISVVNALSTRVEVRVKRDANEYRMTFADGFKDSDLEVIGTVGKRNTGTSVHFWPDPKYFDSAKFSVSRLKHVLKAKAVLCPGLSVVFEDKNTGERVEWHFEDGLRSYLTDAVAELPRLPDEPFCGNLEGSKEAVSWALLWLPEGGESVQESYVNLIPTAQGGTHVNGLRQGLLDAMREFCEFRNLLPRGVKLAPEDVWERIAFVLSMKMQEPQFSGQTKERLSSREAAAFVSGVVKDAFSLWLNEHAEIGLQLAELAISNAGRRLKAGKKVERKKITQGPALPGKLADCAGQEPMRAELFLVEGDSAGGSAKQARDKEFQAIMPLRGKILNTWEVDGGEVLASQEVHDIAVAIGVDPGASDLAQLRYGKICILADADSDGLHIATLLCALFVRHFRPLVEAGHVYVAMPPLYRIDLGKDIYYALDEAERDGILERLAAEKKRGKPQVTRFKGLGEMNPLQLRETTMDPNTRRLVQLTLEDATGTLEIMDMLLAKKRAGDRKSWLESKGNLAEVLV"},"dna_sequence":{"accession":"NC_002516.2","fmin":"5576027","fmax":"5577917","strand":"-","sequence":"TCAGACCAGCACCTCGGCCAGGTTGCCCTTGCTTTCCAGCCAGGACTTGCGGTCACCGGCGCGCTTCTTGGCCAGCAGCATGTCCATGATCTCCAGGGTACCGGTGGCGTCCTCCAGGGTGAGCTGGACCAGCCGCCGGGTATTCGGATCCATGGTGGTCTCGCGCAGTTGCAACGGATTCATTTCGCCAAGGCCCTTGAAGCGGGTGACCTGCGGCTTGCCGCGCTTCTTCTCTGCGGCCAGGCGCTCGAGGATGCCGTCGCGCTCGGCTTCGTCGAGGGCGTAGTAGATGTCCTTGCCGAGGTCGATGCGGTACAGCGGCGGCATCGCCACGTAGACGTGGCCGGCTTCCACCAGCGGGCGGAAATGGCGGACGAACAGCGCGCAGAGCAGCGTGGCGATGTGCAGCCCGTCGGAGTCGGCATCCGCGAGGATACAGATCTTGCCGTAGCGCAGCTGGGCCAGGTCACTGGCACCCGGATCGACGCCGATGGCCACCGCGATGTCGTGGACCTCCTGGCTGGCGAGCACCTCGCCGCCGTCCACTTCCCAGGTGTTCAGGATCTTTCCGCGCAGCGGCATGATCGCCTGGAATTCCTTGTCCCGCGCCTGCTTCGCCGAGCCGCCGGCGGAGTCGCCCTCGACCAGGAACAGTTCCGCGCGCATCGGTTCCTGTCCGGCGCAGTCGGCCAGTTTGCCGGGCAGCGCCGGCCCCTGGGTGATCTTCTTGCGCTCGACCTTCTTGCCCGCCTTGAGGCGACGCCCGGCGTTGCTGATCGCCAGTTCCGCCAGTTGCAGGCCGATTTCGGCGTGCTCGTTGAGCCACAGGCTGAAGGCGTCCTTCACCACGCCCGAGACGAACGCCGCCGCCTCGCGGGACGACAGGCGCTCCTTGGTCTGCCCGGAGAACTGCGGCTCCTGCATCTTCATCGAGAGGACGAAGGCGATCCGCTCCCAGACGTCCTCGGGCGCCAGCTTGACGCCGCGCGGCAACAGGTTGCGGAACTCGCAGAACTCGCGCATGGCGTCGAGCAGGCCCTGGCGCAGGCCGTTCACATGGGTGCCGCCCTGGGCCGTGGGAATCAGGTTGACGTAGCTTTCCTGCACCGACTCACCGCCCTCGGGCAGCCACAGCAGGGCCCAGCTCACCGCTTCCTTGGAACCTTCGAGGTTGCCGCAGAAGGGTTCATCGGGCAGGCGCGGCAGCTCGGCGACCGCGTCGGTCAGGTAGGAGCGCAGGCCGTCCTCGAAGTGCCACTCGACGCGCTCGCCGGTGTTCTTGTCCTCGAACACCACGCTCAGGCCCGGGCACAGCACCGCCTTGGCCTTGAGCACATGCTTGAGGCGGCTGACCGAGAACTTCGCCGAATCGAAATACTTCGGATCCGGCCAGAAATGCACGCTGGTACCGGTATTGCGCTTGCCGACCGTGCCGATGACTTCCAGATCGCTGTCCTTGAAGCCGTCGGCGAAGGTCATCCGGTACTCGTTGGCGTCGCGCTTGACGCGTACCTCGACCCGGGTCGAGAGCGCGTTCACCACCGAGATGCCGACCCCGTGCAAGCCGCCGGAGAACTGGTAGTTCTTGTTCGAGAACTTGCCGCCGGCATGCAGCTTGGTAAGGATCAGCTCGACGCCCGGCACGCCCTCTTCCGGGTGGATGTCCACCGGCATGCCGCGGCCATCGTCGATGACTTCCAGCGAGTTGTCCTGGTGCAGGATCACCTGCACGCTCTTCGCATGGCCGGCCAGGGCTTCGTCGACGCTGTTGTCGATGACTTCCTGGGCCAGATGGTTGGGGCGGGTGGTGTCGGTGTACATCCCCGGGCGCTTGCGCACCGGGTCGAGGCCGGAAAGGACTTCGATGGCGTCTGCGTTGTAAGTAGCCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3003685","ARO_id":"40320","ARO_name":"Pseudomonas aeruginosa parE conferring resistance to fluoroquinolones","ARO_description":"Point mutation in Pseudomonas aeruginosa parE resulting in sensitivity to fluoroquinolones (ciprofloxacin). In combination with a gyrase mutation (gyrA or gyrB), it confers a high level of resistance to ciprofloxacin.","ARO_category":{"39897":{"category_aro_accession":"3003313","category_aro_cvterm_id":"39897","category_aro_name":"fluoroquinolone resistant parE","category_aro_description":"ParE is a subunit of topoisomerase IV, necessary for cell survival. Point mutations in ParE prevent fluoroquinolones from inhibiting DNA synthesis, thus conferring resistance.","category_aro_class_name":"AMR Gene Family"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2200":{"model_id":"2200","model_name":"APH(3')-VI","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"3387":{"protein_sequence":{"accession":"AGI04227.1","sequence":"MELPNIIQQFIGNSVLEPNKIGQSPSDVYSFNRNNETFFLKRSSTLYTETTYSVSREAKMLSWLSEKLKVPELIMTFQDEQFELMITKAINAKPISALFLTDQELLAIYKEALNLLNSVAIIDCPFISNIDHRLKESKFFIDNQLLDDIDQDDFDAELWGDHRTYLSLWNELTETRVEERLVFSHGDITDSNIFIDKFNEIYFLDLGRAGLADEFVDISFVERCLREDASEETAKIFLKHLKNDRPDKRNYFLKLDELN"},"dna_sequence":{"accession":"KC170992.1","fmin":"8362","fmax":"9142","strand":"+","sequence":"ATGGAATTGCCCAATATTATTCAACAATTTATTGGAAACAGCGTTTTAGAGCCAAATAAAATTGGTCAGTCGCCATCGGATGTTTATTCTTTTAATCGAAATAATGAAACTTTTTTTCTTAAGCGATCTAGCACTTTATATACAGAGACCACATACAGTGTCTCTCGCGAAGCGAAAATGTTGAGTTGGCTCTCTGAGAAATTAAAGGTGCCTGAACTCATCATGACTTTTCAGGATGAGCAGTTTGAATTAATGATCACTAAAGCGATCAATGCAAAACCAATTTCAGCGCTTTTTTTAACAGACCAAGAATTGCTTGCTATCTATAAGGAGGCACTCAATCTGTTAAATTCAGTTGCTATTATTGATTGTCCATTTATTTCAAACATTGATCATCGGTTAAAAGAGTCAAAATTTTTTATTGATAACCAACTCCTTGACGATATAGATCAAGATGATTTTGACGCTGAATTATGGGGAGACCATAGAACTTACCTAAGTCTATGGAATGAGTTAACTGAGACTCGTGTTGAAGAAAGATTGGTTTTTTCTCATGGCGATATCACGGATAGTAATATTTTTATAGATAAATTCAATGAAATTTACTTTTTAGATCTTGGCCGTGCTGGGTTAGCTGATGAATTTGTAGATATATCCTTTGTTGAACGTTGCCTAAGAGAGGATGCCTCGGAGGAAACTGCTAAAATATTTTTAAAGCATTTAAAAAATGATAGACCTGACAAAAGGAATTATTTTTTAAAACTTGATGAATTGAATTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3003687","ARO_id":"40322","ARO_name":"APH(3')-VI","ARO_description":"APH(3')-VI is an aminoglycoside phosphoryltransferase that acts on the 3-OH of target of aminoglycosides.","ARO_category":{"36265":{"category_aro_accession":"3000126","category_aro_cvterm_id":"36265","category_aro_name":"APH(3')","category_aro_description":"Phosphorylation of 2-deoxystreptamine aminoglycosides on the hydroxyl group at position 3'","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2203":{"model_id":"2203","model_name":"MCR-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"3390":{"protein_sequence":{"accession":"AKF16168","sequence":"MMQHTSVWYRRSVSPFVLVASVAVFLTATANLTFFDKISQTYPIADNLGFVLTIAVVLFGAMLLITTLLSSYRYVLKPVLILLLIMGAVTSYFTDTYGTVYDTTMLQNALQTDQAETKDLLNAAFIMRIIGLGVLPSLLVAFVKVDYPTWGKGLMRRLGLIVASLALILLPVVAFSSHYASFFRVHKPLRSYVNPIMPIYSVGKLASIEYKKASAPKDTIYHAKDAVQATKPDMRKPRLVVFVVGETARADHVSFNGYERDTFPQLAKIDGVTNFSNVTSCGTSTAYSVPCMFSYLGADEYDVDTAKYQENVLDTLDRLGVSILWRDNNSDSKGVMDKLPKAQFADYKSATNNAICNTNPYNECRDVGMLVGLDDFVAANNGKDMLIMLHQMGNHGPAYFKRYDEKFAKFTPVCEGNELAKCEHQSLINAYDNALLATDDFIAQSIQWLQTHSNAYDVSMLYVSDHGESLGENGVYLHGMPNAFAPKEQRSVPAFFWTDKQTGITPMATDTVLTHDAITPTLLKLFDVTADKVKDRTAFIR"},"dna_sequence":{"accession":"KP347127","fmin":"22412","fmax":"24038","strand":"+","sequence":"ATGATGCAGCATACTTCTGTGTGGTACCGACGCTCGGTCAGTCCGTTTGTTCTTGTGGCGAGTGTTGCCGTTTTCTTGACCGCGACCGCCAATCTTACCTTTTTTGATAAAATCAGCCAAACCTATCCCATCGCGGACAATCTCGGCTTTGTGCTGACGATCGCTGTCGTGCTCTTTGGCGCGATGCTACTGATCACCACGCTGTTATCATCGTATCGCTATGTGCTAAAGCCTGTGTTGATTTTGCTATTAATCATGGGCGCGGTGACCAGTTATTTTACTGACACTTATGGCACGGTCTATGATACGACCATGCTCCAAAATGCCCTACAGACCGACCAAGCCGAGACCAAGGATCTATTAAACGCAGCGTTTATCATGCGTATCATTGGTTTGGGTGTGCTACCAAGTTTGCTTGTGGCTTTTGTTAAGGTGGATTATCCGACTTGGGGCAAGGGTTTGATGCGCCGATTGGGCTTGATCGTGGCAAGTCTTGCGCTGATTTTACTGCCTGTGGTGGCGTTCAGCAGTCATTATGCCAGTTTCTTTCGCGTGCATAAGCCGCTGCGTAGCTATGTCAATCCGATCATGCCAATCTACTCGGTGGGTAAGCTTGCCAGTATTGAGTATAAAAAAGCCAGTGCGCCAAAAGATACCATTTATCACGCCAAAGACGCGGTACAAGCAACCAAGCCTGATATGCGTAAGCCACGCCTAGTGGTGTTCGTCGTCGGTGAGACGGCACGCGCCGATCATGTCAGCTTCAATGGCTATGAGCGCGATACTTTCCCACAGCTTGCCAAGATCGATGGCGTGACCAATTTTAGCAATGTCACATCGTGCGGCACATCGACGGCGTATTCTGTGCCGTGTATGTTCAGCTATCTGGGCGCGGATGAGTATGATGTCGATACCGCCAAATACCAAGAAAATGTGCTGGATACGCTGGATCGCTTGGGCGTAAGTATCTTGTGGCGTGATAATAATTCGGACTCAAAAGGCGTGATGGATAAGCTGCCAAAAGCGCAATTTGCCGATTATAAATCCGCGACCAACAACGCCATCTGCAACACCAATCCTTATAACGAATGCCGCGATGTCGGTATGCTCGTTGGCTTAGATGACTTTGTCGCTGCCAATAACGGCAAAGATATGCTGATCATGCTGCACCAAATGGGCAATCACGGGCCTGCGTATTTTAAGCGATATGATGAAAAGTTTGCCAAATTCACGCCAGTGTGTGAAGGTAATGAGCTTGCCAAGTGCGAACATCAGTCCTTGATCAATGCTTATGACAATGCCTTGCTTGCCACCGATGATTTCATCGCTCAAAGTATCCAGTGGCTGCAGACGCACAGCAATGCCTATGATGTCTCAATGCTGTATGTCAGCGATCATGGCGAAAGTCTGGGTGAGAACGGTGTCTATCTACATGGTATGCCAAATGCCTTTGCACCAAAAGAACAGCGCAGTGTGCCTGCATTTTTCTGGACGGATAAGCAAACTGGCATCACGCCAATGGCAACCGATACCGTCCTGACCCATGACGCGATCACGCCGACATTATTAAAGCTGTTTGATGTCACCGCGGACAAAGTCAAAGACCGCACCGCATTCATCCGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3003689","ARO_id":"40335","ARO_name":"MCR-1","ARO_description":"MCR-1 is a plasmid-borne phosphoethanolamine transferase that interferes with binding of colistin to the cell membrane via addition of phosphoethanolamine to lipid A, resulting reduction in negative charge of the cell membrane.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2202":{"model_id":"2202","model_name":"AAC(3)-Ib\/AAC(6')-Ib''","model_type":"protein domain meta-model","model_type_id":"40326","model_description":"A meta-model used to detect specific domains of proteins that confer resistance to antibiotic(s) relative to wild type. These models include reference sequences, a curated BLASTP cut-off for each of the genes, and directionality of the fused genes (if known).","model_param":{"40327":{"param_type":"domain order","param_description":"A parameter to describe the genes in a fusion protein. The parameter is defined by Cvterm IDs, separated by commas, with the ordering number preceding a colon. If the ordering of one or more parameters is unknown, it is designated as 0. Examples: 1:30003,2:30111 or 0:32224,0:33555","param_type_id":"40327","param_value":{"7702":"1:38930,2:38946"}}},"ARO_accession":"3002600","ARO_id":"39000","ARO_name":"AAC(3)-Ib\/AAC(6')-Ib''","ARO_description":"AAC(3)-Ib\/AAC(6')-Ib'' is an integron-encoded aminoglycoside acetyltransferase in P. aeruginosa","ARO_category":{"36461":{"category_aro_accession":"3000322","category_aro_cvterm_id":"36461","category_aro_name":"AAC(3)","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 3.","category_aro_class_name":"AMR Gene Family"},"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2204":{"model_id":"2204","model_name":"AAC(6')-IId","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"3392":{"protein_sequence":{"accession":"AGL46466.1","sequence":"MTEHDLAMLYEWLNRSHIVEWWGGEEARPTLADVQEQYLPSVLAQESVTPYIAMLNGEPIGYAQSYVALGSGDGWWEEETDPGVRGIDQSLANASQLGKGLGTKLVRALVELLFNDPEVTKIQTDPSPSNLRAIRCYEKAGFERQGTVTTPDGPAVYMVQTRQAFERTRSDA"},"dna_sequence":{"accession":"KC543497.1","fmin":"404932","fmax":"405451","strand":"+","sequence":"ATGACTGAGCATGACCTTGCGATGCTCTATGAGTGGCTAAATCGATCTCATATCGTCGAGTGGTGGGGCGGAGAAGAAGCACGCCCGACACTTGCTGACGTACAGGAACAGTACTTGCCAAGCGTTTTAGCGCAAGAGTCCGTCACTCCATACATTGCAATGCTGAATGGAGAGCCGATTGGGTATGCCCAGTCGTACGTTGCTCTTGGAAGCGGGGACGGATGGTGGGAAGAAGAAACCGATCCAGGAGTACGCGGAATAGACCAGTCACTGGCGAATGCATCACAACTGGGCAAAGGCTTGGGAACCAAGCTGGTTCGAGCTCTGGTTGAGTTGCTGTTCAATGATCCCGAGGTCACCAAGATCCAAACGGACCCGTCGCCGAGCAACTTGCGAGCGATCCGATGCTACGAGAAAGCGGGGTTTGAGAGGCAAGGTACCGTAACCACCCCAGATGGTCCAGCCGTGTACATGGTTCAAACACGCCAGGCATTCGAGCGAACACGCAGTGATGCCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40337","NCBI_taxonomy_name":"Pseudomonas aeruginosa PA96","NCBI_taxonomy_id":"1457392"}}}},"ARO_accession":"3002548","ARO_id":"38948","ARO_name":"AAC(6')-IId","ARO_description":"AAC(6')-IId is an integron-encoded aminoglycoside acetyltransferase in P. aeruginosa, E. cloacae, and C. freundii.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2205":{"model_id":"2205","model_name":"mexJ","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"690"}},"model_sequences":{"sequence":{"3399":{"protein_sequence":{"accession":"NP_252367.1","sequence":"MYRHIPLVALSLFSSLFLAACGNGTPPPAAARPAIVVQPQPAGEVSQAFPGEIRARHEPELAFRIGGKVIRRLVEVGERVKKDQPLAELDPQDVRLQLEAARAQVSAAEANLQTVRAEYRRYRTLLDRNLVSHSQFENIQNSYRAGEARLKQIRAEFNVADNQAGYAVLRSPQDGVIASRRVEVGQVVAAGQTVFSLAADGEREVLIGLPEHSFERFRIGQPVSVELWSQRDRRFAGHIRELSPAADPQSRTFAARVAFDDRATPAELGQSARVYVAAAEAVPLSVPLSALTAEAGQAFVWVVEPGSSTLRRQAVRTGPYAEDRVPVLEGLKAGDWVVATGVQVLREGQQVRPIDRANRTVKLAAKE"},"dna_sequence":{"accession":"NC_002516.2","fmin":"4119269","fmax":"4120373","strand":"-","sequence":"CTACTCCTTGGCCGCCAGTTTCACCGTGCGGTTGGCCCGGTCGATCGGACGCACCTGCTGCCCTTCGCGAAGCACCTGGACCCCGGTGGCCACCACCCAGTCGCCAGCCTTCAGGCCTTCGAGCACCGGCACCCGGTCCTCGGCATAGGGACCGGTGCGCACCGCCTGCCGGCGCAGGGTCGAGCTGCCCGGCTCGACCACCCAGACGAACGCCTGGCCGGCCTCTGCGGTCAGCGCCGACAAGGGAACCGATAACGGCACCGCCTCGGCGGCGGCGACGTAGACCCGCGCGCTCTGGCCCAGTTCGGCCGGAGTCGCGCGGTCGTCGAAGGCCACCCGGGCGGCGAAGGTACGCGATTGCGGATCGGCCGCGGGCGAGAGCTCGCGGATATGCCCGGCGAAGCGTCTGTCGCGTTGCGACCAGAGTTCGACCGACACCGGCTGGCCGATGCGGAAACGTTCGAAGCTGTGTTCCGGCAGGCCGATCAGCACCTCGCGTTCGCCGTCGGCGGCCAGGCTGAAGACCGTCTGTCCGGCCGCCACCACCTGGCCCACCTCGACGCGCCGGCTGGCGATCACGCCATCCTGGGGCGAGCGCAGCACGGCGTAGCCGGCCTGGTTGTCGGCGACGTTGAATTCGGCGCGGATCTGCTTCAGCCGCGCCTCGCCGGCGCGGTAGCTGTTCTGGATGTTCTCGAACTGGGAATGGCTGACCAGGTTGCGGTCGAGCAAGGTGCGGTAGCGCCGGTACTCGGCGCGCACGGTCTGCAAGTTGGCCTCGGCGGCACTGACCTGGGCCCGCGCCGCCTCCAGTTGCAGGCGCACGTCCTGGGGATCGAGTTCGGCCAGGGGCTGGTCCTTCTTTACCCGCTCGCCGACTTCCACCAGCCGGCGGATGACCTTGCCGCCGATGCGGAAGGCCAGCTCCGGCTCGTGGCGGGCGCGGATCTCGCCGGGAAAGGCCTGGCTCACCTCCCCCGCCGGCTGGGGCTGGACGACGATCGCCGGACGCGCCGCGGCTGGCGGCGGCGTGCCGTTGCCGCAGGCGGCGAGGAACAGGGAGGAAAACAGGGACAGGGCGACGAGCGGGATATGGCGGTACAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3003692","ARO_id":"40340","ARO_name":"MexJ","ARO_description":"mexJ is the membrane fusion protein of the MexJK multidrug efflux protein.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2206":{"model_id":"2206","model_name":"mexK","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1900"}},"model_sequences":{"sequence":{"3463":{"protein_sequence":{"accession":"AAG07064.1","sequence":"MSFNLSAWALQNRQIVLYLMILLGAVGALSYSKLGQSEDPPFTFKAMVVQTNWPGASAEEVARQVTERIEKKLMETGDYDRIVSFSRPGVSQVTFMAREDIHSSEIPELWYQIRKKISDIRATLPQSIQGPFFNDEFGTTYGNIYALTGKGFDYAVMKDYADRLQLQLQRIRNVGKVELIGLQDEKIWIDLSNTKLATLGLPLAAVQKALEEQNAVASSGFFETASDRVQLRVSGRFDSVEEIRDFPIRVGDRTFRIGDVAEVRRGFNDPPAPRMRFMGEDAIGLAVAMKPGGDILVLGKALETEFARLQQSLPAGLELRKVSDQPAAVRTGVGEFIRVLAEALVIVLLVSFFSLGLRTGLVVALSIPLVLAMTFAAMHYFGIGLHKISLGALVLALGLLVDDAIIAVEMMAVKMEQGYDRLKAASFAWTSTAFPMLTGTLITAAGFLPIATAQSGTGEYTRSLFQVVTIALVVSWFAAVVFVPYLGAKLLPDLARLHAQKHGGSADGYDPYATAFYQRFRRLVEWCVRYRKTVIVLTLAAFVGALLLFRLVPQQFFPPSARLELLLDIKLAEGASLRSTGEEVQRLEKMLQGHDGIDNYVAYVGTGSPRFYLPLDQQLPAASFAQVVVLAKDLESREALRKWLIERMNEDFPHLRSRISRLENGPPVGYPVQFRVSGEDIPQVRELARKVADKMRENPHVVNVHLDWEEPSKVVYLSIDQERARALGVSTASLSQFLQSALTGSHVSFFREDNELIEILLRGTEQERRDLSLLPSLAVPTENGRSVALSQIATLEYGFEEGIIWHRNRLPTVTVRADIYDDSLPATLVAQIAPTLEPIRAELPDGYLLEVGGTVEDAAKGQSSVNAGVPLFIVVVLSLLMVQLRSFSRMAMVFLTAPLGLIGVTLFLLLFRQPFGFVAMLGTIALAGMIMRNSVILVDQIEQDISHGLDRWHAIIEATVRRFRPIVLTALAAVLAMIPLSRSVFFGPMAVAIMGGLIVATVLTLLFLPALYAAWFRVKKDEARA"},"dna_sequence":{"accession":"AE004091.2","fmin":"4116187","fmax":"4119265","strand":"-","sequence":"TCAGGCCCGCGCCTCGTCCTTCTTCACGCGGAACCAGGCGGCATAGAGCGCCGGCAGGAACAGCAGGGTGAGCACGGTGGCGACGATCAGCCCGCCCATGATCGCCACCGCCATCGGCCCGAAGAACACGCTGCGCGACAGCGGGATCATCGCCAGCACCGCCGCCAGCGCGGTCAGCACGATGGGCCTGAAACGCCGCACGGTAGCCTCGATGATGGCGTGCCAGCGATCCAGTCCATGGCTGATGTCCTGTTCGATCTGGTCCACCAGGATCACCGAGTTGCGCATGATCATGCCGGCCAGGGCGATGGTCCCGAGCATCGCCACGAAGCCGAACGGCTGGCGGAACAGCAGCAGGAACAGGGTCACGCCGATCAGGCCCAGCGGTGCGGTGAGGAATACCATCGCCATCCGCGAGAAGCTGCGCAACTGCACCATCAGCAGGCTCAACACCACCACGATGAACAGCGGCACGCCGGCGTTCACCGAACTCTGGCCCTTCGCCGCGTCCTCCACCGTGCCGCCCACCTCCAGCAGGTAGCCGTCCGGCAACTCGGCGCGGATCGGTTCCAGGGTCGGGGCGATCTGCGCGACCAGGGTCGCCGGCAGCGAATCGTCGTAGATATCGGCGCGCACGGTGACCGTCGGCAGGCGGTTGCGGTGCCAGATGATGCCCTCTTCGAAGCCGTATTCGAGCGTAGCGATCTGCGACAGCGCCACGCTCCGGCCATTCTCGGTCGGCACCGCCAGGCTCGGCAGCAACGACAGGTCACGACGCTCCTGCTCGGTGCCGCGCAGGAGGATCTCGATCAGCTCGTTGTCTTCGCGGAAGAAGCTCACGTGCGAGCCGGTCAGCGCGCTCTGCAGGAACTGCGACAGGCTGGCGGTGCTCACCCCCAGGGCACGGGCGCGCTCCTGGTCGATGCTCAGGTACACCACCTTGCTCGGCTCTTCCCAATCCAGGTGCACATTCACCACGTGCGGGTTCTCGCGCATCTTGTCGGCGACCTTGCGCGCCAGTTCGCGAACCTGCGGGATGTCCTCGCCGGAAACCCGGAACTGCACCGGATAGCCCACCGGCGGCCCGTTCTCCAGGCGACTGATGCGGCTGCGCAGGTGCGGGAAGTCCTCGTTCATCCGCTCGATCAGCCACTTGCGCAGCGCCTCGCGGCTCTCCAGGTCCTTGGCCAGCACCACCACCTGGGCGAAGCTGGCCGCCGGCAATTGCTGGTCCAGCGGCAGGTAGAAGCGGGGCGAGCCGGTGCCGACGTAGGCCACGTAGTTGTCGATGCCGTCATGGCCCTGCAGCATTTTTTCCAGGCGCTGGACTTCCTCGCCGGTAGAGCGCAGTGAGGCACCCTCCGCCAGCTTGATGTCCAGCAGCAGCTCCAGGCGCGCCGAGGGCGGGAAGAACTGCTGCGGCACCAGGCGGAACAGCAGCAGCGCGCCGACGAAGGCCGCGAGAGTCAGGACGATCACCGTCTTGCGGTAGCGCACGCACCACTCCACCAGACGCCGGAAGCGCTGGTAGAAGGCCGTAGCATAGGGATCGTAGCCATCGGCGCTGCCGCCGTGCTTCTGCGCGTGCAACCTGGCCAGGTCCGGCAGCAGCTTGGCCCCCAGGTAGGGAACGAAGACCACCGCGGCGAACCAGGAGACCACCAGGGCGATGGTCACCACCTGGAACAACGAGCGGGTGTATTCGCCGGTGCCGGACTGCGCGGTGGCGATCGGCAGGAAGCCGGCGGCGGTGATCAGGGTGCCGGTGAGCATCGGGAAGGCGGTGCTGGTCCAGGCGAAGCTGGCCGCCTTGAGGCGGTCGTAGCCCTGCTCCATCTTCACCGCCATCATCTCCACCGCGATGATCGCGTCGTCCACCAGTAATCCCAGCGCCAGCACCAGGGCGCCGAGGGAGATCTTGTGCAGGCCGATGCCGAAGTAATGCATGGCGGCGAAGGTCATCGCCAGCACCAGCGGGATCGACAGCGCCACCACCAGGCCGGTGCGCAGGCCGAGGGAGAAGAAGCTCACCAGCAGGACGATCACCAGCGCCTCGGCCAGCACCCGGATGAACTCGCCGACCCCGGTACGTACCGCCGCCGGCTGGTCGGACACCTTGCGCAGTTCCAGTCCGGCCGGCAGCGACTGCTGCAGGCGGGCGAACTCGGTTTCCAGGGCCTTGCCCAGCACCAGGATGTCGCCGCCCGGCTTCATCGCTACCGCCAGGCCGATGGCGTCCTCGCCCATGAAGCGCATGCGCGGCGCCGGCGGATCGTTGAAGCCGCGGCGAACCTCGGCCACGTCGCCGATGCGGAAGGTGCGGTCGCCGACGCGGATGGGGAAGTCGCGGATCTCCTCCACCGAATCGAAACGCCCGGAAACGCGCAACTGCACGCGGTCGCTGGCGGTCTCGAAGAACCCGGAGGAGGCCACCGCGTTCTGTTCCTCCAGCGCCTTCTGTACCGCCGCCAGGGGCAGGCCGAGGGTGGCCAGCTTGGTGTTGGACAGGTCGATCCAGATCTTCTCGTCCTGCAGGCCGATCAGCTCGACCTTGCCGACGTTCCTGATCCGCTGCAATTGCAGTTGCAGGCGGTCGGCATAGTCCTTCATCACCGCGTAGTCGAAGCCCTTGCCGGTGAGCGCATAGATGTTGCCGTAGGTGGTGCCGAACTCGTCGTTGAAGAACGGGCCCTGGATGCTTTGCGGCAAGGTGGCGCGAATGTCGCTGATCTTCTTGCGGATCTGGTACCAGAGTTCGGGGATCTCGCTGGAATGGATGTCCTCGCGGGCCATGAAGGTCACCTGCGAGACGCCGGGGCGGGAGAAGGACACGATGCGATCGTAGTCGCCGGTTTCCATCAGCTTCTTCTCGATACGCTCGGTGACCTGCCGGGCCACCTCTTCGGCGCTGGCGCCCGGCCAGTTGGTCTGCACCACCATGGCCTTGAAGGTGAACGGCGGGTCTTCGCTCTGCCCCAGCTTGCTGTAGGACAGCGCGCCGACCGCGCCAAGCAGGATCATCAGGTACAGGACGATCTGGCGATTCTGCAACGCCCAGGCGGAAAGGTTGAAGGACAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3003693","ARO_id":"40341","ARO_name":"MexK","ARO_description":"mexK is the inner membrane resistance-nodulation-cell division (RND) transporter in the MexJK multidrug efflux protein.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2207":{"model_id":"2207","model_name":"mexV","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"650"}},"model_sequences":{"sequence":{"3464":{"protein_sequence":{"accession":"AAG07762.1","sequence":"MLLRRMLIMLAAVIAVVAILAGYKVYSIRQQIALFSAPKPPISVTASLAEKRPWQSRLPAIGSLKAFQGVTLTAEVSGTVRDVLFLSGDQVKLDQPLIQLESDVEEATLRTAEADLGLARAEYQRGRELIGSKAISKSEFDRLAAQWAKTSATVAELKAALAKKRVLAPFAGTIGIRQVDVGDYVSPGTPIATLQDLSTLLLDFHLPEQDFPLLSRGQLVKVRVAAYPAQVFDAEIAAINPKVDNETRNLQVRAALENPDGKLLPGMFANLEVMLPGEEQRVVVPETAITFTLYGDSIYVVGQKKDEQGQVSKDDKGQPQQVVERRFVRIGERREGLAVVLEGLEGGEQVVTSGQLKLDNGAAVAIVAERDLQQEH"},"dna_sequence":{"accession":"AE004091.2","fmin":"4903465","fmax":"4904596","strand":"+","sequence":"ATGTTGCTCCGCCGCATGTTGATCATGCTCGCCGCGGTGATCGCCGTGGTGGCGATTCTCGCCGGCTACAAGGTCTACTCCATCCGTCAGCAGATCGCCCTTTTCAGCGCACCGAAACCGCCGATCAGCGTGACCGCCAGCCTGGCCGAAAAGCGTCCCTGGCAGAGCCGCCTGCCAGCCATCGGCAGCCTCAAGGCATTCCAGGGCGTGACCCTCACCGCCGAAGTCTCCGGCACGGTACGCGACGTACTGTTCCTTTCCGGCGACCAGGTGAAGCTGGACCAACCGCTGATCCAGTTGGAAAGCGACGTCGAGGAAGCCACCCTGCGCACTGCCGAGGCCGATCTCGGCCTGGCCAGGGCCGAGTACCAGCGCGGCCGCGAACTGATCGGCAGCAAGGCCATCTCGAAAAGCGAATTCGATCGTCTCGCCGCGCAGTGGGCCAAGACCAGCGCCACCGTCGCCGAGCTGAAGGCGGCGCTGGCGAAGAAGCGCGTGCTCGCGCCCTTCGCCGGGACCATCGGCATCCGCCAGGTGGACGTCGGCGACTACGTCTCGCCCGGGACGCCGATCGCCACCTTGCAGGACCTTTCCACCCTGCTCCTGGATTTCCACCTGCCCGAGCAGGACTTCCCCCTGCTCAGCCGCGGCCAACTGGTGAAGGTCCGGGTCGCCGCCTACCCCGCCCAGGTGTTCGACGCCGAGATCGCCGCCATCAACCCCAAGGTCGACAACGAGACCCGCAACCTGCAGGTCCGCGCTGCCCTGGAGAACCCGGACGGCAAGCTGCTGCCGGGCATGTTCGCCAACCTCGAGGTGATGTTGCCTGGCGAGGAACAACGCGTCGTGGTCCCGGAGACGGCGATCACCTTCACCCTCTACGGCGACTCGATCTACGTCGTCGGGCAGAAGAAGGACGAGCAGGGCCAGGTGTCGAAGGATGACAAGGGCCAGCCGCAACAGGTCGTCGAGCGCCGCTTCGTCAGGATCGGCGAACGCCGCGAAGGCCTGGCGGTGGTGCTCGAAGGCCTTGAGGGCGGCGAGCAGGTAGTGACTTCCGGGCAACTGAAGCTCGACAACGGCGCCGCGGTGGCCATCGTCGCCGAGCGGGACCTCCAGCAAGAGCACTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3003030","ARO_id":"39464","ARO_name":"MexV","ARO_description":"MexV is the membrane fusion protein of the MexVW-OprM multidrug efflux complex.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavin","category_aro_description":"Acriflavin is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36193":{"category_aro_accession":"3000054","category_aro_cvterm_id":"36193","category_aro_name":"acridine dye","category_aro_description":"Acridine dyes are cell permeable, basic molecules with an acridine chromophore. These compounds intercalate DNA. The image shown represents the core structure of the acridine family, with specific dyes containing varying substituents.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2208":{"model_id":"2208","model_name":"mexW","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1900"}},"model_sequences":{"sequence":{"3462":{"protein_sequence":{"accession":"AAG07763.1","sequence":"MAFTDPFIRRPVLASVVSLLIVLLGMQAFSKLVIREYPQMENALITVTTLYAGANAETIQGYITQPLQQSLASAEGIDYMTSVSRQNYSTISIYARIGANTDRLVTELLAKSNEVKSQLPPDAEDPVLQKEAADASALMYISFYSEQMNNPQITDYLSRVIQPKLATLPGIAEAEILGNQVFAMRLWLDPVKMAAFGVTAGEINQAVQQYNFLAAAGEVKGQLVVTSVNASTDLKSPQAFAAIPVKTDGDRRVLMGDVARVELGAASYDAISSFNGIPSVYIGIKGTPSANPLDVIKEVRAKMPELEEQLPPNLKVSIAYDATRFIQASIDEVVKTLGEAVLIVIVVVFLFLGAFRSVLIPVVTIPLSMIGVLFFMQAMGYSINLLTLLAMVLAIGLVVDDAIVVVENIHRHIEEGKPPFEAALEGAREIAVPVVSMTITLAAVYAPIGFLTGLTGALFKEFAFTLAGAVIISGIVALTLSPMMCSRLLRHEENPSGLAHRLDLIFEGLKQRYQRALHGTLDTRPVVLVFAVLVLALIPVLLMFTKKELAPEEDQGIVFLMTNSPQTANLDYLNRYTAEFEGIFRSFPEYYSAFQINGYNGVQAGIGGMLLKPWDEREKSQMELLHAVQAKLNEIPGVQIFAFNLPSLPGTGEGLPFQFVLNTANDYESLLQVAQRVKQRASESGKFAFLDLDLAFDKPELVVDIDREKAAQMGVSMQDLGVALASLLGEGEINRFTIDGRSYKVIAQVERPYRDNPGWLGSYYVKSRNGQLVALSTLIETHERARPRQLNQFQQLNSAIISGFPIVSMGEAIETVQQIAREEAPRGFAVDYAGASRQYVQEGSALLVTFGLALAIIFLVLAAQFESFRDPLVIMVTVPLSICGALIPLFLGVSSLNIYTQVGLVTLIGLISKHGILIVEFANQLRHEQGLGRREAIEQAAAIRLRPVLMTTAAMVLGVIPLILATGAGAVSRFDIGIVIATGMSVGTLFTLFVLPCIYTLVARPDAPPGVTQAANAH"},"dna_sequence":{"accession":"NC_002516.2","fmin":"4904646","fmax":"4907703","strand":"+","sequence":"ATGGCTTTTACCGATCCGTTCATCCGTCGTCCGGTCCTGGCGAGCGTGGTCAGCCTGCTGATCGTCCTGCTCGGCATGCAGGCCTTCAGCAAGCTGGTGATCCGCGAGTATCCGCAAATGGAGAACGCGCTGATCACGGTGACCACGCTCTACGCCGGCGCCAACGCGGAAACCATCCAGGGCTACATCACCCAGCCGCTGCAGCAGAGCCTGGCCAGCGCCGAAGGCATCGACTACATGACCTCGGTGAGCCGGCAGAACTATTCGACCATCTCCATCTACGCGCGGATCGGCGCCAATACCGATCGCCTGGTCACCGAGCTGCTGGCCAAGTCCAACGAAGTGAAGAGCCAGCTGCCGCCGGACGCCGAGGACCCGGTGCTGCAGAAGGAGGCCGCGGACGCCTCGGCGCTGATGTACATCAGCTTCTACAGCGAGCAGATGAACAACCCGCAGATCACCGACTACCTGTCGCGGGTGATCCAGCCCAAGCTGGCGACCCTGCCCGGTATCGCCGAGGCGGAGATCCTCGGCAACCAGGTGTTCGCCATGCGCCTGTGGCTGGACCCGGTGAAGATGGCCGCGTTCGGCGTCACCGCCGGCGAGATCAACCAGGCGGTGCAGCAGTACAACTTCCTCGCCGCCGCCGGCGAGGTGAAGGGCCAGTTGGTGGTCACCAGCGTCAATGCTTCCACCGACCTCAAGTCGCCCCAGGCCTTCGCCGCCATCCCGGTGAAGACCGACGGCGACCGCCGGGTGCTGATGGGTGATGTCGCACGGGTCGAACTGGGCGCCGCCAGCTACGACGCGATCAGTTCGTTCAATGGGATTCCCTCGGTCTACATCGGCATCAAGGGCACGCCCAGCGCCAACCCGCTGGACGTGATCAAGGAAGTGCGGGCGAAGATGCCCGAACTGGAAGAGCAATTGCCGCCCAACCTCAAGGTGTCCATCGCCTACGACGCCACGCGCTTCATTCAGGCCTCCATCGATGAAGTGGTGAAGACCCTCGGCGAGGCGGTGCTGATCGTCATCGTGGTGGTGTTCCTGTTCCTCGGCGCGTTCCGTTCGGTACTGATCCCGGTGGTGACCATTCCGCTGTCGATGATCGGCGTATTGTTCTTCATGCAGGCCATGGGCTACTCGATCAACCTGCTGACCCTGCTGGCGATGGTCCTGGCCATCGGCCTGGTGGTGGACGACGCGATCGTGGTGGTGGAAAACATCCACCGCCACATCGAGGAGGGCAAGCCGCCCTTCGAGGCTGCCCTGGAGGGCGCGCGGGAGATCGCCGTACCGGTGGTCAGCATGACCATCACCCTCGCCGCGGTCTACGCGCCGATCGGCTTCCTCACCGGCCTCACCGGCGCCCTGTTCAAGGAGTTCGCCTTCACCCTGGCCGGCGCGGTGATCATTTCCGGGATCGTCGCCCTGACCCTGTCGCCGATGATGTGCTCGCGCCTGTTGCGCCACGAGGAGAATCCCTCGGGCCTGGCGCATCGCCTCGACCTGATCTTCGAGGGCCTGAAGCAACGCTACCAGCGCGCCCTCCACGGCACCCTGGACACCCGTCCGGTGGTCCTGGTGTTCGCCGTGCTGGTACTGGCGCTGATCCCGGTACTGCTGATGTTCACCAAGAAGGAGCTGGCGCCGGAAGAGGACCAGGGCATCGTGTTCCTCATGACCAACTCGCCGCAAACCGCCAACCTCGACTACCTGAATCGCTACACCGCCGAGTTCGAAGGCATCTTCCGCAGCTTCCCGGAGTATTACTCGGCGTTCCAGATCAACGGCTACAACGGCGTCCAGGCCGGCATCGGCGGCATGCTGCTCAAGCCCTGGGACGAACGCGAAAAGAGCCAGATGGAATTGCTCCATGCGGTGCAGGCGAAGCTCAACGAGATTCCCGGCGTGCAGATCTTCGCCTTCAACCTGCCGTCGCTACCGGGCACCGGCGAGGGCCTGCCATTCCAGTTCGTGCTCAACACCGCCAACGACTACGAGTCGCTGCTGCAAGTGGCGCAACGGGTGAAGCAGCGCGCCAGCGAGTCCGGCAAGTTCGCCTTCCTCGATCTCGACCTGGCGTTCGACAAACCCGAGCTGGTGGTCGACATCGACCGCGAGAAGGCCGCGCAGATGGGCGTCTCCATGCAGGACCTGGGGGTGGCGCTGGCCAGCCTGCTCGGCGAGGGCGAGATCAACCGCTTCACCATCGACGGGCGCAGCTACAAGGTCATCGCCCAGGTCGAACGCCCCTATCGCGACAATCCCGGCTGGCTCGGCAGCTACTACGTGAAGAGCCGCAACGGCCAACTGGTCGCCCTCTCGACCCTGATCGAGACCCACGAACGGGCACGGCCACGGCAACTGAACCAGTTCCAGCAGCTCAACTCGGCGATCATCTCCGGCTTCCCCATCGTCAGCATGGGCGAGGCCATCGAGACGGTTCAGCAGATCGCCCGCGAGGAAGCCCCGCGTGGCTTCGCCGTCGACTACGCCGGCGCTTCCCGGCAATACGTGCAGGAAGGCAGCGCATTGCTGGTCACCTTCGGACTGGCCCTGGCGATCATCTTCCTGGTCCTCGCCGCACAGTTCGAAAGCTTCCGCGATCCGCTGGTGATCATGGTCACCGTGCCGCTGTCGATCTGCGGTGCGCTGATACCGCTGTTCCTCGGCGTGTCGAGCCTGAACATCTATACCCAGGTCGGCCTGGTGACCCTGATCGGCCTGATCAGCAAACACGGCATCCTGATCGTCGAGTTCGCCAACCAGTTGCGCCACGAACAGGGGCTGGGGCGTCGCGAGGCCATCGAGCAGGCCGCCGCGATCCGCCTGCGGCCAGTACTGATGACCACCGCGGCGATGGTGCTCGGGGTGATCCCGCTGATCCTCGCCACCGGCGCCGGGGCGGTCAGTCGCTTCGACATCGGCATCGTGATCGCGACCGGCATGTCGGTGGGCACCCTCTTCACCCTGTTCGTCCTGCCGTGCATCTACACCCTGGTGGCCAGGCCGGATGCCCCGCCAGGCGTGACGCAAGCGGCAAACGCACACTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3003031","ARO_id":"39465","ARO_name":"MexW","ARO_description":"MexW is the RND-type membrane protein of the efflux complex MexVW-OprM.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavin","category_aro_description":"Acriflavin is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36193":{"category_aro_accession":"3000054","category_aro_cvterm_id":"36193","category_aro_name":"acridine dye","category_aro_description":"Acridine dyes are cell permeable, basic molecules with an acridine chromophore. These compounds intercalate DNA. The image shown represents the core structure of the acridine family, with specific dyes containing varying substituents.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2213":{"model_id":"2213","model_name":"opmE","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"850"}},"model_sequences":{"sequence":{"3407":{"protein_sequence":{"accession":"BAE06009.1","sequence":"MKPYLRSSLSALILLGGCAAVGPDYAPPSASAPASFGAMPAGIDGSGVEIEWWRGFDEPALESLIQRALAANLDIALAGARLDEAKALLRENREEFLPRGGPAFDYQARRRGEVETPAGQQRDIETYRGALDASWEIDLFGRVRRSVEAAEAQAGSREALLRNVQASVAATVAMSWFQLQGIEAELAVVHDIAGNQRDSLEMVERLVSAGSAHEFDRLRAEALLHNVEAAVPDLERRRAATRNALAVLLAEAPQAFSPPVARASGERLTLRTLGVGDPAGLLARRADIAAAERNLAAATARIGVETAGLYPQVEVRGSIGLVAGNLDALDESGTSFNVLNPVIRWALLDRGRVWARIAASEARAQEALILYDRTVLRALQETDDAFNGYGAAADRLRLRLLEATANREAARLARERFVQGDGEYLDVLEAERSDYLSRRALSIARTEQRLAVVGIYKALGGGWEACAGARRCGVATDDTSPGVARQRDSRS"},"dna_sequence":{"accession":"AB219524.1","fmin":"4334","fmax":"5810","strand":"+","sequence":"ATGAAGCCATACCTGCGGTCTTCGTTGAGCGCGCTGATCCTGCTGGGCGGCTGTGCCGCGGTGGGGCCCGACTATGCGCCGCCGAGCGCGTCCGCACCGGCCAGCTTCGGCGCGATGCCGGCGGGTATCGATGGCAGTGGCGTGGAGATCGAGTGGTGGCGCGGGTTCGACGAGCCAGCCCTGGAGTCTCTGATCCAGCGGGCGCTCGCGGCGAACCTCGACATCGCCCTTGCCGGCGCGCGCCTGGACGAAGCGAAGGCGCTGCTGCGCGAGAACCGCGAAGAGTTCCTGCCGCGCGGCGGCCCGGCGTTCGATTACCAGGCCCGGCGGCGCGGCGAGGTGGAAACACCGGCCGGCCAGCAGCGCGACATCGAGACCTATCGCGGCGCGCTGGATGCTTCCTGGGAAATCGACCTGTTCGGCCGGGTGCGGCGCTCGGTGGAGGCCGCCGAGGCGCAGGCGGGCTCGCGCGAGGCCCTGCTGCGCAACGTGCAGGCGAGCGTCGCGGCTACGGTTGCCATGTCCTGGTTCCAGCTACAGGGCATCGAGGCCGAACTTGCGGTGGTCCATGACATCGCCGGCAACCAGCGCGACAGCCTGGAGATGGTCGAACGCCTGGTCAGCGCCGGCTCCGCCCACGAGTTCGACCGGTTGCGCGCCGAAGCGTTATTGCACAACGTCGAGGCGGCCGTGCCCGACCTCGAACGGCGCCGCGCCGCCACCCGCAATGCGCTGGCCGTTCTCCTCGCGGAAGCCCCGCAGGCCTTCAGCCCGCCGGTCGCCCGTGCCTCCGGGGAAAGGCTGACGCTCCGCACCCTCGGGGTCGGCGACCCGGCGGGACTGCTGGCGCGTCGCGCTGACATCGCCGCGGCCGAACGCAACCTGGCGGCCGCGACCGCACGTATCGGCGTCGAGACCGCGGGGCTGTATCCGCAGGTCGAGGTACGCGGCTCGATCGGCCTGGTCGCCGGCAATCTCGATGCTTTGGACGAGAGTGGTACGTCCTTCAACGTCCTGAACCCGGTGATTCGCTGGGCGTTACTCGACCGCGGTCGCGTGTGGGCGCGGATCGCCGCCAGCGAAGCCCGTGCGCAGGAGGCATTGATCCTCTACGACCGGACGGTACTGCGCGCCCTGCAGGAGACCGATGATGCCTTCAACGGCTATGGCGCTGCCGCTGACAGGCTCCGCCTGCGCCTGCTCGAGGCGACGGCCAATCGCGAGGCGGCGCGCCTGGCCCGGGAGCGCTTCGTCCAGGGGGACGGCGAGTACCTGGACGTGCTCGAGGCGGAACGCTCGGACTACCTCAGCCGGCGCGCATTGAGCATCGCGCGCACCGAGCAGCGCCTTGCCGTCGTGGGTATCTACAAGGCGCTGGGGGGTGGCTGGGAGGCCTGCGCGGGGGCGCGGCGCTGTGGCGTGGCTACCGACGATACCTCTCCAGGCGTGGCACGGCAGCGCGACAGTCGCTCCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3003700","ARO_id":"40352","ARO_name":"opmE","ARO_description":"opmE is an outer membrane factor protein that is part of the multidrug efflux pump MexPQ-OpmE.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavin","category_aro_description":"Acriflavin is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36309":{"category_aro_accession":"3000170","category_aro_cvterm_id":"36309","category_aro_name":"imipenem","category_aro_description":"Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"37626":{"category_aro_accession":"3001227","category_aro_cvterm_id":"37626","category_aro_name":"kitasamycin","category_aro_description":"Kitasamycin is a macrolide antibiotic and is produced by Streptoverticillium kitasatoense. The drug has antimicrobial activity against a wide spectrum of pathogens.","category_aro_class_name":"Antibiotic"},"40353":{"category_aro_accession":"3003701","category_aro_cvterm_id":"40353","category_aro_name":"rokitamycin","category_aro_description":"Rokitamycin is a macrolide antibiotic. Synthesized from strains of Streptomyces kitasatoensis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36193":{"category_aro_accession":"3000054","category_aro_cvterm_id":"36193","category_aro_name":"acridine dye","category_aro_description":"Acridine dyes are cell permeable, basic molecules with an acridine chromophore. These compounds intercalate DNA. The image shown represents the core structure of the acridine family, with specific dyes containing varying substituents.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2216":{"model_id":"2216","model_name":"mexM","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"650"}},"model_sequences":{"sequence":{"3409":{"protein_sequence":{"accession":"BAE06005.1","sequence":"MQALRSGGGRVLVGVLAAGLVAFGGWAWLGGDAGAKAAPAPARVPVIVARVERRDVEQQVSGIGTVTSLHNVVIRTQIDGQLTRLLVSEGQMVEAGELLATIDDRAVVAALEQAQASRASNQAQLKSAEQDLQRYRSLYAERAVSRQLLDQQQATVDQLRATLKANDATINAERVRLSYTRITSPVSGKVGIRNVDVGNLVRVGDSLGLFSVTQIAPISVVFSLQQEQLLQLQALLGGEAAVRAYSRDGGSALGEGRLLTIDNQIDSSTGTIRVRASFDNRQARLWPGQFVAVSLHTGVRRDQLVLSSKAVRRGLEGNFVYRVADDRVEAVPVRVLQDIDGLSVVEGLASGDQVVVDGHSRLMPGALVDIQEPRPSLAQATERRP"},"dna_sequence":{"accession":"AB219523.1","fmin":"21","fmax":"1179","strand":"+","sequence":"ATGCAGGCGTTGCGCAGTGGTGGGGGACGGGTCCTGGTGGGCGTGCTGGCGGCGGGCCTGGTCGCCTTCGGCGGTTGGGCATGGCTCGGCGGCGACGCCGGGGCGAAGGCGGCGCCCGCGCCGGCCAGGGTCCCGGTGATCGTGGCGCGGGTGGAGCGGCGCGACGTCGAGCAACAGGTCAGCGGCATCGGCACGGTGACTTCGTTGCACAACGTGGTGATCCGCACCCAGATCGACGGCCAGTTGACCCGCCTGCTGGTGAGCGAAGGGCAGATGGTCGAGGCGGGCGAGTTACTGGCGACCATCGATGACCGCGCCGTCGTCGCCGCGCTGGAGCAGGCGCAGGCCTCCAGGGCGAGCAACCAGGCCCAGCTGAAATCCGCCGAGCAGGACCTGCAACGCTACCGCAGCCTGTATGCCGAGCGTGCGGTGTCACGCCAACTGCTGGACCAGCAGCAGGCGACGGTCGACCAGTTGCGCGCGACCCTGAAGGCCAACGATGCCACCATCAACGCCGAGCGGGTGCGCCTGTCCTACACCCGGATCACCTCGCCGGTATCCGGCAAGGTCGGTATCCGCAACGTCGATGTCGGCAACCTGGTGCGGGTCGGCGACAGTCTCGGCCTGTTCAGCGTGACCCAGATCGCACCGATCTCCGTAGTCTTCTCCCTGCAACAGGAACAGTTGCTCCAGTTGCAGGCGCTGCTCGGCGGCGAGGCGGCGGTGCGCGCCTACAGCCGCGACGGCGGGAGCGCGCTGGGCGAGGGCCGGTTGCTGACCATCGACAACCAGATCGACAGTTCCACCGGCACCATCCGCGTGCGCGCCTCCTTCGATAACCGCCAGGCCCGGCTCTGGCCCGGGCAGTTCGTCGCGGTGAGCCTGCACACCGGGGTCCGGCGCGACCAGTTGGTGCTGTCGAGCAAGGCGGTGCGCCGCGGCCTGGAGGGCAATTTCGTCTACCGGGTCGCCGACGACCGGGTCGAGGCGGTGCCGGTGCGGGTGCTCCAGGACATCGACGGCCTCAGTGTGGTGGAAGGCCTGGCCAGCGGTGACCAGGTGGTGGTGGACGGCCACTCGCGGCTGATGCCCGGCGCCCTGGTCGATATCCAGGAGCCGCGCCCGAGCCTGGCCCAGGCCACGGAGCGGCGGCCGTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3003704","ARO_id":"40358","ARO_name":"mexM","ARO_description":"mexM is the membrane fusion protein of the MexMN-OprM multidrug efflux complex.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2217":{"model_id":"2217","model_name":"mexN","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1900"}},"model_sequences":{"sequence":{"3410":{"protein_sequence":{"accession":"BAE06006.1","sequence":"MTPRAGISGWCVRHPIATALLTLASLLLGLLAFLRLGVAPLPEADFPTIQINALLPGGSPETMASSVATPLEVQFSAIPGITEMTSSSALGTTTLTLQFSLDKSIDVAAQEVQAAINAAAGRLPVDMPNLPTWRKVNPADSPIMILRVNSEMMPLIELSDYAETILARQLSQVNGVGQIFVVGQQRPAIRIQAQPEKLAAYQLTLADLRQSLQSASVNLAKGALYGEGRVSTLAANDQLFNASDYDDLVVAYRQGAPVFLKDVARIVSAPEDDYVQAWPNGVPGVALVILRQPGANIVDTADAIQAALPRLREMLPATIEVDVLNDRTRTIRSSLHEVELTLLLTIGLVVLVMGLFLRQLSATLIVATVLAVSLSASFAAMYVLGFTLNNLTLVALIIAVGFIVDDAIVVVENIHRHLEAGASKVEAALKGAAEIGFTVISISFSLIAAFIPLLFMGGIVGRLFREFAVSVTVAILISVVASLTLAPMLASRFMPALRHAEAPRKGFAEWLTGGYERGLRWALGHQRLMLVGFAFTVLVAVAGYVGIPKGFFPLQDTAFVIGTSQAAEDISYDDMVAKHRQLAEIIASDPAVQSYNHAVGVTGGSQSLANGRFWIVLKDRGERDVSVGEFIDRLRPQLAKVPGIMLYLRAAQDINLSSGPSRTQYQYALRSSDSTQLALWAQRLTERLKQVPGLMDVSNDLQVGASVTALDIDRVAAARFGLSAEDVSQTLYDAFGQRQVGEYQTEVNQYKVVLELDARQRGRAESLDWFYLRSPLSGEMVPLSAIAKVAAPRSGPLQINHNGMFPAVNLSFNLAAGVSLGEAVQAVQRAQEEIGMPSTIIGVFQGAAQAFQSSLASQPLLILAALIAVYIILGVLYESFVHPLTILSTLPSAGIGAVFLLWAWGQDFSIMALIGIVLLIGIVKKNGILMVDFAIVAQREQGMSAEQAIYQACLTRFRPIMMTTLAALLGAIPLMIGFGTGSELRQPLGIAVVGGLLVSQVLTLFSTPVVYLALERLFHRRGTTTSDGGTAGATAT"},"dna_sequence":{"accession":"AB219523.1","fmin":"1175","fmax":"4286","strand":"+","sequence":"GTGACGCCGCGCGCCGGGATTTCCGGCTGGTGCGTACGGCACCCGATCGCCACCGCGCTGCTGACCCTGGCCTCGCTGCTGCTGGGGCTGCTGGCGTTCCTCCGGCTCGGTGTGGCGCCGTTGCCGGAGGCGGACTTCCCGACCATCCAGATCAACGCCTTGCTGCCCGGCGGTAGCCCGGAGACCATGGCCTCGTCGGTGGCCACCCCCTTGGAAGTGCAGTTCAGCGCGATTCCCGGGATCACCGAGATGACTTCCAGCAGCGCCCTGGGCACCACCACCCTGACCCTGCAGTTCAGCCTCGACAAGAGCATCGACGTCGCCGCCCAGGAGGTCCAGGCGGCGATCAACGCCGCGGCCGGGCGGCTGCCGGTGGACATGCCGAACCTGCCGACCTGGCGCAAGGTCAACCCGGCGGACAGCCCGATCATGATCCTGCGGGTCAACTCGGAGATGATGCCGCTGATCGAACTCAGCGATTACGCCGAGACCATCCTCGCCCGCCAGCTCAGCCAGGTGAACGGCGTGGGGCAGATCTTCGTGGTCGGCCAGCAGCGCCCGGCGATCCGCATCCAGGCCCAGCCGGAGAAGCTCGCCGCCTACCAGCTGACCCTGGCCGACCTGCGCCAGTCGTTGCAGTCGGCCAGCGTCAACCTGGCCAAGGGCGCGCTCTACGGCGAGGGGCGGGTGTCGACCCTCGCGGCCAACGACCAGTTGTTCAACGCCAGCGACTATGACGACCTGGTGGTCGCCTACCGCCAGGGCGCGCCGGTGTTCCTCAAGGACGTGGCGCGGATCGTCTCGGCGCCCGAGGACGACTACGTGCAGGCCTGGCCGAACGGCGTGCCCGGGGTGGCGCTGGTGATCCTGCGCCAGCCTGGGGCGAACATCGTCGATACCGCCGACGCGATCCAGGCCGCGCTGCCACGCCTGCGCGAGATGCTCCCGGCGACCATCGAGGTAGACGTGCTCAACGACCGCACCCGGACCATCCGCTCGTCGTTGCACGAGGTCGAACTGACCCTGCTGCTGACCATTGGCCTGGTGGTGCTGGTGATGGGCCTGTTCCTCCGCCAGCTGTCGGCGACCCTGATCGTCGCCACGGTGCTGGCGGTGTCCCTGAGCGCCAGCTTCGCGGCGATGTACGTGCTCGGCTTCACCCTCAACAACCTGACCCTGGTGGCGCTGATCATCGCTGTCGGCTTCATCGTCGACGACGCCATCGTGGTCGTGGAGAACATCCACCGACACCTGGAAGCGGGCGCCTCGAAGGTCGAGGCGGCGCTCAAGGGCGCGGCGGAGATCGGCTTTACCGTGATTTCCATCAGCTTCTCGCTGATCGCCGCGTTCATTCCCCTGCTGTTCATGGGCGGGATCGTCGGCCGGCTGTTCCGCGAATTCGCGGTCAGCGTGACGGTGGCGATCCTGATCTCGGTGGTCGCTTCGCTGACCCTGGCGCCGATGCTGGCTTCGCGCTTCATGCCGGCATTGCGGCATGCCGAAGCGCCGAGAAAGGGCTTCGCCGAATGGCTGACCGGCGGCTACGAACGCGGCCTGCGCTGGGCGCTCGGGCACCAGCGGCTGATGCTGGTCGGCTTCGCCTTTACCGTGCTGGTGGCGGTGGCCGGCTACGTCGGGATTCCCAAGGGTTTCTTCCCCTTGCAGGACACCGCCTTCGTCATCGGCACGAGCCAGGCTGCCGAGGATATCTCCTACGACGACATGGTCGCCAAGCACCGGCAACTGGCCGAGATCATCGCCAGCGACCCGGCGGTGCAGAGCTACAACCATGCGGTGGGCGTCACCGGCGGTAGCCAGAGCCTGGCCAACGGACGTTTCTGGATCGTCCTCAAGGACCGTGGCGAGCGCGATGTCTCGGTCGGCGAGTTCATCGACCGGCTGCGCCCGCAACTGGCCAAGGTGCCGGGAATCATGCTCTACCTGCGCGCGGCGCAGGACATCAACCTCAGTTCCGGACCCTCGCGGACCCAGTACCAGTACGCCCTGCGCAGCAGCGACAGCACCCAGCTGGCGCTCTGGGCGCAACGCCTCACCGAGCGCCTGAAGCAGGTGCCGGGGCTGATGGATGTGTCCAACGACCTGCAGGTCGGCGCCAGCGTCACCGCGCTGGACATCGACCGGGTGGCCGCGGCGCGTTTCGGCCTCAGCGCCGAGGATGTCAGCCAGACCCTCTACGACGCCTTCGGCCAGCGCCAGGTCGGCGAGTACCAGACCGAGGTCAACCAGTACAAGGTGGTCCTCGAACTCGATGCGCGCCAGCGCGGCCGCGCGGAAAGCCTGGACTGGTTCTACCTGCGCTCGCCGCTGAGCGGCGAGATGGTCCCGCTGTCGGCCATCGCCAAGGTCGCGGCGCCGCGCTCCGGGCCGCTGCAGATCAACCACAACGGCATGTTCCCGGCGGTCAACCTGTCCTTCAACCTGGCTGCCGGGGTGTCCCTCGGCGAGGCGGTGCAGGCGGTGCAGCGCGCCCAGGAGGAGATCGGCATGCCCTCGACCATTATCGGCGTGTTCCAGGGCGCGGCGCAGGCCTTCCAGAGCTCGCTGGCCTCGCAACCGCTGCTGATCCTCGCCGCGCTGATCGCGGTGTACATCATCCTCGGCGTGCTCTACGAGAGTTTCGTACATCCGCTGACGATCCTCTCGACCCTGCCCTCGGCGGGGATCGGCGCGGTGTTCCTGCTCTGGGCCTGGGGCCAGGACTTCTCGATCATGGCGCTGATCGGCATCGTGCTGCTGATCGGCATCGTCAAGAAGAACGGCATCCTCATGGTCGACTTCGCCATCGTCGCCCAGCGCGAGCAGGGCATGAGCGCGGAGCAGGCGATCTACCAGGCCTGCCTGACCCGTTTCCGGCCGATCATGATGACCACCCTGGCCGCGCTGCTGGGCGCGATACCCCTGATGATCGGCTTCGGCACCGGTTCCGAGCTGCGCCAGCCTCTGGGCATCGCGGTGGTCGGCGGGCTGCTGGTGAGCCAGGTGCTGACCCTGTTCAGCACGCCGGTGGTATACCTGGCCCTGGAGCGGCTGTTCCACCGGCGCGGGACGACGACCTCGGACGGCGGAACCGCTGGGGCGACGGCGACATGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3003705","ARO_id":"40359","ARO_name":"mexN","ARO_description":"MexN is the inner membrane transporter of the MexMN-OprM multidrug efflux complex.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2219":{"model_id":"2219","model_name":"mexL","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"3412":{"protein_sequence":{"accession":"NP_252368.1","sequence":"MSESTSSVGPGRPKDPAKREAILEAAKRLFLCNGYDGSSMEAIASEAGVSKLTVYSHFTDKETLFSEAVKAKCAEQLPALYFQLAEGAPLEKVLLNIARGFHRLINSHEAIALTRLMAAQAGQNPKLSELFFEAGPKQVIDEMERLLEQARRSGKLAFPDARHAAEHFFMLVKGCANYRLLIGCAEPLDEAEGERHVEEVVALFLRAFAAGG"},"dna_sequence":{"accession":"AE004091.2","fmin":"4120468","fmax":"4121107","strand":"+","sequence":"ATGTCAGAATCCACCTCCTCCGTCGGTCCCGGCCGGCCCAAGGACCCGGCCAAACGGGAAGCCATTCTCGAGGCGGCCAAGCGCCTGTTCCTCTGCAACGGCTACGACGGCAGCAGCATGGAAGCCATCGCCTCGGAAGCCGGCGTTTCCAAGCTCACCGTCTACAGCCACTTCACCGACAAGGAAACCCTGTTCAGCGAAGCGGTGAAGGCCAAGTGCGCCGAGCAGCTTCCCGCCCTGTACTTCCAGCTGGCCGAAGGCGCGCCACTGGAAAAGGTCCTGCTGAATATCGCCCGCGGCTTCCACCGGCTGATCAACAGCCACGAGGCGATCGCCCTGACCCGCCTGATGGCCGCGCAGGCCGGGCAGAACCCCAAGCTTTCCGAGCTGTTCTTCGAGGCCGGGCCGAAGCAGGTGATCGACGAGATGGAACGCCTCCTCGAGCAGGCCCGCCGCAGCGGCAAGCTGGCGTTCCCGGACGCGCGCCACGCCGCCGAACACTTCTTCATGCTGGTCAAGGGCTGCGCCAATTACCGTCTGTTGATCGGCTGCGCCGAACCGCTGGACGAGGCCGAAGGCGAGCGGCACGTGGAAGAAGTGGTGGCGCTGTTCCTGCGCGCCTTCGCCGCGGGCGGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3003710","ARO_id":"40364","ARO_name":"MexL","ARO_description":"MexL is a specific repressor of mexJK transcription and autoregulates its own expression.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2221":{"model_id":"2221","model_name":"VEB-1a","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"3415":{"protein_sequence":{"accession":"AAK14293.1","sequence":"MKIVKRILLVLLSLFFTVVYSNAQTDNLTLKIENVLKAKNARIGVAIFNSNEKDTLKINNDFHFPMQSVMKFPIALAVLSEIDKGNLSFEQKIEITPQDLLPKTWSPIKEEFPNGTTLTIEQILNYTVSESDNIGCDILLKLIGGTDSVQKFLNANHFTDISIKANEEQMHKDWNTQYQNWATPTAMNKLLIDTYNNKNQLLSKKSYDFIWKIMRETTTGSNRLKGQLPKNTIVAHKTGTSGINNGIAAATNDVGVITLPNGQLIFISVFVAESKETSEINEKIISDIAKITWNYYLNK"},"dna_sequence":{"accession":"AF324833.1","fmin":"0","fmax":"900","strand":"+","sequence":"ATGAAAATCGTAAAAAGGATATTATTAGTATTGTTAAGTTTATTTTTTACAGTTGTGTATTCAAATGCTCAAACTGACAACTTAACTTTGAAAATTGAGAATGTTTTAAAGGCAAAAAATGCCAGAATAGGAGTAGCAATATTCAACAGCAATGAGAAGGATACTTTGAAGATTAATAACGACTTCCATTTCCCGATGCAAAGCGTTATGAAATTTCCGATTGCTTTAGCCGTTTTGTCTGAGATAGATAAAGGGAATCTTTCTTTTGAACAAAAAATAGAGATTACCCCTCAAGACCTTTTGCCTAAAACGTGGAGTCCGATTAAAGAGGAATTCCCTAATGGAACAACTTTGACGATTGAACAAATACTAAATTATACAGTATCAGAGAGCGACAATATTGGTTGTGATATTTTGCTAAAATTAATCGGAGGAACTGATTCTGTTCAAAAATTCTTGAATGCTAATCATTTCACTGATATTTCAATCAAAGCAAACGAAGAACAAATGCACAAGGATTGGAATACCCAATATCAAAATTGGGCAACCCCAACAGCGATGAACAAACTGTTAATAGATACTTATAATAATAAGAACCAATTACTTTCTAAAAAAAGTTATGATTTTATTTGGAAAATTATGAGAGAAACAACAACAGGAAGTAACCGATTAAAAGGACAATTACCAAAGAATACAATTGTTGCTCATAAAACAGGGACTTCCGGAATAAATAATGGAATTGCAGCAGCCACTAATGATGTTGGGGTAATTACTTTACCGAATGGACAATTAATTTTTATAAGCGTATTTGTTGCAGAGTCCAAAGAAACTTCGGAAATTAATGAAAAGATTATTTCAGACATTGCAAAAATAACGTGGAATTACTATTTGAATAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3003711","ARO_id":"40365","ARO_name":"VEB-1a","ARO_description":"VEB-1a is a beta-lactamase that is found in Pseudomonas aeruginosa.","ARO_category":{"36182":{"category_aro_accession":"3000043","category_aro_cvterm_id":"36182","category_aro_name":"VEB beta-lactamase","category_aro_description":"VEB beta-lactamases or Vietnamese extended-spectrum beta-lactamases are class A beta-lactamases that confer high-level resistance to oxyimino cephalosporins and to aztreonam","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2222":{"model_id":"2222","model_name":"VEB-1b","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"3416":{"protein_sequence":{"accession":"AAK14294.1","sequence":"MKIVKRILLVLLSLFFTVEYSNAQTDNLTLKIENVLKAKNARIGVAIFNSNEKDTLKINNDFHFPMQSVMKFPIALAVLSEIDKGNLSFEQKIEITPQDLLPKTWSPIKEEFPNGTTLTIEQILNYTVSESDNIGCDILLKLIGGTDSVQKFLNANHFTDISIKANEEQMHKDWNTQYQNWATPTAMNKLLIDTYNNKNQLLSKKSYDFIWKIMRETTTGSNRLKGQLPKNTIVAHKTGTSGINNGIAAATNDVGVITLPNGQLIFISVFVAESKETSEINEKIISDIAKITWNYYLNK"},"dna_sequence":{"accession":"AF324834.1","fmin":"0","fmax":"900","strand":"+","sequence":"ATGAAAATCGTAAAAAGGATATTATTAGTATTGTTAAGTTTATTTTTTACAGTTGAGTATTCAAATGCTCAAACTGACAACTTAACTTTGAAAATTGAGAATGTTTTAAAGGCAAAAAATGCCAGAATAGGAGTAGCAATATTCAACAGCAATGAGAAGGATACTTTGAAGATTAATAACGACTTCCATTTCCCGATGCAAAGCGTTATGAAATTTCCGATTGCTTTAGCCGTTTTGTCTGAGATAGATAAAGGGAATCTTTCTTTTGAACAAAAAATAGAGATTACCCCTCAAGACCTTTTGCCTAAAACGTGGAGTCCGATTAAAGAGGAATTCCCTAATGGAACAACTTTGACGATTGAACAAATACTAAATTATACAGTATCAGAGAGCGACAATATTGGTTGTGATATTTTGCTAAAATTAATCGGAGGAACTGATTCTGTTCAAAAATTCTTGAATGCTAATCATTTCACTGATATTTCAATCAAAGCAAACGAAGAACAAATGCACAAGGATTGGAATACCCAATATCAAAATTGGGCAACCCCAACAGCGATGAACAAACTGTTAATAGATACTTATAATAATAAGAACCAATTACTTTCTAAAAAAAGTTATGATTTTATTTGGAAAATTATGAGAGAAACAACAACAGGAAGTAACCGATTAAAAGGACAATTACCAAAGAATACAATTGTTGCTCATAAAACAGGGACTTCCGGAATAAATAATGGAATTGCAGCAGCCACTAATGATGTTGGGGTAATTACTTTACCGAATGGACAATTAATTTTTATAAGCGTATTTGTTGCAGAGTCCAAAGAAACTTCGGAAATTAATGAAAAGATTATTTCAGACATTGCAAAAATAACGTGGAATTACTATTTGAATAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3003712","ARO_id":"40366","ARO_name":"VEB-1b","ARO_description":"VEB-1b is a beta-lactamase that is found in Pseudomonas aeruginosa.","ARO_category":{"36182":{"category_aro_accession":"3000043","category_aro_cvterm_id":"36182","category_aro_name":"VEB beta-lactamase","category_aro_description":"VEB beta-lactamases or Vietnamese extended-spectrum beta-lactamases are class A beta-lactamases that confer high-level resistance to oxyimino cephalosporins and to aztreonam","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2191":{"model_id":"2191","model_name":"AAC(6')-Iaj","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"3379":{"protein_sequence":{"accession":"BAM46120.1","sequence":"MEYSIINIVEQNNYQIDAARILTNTFLDIGNKTWPTIQSAIDEVEECIDLPNICIGLIHNNQLIGWVGLRPMYDKTWELHPLVVRTDYQSKGIGSVLLAEVEKRAREVGIIGIILGTDDEYNKTSLSEITIDENNIFDAIQNIKNIHNHPYEFYQKNGYMIVGIIPNANGLRKPDIWMWKSLLN"},"dna_sequence":{"accession":"AB709942","fmin":"1194","fmax":"1749","strand":"+","sequence":"ATGGAATATTCAATTATCAATATAGTAGAGCAAAACAATTATCAGATCGATGCTGCAAGAATTCTTACAAATACTTTTCTTGATATAGGTAATAAAACTTGGCCAACTATTCAAAGCGCAATCGATGAAGTCGAAGAGTGTATTGATCTGCCCAATATATGTATAGGTTTAATTCATAACAATCAATTAATTGGATGGGTCGGATTACGTCCGATGTATGATAAAACGTGGGAATTGCACCCATTAGTTGTAAGAACTGACTATCAAAGTAAGGGGATCGGTAGTGTATTACTTGCTGAAGTTGAAAAAAGGGCAAGAGAAGTTGGAATAATTGGAATAATATTAGGAACTGATGATGAATATAACAAAACAAGTCTTTCTGAAATAACTATAGATGAAAATAATATATTCGATGCAATACAAAATATTAAGAATATACATAATCATCCATATGAGTTTTACCAAAAAAATGGATATATGATTGTTGGAATAATTCCAAATGCAAATGGACTAAGAAAACCCGATATTTGGATGTGGAAAAGTCTACTCAATTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3003677","ARO_id":"40309","ARO_name":"AAC(6')-Iaj","ARO_description":"AAC(6')-Iaj is a functional acetyltransferase that modifies the amino groups at the 6' positions of aminoglycosides and contributes to aminoglycoside resistance of P. aeruginosa","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2227":{"model_id":"2227","model_name":"VCC-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"3430":{"protein_sequence":{"accession":"ALU64000","sequence":"MKRIAMYVALSISTSTAFADEHNKNMADIEAAFEGRVGVYAINTGSGKAYSYRANERFPLCSSFKAFLAAAVLKMDQDSPGVLLEKVNYHNRTMEPHSPITEKFQSQGMAVGELAAATLQYSDNGAANLLMEKYIKGPEGMTQFMNSIGDTKFRLDRWELDLNSAIPGDERDTSTPKAVAESLNKLISNTVLDNYHQEIFKKWMIGNTTGDNRIRAAVPDGWVVGDKTGTCGKYGTANDHAFILQGNNAAPLILSIYTTRKGEHMKHDDEVIAKAARIAIENVK"},"dna_sequence":{"accession":"KT818596","fmin":"10010","fmax":"10865","strand":"+","sequence":"ATGAAACGTATTGCTATGTATGTTGCATTATCAATCTCTACTTCAACAGCTTTCGCTGATGAGCACAACAAAAATATGGCTGATATTGAAGCTGCTTTTGAGGGGCGTGTCGGTGTTTACGCAATAAACACTGGCAGCGGCAAGGCATATTCATATCGAGCTAACGAACGCTTCCCCTTATGTAGTTCATTTAAAGCATTTTTGGCGGCAGCAGTTTTAAAAATGGATCAAGATAGTCCTGGAGTCCTGCTTGAAAAAGTAAATTATCATAACAGAACTATGGAACCCCATTCACCCATAACAGAGAAATTTCAGTCACAAGGAATGGCCGTAGGGGAACTGGCTGCTGCAACACTTCAGTATAGTGATAATGGTGCTGCTAACCTTCTCATGGAGAAATATATAAAAGGACCAGAGGGCATGACTCAGTTCATGAACAGTATTGGTGATACTAAGTTTAGGTTGGACCGATGGGAGTTGGACCTTAATAGTGCTATACCTGGAGATGAACGTGACACATCAACACCGAAGGCCGTGGCAGAAAGTCTGAATAAGTTAATATCAAATACCGTCTTAGACAACTACCATCAAGAGATATTCAAAAAGTGGATGATCGGTAATACTACAGGAGATAATAGAATAAGAGCTGCTGTGCCTGATGGTTGGGTTGTCGGTGATAAAACGGGAACTTGCGGAAAGTATGGCACAGCAAACGATCATGCGTTTATTTTACAAGGTAATAATGCTGCCCCTCTGATTTTATCTATATATACAACCAGAAAGGGAGAACATATGAAGCATGATGATGAGGTGATTGCTAAAGCAGCTAGGATTGCAATAGAAAATGTAAAGTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36789","NCBI_taxonomy_name":"Vibrio cholerae","NCBI_taxonomy_id":"666"}}}},"ARO_accession":"3003713","ARO_id":"40367","ARO_name":"VCC-1","ARO_description":"VCC-1 is a Class A carbapenemase isolated from Vibrio cholerae and exhibits resistance to penicillins, carbapenems and monobactam antibiotics.","ARO_category":{"41360":{"category_aro_accession":"3004196","category_aro_cvterm_id":"41360","category_aro_name":"VCC beta-lactamase","category_aro_description":"VCC beta-lactamases are Class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2228":{"model_id":"2228","model_name":"PEDO-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"3429":{"protein_sequence":{"accession":"AJP77059","sequence":"MKIKFIFCLLLFPLFVFSQNVQEPTDTPKEWSAAYAPFRIVGNVYYVGTYDLACYLITTPKGNILINTGLRSSAAQIKKNVELLGFNFKDIKILLTTQAHYDHLGAMAEIKKLTGAKMMVDEKDASVMKDGGRTDYALGNGKTTYAPIIPDRLLKDGDQIQLGNTSIVMLHHPGHTKGSCSFMLKTKDETRDYSVLIANMPSIVTEKKFSEIPAYPQIEKDYAYTLSSLKKLSFDIWLSSHASQFCLHEKHKPGDKYNPTAFIDRAGYDKVLNSLQLEFDKKIGKK"},"dna_sequence":{"accession":"KP109677","fmin":"4318","fmax":"5179","strand":"+","sequence":"ATGAAAATTAAATTTATTTTTTGCCTCTTGCTTTTTCCGCTCTTTGTATTTTCACAAAATGTACAAGAACCTACCGATACGCCAAAAGAGTGGTCGGCTGCTTATGCCCCATTCCGCATTGTTGGGAATGTTTATTATGTTGGCACTTACGATCTGGCCTGCTACCTTATTACCACTCCGAAAGGAAATATACTGATCAATACCGGACTGCGTTCCTCGGCTGCGCAGATCAAAAAAAACGTGGAACTTTTGGGCTTTAACTTTAAAGACATCAAAATCCTGCTGACCACACAGGCACATTACGACCATTTGGGTGCTATGGCGGAGATCAAGAAACTTACTGGTGCAAAAATGATGGTTGATGAAAAAGATGCCAGTGTGATGAAGGATGGCGGCCGTACGGATTACGCACTGGGTAACGGAAAAACAACCTACGCTCCTATTATACCAGACCGTTTATTAAAGGATGGAGATCAGATCCAGCTCGGAAATACCAGTATTGTAATGCTCCACCACCCCGGCCATACTAAAGGATCATGCAGTTTTATGCTTAAAACTAAAGATGAAACAAGAGACTATTCGGTGCTGATTGCGAATATGCCCAGTATTGTTACCGAAAAAAAGTTTTCTGAAATACCAGCTTATCCGCAAATTGAAAAAGATTACGCCTATACTTTAAGTTCGCTCAAAAAATTATCATTTGATATCTGGTTGTCGTCTCATGCAAGCCAGTTTTGTCTGCACGAGAAACATAAACCTGGCGATAAATATAATCCTACCGCTTTTATAGATCGTGCAGGATACGATAAGGTATTAAACAGCCTTCAGCTCGAATTTGATAAAAAGATTGGCAAGAAATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40283","NCBI_taxonomy_name":"Pedobacter sp. SI-33","NCBI_taxonomy_id":"1620222"}}}},"ARO_accession":"3003670","ARO_id":"40288","ARO_name":"PEDO-1","ARO_description":"PEDO-1 is a subclass B3 metallo-beta lactamase isolated from Pedobacter roseus exhibiting resistance to carbapenems.","ARO_category":{"41384":{"category_aro_accession":"3004220","category_aro_cvterm_id":"41384","category_aro_name":"subclass B3 PEDO beta-lactamase","category_aro_description":"PEDO family enzymes that are classified under subclass B3 (metallo-) beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2229":{"model_id":"2229","model_name":"PEDO-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"3428":{"protein_sequence":{"accession":"AJP77071","sequence":"MKKIFLMVLFSCSLLGFAQTVTEPANNPKEWSQATEPFRIAGNLYYVGTYDLASYLIVTEKGNILINTGLANSLSIIKENIKALGFDYKSIKILLLTQAHFDHLGAMSEIKKETGAKLYVDEKDADALETGGKLDYELGKYGISFKPVKPDFLLKNNDKIKLGNTTLTMLHHPGHTKGSCSFIFDTKDKNSSYKILIANMPSIIVDRKFSEIASYKDIQKDYTETFKAMKKLDFDLWVASHASQFELHDKRKSGAPYNPKIFMDKSKFFKNLEDLENIFLEKIKN"},"dna_sequence":{"accession":"KP109678","fmin":"5817","fmax":"6675","strand":"+","sequence":"ATGAAAAAAATATTTTTAATGGTTTTATTTTCTTGCAGTCTGTTGGGTTTTGCTCAAACAGTAACAGAGCCGGCTAATAATCCAAAAGAATGGTCTCAAGCTACAGAGCCATTTAGAATTGCAGGTAATCTATATTATGTTGGCACTTATGATTTAGCTTCTTATTTAATTGTAACAGAAAAAGGAAATATATTAATAAATACAGGTTTAGCTAATTCGCTTTCAATAATAAAAGAAAATATAAAAGCTTTGGGATTTGATTATAAATCAATCAAAATTTTGCTCTTAACCCAAGCTCATTTTGATCATTTGGGTGCGATGTCTGAGATTAAAAAAGAAACCGGTGCAAAACTTTATGTAGATGAGAAAGATGCGGACGCTCTTGAAACAGGCGGAAAATTGGATTATGAGCTTGGAAAATATGGCATAAGTTTCAAGCCTGTAAAACCTGATTTCCTATTGAAGAATAACGATAAGATTAAATTAGGCAACACTACTTTAACAATGCTTCATCATCCTGGGCATACTAAAGGATCGTGTAGTTTTATATTTGATACAAAAGATAAAAATTCTAGCTACAAAATTTTGATTGCCAATATGCCATCCATAATTGTTGATAGAAAATTCTCAGAAATAGCATCATATAAAGATATCCAAAAAGATTATACCGAAACTTTTAAAGCAATGAAAAAGCTTGACTTTGATCTTTGGGTTGCCTCTCATGCAAGTCAGTTTGAGCTCCATGATAAACGTAAATCAGGAGCCCCTTATAATCCAAAAATCTTTATGGATAAAAGTAAATTTTTCAAGAATCTTGAAGATCTGGAAAATATTTTCCTCGAAAAAATAAAAAATTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40284","NCBI_taxonomy_name":"Pedobacter sp. ALS-14","NCBI_taxonomy_id":"1620221"}}}},"ARO_accession":"3003714","ARO_id":"40368","ARO_name":"PEDO-2","ARO_description":"PEDO-2 is a subclass B3 metallo-beta lactamase isolated from Pedobacter borealis exhibiting carbapenem resistance.","ARO_category":{"41384":{"category_aro_accession":"3004220","category_aro_cvterm_id":"41384","category_aro_name":"subclass B3 PEDO beta-lactamase","category_aro_description":"PEDO family enzymes that are classified under subclass B3 (metallo-) beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2230":{"model_id":"2230","model_name":"PEDO-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"3427":{"protein_sequence":{"accession":"AJP77076","sequence":"MRYLLSFLLCLSAFASFAQNPKIKIKHLTGDLYVYTTYNTYKGALTDANAVYLVTNKGVVVIDAPWDATQFQPFLDSIQTKHHQKVVLAIATHSHGDRAGGLAFFKSKGIKTYTNKLTDEILKTNKEPRAAYTFTNDTTFTVGQYKINTYYAGKGHTKDNLVVWFPKDKVLFGGCLIKSIEANDLGYIGESDLAAWPKSIEKLKQKYPDTKIVITGHAAWGNRESLDHTLKLLREKK"},"dna_sequence":{"accession":"KP109679","fmin":"2260","fmax":"2974","strand":"+","sequence":"CTACTTTTTCTCCCTCAATAGCTTTAGGGTATGGTCTAGAGATTCCCTGTTTCCCCAGGCAGCGTGTCCGGTAATAACAATTTTGGTATCAGGATATTTCTGTTTTAACTTTTCGATGCTTTTTGGCCATGCGGCTAAATCGGATTCTCCAATATAGCCCAAATCATTGGCTTCGATGCTTTTAATCAGGCAGCCACCGAATAAAACTTTGTCTTTTGGAAACCAAACTACCAGATTATCCTTTGTATGCCCCTTGCCGGCATAGTAGGTGTTTATTTTATATTGTCCCACTGTAAAAGTAGTGTCGTTGGTAAAGGTGTAGGCTGCGCGTGGCTCTTTATTAGTTTTCAGAATTTCGTCGGTTAATTTATTGGTATAGGTTTTTATGCCCTTACTTTTAAAGAACGCTAAACCGCCTGCGCGGTCGCCATGCGAATGTGTGGCAATGGCCAGCACTACTTTTTGGTGATGTTTGGTCTGAATAGAGTCTAAAAAGGGCTGGAACTGCGTAGCATCCCAAGGGGCATCGATTACTACAACACCTTTATTGGTAACCAGGTAAACCGCATTTGCATCTGTTAAAGCGCCTTTGTAGGTATTGTATGTGGTGTAAACATAAAGATCGCCAGTTAAATGTTTGATTTTTATTTTTGGATTTTGCGCGAAAGAGGCAAAGGCAGATAAACAAAGTAAAAAGGAAAGAAGATAACGCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40285","NCBI_taxonomy_name":"Pedobacter sp. Stok-3","NCBI_taxonomy_id":"1620223"}}}},"ARO_accession":"3003715","ARO_id":"40369","ARO_name":"PEDO-3","ARO_description":"PEDO-3 is a class B1 metallo-beta lactamase isolated from Pedobacter kyungheensis exhibiting resistance to carbapenems.","ARO_category":{"41391":{"category_aro_accession":"3004227","category_aro_cvterm_id":"41391","category_aro_name":"subclass B1 PEDO beta-lactamase","category_aro_description":"Beta-lactamases that are part of the PEDO gene family and are classified as subclass B1 (metallo-) beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2231":{"model_id":"2231","model_name":"CPS-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"3431":{"protein_sequence":{"accession":"AJP77054","sequence":"MRNLTLLFLLCLSFFGTAQTVTEPKNNPAEWSKDYEPFKIVGNLYYVGTYDLASYLIVTDKGNILINTGLADSYSTIKKNIEKFGFKYKDIKILTLTQAHYDHMGAMAQIKKETGAKLYVDEKDAAELKSGGKSDYEMGKYGVTFEPVHPDFLLKNNAKIKLGNTVLTLLHHPGHTKGSCSFLFETKEGNKNYKVLIANLPSIIIDHKFSDVKKYPTIQKDYGYTFEAMKKINFDVWVASHASQFDLHKKRKEGDSYNPKLFMDKENYFKRLKDLENDYLEKVKEDSAKK"},"dna_sequence":{"accession":"KP109675","fmin":"1328","fmax":"2201","strand":"+","sequence":"ATGAGAAACCTGACACTTTTATTTTTACTATGCCTATCTTTTTTTGGAACTGCACAAACCGTAACAGAGCCTAAAAATAATCCGGCAGAATGGTCAAAAGACTATGAACCTTTCAAAATTGTGGGGAATTTATATTATGTAGGAACTTACGATCTTGCATCTTATCTTATCGTGACCGATAAAGGCAATATTTTGATCAACACAGGTTTGGCGGATTCTTATTCTACCATTAAAAAAAATATCGAAAAGTTTGGTTTTAAGTATAAAGATATCAAAATTCTTACCTTAACGCAGGCACATTATGATCACATGGGAGCAATGGCTCAAATAAAAAAAGAAACCGGTGCAAAACTTTATGTTGACGAAAAAGATGCTGCAGAACTTAAAAGTGGTGGAAAATCTGACTACGAAATGGGAAAATACGGCGTTACTTTCGAACCTGTGCATCCTGATTTTCTTTTGAAAAACAATGCTAAAATAAAATTGGGAAATACGGTATTAACCTTGCTTCATCATCCCGGTCATACAAAAGGATCTTGCAGTTTCTTATTTGAAACCAAAGAAGGAAACAAAAATTACAAAGTTTTGATCGCCAATTTACCTTCAATTATTATTGACCATAAATTTTCTGATGTAAAGAAATATCCTACCATTCAGAAAGATTATGGATACACTTTTGAGGCCATGAAAAAAATAAATTTCGATGTTTGGGTAGCTTCGCATGCAAGTCAGTTTGATCTTCATAAAAAGCGGAAAGAAGGAGATTCTTACAATCCGAAATTGTTTATGGATAAAGAAAATTATTTTAAAAGGCTTAAAGATCTGGAAAACGATTATCTGGAAAAAGTAAAAGAAGATTCAGCGAAAAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40281","NCBI_taxonomy_name":"Chryseobacterium sp. Stok-1","NCBI_taxonomy_id":"1620218"}}}},"ARO_accession":"3003716","ARO_id":"40370","ARO_name":"CPS-1","ARO_description":"CPS-1 is a subclass B3 metallo-beta lactamase isolated from Chyseobacterium piscium exhibiting carbapenem resistance.","ARO_category":{"41385":{"category_aro_accession":"3004221","category_aro_cvterm_id":"41385","category_aro_name":"CPS beta-lactamase","category_aro_description":"CPS beta-lactamases are a subclass B3 family.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2232":{"model_id":"2232","model_name":"ESP-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"3432":{"protein_sequence":{"accession":"AJP77085","sequence":"MKKLTLILSLIIAFFGYAQTVTEPTNHSAEWSQPYEPFRIVGNLYYVGTYDLASYLIVTEKGNILINTGLADSYPQIKANIEKLGFKYKDTKILTLTQAHFDHMGAMADIKAETGAKLYVDEADAAELKSGGKSDYELGKYGVTFKPLTPDFLLKNNGKIKLGNTTLTLLHHPGHTKGSCSFIFETKDENRKYKVVIANMPSIIIDHKFSDVKTYPSIQKDYAYTLEAMKKLDFDVWVASHASQFDLHKKRKEGDAYNPKLFMDKENYFKRLKDLEDDYLEKVKEENKPE"},"dna_sequence":{"accession":"KP109681","fmin":"1642","fmax":"2515","strand":"+","sequence":"ATGAAAAAACTTACCCTAATACTTTCACTGATCATTGCCTTTTTCGGATATGCACAAACCGTAACAGAACCAACCAATCATTCTGCAGAATGGTCGCAACCTTACGAGCCATTCAGAATTGTCGGGAATTTGTATTACGTTGGAACTTATGATTTGGCTTCGTATCTCATTGTGACGGAAAAGGGAAATATCCTTATCAACACAGGTTTGGCGGATTCTTATCCTCAAATAAAAGCGAATATCGAGAAACTCGGATTCAAATACAAAGACACCAAAATCCTGACTTTGACACAAGCGCATTTTGACCATATGGGCGCAATGGCCGATATCAAAGCGGAAACCGGCGCAAAACTTTATGTAGACGAAGCAGATGCTGCGGAACTGAAATCAGGCGGAAAATCGGATTACGAACTGGGAAAATATGGTGTGACTTTCAAACCCTTAACGCCGGATTTTCTTCTGAAAAATAATGGTAAAATAAAATTAGGAAATACCACCTTGACCTTGCTTCATCATCCTGGTCACACAAAAGGTTCGTGCAGTTTTATCTTCGAAACCAAAGATGAAAATCGAAAATATAAAGTTGTGATCGCCAATATGCCATCCATCATCATCGATCATAAATTTTCTGATGTGAAAACTTATCCTTCAATTCAGAAAGATTATGCTTACACTTTGGAGGCGATGAAAAAACTGGATTTCGATGTTTGGGTAGCTTCGCACGCCAGCCAATTCGATCTTCATAAAAAAAGAAAAGAAGGCGATGCTTACAACCCGAAACTATTTATGGATAAAGAGAATTATTTTAAAAGACTGAAAGATTTGGAAGATGATTATCTGGAGAAAGTGAAAGAAGAAAATAAACCAGAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40287","NCBI_taxonomy_name":"Epilithonimonas sp. Stok-2","NCBI_taxonomy_id":"1620219"}}}},"ARO_accession":"3003717","ARO_id":"40371","ARO_name":"ESP-1","ARO_description":"ESP-1 is a subclass B3 metallo-beta lactamase isolated from Epilithonimonas tenax conferring resistance to carbapenems.","ARO_category":{"41386":{"category_aro_accession":"3004222","category_aro_cvterm_id":"41386","category_aro_name":"ESP beta-lactamase","category_aro_description":"ESP family beta-lactamases are subclass B3 (metallo-) beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2233":{"model_id":"2233","model_name":"MSI-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"3433":{"protein_sequence":{"accession":"AJP77057","sequence":"MGARSCSRAWCCSRATRSAPPGRRSGRLSCARCRRPSTGCNPSSTPPITGDIMKHIRLACVAAGLVAAASSVSAIGADWNAPQEPFALFGNSYYVGPHGVASVLITSNQGHILIDGGSDKSPPQIAARIRQLGFKPEDIRFILVSHEHIDHAGGVAELQRLSNAEVLAGAAAVPVLHSGEAGRNDPQYGGLPKMAPVARVRAVRDGEVVKLGPLAVTMHATPGHTQGGASWTWQSNEGGRTANMVYADSLTAFGSGGFRYSGDARYPSARADVERSIAKVAALPCDILVSAHPEVSELWTRYERRAAQGNAAFIDAGACKAYAVKARVKLQEQLARETAKP"},"dna_sequence":{"accession":"KP109676","fmin":"0","fmax":"1026","strand":"+","sequence":"ATGGGCGCACGATCGTGTTCGCGCGCATGGTGCTGCAGCCGCGCGACCCGGAGCGCGCCGCCGGGCCGGCGCTCAGGCAGGCTTTCCTGCGCGCGTTGCCGGCGACCCTCGACAGGCTGTAATCCTTCCTCTACTCCACCCATCACGGGAGACATCATGAAGCACATCCGCCTCGCCTGCGTCGCGGCCGGACTGGTCGCGGCCGCATCCTCCGTCAGCGCCATCGGCGCCGACTGGAACGCGCCGCAGGAACCGTTCGCCCTGTTCGGCAACAGCTACTACGTCGGCCCGCACGGCGTGGCCTCGGTCTTGATCACGTCGAATCAGGGTCACATCCTGATCGACGGCGGCAGCGACAAATCGCCGCCGCAGATCGCCGCGCGCATCCGCCAGCTCGGCTTCAAGCCGGAAGACATCCGCTTCATCCTGGTCTCGCACGAGCACATCGACCATGCGGGCGGTGTCGCCGAGCTGCAGCGCCTGTCGAACGCCGAGGTGCTGGCCGGCGCCGCCGCGGTGCCGGTGCTGCATAGCGGCGAGGCCGGTCGCAACGATCCGCAATACGGCGGCCTGCCGAAGATGGCGCCGGTGGCGCGGGTGCGCGCGGTGCGCGACGGCGAGGTGGTCAAACTCGGGCCGCTGGCGGTGACGATGCACGCCACGCCGGGCCATACGCAGGGTGGCGCCAGCTGGACCTGGCAATCAAACGAAGGCGGACGCACGGCCAACATGGTGTATGCCGACAGCCTGACGGCGTTCGGATCCGGGGGCTTTCGCTACAGCGGCGATGCGCGCTATCCGAGCGCGCGCGCCGACGTCGAGCGATCGATCGCGAAGGTCGCCGCGCTGCCGTGCGACATCCTGGTGTCGGCGCATCCGGAAGTGAGCGAGCTGTGGACCCGGTACGAGCGGCGCGCGGCGCAAGGCAACGCCGCGTTCATCGACGCCGGCGCCTGCAAGGCCTATGCCGTCAAGGCCCGCGTGAAGCTGCAGGAACAACTGGCCAGGGAAACGGCCAAGCCATGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40282","NCBI_taxonomy_name":"Massilia sp. SB1-3","NCBI_taxonomy_id":"1620220"}}}},"ARO_accession":"3003718","ARO_id":"40372","ARO_name":"MSI-1","ARO_description":"MSI-1 is a subclass B3 metallo-beta lactamase isolated from Massilia oculi conferring resistance to carbapenems.","ARO_category":{"41387":{"category_aro_accession":"3004223","category_aro_cvterm_id":"41387","category_aro_name":"MSI beta-lactamase","category_aro_description":"MSI beta-lactamases are a family of subclass B3 (metallo-) beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2234":{"model_id":"2234","model_name":"MSI-OXA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"3434":{"protein_sequence":{"accession":"AJP77058","sequence":"MSHTFIIDRLGASMIKQILAALLLISPLLAQAAEWKESAQVARLFKQEGVSGTFVVYDVAADSYTVHDRQRANTRFIPASTFKIPNTLIALAHGAVANVDEVVPYGGKPVARPEWARDMGLREAIRISNVPVYQEVARRVGLDRMRSELVRMKYGNMQTGTVVDRFWLDGPLKISAVEQTEFLTKLAQGTLPFTNVAMAAVREISRQDGAPELYAKTGWGSRPGEADIGWWVGWLKKDGKLYAFALNMDLPDGAQDKRVSLAKAALRELGLL"},"dna_sequence":{"accession":"KP109676","fmin":"1022","fmax":"1841","strand":"+","sequence":"ATGAGTCACACGTTCATCATCGACCGACTTGGAGCATCCATGATCAAGCAAATTCTCGCAGCACTGTTGTTGATCAGCCCGCTGCTGGCGCAGGCCGCCGAATGGAAGGAAAGCGCGCAGGTGGCGCGCCTGTTCAAGCAGGAAGGCGTGAGCGGCACCTTCGTCGTCTACGACGTGGCCGCCGACAGCTACACGGTGCATGACCGCCAGCGCGCCAACACGCGCTTCATTCCGGCGTCGACCTTCAAGATCCCGAACACGCTGATCGCGCTGGCGCATGGCGCGGTGGCCAACGTCGACGAAGTGGTGCCGTATGGCGGCAAGCCGGTAGCGCGGCCCGAGTGGGCGCGCGACATGGGGCTGCGCGAGGCGATCCGGATCTCGAACGTGCCGGTGTACCAGGAAGTGGCGCGGCGCGTGGGCCTGGACCGGATGCGCTCGGAGCTGGTCCGGATGAAGTACGGGAACATGCAGACCGGGACCGTGGTGGACCGGTTCTGGCTCGATGGGCCTTTGAAGATCAGCGCGGTGGAGCAGACCGAATTTTTGACCAAGCTGGCGCAGGGTACGCTGCCGTTCACCAACGTGGCGATGGCGGCGGTGCGCGAGATCAGCCGTCAGGATGGAGCGCCCGAGCTGTATGCCAAGACCGGGTGGGGCAGTCGGCCGGGCGAGGCCGATATCGGGTGGTGGGTCGGTTGGCTGAAGAAGGATGGCAAGCTGTATGCATTTGCGCTGAATATGGATCTTCCCGATGGTGCGCAGGACAAGCGGGTGTCGCTGGCGAAGGCGGCGTTGCGGGAACTGGGCCTGCTGTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40282","NCBI_taxonomy_name":"Massilia sp. SB1-3","NCBI_taxonomy_id":"1620220"}}}},"ARO_accession":"3003719","ARO_id":"40373","ARO_name":"MSI-OXA","ARO_description":"MSI-OXA is an OXA-85-like class D beta lactamase isolated from Massilia oculi.","ARO_category":{"41406":{"category_aro_accession":"3004242","category_aro_cvterm_id":"41406","category_aro_name":"MSI-OXA family beta-lactamase","category_aro_description":"Members of the MSI-OXA family are class D beta-lactamases that encompass hybrids of MSI-1 and putative OXA homologues.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2235":{"model_id":"2235","model_name":"SPG-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"3435":{"protein_sequence":{"accession":"AJP77080","sequence":"MRPLILLASALAMTAPSGALAQSAEQRAKWNGPREPFRITGNLYYVGTSGLSAYLIAGPRGHVLIDGALPESAPLIAANIRKLGFKLSDVKYLLSNHSHVDHAGGLAELKRLTGAQMVANVADKPDLEAGTTIGRTDIADFPAVKVDRVIGDGDRLTLGPIALVAILTPGHTKGATSWTTRIGSKNVIFTSSISVAGQNLINNINYPNAAADFRASFAKLRALKADIFLSFHAEAFALDEKRARAQAGATDAFVDPNELSRQVDLAEKAFDATLAKQQAANADRR"},"dna_sequence":{"accession":"KP109680","fmin":"1254","fmax":"2112","strand":"+","sequence":"TCAGCGCCGATCCGCATTCGCCGCTTGCTGCTTCGCCAGCGTCGCATCGAAAGCCTTCTCCGCCAGATCGACCTGGCGTGACAATTCGTTCGGATCGACAAAGGCGTCGGTGGCACCCGCCTGCGCCCTGGCGCGTTTTTCATCGAGCGCGAAAGCCTCGGCGTGGAAGCTCAGGAAGATATCTGCCTTCAACGCGCGGAGTTTCGCAAAGCTGGCACGGAAATCGGCGGCGGCGTTCGGATAATTTATATTATTGATAAGATTTTGGCCGGCGACACTGATACTCGATGTGAAGATCACATTCTTGCTGCCAATGCGGGTCGTCCAGCTCGTCGCGCCTTTTGTATGGCCGGGTGTCAGGATGGCGACGAGCGCGATCGGGCCGAGCGTCAGCCGGTCGCCGTCGCCGATCACACGATCGACCTTCACTGCCGGAAAGTCCGCGATATCGGTGCGGCCGATGGTGGTACCTGCTTCGAGATCGGGCTTGTCCGCAACGTTTGCGACCATTTGCGCGCCGGTCAGCCGCTTGAGTTCGGCCAGTCCACCGGCGTGATCGACATGCGAATGGTTGCTGAGCAGATATTTCACATCGGACAGTTTGAAGCCCAGTTTGCGGATGTTCGCGGCGATCAGCGGCGCGCTTTCCGGCAGAGCGCCGTCGATCAGCACATGGCCGCGCGGCCCGGCGATCAGATAGGCCGAAAGCCCGCTGGTGCCGACATAATAGAGATTGCCGGTGATGCGGAATGGCTCGCGCGGCCCGTTCCATTTCGCGCGCTGCTCGGCCGATTGGGCGAGGGCGCCGGATGGGGCTGTCATGGCGAGCGCGGATGCGAGCAGTATCAGGGGGCGCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40286","NCBI_taxonomy_name":"Sphingomonas sp. ALS-13","NCBI_taxonomy_id":"1620224"}}}},"ARO_accession":"3003720","ARO_id":"40374","ARO_name":"SPG-1","ARO_description":"SPG-1 is a subclass B3 metallo-beta lactamase isolated from Sphingomonas sp.","ARO_category":{"41388":{"category_aro_accession":"3004224","category_aro_cvterm_id":"41388","category_aro_name":"SPG beta-lacatamase","category_aro_description":"SPG beta-lactamases are a family of subclass B3 (metallo-) beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2139":{"model_id":"2139","model_name":"vanSD","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3440":{"protein_sequence":{"accession":"ACM47284","sequence":"MKNRNKTSHEDDYLLFKNRLSVKILLMMACSILIIAGVYLFILKDNFANVVVAILDSFIYHDRDEAVVVYLRTFKAYEIWLFLIAVMGVFFMIFRRYLDSISKYFKEINRGIDTLVNEDANDITLPPELASTERKINSIRHTLTKRKTDAELAEQRKNDLVMYLAHDLKTPLSSVIGYLNLLRDENQISEELREKYLSISLDKAERLEELINEFFEITRLIFQISRLCTAKSI"},"dna_sequence":{"accession":"EU999036","fmin":"688","fmax":"1390","strand":"+","sequence":"TTGAAAAATAGAAATAAAACCAGTCATGAAGATGACTATTTACTTTTTAAAAACAGATTGTCCGTTAAAATATTGCTTATGATGGCGTGCTCCATTCTGATTATTGCGGGTGTTTATCTGTTTATCTTAAAAGATAATTTTGCAAATGTCGTGGTAGCCATTTTAGACAGCTTTATCTATCATGATCGGGATGAGGCGGTGGTTGTTTATCTGAGAACCTTTAAGGCGTATGAGATATGGCTTTTCCTGATAGCGGTTATGGGTGTGTTTTTTATGATCTTTCGCCGCTATCTGGACAGCATTTCAAAATATTTTAAGGAGATCAACCGTGGGATCGATACTTTGGTGAATGAGGATGCCAACGATATCACATTGCCTCCGGAGTTGGCTTCGACCGAAAGGAAAATCAATTCCATACGGCATACCCTGACGAAACGGAAAACGGACGCTGAGCTTGCAGAGCAAAGGAAAAACGACCTTGTCATGTATCTGGCCCATGACCTGAAGACCCCGCTTTCATCGGTCATAGGATATTTGAACCTATTAAGGGATGAGAATCAGATCTCCGAGGAACTCAGGGAAAAATATCTGTCCATATCATTGGATAAGGCTGAGCGTCTGGAAGAGCTGATCAATGAGTTTTTTGAAATTACGAGGTTAATCTTTCAAATATCACGCTTGTGTACAGCAAAATCAATCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002934","ARO_id":"39368","ARO_name":"vanSD","ARO_description":"vanSD is a mutated vanS variant found in the vanD gene cluster that caused constitutive expression of vanD peptidoglycan synthesis","ARO_category":{"36210":{"category_aro_accession":"3000071","category_aro_cvterm_id":"36210","category_aro_name":"vanS","category_aro_description":"VanS is similar to histidine protein kinases like EnvZ and acts as a response regulator by activating VanR. VanS is required for high level transcription of other van glycopeptide resistance genes.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2240":{"model_id":"2240","model_name":"vanJ","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"3441":{"protein_sequence":{"accession":"NP_627787","sequence":"MVLRSAARPELWKRAPVLTVSALLLGLVMMLHAEIPNRFGSVGSLVETFLPWFGLFVPVLAAGALWRRSAAAVTALVLPVTVWLSLFGGLLGDKSGAGGEFTMASHNVGAENPDPAGTARDLAASGVDVLALEEITAQDREVYEKGLAREYPYHTVQGTVGLWSKLPLSGTRPVDIATDYGPLADTKPADVTMAGNRALRTTVATERGPLVVYVAHLGSVRLNPRAGFWTDSRDRNAWALGEALAADRSERIALLGDLNGTVDDRALAGITSQLHSVQEAAGNGFGFTWPAKFPVARIDQILVRGVEPTGSWTLPATGSDHLPVAAGVSW"},"dna_sequence":{"accession":"NC_003888","fmin":"3968821","fmax":"3969814","strand":"+","sequence":"GTGGTGCTCCGCAGCGCCGCCCGGCCGGAGCTCTGGAAGCGTGCGCCGGTACTCACGGTGTCGGCGCTGTTGCTGGGCCTCGTGATGATGCTGCACGCGGAGATTCCAAATCGGTTCGGGTCCGTCGGCAGCCTGGTCGAGACCTTCCTGCCGTGGTTCGGTCTGTTCGTCCCCGTGCTGGCCGCCGGAGCGCTGTGGCGCCGCTCCGCCGCCGCGGTGACCGCGCTGGTGCTGCCGGTCACGGTGTGGCTGAGCCTCTTCGGCGGGCTGCTCGGCGACAAGTCAGGCGCGGGCGGCGAATTCACCATGGCCTCCCACAACGTCGGCGCCGAGAACCCGGACCCGGCCGGCACCGCCCGCGACCTGGCTGCCTCCGGAGTGGACGTACTGGCGCTGGAGGAGATCACCGCACAGGACCGGGAGGTGTATGAGAAGGGGCTGGCCAGGGAGTATCCGTACCACACGGTGCAGGGCACGGTCGGGTTGTGGAGCAAGCTGCCGCTGTCGGGCACGCGGCCGGTCGACATCGCGACGGACTACGGGCCGCTGGCGGACACCAAACCGGCCGACGTCACGATGGCCGGCAACCGAGCGCTGCGCACCACGGTGGCCACGGAAAGGGGCCCGCTGGTGGTGTACGTGGCCCACCTGGGCTCCGTACGGCTCAATCCTCGGGCGGGGTTCTGGACGGACTCCCGCGACCGGAACGCGTGGGCGCTCGGCGAGGCCCTCGCCGCCGACCGCAGTGAGCGGATCGCGCTGCTCGGCGACCTGAACGGCACCGTGGACGACCGCGCGTTGGCGGGCATCACCTCGCAGCTGCACTCGGTCCAGGAGGCGGCCGGGAACGGGTTCGGCTTCACCTGGCCGGCGAAGTTCCCGGTGGCGCGGATCGACCAGATCCTGGTGCGCGGCGTGGAGCCGACCGGTTCGTGGACGCTGCCCGCCACCGGCAGCGACCACCTGCCTGTGGCGGCGGGGGTCAGCTGGTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36881","NCBI_taxonomy_name":"Streptomyces coelicolor A3(2)","NCBI_taxonomy_id":"100226"}}}},"ARO_accession":"3002914","ARO_id":"39348","ARO_name":"vanJ","ARO_description":"vanJ is a novel membrane protein that confers resistance to teicoplanin and its derivatives in Streptomyces coelicolor by recycling undecaprenol pyrophosphate during cell wall biosynthesis.","ARO_category":{"41419":{"category_aro_accession":"3004255","category_aro_cvterm_id":"41419","category_aro_name":"vanJ membrane protein","category_aro_description":"vanJ and vanJ homologue proteins confer resistance to the teicoplanin.","category_aro_class_name":"AMR Gene Family"},"35948":{"category_aro_accession":"0000029","category_aro_cvterm_id":"35948","category_aro_name":"teicoplanin","category_aro_description":"Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation  and transpeptidation.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2242":{"model_id":"2242","model_name":"vanWI","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3449":{"protein_sequence":{"accession":"WP_005813024.1","sequence":"MLRRKPWVFLLVILFSQLSLSILLGATVTYGAGYAKAPEGLTVWEKDLGGMTKDEAYAVLAEVIPKAVVYDRTVYFLELNQTDQDLKDYLASQYIISTGNVITDAFEYLHRMSRTIPSPELLNQEEVLAQLRKFALDIDQPGKAAEAYYENGEIVIEEGSLGVRLDVDKSWEQLQQSIGMETVPLVTEVIVVHPTTAELEKVKDPLGDYTTYFNPSFHERVTNVRLAAEAINGLILPPGGEFSFNDTVGKREPERGYLPALMYMGNRVVTDDGGGICQDSTTLYQATKQARLEVLERYSHSLPVSYVPLGQDATVAYGALDFRFRNTTQGYLLLNAATGGNWIRVRIFGVADSEHPALDEPDGYPVKPREWSK"},"dna_sequence":{"accession":"NC_007907.1","fmin":"2195400","fmax":"2196522","strand":"-","sequence":"TTACTTTGACCATTCTCTGGGTTTTACAGGATAACCGTCCGGTTCGTCAAGGGCAGGGTGTTCAGAATCGGCCACACCGAAAATTCTTACCCGAATCCAATTGCCGCCTGTAGCTGCATTAAGCAGCAAATAACCCTGAGTCGTGTTCCGAAAGCGGAAATCCAGCGCTCCATAAGCAACCGTAGCATCCTGCCCCAACGGAACATAGGAAACCGGCAGAGAATGGCTGTATCTTTCCAGCACTTCCAGCCTGGCCTGTTTGGTCGCTTGATAAAGAGTGGTCGAATCCTGGCAAATCCCTCCGCCATCATCTGTGACAACTCTATTGCCCATATACATTAAAGCCGGCAAATACCCTCTTTCAGGCTCACGTTTTCCCACCGTATCATTAAAGGAGAATTCACCACCCGGCGGAAGAATAAGTCCATTGATCGCTTCAGCCGCAAGCCGTACATTGGTAACCCGTTCATGAAAGGAAGGGTTAAAATAGGTGGTGTAATCCCCCAAGGGATCTTTGACCTTCTCTAATTCGGCCGTAGTAGGGTGAACCACTATGACCTCCGTAACAAGCGGCACCGTCTCCATGCCTATGCTTTGCTGCAGTTGTTCCCATGATTTGTCCACATCAAGTCTGACTCCCAAACTGCCCTCTTCGATGACGATCTCGCCATTCTCATAATAGGCTTCAGCCGCCTTACCCGGCTGATCGATATCCAGGGCGAACTTGCGGAGCTGAGCAAGAACTTCCTCCTGATTGAGTAACTCAGGAGACGGGATAGTCCTTGACATTCTGTGCAGGTACTCAAAGGCATCCGTAATAACATTTCCGGTGGAAATGATGTATTGACTTGCCAGATAGTCCTTTAGATCTTGATCGGTTTGGTTTAGCTCCAAGAAATAAACCGTCCGGTCATAGACGACTGCCTTGGGGATTACTTCGGCAAGGACTGCATAGGCCTCATCCTTGGTCATCCCACCCAGATCTTTTTCCCAAACCGTCAACCCCTCGGGTGCCTTCGCATAACCCGCACCGTAGGTTACCGTAGCCCCCAAAAGTATAGATAAGCTAAGCTGACTAAATAAAATTACCAAAAGAAAGACCCATGGTTTCCTTCTTAACAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40382","NCBI_taxonomy_name":"Desulfitobacterium hafniense","NCBI_taxonomy_id":"49338"}}}},"ARO_accession":"3003724","ARO_id":"40380","ARO_name":"vanWI","ARO_description":"VanWI is a vanW variant found in the vanI gene cluster","ARO_category":{"36011":{"category_aro_accession":"3000002","category_aro_cvterm_id":"36011","category_aro_name":"vanW","category_aro_description":"vanW is an accessory gene, with unknown function, found on vancomycin resistance operons.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2244":{"model_id":"2244","model_name":"vanSI","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3448":{"protein_sequence":{"accession":"WP_011461302.1","sequence":"MAIKLKSEKSKRKNDYSKLKRKLFLQMLLLVSATAATVILMRSVIQKNFSVGDSIVEFLKNTFYLRDSDAVIIYRYIFLHNIEVITFIVILIFLVILLGFSISWFTKYFDEISDGMDKLVGESTAEIALSAELGFMENKLNQIKSNLEKQKKAALEAEQRKNDLVVYLAHDIKTPLTSVIGYLSLLDEAPDMPPEQKAKYVGITLEKAYRLEQLINEFFEITRFNLQTIVLNKEKINLLFMLQQLADEFYPMLTPAQGKQVSVNVPEGLTLWGDADKLARVFNNILKNALAYSYENSVIDISAQKQDKNTVITFTNQGNPIPQEKLETIFEKFFRLDTSRSTNTGGSGLGLAIAKEIANAHGGNIFVQSNSEKTVFTVVLPQKQEKATDRHC"},"dna_sequence":{"accession":"NC_007907.1","fmin":"4200836","fmax":"4202015","strand":"-","sequence":"TTAGCAATGCCGATCGGTTGCCTTTTCTTGTTTTTGCGGAAGCACGACAGTAAATACGGTCTTTTCTGAATTACTTTGCACGAAAATATTGCCTCCATGGGCGTTGGCTATTTCTTTGGCTATAGCCAATCCAAGTCCGGAACCGCCTGTATTGGTAGAGCGGGATGTGTCCAGCCGAAAGAACTTCTCAAATATCGTTTCCAGTTTTTCTTGTGGGATCGGATTACCTTGATTCGTAAACGTTATAACAGTGTTTTTGTCCTGCTTTTGAGCAGAAATATCGATGACGCTGTTTTCATAGCTATAGGCCAGCGCATTTTTCAAAATATTATTGAACACACGGGCCAGTTTGTCGGCATCCCCCCACAGTGTGAGACCTTCAGGGACATTGACGGACACCTGCTTTCCCTGGGCAGGCGTCAGCATGGGATAGAATTCATCGGCCAACTGCTGGAGCATAAACAGTAAATTGATTTTTTCTTTATTCAAGACAATCGTTTGCAGATTAAATCTTGTGATCTCAAAAAACTCATTGATCAGCTGCTCCAAGCGATACGCTTTTTCCAAGGTAATACCGACATATTTTGCCTTCTGTTCCGGAGGCATATCGGGTGCTTCATCGAGAAGACTTAAGTATCCTATCACGGAGGTCAGGGGTGTCTTGATATCATGAGCCAAATAAACGACCAGATCATTTTTACGCTGCTCTGCTTCAAGAGCAGCTTTCTTTTGTTTTTCCAAGTTGCTTTTTATCTGATTCAGCTTATTTTCCATAAAACCCAATTCCGCTGATAAGGCAATTTCGGCAGTAGACTCCCCAACAAGTTTATCCATTCCGTCACTGATTTCGTCAAAATATTTAGTAAACCAGGAGATTGAAAAACCAAGCAAAATAACCAAGAATATAAGAATTACAATAAATGTAATAACTTCTATATTATGAAGAAATATATAACGATAAATTATTACAGCATCGCTGTCACGCAGATAAAAGGTATTCTTTAAAAATTCTACAATACTGTCTCCAACACTAAAGTTCTTTTGAATTACAGAACGCATGAGGATCACAGTTGCTGCCGTGGCAGAAACCAGCAGAAGCATTTGCAAAAATAATTTTCTTTTTAATTTTGAATAATCATTTTTTCTTTTGCTTTTCTCACTTTTCAATTTTATAGCCAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40382","NCBI_taxonomy_name":"Desulfitobacterium hafniense","NCBI_taxonomy_id":"49338"}}}},"ARO_accession":"3003726","ARO_id":"40383","ARO_name":"vanSI","ARO_description":"VanSI is a vanS variant found in the vanI gene cluster; it is a histidine kinase.","ARO_category":{"36210":{"category_aro_accession":"3000071","category_aro_cvterm_id":"36210","category_aro_name":"vanS","category_aro_description":"VanS is similar to histidine protein kinases like EnvZ and acts as a response regulator by activating VanR. VanS is required for high level transcription of other van glycopeptide resistance genes.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2248":{"model_id":"2248","model_name":"fusD","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"375"}},"model_sequences":{"sequence":{"3506":{"protein_sequence":{"accession":"WP_011303797","sequence":"MEKQLYPYQFNYIKERVAHLVNAYNSVNDPNTIASIKDVTRDEILSTFNSRNTTIRSNVEKLMNVQLTKEQAQKILTTIQMYVKPFEHPSNKQVTNLFKKVKKLKTPLISDEVLQTSTYIGWNDIASNRKFIIYYDNFGKLNGVYGDISNQTVKSFCSICNKESRVALFMRKTRTGNDGQYTKKGDYICFDSTLCNHQISDLSHFHHFLNKIQ"},"dna_sequence":{"accession":"NZ_CP014057","fmin":"2256545","fmax":"2257187","strand":"+","sequence":"ATGGAAAAACAACTTTACCCTTATCAATTTAATTATATAAAAGAACGCGTTGCACATTTAGTCAATGCTTATAATTCGGTCAACGATCCCAATACAATCGCTTCAATCAAAGATATCACACGCGATGAAATACTCAATACATTTAACTCGAGAGACACTACAATTCGTTCAAATGTTGAAAAGCTCATGAATGTACAACTAACTAAAGAACAAGCTCAAAAAATTTTAACGACCATACAAATGTATGTTAAGCCATTTGAACATCCGAGTAAAAAGCAAGTCACTAACCTTTTTAAAAAAGTTAAAAAGCTAAAAACACCTCTTATCAGTGATGAAGTACTACAAACAAGTACGTATATCGGTTGGAATGATATTGCTTCAAATAGAAAATTCATCATTTATTATGATAACTTTGGAAAATTAAACGGTGTATACGGAGACATTTCTAACCAAACTGTCAAAGGTTTCTGCTCTATTTGCAATAAAGAATCCCGTGTTGCTCTATTTATGCGAAAAACACGTACTGGCAATGATGGCCAATATACCAAAAAAGGTGACTACATTTGTTTTGATAGCACATTATGTAACCATCAAATATCCGATTTATCGCACTTCCATCATTTTTTGAATAAGATTCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40387","NCBI_taxonomy_name":"Staphylococcus saprophyticus","NCBI_taxonomy_id":"29385"}}}},"ARO_accession":"3003731","ARO_id":"40386","ARO_name":"fusD","ARO_description":"A specific fusidic acid resistance gene conferring intrinsic resistance in the bacteria Staphylococcus saprophyticus.","ARO_category":{"39459":{"category_aro_accession":"3003025","category_aro_cvterm_id":"39459","category_aro_name":"fusidic acid inactivation enzyme","category_aro_description":"Enzymes that confer resistance to fusidic acid by inactivation","category_aro_class_name":"AMR Gene Family"},"37139":{"category_aro_accession":"3000759","category_aro_cvterm_id":"37139","category_aro_name":"fusidic acid","category_aro_description":"Fusidic acid is the only commercially available fusidane, a group of steroid-like antibiotics. It is most active against Gram-positive bacteria, and acts by inhibiting elongation factor G to  block protein synthesis.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2249":{"model_id":"2249","model_name":"LpxA","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3337":"Q72K","3335":"H159D","3336":"G68D"},"clinical":{"3337":"Q72K","3335":"H159D","3336":"G68D"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"},"41343":{"param_type":"deletion mutation from nucleotide sequence","param_description":"A subtype of the deletion mutation detection model parameter. This parameter is used when a set of deletion mutations is reported in a nucleotide sequence format. Such mutations may be of variable length - possibly causing a frameshift, but not premature termination of functional knockout. Mutation parameters of this type are reported in the CARD with the notation: [-]nt[position]:[nucleotides].","param_type_id":"41343","param_value":{"8021":"-nt364:445","8022":"-nt391:30","8023":"-nt76:2"}}},"model_sequences":{"sequence":{"3505":{"protein_sequence":{"accession":"AJF82049.1","sequence":"MSNHDLIHSTAIIDPSAVIASDVQIGPYCIIGPQVTIGAGTKLHSHVVVGGFTRIGQNNEIFQFASVGEVCQDLKYKGEETWLEIGNNNLIREHCSLHRGTVQDNALTKIGSHNLLMVNTHIAHDCIVGDHNIFANNVGVAGHVHIGDHVIVGGNSGIHQFCKIDSYSMIGGASLILKDVPAYVMASGNPAHAFGINIEGMRRKGWSKNTIQGLREAYKLIFKSGLTSVQAIDQIKSEILPSVPEAQLLIDSLEQSERGIVR"},"dna_sequence":{"accession":"CP010781.1","fmin":"2255674","fmax":"2256463","strand":"-","sequence":"TTAGCGCACAATTCCACGCTCTGATTGTTCAAGAGAATCAATCAAGAGTTGAGCTTCTGGAACTGAAGGTAAAATTTCACTTTTAATTTGGTCAATAGCTTGAACAGAAGTTAATCCAGATTTAAATATCAATTTATAAGCTTCTCTTAAGCCTTGAATTGTATTTTTAGACCAACCTTTTCTTCGCATACCTTCAATATTTATACCAAACGCATGTGCAGGGTTACCAGAAGCCATCACATAGGCTGGAACATCTTTAAGGATCAAAGAAGCCCCACCAATCATGCTATAAGAATCGATCTTACAGAATTGATGAATTCCAGAATTACCACCCACAATAACGTGATCACCAATATGTACATGTCCAGCGACACCTACATTATTAGCAAAGATATTATGGTCACCTACGATACAATCATGTGCAATATGTGTATTTACCATTAATAGGTTATGACTACCTATCTTGGTTAATGCATTATCTTGCACCGTACCTCTATGTAAGCTGCAATGTTCGCGAATTAGATTATTGTTACCAATTTCAAGCCACGTTTCTTCACCTTTATATTTGAGGTCTTGGCAAACTTCGCCAACACTTGCAAATTGAAAGATTTCGTTATTTTGGCCAATTCTGGTAAAACCACCTACAACCACATGAGAATGTAATTTAGTACCAGCACCAATAGTCACTTGAGGACCGATAATACAATAAGGTCCTATTTGAACATCTGAAGCAATCACTGCAGATGGATCAATAATGGCGGTAGAATGGATTAAATCGTGATTGCTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003573","ARO_id":"40183","ARO_name":"LpxA","ARO_description":"The LpxA gene is widely known to be involved in the biosynthesis of lipid A in Gram-negative bacteria and mutations to this gene may cause resistance to antimicrobial peptides that target the outer membrane","ARO_category":{"40191":{"category_aro_accession":"3003581","category_aro_cvterm_id":"40191","category_aro_name":"Acinetobacter mutant Lpx gene conferring resistance to colistin","category_aro_description":"These genes are involved in the biosynthesis of lipid A in Gram-negative bacteria and mutations to this gene may cause resistance to antimicrobial peptides that target the outer membrane. Mutation by absence or insertion of ISAba11 sequence is a known cause of resistance in Acinetobacter baumannii\u25bf.","category_aro_class_name":"AMR Gene Family"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2251":{"model_id":"2251","model_name":"LpxC","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3342":"P30L"},"clinical":{"3342":"P30L"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"},"41343":{"param_type":"deletion mutation from nucleotide sequence","param_description":"A subtype of the deletion mutation detection model parameter. This parameter is used when a set of deletion mutations is reported in a nucleotide sequence format. Such mutations may be of variable length - possibly causing a frameshift, but not premature termination of functional knockout. Mutation parameters of this type are reported in the CARD with the notation: [-]nt[position]:[nucleotides].","param_type_id":"41343","param_value":{"8019":"-nt858:84","8020":"-nt135:1"}}},"model_sequences":{"sequence":{"3508":{"protein_sequence":{"accession":"AJF83452.1","sequence":"MVKQRTLNRVVKASGIGLHSGQKVMINFIPHTVDGGIVFRRIDLDPPVDIPANALLIQEAFMCSNLVTGDIKVGTIEHVMSAIAGLGIDNLIVEVSASEVPIMDGSAGPFIYLLMQGGLREQDAPKKFIKILKPVEALIDDKKAIFSPHNGFQLNFTIDFDHPAFAKEYQSATIDFSTETFVYEVSEARTFGFMKDLDYLKANNLALGASLDNAIGVDDTGVVNEEGLRFADEFVRHKILDAVGDLYLLGHQIIAKFDGYKSGHALNNQLLRNVQSDPSNYEIVTFDDEKDCPIPYVSVT"},"dna_sequence":{"accession":"CP010781.1","fmin":"3758031","fmax":"3758934","strand":"-","sequence":"TTATGTCACACTCACGTATGGAATTGGACAGTCTTTCTCGTCATCAAATGTTACAATTTCATAATTACTCGGATCGCTTTGAACATTGCGTAATAGCTGATTATTTAAGGCATGTCCTGATTTATAGCCATCAAACTTGGCAATAATTTGATGACCAAGTAAATACAAATCACCAACTGCATCTAAAATTTTGTGACGAACAAACTCATCGGCAAATCGTAAACCTTCTTCGTTTACAACACCTGTATCATCTACGCCAATTGCATTATCTAGACTTGCTCCTAAAGCTAAATTATTTGCTTTAAGGTAATCCAAGTCTTTCATAAAACCAAAAGTTCGTGCCTCACTGACCTCATACACAAACGTTTCAGTAGAAAAATCGATAGTTGCAGACTGATATTCTTTGGCAAATGCAGGATGATCAAAATCAATCGTAAAGTTAAGCTGAAAGCCATTATGCGGGCTGAATATTGCTTTTTTATCATCAATTAAAGCCTCAACTGGCTTTAATATTTTTATAAATTTCTTAGGAGCATCTTGTTCACGCAAGCCACCTTGCATGAGCAAATAAATAAATGGACCAGCACTACCATCCATAATTGGAACTTCAGAAGCAGACACTTCCACAATTAAGTTATCGATTCCTAAACCGGCAATCGCACTCATCACATGTTCGATTGTCCCGACTTTAATATCGCCAGTAACAAGATTTGAACACATAAATGCTTCTTGAATCAGCAATGCATTAGCAGGAATATCGACAGGTGGATCCAAATCGATACGGCGAAATACAATACCTCCATCCACGGTATGTGGAATGAAATTGATCATCACTTTTTGACCGCTATGAAGACCTATTCCACTCGCTTTTACCACACGATTGAGAGTACGCTGTTTCACCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003574","ARO_id":"40184","ARO_name":"LpxC","ARO_description":"The LpxC gene is widely known to be involved in the biosynthesis of lipid A in Gram-negative bacteria and mutations to this gene may cause resistance to antimicrobial peptides that target the outer membrane","ARO_category":{"40191":{"category_aro_accession":"3003581","category_aro_cvterm_id":"40191","category_aro_name":"Acinetobacter mutant Lpx gene conferring resistance to colistin","category_aro_description":"These genes are involved in the biosynthesis of lipid A in Gram-negative bacteria and mutations to this gene may cause resistance to antimicrobial peptides that target the outer membrane. Mutation by absence or insertion of ISAba11 sequence is a known cause of resistance in Acinetobacter baumannii\u25bf.","category_aro_class_name":"AMR Gene Family"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2257":{"model_id":"2257","model_name":"Planobispora rosea EF-Tu mutants conferring resistance to inhibitor GE2270A","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3418":"G261S","3419":"V278A","3420":"G279A","3421":"V295C"},"clinical":{"3418":"G261S","3419":"V278A","3420":"G279A","3421":"V295C"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3512":{"protein_sequence":{"accession":"AAB39605.1","sequence":"MAKAKFERTKPHMNIGTIGHIDHGKTTLTAAITKVLHDRYPELNKATPFDKIDKAPEEKARGITISIAHVEYQTEKRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATAGPMPQTKEHVLLARQVGVPYIVVALNKADMVDDEEILELVELEVRELLSAQEFPGDDLPVVRVSALKALEGDEKWADSIIELMNAVDENIPEPPRDTDKPFLMPIEDVFSITGRGTVVTGRIERGVVKVNEQVDIIGIKSEKTTTTVTSIEMFNKMLDEGHAGDNAALLLRGIKREQVERGQCIIKPGTTTPHTEFEAQVYILSKDEGGRHTPFFNNYRPQFYFRTTDVTGVVNLPEGTEMVMPGDNTEMTVQLIQPIAMEEGLKFAIREGGRTVGAGRVTKILK"},"dna_sequence":{"accession":"U67308.1","fmin":"476","fmax":"1670","strand":"+","sequence":"GTGGCCAAGGCCAAGTTCGAGCGGACCAAGCCGCACATGAACATCGGCACCATTGGGCATATCGACCACGGCAAGACCACTCTGACCGCGGCGATCACCAAGGTGCTCCACGACCGGTACCCCGAGCTGAACAAGGCGACCCCGTTCGACAAGATCGACAAGGCGCCCGAGGAGAAGGCTCGTGGCATCACGATCTCCATCGCGCACGTCGAGTACCAGACCGAGAAGCGCCACTACGCCCACGTGGACTGCCCCGGTCACGCCGACTACGTGAAGAACATGATCACCGGTGCTGCTCAGATGGACGGCGCCATCCTCGTGGTCGCCGCCACCGCCGGCCCGATGCCGCAGACGAAGGAGCACGTCCTCCTGGCCCGTCAGGTCGGCGTCCCCTACATCGTCGTGGCCCTGAACAAGGCCGACATGGTGGACGACGAGGAGATCCTGGAGCTCGTCGAGCTCGAGGTCCGCGAGCTGCTCTCGGCTCAGGAGTTCCCCGGCGACGACCTGCCGGTCGTGCGCGTCTCCGCTCTCAAGGCCCTCGAGGGCGACGAGAAGTGGGCCGACAGCATCATCGAGCTGATGAACGCTGTGGACGAGAACATCCCCGAGCCGCCGCGTGACACCGACAAGCCGTTCCTCATGCCGATCGAGGACGTCTTCTCGATCACCGGTCGTGGAACCGTCGTCACCGGCCGTATCGAGCGCGGTGTCGTCAAGGTCAACGAGCAGGTCGACATCATCGGCATCAAGAGCGAGAAGACCACGACCACCGTCACCAGCATCGAGATGTTCAACAAGATGCTGGACGAGGGCCACGCGGGTGACAACGCGGCCCTGCTGCTCCGCGGCATCAAGCGTGAGCAGGTCGAGCGCGGCCAGTGCATCATCAAGCCGGGCACGACCACCCCGCACACCGAGTTCGAGGCTCAGGTCTACATCCTGTCCAAGGACGAGGGCGGCCGCCACACGCCGTTCTTCAACAACTACCGTCCGCAGTTCTACTTCCGTACGACTGACGTGACCGGTGTCGTGAACCTGCCCGAGGGCACCGAGATGGTCATGCCCGGTGACAACACCGAGATGACCGTCCAGCTCATCCAGCCGATCGCGATGGAGGAAGGCCTCAAGTTCGCGATCCGTGAGGGTGGCCGGACCGTCGGCGCCGGCCGCGTCACCAAGATCCTCAAGTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40395","NCBI_taxonomy_name":"Planobispora rosea","NCBI_taxonomy_id":"35762"}}}},"ARO_accession":"3003361","ARO_id":"39945","ARO_name":"Planobispora rosea EF-Tu mutants conferring resistance to inhibitor GE2270A","ARO_description":"Sequence variants of Planobispora rosea elongation factor Tu that confer resistance to inhibitor GE2270A","ARO_category":{"37711":{"category_aro_accession":"3001312","category_aro_cvterm_id":"37711","category_aro_name":"elfamycin resistant EF-Tu","category_aro_description":"Sequence variants of elongation factor Tu that confer resistance to elfamycin antibiotics.","category_aro_class_name":"AMR Gene Family"},"36725":{"category_aro_accession":"3000586","category_aro_cvterm_id":"36725","category_aro_name":"pulvomycin","category_aro_description":"Pulvomycin is a polyketide antibiotic that binds elongation factor Tu (EF-Tu) to inhibit protein biosynthesis by preventing the formation of the ternary complex (EF-Tu*GTP*aa-tRNA). Phenotypically, it was shown that pulvomycin sensitivity is dominant over resistance.","category_aro_class_name":"Antibiotic"},"37636":{"category_aro_accession":"3001237","category_aro_cvterm_id":"37636","category_aro_name":"GE2270A","category_aro_description":"GE2270A is the model molecule of cyclic thiazolyl peptide elfamycins. GE2270A is produced by Planobispora rosea. Biosynthesis of the molecule has been shown to originate as a ribosomally synthesized peptide that undergoes significant post-translational modification. Clinical use of cyclic thiazolyl peptides is hindered by their low water solubility and bioavailability.","category_aro_class_name":"Antibiotic"},"37641":{"category_aro_accession":"3001242","category_aro_cvterm_id":"37641","category_aro_name":"enacyloxin IIa","category_aro_description":"Enacyloxin IIa is structurally distinct but acts in a similar mechanism to kirromycin-like elfamycins. It prohibits the transfer of the amino acid at the A site to the elongating peptide chain. It is most likely that the mechanism of action is that EF-Tu*GDP is locked in the EF-Tu*GTP form, and EF-Tu*GDP*aa-tRNA is immobilized on the ribosome. It is an open question whether enacyloxin IIa actually belongs to the kirromycin-like group of elfamycins due to their high similarity.","category_aro_class_name":"Antibiotic"},"39998":{"category_aro_accession":"3003414","category_aro_cvterm_id":"39998","category_aro_name":"LFF571","category_aro_description":"LFF571 is a novel semi-synthetic thiopeptide antibiotic derived from GE2270. It has been shown to possess potent in vitro and in vivo activity against Gram-positive bacteria. It is hypothesized that it a translation inhibitor leading to cell death.","category_aro_class_name":"Antibiotic"},"37618":{"category_aro_accession":"3001219","category_aro_cvterm_id":"37618","category_aro_name":"elfamycin antibiotic","category_aro_description":"Elfamycins are molecules that inhibit bacterial elongation factor Tu (EF-Tu), a key protein which brings aminoacyl-tRNA (aa-tRNA) to the ribosome during protein synthesis. Elfamycins defined by their target (EF-Tu), rather than a conserved chemical backbone. Elfamycins follow two mechanisms to disrupt protein synthesis: 1. kirromycins and enacyloxin fix EF-Tu in the GTP bound conformation and lock EF-Tu onto the ribosome, and 2. pulvomycin and GE2270 cover the binding site of aa-tRNA disallowing EF-Tu from being charged with aa-tRNA. All elfamycins cause increased the affinity of EF-Tu for GTP.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2259":{"model_id":"2259","model_name":"mphG","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"3513":{"protein_sequence":{"accession":"BAL43359","sequence":"MKNRDIQKLAERNGLILSDEMSFNEMGIDFKVGFATDRDGTKWLLRIPRRTTLGEQIANEKRILQLVSKYLSVQVPDWRIANEKLVAYPLLDGKPALTYDAETYEVTWNMSKENDLYIPSLAKALIELHSIPTEEVLRNNLKILTPEQVRNEISERLILVKSELGINAELELRYQKWLDNDALWPNFTKFIHGDLYAGHTLTHHNGEVCGIIDWSTAQVSDIAQDFSGHVTVFGEESLKNLIAAYEKQGGEVWDKLFEQAVERAAAAPLAYGYFALETQDEIHLSSAKLQLGVE"},"dna_sequence":{"accession":"AB571865","fmin":"143423","fmax":"144308","strand":"-","sequence":"CTACTCAACACCTAACTGTAATTTTGCAGAACTAAGATGAATTTCATCTTGTGTTTCTAAAGCAAAATATCCATAAGCTAGAGGTGCGGCAGCAGCTCGTTCAACTGCTTGTTCAAACAGTTTATCCCATACTTCTCCACCTTGTTTTTCGTATGCCGCAATTAAATTTTTCAGACTTTCTTCACCGAAAACAGTAACGTGACCTGAAAAATCTTGTGCTATATCGCTGACTTGTGCAGTTGACCAATCAATAATTCCACAAACTTCTCCATTATGATGAGTAAGTGTATGACCTGCATACAAATCACCGTGAATGAATTTTGTAAAATTCGGCCATAAGGCATCATTATCCAGCCATTTTTGGTACCGAAGTTCTAATTCGGCATTTATCCCTAATTCAGATTTCACCAAAATCAATCTTTCAGAAATCTCATTTCTAACCTGTTCAGGTGTCAAAATTTTTAGATTATTACGAAGTACTTCTTCCGTAGGAATTGAATGAAGTTCTATAAGTGCTTTCGCTAATGATGGTATATAAAGGTCGTTTTCTTTAGACATATTCCAGGTTACTTCATAAGTCTCCGCATCATAAGTAAGTGCAGGTTTTCCATCGAGCAAAGGATAGGCTACCAGTTTTTCATTAGCTATACGCCAATCAGGAACTTGAACCGAAAGGTATTTCGACACCAATTGAAGAATGCGTTTCTCATTCGCAATCTGTTCGCCTAAGGTTGTTCTTCTTGGAATACGCAACAACCACTTTGTGCCATCCCTATCTGTAGCGAAACCAACCTTAAAATCAATTCCCATTTCATTAAAACTCATTTCATCCGAAAGAATTAACCCATTTCTTTCCGCTAATTTTTGAATATCTCTATTTTTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40398","NCBI_taxonomy_name":"Photobacterium damselae subsp. damselae","NCBI_taxonomy_id":"85581"}}}},"ARO_accession":"3003742","ARO_id":"40397","ARO_name":"mphG","ARO_description":"The mphG gene encodes a macrolide 2'-phosphotransferase found in Photobacterium damselae sharing sequence similarity to mphA in E. coli.","ARO_category":{"36472":{"category_aro_accession":"3000333","category_aro_cvterm_id":"36472","category_aro_name":"macrolide phosphotransferase (MPH)","category_aro_description":"Macrolide phosphotransferases (MPH) are enzymes encoded by macrolide phosphotransferase genes (mph genes). These enzymes phosphorylate macrolides in GTP dependent manner at 2'-OH of desosamine sugar thereby inactivating them. Characterized MPH's are differentiated based on their substrate specificity.","category_aro_class_name":"AMR Gene Family"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2215":{"model_id":"2215","model_name":"Pseudomonas aeruginosa gyrA and parC conferring resistance to fluoroquinolone","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3986":"S80L"},"clinical":{"3986":"S80L"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1400"}},"model_sequences":{"sequence":{"3408":{"protein_sequence":{"accession":"BAA37152.1","sequence":"MSESLDLSLEGVERRSLAEFTEQAYLNYSMYVIMDRALPHIGDGLKPVQRRIVYAMSELGLDADSKHKKSARTVGDVLGKFHPHGDSACYEAMVLMAQPFSYRYPLVDGQGNWGAPDDPKSFAAMRYTEARLSRYSEVLLSELGQGTVDWVPNFDGTLDEPAVLPARLPNLLLNGTTGIAVGMATDVPPHNLREVASACVRLLDQPGATVAELCEHVPGPDFPTEAEIITPRADLQKVYETGRGSVRMRAVYRFEDGDIVIHALPHQVSGSKVLEQIAGQMQAKKLPMVADLRDESDHENPTRIVIIPRSNRVDVEELMTHLFATTDLETSYRVNLNIIGLDGKPAVKDLRQLLSEWLQFRIGTVRRRLQFRLDKVERRLHLLDGLLIAFLNLDEVIHIIRTEDQPKAVLMERFELSEVQADYILDTRLRQLARLEEMKIRGEQEELLKEQKRLQTLLGSEAKLKKLVREELIKDAETYGDDRRSPIVARAEARALSETELMPTEPVTVVLSEKGWVRCAKGHDIDAAGLSYKAGDGFKAAAPGRSNQYAVFIDSTGRSYSLPAHSLPSARGQGEPLSGRLTPPPGASFECVLLPDDDALFVIASDAGYGFVVKGEDLQAKNKAGKALLSLPNGSAVVAPRPVRDVEQDWLAAVTTEGRLLLFKVSDLPQLGKGKGNKIIGIPGERVASREEYLTDLAVLPAGATLVLQAGKRTLSLKGDDLEHYKGERGRRGNKLPRGFQRVDSLLVDIPPQD"},"dna_sequence":{"accession":"AB003428.1","fmin":"151","fmax":"2416","strand":"+","sequence":"ATGAGCGAATCCCTCGATCTGAGCCTGGAAGGGGTCGAACGCCGGTCGTTGGCCGAGTTCACCGAGCAGGCCTATCTGAACTATTCCATGTACGTGATCATGGACCGCGCCCTGCCGCATATCGGCGACGGCCTGAAACCGGTGCAGCGACGCATCGTCTACGCCATGAGCGAACTGGGGCTGGATGCCGATTCCAAGCACAAGAAGTCGGCGCGCACCGTCGGCGACGTGCTCGGCAAGTTCCACCCGCACGGCGACTCGGCCTGCTACGAGGCCATGGTGCTGATGGCGCAGCCGTTCTCCTATCGCTATCCGCTGGTGGACGGCCAGGGCAACTGGGGGGCTCCGGACGATCCCAAGTCCTTCGCCGCCATGCGTTATACCGAGGCGCGCCTGTCGCGCTATTCCGAGGTGCTGCTCAGCGAACTGGGCCAGGGTACCGTGGACTGGGTACCGAACTTCGACGGCACCCTCGACGAGCCGGCCGTGCTGCCGGCCCGCCTGCCCAACCTGCTGCTCAACGGCACCACCGGCATCGCGGTGGGCATGGCCACCGACGTGCCGCCGCACAACCTGCGGGAAGTCGCGTCGGCCTGCGTGCGCCTGCTCGACCAGCCGGGCGCGACGGTCGCCGAATTGTGCGAACACGTGCCGGGCCCGGACTTCCCCACCGAAGCCGAGATCATCACCCCGCGCGCCGACCTGCAGAAGGTCTACGAGACCGGCCGCGGTTCGGTGCGCATGCGCGCGGTGTACCGCTTCGAGGACGGCGATATCGTCATCCACGCCCTGCCGCACCAGGTGTCCGGTTCCAAGGTGCTGGAACAGATCGCCGGGCAGATGCAGGCCAAGAAGCTGCCGATGGTGGCCGACCTGCGCGACGAGTCGGACCACGAGAACCCGACCCGCATCGTCATCATCCCGCGTTCGAACCGGGTCGATGTCGAAGAGCTGATGACCCATCTGTTCGCCACCACCGACCTGGAGACCAGCTACCGGGTCAACCTGAACATCATCGGCCTCGACGGCAAGCCGGCAGTCAAGGACCTGCGCCAGTTGCTCTCGGAGTGGCTGCAGTTCCGCATCGGCACCGTGCGTCGACGCCTGCAGTTCCGCCTGGACAAGGTCGAGCGCCGCCTGCATCTGCTGGATGGCTTGCTGATCGCCTTCCTCAACCTCGACGAGGTGATCCACATCATCCGCACCGAGGACCAGCCCAAGGCGGTGCTGATGGAGCGCTTCGAACTCAGCGAGGTGCAGGCCGACTACATCCTCGACACCCGCCTGCGCCAGTTGGCACGCCTGGAAGAGATGAAGATCCGCGGCGAGCAGGAAGAGTTGCTGAAGGAGCAGAAGCGCCTGCAGACCCTGCTCGGCAGCGAGGCCAAGCTGAAGAAGCTGGTGCGCGAGGAGCTGATCAAGGACGCCGAGACCTACGGCGACGACCGCCGTTCGCCGATCGTCGCCCGCGCCGAGGCCCGCGCGCTGTCGGAAACCGAGCTGATGCCCACCGAACCGGTGACCGTGGTGCTCTCGGAAAAAGGCTGGGTGCGTTGCGCCAAGGGCCACGACATCGACGCCGCCGGCCTCTCCTACAAGGCCGGCGACGGCTTCAAGGCCGCCGCGCCGGGACGCTCGAACCAGTATGCGGTGTTCATCGACTCCACCGGGCGCAGCTACTCGCTGCCGGCCCACAGCCTGCCGTCCGCGCGAGGCCAGGGCGAGCCACTCAGCGGCCGGCTGACGCCGCCGCCGGGGGCCAGCTTCGAATGCGTGCTGCTGCCGGACGACGATGCGCTGTTCGTGATCGCTTCCGACGCCGGCTATGGTTTCGTGGTCAAGGGCGAGGACCTGCAGGCCAAGAACAAGGCCGGCAAGGCCCTGCTCAGCCTGCCCAACGGCTCCGCCGTGGTGGCGCCGCGCCCGGTGCGCGATGTGGAGCAGGATTGGCTGGCGGCCGTGACGACCGAGGGCCGTCTGCTATTGTTCAAGGTCTCCGACCTGCCGCAGCTCGGCAAGGGCAAGGGCAACAAGATCATCGGCATCCCCGGCGAACGCGTGGCCAGCCGCGAGGAATACCTCACCGACCTGGCTGTTCTGCCAGCCGGGGCGACGTTGGTCCTGCAGGCCGGAAAGCGTACCCTGTCGCTCAAGGGCGACGACCTGGAACACTACAAGGGGGAGCGAGGCCGGCGAGGCAACAAGCTGCCGCGCGGTTTCCAGCGCGTCGACAGCCTGCTGGTGGATATTCCGCCACAGGATTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3003702","ARO_id":"40355","ARO_name":"Pseudomonas aeruginosa gyrA and parC conferring resistance to fluoroquinolone","ARO_description":"Point mutation in Pseudomonas aeruginosa parC resulting in fluoroquinolone resistance also requiring a gyrA mutation.","ARO_category":{"36913":{"category_aro_accession":"3000619","category_aro_cvterm_id":"36913","category_aro_name":"fluoroquinolone resistant parC","category_aro_description":"ParC is a subunit of topoisomerase IV, which decatenates and relaxes DNA to allow access to genes for transcription or translation. Point mutations in ParC prevent fluoroquinolone antibiotics from inhibiting DNA synthesis, and confer low-level resistance. Higher-level resistance results from both gyrA and parC mutations.","category_aro_class_name":"AMR Gene Family"},"39876":{"category_aro_accession":"3003292","category_aro_cvterm_id":"39876","category_aro_name":"fluoroquinolone resistant gyrA","category_aro_description":"DNA gyrase is responsible for DNA supercoiling and consists of two alpha and two beta subunits. GyrA point mutations confer resistance by preventing fluoroquinolone antibiotics from binding the alpha-subunit.","category_aro_class_name":"AMR Gene Family"},"40471":{"category_aro_accession":"3003786","category_aro_cvterm_id":"40471","category_aro_name":"fluoroquinolone self resistant parC","category_aro_description":"Inherent parC resistance to fluoroquinolone from an antibiotic producer. The presence of these genes confers self-resistance to the antibiotic it produces.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"37142":{"category_aro_accession":"3000762","category_aro_cvterm_id":"37142","category_aro_name":"pefloxacin","category_aro_description":"Pefloxacin is structurally and functionally similar to norfloxacin. It is poorly active against mycobacteria, while anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"40338":{"category_aro_accession":"3003690","category_aro_cvterm_id":"40338","category_aro_name":"sitafloxacin","category_aro_description":"Sitafloxacin is a fluoroquinolone active against multi-resistant Gram-positive and negative pathogens. Sitafloxacin shows inhibitory activity against DNA gyrase and topoisomerase IV, which blocks bacterial DNA replication, thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"40463":{"category_aro_accession":"3003780","category_aro_cvterm_id":"40463","category_aro_name":"nybomycin","category_aro_description":"A  heterocyclic antibiotic that targets mutant gyrA (type II topoisomerase) containing an S84L substitution, counteracting acquired quinolone resistance. It is effective against quinolone-resistant Gram-positive bacteria including S. aureus and E. faecalis. Due to its ability to counteract quinolone resistance by targeting the mutant form of the gyrA protein, it is classified as a reverse antibiotic (RA).","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2224":{"model_id":"2224","model_name":"Pseudomonas aeruginosa oprD with mutation conferring resistance to imipenem","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3176":"Q142X"},"clinical":{"3176":"Q142X"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"3421":{"protein_sequence":{"accession":"NP_249649.1","sequence":"MKVMKWSAIALAVSAGSTQFAVADAFVSDQAEAKGFIEDSSLDLLLRNYYFNRDGKSGSGDRVDWTQGFLTTYESGFTQGTVGFGVDAFGYLGLKLDGTSDKTGTGNLPVMNDGKPRDDYSRAGGAVKVRISKTMLKWGEMQPTAPVFAAGGSRLFPQTATGFQLQSSEFEGLDLEAGHFTEGKEPTTVKSRGELYATYAGETAKSADFIGGRYAITDNLSASLYGAELEDIYRQYYLNSNYTIPLASDQSLGFDFNIYRTNDEGKAKAGDISNTTWSLAAAYTLDAHTFTLAYQKVHGDQPFDYIGFGRNGSGAGGDSIFLANSVQYSDFNGPGEKSWQARYDLNLASYGVPGLTFMVRYINGKDIDGTKMSDNNVGYKNYGYGEDGKHHETNLEAKYVVQSGPAKDLSFRIRQAWHRANADQGEGDQNEFRLIVDYPLSIL"},"dna_sequence":{"accession":"NC_002516.2","fmin":"1043982","fmax":"1045314","strand":"-","sequence":"TTACAGGATCGACAGCGGATAGTCGACGATCAGGCGGAACTCGTTCTGGTCGCCTTCGCCCTGGTCGGCGTTGGCACGGTGCCAGGCCTGGCGGATGCGGAACGACAGGTCCTTGGCCGGACCGGACTGGACCACGTACTTGGCTTCGAGGTTGGTTTCGTGGTGCTTGCCATCCTCGCCGTAGCCGTAGTTCTTATAGCCGACGTTGTTGTCAGACATCTTGGTGCCATCGATGTCCTTGCCATTGATATAGCGGACCATGAAAGTCAGGCCGGGAACGCCATAGGAGGCTAGGTTCAGGTCGTAGCGAGCCTGCCAGGATTTCTCGCCAGGGCCGTTGAAGTCGGAGTACTGGACAGAGTTGGCGAGGAAAATCGAGTCGCCACCTGCGCCAGAGCCGTTGCGGCCGAAGCCGATATAATCAAACGGCTGATCGCCATGGACCTTCTGGTAGGCCAAGGTGAAAGTGTGCGCATCCAGAGTGTAGGCTGCCGCCAGGGACCAAGTGGTGTTGCTGATGTCGCCGGCCTTGGCCTTGCCTTCATCGTTTGTGCGGTAGATGTTGAAATCGAAGCCCAGCGATTGGTCGGATGCCAGTGGGATGGTGTAGTTGCTGTTCAGGTAATACTGGCGATAGATGTCTTCGAGTTCGGCGCCGTACAGGGAGGCGCTGAGGTTATCGGTGATTGCGTAGCGGCCCCCAATGAAATCGGCGCTCTTGGCGGTCTCGCCTGCGTAGGTGGCATAGAGTTCGCCACGCGATTTGACGGTGGTCGGCTCCTTGCCCTCGGTGAAGTGGCCTGCCTCGAGGTCGAGCCCTTCGAATTCGCTGCTCTGCAGCTGGAAGCCGGTCGCGGTCTGCGGGAACAGGCGGCTGCCGCCAGCGGCGAAGACCGGGGCGGTCGGTTGCATCTCGCCCCACTTCAGCATGGTCTTGGAGATGCGCACCTTCACGGCGCCGCCGGCGCGGCTGTAGTCATCGCGCGGCTTGCCGTCGTTCATCACCGGCAGGTTGCCGGTGCCGGTCTTGTCGGAGGTGCCGTCGAGCTTCAGGCCCAGGTAGCCGAAGGCATCGACGCCGAAGCCCACAGTGCCTTGGGTGAAGCCGGATTCATAGGTGGTGAGGAAGCCTTGGGTCCAGTCGACGCGGTCCCCGCTGCCGCTCTTGCCGTCACGGTTGAAATAGTAGTTGCGGAGCAGCAGGTCGAGGCTGCTGTCTTCGATGAACCCCTTCGCTTCGGCCTGATCGCTGACGAATGCGTCGGCCACGGCGAACTGAGTGCTACCTGCGGAAACCGCCAGTGCAATGGCGCTCCACTTCATCACTTTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3003686","ARO_id":"40321","ARO_name":"Pseudomonas aeruginosa oprD with mutation conferring resistance to imipenem","ARO_description":"oprD is an outer membrane porin which facilitates the uptake of basic amino acids and imipenem in Pseudomonas aeruginosa.","ARO_category":{"41442":{"category_aro_accession":"3004278","category_aro_cvterm_id":"41442","category_aro_name":"Outer Membrane Porin (Opr)","category_aro_description":"The Opr family consists of porins in Pseudomonas species, and other Gram-negative bacteria, that exhibit a variety of substrate selectivities.","category_aro_class_name":"AMR Gene Family"},"36309":{"category_aro_accession":"3000170","category_aro_cvterm_id":"36309","category_aro_name":"imipenem","category_aro_description":"Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36383":{"category_aro_accession":"3000244","category_aro_cvterm_id":"36383","category_aro_name":"reduced permeability to antibiotic","category_aro_description":"Reduction in permeability to antibiotic, generally through reduced production of porins, can provide resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2241":{"model_id":"2241","model_name":"vanI","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"4298":{"protein_sequence":{"accession":"KTE89608.1","sequence":"MTKLKIAIIFGGCSEEHPVSVKSAGEVAKNLDPEKYEPFYIGITKDGVWQLCHYPEVNWEKGSCRPAILSPDRSVQGLLVLEQGQYQRIPLDLVFPVLHGKFGEDGAMQGLLELSGIPYVGCDIPSSALCMDKSLAYIVAGKAGIATPKFRTVTVKETIDAERLTYPVYVKPARSGSSFGVTKVCRQEELLNAVEIASQYDSKVLIEETVIGTEIGCAIFGNDLDLIAGEVDQIRLSHGFFRIHQENEPEKGSENSTLIVPAGISAEARSRVQETAKAIYRALGCRGLARVDMFLKEDGTVILNEVNTLPGMTSYSRFPRMMAAAGLPFAEVIDRLVSLALKGKTGTN"},"dna_sequence":{"accession":"LOCK01000072.1","fmin":"166343","fmax":"167390","strand":"-","sequence":"TCAATTGGTTCCTGTTTTTCCTTTCAAGGCCAACGAGACAAGCCGGTCGATCACTTCGGCAAAGGGCAAGCCTGCGGCCGCCATCATTCTCGGAAAACGGCTGTATGAGGTCATGCCGGGCAAGGTATTCACCTCGTTGAGGATTACTGTTCCATCTTCTTTCAGAAACATATCCACCCGCGCCAGTCCCCTGCAGCCCAAAGCGCGATAGATGGCTTTTGCCGTCTCCTGAACACGCGAGCGCGCCTCTGCCGAAATGCCGGCGGGAACGATTAGTGTTGAGTTTTCGGAACCCTTTTCCGGCTCATTCTCCTGATGGATTCTGAAAAAGCCATGAGACAGACGAATCTGATCGACCTCGCCGGCGATCAAATCCAGATCGTTCCCAAATATCGCACACCCTATCTCAGTGCCGATGACAGTCTCTTCAATCAGCACCTTCGAGTCATACTGGCTGGCGATTTCCACCGCATTCAGCAATTCTTCTTGGCGGCATACCTTAGTGACGCCGAAGGATGAACCCGAACGGGCCGGCTTGACATAAACGGGATAAGTAAGCCGTTCAGCGTCAATGGTTTCCTTCACCGTGACCGTCCGGAACTTTGGCGTGGCAATTCCTGCCTTTCCAGCGACGATATAAGCCAGGGATTTGTCCATGCACAGAGCCGAACTCGGGATATCACAGCCCACATAGGGGATGCCGGAAAGCTCCAGCAAGCCTTGCATCGCCCCATCCTCGCCAAATTTGCCATGCAGAACGGGAAACACCAGATCCAAAGGTATCCTTTGGTATTGTCCCTGCTCCAGAACAAGCAATCCCTGGACGCTTCTGTCCGGTGACAGGATAGCCGGACGGCAGCTGCCCTTTTCCCAATTGACCTCAGGGTAGTGGCAAAGCTGCCAAACCCCATCTTTCGTAATCCCGATATAGAAGGGTTCATACTTTTCGGGATCCAGGTTTTTGGCGACCTCCCCAGCAGATTTAACGGAGACGGGATGTTCTTCGGAACAGCCTCCGAAGATAATTGCAATTTTCAACTTAGTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40382","NCBI_taxonomy_name":"Desulfitobacterium hafniense","NCBI_taxonomy_id":"49338"}}}},"ARO_accession":"3003723","ARO_id":"40377","ARO_name":"vanI","ARO_description":"VanI is a D-Ala-D-Lac ligase that reduces vancomycin binding affinity, helping to confer vancomycin resistance as part of the VanI resistance gene cluster in Desulfitobacterium spp. and Desulfosporosinus spp.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"39340":{"category_aro_accession":"3002906","category_aro_cvterm_id":"39340","category_aro_name":"van ligase","category_aro_description":"van ligases synthesize alternative substrates for peptidoglycan synthesis that reduce vancomycin binding affinity.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2245":{"model_id":"2245","model_name":"vanKI","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3447":{"protein_sequence":{"accession":"WP_011461306","sequence":"MLNVDKISEETYYAFISQADLGNFMQYPSWAKVKTEWTSDLLGWFTPDNKLAGCGLILYRKMPCLNRYLAYCPRGPLIDWQSPNLREWFEPLVAYLRSKQVFSIKIDPPVVQAKWSAPTIKTFLGQAREQGSKGKVLRDLPPDEDYTTVQQVQQQLRQMGWRKQRGDTGFAATQPQYVYRLPLEGRSLEEVFAGFHTNWRRNVKKAERLGVKVRVGTEQDLPAFYELLKVTSERDHFKVRSFSYFSNLYRSLKAEAADRIALYLAEDEEELLAATLAVHSNAHSWYLYGASSNVKREKAPNHAIQWRMIQDAYQLKAYTYDFRGISPTLDESDPLFGLLRFKLGFGGEACEMISAWDYPLQPLLYRAFQLYLKRR"},"dna_sequence":{"accession":"NC_007907","fmin":"4204949","fmax":"4206077","strand":"-","sequence":"CTACCGCCGTTTTAAGTACAGCTGGAAAGCCCGGTATAATAAAGGCTGCAGGGGGTAGTCCCAAGCACTGATCATTTCACAAGCCTCGCCTCCAAAGCCCAATTTAAATCTCAACAACCCAAACAGGGGGTCAGATTCATCCAGGGTAGGGCTGATGCCTCTAAAATCATAGGTGTAGGCCTTAAGCTGATAAGCATCTTGAATCATCCGCCACTGGATAGCATGATTCGGGGCCTTCTCCCGTTTTACATTGCTGCTGGCCCCGTAAAGATACCATGAGTGGGCGTTGGAATGGACGGCTAAGGTAGCAGCCAATAATTCCTCTTCATCTTCCGCCAGATAAAGAGCAATACGGTCTGCCGCTTCAGCCTTTAAGGACCGGTACAGATTGGAAAAGTAGGAGAAACTGCGCACCTTGAAGTGATCCCGTTCTGAAGTTACCTTCAGCAGCTCATAAAAAGCCGGTAAATCCTGTTCGGTCCCGACCCGGACCTTGACGCCCAAACGCTCGGCCTTTTTAACATTGCGCCTCCAGTTGGTATGAAAACCGGCGAAGACCTCCTCCAGGCTGCGCCCCTCTAAGGGCAGGCGGTAAACATATTGGGGCTGGGTCGCAGCGAAACCCGTATCCCCCCGCTGCTTCCGCCAACCCATTTGCCGTAATTGCTGCTGCACTTGTTGGACCGTTGTGTAGTCTTCGTCCGGCGGCAAATCGCGCAAAACTTTCCCTTTGCTGCCCTGTTCACGGGCTTGCCCTAAAAACGTTTTAATGGTGGGGGCAGACCATTTTGCCTGGACCACCGGAGGATCGATCTTGATACTGAAAACCTGCTTGCTTCTCAAATAAGCCACAAGAGGTTCGAACCATTCCCTGAGGTTGGGGCTCTGCCAGTCAATAAGGGGACCGCGGGGACAATACGCCAGGTACCGGTTAAGGCAGGGCATTTTCCGGTATAAGATCAAACCACACCCTGCCAATTTATTGTCCGGGGTGAACCACCCCAATAAATCGCTGGTCCACTCAGTTTTGACCTTGGCCCAGGAAGGATACTGCATAAAATTGCCTAGATCCGCTTGAGAAATGAACGCATAATAGGTTTCTTCACTTATCTTGTCAACGTTTAACAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40382","NCBI_taxonomy_name":"Desulfitobacterium hafniense","NCBI_taxonomy_id":"49338"}}}},"ARO_accession":"3003727","ARO_id":"40384","ARO_name":"vanKI","ARO_description":"VanKI is a peptidoglycan bridge formation protein also known as FemAB that is part of the VanI glycopeptide resistance gene cluster.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"39349":{"category_aro_accession":"3002915","category_aro_cvterm_id":"39349","category_aro_name":"vanK","category_aro_description":"VanK is a member of the Fem family of enzymes that add the cross-bridge amino acids to the stem pentapeptide of cell wall precursors in Streptomyces coelicolor that confers inducible, high-level vancomycin resistance","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2246":{"model_id":"2246","model_name":"vanRI","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"3450":{"protein_sequence":{"accession":"WP_011461303","sequence":"MAANILIVDDEQAIADLVEVYLKNENYNLFKFYNGKDALDCIEKEKLDLAILDVMLPDVDGFSICRQIREKHNFPVIMLTAKEEEIDKITGLTLGADDYITKPFRPLELIARVKAQLRRFTKYNSAEPNQEEHVIAFSGLVLDMDTHECTLNEKKLSLTPTEFSILWVLCSNRGRVVSSEELFSEVWGDKYFTNSNNTVMVHIRHLREKMQDSAEHPKYIKTVWGVGYKIEK"},"dna_sequence":{"accession":"NC_007907","fmin":"4201992","fmax":"4202691","strand":"-","sequence":"TCACTTTTCAATTTTATAGCCAACCCCCCATACCGTTTTGATATATTTAGGATGTTCCGCGCTGTCTTGCATTTTTTCCCTTAAATGCCGGATATGCACCATGACCGTATTATTGCTGTTGGTGAAATACTTGTCTCCCCATACCTCACTGAACAATTCTTCCGAACTGACTACCCGGCCGCGGTTGGAGCAAAGGACCCAAAGAATGGAGAACTCCGTAGGCGTGAGGGATAGTTTTTTTTCATTCAAGGTACATTCATGGGTATCCATGTCTAAGACCAAGCCGGAAAAGGCAATCACGTGTTCCTCTTGGTTTGGCTCTGCAGAATTATACTTGGTAAATCTCCGCAGCTGCGCCTTGACGCGGGCAATCAGCTCCAAGGGACGGAACGGCTTGGTGATATAGTCGTCCGCGCCTAAGGTCAGCCCGGTAATCTTATCGATTTCTTCTTCCTTGGCTGTCAGCATGATCACCGGAAAATTATGCTTTTCCCGGATTTGCCGGCAGATTGAAAAACCGTCTACATCAGGGAGCATGACATCCAAAATGGCGAGATCCAGTTTTTCCTTTTCAATACAGTCAAGGGCATCCTTGCCGTTATAAAATTTAAAGAGATTATAGTTCTCATTTTTCAGATAAACTTCCACCAAATCGGCAATAGCTTGTTCATCATCAACAATCAAAATATTAGCAGCCAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40382","NCBI_taxonomy_name":"Desulfitobacterium hafniense","NCBI_taxonomy_id":"49338"}}}},"ARO_accession":"3003728","ARO_id":"40385","ARO_name":"vanRI","ARO_description":"VanRI is the regulatory transcriptional activator in the VanSR regulator within the VanI glycopeptide resistance gene cluster.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36713":{"category_aro_accession":"3000574","category_aro_cvterm_id":"36713","category_aro_name":"vanR","category_aro_description":"VanR is a OmpR-family transcriptional activator in the VanSR regulatory system. When activated by VanS, it promotes cotranscription of VanA, VanH, and VanX.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2243":{"model_id":"2243","model_name":"vanXI","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"375"}},"model_sequences":{"sequence":{"4230":{"protein_sequence":{"accession":"WP_015943580.1","sequence":"MKSDFVFVDELVSGIRWDAKYATWDNFTGKPVDGYAANRIVGTRALCAALEKARENAASLGFGLLLWDGYRPQCAVDCFLRWSKQPEDGRTKQKHYPNIDRSEIIEKGYVAAKSGHSRGSAIDLTLYHLASGTLVPMGGDFDLMDSVSHHGAHGISQAEARNRQYLCSIMEASGFVSYACEWWHYSLKHEPYPNTYFDFLIA"},"dna_sequence":{"accession":"NG_055644.1","fmin":"100","fmax":"709","strand":"+","sequence":"ATGAAAAGTGATTTTGTCTTTGTGGACGAGTTGGTATCAGGAATACGTTGGGATGCTAAATACGCCACCTGGGATAATTTTACCGGCAAACCGGTGGACGGCTATGCAGCCAATCGAATTGTCGGTACGAGAGCGTTGTGCGCGGCCTTGGAAAAAGCACGGGAAAACGCCGCATCCTTGGGCTTTGGCTTGCTTCTTTGGGATGGTTACCGCCCTCAATGCGCCGTAGATTGCTTTCTGCGCTGGTCTAAACAGCCGGAAGATGGCCGGACGAAACAGAAACACTATCCGAATATTGACCGATCCGAGATCATCGAAAAAGGATATGTGGCTGCCAAGTCGGGCCACAGCCGGGGCAGCGCCATTGATTTAACCCTTTATCATTTAGCTTCCGGAACACTTGTGCCCATGGGCGGTGATTTTGATTTGATGGATTCAGTCTCACATCATGGCGCACATGGAATCAGCCAAGCCGAAGCGAGAAACCGTCAATATCTTTGTTCGATCATGGAGGCCAGCGGTTTTGTTTCCTACGCTTGCGAGTGGTGGCATTACAGCCTGAAACACGAACCTTATCCCAACACTTACTTTGATTTTCTCATCGCCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40382","NCBI_taxonomy_name":"Desulfitobacterium hafniense","NCBI_taxonomy_id":"49338"}}}},"ARO_accession":"3003725","ARO_id":"40381","ARO_name":"vanXI","ARO_description":"VanXI is a VanX variant found in the VanI glycopeptide resistance gene cluster. It is a D-Ala-D-Ala dipeptidase.","ARO_category":{"36020":{"category_aro_accession":"3000011","category_aro_cvterm_id":"36020","category_aro_name":"vanX","category_aro_description":"VanX is a D,D-dipeptidase that cleaves D-Ala-D-Ala but not D-Ala-D-Lac, ensuring that the latter dipeptide that has reduced binding affinity with vancomycin is used to synthesize peptidoglycan substrate.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2223":{"model_id":"2223","model_name":"mexZ","model_type":"protein overexpression model","model_type_id":"41091","model_description":"This model detects protein overexpression based on the presence of mutations.The detection of the protein without an associated mutation indicates that the protein is likely to be expressed at low or basal levels. The detection of the protein with the mutation indicates that the protein is likely overexpressed. This model reflects how certain proteins are functional with and without mutations. For example, efflux pump subunits and regulators are functional with mutations and without mutations. Without mutations, efflux pump subunits and regulators are usually expressed at a low level. When an efflux pump regulator has a mutation, it can cause the overexpression of the efflux pump it is responsible for regulating, leading to resistance to specific drugs. Protein overexpression models have two parameters: a curated BLASTP cutoff, and a curated set of mutations (single resistance variants, frameshift mutations, indels, etc.) shown clinically to confer resistance. This model type is a combination of the protein homolog and protein variant model. A detected hit can be categorized as Perfect, Strict, or Loose with no mutation(s) or as Strict or Loose with mutation(s).","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3168":"G195E","3173":"V44A","3174":"G46S","3175":"Q10Z"},"clinical":{"3168":"G195E","3173":"V44A","3174":"G46S","3175":"Q10Z"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"390"}},"model_sequences":{"sequence":{"3420":{"protein_sequence":{"accession":"NP_250710.1","sequence":"MARKTKEESQKTRDGILDAAERVFLEKGVGTTAMADLADAAGVSRGAVYGHYKNKIEVCLAMCDRAFGQIEVPDENARVPALDILLRAGMGFLRQCCEPGSVQRVLEILYLKCERSDENEPLLRRRELLEKQGQRFGLRQIRRAVERGELPARLDVELASIYLQSLWDGICGTLAWTERLRDDPWNRAERMFRAGLDSLRSSPYLLLADA"},"dna_sequence":{"accession":"NC_002516.2","fmin":"2212676","fmax":"2213309","strand":"+","sequence":"GTGGCCAGGAAAACCAAAGAGGAATCCCAGAAAACCCGCGACGGCATACTCGATGCCGCCGAGCGGGTTTTCCTGGAAAAGGGCGTGGGCACCACTGCCATGGCCGACCTGGCGGACGCCGCCGGGGTTTCTCGCGGTGCGGTCTACGGCCACTACAAGAACAAGATCGAGGTCTGCCTGGCGATGTGCGACCGCGCCTTCGGCCAGATCGAGGTACCCGACGAAAACGCCAGGGTGCCGGCGCTGGATATCCTCCTGCGCGCCGGCATGGGCTTTCTCCGCCAGTGCTGCGAGCCCGGTTCGGTGCAGCGGGTGCTGGAGATCCTCTACCTCAAGTGCGAACGCAGCGACGAGAACGAGCCGCTGTTGCGCCGCCGCGAGCTGCTCGAGAAGCAGGGGCAACGCTTCGGCCTCCGGCAGATCCGCCGGGCGGTGGAACGCGGCGAACTGCCGGCGCGGCTGGACGTCGAGCTGGCCAGCATCTATCTGCAATCGCTCTGGGACGGCATCTGCGGCACCCTGGCCTGGACCGAGCGCCTGCGCGACGATCCCTGGAACCGCGCCGAACGCATGTTCCGCGCCGGCCTCGACAGCCTGCGCAGTTCTCCCTACCTGTTGCTGGCGGACGCCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3003709","ARO_id":"40363","ARO_name":"MexZ","ARO_description":"MexZ is a transcriptional regulator that downregulates the mexXY multidrug transporter operon, which confers to aminoglycoside resistance on Pseudomonas aeruginosa.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavin","category_aro_description":"Acriflavin is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36193":{"category_aro_accession":"3000054","category_aro_cvterm_id":"36193","category_aro_name":"acridine dye","category_aro_description":"Acridine dyes are cell permeable, basic molecules with an acridine chromophore. These compounds intercalate DNA. The image shown represents the core structure of the acridine family, with specific dyes containing varying substituents.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2260":{"model_id":"2260","model_name":"vatF","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"3514":{"protein_sequence":{"accession":"AAF63432","sequence":"MEDKPILGPDPQCKHPMVGFSQVCFIKNTTQNPNIIIGDYTYYDDPQDSENFERNVLYHYPFIGDKLIIGKFCALAHGVKFIMNGANHKMSGLSTYPFNIFGNGWERVAPSRDELPYKGDTHVGNDVWIGYDVLIMPGVTIGNGAIISSRSVVTRDVPAYSVVGGNPATLIKNRFSAEVIGKLQTIAWWDWPIDAISRNLHLIVAGDIEALARAASEIDHT"},"dna_sequence":{"accession":"AF170730","fmin":"69","fmax":"735","strand":"+","sequence":"ATGGAAGATAAGCCAATATTAGGGCCAGATCCCCAGTGTAAACACCCGATGGTGGGGTTTTCTCAAGTATGCTTTATCAAAAATACCACACAGAATCCGAACATTATTATCGGTGATTATACCTACTACGACGATCCACAAGATTCTGAAAACTTTGAACGTAACGTGCTTTATCACTACCCCTTTATTGGTGATAAGCTGATTATCGGCAAATTCTGTGCATTAGCTCATGGGGTGAAGTTCATTATGAATGGTGCCAACCATAAAATGTCTGGGTTATCGACTTACCCATTCAATATTTTTGGTAACGGTTGGGAAAGAGTCGCCCCGTCCAGGGATGAGCTGCCTTATAAAGGCGATACTCATGTCGGAAATGATGTGTGGATTGGCTATGATGTGTTGATTATGCCAGGTGTCACCATTGGCAATGGGGCAATTATTTCATCACGCTCAGTGGTCACGCGCGATGTGCCCGCTTATAGTGTGGTCGGCGGTAATCCCGCAACACTGATTAAAAATCGCTTCTCAGCCGAGGTTATCGGTAAGCTACAAACCATTGCCTGGTGGGATTGGCCAATAGACGCGATCAGTCGCAATCTACACCTGATCGTTGCCGGTGATATCGAGGCATTAGCGCGAGCAGCCAGCGAGATTGATCACACCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40164","NCBI_taxonomy_name":"Yersinia enterocolitica","NCBI_taxonomy_id":"630"}}}},"ARO_accession":"3003744","ARO_id":"40399","ARO_name":"vatF","ARO_description":"vatF is a streptogramin A acetyl transferase gene isolated from the chromosome of Yersinia enterocolitica.","ARO_category":{"36592":{"category_aro_accession":"3000453","category_aro_cvterm_id":"36592","category_aro_name":"streptogramin vat acetyltransferase","category_aro_description":"vat (Virginiamycin acetyltransferases) enzymes catalyze the transfer of an acetyl group from acetyl-CoA to the secondary alcohol of streptogramin A compounds, thus inactivating virginiamycin-like antibiotics and conferring resistance to these compounds.","category_aro_class_name":"AMR Gene Family"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2261":{"model_id":"2261","model_name":"lnuE","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"3515":{"protein_sequence":{"accession":"AGT57825","sequence":"MGKNNVTEKHLFYILDLLKDLQITYWLDGGWGVDVLTGKQQREHRDIDIDFDSQHTDKLVKKLKEIGYITVVDWMPSRMELKHEEYGYLDIHPLDLKKDGTATQADPKGGFYLFEKDWFTTTNYKNRKIPCISKEAQLLFHSGYELTEKDQFDIKNLNSINQVKKEGHFSNDF"},"dna_sequence":{"accession":"KF287643","fmin":"0","fmax":"522","strand":"+","sequence":"TTGGGAAAAAATAATGTCACAGAAAAACATCTATTTTATATTTTAGATTTACTTAAAGACCTCCAAATAACTTATTGGTTAGACGGTGGATGGGGAGTAGATGTACTCACTGGAAAGCAACAGAGAGAACACAGAGACATAGATATCGATTTTGATTCACAACATACAGACAAATTAGTTAAAAAATTAAAAGAGATTGGATACATCACAGTTGTAGATTGGATGCCTTCCAGAATGGAATTAAAACACGAAGAATACGGATATTTAGATATACATCCCTTAGATTTAAAAAAAGATGGCACAGCAACTCAAGCCGATCCAAAAGGCGGTTTTTATCTATTCGAAAAAGATTGGTTCACAACTACAAATTACAAAAATCGAAAAATACCATGCATTTCAAAAGAAGCACAACTACTTTTTCACTCTGGATATGAATTAACAGAAAAAGACCAATTTGATATTAAAAATTTAAACTCAATAAATCAAGTTAAGAAAGAAGGTCATTTTTCAAATGACTTCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36748","NCBI_taxonomy_name":"synthetic construct","NCBI_taxonomy_id":"32630"}}}},"ARO_accession":"3003762","ARO_id":"40400","ARO_name":"lnuE","ARO_description":"lnuE encodes a lincosamide resistance gene isolated from Streptococcus suis that was truncated by an ISEnfa5-cfr-ISEnfa5 segment insertion. It shares the closest sequence similarity to lnuA.","ARO_category":{"36360":{"category_aro_accession":"3000221","category_aro_cvterm_id":"36360","category_aro_name":"lincosamide nucleotidyltransferase (LNU)","category_aro_description":"Resistance to the lincosamide antibiotic by ATP-dependent modification of the 3' and\/or 4'-hydroxyl groups of the methylthiolincosamide sugar.","category_aro_class_name":"AMR Gene Family"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2262":{"model_id":"2262","model_name":"mefC","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"3516":{"protein_sequence":{"accession":"BAL43360","sequence":"MENRKWFKTYMFIWAGQFASMLTSYAVQFAIVIWLSLEYKSAEVLAYAGIAAMLPQALIGLIAGVYVDRLNRKYVMIFSDAFIALCALLLLVILQNENVNLIWIYILLGLRSVGNAFHAPALQAIAPLIVPQNELIKVAGINQVLHSVCRIGGPAIGTLAIAYLPISKVLYLDLIGALLAILSLVMVKIPNVVAKSKSSAHSIATEFSEGFQTVSKNKGLRYLFLYAMAITFVIMPAAIMFPLLTTGHFAGGKWEIGIVEVVWGGGMLIGGVILSIFKLKGSKVVAVNVMYVLLGLTFILSGVLPASWFVGFVMVTAIGGISLSVFNGCFTAIVQTEVSPEKLGRVFSLYYSLAVLPSVIGLLFTGLIAEVIGVNITFIISGCLAILVGILSFSTRNLMQLGKIKNI"},"dna_sequence":{"accession":"AB571865","fmin":"144312","fmax":"145536","strand":"-","sequence":"TTAAATATTTTTGATTTTACCTAATTGCATTAAGTTGCGAGTGCTAAACGAAAGAATACCCACAAGGATTGCCAAACAACCGCTTATGATAAACGTAATGTTTACACCAATAACTTCTGCAATCAGGCCTGTGAATAATAAACCGATTACACTTGGCAAAACTGCCAAACTATAATAAAGTGAAAATACACGTCCTAATTTTTCAGGACTTACCTCTGTTTGTACAATTGCTGTAAAACAGCCATTGAAAACAGACAGGCTGATACCGCCAATGGCTGTTACCATCACAAATCCTACAAACCAACTTGCAGGTAATACACCACTCAAAATAAATGTAAGTCCCAATAATACATACATAACATTGACTGCGACTACTTTTGAGCCTTTCAATTTGAAAATACTCAGGATGACACCGCCAATAAGCATACCTCCGCCCCAAACCACTTCTACAATTCCTATCTCCCATTTTCCTCCTGCAAAATGCCCTGTTGTGAGCAACGGAAACATAATGGCAGCTGGCATTATAACAAAGGTTATCGCCATTGCATAAAGAAAAAGATAACGCAAACCTTTGTTTTTTGAAACAGTCTGAAACCCTTCCGAAAATTCTGTAGCAATAGAATGTGCAGACGATTTTGACTTCGCAACCACATTGGGAATTTTCACCATCACGAGTGAAAGAATAGCCAGCAATGCTCCAATCAAATCCAAGTACAATACTTTTGAAATAGGAAGATAAGCAATGGCTAATGTGCCAATGGCAGGACCACCAATCCTGCAAACCGAATGTAACACCTGATTAATTCCTGCTACCTTTATCAATTCATTTTGGGGTACAATCAGCGGAGCAATTGCCTGTAGTGCCGGAGCGTGAAAAGCATTACCAACAGAGCGTAAACCCAATAAAATGTATATCCATATAAGATTAACATTTTCATTTTGTAAAATGACGAGTAACAAAAGGGCACAGAGAGCTATAAAAGCATCCGAAAAAATCATTACATATTTACGATTGAGACGGTCAACATATACACCTGCTATTAAGCCTATCAATGCTTGAGGCAACATAGCTGCTATTCCTGCGTAGGCTAAAACTTCGGCTGACTTGTACTCCAGACTAAGCCATATAACAATAGCAAACTGAACAGCATAACTTGTAAGCATTGAAGCAAACTGTCCAGCCCATATAAACATATAGGTCTTAAACCATTTACGGTTTTCCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40398","NCBI_taxonomy_name":"Photobacterium damselae subsp. damselae","NCBI_taxonomy_id":"85581"}}}},"ARO_accession":"3003745","ARO_id":"40401","ARO_name":"mefC","ARO_description":"mefC is a macrolide efflux gene isolated from a plasmid in Photobacterium damselae.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2264":{"model_id":"2264","model_name":"oleC","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"3518":{"protein_sequence":{"accession":"AAA26793","sequence":"MTVRGLVKHYGETKALDGVDLDVREGTVMGVLGPNGAGKTTLVRILSTLITPDSGQATVAGYDVVRQPRQLRRVIGLTGQYASVDEKLPGWENLYLIGRLLDLSRKEARARADELLERFSLTEAARRPAGTYSGGMRRRLDLAASMIGRPAVLYLDEPTTGLDPRTRNEVWDEVKAMVGDGVTVLLTTQYMEEAEQLASELTVVDRGRVIAKGGIEELKARVGGRTLRVRPVDPLQLRPLAGMLDELGITGLASTTVDTETGALLVPILSDEQLTAVVGAVTARGITLSSITTELPSLDEVFLSLTGHRASAPQDAEPARQEVAV"},"dna_sequence":{"accession":"L06249","fmin":"1527","fmax":"2505","strand":"+","sequence":"GTGACCGTACGGGGGCTGGTCAAGCACTACGGCGAGACCAAGGCGCTGGACGGCGTCGACCTGGACGTGCGCGAGGGCACCGTGATGGGTGTGCTCGGGCCGAACGGCGCCGGCAAGACCACCCTCGTCCGCATCCTGTCCACCCTGATCACCCCGGACTCCGGGCAGGCCACCGTGGCCGGCTACGACGTCGTACGCCAGCCCCGGCAGCTGCGCCGGGTCATCGGGCTCACCGGCCAGTACGCGTCGGTGGACGAGAAGCTCCCGGGCTGGGAGAACCTCTACCTGATCGGCCGGCTGCTGGACCTGTCCCGCAAGGAGGCCCGGGCCCGCGCCGACGAGCTGCTGGAGCGGTTCTCGCTGACCGAGGCCGCCCGGCGCCCGGCCGGCACCTACTCCGGCGGTATGCGGCGCCGACTGGACCTGGCCGCCTCGATGATCGGCCGGCCGGCCGTGCTGTACCTGGACGAGCCGACCACCGGCCTCGACCCGCGCACCCGCAACGAGGTGTGGGACGAGGTCAAGGCGATGGTCGGCGACGGCGTCACCGTGCTGCTCACCACCCAGTACATGGAGGAGGCCGAGCAGCTCGCCTCGGAACTGACCGTGGTGGACCGCGGCCGGGTCATCGCCAAGGGCGGCATCGAGGAGCTGAAGGCCCGCGTCGGCGGGCGCACCCTGCGGGTGCGGCCGGTCGACCCGCTCCAGCTGCGCCCGCTCGCCGGCATGCTGGACGAGCTGGGCATCACCGGGCTGGCTTCCACCACCGTGGACACCGAGACCGGGGCCCTGCTGGTGCCGATCCTCAGCGACGAGCAGCTGACCGCCGTGGTCGGCGCGGTCACCGCGCGCGGCATCACGCTGTCCTCCATCACCACCGAACTGCCCAGCCTGGACGAGGTGTTCCTGTCCCTCACCGGCCACCGCGCCAGTGCCCCGCAGGACGCCGAGCCCGCCCGCCAGGAGGTCGCCGTATGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36823","NCBI_taxonomy_name":"Streptomyces antibioticus","NCBI_taxonomy_id":"1890"}}}},"ARO_accession":"3003748","ARO_id":"40404","ARO_name":"oleC","ARO_description":"oleC is an ABC transporter isolated from Streptomyces antibioticus and is involved in oleandomycin secretion.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2265":{"model_id":"2265","model_name":"salA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1090"}},"model_sequences":{"sequence":{"3519":{"protein_sequence":{"accession":"AGN74946","sequence":"MLFLFEEKALEVEHKVLIPELTFSIEDHEHLAIVGVNGVGKSTLLKVIHQDQSVDSAMMEQDLTPYYDWTVMDYIIESYPEIAKIRLQLNHTDMINKYIELDGYIIEGEIVTEAKKLGIKEEQLEQKISTLSGGEQTKVSFLKVKMSKASLLLIDEPTNHMDLEMKEWLTKAFKQEQRAILFVSHDRTFLNETPDAILELSLDGAKKYIGKYDKYKQQKDIEHETLKLQYEKQQKEQAAIEETIKKYKAWYQKAEQSASVRSPYQQKQLSKLAKRFKSKEQQLNRKLDQEHIPNPHKKEKTFSIQHHNFKSHYLVQFNHVSFAYDNRKIFDDVSFYIKRNQNVIVEGRNGTGKSTLIKLILGELEPTKGDITVHPELEIGYFSQDFENLNMHHTVLDEILEIPEMKEADARTILASFYFDKDRINDVVETLSMGEKCRLQFVKLYFSNPHIMILDEPTNYFDIGMQENIIQLIQSFQGSVLIVSHDNYFKSQIKDQTWTIKNHQMTHENVQVKDPINTESMKHHLKELEQYTDERNRETEF"},"dna_sequence":{"accession":"KC693025","fmin":"0","fmax":"1626","strand":"+","sequence":"ATGCTATTTTTATTTGAAGAAAAAGCATTAGAAGTTGAACATAAAGTATTAATACCCGAGTTGACTTTTTCAATAGAGGACCATGAACATTTAGCAATCGTTGGTGTTAATGGTGTTGGAAAATCAACATTATTAAAAGTCATTCATCAAGATCAATCAGTTGATTCAGCGATGATGGAACAAGATTTAACACCTTATTATGATTGGACTGTTATGGATTATATAATTGAATCATATCCTGAAATCGCAAAGATTAGATTGCAACTTAATCATACAGATATGATTAATAAATATATTGAATTAGATGGATACATTATAGAAGGTGAAATCGTAACAGAAGCAAAAAAGCTCGGAATAAAAGAGGAACAACTAGAACAGAAAATTTCTACTTTAAGTGGTGGAGAACAAACAAAAGTATCATTTTTAAAAGTGAAAATGTCTAAAGCATCATTACTATTAATCGATGAACCAACAAACCACATGGATTTAGAAATGAAGGAATGGTTGACGAAAGCTTTTAAACAAGAACAACGTGCTATATTATTTGTATCTCATGACCGAACATTTTTAAATGAAACGCCAGATGCTATATTAGAATTGAGTCTTGATGGGGCTAAGAAGTATATCGGTAAATACGATAAATACAAACAACAAAAAGATATAGAGCATGAAACATTAAAGCTACAGTATGAAAAACAACAAAAAGAACAAGCGGCCATTGAAGAAACGATTAAAAAATATAAAGCATGGTATCAAAAAGCAGAACAAAGTGCTTCTGTGAGAAGCCCATATCAACAAAAACAATTAAGTAAGTTAGCGAAACGGTTTAAATCAAAAGAACAACAATTAAATCGTAAACTTGATCAAGAGCATATCCCAAATCCACATAAAAAAGAGAAAACTTTCTCAATACAACATCATAATTTTAAATCACATTATTTAGTTCAATTTAATCATGTTTCGTTTGCTTATGATAACCGGAAAATATTCGATGATGTATCATTCTATATTAAGCGAAATCAAAATGTTATTGTTGAAGGCAGAAATGGTACAGGTAAATCAACTTTAATCAAATTGATACTCGGTGAACTCGAGCCAACTAAAGGTGATATAACTGTTCATCCAGAATTAGAAATTGGATATTTCTCTCAAGATTTTGAGAATTTAAATATGCATCATACTGTCTTAGATGAAATATTAGAAATTCCTGAAATGAAAGAAGCAGATGCAAGAACCATATTAGCAAGCTTTTATTTTGATAAAGATAGGATAAATGATGTTGTTGAAACACTATCGATGGGTGAAAAATGTAGGTTACAATTTGTAAAATTATATTTTTCAAATCCTCATATTATGATATTAGATGAGCCAACAAACTATTTCGATATTGGCATGCAAGAAAATATCATTCAATTAATACAATCATTTCAAGGTTCGGTCCTTATTGTATCTCATGATAATTATTTTAAATCACAAATTAAAGATCAGACTTGGACTATAAAAAATCATCAAATGACGCATGAAAATGTTCAAGTCAAAGATCCTATTAATACAGAATCTATGAAACATCATTTAAAAGAATTAGAACAATATACAGATGAAAGAAATCGTGAAACAGAGTTCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40406","NCBI_taxonomy_name":"Staphylococcus sciuri subsp. sciuri","NCBI_taxonomy_id":"147467"}}}},"ARO_accession":"3003749","ARO_id":"40405","ARO_name":"salA","ARO_description":"salA is an ABC transporter gene isolated from the chromosome of Staphylococcus sciuri conferring resistance to lincosamides and streptogramins.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"37716":{"category_aro_accession":"3001317","category_aro_cvterm_id":"37716","category_aro_name":"pleuromutilin","category_aro_description":"Pleuromutilin is a natural product antibiotic produced by Clitopilus passeckerianus. Related antibiotics of clinical significance, such as tiamulin and retapamulin, are semi-synthetic derivatives of this compound.","category_aro_class_name":"Antibiotic"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2274":{"model_id":"2274","model_name":"RlmA(II)","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"3534":{"protein_sequence":{"accession":"AJD73064.1","sequence":"MNTNLKPKLQRFASATAFACPICQENLTLLETNFKCCNRHSFDLAKFGYVNLAPQIKQSANYNKENFQNRQQILEAGFYQAILDAVSDLLASSKTTTTILDIGCGEGFYSRKLQESHSEKTFYAFDISKDSVQIAAKSEPNWAVNWFVGDLARLPIKDANMDILLDIFSPANYGEFRRVLSKDGILIKVIPTENHLKEIRQRVQDQLTNKEYSNQDIKEHFQEHFTILSSQTASLTKTITAEQLQALLSMTPLLFHVDQSKIDWSQLTEITIEAEILVGKAF"},"dna_sequence":{"accession":"CP007593.1","fmin":"2148923","fmax":"2149772","strand":"+","sequence":"ATGAATACAAATCTCAAGCCCAAACTTCAGCGTTTTGCTTCTGCGACTGCCTTTGCCTGTCCTATCTGTCAAGAAAATCTGACTCTGTTAGAGACTAATTTCAAGTGCTGCAACCGTCATTCTTTTGACTTGGCGAAATTTGGCTATGTCAATCTAGCACCTCAAATCAAGCAATCTGCTAACTATAACAAGGAAAATTTTCAAAACCGTCAACAAATCCTAGAAGCCGGCTTTTACCAAGCTATCTTAGATGCTGTATCTGACTTGCTTGCAAGCTCAAAAACTACCACAACAATTTTGGATATCGGTTGTGGTGAAGGATTCTATTCTCGCAAACTACAAGAAAGTCACTCTGAAAAAACTTTCTATGCCTTTGACATCTCCAAAGATTCAGTCCAAATCGCTGCTAAAAGTGAACCCAACTGGGCAGTCAATTGGTTTGTTGGCGACTTGGCACGACTTCCTATAAAAGACGCTAACATGGATATTCTGCTTGATATCTTCTCACCTGCCAACTATGGAGAATTTCGTCGCGTTTTATCCAAAGACGGTATCTTGATAAAGGTTATCCCAACTGAAAATCACCTCAAAGAAATCCGTCAAAGAGTACAGGACCAGCTGACAAACAAGGAGTATTCTAACCAAGATATCAAGGAGCATTTCCAGGAACACTTTACCATCCTATCTAGTCAAACTGCCTCTCTGACTAAGACTATCACAGCAGAACAACTCCAAGCCCTACTCAGTATGACTCCTCTCCTCTTTCACGTTGACCAGAGCAAGATTGACTGGAGCCAACTGACAGAGATTACCATCGAAGCAGAGATTTTGGTTGGGAAAGCATTCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35917","NCBI_taxonomy_name":"Streptococcus pneumoniae","NCBI_taxonomy_id":"1313"}}}},"ARO_accession":"3001301","ARO_id":"37700","ARO_name":"RlmA(II)","ARO_description":"RlmA(II) is a methyltransferase found in Streptococcus pneumoniae and confers resistance to mycinamicin, tylosin and lincosamides. Specifically, this enzyme adds a methyl group to guanosine 748 (E. coli numbering) of 23S ribosomal RNA.","ARO_category":{"37697":{"category_aro_accession":"3001298","category_aro_cvterm_id":"37697","category_aro_name":"non-erm 23S ribosomal RNA methyltransferase (G748)","category_aro_description":"Non-erm 23S ribosomal RNA methyltransferases modify guanosine 748 (E. coli numbering) to confer resistance to some macrolides and lincosamides","category_aro_class_name":"AMR Gene Family"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2201":{"model_id":"2201","model_name":"PvrR","model_type":"protein knockout model","model_type_id":"40354","model_description":"An AMR detection model for instances where the absence of a protein - due to large-scale insertion elements, large deletions, or other methods of protein knockout - confers clinical resistance to a known antibiotic. These models include reference sequences. Protein knockout models are currently in development.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"3389":{"protein_sequence":{"accession":"AAM15533.1","sequence":"MSWKSYRVLVVEDQPFQREYLLNLFRERGVQYLVGAGDGAEALRCLKQDRFDLILSDLMMPGMDGIQMILQLPYLKHRPKLALMSSSSQRMMLSASRVAQSLGLSVIDLLPKPTLPKAIGQLLEHLERCLRQKLEPETDETPHGRTALLDALHNEQLVTWFQAKKSLHTGRIVGAEALIRWSHPQHGLLLPSCFMSDVDATGLHEALLWRVLEQTLNAQESWRRAGYEIPVSVNLPPHLLDNQELPDRLYEYVGARGACTSSLCFELTESSVTTLSSNYYAGACRLRMKGFGLAQDDFGQGYSSFYNLVTTPFTELKIDRSLVQGCVEDNGLNAAVISCIELGHRLNLDVVAEGVETCEELNLLRRLGCDRAQGFLISKAVSAREFERQLREDGPSLLV"},"dna_sequence":{"accession":"AF482691.2","fmin":"2796","fmax":"3996","strand":"+","sequence":"ATGAGCTGGAAATCCTATCGGGTGCTGGTGGTCGAAGATCAGCCGTTTCAGCGCGAATACCTGCTCAACCTGTTTCGCGAGCGCGGCGTGCAGTACCTGGTAGGTGCCGGCGACGGCGCGGAGGCGTTGCGCTGCCTGAAGCAGGACAGGTTCGACCTGATCCTCAGCGATCTGATGATGCCGGGCATGGATGGTATCCAAATGATCCTGCAACTGCCGTATCTCAAGCATCGTCCGAAGCTGGCGCTGATGAGCTCCTCGTCGCAGCGGATGATGCTCAGTGCCAGCCGGGTCGCCCAGAGTCTCGGCTTGTCGGTAATCGACCTGTTGCCCAAGCCGACTCTGCCCAAGGCCATCGGCCAACTTCTGGAACACCTGGAAAGATGCCTCAGGCAGAAGCTGGAGCCGGAAACCGACGAGACTCCGCATGGGCGCACGGCGTTGCTGGATGCCCTGCATAACGAGCAACTGGTGACCTGGTTCCAGGCTAAGAAATCCCTCCACACCGGGCGCATAGTCGGCGCCGAGGCGTTGATACGCTGGAGCCACCCGCAGCATGGCCTGTTGCTGCCCAGCTGTTTCATGAGTGATGTCGACGCTACCGGTCTGCACGAGGCGTTGCTCTGGCGCGTGCTCGAACAGACCCTGAACGCCCAGGAATCGTGGCGCAGGGCGGGTTACGAGATTCCGGTTTCGGTGAATCTGCCGCCGCACCTGCTCGATAACCAGGAACTTCCGGATCGACTCTATGAGTACGTCGGCGCTCGCGGGGCTTGTACCAGCTCACTATGTTTCGAGTTGACCGAGAGCAGTGTCACAACTCTGTCAAGTAACTACTATGCAGGTGCCTGTCGCTTGCGCATGAAAGGGTTCGGATTGGCCCAGGACGACTTTGGCCAGGGTTACAGCTCGTTCTATAACCTGGTCACGACGCCTTTCACGGAGCTGAAGATCGACCGCTCCCTAGTCCAGGGATGCGTAGAGGATAACGGCCTCAATGCAGCTGTCATCAGTTGTATTGAGTTGGGTCACCGCCTGAATCTCGACGTGGTGGCCGAAGGCGTGGAGACCTGCGAGGAACTGAATCTTCTTCGTCGTCTTGGCTGCGACCGGGCGCAGGGTTTCCTGATTTCTAAGGCAGTGTCTGCTCGTGAGTTCGAGCGGCAGTTAAGGGAGGACGGCCCCAGCCTCCTTGTTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3003688","ARO_id":"40325","ARO_name":"PvrR","ARO_description":"PvrR is a response regulator that controls the conversion between antibiotic-resistant and antibiotic-susceptible forms of Pseudomonas aeruginosa biofilms through porin deletion\/gene absence","ARO_category":{"41450":{"category_aro_accession":"3004286","category_aro_cvterm_id":"41450","category_aro_name":"phenotypic variant regulator","category_aro_description":"Phenotypic variant regulator proteins play a role in controlling the switch between antibiotic-susceptible and antibiotic-resistant forms of bacteria. The characterized member of this family is the PvrR protein in Pseudomonas aeruginosa, which when absent, confers antibiotic resistance.","category_aro_class_name":"AMR Gene Family"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"40429":{"category_aro_accession":"3003764","category_aro_cvterm_id":"40429","category_aro_name":"resistance by absence","category_aro_description":"Mechanism of antibiotic resistance conferred by deletion of gene (usually a porin)","category_aro_class_name":"Resistance Mechanism"}}},"2277":{"model_id":"2277","model_name":"Bacillus Cluster B intrinsic mph","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"3540":{"protein_sequence":{"accession":"EOO80837.1","sequence":"MNKQKAVEIARKYGLEVKDESIIFNESGLDFLVAYAEDDKGEEWVLRFPRRDDVMPRTIVEKKALDLVNKYATFQVPVWSVYEGDLIAYKKLIGVPAGTIDPEIQNYVWEMDYENVPEQFHQTLAKALASLHTVPKTEALKVGLFVQTAEEARKSMIERMKKVKAKFGVGESLWNRWQAWVKNEELWPQRTGLIHGDVHAGHTMIDKDANLTGFIDWTEAKVTDVSNDFVFQYRVFGEAALEKLINYYRQAGGIYWPAMKEHVIELNAAYPVAIAEFAIISGLEEYEQMAKETLEVNDR"},"dna_sequence":{"accession":"AHEL01000071.1","fmin":"3243","fmax":"4143","strand":"-","sequence":"CTAGCGGTCATTCACTTCCAATGTTTCTTTCGCCATCTGCTCATATTCTTCCAAGCCTGAGATAATCGCAAACTCAGCTATCGCAACAGGGTATGCCGCATTAAGTTCAATGACGTGCTCTTTCATGGCAGGCCAGTAAATCCCACCTGCTTGCCGGTAATAGTTGATCAGTTTCTCCAGGGCTGCCTCCCCGAATACCCGGTACTGGAAAACAAAGTCATTTGATACATCCGTTACTTTTGCTTCGGTCCAGTCGATAAAACCTGTTAAGTTAGCATCTTTATCAATCATCGTGTGGCCAGCATGAACATCCCCATGAATCAGACCTGTTCTCTGAGGCCACAATTCCTCATTTTTTACCCAGGCCTGCCAGCGGTTCCATAAGGATTCGCCTACGCCAAACTTCGCTTTAACCTTTTTCATACGCTCAATCATCGATTTTCTTGCCTCTTCTGCTGTCTGGACAAACAGGCCTACTTTAAGAGCCTCTGTTTTCGGAACTGTGTGTAGCGAAGCCAACGCTTTGGCTAATGTCTGGTGAAATTGTTCAGGCACATTTTCATAATCCATCTCCCACACATAGTTTTGAATCTCCGGATCAATCGTGCCTGCTGGCACTCCGATTAACTTTTTATAAGCTATTAGATCGCCTTCATAAACCGACCAGACTGGAACCTGAAAAGTGGCATATTTATTTACAAGATCCAGTGCTTTCTTCTCCACTATCGTCCTTGGCATCACATCGTCCCGTCTCGGAAACCTTAGCACCCATTCTTCGCCTTTATCGTCTTCTGCATAAGCAACCAGAAAATCTAAACCGGACTCGTTGAATATGATGGACTCATCTTTAACTTCCAAACCATACTTTCTTGCTATTTCTACCGCTTTCTGTTTGTTCAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39641","NCBI_taxonomy_name":"Bacillus cereus K-5975c","NCBI_taxonomy_id":"1053217"}}}},"ARO_accession":"3003767","ARO_id":"40436","ARO_name":"Bacillus Cluster B intrinsic mph","ARO_description":"Bacillus Cluster B mph are chromosomally-encoded macrolide phosphotransferases that inactivate 14-, 15- and 16-membered macrolides.","ARO_category":{"36472":{"category_aro_accession":"3000333","category_aro_cvterm_id":"36472","category_aro_name":"macrolide phosphotransferase (MPH)","category_aro_description":"Macrolide phosphotransferases (MPH) are enzymes encoded by macrolide phosphotransferase genes (mph genes). These enzymes phosphorylate macrolides in GTP dependent manner at 2'-OH of desosamine sugar thereby inactivating them. Characterized MPH's are differentiated based on their substrate specificity.","category_aro_class_name":"AMR Gene Family"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2278":{"model_id":"2278","model_name":"Bifidobacteria intrinsic ileS conferring resistance to mupirocin","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"2200"}},"model_sequences":{"sequence":{"3541":{"protein_sequence":{"accession":"YP_003971446","sequence":"MSETTNSHVYPKANEGGETASVAPNPSFPNMEETVLKYWDKDDTFNKSVERNPSGDHSQNEFVFFDGPPFANGLPHYGHLLTGYAKDVIPRYQTMKGRKVNRVFGWDTHGLPAELEAQKELGIDSVDQIEKMGIDKFNDACRASVLKYTHEWQDYVHRQARWVDFEHGYKTLNIPYMESVMWAFKQLYEKGLAYQGYRVLPYCPKDQTPLSAHELRMDADVYQDRQDTTVSVAVKLRDEEDAYAVFWTTTPWTVPTNFAIVVGADIDYVEVRPTQGKYAGKKFYFGKPLLSKYEKELGEDYEVVRELKGSEMAGWRYWPVFPYFAGDKAESEGNVPGPEGYQIFTADYVDTVEGTGLVHQAPYGEDDMNTLNAHGIKSTDVLDAGCRFTAQCPDYEGMYVFDANKPILRNLRNGDGPLAEIPAEHRAILFQEKSYVHSYPHCWRCATPLIYKPVSSWFVSVTKIKPRLLELNQQINWIPENVKDGQFGKWLANARDWSISRNRFWGSPIPVWVSDDPKYPRVDVYGSLEELKADFGDYPRDKDGNVNMHRPWIDNLTRVNPDDPTGKSHMHRISDVLDCWFESGSMSFAQFHYPFENKEKFEQHFPADYIVEYIGQTRGWFYLLHVMATALFDRPAFKNVICHGIVLGSDGQKMSKHLRNYPDVNGVFDKYGSDAMRWFLMSSPILRGGNLIVTAEGIRDTVRQVMLPVWSSYYFFTLYANAANGGAGFDARQLRADEVAGLPEMDRYLLARTRRLVERVEKSLDEFAISDACDAASDFIDVLTNWYIRNTRDRFWKEDVNAFNTLYTVLEVFMRVLAPLAPMESESVWRGLTGGESVHLADWPYVADEKTGEATELGRVLVDDPALVDAMEKVREIVSGALSLRKAAQIRVRQPLAKLTVVVEDVDAVKAYDEILKSELNIKDIEFCTMEDAGSQGLKIVHELKVNARAAGPRLGKQVQFAIKASKTGAWHVDAATGAPVVETPNGEVALEAGEYELINRVEEENAAEADASVSAALPTGGFVILDTVLTADLEAEGYARDVIRAVQDARKAADLDIADRIALVLTVPSANVADVERFRDLIAHETLATSFAVKEGAELGVEVAKA"},"dna_sequence":{"accession":"NC_014638","fmin":"1610636","fmax":"1613960","strand":"-","sequence":"TCACGCCTTGGCGACCTCCACGCCCAGCTCGGCACCTTCCTTCACCGCGAAGGAGGTGGCCAGCGTCTCATGGGCGATCAGATCGCGGAACCGCTCGACATCGGCCACATTGGCGGACGGCACGGTCAGCACCAGGGCGATGCGATCGGCGATGTCCAGGTCGGCGGCCTTGCGGGCGTCCTGCACGGCGCGAATCACGTCGCGGGCGTAGCCCTCGGCCTCCAGGTCGGCGGTCAGCACGGTATCGAGAATCACGAAACCGCCGGTAGGCAGAGCGGCCGACACGGAAGCGTCGGCCTCGGCGGCGTTCTCCTCCTCCACGCGGTTGATTAGCTCGTATTCGCCAGCCTCCAGCGCAACCTCGCCGTTCGGCGTCTCGACGACCGGAGCACCGGTCGCGGCATCGACATGCCAGGCACCGGTCTTGGACGCCTTGATGGCGAACTGGACCTGCTTGCCGAGGCGCGGGCCGGCGGCGCGGGCGTTGACCTTCAGCTCGTGCACGATCTTCAGCCCCTGCGAACCGGCATCCTCCATCGTGCAGAACTCAATATCCTTTATATTAAGCTCTGACTTGAGAATTTCGTCGTACGCCTTGACGGCATCCACATCCTCGACCACGACGGTGAGCTTGGCGAGCGGCTGGCGCACACGGATCTGGGCGGCCTTGCGCAACGACAGAGCGCCGGAGACGATCTCGCGCACCTTCTCCATCGCGTCCACCAGTGCCGGGTCGTCGACCAGCACACGGCCAAGCTCGGTCGCCTCACCGGTCTTCTCGTCCGCGACGTACGGCCAATCGGCCAGATGCACGGATTCGCCGCCGGTCAGGCCACGCCACACGGATTCGGACTCCATCGGGGCGAGCGGCGCGAGAACGCGCATGAACACCTCAAGCACGGTGTACAGCGTGTTGAACGCATTCACGTCCTCCTTCCAGAAGCGATCACGGGTGTTGCGGATGTACCAGTTGGTGAGCACGTCGATGAAGTCACTCGCCGCATCGCACGCGTCAGAAATCGCGAACTCGTCGAGCGACTTCTCTACACGCTCTACGAGCCTGCGGGTGCGGGCCAGCAGGTAACGATCCATCTCAGGCAGACCCGCCACCTCGTCCGCGCGCAGCTGACGGGCGTCGAAGCCGGCCCCGCCATTGGCCGCGTTCGCATACAGCGTGAAGAAGTAGTAGGAGCTCCACACCGGCAGCATGACCTGGCGCACGGTGTCGCGGATGCCCTCAGCGGTAACAATGAGGTTGCCGCCGCGCAGGATCGGCGACGACATAAGGAACCAGCGCATGGCGTCGGAACCGTACTTGTCGAACACGCCGTTCACGTCCGGGTAGTTGCGCAGGTGCTTCGACATCTTCTGGCCGTCGGAACCGAGCACGATGCCGTGGCAGATCACGTTCTTGAACGCCGGGCGGTCGAACAGCGCGGTGGCCATCACGTGCAGCAGGTAGAACCAGCCGCGGGTCTGGCCGATGTATTCGACAATGTAGTCGGCCGGGAAGTGCTGCTCGAACTTCTCCTTGTTCTCGAACGGGTAGTGGAACTGCGCGAACGACATCGAACCGGATTCGAACCAGCAGTCGAGCACGTCGCTGATACGGTGCATGTGGCTCTTGCCGGTCGGGTCGTCCGGGTTGACGCGCGTGAGGTTGTCGATCCACGGACGGTGCATGTTGACGTTGCCGTCCTTGTCGCGCGGGTAGTCGCCGAAGTCGGCCTTGAGCTCCTCCAACGAACCGTACACGTCGACGCGCGGGTACTTCGGGTCATCGCTCACCCACACCGGGATCGGCGAACCCCAGAAGCGGTTGCGGGAGATCGACCAGTCGCGCGCGTTGGCGAGCCACTTACCGAACTGACCATCCTTGACATTCTCAGGAATCCAGTTGATCTGCTGGTTGAGCTCCAACAGGCGCGGCTTGATCTTCGTCACCGACACGAACCATGAGCTCACAGGCTTGTAGATCAGCGGCGTGGCGCAACGCCAGCAATGCGGGTAGGAGTGCACATAGCTCTTCTCCTGGAACAGGATCGCGCGATGCTCGGCCGGGATCTCGGCCAGCGGGCCGTCTCCGTTGCGCAGGTTGCGCAGGATCGGCTTGTTCGCGTCGAACACGTACATGCCCTCGTAATCGGGGCACTGCGCGGTGAAGCGGCAGCCGGCGTCGAGCACGTCAGTGCTCTTGATGCCGTGCGCGTTCAGCGTGTTCATATCGTCCTCACCATAGGGAGCCTGGTGAACCAGGCCGGTACCCTCGACGGTGTCTACGTAGTCCGCGGTAAAGATTTGGTAGCCTTCGGGCCCCGGCACGTTGCCCTCAGACTCGGCTTTGTCGCCAGCGAAGTACGGGAACACCGGCCAGTAACGCCAACCGGCCATCTCGGAGCCCTTGAGCTCGCGCACGACCTCGTAATCCTCGCCGAGCTCCTTCTCGTACTTGGAGAGCAGGGGCTTGCCGAAGTAGAACTTCTTGCCGGCGTACTTGCCCTGCGTCGGGCGCACCTCGACATAGTCGATGTCAGCGCCGACGACGATCGCGAAGTTAGTGGGCACGGTCCACGGCGTGGTGGTCCAGAAGACCGCGTAGGCGTCCTCCTCGTCGCGCAGCTTCACGGCCACCGACACGGTGGTGTCCTGACGATCCTGATACACGTCGGCGTCCATGCGCAGCTCGTGCGCCGAAAGCGGCGTCTGATCCTTCGGGCAGTACGGCAGCACGCGGTAGCCCTGGTACGCCAGGCCCTTCTCGTACAGCTGCTTGAACGCCCACATCACCGACTCCATATACGGGATGTTCAGCGTCTTGTACCCGTGCTCGAAGTCGACCCAGCGGGCCTGACGATGCACGTAATCCTGCCATTCGTGCGTGTACTTCAGGACGGAGGCGCGGCAGGCGTCATTGAACTTGTCGATGCCCATCTTCTCGATCTGGTCGACCGAGTCGATGCCGAGCTCCTTCTGCGCCTCCAGCTCGGCGGGCAGACCGTGCGTGTCCCAGCCGAACACGCGGTTGACCTTGCGGCCCTTCATGGTCTGGTAGCGCGGGATCACGTCCTTCGCGTAACCGGTCAGCAGGTGGCCGTAGTGCGGCAGGCCGTTCGCGAACGGCGGGCCGTCGAAGAACACGAACTCGTTCTGACTATGGTCGCCGGAAGGGTTGCGTTCAACGGACTTGTTGAAGGTGTCGTCCTTGTCCCAATACTTCAGGACGGTTTCCTCCATGTTGGGGAAACTCGGGTTCGGCGCGACGCTGGCGGTCTCGCCGCCCTCGTTCGCCTTGGGATACACGTGGGAATTGGTGGTTTCGCTCAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40437","NCBI_taxonomy_name":"Bifidobacterium bifidum PRL2010","NCBI_taxonomy_id":"702459"}}}},"ARO_accession":"3003730","ARO_id":"40419","ARO_name":"Bifidobacterium ileS conferring resistance to mupirocin","ARO_description":"Bifidobacteria have an intrinsically resistant form of ileS (isoleucyl-tRNA synthetase) that confers resistance to mupirocin.","ARO_category":{"36585":{"category_aro_accession":"3000446","category_aro_cvterm_id":"36585","category_aro_name":"antibiotic resistant isoleucyl-tRNA synthetase (ileS)","category_aro_description":"Mupirocin inhibits protein synthesis by interfering with isoleucyl-tRNA synthetase (ileS).  Mutations in ileS can confer low-level mupirocin resistance.","category_aro_class_name":"AMR Gene Family"},"36693":{"category_aro_accession":"3000554","category_aro_cvterm_id":"36693","category_aro_name":"mupirocin","category_aro_description":"Mupirocin, also known as pseudomonic acid, is a bacteriostatic polyketide antibiotic from Pseudomonas fluorescens used to treat S. aureus and MRSA. It inhibits Ile tRNA synthetase.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2279":{"model_id":"2279","model_name":"Listeria monocytogenes mprF","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1650"}},"model_sequences":{"sequence":{"3543":{"protein_sequence":{"accession":"NP_465220","sequence":"MKEKLMQAYAWFQKNSTVVKIVFITFVMAFVIFEIINIATGIDYPSLKENLTSQSPEQIFIMFIVGLIAVTPMLLYDYVIVKLLPGKFSPSHVIASGWITNTFTNIGGFGGVLGASLRASFYGKNASHKEILLAISKIALFLVSGLSIYCLVSLATLLIPGFADHFVNYWPWLLAGGLYFPILFTITKWKSKSLFVDLPIKRELTLIIASLLEWGFAFGCFAIIGTLMGEPVDIFKVFPLFVIASVIGIASMVPGGVGTFDVVMILGLSQLGVSQELALAWMLFYRIFYYIIPFVVGLLFFVQKAGKKVNDFLEGLPLLFLQKVAHRFLVIFVYGSGLLLILSSAVPNAIYHVPFLYKIMPFNFLFTSQITIVAFGFLLLGLARGIECKTKKAYIITVIVLGCAIFNTLARVFSMKQAIFLGIVLLCLFLARNEFYREKLVYTWSKVIIDSIIFIVCLAGYIVIGIYNSPNIKHSKEIPDYLRIASEHLWLVGFVGVFIAVVSLVIIYIYLSTTKEKLGSPFEAVKVREHLAKWGGNEVSHTMFLRDKLLFWAAEGEVLFSYRIIADKMVIMGEPTGNMDKMEAAIEEVMMNADRFGYRPVFYEVRGTMIPYLHDHGFDFIKLGEEGFVDVQNFTMSGKKKKGERALMNKLEREGYTFEIIEPPFNHDTWTTLRAVSDEWLDGREEKGFSLGFFDTYYLEQAPIAIAKNGEGTIVGFASMMPSYTDEMTSIDLMRYSKEAPSGIMDFLFINLFEKAKEDGFQTFNAGMAPLANVGESKYAFLGERLAGLVYRYSQGFYGFKGLRNFKSKYVTEWEQKFVAFRKRSSIAFTMLQLMILVGKKRPLANSQVVLDFPLEEETKKPDSE"},"dna_sequence":{"accession":"NC_003210","fmin":"1758693","fmax":"1761291","strand":"-","sequence":"TTACTCAGAATCTGGTTTTTTTGTTTCTTCTTCGAGTGGGAAATCAAGGACTACTTGGCTATTTGCAAGTGGTCGTTTTTTACCAACAAGAATCATTAATTGTAACATGGTGAAAGCAATGGAACTTCTTTTTCTAAAGGCAACAAATTTTTGTTCCCATTCTGTAACATATTTGGATTTAAAATTACGTAATCCTTTGAAACCGTAAAAACCTTGACTATAACGGTATACAAGTCCGGCTAATCGTTCACCTAGGAAAGCATATTTACTTTCCCCAACATTGGCAAGTGGTGCCATACCGGCATTAAATGTTTGGAAGCCATCTTCTTTGGCTTTTTCGAATAGGTTAATGAAAAGGAAATCCATAATACCTGATGGCGCTTCTTTGGAGTAACGCATTAAATCAATCGAAGTCATTTCGTCTGTATATGACGGCATCATCGAAGCAAATCCAACGATAGTACCTTCTCCGTTTTTAGCGATAGCAATCGGAGCTTGTTCGAGATAATACGTATCGAAGAATCCTAATGAGAAACCTTTTTCTTCCCTACCATCTAGCCACTCATCAGAAACTGCTCGTAAAGTTGTCCAAGTGTCGTGATTGAATGGTGGTTCTATTATTTCAAAAGTATAACCTTCTCGTTCTAATTTATTCATGAGAGCTCGCTCACCTTTTTTCTTTTTACCACTCATTGTAAAGTTTTGGACGTCGACAAAACCTTCCTCGCCAAGCTTGATAAAGTCAAATCCGTGATCATGTAAATATGGAATCATCGTGCCCCGGACTTCATAGAAAACAGGTCGATAGCCAAATCTATCAGCGTTCATCATTACCTCTTCAATCGCTGCTTCCATTTTGTCCATGTTCCCAGTTGGTTCGCCCATGATGACCATTTTGTCCGCAATGATTCGGTAAGAGAAAAGTACTTCCCCCTCTGCTGCCCAAAATAGCAGTTTATCACGTAAGAACATCGTATGACTGACTTCATTTCCGCCCCATTTCGCTAAATGTTCGCGTACTTTGACTGCTTCAAATGGAGAGCCAAGTTTTTCTTTTGTTGTGGATAAATAAATGTAAATAATGACTAAACTAACAACGGCGATAAATACGCCAACGAAGCCGACTAACCATAAATGCTCTGAGGCAATGCGTAAATAGTCAGGGATTTCTTTGGAGTGTTTGATATTTGGTGAGTTGTAAATACCGATAACAATGTAACCTGCCAGACATACGATGAAAATAATGCTATCAATAATTACTTTACTCCAAGTATAAACCAGTTTTTCTCGGTAAAATTCGTTTCGAGCTAAGAATAAACATAACAGCACAATTCCTAAAAAGATTGCCTGCTTCATCGAAAATACGCGAGCAAGTGTGTTGAAAATCGCGCAACCTAGAACAATTACTGTAATAATATACGCTTTCTTTGTTTTACATTCAATCCCTCTCGCAAGCCCCAGTAGTAAAAAGCCAAATGCAACAATGGTAATTTGGGAAGTGAATAAGAAATTAAACGGCATAATTTTGTATAAGAATGGCACATGGTAAATAGCGTTTGGTACGGCGGAAGACAAAATTAACAATAACCCAGAGCCGTAAACAAAAATAACTAAGAAGCGATGGGCCACTTTTTGTAAGAATAATAACGGTAATCCTTCTAAAAAGTCATTTACTTTTTTACCAGCTTTTTGGACGAAGAAAAGTAGTCCCACTACAAAAGGAATAATATAGTAGAAAATTCGGTAAAATAGCATCCAAGCGAGCGCTAATTCTTGAGAAACACCTAATTGGCTAAGTCCAAGAATCATCACGACGTCAAATGTCCCTACTCCACCAGGTACCATCGAAGCAATCCCAATTACCGAAGCAATAACAAATAACGGGAACACTTTGAAAATATCGACTGGTTCTCCCATCAATGTACCGATAATCGCGAAACATCCAAAAGCGAAGCCCCACTCCAAAAGAGAAGCGATAATTAACGTTAATTCTCTTTTGATAGGTAAATCAACAAAGAGTGACTTACTTTTCCATTTCGTAATAGTAAATAAAATCGGGAAGTAAAGACCACCCGCAAGAAGCCATGGCCAGTAATTAACAAAATGATCTGCAAATCCTGGAATGAGTAAAGTGGCTAATGATACTAAACAGTAAATCGATAAACCAGATACTAAAAATAAAGCAATCTTAGAAATAGCTAGTAAAATTTCCTTATGAGATGCATTTTTCCCATAAAAACTTGCTCTTAAACTGGCACCTAATACGCCACCAAAACCGCCAATATTAGTAAAGGTATTCGTAATCCAACCAGAGGCAATCACATGACTTGGCGAAAACTTTCCAGGTAACAACTTAACGATGACATAATCATACAAAAGCATTGGAGTGACAGCAATTAAGCCCACGATAAACATAATAAATATTTGTTCCGGGCTTTGAGAAGTTAAATTTTCTTTTAGCGACGGATAGTCAATCCCCGTCGCAATATTAATAATTTCAAAAATAACAAAAGCCATCACAAAAGTAATAAAAACGATTTTTACGACGGTACTATTTTTTTGAAACCAGGCATAGGCTTGCATTAATTTTTCTTTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40443","NCBI_taxonomy_name":"Listeria monocytogenes EGD-e","NCBI_taxonomy_id":"169963"}}}},"ARO_accession":"3003770","ARO_id":"40442","ARO_name":"Listeria monocytogenes mprF","ARO_description":"MprF is a integral membrane protein that modifies the negatively-charged phosphatidylglycerol on the membrane surface. This confers resistance to cationic peptides that disrupt the cell membrane, including defensins.","ARO_category":{"37243":{"category_aro_accession":"3000863","category_aro_cvterm_id":"37243","category_aro_name":"defensin resistant mprF","category_aro_description":"MprF is a integral membrane protein that modifies the negatively-charged phosphatidylglycerol on the membrane surface of both Gram-positive and Gram-negative bacteria. This confers resistance to cationic peptides that disrupt the cell membrane, including defensins.","category_aro_class_name":"AMR Gene Family"},"37037":{"category_aro_accession":"3000693","category_aro_cvterm_id":"37037","category_aro_name":"defensin","category_aro_description":"Defensins are natural cationic peptides that have antibiotic properties. It is part of the innate immune system of plants and animals.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2281":{"model_id":"2281","model_name":"Brucella suis mprF","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1650"}},"model_sequences":{"sequence":{"3545":{"protein_sequence":{"accession":"Q8FW76","sequence":"MLWWDDISMSLIDDEIPSSQPQVSGRHFGWLKQYQHFLFPIAGIAIALLAIYVLENLLRHTSRTETLAALHNISWTTLALAVFFTALSYAAVALYDVVAVDTIAPNQIPRRIAAVAGAAGYAISNALGFSLLTGGALRYRIYAAEGISLADIGKIVGTSWFAIWFALIIMVGAALLIDPQDVPFLSAIDIRIDIVAGILILGGIGWLIYWLSHGERNVSIGSFSLRLPNSKGALTQIFAGVVDVGAAAATLYVLLPEGAVPSFAVFALVYVIAIVLGIASHAPGGLGAFEATIIAGLGLGGKPDAIAGLLAYRLIYTVLPLVVATAGILIWEVMRRRHMLDKQARFAKRLVEPLVPGLSASIIFLGGIILLISGATPDMRYRVKLLSDIVPEFLVEMSHLAASLVGVALLIVARGLSKRLERAWVAAMVLLLCGAVFSIAKGLDWEEASILCLFALSLWGFRDSFYRRPIAGPFELSWNWIATVGTTVLVSTWLGFFVYRHIEYSSDLWWDFAWNGNAPRFLRATVLVFAVVAAVGLHSIINRHGQRRRKVDHSIPDAVPALVARCPHTDAALAMLGDKQFLLAPDDSAFIMYAQSGGSLIALGEPIGDAEAGKELAWSFHSLADRLALRTVFYGVGPQSLPLFLDMGLIALKLGEVARVDLTDFSLEGPRRQPFRYADRKVDKDGLTFEIIPAADVPPLIPRLRAISDAWLDHKSGSEKGFSLGYFNDEYLKRFDIAVLKKDGEIVAFANIWRGADKYEITVDLMRYMPNVHKLLMDALFAKLLTFSKQEGYKWFNLGAAPLSGLSGSRLASRWNRFGSFIYRRGADLYHFDGLKAFKEKFDPVWTPHYMVCPGGLETPRALLDATTLINGSPLEFIRK"},"dna_sequence":{"accession":"AE014292","fmin":"568280","fmax":"570923","strand":"+","sequence":"TTGCTCTGGTGGGACGACATTTCGATGAGCCTGATTGATGATGAAATACCTTCTTCGCAACCGCAAGTGTCAGGTAGGCATTTCGGCTGGTTGAAACAATATCAGCATTTTCTGTTTCCAATCGCAGGCATCGCCATTGCGTTATTGGCTATTTATGTTCTGGAAAATCTTCTCAGGCACACCTCCCGCACCGAAACGCTTGCAGCCCTTCACAATATTTCATGGACGACGCTCGCACTGGCCGTCTTTTTCACAGCATTAAGCTATGCCGCAGTGGCGCTTTATGATGTCGTGGCGGTGGACACCATAGCGCCCAACCAGATACCGCGCCGCATCGCGGCGGTGGCGGGTGCTGCGGGCTATGCGATTTCCAACGCGCTCGGCTTCTCGCTCCTGACCGGCGGGGCGCTGCGTTATCGCATTTATGCCGCAGAAGGCATAAGCCTGGCCGATATCGGCAAGATCGTCGGCACCTCATGGTTCGCCATCTGGTTCGCCCTCATCATCATGGTGGGCGCAGCCCTGCTGATCGATCCGCAGGACGTGCCTTTTCTTTCCGCCATCGATATACGGATTGATATTGTCGCAGGCATTCTCATCCTTGGCGGCATTGGCTGGCTGATCTACTGGCTTTCGCATGGCGAACGCAATGTCAGCATCGGTTCGTTCAGCCTGCGCCTGCCCAATTCAAAAGGCGCGCTCACGCAGATTTTTGCGGGCGTGGTGGATGTGGGCGCTGCCGCGGCCACGCTCTATGTGCTGTTGCCGGAAGGGGCTGTGCCAAGCTTCGCCGTCTTTGCGCTCGTTTATGTCATCGCCATCGTGCTTGGCATTGCAAGCCACGCGCCAGGCGGCCTCGGCGCTTTTGAGGCAACAATCATCGCAGGGCTTGGCCTCGGTGGAAAACCCGATGCAATTGCGGGCCTGCTGGCCTATCGCCTCATTTACACGGTTCTTCCCCTCGTGGTTGCCACCGCCGGAATCCTCATCTGGGAGGTCATGCGCCGCCGCCATATGCTCGACAAGCAGGCCCGATTCGCCAAGCGGCTGGTGGAGCCGCTGGTTCCGGGGCTTTCAGCCAGCATCATCTTTCTCGGTGGCATCATCCTGCTTATCTCAGGCGCCACGCCCGATATGCGCTATCGTGTGAAGTTGCTGTCCGACATCGTGCCGGAATTTCTTGTGGAGATGTCGCATCTGGCGGCAAGCCTCGTCGGCGTTGCTCTTCTCATCGTCGCGCGCGGCCTTTCCAAACGGCTGGAGCGCGCCTGGGTGGCCGCGATGGTGCTTCTTCTTTGCGGCGCGGTGTTTTCGATCGCAAAAGGACTGGACTGGGAAGAGGCAAGCATTTTGTGCCTTTTTGCCCTTTCACTCTGGGGCTTTCGCGATTCCTTCTACCGTCGTCCGATTGCCGGCCCGTTTGAACTGAGCTGGAACTGGATCGCAACCGTTGGAACCACGGTTCTCGTGTCCACCTGGCTTGGTTTTTTCGTCTACCGCCATATCGAATATTCAAGCGATCTCTGGTGGGATTTCGCGTGGAACGGCAACGCCCCGCGTTTCCTGCGCGCCACCGTTCTGGTTTTCGCAGTCGTGGCGGCAGTCGGCCTTCATTCGATCATCAACCGGCATGGCCAGCGCAGGCGCAAGGTTGATCATTCCATCCCCGATGCCGTGCCCGCACTCGTCGCCCGGTGCCCGCATACAGATGCAGCCCTTGCCATGCTGGGCGACAAGCAATTTCTGCTGGCGCCCGACGACAGCGCGTTCATCATGTATGCGCAGTCGGGCGGCAGCCTGATCGCGCTTGGCGAGCCTATCGGCGATGCCGAAGCGGGCAAGGAACTTGCCTGGTCTTTCCATTCGCTTGCCGACCGTCTGGCGCTGCGCACTGTCTTCTATGGTGTCGGCCCGCAAAGCCTGCCGCTTTTCCTCGATATGGGCCTGATTGCGCTCAAGCTGGGTGAAGTCGCACGCGTTGACCTGACAGATTTTTCGCTGGAAGGCCCGCGCCGCCAGCCCTTCCGTTATGCCGACCGCAAGGTGGACAAGGATGGGCTGACCTTCGAGATTATCCCTGCTGCGGACGTGCCGCCGCTGATCCCGCGCCTGCGCGCAATTTCCGACGCTTGGCTCGACCATAAATCAGGCAGCGAAAAGGGTTTTTCGCTTGGCTATTTCAACGATGAGTATTTAAAGCGTTTCGATATTGCCGTGCTGAAGAAAGACGGCGAAATCGTTGCTTTCGCCAATATATGGCGCGGTGCCGACAAGTATGAGATCACGGTCGACCTGATGCGCTACATGCCCAATGTGCACAAGCTCCTGATGGATGCGCTGTTCGCCAAGCTGCTGACCTTTTCCAAGCAAGAAGGCTACAAATGGTTCAACCTTGGCGCGGCCCCGCTTTCCGGCCTTAGCGGCAGCAGGCTTGCCTCGCGCTGGAACCGTTTCGGCTCGTTCATCTATCGCCGTGGGGCCGATCTTTATCACTTCGACGGGCTCAAAGCCTTCAAGGAAAAATTCGATCCCGTCTGGACCCCGCATTATATGGTTTGCCCCGGCGGGCTTGAAACGCCGCGCGCCCTTCTTGATGCCACAACACTGATTAACGGCAGCCCTTTGGAGTTCATTCGCAAATGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40446","NCBI_taxonomy_name":"Brucella suis","NCBI_taxonomy_id":"29461"}}}},"ARO_accession":"3003772","ARO_id":"40445","ARO_name":"Brucella suis mprF","ARO_description":"MprF is a integral membrane protein that modifies the negatively-charged phosphatidylglycerol on the membrane surface. This confers resistance to cationic peptides that disrupt the cell membrane, including defensins.","ARO_category":{"37243":{"category_aro_accession":"3000863","category_aro_cvterm_id":"37243","category_aro_name":"defensin resistant mprF","category_aro_description":"MprF is a integral membrane protein that modifies the negatively-charged phosphatidylglycerol on the membrane surface of both Gram-positive and Gram-negative bacteria. This confers resistance to cationic peptides that disrupt the cell membrane, including defensins.","category_aro_class_name":"AMR Gene Family"},"37037":{"category_aro_accession":"3000693","category_aro_cvterm_id":"37037","category_aro_name":"defensin","category_aro_description":"Defensins are natural cationic peptides that have antibiotic properties. It is part of the innate immune system of plants and animals.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2282":{"model_id":"2282","model_name":"Clostridium perfringens mprF","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"3546":{"protein_sequence":{"accession":"Q0SSM7","sequence":"MWDSLKKSYRHLKNILGFVTDKRNYENIKKLLKNYKILSDISNIIVSVLVFLSGILLIISGIYPSIFYKIKFLDNIYSLSFLRFSHRASILIGLMLIMTSKEVFFKVKRAYYVTLTLLIVGGAFAFIKDLDYKEGIFILGVIILLILSKKSFYRKSIPIKVTKLSGILIVLSIVMIIFASFIHKFNIHFSKNYKYYIDFFHSTKGYLRIALFTYISFIIFVIIWYLTMPKIEDDERYMDADLEKVSKFFKEIDYGTIFSHLVYLKDKKVFWANEGESLIMYSKYKDKIIVLGDPIATKENLYSCIEEFQAFTNLYGYDVVFYEIEEKNFSTYHDAGYYFFKLGEEARIDLEEFNLIGSKKSAFRNTLRRVEREGYNFSIIEPPFNNEVVSQLKEISDKWLGDRKEKGFSLGWFSEDYIQRSPIAILKNEEENKIMGFVTIMDANDGGETVAIDLMRIDKDAPNASMDYLMLNLFLTFKEKGYKYFSLGEAPLSNVGFNTHSHLQEKLARLVYNSGNIFYSFDGLRRYKSKFSPIWQPRYLAYPKFMSLPEVFINLCLLIANSKERVEKK"},"dna_sequence":{"accession":"CP000312","fmin":"1756064","fmax":"1757774","strand":"-","sequence":"TTATTTTTTCTCTACTCTTTCCTTTGAATTAGCTATTAATAAACATAAGTTAATAAACACCTCTGGTAAGGACATAAACTTAGGATATGCTAAATATCTAGGTTGCCAAATTGGAGAAAACTTTGACTTATATCTTCTTAGTCCATCAAAACTATAGAATATATTACCACTATTATAAACTAACCTTGCAAGCTTTTCTTGTAAATGTGAATGAGTGTTAAATCCTACATTAGATAATGGTGCTTCTCCTAAGCTAAAATACTTATATCCTTTTTCTTTAAAGGTTAAGAATAAATTAAGCATTAGGTAATCCATAGAGGCATTTGGAGCATCTTTATCTATTCTCATTAAATCTATTGCTACTGTCTCCCCTCCATCATTAGCATCCATTATTGTTACAAAGCCCATAATCTTATTTTCTTCTTCATTCTTTAAAATAGCTATAGGTGATCTTTGTATATAATCCTCACTAAACCATCCTAAAGAAAATCCCTTTTCTTTTCTGTCCCCTAACCATTTATCAGATATTTCCTTCAATTGACTTACTACCTCATTATTAAAAGGAGGCTCTATAATGCTAAAATTATATCCTTCCCTTTCAACTCTTCTTAAGGTGTTTCTAAAGGCACTCTTTTTAGAACCAATCAAATTAAATTCTTCTAAATCTATCCTTGCCTCTTCTCCTAACTTAAAGAAATAATACCCTGCATCATGATAGGTAGAAAAGTTTTTTTCTTCTATTTCATAAAAGACAACATCATATCCATATAAATTTGTAAAAGCTTGAAACTCTTCTATACAACTATATAGGTTTTCCTTAGTAGCTATAGGATCTCCTAAAACTATTATCTTATCTTTGTACTTGCTATACATTATTAAGGACTCTCCTTCATTAGCCCAAAAGACCTTTTTATCCTTTAAATAAACTAAATGGGAGAATATTGTTCCATAATCTATTTCTTTAAAGAATTTTGATACCTTTTCTAAATCAGCATCCATATACCTTTCGTCATCTTCTATTTTAGGCATTGTTAAATACCATATTATCACAAATATTATAAAGGATATATATGTGAATAATGCTATTCTTAAATACCCCTTTGTGCTATGGAAAAAGTCTATATAGTATTTATAGTTCTTGCTAAAATGTATGTTAAATTTATGTATAAAACTCGCAAAGATAATCATTACAATTGAAAGAACTATTAATATCCCACTTAATTTAGTAACCTTAATAGGAATACTTTTTCTGTAAAAACTCTTTTTTGATAATATTAGAAGTATTATTACTCCTAAAATAAAAATTCCTTCTTTGTAATCTAAATCTTTTATAAAGGCAAAGGCTCCTCCTACTATAAGCAATGTTAATGTAACATAATAAGCTCTTTTTACCTTAAAGAAAACTTCCTTAGAGGTCATTATTAACATTAATCCAATTAATATTGAAGCTCTATGTGAAAACCTTAAAAAAGATAAACTGTATATATTATCTAAAAATTTTATCTTATAAAATATACTAGGATAAATCCCTGAAATTATTAAAAGAATACCACTTAGAAATACCAAAACTGATACTATTATATTTGATATATCACTTAAGATTTTGTAATTTTTTAATAGCTTCTTTATATTTTCATAATTTCTTTTATCAGTAACAAATCCTAAAATATTTTTTAAATGTCTATAACTTTTTTTTAGTGAATCCCACAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40448","NCBI_taxonomy_name":"Clostridium perfringens SM101","NCBI_taxonomy_id":"289380"}}}},"ARO_accession":"3003773","ARO_id":"40447","ARO_name":"Clostridium perfringens mprF","ARO_description":"MprF is a integral membrane protein that modifies the negatively-charged phosphatidylglycerol on the membrane surface. This confers resistance to cationic peptides that disrupt the cell membrane, including defensins.","ARO_category":{"37243":{"category_aro_accession":"3000863","category_aro_cvterm_id":"37243","category_aro_name":"defensin resistant mprF","category_aro_description":"MprF is a integral membrane protein that modifies the negatively-charged phosphatidylglycerol on the membrane surface of both Gram-positive and Gram-negative bacteria. This confers resistance to cationic peptides that disrupt the cell membrane, including defensins.","category_aro_class_name":"AMR Gene Family"},"37037":{"category_aro_accession":"3000693","category_aro_cvterm_id":"37037","category_aro_name":"defensin","category_aro_description":"Defensins are natural cationic peptides that have antibiotic properties. It is part of the innate immune system of plants and animals.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2283":{"model_id":"2283","model_name":"Streptococcus agalactiae mprF","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1650"}},"model_sequences":{"sequence":{"3547":{"protein_sequence":{"accession":"Q8DWT2","sequence":"MLKKLIEKVKSLTSVIKIVFFISVLVLIIVEMIHLKRTISVEQLKSVFGQLSPMNLFLIILVGVIAVLPTTGYDFVLNGLLRTDKSKRYILQTSWCINTFNNLSGFGGLIDIGLRMAFYGKKGQEKSDLREVTRFLPYLISGLSFISVIALIMSHIFHAKASVDYYYLVLIGASMYFPVIYWISGHKGSHYFGDMPSSTRIKLGVVSFFEWGCAAAAFIIIGYLMGIHLPVYKILPLFCIGCAVGIVSLIPGGLGSFELVLFTGFAAEGLPKETVVAWLLLYRLAYYIIPFFAGIYFFIHYLGSQINQRYENVPKELVSTVLQTMVSHLMRILGAFLIFSTAFFENITYIMWLQKLGLDPLQEQMLWQFPGLLLGVCFILLARTIDQKVKNAFPIAIIWITLTLFYLNLGHISWRLSFWFILLLLGLLVIKPTLYKKQFIYSWEERIKDGIIIVSLMGVLFYIAGLLFPIRAHITGGSIERLHYIIAWEPIALATLILTLVYLCLVKILQGKSCQIGDVFNVDRYKKLLQAYGGSSDSGLAFLNDKRLYWYQKNGEDCVAFQFVIVNNKCLIMGEPAGDDTYIREAIESFIDDADKLDYDLVFYSIGQKLTLLLHEYGFDFMKVGEDALVNLETFTLKGNKYKPFRNALNRVEKDGFYFEVVQSPHSQELLNSLEEISNTWLEGRPEKGFSLGYFNKDYFQQAPIALVKNAEHEVVAFANIMPNYEKSIISIDLMRHDKQKIPNGVMDFLFLSLFSYYQEKGYHYFDLGMAPLSGVGRVETSFAKERMAYLVYHFGSHFYSFNGLHKYKKKFTPLWSERYISCSRSSWLICAICALLMEDSKIKIVK"},"dna_sequence":{"accession":"AE009948","fmin":"2111276","fmax":"2113820","strand":"-","sequence":"TTATTTAACAATCTTAATTTTACTATCTTCCATTAATAGGGCACAAATAGCACAAATTAACCAGGACGAACGAGAACAAGAAATATAACGTTCCGACCACAATGGTGTAAACTTCTTCTTATACTTGTGTAAACCATTAAATGAGTAGAAATGACTACCGAAATGATAGACAAGATACGCCATTCTCTCTTTAGCAAAACTTGTTTCAACGCGACCAACTCCTGATAAAGGTGCCATCCCCAAATCAAAATAGTGGTATCCCTTCTCTTGATAATAAGAGAATAATGATAAAAAGAGGAAATCCATAACGCCATTCGGAATTTTCTGTTTATCGTGACGCATTAAATCAATAGAGATAATACTCTTTTCATAGTTTGGCATAATATTAGCAAAAGCAACAACTTCGTGTTCAGCATTTTTTACCAAAGCTATTGGGGCTTGTTGGAAATAATCTTTATTAAAATATCCTAGTGAGAAACCTTTTTCAGGACGTCCTTCTAACCAAGTATTAGAAATCTCTTCCAAACTATTTAGTAGCTCTTGACTATGTGGCGATTGTACAACTTCGAAATAGAAACCATCCTTTTCAACTCTATTTAGGGCATTTCTGAAAGGTTTGTACTTATTCCCTTTAAGAGTAAACGTTTCTAAATTAACTAAAGCATCCTCACCAACTTTCATAAAGTCAAAACCATACTCATGTAAAAGTAGTGTCAACTTCTGTCCAATACTGTAAAAAACAAGGTCATAGTCTAGCTTATCAGCATCATCAATAAACGATTCAATAGCTTCACGAATATAAGTGTCATCACCGGCTGGTTCCCCCATAATAAGACATTTATTATTGACAATTACAAATTGGAACGCAACGCAATCTTCTCCATTTTTTTGGTACCAGTAGAGCCTTTTATCATTTAAAAAGGCTAAACCGCTATCCGAAGAACCACCGTAAGCTTGAAGTAGTTTTTTATAACGATCCACATTGAACACATCACCAATCTGACAAGATTTTCCTTGTAAAATCTTAACCAAACATAAATAAACGAGAGTAAGAATCAACGTAGCCAATGCTATCGGCTCCCATGCTATGATATAATGCAGGCGTTCAATACTACCACCTGTAATATGAGCCCTGATAGGGAATAGTAGTCCTGCAATATAAAATAGAACTCCCATTAAACTAACGATAATGATTCCATCCTTAATACGCTCTTCCCAGCTATAAATAAATTGTTTTTTATAGAGAGTTGGCTTAATGACTAATAAGCCTAACAATAGTAAAATAAACCAGAAAGATAGTCGCCAACTAATATGACCTAAATTAAGATAAAACAATGTCAAAGTAATCCAGATAATAGCAATTGGAAAAGCATTTTTCACTTTTTGATCAATAGTTCTAGCTAAGAGAATAAAACAAACCCCCAGCAATAAACCTGGAAACTGCCATAACATTTGTTCTTGTAATGGGTCCAAGCCTAGCTTCTGCAACCACATAATATAAGTAATATTTTCAAAAAATGCTGTTGAAAATATTAAGAATGCACCTAAAATACGCATCAAATGGCTCACCATGGTTTGTAGAACAGTTGATACTAACTCTTTCGGGACATTTTCATAACGTTGATTTATTTGACTACCTAAATAATGGATAAAGAAATAGATACCTGCAAAGAATGGAATAATATAGTAGGCTAAACGATAAAGTAATAACCATGCAACCACAGTTTCTTTAGGTAGTCCCTCGGCAGCAAACCCTGTAAATAGAACTAATTCAAAACTTCCTAATCCACCGGGAATAAGGGATACAATCCCGACGGCACAACCAATACAAAATAGTGGTAAAATTTTATAAACTGGTAGATGAATGCCCATTAAATAACCGATAATTATAAATGCTGCGGCCGCACATCCCCATTCAAAAAAAGAAACAACACCTAATTTTATACGAGTACTAGATGGCATATCTCCGAAATAATGGCTTCCTTTATGACCAGAAATCCAATAAATAACAGGAAAATACATACTAGCACCAATTAATACCAAATAATAGTAATCAACACTAGCTTTGGCATGAAAAATATGGCTCATGATTAAGGCAATCACACTAATAAATGACAGACCAGAAATAAGATAGGGTAAAAAACGAGTCACTTCTCTTAGGTCACTCTTCTCTTGACCTTTTTTACCATAAAAAGCCATGCGCAACCCAATATCGATTAAGCCACCGAATCCTGACAAGTTATTAAAAGTGTTGATACACCAACTAGTCTGTAAAATATACCTTTTGCTTTTATCTGTACGTAAAAGTCCATTCAGTACAAAGTCATATCCGGTTGTCGGTAAGACAGCGATAACCCCCACAAGGATAATTAAGAAAAGATTCATTGGAGATAATTGCCCAAAAACACTCTTTAGTTGCTCAACAGAAATAGTTCGTTTCAAATGAATCATTTCAACAATAATAAGCACTAAAACAGATATAAAAAATACAATTTTAATCACAGAAGTCAGTGATTTGACTTTTTCAATTAGCTTTTTCAACAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40450","NCBI_taxonomy_name":"Streptococcus agalactiae serogroup V","NCBI_taxonomy_id":"216466"}}}},"ARO_accession":"3003774","ARO_id":"40449","ARO_name":"Streptococcus agalactiae mprF","ARO_description":"MprF is a integral membrane protein that modifies the negatively-charged phosphatidylglycerol on the membrane surface. This confers resistance to cationic peptides that disrupt the cell membrane, including defensins.","ARO_category":{"37243":{"category_aro_accession":"3000863","category_aro_cvterm_id":"37243","category_aro_name":"defensin resistant mprF","category_aro_description":"MprF is a integral membrane protein that modifies the negatively-charged phosphatidylglycerol on the membrane surface of both Gram-positive and Gram-negative bacteria. This confers resistance to cationic peptides that disrupt the cell membrane, including defensins.","category_aro_class_name":"AMR Gene Family"},"37037":{"category_aro_accession":"3000693","category_aro_cvterm_id":"37037","category_aro_name":"defensin","category_aro_description":"Defensins are natural cationic peptides that have antibiotic properties. It is part of the innate immune system of plants and animals.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2276":{"model_id":"2276","model_name":"Staphylococcus aureus ileS with mutation conferring resistance to mupirocin","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3605":"V588F","3606":"V631F"},"clinical":{"3605":"V588F","3606":"V631F"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1800"}},"model_sequences":{"sequence":{"3538":{"protein_sequence":{"accession":"CAA52296.1","sequence":"MDYKETLLMPKTDFPMRGGLPNKEPQIQEKWDAEDQYHKALEKNKGNETFILHDGPPYANGNLHMGHALNKILKDFIVRYKTMQGFYAPYVPGWDTHGLPIEQALTKKGVDRKKMSTAEFREKCKEFALEQIELQKKDFRRLGVRGDFNDPYITLKPEYEAAQIRIFGEMADKGLIYKGKKPVYWSPSSESSLAEAEIEYHDKRSASIYVAFNVKDDKGVVDADAKFIIWTTTPWTIPSNVAITVHPELKYGQYNVNGEKYIIAEALSDAVAEALDWDKASIKLEKEYTGKELEYVVAQHPFLDRESLVINGDHVTTDAGTGCVHTAPGHGEDDYIVGQKYELPVISPIDDKGVFTEEGGQFEGMFYDKANKAVTDLLTEKGALLKLDFITHSYPHDWRTKKPVIFRATPQWFASISKVRQDILDAIENTNFKVNWGKTRIYNMVRDRGEWVISRQRVWGVPLPVFYAENGEIIMTKETVNHVADLFAEHGSNIWFEREAKDLLPEGFTHPGSPNGTFTKETDIMDVWFDSGSSHRGVLETRPELSFPADMYLEGSDQYRGWFNSSITTSVATRGVSPYKFLLSHGFVMDGEGKKMSKSLGNVIVPDQVVKQKGADIARLWVSSTDYLADVRISDEILKQTSDVYRKIRNTLRFMLGNINDFNPDTDSIPESELLEVDRYLLNRLREFTASTINNYENFDYLNIYQEVQNFINVELSNFYLDYGKDILYIEQRDSHIRRSMQTVLYQILVDMTKLLAPILVHTAEEVWSHTPHVKEESVHLADMPKVVEVDQALLDKWRTFMNLRDDVNRALETARNEKVIGKSLEAKVTIASNDKFNASEFLTSFDALHQLFIVSQVKVVDKLDDQATAYEHGDIVIEHADGEKCERCWNYSEDLGAVDELTHLCPRCQQVVKSLV"},"dna_sequence":{"accession":"X74219","fmin":"90","fmax":"2844","strand":"+","sequence":"ATGGATTACAAAGAAACGTTATTAATGCCTAAAACAGATTTCCCAATGCGAGGTGGTTTACCAAACAAGGAACCGCAAATTCAAGAAAAATGGGATGCAGAAGATCAATACCATAAAGCGTTAGAAAAAAATAAAGGTAACGAAACATTCATTTTACATGATGGCCCACCATACGCGAATGGTAACTTACATATGGGACATGCCTTGAACAAAATTTTAAAAGACTTTATTGTACGTTATAAAACTATGCAAGGGTTCTATGCACCATACGTACCAGGTTGGGATACACATGGTTTGCCAATTGAACAAGCATTAACGAAAAAAGGTGTTGACCGTAAGAAAATGTCAACAGCTGAATTCCGTGAGAAATGTAAAGAATTTGCTTTAGAACAAATTGAATTACAGAAAAAAGATTTTAGACGTTTAGGTGTTCGTGGTGACTTTAATGATCCATATATTACATTAAAACCTGAATACGAAGCTGCACAAATTCGTATTTTTGGAGAAATGGCAGATAAAGGTTTAATTTATAAAGGTAAAAAGCCAGTTTATTGGTCTCCTTCAAGTGAGTCTTCATTAGCAGAAGCAGAAATTGAATATCACGATAAACGTTCAGCATCAATTTACGTTGCATTTAACGTTAAAGATGACAAAGGTGTCGTTGATGCAGATGCTAAATTTATTATCTGGACAACAACGCCATGGACAATTCCATCAAATGTTGCGATTACCGTTCATCCAGAATTAAAATACGGTCAATACAATGTAAATGGCGAAAAATATATTATTGCAGAAGCCTTATCTGACGCCGTAGCAGAAGCACTGGATTGGGATAAAGCATCAATCAAATTAGAAAAAGAATACACAGGTAAGGAATTGGAGTATGTTGTAGCACAACATCCATTCTTAGATAGAGAATCGTTAGTGATTAATGGTGATCATGTTACTACAGATGCTGGTACAGGTTGTGTACATACAGCACCAGGTCACGGGGAAGATGACTATATTGTTGGTCAAAAATATGAATTGCCAGTAATTAGTCCAATCGATGATAAAGGTGTATTTACTGAAGAAGGCGGCCAATTTGAAGGAATGTTCTATGATAAAGCTAATAAAGCCGTTACTGATTTATTAACAGAAAAAGGTGCACTATTAAAATTAGACTTTATTACACATAGCTATCCACACGACTGGAGAACAAAAAAACCTGTAATTTTCCGTGCTACACCACAATGGTTTGCTTCAATCAGTAAAGTAAGACAAGATATTTTAGATGCAATCGAAAATACAAACTTCAAAGTAAATTGGGGTAAAACACGTATTTACAATATGGTTCGTGACCGTGGCGAATGGGTTATTTCTCGTCAACGTGTTTGGGGTGTACCGTTACCAGTATTTTATGCTGAAAATGGCGAAATTATCATGACGAAAGAAACAGTGAATCATGTTGCTGATTTATTTGCAGAACACGGTTCAAATATTTGGTTTGAAAGAGAAGCGAAAGACTTACTACCAGAAGGATTTACACATCCAGGCAGCCCTAACGGTACATTTACTAAAGAAACAGACATTATGGACGTTTGGTTTGATTCTGGTTCATCACACCGTGGCGTGTTGGAAACAAGACCGGAATTAAGTTTCCCAGCAGATATGTATTTAGAAGGTAGTGACCAATATCGTGGTTGGTTCAACTCTTCTATTACAACTTCAGTTGCTACAAGAGGAGTATCACCTTATAAATTCTTACTTTCTCATGGTTTTGTTATGGACGGTGAAGGTAAGAAAATGAGTAAATCTTTAGGTAATGTGATTGTACCTGACCAAGTGGTTAAACAAAAAGGTGCTGATATTGCGAGACTTTGGGTAAGTAGTACGGACTATTTAGCTGATGTTAGAATTTCTGATGAAATTTTAAAACAAACATCTGATGTTTATCGTAAAATCAGAAATACATTAAGATTTATGTTAGGTAATATTAATGATTTCAATCCTGATACAGATAGCATTCCTGAATCAGAGTTATTAGAAGTTGATCGTTACTTGCTAAATCGTTTACGTGAATTTACTGCAAGTACGATTAACAACTATGAAAACTTTGACTACTTAAATATTTATCAAGAAGTTCAAAACTTTATCAATGTTGAGTTAAGTAATTTCTATTTGGATTACGGTAAAGATATTTTATATATTGAACAACGTGATTCTCATATCCGTCGTAGTATGCAAACAGTGTTATATCAAATTTTAGTTGATATGACGAAGTTGTTAGCACCAATCTTAGTGCATACAGCTGAAGAAGTTTGGTCTCATACACCACATGTTAAAGAAGAAAGTGTTCACTTAGCAGACATGCCTAAAGTTGTAGAAGTAGATCAAGCTTTATTGGATAAATGGCGTACATTTATGAATTTACGTGATGATGTGAACCGTGCATTAGAAACTGCTCGTAATGAAAAAGTTATTGGTAAATCATTAGAAGCTAAAGTTACGATTGCTAGTAACGATAAATTTAATGCATCTGAATTCTTAACTTCATTTGATGCATTACATCAATTATTTATCGTGTCACAAGTTAAAGTTGTAGATAAGTTAGATGATCAGGCAACAGCTTATGAACATGGTGATATTGTCATCGAACATGCAGATGGTGAAAAATGTGAAAGATGTTGGAACTATTCAGAGGATCTTGGTGCTGTTGATGAATTGACGCATCTATGCCCACGATGCCAACAAGTTGTAAAATCACTTGTATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3003729","ARO_id":"40418","ARO_name":"Staphylococcus aureus ileS with mutation conferring resistance to mupirocin","ARO_description":"Point mutations to the isoleucyl-tRNA synthetase (ileS) in Staphylococcus aureus that confer resistance to mupirocin.","ARO_category":{"36585":{"category_aro_accession":"3000446","category_aro_cvterm_id":"36585","category_aro_name":"antibiotic resistant isoleucyl-tRNA synthetase (ileS)","category_aro_description":"Mupirocin inhibits protein synthesis by interfering with isoleucyl-tRNA synthetase (ileS).  Mutations in ileS can confer low-level mupirocin resistance.","category_aro_class_name":"AMR Gene Family"},"36693":{"category_aro_accession":"3000554","category_aro_cvterm_id":"36693","category_aro_name":"mupirocin","category_aro_description":"Mupirocin, also known as pseudomonic acid, is a bacteriostatic polyketide antibiotic from Pseudomonas fluorescens used to treat S. aureus and MRSA. It inhibits Ile tRNA synthetase.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2284":{"model_id":"2284","model_name":"Escherichia coli murA with mutation conferring resistance to fosfomycin","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3623":"D369N","3624":"L370I","3627":"C115D","3628":"C115E","3639":"C115S"},"clinical":{"3623":"D369N","3624":"L370I"},"experimental":{"3627":"C115D","3628":"C115E","3639":"C115S"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"3548":{"protein_sequence":{"accession":"AIL15701","sequence":"MDKFRVQGPTKLQGEVTISGAKNAALPILFAALLAEEPVEIQNVPKLKDVDTSMKLLSQLGAKVERNGSVHIDARDVNVFCAPYDLVKTMRASIWALGPLVARFGQGQVSLPGGCTIGARPVDLHISGLEQLGATIKLEEGYVKASVDGRLKGAHIVMDKVSVGATVTIMCAATLAEGTTIIENAAREPEIVDTANFLITLGAKISGQGTDRIVIEGVERLGGGVYRVLPDRIETGTFLVAAAISRGKIICRNAQPDTLDAVLAKLRDAGADIEVGEDWISLDMHGKRPKAVNVRTAPHPAFPTDMQAQFTLLNLVAEGTGFITETVFENRFMHVPELSRMGAHAEIESNTVICHGVEKLSGAQVMATDLRASASLVLAGCIAEGTTVVDRIYHIDRGYERIEDKLRALGANIERVKGE"},"dna_sequence":{"accession":"CP009072","fmin":"1414817","fmax":"1416077","strand":"+","sequence":"ATGGATAAATTTCGTGTTCAGGGGCCAACGAAGCTCCAGGGCGAAGTCACAATTTCCGGCGCTAAAAATGCTGCTCTGCCTATCCTTTTTGCCGCACTACTGGCGGAAGAACCGGTAGAGATCCAGAACGTCCCGAAACTAAAAGACGTCGATACATCAATGAAGCTGCTAAGCCAGCTGGGTGCGAAAGTAGAACGTAATGGTTCTGTGCATATTGATGCCCGCGACGTTAATGTATTCTGCGCACCTTACGATCTGGTTAAAACCATGCGTGCTTCTATCTGGGCGCTGGGGCCGCTGGTAGCGCGCTTTGGTCAGGGGCAAGTTTCACTGCCTGGCGGTTGTACGATCGGCGCACGTCCGGTTGATCTACACATTTCTGGCCTCGAACAATTAGGCGCGACCATCAAACTGGAAGAAGGTTACGTTAAAGCTTCCGTCGATGGTCGTTTGAAAGGCGCACATATCGTGATGGATAAAGTCAGCGTTGGCGCAACGGTGACCATCATGTGTGCTGCAACCCTTGCGGAAGGCACCACGATTATTGAAAACGCAGCGCGTGAACCGGAAATCGTCGATACCGCGAACTTCCTGATTACGCTGGGTGCGAAAATTAGCGGTCAGGGCACCGATCGTATCGTCATCGAAGGTGTGGAACGTTTAGGCGGCGGTGTCTATCGCGTGCTGCCGGATCGTATCGAAACCGGTACTTTCCTGGTGGCGGCGGCGATCTCTCGCGGCAAAATTATCTGCCGTAACGCGCAGCCAGATACTCTGGACGCCGTGCTGGCGAAACTGCGTGACGCTGGAGCGGACATCGAAGTCGGCGAGGACTGGATTAGCCTGGATATGCATGGCAAACGTCCGAAGGCTGTTAACGTACGTACCGCGCCGCATCCGGCATTCCCTACCGATATGCAGGCCCAGTTCACGCTGTTGAACCTGGTGGCAGAAGGGACCGGATTCATCACCGAAACGGTCTTTGAAAACCGCTTTATGCATGTGCCAGAGCTGAGCCGTATGGGCGCGCACGCCGAAATCGAAAGCAATACCGTTATTTGTCACGGTGTTGAAAAACTTTCTGGCGCACAGGTTATGGCAACCGATCTGCGTGCATCAGCAAGCCTGGTGCTGGCTGGCTGTATTGCGGAAGGGACGACGGTGGTTGATCGTATTTATCACATCGATCGTGGCTACGAACGCATTGAAGACAAACTACGCGCTTTAGGTGCAAATATTGAGCGTGTGAAAGGCGAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40452","NCBI_taxonomy_name":"Escherichia coli ATCC 25922","NCBI_taxonomy_id":"1322345"}}}},"ARO_accession":"3003775","ARO_id":"40451","ARO_name":"Escherichia coli murA with mutation conferring resistance to fosfomycin","ARO_description":"murA or UDP-N-acetylglucosamine enolpyruvyl transferase catalyses the initial step in peptidoglycan biosynthesis and is inhibited by fosfomycin. Overexpression of murA through mutations such as Asp369Asn and Leu370Ile confers fosfomycin resistance. Extensive evidence has shown the significance of C115 mutations in conferring fosfomycin resistance since this residue represents a primary binding site for the antibiotic across many species.","ARO_category":{"39245":{"category_aro_accession":"3002811","category_aro_cvterm_id":"39245","category_aro_name":"murA transferase","category_aro_description":"murA or UDP-N-acetylglucosamine enolpyruvyl transferase catalyses the initial step in peptidoglycan biosynthesis and is inhibited by fosfomycin. Overexpression of murA through mutations confers fosfomycin resistance.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2290":{"model_id":"2290","model_name":"Mycobacterium tuberculosis intrinsic murA conferring resistance to fosfomycin","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"},"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"8298":"C117D"},"clinical":{"8298":"C117D"}}},"model_sequences":{"sequence":{"3555":{"protein_sequence":{"accession":"CCE36834","sequence":"MAERFVVTGGNRLSGEVAVGGAKNSVLKLMAATLLAEGTSTITNCPDILDVPLMAEVLRGLGATVELDGDVARITAPDEPKYDADFAAVRQFRASVCVLGPLVGRCKRARVALPGGDAIGSRPLDMHQAGLRQLGAHCNIEHGCVVARAETLRGAEIQLEFPSVGATENILMAAVVAEGVTTIHNAAREPDVVDLCTMLNQMGAQVEGAGSPTMTITGVPRLHPTEHRVIGDRIVAATWGIAAAMTRGDISVAGVDPAHLQLVLHKLHDAGATVTQTDASFRVTQYERPKAVNVATLPFPGFPTDLQPMAIALASIADGTSMITENVFEARFRFVEEMIRLGADARTDGHHAVVRGLPQLSSAPVWCSDIRAGAGLVLAGLVADGDTEVHDVFHIDRGYPLFVENLVSLGAEIERVCC"},"dna_sequence":{"accession":"HE608151","fmin":"1472985","fmax":"1474242","strand":"+","sequence":"GTGGCCGAGCGTTTCGTCGTGACTGGGGGCAACCGGTTATCAGGCGAAGTGGCCGTCGGCGGCGCCAAGAACAGCGTGCTCAAGCTCATGGCTGCGACGTTGTTGGCCGAGGGCACCAGCACGATCACCAACTGTCCCGACATCCTCGATGTGCCGCTGATGGCGGAGGTACTGCGTGGTCTGGGCGCCACCGTCGAACTCGACGGTGACGTGGCCCGGATCACCGCACCTGACGAGCCGAAGTACGATGCCGACTTCGCTGCGGTGCGGCAATTCCGCGCCTCGGTCTGTGTGCTGGGACCGCTGGTCGGGCGGTGCAAACGGGCCAGGGTCGCGCTGCCGGGCGGTGACGCGATCGGGTCGCGTCCGTTGGATATGCACCAGGCGGGCCTACGGCAATTGGGTGCCCACTGCAACATCGAGCACGGCTGCGTGGTAGCCCGAGCGGAAACGTTGCGCGGTGCGGAGATTCAGTTGGAGTTCCCCTCGGTGGGAGCCACCGAGAACATCTTGATGGCCGCCGTGGTGGCCGAGGGAGTCACCACTATTCACAATGCGGCTCGAGAACCCGACGTCGTCGACTTGTGCACGATGTTGAACCAGATGGGCGCACAGGTCGAAGGTGCGGGTTCGCCGACAATGACCATCACCGGTGTCCCGCGGCTGCATCCAACCGAGCACCGGGTGATCGGAGACCGTATCGTTGCCGCCACATGGGGCATCGCTGCCGCAATGACCCGTGGTGATATATCAGTGGCGGGCGTAGACCCGGCGCATCTGCAGCTGGTGCTGCACAAATTGCACGACGCGGGCGCAACCGTCACCCAGACTGACGCCAGCTTCCGGGTGACCCAGTACGAGCGTCCGAAGGCTGTCAACGTTGCGACCTTGCCGTTCCCCGGGTTTCCCACGGATCTGCAGCCGATGGCTATCGCTTTGGCGTCGATCGCCGACGGCACATCGATGATCACGGAGAACGTGTTCGAGGCGCGGTTCCGCTTCGTTGAAGAGATGATCCGGCTCGGTGCAGACGCTCGGACCGACGGGCACCACGCCGTGGTGCGGGGCCTCCCGCAGCTGTCGAGCGCTCCGGTGTGGTGTTCGGACATCCGTGCCGGGGCCGGCTTGGTGCTGGCGGGGCTCGTTGCCGACGGCGACACCGAGGTCCACGATGTATTCCACATCGATCGCGGATATCCGTTGTTCGTGGAGAACCTGGTGAGTCTCGGTGCCGAGATCGAACGGGTATGCTGTTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40468","NCBI_taxonomy_name":"Mycobacterium tuberculosis UT205","NCBI_taxonomy_id":"1097669"}}}},"ARO_accession":"3003784","ARO_id":"40467","ARO_name":"Mycobacterium tuberculosis intrinsic murA conferring resistance to fosfomycin","ARO_description":"Mycobacterium tuberculosis murA confers intrinsic resistance to fosfomycin. The presence of an aspartic acid residue in place of the critical cysteine at position 117 that enables fosfomycin binding is believed to be responsible for this intrinsic resistance.","ARO_category":{"39245":{"category_aro_accession":"3002811","category_aro_cvterm_id":"39245","category_aro_name":"murA transferase","category_aro_description":"murA or UDP-N-acetylglucosamine enolpyruvyl transferase catalyses the initial step in peptidoglycan biosynthesis and is inhibited by fosfomycin. Overexpression of murA through mutations confers fosfomycin resistance.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2287":{"model_id":"2287","model_name":"Mycobacterium smegmatis mutant ndh conferring resistance to isoniazid","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3649":"I17T","3650":"T29P","3651":"H46P","3652":"G84D","3653":"L100P","3654":"A115T","3655":"Y122N","3656":"R145C","3657":"F170S","3658":"A187P","3659":"V246A","3660":"V272E","3661":"V300G","3662":"Q335H","3663":"Y361H"},"experimental":{"3649":"I17T","3650":"T29P","3651":"H46P","3652":"G84D","3653":"L100P","3654":"A115T","3655":"Y122N","3656":"R145C","3657":"F170S","3658":"A187P","3659":"V246A","3660":"V272E","3661":"V300G","3662":"Q335H","3663":"Y361H"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"3551":{"protein_sequence":{"accession":"WP_038583059","sequence":"MSHPGATASDRHKVVIIGSGFGGLTAAKTLKRADVDVKLIARTTHHLFQPLLYQVATGIISEGEIAPATRVILRKQKNAQVLLCDVTHIDLENKTVDSVLLGHTYSTPYDSLIIAAGAGQSYFGNDHFAEFAPGMKSIDDALELRGRILGAFEQAERSSDPVRRAKLLTFTVVGAGPTGVEMAGQIAELADQTLRGSFRHIDPTEARVILLDAAPAVLPPMGEKLGKKARARLEKMGVEVQLGAMVTDVDRNGITVKDSDGTIRRIESACKVWSAGVSASPLGKDLAEQSGVELDRAGRVKVQPDLTLPGHPNVFVVGDMAAVEGVPGVAQGAIQGGRYAAKIIKREVSGTSPKIRTPFEYFDKGSMATVSRFSAVAKVGPVEFAGFFAWLCWLVLHLVYLVGFKTKIVTLLSWGVTFLSTKRGQLTITEQQAYARTRIEELEEIAAAVQDTEKAAS"},"dna_sequence":{"accession":"NZ_CP009496","fmin":"3684057","fmax":"3685431","strand":"+","sequence":"ATGAGCCATCCCGGAGCTACGGCGTCGGATCGGCATAAAGTCGTCATCATCGGTTCGGGTTTCGGTGGTCTCACCGCTGCCAAGACCCTCAAGCGCGCTGACGTCGACGTCAAGCTAATCGCCCGTACCACGCACCACCTCTTCCAGCCGCTGCTCTACCAGGTGGCGACCGGCATCATCTCCGAGGGCGAGATCGCCCCGGCCACTCGAGTGATCCTCCGCAAGCAGAAGAACGCCCAGGTCCTTCTCTGCGATGTGACGCACATCGATCTGGAGAACAAGACCGTGGATTCGGTGCTGCTCGGTCACACCTACTCGACGCCCTACGACAGCCTCATCATCGCCGCGGGCGCGGGTCAGTCCTACTTCGGCAACGACCACTTCGCCGAGTTCGCACCCGGCATGAAGTCGATCGACGATGCGCTGGAGCTGCGCGGTCGCATCCTCGGCGCGTTCGAACAGGCCGAGCGCTCCAGCGACCCGGTGCGCCGCGCGAAGTTGCTGACGTTCACCGTCGTCGGCGCGGGCCCGACCGGCGTCGAGATGGCCGGACAGATCGCCGAATTGGCCGACCAGACTTTGCGGGGCAGCTTCCGCCACATCGATCCCACCGAGGCCCGGGTGATCCTGCTCGACGCCGCACCGGCCGTGCTACCGCCCATGGGCGAGAAGCTCGGCAAGAAGGCGCGGGCCCGTCTGGAGAAGATGGGCGTCGAGGTCCAGCTGGGTGCGATGGTCACCGACGTCGACCGCAACGGCATCACCGTCAAGGATTCCGACGGGACCATCCGTCGCATCGAGTCGGCGTGCAAGGTGTGGTCGGCCGGTGTGTCGGCCAGCCCTCTCGGCAAGGATCTCGCCGAGCAGTCGGGTGTCGAACTCGACCGCGCGGGCCGGGTCAAGGTACAGCCCGACCTGACGCTGCCCGGTCACCCGAACGTGTTCGTCGTGGGCGACATGGCGGCCGTCGAGGGCGTGCCCGGTGTGGCGCAGGGCGCCATCCAGGGTGGCCGCTACGCCGCGAAGATCATCAAGCGTGAGGTCAGTGGCACCAGCCCGAAGATCCGCACGCCGTTCGAGTACTTCGACAAGGGCTCGATGGCGACGGTGTCGCGGTTCTCCGCGGTGGCCAAGGTGGGTCCCGTCGAGTTCGCGGGCTTCTTCGCCTGGTTGTGCTGGCTCGTGCTGCACCTGGTGTACCTGGTCGGGTTCAAGACGAAGATCGTCACACTGCTGTCGTGGGGCGTGACGTTCCTGAGCACCAAGCGTGGTCAGCTCACCATCACCGAGCAGCAGGCCTATGCGCGAACCCGCATCGAGGAGCTCGAGGAGATCGCGGCGGCGGTGCAGGACACCGAGAAAGCCGCGTCCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36871","NCBI_taxonomy_name":"Mycobacterium smegmatis","NCBI_taxonomy_id":"1772"}}}},"ARO_accession":"3003778","ARO_id":"40460","ARO_name":"Mycobacterium smegmatis ndh with mutation conferring resistance to isoniazid","ARO_description":"Mutations in the Mycobacterium smegmatis ndh gene that results in increased resistance to isoniazid.","ARO_category":{"40053":{"category_aro_accession":"3003460","category_aro_cvterm_id":"40053","category_aro_name":"antibiotic resistant ndh","category_aro_description":"ndh is a NADH oxidase. It participates in antibiotic resistance by diminishing NADH oxidation and consequently causes an increase in NADH concentration and depletion of NAD+. This alteration of the NADH\/NAD+ ratio prevents the peroxidation reactions required for the activation of INH, as well as the displacement of the NADH-isonicotinic acyl complex from InhA enzyme binding site.","category_aro_class_name":"AMR Gene Family"},"36659":{"category_aro_accession":"3000520","category_aro_cvterm_id":"36659","category_aro_name":"isoniazid","category_aro_description":"Isoniazid is an organic compound that is the first-line anti tuberculosis medication in prevention and treatment. As a prodrug, it is activated by mycobacterial catalase-peroxidases such as M. tuberculosis KatG. Isoniazid inhibits mycolic acid synthesis, which prevents cell wall synthesis in mycobacteria.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2250":{"model_id":"2250","model_name":"fusC","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"375"}},"model_sequences":{"sequence":{"3507":{"protein_sequence":{"accession":"WP_001033157","sequence":"MNKIEVYKFVKVKQLVYQLIKLYRTNDMNSHKTQKDFLLNEINDIFKEKDIDISDFITSIDDVKLTKKKAEHLLNELKVYIQDFEIPSSSQLEKIFRKVKKLKRPDINLIDTKEISYLGWNDNSSNRKYIVYKNLDDKFEGIYGEISPNKVKGFCKICNQESDTSLFLNKTKHNKSSGTYTKKGDYICYDSFKCNQNLDDINNLYEFIVKIK"},"dna_sequence":{"accession":"NC_002953","fmin":"52819","fmax":"53458","strand":"+","sequence":"ATGAATAAAATAGAAGTGTATAAGTTTGTTAAAGTAAAGCAGTTAGTATATCAATTGATTAAGTTATATCGTACAAACGATATGAATTCCCATAAAACACAAAAAGATTTTTTACTAAATGAAATTAATGATATCTTTAAAGAAAAAGATATTGATATCTCGGACTTTATTACATCGATTGACGATGTAAAATTAACTAAGAAAAAAGCAGAACATCTTTTAAATGAATTAAAAGTGTACATCCAAGATTTTGAAATACCTTCATCAAGTCAACTGGAGAAAATTTTTCGTAAAGTAAAAAAATTAAAGAGACCAGATATAAATTTAATTGATACAAAAGAAATTTCATATTTAGGATGGAATGATAATTCTTCTAACCGAAAATATATCGTTTATAAAAATTTAGATGATAAATTCGAAGGTATATATGGCGAAATTTCACCAAATAAAGTAAAAGGATTCTGTAAAATTTGTAATCAGGAATCTGATACATCACTCTTTCTCAATAAAACTAAACATAATAAGAGTAGTGGAACATATACTAAAAAAGGAGATTACATTTGTTATGACAGTTTTAAATGTAATCAGAACCTAGATGATATAAATAATCTTTACGAATTTATTGTTAAAATAAAATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37074","NCBI_taxonomy_name":"Staphylococcus","NCBI_taxonomy_id":"1279"}}}},"ARO_accession":"3003733","ARO_id":"40388","ARO_name":"fusC","ARO_description":"FusC is a fusidic acid resistance gene enabling ribosomal translocase EF-G dissociation from the ribosome that has been detected in Staphylococcus aureus and Staphylococcus intermedius. Its mechanism is believed to be similar to fusB due to its high level of sequence homology.","ARO_category":{"39459":{"category_aro_accession":"3003025","category_aro_cvterm_id":"39459","category_aro_name":"fusidic acid inactivation enzyme","category_aro_description":"Enzymes that confer resistance to fusidic acid by inactivation","category_aro_class_name":"AMR Gene Family"},"37139":{"category_aro_accession":"3000759","category_aro_cvterm_id":"37139","category_aro_name":"fusidic acid","category_aro_description":"Fusidic acid is the only commercially available fusidane, a group of steroid-like antibiotics. It is most active against Gram-positive bacteria, and acts by inhibiting elongation factor G to  block protein synthesis.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"651":{"model_id":"651","model_name":"Staphylococcus aureus mprF","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1600"},"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"8269":"T345A"},"clinical":{"8269":"T345A"}}},"model_sequences":{"sequence":{"59":{"protein_sequence":{"accession":"ADJ67256.1","sequence":"MNQEVKNKIFSILKITFATALFIFVAITLYRELSGINFKDTLVEFSKINRMSLVLLFIGGGASLVILSMYDVILSRALKMDISLGKVLRVSYIINALNAIVGFGGFIGAGVRAMVYKNYTHDKKKLVHFISLILISMLTGLSLLSLLIVFHVFDASLILDKITWVRWVLYVVSFFLPLFIIYSMVRPPDKNNRFVGLYCTLVSCVEWLAAAVVLYFCGVIVDAHVSFMSFIAIFIIAALSGLVSFIPGGFGAFDLVVLLGFKTLGVPEEKVLLMLLLYRFAYYFVPVIIALILSSFEFGTSAKKYIEGSKYFIPAKDVTSFLMSYQKDIIAKIPSLSLAILVFFTSMINLTIVYDALYDGNHLTYYILLAIHTSACLLLLLNVVGIYKQSRRAIIFAMISILLITVATFFTYASYILITWLAIIFVLLIVAFRRARRLKRPVRMRNIVAMLLFSLFILYVNHIFIAGTLYALDIYTIEMHTSVLRYYFWLTILIIAIIIGMIAWLFDYQFSKVRISSKIEDCEEIINQYGGNYLSHLIYSGDKQFFTNENKTAFLMYRYKASSLVVLGDPLGDENAFDELLEAFYNYAEYLGYDVIFYQVTDQHMPLYHNFGNQFFKLGEEAIIDLTQFSTSGKKRRGFRATLNKFDELNISFEIIEPPFSTEFINELQHVSDLWLDNRQEMHFSVGEFNEEYLSKAPIGVMRNEENEVIAFCSLMPTYFNDAISVDLIRWLPELDLPLMDGLYLHMLLWSKEQGYTKFNMGMATLSNVGQLHYSYLRERLAGRVFEHFNGLYRFQGLRRYKSKYNPNWEPRFLVYRKDNSLWESLSKVMRVIRHK"},"dna_sequence":{"accession":"HM140977","fmin":"0","fmax":"2511","strand":"+","sequence":"ATGAATCAGGAAGTTAAAAACAAAATATTTTCAATCTTAAAAATTACGTTTGCTACAGCTTTATTTATTTTTGTAGCAATCACATTGTATCGGGAGTTATCTGGTATTAACTTTAAAGATACGTTGGTTGAATTTAGTAAGATTAACCGTATGTCCTTAGTGTTACTATTTATTGGTGGTGGGGCATCGCTTGTTATTCTATCAATGTATGATGTGATTTTATCTAGAGCTTTAAAAATGGATATATCCTTAGGCAAAGTTTTAAGAGTAAGTTATATCATCAATGCATTGAATGCGATTGTAGGTTTCGGTGGCTTTATTGGTGCAGGCGTTAGAGCAATGGTTTATAAAAACTATACGCATGATAAAAAGAAATTAGTTCACTTTATATCCTTAATACTTATTTCAATGTTGACAGGTTTAAGCTTATTATCATTGCTAATTGTATTCCATGTTTTCGATGCATCTTTAATCTTAGATAAGATTACATGGGTAAGATGGGTATTATATGTAGTGTCATTTTTCTTACCATTATTCATTATTTATTCAATGGTTAGACCACCCGATAAAAACAATCGTTTTGTAGGATTGTACTGCACTTTAGTGTCGTGTGTTGAATGGTTAGCAGCTGCAGTTGTATTATATTTCTGTGGTGTAATTGTTGACGCTCATGTATCATTCATGTCCTTTATTGCAATATTTATCATTGCTGCATTATCAGGTTTAGTCAGCTTTATTCCTGGTGGTTTCGGCGCTTTCGATTTAGTTGTATTACTAGGATTTAAAACTTTAGGTGTCCCTGAGGAAAAAGTATTATTAATGCTACTTCTATATCGTTTTGCGTACTATTTTGTACCGGTAATTATTGCATTAATTTTATCATCATTTGAATTTGGTACATCAGCTAAGAAGTACATTGAGGGATCTAAATACTTTATTCCTGCTAAAGATGTTACGTCATTTTTAATGTCTTATCAAAAGGATATTATTGCTAAAATTCCATCATTATCATTAGCAATTTTAGTATTCTTTACAAGTATGATCAACTTAACGATTGTTTACGATGCTTTATATGATGGAAATCACTTAACGTATTATATTCTATTGGCAATTCATACTAGTGCTTGTTTATTACTTTTACTGAATGTAGTTGGTATTTATAAGCAAAGTAGACGTGCCATTATCTTTGCTATGATTTCAATTTTATTAATCACAGTGGCGACATTCTTCACTTACGCTTCATATATTTTAATAACATGGTTAGCTATTATTTTTGTTCTGCTTATTGTAGCTTTCCGTAGAGCACGTAGGTTGAAACGCCCAGTAAGAATGAGAAATATAGTTGCAATGCTTTTATTCAGTTTATTTATTTTATATGTTAACCATATATTTATTGCTGGAACGTTATATGCATTAGATATTTATACGATTGAAATGCATACATCTGTATTGCGCTATTACTTCTGGCTTACGATTTTAATCATCGCTATCATCATAGGTATGATTGCATGGTTGTTTGATTATCAATTTAGCAAAGTACGTATTTCTTCTAAAATTGAAGATTGCGAGGAGATTATTAATCAGTACGGCGGTAATTATTTGAGTCACTTGATATATAGTGGTGACAAGCAGTTTTTCACTAATGAAAATAAAACAGCATTTTTAATGTATCGTTATAAAGCAAGTTCATTAGTGGTTCTTGGAGATCCGTTAGGTGATGAAAATGCCTTTGATGAATTGTTAGAAGCATTCTATAATTACGCTGAGTATTTAGGCTATGATGTTATATTCTATCAAGTTACAGATCAACACATGCCTTTATATCATAATTTCGGTAACCAATTTTTCAAATTAGGTGAAGAAGCAATTATTGATTTAACGCAATTTTCAACTTCAGGTAAAAAACGCCGTGGATTTAGAGCGACTTTAAATAAATTCGATGAACTTAATATTTCGTTCGAAATTATTGAACCACCGTTTTCAACTGAATTTATAAATGAACTTCAACATGTAAGTGATTTATGGCTAGATAATCGTCAGGAAATGCATTTCTCTGTTGGTGAATTTAATGAAGAATACTTATCTAAAGCGCCAATTGGTGTAATGCGAAATGAAGAAAATGAAGTAATTGCATTTTGTAGTTTAATGCCAACATACTTTAATGATGCCATTTCAGTCGATTTAATTAGATGGTTGCCAGAGTTAGATTTACCATTAATGGATGGTCTATACTTGCATATGTTACTTTGGAGTAAAGAACAAGGTTATACAAAATTTAATATGGGTATGGCAACGTTATCGAACGTTGGTCAATTGCATTATTCATATTTAAGAGAACGACTTGCAGGCCGTGTCTTTGAACATTTCAACGGTCTATATCGTTTCCAAGGATTACGTCGTTATAAATCTAAATATAATCCGAATTGGGAACCACGCTTTTTAGTTTATCGTAAAGATAATTCGCTTTGGGAATCACTTTCTAAAGTAATGCGTGTAATACGTCACAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3003769","ARO_id":"40441","ARO_name":"Staphylococcus aureus mprF","ARO_description":"MprF is a integral membrane protein that modifies the negatively-charged phosphatidylglycerol on the membrane surface. A point mutation in the putative mprF synthase domain is associated with enhanced expression, increased synthesis and reduced daptomycin surface binding. This confers resistance to cationic peptides that disrupt the cell membrane, including defensins.","ARO_category":{"37243":{"category_aro_accession":"3000863","category_aro_cvterm_id":"37243","category_aro_name":"defensin resistant mprF","category_aro_description":"MprF is a integral membrane protein that modifies the negatively-charged phosphatidylglycerol on the membrane surface of both Gram-positive and Gram-negative bacteria. This confers resistance to cationic peptides that disrupt the cell membrane, including defensins.","category_aro_class_name":"AMR Gene Family"},"37037":{"category_aro_accession":"3000693","category_aro_cvterm_id":"37037","category_aro_name":"defensin","category_aro_description":"Defensins are natural cationic peptides that have antibiotic properties. It is part of the innate immune system of plants and animals.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2263":{"model_id":"2263","model_name":"optrA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1300"}},"model_sequences":{"sequence":{"3517":{"protein_sequence":{"accession":"AKA86814","sequence":"MSKATFAIASTNAKEDMKMQYKIINGAVYYDGNMVLENIGIEINDNEKIAIVGRNGCGKTTLLKAIIGEIELEEGTGESEFQVIKTGNPYISYLRQMPFEDESISMVDEVRTVFKTLIDMENKMKQLIDKMENQYDDKIINEYSDISERYMALGGLTYQKEYETMIRSMGFTEADYKKPISEFSGGQRTKIAFIKILLTKPDILLLDEPTNHLDIETIQWLESYLRSYKSTLVIISHDRMFLNRIVDKVYEIEWGETKCYKGNYSAFEEQKRENHIKQQKDYDLQQIEIERITRLIERFRYKPTKAKMVQSKIKLLQRMQILNAPDQYDTKTYMSKFQPRISSSRQVLSASELVIGYDTPLAKVNFNLERGQKLGIVGSNGIGKSTLLKTLMGGVAALSGDFKFGYNVEISYFDQQLAQISGDDTLFEIFQSEYPELNDTEVRTALGSFQFSGDDVFRPVSSLSGGEKVRLTLCKLLYKRTNVLILDEPTNHMDIIGKENLENILCSYQGTIIFVSHDRYFTNKIADRLLVFDKDGVEFVQSTYGEYEKKRMNSEKPFNNIKVEQKVEKNNTVKGDRNSIEKEKVKKEKRIEKLEVLINQYDEELERLNKIISEPNNSSDYIVLTEIQKSIDDVKRCQGNYFNEWEQLMRELEVM"},"dna_sequence":{"accession":"KP399637","fmin":"31476","fmax":"33444","strand":"+","sequence":"TTGTCCAAAGCCACCTTTGCAATTGCTAGTACTAACGCAAAGGAGGATATGAAAATGCAATACAAAATAATTAATGGTGCCGTTTACTATGATGGTAATATGGTGTTGGAAAACATCGGTATTGAAATCAATGATAATGAAAAGATTGCTATTGTTGGTAGAAATGGATGTGGAAAAACAACCTTGCTAAAAGCTATTATAGGCGAAATTGAATTAGAAGAAGGAACTGGTGAAAGTGAGTTTCAAGTAATAAAGACCGGTAACCCTTATATTAGCTATTTAAGACAGATGCCTTTTGAAGATGAAAGTATATCAATGGTGGATGAAGTCCGTACGGTATTTAAGACGCTTATTGATATGGAAAACAAGATGAAACAGCTGATAGATAAAATGGAGAATCAATATGATGATAAAATCATCAATGAATACTCTGATATCAGTGAAAGGTATATGGCTCTTGGAGGTCTAACCTACCAAAAAGAATATGAAACGATGATTCGTAGTATGGGTTTTACTGAAGCAGATTATAAAAAACCCATTTCTGAATTTTCAGGTGGTCAGCGAACTAAGATAGCTTTTATAAAAATACTTTTAACAAAGCCAGACATTCTATTACTTGATGAACCTACTAACCACCTTGATATAGAAACAATACAATGGTTGGAGAGTTATTTGAGAAGTTATAAATCTACATTGGTTATTATTTCCCATGATAGAATGTTTCTTAATCGAATTGTGGATAAGGTTTATGAAATCGAATGGGGAGAGACCAAATGTTATAAAGGTAATTATTCAGCCTTTGAGGAGCAAAAACGAGAAAATCATATCAAACAGCAAAAAGATTACGACTTGCAACAGATAGAAATTGAAAGGATTACACGCTTGATTGAACGTTTTCGTTATAAACCTACGAAAGCTAAAATGGTGCAATCTAAAATTAAATTATTACAGCGTATGCAAATATTAAATGCACCAGACCAATACGATACAAAAACTTATATGTCTAAATTTCAACCGAGAATCAGTAGTTCAAGGCAAGTATTAAGTGCTTCAGAACTTGTGATAGGCTATGATACTCCTCTTGCAAAGGTTAATTTCAACCTTGAAAGGGGACAGAAGCTTGGAATTGTTGGGAGTAATGGTATTGGTAAATCCACGTTGCTTAAAACACTTATGGGTGGTGTGGCAGCATTGTCTGGAGATTTTAAATTCGGATACAATGTTGAAATTAGCTATTTTGACCAACAGCTTGCTCAAATCAGTGGAGATGATACACTATTCGAAATTTTTCAAAGCGAATACCCTGAGCTAAATGACACAGAGGTCAGAACTGCTCTTGGCTCATTTCAGTTTAGTGGAGATGATGTTTTTAGACCGGTGTCCTCTTTGTCAGGTGGAGAAAAGGTTAGATTGACATTATGTAAATTATTATATAAACGTACTAATGTTTTAATCTTAGATGAACCGACAAACCACATGGATATTATTGGAAAAGAGAATTTAGAGAATATCTTATGCAGTTATCAAGGTACAATTATTTTTGTGTCACATGATAGATATTTTACTAATAAGATTGCTGACAGATTACTTGTTTTTGATAAGGATGGTGTAGAGTTTGTACAATCTACTTATGGTGAGTACGAGAAAAAAAGGATGAATTCTGAAAAGCCATTTAATAACATTAAAGTTGAGCAGAAAGTAGAGAAAAATAACACAGTAAAAGGCGATCGTAACTCCATTGAGAAGGAGAAGGTTAAGAAGGAGAAACGAATTGAAAAGCTTGAAGTGTTAATAAATCAATATGATGAAGAATTAGAAAGATTGAATAAAATCATTTCTGAACCAAACAATTCTTCTGATTATATAGTACTGACGGAAATACAAAAATCAATTGATGATGTTAAAAGGTGTCAGGGTAATTATTTTAATGAATGGGAACAGTTGATGAGAGAATTGGAAGTTATGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3003746","ARO_id":"40402","ARO_name":"optrA","ARO_description":"optrA encodes an ABC-transporter gene conferring resistance to oxazolidinones that was isolated from a plasmid in Enterococcus faecalis and Enterococcus faecium.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"36218":{"category_aro_accession":"3000079","category_aro_cvterm_id":"36218","category_aro_name":"oxazolidinone antibiotic","category_aro_description":"Oxazolidinones are a class of synthetic antibiotics discovered the the 1980's.  They inhibit protein synthesis by binding to domain V of the 23S rRNA of the 50S subunit of bacterial ribosomes.  Linezolid is the only member of this class currently in clinical use.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2268":{"model_id":"2268","model_name":"eatAv","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3466":"T450I"},"clinical":{"3466":"T450I"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"3626":{"protein_sequence":{"accession":"AGQ48857.1","sequence":"MSKIEIKNLTFGYDSQGTLLFEQANLNFDTQWKLGLIGRNGRGKTTLLNILQNKLPYQGQVIHQQEFAYFPQQTKDKERLTYYVLNDITDFEIWEIERELQLMQTDPEILWREFSTLSGGEKTKVLLALLFVDDTHFPLIDEPTNHLDISGRKQVAAYLKKKKQGFIVVSHDRGFIDEVVDHVLAIEKSQLELYQGNFSIYEEQKKLRDEFEMAQNEKLKKEVSRLKKTAAEKAEWSRSREGDKTKKQVGFIDTESRRVNKGAVGADAARTMKRSKAIVNRMETQISEKEKLLKDIEYIDSLTMNSQASHHKRLLSVEDLQLGYENLLFEPIHFTIEPHQRVAISGPNGAGKSSIIHYLLGAFNGKVIGEKYQPKHLSISYASQNYEDNRGTLAEFAEKNQVDYQAFLNNLRKLGMERDVFHNKIEQMSMGQRKKVELAKSLSQPAELYIWDEPLNYLDVFNQEQLEQLILNVKPAMLLVEHDQTFLDKVSTEIISLERI"},"dna_sequence":{"accession":"KF010779.1","fmin":"0","fmax":"1503","strand":"+","sequence":"ATGTCTAAAATCGAAATAAAAAATCTGACATTCGGCTACGACAGCCAAGGCACATTATTATTTGAACAAGCAAATCTAAATTTTGACACACAATGGAAACTAGGACTTATCGGACGAAACGGTCGAGGAAAGACAACTTTACTGAATATTCTACAAAACAAACTACCTTATCAAGGGCAAGTAATCCATCAGCAAGAATTTGCCTATTTCCCGCAACAGACAAAAGATAAAGAACGTTTAACCTATTACGTGTTAAATGATATTACGGATTTTGAGATATGGGAAATCGAAAGAGAGCTCCAATTGATGCAAACAGATCCTGAAATCTTATGGAGAGAATTCAGCACACTATCGGGGGGAGAGAAGACAAAAGTCCTACTGGCACTTTTATTTGTGGATGACACTCATTTCCCGTTAATCGATGAACCAACGAATCATTTGGATATCTCTGGTAGAAAACAAGTAGCGGCTTATTTGAAAAAGAAAAAACAAGGCTTCATCGTGGTCAGCCATGACCGGGGATTTATCGATGAAGTAGTGGACCATGTTTTAGCAATCGAAAAAAGTCAACTGGAACTTTATCAAGGGAATTTCTCTATCTATGAAGAACAGAAAAAACTTCGTGATGAATTTGAAATGGCTCAAAATGAAAAATTGAAAAAAGAAGTCAGTAGGCTAAAGAAAACAGCAGCTGAAAAAGCCGAATGGTCTCGTTCCCGAGAAGGAGATAAAACAAAGAAACAAGTCGGATTCATCGATACTGAATCTAGACGAGTGAATAAAGGAGCAGTGGGTGCTGATGCTGCACGGACGATGAAACGATCCAAAGCAATCGTGAATCGGATGGAGACCCAGATCAGCGAGAAAGAAAAACTATTAAAAGATATCGAATATATCGATTCTTTGACGATGAATAGCCAAGCGTCTCACCATAAGCGACTTTTAAGCGTAGAAGATCTTCAATTAGGGTATGAAAATCTGTTATTCGAGCCAATTCATTTTACAATCGAGCCTCATCAGCGGGTGGCGATTTCAGGTCCTAACGGTGCAGGAAAGTCATCCATTATCCATTATCTTCTGGGGGCATTCAACGGCAAGGTTATAGGAGAAAAATACCAGCCAAAACATCTGAGCATTAGTTATGCAAGCCAAAATTATGAAGACAATCGAGGAACGTTGGCGGAATTTGCAGAGAAAAACCAAGTAGACTACCAAGCATTTTTGAACAACCTCCGAAAGCTTGGGATGGAAAGAGATGTTTTTCATAACAAGATCGAGCAGATGAGTATGGGCCAACGGAAAAAAGTGGAATTGGCTAAATCTTTATCACAGCCAGCTGAACTATATATATGGGATGAACCATTGAATTATTTGGATGTCTTCAATCAAGAACAATTAGAACAACTGATCTTGAACGTGAAACCTGCCATGTTACTAGTGGAACATGATCAAACCTTCCTGGATAAAGTATCTACTGAGATTATTTCTCTTGAGAGAATCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3003761","ARO_id":"40408","ARO_name":"eatAv","ARO_description":"eatAv is a mutated form of the wildtype eatA ABC transporter gene isolated from Enterococcus faecium conferring resistance to lincosamides, streptogramin A's and pleuromutilins (LSaP phenotype).","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"37716":{"category_aro_accession":"3001317","category_aro_cvterm_id":"37716","category_aro_name":"pleuromutilin","category_aro_description":"Pleuromutilin is a natural product antibiotic produced by Clitopilus passeckerianus. Related antibiotics of clinical significance, such as tiamulin and retapamulin, are semi-synthetic derivatives of this compound.","category_aro_class_name":"Antibiotic"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2254":{"model_id":"2254","model_name":"Staphylococcus mutant fusA gene conferring resistance to fusidic acid","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"40330":{"param_type":"multiple resistance variants","param_description":"A set of nucleotide or amino acid substitutions that are each required to confer resistance to an antibiotic drug or drug class by co-mutation. Compare to single resistance variant, where only one substitution is required. Multiple resistance variants parameters are indicated on appropriate models using the following notation: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2],...,[wild-type n][position n][mutation n]. When each included substitution is detected in a protein sequence, resistance is conferred. This parameter is not currently included in any detection algorithms.","param_type_id":"40330","param_value":{"3355":"A67T,P406L","3358":"H457Y,S416F","3359":"V90I,H457Q,L461K,A655V","3374":"D189V,L430S","3375":"T387I,E449K","3376":"A70V,A160V,H457Y","3365":"F652S,Y654N","3388":"G452C,R659L"}},"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3356":"H457Y","3357":"L461K","3367":"H457Q","3368":"M453I","3369":"P404L","3370":"A376V","3371":"F441Y","3372":"V90A","3373":"V90I","3377":"L461S","3379":"L461F","3360":"T436I","3361":"G452S","3362":"L456F","3364":"R464C","3366":"P406L","3380":"F88L","3381":"Q115L","3382":"P404Q","3383":"V407F","3384":"D434N","3385":"G451V","3386":"G452C","3387":"G452V","3389":"R464H","3390":"R464S","3391":"R464L"},"clinical":{"3356":"H457Y","3357":"L461K","3367":"H457Q","3368":"M453I","3369":"P404L","3370":"A376V","3371":"F441Y","3372":"V90A","3373":"V90I","3377":"L461S","3379":"L461F"},"experimental":{"3360":"T436I","3361":"G452S","3362":"L456F","3364":"R464C","3366":"P406L","3380":"F88L","3381":"Q115L","3382":"P404Q","3383":"V407F","3384":"D434N","3385":"G451V","3386":"G452C","3387":"G452V","3389":"R464H","3390":"R464S","3391":"R464L"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1350"}},"model_sequences":{"sequence":{"3510":{"protein_sequence":{"accession":"CAG39573","sequence":"MAREFSLEKTRNIGIMAHIDAGKTTTTERILYYTGRIHKIGETHEGASQMDWMEQEQDRGITITSAATTAAWEGHRVNIIDTPGHVDFTVEVERSLRVLDGAVTVLDAQSGVEPQTETVWRQATTYGVPRIVFVNKMDKLGANFEYSVSTLHDRLQANAAPIQLPIGAEDEFEAIIDLVEMKCFKYTNDLGTEIEEIEIPEDHLDRAEEARASLIEAVAETSDELMEKYLGDEEISVSELKEAIRQATTNVEFYPVLCGTAFKNKGVQLMLDAVIDYLPSPLDVKPIIGHRASNPEEEVIAKADDSAEFAALAFKVMTDPYVGKLTFFRVYSGTMTSGSYVKNSTKGKRERVGRLLQMHANSRQEIDTVYSGDIAAAVGLKDTGTGDTLCGEKNDIILESMEFPEPVIHLSVEPKSKADQDKMTQALVKLQEEDPTFHAHTDEETGQVIIGGMGELHLDILVDRMKKEFNVECNVGAPMVSYRETFKSSAQVQGKFSRQSGGRGQYGDVHIEFTPNETGAGFEFENAIVGGVVPREYIPSVEAGLKDAMENGVLAGYPLIDVKAKLYDGSYHDVDSSEMAFKIAASLALKEAAKKCDPVILEPMMKVTIEMPEEYMGDIMGDVTSRRGRVDGMEPRGNAQVVNAYVPLSEMFGYATSLRSNTQGRGTYTMYFDHYAEVPKSIAEDIIKKNKGE"},"dna_sequence":{"accession":"BX571856","fmin":"599702","fmax":"601784","strand":"+","sequence":"ATGGCTAGAGAATTTTCATTAGAAAAAACTCGTAATATCGGTATCATGGCTCACATTGATGCTGGTAAAACGACTACGACTGAACGTATTCTTTATTACACTGGCCGTATCCACAAAATTGGTGAAACACATGAAGGTGCTTCACAAATGGACTGGATGGAGCAAGAACAAGACCGTGGTATTACTATCACATCTGCTGCAACAACAGCAGCTTGGGAAGGTCACCGTGTAAACATTATCGATACACCTGGACACGTAGACTTCACTGTAGAAGTTGAACGTTCATTACGTGTACTTGACGGAGCAGTTACAGTACTTGATGCACAATCAGGTGTTGAACCTCAAACTGAAACAGTTTGGCGTCAGGCTACAACTTATGGTGTTCCACGTATCGTATTTGTAAACAAAATGGACAAATTAGGTGCTAACTTCGAATACTCTGTAAGTACATTACATGATCGTTTACAAGCTAACGCTGCTCCAATCCAATTACCAATTGGTGCGGAAGACGAATTCGAAGCAATCATTGACTTAGTTGAAATGAAATGTTTCAAATATACAAATGATTTAGGTACTGAAATTGAAGAAATTGAAATTCCTGAAGACCACTTAGATAGAGCTGAAGAAGCTCGTGCTAGCTTAATCGAAGCAGTTGCAGAAACTAGCGACGAATTAATGGAAAAATATCTTGGTGACGAAGAAATTTCAGTTTCTGAATTAAAAGAAGCTATCCGCCAAGCTACTACTAACGTAGAATTCTACCCAGTACTTTGTGGTACAGCTTTCAAAAACAAAGGTGTTCAATTAATGCTTGACGCTGTAATTGATTACTTACCTTCACCACTAGACGTTAAACCAATTATTGGTCACCGTGCTAGCAACCCTGAAGAAGAAGTAATCGCGAAAGCAGACGATTCAGCTGAATTCGCTGCATTAGCGTTCAAAGTTATGACTGACCCTTATGTTGGTAAATTAACATTCTTCCGTGTGTACTCAGGTACAATGACATCTGGTTCATACGTTAAGAACTCTACTAAAGGTAAACGTGAACGTGTAGGTCGTTTATTACAAATGCACGCTAACTCACGTCAAGAAATCGATACTGTATACTCTGGAGATATCGCTGCTGCGGTAGGTCTTAAAGATACAGGTACTGGTGATACTTTATGTGGTGAGAAAAATGACATTATCTTGGAATCAATGGAATTCCCAGAGCCAGTTATTCACTTATCAGTAGAGCCAAAATCTAAAGCTGACCAAGATAAAATGACTCAAGCTTTAGTTAAATTACAAGAAGAAGACCCAACATTCCATGCACACACTGACGAAGAAACTGGACAAGTTATCATCGGTGGTATGGGTGAGCTTCACTTAGACATCTTAGTAGACCGTATGAAGAAAGAATTCAACGTTGAATGTAACGTAGGTGCTCCAATGGTTTCATATCGTGAAACATTCAAATCATCTGCACAAGTTCAAGGTAAATTCTCTCGTCAATCTGGTGGTCGTGGTCAATACGGTGATGTTCACATTGAATTCACACCAAACGAAACAGGCGCAGGTTTCGAATTCGAAAACGCTATCGTTGGTGGTGTAGTTCCTCGTGAATACATTCCATCAGTAGAAGCTGGTCTTAAAGATGCTATGGAAAATGGTGTCTTAGCAGGTTATCCATTAATTGATGTTAAAGCTAAATTATATGATGGTTCATACCATGATGTCGATTCATCTGAAATGGCCTTCAAAATTGCTGCATCATTAGCACTTAAAGAAGCTGCTAAAAAATGTGATCCTGTAATCTTAGAACCAATGATGAAAGTAACTATTGAAATGCCTGAAGAGTACATGGGTGATATCATGGGTGACGTAACATCTCGTCGTGGACGTGTTGATGGTATGGAACCTCGTGGTAATGCACAAGTTGTTAATGCTTATGTACCACTTTCAGAAATGTTCGGTTATGCAACATCATTACGTTCAAACACTCAAGGTCGCGGTACTTACACTATGTACTTCGATCACTATGCTGAAGTTCCAAAATCAATCGCTGAAGATATTATCAAGAAAAATAAAGGTGAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35517","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus MRSA252","NCBI_taxonomy_id":"282458"}}}},"ARO_accession":"3003735","ARO_id":"40390","ARO_name":"Staphylococcus aureus fusA with mutation conferring resistance to fusidic acid","ARO_description":"The mutations to this gene are involved in altering the translation elongation factor G (EF-G) in association with the ribosome to prevent fusidic acid from binding EF-G and preventing translation.","ARO_category":{"40389":{"category_aro_accession":"3003734","category_aro_cvterm_id":"40389","category_aro_name":"antibiotic resistant fusA","category_aro_description":"Antibiotic resistant fusA is caused by mutations to the elongation factor G (EF-G) and confers resistance to fusidic acid.","category_aro_class_name":"AMR Gene Family"},"37139":{"category_aro_accession":"3000759","category_aro_cvterm_id":"37139","category_aro_name":"fusidic acid","category_aro_description":"Fusidic acid is the only commercially available fusidane, a group of steroid-like antibiotics. It is most active against Gram-positive bacteria, and acts by inhibiting elongation factor G to  block protein synthesis.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2256":{"model_id":"2256","model_name":"Staphylococcus mutant fusE gene conferring resistance to fusidic acid","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3414":"Q140L"},"clinical":{"3414":"Q140L"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"3504":{"protein_sequence":{"accession":"ADL24064","sequence":"MSRVGKKIIDIPSDVTVTFDGNHVTVKGPKGELSRTLNERMTFKQEENTIEVVRPSDSKEDRTNHGTTRALLNNMVQGVSQGYVKVLELVGVGYRAQMQGKDLILNVGYSHPVEIKAEENITFSVEKNTVVKVEGISKEQVGALASNIRSVRPPEPYKGKGIRYQGEYVRRKEGKTGK"},"dna_sequence":{"accession":"CP002114","fmin":"2306994","fmax":"2307531","strand":"-","sequence":"TTATTTACCAGTTTTACCTTCTTTACGGCGAACGTATTCACCTTGGTAACGAATACCTTTACCTTTGTAAGGCTCTGGAGGTCTTACTGAACGGATGTTAGATGCTAATGCTCCAACTTGTTCTTTTGAAATACCTTCAACTTTAACGACTGTGTTTTTCTCAACTGAGAAAGTAATGTTTTCTTCAGCTTTAATTTCTACTGGGTGAGAATAACCAACGTTAAGGATTAAGTCTTTACCTTGCATTTGAGCACGGTAACCTACACCAACAAGTTCAAGTACTTTTACGTATCCTTGAGAAACACCTTGTACCATATTGTTTAATAAAGCACGAGTTGTACCATGGTTTGTTCTATCTTCTTTAGAATCAGATGGTCTTACAACTTCAATTGTGTTTTCTTCTTGTTTGAATGTCATTCTTTCATTTAAAGTTCTTGATAATTCACCTTTAGGACCTTTAACAGTTACATGATTTCCATCAAAAGTTACTGTTACGTCACTAGGGATGTCAATAATTTTCTTACCAACACGACTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40393","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus JKD6159","NCBI_taxonomy_id":"869816"}}}},"ARO_accession":"3003737","ARO_id":"40392","ARO_name":"Staphylococcus aureus fusE with mutation conferring resistance to fusidic acid","ARO_description":"The mutations to the rplF gene encoding riboprotein L6 have been shown to cause fusidic acid resistance, demonstrating a potential secondary site of action of the antibiotic that is blocked through these mutations. Several types of mutations have been identified that cause resistance, including SNPs, frameshift mutations and early stop codons.","ARO_category":{"40391":{"category_aro_accession":"3003736","category_aro_cvterm_id":"40391","category_aro_name":"antibiotic resistant fusE","category_aro_description":"Antibiotic resistant fusE is caused by mutations in a region of the rplF gene encoding riboprotein L6, and confers resistance to fusidic acid.","category_aro_class_name":"AMR Gene Family"},"37139":{"category_aro_accession":"3000759","category_aro_cvterm_id":"37139","category_aro_name":"fusidic acid","category_aro_description":"Fusidic acid is the only commercially available fusidane, a group of steroid-like antibiotics. It is most active against Gram-positive bacteria, and acts by inhibiting elongation factor G to  block protein synthesis.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2272":{"model_id":"2272","model_name":"Enterococcus faecalis cls conferring resistance to daptomycin","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3581":"R218Q","3603":"H215R","3582":"R267H"},"experimental":{"3581":"R218Q","3603":"H215R","3582":"R267H"}},"41342":{"param_type":"deletion mutation from peptide sequence","param_description":"A subtype of the deletion mutation detection model parameter. This parameter is used when a set of deletion mutations is reported in a peptide sequence format. These are specific to codon deletions, where a multiple of 3 nucleotides are deleted. Mutations of this type are reported in the CARD with the notation: [-][AAs][position range].","param_type_id":"41342","param_value":{"3850":"-K61","3852":"-NFQ74-76"}},"41344":{"param_type":"insertion mutation from peptide sequence","param_description":"A subtype of the insertion mutation detection model parameter. This parameter is used when a set of insertion mutations is reported in a peptide sequence format. These are specific to codon insertions, where a multiple of three nucleotides are inserted. This does not cause a frameshift mutation. Mutation parameters of this type are reported in CARD with the notation: [+][AAs][position range].","param_type_id":"41344","param_value":{"3853":"+AII14-16"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"900"}},"model_sequences":{"sequence":{"3537":{"protein_sequence":{"accession":"AEA93051.1","sequence":"MILSVLTVIYFINAIIAGITILLKPRDVAAIWAWLLVLIALPVFGFFLYLFFGRGLTDKKKFYLQQSDLRELENFQNFQEESFELYSQKMPTEEQQQFTDFFSSLNRMPLTKKNDVEIFTDGTEKFNALMADIKKAQHSIHIEYYAFVTDHIGTKILNLLEEKAAEGVEVRLLYDAFGSKGTKVHHLNELKKNGGFVQTFITSQKALLKFRLNYHDHRKIVVIDGKVGYIGGFNVADQYAGTTKKFGYWRDTHLRIQGPATSLLQMRFLMDWNVSSPEKNRVAYQLDYFFKLEALVPEANTSIQMIASGPNSDREQIKLAFIKLITSAKKRVWIQTPYLVPDDSVLAALKVAAASGVDVKIMIPDKPDHPFIYRATQYYGRLLMKENIEILIYNGGFLHAKTMIMDDEVCTVGSANQDIRSYKLNFEANAVLYDKKIIDQLEAIFLEDRKKCTTMTPEVVRDMSKWLIFKQQISRLFSPIL"},"dna_sequence":{"accession":"CP002621.1","fmin":"376485","fmax":"377931","strand":"+","sequence":"TTGATTCTTAGCGTCTTAACAGTTATTTATTTTATTAATGCAATTATTGCGGGAATTACCATTTTGTTAAAACCTCGAGATGTAGCAGCAATTTGGGCATGGCTACTCGTACTGATTGCTCTACCCGTTTTTGGTTTTTTCTTATATTTATTCTTTGGTCGCGGTTTAACCGACAAAAAGAAATTTTATTTGCAACAAAGTGATTTGCGGGAATTAGAGAATTTTCAGAATTTCCAAGAAGAAAGTTTTGAACTTTATAGTCAAAAGATGCCGACGGAGGAGCAACAACAGTTTACAGACTTTTTTTCCTCGTTAAATAGGATGCCTCTGACTAAGAAAAATGATGTTGAAATTTTTACGGATGGTACGGAAAAATTCAATGCGTTGATGGCGGATATAAAAAAAGCTCAGCACTCCATTCATATTGAATATTATGCCTTTGTAACGGATCATATCGGTACCAAAATTTTGAACTTATTAGAAGAAAAGGCGGCTGAAGGGGTTGAAGTGCGGTTGCTTTACGATGCCTTTGGCTCAAAGGGCACCAAGGTTCATCATTTGAATGAATTGAAAAAAAACGGTGGTTTTGTCCAAACGTTTATTACTTCTCAAAAAGCACTTTTGAAGTTTCGTTTGAATTATCATGATCACCGGAAAATTGTTGTTATTGACGGAAAAGTAGGCTACATTGGCGGCTTTAATGTTGCCGATCAATATGCCGGAACGACTAAAAAGTTTGGCTATTGGCGGGATACACATTTACGGATTCAAGGGCCAGCAACCTCATTACTGCAAATGCGTTTTTTAATGGATTGGAACGTCTCTTCCCCCGAGAAAAATCGTGTGGCGTATCAATTGGATTATTTCTTTAAACTTGAAGCATTGGTGCCAGAGGCAAATACATCCATTCAGATGATTGCCAGTGGTCCTAACAGTGACCGTGAACAAATTAAATTGGCCTTTATTAAATTGATTACTTCTGCCAAGAAAAGAGTCTGGATTCAAACGCCGTATTTAGTTCCTGATGATAGTGTCTTGGCTGCTTTAAAGGTTGCTGCGGCTTCAGGAGTAGATGTTAAAATTATGATTCCAGATAAGCCCGACCATCCGTTTATTTATCGAGCAACACAGTATTACGGCCGCTTATTGATGAAAGAAAATATTGAAATTTTAATTTATAACGGTGGTTTCTTACATGCGAAAACAATGATTATGGATGATGAAGTCTGCACAGTTGGTTCAGCCAATCAAGATATCCGAAGTTACAAATTAAACTTTGAAGCAAATGCTGTGTTATATGATAAAAAAATCATTGATCAATTAGAAGCAATTTTCTTAGAAGATCGAAAAAAATGTACAACAATGACTCCAGAAGTTGTTCGTGACATGTCAAAATGGTTGATTTTTAAACAACAAATTTCACGATTATTTTCACCAATTCTTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40433","NCBI_taxonomy_name":"Enterococcus faecalis OG1RF","NCBI_taxonomy_id":"474186"}}}},"ARO_accession":"3003760","ARO_id":"40417","ARO_name":"Enterococcus faecalis cls with mutation conferring resistance to daptomycin","ARO_description":"cls or cardiolipin synthase is an inner membrane protein involved in membrane synthesis and phosopholipid metabolism, with mutations to the gene being capable of conferring daptomycin resistance.","ARO_category":{"39856":{"category_aro_accession":"3003272","category_aro_cvterm_id":"39856","category_aro_name":"daptomycin resistant cls","category_aro_description":"Cardiolipin synthetase catalyzes the formation of cardiolipin from two phosphatidylglycerol molecules. Cardiolipin is important in membrane translocation and permeabilization. Current known mutations on the enzyme confer resistance to daptomycin.","category_aro_class_name":"AMR Gene Family"},"35985":{"category_aro_accession":"0000068","category_aro_cvterm_id":"35985","category_aro_name":"daptomycin","category_aro_description":"Daptomycin is a novel lipopeptide antibiotic used in the treatment of certain infections caused by Gram-positive organisms. Daptomycin interferes with the bacterial cell membrane, reducing membrane potential and inhibiting cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2285":{"model_id":"2285","model_name":"Staphylococcus aureus murA with mutation conferring resistance to fosfomycin","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3630":"V65L","3631":"G257D","3632":"D278E","3633":"E291D","3634":"Q362R","3635":"T396N"},"clinical":{"3630":"V65L","3631":"G257D","3632":"D278E","3633":"E291D","3634":"Q362R","3635":"T396N"}},"40394":{"param_type":"nonsense mutation","param_description":"A nucleotide substitution resulting in a change from an amino acid codon to a STOP codon. Nonsense mutations truncate protein translation prematurely, resulting in a defective or completely inactive protein. In CARD, nonsense mutations may be attached to models using the notation: [wild type amino acid][position][STOP] (e.g. Q42STOP). This parameter is not currently used in detection algorithms.","param_type_id":"40394","param_value":{"3638":"L42STOP"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"3549":{"protein_sequence":{"accession":"CAG41169","sequence":"MDKIVIKGGNKLTGEVKVEGAKNAVLPILTASLLASDKPSKLVNVPALSDVETINNVLTTLNADVTYKKDENAVVVDATKTLNEEAPYEYVSKMRASILVMGPLLARLGHAIVALPGGCAIGSRPIEQHIKGFEALGAEIHLENGNIYANAKDGLKGTSIHLDFPSVGATQNIIMAASLAKGKTLIENAAKEPEIVDLANYINEMGGRITGAGTDTITINGVESLHGVEHAIIPDRIEAGTLLIAGAITRGDIFVRGAIKEHMASLVYKLEEMGVELEYQEDGIRVRAEGDLQPVDIKTLPHPGFPTDMQSQMMALLLTANGHKVVTETVFENRFMHVAEFKRMNANINVEGRSAKLEGKSQLQGAQVKATDLRAAAALILAGLVADGKTSVTELTHLDRGYVDLHGKLKQLGADIERIND"},"dna_sequence":{"accession":"BX571856","fmin":"2257045","fmax":"2258311","strand":"-","sequence":"TTAATCGTTAATACGTTCAATGTCTGCACCTAATTGCTTCAATTTACCGTGTAAGTCAACATAGCCTCTATCTAGGTGCGTTAATTCAGTAACGCTTGTTTTACCATCAGCAACTAATCCAGCTAAAATTAAGGCTGCTGCTGCTCTTAAATCAGTCGCTTTAACTTGTGCACCTTGCAATTGACTTTTACCTTCAAGTTTAGCACTACGACCTTCTACATTGATATTAGCATTCATACGTTTGAACTCTGCGACATGCATAAAACGATTTTCAAATACAGTTTCAGTTACTACTTTATGTCCGTTTGCTGTTAATAATAATGCCATCATTTGTGACTGCATATCGGTTGGAAAACCAGGATGCGGTAATGTTTTGATGTCAACAGGCTGTAAATCTCCTTCAGCACGTACACGAATACCATCTTCTTGATATTCCAATTCAACGCCCATTTCTTCTAATTTATACACTAAACTAGCCATATGTTCTTTGATTGCACCACGTACAAAAATATCGCCACGAGTAATGGCACCAGCGATCAGTAATGTGCCTGCTTCAATTCTATCTGGAATGATAGCATGTTCTACACCATGTAATGATTCTACACCATTGATTGTAATTGTGTCTGTACCAGCACCAGTAATTCTACCGCCCATTTCATTAATGTAGTTTGCTAAATCAACAATTTCAGGTTCTTTAGCTGCATTTTCAATTAAAGTCTTACCCTTAGCTAATGATGCTGCCATAATAATATTTTGTGTTGCTCCTACACTTGGAAAATCTAAATGAATTGATGTACCTTTTAATCCATCTTTAGCATTAGCATAAATATTACCATTTTCAAGATGAATTTCTGCGCCTAAAGCTTCAAAACCTTTAATGTGTTGCTCAATCGGTCTACTTCCAATTGCACAACCACCAGGCAATGCAACAATAGCATGTCCTAGTCTTGCTAAAAGAGGTCCCATAACTAAAATACTTGCACGCATTTTACTAACATATTCATATGGTGCCTCTTCATTTAGAGTCTTTGTTGCATCAACGACAACAGCATTTTCGTCCTTTTTGTATGTAACGTCAGCATTTAAGGTTGTTAATACATTATTTATTGTTTCTACATCACTTAAAGCTGGAACATTAACTAATTTGCTCGGTTTATCAGAAGCTAATAAAGATGCTGTTAATATAGGTAATACTGCATTTTTAGCACCTTCTACTTTAACTTCACCCGTTAATTTATTTCCACCTTTGATTACTATTTTATCCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35517","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus MRSA252","NCBI_taxonomy_id":"282458"}}}},"ARO_accession":"3003776","ARO_id":"40453","ARO_name":"Staphylococcus aureus murA with mutation conferring resistance to fosfomycin","ARO_description":"murA or UDP-N-acetylglucosamine enolpyruvyl transferase catalyses the initial step in peptidoglycan biosynthesis and is inhibited by fosfomycin. Overexpression of murA through mutations confers fosfomycin resistance.","ARO_category":{"39245":{"category_aro_accession":"3002811","category_aro_cvterm_id":"39245","category_aro_name":"murA transferase","category_aro_description":"murA or UDP-N-acetylglucosamine enolpyruvyl transferase catalyses the initial step in peptidoglycan biosynthesis and is inhibited by fosfomycin. Overexpression of murA through mutations confers fosfomycin resistance.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2271":{"model_id":"2271","model_name":"mupB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"2000"}},"model_sequences":{"sequence":{"3524":{"protein_sequence":{"accession":"AEY83581","sequence":"MENENIIEEQKILNFWKEENIFKKSIDNRKNDNPFVFYDGPPTANGLPHTGHVLGRVIKDLFARYKTMQGFYVERKAGWDTHGLPVELGVEKKLGIKDKNEIEKYGIEKFINECKNSVFMYEKQWREFSELIGYWVDMEKPYKTMDNTYIESIWYILSDFHKKGLLYKGHKVTPYCPSCETSLSSHEVAQGYKEVKDISVILKFPILDSDENFLVWTTTPWSLPGNIALAINAEEIYVKVNYDNEIFIIMESLLQSVFKDEDNIDIVSKHKGKEFVGKEYLAPFPNKSLMNNENSYKVLPADFVTNKDGTGIVHIAPAYGEDDYKLVQENNIPFINVIDSRGKYNQDSPIFKGELAKESDINIIKELTHLNLLFKKEKYEHSYPFCWRCDNPLIYYAMEGWFIKTTAYKNEIKENNQKIEWYPDHIKNGRFGNFLDNMIDWNIGRKRYWGTPLNIWKCSTCSHEFSPKSINDLIQHSIEDIPSDIELHRPYIDNVKCKCQNCGGDMCREEEVIDVWFDSGSMPFAQNHYPFSGPIQNSYPADFIAEGVDQTRGWFYSLLVISTIFKGEAPYKNALSLGHILDSNGQKMSKSKGNVIDPISMIKTYGADSLRWTLVSDSVPWTNKRFSENMVAQSKSRVIDTLKNIFNFYNMYQKIDNYDYTRDTPKQLNLLDNWAISRMNSVIKEVELHLEKYNPTNASRAIGEFINEISNWYIRRSRSRFWSSEMNEDKKSAYFTLRLILINTCKIIAPFTPFTSEEIHLNLTKKSVHLEDFPQAKEEYINLKLEEDMNKVLDIVEKSRSIRNNINIKTKQPLSNMYIYDNNNLDNEFLRKYKDIIKDEINVKKINIVSDLDNFLEYDVKPNFSTLGPKLGKDMKQFQILFKNIKKEEMNKLINDFDKLQKVFDSLGVTIEEKDFIISKIPKKGFSLSSNDSDRLIILDTNLTQELIREGFVRELIRVIQQLRKQQNFNIEERINVVIDIDSDGLLSIKNNINILKENVLINNLKFEKRETMKYFKINQKEIGIQLMSSFTN"},"dna_sequence":{"accession":"JQ231224","fmin":"90","fmax":"3192","strand":"+","sequence":"TTGGAAAACGAGAATATAATAGAAGAACAAAAAATCTTAAATTTTTGGAAAGAAGAAAACATTTTCAAAAAGAGTATTGATAATAGAAAAAATGATAATCCATTTGTTTTTTACGATGGTCCTCCAACTGCCAATGGCTTACCACATACAGGTCACGTGTTAGGAAGAGTAATAAAAGATTTATTTGCTCGATATAAGACAATGCAAGGATTTTATGTTGAAAGAAAAGCTGGGTGGGATACCCATGGACTACCTGTAGAACTTGGTGTTGAAAAAAAACTTGGAATTAAGGATAAAAATGAAATAGAAAAATATGGAATAGAAAAATTTATAAATGAATGTAAAAATAGTGTGTTTATGTATGAAAAACAGTGGAGAGAATTTAGTGAACTAATCGGATATTGGGTAGATATGGAAAAACCGTACAAAACAATGGATAATACGTATATAGAATCAATCTGGTATATATTGTCTGACTTTCATAAAAAAGGTCTTTTATACAAAGGGCATAAAGTTACCCCGTATTGTCCAAGCTGTGAAACTTCTTTAAGTTCTCATGAAGTAGCTCAGGGATATAAGGAAGTAAAAGATATCTCTGTAATCTTAAAATTTCCGATTTTAGACAGTGATGAGAATTTCTTAGTTTGGACGACAACTCCATGGAGCTTACCAGGTAATATAGCTTTAGCCATAAATGCTGAAGAAATATATGTTAAAGTTAATTATGATAATGAAATTTTTATTATCATGGAAAGTTTGTTGCAAAGTGTTTTTAAAGATGAAGACAATATAGATATAGTAAGTAAACATAAAGGAAAAGAATTTGTAGGAAAAGAATACCTCGCTCCTTTCCCTAACAAGTCTCTTATGAACAATGAAAACTCATATAAAGTTTTACCTGCTGATTTTGTTACAAATAAAGATGGTACGGGTATCGTCCATATTGCTCCGGCTTATGGGGAAGATGATTACAAATTAGTTCAAGAAAATAATATACCCTTTATTAATGTTATTGATTCTAGAGGAAAATATAATCAAGATTCTCCTATTTTTAAAGGAGAGCTAGCTAAAGAATCAGATATTAACATTATTAAAGAACTTACACATTTAAATCTACTTTTCAAAAAAGAAAAATATGAACATAGCTATCCTTTTTGTTGGAGATGTGATAATCCATTAATCTATTATGCAATGGAAGGTTGGTTTATAAAAACAACGGCTTATAAAAATGAAATAAAGGAAAACAATCAAAAAATAGAATGGTATCCAGACCATATTAAAAATGGAAGGTTTGGAAATTTCTTAGATAATATGATTGATTGGAATATTGGTAGAAAAAGATATTGGGGCACTCCACTAAATATATGGAAATGCTCCACGTGTTCCCATGAGTTTTCACCTAAAAGCATAAATGATCTAATACAACATTCCATTGAAGATATTCCTTCTGATATAGAATTACATCGACCTTATATAGATAATGTGAAATGTAAATGTCAAAATTGTGGTGGTGACATGTGTAGAGAAGAAGAAGTCATTGATGTATGGTTTGATAGTGGATCGATGCCTTTTGCACAAAATCACTATCCATTTAGTGGTCCCATTCAAAACTCATACCCAGCTGACTTTATAGCTGAAGGAGTTGATCAAACTAGAGGGTGGTTTTATAGCTTATTGGTGATTTCAACAATTTTCAAAGGGGAAGCACCTTATAAAAACGCATTGTCATTAGGACATATATTAGATTCCAATGGACAAAAAATGTCGAAAAGTAAAGGGAATGTTATAGATCCTATATCAATGATAAAAACTTATGGCGCTGATTCTTTAAGATGGACATTAGTTTCTGACAGCGTTCCTTGGACTAACAAAAGGTTTTCAGAAAATATGGTGGCACAATCAAAATCGAGAGTAATTGATACTTTAAAAAATATATTTAACTTCTATAATATGTATCAAAAAATTGATAATTATGACTATACTAGGGATACTCCTAAACAGCTGAATTTACTTGATAATTGGGCTATATCTCGAATGAATTCAGTTATAAAAGAGGTAGAGCTGCATTTAGAAAAATATAACCCTACAAATGCATCAAGAGCTATTGGGGAGTTTATCAATGAAATAAGTAATTGGTATATTAGAAGATCTAGAAGTCGATTTTGGAGTAGTGAAATGAATGAGGATAAAAAGAGTGCGTATTTTACTCTTAGACTTATTTTGATTAATACTTGTAAAATAATAGCTCCTTTCACCCCATTTACTAGCGAGGAAATACATCTAAATCTCACCAAAAAAAGTGTACACTTAGAAGATTTCCCTCAAGCCAAGGAAGAATATATAAATTTAAAACTAGAAGAAGATATGAATAAAGTTTTAGATATTGTCGAAAAATCTAGAAGCATAAGAAATAACATAAACATCAAAACAAAACAACCACTTTCAAACATGTATATATATGACAATAATAATCTTGATAATGAATTTCTAAGAAAATACAAAGACATCATTAAAGATGAAATAAATGTTAAAAAGATAAATATTGTTTCTGATTTAGACAATTTTTTAGAATATGATGTAAAACCGAACTTTTCAACTTTAGGCCCTAAATTAGGAAAAGATATGAAACAATTCCAAATTTTATTTAAAAATATTAAAAAAGAAGAAATGAATAAACTAATCAATGATTTCGATAAACTTCAAAAAGTTTTTGACTCTTTAGGTGTAACAATTGAGGAAAAGGATTTTATTATTAGTAAAATACCTAAAAAGGGATTCTCTCTTTCAAGCAATGACTCTGATCGTCTTATCATTTTAGACACTAATTTGACTCAAGAATTAATTCGCGAAGGGTTTGTCAGAGAATTAATTCGTGTTATTCAACAACTAAGAAAACAACAGAACTTTAATATTGAAGAACGTATAAATGTAGTAATAGACATAGATTCCGATGGTTTACTATCAATTAAAAATAATATCAATATATTGAAAGAAAATGTACTAATTAATAATCTAAAATTTGAGAAAAGAGAAACTATGAAATATTTTAAAATTAATCAGAAAGAAATTGGTATTCAGTTAATGTCTAGCTTTACAAATTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3000510","ARO_id":"36649","ARO_name":"Staphylococcus mupB conferring resistance to mupirocin","ARO_description":"An alternative isoleucyl-tRNA synthetase conferring resistance to mupirocin.","ARO_category":{"36585":{"category_aro_accession":"3000446","category_aro_cvterm_id":"36585","category_aro_name":"antibiotic resistant isoleucyl-tRNA synthetase (ileS)","category_aro_description":"Mupirocin inhibits protein synthesis by interfering with isoleucyl-tRNA synthetase (ileS).  Mutations in ileS can confer low-level mupirocin resistance.","category_aro_class_name":"AMR Gene Family"},"36693":{"category_aro_accession":"3000554","category_aro_cvterm_id":"36693","category_aro_name":"mupirocin","category_aro_description":"Mupirocin, also known as pseudomonic acid, is a bacteriostatic polyketide antibiotic from Pseudomonas fluorescens used to treat S. aureus and MRSA. It inhibits Ile tRNA synthetase.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2270":{"model_id":"2270","model_name":"mupA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"2000"}},"model_sequences":{"sequence":{"3523":{"protein_sequence":{"accession":"CAA53189","sequence":"MTKKYLNTQNEISAFWNTQKIFKKSIDNRKGQESFVFYDGPPTANGLPHAGHVLGRVIKDLVARLKTMQGFYVERKAGWDTHGLPVELEVEKKIGIKGKQDIEKYGIENFINECKKSVFNYEKEWRDFSKDLGYWVDMDSPYITLENNYIESVWNILSTFHKKGLLYKGHKVTPYCTHDQTALSSHEVAQGYKNVKDLSAVVKFQLTNSKDTYFLSWTTTPWTLPANVALAINKDLNYSKIRVENEYYILATDLINSIITEKYEIIDTFSGSNLINLKYIPPFESDGLVNAYYVVDGEFVTNSEGTGIVHIAPAHGEDDYQLVLERDLDFLNVITREGVYNDRFPELVGNKAKNSDIEIIKLLSKKQLLYKKQKYEHNYPHCWRCGNPLIYYAMEGWFIKTTNFKNEIINNNNNIEWFPSHIKEGRMGNFLENMVDWNIGRNRYWGTPLNVWICNDCNHEYAPSSIKDLQNNSINKIDEDIELHRPYVDNITLSCPKCNGKMSRVEEVIDVWFDSGSMPFAQHHYPFDNQKIFNQHFPADFIAEGVDQTRGWFYSLLVISTILKGKSSYKRALSLGHILDSNGKKMSKSKGNVINPTELINKYGADSLRWALISDSAPWNNKRFSENIVAQTKSKFIDTLDNIYKFYNMYNKIDHYNPNNEITKSRNTLDNWALSRLNTLIKESNIYVNNYDFTSAARLINEYTNTISNWYIGDSRGRFWEQGISNDKKDAYNTLYEILTTLSRLVAPFVPFISEKIHYNLTGKSVHLQDYPQYKESFINQALEDEMHTVIKIVELSRQARKNADLKIKQPLSKMVIKPNSQLNLSFLPNYYSIIKDELNIKNIELTDNINDYITYELKLNFSSVGPKLGNKTKNIQTLIDSLSEYDKKSLIESNNFKSLSSDAELTKDDFIIKTLPKDSYQLSEDNDCVILLDKNLSPELIREGHARELIRLIQQLRKKKNLPINQRIDIYIGVTGELLESIKTNKNMFKENFVIKNIHLNVIDEYENTIHFNNKEIKISLLY"},"dna_sequence":{"accession":"X75439","fmin":"476","fmax":"3551","strand":"+","sequence":"TTGACAAAGAAATATTTAAACACCCAGAATGAAATATCAGCATTTTGGAATACTCAAAAGATATTTAAAAAATCAATTGACAATAGAAAAGGACAGGAAAGTTTTGTTTTTTATGACGGCCCCCCAACTGCAAATGGCCTTCCTCATGCTGGCCATGTTCTTGGAAGAGTAATCAAGGATTTAGTTGCAAGATTAAAAACTATGCAAGGTTTTTATGTAGAAAGAAAAGCAGGATGGGATACCCATGGCTTACCAGTTGAATTAGAGGTTGAAAAAAAAATTGGAATTAAAGGAAAACAAGACATTGAAAAGTATGGAATAGAAAATTTTATAAATGAATGTAAAAAAAGTGTATTTAATTATGAAAAAGAATGGCGGGATTTTTCTAAAGATTTAGGATACTGGGTTGACATGGACTCCCCCTATATAACTCTTGAGAATAATTATATTGAAAGTGTATGGAATATATTATCTACATTCCATAAAAAAGGACTATTATATAAGGGACATAAGGTGACTCCTTATTGTACACATGATCAAACCGCTTTAAGTTCTCATGAAGTAGCGCAAGGCTATAAAAACGTTAAAGATTTATCAGCTGTTGTTAAATTTCAACTTACAAATAGTAAAGATACTTATTTCTTAAGTTGGACTACCACTCCCTGGACTTTGCCTGCAAATGTAGCATTAGCTATAAATAAAGATCTTAATTATTCAAAAATTCGGGTAGAAAATGAGTATTATATCTTAGCTACAGATCTAATTAATTCTATAATAACTGAAAAATACGAAATTATTGATACCTTTTCAGGAAGTAATTTAATTAATTTAAAATACATTCCTCCTTTTGAAAGCGACGGTTTAGTTAATGCATATTACGTTGTTGATGGAGAATTTGTTACTAACTCAGAAGGAACTGGTATTGTTCATATAGCACCAGCTCATGGGGAAGATGACTACCAATTGGTTTTAGAGCGTGATTTGGATTTCTTAAATGTTATAACAAGAGAAGGAGTATATAATGATAGGTTCCCTGAATTAGTTGGTAATAAAGCTAAAAATAGTGATATAGAAATCATAAAATTATTATCCAAAAAACAACTTTTATATAAAAAACAAAAATATGAGCATAATTATCCTCATTGTTGGAGATGTGGTAATCCTTTGATATATTATGCGATGGAAGGTTGGTTTATTAAAACAACTAATTTTAAGAATGAAATTATTAACAATAATAATAATATAGAGTGGTTTCCTTCTCATATTAAGGAAGGGAGAATGGGAAATTTCTTAGAAAATATGGTTGATTGGAACATTGGTAGAAATAGATATTGGGGAACACCATTAAATGTATGGATTTGCAATGATTGTAATCACGAATACGCACCAAGTAGTATTAAGGATTTACAAAATAATTCCATCAATAAAATTGATGAAGATATTGAGTTGCATAGACCTTATGTTGATAATATCACTCTTAGTTGCCCTAAGTGTAATGGGAAAATGTCTCGAGTAGAAGAAGTAATCGATGTTTGGTTTGATAGCGGCTCTATGCCGTTTGCTCAGCATCATTATCCTTTTGATAACCAGAAAATTTTTAATCAACACTTTCCAGCTGATTTTATTGCAGAAGGAGTTGATCAAACGAGAGGCTGGTTTTACAGTTTACTAGTAATTTCTACTATTCTAAAAGGAAAATCTTCTTATAAACGTGCTTTATCTTTAGGACATATTCTAGACAGTAATGGTAAAAAAATGTCTAAAAGTAAAGGAAACGTTATTAATCCAACTGAATTAATTAATAAGTACGGAGCCGATTCTTTAAGATGGGCCTTAATTTCGGATAGTGCTCCATGGAATAACAAAAGATTCTCAGAAAATATAGTAGCTCAGACCAAATCGAAATTTATAGATACGCTTGATAATATTTATAAATTTTATAATATGTATAATAAAATAGATCACTATAATCCTAATAATGAAATTACAAAAAGTAGAAATACATTAGATAATTGGGCTCTTTCTCGCTTAAACACCTTAATAAAAGAAAGTAATATTTATGTAAATAATTACGATTTCACTTCCGCAGCCAGATTAATTAACGAATATACCAATACAATAAGTAATTGGTATATCGGAGATTCGAGAGGACGATTTTGGGAACAAGGAATTTCTAACGATAAAAAAGATGCGTACAATACGCTTTATGAAATTTTAACAACTTTATCAAGACTAGTGGCTCCATTTGTTCCATTTATATCTGAAAAAATCCATTATAATTTGACTGGAAAAAGTGTGCATTTACAAGATTATCCACAATATAAAGAAAGTTTTATTAATCAAGCATTGGAAGATGAAATGCATACCGTTATAAAAATTGTAGAATTATCTAGACAGGCTCGCAAAAATGCAGATTTAAAAATTAAGCAACCTTTATCGAAAATGGTGATTAAACCTAATAGTCAATTAAACTTAAGTTTTTTACCTAATTACTATTCAATAATAAAAGACGAATTAAATATAAAAAACATTGAATTAACTGATAATATTAATGACTATATTACCTATGAGCTTAAATTGAATTTTTCTTCTGTGGGACCAAAACTAGGGAACAAAACGAAAAATATTCAAACATTGATAGACTCCCTATCAGAGTATGATAAAAAAAGTTTAATTGAGTCTAATAACTTCAAAAGTTTATCTTCTGATGCTGAGTTAACTAAGGATGATTTTATAATTAAAACCTTACCTAAGGATAGTTATCAACTCAGTGAAGATAATGACTGCGTTATATTATTAGATAAAAATTTATCTCCTGAATTAATTCGCGAAGGACATGCTAGAGAGCTCATTAGATTAATTCAACAATTAAGAAAAAAGAAAAATTTACCAATAAATCAACGTATTGATATTTATATCGGTGTAACTGGGGAATTATTAGAATCAATAAAAACCAATAAAAATATGTTTAAAGAAAATTTCGTGATTAAAAATATACACTTAAATGTTATAGATGAATATGAAAATACTATTCATTTTAATAATAAAGAAATAAAAATTTCCTTATTATATTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3000521","ARO_id":"36660","ARO_name":"Staphylococcus mupA conferring resistance to mupirocin","ARO_description":"An alternative isoleucyl-tRNA synthetase conferring resistance to mupirocin.","ARO_category":{"36585":{"category_aro_accession":"3000446","category_aro_cvterm_id":"36585","category_aro_name":"antibiotic resistant isoleucyl-tRNA synthetase (ileS)","category_aro_description":"Mupirocin inhibits protein synthesis by interfering with isoleucyl-tRNA synthetase (ileS).  Mutations in ileS can confer low-level mupirocin resistance.","category_aro_class_name":"AMR Gene Family"},"36693":{"category_aro_accession":"3000554","category_aro_cvterm_id":"36693","category_aro_name":"mupirocin","category_aro_description":"Mupirocin, also known as pseudomonic acid, is a bacteriostatic polyketide antibiotic from Pseudomonas fluorescens used to treat S. aureus and MRSA. It inhibits Ile tRNA synthetase.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2292":{"model_id":"2292","model_name":"Streptomyces rishiriensis parY mutant conferring resistance to aminocoumarin","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1300"}},"model_sequences":{"sequence":{"3557":{"protein_sequence":{"accession":"AAO47226.2","sequence":"MSTFPAPAAGSRPQDGSDYTARHLMVLDGLEAVRKRPGMYIGSSDSRGLMHCLWEIIDNSVDEALAGACDHIEVILHDDGSVEVTDNGRGIPVDTEPRTGLSGVELAYTKLHAGGKFGGGSYAASGGLHGVGASVVNALSARLDIEVDRHGRTHAISFRRGAPGTYSAPGPDAPFTRAQGLHRTARIPKSRTGTRVRYWADRQIFLKDAKLSLENLHQRARQTAFLVPGLTIVVRDEYGLGEGGSKGEESFRFDGGISEFCEYLAADKPVCDVLRLTGQGTFKETVPVLDEHGQMTPTEVTRELGVDVALRWGTGYDTTLRSFVNIIATPKGGTHVAGFEQAVAKTMNEVLRAKKLLRVAEDDIVKDDALEGLTAVVTVRLAEPQFEGQTKEVLGTSAARRIVNTVISRELKAFLTSTKRDAAAQARVVMEKAVAAARTRIAARQHKDAQRRKTALESSSLPAKLADCRSDDVERSELFIVEGDSALGTAKLARNSEFQALLPIRGKILNVQKSSVTDMLKNAECGAIIQVIGAGSGRTFDIDAARYGKIIMMTDADVDGSHIRTLLLTLFHRYMRPMVESGRVFAAVPPLHRIELVQPKKGQDRYVYTYSDRELRDRLMEFQSKGVRYKDSIQRYKGLGEMDADQLAETTMDPRHRTLRRINLSDLEAAEQVFDLLMGNDVAPRKEFISSSAATLDRSRIDI"},"dna_sequence":{"accession":"AF235050.4","fmin":"38028","fmax":"40140","strand":"+","sequence":"GTGAGTACATTCCCCGCCCCGGCCGCCGGCAGCCGCCCCCAGGACGGCTCCGACTACACCGCACGGCACCTGATGGTGCTCGACGGGCTCGAAGCCGTGCGCAAGCGCCCGGGCATGTACATCGGATCCAGCGACAGCCGCGGTCTGATGCACTGCCTGTGGGAGATCATCGACAACTCCGTGGACGAGGCCCTGGCCGGTGCCTGCGACCACATCGAGGTCATCCTCCACGACGACGGTTCCGTGGAAGTCACCGACAACGGCCGCGGCATCCCCGTGGACACGGAACCCCGCACCGGCCTGTCCGGAGTCGAGCTCGCCTACACCAAACTCCACGCCGGCGGCAAGTTCGGCGGCGGCTCGTACGCCGCCTCCGGCGGCCTGCACGGCGTCGGCGCCTCCGTGGTCAACGCGCTGTCCGCCCGGCTGGACATCGAGGTCGACCGCCACGGCCGCACACACGCCATCAGCTTCCGCCGCGGCGCACCCGGCACCTACTCCGCCCCTGGACCCGACGCCCCCTTCACCCGCGCCCAGGGACTGCACCGGACCGCCAGAATCCCCAAGTCACGGACCGGCACGCGCGTGCGGTACTGGGCCGACCGTCAGATCTTCCTCAAGGACGCCAAGCTCTCCCTGGAGAACCTCCATCAGCGCGCCCGCCAGACGGCGTTCCTGGTGCCGGGCCTGACCATCGTCGTGCGCGATGAGTACGGGCTCGGTGAGGGCGGCAGCAAGGGCGAGGAGTCCTTCCGTTTCGACGGCGGCATCAGCGAGTTCTGCGAGTACCTGGCCGCCGACAAGCCGGTCTGCGACGTCCTGCGCCTCACCGGCCAGGGCACGTTCAAGGAGACGGTCCCGGTCCTGGACGAGCACGGGCAGATGACCCCGACCGAGGTCACCCGCGAGCTCGGCGTGGATGTGGCGCTGCGCTGGGGGACCGGTTACGACACGACGCTGCGGTCGTTCGTCAACATCATCGCCACGCCCAAGGGCGGCACCCATGTCGCCGGGTTCGAGCAGGCCGTGGCCAAGACGATGAACGAGGTGCTGCGGGCCAAGAAGCTGCTGCGCGTCGCGGAGGACGACATCGTCAAGGACGACGCGCTGGAGGGTCTGACGGCCGTCGTCACCGTGCGCCTGGCCGAACCCCAGTTCGAGGGTCAGACCAAGGAGGTCCTGGGCACCTCGGCGGCCCGGCGCATCGTGAACACCGTGATCTCCAGGGAGCTGAAGGCGTTCCTGACCTCCACCAAGCGTGACGCGGCCGCTCAGGCGCGGGTCGTGATGGAGAAGGCGGTCGCCGCCGCGCGCACGCGTATCGCGGCGCGGCAGCACAAGGACGCACAGCGTCGCAAGACGGCGCTGGAGTCCTCGTCCCTGCCCGCCAAGCTGGCCGACTGCCGCAGCGACGACGTCGAGCGCAGCGAACTGTTCATCGTCGAGGGCGACTCGGCGCTCGGTACGGCGAAGCTGGCCCGCAACTCCGAGTTCCAGGCGCTGCTGCCGATCCGGGGCAAGATCCTCAACGTCCAGAAGTCGTCCGTGACCGACATGCTGAAGAACGCCGAGTGCGGGGCGATCATCCAGGTCATAGGGGCGGGCTCCGGGCGGACCTTCGACATCGACGCGGCCCGTTACGGCAAGATCATCATGATGACCGACGCCGATGTGGACGGTTCCCACATCCGGACGCTGTTGCTGACGCTGTTCCATCGCTACATGCGGCCCATGGTCGAGTCGGGCCGGGTGTTCGCCGCGGTGCCGCCGCTGCACCGCATCGAGCTGGTCCAGCCCAAGAAGGGCCAGGACAGGTACGTGTACACGTACTCGGACCGGGAGCTGCGCGACAGGCTCATGGAGTTCCAGAGCAAGGGCGTGAGGTACAAGGACTCCATCCAGCGCTACAAGGGTCTGGGCGAGATGGACGCCGATCAGCTGGCCGAGACGACGATGGACCCGCGTCATCGCACCCTGCGACGCATCAACCTCTCCGACCTGGAGGCCGCCGAGCAGGTCTTCGACCTGCTCATGGGCAACGATGTGGCGCCGCGCAAGGAGTTCATCTCCAGCTCCGCGGCCACGCTGGACCGGTCCAGGATCGATATCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36876","NCBI_taxonomy_name":"Streptomyces rishiriensis","NCBI_taxonomy_id":"68264"}}}},"ARO_accession":"3003318","ARO_id":"39902","ARO_name":"Streptomyces rishiriensis parY mutant conferring resistance to aminocoumarin","ARO_description":"point mutation on the Streptomyces rishiriensis parY resulting in aminocoumarin resistance","ARO_category":{"36619":{"category_aro_accession":"3000480","category_aro_cvterm_id":"36619","category_aro_name":"aminocoumarin resistant parY","category_aro_description":"Expression of parY(R), which encodes an aminocoumarin resistant topoisomerase IV, can confer aminocoumarin resistance.","category_aro_class_name":"AMR Gene Family"},"40472":{"category_aro_accession":"3003787","category_aro_cvterm_id":"40472","category_aro_name":"aminocoumarin self resistant parY","category_aro_description":"Inherent ParY resistant to aminocoumarin from an antibiotic producer. The presence of these genes confers self resistance to the antibiotic it produces","category_aro_class_name":"AMR Gene Family"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36271":{"category_aro_accession":"3000132","category_aro_cvterm_id":"36271","category_aro_name":"clorobiocin","category_aro_description":"Clorobiocin is an aminocoumarin antibiotic produced by Streptomyces roseochromogenes, and binds DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36289":{"category_aro_accession":"3000150","category_aro_cvterm_id":"36289","category_aro_name":"coumermycin A1","category_aro_description":"Coumermycin A1 is an antibiotic produced by Streptomyces rishiriensis, and binds DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2298":{"model_id":"2298","model_name":"SPM-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"3564":{"protein_sequence":{"accession":"CAD37801.1","sequence":"MNSPKSRALLGFMGAFCLLLVAGAPLSAKSSDHVDLPYNLTATKIDSDVFVVTDRDFYSSNVLVAKMLDGTVVIVSSPFENLGTQTLMDWVAKTMKPKKVVAINTHFHLDGTGGNEIYKKMGAETWSSDLTKQLRLEENKKDRIKAAEFYKNEDLKRRILSSHPVPADNVFDLKQGKVFSFSNELVEVSFPGPAHSPDNVVVYFPKKKLLFGGCMIKPKELGYLGDANVKAWPDSARRLKKFDAKIVIPGHGEWGGPEMVNKTIKVAEKAVGEMRL"},"dna_sequence":{"accession":"AJ492820.1","fmin":"404","fmax":"1235","strand":"+","sequence":"ATGAACTCACCTAAATCGAGAGCCCTGCTTGGATTCATGGGCGCGTTTTGTTTGTTGCTCGTTGCGGGAGCGCCATTGTCTGCAAAAAGTTCGGATCATGTCGACTTGCCCTACAATCTAACGGCGACCAAGATTGATTCGGACGTTTTCGTCGTCACAGACCGCGATTTCTATTCTTCGAATGTCTTAGTAGCGAAAATGCTTGATGGGACCGTTGTCATTGTCTCTTCGCCGTTTGAAAATCTGGGTACGCAAACGCTTATGGATTGGGTGGCTAAGACTATGAAGCCGAAGAAAGTAGTAGCCATCAATACGCACTTTCATTTGGACGGCACGGGTGGAAATGAAATTTACAAGAAGATGGGCGCGGAGACGTGGTCGAGCGATCTGACAAAGCAGTTGCGACTTGAGGAAAACAAGAAAGACCGGATAAAAGCAGCTGAGTTCTATAAAAACGAGGATCTGAAGCGAAGGATTCTGAGTTCCCATCCTGTTCCAGCGGATAATGTTTTTGATTTGAAACAAGGCAAGGTCTTCTCGTTTTCTAATGAGCTGGTTGAGGTTTCATTTCCAGGACCGGCTCACTCGCCCGATAATGTCGTCGTATATTTTCCCAAGAAGAAACTGCTGTTTGGCGGCTGCATGATAAAGCCGAAGGAACTTGGTTATCTGGGAGATGCCAATGTGAAGGCATGGCCCGATTCAGCTCGGCGGCTAAAAAAGTTTGATGCGAAAATTGTTATACCTGGACACGGCGAATGGGGCGGACCGGAGATGGTTAACAAGACGATCAAGGTCGCGGAAAAGGCCGTTGGCGAAATGAGACTGTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3003793","ARO_id":"40478","ARO_name":"SPM-1","ARO_description":"Plasmid-mediated SPM metallo-beta-lactamase conferring resistance to carbapenem. Originally isolated from Pseudomonas aeruginosa. Responsible for carbapenem-resistant Pseudomonas aeruginosa (CRPA) outbreaks in Brazil.","ARO_category":{"36719":{"category_aro_accession":"3000580","category_aro_cvterm_id":"36719","category_aro_name":"SPM beta-lactamase","category_aro_description":"Sao Paulo metallo-beta-lactamase (SPM-1) confers resistance to carbapenem in Pseudomonas aeruginosa","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2325":{"model_id":"2325","model_name":"Mrx","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"3600":{"protein_sequence":{"accession":"AAS13767.1","sequence":"MSERRYSPLATLFAATFLFRIGNAVAALALPWFVLSHTKSAAWAGATAASSVIATIIGAWVGGGLVDRFGRAPVALISGVVGGVAMASIPLLDAVGALSNTGLIACVVLGAAFDAPGMAAQDSELPKLGHVAGLSVERVSSLKAVIGNVAILGGPALGGAAIGLLGAAPTLGLTAFCSVLAGLLGAWVLPARAARTMTTTATLSMRAGVAFLWSEPLLRPLFGIVMIFVGIVGANGSVIMPALFVDAGRQVAELGLFSSMMGAGGLLGIAIHASVGARISAQNWLAVAFCGSAVGSLLLSQLPGVPVLMLLGALVGLLTGSVSPILNAAIYNRTPPELLGRVLGTVSAVMLSASPMVMLAAGAFVDLAGPLPGLVVSAVFAGLVALLSLRLQFATMAAAATASAPTHTEGEH"},"dna_sequence":{"accession":"AY522923.1","fmin":"7744","fmax":"8983","strand":"-","sequence":"TCAGTGTTCACCTTCTGTATGGGTTGGGGCGGAGGCTGTGGCTGCCGCCGCCATTGTAGCAAATTGAAGACGGAGCGAGAGTAGAGCCACGAGCCCCGCAAACACGGCCGATACAACGAGGCCAGGGAGCGGACCAGCAAGGTCGACAAACGCGCCGGCCGCAAGCATAACCATGGGCGAGGCTGACAGCATCACCGCCGAGACCGTGCCGAGTACCCGGCCGAGAAGTTCTGGCGGCGTGCGGTTGTAGATGGCAGCGTTGAGAATGGGAGAGACTGAGCCGGTCAGCAGTCCCACGAGCGCGCCCAACAACATCAGCACCGGCACGCCTGGCAACTGTGAAAGCAGAAGCGAGCCCACCGCAGAGCCACAAAATGCCACCGCCAGCCAGTTCTGCGCTGATATCCGGGCGCCGACCGACGCATGAATGGCAATGCCAAGGAGACCACCAGCCCCCATCATTGAGGAGAACAGCCCGAGCTCTGCTACTTGGCGTCCTGCATCTACAAACAGCGCAGGCATGATGACGCTGCCGTTGGCGCCAACGATGCCCACGAAGATCATCACTATACCAAAGAGAGGGCGCAGCAGGGGTTCGCTCCAGAGAAAAGCGACGCCGGCGCGCATGGAGAGAGTCGCCGTCGTGGTCATCGTCCGAGCGGCACGCGCGGGAAGCACCCACGCGCCGAGCAGACCTGCAAGGACGGAGCAGAACGCCGTCAGCCCGAGCGTTGGCGCAGCGCCAAGCAGGCCGATTGCGGCCCCCCCAAGGGCCGGGCCACCTAGAATCGCGACGTTCCCGATCACCGCTTTCAGTGACGAGACGCGCTCAACGGAGAGCCCGGCGACGTGGCCGAGTTTGGGCAGCTCACTGTCCTGCGCGGCCATACCGGGTGCGTCGAACGCGGCACCGAGCACCACGCAAGCGATCAGCCCAGTGTTCGAGAGGGCGCCAACGGCATCGAGCAGTGGGATGCTCGCCATGGCCACGCCGCCCACCACACCCGAGATCAATGCGACGGGCGCGCGCCCGAACCGATCGACGAGGCCACCACCAACCCACGCGCCGATGATGGTCGCGATGACGCTGCTAGCGGCCGTGGCGCCCGCCCAGGCCGCGCTCTTTGTATGAGACAGGACGAACCATGGAAGCGCGAGGGCCGCCACCGCGTTGCCGATCCGGAAGAGAAAGGTCGCCGCGAACAGCGTCGCGAGCGGGCTATATCGACGTTCGCTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36810","NCBI_taxonomy_name":"Aeromonas hydrophila","NCBI_taxonomy_id":"644"}}}},"ARO_accession":"3003839","ARO_id":"40531","ARO_name":"Mrx","ARO_description":"Part of the macrolide inactivation gene cluster in Aeromonas hydrophila","ARO_category":{"36472":{"category_aro_accession":"3000333","category_aro_cvterm_id":"36472","category_aro_name":"macrolide phosphotransferase (MPH)","category_aro_description":"Macrolide phosphotransferases (MPH) are enzymes encoded by macrolide phosphotransferase genes (mph genes). These enzymes phosphorylate macrolides in GTP dependent manner at 2'-OH of desosamine sugar thereby inactivating them. Characterized MPH's are differentiated based on their substrate specificity.","category_aro_class_name":"AMR Gene Family"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2317":{"model_id":"2317","model_name":"mgrB","model_type":"protein knockout model","model_type_id":"40354","model_description":"An AMR detection model for instances where the absence of a protein - due to large-scale insertion elements, large deletions, or other methods of protein knockout - confers clinical resistance to a known antibiotic. These models include reference sequences. Protein knockout models are currently in development.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"75"}},"model_sequences":{"sequence":{"3586":{"protein_sequence":{"accession":"NP_416340.1","sequence":"MKKFRWVVLVVVVLACLLLWAQVFNMMCDQDVQFFSGICAINQFIPW"},"dna_sequence":{"accession":"NC_000913.3","fmin":"1908622","fmax":"1908766","strand":"-","sequence":"TCACCACGGGATAAACTGGTTAATGGCACAAATTCCGCTGAAAAATTGTACATCCTGATCGCACATCATGTTGAATACCTGCGCCCAAAGCAGCAAGCAAGCCAACACCACGACAACCAGAACGACCCATCGAAACTTTTTCAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3003820","ARO_id":"40510","ARO_name":"mgrB","ARO_description":"mgrB is a small transmembrane protein produced in the PhoPQ signalling system. It acts as a negative regulator in this system. Inactivation or down-regulation of mgrB confers colistin resistance by absence as shown in Klebsiella pneumoniae","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"41433":{"category_aro_accession":"3004269","category_aro_cvterm_id":"41433","category_aro_name":"pmr phosphoethanolamine transferase","category_aro_description":"This family of phosphoethanolamine transferase catalyze the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine to lipid A, which impedes the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"},"40429":{"category_aro_accession":"3003764","category_aro_cvterm_id":"40429","category_aro_name":"resistance by absence","category_aro_description":"Mechanism of antibiotic resistance conferred by deletion of gene (usually a porin)","category_aro_class_name":"Resistance Mechanism"}}},"2323":{"model_id":"2323","model_name":"qacH","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"190"}},"model_sequences":{"sequence":{"3598":{"protein_sequence":{"accession":"AAZ42322.1","sequence":"MKNWIFMAVAIFGEVIATSALKSSHGFTRLVPSVVVVAGYGLAFYFLSLALKSIPVGIAYAVWAGLGIVLVAAIAWIFHGQKLDFWAFIGMGLIVSGVAVLNLLSKVSAH"},"dna_sequence":{"accession":"DQ149925.1","fmin":"188","fmax":"521","strand":"+","sequence":"GTGAAGAACTGGATATTTATGGCTGTTGCAATCTTTGGCGAGGTCATCGCAACTTCCGCACTGAAGTCTAGCCATGGATTCACTAGGTTAGTTCCTTCCGTTGTAGTTGTGGCTGGCTACGGGCTTGCGTTCTATTTCTTGTCTCTCGCGCTCAAGTCCATTCCGGTCGGTATTGCTTACGCTGTATGGGCTGGGCTTGGCATCGTGCTTGTGGCAGCTATTGCTTGGATTTTCCATGGCCAAAAACTAGACTTCTGGGCGTTCATTGGCATGGGACTTATCGTCAGTGGCGTCGCCGTTCTAAACCTGCTATCCAAGGTCAGCGCACATTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36789","NCBI_taxonomy_name":"Vibrio cholerae","NCBI_taxonomy_id":"666"}}}},"ARO_accession":"3003836","ARO_id":"40527","ARO_name":"qacH","ARO_description":"qacH is a subunit of the qac multidrug efflux pump in Vibrio cholerae","ARO_category":{"36004":{"category_aro_accession":"0010003","category_aro_cvterm_id":"36004","category_aro_name":"small multidrug resistance (SMR) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Small multidrug resistance (SMR) proteins are a relatively small family of transporters, restricted to prokaryotic cells. They are also the smallest multidrug transporters, with only four transmembrane alpha-helices and no significant extramembrane domain.","category_aro_class_name":"AMR Gene Family"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2324":{"model_id":"2324","model_name":"gadW","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"470"}},"model_sequences":{"sequence":{"3599":{"protein_sequence":{"accession":"ANK04027.1","sequence":"MAHVCSVILVRRSFDIHHEQQKISLHNESILLLDKNLADDFAFCSLDTRRLDIEELTVCHYLQNIRQLPRNLGLHSKDRLLINQSPPIQLVTAIFDSFNDPRVNSPILSKMLYLSCLSMFSHKKELIPLLFNSISTVSGKVERLISFDIAKRWYLRDIAERMYTSESLIKKKLQDENTCFSKILLASRMSMARRLLELRQIPLHTIAEKCGYSSTSYFINTFRQYYGVTPHQFSQHSPGTFS"},"dna_sequence":{"accession":"CP015085.1","fmin":"2551711","fmax":"2552440","strand":"-","sequence":"TCAGGAAAAGGTACCCGGCGAATGTTGCGAAAACTGATGTGGCGTTACACCATAATATTGTCTAAATGTATTTATAAAGTATGACGTACTGCTATAGCCACATTTTTCCGCAATAGTATGCAGAGGTATTTGACGTAACTCGAGTAATCGTCTGGCCATCGACATCCTGGAGGCGAGTAATATTTTACTGAAACAGGTATTTTCATCCTGCAACTTTTTTTTGATGAGACTCTCGCTGGTGTACATTCTTTCTGCGATATCGCGTAGATACCAACGTTTAGCGATATCAAAGCTAATAAGGCGTTCAACTTTTCCTGAAACAGTACTGATACTATTGAAAAGTAAGGGGATCAGTTCTTTCTTATGAGAAAACATTGATAAACAGGAAAGATAGAGCATTTTGCTCAGTATCGGCGAATTGACCCGGGGGTCATTGAAACTATCAAAAATCGCCGTCACCAGCTGTATGGGGGGTGACTGGTTAATTAACAAACGGTCTTTGCTATGCAATCCTAAATTGCGTGGCAACTGACGAATATTTTGTAAGTAATGGCAAACTGTCAGCTCTTCGATATCCAGCCGTCGCGTATCCAGTGAACAAAACGCAAAATCGTCTGCCAAATTTTTATCCAGCAGCAGGATACTCTCGTTATGCAACGATATTTTTTGCTGTTCATGATGAATATCGAATGAACGACGAACGAGGATCACCGAGCAGACATGAGCCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40530","NCBI_taxonomy_name":"Escherichia coli O25b:H4","NCBI_taxonomy_id":"941280"}}}},"ARO_accession":"3003838","ARO_id":"40529","ARO_name":"gadW","ARO_description":"GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and, in situations where GadX is missing, activates gadA and gadBC.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35930":{"category_aro_accession":"0000011","category_aro_cvterm_id":"35930","category_aro_name":"cloxacillin","category_aro_description":"Cloxacillin is a semisynthetic, isoxazolyl penicillin derivative in the beta-lactam class of antibiotics. It interferes with peptidogylcan synthesis and is commonly used for treating penicillin-resistant Staphylococcus aureus infections.","category_aro_class_name":"Antibiotic"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2300":{"model_id":"2300","model_name":"Acinetobacter baumannii AmpC beta-lactamase","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"3566":{"protein_sequence":{"accession":"ACJ42146.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNRSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"CP001182.1","fmin":"2873299","fmax":"2874451","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATCGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTGGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCATTTGGTTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCTGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCTGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35531","NCBI_taxonomy_name":"Acinetobacter baumannii AB0057","NCBI_taxonomy_id":"480119"}}}},"ARO_accession":"3003796","ARO_id":"40481","ARO_name":"Acinetobacter baumannii ampC beta-lactamase","ARO_description":"A class C beta-lactamase found in Acinetobacter baumannii that confers resistance to piperacillin and cefepime.","ARO_category":{"41396":{"category_aro_accession":"3004232","category_aro_cvterm_id":"41396","category_aro_name":"ampC-type beta-lactamase","category_aro_description":"AmpC beta-lactamases are clinically important class C beta-lactamase enzymes which confer resistance to cephalosporins and penicillin-like antibiotics. AmpC beta-lactamases are typically found in Enterobacteriaceae, and were described in Escherichia coli in 1940 as the first reported enzymatic deactivation of penicillin. The name AmpC connects these enzymes functionally across many species, however these enzymes are generally unnamed and not phylogenetically related.","category_aro_class_name":"AMR Gene Family"},"35976":{"category_aro_accession":"0000059","category_aro_cvterm_id":"35976","category_aro_name":"cefepime","category_aro_description":"Cefepime (INN) is a fourth-generation cephalosporin antibiotic developed in 1994. It contains an aminothiazolyl group that decreases its affinity with beta-lactamases. Cefepime shows high binding affinity with penicillin-binding proteins and has an extended spectrum of activity against Gram-positive and Gram-negative bacteria, with greater activity against both Gram-negative and Gram-positive organisms than third-generation agents.","category_aro_class_name":"Antibiotic"},"35995":{"category_aro_accession":"0000078","category_aro_cvterm_id":"35995","category_aro_name":"piperacillin","category_aro_description":"Piperacillin is an acetylureidopenicillin and has an extended spectrum of targets relative to other beta-lactam antibiotics. It inhibits cell wall synthesis in bacteria, and is usually taken with the beta-lactamase inhibitor tazobactam to overcome penicillin-resistant bacteria.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2321":{"model_id":"2321","model_name":"cdeA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"810"}},"model_sequences":{"sequence":{"3596":{"protein_sequence":{"accession":"CAE00499.1","sequence":"MENLFTRKFTTFEFLKFVSPAIISMIFISLYTIIDGIFVSTLVGSDALASINIVLPIINLVCGFGIMMATGGGAIVSIRMGENRQDEANSTFSFIVLFSLIVGILFTVISYFFIKEISILLGATDKLLPYCITYGKVMILCTPFYILKFIFEYFARTDGNSKFSLFLSVIGGVTNIILDYVFIKYFGMGLLGAAVATAIGIILTCVLGIIYFLSNKSTLKLRKPKTDFRLIRDTMINGSSEMVTELSTGITTFLFNVVALKLAGENGLAALTIVLYAHFLMTSVYLGFAAGVSPLISYNFGAENSDKLKETFKHSLKFIFISSLLVFIIALVFAPFIVRVFVNPDNTVFKLALQGLKIFAFAFLFVGINIFASGFFTAFHNGKISAIISFSRAFVFIIIGIIILPPMLNMTGLWLTVPFAEVITIFISILFIKKYKGRYKY"},"dna_sequence":{"accession":"AJ574887.1","fmin":"370","fmax":"1696","strand":"-","sequence":"TTAATACTTATATCTACCTTTATATTTTTTTATAAATAGAATAGATATAAATATGGTTATAACCTCAGCAAATGGAACTGTAAGCCATAATCCAGTCATGTTTAACATAGGAGGAAGAATTATGATTCCTATGATTATAAAAACAAAGGCACGACTAAAAGATATAATAGCTGAAATTTTTCCATTGTGAAATGCTGTAAAAAATCCTGATGCAAATATATTTATACCAACAAACAAAAAAGCAAATGCAAATATTTTTAATCCTTGTAAGGCTAGTTTAAATACTGTGTTATCTGGATTTACAAAGACCCTAACAATAAATGGTGCAAATACTAAAGCAATAATAAACACTAAAAGAGAAGAAATAAATATAAATTTTAGAGAATGTTTAAATGTTTCTTTTAATTTATCACTGTTTTCAGCACCAAAATTATAGCTTATTAATGGAGACACTCCAGCAGCGAATCCTAGATAGACTGATGTCATTAAAAAATGAGCATACAATACTATAGTAAGAGCAGCAAGTCCATTTTCTCCTGCTAATTTTAAAGCTACTACATTAAATAAGAATGTTGTAATTCCTGTAGATAATTCTGTAACCATTTCAGAAGAACCGTTTATCATAGTATCTCTTATAAGTCTAAAATCGGTTTTTGGTTTTCTTAATTTTAGTGTAGATTTATTAGATAAGAAGTAAATAATACCTAAAACACAAGTTAAAATAATACCTATAGCAGTTGCAACTGCAGCTCCTAAAAGACCCATTCCAAAATATTTAATAAATACATAATCCAATATTATATTTGTTACACCACCAATGACTGATAGAAATAAACTAAATTTAGAATTTCCATCAGTTCTTGCAAAGTACTCAAATATAAATTTTAAAATATAAAATGGTGTACATAAAATCATAACTTTACCATAAGTTATACAATATGGTAATAACTTATCTGTTGCACCAAGCAAAATAGATATTTCTTTGATAAAGAAATATGAGATTACTGTGAATAAAATCCCAACAATCAATGAAAACAAAACTATAAAAGAAAATGTAGAGTTGGCTTCATCCTGTCTATTTTCACCCATACGTATAGAAACGATAGCACCTCCACCAGTTGCCATCATTATTCCAAATCCACAAACAAGGTTAATTATAGGTAGTACAATATTTATACTAGCAAGAGCATCAGAACCAACTAATGTCGATACAAAGATGCCATCTATTATTGTGTACAAAGATATAAATATCATGGATATAATTGCAGGAGAAACAAATTTTAGAAATTCAAAAGTAGTGAATTTTCTTGTAAATAAATTTTCCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36807","NCBI_taxonomy_name":"Clostridium difficile","NCBI_taxonomy_id":"1496"}}}},"ARO_accession":"3003835","ARO_id":"40526","ARO_name":"cdeA","ARO_description":"Clostridium difficile and Escherichia coli multidrug efflux transporter with antiporter function. Confers resistance to fluoroquinolones in E. coli and acriflavin in C.difficile.","ARO_category":{"36251":{"category_aro_accession":"3000112","category_aro_cvterm_id":"36251","category_aro_name":"multidrug and toxic compound extrusion (MATE) transporter","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Multidrug and toxic compound extrusion (MATE) transporters utilize the cationic gradient across the membrane as an energy source. Although there is a diverse substrate specificity, almost all MATE transporters recognize fluoroquinolones. Arciflavine, ethidium and aminoglycosides are also good substrates.","category_aro_class_name":"AMR Gene Family"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavin","category_aro_description":"Acriflavin is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36193":{"category_aro_accession":"3000054","category_aro_cvterm_id":"36193","category_aro_name":"acridine dye","category_aro_description":"Acridine dyes are cell permeable, basic molecules with an acridine chromophore. These compounds intercalate DNA. The image shown represents the core structure of the acridine family, with specific dyes containing varying substituents.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2288":{"model_id":"2288","model_name":"Mycobacterium bovis mutant ndh conferring resistance to isoniazid","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"800"},"41345":{"param_type":"insertion mutation from nucleotide sequence","param_description":"A subtype of the insertion mutation detection model parameter. This parameter is used when a set of insertion mutations is reported in a nucleotide sequence format. Such mutations may be of variable length - possibly causing a frameshift, but not causing premature termination or a functional knockout. Mutation parameters of this type are reported in CARD with the notation: [+]nt[position]:[nucleotides].","param_type_id":"41345","param_value":{"8072":"+nt272:A","8073":"+nt439:T"}},"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3664":"R202W","3665":"L239P","3666":"V329A","3667":"D366G"},"experimental":{"3664":"R202W","3665":"L239P","3666":"V329A","3667":"D366G"}}},"model_sequences":{"sequence":{"3552":{"protein_sequence":{"accession":"CAL71877","sequence":"MSPQQEPTAQPPRRHRVVIIGSGFGGLNAAKKLKRADVDIKLIARTTHHLFQPLLYQVATGIISEGEIAPPTRVVLRKQRNVQVLLGNVTHIDLAGQCVVSELLGHTYQTPYDSLIVAAGAGQSYFGNDHFAEFAPGMKSIDDALELRGRILSAFEQAERSSDPERRAKLLTFTVVGAGPTGVEMAGQIAELAEHTLKGAFRHIDSTKARVILLDAAPAVLPPMGAKLGQRAAARLQKLGVEIQLGAMVTDVDRNGITVKDSDGTVRRIESACKVWSAGVSASRLGRDLAEQSRVELDRAGRVQVLPDLSIPRYPNVFVVGDMAAVEGVPGVAQGAIQGAKYVASTIKAELAGANPAEREPFQYFDKGSMATVSRFSAVAKIGPVEFSGFIAWLIWLVLHLAYLIGFKTKITTLLSWTVTFLSTRRGQLTITDQQAFARTRLEQLAELAAEAQGSAASAKVAS"},"dna_sequence":{"accession":"AM408590","fmin":"2102609","fmax":"2104001","strand":"-","sequence":"CTAGCTGGCCACCTTAGCGCTTGCCGCTGAGCCCTGCGCCTCGGCGGCCAGCTCGGCCAGCTGTTCGAGCCGCGTTCGCGCAAATGCCTGCTGGTCGGTGATGGTCAGCTGGCCGCGGCGAGTACTGAGGAAAGTCACCGTCCACGACAGCAGAGTGGTGATCTTGGTCTTGAACCCGATCAGGTACGCCAGGTGCAGCACCAGCCAAATCAGCCAGGCGATAAAGCCGCTGAACTCAACGGGACCGATCTTGGCCACCGCCGAAAACCTCGAAACCGTGGCCATCGATCCCTTGTCGAAGTACTGGAATGGCTCACGCTCCGCCGGGTTGGCGCCGGCCAGTTCGGCCTTGATCGTGCTGGCGACGTATTTCGCCCCCTGGATGGCGCCCTGCGCCACACCCGGCACACCCTCCACAGCGGCCATATCGCCCACCACGAACACGTTCGGGTACCGGGGAATGGACAGGTCGGGCAGCACTTGGACCCGGCCGGCCCGGTCGAGCTCAACCCGTGATTGCTCGGCAAGGTCCCTGCCCAACCGACTGGCCGAAACCCCGGCCGACCAGACCTTGCAGGCCGACTCGATGCGCCGGACGGTGCCGTCGGAGTCCTTGACGGTGATGCCGTTGCGGTCGACGTCGGTGACCATCGCACCCAGCTGGATTTCCACGCCCAGCTTCTGCAACCGGGCAGCCGCCCGCTGACCGAGCTTTGCGCCCATCGGTGGCAGCACCGCCGGGGCGGCGTCAAGCAGAATCACCCGCGCCTTGGTCGAGTCGATGTGCCGGAATGCGCCCTTCAACGTGTGCTCGGCCAGCTCGGCGATCTGTCCGGCCATTTCAACACCGGTGGGGCCAGCCCCGACAACGGTGAATGTCAGTAGCTTGGCCCGCCGTTCCGGATCGCTGGACCGTTCGGCTTGCTCGAAAGCGCTCAATATGCGGCCACGCAACTCCAACGCGTCGTCGATGGACTTCATGCCGGGTGCGAATTCGGCGAAATGGTCGTTGCCGAAATAAGACTGGCCAGCACCCGCGGCGACGATCAGGCTGTCGTAGGGGGTTTGGTAGGTGTGACCGAGCAATTCCGAGACGACGCACTGCCCGGCCAGGTCGATGTGGGTGACGTTGCCCAACAGTACCTGGACATTGCGCTGCTTACGCAGCACGACCCGGGTCGGCGGAGCGATTTCTCCCTCGGAGATAATCCCGGTGGCCACTTGGTACAGCAGCGGCTGGAACAGGTGATGGGTGGTGCGCGCGATCAGCTTGATGTCAACGTCGGCCCGCTTGAGCTTCTTTGCCGCGTTTAGCCCGCCGAACCCAGATCCGATGATCACAACTCGATGCCTACGAGGTGGTTGCGCTGTGGGTTCTTGCTGGGGACTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40462","NCBI_taxonomy_name":"Mycobacterium bovis BCG str. Pasteur 1173P2","NCBI_taxonomy_id":"410289"}}}},"ARO_accession":"3003779","ARO_id":"40461","ARO_name":"Mycobacterium bovis ndh with mutation conferring resistance to isoniazid","ARO_description":"Mutations in the Mycobacterium bovis ndh gene that results in increased resistance to isoniazid.","ARO_category":{"40053":{"category_aro_accession":"3003460","category_aro_cvterm_id":"40053","category_aro_name":"antibiotic resistant ndh","category_aro_description":"ndh is a NADH oxidase. It participates in antibiotic resistance by diminishing NADH oxidation and consequently causes an increase in NADH concentration and depletion of NAD+. This alteration of the NADH\/NAD+ ratio prevents the peroxidation reactions required for the activation of INH, as well as the displacement of the NADH-isonicotinic acyl complex from InhA enzyme binding site.","category_aro_class_name":"AMR Gene Family"},"36659":{"category_aro_accession":"3000520","category_aro_cvterm_id":"36659","category_aro_name":"isoniazid","category_aro_description":"Isoniazid is an organic compound that is the first-line anti tuberculosis medication in prevention and treatment. As a prodrug, it is activated by mycobacterial catalase-peroxidases such as M. tuberculosis KatG. Isoniazid inhibits mycolic acid synthesis, which prevents cell wall synthesis in mycobacteria.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2310":{"model_id":"2310","model_name":"Streptomyces cinnamoneus EF-Tu mutants conferring resistance to elfamycin","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"},"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"8300":"A379T"},"clinical":{"8300":"A379T"}}},"model_sequences":{"sequence":{"3578":{"protein_sequence":{"accession":"CAA67349.1","sequence":"MAKAKFERTKPHVNIGTIGHVDHGKTTLTAAITKVLHDAIPDLNPFTPFDEIDKAPEERQRGITISIAHVEYQTESRHYAHVDCPGHADYIKNMITGAAQMDGAILVVAATDGPMPQTKEHVLLARQSGVPYIVVALNKADMVDDEEIMELVELEVRELLSEYEFDGDNCPVVQVSALKALEGDKEWGEKLLGLMKAVDENIPQPERDVDKPFLMPIEDVFTITGRGTVVTGRIERGVLKVNETVDIIGIKTEKTTTTVTGIEMFRKLLDEGQAGENVGLLLRGIKREDVERGQCIIKPGTVTPHTEFEATAYILSKDEGGRHTPFFNNYRPQFYFRTTDVTGVVTLKEGTEMVMPGDNAEMTVNLIQPVAMEEGLRFTIREGGRTVGAGQVVKINK"},"dna_sequence":{"accession":"X98831.1","fmin":"361","fmax":"1555","strand":"+","sequence":"GTGGCGAAGGCGAAGTTCGAGCGGACTAAGCCGCACGTCAACATCGGCACCATCGGTCACGTCGACCACGGTAAGACGACTCTTACCGCGGCGATCACCAAGGTGCTGCACGACGCGATCCCGGACCTGAACCCCTTCACGCCGTTCGACGAGATCGACAAGGCGCCGGAAGAGCGTCAGCGCGGTATCACGATCTCGATCGCTCACGTTGAGTACCAGACCGAGTCGCGTCACTACGCCCACGTCGACTGCCCGGGTCACGCAGACTACATCAAGAACATGATCACCGGTGCCGCCCAGATGGACGGCGCGATCCTCGTGGTCGCCGCGACCGACGGTCCGATGCCGCAGACCAAGGAGCACGTGCTCCTGGCCCGCCAGTCCGGCGTTCCGTACATTGTGGTGGCCCTGAACAAGGCCGACATGGTGGACGACGAGGAGATCATGGAGCTCGTCGAGCTCGAGGTCCGTGAGCTCCTCTCCGAGTACGAGTTCGACGGCGACAACTGCCCCGTCGTCCAGGTCTCGGCTCTCAAGGCGCTCGAGGGCGACAAGGAGTGGGGCGAGAAGCTCCTCGGCCTCATGAAGGCCGTGGACGAGAACATCCCGCAGCCCGAGCGTGACGTCGACAAGCCGTTCCTGATGCCGATCGAGGACGTCTTCACGATCACCGGTCGTGGCACCGTCGTCACCGGTCGTATCGAGCGCGGTGTCCTCAAGGTCAACGAGACCGTCGACATCATCGGCATCAAGACCGAGAAGACCACCACCACGGTCACCGGTATCGAGATGTTCCGCAAGCTGCTCGACGAGGGCCAGGCCGGTGAGAACGTCGGTCTGCTCCTCCGTGGCATCAAGCGCGAGGACGTCGAGCGCGGCCAGTGCATCATCAAGCCCGGTACGGTCACGCCGCACACCGAGTTCGAGGCCACGGCGTACATCCTGTCGAAGGACGAGGGTGGCCGTCACACCCCGTTCTTCAACAACTACCGTCCGCAGTTCTACTTCCGTACGACTGACGTGACCGGTGTTGTGACCCTCAAGGAGGGCACGGAGATGGTCATGCCCGGCGACAACGCCGAGATGACCGTCAACCTGATCCAGCCTGTCGCGATGGAGGAGGGCCTGCGCTTCACCATCCGTGAGGGTGGCCGCACCGTCGGCGCCGGCCAGGTCGTCAAGATCAACAAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40498","NCBI_taxonomy_name":"Streptomyces cinnamoneus","NCBI_taxonomy_id":"53446"}}}},"ARO_accession":"3003359","ARO_id":"39943","ARO_name":"Streptomyces cinnamoneus EF-Tu mutants conferring resistance to elfamycin","ARO_description":"Sequence variants of Streptomyces cinnamoneus elongation factor Tu that confer resistance to elfamycin antibiotics.","ARO_category":{"37711":{"category_aro_accession":"3001312","category_aro_cvterm_id":"37711","category_aro_name":"elfamycin resistant EF-Tu","category_aro_description":"Sequence variants of elongation factor Tu that confer resistance to elfamycin antibiotics.","category_aro_class_name":"AMR Gene Family"},"40497":{"category_aro_accession":"3003810","category_aro_cvterm_id":"40497","category_aro_name":"kirromycin self resistant EF-Tu","category_aro_description":"Natural producers of kirromycin and kirromycin-like antibiotics (i.e., kirrothrycin) possess self-resistance, which is classified here","category_aro_class_name":"AMR Gene Family"},"36725":{"category_aro_accession":"3000586","category_aro_cvterm_id":"36725","category_aro_name":"pulvomycin","category_aro_description":"Pulvomycin is a polyketide antibiotic that binds elongation factor Tu (EF-Tu) to inhibit protein biosynthesis by preventing the formation of the ternary complex (EF-Tu*GTP*aa-tRNA). Phenotypically, it was shown that pulvomycin sensitivity is dominant over resistance.","category_aro_class_name":"Antibiotic"},"37633":{"category_aro_accession":"3001234","category_aro_cvterm_id":"37633","category_aro_name":"kirromycin","category_aro_description":"Kirromycin, also known as mocimycin, is the representative molecule of its own class of elfamycins which is composed of more than 10 analogs. Kirromycin binds to the domain 1,2 interface of elongation factor Tu. This interaction maintains the EF-Tu*GTP conformation even after GTP is hydrolyzed to GDP. EF-Tu*GDP normally releases aa-tRNA and then exits the ribosome; however, kirromycin*EF-Tu*GDP*aa-tRNA forms a strong complex and remains bound to the ribosome, prohibits translocation of the peptide chain and translation is halted.","category_aro_class_name":"Antibiotic"},"37636":{"category_aro_accession":"3001237","category_aro_cvterm_id":"37636","category_aro_name":"GE2270A","category_aro_description":"GE2270A is the model molecule of cyclic thiazolyl peptide elfamycins. GE2270A is produced by Planobispora rosea. Biosynthesis of the molecule has been shown to originate as a ribosomally synthesized peptide that undergoes significant post-translational modification. Clinical use of cyclic thiazolyl peptides is hindered by their low water solubility and bioavailability.","category_aro_class_name":"Antibiotic"},"37641":{"category_aro_accession":"3001242","category_aro_cvterm_id":"37641","category_aro_name":"enacyloxin IIa","category_aro_description":"Enacyloxin IIa is structurally distinct but acts in a similar mechanism to kirromycin-like elfamycins. It prohibits the transfer of the amino acid at the A site to the elongating peptide chain. It is most likely that the mechanism of action is that EF-Tu*GDP is locked in the EF-Tu*GTP form, and EF-Tu*GDP*aa-tRNA is immobilized on the ribosome. It is an open question whether enacyloxin IIa actually belongs to the kirromycin-like group of elfamycins due to their high similarity.","category_aro_class_name":"Antibiotic"},"39998":{"category_aro_accession":"3003414","category_aro_cvterm_id":"39998","category_aro_name":"LFF571","category_aro_description":"LFF571 is a novel semi-synthetic thiopeptide antibiotic derived from GE2270. It has been shown to possess potent in vitro and in vivo activity against Gram-positive bacteria. It is hypothesized that it a translation inhibitor leading to cell death.","category_aro_class_name":"Antibiotic"},"37618":{"category_aro_accession":"3001219","category_aro_cvterm_id":"37618","category_aro_name":"elfamycin antibiotic","category_aro_description":"Elfamycins are molecules that inhibit bacterial elongation factor Tu (EF-Tu), a key protein which brings aminoacyl-tRNA (aa-tRNA) to the ribosome during protein synthesis. Elfamycins defined by their target (EF-Tu), rather than a conserved chemical backbone. Elfamycins follow two mechanisms to disrupt protein synthesis: 1. kirromycins and enacyloxin fix EF-Tu in the GTP bound conformation and lock EF-Tu onto the ribosome, and 2. pulvomycin and GE2270 cover the binding site of aa-tRNA disallowing EF-Tu from being charged with aa-tRNA. All elfamycins cause increased the affinity of EF-Tu for GTP.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2294":{"model_id":"2294","model_name":"Campylobacter jejuni gyrA conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3817":"T86I"},"clinical":{"3817":"T86I"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1200"}},"model_sequences":{"sequence":{"4439":{"protein_sequence":{"accession":"YP_002344422.1","sequence":"MENIFSKDSDIELVDIENSIKSSYLDYSMSVIIGRALPDARDGLKPVHRRILYAMQNDEAKSRTDFVKSARIVGAVIGRYHPHGDTAVYDALVRMAQDFSMRYPSITGQGNFGSIDGDSAAAMRYTEAKMSKLSHELLKDIDKDTVDFVPNYDGSESEPDVLPSRVPNLLLNGSSGIAVGMATNIPPHSLNELIDGLLYLLDNKDASLEEIMQFIKGPDFPTGGIIYGKKGIIEAYRTGRGRVKVRAKTHIEKKTNKDVIVIDELPYQTNKARLIEQIAELVKERQIEGISEVRDESNKEGIRVVIELKREAMSEIVLNNLFKSTTMESTFGVIMLAIHNKEPKIFSLLELLNLFLTHRKTVIIRRTIFELQKARARAHILEGLKIALDNIDEVIALIKNSSDNNTARDSLVAKFGLSELQANAILDMKLGRLTGLEREKIENELAELMKEIARLEEILKSETLLENLIRDELKEIRSKFDVPRITQIEDDYDDIDIEDLIPNENMVVTITHRGYIKRVPSKQYEKQKRGGKGKLAVTTYDDDFIESFFTANTHDTLMFVTDRGQLYWLKVYKIPEGSRTAKGKAVVNLINLQAEEKIMAIIPTTDFDESKSLCFFTKNGIVKRTNLSEYQNIRSVGVRAINLDENDELVTAIIVQRDEDEIFATGGEENLENQEIENLDDENLENEESVSTQGKMLFAVTKKGMCIKFPLAKVREIGRVSRGVTAIKFKEKNDELVGAVVIENDEQEILSISAKGIGKRTNAGEYRLQSRGGKGVICMKLTEKTKDLISVVIVDETMDLMALTSSGKMIRVDMQSIRKAGRNTSGVIVVNVENDEVVSIAKCPKEENDEDELSDENFGLDLQ"},"dna_sequence":{"accession":"NC_002163.1","fmin":"957630","fmax":"960222","strand":"-","sequence":"TTATTGCAAATCTAAACCAAAGTTTTCATCGCTTAACTCATCCTCGTCATTTTCCTCTTTAGGACACTTAGCGATGCTAACCACCTCGTCATTTTCCACATTAACTACAATGACACCACTCGTATTACGCCCTGCTTTTCTAATGCTTTGCATATCAACACGTATCATCTTACCTGAACTTGTAAGAGCCATTAAATCCATAGTTTCATCTACTATAACTACGCTAATAAGATCTTTGGTTTTTTCTGTAAGTTTCATACAAATTACACCCTTACCACCTCTGCTTTGCAATCTATATTCTCCAGCATTGGTGCGTTTTCCTATACCTTTTGCACTTATGCTTAAAATTTCTTGCTCATCATTTTCTATAACAACTGCACCTACTAATTCGTCATTTTTCTCTTTAAACTTAATAGCCGTCACCCCACGACTTACACGGCCGATTTCACGCACTTTAGCAAGTGGGAATTTGATACACATACCTTTTTTGGTTACTGCAAAGAGCATTTTACCTTGTGTGCTTACACTTTCTTCATTTTCAAGATTTTCATCATCTAAATTTTCAATTTCTTGATTTTCTAAATTTTCTTCACCACCAGTGGCAAAAATTTCATCTTCATCTCTTTGAACAATAATAGCAGTTACCAACTCATCATTTTCATCCAAGTTGATCGCTCTAACTCCTACACTTCTGATATTTTGATATTCACTCAAATTTGTACGCTTTACAATACCATTTTTAGTAAAGAAACATAAAGATTTGCTCTCATCAAAATCCGTGGTTGGAATAATAGCCATGATTTTTTCTTCAGCTTGTAAATTGATAAGATTTACCACTGCTTTTCCTTTAGCCGTTCTTGAGCCTTCAGGAATTTTATAAACTTTAAGCCAATAAAGCTGTCCACGATCTGTTACAAACATAAGCGTATCATGTGTATTTGCCGTAAAGAAACTTTCTATAAAATCATCATCATAAGTCGTAACGGCTAATTTTCCTTTTCCACCTCGTTTTTGTTTTTCATATTGTTTACTAGGCACACGCTTAATATAACCACGATGTGTGATAGTTACAACCATATTTTCATTAGGAATCAAATCTTCAATATCAATATCATCGTAATCATCTTCAATTTGAGTAATACGTGGCACATCAAATTTACTTCTAATTTCTTTTAATTCATCGCGAATTAAATTTTCAAGCAAGGTTTCACTTTTTAAAATTTCTTCAAGTCTTGCAATTTCTTTCATTAATTCTGCAAGTTCATTTTCGATTTTTTCTCTTTCAAGTCCTGTTAAACGACCAAGTTTCATATCTAAAATAGCATTGGCTTGAAGCTCACTAAGACCAAATTTAGCTACTAAAGAATCTCTTGCGGTATTATTATCAGAACTATTTTTAATTAAAGCAATCACTTCATCTATATTATCAAGTGCAATTTTAAGACCTTCTAAAATATGAGCTCTTGCTCTTGCCTTTTGAAGTTCAAAAATCGTTCTTCTAATAATAACTGTTTTTCTATGAGTTAAGAAAAGATTTAAAAGTTCCAACAAAGAGAAAATTTTAGGTTCTTTATTATGAATTGCCAACATAATCACACCAAAAGTACTTTCCATAGTGGTAGATTTAAATAGATTATTTAAAACAATTTCACTCATAGCCTCACGTTTAAGCTCTATAACAACGCGGATTCCTTCTTTATTGCTCTCATCTCTTACTTCAGATATTCCTTCAATTTGCCTTTCTTTAACAAGCTCTGCAATCTGCTCTATAAGCCTAGCTTTATTGGTTTGATAAGGAAGCTCATCGATAACAATAACATCTTTATTTGTCTTTTTTTCAATATGAGTTTTAGCTCGCACTTTCACGCGACCACGCCCTGTGCGATAAGCTTCTATAATACCTTTTTTACCATAAATTATTCCACCTGTTGGAAAATCTGGACCTTTGATAAACTGCATAATCTCTTCTAGGCTTGCATCTTTATTATCAAGCAAATATAAAAGTCCATCTATCAACTCATTTAAACTATGAGGTGGGATGTTTGTCGCCATACCTACAGCTATACCACTTGAACCATTTAATAATAAATTTGGAACCCTAGAAGGTAAAACATCAGGTTCGCTTTCTGAACCATCATAATTTGGAACAAAATCGACCGTATCTTTATCTATATCTTTTAAAAGCTCATGAGAAAGTTTACTCATTTTTGCTTCAGTATAACGCATCGCAGCGGCACTATCACCATCTATAGATCCAAAGTTGCCTTGTCCTGTAATACTTGGATATCTCATAGAAAAATCTTGAGCCATTCTAACCAAAGCATCATAAACTGCTGTATCTCCATGTGGGTGATAACGACCTATAACAGCACCCACTATACGGGCTGATTTGACAAAATCTGTTCTACTTTTTGCCTCATCATTTTGCATAGCATATAAAATTCTTCTATGAACAGGCTTTAAACCATCTCTTGCGTCAGGCAAAGCACGACCTATAATAACACTCATAGAATAGTCTAAATAACTACTTTTTATAGAATTTTCTATATCTACAAGTTCAATATCAGAATCTTTGCTAAAAATATTCTCCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36956","NCBI_taxonomy_name":"Campylobacter jejuni subsp. jejuni NCTC 11168","NCBI_taxonomy_id":"192222"}}}},"ARO_accession":"3003789","ARO_id":"40474","ARO_name":"Campylobacter jejuni gyrA conferring resistance to fluoroquinolones","ARO_description":"Campylobacter jejuni is a major bacterial infectious agent associated with gastroenteritis. Quinolone resistance is reportedly conferred by a single C-257-T nucleotide substitution in the gyrA gene.","ARO_category":{"39876":{"category_aro_accession":"3003292","category_aro_cvterm_id":"39876","category_aro_name":"fluoroquinolone resistant gyrA","category_aro_description":"DNA gyrase is responsible for DNA supercoiling and consists of two alpha and two beta subunits. GyrA point mutations confer resistance by preventing fluoroquinolone antibiotics from binding the alpha-subunit.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"40463":{"category_aro_accession":"3003780","category_aro_cvterm_id":"40463","category_aro_name":"nybomycin","category_aro_description":"A  heterocyclic antibiotic that targets mutant gyrA (type II topoisomerase) containing an S84L substitution, counteracting acquired quinolone resistance. It is effective against quinolone-resistant Gram-positive bacteria including S. aureus and E. faecalis. Due to its ability to counteract quinolone resistance by targeting the mutant form of the gyrA protein, it is classified as a reverse antibiotic (RA).","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2314":{"model_id":"2314","model_name":"Acinetobacter baumannii gyrA conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"4497":"G81C","4498":"S83L"},"clinical":{"4497":"G81C","4498":"S83L"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1500"}},"model_sequences":{"sequence":{"3583":{"protein_sequence":{"accession":"AJF82744.1","sequence":"MSVSEIRPIAIEDELKHSYLDYAMSVIVSRALPDVRDGLKPVHRRVLYAMHELGNDYNKAYKKSARVVGDVIGKYHPHGDSAVYETIVRMAQDFSLRYLLVDGQGNFGSIDGDSAAAMRYTEVRMTKLAHELLADLEKDTVDWEDNYDGSERIPEVLPTRVPNLLINGAAGIAVGMATNMAPHNMTEVVNACLAYADNPNISIEGLMEYITGPDFPTGGIIYGKSGIVDAYRTGKGRLHIRGKYHFEEDEKTGRTTIVFTEIPYQVNKARVIERIAELVKEKKLEGISELRDESDKEGMRIAIDLKRGENAEVVVNNLFLNTQLENSFSINMVCLDNGQPKLMNLKDIIAAFIRHRQEVVTRRTMFELRKARERGHILEGLTVALANIDEIIETIKTSANPAEARERLLAGEWAGGGVVALLEKAGAISVRPDEIEGEDPNRPFGLSDSIYRLSPTQVGAILELRLHRLTGLEQDKLHAEYTEILGQIAELTAILNDFNLLMGVIREELAQVLQQYGDARRTEIVESRVDFCREDLIPEEQVVLTVSQTGYAKTQPLSDYQAQRRGGRGKSATSMKDDDFIQHLIVASNHATVLCFTNVGKVYRLKVFEVPQASRGAKGRPIVNLLPLDATETVTAILPLTEFPENHYVFMATASGTVKRVELEQFANIRSNGLRAIELNEEDTLIGVAITDGNQQIMLFSNEGKAIRFAETDVRAMGRTAKGVRGMRVSFASSTLSEEDADVENDDSDDNDDSTDSSLVSRIVSLVVVPETGEVLCASANGYGKRTPVNDFPTKKRGGKGVIAIKTSERNGELVGAVSIDETKELLLISDGGTLVRTRAAEVAMTGRNAQGVRLIRLSEEETLVGVVSIEAVEDEEELLEGEVDTTETDSEEAVSNNEDTSEE"},"dna_sequence":{"accession":"CP010781.1","fmin":"2990040","fmax":"2992755","strand":"-","sequence":"TTACTCTTCAGAAGTATCTTCATTATTAGATACAGCTTCTTCGCTATCAGTTTCAGTCGTATCTACTTCACCTTCAAGAAGTTCTTCTTCGTCTTCTACAGCTTCAATTGAAACTACGCCAACGAGCGTTTCTTCTTCGCTTAAACGGATCAGACGAACACCTTGAGCATTACGGCCTGTCATTGCAACTTCTGCAGCACGCGTACGAACAAGCGTACCACCATCAGAAATTAATAATAACTCTTTGGTTTCATCAATAGAAACTGCACCAACTAGCTCACCGTTACGTTCACTTGTCTTGATCGCAATAACACCCTTACCACCACGTTTCTTGGTCGGGAAGTCATTTACTGGAGTACGTTTACCATAACCGTTGGCACTCGCACACAGTACTTCGCCTGTCTCAGGTACAACAACAAGCGATACGATGCGACTTACTAGACTTGAATCTGTTGAATCATCATTATCATCTGAATCATCATTTTCAACATCTGCATCTTCTTCACTTAAGGTGCTGCTTGCAAAACTCACGCGCATACCGCGTACACCTTTCGCTGTACGACCCATTGCACGTACGTCAGTTTCAGCAAAACGAATTGCCTTACCTTCGTTAGAGAACAACATGATTTGCTGATTACCATCAGTAATCGCAACACCAATTAAAGTATCTTCTTCATTAAGTTCAATAGCACGTAGACCATTTGAACGAATGTTTGCAAATTGCTCTAACTCAACACGCTTAACCGTACCAGAAGCTGTCGCCATAAACACATAGTGGTTTTCCGGGAACTCGGTTAACGGCAAGATTGCGGTTACGGTTTCTGTTGCATCTAGAGGTAACAAGTTCACGATTGGACGGCCTTTTGCCCCACGTGATGCTTGAGGAACTTCAAATACTTTCAGACGGTACACTTTACCCACATTGGTAAAGCAAAGTACGGTCGCATGGTTCGATGCCACAATCAGATGTTGAATAAAGTCATCATCTTTCATTGAGGTTGCAGACTTACCACGTCCACCACGGCGCTGTGCCTGATAGTCTGAAAGAGGTTGAGTTTTTGCATAACCCGTTTGCGAAACCGTTAATACCACTTGCTCTTCAGGAATTAAATCTTCACGGCAGAAATCCACACGAGATTCAACAATTTCGGTACGACGTGCATCGCCATATTGTTGTAAAACTTGTGCCAACTCTTCGCGAATAACACCCATTAACAAGTTAAAGTCATTTAAAATTGCAGTAAGTTCAGCAATTTGACCTAAAATTTCAGTATATTCCGCATGTAACTTGTCTTGTTCAAGACCAGTTAAACGGTGTAAACGTAATTCTAAAATTGCGCCTACTTGTGTTGGTGACAGACGATAAATTGAATCACTTAAACCAAATGGACGATTTGGATCTTCACCTTCAATTTCATCTGGGCGAACAGAAATTGCACCAGCTTTTTCAAGTAGTGCAACAACGCCACCACCTGCCCACTCACCCGCAAGTAAACGCTCACGCGCTTCAGCAGGGTTTGCAGAAGTTTTGATGGTTTCAATAATTTCATCAATATTGGCTAAGGCAACTGTCAAGCCTTCCAAGATATGACCACGTTCACGTGCTTTACGTAATTCGAACATGGTACGGCGTGTCACAACTTCTTGGCGGTGACGAATAAATGCCGCAATAATATCTTTTAGATTCATCAATTTTGGTTGTCCATTGTCTAGACAAACCATGTTGATGCTGAATGAGTTTTCAAGCTGGGTATTTAAGAATAAGTTATTTACAACGACTTCTGCGTTTTCACCGCGTTTCAAGTCAATTGCAATACGCATACCTTCTTTATCAGACTCATCACGAAGTTCTGAAATACCTTCAAGCTTTTTCTCTTTTACTAACTCGGCAATACGTTCAATAACTCTTGCTTTGTTTACTTGATATGGAATTTCAGTAAAGACGATGGTTGTACGACCTGTCTTTTCATCTTCTTCGAAATGGTATTTACCACGAATGTGTAAACGACCTTTACCGGTACGGTAGGCATCAACAATACCTGATTTACCGTAAATAATACCGCCTGTAGGGAAGTCAGGACCAGTAATGTATTCCATCAATCCTTCAATCGAGATATTCGGATTGTCAGCATAAGCCAAACAAGCATTCACAACTTCTGTCATGTTGTGTGGTGCCATGTTAGTTGCCATACCTACAGCAATACCAGCAGCACCGTTAATTAATAAGTTTGGAACACGTGTCGGAAGTACTTCAGGGATACGTTCCGAACCGTCGTAGTTATCTTCCCAGTCAACTGTGTCTTTTTCTAAATCTGCAAGAAGCTCATGTGCCAGCTTAGTCATACGGACTTCGGTATAACGCATTGCCGCAGCGCTATCACCATCGATCGAACCGAAGTTACCCTGACCATCAACCAATAAATAACGTAAGCTAAAGTCTTGAGCCATACGAACAATGGTTTCATAAACAGCTGAGTCACCATGCGGGTGATATTTACCGATTACGTCCCCAACGACACGAGCAGATTTCTTGTAGGCTTTGTTATAGTCATTGCCCAATTCGTGCATGGCATAAAGCACACGACGGTGAACAGGTTTAAGACCGTCTCTCACATCCGGCAATGCACGAGATACAATTACACTCATCGCGTAATCTAAATATGAATGCTTGAGTTCGTCCTCAATGGCAATCGGTCGGATTTCCGATACGCTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003817","ARO_id":"40507","ARO_name":"Acinetobacter baumannii gyrA conferring resistance to fluoroquinolones","ARO_description":"Mutations in the A subunit of DNA gyrase reduce its affinity for fluoroquinolones, thereby conferring resistance.","ARO_category":{"39876":{"category_aro_accession":"3003292","category_aro_cvterm_id":"39876","category_aro_name":"fluoroquinolone resistant gyrA","category_aro_description":"DNA gyrase is responsible for DNA supercoiling and consists of two alpha and two beta subunits. GyrA point mutations confer resistance by preventing fluoroquinolone antibiotics from binding the alpha-subunit.","category_aro_class_name":"AMR Gene Family"},"35942":{"category_aro_accession":"0000023","category_aro_cvterm_id":"35942","category_aro_name":"enoxacin","category_aro_description":"Enoxacin belongs to a group called fluoroquinolones. Its mode of action depends upon blocking bacterial DNA replication by binding itself to DNA gyrase and causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37004":{"category_aro_accession":"3000660","category_aro_cvterm_id":"37004","category_aro_name":"lomefloxacin","category_aro_description":"Lomefloxacin is a difluoropiperazinyl quinolone, sharing similar activities with other fluoroquinolones. It is used to treat urinary tract infections. Relative to other fluoroquinolones, it has a longer half life and has higher serum concentrations.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"37008":{"category_aro_accession":"3000664","category_aro_cvterm_id":"37008","category_aro_name":"trovafloxacin","category_aro_description":"Trovafloxacin is a trifluoroquinalone with a broad spectrum of activity that acts by inhibiting the uncoiling of supercoiled DNA. While potent against many Gram-positive and Gram-negative bacteria, it is less active against pseudomonads and Cl. difficile. It is usually taken as the prodrug trovafloxacin mesylate or alatrofloxacin mesylate for oral or intravenous administration, respectively.","category_aro_class_name":"Antibiotic"},"37009":{"category_aro_accession":"3000665","category_aro_cvterm_id":"37009","category_aro_name":"grepafloxacin","category_aro_description":"Grepafloxacin is a broad-spectrum antibacterial quinoline. It is no longer taken due to its high toxicity.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"37142":{"category_aro_accession":"3000762","category_aro_cvterm_id":"37142","category_aro_name":"pefloxacin","category_aro_description":"Pefloxacin is structurally and functionally similar to norfloxacin. It is poorly active against mycobacteria, while anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"40463":{"category_aro_accession":"3003780","category_aro_cvterm_id":"40463","category_aro_name":"nybomycin","category_aro_description":"A  heterocyclic antibiotic that targets mutant gyrA (type II topoisomerase) containing an S84L substitution, counteracting acquired quinolone resistance. It is effective against quinolone-resistant Gram-positive bacteria including S. aureus and E. faecalis. Due to its ability to counteract quinolone resistance by targeting the mutant form of the gyrA protein, it is classified as a reverse antibiotic (RA).","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2305":{"model_id":"2305","model_name":"Enterococcus faecalis gshF with mutation conferring daptomycin resistance","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3891":"E554K"},"experimental":{"3891":"E554K"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1500"}},"model_sequences":{"sequence":{"3572":{"protein_sequence":{"accession":"WP_002389492","sequence":"MNYRELMQKKNVRPYVLMARFGLEKENQRSTREGLLATTDHPTVFGNRSYHPYIQTDFSETQLELITPVANSGTEMLRFLDAIHDVARRSIPEDEMLWPLSMPPQLPTKDEEIKIAKLDQYDAVLYRRYLAKEYGKRKQMVSGIHFNFEYDQALIQQLYDEQSEVTDCKQFKTKVYMKVARNFLRYRWLITYLFGASPVSEDGYFRVYDDQPQEPIRSIRNSTYGYRNHDNVKVSYASLERYLEDIHRMVENGLLSEEKEFYAPVRLRGGKQMSDLPKTGIRYIELRNLDLNPFSRLGIVEDTVDFLHYFMLYLLWTDEKEEADEWVKTGDILNEQVALGHPHETIKLIAEGDRIFSEMIDMLDALGIRKGKEVVGKYYQQLRNPQDTVSGKMWTIIQENSNSELGNIFGNQYQSMAFERPYQLAGFREMELSTQIFLFDAIQKGLEIEILDEQEQFLKLQHGEHIEYVKNANMTSKDNYVVPLIMENKTVTKKILSAAGFHVPGGEEFSSFIEAQEAHLRYANKAFVVKPKSTNYGLGITIFKEGASLEDFTEALRIAFKEDTAVLIEEFLPGTEYRFFVLDNDVKAIMLRVPANVTGDGKHTVEELVAAKNSDPLRGTNHRAPLELIQLNDLEKLMLKEQGLTIYSVPEKEQIVYLRENSNVSTGGDSIDMTDVIDDSYKQIAIEAVAALGAKICGIDLIIPDKDVKGTRDSLTYGIIEANFNPAMHMHVYPYAGQGRRLTMDVLKLLYPEVVQ"},"dna_sequence":{"accession":"NZ_CP014949","fmin":"1661364","fmax":"1663635","strand":"-","sequence":"TTATTGAACCACTTCTGGGTATAAAAGTTTTAAAACGTCCATTGTCAAGCGTCTACCCTGTCCAGCGTATGGATACACATGCATGTGCATGGCTGGATTAAAGTTTGCTTCGATAATCCCGTACGTTAAGCTATCACGTGTGCCTTTTACGTCTTTGTCAGGAATGATTAAATCAATGCCACAAATTTTGGCTCCTAAAGCAGCTACGGCCTCAATGGCGATTTGTTTATAACTATCATCAATGACATCGGTCATATCAATCGAATCCCCGCCCGTGCTAACATTAGAATTTTCTCGCAAGTACACGATTTGCTCTTTTTCTGGCACAGAATAGATAGTTAAACCTTGTTCTTTCAACATTAGTTTTTCTAAATCATTTAACTGGATTAATTCTAGTGGTGCACGGTGATTGGTCCCCCGCAATGGATCACTATTTTTAGCGGCCACCAATTCTTCTACAGTGTGTTTGCCATCTCCGGTAACATTGGCTGGCACGCGCAACATGATGGCTTTTACATCATTATCTAACACAAAGAACCGATATTCTGTTCCAGGTAAAAACTCTTCAATTAAAACCGCTGTGTCCTCTTTAAAAGCAATCCGTAACGCTTCCGTAAAGTCTTCCAACGAAGCGCCTTCTTTAAAAATGGTAATTCCTAAACCGTAATTCGTTGATTTTGGTTTCACGACAAACGCTTTATTGGCGTAGCGTAAATGTGCTTCTTGTGCCTCAATAAAAGATGAAAATTCTTCACCGCCAGGCACATGGAACCCTGCTGCAGACAAAATTTTCTTTGTCACGGTTTTGTTTTCCATAATCAATGGTACCACGTAGTTATCTTTGCTAGTCATGTTGGCATTTTTGACGTATTCAATGTGCTCGCCATGTTGCAGTTTCAAAAATTGCTCTTGTTCATCTAAAATTTCGATTTCCAAACCTTTTTGAATCGCATCAAACAAGAAAATTTGTGTGGATAATTCCATCTCACGGAAACCAGCTAATTGATAAGGGCGTTCAAAGGCCATACTTTGATATTGGTTTCCAAAAATATTTCCCAGTTCACTGTTGGAGTTTTCTTGAATAATCGTCCACATTTTGCCAGAAACGGTGTCTTGTGGATTCCGCAGTTGTTGATAATACTTACCGACAACTTCTTTGCCTTTACGAATGCCTAGAGCATCTAACATATCAATCATTTCTGAAAAAATCCGATCGCCTTCTGCAATTAACTTAATCGTTTCATGAGGATGACCAAGAGCCACTTGTTCATTTAAAATATCGCCAGTTTTTACCCATTCATCCGCTTCTTCTTTTTCATCTGTCCACAATAAATACAACATGAAATAATGTAAGAAATCCACAGTATCTTCCACAATGCCTAAACGTGAAAAAGGATTTAAGTCTAAATTACGCAACTCGATATAGCGAATACCTGTTTTAGGCAGATCAGACATTTGTTTCCCACCACGTAAGCGCACAGGCGCATAAAATTCTTTTTCTTCAGAAAGTAAACCATTTTCCACCATGCGATGAATATCTTCTAAATAGCGTTCCAATGAGGCATACGATACTTTCACATTGTCATGATTTCTGTAGCCATACGTACTATTCCGAATACTGCGAATGGGTTCTTGCGGTTGGTCGTCATAGACTCTAAAGTAGCCGTCTTCACTAACTGGCGAAGCCCCAAAAAGATACGTAATTAACCAACGATAACGTAAAAAGTTACGGGCAACTTTCATGTACACTTTCGTTTTAAATTGTTTGCAATCTGTCACTTCGGATTGTTCATCATATAATTGCTGAATCAGGGCTTGGTCATATTCAAAATTAAAATGAATTCCGCTGACCATTTGTTTTCGTTTGCCATACTCTTTTGCCAAATAACGACGATATAACACTGCATCATATTGATCTAATTTAGCAATTTTAATCTCTTCATCTTTTGTTGGTAATTGTGGCGGCATACTTAATGGCCACAGCATTTCATCTTCTGGAATCGAACGACGAGCCACATCGTGAATGGCATCTAAAAAACGAAGCATTTCTGTGCCGCTATTTGCTACAGGCGTGATTAGTTCTAATTGTGTTTCACTAAAATCTGTTTGAATATATGGATGATAAGAACGGTTACCAAAAACCGTGGGATGATCAGTTGTCGCTAAAAGCCCTTCTCGTGTACTACGTTGGTTTTCTTTTTCTAAACCAAAACGAGCCATCAATACGTAAGGACGAACATTTTTCTTTTGCATTAATTCTCTATAATTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3003805","ARO_id":"40490","ARO_name":"Enterococcus faecalis gshF with mutation conferring daptomycin resistance","ARO_description":"gshF is a bifunctional glutamate-cysteine ligase\/ glutathione synthetase that when mutated, confers daptomycin resistance.","ARO_category":{"40491":{"category_aro_accession":"3003806","category_aro_cvterm_id":"40491","category_aro_name":"daptomycin resistant gshF","category_aro_description":"Mutations to the glutathione synthetase gshF confers daptomycin resistance.","category_aro_class_name":"AMR Gene Family"},"35985":{"category_aro_accession":"0000068","category_aro_cvterm_id":"35985","category_aro_name":"daptomycin","category_aro_description":"Daptomycin is a novel lipopeptide antibiotic used in the treatment of certain infections caused by Gram-positive organisms. Daptomycin interferes with the bacterial cell membrane, reducing membrane potential and inhibiting cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2301":{"model_id":"2301","model_name":"Enterococcus faecalis YybT with mutation conferring daptomycin resistance","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3878":"I440S"},"experimental":{"3878":"I440S"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1250"}},"model_sequences":{"sequence":{"3568":{"protein_sequence":{"accession":"WP_002356022","sequence":"MQKKRIQKNGFLIVVGLLLVEFLLYFLLTNKWLLLAVIIALDIFLLVVIRLLIRDVEITNVEKIQEASSIAEQSLDYVVNEVPVGIITYNGETRAVEWLNPYAASIFNKDNQLTLTASQVTSYLELAERNQDIFTIDENTYRFSVNKEQHTITFEDITKESNLYQEKVEMQTAIGIVSVDNYDDVTDTMDEKEISYLNSFITTMVSDWMDQYKVFYKRINAERYFFIAQWEDIQKMMDEKFSILDTIRKESANHEVAITLSMGIAYGGPTLDQTGTTAQTNLDTALVRGGDQVVVKEAKDEAKPLFFGGKTAVTTKRSQVRSRAMSMAIKGIIAESADIYIMGHRYPDMDALGSAFGVARLASFNNRKAWIVLDENEIIPDVKRVLEAIKEYPELEERIISPKEAMKRKKESSLLVMVDYHKPSLSISQELYERFDKVVIIDHHRRGDEFPAKPLLSYIESSASSASELVTELIEYQSNSANKLQAFEATMMLAGIVVDTKSFNTRTTARTFDVASYLRTCGADSSLVQYLLSSDLTSYLEMNNLISKSEYVTKDTVVVAGSEDKEYDSVTAAKTADTLLSMAGINAAFVITKRTDQQIGISARSNGSINVQIIMENLGGGGHFTNAAVQLSNVTVAEVKEQLLDVIRQNINEMYEQE"},"dna_sequence":{"accession":"NZ_CP014949","fmin":"1905748","fmax":"1907725","strand":"+","sequence":"ATGCAAAAGAAGAGAATTCAAAAAAACGGTTTCTTAATTGTTGTGGGTCTTCTCTTAGTAGAATTTCTCCTCTATTTCTTACTAACAAATAAATGGCTGCTATTGGCGGTAATTATCGCATTAGATATCTTTCTCTTAGTGGTTATTCGGCTGTTGATTAGAGATGTAGAAATTACGAACGTAGAAAAGATTCAAGAAGCAAGTTCCATTGCTGAACAATCGTTGGATTATGTTGTAAATGAAGTACCTGTGGGAATTATTACGTATAACGGGGAAACACGCGCGGTAGAATGGCTTAATCCTTATGCTGCTTCTATTTTTAATAAAGACAATCAGCTAACGTTAACCGCTAGCCAAGTGACGTCTTATTTAGAATTAGCAGAACGAAACCAAGATATTTTTACGATTGACGAAAATACCTATCGCTTTAGCGTCAATAAAGAACAACATACAATTACTTTTGAAGATATCACTAAAGAAAGTAATTTGTATCAAGAAAAAGTCGAAATGCAAACGGCTATTGGCATTGTGTCTGTCGATAATTATGATGATGTCACCGATACAATGGACGAGAAAGAAATTTCTTATTTGAATAGTTTCATTACGACGATGGTTTCTGATTGGATGGACCAATACAAAGTTTTTTATAAGCGAATCAACGCAGAACGTTATTTTTTCATTGCCCAATGGGAAGATATTCAAAAAATGATGGACGAAAAATTTTCTATTTTGGATACGATCCGTAAGGAATCAGCTAACCATGAAGTAGCCATTACGTTAAGTATGGGGATTGCTTATGGGGGGCCAACCTTAGATCAAACCGGGACCACGGCTCAAACAAACCTAGATACAGCTTTAGTACGTGGCGGCGATCAAGTGGTTGTAAAAGAAGCCAAAGATGAAGCGAAGCCGTTATTTTTTGGTGGAAAAACGGCAGTAACGACGAAACGTTCCCAAGTACGTTCTCGCGCAATGAGCATGGCAATTAAGGGAATTATTGCGGAATCAGCTGACATCTATATTATGGGCCATCGTTATCCAGATATGGATGCGTTAGGTTCAGCATTTGGTGTTGCTCGTTTAGCCTCGTTTAATAATCGAAAAGCGTGGATTGTTTTAGATGAAAATGAAATCATTCCCGATGTCAAAAGAGTGTTAGAGGCGATTAAAGAGTACCCAGAATTAGAAGAGCGCATTATTAGTCCTAAAGAGGCCATGAAGCGCAAGAAAGAAAGTAGCTTATTAGTTATGGTAGATTACCATAAACCGTCTCTATCGATCTCACAAGAGCTCTATGAGCGTTTTGATAAAGTGGTAATCATTGATCACCATCGACGAGGAGACGAATTTCCAGCAAAACCCTTGCTTTCTTATATTGAATCTTCTGCCTCTTCTGCTTCAGAATTAGTCACAGAATTGATCGAATACCAAAGTAATAGCGCAAATAAACTGCAGGCCTTTGAAGCAACCATGATGTTGGCGGGAATTGTGGTTGATACGAAAAGTTTCAATACACGAACGACGGCGCGAACATTTGATGTGGCTAGTTATTTACGAACTTGTGGAGCAGACTCATCTTTAGTACAATATCTATTAAGTTCTGATCTTACAAGCTATCTGGAAATGAACAACTTAATCTCTAAAAGCGAATATGTCACAAAAGATACCGTCGTTGTTGCAGGGAGTGAAGACAAAGAATATGATAGTGTCACAGCTGCCAAAACAGCGGACACATTACTTTCTATGGCAGGGATTAATGCAGCATTTGTCATTACCAAGCGGACGGATCAACAGATTGGCATTAGTGCTCGGAGTAATGGTTCAATTAATGTCCAAATTATTATGGAAAATTTAGGTGGTGGCGGTCACTTTACTAATGCGGCAGTACAATTATCAAACGTAACAGTAGCAGAAGTAAAAGAGCAACTACTTGATGTAATTCGTCAAAATATTAATGAAATGTATGAACAGGAGTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37056","NCBI_taxonomy_name":"Enterococcus","NCBI_taxonomy_id":"1350"}}}},"ARO_accession":"3003797","ARO_id":"40482","ARO_name":"Enterococcus faecalis YybT with mutation conferring daptomycin resistance","ARO_description":"YybT has phosphodiesterase activity towards cyclic dinucleotides using a c-di-GMP hydrolyzing phosphodiesterase domain. Mutations to the gene confer resistance to daptomycin.","ARO_category":{"40483":{"category_aro_accession":"3003798","category_aro_cvterm_id":"40483","category_aro_name":"daptomycin resistant YybT","category_aro_description":"Mutations to the YybT gene confers daptomycin resistance","category_aro_class_name":"AMR Gene Family"},"35985":{"category_aro_accession":"0000068","category_aro_cvterm_id":"35985","category_aro_name":"daptomycin","category_aro_description":"Daptomycin is a novel lipopeptide antibiotic used in the treatment of certain infections caused by Gram-positive organisms. Daptomycin interferes with the bacterial cell membrane, reducing membrane potential and inhibiting cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2306":{"model_id":"2306","model_name":"Escherichia coli acrR with mutation conferring multidrug antibiotic resistance","model_type":"protein overexpression model","model_type_id":"41091","model_description":"This model detects protein overexpression based on the presence of mutations.The detection of the protein without an associated mutation indicates that the protein is likely to be expressed at low or basal levels. The detection of the protein with the mutation indicates that the protein is likely overexpressed. This model reflects how certain proteins are functional with and without mutations. For example, efflux pump subunits and regulators are functional with mutations and without mutations. Without mutations, efflux pump subunits and regulators are usually expressed at a low level. When an efflux pump regulator has a mutation, it can cause the overexpression of the efflux pump it is responsible for regulating, leading to resistance to specific drugs. Protein overexpression models have two parameters: a curated BLASTP cutoff, and a curated set of mutations (single resistance variants, frameshift mutations, indels, etc.) shown clinically to confer resistance. This model type is a combination of the protein homolog and protein variant model. A detected hit can be categorized as Perfect, Strict, or Loose with no mutation(s) or as Strict or Loose with mutation(s).","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3903":"R45C"},"clinical":{"3903":"R45C"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"375"}},"model_sequences":{"sequence":{"3575":{"protein_sequence":{"accession":"NP_414997.1","sequence":"MARKTKQEAQETRQHILDVALRLFSQQGVSSTSLGEIAKAAGVTRGAIYWHFKDKSDLFSEIWELSESNIGELELEYQAKFPGDPLSVLREILIHVLESTVTEERRRLLMEIIFHKCEFVGEMAVVQQAQRNLCLESYDRIEQTLKHCIEAKMLPADLMTRRAAIIMRGYISGLMENWLFAPQSFDLKKEARDYVAILLEMYLLCPTLRNPATNE"},"dna_sequence":{"accession":"NC_000913.3","fmin":"485760","fmax":"486408","strand":"+","sequence":"ATGGCACGAAAAACCAAACAAGAAGCGCAAGAAACGCGCCAACACATCCTCGATGTGGCTCTACGTCTTTTCTCACAGCAGGGGGTATCATCCACCTCGCTGGGCGAGATTGCAAAAGCAGCTGGCGTTACGCGCGGTGCAATCTACTGGCATTTTAAAGACAAGTCGGATTTGTTCAGTGAGATCTGGGAACTGTCAGAATCCAATATTGGTGAACTAGAGCTTGAGTATCAGGCAAAATTCCCTGGCGATCCACTCTCAGTATTAAGAGAGATATTAATTCATGTTCTTGAATCCACGGTGACAGAAGAACGGCGTCGATTATTGATGGAGATTATATTCCACAAATGCGAATTTGTCGGAGAAATGGCTGTTGTGCAACAGGCACAACGTAATCTCTGTCTGGAAAGTTATGACCGTATAGAACAAACGTTAAAACATTGTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATATTTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCTTACTGGAGATGTATCTCCTGTGCCCCACGCTTCGTAATCCTGCCACTAACGAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3003807","ARO_id":"40492","ARO_name":"Escherichia coli acrR with mutation conferring multidrug antibiotic resistance","ARO_description":"AcrR is a repressor of the AcrAB-TolC multidrug efflux complex. AcrR mutations result in high level antibiotic resistance. The mutations associated with this model are specific to E. coli.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2307":{"model_id":"2307","model_name":"CarO","model_type":"protein knockout model","model_type_id":"40354","model_description":"An AMR detection model for instances where the absence of a protein - due to large-scale insertion elements, large deletions, or other methods of protein knockout - confers clinical resistance to a known antibiotic. These models include reference sequences. Protein knockout models are currently in development.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"425"}},"model_sequences":{"sequence":{"3576":{"protein_sequence":{"accession":"AKL79742.1","sequence":"MKVLRVLVTTTALLAAGAAMADEAVVHDSYAFDKNQLIPVGARAEVGTTGYGGALLWQANPYVGLALGYNGGDISWRDDLSINGTKYDVDMDNNNVYLNAEIRPWGASTNRWAQGLYVAAGAAYLDNDYDLTKRSQDGTIKVNGNNYNFNGSVDGKLSYKNDIAPYLGFGFAPKINKNWGVFGEVGAYYTGNPTVNLKSNGTFVNVNGADFDKDLRAEENKIRNDDKYQWLPVGKVGVNFFW"},"dna_sequence":{"accession":"KP658477.1","fmin":"0","fmax":"729","strand":"+","sequence":"ATGAAAGTATTACGTGTTTTAGTGACAACTACAGCTTTACTTGCTGCTGGTGCTGCAATGGCGGATGAAGCTGTTGTTCATGACAGCTATGCATTCGATAAAAACCAATTAATTCCAGTAGGCGCTCGTGCTGAAGTAGGTACTACAGGTTACGGTGGTGCTTTGTTATGGCAAGCAAACCCATATGTAGGTTTAGCATTGGGTTATAACGGCGGTGACATTTCTTGGCGAGATGACTTATCAATTAATGGTACTAAATATGACGTTGATATGGATAATAACAACGTATATTTAAATGCCGAAATTCGCCCATGGGGTGCAAGTACTAACCGTTGGGCTCAAGGCTTATATGTAGCTGCAGGTGCGGCGTATTTAGATAACGATTATGACCTAACTAAACGTTCACAAGATGGGACTATTAAAGTAAATGGTAATAATTATAACTTTAATGGGTCAGTGGATGGTAAATTAAGTTATAAAAATGATATCGCTCCTTATTTAGGTTTTGGTTTTGCACCTAAAATCAATAAAAACTGGGGCGTATTCGGTGAAGTAGGTGCTTACTATACTGGTAACCCAACAGTAAATCTTAAATCAAATGGTACTTTTGTTAATGTTAACGGTGCTGACTTTGATAAAGATTTACGTGCTGAAGAAAATAAAATCCGTAACGACGATAAATATCAATGGTTGCCAGTTGGTAAAGTTGGTGTGAACTTCTTCTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003808","ARO_id":"40493","ARO_name":"carO","ARO_description":"carO is a transmembrane beta-barrel involved in the influx of carbapenem antibiotics in Acinetobacter baumannii. Disruption of the carO gene by distinct insertion elements results in a loss of carO expression causing resistance to carbapenem antibiotics. Homologs of carO have been identified in genera Acinetobacter, Moraxella and Psychrobacter.","ARO_category":{"41447":{"category_aro_accession":"3004283","category_aro_cvterm_id":"41447","category_aro_name":"CarO porin","category_aro_description":"The imipenum resistance-associated CarO porin family is composed of the CarO porin originally identified in Acinetobacter baumannii. The loss of these porins is associated with imipenem and meropenem multi-drug resistance. The channels formed by CarO porins show slight cation selectivity.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36383":{"category_aro_accession":"3000244","category_aro_cvterm_id":"36383","category_aro_name":"reduced permeability to antibiotic","category_aro_description":"Reduction in permeability to antibiotic, generally through reduced production of porins, can provide resistance.","category_aro_class_name":"Resistance Mechanism"},"40429":{"category_aro_accession":"3003764","category_aro_cvterm_id":"40429","category_aro_name":"resistance by absence","category_aro_description":"Mechanism of antibiotic resistance conferred by deletion of gene (usually a porin)","category_aro_class_name":"Resistance Mechanism"}}},"2286":{"model_id":"2286","model_name":"Borrelia burgdorferi murA with mutation conferring resistance to fosfomycin","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3640":"D116C"},"experimental":{"3640":"D116C"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"4409":{"protein_sequence":{"accession":"NP_212606.2","sequence":"MHSYIVEGGYKIGGQITASGNKNAALPCILAALLTDEEVILENIPNINDVKVVLDILNDIGADIAREGNTLKIKVLNIVKTEIDSSFTDLIRASILLLGPFVSRFGKIDMALPGGDVIGKRRLDTHFYGLCKLGAKLSTKDRRIVLKANKLVGAEMFLDEASVTATENIIMAAVLAEGNTVIMNAACEPHVQDLCNMLNSMGANILGIGSNVLEIKGVKKLSGTVFRIGADFMQVGSLISLAALTGGELEIKKADPQHFRLIRHVYSRLGINFEYDRENVYVRNKQELKVKLDFGGHIPKIDDGPWPAFPTDLMSIIVVTATQVEGTVLVFEKMFESRMFFVDKLIKMGARIVLCDPHRVVVTGKSSLKGNVLSSPDVRAGMSLLIAAFVAEGRSEIQNVYQIERGYEDVVNKLINLGAKIKKVKSQ"},"dna_sequence":{"accession":"NC_001318.1","fmin":"490643","fmax":"491927","strand":"+","sequence":"ATGCATAGTTATATTGTAGAAGGCGGCTATAAGATAGGTGGTCAAATTACAGCTAGTGGGAATAAGAACGCTGCTTTACCCTGTATTTTGGCTGCTTTACTTACCGATGAAGAGGTTATTTTAGAAAATATTCCTAATATTAATGATGTAAAAGTTGTTTTAGATATTTTAAATGACATAGGAGCAGATATTGCAAGAGAGGGAAATACTTTAAAAATAAAAGTTTTAAATATTGTGAAAACAGAAATAGATTCTTCTTTTACAGATTTAATTAGGGCTTCCATACTTTTATTAGGGCCTTTTGTTTCTAGGTTTGGAAAAATAGATATGGCGCTTCCAGGAGGAGATGTGATTGGAAAGAGGAGGCTTGATACTCATTTTTACGGGCTTTGCAAGCTGGGGGCCAAGTTAAGCACAAAAGATAGAAGGATTGTTTTAAAGGCTAACAAGCTTGTTGGCGCTGAAATGTTTTTAGATGAAGCTTCTGTTACAGCCACAGAAAATATCATTATGGCTGCAGTTCTTGCTGAAGGAAATACTGTTATTATGAACGCTGCTTGTGAGCCACATGTTCAAGATTTGTGTAATATGTTAAATTCAATGGGCGCTAATATTTTAGGAATTGGTTCAAATGTTTTAGAAATAAAAGGTGTAAAAAAATTAAGTGGGACCGTATTTAGAATAGGAGCCGATTTCATGCAAGTTGGTTCTTTAATTAGCCTTGCTGCATTAACAGGGGGTGAGTTGGAAATTAAAAAAGCAGATCCCCAACATTTCAGATTAATTAGGCATGTATATTCAAGACTTGGCATTAATTTTGAATATGACAGGGAAAATGTATATGTAAGAAATAAACAAGAATTAAAAGTTAAGTTAGATTTTGGTGGGCACATTCCAAAAATTGATGATGGCCCATGGCCAGCCTTTCCAACAGACCTTATGAGTATTATTGTAGTTACTGCAACGCAAGTAGAAGGCACAGTTTTAGTTTTTGAGAAGATGTTTGAATCTAGGATGTTTTTTGTAGATAAATTAATAAAAATGGGTGCTCGAATTGTGCTTTGTGATCCACACCGCGTAGTAGTTACGGGCAAATCTTCTCTTAAAGGCAATGTTTTGTCTTCTCCGGATGTACGAGCGGGAATGTCTCTTCTTATTGCTGCTTTTGTTGCTGAAGGTCGCAGCGAGATTCAAAATGTTTATCAAATTGAAAGAGGATACGAAGATGTAGTTAACAAATTGATTAATTTGGGTGCAAAAATCAAGAAAGTTAAAAGTCAATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40455","NCBI_taxonomy_name":"Borrelia burgdorferi B31","NCBI_taxonomy_id":"224326"}}}},"ARO_accession":"3003777","ARO_id":"40454","ARO_name":"Borrelia burgdorferi murA with mutation conferring resistance to fosfomycin","ARO_description":"murA or UDP-N-acetylglucosamine enolpyruvyl transferase catalyses the initial step in peptidoglycan biosynthesis and is inhibited by fosfomycin. Mutations to the murA enzyme confers resistance to the antibiotic.","ARO_category":{"39245":{"category_aro_accession":"3002811","category_aro_cvterm_id":"39245","category_aro_name":"murA transferase","category_aro_description":"murA or UDP-N-acetylglucosamine enolpyruvyl transferase catalyses the initial step in peptidoglycan biosynthesis and is inhibited by fosfomycin. Overexpression of murA through mutations confers fosfomycin resistance.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2293":{"model_id":"2293","model_name":"Bacillus subtilis pgsA mutations conferring resistance to daptomycin","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3815":"A64V"},"experimental":{"3815":"A64V"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3558":{"protein_sequence":{"accession":"BAA85265","sequence":"MKKELSFHEKLLKLTKQQKKKTNKHVFIAIPIVFVLMFAFMWAGKAETPKVKTYSDDVLSASFVGDIMMGRYVEKVTEQKGADSIFQYVEPIFRASDYVAGNFENPVTYQKNYKQADKEIHLQTNKESVKVLKDMNFTVLNSANNHAMDYGVQGMKDTLGEFAKQNLDIVGAGYSLSDAKKKISYQKVNGVTIATLGFTDVSGKGFAAKKNTPGVLPADPEIFIPMISEAKKHADIVVVQSHWGQEYDNDPNDRQRQLARAMSDAGADIIVGHHPHVLEPIEVYNGTVIFYSLGNFVFDQGWTRTRDSALVQYHLKKNGTGRFEVTPIDIHEATPAPVKKDSLKQKTIIRELTKDSNFAWKVEDGKLTFDIDHSDKLKSK"},"dna_sequence":{"accession":"AB016245","fmin":"1664","fmax":"2807","strand":"+","sequence":"ATGAAAAAAGAACTGAGCTTTCATGAAAAGCTGCTAAAGCTGACAAAACAGCAAAAAAAGAAAACCAATAAGCACGTATTTATTGCCATTCCGATCGTTTTTGTCCTTATGTTCGCTTTCATGTGGGCGGGAAAAGCGGAAACGCCGAAGGTCAAAACGTATTCTGACGACGTACTCTCAGCCTCATTTGTAGGCGATATTATGATGGGACGCTATGTTGAAAAAGTAACGGAGCAAAAAGGGGCAGACAGTATTTTTCAATATGTTGAACCGATCTTTAGAGCCTCGGATTATGTAGCAGGAAACTTTGAAAACCCGGTAACCTATCAAAAGAATTATAAACAAGCAGATAAAGAGATTCATCTGCAGACGAATAAGGAATCAGTGAAAGTCTTGAAGGATATGAATTTCACGGTTCTCAACAGCGCCAACAACCACGCAATGGATTACGGCGTTCAGGGCATGAAAGATACGCTTGGAGAATTTGCGAAGCAAAATCTTGATATCGTTGGAGCGGGATACAGCTTAAGTGATGCGAAAAAGAAAATTTCGTACCAGAAAGTCAACGGGGTAACGATTGCGACGCTTGGCTTTACCGATGTGTCCGGGAAAGGTTTCGCGGCTAAAAAGAATACGCCGGGCGTGCTGCCCGCAGATCCTGAAATCTTCATCCCTATGATTTCAGAAGCGAAAAAACATGCTGACATTGTTGTTGTGCAGTCACACTGGGGCCAAGAGTATGACAATGATCCAAACGACCGCCAGCGCCAGCTTGCAAGAGCCATGTCTGATGCGGGAGCTGACATCATCGTCGGCCATCATCCGCACGTCTTAGAACCGATTGAAGTATATAACGGAACCGTCATTTTCTACAGCCTCGGCAACTTTGTCTTTGACCAAGGCTGGACGAGAACAAGAGACAGTGCACTGGTTCAGTATCACCTGAAGAAAAATGGAACAGGCCGCTTTGAAGTGACACCGATCGATATCCATGAAGCGACACCTGCACCTGTGAAAAAAGACAGCCTTAAACAGAAAACCATTATTCGCGAACTGACGAAAGACTCTAATTTCGCTTGGAAAGTAGAAGACGGAAAACTGACGTTTGATATTGATCATAGTGACAAACTAAAATCTAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36833","NCBI_taxonomy_name":"Bacillus subtilis","NCBI_taxonomy_id":"1423"}}}},"ARO_accession":"3003788","ARO_id":"40473","ARO_name":"Bacillus subtilis pgsA with mutation conferring resistance to daptomycin","ARO_description":"Point mutations that occur within the Bacillus subtilis pgsA gene resulting in resistance to daptomycin.","ARO_category":{"39627":{"category_aro_accession":"3003080","category_aro_cvterm_id":"39627","category_aro_name":"daptomycin resistant pgsA","category_aro_description":"pgsA or phosphatidylglycerophosphate synthetase is an integral membrane protein involved in phospholipid biosynthesis. It is a CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase. Laboratory experiments have detected mutations conferring daptomycin resistance in Entercoccus.","category_aro_class_name":"AMR Gene Family"},"35985":{"category_aro_accession":"0000068","category_aro_cvterm_id":"35985","category_aro_name":"daptomycin","category_aro_description":"Daptomycin is a novel lipopeptide antibiotic used in the treatment of certain infections caused by Gram-positive organisms. Daptomycin interferes with the bacterial cell membrane, reducing membrane potential and inhibiting cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2299":{"model_id":"2299","model_name":"Staphylococcus aureus walK with mutation conferring daptomycin resistance","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3875":"L10F","3887":"S221P","3888":"R263C"},"experimental":{"3875":"L10F","3887":"S221P","3888":"R263C"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1150"}},"model_sequences":{"sequence":{"3565":{"protein_sequence":{"accession":"CAG39047","sequence":"MKWLKQLQSLHTKLVIVYVLLIIIGMQIIGLYFTNNLEKELLDNFKKNITQYAKQLEISIEKVYDEKGSVNAQKDIQNLLSEYANRQEIGEIRFIDKDQIIIATTKQSNRSLINQKANDSSVQKALSLGQSNDHLILKDYGGGKDRVWVYNIPVKVDKKVIGNIYIESKINDVYNQLNNINQIFIVGTAISLLITVILGFFIARTITKPITDMRNQTVEMSRGNYTQRVKIYGNDEIGELALAFNNLSKRVQEAQANTESEKRRLDSVITHMSDGIIATDRRGRIRIVNDMALKMLGMAKEDIIGYYMLSVLSLEDEFKLEEIQENNDSFLLDLNEEEGLIARVNFSTIVQETGFVTGYIAVLHDVTEQQQVERERREFVANVSHELRTPLTSMNSYIEALEEGAWKDEELAPQFLSVTREETERMIRLVNDLLQLSKMDNESDQINKEIIDFNMFINKIINRHEMSTKDTTFIRDIPKKTIFTEFDPDKMTQVFDNVITNAMKYSRGDKRVEFHVKQNPLYNRMTIRIKDNGIGIPINKVDKIFDRFYRVDKARTRKMGGTGLGLAISKEIVEAHNGRIWANSVEGQGTSIFITLPCEVIEDGDWDE"},"dna_sequence":{"accession":"BX571856","fmin":"25616","fmax":"27443","strand":"+","sequence":"ATGAAGTGGCTAAAACAACTACAATCCCTTCATACTAAACTTGTAATTGTTTATGTATTACTGATTATCATTGGTATGCAAATTATCGGGCTGTATTTTACAAATAACCTTGAAAAAGAGCTGCTTGATAATTTTAAGAAGAATATTACGCAGTACGCTAAGCAATTAGAAATTAGTATTGAAAAAGTATATGACGAAAAGGGCTCCGTAAATGCACAAAAAGATATTCAAAATTTATTAAGTGAGTATGCCAACCGTCAAGAAATTGGAGAAATTCGTTTTATAGATAAAGACCAAATTATTATTGCGACGACGAAGCAGTCTAACCGTAGTCTAATCAATCAAAAAGCGAATGATAGTTCTGTCCAAAAAGCACTATCACTAGGACAATCAAACGATCATTTAATTTTAAAAGATTATGGCGGTGGTAAGGACCGTGTCTGGGTATATAATATCCCCGTTAAAGTCGATAAAAAGGTAATTGGTAATATTTATATCGAATCAAAAATTAATGACGTTTATAACCAATTAAATAATATAAATCAAATATTCATTGTTGGTACAGCTATTTCATTATTAATCACAGTCATCCTAGGATTCTTTATAGCGCGAACGATTACCAAACCAATCACCGATATGCGTAACCAGACGGTTGAAATGTCCAGAGGTAACTATACGCAACGTGTGAAGATTTATGGTAATGATGAAATTGGCGAATTAGCTTTAGCATTTAATAACTTGTCTAAACGTGTACAAGAAGCGCAGGCTAATACTGAAAGTGAGAAACGTAGACTGGACTCAGTTATCACCCATATGAGTGATGGTATTATTGCAACAGACCGTCGTGGACGTATTCGTATTGTCAATGATATGGCACTTAAGATGCTTGGTATGGCGAAAGAAGACATCATCGGATATTACATGTTAAGTGTATTAAGTCTTGAAGATGAATTTAAACTTGAAGAAATTCAAGAGAATAATGATAGTTTCTTATTAGATTTAAATGAAGAAGAAGGTCTAATCGCACGTGTTAACTTTAGTACGATTGTGCAGGAAACAGGATTTGTAACGGGTTATATCGCTGTGTTACATGACGTGACTGAACAACAACAAGTTGAACGTGAGCGTCGTGAATTTGTTGCCAATGTATCACATGAGTTACGTACACCTTTAACTTCTATGAATAGTTACATTGAAGCACTTGAAGAAGGTGCATGGAAAGATGAGGAACTTGCGCCACAATTTTTATCTGTTACCCGTGAAGAAACAGAACGAATGATTCGACTGGTCAATGACTTGCTACAGTTATCTAAAATGGATAATGAGTCTGATCAAATCAATAAAGAAATTATCGACTTTAACATGTTCATTAATAAAATTATTAATCGACATGAAATGTCTACGAAAGATACAACATTTATTCGAGATATTCCGAAAAAGACGATTTTCACAGAATTTGATCCTGATAAAATGACGCAAGTATTTGATAATGTCATTACAAATGCGATGAAATATTCTAGAGGCGATAAACGTGTCGAGTTCCACGTGAAACAAAATCCACTTTATAATCGAATGACGATTCGTATTAAAGATAATGGCATCGGTATTCCTATCAATAAAGTCGATAAGATATTCGACCGATTCTATCGTGTAGATAAGGCACGTACGCGTAAAATGGGTGGTACTGGATTAGGACTAGCCATTTCGAAAGAGATCGTGGAAGCTCACAATGGTCGTATTTGGGCAAACAGTGTAGAAGGTCAAGGCACATCTATCTTTATCACACTTCCATGTGAAGTCATTGAAGACGGTGATTGGGATGAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35517","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus MRSA252","NCBI_taxonomy_id":"282458"}}}},"ARO_accession":"3003794","ARO_id":"40479","ARO_name":"Staphylococcus aureus walK with mutation conferring resistance to daptomycin","ARO_description":"walK is the histidine kinase sensor of a two-component regulatory system controlling peptidoglycan metabolism through regulation of the expression of most of the peptidoglycan hydrolase genes. Mutations in the gene have been found that confer daptomycin resistance.","ARO_category":{"40480":{"category_aro_accession":"3003795","category_aro_cvterm_id":"40480","category_aro_name":"daptomycin resistant walK","category_aro_description":"Mutations to the walK gene, part of a cell wall metabolism 2-component regulatory system, confers resistance to antibiotics, specifically daptomycin.","category_aro_class_name":"AMR Gene Family"},"35985":{"category_aro_accession":"0000068","category_aro_cvterm_id":"35985","category_aro_name":"daptomycin","category_aro_description":"Daptomycin is a novel lipopeptide antibiotic used in the treatment of certain infections caused by Gram-positive organisms. Daptomycin interferes with the bacterial cell membrane, reducing membrane potential and inhibiting cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2315":{"model_id":"2315","model_name":"Acinetobacter baumannii parC conferring resistance to fluoroquinolone","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3988":"S80L","3989":"S83L","3990":"D87E"},"clinical":{"3988":"S80L","3989":"S83L","3990":"D87E"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1400"}},"model_sequences":{"sequence":{"3584":{"protein_sequence":{"accession":"ALJ89624.1","sequence":"MTSLAHHATENRSVAEFTEQAYLNYAMYVIMDRALPHISDGLKPVQRRIVYAMSELGLKSSGKPKKSARTVGDVLGKYHPHGDLACYEAMVLMAQPFSYRYPLIEGQGNWGSPDDPKSFAAMRYTEAKLSAYSELLLSELGQGTSEWQDNFDGSLKEPITLPARVPNILLNGTTGIAVGMATDIPPHNLREVVKGTIALIRNPQTSDEKLAEYIPAPDLPTKAEIITPPEELLKIQTTGRGSYRMRAVYTIEKNEIVITELPYQVSGSKVITQIADQMQAKKLPLVVDVRDESDHENPTRLVIVLRSNRIDAEAVMSHLFATTDLESSYRVNLNMIGEDGRPQVKSIRRILLEWIEIRKKTVTRRLQYHLNRIEKRLHILAGLLIAYLDIDTVIRIIREEDQPKPVLMEHFNIDEIQAEAILELKLRHLAKLEEMEIRHEQDELSAKAAIIREQLENPESLKNLIISELKEDAKKFGDERRSPIVARAEAVQIKEQDLMPAETVTVVLSEAGWVRAAKGADVDAENLNYRAGDQYLSHAVGKTNQRVYFLDETGRSYALPISNLPSARGLGDPLSSKLSPASGVSFIQVYLDDDESELIAASSAGYGFKTQTKQLDTNAKAGKTFLTVPDKAKALPLISAQNMTHLAVLSSAGRLLILDLAELPNLNKGKGNKLIQLEGKEQILSMTTLNLDEIIQVVAGQQHLKLKGDDLQKYMGKRASKGQLLPRGYQKANKLLIQR"},"dna_sequence":{"accession":"CP012952.1","fmin":"3861302","fmax":"3863522","strand":"-","sequence":"TTATCTCTGAATCAACAGTTTATTTGCTTTTTGATATCCACGTGGTAAGAGCTGACCTTTCGAAGCACGTTTACCCATGTATTTTTGTAGATCATCACCTTTTAATTTGAGATGTTGTTGACCTGCAACCACCTGAATTATTTCATCTAAGTTCAGGGTTGTCATGGATAAAATTTGCTCTTTGCCTTCAAGTTGTATCAACTTATTACCTTTACCTTTATTTAAATTTGGTAGTTCTGCCAAATCTAAAATTAACAAACGCCCTGCTGAGCTCAGTACAGCCAAATGCGTCATGTTTTGGGCAGAAATGAGTGGTAAAGCCTTTGCCTTATCCGGAACCGTTAAGAATGTCTTACCGGCTTTCGCATTGGTATCTAATTGCTTGGTTTGCGTTTTAAAACCATAACCTGCCGAACTTGCAGCAATCAATTCAGACTCATCATCATCTAAATAAACCTGAATAAACGATACGCCACTTGCTGGTGATAATTTAGAACTTAATGGATCCCCCAAGCCTCTCGCTGAAGGTAAGTTACTAATTGGCAAGGCATAGCTGCGCCCTGTTTCATCAAGGAAGTAAACTCGCTGATTGGTTTTCCCGACAGCATGACTTAAATATTGGTCCCCAGCACGGTAGTTGAGATTTTCGGCATCCACATCCGCACCTTTTGCCGCACGAACCCAGCCTGCTTCAGACAAAACCACCGTTACCGTTTCAGCTGGCATTAAATCCTGTTCTTTAATTTGAACTGCTTCAGCACGTGCAACAATTGGAGAACGGCGCTCATCACCGAACTTTTTCGCATCTTCTTTTAATTCACTGATAATTAGGTTTTTTAAAGATTCAGGATTTTCGAGTTGTTCACGAATAATGGCAGCTTTCGCAGAAAGTTCATCTTGTTCATGACGGATTTCCATCTCTTCAAGCTTTGCCAAATGACGTAATTTAAGCTCTAAAATCGCCTCGGCCTGTATCTCATCAATATTAAAGTGTTCCATCAAGACTGGCTTAGGCTGGTCTTCTTCACGAATAATACGAATGACTGTATCAATATCGAGATAAGCAATTAAAAGACCTGCCAAAATATGCAGGCGCTTTTCAATACGGTTTAAATGGTACTGCAAACGACGAGTTACCGTTTTTTTACGGATCTCGATCCATTCAAGCAAAATACGACGAATTGATTTCACCTGAGGACGGCCATCTTCGCCAATCATGTTCAAATTGACACGATAGCTTGATTCTAAATCGGTGGTCGCAAATAAGTGGCTCATCACTGCTTCCGCATCAATACGGTTAGAGCGCAGTACAATCACGAGTCGTGTCGGGTTTTCATGATCCGATTCATCACGCACGTCGACAACTAATGGCAGCTTTTTAGCCTGCATCTGGTCAGCAATTTGAGTAATTACCTTAGAACCAGAGACTTGATATGGCAGCTCAGTAATTACAATTTCATTTTTCTCAATGGTATATACCGCTCGCATACGATAACTACCACGACCAGTGGTCTGGATTTTGAGTAATTCTTCTGGCGGGGTAATAATTTCAGCTTTGGTTGGTAAATCCGGAGCCGGAATATATTCAGCTAATTTTTCGTCCGAGGTTTGCGGATTACGGATTAAAGCAATTGTGCCTTTTACAACTTCACGCAAATTATGTGGCGGGATATCAGTTGCCATCCCAACAGCAATACCTGTCGTACCATTAAGAAGAATATTAGGTACACGCGCAGGTAAAGTGATCGGTTCTTTTAAAGAACCATCAAAGTTATCTTGCCATTCGCTAGTGCCCTGACCTAATTCGCTCAGCAATAATTCACTATAAGCCGAGAGTTTTGCTTCGGTATAACGCATCGCAGCAAAAGACTTAGGATCATCAGGTGAGCCCCAGTTCCCCTGACCTTCGATTAAAGGATAGCGGTAACTAAATGGCTGAGCCATGAGTACCATGGCTTCATAACATGCCAAGTCACCATGTGGGTGGTATTTACCAAGTACATCACCCACTGTACGCGCTGATTTTTTTGGCTTGCCACTGCTTTTTAAGCCTAGCTCGCTCATGGCATAGACAATACGGCGCTGTACGGGCTTTAAGCCATCACTGATATGCGGTAATGCACGGTCCATAATGACGTACATGGCATAATTCAAGTAAGCCTGTTCAGTAAATTCGGCTACAGAGCGGTTTTCTGTCGCATGATGCGCAAGGCTGGTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003818","ARO_id":"40508","ARO_name":"Acinetobacter baumannii parC conferring resistance to fluoroquinolone","ARO_description":"Mutations in Acinetobacter baumannii parC that result in resistance to fluoroquinolones.","ARO_category":{"36913":{"category_aro_accession":"3000619","category_aro_cvterm_id":"36913","category_aro_name":"fluoroquinolone resistant parC","category_aro_description":"ParC is a subunit of topoisomerase IV, which decatenates and relaxes DNA to allow access to genes for transcription or translation. Point mutations in ParC prevent fluoroquinolone antibiotics from inhibiting DNA synthesis, and confer low-level resistance. Higher-level resistance results from both gyrA and parC mutations.","category_aro_class_name":"AMR Gene Family"},"35942":{"category_aro_accession":"0000023","category_aro_cvterm_id":"35942","category_aro_name":"enoxacin","category_aro_description":"Enoxacin belongs to a group called fluoroquinolones. Its mode of action depends upon blocking bacterial DNA replication by binding itself to DNA gyrase and causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37004":{"category_aro_accession":"3000660","category_aro_cvterm_id":"37004","category_aro_name":"lomefloxacin","category_aro_description":"Lomefloxacin is a difluoropiperazinyl quinolone, sharing similar activities with other fluoroquinolones. It is used to treat urinary tract infections. Relative to other fluoroquinolones, it has a longer half life and has higher serum concentrations.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"37008":{"category_aro_accession":"3000664","category_aro_cvterm_id":"37008","category_aro_name":"trovafloxacin","category_aro_description":"Trovafloxacin is a trifluoroquinalone with a broad spectrum of activity that acts by inhibiting the uncoiling of supercoiled DNA. While potent against many Gram-positive and Gram-negative bacteria, it is less active against pseudomonads and Cl. difficile. It is usually taken as the prodrug trovafloxacin mesylate or alatrofloxacin mesylate for oral or intravenous administration, respectively.","category_aro_class_name":"Antibiotic"},"37009":{"category_aro_accession":"3000665","category_aro_cvterm_id":"37009","category_aro_name":"grepafloxacin","category_aro_description":"Grepafloxacin is a broad-spectrum antibacterial quinoline. It is no longer taken due to its high toxicity.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"37142":{"category_aro_accession":"3000762","category_aro_cvterm_id":"37142","category_aro_name":"pefloxacin","category_aro_description":"Pefloxacin is structurally and functionally similar to norfloxacin. It is poorly active against mycobacteria, while anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2295":{"model_id":"2295","model_name":"Enterococcus faecium liaF mutant conferring daptomycin resistance","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3859":"I144T","3860":"L39F"},"clinical":{"3859":"I144T","3860":"L39F"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"3561":{"protein_sequence":{"accession":"CUX99269.1","sequence":"MNSSWRFFVVVEALLLLFAVWQIVNNTGLLLLVIFGIFNIYLAMRKYPRTKFQNFQLILGSLVIFFSLVNSPALWMMVVLAVLFIGLKGVEISGIDLTKNAFWRKKQIMMVQTEQLKTHNNERKRQQLFGNQRIGNDVYEWDDINIAIISGDTIIDLGNTLLPKDDNIVIVRKGIGRTRILVPLGVAIRLEHATLVGNVLFEEEQFSLKNEQIKICSSDYDENPRRLKIITNTLVGDVEVIRI"},"dna_sequence":{"accession":"LN999844.1","fmin":"1854250","fmax":"1854982","strand":"-","sequence":"TCATATTCGTATCACCTCGACATCTCCAACCAAGGTATTGGTAATGATCTTCAATCTGCGAGGATTTTCATCATAATCACTGCTGCAGATTTTGATCTGTTCATTTTTTAAGGAAAACTGCTCTTCTTCAAACAAGACATTTCCTACTAATGTCGCATGCTCTAATCGAATAGCCACTCCCAGGGGTACTAAGATCCGTGTTCTGCCTATCCCTTTTCTTACAATCACAATATTATCATCTTTTGGCAAAAGTGTATTGCCCAAATCGATGATAGTATCACCAGAAATGATGGCAATGTTGATATCATCCCATTCATAGACGTCGTTTCCAATACGTTGGTTACCAAATAATTGCTGTCTTTTACGCTCATTATTATGTGTTTTTAATTGCTCTGTTTGGACCATCATGATCTGTTTTTTTCGCCAAAAAGCATTTTTTGTCAAATCTATTCCTGAAATCTCTACACCTTTCAGGCCGATAAATAAAACGGCCAATACAACCATCATCCATAAAGCAGGACTGTTGACTAAGCTAAAAAAAATGACCAAGCTCCCTAAGATCAATTGAAAATTTTGAAATTTAGTACGAGGATATTTGCGCATAGCTAGATATATATTGAAAATACCGAATATTACTAAAAGCAAAAGTCCAGTATTGTTTACGATTTGCCAAACAGCAAATAACAGCAGCAGTGCTTCGACTACCACAAAAAAACGCCAAGAACTATTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3003790","ARO_id":"40475","ARO_name":"Enterococcus faecium liaF mutant conferring daptomycin resistance","ARO_description":"liaF is an accessory protein that acts as a negative regulator of liaRS signal transduction pathway. Mutations confer daptomycin resistance.","ARO_category":{"41426":{"category_aro_accession":"3004262","category_aro_cvterm_id":"41426","category_aro_name":"daptomycin resistant liaF","category_aro_description":"Mutations to the liaF accessory protein that confer resistance to daptomycin.","category_aro_class_name":"AMR Gene Family"},"35985":{"category_aro_accession":"0000068","category_aro_cvterm_id":"35985","category_aro_name":"daptomycin","category_aro_description":"Daptomycin is a novel lipopeptide antibiotic used in the treatment of certain infections caused by Gram-positive organisms. Daptomycin interferes with the bacterial cell membrane, reducing membrane potential and inhibiting cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2296":{"model_id":"2296","model_name":"Enterococcus faecalis liaS mutant conferring daptomycin resistance","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3865":"A180T"},"clinical":{"3865":"A180T"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"650"}},"model_sequences":{"sequence":{"4418":{"protein_sequence":{"accession":"AAO82600.1","sequence":"MTDRISRRMISLYASLSTFIVILITLFSYFHSIKQNRWLLELLQRKVFYLPLIVHIVLISLLIGLLTFLLISLVQKGQYGRIEEKLRLLANGNYESPVLNKPTTSENQDHYLTEVEQDIWSIKNKLLEMSKELQLLNSRPQLMDGQTKEEILENERHRLARELHDSVSQQLFAAMMMLSALNEQAQRTETPEPYRKQLAMVAEIINASQSEMRALLLHLRPISLEGKSLRKGIEQLLKELQTKIKIELIWDVEDVHLNSSIEDHLFRIVQELLSNTLRHAKAKELEVYLHQVDKNVLLRIVDDGVGFDMKEQSNKAGSYGLNNIRERVVGMGGTVKIISFKGQGTSVEIKVPVIKEETASDQSNVSG"},"dna_sequence":{"accession":"AE016830.1","fmin":"2789720","fmax":"2790824","strand":"-","sequence":"TCATCCACTAACATTACTTTGATCACTTGCAGTTTCCTCCTTTATGACAGGAACTTTAATTTCAACGCTGGTTCCCTGCCCTTTAAAACTAATAATTTTAACTGTACCGCCCATGCCGACAACACGTTCTCGAATATTATTTAAGCCATAACTACCGGCTTTATTACTTTGTTCCTTCATATCAAAGCCGACACCATCATCAACAATACGCAATAACACGTTTTTATCGACTTGGTGTAAGTATACCTCTAATTCCTTTGCTTTGGCATGTCTTAAGGTATTTGAAAGTAACTCCTGCACAATTCGGAAAAGATGATCCTCAATGCTGCTATTTAAATGAACATCTTCAACATCCCAAATCAATTCAATTTTAATTTTTGTTTGTAGTTCTTTCAGTAATTGTTCAATACCTTTACGCAAACTTTTTCCTTCTAGACTGATAGGACGCAAGTGCAATAGTAGCGCGCGCATTTCCGATTGGGAGGCATTAATGATTTCTGCCACCATGGCTAGTTGTTTACGATATGGTTCCGGGGTTTCTGTTCGTTGTGCTTGTTCATTTAATGCAGACAACATCATCATGGCTGCAAAAAGTTGTTGACTGACTGAATCATGCAACTCCCGCGCCAAACGATGCCGCTCGTTCTCTAAAATTTCTTCTTTTGTTTGCCCATCCATTAATTGCGGTCGACTGTTTAATAATTGCAATTCTTTAGACATCTCTAATAATTTATTTTTAATCGACCAAATATCTTGTTCGACTTCGGTTAGATAATGGTCTTGATTTTCACTGGTCGTTGGTTTGTTTAAGACTGGACTTTCATAATTACCGTTGGCCAATAACCGAAGTTTTTCTTCAATCCGTCCATATTGCCCTTTTTGAACCAATGAAATCAGTAAAAAGGTCAATAAGCCTATTAGTAAGGATATGAGAACAATGTGCACAATTAGTGGTAAATAAAAGACTTTTCTCTGAAGAAGCTCTAATAACCACCGGTTTTGTTTAATCGAATGAAAATATGAAAACAATGTAATTAAGATAACAATAAAGGTGCTAAGGGACGCATATAATGAAATCATGCGTCTTGAAATCCGATCGGTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37592","NCBI_taxonomy_name":"Enterococcus faecalis V583","NCBI_taxonomy_id":"226185"}}}},"ARO_accession":"3003791","ARO_id":"40476","ARO_name":"Enterococcus faecalis liaS mutant conferring daptomycin resistance","ARO_description":"liaS is a histidine kinase found in the liaFSR signal transduction pathway. Mutations confer daptomycin resistance.","ARO_category":{"41428":{"category_aro_accession":"3004264","category_aro_cvterm_id":"41428","category_aro_name":"daptomycin resistant liaS","category_aro_description":"Mutations in the liaS histidine kinase that confer daptomycin resistance.","category_aro_class_name":"AMR Gene Family"},"35985":{"category_aro_accession":"0000068","category_aro_cvterm_id":"35985","category_aro_name":"daptomycin","category_aro_description":"Daptomycin is a novel lipopeptide antibiotic used in the treatment of certain infections caused by Gram-positive organisms. Daptomycin interferes with the bacterial cell membrane, reducing membrane potential and inhibiting cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2297":{"model_id":"2297","model_name":"Enterococcus faecalis liaR mutant conferring daptomycin resistance","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3870":"D191N"},"experimental":{"3870":"D191N"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"3563":{"protein_sequence":{"accession":"NP_816529","sequence":"MIKVMLVDDHEMVRLGVSSYLSIQEDIEVVGEAENGKIGYEKALELRPDVILMDLVMEEMDGIDSTKAILKDWPEAKIIIVTSFIDDEKVYPAIEAGAAGYLLKTSTAHEIADAIRATYRGERVLEPEVTHKMMERLTKKQEPVLHEDLTNREHEILMLIAQGKSNQEIADELFITLKTVKTHVSNILAKLDVDDRTQAAIYAFQHGLAK"},"dna_sequence":{"accession":"NC_004668","fmin":"2789113","fmax":"2789746","strand":"-","sequence":"TTATTTGGCTAAACCATGTTGAAAAGCATAAATCGCCGCTTGGGTCCGATCATCCACATCTAGTTTTGCTAAAATGTTTGAAACATGTGTTTTAACTGTTTTCAAAGTGATAAAGAGTTCATCAGCTATTTCCTGATTACTTTTACCTTGTGCAATCAACATTAAAATTTCGTGTTCCCGGTTTGTCAAATCTTCGTGCAACACCGGCTCTTGTTTTTTTGTTAACCGTTCCATCATCTTATGCGTCACTTCAGGTTCCAACACACGCTCTCCGCGATAAGTCGCCCGAATTGCATCAGCAATCTCATGTGCTGTTGATGTCTTTAATAGGTAGCCCGCTGCACCAGCTTCAATCGCCGGATACACTTTTTCATCATCAATAAAACTCGTCACAATAATAATCTTGGCTTCTGGCCAATCTTTCAAGATCGCTTTTGTTGAATCAATGCCGTCCATTTCTTCCATTACCAAATCCATCAAAATAACATCTGGACGTAGTTCCAATGCTTTTTCATAGCCAATCTTACCGTTTTCTGCTTCGCCTACGACTTCTATATCCTCTTGAATAGATAAATATGATGAAACGCCTAAACGGACCATTTCATGGTCATCCACTAACATTACTTTGATCAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37592","NCBI_taxonomy_name":"Enterococcus faecalis V583","NCBI_taxonomy_id":"226185"}}}},"ARO_accession":"3003792","ARO_id":"40477","ARO_name":"Enterococcus faecalis liaR mutant conferring daptomycin resistance","ARO_description":"liaR is a response regulator found in the liaFSR signal transduction pathway. Mutations confer daptomycin resistance.","ARO_category":{"41427":{"category_aro_accession":"3004263","category_aro_cvterm_id":"41427","category_aro_name":"daptomycin resistant liaR","category_aro_description":"Mutations to the liaR response regulator that confer resistance to daptomycin.","category_aro_class_name":"AMR Gene Family"},"35985":{"category_aro_accession":"0000068","category_aro_cvterm_id":"35985","category_aro_name":"daptomycin","category_aro_description":"Daptomycin is a novel lipopeptide antibiotic used in the treatment of certain infections caused by Gram-positive organisms. Daptomycin interferes with the bacterial cell membrane, reducing membrane potential and inhibiting cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2308":{"model_id":"2308","model_name":"Acinetobacter OprD conferring resistance to imipenem","model_type":"protein knockout model","model_type_id":"40354","model_description":"An AMR detection model for instances where the absence of a protein - due to large-scale insertion elements, large deletions, or other methods of protein knockout - confers clinical resistance to a known antibiotic. These models include reference sequences. Protein knockout models are currently in development.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"4419":{"protein_sequence":{"accession":"AHB92962.1","sequence":"MLKAQKLTLAVLISAAIISSAQASEQSEAKGFVEDANGSILFRTGYISRDKKNGVDDTSSFAQTAIVNIESGFTPGIVGFGVGVVGDGSFKIGANKNAGNNMIPRETGFNDEGVLTKGAGDSYDHWARGGGSVKARFSNTTVRYGTQVLDLPVLASNTARLVPEYFTGTLLTSHEIKDLEVIAGKFTKDQYSDQVNTDGRHLDRAIVWGAKYKFDDNLNASYYGLDSKDKLERHYLNVNYKQPLANDSSLTYDFSGYHTKFDEGASTYSQTTDDLSNRKNNIWAISTAYNTGPHNIMVAYQQNSGNVGYDYGENADGGQSIYLPNSYLSDFIGNDEKSAQIQYSLDFGKLGVLPGLNWTTAFVYGWDIKVKGLTDDAEEREFFNQVKYTVQSGFAKDASLRIRNSYYRASNAYQTNAYIGDTNEWRIFLDIPVKLF"},"dna_sequence":{"accession":"CP006768.1","fmin":"3513469","fmax":"3514780","strand":"+","sequence":"ATGCTAAAAGCACAAAAACTTACATTAGCAGTTCTCATTTCTGCGGCAATAATTTCCTCAGCTCAGGCAAGCGAGCAAAGTGAGGCAAAAGGATTTGTTGAAGATGCGAACGGTTCTATTCTCTTCCGTACAGGTTACATCAGCCGTGACAAAAAAAATGGCGTAGATGACACCAGTTCATTTGCTCAAACAGCAATCGTAAATATTGAATCTGGCTTTACTCCTGGTATTGTTGGTTTCGGTGTGGGCGTTGTTGGTGACGGTTCATTTAAAATCGGCGCAAATAAAAACGCTGGCAATAACATGATTCCACGTGAAACTGGTTTCAATGACGAAGGCGTGCTAACAAAAGGTGCTGGTGATTCTTACGATCACTGGGCTCGTGGTGGCGGTAGCGTAAAAGCACGTTTCTCAAATACAACTGTACGTTACGGTACTCAAGTACTTGACCTGCCAGTTCTTGCAAGTAATACAGCACGTTTAGTGCCTGAATACTTCACAGGTACTTTATTAACCAGCCATGAAATTAAAGATTTAGAAGTGATTGCTGGTAAATTCACTAAAGATCAATATTCTGACCAAGTGAACACCGATGGCCGTCATCTTGACCGTGCAATTGTGTGGGGTGCTAAATACAAGTTTGATGATAATTTAAATGCATCTTACTATGGTTTAGATAGTAAAGATAAACTTGAACGTCATTACCTCAATGTAAACTATAAACAACCATTGGCGAATGACAGCTCATTAACTTACGATTTCAGTGGTTATCACACTAAGTTTGATGAAGGTGCTTCTACTTATTCACAAACTACTGATGACCTATCTAACCGTAAAAACAATATTTGGGCAATTTCTACAGCCTATAATACTGGTCCACATAACATCATGGTGGCTTACCAACAAAACAGTGGTAATGTCGGTTATGACTATGGTGAAAATGCTGACGGCGGTCAAAGTATTTATCTGCCAAATTCTTATTTGTCTGATTTCATCGGTAATGATGAAAAATCAGCACAAATCCAATATAGCCTCGATTTCGGTAAGTTAGGCGTATTACCTGGCTTAAACTGGACCACTGCATTTGTATACGGTTGGGACATCAAAGTTAAAGGTTTAACTGATGATGCTGAAGAACGCGAATTCTTTAACCAAGTGAAATACACAGTTCAAAGTGGTTTCGCTAAAGATGCAAGCCTTCGTATTCGTAACTCATACTACCGTGCAAGCAATGCTTATCAAACGAATGCCTACATCGGTGATACCAATGAATGGCGTATTTTCTTAGATATTCCTGTGAAATTATTCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40496","NCBI_taxonomy_name":"Acinetobacter baumannii ZW85-1","NCBI_taxonomy_id":"1400867"}}}},"ARO_accession":"3003809","ARO_id":"40495","ARO_name":"Acinetobacter baumannii OprD conferring resistance to imipenem","ARO_description":"An outer member protein (OMP) found in Acinetobacter baumannii involved in the uptake of imipenem and basic amino acids. This porin is homologous to Pseudomonas aeruginosa OprD, which performs an identical function.","ARO_category":{"41442":{"category_aro_accession":"3004278","category_aro_cvterm_id":"41442","category_aro_name":"Outer Membrane Porin (Opr)","category_aro_description":"The Opr family consists of porins in Pseudomonas species, and other Gram-negative bacteria, that exhibit a variety of substrate selectivities.","category_aro_class_name":"AMR Gene Family"},"36309":{"category_aro_accession":"3000170","category_aro_cvterm_id":"36309","category_aro_name":"imipenem","category_aro_description":"Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36383":{"category_aro_accession":"3000244","category_aro_cvterm_id":"36383","category_aro_name":"reduced permeability to antibiotic","category_aro_description":"Reduction in permeability to antibiotic, generally through reduced production of porins, can provide resistance.","category_aro_class_name":"Resistance Mechanism"},"40429":{"category_aro_accession":"3003764","category_aro_cvterm_id":"40429","category_aro_name":"resistance by absence","category_aro_description":"Mechanism of antibiotic resistance conferred by deletion of gene (usually a porin)","category_aro_class_name":"Resistance Mechanism"}}},"2326":{"model_id":"2326","model_name":"TLA-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"3603":{"protein_sequence":{"accession":"WP_059512353.1","sequence":"MKKHLIVIAFCALFASAFAAKGTDSLKNSAKGTDSLKNSIEKYLKDKKAKVGVAVLGIEDNFKLNVNEKHHYPMQSTYKFHLALAVLDKLDKENISVDKKLFVKKSDLQPNTWSPLKDKYPNGNLELSFSEIIKSTVSHSDNNGCDILFRFVGGTNKVHNFISKLGVKNISIKATEEEMHKAWNVQYTNWTTPDATVQLLKKFYKNEILSKNSYDFLLNTMIETTTGPKRLKGLLPDGTVVAHKTGSSDTNNKGITAATNDIGIITLPNGKHFAIAVYVSDSSEKSDVNEKIIAEICKSVWDYLVKDGK"},"dna_sequence":{"accession":"NG_050312","fmin":"100","fmax":"1030","strand":"+","sequence":"ATGAAAAAACATCTTATTGTAATTGCATTTTGTGCGCTTTTTGCTTCTGCCTTTGCGGCTAAAGGTACGGATTCGCTTAAAAACAGTGCTAAAGGTACGGATTCGCTTAAAAACAGTATTGAAAAATATCTTAAAGATAAAAAAGCAAAAGTCGGTGTTGCCGTTTTGGGAATTGAAGATAATTTTAAATTGAACGTTAACGAAAAGCATCACTATCCTATGCAAAGTACTTATAAATTCCATTTAGCGTTGGCAGTGCTTGATAAACTTGATAAAGAGAATATTTCCGTTGACAAGAAGCTTTTTGTAAAGAAATCCGACCTTCAACCGAATACTTGGAGCCCGCTAAAAGATAAATATCCTAACGGAAATTTGGAATTGTCATTTAGTGAAATTATTAAGTCTACAGTTTCTCACAGCGATAACAACGGCTGCGATATTCTTTTCAGATTTGTCGGCGGAACAAATAAAGTCCACAATTTTATTAGCAAGCTTGGCGTTAAGAATATTTCTATCAAAGCTACAGAAGAAGAAATGCACAAGGCATGGAATGTACAATATACCAATTGGACAACTCCCGATGCTACCGTTCAGCTCTTAAAGAAGTTCTACAAAAATGAAATACTCTCAAAAAATAGTTACGACTTTTTGCTTAATACCATGATTGAAACTACTACCGGACCTAAACGACTCAAAGGACTTTTGCCGGATGGAACTGTTGTTGCGCATAAAACCGGAAGCTCAGATACTAACAATAAAGGAATTACTGCTGCCACAAATGATATCGGTATTATTACTTTGCCGAACGGCAAGCACTTTGCCATTGCTGTTTATGTGTCGGATTCAAGCGAAAAGAGCGATGTTAACGAAAAAATTATTGCCGAAATTTGCAAAAGCGTTTGGGATTATCTAGTTAAGGATGGGAAATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40532","NCBI_taxonomy_name":"Enterobacteriaceae","NCBI_taxonomy_id":"543"}}}},"ARO_accession":"3003204","ARO_id":"39788","ARO_name":"TLA-3","ARO_description":"TLA-3 is a beta-lactamase found in a transferable plasmid of Serratia marcescens clinical isolate. It confers resistance to ceftazidime, cefotaxime and cefepime, but not to cefmetazole and meropenem","ARO_category":{"39785":{"category_aro_accession":"3003201","category_aro_cvterm_id":"39785","category_aro_name":"TLA beta-lactamase","category_aro_description":"The TLA beta-lactamases are resistant to expanded-spectrum cephalosporins, aztreonam, ciprofloxacin, and ofloxacin but was susceptible to amikacin, cefotetan, and imipenem.","category_aro_class_name":"AMR Gene Family"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2328":{"model_id":"2328","model_name":"MUS-2 beta-lactamase","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"3605":{"protein_sequence":{"accession":"WP_063860852","sequence":"MHRILSVITMLICTTLVHAQSDKLKIKQLNDNMYIYTTYQEFQGVTYSSNSMYVLTDEGAILIDTPWDKDQYEPLLEYIRSNHNKEVKWVITTHFHEDRSGGLGYFNSIGAQTYTYALTNEILKERNEPQAQYSFNKEKQFTFGNEKLAVYFLGEGHSLDNTVVWFPKEEVLYGGCLIKSAEATTIGNIADGNVIAWPKTIEAVKQKFKNAKVIIPGHDEWDMIGHIENTERILSAYNQQHSTKND"},"dna_sequence":{"accession":"NG_049325","fmin":"0","fmax":"741","strand":"+","sequence":"ATGCACAGAATACTTAGTGTCATAACGATGTTAATCTGTACTACATTAGTACACGCTCAATCTGACAAGCTAAAAATCAAACAACTCAATGATAATATGTATATATACACTACTTATCAAGAGTTTCAAGGAGTAACATACTCTTCTAATTCGATGTACGTACTGACAGATGAAGGTGCTATTCTAATAGACACACCTTGGGATAAAGATCAGTACGAACCTCTATTAGAGTACATCAGATCGAATCATAACAAAGAGGTTAAATGGGTCATCACTACCCACTTCCACGAAGATCGTTCTGGTGGATTAGGTTACTTTAACAGTATAGGAGCACAGACGTATACCTATGCATTGACCAATGAAATATTAAAAGAACGCAATGAACCACAAGCTCAATATTCTTTTAATAAAGAAAAACAGTTTACCTTTGGCAATGAGAAGTTGGCTGTATACTTTTTAGGAGAAGGACATTCACTAGATAATACCGTAGTCTGGTTTCCAAAAGAAGAAGTACTATACGGAGGGTGCCTGATTAAGAGTGCCGAAGCTACCACTATAGGTAATATAGCCGATGGTAACGTGATAGCTTGGCCTAAGACTATCGAAGCCGTAAAACAAAAATTTAAGAATGCTAAAGTCATTATACCAGGACATGATGAATGGGATATGATAGGGCATATCGAGAATACTGAGCGTATATTATCAGCATACAATCAACAACATTCAACTAAAAACGATTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39072","NCBI_taxonomy_name":"Myroides odoratimimus","NCBI_taxonomy_id":"76832"}}}},"ARO_accession":"3003842","ARO_id":"40535","ARO_name":"MUS-2","ARO_description":"MUS-2 is a chromosome-encoded beta-lactamase from Myroides odoratimimus.","ARO_category":{"41143":{"category_aro_accession":"3004067","category_aro_cvterm_id":"41143","category_aro_name":"MUS beta-lactamase","category_aro_description":"Subclass B1 (metallo-) beta-lactamases found in Myroides spp., which confer resistance to carbapenam class beta-lactamase antibiotics.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2329":{"model_id":"2329","model_name":"MOX-9","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3606":{"protein_sequence":{"accession":"WP_042649345","sequence":"MQQQVRMTLLMASTLLWAGLAQATADTQADPLRPLVDASIRPVLKEHRIPGMAVAVLKDGKAHYFNYGVANRESGARVSEQTLFEIGSVSKTLTATLGAYAVVKGALKLDDKVSQHGPWLKGSAFDGITMAELATYSAGGLPLQFPDEVDSIDKMRAYYRQWTPAYRAGSHRQYSNPSIGLFGHLAAQSLGQPFEQLMSQTLLPGLGLEHTYLKVPAEAMANYAYGYSKEDKPIRVNPGVLADEAYGIKTSSADLLKFVGANMTGTGDEAMQQAIALTHKGVYSVGAMTQGLGWESYAYPVTEETLLAGNSGKVILEANPTAPASNETGSQVLFNKTGSTGGFGAYVAFVPAKGIGIVMLANRNYPIQARVETAHAILSKLAE"},"dna_sequence":{"accession":"NG_049322","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCAACAACAGGTGCGGATGACATTGCTGATGGCGAGCACGCTGCTCTGGGCCGGTCTGGCCCAGGCCACGGCGGACACCCAGGCCGATCCCCTGCGCCCCCTGGTGGATGCCAGTATCCGGCCCGTGCTCAAGGAGCACCGGATCCCCGGCATGGCGGTGGCGGTGCTGAAAGATGGCAAGGCCCACTACTTCAACTACGGGGTGGCCAACCGGGAGAGCGGGGCCCGTGTCAGCGAGCAGACCCTGTTCGAGATTGGATCGGTCAGCAAGACTCTTACGGCAACGCTTGGGGCTTATGCCGTGGTGAAGGGGGCGCTCAAGCTCGATGACAAGGTGAGTCAGCATGGGCCCTGGCTGAAAGGATCGGCTTTTGACGGTATCACCATGGCCGAGCTCGCCACCTACAGCGCCGGGGGCTTGCCGCTGCAATTCCCCGACGAGGTGGATTCCATCGACAAGATGCGTGCCTACTATCGCCAGTGGACGCCTGCCTATCGGGCGGGCAGCCATCGCCAGTACTCCAACCCCAGCATCGGCCTGTTCGGCCATCTCGCGGCCCAGAGCCTGGGCCAACCCTTTGAACAGTTGATGAGCCAGACCCTGCTGCCCGGGCTTGGTCTCGAGCACACCTATCTCAAGGTCCCTGCCGAGGCCATGGCGAACTACGCCTATGGCTACTCGAAAGAGGACAAGCCTATCAGGGTCAACCCGGGGGTCCTGGCGGACGAGGCCTATGGCATCAAGACCAGCTCGGCGGATCTGCTGAAGTTTGTCGGCGCCAACATGACAGGCACCGGGGACGAGGCGATGCAGCAGGCGATTGCCCTGACCCACAAGGGGGTTTACTCGGTGGGTGCCATGACTCAGGGGCTCGGCTGGGAGAGTTATGCCTATCCCGTGACCGAAGAGACCTTGCTTGCAGGCAACTCGGGCAAGGTGATCCTCGAGGCCAACCCGACGGCGCCCGCCTCCAACGAGACGGGTAGCCAGGTGCTCTTCAACAAGACCGGCTCCACCGGCGGCTTTGGTGCCTATGTGGCCTTTGTGCCAGCCAAGGGGATTGGCATCGTCATGCTGGCCAATCGCAACTATCCCATCCAGGCCAGGGTAGAGACGGCCCACGCCATCCTGAGCAAGCTGGCCGAGTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40536","NCBI_taxonomy_name":"Gammaproteobacteria","NCBI_taxonomy_id":"1236"}}}},"ARO_accession":"3002191","ARO_id":"38591","ARO_name":"MOX-9","ARO_description":"MOX-9 is a beta-lactamase found in Citrobacter freundii.","ARO_category":{"36222":{"category_aro_accession":"3000083","category_aro_cvterm_id":"36222","category_aro_name":"MOX beta-lactamase","category_aro_description":"MOX beta-lactamases are plasmid-mediated AmpC-type beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2331":{"model_id":"2331","model_name":"kdpE","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"3608":{"protein_sequence":{"accession":"NP_415222.1","sequence":"MTNVLIVEDEQAIRRFLRTALEGDGMRVFEAETLQRGLLEAATRKPDLIILDLGLPDGDGIEFIRDLRQWSAVPVIVLSARSEESDKIAALDAGADDYLSKPFGIGELQARLRVALRRHSATTAPDPLVKFSDVTVDLAARVIHRGEEEVHLTPIEFRLLAVLLNNAGKVLTQRQLLNQVWGPNAVEHSHYLRIYMGHLRQKLEQDPARPRHFITETGIGYRFML"},"dna_sequence":{"accession":"NC_000913.3","fmin":"721055","fmax":"721733","strand":"-","sequence":"TCAAAGCATAAACCGATAGCCAATACCGGTTTCAGTAATGAAATGGCGTGGGCGGGCGGGATCCTGTTCCAGTTTTTGTCGCAGATGTCCCATATAAATACGCAAATAGTGACTGTGTTCGACCGCGTTTGGCCCCCACACCTGGTTAAGGAGCTGGCGCTGGGTGAGTACTTTTCCGGCATTGTTGAGCAGCACCGCCAGCAGGCGGAACTCAATTGGTGTGAGATGCACCTCTTCCTCACCCCGGTGAATCACGCGGGCGGCTAAATCGACGGTAACATCGGAAAATTTTACCAGCGGATCGGGCGCGGTGGTGGCAGAGTGGCGGCGTAATGCGACGCGCAGACGGGCCTGCAATTCGCCAATGCCAAACGGCTTACTCAGATAATCATCCGCTCCGGCATCCAGCGCGGCGATTTTGTCGCTCTCTTCGCTGCGTGCGGAAAGCACAATCACCGGCACCGCGCTCCACTGGCGCAGGTCGCGGATAAACTCAATCCCATCACCATCGGGCAGGCCGAGATCGAGAATAATCAAATCTGGCTTACGGGTTGCCGCTTCCAGCAAGCCGCGTTGCAGCGTTTCGGCCTCAAAGACGCGCATCCCGTCGCCCTCCAGCGCCGTGCGCAGAAAGCGACGAATAGCCTGTTCATCTTCAACAATCAGAACGTTTGTCAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3003841","ARO_id":"40534","ARO_name":"kdpE","ARO_description":"kdpE is a transcriptional activator that is part of the two-component system KdpD\/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.","ARO_category":{"41098":{"category_aro_accession":"3004046","category_aro_cvterm_id":"41098","category_aro_name":"kdpDE","category_aro_description":"kdpDE is a two-component regulatory system in Escherichia coli, well studied for its role in potassium transport and homeostasis. kdpE is also implicated in virulence loci regulation and overexpression of kdpE is shown to confer resistance to aminoglycoside antibiotics.","category_aro_class_name":"AMR Gene Family"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2333":{"model_id":"2333","model_name":"LEN-26","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"3610":{"protein_sequence":{"accession":"WP_025712239","sequence":"MRYVRLCVISLLANLPLAVYAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGVEQLDRRIHYRQQDLVDYSPVSEKHLTDGMTIGELCAAAITMSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDMRDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGARGIVALLGPDGKAERIVVIYMRDTPATIAERNQQIAAIGAALIEHWQR"},"dna_sequence":{"accession":"NG_049281","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCAACCTGCCACTAGCGGTATACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGGTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTACCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTGACCGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACATGCGCGACACCACTACCCCGGCCAGCATGGCCGCCACGCTGCGTAAACTACTGACTGCGCAGCATCTGAGCGCCCGTTCACAGCAGCAGCTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGACAAGACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAAGCGGAGCGCATTGTGGTGATTTATATGCGGGATACGCCGGCGACCATCGCCGAGCGTAACCAGCAGATCGCCGCTATCGGCGCGGCGCTGATCGAGCACTGGCAGCGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37059","NCBI_taxonomy_name":"Klebsiella","NCBI_taxonomy_id":"570"}}}},"ARO_accession":"3002474","ARO_id":"38874","ARO_name":"LEN-26","ARO_description":"LEN-26 is a beta-lactamase found in Escherichia coli and Klebsiella pneumoniae.","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2335":{"model_id":"2335","model_name":"ADC-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3628":{"protein_sequence":{"accession":"WP_004746565.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFINANLNPQKYPTDIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_048644.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCTCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCCACCTTACCGGATATGTTGAGTTTTATTAATGCCAACCTTAACCCACAAAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAGCCTAATAAAGTGACTGCTATTTCAAAAGAGCCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40546","NCBI_taxonomy_name":"Proteobacteria","NCBI_taxonomy_id":"1224"}}}},"ARO_accession":"3003848","ARO_id":"40545","ARO_name":"ADC-2","ARO_description":"ADC-2 is a beta-lactamase found in Oligella urethralis.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2375":{"model_id":"2375","model_name":"Rm3 beta-lactamase","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"3669":{"protein_sequence":{"accession":"AGU01679.2","sequence":"MSLTPPRALVLALLLASPGTQAQTPAPATPPTPGCEVCATWNADQAPFRLFGNTYYVGMKGLSSVLVTSPQGHVLIDGGLPESAPKIIANIGALGFRIEDVKLILNSHGHIDHAGGLAELQRRSNALVAASPSAALDLASGEVGPDDPQYHALPKYPPVKDMRLARDGGQFNVGPVYLTAHATPGHTPGGLSWTWQSCDGPRCLNMVYADSINAVSRPGFKFSASSEYPNALADLRHSFETLEKLPCDVLISAHPEASQLWQRLEASATGGSDAFVDPQACRAYVAAARTLLDSRLDQEKQQ"},"dna_sequence":{"accession":"KF485393.2","fmin":"6723","fmax":"7632","strand":"+","sequence":"ATGTCCCTCACACCACCACGCGCGCTGGTCCTGGCCCTGCTGCTGGCCAGCCCCGGCACCCAGGCGCAAACACCGGCTCCAGCCACACCGCCAACGCCGGGCTGCGAAGTCTGCGCCACCTGGAATGCCGACCAGGCACCGTTCCGCCTCTTCGGCAATACCTATTACGTGGGCATGAAAGGCCTCAGTTCCGTGCTGGTGACGTCGCCGCAGGGCCATGTGCTGATCGATGGCGGCTTGCCGGAATCGGCGCCCAAGATCATCGCCAATATCGGCGCGCTGGGCTTTCGCATAGAGGACGTCAAGCTGATCCTCAATTCGCACGGCCATATCGACCATGCGGGCGGCCTGGCCGAACTGCAGCGGCGCAGCAATGCCCTGGTGGCGGCCAGCCCGTCGGCCGCGCTGGACCTGGCGTCGGGCGAAGTGGGCCCGGACGACCCGCAATACCATGCGCTGCCCAAATATCCGCCCGTCAAGGACATGCGCCTGGCGCGCGACGGCGGCCAGTTCAATGTCGGCCCCGTCTACCTGACGGCGCATGCCACGCCAGGGCACACGCCCGGGGGCCTGAGCTGGACGTGGCAATCGTGCGACGGTCCCCGCTGCCTGAACATGGTCTACGCGGACAGCATCAACGCCGTCTCGCGCCCCGGTTTCAAGTTCAGCGCCAGCAGTGAGTATCCGAACGCCCTGGCGGACTTGCGCCACAGCTTCGAGACCCTGGAAAAACTGCCCTGCGACGTGCTCATTTCGGCGCATCCGGAGGCGTCGCAATTGTGGCAACGACTGGAAGCGAGCGCCACGGGCGGCAGCGATGCCTTCGTCGATCCGCAGGCCTGCCGCGCCTACGTGGCGGCGGCGCGCACCTTGCTCGACTCTCGTCTGGACCAGGAAAAACAGCAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3003894","ARO_id":"40596","ARO_name":"Rm3","ARO_description":"Rm3 is a class B3 metallo-beta-lactamase isolated from a metagenomic soil sample in Yorkshire, United Kingdom, shown to confer resistance to clinically used penicillins, cephalosporins, and carbapenems.","ARO_category":{"41389":{"category_aro_accession":"3004225","category_aro_cvterm_id":"41389","category_aro_name":"Rm3 family beta-lactamase","category_aro_description":"A family encompassing subclass B3 Rm3-like beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1670":{"model_id":"1670","model_name":"nalC","model_type":"protein overexpression model","model_type_id":"41091","model_description":"This model detects protein overexpression based on the presence of mutations.The detection of the protein without an associated mutation indicates that the protein is likely to be expressed at low or basal levels. The detection of the protein with the mutation indicates that the protein is likely overexpressed. This model reflects how certain proteins are functional with and without mutations. For example, efflux pump subunits and regulators are functional with mutations and without mutations. Without mutations, efflux pump subunits and regulators are usually expressed at a low level. When an efflux pump regulator has a mutation, it can cause the overexpression of the efflux pump it is responsible for regulating, leading to resistance to specific drugs. Protein overexpression models have two parameters: a curated BLASTP cutoff, and a curated set of mutations (single resistance variants, frameshift mutations, indels, etc.) shown clinically to confer resistance. This model type is a combination of the protein homolog and protein variant model. A detected hit can be categorized as Perfect, Strict, or Loose with no mutation(s) or as Strict or Loose with mutation(s).","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"4363":"S209R","4364":"R97G","4366":"A186T","7533":"G71E"},"clinical":{"4363":"S209R","4364":"R97G","4366":"A186T","7533":"G71E"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"187":{"protein_sequence":{"accession":"NP_252410.1","sequence":"MNDASPRLTERGRQRRRAMLDAATQAFLEHGFEGTTLDMVIERAGGSRGTLYSSFGGKEGLFAAVIAHMIGEIFDDSADQPRPAATLSATLEHFGRRFLTSLLDPRCQSLYRLVVAESPRFPAIGKSFYEQGPQQSYLLLSERLAAVAPHMDEETLYAVACQFLEMLKADLFLKALSVADFQPTMALLETRLKLSVDIIACYLEHLSQSPAQG"},"dna_sequence":{"accession":"NC_002516","fmin":"4166517","fmax":"4167159","strand":"+","sequence":"ATGAACGATGCTTCTCCCCGTCTGACCGAACGCGGCAGGCAACGCCGCCGCGCCATGCTCGACGCCGCTACCCAGGCCTTTCTCGAACACGGTTTCGAAGGCACCACCCTGGACATGGTGATAGAACGGGCCGGTGGTTCACGGGGGACCCTGTACAGCTCCTTCGGCGGCAAGGAGGGCCTGTTCGCCGCGGTGATCGCCCACATGATCGGGGAAATCTTCGACGACAGCGCCGATCAGCCGCGCCCCGCCGCCACGCTGAGCGCCACCCTCGAGCATTTCGGCCGGCGCTTTCTCACCAGCCTGCTCGATCCCCGCTGCCAGAGCCTCTATCGCCTGGTGGTGGCGGAATCCCCGCGGTTTCCGGCGATCGGCAAGTCCTTCTACGAGCAGGGGCCGCAGCAGAGCTATCTGCTGCTCAGCGAGCGACTGGCCGCGGTCGCTCCTCACATGGACGAGGAAACGCTCTACGCGGTGGCCTGCCAGTTTCTCGAGATGCTCAAGGCCGACCTGTTCCTCAAGGCCCTCAGCGTGGCCGACTTCCAGCCGACCATGGCGCTGCTGGAAACCCGCCTCAAGCTGTCGGTGGACATCATCGCCTGCTACCTGGAACACCTGTCGCAGAGCCCCGCGCAGGGCTGAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3000818","ARO_id":"37198","ARO_name":"nalC","ARO_description":"NalC is a repressor of PA3720-PA3719, which are positive regulators of MexAB-OprM. Thus, nalC mutants confer multidrug resistance.","ARO_category":{"35996":{"category_aro_accession":"0000079","category_aro_cvterm_id":"35996","category_aro_name":"clavulanate","category_aro_description":"Clavulanic acid is a beta-lactamase inhibitor (marketed by GlaxoSmithKline, formerly Beecham) combined with penicillin group antibiotics to overcome certain types of antibiotic resistance. It is used to overcome resistance in bacteria that secrete beta-lactamase, which otherwise inactivates most penicillins.","category_aro_class_name":"Adjuvant"},"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35979":{"category_aro_accession":"0000062","category_aro_cvterm_id":"35979","category_aro_name":"ceftriaxone","category_aro_description":"Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36468":{"category_aro_accession":"3000329","category_aro_cvterm_id":"36468","category_aro_name":"sulfamethoxazole","category_aro_description":"Sulfamethoxazole is a sulfonamide antibiotic usually taken with trimethoprim, a diaminopyrimidine antibiotic. Sulfamethoxazole inhibits dihydropteroate synthase, essential to tetrahydrofolic acid biosynthesis. This pathway generates compounds used in the synthesis of many amino acids and nucleotides.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36689":{"category_aro_accession":"3000550","category_aro_cvterm_id":"36689","category_aro_name":"aztreonam","category_aro_description":"Aztreonam was the first monobactam discovered, and is greatly effective against Gram-negative bacteria while inactive against Gram-positive bacteria. Artreonam is a poor substrate for beta-lactamases, and may even act as an inhibitor. In Gram-negative bacteria, Aztreonam interferes with filamentation, inhibiting cell division and leading to cell death.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"40362":{"category_aro_accession":"3003708","category_aro_cvterm_id":"40362","category_aro_name":"panipenem","category_aro_description":"Panipenem is a carbapenem antibacterial agent with a broad spectrum of in vitro activity covering a wide range of Gram-negative and Gram-positive aerobic and anaerobic bacterial.  It is used in combination with betamipron to inhibit panipenem uptake into the renal tubule and prevent nephrotoxicity.","category_aro_class_name":"Antibiotic"},"40957":{"category_aro_accession":"3004024","category_aro_cvterm_id":"40957","category_aro_name":"trimethoprim-sulfamethoxazole","category_aro_description":"An antibiotic cocktail containing the diaminopyrimidine antibiotic Trimethoprim and the sulfonamide antibiotic sulfamethoxazole (1 TMP:5 SMX).","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36421":{"category_aro_accession":"3000282","category_aro_cvterm_id":"36421","category_aro_name":"sulfonamide antibiotic","category_aro_description":"Sulfonamides are broad spectrum, synthetic antibiotics that contain the sulfonamide group. Sulfonamides inhibit dihydropteroate synthase, which catalyzes the conversion of p-aminobenzoic acid to dihydropteroic acid as part of the tetrahydrofolic acid biosynthetic pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor of many nucleotides and amino acids. Many sulfamides are taken with trimethoprim, an inhibitor of dihydrofolate reductase, also disturbing the trihydrofolic acid synthesis pathway.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2373":{"model_id":"2373","model_name":"Escherichia coli UhpT with mutation conferring resistance to fosfomycin","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"4358":"E350Q"},"clinical":{"4358":"E350Q"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"850"}},"model_sequences":{"sequence":{"3667":{"protein_sequence":{"accession":"CDJ73208","sequence":"MLAFLNQVRKPTLDLPLEVRRKMWFKPFMQSYLVVFIGYLTMYLIRKNFNIAQNDMISTYGLSMTQLGMIGLGFSITYGVGKTLVSYYADGKNTKQFLPFMLILSAICMLGFSASMGSGSVSLFLMIAFYALSGFFQSTGGSCSYSTITKWTPRRKRGTFLGFWNISHNLGGAGAAGVALFGANYLFDGHVIGMFIFPSIIALIVGFIGLRYGSDSPESYGLGKAEELFGEEISEEDKETESTDMTKWQIFVEYVLKNKVIWLLCFANIFLYVVRIGIDQWSTVYAFQELKLSKAVAIQGFTLFEAGALVGTLLWGWLSDLANGRRGLVACIALALIIATLGVYQHASNEYIYLASLFALGFLVFGPQLLIGVAAVGFVPKKAIGAADGIKGTFAYLIGDSFAKLGLGMIADGTPVFGLTGWAGTFAALDIAAIGCICLMAIVAVMEERKIRREKKIQQLTVA"},"dna_sequence":{"accession":"HG738867","fmin":"2934266","fmax":"2935658","strand":"+","sequence":"ATGCTGGCTTTCTTAAACCAGGTTCGCAAGCCGACCCTGGACCTTCCGCTCGAAGTGCGGCGCAAAATGTGGTTCAAACCGTTCATGCAATCCTACCTGGTGGTCTTTATCGGCTACCTGACGATGTACCTGATTCGCAAGAACTTTAACATCGCGCAGAACGATATGATTTCGACCTACGGGTTGAGCATGACGCAGCTGGGGATGATCGGCCTGGGTTTCTCCATCACTTATGGCGTGGGTAAAACGCTGGTTTCCTACTACGCCGACGGCAAAAACACCAAACAATTCCTGCCGTTCATGCTGATCCTCTCTGCTATTTGTATGCTGGGCTTCAGTGCCAGTATGGGCAGCGGCTCGGTTAGCCTGTTCCTGATGATTGCCTTCTACGCCTTAAGCGGCTTTTTCCAGAGTACCGGCGGTTCGTGCAGTTACTCCACCATCACCAAATGGACGCCGCGTCGTAAACGCGGGACATTCCTCGGTTTCTGGAATATTTCTCACAACCTTGGCGGTGCAGGCGCAGCAGGTGTGGCGCTGTTCGGGGCAAATTACCTGTTCGATGGCCATGTCATCGGCATGTTTATCTTCCCGTCGATTATCGCGCTGATTGTCGGTTTTATCGGCCTGCGTTACGGCAGCGACTCCCCGGAATCTTATGGCCTCGGCAAAGCTGAAGAACTGTTCGGCGAGGAGATCAGCGAAGAGGACAAAGAGACAGAATCTACCGATATGACCAAGTGGCAGATCTTTGTTGAGTATGTGCTGAAAAACAAAGTGATCTGGCTGCTGTGCTTCGCCAACATTTTCCTCTATGTGGTACGTATTGGTATCGACCAGTGGTCAACCGTATACGCGTTCCAGGAACTGAAACTCTCTAAAGCGGTGGCGATTCAGGGCTTTACGCTGTTTGAAGCTGGTGCGCTGGTCGGTACGCTGCTGTGGGGCTGGCTCTCTGACCTGGCGAACGGTCGCCGTGGCCTGGTGGCCTGCATCGCGCTGGCGCTGATTATCGCCACGCTCGGTGTGTATCAACATGCCAGTAACGAATATATCTATCTGGCTTCTCTCTTTGCGTTGGGTTTCCTGGTCTTTGGCCCGCAATTGTTGATTGGTGTGGCTGCTGTTGGCTTTGTACCTAAAAAAGCGATTGGCGCTGCCGATGGTATTAAAGGCACCTTTGCTTACCTGATTGGTGACAGCTTTGCCAAGTTAGGTCTGGGAATGATTGCCGATGGGACGCCGGTATTCGGCCTTACCGGCTGGGCAGGCACCTTCGCCGCGCTGGATATCGCCGCGATTGGTTGTATCTGCCTGATGGCGATAGTGGCGGTAATGGAAGAACGCAAAATCCGCCGCGAGAAAAAAATTCAGCAGTTGACAGTGGCATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40589","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MC4100","NCBI_taxonomy_id":"1403831"}}}},"ARO_accession":"3003890","ARO_id":"40592","ARO_name":"Escherichia coli UhpT with mutation conferring resistance to fosfomycin","ARO_description":"Mutations to the active importer UhpT, which is involved with the uptake of many phosphorylated sugars, confer resistance to fosfomycin by reducing import of the drug into the bacteria.","ARO_category":{"41412":{"category_aro_accession":"3004248","category_aro_cvterm_id":"41412","category_aro_name":"UhpT","category_aro_description":"UhpT encodes a transporter that can import fosfomycin-type drugs into bacterial cells. Mutations to UhpT confer resistance.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2372":{"model_id":"2372","model_name":"Escherichia coli GlpT with mutation conferring resistance to fosfomycin","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"4320":"E448K"},"clinical":{"4320":"E448K"}},"40330":{"param_type":"multiple resistance variants","param_description":"A set of nucleotide or amino acid substitutions that are each required to confer resistance to an antibiotic drug or drug class by co-mutation. Compare to single resistance variant, where only one substitution is required. Multiple resistance variants parameters are indicated on appropriate models using the following notation: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2],...,[wild-type n][position n][mutation n]. When each included substitution is detected in a protein sequence, resistance is conferred. This parameter is not currently included in any detection algorithms.","param_type_id":"40330","param_value":{"4321":"E448K, G33R","4322":"E448K, Q444E, E443Q, L297F","4323":"E448K, G302D"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"850"},"41343":{"param_type":"deletion mutation from nucleotide sequence","param_description":"A subtype of the deletion mutation detection model parameter. This parameter is used when a set of deletion mutations is reported in a nucleotide sequence format. Such mutations may be of variable length - possibly causing a frameshift, but not premature termination of functional knockout. Mutation parameters of this type are reported in the CARD with the notation: [-]nt[position]:[nucleotides].","param_type_id":"41343","param_value":{"8144":"-nt602:20"}}},"model_sequences":{"sequence":{"3666":{"protein_sequence":{"accession":"CDJ72593","sequence":"MLSIFKPAPHKARLPAAEIDPTYRRLRWQIFLGIFFGYAAYYLVRKNFALAMPYLVEQGFSRGDLGFALSGISIAYGFSKFIMGSVSDRSNPRVFLPAGLILAAAVMLFMGFVPWATSSIAVMFVLLFLCGWFQGMGWPPCGRTMVHWWSQKERGGIVSVWNCAHNVGGGIPPLLFLLGMAWFNDWHAALYMPAFCAILVALFAFAMMRDTPQSCGLPPIEEYKNDYPDDYNEKAEQELTAKQIFMQYVLPNKLLWYIAIANVFVYLLRYGILDWSPTYLKEVKHFALDKSSWAYFLYEYAGIPGTLLCGWMSDKVFRGNRGATGVFFMTLVTIATIVYWMNPAGNPTVDMICMIVIGFLIYGPVMLIGLHALELAPKKAAGTAAGFTGLFGYLGGSVAASAIVGYTVDFFGWDGGFMVMIGGSILAVILLIVVMIGEKRRHEQLLQERNGG"},"dna_sequence":{"accession":"HG738867","fmin":"2233288","fmax":"2234647","strand":"-","sequence":"TTAGCCTCCGTTGCGTTCTTGCAGTAATTGTTCATGGCGACGTTTTTCGCCAATCATCACAACAATCAACAAGATAACCGCCAGAATGCTGCCGCCAATCATTACCATAAAGCCGCCATCCCAGCCGAAGAAGTCCACGGTGTAGCCAACAATCGCGCTCGCCGCCACCGAACCGCCCAGGTAACCAAACAGCCCGGTAAAGCCCGCTGCCGTACCTGCCGCTTTTTTCGGTGCCAGTTCCAGCGCATGCAGACCGATCAGCATCACAGGACCGTAGATCAGGAAGCCGATAACAATCATACAAATCATATCGACGGTTGGGTTACCTGCCGGGTTCATCCAGTAAACGATAGTCGCGATGGTCACCAGTGTCATAAAGAAAACGCCGGTTGCCCCACGGTTGCCACGGAAGACTTTATCCGACATCCAGCCGCACAGCAGAGTGCCCGGAATACCTGCATATTCATAAAGGAAGTAGGCCCAGGAGGATTTATCTAGCGCGAAATGCTTAACCTCTTTCAGATAAGTCGGTGACCAGTCGAGGATGCCGTAACGCAGCAGATAAACGAACACGTTGGCGATGGCGATATACCACAGCAGTTTGTTCGGCAGTACGTACTGCATGAAGATTTGCTTCGCCGTCAGCTCCTGTTCCGCTTTTTCGTTATAGTCGTCCGGATAATCATTTTTGTACTCTTCGATCGGCGGCAAGCCACAGGATTGCGGGGTATCGCGCATCATCGCAAAGGCGAATAATGCCACCAGAATGGCGCAGAAAGCAGGCATATAGAGCGCCGCATGCCAGTCATTGAACCAGGCCATCCCCAGCAGGAACAGCAGCGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGTGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTACAAACATCACCGCAATGCTCGACGTCGCCCATGGCACAAAGCCCATAAACAACATCACTGCCGCCGCCAGAATCAAACCTGCGGGCAGGAAAACGCGCGGATTCGAGCGATCCGATACCGAACCCATGATGAATTTCGAAAATCCATAAGCAATCGAGATCCCCGAAAGGGCAAAACCTAAATCACCGCGTGAGAATCCCTGCTCAACCAGATAAGGCATAGCAAGCGCAAAGTTCTTACGAACCAAATAGTAAGCCGCATAGCCAAAGAATATCCCCAGGAAAATTTGCCAGCGCAATCGACGATAAGTCGGATCGATCTCCGCGGCAGGTAAGCGCGCTTTGTGTGGCGCTGGTTTAAAAATACTCAACAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40589","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MC4100","NCBI_taxonomy_id":"1403831"}}}},"ARO_accession":"3003889","ARO_id":"40588","ARO_name":"Escherichia coli GlpT with mutation conferring resistance to fosfomycin","ARO_description":"Point mutations to the active importer GlpT, which is involved with the uptake of many phosphorylated sugars, confer resistance to fosfomycin by reducing import of the drug into the bacteria.","ARO_category":{"41411":{"category_aro_accession":"3004247","category_aro_cvterm_id":"41411","category_aro_name":"GlpT","category_aro_description":"Fosfomycin is transported bacterial cells through transporters, one of them being glycerol-3-phosphate, which is encoded by the GlpT gene. Mutations in the GlpT gene can confer resistance to fosfomycin.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"383":{"model_id":"383","model_name":"Pseudomonas mutant PhoQ conferring resistance to colistin","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"4370":"K123Q","4371":"V260G"},"experimental":{"4370":"K123Q","4371":"V260G"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"860"}},"model_sequences":{"sequence":{"3672":{"protein_sequence":{"accession":"NP_249871.1","sequence":"MIRSLRIRLMLGAAALAVLFMLALLPALQRAFGIALENTIEQRLAADVATLVSAARVEKGRLVMPEHLPVEEFNLPEAKVLGYIYDQNGDLLWRSTSAADESINYTPRYDGRGNEFHTTRDAKGEEFFVFDVEIDLLRGKQAAYSIVTMQSVSEFESLLKGFREQLYLWLGGALLVLLGLLWLGLTWGFRAMRGLSSELDQIESGERESLSEEHPRELLRLTHSLNRLLRSEHKQRERYRHSLGDLAHSLKTPLAVLQGVGDQLAEEPGNREQVRVLQGQIERMSQQIGYQLQRASLRKSGLVRHREQLAPLVETLCDALDKVYRDKRVSLQRDFSPSFSVPVERGALLELLGNLLENAYRLCLGRVRVGARLGPGYSELWVEDDGPGVPAEQRARIIRRGERADTQHPGQGIGLAVALDIIESYDGELSLDDSELGGACFRIRFATV"},"dna_sequence":{"accession":"NC_002516.2","fmin":"1278361","fmax":"1279708","strand":"+","sequence":"GTGATCCGTTCCCTGCGCATCCGTCTGATGCTCGGCGCCGCCGCCCTGGCGGTGCTGTTCATGCTGGCGCTGCTGCCGGCCCTGCAGCGGGCCTTCGGCATCGCCCTGGAGAACACCATCGAGCAGCGCCTGGCCGCCGACGTGGCGACCCTGGTCTCGGCGGCGCGGGTGGAGAAGGGCCGCCTGGTGATGCCCGAGCACCTGCCGGTGGAGGAGTTCAACCTGCCGGAGGCCAAGGTCCTCGGCTATATCTACGACCAGAATGGCGATCTGCTCTGGCGCTCCACCTCGGCGGCCGACGAGTCGATCAACTACACGCCGCGCTACGACGGCCGCGGCAACGAATTCCACACCACCCGCGATGCGAAGGGCGAGGAGTTCTTCGTGTTCGACGTCGAGATCGACCTGCTGCGCGGCAAGCAGGCGGCCTACAGCATCGTCACCATGCAATCGGTCAGCGAGTTCGAGAGCCTGCTCAAGGGGTTCCGCGAGCAGCTCTACCTGTGGCTCGGCGGCGCCCTGCTGGTCTTGCTCGGGCTGCTCTGGCTGGGTCTGACCTGGGGCTTCCGGGCGATGCGCGGGTTGAGTTCCGAGCTGGACCAGATCGAATCCGGCGAGCGCGAGAGCCTGAGCGAGGAGCATCCGCGCGAGCTGCTGCGCCTGACCCACTCGCTTAACCGCCTGTTGCGCAGCGAGCACAAACAGCGCGAGCGCTACCGCCACTCCCTCGGCGACCTGGCGCACAGTCTGAAGACGCCGCTGGCGGTCTTGCAGGGGGTCGGCGACCAGCTCGCCGAGGAGCCCGGCAACCGCGAGCAGGTGCGGGTGCTACAGGGCCAGATCGAGCGCATGAGCCAGCAGATAGGCTATCAGTTGCAGCGCGCCAGCCTGCGCAAGAGCGGCCTGGTACGCCATCGCGAGCAACTGGCGCCGCTGGTGGAGACCCTGTGCGACGCGCTGGACAAGGTCTATCGCGACAAGCGGGTAAGCCTGCAGCGGGACTTCTCGCCGTCCTTCAGCGTGCCGGTGGAGCGCGGCGCGCTGCTGGAACTGCTCGGCAACCTGCTGGAGAACGCCTATCGCCTGTGCCTGGGCCGGGTCCGCGTGGGCGCCCGGCTGGGGCCGGGTTACTCGGAGCTGTGGGTCGAGGACGACGGTCCCGGAGTGCCTGCCGAACAGCGCGCACGAATCATCCGCCGCGGCGAGCGCGCCGATACCCAGCACCCGGGGCAGGGCATCGGCCTGGCCGTGGCGCTGGACATCATCGAGAGCTACGACGGCGAACTGAGCCTGGACGATTCCGAGCTGGGCGGCGCCTGCTTCCGCATACGTTTCGCTACAGTCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3003896","ARO_id":"40598","ARO_name":"Pseudomonas mutant PhoQ conferring resistance to colistin","ARO_description":"Mutations in Pseudomonas aeruginosa PhoQ of the two-component PhoPQ regulatory system. Presence of mutation confers resistance to colistin","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"41433":{"category_aro_accession":"3004269","category_aro_cvterm_id":"41433","category_aro_name":"pmr phosphoethanolamine transferase","category_aro_description":"This family of phosphoethanolamine transferase catalyze the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine to lipid A, which impedes the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"660":{"model_id":"660","model_name":"Streptococcus pneumoniae parC conferring resistance to fluoroquinolone","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3979":"D84H","3980":"S80F","3981":"S80Y"},"clinical":{"3979":"D84H","3980":"S80F"},"experimental":{"3981":"S80Y"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1400"}},"model_sequences":{"sequence":{"2068":{"protein_sequence":{"accession":"AAK74984.1","sequence":"MSNIQNMSLEDIMGERFGRYSKYIIQDRALPDIRDGLKPVQRRILYSMNKDSNTFDKSYRKSAKSVGNIMGNFHPHGDSSIYDAMVRMSQNWKNREILVEMHGNNGSMDGDPPAAMRYTEARLSEIAGYLLQDIEKKTVPFAWNFDDTEKEPTVLPAAFPNLLVNGSTGISAGYATDIPPHNLAEVIDAAVYMIDHPTAKIDKLMEFLPGPDFPTGAIIQGRDEIKKAYETGKGRVVVRSKTEIEKLKGGKEQIVIIEIPYEINKANLVKKIDDVRVNNKVAGIAEVRDESDRDGLRIAIELKKDANTELVLNYLFKYTDLQINYNFNMVAIDNFTPRQVGIVPILSSYIAHRREVILARSRFDKEKAEKRLHIVEGLIRVISILDEVIALIRASENKADAKENLKVSYDFTEEQAEAIVTLQLYRLTNTDVVVLQEEEAELREKIAMLAAIIGDERTMYNLMKKELREVKKKFATPRLSSLEDTAKAIEIDTASLIAEEDTYVSVTKAGYIKRTSPRSFAASTLEEIGKRDDDRLIFVQSAKTTQHLLMFTSLGNVIYRPIHELADIRWKDIGEHLSQTITNFETNEEILYVEVLDQFDDATTYFAVTRLGQIKRVERKEFTPWRTYRSKSVKYAKLKDDTDQIVAVAPIKLDDVVLVSQNGYALRFNIEEVPVVGAKAAGVKAMNLKEDDVLQSGFICNTSSFYLLTQRGSLKRVSIEEILATSRAKRGLQVLRELKNKPHRVFLAGAVAEQGFVGDFFSTEVDVNDQTLLVQSNKGTIYESRLQDLNLSERTSNGSFISDTISDEEVFDAYLQEVVTEDK"},"dna_sequence":{"accession":"AE005672","fmin":"800699","fmax":"803171","strand":"+","sequence":"ATGTCTAACATTCAAAACATGTCCCTGGAGGACATCATGGGAGAGCGCTTTGGTCGCTACTCCAAGTACATTATTCAAGACCGGGCTTTGCCAGATATTCGTGATGGGTTGAAGCCGGTTCAGCGCCGTATTCTTTATTCTATGAATAAGGATAGCAATACTTTTGACAAGAGCTACCGTAAGTCGGCCAAGTCAGTCGGGAACATCATGGGGAATTTCCACCCACACGGGGATTCTTCTATCTATGATGCCATGGTTCGTATGTCACAGAACTGGAAAAATCGTGAGATTCTAGTTGAAATGCACGGTAATAACGGTTCTATGGACGGAGATCCTCCTGCGGCTATGCGTTATACTGAGGCACGTTTGTCTGAAATTGCAGGCTACCTTCTTCAGGATATCGAGAAAAAGACAGTTCCTTTTGCATGGAACTTTGACGATACGGAGAAAGAACCAACGGTCTTGCCAGCAGCCTTTCCAAACCTCTTGGTCAATGGTTCGACTGGGATTTCGGCTGGTTATGCCACAGACATTCCTCCCCATAATTTAGCTGAGGTCATAGATGCTGCAGTTTACATGATTGACCACCCAACTGCAAAGATTGATAAACTCATGGAATTCTTGCCTGGACCAGACTTCCCTACAGGGGCTATTATTCAGGGTCGTGATGAAATCAAGAAAGCTTATGAGACTGGGAAAGGGCGCGTGGTTGTTCGTTCCAAGACTGAAATTGAAAAGCTAAAAGGTGGTAAGGAACAAATCGTTATTATTGAGATTCCTTATGAAATCAATAAGGCCAATCTAGTCAAGAAAATCGATGATGTTCGTGTTAATAACAAGGTAGCTGGGATTGCTGAGGTTCGTGATGAGTCTGACCGTGATGGTCTTCGTATCGCTATCGAACTTAAGAAAGACGCTAATACTGAGCTTGTTCTCAACTACTTATTTAAGTACACCGACCTACAAATCAACTACAACTTTAATATGGTGGCGATTGACAATTTCACACCTCGTCAGGTTGGGATTGTTCCAATCCTGTCTAGCTATATCGCTCACCGTCGAGAAGTGATTTTGGCGCGTTCACGCTTTGACAAAGAAAAGGCTGAGAAACGTCTCCATATCGTCGAAGGTTTGATTCGTGTGATTTCGATTTTGGATGAAGTCATTGCTCTTATCCGTGCTTCTGAGAATAAGGCGGACGCCAAGGAAAACCTCAAAGTTAGCTATGATTTTACGGAAGAACAGGCTGAGGCTATCGTAACTTTGCAACTGTACCGTTTGACCAATACCGATGTGGTTGTCTTGCAGGAAGAAGAAGCAGAGCTTCGTGAGAAGATTGCTATGCTGGCGGCTATTATCGGTGATGAAAGGACTATGTACAATCTCATGAAGAAAGAACTTCGTGAGGTCAAGAAGAAATTTGCAACTCCTCGTTTGAGTTCTTTAGAAGACACTGCGAAAGCAATTGAGATTGATACAGCTAGTCTTATCGCTGAGGAAGATACCTACGTCAGCGTGACCAAGGCAGGTTACATCAAGCGTACCAGTCCACGTTCCTTTGCGGCTTCCACCTTGGAAGAAATTGGCAAGCGTGATGATGACCGTTTGATTTTTGTTCAATCTGCCAAGACAACCCAGCACCTCTTGATGTTCACAAGTCTTGGAAATGTCATCTACAGACCAATCCATGAGTTGGCAGATATTCGTTGGAAGGACATCGGAGAGCATCTGAGCCAAACCATCACAAACTTTGAAACGAATGAAGAAATCCTTTATGTGGAAGTACTGGATCAGTTTGACGATGCGACAACCTACTTTGCAGTGACTCGCCTTGGTCAAATCAAACGGGTAGAGCGAAAAGAATTCACTCCATGGCGGACCTATAGATCTAAGTCTGTCAAGTATGCTAAGCTCAAAGACGATACAGATCAGATTGTAGCAGTGGCTCCGATTAAACTAGATGATGTTGTCTTGGTTAGTCAAAATGGTTATGCCCTGCGTTTCAATATCGAAGAGGTTCCGGTTGTCGGTGCTAAGGCAGCAGGTGTCAAGGCTATGAATTTGAAAGAAGATGATGTCCTCCAATCTGGCTTTATCTGTAATACTTCGTCCTTCTACCTCTTGACCCAGCGTGGAAGCTTGAAACGTGTTTCCATTGAGGAAATTCTAGCAACCAGCCGTGCCAAACGAGGATTACAAGTCTTGCGTGAGTTGAAAAACAAACCGCATCGTGTCTTCTTGGCAGGAGCAGTTGCAGAGCAAGGATTTGTTGGCGATTTCTTCAGTACGGAAGTGGATGTGAACGACCAAACTCTGCTTGTCCAATCCAATAAAGGAACAATCTATGAAAGCCGATTGCAAGACTTGAACTTGTCAGAACGCACTAGCAATGGAAGCTTCATTTCTGACACGATTTCAGATGAAGAAGTTTTTGACGCTTATCTTCAGGAAGTAGTTACTGAAGATAAATAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40078","NCBI_taxonomy_name":"Streptococcus pneumoniae TIGR4","NCBI_taxonomy_id":"170187"}}}},"ARO_accession":"3003311","ARO_id":"39895","ARO_name":"Streptococcus pneumoniae parC conferring resistance to fluoroquinolone","ARO_description":"Point mutation in Streptococcus pneumoniae parC resulting in fluoroquinolone resistance","ARO_category":{"36913":{"category_aro_accession":"3000619","category_aro_cvterm_id":"36913","category_aro_name":"fluoroquinolone resistant parC","category_aro_description":"ParC is a subunit of topoisomerase IV, which decatenates and relaxes DNA to allow access to genes for transcription or translation. Point mutations in ParC prevent fluoroquinolone antibiotics from inhibiting DNA synthesis, and confer low-level resistance. Higher-level resistance results from both gyrA and parC mutations.","category_aro_class_name":"AMR Gene Family"},"40471":{"category_aro_accession":"3003786","category_aro_cvterm_id":"40471","category_aro_name":"fluoroquinolone self resistant parC","category_aro_description":"Inherent parC resistance to fluoroquinolone from an antibiotic producer. The presence of these genes confers self-resistance to the antibiotic it produces.","category_aro_class_name":"AMR Gene Family"},"35942":{"category_aro_accession":"0000023","category_aro_cvterm_id":"35942","category_aro_name":"enoxacin","category_aro_description":"Enoxacin belongs to a group called fluoroquinolones. Its mode of action depends upon blocking bacterial DNA replication by binding itself to DNA gyrase and causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37004":{"category_aro_accession":"3000660","category_aro_cvterm_id":"37004","category_aro_name":"lomefloxacin","category_aro_description":"Lomefloxacin is a difluoropiperazinyl quinolone, sharing similar activities with other fluoroquinolones. It is used to treat urinary tract infections. Relative to other fluoroquinolones, it has a longer half life and has higher serum concentrations.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"37008":{"category_aro_accession":"3000664","category_aro_cvterm_id":"37008","category_aro_name":"trovafloxacin","category_aro_description":"Trovafloxacin is a trifluoroquinalone with a broad spectrum of activity that acts by inhibiting the uncoiling of supercoiled DNA. While potent against many Gram-positive and Gram-negative bacteria, it is less active against pseudomonads and Cl. difficile. It is usually taken as the prodrug trovafloxacin mesylate or alatrofloxacin mesylate for oral or intravenous administration, respectively.","category_aro_class_name":"Antibiotic"},"37009":{"category_aro_accession":"3000665","category_aro_cvterm_id":"37009","category_aro_name":"grepafloxacin","category_aro_description":"Grepafloxacin is a broad-spectrum antibacterial quinoline. It is no longer taken due to its high toxicity.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"37142":{"category_aro_accession":"3000762","category_aro_cvterm_id":"37142","category_aro_name":"pefloxacin","category_aro_description":"Pefloxacin is structurally and functionally similar to norfloxacin. It is poorly active against mycobacteria, while anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2334":{"model_id":"2334","model_name":"ADC-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3627":{"protein_sequence":{"accession":"WP_004714775.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLGAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNRFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_048633.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGGTGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACCGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003847","ARO_id":"40544","ARO_name":"ADC-1","ARO_description":"ADC-1 is a beta-lactamase found in Acinetobacter baumannii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2336":{"model_id":"2336","model_name":"ADC-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3629":{"protein_sequence":{"accession":"WP_063857798.1","sequence":"MRFKKISCLLLSPLFFFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIYANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLSAIKK"},"dna_sequence":{"accession":"NG_048651","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTTTTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACTGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCCTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCTGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCCACCTTACCGGATATGTTGAGTTTTATTTATGCCAACCTTAACCCACAGAAATATCCGGCTGATATTCAAAGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAGCCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAGTGCAATAAAGAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003849","ARO_id":"40547","ARO_name":"ADC-3","ARO_description":"ADC-3 is a beta-lactamase found in Acinetobacter baumannii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2337":{"model_id":"2337","model_name":"ADC-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3630":{"protein_sequence":{"accession":"WP_063857801.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIYANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNRFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_048655.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACTGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCTGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCCACCCTTCCGGATATGTTGAGTTTTATTTATGCCAACCTTAACCCACAGAAATATCCGGCTGATATTCAAAGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACCGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003850","ARO_id":"40548","ARO_name":"ADC-4","ARO_description":"ADC-4 is a beta-lactamase found in Acinetobacter baumannii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2339":{"model_id":"2339","model_name":"ADC-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3632":{"protein_sequence":{"accession":"WP_017725267.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTLFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPAMLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_048669.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTGTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCAACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCGGCAGATATTCAACGTGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAATGTTACAAACTTTACTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACGTATGTGGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCGTATGCAGTTTTAAATGCAATAAAGAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003852","ARO_id":"40551","ARO_name":"ADC-6","ARO_description":"ADC-6 is a beta-lactamase found in Acinetobacter baumannii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2340":{"model_id":"2340","model_name":"ADC-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3633":{"protein_sequence":{"accession":"WP_063857816.1","sequence":"MRFKKISCLLLSPLFIFSTSIYADNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSNTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPTDIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTSGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYVVLNAIKK"},"dna_sequence":{"accession":"NG_048677.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTTTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGACAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCTGTAAATAGCAATACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCTGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCCACCTTACCGGATATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAGCGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGTTGTGCTGAATGCAATAAAGAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003853","ARO_id":"40552","ARO_name":"ADC-7","ARO_description":"ADC-7 is a beta-lactamase that is found in Acinetobacter baumannii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2341":{"model_id":"2341","model_name":"ADC-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"4033":{"protein_sequence":{"accession":"CAL25116.3","sequence":"MMKDILGNLDNVPFKIMTGCIAGLLSCGTVAQSTVQQSIQQSVDRHFKPLMAQYQISGMAIAVSINGQHYYQNYGVASKQTEQNVSEHTLFELGSVSKLFNATLTGYAQAQGQLKLSDHPAQYFPELKNTAVNQATLLNLGTYTAGGFPLQFPEQIKTTQDMTQYFQHWQPKAAPRRIREYSNPSIGLMGYVTALAMKNSYSNLIENTLFPALGMHHSYINVPAAQMSNYAWGYQADQAIRVSPGMFDAEAYGIKSNTADMLKFLDAQINPQNLKPTLRKAIQTTQMGYFRVGQMRQGLGWEQYTYPVSLTTLLAGNSAKMALQPQPVTGISKPITAPQQALLNKTGATNGFSAYVVVIPSQKIGLVMLANRNFPNDARVKAAYATLQQILNADIQK"},"dna_sequence":{"accession":"AM293332.3","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGATGAAAGACATATTAGGTAACTTAGATAACGTGCCATTTAAGATCATGACAGGCTGTATTGCAGGACTATTGTCCTGTGGTACGGTCGCTCAATCGACAGTCCAACAATCAATTCAACAAAGTGTAGATCGACATTTTAAGCCCCTTATGGCTCAGTATCAAATTTCAGGAATGGCGATTGCGGTCAGCATAAATGGGCAACATTACTATCAGAATTATGGCGTAGCATCTAAACAGACCGAGCAAAATGTCTCTGAACATACTCTATTTGAGTTGGGTTCGGTGAGTAAGCTCTTTAATGCAACGCTGACGGGATATGCTCAAGCACAAGGTCAACTTAAGTTGAGTGATCATCCTGCCCAATATTTTCCAGAATTAAAAAATACAGCAGTGAATCAGGCGACTCTCCTGAATCTGGGGACCTATACCGCAGGTGGTTTTCCGCTACAGTTTCCTGAGCAGATCAAGACAACACAAGACATGACTCAGTATTTTCAGCACTGGCAGCCTAAAGCGGCTCCAAGACGTATTCGAGAATATTCAAATCCAAGCATTGGCTTGATGGGCTATGTCACCGCACTTGCGATGAAAAATAGCTATTCAAATCTAATTGAAAATACGTTATTCCCTGCGTTGGGGATGCATCATAGCTATATCAACGTTCCAGCAGCGCAGATGTCAAATTATGCATGGGGATATCAGGCAGATCAGGCGATACGTGTCTCACCAGGTATGTTTGATGCAGAGGCGTATGGCATCAAAAGTAACACTGCCGATATGCTTAAATTTCTAGATGCTCAAATAAATCCCCAAAATCTAAAACCCACGCTCCGAAAGGCCATACAAACCACTCAGATGGGTTATTTTCGGGTGGGACAGATGCGACAGGGCTTGGGTTGGGAGCAATATACTTATCCAGTATCCTTAACAACCTTGCTGGCGGGAAATTCCGCTAAAATGGCTCTACAGCCTCAACCTGTTACAGGCATTTCAAAACCTATCACTGCTCCGCAGCAGGCCCTTTTGAATAAAACTGGTGCAACCAATGGTTTTTCGGCTTATGTGGTGGTTATTCCGAGCCAAAAGATTGGACTGGTGATGCTTGCCAATCGTAATTTTCCCAATGATGCACGGGTGAAAGCAGCTTATGCCACACTACAGCAAATCCTCAATGCAGATATTCAGAAATGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41144","NCBI_taxonomy_name":"Acinetobacter sp. ADP1","NCBI_taxonomy_id":"62977"}}}},"ARO_accession":"3003854","ARO_id":"40553","ARO_name":"ADC-8","ARO_description":"ADC-8 is a beta-lactamase found in Acinetobacter sp.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2338":{"model_id":"2338","model_name":"ADC-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3631":{"protein_sequence":{"accession":"WP_038405930.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLTPQKYPTDIQRAINETHQGFYQVGTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_048660.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTACCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTGATCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGCAACCTCGCTTTACAATTTCCAGATGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTGGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTTGATGCCCCAGCATACGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTACCCCACAGAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTCGGCACCATGTATCAGGCACTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTGGTCTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40550","NCBI_taxonomy_name":"Acinetobacter calcoaceticus\/baumannii complex","NCBI_taxonomy_id":"909768"}}}},"ARO_accession":"3003851","ARO_id":"40549","ARO_name":"ADC-5","ARO_description":"ADC-5 is a beta-lactamase found in Acinetobacter pittii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2342":{"model_id":"2342","model_name":"ADC-12","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3635":{"protein_sequence":{"accession":"WP_063857787.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDREIKKLVDQNFKPLLDKYDVPGMAVGVIQNNKKYETYYGLQSVQDKKSVSSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKEWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPGLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLKFINANLNPQKYPKDTQRAINETHQGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGSYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_048636","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCGAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCTTTATTAGATAAATATGATGTGCCGGGTATGGCCGTGGGCGTTATTCAGAATAATAAAAAATATGAAACGTATTATGGTCTTCAATCTGTTCAAGATAAAAAATCCGTAAGTAGCAGTACCATTTTTGAACTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCAACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGAATGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGGCCTTGGCTTAAAACATAGCTATGTAAATGTACCGAAGACCCAGATGCAAAACTATGCTTTTGGCTATAATCAAGAAAATCAGCCAATTCGTGTTAACCCCGGTCCGCTAGATGCTCCAGCATATGGGGTTAAATCGACGCTACCCGATATGCTTAAGTTTATTAATGCCAACCTCAACCCACAGAAATATCCGAAAGATACTCAACGTGCAATTAATGAAACACATCAAGGTTTCTACCAAGTCGGCACGATGTATCAGGCACTTGGTTGGGAAGAATTTTCTTATCCAGCGCCTTTACAAACTTTATTAGACAGTAATTCAGAGCAAATCGTGATGAAGCCTAATAAAGTGACTGCCATTTCCAAAGAACCTTCAGTTAAGATGTTCCACAAAACTGGCTCAACAAATGGCTTTGGATCTTATGTGGTGTTTATTCCAAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCAGTATTGAATGCAATAAAGAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3003856","ARO_id":"40555","ARO_name":"ADC-12","ARO_description":"ADC-12 is a beta-lactamase found in Acinetobacter pittii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2374":{"model_id":"2374","model_name":"Escherichia coli UhpA with mutation conferring resistance to fosfomycin","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"4362":"G97D"},"clinical":{"4362":"G97D"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"3668":{"protein_sequence":{"accession":"CDJ73205","sequence":"MITVALIDDHLIVRSGFAQLLGLEPDLQVVAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQLPKGMATIMLSVHDSPALVEQALNAGARGFLSKRCSPDELIAAVHTVATGGCYLTPDIAIKLASGRQDPLTKRERQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSNDVELARRMFDGW"},"dna_sequence":{"accession":"HG738867","fmin":"2930707","fmax":"2931298","strand":"+","sequence":"ATGATCACCGTTGCCCTTATAGACGATCACCTCATCGTCCGCTCCGGCTTTGCGCAGCTGCTGGGGCTGGAACCTGATTTGCAGGTAGTTGCCGAGTTTGGTTCGGGGCGCGAGGCGCTGGCGGGGCTGCCGGGGCGCGGTGTGCAGGTGTGTATTTGCGATATCTCCATGCCCGATATCTCCGGTCTGGAGCTGCTAAGCCAGCTGCCGAAAGGTATGGCGACGATTATGCTCTCCGTTCACGACAGTCCTGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCACGCGGCTTTCTTTCCAAACGCTGTAGCCCGGATGAACTCATTGCTGCGGTGCATACGGTTGCCACGGGCGGCTGTTATCTGACGCCGGATATTGCCATTAAACTGGCATCCGGTCGTCAGGACCCGCTAACCAAACGTGAACGCCAGGTGGCGGAAAAACTGGCGCAAGGAATGGCGGTGAAAGAGATTGCCGCCGAACTGGGCTTGTCACCGAAAACGGTACACGTCCATCGCGCCAATCTGATGGAAAAACTGGGCGTCAGTAACGACGTAGAGCTGGCGCGCCGCATGTTTGATGGCTGGTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40589","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MC4100","NCBI_taxonomy_id":"1403831"}}}},"ARO_accession":"3003893","ARO_id":"40595","ARO_name":"Escherichia coli UhpA with mutation conferring resistance to fosfomycin","ARO_description":"uhpA is a positive activator of the fosfomycin importer uhpT, thus mutations to uhpA confer fosfomycin resistance by reducing uhpT expression. Both knockout and amino acid substitution mutations have been found that confer resistance, with the Protein Knockout model describing the large, knockout mutations causing loss of function of the gene, and the Protein Variant model describing the amino acid substitutions.","ARO_category":{"41412":{"category_aro_accession":"3004248","category_aro_cvterm_id":"41412","category_aro_name":"UhpT","category_aro_description":"UhpT encodes a transporter that can import fosfomycin-type drugs into bacterial cells. Mutations to UhpT confer resistance.","category_aro_class_name":"AMR Gene Family"},"41413":{"category_aro_accession":"3004249","category_aro_cvterm_id":"41413","category_aro_name":"UhpA","category_aro_description":"UhpA acts as a positive regulator of UhpT, which is a transporter to bring fosfomycin drugs into bacterial cells. Mutations in UhpA that negatively impact the expression of UhpT can confer resistance.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2376":{"model_id":"2376","model_name":"Escherichia coli UhpA with mutation conferring resistance to fosfomycin","model_type":"protein knockout model","model_type_id":"40354","model_description":"An AMR detection model for instances where the absence of a protein - due to large-scale insertion elements, large deletions, or other methods of protein knockout - confers clinical resistance to a known antibiotic. These models include reference sequences. Protein knockout models are currently in development.","model_sequences":{"sequence":{"3671":{"protein_sequence":{"accession":"CDJ73205","sequence":"MITVALIDDHLIVRSGFAQLLGLEPDLQVVAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQLPKGMATIMLSVHDSPALVEQALNAGARGFLSKRCSPDELIAAVHTVATGGCYLTPDIAIKLASGRQDPLTKRERQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSNDVELARRMFDGW"},"dna_sequence":{"accession":"HG738867","fmin":"2930707","fmax":"2931298","strand":"+","sequence":"ATGATCACCGTTGCCCTTATAGACGATCACCTCATCGTCCGCTCCGGCTTTGCGCAGCTGCTGGGGCTGGAACCTGATTTGCAGGTAGTTGCCGAGTTTGGTTCGGGGCGCGAGGCGCTGGCGGGGCTGCCGGGGCGCGGTGTGCAGGTGTGTATTTGCGATATCTCCATGCCCGATATCTCCGGTCTGGAGCTGCTAAGCCAGCTGCCGAAAGGTATGGCGACGATTATGCTCTCCGTTCACGACAGTCCTGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCACGCGGCTTTCTTTCCAAACGCTGTAGCCCGGATGAACTCATTGCTGCGGTGCATACGGTTGCCACGGGCGGCTGTTATCTGACGCCGGATATTGCCATTAAACTGGCATCCGGTCGTCAGGACCCGCTAACCAAACGTGAACGCCAGGTGGCGGAAAAACTGGCGCAAGGAATGGCGGTGAAAGAGATTGCCGCCGAACTGGGCTTGTCACCGAAAACGGTACACGTCCATCGCGCCAATCTGATGGAAAAACTGGGCGTCAGTAACGACGTAGAGCTGGCGCGCCGCATGTTTGATGGCTGGTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40589","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MC4100","NCBI_taxonomy_id":"1403831"}}}},"ARO_accession":"3003893","ARO_id":"40595","ARO_name":"Escherichia coli UhpA with mutation conferring resistance to fosfomycin","ARO_description":"uhpA is a positive activator of the fosfomycin importer uhpT, thus mutations to uhpA confer fosfomycin resistance by reducing uhpT expression. Both knockout and amino acid substitution mutations have been found that confer resistance, with the Protein Knockout model describing the large, knockout mutations causing loss of function of the gene, and the Protein Variant model describing the amino acid substitutions.","ARO_category":{"41412":{"category_aro_accession":"3004248","category_aro_cvterm_id":"41412","category_aro_name":"UhpT","category_aro_description":"UhpT encodes a transporter that can import fosfomycin-type drugs into bacterial cells. Mutations to UhpT confer resistance.","category_aro_class_name":"AMR Gene Family"},"41413":{"category_aro_accession":"3004249","category_aro_cvterm_id":"41413","category_aro_name":"UhpA","category_aro_description":"UhpA acts as a positive regulator of UhpT, which is a transporter to bring fosfomycin drugs into bacterial cells. Mutations in UhpA that negatively impact the expression of UhpT can confer resistance.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2383":{"model_id":"2383","model_name":"ANT(4')-Ib","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"3702":{"protein_sequence":{"accession":"YP_006938491.1","sequence":"MNGPIIMTREERMKIVHEIKERILDKYGDDVKAIGVYGSLGRQTDGPYSDIEMMCVMSTEEAEFSHEWTTGEWKVEVNFDSEEILLDYASQVESDWPLTHGQFFSILPIYDSGGYLEKVYQTAKSVEAQTFHDAICALIVEELFEYAGKWRNIRVQGPTTFLPSLTVQVAMAGAMLIGLHHRICYTTSASVLTEAVKQSDLPSGYDHLCQFVMSGQLSDSEKLLESLENFWNGIQEWTERHGYIVDVSKRIPF"},"dna_sequence":{"accession":"NC_013342.1","fmin":"26737","fmax":"27499","strand":"-","sequence":"TCAAAATGGTATGCGTTTTGACACATCCACTATATATCCGTGTCGTTCTGTCCACTCCTGAATCCCATTCCAGAAATTCTCTAGCGATTCCAGAAGTTTCTCAGAGTCGGAAAGTTGACCAGACATTACGAACTGGCACAGATGGTCATAACCTGAAGGAAGATCTGATTGCTTAACTGCTTCAGTTAAGACCGAAGCGCTCGTCGTATAACAGATGCGATGATGCAGACCAATCAACATGGCACCTGCCATTGCTACCTGTACAGTCAAGGATGGTAGAAATGTTGTCGGTCCTTGCACACGAATATTACGCCATTTGCCTGCATATTCAAACAGCTCTTCTACGATAAGGGCACAAATCGCATCGTGGAACGTTTGGGCTTCTACCGATTTAGCAGTTTGATACACTTTCTCTAAGTATCCACCTGAATCATAAATCGGCAAAATAGAGAAAAATTGACCATGTGTAAGCGGCCAATCTGATTCCACCTGAGATGCATAATCTAGTAGAATCTCTTCGCTATCAAAATTCACTTCCACCTTCCACTCACCGGTTGTCCATTCATGGCTGAACTCTGCTTCCTCTGTTGACATGACACACATCATCTCAATATCCGAATAGGGCCCATCAGTCTGACGACCAAGAGAGCCATAAACACCAATAGCCTTAACATCATCCCCATATTTATCCAATATTCGTTCCTTAATTTCATGAACAATCTTCATTCTTTCTTCTCTAGTCATTATTATTGGTCCATTCAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3003905","ARO_id":"40608","ARO_name":"ANT(4')-Ib","ARO_description":"Kanamycin nucleotidyltransferase sequence from Staphylococcus aureus plasmid. Confers resistance to kanamycin, neomycin and other aminoglycosides","ARO_category":{"36368":{"category_aro_accession":"3000229","category_aro_cvterm_id":"36368","category_aro_name":"ANT(4')","category_aro_description":"Nucleotidylylation of 2-deoxystreptamine aminoglycosides at the hydroxyl group at position 4'","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2404":{"model_id":"2404","model_name":"Neisseria gonorrhoeae gyrA conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"4449":"S91F","4450":"D95G","4451":"D95N"},"clinical":{"4449":"S91F","4450":"D95G","4451":"D95N"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1500"}},"model_sequences":{"sequence":{"3730":{"protein_sequence":{"accession":"YP_207769.1","sequence":"MTDATIRHDHKFALETLPVSLEDEMRKSYLDYAMSVIVGRALPDVRDGLKPVHRRVLYAMHELKNNWNAAYKKSARIVGDVIGKYHPHGDSAVYDTIVRMAQNFAMRYVLIDGQGNFGSVDGLAAAAMRYTEIRMAKISHEMLADIEEETVNFGPNYDGSEHEPLVLPTRFPTLLVNGSSGIAVGMATNIPPHNLTDTINACLRLLDEPKTEIDELIDIIQAPDFPTGATIYGLGGVREGYKTGRGRVVIRGKTHIEPIGKNGEREAIVIDEIPYQVNKAKLVEKIGDLVREKTLEGISELRDESDKSGMRVVIELKRNENAEVVLNQLYKLTPLQDSFGINMVVLVDGQPRLLNLKQILSEFLRHRREVVTRRTLFRLKKARHEGHIAEGKAVALSNIDEIIKLIKESPNAAEAKEKLLARPWRSSLVEEMLTRSGLDLEMMRPEGLAANIGLKKQGYYLSEIQADAILRMSLRNLTGLDQKEIIESYKNLMGKIIDFVDILSKPERITQIIRDELEEIKTNYGDERRSEINPFGGDIADEDLIPQREMVVTLTHGGYIKTQPTTDYQAQRRGGRGKQAAATKDEDFIETLFVANTHDYLMCFTNLGKCHWIKVYKLPEGGRNSRGRPINNVIQLEEGEKVSAILAVREFPEDQYVFFATAQGMVKKVQLSAFKNVRAQGIKAIALKEGDYLVGAAQTGGADDIMLFSNLGKAIRFNEYWEKSGNDEAEDADIETEISDDLEDETADNENTLPSGKNGVRPSGRGSGGLRGMRLPADGKIVSLITFAPETEESGLQVLTATANGYGKRTPIADYSRKNKGGQGSIAINTGERNGDLVAATLVGETDDLMLITSGGVLIRTKVEQIRETGRAAAGVKLINLDEGETLVSLERVAEDESELSGASVISNVTEPEAEN"},"dna_sequence":{"accession":"NC_002946.2","fmin":"618438","fmax":"621189","strand":"-","sequence":"TCAGTTCTCGGCTTCCGGTTCGGTTACATTGGAAATTACAGAAGCGCCGGAGAGTTCGGATTCGTCTTCGGCAACACGTTCCAGCGATACCAAGGTTTCGCCTTCGTCCAAGTTAATCAGTTTCACGCCTGCTGCGGCGCGGCCGGTTTCGCGGATTTGTTCGACTTTGGTACGGATAAGCACGCCGCCGCTGGTAATCAGCATCAAATCGTCGGTTTCGCCGACCAAGGTTGCGGCGACCAAATCGCCGTTGCGCTCGCCGGTGTTAATGGCAATACTGCCTTGCCCGCCTTTGTTTTTGCGGCTGTAATCGGCAATCGGGGTGCGTTTTCCGTATCCGTTGGCGGTGGCGGTTAAAACTTGCAAACCGCTTTCTTCGGTTTCAGGGGCGAAGGTAATCAGGCTGACGATTTTGCCGTCGGCAGGCAGGCGCATACCGCGCAAACCGCCGCTGCCGCGACCGGACGGACGCACGCCGTTTTTGCCGCTTGGCAGGGTGTTTTCGTTGTCGGCGGTTTCGTCTTCGAGGTCGTCTGAAATCTCGGTTTCGATGTCGGCATCTTCCGCTTCGTCGTTGCCGGATTTTTCCCAGTATTCGTTGAAGCGGATGGCTTTGCCCAAGTTGGAGAACAACATAATGTCGTCCGCACCGCCTGTTTGCGCAGCGCCGACGAGGTAGTCGCCTTCTTTGAGTGCGATGGCTTTAATGCCTTGGGCGCGGACGTTTTTAAAGGCGGAAAGTTGGACTTTTTTCACCATTCCCTGCGCGGTGGCGAAGAAGACGTATTGGTCTTCGGGAAACTCGCGTACTGCCAGAATCGCGCTGACTTTTTCGCCTTCTTCCAGCTGGATGACGTTGTTAATCGGACGGCCGCGGCTGTTGCGTCCGCCTTCGGGCAGTTTGTAAACCTTAATCCAGTGGCACTTGCCGAGGTTGGTAAAACACATCAAATAGTCATGCGTGTTGGCAACAAACAGGGTTTCGATAAAGTCTTCGTCTTTGGTGGCAGCCGCCTGTTTGCCGCGCCCGCCGCGACGCTGAGCCTGATAGTCGGTGGTCGGCTGGGTTTTTATATAGCCGCCGTGGGTCAGGGTCACGACCATTTCGCGTTGCGGAATCAGGTCTTCATCGGCAATGTCGCCGCCGAACGGGTTGATTTCGCTGCGGCGTTCGTCGCCATAGTTGGTTTTGATTTCTTCCAGTTCGTCACGGATGATTTGGGTAATGCGTTCGGGTTTGGAGAGGATATCCACAAAGTCGATGATTTTACCCATCAGGTTTTTGTAGCTTTCGATAATTTCTTTCTGATCGAGGCCGGTCAGGTTTCGCAGGCTCATGCGTAAAATAGCATCTGCCTGAATCTCGCTCAGGTAATAACCTTGTTTTTTCAGACCAATGTTTGCAGCCAATCCTTCCGGACGCATCATTTCCAAATCCAGACCGGAACGCGTCAGCATTTCTTCAACGAGGCTGCTGCGCCAAGGGCGCGCAAGCAGTTTTTCTTTGGCCTCGGCCGCGTTGGGCGATTCTTTGATGAGCTTGATGATTTCATCGATATTGGACAGTGCGACGGCTTTGCCTTCGGCGATATGCCCTTCATGGCGTGCCTTCTTCAGCCGGAAAAGCGTACGTCGGGTAACGACTTCGCGGCGGTGGCGCAGGAATTCGGAGAGAATCTGTTTCAGGTTTAACAGGCGCGGTTGTCCGTCGACCAAAACAACCATATTGATGCCGAAACTGTCTTGCAGCGGAGTCAGTTTGTAGAGTTGGTTTAAGACGACTTCGGCATTTTCGTTGCGTTTCAGCTCGATAACGACGCGCATCCCGGATTTGTCGGATTCGTCGCGGAGCTCGGAAATGCCTTCCAGCGTTTTTTCCCGAACCAAATCGCCGATTTTCTCGACCAACTTGGCTTTGTTGACCTGATAGGGGATTTCGTCGATAACGATGGCTTCGCGTTCGCCGTTTTTGCCTATGGGTTCGATATGGGTCTTACCGCGTATAACGACGCGGCCGCGGCCTGTTTTATAGCCTTCGCGCACGCCGCCCAAGCCGTAGATGGTTGCCCCGGTCGGGAAGTCGGGGGCTTGGATAATGTCGATCAGTTCGTCGATTTCGGTTTTGGGTTCGTCCAAAAGACGCAGACAGGCGTTGATGGTGTCGGTGAGGTTGTGCGGCGGGATGTTGGTCGCCATACCGACGGCGATACCGGACGAGCCGTTGACGAGCAGTGTGGGGAAACGGGTCGGCAGTACAAGCGGCTCGTGTTCGCTACCGTCGTAGTTCGGGCCGAAATTAACGGTTTCTTCCTCAATGTCTGCCAGCATTTCATGTGAGATTTTCGCCATGCGGATTTCGGTATAGCGCATGGCTGCGGCGGCAAGCCCGTCCACCGATCCGAAGTTGCCCTGTCCGTCTATCAGCACATAACGCATAGCGAAATTTTGCGCCATACGGACGATGGTGTCGTAAACTGCGGAATCGCCGTGGGGGTGGTATTTACCGATGACGTCGCCGACGATGCGCGCCGATTTTTTGTAGGCGGCATTCCAGTTATTTTTCAGCTCGTGCATCGCGTACAGTACGCGCCGGTGCACCGGCTTTAGGCCGTCGCGAACGTCCGGCAGCGCGCGCCCGACAATGACGCTCATGGCGTAGTCGAGATAGCTTTTGCGCATTTCGTCTTCAAGGCTGACGGGCAGGGTTTCGAGGGCGAATTTGTGGTCGTGGCGGATGGTTGCGTCGGTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40638","NCBI_taxonomy_name":"Neisseria gonorrhoeae FA 1090","NCBI_taxonomy_id":"242231"}}}},"ARO_accession":"3003928","ARO_id":"40637","ARO_name":"Neisseria gonorrhoeae gyrA conferring resistance to fluoroquinolones","ARO_description":"Point mutation in Neisseria gonorrhoeae DNA gyrase subunit A. Decreases affinity between fluoroquinolone antibiotic molecule and gyrA, thereby conferring resistance to fluoroquinolone","ARO_category":{"39876":{"category_aro_accession":"3003292","category_aro_cvterm_id":"39876","category_aro_name":"fluoroquinolone resistant gyrA","category_aro_description":"DNA gyrase is responsible for DNA supercoiling and consists of two alpha and two beta subunits. GyrA point mutations confer resistance by preventing fluoroquinolone antibiotics from binding the alpha-subunit.","category_aro_class_name":"AMR Gene Family"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"40463":{"category_aro_accession":"3003780","category_aro_cvterm_id":"40463","category_aro_name":"nybomycin","category_aro_description":"A  heterocyclic antibiotic that targets mutant gyrA (type II topoisomerase) containing an S84L substitution, counteracting acquired quinolone resistance. It is effective against quinolone-resistant Gram-positive bacteria including S. aureus and E. faecalis. Due to its ability to counteract quinolone resistance by targeting the mutant form of the gyrA protein, it is classified as a reverse antibiotic (RA).","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2387":{"model_id":"2387","model_name":"Erm(47)","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"3705":{"protein_sequence":{"accession":"ANZ79476.1","sequence":"MNRKSVRFGQNFVTSINDINKICKKIDVNSNDVYFEIGPGKGHFTQYFVERAKEVIAIEIDSELIPILNNKFSDLDNIKIINHDFMSYELPSTFKYKVFGNIPFNLSTSIIRKLSLEKYADEIYLIVELGFAKRLEDLNRKMGLMLAPFYEISILYNIPKRYFHPIPSVEVVLIKLKRTSYNMSMKEYIKYEDFIEKWVKKDYNVLFTKNQLKQAIRYGNIDNLRILKVDQILSIFESYKLFNGLK"},"dna_sequence":{"accession":"KU612222.1","fmin":"80337","fmax":"81078","strand":"+","sequence":"ATGAACAGAAAAAGTGTTAGATTTGGACAAAATTTTGTAACTTCTATTAATGATATAAACAAAATATGTAAGAAGATAGACGTGAATTCTAATGATGTTTATTTTGAAATTGGTCCAGGTAAAGGGCATTTTACTCAATACTTTGTGGAAAGGGCTAAAGAGGTAATTGCTATTGAAATAGACAGTGAATTAATTCCTATATTAAACAACAAATTTTCAGATCTAGATAATATAAAAATTATTAATCATGACTTTATGTCTTATGAATTACCATCTACATTTAAGTATAAAGTTTTTGGAAATATTCCATTTAATTTGAGTACTTCTATTATTCGTAAACTTAGTTTAGAAAAATATGCAGATGAGATTTACTTAATAGTGGAATTAGGGTTTGCAAAAAGATTAGAAGACTTAAACCGTAAAATGGGACTAATGTTAGCTCCATTTTATGAAATTTCAATTTTATACAATATTCCAAAAAGATATTTTCATCCCATACCCAGTGTTGAGGTAGTGCTGATAAAACTAAAAAGAACTTCCTATAATATGTCCATGAAAGAATATATAAAGTATGAAGACTTTATAGAAAAATGGGTAAAAAAGGATTATAATGTTTTATTTACAAAAAATCAGCTAAAACAAGCAATCAGATATGGAAATATTGATAATTTAAGAATCCTAAAAGTTGATCAAATTCTATCCATATTTGAAAGTTACAAATTATTTAATGGGTTAAAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40615","NCBI_taxonomy_name":"Helcococcus kunzii","NCBI_taxonomy_id":"40091"}}}},"ARO_accession":"3003908","ARO_id":"40614","ARO_name":"Erm(47)","ARO_description":"Chromosome-encoded gene conferring MLSB resistance. Identified from Helcococcus kunzii.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"639":{"model_id":"639","model_name":"AAC(3)-IV","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"3715":{"protein_sequence":{"accession":"ABB43029.1","sequence":"MQYEWRKAELIGQLLNLGVTPGGVLLVHSSFRSVRPLEDGPLGLIEALRAALGPGGTLVMPSWSGLDDEPFDPATSPVTPDLGVVSDTFWRLPNVKRSAHPFAFAAAGPQAEQIISDPLPLPPHSPASPVARVHELDGQVLLLGVGHDANTTLHLAELMAKVPYGVPRHCTILQDGKLVRVDYLENDHCCERFALADRWLKEKSLQKEGPVGHAFARLIRSRDIVATALGQLGRDPLIFLHPPEAGCEECDAARQSIG"},"dna_sequence":{"accession":"DQ241380.1","fmin":"0","fmax":"777","strand":"+","sequence":"GTGCAATACGAATGGCGAAAAGCCGAGCTCATCGGTCAGCTTCTCAACCTTGGGGTTACCCCCGGCGGTGTGCTGCTGGTCCACAGCTCCTTCCGTAGCGTCCGGCCCCTCGAAGATGGGCCACTTGGACTGATCGAGGCCCTGCGTGCTGCGCTGGGTCCGGGAGGGACGCTCGTCATGCCCTCGTGGTCAGGTCTGGACGACGAGCCGTTCGATCCTGCCACGTCGCCCGTTACACCGGACCTTGGAGTTGTCTCTGACACATTCTGGCGCCTGCCAAATGTAAAGCGCAGCGCCCATCCATTTGCCTTTGCGGCAGCGGGGCCACAGGCAGAGCAGATCATCTCTGATCCATTGCCCCTGCCACCTCACTCGCCTGCAAGCCCGGTCGCCCGTGTCCATGAACTCGATGGGCAGGTACTTCTCCTCGGCGTGGGACACGATGCCAACACGACGCTGCATCTTGCCGAGTTGATGGCAAAGGTTCCCTATGGGGTGCCGAGACACTGCACCATTCTTCAGGATGGCAAGTTGGTACGCGTCGATTATCTCGAGAATGACCACTGCTGTGAGCGCTTTGCCTTGGCGGACAGGTGGCTCAAGGAGAAGAGCCTTCAGAAGGAAGGTCCAGTCGGTCATGCCTTTGCTCGGTTGATCCGCTCCCGCGACATTGTGGCGACAGCCCTGGGTCAACTGGGCCGAGATCCGTTGATCTTCCTGCATCCGCCAGAGGCGGGATGCGAAGAATGCGATGCCGCTCGCCAGTCGATTGGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002539","ARO_id":"38939","ARO_name":"AAC(3)-IV","ARO_description":"AAC(3)-IV is a plasmid-encoded aminoglycoside acetyltransferase in E. coli, C. jejuni and P. stutzeri","ARO_category":{"36461":{"category_aro_accession":"3000322","category_aro_cvterm_id":"36461","category_aro_name":"AAC(3)","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 3.","category_aro_class_name":"AMR Gene Family"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2396":{"model_id":"2396","model_name":"OXA-368","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"3721":{"protein_sequence":{"accession":"AMB19637.1","sequence":"MKTFAAYVIIACLSSTALAGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPVSTFKIPSAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGDIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG"},"dna_sequence":{"accession":"KT736121.1","fmin":"0","fmax":"2721","strand":"+","sequence":"TCAGCCGGGCGACAAGTGCAAGGCCAAGGCGTCCAGCGGGCTGGAGGTGCCTCCGGCAGCGACTTTCAGCACATGCGTGTAGATCATCGTCGTGCTCACGTCCGAATGCCCCAACAACTCTTGCACCGTTCGGATGTCTGTGCCTGCTTGCAGCAAGTGGGTGGCGAATGAGTGGCGCAGGGTGTGGACAGATACGTGTTTGGCAATGCCAGCCTGAACTACCGCTTTTTTTAGTTGCCGGTTCAGTCTTTCCTCAAACAAGTGGTGGCGGCGCTCAACGCCGGTTTGTGGGTCCACAGACAGCTTGGCCGATGGAAACACCCAGAACCAGGCCCAGCTCTCGCCCGCCCTGGGGTACTTGCGCTCCAGTGCATGAGGCAGATACACGCCTCCGCGCCCCGTGGCACGGTCCTGCCCCCACACAGCGCGGACCTGAATCAGCTGCGCCCGCAACCGAGGTACGAGCGCCCTGGGCAGCATCACCACGCGGTCCTTGTCGCCCTTGCCGCTGCGCACAATGATCGCGTGGCGGTCGAAATCCACATCCTTGACCCGCAGGCCCAGCGCTTCGCGCAGGCGCAACCCACTGCCGTAAAGCAGGGCGGCCAACAGCGCTTCGGTGCCCGCCATGTGCGAAAGCAACGTCTGAACCTCCTGCACCGTCAGCACCACCGGAATCCGCTTGCGTTCTGGCGGCCGACCAATCTGCTGCATCCACGGCAATTCCATGCCCAGCACCTGCCGATACAAGAACAACAGCGCGTTGAGCGCCTGCCGGTGGGTGGCCGGCGCCACTTGCTTCTCGGTGGCGAGCATGGTCAGAAAACCCTCGACTTCAGCTTGCCCCATTTCGCGCGGATGTCGAAACCCACCATGGCTGCGGGCCGTCCACAACACAAATGCCTTGGCCCAGTAGACATAAGCTTTCTCGGTCTGTAGGCTGTAATGCAGGTAGCGAACCCGTTCGCGCACCTGATCGAGCAGCTTGATGGATCGGGGAGGGAACCAGTCAGGTTTGTCATTTCTGTTATACCTGTTCATGCATCCGGTATGATGCTTTACAGAATTGATTTCAAACACTTTTTTTGGGTGCCGTGCGACATTGTTTAACGACCACGGTTGTGGGTATCCGGTGTTTGGTCAGATAAACCATAAGTTAGCCACCAAGAAGGTGCCATGAAAACATTTGCCGCATATGTAATTATCGCGTGTCTTTCGAGTACGGCATTAGCTGGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTCTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATGACTTAGCTCGTGCATCAAAGGAATATCTTCCAGTATCAACATTTAAGATCCCCAGCGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAGCAATGGGAAAGAGACTTGACCTTAAGAGGGGCAATACAAGTTTCAGCTGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCCTATGGCAACCAGAATATCAGTGGTGACATTGACAAATTCTGGTTGGAAGGCCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATATTTAAATAAATTGTCAGCATCTAAAGAAAACCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCGGCACCTGAATATCTAGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGGTGGGTTGAGAAGGAGACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAGTAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGAAAGTGAGGGCATCATTGGTGGCTAACAAGTCGCTCAAGGTCGCTCCCTGCGGTCGCTGGACAGTCCCAGTCGGCGCATGCTTCGCATTTTATGCGCCGCCTGTGCCTGCCCCTTAGCTCCAACGTTAGGCATCACAAAGTACAGCATCGTGACCAACAGCAACGATTCCGTCACACTGCGCCTCATGACTGAGCATGACCTTGCGATGCTCTATGAGTGGCTAAATCGATCTCATATCGTCGAGTGGTGGGGCGGAGAAGAAGCACGCCCGACACTTGCTGACGTACAGGAACAGTACTTGCCAAGCGTTTTAGCGCAAGAGTCCGTCACTCCATACATTGCAATGCTGAATGGAGAGCCGATTGGGTATGCCCAGTCGTACGTTGCTCTTGGAAGCGGGGACGGATGGTGGGAAGAAGAAACCGATCCAGGAGTACGCGGAATAGACCAGTCACTGGCGAATGCATCACAACTGGGCAAAGGCTTGGGAACCAAGCTGGTTCGAGCTCTGGTTGAGTTGCTGTTCAATGATCCCGAGGTCACCAAGATCCAAACGGACCCGTCGCCGAGCAACTTGCGAGCGATCCGATGCTACGAGAAAGCGGGGTTTGAGAGGCAAGGTACCGTAACCACCCCAGATGGTCCAGCCGTGTACATGGTTCAAACACGCCAGGCATTCGAGCGAACACGCAGTGTTGCCTAACCCTTCCATCGAGGGGGACGTCCAAGGGCTGGCGCCCTTGGCCGCCCCTCATGTCAAACGTTGAGC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36957","NCBI_taxonomy_name":"Aeromonas sobria","NCBI_taxonomy_id":"646"}}}},"ARO_accession":"3001555","ARO_id":"37955","ARO_name":"OXA-368","ARO_description":"OXA-368 is a beta-lactamase found in Aeromonas sobria. From the Lahey list of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2398":{"model_id":"2398","model_name":"TEM-220","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"3723":{"protein_sequence":{"accession":"AIW68620.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTTPATMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"KM998962.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGCAACAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36806","NCBI_taxonomy_name":"Neisseria gonorrhoeae","NCBI_taxonomy_id":"485"}}}},"ARO_accession":"3003158","ARO_id":"39735","ARO_name":"TEM-220","ARO_description":"From the Lahey list of beta-lactamases.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2399":{"model_id":"2399","model_name":"oqxA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"670"}},"model_sequences":{"sequence":{"3725":{"protein_sequence":{"accession":"YP_001693237.1","sequence":"MSLQKTWGNIHLTALGAMMLSFLLVGCDDSVAQNAAPPAPTVSAAKVLVKSISQWDSFNGRIEAVESVQLRPRVSGYIDKVNYTDGQEVKKGQVLFTIDDRTYRAALEQAQAALARAKTQASLAQSEANRTDKLVHTNLVSREEWEQRRSAAVQAQADIRAAQAAVDAAQLNLDFTKVTAPIDGRASRALITSGNLVTAGDTASVLTTLVSQKTVYVYFDVDESTYLHYQNLARRGQGASSDNQALPVEIGLVGEEGYPHQGKVDFLDNQLTPSTGTIRMRALLDNSQRLFTPGLFARVRLPGSAEFKATLIDDKAVLTDQDRKYVYIVDKDGKAQRRDITPGRLADGLRIVQKGLNPGDSVIVDGLQKVFMPGMPVNAKTVAMTSSATLN"},"dna_sequence":{"accession":"NC_010378.1","fmin":"46651","fmax":"47827","strand":"+","sequence":"ATGAGCCTGCAAAAAACCTGGGGAAACATTCACCTGACCGCGCTCGGCGCGATGATGCTCTCCTTTCTGCTCGTCGGCTGCGACGACAGCGTCGCACAGAATGCTGCGCCTCCCGCCCCGACGGTCAGCGCCGCTAAGGTGCTGGTGAAGTCGATCAGTCAGTGGGATAGTTTTAACGGTCGCATTGAAGCGGTGGAGAGCGTTCAGCTTCGCCCTCGCGTCTCGGGATACATTGATAAAGTGAATTACACTGACGGCCAGGAGGTGAAAAAGGGCCAGGTGCTGTTCACGATAGATGACAGAACCTATCGCGCCGCGCTGGAGCAGGCGCAGGCGGCGTTGGCAAGAGCCAAAACGCAGGCCAGCCTCGCGCAAAGCGAGGCGAACCGCACCGATAAATTAGTCCATACCAACCTCGTCTCCCGTGAAGAGTGGGAGCAGCGCCGGTCAGCCGCGGTTCAGGCGCAGGCCGACATTCGCGCCGCGCAGGCGGCGGTGGATGCCGCGCAGCTTAACCTCGACTTCACCAAAGTGACCGCCCCTATTGACGGCCGCGCCAGCCGGGCGCTGATCACCAGCGGTAACCTGGTCACCGCGGGCGACACCGCCAGCGTGCTCACCACCCTGGTCTCGCAAAAGACGGTGTACGTCTACTTTGACGTCGACGAGTCAACCTACCTCCACTATCAAAACCTCGCCCGCCGCGGGCAAGGCGCGTCCAGCGATAATCAGGCGCTCCCGGTGGAGATTGGCCTGGTGGGCGAGGAGGGTTACCCCCACCAGGGCAAAGTGGATTTTCTCGATAATCAGTTAACGCCGAGTACCGGCACCATCCGCATGCGTGCGCTGCTGGATAACTCGCAGCGTCTGTTCACGCCGGGGCTGTTTGCCCGCGTGCGTCTGCCGGGCAGCGCAGAGTTCAAAGCCACGCTGATCGACGACAAAGCGGTACTGACCGATCAGGATCGTAAATACGTCTATATCGTTGATAAAGATGGTAAAGCACAGCGCCGCGACATTACCCCAGGGCGGCTGGCAGACGGTTTACGCATCGTTCAGAAGGGGTTGAATCCTGGGGATAGCGTCATCGTCGACGGCTTACAAAAAGTGTTTATGCCGGGTATGCCGGTTAACGCCAAAACCGTTGCCATGACCTCCAGCGCCACCCTTAACTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3003922","ARO_id":"40631","ARO_name":"oqxA","ARO_description":"RND efflux pump conferring resistance to fluoroquinolone","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35992":{"category_aro_accession":"0000075","category_aro_cvterm_id":"35992","category_aro_name":"nitrofurantoin","category_aro_description":"Nitrofurantoin is an antibiotic used to treat urinary tract infections. It inhibits enzyme synthesis by inhibiting essential enzymes involved in the citric acid cycle, as well as those involved in DNA, RNA, and protein synthesis. It is marketed under the following brand names: Furadantin, Macrobid, Macrodantin, Nitro Macro and Urantoin.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"41240":{"category_aro_accession":"3004116","category_aro_cvterm_id":"41240","category_aro_name":"nitrofuran antibiotic","category_aro_description":"Nitrofurans are chemotherapeutic agents with antibacterial and antiprotozoal activity.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2400":{"model_id":"2400","model_name":"oqxB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"2000"}},"model_sequences":{"sequence":{"3726":{"protein_sequence":{"accession":"YP_001693238","sequence":"MDFSRFFIDRPIFAAVLSILIFITGLIAIPLLPVSEYPDVVPPSVQVRAEYPGANPKVIAETVATPLEEAINGVENMMYMKSVAGSDGVLVTTVTFRPGTDPDQAQVQVQNRVAQAEARLPEDVRRLGITTQKQSPTLTLVVHLFSPGGKYDSLYMRNYATLKVKDELARLPGVGQIQIFGSGEYAMRVWLDPNKVAARGLTASDVVTAMQEQNVQVSAGQLGAEPLPQESDFLISINAQGRLHTEEEFGNIILKTAQDGSLVRLRDVARIEMGSGSYALRSQLNNKDAVGIGIFQSPGANAIDLSNAVRAKMAELATRFPEDMQWAAPYDPTVFVRDSIRAVVQTLLEAVVLVVLVVILFLQTWRASIIPLIAVPVSVVGTFSILYLLGFSLNTLSLFGLVLAIGIVVDDAIVVVENVERNIEEGLAPLAAAHQAMREVSGPIIAIALVLCAVFVPMAFLSGVTGQFYKQFAVTIAISTVISAINSLTLSPALAALLLKPHGAKKDLPTRLIDRLFGWIFRPFNRFFLRSSNGYQGLVGKTLGRRGAVFAVYLLLLCAAGVMFKVVPGGFIPTQDKLYLIGGVKMPEGSSLARTDAVIRKMSEIGMNTEGVDYAVAFPGLNALQFTNTPNTGTVFFGLKPFDQRKHTAAEINAEINAKIAQIQQGFGFSILPPPILGLGQGSGYSLYIQDRGGLGYGALQSAVNAMSGAIMQTPGMHFPISTYQANVPQLDVQVDRDKAKAQGVSLTDLFGTLQTYLGSSYVNDFNQFGRTWRVMAQADGPYRESVEDIANLRTRNNQGEMVPIGSMVNISTTYGPDPVIRYNGYPAADLIGDADPRVLSSSQAMTHLEELSKQILPNGMNIEWTDLSFQQATQGNTALIVFPVAVLLAFLVLAALYESWTLPLAVILIVPMTMLSALFGVWLTGGDNNVFVQVGLVVLMGLACKNAILIVEFARELEIQGKGIMEAALEACRLRLRPIVMTSIAFIAGTIPLILGHGAGAEVRGVTGITVFSGMLGVTLFGLFLTPVFYVTLRKLVTRRKPVQEDLPA"},"dna_sequence":{"accession":"NC_010378.1","fmin":"47850","fmax":"51003","strand":"+","sequence":"ATGGACTTTTCCCGCTTTTTTATCGACAGGCCGATTTTCGCCGCGGTGCTGTCGATTTTAATTTTTATCACCGGGTTAATCGCTATCCCACTGCTGCCGGTGAGCGAATATCCGGATGTCGTCCCGCCGAGCGTCCAGGTGCGCGCGGAGTATCCCGGCGCCAACCCGAAAGTGATTGCCGAGACCGTGGCGACGCCGCTGGAGGAAGCGATCAACGGCGTTGAAAACATGATGTACATGAAATCGGTCGCCGGCTCCGACGGCGTGCTGGTCACCACCGTCACCTTCCGCCCGGGTACCGACCCGGATCAGGCGCAGGTTCAGGTGCAGAACCGCGTCGCGCAGGCCGAAGCGCGTCTGCCGGAGGATGTACGCCGTCTGGGGATCACCACCCAGAAGCAGTCTCCGACGCTGACCCTGGTGGTGCATCTGTTCTCCCCCGGCGGGAAGTACGACTCGCTGTATATGCGCAACTACGCCACGCTGAAAGTGAAGGATGAGCTGGCGCGCCTGCCCGGCGTCGGCCAGATCCAGATTTTTGGCTCCGGTGAATATGCGATGCGCGTCTGGCTGGATCCCAATAAGGTCGCTGCCCGCGGTCTGACGGCCTCGGATGTGGTGACGGCGATGCAGGAGCAAAACGTCCAGGTGTCTGCCGGACAGCTTGGCGCCGAGCCGCTGCCGCAGGAGAGCGATTTCCTGATCTCCATTAACGCCCAGGGCCGTCTGCATACCGAAGAAGAGTTTGGCAATATCATTCTGAAAACGGCGCAGGATGGCTCGCTGGTCCGCCTGCGCGACGTGGCGCGCATCGAGATGGGTTCCGGTAGCTATGCGCTGCGCTCCCAGCTCAACAATAAGGATGCGGTCGGGATCGGTATCTTCCAGTCACCCGGCGCTAACGCCATCGATCTGTCGAACGCGGTACGCGCCAAAATGGCCGAGCTGGCCACCCGCTTCCCGGAAGATATGCAATGGGCGGCGCCGTACGACCCGACGGTTTTCGTCCGCGACTCCATCCGCGCGGTGGTGCAGACGCTGCTGGAGGCGGTAGTGCTGGTGGTGCTGGTAGTGATCCTGTTCCTGCAGACCTGGCGCGCGTCGATTATCCCGTTGATCGCTGTGCCGGTATCGGTGGTGGGTACCTTCAGCATTCTCTATCTGCTGGGCTTCTCGCTGAATACCCTGAGCCTGTTCGGGCTGGTACTGGCTATCGGTATCGTGGTGGACGACGCCATCGTGGTGGTGGAGAACGTCGAGCGTAATATCGAAGAGGGGCTTGCGCCGCTTGCCGCGGCGCATCAGGCGATGCGTGAGGTCTCCGGGCCGATTATCGCCATTGCGCTGGTGCTGTGTGCGGTGTTCGTGCCGATGGCGTTTCTCTCCGGGGTCACCGGCCAGTTCTACAAACAGTTCGCGGTGACCATCGCCATCTCGACGGTGATCTCGGCCATCAACTCGCTGACGCTCTCCCCGGCGCTGGCGGCCCTGCTGTTAAAGCCGCACGGCGCGAAGAAAGACCTCCCTACCCGGCTGATCGATCGCCTGTTTGGCTGGATTTTCCGTCCGTTTAACCGCTTTTTCCTGCGCAGCTCGAACGGCTATCAGGGACTGGTAGGCAAAACGCTTGGACGCCGTGGCGCAGTGTTTGCGGTGTACCTGCTGCTGCTCTGCGCCGCTGGGGTGATGTTTAAAGTCGTCCCCGGCGGGTTTATTCCCACCCAGGATAAGCTGTATCTCATTGGCGGCGTGAAGATGCCGGAAGGGTCGTCGCTGGCGCGCACCGACGCGGTGATCCGCAAAATGAGCGAGATCGGGATGAATACCGAAGGGGTCGACTATGCGGTCGCTTTCCCGGGGCTTAACGCGCTGCAGTTCACCAACACGCCGAATACCGGGACGGTCTTTTTTGGCCTGAAACCGTTCGACCAGCGCAAACACACGGCGGCGGAAATTAACGCGGAGATCAACGCCAAAATCGCGCAAATCCAGCAGGGCTTTGGCTTTTCCATCCTGCCGCCGCCGATTTTAGGTCTGGGTCAGGGTTCCGGCTACTCCCTGTACATCCAGGATCGCGGAGGGCTGGGCTATGGCGCGCTGCAAAGCGCGGTGAATGCGATGTCCGGGGCGATTATGCAGACGCCGGGGATGCACTTCCCGATCTCGACTTACCAGGCTAACGTGCCGCAGCTGGACGTGCAGGTCGATCGCGATAAGGCGAAAGCGCAGGGGGTATCGCTAACCGATCTGTTCGGTACGCTGCAGACCTATCTCGGCTCGTCTTATGTCAATGACTTTAACCAGTTCGGGCGTACCTGGCGCGTGATGGCCCAGGCTGACGGACCATACCGCGAGAGCGTGGAAGATATCGCCAATCTGCGCACCCGCAATAATCAGGGCGAAATGGTACCGATCGGCAGTATGGTGAATATCAGTACCACCTACGGGCCGGATCCGGTGATCCGCTACAACGGTTATCCGGCGGCGGACCTGATTGGCGATGCCGATCCGCGGGTCCTCTCTTCTTCGCAGGCGATGACGCATCTGGAAGAGCTGTCGAAGCAGATCCTGCCGAATGGGATGAATATTGAGTGGACGGATCTCAGCTTCCAGCAGGCCACCCAGGGCAACACGGCGCTGATCGTCTTCCCGGTGGCGGTGCTGCTGGCATTCCTCGTACTGGCCGCGCTGTATGAAAGCTGGACCCTGCCGCTGGCGGTGATCCTTATCGTACCGATGACGATGCTCTCCGCGCTGTTTGGCGTCTGGCTGACCGGGGGCGATAACAACGTCTTCGTGCAGGTGGGTCTGGTGGTCCTGATGGGCCTGGCCTGTAAAAACGCCATTCTGATCGTCGAGTTTGCCCGCGAGCTGGAGATCCAGGGGAAAGGCATCATGGAAGCGGCGCTGGAGGCATGCCGCCTGCGTCTGCGCCCGATCGTGATGACCTCCATCGCCTTTATCGCCGGGACCATTCCGCTGATCCTCGGCCACGGCGCGGGGGCGGAAGTCCGCGGCGTCACCGGGATCACGGTGTTCTCCGGGATGCTGGGCGTGACGCTCTTCGGTCTGTTCCTGACGCCGGTGTTTTACGTGACGCTACGGAAACTGGTGACCCGCAGGAAGCCGGTCCAGGAGGATCTGCCCGCCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3003923","ARO_id":"40632","ARO_name":"oqxB","ARO_description":"RND efflux pump conferring resistance to fluoroquinolone","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35992":{"category_aro_accession":"0000075","category_aro_cvterm_id":"35992","category_aro_name":"nitrofurantoin","category_aro_description":"Nitrofurantoin is an antibiotic used to treat urinary tract infections. It inhibits enzyme synthesis by inhibiting essential enzymes involved in the citric acid cycle, as well as those involved in DNA, RNA, and protein synthesis. It is marketed under the following brand names: Furadantin, Macrobid, Macrodantin, Nitro Macro and Urantoin.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"41240":{"category_aro_accession":"3004116","category_aro_cvterm_id":"41240","category_aro_name":"nitrofuran antibiotic","category_aro_description":"Nitrofurans are chemotherapeutic agents with antibacterial and antiprotozoal activity.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2401":{"model_id":"2401","model_name":"Haemophilus parainfluenzae gyrA conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"4438":"S84Y"},"clinical":{"4438":"S84Y"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1500"}},"model_sequences":{"sequence":{"3727":{"protein_sequence":{"accession":"WP_014065640.1","sequence":"MTDSIHSSITPVNIEEELKSSYLDYAMSVIVGRALPDVRDGLKPVHRRVLFSMDQSGITAGKKYVKSARVVGDVIGKYHPHGDSAVYDTIVRMAQPFSLRYMLVDGQGNFGSIDGDAPAAMRYTEVRMQKITQALLTDLDKETVNFSPNYDGELMIPDVLPTRIPALLANGSSGIAVGMATNIPPHNLNEVLDGCLAYIDNENITIDELMQYIPGPDFPTAALINGRKGIEEAYRTGRGKVYVRARASVETTDKGKEQIIVTELPYQVNKAKLVEKIAELIKDKKIEGISNIIDLSNKEGIRIEIDIKRDAVGEVVLNHLYALTQMQVTFGINMVALDHGQPRLFNLKQIIEAFVMHRREVVIRRSLFELRKARERTHILEGLAVATSNIDEIIDIIRQSKERKEAAEKLISRPWKLNNEILGLLDAAARPAELAAEFGIKGSDYYLSPEQVDAILELRLHRLTGLATEEVINEYKELLVKIAELLHIINSPERLMEVIREELEQVRAQFADERRTEITAASGDIDLEDLIAQEDVVVTLSHEGYVKYQPLTDYEAQRRGGKGKSATKMKDEDFIEKLLVANTHDTILCFSSRGRLYWLKVYQLPQASRGARGRPIVNILPLQENERITAILPISAYEEDKFVIMATAGGIVKKIALTEFSRPRSSGIIALNLRDEDELIGVDITDGSNEIMLFSSQGRVVRFAESAVRAMGRLATGVRGIKLALTNDIADDESAVEIEEVSDDNAEETLDLNIDKVVSLVVPKNDGAILTATQNGYGKRTQLSEYPTKSRNTKGVISIKVSERNGKVVAATQVEETDQIMLITDAGTLVRTRVSEVSIVGRNTQGVRLIRTAEDEHVVSLERVCDVDDEDEGTEDVTSEE"},"dna_sequence":{"accession":"NC_015964.1","fmin":"1996520","fmax":"1999166","strand":"+","sequence":"ATGACGGATTCAATCCATTCCTCTATTACCCCAGTCAATATTGAAGAAGAACTAAAATCTTCTTACCTTGACTACGCCATGTCGGTGATTGTTGGGCGTGCTTTGCCTGATGTGCGTGACGGTTTAAAACCGGTGCATCGACGTGTGCTTTTCTCCATGGATCAATCTGGCATCACTGCCGGCAAAAAATACGTAAAATCTGCCCGTGTGGTAGGTGATGTAATCGGTAAATATCACCCGCACGGTGATTCTGCAGTGTACGACACCATTGTGCGTATGGCACAGCCGTTCTCATTGCGCTACATGTTGGTAGATGGGCAAGGTAACTTCGGTTCAATCGACGGTGATGCGCCAGCGGCAATGCGTTATACCGAAGTCCGTATGCAAAAAATCACCCAAGCGTTATTAACTGACTTGGATAAAGAAACCGTAAATTTCTCGCCAAACTATGATGGCGAATTAATGATTCCGGATGTATTACCAACTCGTATTCCTGCACTTTTAGCAAACGGTTCTTCCGGTATTGCGGTGGGGATGGCAACCAACATTCCACCACACAACTTAAATGAAGTTTTAGATGGATGCTTGGCTTATATTGATAACGAAAACATCACCATTGATGAGTTAATGCAATATATCCCGGGCCCAGACTTCCCAACAGCGGCATTAATTAATGGCCGTAAAGGGATTGAAGAAGCTTATCGCACTGGTCGCGGCAAAGTGTATGTTCGCGCTCGCGCTAGCGTAGAAACCACAGATAAAGGCAAAGAGCAAATTATTGTGACCGAATTGCCTTATCAAGTGAACAAAGCCAAATTAGTGGAAAAAATTGCTGAGCTTATCAAAGATAAAAAAATCGAAGGCATCAGCAATATTATCGACCTTTCGAACAAAGAAGGGATTCGCATTGAAATTGACATCAAACGTGATGCCGTAGGCGAAGTAGTATTAAATCACCTCTATGCGCTTACCCAAATGCAGGTAACCTTCGGGATTAACATGGTGGCCTTGGATCACGGTCAACCACGTTTATTCAACTTAAAACAAATCATTGAAGCCTTTGTGATGCACCGTCGCGAAGTGGTGATTCGCCGTTCTTTATTTGAATTGCGTAAAGCCCGCGAGCGTACCCATATTTTAGAAGGTTTAGCGGTTGCAACATCAAATATCGATGAAATCATCGATATCATCCGTCAATCGAAAGAGCGTAAAGAAGCGGCAGAAAAATTAATCTCTCGCCCTTGGAAATTGAATAACGAAATTTTAGGTTTACTTGATGCAGCGGCACGTCCAGCTGAGTTAGCGGCTGAATTTGGTATTAAAGGTTCGGATTACTATCTTTCTCCAGAACAAGTTGATGCAATCTTAGAACTTCGCTTGCATCGTTTAACCGGTCTTGCTACCGAAGAAGTAATCAATGAATACAAAGAGTTATTGGTTAAAATTGCAGAACTTCTCCACATCATCAACAGCCCTGAGCGTTTGATGGAAGTGATTCGTGAAGAGCTTGAACAAGTACGCGCACAATTCGCGGATGAACGTCGTACCGAAATTACTGCGGCTTCTGGTGATATTGATTTAGAAGATTTAATTGCTCAAGAAGATGTGGTAGTGACCCTTTCTCACGAAGGTTATGTGAAATATCAACCGCTTACCGACTACGAAGCACAACGTCGTGGTGGTAAAGGTAAATCCGCAACGAAGATGAAAGATGAAGACTTCATTGAAAAACTCTTAGTAGCGAATACTCACGATACGATTCTCTGTTTCTCTAGCCGCGGTCGCTTATATTGGTTGAAAGTCTATCAATTACCACAAGCAAGCCGTGGTGCGCGTGGTCGTCCGATTGTGAATATTCTACCGTTGCAAGAAAACGAGCGTATCACCGCAATCTTGCCAATCTCTGCTTATGAAGAAGATAAATTCGTCATCATGGCAACGGCTGGTGGTATTGTGAAGAAAATTGCGCTAACCGAATTCAGCCGTCCACGTTCAAGCGGTATCATCGCCTTGAACTTACGTGATGAAGATGAATTAATCGGCGTGGATATCACCGATGGTTCTAACGAAATCATGTTGTTCTCTTCGCAAGGTCGCGTAGTACGTTTCGCTGAAAGTGCAGTGCGTGCAATGGGTCGTTTAGCAACAGGTGTACGCGGTATTAAACTCGCCCTAACCAACGACATCGCTGACGATGAAAGTGCGGTCGAAATTGAAGAGGTTTCCGATGATAATGCAGAAGAAACCCTCGATCTCAATATCGATAAAGTGGTTTCCTTAGTTGTGCCGAAAAATGACGGCGCAATCCTTACGGCGACGCAAAACGGTTACGGTAAACGCACACAATTAAGCGAATACCCAACCAAATCCCGTAATACCAAAGGGGTGATTTCGATTAAAGTGAGCGAACGTAACGGTAAAGTCGTTGCGGCGACACAAGTGGAAGAAACCGACCAAATTATGCTTATCACTGATGCGGGTACCTTAGTGCGTACTCGTGTAAGTGAAGTGAGCATCGTTGGCCGTAACACCCAAGGGGTTCGTTTAATTCGTACCGCAGAAGATGAGCACGTAGTCAGTCTTGAACGTGTTTGTGATGTGGATGATGAAGACGAAGGCACTGAAGATGTGACTTCTGAAGAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36927","NCBI_taxonomy_name":"Haemophilus parainfluenzae","NCBI_taxonomy_id":"729"}}}},"ARO_accession":"3003924","ARO_id":"40633","ARO_name":"Haemophilus parainfluenzae gyrA conferring resistance to fluoroquinolones","ARO_description":"Point mutation of Haemophilus parainfluenzae gyrA resulted in the lowered affinity between fluoroquinolones and GyrA. Thus, conferring resistance. Both Ser and Tyr are hydrophilic amino acids, however Tyr has an additional bulky hydrophobic group which could affect the interaction between the DNA gyrase with quinolones","ARO_category":{"39876":{"category_aro_accession":"3003292","category_aro_cvterm_id":"39876","category_aro_name":"fluoroquinolone resistant gyrA","category_aro_description":"DNA gyrase is responsible for DNA supercoiling and consists of two alpha and two beta subunits. GyrA point mutations confer resistance by preventing fluoroquinolone antibiotics from binding the alpha-subunit.","category_aro_class_name":"AMR Gene Family"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"40463":{"category_aro_accession":"3003780","category_aro_cvterm_id":"40463","category_aro_name":"nybomycin","category_aro_description":"A  heterocyclic antibiotic that targets mutant gyrA (type II topoisomerase) containing an S84L substitution, counteracting acquired quinolone resistance. It is effective against quinolone-resistant Gram-positive bacteria including S. aureus and E. faecalis. Due to its ability to counteract quinolone resistance by targeting the mutant form of the gyrA protein, it is classified as a reverse antibiotic (RA).","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2402":{"model_id":"2402","model_name":"Haemophilus parainfluenzae parC conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"4440":"S84F"},"clinical":{"4440":"S84F"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1400"}},"model_sequences":{"sequence":{"3728":{"protein_sequence":{"accession":"WP_041918279.1","sequence":"MSNINYEGIEQMPLRTFTEKAYLNYSMYVIMDRALPFIGDGLKPVQRRIVYAMSELGLNAAAKFKKSARTVGDVLGKFHPHGDSACYEAMVLMAQPFSYRYPLVDGQGNWGAPDDPKSFAAMRYTESRLSKISEILLSELGQGTVDFQPNFDGTLEEPQYLPARLPHILLNGTTGIAVGMATDIPPHNINEVADAAVMLLDNPKAGLDDVLNIIQGPDFPTEAEIISPKDDIRKMYETGRGSIKMRATWHKEDGEIIISALPHQSSPSKIIAQIAEQMTAKKLPMVEDIRDEADYENPVRIVLVPRSNRVDTDALMAHLFATTDLEKSYRVNMNMIGLDHKPAVKGLLQVLIEWLTFRRTTVTRRLQHRLDKVLARLHILDGLMIAFLNIDEVIEIIRTEDEPKQVLMARFNLSDEQAEAILNLRLRHLAKLEEHQLQAEKDKLEEERSNLELILGSERRLNTLIKKEIQEDAKKYASPRMSQLVEREEAKAISESEMTPAEPVTVILSEMGWVRCAKGHDIDPEGLSYKAGDKYLAHACGKSNQPVIFIDSTGRSYALDPLSLPSARSQGEPLTGKLTLPAGATIEQVIMEPEKQELLMASDAGYGFICKFEDLIARNKAGKALISLPENAKVLKPETLSESTSLLVSLTSAGRMLIFPVRDLPALSKGKGNKIISIPAANAKARSELLVKLFLISEQASLEFHSGKRKITLKPEDLQKFRAERGRKGSQLPRGLHSNVDIVVVEPEHNS"},"dna_sequence":{"accession":"NC_015964.1","fmin":"1905162","fmax":"1907418","strand":"+","sequence":"ATGAGCAATATTAATTACGAAGGCATCGAGCAGATGCCACTTCGCACCTTTACAGAAAAGGCTTACCTTAATTATTCAATGTACGTCATCATGGATCGTGCATTGCCTTTTATTGGCGATGGCTTAAAGCCTGTTCAACGTCGTATTGTCTATGCGATGTCTGAACTGGGTTTAAATGCCGCGGCAAAATTTAAAAAGTCCGCGCGTACCGTCGGTGATGTGTTAGGTAAATTCCATCCACATGGTGACTCTGCTTGTTATGAAGCCATGGTATTAATGGCTCAGCCTTTTTCTTATCGTTATCCTTTGGTAGATGGGCAAGGAAACTGGGGGGCGCCAGATGATCCTAAATCATTTGCGGCAATGCGTTATACAGAATCTCGCCTGTCCAAAATCTCTGAAATTTTATTATCTGAATTAGGCCAAGGCACTGTTGATTTCCAACCGAACTTTGATGGTACCTTAGAAGAACCTCAATATTTGCCTGCACGTTTGCCTCATATTCTGTTAAACGGCACCACCGGGATTGCCGTCGGGATGGCAACCGATATTCCACCACATAATATTAATGAAGTGGCGGATGCCGCTGTTATGCTATTAGATAATCCAAAAGCAGGATTAGATGATGTACTCAATATCATTCAAGGCCCGGATTTCCCAACTGAAGCGGAAATTATTTCACCAAAAGATGATATTCGCAAAATGTATGAAACCGGTCGTGGTTCTATCAAAATGCGTGCAACATGGCATAAAGAAGACGGTGAAATCATCATTAGTGCACTTCCTCATCAATCTTCACCATCAAAAATCATTGCGCAAATTGCTGAACAAATGACAGCAAAAAAATTGCCAATGGTGGAAGATATTCGTGATGAAGCAGATTATGAAAACCCTGTACGTATCGTGCTTGTGCCACGTTCAAATCGTGTTGATACGGATGCCTTAATGGCGCATTTATTTGCGACGACTGATCTCGAAAAAAGCTATCGTGTAAATATGAATATGATCGGACTTGATCATAAACCAGCCGTAAAAGGCCTACTTCAAGTTCTTATCGAATGGCTGACATTCCGTCGTACTACCGTGACACGTCGTTTACAACATCGTTTAGATAAAGTACTCGCTCGTTTGCACATTTTAGATGGTTTGATGATTGCCTTCCTCAATATTGACGAAGTGATTGAGATTATTCGTACTGAAGATGAACCAAAACAAGTTTTAATGGCTCGCTTTAACTTAAGTGATGAACAGGCAGAAGCCATTTTAAACTTACGTTTACGCCATTTGGCCAAATTAGAAGAACATCAATTACAAGCTGAAAAAGATAAACTCGAAGAAGAGCGGTCAAATTTAGAGTTAATTTTAGGATCTGAACGTCGCTTAAATACCTTGATCAAAAAAGAAATTCAAGAAGATGCGAAAAAATACGCCAGCCCTAGAATGTCTCAATTAGTTGAACGTGAAGAAGCGAAAGCCATTTCTGAAAGTGAAATGACTCCGGCTGAACCCGTTACCGTTATCTTATCTGAAATGGGCTGGGTACGCTGTGCAAAAGGTCATGACATTGATCCGGAAGGATTAAGCTATAAAGCAGGCGATAAATATCTGGCTCACGCTTGCGGTAAAAGTAATCAGCCTGTAATCTTTATTGACAGCACGGGGCGTAGCTATGCTTTAGATCCATTAAGCTTGCCTTCTGCGCGTTCACAAGGTGAACCACTCACCGGTAAACTGACATTACCGGCCGGTGCGACCATTGAACAGGTTATTATGGAACCTGAAAAACAAGAATTATTGATGGCATCAGATGCAGGATATGGTTTTATTTGCAAATTTGAAGATTTAATTGCGCGTAATAAAGCAGGAAAAGCCTTGATTTCTTTGCCAGAAAATGCGAAAGTCTTGAAACCTGAGACACTTTCCGAGTCGACCTCACTTCTTGTGTCCCTCACTTCAGCGGGTCGAATGCTGATTTTTCCGGTACGGGATTTACCGGCATTATCAAAAGGGAAAGGCAACAAAATCATCAGTATTCCAGCAGCGAATGCAAAAGCGCGGTCAGAATTATTAGTGAAATTGTTCTTAATTTCAGAGCAAGCTAGCCTTGAGTTCCATTCCGGTAAACGAAAAATCACATTAAAACCGGAAGATCTGCAAAAATTCCGAGCGGAACGCGGCAGAAAAGGCTCCCAATTACCACGTGGATTACATAGCAATGTTGATATTGTGGTAGTTGAACCCGAACACAACTCATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36927","NCBI_taxonomy_name":"Haemophilus parainfluenzae","NCBI_taxonomy_id":"729"}}}},"ARO_accession":"3003925","ARO_id":"40634","ARO_name":"Haemophilus parainfluenzae parC conferring resistance to fluoroquinolones","ARO_description":"Point mutation of Haemophilus parainfluenzae parC resulted in the lowered affinity between fluoroquinolones and ParC. Thus, conferring resistance.","ARO_category":{"36913":{"category_aro_accession":"3000619","category_aro_cvterm_id":"36913","category_aro_name":"fluoroquinolone resistant parC","category_aro_description":"ParC is a subunit of topoisomerase IV, which decatenates and relaxes DNA to allow access to genes for transcription or translation. Point mutations in ParC prevent fluoroquinolone antibiotics from inhibiting DNA synthesis, and confer low-level resistance. Higher-level resistance results from both gyrA and parC mutations.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"37142":{"category_aro_accession":"3000762","category_aro_cvterm_id":"37142","category_aro_name":"pefloxacin","category_aro_description":"Pefloxacin is structurally and functionally similar to norfloxacin. It is poorly active against mycobacteria, while anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2403":{"model_id":"2403","model_name":"Salmonella enterica gyrA conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"4443":"S97P","4444":"S83F","4445":"D87N","4446":"D87Y"},"clinical":{"4443":"S97P","4444":"S83F","4445":"D87N","4446":"D87Y"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1500"}},"model_sequences":{"sequence":{"3729":{"protein_sequence":{"accession":"NP_461214.1","sequence":"MSDLAREITPVNIEEELKSSYLDYAMSVIVGRALPDVRDGLKPVHRRVLYAMNVLGNDWNKAYKKSARVVGDVIGKYHPHGDSAVYDTIVRMAQPFSLRYMLVDGQGNFGSIDGDSAAAMRYTEIRLAKIAHELMADLEKETVDFVDNYDGTEKIPDVMPTKIPNLLVNGSSGIAVGMATNIPPHNLTEVINGCLAYIDNEDISIEGLMEHIPGPDFPTAAIINGRRGIEEAYRTGRGKVYIRARAEVEADAKTGRETIIVHEIPYQVNKARLIEKIAELVKDKRVEGISALRDESDKDGMRIVIEVKRDAVGEVVLNNLYSQTQLQVSFGINMVALHHGQPKIMNLKDIISAFVRHRREVVTRRTIFELRKARDRAHILEALAIALANIDPIIELIRRAPTPAEAKAALISRPWDLGNVAAMLERAGDDAARPEWLEPEFGVRDGQYYLTEQQAQAILDLRLQKLTGLEHEKLLDEYKELLEQIAELLHILGSADRLMEVIREEMELIRDQFGDERRTEITANSADINIEDLISQEDVVVTLSHQGYVKYQPLTDYEAQRRGGKGKSAARIKEEDFIDRLLVANTHDTILCFSSRGRLYWMKVYQLPEASRGARGRPIVNLLPLEANERITAILPVREYEEGVNVFMATASGTVKKTALTEFSRPRSAGIIAVNLNDGDELIGVDLTSGSDEVMLFSAAGKVVRFKEDAVRAMGRTATGVRGIKLAGDDKVVSLIIPRGEGAILTVTQNGYGKRTAADEYPTKSRATQGVISIKVTERNGSVVGAVQVDDCDQIMMITDAGTLVRTRVSEISVVGRNTQGVILIRTAEDENVVGLQRVAEPVDDEELDAIDGSVAEGDEDIAPEAESDDDVADDADE"},"dna_sequence":{"accession":"NC_003197.1","fmin":"2373710","fmax":"2376347","strand":"-","sequence":"TTACTCGTCAGCGTCATCCGCAACGTCGTCATCGCTTTCCGCTTCCGGGGCGATATCCTCATCCCCTTCCGCCACGCTGCCGTCGATAGCGTCGAGTTCTTCGTCATCTACCGGTTCAGCAACGCGTTGCAGACCCACCACGTTTTCATCTTCCGCCGTGCGGATAAGGATAACGCCCTGGGTATTACGTCCCACTACGCTGATCTCGGACACACGGGTACGCACCAGAGTACCGGCATCCGTGATCATCATGATCTGGTCGCAATCGTCTACCTGTACCGCACCGACAACGGAACCGTTGCGCTCGGTCACTTTGATAGAGATAACGCCCTGCGTCGCACGAGACTTGGTCGGGTACTCGTCCGCTGCGGTACGCTTCCCGTAGCCGTTTTGCGTTACGGTCAGAATAGCGCCTTCGCCGCGTGGGATGATCAGAGAGACGACTTTATCGTCTCCCGCCAGCTTAATACCGCGCACACCGGTCGCGGTACGCCCCATCGCACGGACGGCGTCTTCTTTGAAGCGCACCACTTTACCCGCGGCCGAGAACAGCATGACTTCGTCAGAACCAGAAGTCAGGTCAACGCCAATCAGCTCGTCGCCGTCGTTGAGGTTCACCGCGATAATACCGGCGGAACGCGGACGGCTGAATTCGGTCAGCGCCGTTTTCTTCACGGTACCGCTGGCGGTCGCCATAAAGACGTTGACGCCTTCTTCATACTCACGAACCGGCAGAATCGCGGTGATACGTTCGTTGGCTTCCAGCGGCAGCAGGTTGACGATCGGACGACCGCGCGCGCCGCGGCTGGCTTCCGGCAGCTGATAGACCTTCATCCAGTACAGACGGCCCCGGCTGGAGAAGCAGAGGATGGTGTCATGGGTGTTAGCCACCAGCAGGCGGTCGATAAAGTCTTCTTCTTTAATACGCGCGGCAGATTTACCTTTCCCACCACGACGTTGCGCTTCGTAATCTGTCAGCGGTTGATATTTGACGTAACCCTGGTGAGACAGCGTCACGACAACATCTTCCTGGCTAATCAGATCTTCGATATTAATATCGGCGCTGTTGGCGGTGATTTCGGTACGACGCTCATCGCCGAACTGATCGCGAATTAACTCCATCTCTTCGCGGATCACTTCCATCAGGCGATCGGCGCTGCCCAGAATGTGCAGCAATTCAGCAATCTGCTCCAGCAGCTCTTTGTATTCGTCGAGCAGTTTTTCATGCTCCAGGCCGGTCAGTTTCTGCAAACGCAGATCCAGAATCGCCTGCGCCTGCTGTTCAGTCAGGTAGTACTGACCGTCACGCACGCCAAATTCTGGCTCCAGCCATTCCGGACGCGCGGCGTCATCACCAGCGCGCTCCAGCATCGCAGCAACGTTGCCCAGATCCCACGGACGCGAAATCAGCGCCGCTTTTGCTTCCGCCGGCGTTGGCGCGCGGCGAATCAGTTCGATAATCGGGTCGATGTTGGCCAGCGCAATCGCCAGAGCTTCAAGGATATGCGCACGGTCACGGGCTTTACGCAGTTCAAAAATAGTCCGACGCGTCACCACTTCACGGCGGTGGCGCACGAACGCTGAAATGATATCTTTCAGGTTCATGATCTTCGGCTGGCCGTGATGCAGCGCCACCATGTTAATACCGAAGGAAACCTGTAGCTGGGTCTGGGAGTAGAGATTATTAAGCACCACCTCGCCCACCGCATCGCGTTTCACTTCAATCACGATGCGCATCCCGTCTTTGTCGGATTCGTCACGCAGCGCGCTGATGCCTTCCACGCGTTTATCTTTCACCAGCTCGGCGATTTTCTCGATCAGGCGCGCTTTGTTCACCTGATAGGGAATTTCATGGACGATGATGGTTTCACGGCCCGTTTTGGCGTCAGCTTCAACTTCCGCGCGGGCGCGAATGTACACTTTGCCACGACCGGTGCGGTAGGCTTCTTCGATACCACGACGACCGTTGATGATCGCGGCGGTCGGGAAGTCCGGCCCCGGAATATGTTCCATCAGCCCTTCAATGCTGATGTCTTCGTTGTCGATATACGCCAGGCAGCCGTTAATCACTTCCGTCAGGTTGTGCGGCGGGATATTCGTCGCCATACCTACTGCGATACCGGAAGAACCGTTCACCAGCAGATTCGGAATTTTGGTCGGCATGACGTCCGGAATTTTTTCCGTACCGTCATAGTTATCCACGAAATCCACCGTCTCTTTTTCGAGATCGGCCATCAGTTCGTGGGCGATTTTCGCCAGACGGATCTCCGTATAACGCATTGCCGCCGCGGAGTCGCCGTCAATAGAACCGAAGTTACCCTGACCATCCACCAGCATGTAACGCAGCGAGAATGGCTGCGCCATACGAACGATGGTGTCATACACTGCGGAATCGCCGTGGGGATGGTATTTACCGATTACGTCACCAACGACACGGGCAGATTTTTTATAGGCTTTGTTCCAGTCATTGCCCAATACGTTCATGGCGTAAAGTACGCGACGGTGTACCGGCTTCAGGCCATCTCGGACATCCGGCAGCGCACGGCCAACAATGACCGACATCGCATAATCCAGATAGGAGCTCTTCAGCTCCTCCTCAATGTTGACCGGTGTAATTTCTCTCGCAAGGTCGCTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35734","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium str. LT2","NCBI_taxonomy_id":"99287"}}}},"ARO_accession":"3003926","ARO_id":"40635","ARO_name":"Salmonella enterica gyrA conferring resistance to fluoroquinolones","ARO_description":"Point mutations in Salmonella gyrA that confer resistance to Nalidixic acid, a fluoroquinolone antibiotic. These mutations have also been shown to reduce susceptibility to ciprofloxacin.","ARO_category":{"39876":{"category_aro_accession":"3003292","category_aro_cvterm_id":"39876","category_aro_name":"fluoroquinolone resistant gyrA","category_aro_description":"DNA gyrase is responsible for DNA supercoiling and consists of two alpha and two beta subunits. GyrA point mutations confer resistance by preventing fluoroquinolone antibiotics from binding the alpha-subunit.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"40463":{"category_aro_accession":"3003780","category_aro_cvterm_id":"40463","category_aro_name":"nybomycin","category_aro_description":"A  heterocyclic antibiotic that targets mutant gyrA (type II topoisomerase) containing an S84L substitution, counteracting acquired quinolone resistance. It is effective against quinolone-resistant Gram-positive bacteria including S. aureus and E. faecalis. Due to its ability to counteract quinolone resistance by targeting the mutant form of the gyrA protein, it is classified as a reverse antibiotic (RA).","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2405":{"model_id":"2405","model_name":"Neisseria gonorrhoeae parC conferring resistance to fluoroquinolone","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"4454":"S87R","4455":"E91G"},"clinical":{"4454":"S87R","4455":"E91G"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1400"}},"model_sequences":{"sequence":{"3731":{"protein_sequence":{"accession":"YP_208330.1","sequence":"MNTQPHASHTDSNTLMLGRYAERAYLEYAMSVVKGRALPEVSDGQKPVQRRILFAMRDMGLTAGAKPVKSARVVGEILGKYHPHGDSSAYEAMVRMAQDFTLRYPLIDGIGNFGSRDGDGAAAMRYTEARLTPIAELLLSEINQGTVDFMPNYDGAFDEPLHLPARLPMVLLNGASGIAVGMATEIPSHNLNEVTQAAIALLKKPTLETADLMQYIPAPDFAGGGQIITPADELRRIYETGKGSVRVRARYEIEKLARGQWRVIVTELPPNANSAKILAEIEEQTNPKPKAGKKQLNQDRLNTKKLMLDLIDRVRDESDGEHPVRLVFEPKSSRIDTDTFINTLMAQTSLEGNVSMNLVMMGLDNRPAQKNLKTILQEWLDFRVVTVTRRLKFRLNQVEKRLHILEGRLKVFLHIDEVIKVIRESDDPKADLMAVFGLTEIQAEDILEIRLRQLARLEGFKLEKELNELREEQGRLNIFLGDENEKRKLIIKEMQADMKQFGDARRTLVEEAGRAVLTQTAADEPITLILSEKGWIRSRAGHNLDLSQTAFKEGDRLKQTLEGRTVLPVVILDSSGRTYSIDAAEIPGGRGDGVPVSSLIELQNGAKPVAMLTGLPEQHYLLSSSGGYGFIAKLGDMVGRVKAGKVVMTADSGETVLPPVAVYASSFINPDCKIIAATSQNRALAFPIGELKIMAKGKGLQIIGLNAGESMTHTAVSSEPEILIESEGRRGAAHKDRLPVALIEAKRGKKGRLLPISGSLKQLSSPK"},"dna_sequence":{"accession":"NC_002946.2","fmin":"1210523","fmax":"1212827","strand":"+","sequence":"ATGAATACGCAACCGCACGCTTCCCATACCGATTCCAACACGCTGATGCTCGGCCGATACGCCGAACGCGCCTATCTCGAATACGCCATGAGCGTGGTCAAAGGCCGCGCGCTGCCTGAAGTTTCAGACGGCCAAAAGCCCGTGCAGCGGCGCATTTTGTTTGCCATGCGCGATATGGGTTTGACGGCGGGGGCGAAGCCGGTGAAATCGGCGCGCGTGGTCGGCGAGATTTTGGGTAAATACCATCCGCACGGCGACAGTTCCGCCTATGAGGCGATGGTGCGCATGGCTCAGGATTTTACCTTGCGCTACCCCTTAATCGACGGCATCGGCAACTTCGGTTCGCGCGACGGCGACGGGGCGGCGGCGATGCGTTACACCGAAGCGCGGCTGACGCCGATTGCGGAATTGCTGTTGTCCGAAATCAATCAGGGGACGGTGGATTTTATGCCGAACTACGACGGCGCGTTTGACGAGCCGCTGCACCTTCCCGCCCGCTTGCCTATGGTGTTGCTCAACGGCGCGTCGGGCATCGCGGTGGGTATGGCGACCGAGATTCCGTCGCACAATTTGAACGAAGTCACGCAGGCGGCGATTGCACTGTTGAAGAAACCGACGCTGGAAACCGCCGACCTGATGCAATATATTCCTGCTCCCGATTTTGCCGGCGGCGGTCAAATCATCACGCCGGCGGACGAATTGCGCCGTATTTACGAAACCGGCAAGGGCAGCGTGCGCGTGCGTGCGCGTTATGAAATCGAGAAATTGGCGCGCGGACAGTGGCGCGTCATCGTAACCGAACTGCCGCCGAACGCCAACTCCGCCAAAATCCTTGCCGAAATCGAAGAGCAAACCAACCCGAAACCGAAAGCGGGTAAAAAGCAGCTCAACCAAGACCGGCTCAATACCAAAAAGCTGATGCTGGATTTAATCGACCGCGTGCGCGACGAGTCCGACGGCGAACATCCCGTGCGCCTTGTATTTGAACCGAAATCCAGCCGCATCGATACCGATACCTTCATCAACACGCTGATGGCGCAAACTTCGCTGGAAGGCAATGTGTCCATGAACTTGGTGATGATGGGTTTGGACAACCGCCCCGCGCAGAAAAACCTGAAAACGATTTTGCAGGAATGGCTGGATTTCCGCGTCGTTACCGTAACACGCCGTCTGAAATTCCGTTTAAACCAAGTGGAAAAACGGCTGCACATCCTCGAAGGCCGTCTGAAAGTCTTTCTGCACATCGACGAAGTGATTAAAGTCATCCGCGAATCGGACGACCCGAAAGCCGATTTGATGGCGGTGTTCGGGCTGACCGAAATCCAAGCCGAAGACATTTTGGAAATCCGCCTGCGTCAGCTGGCGCGTTTGGAAGGTTTCAAACTCGAAAAAGAATTGAACGAATTGCGCGAAGAACAAGGCCGTCTGAATATCTTTTTGGGCGACGAAAACGAAAAACGCAAGCTGATTATCAAAGAGATGCAGGCGGACATGAAGCAGTTCGGCGACGCGCGCCGCACGCTGGTGGAAGAGGCCGGACGCGCCGTGCTGACACAAACCGCCGCCGACGAACCCATCACGCTGATTTTGTCGGAAAAAGGCTGGATACGCAGCCGTGCCGGACATAATCTCGATTTGAGCCAAACCGCGTTCAAAGAAGGCGACCGCCTCAAACAAACCCTTGAAGGCCGCACTGTTTTACCCGTCGTCATCCTCGATTCATCGGGCAGAACCTACTCGATCGATGCCGCCGAAATCCCCGGCGGACGCGGCGACGGCGTACCGGTTTCCTCCTTAATCGAGTTGCAAAACGGCGCGAAACCCGTCGCGATGTTGACAGGATTGCCGGAACAACATTATTTATTATCAAGCAGCGGCGGCTACGGCTTTATCGCCAAGCTGGGCGATATGGTCGGACGCGTGAAAGCGGGCAAAGTGGTGATGACCGCAGACAGCGGCGAAACCGTCCTGCCGCCGGTTGCCGTCTATGCCTCCTCGTTCATCAACCCCGACTGCAAAATCATTGCAGCCACCAGTCAAAACCGCGCCCTCGCCTTCCCCATCGGCGAATTGAAAATTATGGCGAAAGGCAAAGGACTGCAAATCATCGGATTAAACGCCGGCGAATCGATGACGCATACCGCCGTTTCTTCCGAGCCGGAAATCCTGATTGAAAGCGAAGGCAGGCGCGGCGCGGCGCACAAAGACCGCCTCCCCGTCGCCCTGATTGAGGCAAAACGCGGCAAAAAAGGCAGACTGTTGCCCATATCGGGCAGCCTGAAACAGCTTTCTTCCCCCAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40638","NCBI_taxonomy_name":"Neisseria gonorrhoeae FA 1090","NCBI_taxonomy_id":"242231"}}}},"ARO_accession":"3003929","ARO_id":"40639","ARO_name":"Neisseria gonorrhoeae parC conferring resistance to fluoroquinolone","ARO_description":"Point mutations in Neisseria gonorrhoeae parC protein that confer resistance to fluoroquinolone by reducing affinity to antibiotic binding site","ARO_category":{"36913":{"category_aro_accession":"3000619","category_aro_cvterm_id":"36913","category_aro_name":"fluoroquinolone resistant parC","category_aro_description":"ParC is a subunit of topoisomerase IV, which decatenates and relaxes DNA to allow access to genes for transcription or translation. Point mutations in ParC prevent fluoroquinolone antibiotics from inhibiting DNA synthesis, and confer low-level resistance. Higher-level resistance results from both gyrA and parC mutations.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"37142":{"category_aro_accession":"3000762","category_aro_cvterm_id":"37142","category_aro_name":"pefloxacin","category_aro_description":"Pefloxacin is structurally and functionally similar to norfloxacin. It is poorly active against mycobacteria, while anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2406":{"model_id":"2406","model_name":"rpsJ","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"4457":"V57M","4458":"V57L"},"clinical":{"4457":"V57M","4458":"V57L"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"3732":{"protein_sequence":{"accession":"YP_208874.1","sequence":"MANQKIRIRLKAYDYALIDRSAQEIVETAKRTGAVVKGPIPLPTKIERFNILRSPHVNKTSREQLEIRTHLRLMDIVDWTDKTTDALMKLDLPAGVDVEIKVQ"},"dna_sequence":{"accession":"NC_002946.2","fmin":"1807358","fmax":"1807670","strand":"-","sequence":"TTATTGGACTTTAATTTCTACATCAACACCGGCCGGCAAATCCAGCTTCATCAGCGCATCGGTAGTTTTATCGGTCCAATCCACGATGTCCATCAGGCGCAAATGGGTGCGGATTTCCAATTGTTCACGGGAAGTTTTGTTCACGTGCGGAGAACGCAAAATGTTGAAACGCTCGATTTTGGTCGGCAAAGGAATCGGGCCTTTTACAACAGCACCGGTACGTTTTGCAGTTTCAACGATTTCTTGTGCAGAACGGTCAATCAGGGCGTAATCATAAGCTTTCAGGCGGATACGGATTTTTTGGTTTGCCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40638","NCBI_taxonomy_name":"Neisseria gonorrhoeae FA 1090","NCBI_taxonomy_id":"242231"}}}},"ARO_accession":"3003930","ARO_id":"40640","ARO_name":"rpsJ","ARO_description":"rpsJ is a tetracycline resistance protein identified in Neisseria gonorrhoeae. Tetracycline resistance is conferred by binding to the ribosome as a 30S ribosomal protection protein.","ARO_category":{"35921":{"category_aro_accession":"0000002","category_aro_cvterm_id":"35921","category_aro_name":"tetracycline-resistant ribosomal protection protein","category_aro_description":"A family of proteins known to bind to the 30S ribosomal subunit. This interaction prevents tetracycline and tetracycline derivatives from inhibiting ribosomal function. Thus, these proteins confer elevated resistance to tetracycline derivatives as a ribosomal protection protein.","category_aro_class_name":"AMR Gene Family"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2407":{"model_id":"2407","model_name":"Capnocytophaga gingivalis gyrA conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"4461":"G80N"},"clinical":{"4461":"G80N"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1500"}},"model_sequences":{"sequence":{"3733":{"protein_sequence":{"accession":"EEK14408.1","sequence":"MVEGEKLIPINIEDQMKTAYIDYSMSVIVSRALPDVRDGLKPVHRRVLFGMHELGVRSNTAHKKSARIVGEVLGKYHPHGDSSVYDTMVRMAQWWNMRYMLVDGQGNFGSIDGDSPAAMRYTEARMRKMAEDMLIDIDKETVDHSLNFDDTLLEPTVLPTRIPNLLVNGSSGIAVGMATNMPPHNLAEVVDGIIAYLGNQDITIDELMEYIKAPDFPTGGIIYGYDGVREAFKTGRGRVVIRAKAHFEEVNGRDCIVVTEVPYQVNPETMREQTSNLVKEGKLEGLADIVDQTGKGGMRIVYELKKDAIPNVVLNNLFKHTALQSSFSVNNIALVNGRPQQLNLKDLIYHFVEHRHDVVYRRTEYELKKAKERIHILEGFMKVMATEDTMGKAIEIIRFHDKPKEDLMTEFELTEIQAEAILALQLRRINKLLILQTKEEYEQLLAQIIDLEDILARKERRTEIIKEELLEIKSKYGDERRSVIEYAGGDISIEDIIPDDQVVITISNAGYIKRTSVNEYKTQARGGVGQKASATRDKDFIEHLFIGTNHQYMLFFTEKGKCFWLRVYEIPEGGKNTKGRAIQNLINIEPDDLVKAVICTHDLKEKDYTNSHYVIMATKKGIIKKTSLEQYSRPRQNGIVAITIKEDDELLEARLTSGNSQIMLAVKSGKAIRFPEDKVRAVGRSGSGVRGISLDSDKDEVIGMIAIENPLEETVLVVSENGYGKRTFIDEPETGEAVYRITNRGGKGVKTISITEKTGNLVAIKSVLEEDDLMIINKSGMAIRLPVSGLRVMGRATQGVRLINIKGNDSIAAVAKVMKEDEDENTTEEIENPTEE"},"dna_sequence":{"accession":"ACLQ01000019.1","fmin":"24238","fmax":"26749","strand":"+","sequence":"ATGGTTGAAGGAGAAAAACTCATTCCTATTAACATAGAAGACCAGATGAAGACAGCCTACATTGACTATTCAATGTCAGTGATTGTCTCAAGAGCTTTGCCCGATGTACGCGATGGGCTGAAGCCTGTACATCGTCGTGTACTCTTTGGAATGCACGAGCTTGGCGTACGTAGCAACACCGCTCATAAGAAATCAGCCCGTATCGTAGGGGAAGTACTCGGTAAGTACCATCCACACGGCGATTCTTCCGTATATGACACAATGGTACGTATGGCACAATGGTGGAACATGCGCTATATGCTTGTAGATGGGCAAGGTAACTTTGGTTCTATCGATGGAGACTCTCCTGCAGCTATGCGTTATACCGAGGCGAGAATGAGAAAAATGGCCGAGGATATGCTGATAGATATCGACAAAGAAACAGTAGATCACAGCCTGAACTTTGACGATACCCTACTCGAACCTACTGTATTGCCTACCCGCATCCCTAACCTACTGGTGAATGGGTCTTCGGGTATTGCTGTAGGTATGGCTACCAATATGCCACCTCATAATCTTGCTGAAGTAGTTGATGGTATAATTGCTTATCTTGGCAATCAAGATATTACCATCGATGAACTTATGGAATATATCAAGGCTCCTGACTTCCCTACAGGTGGAATCATCTATGGCTATGATGGAGTAAGAGAAGCCTTCAAGACTGGACGTGGACGTGTAGTAATCCGCGCCAAGGCTCATTTTGAAGAAGTTAATGGTCGTGACTGTATTGTCGTAACTGAAGTTCCCTATCAAGTGAACCCAGAGACGATGCGTGAACAGACTTCGAACCTTGTCAAAGAAGGCAAACTCGAAGGCCTAGCCGATATCGTAGATCAAACAGGTAAAGGAGGAATGCGCATCGTATATGAACTCAAAAAAGATGCTATTCCCAACGTAGTGCTGAATAACCTCTTCAAACACACAGCATTACAATCCTCCTTCAGTGTCAATAATATTGCCTTGGTCAATGGACGCCCTCAGCAACTGAACCTCAAGGACTTAATATATCACTTTGTAGAACATCGCCACGATGTAGTATACAGACGTACTGAGTATGAGCTCAAAAAAGCCAAAGAACGTATCCATATCTTGGAAGGGTTCATGAAGGTGATGGCCACAGAAGACACTATGGGGAAAGCTATTGAAATCATCCGTTTTCATGACAAGCCCAAAGAGGATTTGATGACCGAGTTCGAGCTTACCGAAATACAAGCTGAAGCTATCTTAGCCTTACAGCTACGTCGTATCAATAAGCTATTAATCCTTCAAACCAAAGAAGAATATGAGCAATTATTAGCACAAATTATTGATTTGGAAGATATCCTTGCTCGCAAAGAACGCCGTACCGAGATTATCAAAGAAGAACTCTTGGAAATAAAATCCAAATATGGAGACGAACGTCGTTCTGTCATAGAATATGCAGGGGGTGATATCTCCATTGAGGATATTATCCCTGATGATCAAGTGGTTATTACCATTTCCAACGCAGGTTACATAAAGCGTACTTCTGTCAATGAATACAAAACCCAAGCACGTGGTGGTGTAGGACAAAAAGCCTCTGCTACTCGTGATAAGGACTTCATAGAGCATCTGTTCATAGGTACCAACCACCAGTATATGCTGTTCTTTACAGAGAAAGGTAAGTGTTTTTGGCTCAGGGTGTATGAGATTCCTGAAGGAGGTAAAAATACCAAAGGACGCGCCATACAGAACCTTATCAATATCGAACCCGATGACCTTGTTAAGGCAGTCATCTGTACCCATGACCTCAAGGAAAAAGACTATACCAATAGTCACTATGTCATCATGGCTACTAAAAAAGGGATTATTAAGAAAACCAGCTTAGAACAATATTCACGTCCACGCCAGAATGGTATCGTTGCCATCACTATCAAAGAAGATGATGAGCTATTAGAAGCACGTCTTACCTCTGGCAACAGCCAAATCATGCTAGCTGTCAAGTCTGGAAAGGCTATTCGCTTCCCAGAGGACAAGGTGAGAGCTGTAGGGCGTAGTGGCTCTGGAGTACGAGGTATCTCTTTGGATAGTGACAAAGATGAGGTAATCGGAATGATTGCCATAGAAAATCCTCTGGAAGAAACCGTATTGGTAGTTTCCGAGAATGGTTATGGTAAGCGTACCTTTATCGATGAACCAGAGACAGGAGAAGCAGTATATCGTATTACCAACCGTGGAGGAAAAGGAGTCAAGACTATTTCTATCACAGAGAAAACAGGTAATCTGGTAGCAATCAAGTCAGTTTTGGAAGAAGACGATCTGATGATTATCAATAAGTCGGGTATGGCTATTCGCCTCCCTGTAAGTGGACTCCGTGTGATGGGACGTGCTACCCAAGGAGTACGCCTTATCAATATCAAAGGAAATGACTCTATTGCCGCAGTAGCAAAGGTTATGAAAGAAGATGAGGATGAAAATACTACCGAAGAGATAGAAAACCCAACAGAAGAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40642","NCBI_taxonomy_name":"Capnocytophaga gingivalis ATCC 33624","NCBI_taxonomy_id":"553178"}}}},"ARO_accession":"3003931","ARO_id":"40641","ARO_name":"Capnocytophaga gingivalis gyrA conferring resistance to fluoroquinolones","ARO_description":"Point mutation in Capnocytophaga gingivalis that decreases binding affinity of fluoroquinolone antibiotics to gyrA, thereby conferring resistance.","ARO_category":{"39876":{"category_aro_accession":"3003292","category_aro_cvterm_id":"39876","category_aro_name":"fluoroquinolone resistant gyrA","category_aro_description":"DNA gyrase is responsible for DNA supercoiling and consists of two alpha and two beta subunits. GyrA point mutations confer resistance by preventing fluoroquinolone antibiotics from binding the alpha-subunit.","category_aro_class_name":"AMR Gene Family"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"40463":{"category_aro_accession":"3003780","category_aro_cvterm_id":"40463","category_aro_name":"nybomycin","category_aro_description":"A  heterocyclic antibiotic that targets mutant gyrA (type II topoisomerase) containing an S84L substitution, counteracting acquired quinolone resistance. It is effective against quinolone-resistant Gram-positive bacteria including S. aureus and E. faecalis. Due to its ability to counteract quinolone resistance by targeting the mutant form of the gyrA protein, it is classified as a reverse antibiotic (RA).","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2410":{"model_id":"2410","model_name":"Salmonella enterica parC conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"4487":"W106G"},"clinical":{"4487":"W106G"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1400"}},"model_sequences":{"sequence":{"3739":{"protein_sequence":{"accession":"NP_462089.1","sequence":"MSDMAERLALHEFTENAYLNYSMYVIMDRALPFIGDGLKPVQRRIVYAMSELGLNATAKFKKSARTVGDVLGKYHPHGDSACYEAMVLMAQPFSYRYPLVDGQGNWGAPDDPKSFAAMRYTESRLSKYAELLLSELGQGTADWVPNFDGTMQEPKMLPARLPNILLNGTTGIAVGMATDIPPHNLREVAKAAITLIEQPKTTLDQLLDIVQGPDYPTEAEIITPRAEIRKIYENGRGSVRMRAVWTKEDGAVVISALPHQVSGAKVLEQIAAQMRNKKLPMVDDLRDESDHENPTRLVIVPRSNRVDMEQVMNHLFATTDLEKSYRINLNMIGLDGRPAVKNLLEILTEWLAFRRDTVRRRLNYRLEKVLKRLHILEGLLVAFLNIDEVIEIIRSEDEPKPALMSRFGISETQAEAILELKLRHLAKLEEMKIRGEQDELEKERDQLQGILASERKMNTLLKKELQADADAYGDDRRSPLREREEAKAMSEHDMLPSEPVTIVLSQMGWVRSAKGHDIDAPGLNYKAGDSFKAAVKGKSNQPVVFIDTTGRSYAIDPITLPSARGQGEPLTGKLTLPPGATVEHMLMEGDDQKLLMASDAGYGFVCTFNDLVARNRAGKTLITLPENAHVMPPLVIEDEHDMLLAITQAGRMLMFPVDSLPQLSKGKGNKIINIPSAEAAKGDDGLAHLYVLPPQSTLTIHVGKRKIKLRPEELQKVVGERGRRGTLMRGLQRIDRIEIDSPHRVSHGDSEE"},"dna_sequence":{"accession":"NC_003197.1","fmin":"3336946","fmax":"3339205","strand":"-","sequence":"TTACTCTTCGCTGTCGCCATGACTTACGCGATGCGGCGAATCAATCTCAATGCGATCGATACGCTGCAGGCCGCGCATTAATGTGCCACGGCGTCCGCGTTCACCGACCACCTTTTGTAACTCTTCAGGGCGCAGTTTGATTTTGCGCTTCCCGACATGGATAGTCAGAGTGCTTTGTGGCGGCAGCACGTACAGGTGCGCCAGTCCATCATCGCCTTTCGCCGCTTCTGCAGAGGGGATATTAATGATCTTATTCCCTTTGCCTTTCGACAGCTGCGGCAGAGAGTCTACCGGGAACATCAACATCCGTCCGGCCTGGGTAATCGCCAGCAGCATATCGTGCTCGTCTTCAATCACCAGCGGCGGCATGACGTGCGCATTTTCCGGCAGTGTAATCAATGTCTTACCGGCACGGTTACGGGCAACCAGATCGTTAAACGTACAAACGAAGCCGTAGCCCGCATCCGACGCCATCAGCAGTTTCTGGTCATCGCCTTCCATCAGCATATGCTCTACGGTCGCCCCCGGCGGCAGCGTGAGTTTGCCGGTCAGCGGCTCGCCCTGCCCACGCGCCGACGGAAGCGTAATGGGATCAATAGCATAGCTGCGCCCGGTGGTATCAATAAACACCACCGGTTGATTGCTCTTACCTTTCACCGCGGCTTTAAAGCTGTCGCCCGCTTTATAGTTAAGCCCCGGCGCATCAATATCATGACCTTTGGCGCTGCGCACCCAGCCCATCTGCGACAGCACGATAGTCACCGGTTCGGACGGCAGCATATCGTGTTCGCTCATCGCTTTAGCTTCTTCGCGCTCACGCAGCGGAGAACGGCGATCGTCGCCATAGGCATCGGCGTCCGCCTGTAGTTCTTTTTTCAGCAAGGTATTCATTTTGCGTTCGGACGCGAGAATGCCCTGCAACTGGTCCCTCTCTTTTTCCAGCTCGTCCTGCTCGCCGCGAATTTTCATCTCTTCCAGTTTGGCGAGATGGCGCAGTTTCAGTTCGAGAATCGCTTCCGCCTGGGTTTCGCTGATGCCGAAACGCGACATCAGCGCGGGTTTTGGCTCGTCTTCGCTACGGATAATCTCAATCACTTCGTCGATGTTGAGAAACGCCACCAGCAAACCTTCGAGGATATGCAGGCGCTTAAGCACTTTCTCCAGACGATAGTTCAGACGACGGCGCACCGTGTCGCGGCGGAACGCCAGCCACTCGGTGAGGATCTCCAGCAGGTTTTTCACCGCCGGACGACCATCCAGACCGATCATGTTCAGGTTAATACGGTAGCTTTTTTCCAGATCGGTGGTGGCGAACAGATGGTTCATCACCTGTTCCATATCCACACGGTTGGAGCGTGGCACAATCACTAAACGCGTCGGGTTTTCGTGATCCGATTCATCGCGCAGATCGTCCACCATCGGCAGTTTTTTATTACGCATCTGCGCAGCAATCTGCTCCAGCACTTTCGCGCCAGAGACCTGATGCGGCAGCGCGGAAATTACCACAGCGCCGTCTTCTTTGGTCCATACCGCGCGCATACGCACGGAGCCCCGCCCGTTTTCGTAAATTTTACGAATTTCCGCACGTGGGGTAATGATCTCCGCTTCGGTCGGGTAATCCGGCCCCTGAACGATATCCAGCAACTGATCCAGCGTCGTTTTCGGCTGCTCAATCAGCGTAATCGCCGCTTTCGCCACTTCGCGCAGGTTGTGCGGCGGGATATCTGTTGCCATGCCCACCGCAATACCGGTGGTGCCGTTCAGCAGGATGTTCGGCAGACGCGCCGGTAACATTTTCGGTTCCTGCATGGTGCCGTCGAAGTTTGGCACCCAGTCCGCCGTCCCCTGACCGAGTTCGCTTAACAGCAGCTCGGCGTATTTGGACAGGCGGGATTCGGTATAACGCATCGCCGCGAATGACTTCGGATCATCCGGCGCGCCCCAGTTCCCCTGGCCATCGACCAGCGGGTAACGGTAAGAGAACGGCTGCGCCATCAGCACCATGGCTTCATAGCAGGCGCTGTCGCCATGCGGGTGATACTTACCCAGTACGTCACCAACGGTACGGGCGGATTTTTTAAATTTAGCGGTGGCGTTCAGCCCCAGCTCTGACATCGCATAGACGATGCGGCGCTGTACCGGCTTCAGGCCGTCGCCAATAAACGGCAACGCACGATCCATGATCACGTACATGGAGTAGTTTAAGTAGGCGTTTTCCGTAAATTCATGTAGCGCAAGGCGCTCTGCCATATCGCTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35734","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium str. LT2","NCBI_taxonomy_id":"99287"}}}},"ARO_accession":"3003939","ARO_id":"40662","ARO_name":"Salmonella enterica parC conferring resistance to fluoroquinolones","ARO_description":"Point mutations in Salmonella parC gene implicated in decreased susceptibility to fluoroquinolone antibiotics, primarily ciprofloxacin and nalidixic acid.","ARO_category":{"36913":{"category_aro_accession":"3000619","category_aro_cvterm_id":"36913","category_aro_name":"fluoroquinolone resistant parC","category_aro_description":"ParC is a subunit of topoisomerase IV, which decatenates and relaxes DNA to allow access to genes for transcription or translation. Point mutations in ParC prevent fluoroquinolone antibiotics from inhibiting DNA synthesis, and confer low-level resistance. Higher-level resistance results from both gyrA and parC mutations.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"37142":{"category_aro_accession":"3000762","category_aro_cvterm_id":"37142","category_aro_name":"pefloxacin","category_aro_description":"Pefloxacin is structurally and functionally similar to norfloxacin. It is poorly active against mycobacteria, while anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2395":{"model_id":"2395","model_name":"apmA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"3717":{"protein_sequence":{"accession":"CBL58181.1","sequence":"MKTRLEQVLERYLNGREVAVWGVPTRRLLRALKPFKFHTADRVDPQYHYVVAVTDDDLTDFLSDEQSKSFQYANDYLTFDDEGGELPFERMCFNVPVGRQTYFGDGVVGACENGYIKSIGQFTSINGTAEIHANHQLNMTFVSDDIQNFFNEESMAVFQEKLRKDPKHPYAYSKEPMTIGSDVYIGAHAFINASTVTSIGDGAIIGSGAVVLENVPPFAVVVGVPARIKRYRFSKEMIETLLRVKWWDWSIEEINENVDALISPELFMKKYGSL"},"dna_sequence":{"accession":"FN806789.3","fmin":"2693","fmax":"3518","strand":"+","sequence":"ATGAAAACCAGACTTGAACAAGTTTTAGAACGTTATCTCAACGGACGCGAGGTAGCTGTATGGGGTGTTCCGACACGCCGTTTGCTTCGTGCATTAAAACCTTTTAAATTTCATACTGCCGATCGTGTTGATCCTCAATATCATTATGTTGTTGCTGTAACCGATGACGACTTAACCGACTTTTTATCCGATGAACAGAGCAAGTCGTTTCAATACGCGAATGACTACCTTACGTTTGACGACGAGGGAGGCGAACTTCCGTTTGAACGAATGTGCTTCAATGTCCCCGTTGGCAGGCAAACGTATTTTGGAGACGGTGTCGTAGGAGCTTGCGAAAACGGGTATATCAAGAGCATCGGCCAATTTACATCGATTAACGGCACGGCAGAGATCCATGCGAACCATCAGTTAAACATGACCTTTGTAAGCGACGATATTCAAAACTTCTTCAACGAAGAAAGCATGGCTGTATTCCAAGAAAAGCTGCGAAAAGACCCGAAACACCCTTATGCTTATAGCAAAGAACCTATGACCATAGGTAGCGATGTTTATATCGGCGCACATGCATTCATCAATGCTTCCACTGTGACAAGCATCGGTGACGGTGCAATAATTGGCTCAGGGGCAGTAGTTCTGGAAAATGTTCCTCCTTTTGCTGTCGTCGTTGGTGTCCCTGCGAGAATCAAGCGTTACCGCTTCTCAAAGGAGATGATTGAAACCCTCCTTCGTGTCAAATGGTGGGACTGGAGTATAGAGGAAATTAACGAAAATGTTGATGCGCTTATATCACCTGAACTATTTATGAAAAAGTACGGGAGTTTGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3003918","ARO_id":"40626","ARO_name":"apmA","ARO_description":"Plasmid-borne apramycin-resistant aminocyclitol acetyltransferase gene identified from bovine MRSA.","ARO_category":{"41422":{"category_aro_accession":"3004258","category_aro_cvterm_id":"41422","category_aro_name":"amp acetyltransferase","category_aro_description":"A family of acetyltransferases that confer resistance to apramycin.","category_aro_class_name":"AMR Gene Family"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2411":{"model_id":"2411","model_name":"Shigella flexneri gyrA conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"4489":"N57K","4490":"H80P"},"clinical":{"4489":"N57K","4490":"H80P"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1500"}},"model_sequences":{"sequence":{"3741":{"protein_sequence":{"accession":"NP_708120.1","sequence":"MSDLAREITPVNIEEELKSSYLDYAMSVIVGRALPDVRDGLKPVHRRVLYAMNVLGNDWNKAYKKSARVVGDVIGKYHPHGDSAVYDTIVRMAQPFSLRYMLVDGQGNFGSIDGDSAAAMRYTEIRLAKIAHELMADLEKETVDFVDNYDGTEKIPDVMPTKIPNLLVNGSSGIAVGMATNIPPHNLTEVINGCLAYIDDEDISIEGLMEHIPGPDFPTAAIINGRRGIEEAYRTGRGKVYIRARAEVEVDAKTGRETIIVHEIPYQVNKARLIEKIAELVKEKRVEGISALRDESDKDGMRIVIEVKRDAVGEVVLNNLYSQTQLQVSFGINMVALHHGQPKIMNLKDIIAAFVRHRREVVTRRTIFELRKARDRAHILEALAVALANIDPIIELIRHAPTPAEAKTALVANPWQLGNVAAMLERAGDDAARPEWLEPEFGVRDGLYYLTEQQAQAILDLRLQKLTGLEHEKLLDEYKELLDQIAELLRILGSADRLMEVIREELELVREQFGDKRRTEITANSADINLEDLITQEDVVVTLSHQGYVKYQPLSEYEAQRRGGKGKSAARIKEEDFIDRLLVANTHDHILCFSSRGRVYSMKVYQLPEATRGARGRPIVNLLPLEQDERITAILPVTEFEEGVKVFMATANGTVKKTVLTEFNRLRTAGKVAIKLVDGDELIGVDLTSGEDEVMLFSAEGKVVRFKESSVRAMGCNTTGVRGIRLGEGDKVVSLIVPRGDGAILTATQNGYGKRTAVAEYPTKSRATKGVISIKVTERNGLVVGAVQVDDCDQIMMITDAGTLVRTRVSEISIVGRNTQGVILIRTAEDENVVGLQRVAEPVDEEDLDTIDGSAAEGDDEIAPEVDVDDEPEEE"},"dna_sequence":{"accession":"NC_004337.2","fmin":"2352231","fmax":"2354859","strand":"-","sequence":"TTATTCTTCTTCTGGCTCGTCGTCAACGTCCACTTCCGGAGCAATTTCATCATCCCCTTCCGCGGCACTGCCGTCGATGGTATCCAGATCTTCCTCGTCAACCGGTTCAGCAACACGCTGCAGACCCACTACGTTTTCATCTTCCGCAGTACGGATGAGGATCACGCCCTGGGTGTTACGGCCCACGATGCTGATTTCTGAAACGCGAGTACGTACCAGCGTACCGGCATCGGTGATCATCATGATCTGGTCGCAGTCATCTACCTGCACCGCGCCAACCACTAAACCGTTACGTTCGGTAACCTTGATGGAGATAACCCCTTTCGTCGCACGCGACTTGGTTGGGTATTCCGCCACTGCAGTACGTTTACCGTAACCGTTTTGCGTTGCGGTGAGGATTGCGCCATCGCCACGAGGCACGATCAGAGAGACGACTTTATCGCCTTCACCTAAGCGAATACCGCGCACACCAGTGGTATTGCAGCCCATCGCACGGACAGAAGACTCTTTAAAGCGCACCACTTTACCTTCGGCGGAGAACAGCATTACTTCATCTTCGCCACTGGTCAGATCAACGCCGATCAGCTCATCGCCGTCAACCAGTTTGATCGCCACTTTACCGGCGGTACGCAGACGGTTGAATTCGGTGAGGACGGTTTTCTTCACAGTACCGTTAGCGGTCGCCATGAAGACTTTCACGCCTTCTTCAAACTCGGTCACCGGCAGGATCGCGGTGATACGTTCGTCCTGTTCCAGCGGTAGCAGGTTGACGATCGGACGACCGCGCGCGCCACGAGTGGCTTCCGGCAACTGGTAAACTTTCATCGAATAGACGCGACCACGGCTGGAGAAGCACAGAATATGGTCGTGCGTGTTCGCCACCAGCAGTCGGTCGATAAAGTCTTCTTCTTTAATACGTGCGGCAGATTTACCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATATTTAACGTAGCCCTGGTGAGAGAGCGTCACGACCACATCTTCCTGGGTGATCAGATCTTCCAGGTTGATGTCTGCGCTGTTGGCGGTGATTTCAGTACGACGTTTGTCACCGAACTGTTCACGAACCAGCTCCAGCTCTTCGCGGATCACTTCCATCAGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCGATCTGATCCAGCAGCTCTTTGTATTCGTCGAGCAGTTTTTCGTGCTCAAGGCCGGTCAGTTTCTGCAAACGCAGATCCAGAATCGCCTGAGCTTGCTGTTCGGTCAGGTAGTACAGACCATCACGCACGCCGAACTCTGGCTCCAGCCATTCCGGACGCGCAGCATCGTCGCCAGCACGTTCCAACATGGCGGCAACGTTGCCCAGCTGCCACGGATTAGCAACCAGCGCAGTTTTCGCTTCTGCAGGCGTCGGCGCATGACGGATCAGTTCGATGATCGGGTCAATGTTCGCCAGCGCCACGGCTAATGCTTCAAGGATATGAGCACGATCGCGAGCTTTACGCAGTTCGAAAATAGTACGACGGGTCACCACTTCACGGCGGTGACGAACAAACGCCGCGATGATGTCTTTCAGGTTCATGATCTTCGGCTGACCATGGTGCAATGCCACCATGTTGATACCGAAAGAAACCTGCAACTGGGTCTGGGAGTAGAGGTTGTTGAGCACAACTTCACCGACCGCATCGCGTTTCACTTCAATCACGATGCGCATACCGTCTTTGTCAGACTCGTCACGCAGCGCGCTGATGCCTTCCACGCGTTTTTCTTTTACCAGTTCCGCAATCTTCTCGATCAGGCGCGCTTTGTTTACCTGATACGGAATTTCGTGGACGATAATGGTTTCACGTCCGGTTTTGGCGTCAACTTCCACTTCAGCACGGGCGCGGATATATACCTTGCCGCGACCGGTACGGTAAGCTTCTTCAATACCGCGACGACCGTTAATGATTGCCGCCGTCGGGAAGTCCGGCCCCGGGATGTGTTCCATCAGCCCTTCAATGCTGATGTCTTCATCATCGATATACGCCAGACAACCGTTGATGACTTCCGTCAGGTTGTGCGGCGGGATGTTGGTTGCCATACCTACGGCGATACCGGAAGAACCGTTCACCAGCAGGTTAGGAATTTTGGTTGGCATGACGTCGGGAATTTTTTCCGTGCCGTCATAGTTATCAACGAAATCGACCGTCTCTTTTTCGAGATCGGCCATCAGTTCATGGGCAATTTTCGCCAGACGGATTTCCGTATAACGCATTGCCGCCGCAGAGTCGCCGTCGATGGAACCGAAGTTACCCTGACCGTCTACCAGCATGTAACGCAGCGAGAATGGCTGCGCCATACGGACGATCGTGTCATAAACCGCCGAGTCACCATGGGGATGGTATTTACCGATTACGTCACCAACGACACGGGCAGATTTTTTATAGGCTTTGTTCCAGTCATTGCCTAGTACGTTCATGGCGTAAAGTACGCGACGGTGTACCGGCTTCAGGCCATCTCGGACATCTGGCAGCGCACGGCCAACAATGACCGACATCGCATAATCCAGATAGGAGCTCTTTAGCTCTTCCTCAATGTTGACCGGTGTAATTTCTCTCGCAAGGTCGCTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40665","NCBI_taxonomy_name":"Shigella flexneri 2a str. 301","NCBI_taxonomy_id":"198214"}}}},"ARO_accession":"3003940","ARO_id":"40664","ARO_name":"Shigella flexneri gyrA conferring resistance to fluoroquinolones","ARO_description":"Point mutations in Shigella flexneri gyrA observed to confer resistance to fluoroquinolone antibiotics.","ARO_category":{"39876":{"category_aro_accession":"3003292","category_aro_cvterm_id":"39876","category_aro_name":"fluoroquinolone resistant gyrA","category_aro_description":"DNA gyrase is responsible for DNA supercoiling and consists of two alpha and two beta subunits. GyrA point mutations confer resistance by preventing fluoroquinolone antibiotics from binding the alpha-subunit.","category_aro_class_name":"AMR Gene Family"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"40463":{"category_aro_accession":"3003780","category_aro_cvterm_id":"40463","category_aro_name":"nybomycin","category_aro_description":"A  heterocyclic antibiotic that targets mutant gyrA (type II topoisomerase) containing an S84L substitution, counteracting acquired quinolone resistance. It is effective against quinolone-resistant Gram-positive bacteria including S. aureus and E. faecalis. Due to its ability to counteract quinolone resistance by targeting the mutant form of the gyrA protein, it is classified as a reverse antibiotic (RA).","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2412":{"model_id":"2412","model_name":"Shigella flexneri parC conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"4492":"A85T","4493":"D111H","4494":"S129P"},"clinical":{"4492":"A85T","4493":"D111H","4494":"S129P"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1400"}},"model_sequences":{"sequence":{"3742":{"protein_sequence":{"accession":"NP_708834.1","sequence":"MSDMAERLALHEFTENAYLNYSMYVIMDRALPFIGDGLKPVQRRIVYAMSELGLNASAKFKKSARTVGDVLGKYHPHGDSACYEAMVLMAQPFSYRYPLVDGQGNWGAPDDPKSFAAMRYTESRLSKYSELLLSELGQGTADWVPNFDGTLQEPKMLPARLPNILLNGTTGIAVGMATDIPPHNLREVAQAAIALIDQPKTTLDQLLDIVQGPDYPTEAEIITSRAEIRKIYENGRGSVRMRAVWKKEDGAVVISALPHQVSGARVLEQIAAQMRNKKLPMVDDLRDESDHENPTRLVIVPRSNRVDMDQVMNHLFATTDLEKSYRINLNMIGLDGRPAVKNLLEILSEWLVFRRDTVRRRLNYRLEKVLKRLHILEGLLVAFLNIDEVIEIIRNEDEPKPALMSRFGLTETQAEAILELKLRHLAKLEEMKIRGEQSELEKERDQLQGILASERKMNNLLKKELQADAQAYGDDRRSPLQEREEAKAMSEHDMLPSEPVTIVLSQMGWVRSAKGHDIDAPGLNYKAGDSFKAAVKGKSNQPVVFVDSTGRSYAIDPITLPSARGQGEPLTGKLTLPPGATVDHMLMESDDQKLLMASDAGYGFVCTFNDLVARNRAGKALITLPENAHVMPPVVIEDASDMLLAITQAGRMLMFPVSDLPQLSKGKGNKIINIPSAEAARGEDGLAQLYVLPPQSTLTIHVGKRKIKLRPEELQKVTGERGRRGTLMRGLQRIDRVEIDSPRRASSGDSEE"},"dna_sequence":{"accession":"NC_004337.2","fmin":"3159154","fmax":"3161413","strand":"-","sequence":"TTACTCTTCGCTATCACCGCTGCTGGCACGGCGAGGAGAGTCGATCTCAACACGATCGATACGCTGCAAACCGCGCATCAACGTACCGCGGCGTCCACGTTCGCCAGTGACTTTCTGTAGCTCTTCCGGACGCAGTTTAATTTTGCGTTTCCCAACATGAATGGTCAGCGTGCTTTGCGGCGGCAGAACGTACAGTTGCGCCAGACCATCCTCGCCACGCGCGGCTTCTGCCGATGGAATGTTGATAATCTTGTTGCCTTTGCCCTTCGACAGCTGCGGCAGATCGCTTACCGGGAACATCAACATACGGCCTGCCTGAGTGATTGCCAGCAGCATATCGGAAGCATCTTCAATCACCACCGGCGGCATAACATGGGCATTTTCCGGTAAGGTGATCAAAGCCTTACCCGCACGGTTACGCGCTACCAGATCGTTAAAGGTGCAGACGAAACCGTAACCCGCATCGGAAGCCATCAGCAGTTTCTGATCGTCGCTTTCCATCAGCATATGGTCAACGGTCGCCCCAGGCGGCAACGTTAATTTGCCGGTGAGTGGTTCGCCCTGACCACGCGCCGACGGCAGCGTAATCGGGTCGATGGCATAGCTACGACCGGTGGAATCAACAAACACTACCGGTTGGTTACTCTTACCTTTCACCGCCGCTTTGAAGCTATCACCCGCTTTATAATTCAGGCCCGGCGCGTCGATATCATGGCCTTTAGCGCTGCGTACCCAGCCCATCTGCGACAGCACAATGGTGACAGGTTCAGACGGCAGCATGTCGTGCTCGCTCATCGCTTTCGCTTCTTCGCGTTCCTGCAACGGCGAACGACGATCGTCACCGTAGGCTTGCGCGTCTGCCTGCAGTTCTTTCTTCAGCAGGTTATTCATTTTACGCTCGGAAGCCAAAATGCCCTGCAACTGGTCGCGCTCTTTTTCCAGCTCACTCTGCTCACCGCGAATCTTCATCTCTTCCAGTTTGGCAAGATGACGCAGTTTCAGTTCGAGGATCGCTTCCGCCTGGGTTTCCGTAAGGCCAAACCGCGACATCAGCGCCGGTTTCGGTTCATCTTCGTTACGAATGATCTCAATCACTTCGTCGATGTTGAGAAACGCCACCAGCAAACCTTCCAGGATATGCAGGCGCTTGAGGACTTTCTCCAGACGATAGTTCAGTCGGCGGCGCACGGTATCGCGACGGAACACCAGCCATTCGGAGAGGATTTCCAGCAGGTTTTTCACCGCCGGACGACCATCCAGACCGATCATATTGAGGTTAATGCGATAGCTCTTTTCCAGATCGGTGGTAGCGAAGAGGTGGTTCATCACCTGATCCATATCCACGCGGTTGGAACGCGGCACAATCACCAGACGGGTCGGGTTCTCGTGGTCAGATTCATCGCGCAGATCGTCAACCATCGGCAGCTTTTTGTTGCGCATTTGCGCAGCAATTTGCTCCAGTACGCGCGCACCTGAAACCTGATGCGGTAATGCGCTGATAACCACCGCGCCATCTTCTTTCTTCCACACCGCGCGCATACGCACTGAACCACGTCCGTTCTCGTAGATTTTACGAATCTCGGCGCGCGAAGTGATAATTTCCGCTTCAGTCGGATAATCCGGCCCCTGCACGATATCCAGCAGCTGATCGAGCGTAGTTTTCGGCTGGTCGATTAATGCGATTGCCGCCTGAGCTACTTCACGCAGGTTATGCGGTGGAATATCGGTCGCCATGCCGACGGCAATACCGGTGGTGCCGTTAAGCAAAATGTTTGGCAGACGGGCAGGTAGCATTTTCGGCTCCTGCAAAGTGCCGTCGAAGTTTGGCACCCAGTCAGCCGTCCCCTGCCCCAGCTCGCTCAATAGCAGCTCGGAATATTTCGACAACCGGGATTCGGTGTAACGCATTGCCGCGAACGATTTCGGATCGTCCGGCGCGCCCCAGTTCCCCTGACCATCAACCAGCGGATAACGGTAAGAGAACGGCTGCGCCATCAGGACCATCGCTTCATAACAGGCGCTATCGCCGTGCGGATGGTATTTACCCAGTACGTCACCGACGGTACGGGCCGATTTTTTAAATTTGGCGCTGGCATTCAGGCCCAGTTCAGACATCGCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACATGGAGTAGTTTAAGTAGGCGTTTTCCGTAAATTCATGTAGCGCAAGGCGCTCTGCCATATCGCTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40665","NCBI_taxonomy_name":"Shigella flexneri 2a str. 301","NCBI_taxonomy_id":"198214"}}}},"ARO_accession":"3003941","ARO_id":"40666","ARO_name":"Shigella flexneri parC conferring resistance to fluoroquinolones","ARO_description":"Point mutation in parC conferring resistance to fluoroquinolone antibiotics in Shigella flexneri,","ARO_category":{"36913":{"category_aro_accession":"3000619","category_aro_cvterm_id":"36913","category_aro_name":"fluoroquinolone resistant parC","category_aro_description":"ParC is a subunit of topoisomerase IV, which decatenates and relaxes DNA to allow access to genes for transcription or translation. Point mutations in ParC prevent fluoroquinolone antibiotics from inhibiting DNA synthesis, and confer low-level resistance. Higher-level resistance results from both gyrA and parC mutations.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"37142":{"category_aro_accession":"3000762","category_aro_cvterm_id":"37142","category_aro_name":"pefloxacin","category_aro_description":"Pefloxacin is structurally and functionally similar to norfloxacin. It is poorly active against mycobacteria, while anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2409":{"model_id":"2409","model_name":"Neisseria meningititis PBP2 conferring resistance to beta-lactam","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"4464":"G482S","4466":"F504L","4467":"A510V","4468":"I312M","4469":"V316T","4470":"N512Y","4471":"G545S","4472":"A501P"},"experimental":{"4464":"G482S","4466":"F504L","4467":"A510V","4468":"I312M","4469":"V316T","4470":"N512Y","4471":"G545S","4472":"A501P"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"3738":{"protein_sequence":{"accession":"NP_273462.1","sequence":"MLIKSEYKPRMLPKEEQVKKPMTSNGRISFVLMAIAVLFAGLIARGLYLQTVTYNFLKEQGDNRIVRTQTLPATRGTVSDRNGAVLALSAPTESLFAVPKEMKEMPSAAQLERLSELVDVPVDVLRNKLEQKGKSFIWIKRQLDPKVAEEVKALGLENFVFEKELKRHYPMGNLFAHVIGFTDIDGKGQEGLELSLEDSLHGEDGAEVVLRDRQGNIVDSLDSPRNKAPKNGKDIILSLDQRIQTLAYEELNKAVEYHQAKAGTVVVLDARTGEILALANTPAYDPNRPGRADSEQRRNRAVTDMIEPGSAIKPFVIAKALDAGKTDLNERLNTQPYKIGPSPVRDTHVYPSLDVRGIMQKSSNVGTSKLSARFGAEEMYDFYHELGIGVRMHSGFPGETAGLLRNWRRWRPIEQATMSFGYGLQLSLLQLARAYTALTHDGVLLPVSFEKQAVAPQGKRIFKESTAREVRNLMVSVTEPGGTGTAGAVDGFDVGAKTGTARKFVNGRYADNKHIATFIGFAPAKNPRVIVAVTIDEPTAHGYYGGVVAGPPFKKIMGGSLNILGISPTKPLTAAAVKTPS"},"dna_sequence":{"accession":"NC_003112.2","fmin":"419828","fmax":"421574","strand":"+","sequence":"ATGTTGATTAAGAGCGAATATAAGCCTCGGATGCTGCCCAAAGAAGAGCAGGTCAAAAAGCCGATGACCAGTAACGGACGGATCAGCTTCGTCCTGATGGCAATAGCGGTCTTGTTTGCCGGTCTGATTGCTCGCGGACTGTATCTGCAGACGGTAACGTATAACTTTTTGAAAGAACAGGGCGACAACCGGATTGTGCGGACTCAAACATTGCCGGCTACACGCGGTACGGTTTCGGACCGGAACGGTGCGGTTTTGGCGTTGAGTGCGCCGACGGAGTCCCTGTTTGCCGTGCCTAAAGAGATGAAGGAAATGCCGTCTGCCGCACAATTGGAACGCCTGTCCGAGCTTGTCGATGTGCCGGTTGATGTTTTGAGGAACAAGCTCGAACAGAAAGGCAAGTCGTTTATCTGGATTAAGCGGCAGCTCGATCCCAAGGTTGCCGAAGAGGTCAAAGCCTTGGGTTTGGAAAACTTTGTATTTGAAAAAGAATTAAAACGCCATTACCCGATGGGCAACCTGTTTGCACACGTCATCGGATTTACCGATATTGACGGCAAAGGTCAGGAAGGTTTGGAACTTTCGCTTGAAGACAGCCTGCATGGCGAAGACGGCGCGGAAGTCGTTTTGCGGGACCGGCAGGGCAATATTGTGGACAGCTTGGACTCCCCGCGCAATAAAGCCCCGAAAAACGGCAAAGACATCATCCTTTCCCTCGATCAGAGGATTCAGACCTTGGCCTATGAAGAGTTGAACAAGGCGGTCGAATACCATCAGGCAAAAGCCGGAACGGTGGTGGTTTTGGATGCCCGCACGGGGGAAATCCTCGCCTTGGCCAATACGCCCGCCTACGATCCCAACAGGCCCGGCCGGGCAGACAGCGAACAGCGGCGCAACCGTGCCGTAACCGATATGATCGAACCCGGTTCGGCAATCAAACCGTTTGTGATTGCGAAGGCATTGGATGCGGGCAAAACCGATTTGAACGAACGGCTGAATACGCAGCCTTATAAAATCGGACCGTCTCCCGTGCGCGATACCCATGTTTACCCCTCTTTGGATGTGCGCGGCATCATGCAGAAATCGTCCAACGTCGGCACAAGCAAACTGTCTGCGCGTTTCGGTGCCGAAGAAATGTATGACTTCTATCATGAGTTGGGCATCGGTGTGCGTATGCACTCGGGCTTTCCGGGCGAAACTGCAGGTTTGTTGAGAAATTGGCGCAGGTGGCGGCCTATCGAACAGGCGACGATGTCTTTCGGTTACGGCCTGCAATTGAGCCTGCTGCAATTGGCGCGCGCCTATACCGCACTGACGCACGACGGCGTTTTACTGCCGGTCAGCTTTGAAAAACAGGCGGTTGCGCCGCAAGGCAAACGCATATTCAAAGAATCGACCGCGCGCGAGGTACGCAATCTGATGGTTTCCGTAACCGAGCCGGGCGGCACCGGTACGGCGGGTGCGGTGGACGGTTTCGATGTCGGCGCGAAAACCGGCACGGCGCGCAAGTTCGTCAACGGGCGTTATGCCGACAACAAACACATCGCTACCTTTATCGGTTTTGCCCCCGCCAAAAATCCCCGTGTGATTGTGGCGGTAACCATTGACGAACCGACTGCCCACGGTTATTACGGCGGCGTAGTGGCAGGGCCGCCCTTCAAAAAAATTATGGGCGGCAGCCTGAACATCTTGGGCATTTCCCCGACCAAGCCACTGACCGCCGCAGCCGTCAAAACACCGTCTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39597","NCBI_taxonomy_name":"Neisseria meningitidis MC58","NCBI_taxonomy_id":"122586"}}}},"ARO_accession":"3003937","ARO_id":"40660","ARO_name":"Neisseria meningititis PBP2 conferring resistance to beta-lactam","ARO_description":"Point mutation in Neisseria meningititis PBP2 (penA) decreases affinity between beta-lactam antibiotic molecule and PBP2, thereby conferring resistance to beta-lactam.","ARO_category":{"40661":{"category_aro_accession":"3003938","category_aro_cvterm_id":"40661","category_aro_name":"Penicillin-binding protein mutations conferring resistance to beta-lactam antibiotics","category_aro_description":"Mutations in PBP transpeptidases that change the affinity for penicillin thereby conferring resistance to penicillin antibiotics","category_aro_class_name":"AMR Gene Family"},"35927":{"category_aro_accession":"0000008","category_aro_cvterm_id":"35927","category_aro_name":"cefoxitin","category_aro_description":"Cefoxitin is a cephamycin antibiotic often grouped with the second generation cephalosporins. Cefoxitin is bactericidal and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. Cefoxitin's 7-alpha-methoxy group and 3' leaving group make it a poor substrate for most beta-lactamases.","category_aro_class_name":"Antibiotic"},"35930":{"category_aro_accession":"0000011","category_aro_cvterm_id":"35930","category_aro_name":"cloxacillin","category_aro_description":"Cloxacillin is a semisynthetic, isoxazolyl penicillin derivative in the beta-lactam class of antibiotics. It interferes with peptidogylcan synthesis and is commonly used for treating penicillin-resistant Staphylococcus aureus infections.","category_aro_class_name":"Antibiotic"},"35934":{"category_aro_accession":"0000015","category_aro_cvterm_id":"35934","category_aro_name":"methicillin","category_aro_description":"Derived from penicillin to combat penicillin-resistance, methicillin is insensitive to beta-lactamases (also known as penicillinases) secreted by many penicillin-resistant bacteria. Methicillin is bactericidal, and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Antibiotic"},"35961":{"category_aro_accession":"0000043","category_aro_cvterm_id":"35961","category_aro_name":"carbenicillin","category_aro_description":"Carbenicillin is a semi-synthetic antibiotic belonging to the carboxypenicillin subgroup of the penicillins. It has gram-negative coverage which includes Pseudomonas aeruginosa but limited gram-positive coverage. The carboxypenicillins are susceptible to degradation by beta-lactamase enzymes. Carbenicillin antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Antibiotic"},"35971":{"category_aro_accession":"0000054","category_aro_cvterm_id":"35971","category_aro_name":"penicillin","category_aro_description":"Penicillin (sometimes abbreviated PCN) is a beta-lactam antibiotic used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms. It works by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Antibiotic"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35975":{"category_aro_accession":"0000058","category_aro_cvterm_id":"35975","category_aro_name":"cefazolin","category_aro_description":"Cefazolin (INN), also known as cefazoline or cephazolin, is a first generation cephalosporin antibiotic. It is administered parenterally, and is active against a broad spectrum of bacteria.","category_aro_class_name":"Antibiotic"},"35976":{"category_aro_accession":"0000059","category_aro_cvterm_id":"35976","category_aro_name":"cefepime","category_aro_description":"Cefepime (INN) is a fourth-generation cephalosporin antibiotic developed in 1994. It contains an aminothiazolyl group that decreases its affinity with beta-lactamases. Cefepime shows high binding affinity with penicillin-binding proteins and has an extended spectrum of activity against Gram-positive and Gram-negative bacteria, with greater activity against both Gram-negative and Gram-positive organisms than third-generation agents.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35978":{"category_aro_accession":"0000061","category_aro_cvterm_id":"35978","category_aro_name":"ceftobiprole","category_aro_description":"Ceftobiprole (Zeftera\/Zevtera) is a next generation (5th generation) cephalosporin antibiotic with activity against methicillin-resistant Staphylococcus aureus, penicillin-resistant Streptococcus pneumoniae, Pseudomonas aeruginosa, and Enterococci. Ceftobiprole inhibits transpeptidases essential to building cell walls, and is a poor substrate for most beta-lactamases.","category_aro_class_name":"Antibiotic"},"35979":{"category_aro_accession":"0000062","category_aro_cvterm_id":"35979","category_aro_name":"ceftriaxone","category_aro_description":"Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"35980":{"category_aro_accession":"0000063","category_aro_cvterm_id":"35980","category_aro_name":"cefuroxime","category_aro_description":"Cefuroxime is a second-generation cephalosporin antibiotic with increased stability with beta-lactamases than first-generation cephalosporins. Cefuroxime is active against Gram-positive organisms but less active against methicillin-resistant strains.","category_aro_class_name":"Antibiotic"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"35987":{"category_aro_accession":"0000070","category_aro_cvterm_id":"35987","category_aro_name":"ertapenem","category_aro_description":"Ertapenem is a carbapenem antibiotic and is highly resistant to beta-lactamases like other carbapenems. It inhibits bacterial cell wall synthesis.","category_aro_class_name":"Antibiotic"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"35995":{"category_aro_accession":"0000078","category_aro_cvterm_id":"35995","category_aro_name":"piperacillin","category_aro_description":"Piperacillin is an acetylureidopenicillin and has an extended spectrum of targets relative to other beta-lactam antibiotics. It inhibits cell wall synthesis in bacteria, and is usually taken with the beta-lactamase inhibitor tazobactam to overcome penicillin-resistant bacteria.","category_aro_class_name":"Antibiotic"},"36309":{"category_aro_accession":"3000170","category_aro_cvterm_id":"36309","category_aro_name":"imipenem","category_aro_description":"Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.","category_aro_class_name":"Antibiotic"},"36689":{"category_aro_accession":"3000550","category_aro_cvterm_id":"36689","category_aro_name":"aztreonam","category_aro_description":"Aztreonam was the first monobactam discovered, and is greatly effective against Gram-negative bacteria while inactive against Gram-positive bacteria. Artreonam is a poor substrate for beta-lactamases, and may even act as an inhibitor. In Gram-negative bacteria, Aztreonam interferes with filamentation, inhibiting cell division and leading to cell death.","category_aro_class_name":"Antibiotic"},"36976":{"category_aro_accession":"3000632","category_aro_cvterm_id":"36976","category_aro_name":"benzylpenicillin","category_aro_description":"Benzylpenicillin, commonly referred to as penicillin G, is effective against both Gram-positive and Gram-negative bacteria. It is unstable in acid.","category_aro_class_name":"Antibiotic"},"36977":{"category_aro_accession":"3000633","category_aro_cvterm_id":"36977","category_aro_name":"phenoxymethylpenicillin","category_aro_description":"Phenoxymethylpenicillin, or penicillin V, is a penicillin derivative that is acid stable but less active than benzylpenicillin (penicillin G).","category_aro_class_name":"Antibiotic"},"36978":{"category_aro_accession":"3000634","category_aro_cvterm_id":"36978","category_aro_name":"propicillin","category_aro_description":"Propicillin is an orally taken penicillin derivative that has high absorption but poor activity.","category_aro_class_name":"Antibiotic"},"36979":{"category_aro_accession":"3000635","category_aro_cvterm_id":"36979","category_aro_name":"dicloxacillin","category_aro_description":"Dicloxacillin is a penicillin derivative that has an extra chlorine atom in comparison to cloxacillin. While more active than cloxacillin, its high affinity for serum protein reduces its activity in human serum in vitro.","category_aro_class_name":"Antibiotic"},"36980":{"category_aro_accession":"3000636","category_aro_cvterm_id":"36980","category_aro_name":"flucloxacillin","category_aro_description":"Flucloxacillin is similar to cloxacillin, with an extra additional fluorine atom.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"36982":{"category_aro_accession":"3000638","category_aro_cvterm_id":"36982","category_aro_name":"azlocillin","category_aro_description":"Azlocillin is a semisynthetic derivative of penicillin that is notably active against Ps. aeruginosa and other Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36983":{"category_aro_accession":"3000639","category_aro_cvterm_id":"36983","category_aro_name":"mezlocillin","category_aro_description":"Mezlocillin is a penicillin derivative taken parenterally.","category_aro_class_name":"Antibiotic"},"36984":{"category_aro_accession":"3000640","category_aro_cvterm_id":"36984","category_aro_name":"doripenem","category_aro_description":"Doripenem is a carbapenem with a broad range of activity against Gram-positive and Gram-negative bacteria, and along with meropenem, it is the most active beta-lactam antibiotic against Pseudomonas aeruginosa. It inhibits bacterial cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36985":{"category_aro_accession":"3000641","category_aro_cvterm_id":"36985","category_aro_name":"cefalexin","category_aro_description":"Cefalexin is a cephalosporin antibiotic that causes filamentation. It is resistant to staphylococcal beta-lactamase, but degraded by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"36986":{"category_aro_accession":"3000642","category_aro_cvterm_id":"36986","category_aro_name":"cefadroxil","category_aro_description":"Cefadroxil, or p-hydroxycephalexin, is an cephalosporin antibiotic similar to cefalexin.","category_aro_class_name":"Antibiotic"},"36987":{"category_aro_accession":"3000643","category_aro_cvterm_id":"36987","category_aro_name":"cefotiam","category_aro_description":"Cefotiam is a cephalosporin antibiotic with similar activity to cefuroxime but more active against enterobacteria. It is consumed orally as the prodrug cefotiam hexetil.","category_aro_class_name":"Antibiotic"},"36988":{"category_aro_accession":"3000644","category_aro_cvterm_id":"36988","category_aro_name":"cefaclor","category_aro_description":"Cefaclor is a semisynthetic cephalosporin derived from cephalexin. It has broad-spectrum antibiotic activity.","category_aro_class_name":"Antibiotic"},"36989":{"category_aro_accession":"3000645","category_aro_cvterm_id":"36989","category_aro_name":"cefotaxime","category_aro_description":"Cefotaxime is a semisynthetic cephalosporin taken parenterally. It is resistant to most beta-lactamases and active against Gram-negative rods and cocci due to its aminothiazoyl and methoximino functional groups.","category_aro_class_name":"Antibiotic"},"36990":{"category_aro_accession":"3000646","category_aro_cvterm_id":"36990","category_aro_name":"cefixime","category_aro_description":"Cefixime is a cephalosporin resistant to most beta-lactamases. It is active against many enterobacteria, but activity against staphylococci is poor.","category_aro_class_name":"Antibiotic"},"36991":{"category_aro_accession":"3000647","category_aro_cvterm_id":"36991","category_aro_name":"cefpodoxime","category_aro_description":"Cefpodoxime is a semisynthetic cephalosporin that acts similarly to cefotaxime with broad-spectrum activity. It is stable to many plasmid-mediated beta-lactamses. Cefpodoxime is consumed as the prodrug cefpodoxime proxetil.","category_aro_class_name":"Antibiotic"},"36992":{"category_aro_accession":"3000648","category_aro_cvterm_id":"36992","category_aro_name":"ceftibuten","category_aro_description":"Ceftibuten is a semisynthetic cephalosporin active against Gram-negative bacilli. It is resistant against many plasmid-mediated beta-lactamases.","category_aro_class_name":"Antibiotic"},"36993":{"category_aro_accession":"3000649","category_aro_cvterm_id":"36993","category_aro_name":"cefditoren","category_aro_description":"Cefditoren is a semisynthetic cephalosporin active against staphylococci, streptococci, and and most enterobacteria. It is resistant to staphylococcal and most enterobacterial beta-lactamases, and is usually taken as the prodrug cefditoren pivoxil.","category_aro_class_name":"Antibiotic"},"36994":{"category_aro_accession":"3000650","category_aro_cvterm_id":"36994","category_aro_name":"cefdinir","category_aro_description":"Cefdinir is similar to cefixime with a modified side-chain at its 7-amino position. It also shares similar activity with cefixime but is more active against staphylococci. It has also be shown to enhance phagocytosis.","category_aro_class_name":"Antibiotic"},"36995":{"category_aro_accession":"3000651","category_aro_cvterm_id":"36995","category_aro_name":"ceftaroline","category_aro_description":"Ceftaroline is a novel cephalosporin active against methicillin resistant Staphylococcus aureus. Like other cephalosporins it binds penicillin-binding proteins to inhibit cell wall synthesis. It strongly binds with PBP2a, associated with methicillin resistance. It is taken orally as the prodrug ceftaroline fosamil.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"37085":{"category_aro_accession":"3000705","category_aro_cvterm_id":"37085","category_aro_name":"isopenicillin N","category_aro_description":"Isopenicillin N is a natural penicillin derivative produced by Penicillium chrysogenum with activity similar to penicillin N.","category_aro_class_name":"Antibiotic"},"37086":{"category_aro_accession":"3000706","category_aro_cvterm_id":"37086","category_aro_name":"penicillin N","category_aro_description":"Penicillin N is a penicillin derivative produced by Cephalosporium acremonium.","category_aro_class_name":"Antibiotic"},"37141":{"category_aro_accession":"3000761","category_aro_cvterm_id":"37141","category_aro_name":"mecillinam","category_aro_description":"Mecillinam is a broad-spectrum beta-lactam antibiotic that was semi-synthetically derived to have a different drug centre, being a 6-alpha-amidinopenicillanate instead of a 6-alpha-acylaminopenicillanate. Contrasting most beta-lactam drugs, mecillinam is most active against Gram-negative bacteria. It binds specifically to penicillin binding protein 2 (PBP2).","category_aro_class_name":"Antibiotic"},"40928":{"category_aro_accession":"3004001","category_aro_cvterm_id":"40928","category_aro_name":"cefmetazole","category_aro_description":"Cefmetazole is a semi-synthetic cephamycin antibiotic with broad spectrum antibiotic activity against both gram-positive and gram-negative bacteria, that disrupt cell wall synthesis through binding to PBPs causing cell lysis.","category_aro_class_name":"Antibiotic"},"40929":{"category_aro_accession":"3004002","category_aro_cvterm_id":"40929","category_aro_name":"cefonicid","category_aro_description":"Cefonicid is a second-generation cephalosporin-class beta-lactam antibiotic with broad spectrum activity. Particularly used against urinary tract infections and lower respiratory infections. Causes cell lysis by inactivation of PBPs through binding, inhibiting peptidoglycan synthesis.","category_aro_class_name":"Antibiotic"},"40932":{"category_aro_accession":"3004005","category_aro_cvterm_id":"40932","category_aro_name":"cefprozil","category_aro_description":"Cefprozil is a cephalosporin and beta-lactam antibiotic with bactericidal activity. It selectively binds to PBPs and inhibits peptidoglycan synthesis, a major cell wall component, resulting in cell lysis.","category_aro_class_name":"Antibiotic"},"40933":{"category_aro_accession":"3004006","category_aro_cvterm_id":"40933","category_aro_name":"ceftiofur","category_aro_description":"Ceftiofur is a third-generation broad spectrum cephalosporin and beta-lactam antibiotic. It causes cell lysis by disrupting peptidoglycan cross-linkage and cell wall formation by binding to PBPs.","category_aro_class_name":"Antibiotic"},"40934":{"category_aro_accession":"3004007","category_aro_cvterm_id":"40934","category_aro_name":"ceftizoxime","category_aro_description":"Ceftizoxime is a third-generation cephalosporin and broad spectrum beta-lactam antibiotic. Ceftizoxime causes bacterial cell lysis through peptidoglycan cross-linking inhibition by binding to PBPs.","category_aro_class_name":"Antibiotic"},"40935":{"category_aro_accession":"3004008","category_aro_cvterm_id":"40935","category_aro_name":"cephapirin","category_aro_description":"Cephapirin is a first-generation cephalosporin and broad spectrum beta-lactam antibiotic. Inactivation of penicillin-binding proteins through cephapirin binding disrupts peptidoglycan cross-linking, resulting in cell lysis.","category_aro_class_name":"Antibiotic"},"40936":{"category_aro_accession":"3004009","category_aro_cvterm_id":"40936","category_aro_name":"cefradine","category_aro_description":"Cefradine is a first-generation cephalosporin and broad spectrum beta-lactam antibiotic. Cefradine binding to penicillin-binding proteins disrupts cell wall peptidoglycan cross-linkage, resulting in cell lysis.","category_aro_class_name":"Antibiotic"},"40943":{"category_aro_accession":"3004016","category_aro_cvterm_id":"40943","category_aro_name":"loracarbef","category_aro_description":"Loracarbef is a second-generation cephalosporin (carbacephem) and broad spectrum beta-lactam antibiotic. Loracarbef inhibits PBPs through binding, disrupting peptidoglycan cell wall cross-linkage and resulting in cell death.","category_aro_class_name":"Antibiotic"},"40944":{"category_aro_accession":"3004017","category_aro_cvterm_id":"40944","category_aro_name":"moxalactam","category_aro_description":"Moxalactam (Latamoxef) is a broad spectrum cephalosporin (oxacephem) and beta-lactam antibiotic. Moxalactam binding to PBPs inhibits peptidoglycan cross-linkage in the cell wall, resulting in cell death. Moxalactam is proposed to be effective against meningitides as it passes the blood-brain barrier.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2416":{"model_id":"2416","model_name":"abcA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"3000"}},"model_sequences":{"sequence":{"3747":{"protein_sequence":{"accession":"XP_753111.1","sequence":"MNESHEAGKNSSTNVEEREEEVLRLARQFTEQSSYSTAGQTPFAAEAGSALDPNGERFNARAWCKAMLQMHIGDKEAHPLRTLGVAFSNLNVHGFGSDTDYQKSVGNVWLKTLSLARIAFGQKQRKVDILQNLEGLVEAGEMLVVLGPPGSGCSTFLKTIAGETYGFHVDKNSNINFQGIAKQMAHEFRGEAIYTAEVDVHFPKLTVGDTLYFAARARTPRHIPGGVNATQYAGHMRDVIMAMFGISHTKNTIVGNDFIRGVSGGERKRVSIAEACLSNAPLQCWDNSTRGLDSANAIEFCKTLRMQADINGTTACVSLYQAPQAAYDYFDKVLVLYEGREIYFGPTSMAKHYFLQMGFVCPDRQTDADFLTSMTSHLERVVQPGYEDRVPRTPDEFAARWKASPQRAQLMQHIKSYNAKFALDGEYLDKFKQSRRAQQAKAQRVSSPYTLSYVQQVKLCLWRGYQRLKADPSVTISSLFGNTIISLVIASIFYNLKADTSTFFQRGALLFFAVLMNALGCGLEMLTLYAQRGIIEKHSRYALYHPSAEAFSSMIMDLPYKILNAITSNIVLYFMTNLRREPGAFFFFVFTSFILTLTMSMFFRSMASLSRSLVQVLPFSAVLLLGLSMYTGFAIPTGYMLGWARWIAYINPISYGFESLMINEFHNRDFPCMDYVPSGPGYTDVGLNNRVCSTVRSVPGQAFVNGNAYIESAYSYTASHKWRNIGVIFAYMFLLGAVYLVATDFITEKKPKGEILVFPRGHKALKKGKSDEDLEGGGGRSATVEKIGSDGLAMIERQTAIFQWKDVCFDIKIGKENCRILDHVDGWVKPGILTALMGVSGAGKTTLLDVLATRTTMGIISGEMLVDGQPRDESFQRKTGYAQQQDLHLSTATVREALEFSALLRQSAHVPRQEKIDYVTEVIKLLDMTEYADAVIGVPGEGLNVEQRKRLTIGVELAARPQLLLFLDEPTSGLDSQTSWAILDLLDKLKKNGQAILCTIHQPSAMLFQRFDRLLFLQAGGRTVYFGEIGQNSQILIDYFVRNGAPPCPPDANPAEWMLDVIGAAPGSHTSINWFETWRRSPEYARVQEHLAELKHERRHQTNLFRTTSGQKREDKDSYREFAAPFWAQLYQVQVRVFQQIWRSPTYIYSKTALCVLSALFVGFSLFHTPNTIQGLQNQMFGIFMLLTLFGQLIQQIMPHFVAQRALYEVRDRPAKTYSWKAFLIANIVVELPWNSLMSVLMFLCWYYPIGLYRNAEPTDAVHLRGTQMWLMIWTFLLFSSTFAHFMIAAFDAAENAGNLGNLLFLLCLLFCGVLATPDQLPRFWIFMYRVSPFTYLVSGMLSVGISNTNVTCADNEYLRFDPVNGTCGEYMGSYMSNLGGYLADEMATANCSFCPIKETNVFLGRVSSSYSDIWRNFGLMWVFIVFNIFAACSLYWWVRVPRDKKPVAKAE"},"dna_sequence":{"accession":"NC_007194.1","fmin":"4771163","fmax":"4775731","strand":"-","sequence":"TCACTCGGCCTTTGCAACTGGCTTCTTGTCTCGTGGAACACGAACCCACCAGTACAGCGAACAAGCTGCAAAGATATTGAAAACAATAAATACCCACATGAGCCCAAAGTTCCTCCAGATATCCGAGTAACTCGACGAAACTCTACCGAGGAACACATTCGTCTCCTTGATCGGGCAGAAGCTGCAGTTCGCAGTCGCCATCTCGTCTGCAAGGTACCCGCCCAGATTCGACATGTATGAGCCCATGTACTCGCCGCAAGTCCCATTGACGGGGTCAAAGCGCAGATACTCATTGTCCGCGCAGGTGACATTCGTATTCGATATACCCACAGACAACATCCCGCTCACCAGATATGTAAACGGCGAAACGCGATACATGAAGATCCAGAACCGTGGGAGCTGATCCGGTGTCGCTAGCACGCCGCAGAAAAGCAGACAAAGCAGGAAAAGCAGGTTTCCGAGGTTTCCCGCGTTCTCGGCGGCGTCAAACGCTGCGATCATAAAATGGGCAAAGGTGGACGAGAAGAGAAGGAAGGTCCAGATCATCAGCCACATTTGCGTGCCCCGCAAGTGCACCGCATCAGTTGGTTCGGCATTGCGGTAAAGACCAATCGGGTAGTACCAGCACAGGAACATAAGGACGGACATGAGCGAGTTCCAGGGGAGTTCAACAACGATGTTGGCGATGAGGAAGGCTTTCCAAGAGTAGGTTTTTGCAGGTCGGTCGCGGACTTCATACAGCGCGCGCTGGGCGACGAAATGCGGCATGATTTGTTGGATAAGCTGGCCGAACAGGGTAAGTAGCATGAAGATGCCGAACATTTGATTCTGGAGGCCTTGGATGGTGTTGGGTGTATGGAAAAGGGAGAAGCCGACGAAGAGAGCGGATAACACGCAGAGAGCGGTCTTGGAGTAGATGTAGGTGGGTGACCGCCAGATTTGCTGGAAGACTCGTACTTGGACTTGGTAGAGCTGGGCCCAGAAAGGAGCAGCGAACTCGCGGTAGCTGTCTTTGTCTTCGCGCTTTTGGCCGGATGTAGTGCGGAACAGGTTTGTTTGGTGGCGACGTTCGTGTTTCAGTTCAGCAAGGTGCTCTTGGACTCGTGCATATTCGGGGGATCGACGCCAGGTCTCGAACCAGTTGATGCTGGTGTGTGATCCGGGAGCGGCACCGATCACATCCAGCATCCATTCGGCAGGATTCGCATCCGGAGGACATGGAGGGGCACCGTTGCGGACGAAGTAGTCAATCAGTATTTGCGAGTTCTGACCGATTTCTCCAAAGTAGACAGTACGACCCCCAGCTTGAAGGAAGAGGAGACGATCAAAGCGCTGAAACAGCATGGCAGATGGTTGATGGATGGTACACACTTGGAACACATTAATGACAGCGATAAACGCCGGATCAGACACTTACAAATAGCCTGGCCGTTCTTCTTCAGTTTATCGAGGAGATCAAGAATAGCCCAGGATGTCTGAGAATCAAGTCCTGAGGTCGGTTCGTCTAGGAAAAGGCTGCGCACGCAACATGATGCGCCTATCCCCGCAATGGGGACAAACGCAATACACTCAGTCAGTAATTTGCCCAAGGCCGCAGTAATTGCTGGAGGGCACAAACTTACAGGAGTTGGGGTCTGGCTGCAAGCTCTACCCCGATTGTGAGACGTTTACGTTGCTCAACGTTCAGGCCTTCACCAGGCACCCCAATAACGGCATCAGCATACTCCGTCATGTCAAGAAGCTTGATCACTTCTGTCACGTAGTCAATCTTCTCTTGACGAGGAACGTGAGCAGATTGACGTAGAAGAGCAGAGAACTCAAGTGCCTCGCGCACGGTAGCAGTACTCAAATGCAGATCTTGTTGCTGAGCATAGCCGGTCTTACGTTGAAAGGACTCATCACGCGGTTGACCATCGACGAGCATTTCTCCACTGATAATCCCCATCGTGGTGCGCGTAGCAAGGACATCCAAGAGCGTGGTCTTTCCAGCACCCGAAACACCCATAAGCGCCGTCAAGATTCCCGGTTTGACCCATCCGTCAACATGGTCAAGAATCCTGCAATTCTCCTTTCCAATCTTGATATCGAAGCAGACATCCTTCCACTGGAAGATTGCGGTTTGGCGTTCAATCATGGCAAGGCCATCTGAGCCGATCTTCTCGACTGTGGCGCTGCGGCCACCACCCCCTTCAAGATCCTCATCTGACTTGCCTTTCTTCAGAGCCTTGTGTCCGCGAGGAAATACCAGGATCTCGCCCTTCGGCTTCTTCTCGGTGATGAAGTCAGTAGCAACGAGATAGACCGCCCCAAGCAGGAACATGTAAGCGAATATGACACCGATGTTTCTCCATTTGTGAGAAGCGGTATAGCTATATGCTGACTCAATGTAAGCATTGCCATTGACAAAGGCTTGTCCAGGCACTGATCTGACGGTGGAGCAAACACGGTTGTTGAGCCCGACATCCGTATAGCCAGGACCCGATGGGACATAGTCCATGCACGGGAAATCGCGGTTGTGGAACTCATTGATCATCAGTGACTCAAAGCCATAGCTGATGGGATTGATGTACGCAATCCAGCGAGCCCAGCCCAGCATATATCCAGTCGGGATAGCGAACCCAGTGTACATGCTGAGACCGAGAAGTAGCACGGCGGAGAAGGGCAGAACTTGGACAAGGGATCTGGATAGCGATGCCATAGACCGGAAGAACATGGACATGGTCAGAGTCAGGATGAACGAAGTGAAGACAAAGAAGAAGAAAGCCCCGGGTTCTCTCCTCAAGTTGGTCATGAAGTACAGAACTATATTGGACGTAATGGCGTTGAGAATCTTATAGGGCAAATCCATTATCATTGATGAAAAAGCTTCAGCAGATGGATGGTAGAGAGCGTATCGGGAGTGCTTCTCGATGATCCCTCGTTGCGCGTATAGAGTCAGCATTTCAAGGCCGCAGCCAAGAGCGTTCATAAGAACAGCAAAGAAGAGAAGAGCACCACGCTGAAAAAAGGTGCTGGTGTCAGCCTTGAGGTTGTAGAAGATACTGGCGATAACTAGGGATATGATAGTATTTCCGAATAATGAAGAGATTGTGACACTGGGGTCAGCCTTCAATCGTTGATACCCGCGCCACAGGCACAGTTTCACCTGTTGGACATAGGAAAGAGTGTAGGGTGATGATACCCGCTGAGCCTTGGCTTGCTGGGCTCGCCGAGATTGCTTAAACTTATCCAGGTATTCCCCATCCAGTGCGAACTTTGCATTATAACTCTTGATGTGTTGCATCAGCTGTGCTCGCTGTGGTGAGGCCTTCCATCGTGCAGCGAACTCATCAGGTGTTCGAGGTACGCGATCTTCATAACCAGGCTGAACAACACGCTCAAGATGGCTAGTCATAGATGTGAGAAAGTCGGCATCGGTTTGCCGGTCAGGGCATACGAAGCCCATCTGAAGGAAGTAGTGCTTCGCCATGGATGTGGGACCAAAGTAGATCTCGCGACCTTCGTATAGGACCAGGACCTTATCGAAATAGTCGTACGCAGCCTGGGGAGCTTGATATAGAGAGACACAGGCTGTGGTGCCATTGATATCTGCCTGCATGCGTAAGGTTTTGCAGAACTCAATGGCATTCGCACTATCAAGACCACGAGTCGAATTGTCCCAACATTGCAGCGGTGCATTGCTGAGACAAGCTTCCGCAATGCTAACCCGCTTGCGCTCTCCACCAGATACACCGCGGATGAAGTCGTTTCCGACAATTGTGTTCTTCGTATGGCTGATACCAAACATGGCCATGATCACGTCTCGCATGTGGCCGGCATACTGGGTCGCATTCACCCCCCCAGGAATGTGTCGTGGTGTTCGGGCACGAGCCGCGAAATAAAGGGTATCTCCAACCGTGAGCTTGGGGAAGTGGACATCAACCTCTGCGGTATAGATGGCTTCACCCCTGAACTCGTGGGCCATCTGCTTTGCGCTCACGCCTGACCGAAATTAGCAAAGCAGCACCCTGCTCTTGTGTCAAGTTAAACATGCCTTGGAAATTGATGTTTGAGTTTTTGTCCACATGAAAGCCGTAAGTCTCTCCAGCAATGGTCTTCAAAAAAGTGGAGCATCCAGATCCAGGGGGTCCAAGTACGACGAGCATCTCTCCAGCCTCCACCAATCCTTCCAAGTTCTGCAAAATGTCGACTTTGCGCTGCTTTTGACCAAATGCTATTCTTGCCAGGCTGAGCGTCTTTAACCAGACATTGCCGACGCTTTTCTGGTAATCAGTGTCGGAACCGAAACCATGCACATTGAGATTGCTGAAGGCGACCCCCAAGGTTCGCAGTGGGTGTGCCTCCTTGTCCCCAATGTGCATCTGCAGCATGGCCTTGCACCATGCCCGAGCGTTGAAGCGTTCACCATTGGGGTCCAGGGCCGATCCGGCCTCCGCAGCAAAGGGGGTTTGTCCCGCCGTGGAATAGCTGCTCTGCTCTGTGAACTGTCTGGCTAGCCGAAGAACCTCCTCTTCCCTCTCCTCCACATTGGTAGAGGAATTTTTTCCAGCTTCATGACTTTCATTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40696","NCBI_taxonomy_name":"Aspergillus fumigatus Af293","NCBI_taxonomy_id":"330879"}}}},"ARO_accession":"3003942","ARO_id":"40695","ARO_name":"abcA","ARO_description":"AbcA is a multidrug resistant ABC transporter that confers resistance to methicillin, daptomycin, cefotaxime, and moenomycin.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"35934":{"category_aro_accession":"0000015","category_aro_cvterm_id":"35934","category_aro_name":"methicillin","category_aro_description":"Derived from penicillin to combat penicillin-resistance, methicillin is insensitive to beta-lactamases (also known as penicillinases) secreted by many penicillin-resistant bacteria. Methicillin is bactericidal, and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Antibiotic"},"35985":{"category_aro_accession":"0000068","category_aro_cvterm_id":"35985","category_aro_name":"daptomycin","category_aro_description":"Daptomycin is a novel lipopeptide antibiotic used in the treatment of certain infections caused by Gram-positive organisms. Daptomycin interferes with the bacterial cell membrane, reducing membrane potential and inhibiting cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36989":{"category_aro_accession":"3000645","category_aro_cvterm_id":"36989","category_aro_name":"cefotaxime","category_aro_description":"Cefotaxime is a semisynthetic cephalosporin taken parenterally. It is resistant to most beta-lactamases and active against Gram-negative rods and cocci due to its aminothiazoyl and methoximino functional groups.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2397":{"model_id":"2397","model_name":"pgpB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"3724":{"protein_sequence":{"accession":"BAG33043.1","sequence":"MEYILEVERNLFLTLNGVQHPLLDGFFYLISAKWTWVIMSIAFLFFLFYKKPTKEALFIVGAVLLSVLICDQLSSSFFKPFFARFRPSHHPDFIDYVKTVYGYRGGKYGFISGHTTNYISLALFTSRIFRNKFYTWTIWSVVALVIYSRIYIGVHFITDIIPGIAVGLIVGHFVYKVYLYARSRWLGASCPAHPSAVYAGDSIRLWTLSLIGFVFAMLCMSRQLTEILQYYVFLLF"},"dna_sequence":{"accession":"AP009380.1","fmin":"573191","fmax":"573902","strand":"-","sequence":"TCAGAAGAGCAGGAAGACATAGTACTGTAGTATCTCCGTCAACTGGCGGGACATACACAGCATGGCAAAGACAAAGCCGATGAGGCTAAGTGTCCAGAGCCGAATGGAATCGCCGGCATAGACTGCCGACGGATGGGCAGGGCATGAGGCTCCCAACCAACGGGAACGTGCATACAGATAGACTTTATAAACAAAGTGTCCTACGATAAGTCCGACGGCGATACCCGGGATAATATCGGTGATGAAATGCACTCCGATATAAATACGGCTATAGATGACGAGTGCGACGACGCTCCAGATCGTCCACGTGTAGAATTTATTCCGAAAAATACGGCTCGTAAATAATGCCAGCGATATGTAGTTCGTCGTATGCCCTGAGATAAATCCGTACTTTCCTCCCCGATAGCCGTAGACCGTCTTCACATAGTCGATAAAATCAGGGTGGTGCGAAGGGCGGAATCTTGCGAAGAAAGGCTTGAAAAAAGAAGAGGAGAGTTGATCGCAGATGAGTACGCTCAATAAGACTGCTCCTACGATGAAGAGAGCTTCCTTTGTCGGTTTCTTATAAAAAAGGAAGAACAGAAACGCGATGGACATTATCACCCAAGTCCATTTGGCCGAGATCAAATAGAAAAAACCGTCCAACAAAGGATGCTGTACTCCGTTCAGAGTCAAAAAGAGGTTCCTTTCTACTTCAAGAATGTATTCCAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40629","NCBI_taxonomy_name":"Porphyromonas gingivalis ATCC 33277","NCBI_taxonomy_id":"431947"}}}},"ARO_accession":"3003920","ARO_id":"40628","ARO_name":"pgpB","ARO_description":"A gene that produces the protein lipid A 4\u2019-phosphatase","ARO_category":{"41451":{"category_aro_accession":"3004287","category_aro_cvterm_id":"41451","category_aro_name":"lipid A phosphatase","category_aro_description":"The antimicrobial activity of certain antibiotics, such as peptide antibiotics, is proposed to be initiated through binding to the lipid A moiety of lipopolysaccharides. Thus, covalent modification of Gram-negative bacterial lipid A by phosphatases is a mechanism to reduce the susceptibility of the bacteria to antibiotics.","category_aro_class_name":"AMR Gene Family"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1035":{"model_id":"1035","model_name":"Streptococcus pneumoniae PBP2b conferring resistance to amoxicillin","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"4480":"T445A","4481":"E475G","4482":"T488A"},"clinical":{"4480":"T445A","4481":"E475G","4482":"T488A"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1300"}},"model_sequences":{"sequence":{"3737":{"protein_sequence":{"accession":"NP_359110.1","sequence":"MRLICMRKFNSHSIPIRLNLLFSIVILLFMTIIGRLLYMQVLNKDFYEKKLASASQTKITSSSARGEIYDASGKPLVENTLKQVVSFTRSNKMTATDLKETAKKLLTYVSISSPNLTERQLADYYLADPEIYKKIVEALPSEKRLDSDGNRLSESELYNNAVDSVQTSQLNYTEDEKKEIYLFSQLNAVGNFATGTIATDPLNDSQVAVIASISKEMPGISISTSWDRKVLETSLSSIVGSVSSEKAGLPAEEAEAYLKKGYSLNDRVGTSYLEKQYEETLQGKRSVKEIHLDKYGNMESVDTIEEGSKGNNIKLTIDLAFQDSVDALLKSYFNSELENGGAKYSEGVYAVALNPKTGAVLSMSGIKHDLKTGELTPDSLGTVTNVFVPGSVVKAATISSGWENGVLSGNQTLTDQSIVFQGSAPINSWYTQAYGSFPITAVQALEYSSNTYMVQTALGLMGQTYQPNMFVGTSNLESAMEKLRSTFGEYGLGTATGIDLPDESTGFVPKEYSFANYITNAFGQFDNYTPMQLAQYVATIANNGVRVAPRIVEGIYGNNDKGGLGDLIQQLQPTEMNKVNISDSDMSILHQGFYQVAHGTSGLTTGRAFSNGALVSISGKTGTAESYVADGQQATNTNAVAYAPSDNPQIAVAVVFPHNTNLTNGVGPSIARDIINLYQKYHPMN"},"dna_sequence":{"accession":"NC_003098.1","fmin":"1494215","fmax":"1496273","strand":"-","sequence":"CTAATTCATTGGATGGTATTTTTGATACAGATTGATAATGTCACGCGCAATGGAAGGTCCTACACCATTTGTTAGATTGGTATTATGAGGAAAGACCACTGCGACAGCGATTTGGGGATTATCAGATGGGGCATAGGCCACCGCATTGGTATTGGTTGCTTGCTGACCATCTGCCACATAGCTTTCGGCTGTACCTGTTTTTCCGCTAATGGATACCAAGGCACCATTTGAAAAGGCACGTCCAGTTGTCAATCCACTAGTACCATGGGCAACCTGATAAAAACCTTGGTGCAAGATGCTCATATCGGAGTCGGATATATTGACCTTATTCATCTCTGTCGGTTGCAGTTGCTGAATCAAGTCACCCAGTCCTCCCTTATCATTATTACCATAAATGCCTTCAACAATACGAGGAGCCACACGAACACCATTATTTGCAATAGTTGCTACATACTGAGCCAACTGCATCGGCGTATAGTTATCAAACTGCCCAAAGGCATTAGTAATGTAATTAGCAAAGCTATACTCTTTGGGAACAAATCCAGTAGATTCATCTGGTAGGTCAATTCCTGTCGCAGTACCCAAGCCATATTCGCCAAAGGTTGAACGCAGTTTCTCCATAGCAGACTCTAGATTGCTGGTGCCGACAAACATATTGGGTTGATAGGTTTGCCCCATAAGACCTAAGGCTGTTTGGACCATATAGGTATTTGATGAATACTCCAGAGCTTGGACCGCTGTGATAGGGAATGAACCGTAAGCCTGAGTATACCAAGAATTGATGGGAGCTGAACCTTGGAAGACAATGGACTGGTCTGTCAAGGTCTGGTTTCCTGACAAGACTCCATTTTCCCAACCTGAGCTGATGGTCGCCGCCTTGACAACCGAACCTGGAACAAAGACATTGGTTACCGTTCCCAAGGAATCAGGCGTCAACTCTCCCGTTTTCAAGTCATGTTTAATCCCTGACATAGACAAAACCGCACCTGTTTTTGGGTTAAGGGCGACTGCATAGACACCTTCAGAATACTTGGCTCCACCATTTTCTAGCTCAGAATTGAAATAACTTTTCAGTAAAGCATCCACGCTATCTTGGAAAGCCAAATCAATGGTCAGTTTGATATTGTTTCCCTTACTACCTTCCTCAATTGTATCCACGCTTTCCATATTGCCATATTTATCCAGATGGATTTCTTTTACCGAGCGTTTTCCTTGTAAGGTCTCTTCATATTGCTTTTCCAAATAGGAGGTTCCTACACGGTCATTTAGAGAATAGCCTTTTTTAAGATAGGCTTCTGCTTCTTCCGCTGGGAGACCAGCTTTTTCACTGGATACACTCCCAACTATAGAAGAAAGGGAAGTTTCCAAAACCTTTCTATCCCAAGAAGTAGAAATACTAATGCCAGGCATCTCCTTTGAAATAGAGGCAATAACAGCCACCTGAGAATCATTTAGAGGATCTGTAGCAATGGTTCCTGTCGCAAAGTTTCCAACAGCATTTAACTGACTAAAAAGATAGATTTCTTTCTTTTCATCCTCTGTATAGTTTAGTTGACTCGTTTGTACACTATCGACCGCATTGTTATACAGTTCTGATTCGGATAGACGATTGCCATCTGAATCCAAGCGTTTCTCGCTTGGGAGAGCTTCCACTATTTTTTTATAGATTTCAGGATCAGCCAAATAGTAATCCGCCAGCTGGCGTTCTGTCAAATTTGGAGAACTGATGCTCACATAAGTCAGTAACTTTTTAGCTGTTTCTTTTAAGTCTGTAGCCGTCATTTTATTGCTACGCGTAAAGGAAACAACCTGCTTTAACGTATTTTCTACCAAAGGTTTTCCACTAGCATCATAAATTTCCCCACGGGCTGAACTGCTTGTAATCTTGGTCTGACTAGCTGAGGCTAGCTTTTTTTCGTAAAAATCCTTGTTCAAAACCTGCATATACAACAAACGACCAATAATGGTCATAAAGAGTAAAATGACGATTGAAAACAATAAATTAAGCCGAATCGGAATCGAATGGCTGTTAAATTTTCTCATACAAATCAGTCTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39596","NCBI_taxonomy_name":"Streptococcus pneumoniae R6","NCBI_taxonomy_id":"171101"}}}},"ARO_accession":"3003042","ARO_id":"39476","ARO_name":"Streptococcus pneumoniae PBP2b conferring resistance to amoxicillin","ARO_description":"PBP2b is a penicillin-binding protein found in Streptococcus pneumoniae","ARO_category":{"40661":{"category_aro_accession":"3003938","category_aro_cvterm_id":"40661","category_aro_name":"Penicillin-binding protein mutations conferring resistance to beta-lactam antibiotics","category_aro_description":"Mutations in PBP transpeptidases that change the affinity for penicillin thereby conferring resistance to penicillin antibiotics","category_aro_class_name":"AMR Gene Family"},"35927":{"category_aro_accession":"0000008","category_aro_cvterm_id":"35927","category_aro_name":"cefoxitin","category_aro_description":"Cefoxitin is a cephamycin antibiotic often grouped with the second generation cephalosporins. Cefoxitin is bactericidal and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. Cefoxitin's 7-alpha-methoxy group and 3' leaving group make it a poor substrate for most beta-lactamases.","category_aro_class_name":"Antibiotic"},"35930":{"category_aro_accession":"0000011","category_aro_cvterm_id":"35930","category_aro_name":"cloxacillin","category_aro_description":"Cloxacillin is a semisynthetic, isoxazolyl penicillin derivative in the beta-lactam class of antibiotics. It interferes with peptidogylcan synthesis and is commonly used for treating penicillin-resistant Staphylococcus aureus infections.","category_aro_class_name":"Antibiotic"},"35934":{"category_aro_accession":"0000015","category_aro_cvterm_id":"35934","category_aro_name":"methicillin","category_aro_description":"Derived from penicillin to combat penicillin-resistance, methicillin is insensitive to beta-lactamases (also known as penicillinases) secreted by many penicillin-resistant bacteria. Methicillin is bactericidal, and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Antibiotic"},"35961":{"category_aro_accession":"0000043","category_aro_cvterm_id":"35961","category_aro_name":"carbenicillin","category_aro_description":"Carbenicillin is a semi-synthetic antibiotic belonging to the carboxypenicillin subgroup of the penicillins. It has gram-negative coverage which includes Pseudomonas aeruginosa but limited gram-positive coverage. The carboxypenicillins are susceptible to degradation by beta-lactamase enzymes. Carbenicillin antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Antibiotic"},"35971":{"category_aro_accession":"0000054","category_aro_cvterm_id":"35971","category_aro_name":"penicillin","category_aro_description":"Penicillin (sometimes abbreviated PCN) is a beta-lactam antibiotic used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms. It works by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Antibiotic"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35975":{"category_aro_accession":"0000058","category_aro_cvterm_id":"35975","category_aro_name":"cefazolin","category_aro_description":"Cefazolin (INN), also known as cefazoline or cephazolin, is a first generation cephalosporin antibiotic. It is administered parenterally, and is active against a broad spectrum of bacteria.","category_aro_class_name":"Antibiotic"},"35976":{"category_aro_accession":"0000059","category_aro_cvterm_id":"35976","category_aro_name":"cefepime","category_aro_description":"Cefepime (INN) is a fourth-generation cephalosporin antibiotic developed in 1994. It contains an aminothiazolyl group that decreases its affinity with beta-lactamases. Cefepime shows high binding affinity with penicillin-binding proteins and has an extended spectrum of activity against Gram-positive and Gram-negative bacteria, with greater activity against both Gram-negative and Gram-positive organisms than third-generation agents.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35978":{"category_aro_accession":"0000061","category_aro_cvterm_id":"35978","category_aro_name":"ceftobiprole","category_aro_description":"Ceftobiprole (Zeftera\/Zevtera) is a next generation (5th generation) cephalosporin antibiotic with activity against methicillin-resistant Staphylococcus aureus, penicillin-resistant Streptococcus pneumoniae, Pseudomonas aeruginosa, and Enterococci. Ceftobiprole inhibits transpeptidases essential to building cell walls, and is a poor substrate for most beta-lactamases.","category_aro_class_name":"Antibiotic"},"35979":{"category_aro_accession":"0000062","category_aro_cvterm_id":"35979","category_aro_name":"ceftriaxone","category_aro_description":"Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"35980":{"category_aro_accession":"0000063","category_aro_cvterm_id":"35980","category_aro_name":"cefuroxime","category_aro_description":"Cefuroxime is a second-generation cephalosporin antibiotic with increased stability with beta-lactamases than first-generation cephalosporins. Cefuroxime is active against Gram-positive organisms but less active against methicillin-resistant strains.","category_aro_class_name":"Antibiotic"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"35987":{"category_aro_accession":"0000070","category_aro_cvterm_id":"35987","category_aro_name":"ertapenem","category_aro_description":"Ertapenem is a carbapenem antibiotic and is highly resistant to beta-lactamases like other carbapenems. It inhibits bacterial cell wall synthesis.","category_aro_class_name":"Antibiotic"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"35995":{"category_aro_accession":"0000078","category_aro_cvterm_id":"35995","category_aro_name":"piperacillin","category_aro_description":"Piperacillin is an acetylureidopenicillin and has an extended spectrum of targets relative to other beta-lactam antibiotics. It inhibits cell wall synthesis in bacteria, and is usually taken with the beta-lactamase inhibitor tazobactam to overcome penicillin-resistant bacteria.","category_aro_class_name":"Antibiotic"},"36309":{"category_aro_accession":"3000170","category_aro_cvterm_id":"36309","category_aro_name":"imipenem","category_aro_description":"Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.","category_aro_class_name":"Antibiotic"},"36689":{"category_aro_accession":"3000550","category_aro_cvterm_id":"36689","category_aro_name":"aztreonam","category_aro_description":"Aztreonam was the first monobactam discovered, and is greatly effective against Gram-negative bacteria while inactive against Gram-positive bacteria. Artreonam is a poor substrate for beta-lactamases, and may even act as an inhibitor. In Gram-negative bacteria, Aztreonam interferes with filamentation, inhibiting cell division and leading to cell death.","category_aro_class_name":"Antibiotic"},"36976":{"category_aro_accession":"3000632","category_aro_cvterm_id":"36976","category_aro_name":"benzylpenicillin","category_aro_description":"Benzylpenicillin, commonly referred to as penicillin G, is effective against both Gram-positive and Gram-negative bacteria. It is unstable in acid.","category_aro_class_name":"Antibiotic"},"36977":{"category_aro_accession":"3000633","category_aro_cvterm_id":"36977","category_aro_name":"phenoxymethylpenicillin","category_aro_description":"Phenoxymethylpenicillin, or penicillin V, is a penicillin derivative that is acid stable but less active than benzylpenicillin (penicillin G).","category_aro_class_name":"Antibiotic"},"36978":{"category_aro_accession":"3000634","category_aro_cvterm_id":"36978","category_aro_name":"propicillin","category_aro_description":"Propicillin is an orally taken penicillin derivative that has high absorption but poor activity.","category_aro_class_name":"Antibiotic"},"36979":{"category_aro_accession":"3000635","category_aro_cvterm_id":"36979","category_aro_name":"dicloxacillin","category_aro_description":"Dicloxacillin is a penicillin derivative that has an extra chlorine atom in comparison to cloxacillin. While more active than cloxacillin, its high affinity for serum protein reduces its activity in human serum in vitro.","category_aro_class_name":"Antibiotic"},"36980":{"category_aro_accession":"3000636","category_aro_cvterm_id":"36980","category_aro_name":"flucloxacillin","category_aro_description":"Flucloxacillin is similar to cloxacillin, with an extra additional fluorine atom.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"36982":{"category_aro_accession":"3000638","category_aro_cvterm_id":"36982","category_aro_name":"azlocillin","category_aro_description":"Azlocillin is a semisynthetic derivative of penicillin that is notably active against Ps. aeruginosa and other Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36983":{"category_aro_accession":"3000639","category_aro_cvterm_id":"36983","category_aro_name":"mezlocillin","category_aro_description":"Mezlocillin is a penicillin derivative taken parenterally.","category_aro_class_name":"Antibiotic"},"36984":{"category_aro_accession":"3000640","category_aro_cvterm_id":"36984","category_aro_name":"doripenem","category_aro_description":"Doripenem is a carbapenem with a broad range of activity against Gram-positive and Gram-negative bacteria, and along with meropenem, it is the most active beta-lactam antibiotic against Pseudomonas aeruginosa. It inhibits bacterial cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36985":{"category_aro_accession":"3000641","category_aro_cvterm_id":"36985","category_aro_name":"cefalexin","category_aro_description":"Cefalexin is a cephalosporin antibiotic that causes filamentation. It is resistant to staphylococcal beta-lactamase, but degraded by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"36986":{"category_aro_accession":"3000642","category_aro_cvterm_id":"36986","category_aro_name":"cefadroxil","category_aro_description":"Cefadroxil, or p-hydroxycephalexin, is an cephalosporin antibiotic similar to cefalexin.","category_aro_class_name":"Antibiotic"},"36987":{"category_aro_accession":"3000643","category_aro_cvterm_id":"36987","category_aro_name":"cefotiam","category_aro_description":"Cefotiam is a cephalosporin antibiotic with similar activity to cefuroxime but more active against enterobacteria. It is consumed orally as the prodrug cefotiam hexetil.","category_aro_class_name":"Antibiotic"},"36988":{"category_aro_accession":"3000644","category_aro_cvterm_id":"36988","category_aro_name":"cefaclor","category_aro_description":"Cefaclor is a semisynthetic cephalosporin derived from cephalexin. It has broad-spectrum antibiotic activity.","category_aro_class_name":"Antibiotic"},"36989":{"category_aro_accession":"3000645","category_aro_cvterm_id":"36989","category_aro_name":"cefotaxime","category_aro_description":"Cefotaxime is a semisynthetic cephalosporin taken parenterally. It is resistant to most beta-lactamases and active against Gram-negative rods and cocci due to its aminothiazoyl and methoximino functional groups.","category_aro_class_name":"Antibiotic"},"36990":{"category_aro_accession":"3000646","category_aro_cvterm_id":"36990","category_aro_name":"cefixime","category_aro_description":"Cefixime is a cephalosporin resistant to most beta-lactamases. It is active against many enterobacteria, but activity against staphylococci is poor.","category_aro_class_name":"Antibiotic"},"36991":{"category_aro_accession":"3000647","category_aro_cvterm_id":"36991","category_aro_name":"cefpodoxime","category_aro_description":"Cefpodoxime is a semisynthetic cephalosporin that acts similarly to cefotaxime with broad-spectrum activity. It is stable to many plasmid-mediated beta-lactamses. Cefpodoxime is consumed as the prodrug cefpodoxime proxetil.","category_aro_class_name":"Antibiotic"},"36992":{"category_aro_accession":"3000648","category_aro_cvterm_id":"36992","category_aro_name":"ceftibuten","category_aro_description":"Ceftibuten is a semisynthetic cephalosporin active against Gram-negative bacilli. It is resistant against many plasmid-mediated beta-lactamases.","category_aro_class_name":"Antibiotic"},"36993":{"category_aro_accession":"3000649","category_aro_cvterm_id":"36993","category_aro_name":"cefditoren","category_aro_description":"Cefditoren is a semisynthetic cephalosporin active against staphylococci, streptococci, and and most enterobacteria. It is resistant to staphylococcal and most enterobacterial beta-lactamases, and is usually taken as the prodrug cefditoren pivoxil.","category_aro_class_name":"Antibiotic"},"36994":{"category_aro_accession":"3000650","category_aro_cvterm_id":"36994","category_aro_name":"cefdinir","category_aro_description":"Cefdinir is similar to cefixime with a modified side-chain at its 7-amino position. It also shares similar activity with cefixime but is more active against staphylococci. It has also be shown to enhance phagocytosis.","category_aro_class_name":"Antibiotic"},"36995":{"category_aro_accession":"3000651","category_aro_cvterm_id":"36995","category_aro_name":"ceftaroline","category_aro_description":"Ceftaroline is a novel cephalosporin active against methicillin resistant Staphylococcus aureus. Like other cephalosporins it binds penicillin-binding proteins to inhibit cell wall synthesis. It strongly binds with PBP2a, associated with methicillin resistance. It is taken orally as the prodrug ceftaroline fosamil.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"37085":{"category_aro_accession":"3000705","category_aro_cvterm_id":"37085","category_aro_name":"isopenicillin N","category_aro_description":"Isopenicillin N is a natural penicillin derivative produced by Penicillium chrysogenum with activity similar to penicillin N.","category_aro_class_name":"Antibiotic"},"37086":{"category_aro_accession":"3000706","category_aro_cvterm_id":"37086","category_aro_name":"penicillin N","category_aro_description":"Penicillin N is a penicillin derivative produced by Cephalosporium acremonium.","category_aro_class_name":"Antibiotic"},"37141":{"category_aro_accession":"3000761","category_aro_cvterm_id":"37141","category_aro_name":"mecillinam","category_aro_description":"Mecillinam is a broad-spectrum beta-lactam antibiotic that was semi-synthetically derived to have a different drug centre, being a 6-alpha-amidinopenicillanate instead of a 6-alpha-acylaminopenicillanate. Contrasting most beta-lactam drugs, mecillinam is most active against Gram-negative bacteria. It binds specifically to penicillin binding protein 2 (PBP2).","category_aro_class_name":"Antibiotic"},"40928":{"category_aro_accession":"3004001","category_aro_cvterm_id":"40928","category_aro_name":"cefmetazole","category_aro_description":"Cefmetazole is a semi-synthetic cephamycin antibiotic with broad spectrum antibiotic activity against both gram-positive and gram-negative bacteria, that disrupt cell wall synthesis through binding to PBPs causing cell lysis.","category_aro_class_name":"Antibiotic"},"40929":{"category_aro_accession":"3004002","category_aro_cvterm_id":"40929","category_aro_name":"cefonicid","category_aro_description":"Cefonicid is a second-generation cephalosporin-class beta-lactam antibiotic with broad spectrum activity. Particularly used against urinary tract infections and lower respiratory infections. Causes cell lysis by inactivation of PBPs through binding, inhibiting peptidoglycan synthesis.","category_aro_class_name":"Antibiotic"},"40932":{"category_aro_accession":"3004005","category_aro_cvterm_id":"40932","category_aro_name":"cefprozil","category_aro_description":"Cefprozil is a cephalosporin and beta-lactam antibiotic with bactericidal activity. It selectively binds to PBPs and inhibits peptidoglycan synthesis, a major cell wall component, resulting in cell lysis.","category_aro_class_name":"Antibiotic"},"40933":{"category_aro_accession":"3004006","category_aro_cvterm_id":"40933","category_aro_name":"ceftiofur","category_aro_description":"Ceftiofur is a third-generation broad spectrum cephalosporin and beta-lactam antibiotic. It causes cell lysis by disrupting peptidoglycan cross-linkage and cell wall formation by binding to PBPs.","category_aro_class_name":"Antibiotic"},"40934":{"category_aro_accession":"3004007","category_aro_cvterm_id":"40934","category_aro_name":"ceftizoxime","category_aro_description":"Ceftizoxime is a third-generation cephalosporin and broad spectrum beta-lactam antibiotic. Ceftizoxime causes bacterial cell lysis through peptidoglycan cross-linking inhibition by binding to PBPs.","category_aro_class_name":"Antibiotic"},"40935":{"category_aro_accession":"3004008","category_aro_cvterm_id":"40935","category_aro_name":"cephapirin","category_aro_description":"Cephapirin is a first-generation cephalosporin and broad spectrum beta-lactam antibiotic. Inactivation of penicillin-binding proteins through cephapirin binding disrupts peptidoglycan cross-linking, resulting in cell lysis.","category_aro_class_name":"Antibiotic"},"40936":{"category_aro_accession":"3004009","category_aro_cvterm_id":"40936","category_aro_name":"cefradine","category_aro_description":"Cefradine is a first-generation cephalosporin and broad spectrum beta-lactam antibiotic. Cefradine binding to penicillin-binding proteins disrupts cell wall peptidoglycan cross-linkage, resulting in cell lysis.","category_aro_class_name":"Antibiotic"},"40943":{"category_aro_accession":"3004016","category_aro_cvterm_id":"40943","category_aro_name":"loracarbef","category_aro_description":"Loracarbef is a second-generation cephalosporin (carbacephem) and broad spectrum beta-lactam antibiotic. Loracarbef inhibits PBPs through binding, disrupting peptidoglycan cell wall cross-linkage and resulting in cell death.","category_aro_class_name":"Antibiotic"},"40944":{"category_aro_accession":"3004017","category_aro_cvterm_id":"40944","category_aro_name":"moxalactam","category_aro_description":"Moxalactam (Latamoxef) is a broad spectrum cephalosporin (oxacephem) and beta-lactam antibiotic. Moxalactam binding to PBPs inhibits peptidoglycan cross-linkage in the cell wall, resulting in cell death. Moxalactam is proposed to be effective against meningitides as it passes the blood-brain barrier.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2386":{"model_id":"2386","model_name":"cipA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"3704":{"protein_sequence":{"accession":"WP_015735625.1","sequence":"MKYLSKYEKIRKILSALNQPNYRYSQITEAIFKNKIGNFEAMNNLPKPVRNELIKELGNNVLSITPKMEQKSNQVSKILFAIPGDEYIESVRLSYQTGWESYCISSQCGCGFGCTFCATGTLGLKRNLTTDEITDQLLYFTLNNHPLDSVSFMGMGEALANPYVFDALHLLTDPKLFGLGHRRITVSTIGLLPGVKKLTKEFPQINLTFSLHSPFHDQRSELMPINNHFPLEEVMTVLDEHIQQTKRKVYIAYILLRGINDSTKHAKAVADLLRERGSWEHLYHVNLIPYNSTDATSQSFVESDQNSINMFLRILKSKGIHVTVRTQFGSDINAACGQLYGSNGNI"},"dna_sequence":{"accession":"NC_013406.1","fmin":"3931126","fmax":"3932167","strand":"-","sequence":"TTAAATGTTACCGTTTGATCCATATAGTTGACCGCATGCTGCGTTGATGTCTGATCCGAATTGGGTCCTCACGGTGACATGGATTCCCTTTGACTTCAAGATTCTAAGGAACATATTGATGCTGTTCTGATCCGACTCTACAAAACTTTGTGATGTGGCATCAGTGGAATTGTATGGAATTAGATTGACGTGATATAAATGTTCCCACGACCCTCTTTCACGCAACAAATCAGCAACGGCTTTAGCATGTTTAGTTGAATCGTTGATACCCCTTAGCAGGATATAAGCAATGTAAACCTTTCGCTTTGTTTGCTGAATATGCTCGTCCAACACGGTCATAACTTCTTCTAATGGAAAATGATTGTTAATGGGCATTAACTCGCTTCTCTGATCATGAAATGGTGAATGAAGCGAGAACGTTAAATTAATCTGTGGAAATTCCTTCGTCAACTTTTTTACTCCAGGTAATAAACCTATGGTAGAAACCGTAATCCTTCGATGTCCTAAACCGAAAAGTTTAGGATCCGTCAGCAAATGCAAAGCATCAAATACATATGGATTTGCAAGTGCCTCTCCCATTCCCATAAAAGACACACTGTCCAAGGGATGGTTATTCAAAGTAAAATAAAGCAGTTGATCCGTTATTTCATCCGTTGTAAGATTCCTCTTCAAACCGAGTGTTCCCGTAGCGCAAAATGTACAACCAAATCCGCAACCGCACTGCGAAGAGATACAATAGGATTCCCAGCCCGTTTGATAACTTAACCTTACGGATTCAATGTATTCATCGCCTGGGATAGCAAACAGAATTTTGCTAACTTGGTTGGATTTCTGCTCCATTTTCGGTGTGATGCTTAACACATTGTTTCCAAGCTCTTTGATTAATTCATTTCTTACAGGCTTAGGCAAGTTGTTCATTGCTTCGAAATTTCCGATCTTGTTCTTGAAGATTGCCTCTGTTATTTGCGAATATCTATAATTCGGTTGATTTAGAGCCGATAAGATCTTACGTATTTTTTCATACTTAGATAAATACTTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40613","NCBI_taxonomy_name":"Paenibacillus sp. Y412MC10","NCBI_taxonomy_id":"481743"}}}},"ARO_accession":"3003907","ARO_id":"40612","ARO_name":"cipA","ARO_description":"Cfr-like methyltransferase enzyme conferring resistance to multiple clinically relevant antibiotic classes.","ARO_category":{"36341":{"category_aro_accession":"3000202","category_aro_cvterm_id":"36341","category_aro_name":"Cfr 23S ribosomal RNA methyltransferase","category_aro_description":"Cfr genes produce enzymes which catalyze the methylation of the 23S rRNA subunit at position 8 of adenine-2503. Methylation of 23S rRNA at this site confers resistance to some classes of antibiotics, including streptogramins, chloramphenicols, florfenicols, linezolids and clindamycin.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"35989":{"category_aro_accession":"0000072","category_aro_cvterm_id":"35989","category_aro_name":"linezolid","category_aro_description":"Linezolid is a synthetic antibiotic used for the treatment of serious infections caused by Gram-positive bacteria that are resistant to several other antibiotics. It inhibits protein synthesis by binding to domain V of the 23S rRNA of the 50S subunit of bacterial ribosomes.","category_aro_class_name":"Antibiotic"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37015":{"category_aro_accession":"3000671","category_aro_cvterm_id":"37015","category_aro_name":"tiamulin","category_aro_description":"Tiamulin is a pleuromutilin derivative currently used in veterinary medicine. It binds to the 23 rRNA of the 50S ribosomal subunit to inhibit protein translation.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"36218":{"category_aro_accession":"3000079","category_aro_cvterm_id":"36218","category_aro_name":"oxazolidinone antibiotic","category_aro_description":"Oxazolidinones are a class of synthetic antibiotics discovered the the 1980's.  They inhibit protein synthesis by binding to domain V of the 23S rRNA of the 50S subunit of bacterial ribosomes.  Linezolid is the only member of this class currently in clinical use.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2394":{"model_id":"2394","model_name":"Staphylococcus aureus menA with mutation conferring resistance to lysocin","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"4430":"G33D"},"experimental":{"4430":"G33D"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"3718":{"protein_sequence":{"accession":"YP_499533.1","sequence":"MSNQYQQYSTVKKYWHLMRPHTLTASVVPVLVGTAASKIYFLGSEDHIKISLFIAMLLACLLIQAATNMFNEYYDYKKGLDDHESVGIGGAIVRNGMSPELVLRLAIAFYILAAILGLFLAANSSFWLLPVGLVCMAVGYLYTGGPFPISWTPFGELFSGVFMGMFIIVIAFFIQTGNIQSYVIWLSVPIVITIGLINMANNIRDRVKDKASGRKTLPILLGKNASLTFMAIMYFIAYAFIVLTIIIKPGGSLFYLLALLSFPMPVKVIRRFKKNDTPPTMMPAMAAAGKTNTFFGLLYALGIYISALFAGI"},"dna_sequence":{"accession":"NC_007795.1","fmin":"951801","fmax":"952740","strand":"-","sequence":"TTAAATGCCTGCAAATAATGCACTAATATAAATACCTAATGCATATAATAAACCGAAAAATGTATTTGTTTTACCAGCAGCAGCCATTGCTGGCATCATTGTAGGCGGTGTATCATTCTTCTTGAAACGTCTGATAACTTTAACAGGCATTGGGAATGATAACAACGCAAGTAAGTAAAATAATGAGCCACCAGGTTTAATAATGATCGTAAGTACAATAAAGGCATAAGCGATAAAGTACATGATTGCCATAAATGTTAAAGAAGCATTTTTACCTAATAGAATGGGTAAAGTTTTGCGACCACTTGCTTTATCTTTGACACGGTCGCGAATATTGTTAGCCATATTAATTAAACCGATAGTGATTACTATAGGTACACTTAACCAAATTACATAACTTTGAATATTGCCAGTTTGAATAAAGAATGCAATAACGATAATAAACATACCCATAAATACGCCTGAGAATAATTCACCGAAAGGCGTCCATGAAATAGGGAAAGGGCCACCTGTATATAGGTAACCAACAGCCATACATACTAATCCAACTGGTAATAACCAAAATGAAGAGTTAGCAGCTAAAAACAAACCTAATATTGCTGCTAAGATGTAAAATGCAATGGCTAATCGTAGCACAAGCTCTGGGCTCATACCGTTGCGAACAATGGCACCACCAATGCCTACAGATTCATGATCATCGAGGCCTTTTTTATAATCATAGTATTCATTAAACATATTAGTTGCTGCTTGAATAAGTAAGCATGCTAGTAACATGGCAATGAATAGGCTGATTTTAATATGATCTTCGCTACCAAGAAAATATATTTTAGATGCTGCTGTACCAACTAAAACGGGTACTACGGAAGCAGTTAATGTATGAGGACGCATTAAATGCCAATATTTCTTAACTGTAGAATATTGCTGATATTGATTACTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35511","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus NCTC 8325","NCBI_taxonomy_id":"93061"}}}},"ARO_accession":"3003917","ARO_id":"40625","ARO_name":"Staphylococcus aureus menA with mutation conferring resistance to lysocin","ARO_description":"menA encodes a 1,4-dihydroxy-2-naphthoate octaprenyltransferase, with mutations to the protein conferring resistance to lysocin E.","ARO_category":{"41429":{"category_aro_accession":"3004265","category_aro_cvterm_id":"41429","category_aro_name":"lysocin resistant menA","category_aro_description":"Mutations to demA confer lycosin resistance.","category_aro_class_name":"AMR Gene Family"},"40623":{"category_aro_accession":"3003915","category_aro_cvterm_id":"40623","category_aro_name":"Lysocin E","category_aro_description":"A drug which binds to menaquinone in the bacterial cell membrane. Binding of Lysocin to menaquinone facilitates lysis of the cell.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2380":{"model_id":"2380","model_name":"Staphylococcus aureus GlpT with mutation conferring resistance to fosfomycin","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"4385":"W137R","4386":"F3I","4387":"L27F","4388":"A100V","4389":"V213I","4390":"G352D"},"clinical":{"4385":"W137R","4386":"F3I","4387":"L27F","4388":"A100V","4389":"V213I","4390":"G352D"}},"40394":{"param_type":"nonsense mutation","param_description":"A nucleotide substitution resulting in a change from an amino acid codon to a STOP codon. Nonsense mutations truncate protein translation prematurely, resulting in a defective or completely inactive protein. In CARD, nonsense mutations may be attached to models using the notation: [wild type amino acid][position][STOP] (e.g. Q42STOP). This parameter is not currently used in detection algorithms.","param_type_id":"40394","param_value":{"4391":"W355STOP"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"800"},"41343":{"param_type":"deletion mutation from nucleotide sequence","param_description":"A subtype of the deletion mutation detection model parameter. This parameter is used when a set of deletion mutations is reported in a nucleotide sequence format. Such mutations may be of variable length - possibly causing a frameshift, but not premature termination of functional knockout. Mutation parameters of this type are reported in the CARD with the notation: [-]nt[position]:[nucleotides].","param_type_id":"41343","param_value":{"8145":"-nt248:G","8146":"-nt225:TGGATTTA"}},"41345":{"param_type":"insertion mutation from nucleotide sequence","param_description":"A subtype of the insertion mutation detection model parameter. This parameter is used when a set of insertion mutations is reported in a nucleotide sequence format. Such mutations may be of variable length - possibly causing a frameshift, but not causing premature termination or a functional knockout. Mutation parameters of this type are reported in CARD with the notation: [+]nt[position]:[nucleotides].","param_type_id":"41345","param_value":{"8147":"+nt392:T"}}},"model_sequences":{"sequence":{"3678":{"protein_sequence":{"accession":"CAG39357","sequence":"MNFLKPAKHIKPLPENQIDDTYKRLRLQVFLGIFIGYAGYYLLRKNFSLAMPALQEQGFTKAELGFALSAVSIAYGFSKFFMGTVSDRSNARIFLVLGLVLTAIVNLLMGFVPFFTSGIGIMFVLLFLNGWFQGMGWPPSGRVLVHWFSVSERGSKTALWNVAHNVGGGIMAPIAAWGITTTAFINFGYLKGFEGVFIYPALLALIIAAISYILIRDTPQSQGLPPIEIYKNDFATSDKKTLETELTTKEILFKYVLNNKWVWAIAFANIFVYFVRYGVLDWAPVYLSEEKHFDLKASGWAYFLYEWAGIPGTLLCGYISDKLFKGRRGPAGFFFMLGVTVFVLIYWLNPPGNAWLDNVSLIAIGFLIYGPVMLIGLQALDYVPKKAAGTAAGLTGLFGYLFGAVMANIVLGAVVDKFGWDVGFILLTAISVFAMLSFILTWNKVGQETVHH"},"dna_sequence":{"accession":"KT372193","fmin":"0","fmax":"1359","strand":"+","sequence":"ATGAATTTTCTTAAACCTGCAAAGCATATTAAGCCTTTGCCAGAAAATCAGATAGATGATACCTATAAACGATTACGTCTCCAAGTATTTCTTGGTATTTTCATCGGTTACGCTGGGTACTATTTATTACGTAAAAACTTTTCATTAGCGATGCCAGCATTGCAAGAGCAAGGTTTTACAAAAGCGGAACTAGGTTTTGCACTTTCTGCTGTTTCCATCGCATATGGATTTAGTAAGTTCTTTATGGGTACTGTAAGTGATCGGAGCAATGCTCGGATATTCTTAGTTCTTGGATTAGCACTCACTGCTATCGTCAATTTGTTAATGGGATTTGTACCGTTCTTTACATCAGGTATCGGTATTATGTTTGTCCTATTATTCTTAAATGGATGGTTTCAAGGTATGGGCTGGCCACCTTCAGGCCGTGTTCTCGTTCACTGGTTTAGTGTAAGTGAACGCGGAAGTAAGACTGCCCTTTGGAACGTTGCGCATAATGTTGGTGGAGGTATTATGGCACCTATTGCTGCTTGGGGTATTACAACAACAGCATTTATCAACTTTGGTTATTTAAAAGGTTTCGAAGGTGTATTCATTTACCCTGCACTCTTAGCACTTATCATTGCCGCAATTTCATACGTATTGATTAGAGACACACCTCAATCTCAAGGTTTACCTCCAATCGAAATTTATAAAAACGACTTTGCTACAAGCGATAAGAAAACATTAGAAACAGAATTAACTACAAAAGAAATTTTATTTAAATATGTACTGAACAATAAATGGGTATGGGCAATTGCCTTTGCAAATATATTTGTTTATTTCGTGCGTTATGGTGTACTTGATTGGGCGCCAGTCTACTTAAGTGAAGAAAAACATTTCGACTTAAAAGCATCAGGTTGGGCATACTTCTTATACGAATGGGCTGGAATTCCTGGTACATTATTATGTGGTTACATTTCTGATAAATTATTCAAAGGTCGTCGTGGACCTGCAGGTTTCTTCTTTATGTTAGGTGTCACAGTATTTGTATTAATTTATTGGTTAAATCCTCCAGGCAATGCTTAGTTAGACAATGTCTCATTAATTGCCATTGGTTTCTTAATATATGGACCAGTTATGTTAATTGGTTTACAAGCATTAGATTATGTACCTAAAAAAGCAGCTGGCACAGCAGCTGGATTAACAGGATTATTTGGTTATCTGTTTGGTGCTGTAATGGCCAACATCGTCTTAGGTGCTGTAGTTGATAAATTCGGATGGGATGTCGGTTTTATTTTATTAACAGCAATCAGTGTGTTTGCAATGTTGAGCTTTATCCTCACTTGGAATAAAGTAGGACAAGAAACCGTTCATCATTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35517","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus MRSA252","NCBI_taxonomy_id":"282458"}}}},"ARO_accession":"3003901","ARO_id":"40603","ARO_name":"Staphylococcus aureus GlpT with mutation conferring resistance to fosfomycin","ARO_description":"Mutations to the active importer GlpT, which is involved with the uptake of many phosphorylated sugars, confer resistance to fosfomycin by reducing import of the drug into the bacteria.","ARO_category":{"41411":{"category_aro_accession":"3004247","category_aro_cvterm_id":"41411","category_aro_name":"GlpT","category_aro_description":"Fosfomycin is transported bacterial cells through transporters, one of them being glycerol-3-phosphate, which is encoded by the GlpT gene. Mutations in the GlpT gene can confer resistance to fosfomycin.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2378":{"model_id":"2378","model_name":"Escherichia coli CyaA with mutation conferring resistance to fosfomycin","model_type":"protein knockout model","model_type_id":"40354","model_description":"An AMR detection model for instances where the absence of a protein - due to large-scale insertion elements, large deletions, or other methods of protein knockout - confers clinical resistance to a known antibiotic. These models include reference sequences. Protein knockout models are currently in development.","model_sequences":{"sequence":{"3676":{"protein_sequence":{"accession":"CDJ73082","sequence":"MYLYIETLKQRLDAINQLRVDRALAAMGPAFQQVYSLLPTLLHYHHPLMPGYLDGNVPKGICLYTPDETQRHYLNELELYRGMSVQDPPKGELPITGVYTMGSTSSVGQSCSSDLDIWVCHQSWLDSEERQLLQRKCSLLENWAASLGVEVSFFLIDENRFRHNESGSLGGEDCGSTQHILLLDEFYRTAVRLAGKRILWNMVPCDEEEHYDDYVMTLYAQGVLTPNEWLDLGGLSSLSAEEYFGASLWQLYKSIDSPYKAVLKTLLLEAYSWEYPNPRLLAKDIKQRLHDGEIVSFGLDPYCMMLERVTEYLTAIEDFTRLDLVRRCFYLKVCEKLSRERACVGWRRAVLSQLVSEWGWDEARLAMLDNRANWKIDQVREAHNELLDAMMQSYRNLIRFARRNNLSVSASPQDIGVLTRKLYAAFEALPGKVTLVNPQISPDLSEPNLTFIYVPPGRANRSGWYLYNRAPNIESIISHQPLEYNRYLNKLVAWAWFNGLLTSRTRLYIKGNGIVDLPKLQEMVADVSHHFPLRLPAPTPKALYSPCEIRHLAIIVNLEYDPTAAFRNQVVHFDFRKLDVFSFGENQNCLVGSVDLLYRNSWNEVRTLHFNGEQSMIEALKTILGKMHQDAAPPDSVEVFCYSQHLRGLIRTRVQQLVSECIELRLSSTRQETGRFKALRVSGQTWGLFFERLNVSVQKLENAIEFYGAISHNKLHGLSVQVETNHVKLPAVVDGFASEGIIQFFFEETQDENGFNIYILDESNRVEVYHHCEGSKEELVRDVSRFYSSSHDRFTYGSSFINFNLPQFYQIVKVDGREQVIPFRTKSIGNMPPANQDHDTPLLQQYFS"},"dna_sequence":{"accession":"HG738867","fmin":"2786398","fmax":"2788945","strand":"-","sequence":"TCACGAAAAATATTGCTGTAATAGCGGCGTATCGTGATCCTGATTGGCAGGCGGCATGTTACCGATAGATTTTGTGCGGAACGGAATCACCTGTTCACGACCATCAACCTTCACAATCTGATAGAACTGCGGCAGGTTGAAGTTGATGAAGCTTGAGCCGTAGGTAAAGCGGTCATGCGATGACGAGTAGAAGCGACTGACGTCACGTACCAGCTCCTCTTTGCTGCCTTCGCAGTGGTGATATACCTCAACCCGGTTGCTTTCGTCGAGAATGTAGATATTAAAGCCATTCTCGTCTTGCGTTTCTTCGAAAAAGAACTGGATGATCCCTTCGCTGGCAAAGCCGTCCACCACCGCCGGTAATTTGACGTGATTGGTTTCAACCTGCACTGACAGGCCGTGCAGTTTGTTATGCGAAATCGCGCCATAAAACTCGATGGCGTTTTCCAGTTTCTGTACCGATACATTCAGGCGTTCGAAGAACAACCCCCAGGTTTGACCAGAAACGCGCAGCGCCTTGAAACGCCCGGTTTCCTGGCGGGTGCTGGAAAGACGCAATTCAATACACTCAGAAACCAGTTGCTGCACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACAGAAGACTTCCACGCTATCTGGCGGTGCGGCGTCCTGATGCATTTTGCCGAGAATAGTTTTCAGGGCTTCGATCATCGATTGCTCGCCGTTGAAGTGCAGCGTACGCACTTCGTTCCACGAGTTGCGGTACAGCAGGTCAACGCTACCTACCAGGCAATTTTGATTCTCGCCAAAGCTGAAGACATCCAGCTTACGGAAATCGAAATGCACCACCTGATTGCGGAACGCCGCTGTCGGGTCATATTCCAGGTTAACGATAATCGCCAGATGGCGGATCTCACACGGGCTGTAGAGCGCCTTCGGTGTCGGTGCAGGTAAGCGCAGCGGGAAATGGTGCGACACGTCGGCGACCATCTCCTGCAACTTAGGCAAATCGACAATGCCGTTACCTTTAATATACAAACGGGTGCGCGAGGTCAGCAGGCCGTTAAACCATGCCCACGCCACCAGTTTATTCAGGTAACGGTTATATTCCAGCGGCTGATGGCTGATGATCGACTCAATATTTGGCGCGCGGTTATACAGATACCAACCTGAACGGTTAGCCCGGCCCGGCGGCACATAAATAAAGGTCAGATTCGGTTCCGAGAGATCGGGTGAAATCTGCGGGTTTACCAGCGTCACTTTACCTGGTAATGCTTCAAACGCGGCATACAGCTTACGCGTCAGCACGCCGATATCCTGCGGACTGGCGGAGACGCTAAGGTTATTGCGACGCGCAAAGCGGATCAGATTACGGTAGCTCTGCATCATCGCGTCGAGCAACTCGTTGTGCGCCTCACGCACCTGATCAATCTTCCAGTTAGCGCGGTTATCGAGCATTGCCAGACGAGCTTCGTCCCAACCCCACTCGCTCACTAACTGGCTCAACACTGCGCGACGCCAGCCTACGCAGGCGCGTTCACGGCTGAGCTTTTCGCACACTTTTAAATAGAAGCAGCGACGTACTAAATCCAGACGGGTAAAATCTTCAATCGCCGTCAGGTATTCAGTAACACGCTCCAGCATCATGCAGTATGGATCGAGACCAAACGATACAATCTCGCCGTCGTGCAAACGCTGTTTGATATCTTTCGCCAGCAGACGTGGGTTCGGGTATTCCCAGGAATAGGCTTCCAGCAGCAGTGTTTTCAGTACCGCTTTGTATGGGGAATCGATACTCTTGTAGAGCTGCCAAAGGCTGGCACCAAAGTACTCTTCAGCAGAAAGCGAGCTTAAGCCACCGAGATCCAGCCATTCATTTGGCGTCAGCACGCCCTGCGCGTAAAGCGTCATCACATAGTCGTCGTAATGCTCTTCTTCGTCGCACGGCACCATATTCCACAGAATACGCTTACCGGCGAGACGCACGGCGGTACGATAAAATTCGTCAAGCAGCAGTATATGCTGGGTGGAGCCACAATCTTCGCCCCCCAGGCTGCCGCTTTCATTATGACGGAAGCGGTTTTCATCAATCAGGAAGAAGCTGACTTCCACACCCAGCGAGGCGGCCCAGTTTTCCAGCAGGCTACATTTACGTTGTAGCAATTGGCGCTCTTCGCTATCGAGCCAGGATTGATGACAGACCCAGATATCCAGGTCAGAGGAACAACTTTGCCCTACGGACGAGGTGCTGCCCATGGTGTATACACCAGTAATTGGAAGCTCACCTTTCGGCGGATCCTGTACTGACATTCCACGATACAGTTCAAGCTCGTTCAGGTAGTGGCGTTGAGTTTCATCAGGCGTGTAAAGGCAAATGCCTTTGGGAACGTTACCATCAAGGTAACCCGGCATTAGCGGATGGTGATAGTGCAACAATGTCGGCAGTAGACTGTAGACCTGTTGGAATGCAGGCCCCATAGCAGCAAGCGCGCGATCCACACGCAATTGATTTATGGCATCCAGTCTCTGTTTCAGAGTCTCAATATAGAGGTACAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40589","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MC4100","NCBI_taxonomy_id":"1403831"}}}},"ARO_accession":"3003900","ARO_id":"40602","ARO_name":"Escherichia coli CyaA with mutation conferring resistance to fosfomycin","ARO_description":"CyaA (adenylate cyclase) is involved with the synthesis of cyclic AMP which regulates the fosfomycin transporter glpT. As a result, mutations to cyaA confer resistance to fosfomycin.","ARO_category":{"41415":{"category_aro_accession":"3004251","category_aro_cvterm_id":"41415","category_aro_name":"cya adenylate cyclase","category_aro_description":"Adenylate cyclases encoded by cya genes, which are involved in the synthesis cyclic AMP which regulates the fosfomycin transporter glpT. Mutations in cya genes can confer resistance to fosfomycin.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2379":{"model_id":"2379","model_name":"Escherichia coli CyaA with mutation conferring resistance to fosfomycin","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"4382":"S352T"},"clinical":{"4382":"S352T"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1650"}},"model_sequences":{"sequence":{"3677":{"protein_sequence":{"accession":"CDJ73082","sequence":"MYLYIETLKQRLDAINQLRVDRALAAMGPAFQQVYSLLPTLLHYHHPLMPGYLDGNVPKGICLYTPDETQRHYLNELELYRGMSVQDPPKGELPITGVYTMGSTSSVGQSCSSDLDIWVCHQSWLDSEERQLLQRKCSLLENWAASLGVEVSFFLIDENRFRHNESGSLGGEDCGSTQHILLLDEFYRTAVRLAGKRILWNMVPCDEEEHYDDYVMTLYAQGVLTPNEWLDLGGLSSLSAEEYFGASLWQLYKSIDSPYKAVLKTLLLEAYSWEYPNPRLLAKDIKQRLHDGEIVSFGLDPYCMMLERVTEYLTAIEDFTRLDLVRRCFYLKVCEKLSRERACVGWRRAVLSQLVSEWGWDEARLAMLDNRANWKIDQVREAHNELLDAMMQSYRNLIRFARRNNLSVSASPQDIGVLTRKLYAAFEALPGKVTLVNPQISPDLSEPNLTFIYVPPGRANRSGWYLYNRAPNIESIISHQPLEYNRYLNKLVAWAWFNGLLTSRTRLYIKGNGIVDLPKLQEMVADVSHHFPLRLPAPTPKALYSPCEIRHLAIIVNLEYDPTAAFRNQVVHFDFRKLDVFSFGENQNCLVGSVDLLYRNSWNEVRTLHFNGEQSMIEALKTILGKMHQDAAPPDSVEVFCYSQHLRGLIRTRVQQLVSECIELRLSSTRQETGRFKALRVSGQTWGLFFERLNVSVQKLENAIEFYGAISHNKLHGLSVQVETNHVKLPAVVDGFASEGIIQFFFEETQDENGFNIYILDESNRVEVYHHCEGSKEELVRDVSRFYSSSHDRFTYGSSFINFNLPQFYQIVKVDGREQVIPFRTKSIGNMPPANQDHDTPLLQQYFS"},"dna_sequence":{"accession":"HG738867","fmin":"2786398","fmax":"2788945","strand":"-","sequence":"TCACGAAAAATATTGCTGTAATAGCGGCGTATCGTGATCCTGATTGGCAGGCGGCATGTTACCGATAGATTTTGTGCGGAACGGAATCACCTGTTCACGACCATCAACCTTCACAATCTGATAGAACTGCGGCAGGTTGAAGTTGATGAAGCTTGAGCCGTAGGTAAAGCGGTCATGCGATGACGAGTAGAAGCGACTGACGTCACGTACCAGCTCCTCTTTGCTGCCTTCGCAGTGGTGATATACCTCAACCCGGTTGCTTTCGTCGAGAATGTAGATATTAAAGCCATTCTCGTCTTGCGTTTCTTCGAAAAAGAACTGGATGATCCCTTCGCTGGCAAAGCCGTCCACCACCGCCGGTAATTTGACGTGATTGGTTTCAACCTGCACTGACAGGCCGTGCAGTTTGTTATGCGAAATCGCGCCATAAAACTCGATGGCGTTTTCCAGTTTCTGTACCGATACATTCAGGCGTTCGAAGAACAACCCCCAGGTTTGACCAGAAACGCGCAGCGCCTTGAAACGCCCGGTTTCCTGGCGGGTGCTGGAAAGACGCAATTCAATACACTCAGAAACCAGTTGCTGCACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACAGAAGACTTCCACGCTATCTGGCGGTGCGGCGTCCTGATGCATTTTGCCGAGAATAGTTTTCAGGGCTTCGATCATCGATTGCTCGCCGTTGAAGTGCAGCGTACGCACTTCGTTCCACGAGTTGCGGTACAGCAGGTCAACGCTACCTACCAGGCAATTTTGATTCTCGCCAAAGCTGAAGACATCCAGCTTACGGAAATCGAAATGCACCACCTGATTGCGGAACGCCGCTGTCGGGTCATATTCCAGGTTAACGATAATCGCCAGATGGCGGATCTCACACGGGCTGTAGAGCGCCTTCGGTGTCGGTGCAGGTAAGCGCAGCGGGAAATGGTGCGACACGTCGGCGACCATCTCCTGCAACTTAGGCAAATCGACAATGCCGTTACCTTTAATATACAAACGGGTGCGCGAGGTCAGCAGGCCGTTAAACCATGCCCACGCCACCAGTTTATTCAGGTAACGGTTATATTCCAGCGGCTGATGGCTGATGATCGACTCAATATTTGGCGCGCGGTTATACAGATACCAACCTGAACGGTTAGCCCGGCCCGGCGGCACATAAATAAAGGTCAGATTCGGTTCCGAGAGATCGGGTGAAATCTGCGGGTTTACCAGCGTCACTTTACCTGGTAATGCTTCAAACGCGGCATACAGCTTACGCGTCAGCACGCCGATATCCTGCGGACTGGCGGAGACGCTAAGGTTATTGCGACGCGCAAAGCGGATCAGATTACGGTAGCTCTGCATCATCGCGTCGAGCAACTCGTTGTGCGCCTCACGCACCTGATCAATCTTCCAGTTAGCGCGGTTATCGAGCATTGCCAGACGAGCTTCGTCCCAACCCCACTCGCTCACTAACTGGCTCAACACTGCGCGACGCCAGCCTACGCAGGCGCGTTCACGGCTGAGCTTTTCGCACACTTTTAAATAGAAGCAGCGACGTACTAAATCCAGACGGGTAAAATCTTCAATCGCCGTCAGGTATTCAGTAACACGCTCCAGCATCATGCAGTATGGATCGAGACCAAACGATACAATCTCGCCGTCGTGCAAACGCTGTTTGATATCTTTCGCCAGCAGACGTGGGTTCGGGTATTCCCAGGAATAGGCTTCCAGCAGCAGTGTTTTCAGTACCGCTTTGTATGGGGAATCGATACTCTTGTAGAGCTGCCAAAGGCTGGCACCAAAGTACTCTTCAGCAGAAAGCGAGCTTAAGCCACCGAGATCCAGCCATTCATTTGGCGTCAGCACGCCCTGCGCGTAAAGCGTCATCACATAGTCGTCGTAATGCTCTTCTTCGTCGCACGGCACCATATTCCACAGAATACGCTTACCGGCGAGACGCACGGCGGTACGATAAAATTCGTCAAGCAGCAGTATATGCTGGGTGGAGCCACAATCTTCGCCCCCCAGGCTGCCGCTTTCATTATGACGGAAGCGGTTTTCATCAATCAGGAAGAAGCTGACTTCCACACCCAGCGAGGCGGCCCAGTTTTCCAGCAGGCTACATTTACGTTGTAGCAATTGGCGCTCTTCGCTATCGAGCCAGGATTGATGACAGACCCAGATATCCAGGTCAGAGGAACAACTTTGCCCTACGGACGAGGTGCTGCCCATGGTGTATACACCAGTAATTGGAAGCTCACCTTTCGGCGGATCCTGTACTGACATTCCACGATACAGTTCAAGCTCGTTCAGGTAGTGGCGTTGAGTTTCATCAGGCGTGTAAAGGCAAATGCCTTTGGGAACGTTACCATCAAGGTAACCCGGCATTAGCGGATGGTGATAGTGCAACAATGTCGGCAGTAGACTGTAGACCTGTTGGAATGCAGGCCCCATAGCAGCAAGCGCGCGATCCACACGCAATTGATTTATGGCATCCAGTCTCTGTTTCAGAGTCTCAATATAGAGGTACAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40589","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MC4100","NCBI_taxonomy_id":"1403831"}}}},"ARO_accession":"3003900","ARO_id":"40602","ARO_name":"Escherichia coli CyaA with mutation conferring resistance to fosfomycin","ARO_description":"CyaA (adenylate cyclase) is involved with the synthesis of cyclic AMP which regulates the fosfomycin transporter glpT. As a result, mutations to cyaA confer resistance to fosfomycin.","ARO_category":{"41415":{"category_aro_accession":"3004251","category_aro_cvterm_id":"41415","category_aro_name":"cya adenylate cyclase","category_aro_description":"Adenylate cyclases encoded by cya genes, which are involved in the synthesis cyclic AMP which regulates the fosfomycin transporter glpT. Mutations in cya genes can confer resistance to fosfomycin.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2381":{"model_id":"2381","model_name":"Staphylococcus aureus UhpT with mutation conferring resistance to fosfomycin","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"4396":"G358V","4397":"G112E","4398":"W425R"},"clinical":{"4396":"G358V","4397":"G112E","4398":"W425R"}},"40394":{"param_type":"nonsense mutation","param_description":"A nucleotide substitution resulting in a change from an amino acid codon to a STOP codon. Nonsense mutations truncate protein translation prematurely, resulting in a defective or completely inactive protein. In CARD, nonsense mutations may be attached to models using the notation: [wild type amino acid][position][STOP] (e.g. Q42STOP). This parameter is not currently used in detection algorithms.","param_type_id":"40394","param_value":{"4399":"Y314STOP","4400":"W228STOP"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"850"},"41343":{"param_type":"deletion mutation from nucleotide sequence","param_description":"A subtype of the deletion mutation detection model parameter. This parameter is used when a set of deletion mutations is reported in a nucleotide sequence format. Such mutations may be of variable length - possibly causing a frameshift, but not premature termination of functional knockout. Mutation parameters of this type are reported in the CARD with the notation: [-]nt[position]:[nucleotides].","param_type_id":"41343","param_value":{"8148":"-nt431:ATTCAACGATTT","8149":"-nt27:T"}},"41345":{"param_type":"insertion mutation from nucleotide sequence","param_description":"A subtype of the insertion mutation detection model parameter. This parameter is used when a set of insertion mutations is reported in a nucleotide sequence format. Such mutations may be of variable length - possibly causing a frameshift, but not causing premature termination or a functional knockout. Mutation parameters of this type are reported in CARD with the notation: [+]nt[position]:[nucleotides].","param_type_id":"41345","param_value":{"8150":"+nt904:T"}}},"model_sequences":{"sequence":{"3679":{"protein_sequence":{"accession":"CAG39240","sequence":"MNFFDIHKIPNKGIPLSVQRKLWLRNFMQAFFVVFFVYMAMYLIRNNFKAAQPFLKEEIGLSTLELGYIGLAFSITYGLGKTLLGYFVDGRNTKRIISFLLILSAITVLIMGFVLSYFGSVMGLLIVLWGLNGVFQSVGGPASYSTISRWAPRTKRGRYLGFWNTSHNIGGAIAGGVALWGANVFFHGNVIGMFIFPSVIALLIGIATLFIGKDDPEELGWNRAEEIWEEPVDKENIDSQGMTKWEIFKKYILGNPVIWILCVSNVFVYIVRIGIDNWAPLYVSEHLHFSKGDAVNTIFYFEIGALVASLLWGYVSDLLKGRRAIVAIGCMFMITFVVLFYTNATSVMMVNISLFALGALIFGPQLLIGVSLTGFVPKNAISVANGMTGSFAYLFGDSMAKVGLAAIADPTRNGLNIFGYTLSGWTDVFIVFYVALFLGMILLGIVAFYEEKKIRSLKI"},"dna_sequence":{"accession":"KT372207","fmin":"0","fmax":"1380","strand":"+","sequence":"ATGAACTTTTTTGATATCCATAAGATTCCGAACAAAGGCATTCCATTATCGGTACAACGTAAATTATGGCTTAGAAACTTCATGCAAGCTTTCTTTGTAGTGTTCTTTGTTTATATGGCTATGTATTTAATTCGAAACAACTTTAAGGCGGCCCAACCGTTTTTAAAAGAGGAAATTGGATTATCTACATTAGAACTTGGTTATATCGGATTAGCATTTAGTATCACGTACGGTTTAGGGAAAACATTACTTGGATATTTTGTCGATGGACGTAACACAAAACGTATTATCTCGTTCTTACTTATCTTATCTGCGATTACAGTTTTAATTATGGGATTTGTTTTAAGTTACTTTGGTTCTGTAATGGGATTATTAATTGTACTTTGGGGACTTAACGGGGTGTTCCAATCAGTTGGTGGACCTGCAAGTTATTCAACGATTTCAAGATGGGCGCCAAGAACGAAACGTGGCCGATACTTAGGATTTTGGAATACATCACATAATATCGGTGGTGCCATTGCAGGTGGTGTTGCACTTTGGGGTGCTAATGTATTCTTCCATGGAAATGTTATAGGGATGTTCATTTTCCCATCGGTGATTGCATTACTTATTGGTATCGCAACATTATTTATCGGAAAAGATGATCCAGAAGAATTAGGATGGAATCGTGCTGAAGAAATTTAGGAAGAGCCGGTCGATAAAGAAAATATTGATTCTCAAGGTATGACGAAATGGGAGATCTTTAAAAAATATATCCTGGGAAATCCTGTTATATGGATTCTATGTGTTTCAAACGTCTTTGTATACATTGTACGAATCGGTATTGATAACTGGGCACCGTTATATGTGTCAGAGCATTTACACTTTAGTAAAGGCGATGCAGTTAATACGATATTCTACTTTGAAATTGGTGCATTAGTTGCAAGTTTATTATGGGGCTACGTATCAGACTTATTAAAAGGTCGTCGTGCAATTGTAGCTATTGGCTGTATGTTTATGATTACATTTGTTGTCTTATTCTACACAAATGCTACAAGTGTCATGATGGTTAACATTTCATTGTTTGCATTAGGTGCGTTAATCTTTGGTCCGCAATTATTAATTGGTGTATCATTAACTGGTTTTGTTCCTAAAAATGCCATCAGTGTAGCAAACGGAATGACAGGTTCATTCGCGTATCTATTCGGTGACTCAATGGCGAAAGTTGGTTTGGCGGCTATTGCTGATCCAACACGTAACGGTTTAAACATCTTTGGATATACATTAAGTGGATGGACAGATGTTTTCATCGTCTTCTATGTTGCATTATTCCTAGGCATGATTCTATTAGGAATCGTTGCTTTCTATGAAGAAAAGAAAATTAGAAGTTTAAAAATTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35517","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus MRSA252","NCBI_taxonomy_id":"282458"}}}},"ARO_accession":"3003902","ARO_id":"40604","ARO_name":"Staphylococcus aureus UhpT with mutation conferring resistance to fosfomycin","ARO_description":"Mutations to the active importer UhpT, which is involved with the uptake of many phosphorylated sugars, confer resistance to fosfomycin by reducing import of the drug into the bacteria.","ARO_category":{"41412":{"category_aro_accession":"3004248","category_aro_cvterm_id":"41412","category_aro_name":"UhpT","category_aro_description":"UhpT encodes a transporter that can import fosfomycin-type drugs into bacterial cells. Mutations to UhpT confer resistance.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2421":{"model_id":"2421","model_name":"efrA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"960"}},"model_sequences":{"sequence":{"3752":{"protein_sequence":{"accession":"CDO61513.1","sequence":"NILLGYFGARITTNIVRDIRDDLFEKIQTFSHSEYESIGVSSLITRTTNDAYQIMLFMGNILRLGFMTPVMFIASLYMVMRTSPSLGMYVLGALPFLLLAVVGIARLSEPLSKKQQKNLDGINGILRENLSGLRVIRAFVNEKFEESRFNKVNETYTKSSKSLFRLMAAAQPGFFFLFNIVMVLIIWSGTVQISHGDLEVGNLIAFIEYIFHALFSFMLFASVLMMYPRAAVSASRIQEALDMEPAIREEEGVTETATKGYLEFKNVTFAYPGHAESPVIRNVSFKASPGETVAFIGSTGSGKSTLIQLIPRFYDVSEGEILIDGVNVKEYKLSALRNKIGYIPQKALLFTGTIADNLRYGKEDATLEEMERAIDIAQATEFVSQKPQGYDEPLSEGGTNFSGGQKQRLAIARAIIRNPEIYIFDDSFSALDYQTDANLRARLKKETTESTVLIVAQRVGTIMHADRIVCFKRRRRGRKFGHQPF"},"dna_sequence":{"accession":"HG970100.1","fmin":"0","fmax":"1457","strand":"+","sequence":"AATATTTTGCTAGGGTACTTTGGTGCCAGAATTACAACAAACATTGTTCGTGATATTCGTGATGATTTATTTGAAAAGATTCAAACTTTCTCACACAGTGAATATGAAAGTATTGGGGTTTCTTCCTTAATTACGCGAACTACCAATGATGCATACCAAATTATGCTCTTCATGGGAAATATTTTACGTCTTGGCTTTATGACGCCAGTGATGTTTATTGCCAGTCTTTACATGGTGATGCGAACGAGTCCGTCGTTAGGAATGTACGTTTTAGGTGCCTTGCCTTTTCTGCTGCTAGCAGTTGTCGGAATTGCTCGTTTGTCAGAACCGTTATCTAAAAAGCAACAAAAGAACTTAGATGGAATCAATGGGATTTTAAGAGAAAATCTTTCTGGATTGCGGGTAATACGCGCATTTGTTAATGAAAAATTTGAAGAATCTCGTTTTAATAAAGTCAATGAAACTTACACTAAAAGTTCAAAAAGTCTGTTTCGTTTAATGGCAGCAGCCCAACCAGGGTTCTTTTTCTTATTTAATATTGTGATGGTCTTAATCATTTGGAGCGGGACTGTTCAAATCAGCCATGGGGATTTAGAAGTTGGGAATTTAATTGCTTTTATTGAATATATTTTTCATGCGCTGTTCTCGTTTATGTTATTTGCCAGTGTCTTAATGATGTATCCACGGGCTGCGGTTTCGGCTTCACGGATTCAAGAAGCCTTAGACATGGAACCAGCTATTCGTGAAGAAGAAGGCGTAACAGAAACAGCTACTAAAGGCTATCTAGAGTTTAAAAATGTAACCTTTGCCTATCCTGGACATGCGGAAAGCCCAGTTATTCGCAATGTAAGTTTTAAGGCGTCACCTGGTGAAACAGTGGCCTTTATTGGGAGCACAGGTAGTGGGAAATCAACATTAATTCAATTGATTCCACGGTTTTATGATGTATCAGAAGGTGAAATTTTAATCGATGGAGTGAACGTAAAAGAGTACAAACTTAGTGCATTACGCAATAAGATTGGCTATATTCCACAAAAAGCGTTACTTTTTACTGGTACAATTGCTGATAATCTTCGCTACGGTAAGGAAGATGCGACGTTAGAAGAAATGGAACGAGCAATTGACATTGCTCAAGCAACAGAATTTGTTTCACAAAAACCGCAAGGCTATGATGAACCTCTTTCAGAAGGTGGCACGAACTTTTCTGGTGGTCAAAAACAACGTTTAGCTATCGCACGGGCGATTATTCGCAATCCGGAAATTTATATATTTGATGATAGTTTTTCTGCGTTAGATTATCAAACAGATGCAAATTTACGAGCGCGTCTGAAAAAAGAAACAACAGAATCCACTGTTTTAATTGTGGCACAACGTGTTGGAACAATTATGCATGCGGACCGCATTGTTTGTTTTAAACGAAGGCGACGTGGTCGGAAATTTGGGCACCAACCATTTCA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3003948","ARO_id":"40703","ARO_name":"efrA","ARO_description":"efrA is a part of the EfrAB efflux pump, and both efrA and efrB are necessary to confer drug resistance.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2422":{"model_id":"2422","model_name":"efrB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"710"}},"model_sequences":{"sequence":{"3753":{"protein_sequence":{"accession":"CDO61516.1","sequence":"LDTCRIFRRNAKSPVNIAKHAKFIRRLKWLCSENMTGFSVLKLYVRKKKPLKGFKQVNHRFKWFGFKASFISGLMLPLVQMTAYGTYIGVAVLGSYYVVAGVIVVGQLQAFIQYIWQISQPMGNITQLSAALQSASASTMRIFEILDEPEEELNEQDVPLPEPILGSVEFENVSFSYDPEKPLIRNLNFKVDAGQMVAIVGPTGAGKTTLINLLMRFYDVTEGAIKIDGIDTKKMNRSDVRSVFGMVLQDAWLYKGTIADNIRFGKLDATDYEVVDAAKTANVDHFIRTMPDGYEMEINSEGDNVSLGQKQLLTIARAVISDPKILILDEATSSVDTRLEALIQKAMDRVMEGRTSFVIAHR"},"dna_sequence":{"accession":"HG970103.1","fmin":"0","fmax":"1086","strand":"+","sequence":"TTAGATACGTGTCGCATATTCAGGAGGAATGCTAAATCACCAGTAAATATTGCAAAGCATGCAAAATTCATTAGGAGACTTAAATGGTTATGTTCAGAAAATATGACTGGGTTCAGTGTCTTAAAACTATATGTTCGGAAAAAGAAACCCTTGAAAGGCTTTAAACAAGTCAATCATCGTTTTAAATGGTTTGGCTTCAAAGCATCCTTTATCTCAGGATTAATGTTGCCATTGGTTCAAATGACCGCTTATGGGACCTATATCGGGGTAGCTGTCCTTGGTAGTTACTATGTGGTTGCTGGTGTGATCGTAGTGGGGCAGTTACAAGCGTTTATTCAATATATTTGGCAAATTAGCCAACCAATGGGGAATATTACGCAGTTGTCTGCAGCTTTACAAAGCGCTTCAGCTTCGACCATGCGGATTTTTGAAATCCTAGATGAACCAGAAGAAGAACTTAACGAACAAGATGTTCCTTTGCCAGAACCTATTTTAGGCTCTGTTGAATTTGAAAATGTCAGCTTTAGTTATGACCCAGAAAAACCGTTAATTCGTAATTTGAACTTTAAAGTTGATGCGGGCCAAATGGTTGCGATTGTGGGACCAACTGGCGCTGGGAAAACAACCTTAATCAACTTACTGATGCGTTTTTATGATGTAACAGAAGGCGCCATTAAAATTGATGGTATTGACACAAAAAAAATGAACCGTAGTGATGTCCGATCTGTATTTGGAATGGTATTGCAAGATGCTTGGTTGTATAAAGGTACCATTGCAGATAACATTCGTTTTGGGAAGTTGGATGCCACGGATTATGAAGTTGTCGATGCAGCGAAAACGGCCAATGTGGATCACTTCATTCGGACAATGCCAGATGGGTATGAAATGGAAATCAATTCTGAGGGAGATAACGTTTCCCTTGGTCAAAAACAATTGTTGACCATTGCCCGAGCGGTAATTTCTGATCCGAAAATTTTGATTTTAGATGAGGCGACTAGTTCAGTCGATACACGCTTGGAAGCCTTAATTCAAAAAGCAATGGATCGTGTTATGGAAGGACGAACGAGTTTCGTTATTGCCCACCGT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3003949","ARO_id":"40704","ARO_name":"efrB","ARO_description":"efrB is a part of the EfrAB efflux pump, and both efrA and efrB are necessary to confer multidrug resistance.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2423":{"model_id":"2423","model_name":"msbA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"3754":{"protein_sequence":{"accession":"NP_415434.1","sequence":"MHNDKDLSTWQTFRRLWPTIAPFKAGLIVAGVALILNAASDTFMLSLLKPLLDDGFGKTDRSVLVWMPLVVIGLMILRGITSYVSSYCISWVSGKVVMTMRRRLFGHMMGMPVSFFDKQSTGTLLSRITYDSEQVASSSSGALITVVREGASIIGLFIMMFYYSWQLSIILIVLAPIVSIAIRVVSKRFRNISKNMQNTMGQVTTSAEQMLKGHKEVLIFGGQEVETKRFDKVSNRMRLQGMKMVSASSISDPIIQLIASLALAFVLYAASFPSVMDSLTAGTITVVFSSMIALMRPLKSLTNVNAQFQRGMAACQTLFTILDSEQEKDEGKRVIERATGDVEFRNVTFTYPGRDVPALRNINLKIPAGKTVALVGRSGSGKSTIASLITRFYDIDEGEILMDGHDLREYTLASLRNQVALVSQNVHLFNDTVANNIAYARTEQYSREQIEEAARMAYAMDFINKMDNGLDTVIGENGVLLSGGQRQRIAIARALLRDSPILILDEATSALDTESERAIQAALDELQKNRTSLVIAHRLSTIEKADEIVVVEDGVIVERGTHNDLLEHRGVYAQLHKMQFGQ"},"dna_sequence":{"accession":"NC_000913.3","fmin":"966620","fmax":"968369","strand":"+","sequence":"ATGCATAACGACAAAGATCTCTCTACGTGGCAGACATTCCGCCGACTGTGGCCAACCATTGCGCCTTTCAAAGCGGGTCTGATCGTGGCGGGCGTAGCGTTAATCCTCAACGCAGCCAGCGATACCTTCATGTTATCGCTCCTTAAGCCACTTCTTGATGATGGCTTTGGTAAAACAGATCGCTCCGTGCTGGTGTGGATGCCGCTGGTGGTGATCGGGCTGATGATTTTACGTGGTATCACCAGCTATGTCTCCAGCTACTGTATCTCCTGGGTATCAGGAAAGGTGGTAATGACCATGCGTCGCCGCCTGTTTGGTCACATGATGGGAATGCCAGTTTCATTCTTTGACAAACAGTCAACGGGTACGCTGTTGTCACGTATTACCTACGATTCCGAACAGGTTGCTTCTTCTTCTTCCGGCGCACTGATTACTGTTGTGCGTGAAGGTGCGTCGATCATCGGCCTGTTCATCATGATGTTCTATTACAGTTGGCAACTGTCGATCATTTTGATTGTGCTGGCACCGATTGTTTCGATTGCGATTCGCGTTGTATCGAAGCGTTTTCGCAACATCAGTAAAAACATGCAGAACACCATGGGGCAGGTGACCACCAGCGCAGAACAAATGCTGAAGGGCCACAAAGAAGTATTGATTTTCGGTGGTCAGGAAGTGGAAACGAAACGCTTTGATAAAGTCAGCAACCGAATGCGTCTTCAGGGGATGAAAATGGTTTCAGCCTCTTCCATCTCTGATCCGATCATTCAGCTGATCGCCTCTTTGGCGCTGGCGTTTGTTCTGTATGCGGCGAGCTTCCCAAGTGTCATGGATAGCCTGACTGCCGGTACGATTACCGTTGTTTTCTCTTCAATGATTGCACTGATGCGTCCGCTGAAATCGCTGACCAACGTTAACGCCCAGTTCCAGCGCGGTATGGCGGCTTGTCAGACGCTGTTTACCATTCTGGACAGTGAGCAGGAGAAAGATGAAGGTAAGCGCGTGATCGAGCGTGCGACTGGCGACGTGGAATTCCGCAATGTCACCTTTACTTATCCGGGACGTGACGTACCTGCATTGCGTAACATCAACCTGAAAATTCCGGCAGGGAAGACGGTTGCTCTGGTTGGACGCTCTGGTTCGGGTAAATCAACCATCGCCAGCCTGATCACGCGTTTTTACGATATTGATGAAGGCGAAATCCTGATGGATGGTCACGATCTGCGCGAGTATACCCTGGCGTCGTTACGTAACCAGGTTGCTCTGGTGTCGCAGAATGTCCATCTGTTTAACGATACGGTTGCTAACAACATTGCTTACGCACGGACTGAACAGTACAGCCGTGAGCAAATTGAAGAAGCGGCGCGTATGGCCTACGCCATGGACTTCATCAATAAGATGGATAACGGTCTCGATACAGTGATTGGTGAAAACGGCGTGCTGCTCTCTGGCGGTCAGCGTCAGCGTATTGCTATCGCTCGAGCCTTGTTGCGTGATAGCCCGATTCTGATTCTGGACGAAGCTACCTCGGCTCTGGATACCGAATCCGAACGTGCGATTCAGGCGGCACTGGATGAGTTGCAGAAAAACCGTACCTCTCTGGTGATTGCCCACCGCTTGTCTACCATTGAAAAGGCAGACGAAATCGTGGTCGTCGAGGATGGTGTCATTGTGGAACGCGGTACGCATAACGATTTGCTTGAGCACCGCGGCGTTTACGCGCAACTTCACAAAATGCAGTTTGGCCAATGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3003950","ARO_id":"40720","ARO_name":"msbA","ARO_description":"MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A, a major component of the bacterial outer cell membrane, and is the only bacterial ABC transporter that is essential for cell viability.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"37033":{"category_aro_accession":"3000689","category_aro_cvterm_id":"37033","category_aro_name":"metronidazole","category_aro_description":"Metronidazole is a nitroimidazole that is active against anaerobic bacteria and protozoa. It is not effective against aerobic bacteria. Nitroimidazoles act by oxidizing DNA causing strand breaks and cell death.","category_aro_class_name":"Antibiotic"},"41239":{"category_aro_accession":"3004115","category_aro_cvterm_id":"41239","category_aro_name":"nitroimidazole antibiotic","category_aro_description":"Nitroimidazoles are a group of drugs that have both antiprotozoal and antibacterial activity, classified with respect to the location of the nitro functional group.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2425":{"model_id":"2425","model_name":"hmrM","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"900"}},"model_sequences":{"sequence":{"3756":{"protein_sequence":{"accession":"WP_014550864.1","sequence":"MNFRLLSQYHTDIKKLIKISLPILLAQIAQNSMGLADTIMAGRVSSTDMAAISIGASIWMPLMFFGQGLLLALPPTISYLNGSGQHHRIAHQVRQGIWLVLGVSIPLGLLIYFCEIPLQYMQMESKMSDLARNYLHAMLWGLPAYLMLINFRCLNDGIEKTKPAMVITFLGLLINIPLNYIFIYGKFGMPAFGAVGCGIATAIVNWAMCLMMIFYSYTNTQERSLKVFSQLIEMPNPKTLKKLLRLGLPIAIAICCEVALYALTSLMLSPLGATIVASHQITLNTSSFIFMFPMSIGMATTILVGQALGAGSPQNAKKIGYAALLLGLTVTIVTALITIFFRYEIASIFVTDEIVIAMAANLLLFAALYQFSDTIQMVVGGILRGYKDTKVILYITLFSYWVIGVPLGYTLGRTDWLVPHIDAKGFWIAFVVSLTFAAFLLSLRMKKMQAMNDNAILQRLEKLK"},"dna_sequence":{"accession":"NC_017452.1","fmin":"1144673","fmax":"1146068","strand":"-","sequence":"TTATTTAAGTTTTTCTAAACGTTGTAAAATAGCGTTGTCGTTCATAGCTTGCATTTTTTTCATTCTCAAAGAAAGTAAGAATGCCGCAAAAGTGAGCGAGACCACAAAGGCAATCCAGAAACCTTTCGCATCAATGTGTGGCACAAGCCAATCTGTACGACCTAGCGTATAACCAAGTGGCACACCAATTACCCAATAAGAGAAAAGGGTAATGTATAAAATGACTTTAGTATCTTTATAACCACGTAAAATACCACCAACCACCATTTGAATGGTATCTGAAAATTGATAAAGTGCGGCAAATAATAATAGATTTGCTGCCATGGCGATGACAATTTCATCTGTCACGAAGATCGATGCAATTTCATAACGGAAAAAAATCGTAATTAATGCAGTAACAATTGTCACAGTTAGCCCTAATAATAATGCGGCATAGCCAATTTTCTTCGCATTTTGTGGAGAACCTGCACCCAATGCTTGTCCAACTAAAATCGTCGTTGCCATACCAATCGACATAGGGAACATAAAAATAAAAGAACTAGTATTCAGCGTAATTTGATGGCTTGCCACAATAGTTGCACCCAGCGGAGAAAGCATTAAGGACGTAAGTGCATATAACGCCACTTCGCAACAAATTGCAATGGCAATGGGTAATCCTAAACGCAGTAATTTTTTAAGTGTTTTCGGATTTGGCATTTCAATTAATTGACTAAATACTTTTAGTGAACGTTCTTGAGTATTCGTGTAGGAATAGAAAATCATCATTAAGCACATTGCCCAGTTCACAATAGCTGTCGCAATACCACAGCCCACCGCACCAAAAGCAGGCATACCAAATTTTCCATAAATAAAAATGTAATTAAGCGGAATATTAATCAATAAACCTAAAAAGGTAATGACCATCGCAGGCTTGGTTTTCTCAATCCCATCATTTAAACAACGAAAATTAATCAGCATCAAATAAGCTGGCAATCCCCACAACATCGCGTGTAAATAATTGCGTGCTAAATCTGACATTTTGCTTTCCATTTGCATATATTGCAGCGGAATTTCACAGAAATAAATCAGTAAACCTAAAGGAATACTCACGCCTAACACAAGCCAAATGCCTTGGCGAACTTGATGTGCAATGCGATGGTGTTGGCCTGAACCATTCAAATAAGAAATTGTAGGCGGCAATGCCAACAATAAACCTTGCCCAAAAAACATCAATGGCATCCAAATTGAAGCACCAATAGAAATGGCTGCCATATCAGTGGAACTCACTCGCCCCGCCATAATGGTATCCGCTAATCCCATTGAGTTTTGTGCAATTTGCGCTAATAAAATAGGCAAGGAAATTTTAATCAACTTTTTAATATCAGTGTGGTATTGAGATAAAAGACGAAAATTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36768","NCBI_taxonomy_name":"Haemophilus influenzae","NCBI_taxonomy_id":"727"}}}},"ARO_accession":"3003953","ARO_id":"40723","ARO_name":"hmrM","ARO_description":"hmrM is a multidrug efflux pump belonging to the MATE family and functions as a  Na+\/drug antiporter.","ARO_category":{"36251":{"category_aro_accession":"3000112","category_aro_cvterm_id":"36251","category_aro_name":"multidrug and toxic compound extrusion (MATE) transporter","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Multidrug and toxic compound extrusion (MATE) transporters utilize the cationic gradient across the membrane as an energy source. Although there is a diverse substrate specificity, almost all MATE transporters recognize fluoroquinolones. Arciflavine, ethidium and aminoglycosides are also good substrates.","category_aro_class_name":"AMR Gene Family"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavin","category_aro_description":"Acriflavin is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36193":{"category_aro_accession":"3000054","category_aro_cvterm_id":"36193","category_aro_name":"acridine dye","category_aro_description":"Acridine dyes are cell permeable, basic molecules with an acridine chromophore. These compounds intercalate DNA. The image shown represents the core structure of the acridine family, with specific dyes containing varying substituents.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2426":{"model_id":"2426","model_name":"efmA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"3757":{"protein_sequence":{"accession":"BAG75524.1","sequence":"MENEQSVVLTNWKRNYLFFLSGQFLSGITSMVVQYAIIWYLTRETGSATILSFATLLGMIPMVLLSPFVGPLVDRWDKKALLIVTDIIVAIFALILAVVGTISESFPIWLVFVSLFMRSVAQTFQMPTIQSIMPTIVPSSHITRTNGQLGMVQSANFIIAPALGAALFSVVPVNYLILLDVLGAVFGVGLLIFVKIPKVSPEILEVPLTIFKDAKFGLQQLMDNKGLWYITINGAFVMLLFMPAISLYPLMTLDYFGGSVGQAGAVEVVYAVGMLLGGALISFIGTWKDRMKPIIIAYIIMGLTIGASGLVPNDSQGFLYFLILNAGAGCATPYFNTLLMAMIQQSYESNVLGRVLGNFNSLMNLAGPIGLLFAGPLADRLGVEKMFLFSGIGILLCGIVLFLTSAARNYDKELQKKLVKEHHEQKDE"},"dna_sequence":{"accession":"AB467372.1","fmin":"284","fmax":"1571","strand":"+","sequence":"ATGGAAAATGAACAGTCGGTCGTTTTAACGAATTGGAAGAGAAATTATTTGTTCTTTTTATCGGGACAGTTTTTGTCAGGAATCACTAGTATGGTCGTCCAATATGCGATCATCTGGTATTTGACAAGAGAAACCGGTTCGGCGACAATTTTGAGTTTTGCTACTTTACTAGGAATGATTCCCATGGTTTTACTAAGCCCATTTGTAGGACCGCTAGTGGATCGCTGGGATAAAAAAGCTCTTTTGATTGTCACGGATATTATTGTAGCGATTTTCGCGCTTATTTTAGCAGTAGTCGGAACGATTTCAGAATCCTTCCCGATTTGGCTAGTTTTTGTGTCTTTGTTTATGCGTTCGGTCGCACAAACATTCCAAATGCCAACGATCCAGTCGATTATGCCGACAATCGTTCCATCTTCTCACATAACAAGGACGAATGGACAGTTAGGAATGGTCCAATCAGCGAATTTCATCATTGCGCCAGCTCTAGGTGCGGCTTTGTTTTCAGTCGTTCCTGTCAATTACCTTATTTTATTAGATGTATTGGGGGCAGTTTTTGGTGTCGGCTTATTGATTTTTGTGAAGATCCCAAAAGTTTCTCCTGAAATATTGGAAGTTCCGCTTACTATTTTTAAAGATGCAAAATTTGGGCTGCAGCAATTGATGGATAATAAAGGGTTATGGTACATAACGATCAATGGTGCATTTGTGATGCTGTTGTTCATGCCAGCAATCAGTCTGTATCCATTGATGACGCTAGATTACTTTGGTGGTTCCGTTGGACAGGCGGGAGCAGTGGAAGTAGTCTACGCAGTCGGAATGCTCTTAGGCGGTGCACTGATCAGTTTTATAGGAACATGGAAAGACCGAATGAAACCTATTATTATAGCCTACATCATTATGGGCCTGACGATCGGTGCAAGCGGATTGGTTCCAAACGATAGTCAAGGGTTCTTGTACTTTCTTATCTTGAATGCAGGAGCAGGTTGTGCAACGCCATATTTCAATACACTGCTGATGGCAATGATCCAGCAGAGTTATGAATCGAATGTTTTAGGTCGTGTCTTAGGGAACTTCAACTCTTTGATGAACCTGGCAGGTCCAATTGGATTATTATTTGCAGGACCATTAGCTGATCGTTTAGGGGTAGAAAAAATGTTCTTGTTTTCCGGAATCGGGATTTTATTATGCGGAATCGTTTTATTTTTAACGTCAGCTGCCCGAAATTATGATAAAGAATTACAGAAAAAACTGGTAAAAGAACACCATGAGCAAAAAGACGAATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3003954","ARO_id":"40724","ARO_name":"efmA","ARO_description":"efmA is an MFS transporter permease in  E. faecium.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2427":{"model_id":"2427","model_name":"efpA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"3758":{"protein_sequence":{"accession":"NP_217362.1","sequence":"MTALNDTERAVRNWTAGRPHRPAPMRPPRSEETASERPSRYYPTWLPSRSFIAAVIAIGGMQLLATMDSTVAIVALPKIQNELSLSDAGRSWVITAYVLTFGGLMLLGGRLGDTIGRKRTFIVGVALFTISSVLCAVAWDEATLVIARLSQGVGSAIASPTGLALVATTFPKGPARNAATAVFAAMTAIGSVMGLVVGGALTEVSWRWAFLVNVPIGLVMIYLARTALRETNKERMKLDATGAILATLACTAAVFAFSIGPEKGWMSGITIGSGLVALAAAVAFVIVERTAENPVVPFHLFRDRNRLVTFSAILLAGGVMFSLTVCIGLYVQDILGYSALRAGVGFIPFVIAMGIGLGVSSQLVSRFSPRVLTIGGGYLLFGAMLYGSFFMHRGVPYFPNLVMPIVVGGIGIGMAVVPLTLSAIAGVGFDQIGPVSAIALMLQSLGGPLVLAVIQAVITSRTLYLGGTTGPVKFMNDVQLAALDHAYTYGLLWVAGAAIIVGGMALFIGYTPQQVAHAQEVKEAIDAGEL"},"dna_sequence":{"accession":"NC_000962.3","fmin":"3153038","fmax":"3154631","strand":"-","sequence":"TTACAGCTCGCCGGCGTCGATCGCTTCCTTGACCTCCTGCGCATGGGCAACCTGCTGCGGCGTATACCCGATAAACAGCGCCATACCGCCGACGATGATGGCCGCTCCGGCCACCCACAGCAGGCCGTAGGTGTAGGCGTGGTCAAGCGCGGCCAACTGCACGTCGTTCATGAACTTCACCGGACCGGTGGTACCGCCCAGGTACAGCGTGCGCGACGTGATCACAGCCTGGATGACGGCGAGCACCAGCGGACCGCCCAGGCTCTGCAGCATCAGCGCAATTGCCGATACCGGACCGATCTGGTCGAAGCCGACGCCAGCGATCGCCGACAGAGTCAGCGGGACGACGGCCATGCCGATGCCAATCCCGCCGACGACGATCGGCATGACCAGGTTGGGGAAGTAGGGCACACCACGGTGCATGAAAAATGAGCCGTACAGCATGGCGCCGAATAGCAGATATCCGCCGCCGATGGTCAACACCCGTGGCGAAAACCGGGACACCAGCTGCGAGGACACACCTAGGCCGATTCCCATCGCGATGACGAACGGGATGAAACCTACGCCCGCGCGTAGCGCGCTGTAGCCCAAGATGTCCTGCACGTACAGGCCGATGCAGACGGTCAGGCTGAACATGACGCCGCCGGCCAACAGGATCGCGCTGAACGTGACCAACCGGTTGCGGTCGCGGAACAAGTGGAACGGCACGACGGGGTTCTCGGCAGTGCGCTCCACGATGACAAACGCGACAGCGGCCGCCAAGGCCACCAGGCCCGAACCGATGGTAATGCCTGACATCCAGCCCTTTTCAGGACCGATCGAGAAGGCGAAAACCGCCGCGGTGCATGCCAGCGTGGCCAGTATGGCCCCGGTGGCGTCGAGCTTCATCCGTTCTTTGTTGGTTTCCCGTAGGGCGGTGCGGGCCAGGTAGATCATCACCAGCCCGATCGGCACGTTCACCAGGAACGCCCACCGCCATGACACCTCGGTCAGTGCTCCGCCGACCACCAGCCCCATCACCGACCCGATCGCGGTCATCGCGGCGAACACCGCCGTCGCGGCGTTGCGGGCAGGTCCCTTGGGGAACGTGGTCGCCACCAGCGCCAGACCGGTCGGAGATGCGATGGCCGACCCCACACCCTGGGACAACCGGGCGATCACCAACGTCGCCTCGTCCCAGGCGACCGCGCACAGCACCGACGAGATGGTGAATAGCGCAACGCCAACAATGAAGGTGCGTTTGCGCCCGATGGTGTCGCCAAGCCGGCCGCCGAGCAGCATCAGCCCGCCGAAGGTCAGCACGTAGGCGGTGATCACCCAGCTGCGGCCGGCATCAGACAAGCTCAGCTCGTTTTGAATCTTAGGTAGCGCGACGATGGCGACGGTGCTGTCCATGGTCGCCAGCAGCTGCATCCCGCCGATAGCAATAACCGCAGCGATAAAGCTGCGCGAGGGCAGCCAAGTCGGGTAGTACCTGCTGGGGCGCTCTGAAGCGGTCTCCTCCGAGCGCGGCGGGCGCATCGGGGCCGGACGGTGTGGGCGTCCGGCTGTCCAGTTACGGACCGCCCGCTCTGTGTCGTTGAGAGCCGTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3003955","ARO_id":"40726","ARO_name":"efpA","ARO_description":"efpA is an MFS transporter found in Mycobacterium tuberculosis.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36659":{"category_aro_accession":"3000520","category_aro_cvterm_id":"36659","category_aro_name":"isoniazid","category_aro_description":"Isoniazid is an organic compound that is the first-line anti tuberculosis medication in prevention and treatment. As a prodrug, it is activated by mycobacterial catalase-peroxidases such as M. tuberculosis KatG. Isoniazid inhibits mycolic acid synthesis, which prevents cell wall synthesis in mycobacteria.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2428":{"model_id":"2428","model_name":"farA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"730"}},"model_sequences":{"sequence":{"3759":{"protein_sequence":{"accession":"NP_273367.1","sequence":"MDTHTDETKLQNTQAKRKRRLTALTLLFALAAAAAGSAFFLWWQHEEETEDAYVAGRVVQVTPQKGGTVRKVLHDDTDAVKKGDVLAVLDDDNDVLAYERAKNELVQAVRQNRRQNAATSQAGAQVALRRADLARAQDDLRRRSALAESGAVSAEELAHARAAVSQAQAAVKAALAEESSARAALGGQVSLREQPAVQTAIGRLKDAWLNLQRTQIRAPADGQVAKRSVQVGQQVAAGAPLMAVVPLSDVWVDANFKETQLRHMKIGQPAELVSDLYGKQIVYRGRVAGFSAGTGSAFSLIPAQNATGNWIKVVQRVPVRIVLNREDVDRHPLRIGLSMTVKVDTSAAGAPVSKTPGAALPEMESTDWSEVDRTVDEILGQSAP"},"dna_sequence":{"accession":"NC_003112.2","fmin":"329612","fmax":"330767","strand":"+","sequence":"ATGGATACGCACACGGACGAAACAAAACTTCAAAACACGCAAGCCAAACGCAAACGCCGCCTGACGGCATTGACGCTGCTGTTCGCGCTTGCCGCCGCAGCCGCCGGGTCGGCGTTTTTTTTATGGTGGCAGCACGAAGAGGAAACGGAAGACGCTTATGTTGCCGGACGCGTGGTTCAGGTTACGCCGCAAAAGGGCGGTACGGTGCGGAAGGTTTTGCACGACGATACGGATGCCGTGAAAAAAGGCGACGTGCTGGCGGTATTGGACGACGATAATGATGTGCTGGCTTACGAGCGGGCAAAAAACGAGCTGGTTCAGGCGGTGCGGCAAAACCGCCGGCAAAATGCCGCCACTTCGCAGGCGGGGGCGCAGGTTGCCTTGCGCCGGGCGGATTTGGCACGCGCACAGGATGATTTGCGCCGCCGGTCTGCTTTGGCGGAATCGGGCGCGGTGTCCGCCGAAGAGCTGGCACACGCCCGTGCGGCAGTGTCTCAGGCGCAGGCGGCGGTCAAAGCGGCTTTGGCGGAAGAATCTTCGGCACGTGCGGCTTTGGGCGGTCAGGTTTCTTTGCGCGAACAGCCGGCGGTTCAGACGGCAATCGGCAGGTTGAAAGATGCGTGGTTGAACCTTCAGCGGACGCAAATCCGCGCGCCGGCGGACGGTCAGGTGGCGAAGCGTTCGGTGCAGGTCGGGCAGCAGGTGGCGGCAGGCGCGCCGCTGATGGCGGTGGTGCCGCTGTCGGATGTGTGGGTGGATGCTAATTTTAAAGAGACGCAGTTGCGGCATATGAAAATCGGACAGCCTGCCGAGCTGGTGTCCGATTTGTACGGCAAACAAATTGTTTATCGCGGCAGGGTGGCAGGTTTTTCGGCAGGTACGGGCAGCGCGTTTTCGCTGATTCCGGCGCAAAACGCAACGGGCAACTGGATTAAAGTGGTGCAGCGCGTCCCCGTCCGTATCGTGCTGAACCGCGAAGATGTGGACAGGCATCCGTTGCGTATCGGTTTGTCGATGACGGTTAAAGTGGATACTTCCGCCGCAGGCGCGCCTGTTTCAAAAACGCCGGGTGCGGCATTGCCGGAAATGGAAAGTACCGACTGGTCGGAAGTCGATCGGACGGTCGATGAAATCCTCGGGCAATCCGCGCCCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39597","NCBI_taxonomy_name":"Neisseria meningitidis MC58","NCBI_taxonomy_id":"122586"}}}},"ARO_accession":"3003961","ARO_id":"40732","ARO_name":"farA","ARO_description":"farA is the membrane fusion protein that is part of the farAB efflux pump.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"40728":{"category_aro_accession":"3003957","category_aro_cvterm_id":"40728","category_aro_name":"palmitic acid","category_aro_description":"Palmitic acid is the most common saturated fatty acid found in animals, plants, and microorganisms. Palmitic acid is found to have antibacterial properties.","category_aro_class_name":"Antibiotic"},"40729":{"category_aro_accession":"3003958","category_aro_cvterm_id":"40729","category_aro_name":"oleic acid","category_aro_description":"Oleic acid is a fatty acid that occurs naturally in various animal and vegetable fats and oils. Oleic acid is found to have antibacterial activity, particularly in inhibiting the growth of several Gram-positive bacterial species.","category_aro_class_name":"Antibiotic"},"40730":{"category_aro_accession":"3003959","category_aro_cvterm_id":"40730","category_aro_name":"linoleic acid","category_aro_description":"Linoleic acid is a polyunsaturated omega-6 fatty acid. Linoleic acid has been found to have antibacterial activity, particularly in inhibiting the growth of Gram-positive bacterial species.","category_aro_class_name":"Antibiotic"},"40727":{"category_aro_accession":"3003956","category_aro_cvterm_id":"40727","category_aro_name":"antibacterial free fatty acids","category_aro_description":"Amongst the diverse and potent biological activities of free fatty acids (FFAs) is the ability to kill or inhibit the growth of bacteria. The antibacterial properties of FFAs are used by many organisms to defend against parasitic or pathogenic bacteria. The prime target of FFA action is the cell membrane, where FFAs disrupt the electron transport chain and oxidative phosphorylation. Besides interfering with cellular energy production, FFA action may also result from the inhibition of enzyme activity, impairment of nutrient uptake, generation of peroxidation and auto-oxidation degradation products or direct lysis of bacterial cells.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2429":{"model_id":"2429","model_name":"farB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"990"}},"model_sequences":{"sequence":{"3760":{"protein_sequence":{"accession":"NP_273368.1","sequence":"MDYPPLKGAALAWVTLSLGLAVFMEVLDTTIANVAVPVIAGNLGAATTQGTWVITSFSVANAVSVPLTGFLAKRIGEVKLFTAAAVGFVITSWLCGIAPNLQSLVVFRILQGFIAGPLIPLSQSLLMASYPPAKRTLALALWAMTVVVAPVLGPILGGWISGNWHWGWIFFINIPIGIISAWITWKHLKYRETETVKMPTDYVGLTLMVVGIGALQMMLDRGKELDWFASGEIITLGVVALVCLSYFIVWELGEKYPIVDLSLFKDRNFTVGVIATSLGFMVYMGTLTLLPLVLQTNLGYTSTWAGLAAAPVGILPVFLSPLIGRFGNKIDMRLFVTASFLTFAFTFYWRTDFYADMDIGNVIWPQFWQGVGVAMFFLPLTTITLSHMKGGQIAAAGSLSNFLRVLMGGVGVSVVSTLWERREALHHTRFAEHITPYSATLHETAAHLSQHGVSDIQTLGIINNTITQQGFIIGSNEIFMAGSLLFIIMIPVIWLAKPPFHNGGGGGH"},"dna_sequence":{"accession":"NC_003112.2","fmin":"330790","fmax":"332317","strand":"+","sequence":"ATGGATTATCCACCGCTTAAGGGTGCGGCATTGGCGTGGGTTACGCTGTCTTTGGGGCTTGCCGTATTTATGGAAGTTTTAGATACGACTATCGCCAATGTCGCCGTTCCCGTCATCGCCGGCAACCTCGGTGCGGCAACCACTCAGGGGACGTGGGTCATCACTTCCTTTTCTGTGGCAAACGCCGTTTCCGTGCCGCTGACGGGCTTTTTGGCAAAACGCATCGGCGAGGTCAAATTGTTTACCGCCGCCGCTGTCGGTTTCGTCATCACATCGTGGCTGTGCGGTATTGCCCCCAACCTTCAGTCGCTGGTTGTTTTCCGCATCTTGCAGGGCTTTATCGCCGGGCCGCTGATTCCCTTGTCGCAAAGCCTGTTAATGGCATCCTATCCGCCCGCAAAACGGACGCTGGCACTGGCATTGTGGGCAATGACCGTCGTTGTCGCCCCTGTTCTCGGGCCGATACTCGGCGGCTGGATTTCCGGAAACTGGCATTGGGGTTGGATTTTCTTCATTAATATCCCTATCGGTATCATATCGGCATGGATTACATGGAAACATTTGAAATATCGGGAAACGGAAACCGTTAAAATGCCGACCGACTATGTCGGGCTTACATTGATGGTAGTCGGTATCGGCGCGTTACAGATGATGCTGGACAGGGGTAAGGAACTCGACTGGTTCGCCTCTGGAGAAATCATTACCTTGGGCGTAGTCGCACTGGTGTGCTTGTCGTATTTTATTGTTTGGGAATTGGGAGAAAAATATCCGATTGTCGATTTATCGCTGTTTAAAGATCGGAATTTTACCGTCGGCGTCATTGCCACGTCATTGGGTTTTATGGTGTATATGGGGACGCTGACCCTGCTGCCGTTAGTGTTGCAGACCAACCTGGGCTATACCTCCACGTGGGCAGGGCTTGCCGCCGCACCTGTCGGCATCCTGCCTGTTTTCCTGTCTCCGTTAATCGGCAGGTTCGGCAATAAAATCGATATGCGCCTGTTCGTAACTGCCAGCTTCCTGACCTTTGCCTTTACTTTCTATTGGCGTACGGATTTTTATGCCGATATGGATATTGGCAACGTCATCTGGCCGCAGTTTTGGCAGGGTGTCGGTGTCGCCATGTTTTTTCTGCCGCTGACCACCATCACACTGTCGCATATGAAGGGCGGGCAGATTGCCGCCGCAGGCAGCCTGTCGAATTTCTTGCGCGTGCTGATGGGCGGTGTCGGCGTATCCGTCGTCAGCACCCTGTGGGAACGGCGCGAAGCGTTGCACCACACACGCTTTGCCGAACACATCACGCCCTATTCCGCAACATTGCACGAAACGGCCGCTCATTTGTCCCAGCACGGCGTTTCCGACATTCAAACCCTAGGCATCATCAACAATACCATTACCCAGCAGGGTTTTATTATCGGCTCGAACGAAATCTTTATGGCGGGCAGCTTGTTATTCATTATCATGATACCCGTCATATGGCTGGCAAAACCGCCGTTCCACAACGGCGGCGGCGGTGGACATTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39597","NCBI_taxonomy_name":"Neisseria meningitidis MC58","NCBI_taxonomy_id":"122586"}}}},"ARO_accession":"3003962","ARO_id":"40733","ARO_name":"farB","ARO_description":"farB is the cytoplasmic transporter protein that is part of the farAB efflux pump. farB corresponds to 3 loci in Pseudomonas aeruginosa PAO1 and 3 loci in Pseudomonas aeruginosa LESB58.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"40728":{"category_aro_accession":"3003957","category_aro_cvterm_id":"40728","category_aro_name":"palmitic acid","category_aro_description":"Palmitic acid is the most common saturated fatty acid found in animals, plants, and microorganisms. Palmitic acid is found to have antibacterial properties.","category_aro_class_name":"Antibiotic"},"40729":{"category_aro_accession":"3003958","category_aro_cvterm_id":"40729","category_aro_name":"oleic acid","category_aro_description":"Oleic acid is a fatty acid that occurs naturally in various animal and vegetable fats and oils. Oleic acid is found to have antibacterial activity, particularly in inhibiting the growth of several Gram-positive bacterial species.","category_aro_class_name":"Antibiotic"},"40730":{"category_aro_accession":"3003959","category_aro_cvterm_id":"40730","category_aro_name":"linoleic acid","category_aro_description":"Linoleic acid is a polyunsaturated omega-6 fatty acid. Linoleic acid has been found to have antibacterial activity, particularly in inhibiting the growth of Gram-positive bacterial species.","category_aro_class_name":"Antibiotic"},"40727":{"category_aro_accession":"3003956","category_aro_cvterm_id":"40727","category_aro_name":"antibacterial free fatty acids","category_aro_description":"Amongst the diverse and potent biological activities of free fatty acids (FFAs) is the ability to kill or inhibit the growth of bacteria. The antibacterial properties of FFAs are used by many organisms to defend against parasitic or pathogenic bacteria. The prime target of FFA action is the cell membrane, where FFAs disrupt the electron transport chain and oxidative phosphorylation. Besides interfering with cellular energy production, FFA action may also result from the inhibition of enzyme activity, impairment of nutrient uptake, generation of peroxidation and auto-oxidation degradation products or direct lysis of bacterial cells.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2430":{"model_id":"2430","model_name":"hp1181","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"850"}},"model_sequences":{"sequence":{"3761":{"protein_sequence":{"accession":"NP_207972.1","sequence":"MFKKIFPLALVSSLRFLGLFIVLPVISLYADSFHSSSPLLVGLAVGGAYLTQIVFQTPMGILSDKIGRKVVVMVCLLLFLAGSLVCFIANDIVWLVIGRFIQGMGALGGVISAMVADEVKEEERTKAMAIMGAFIFISFTISMAIGPGVVAFLGGAKWLFLLTAILTLLSLLMLLKVKDAPKISYQIKNIKAYQPNSKALYLLYLSSFFEKAFMTLIFVLIPLALVNEFHKDESFLILVYVPGALLGVLSMGIASVMAEKYNKPKGVMLSGVLLFIVSYLCLFLADSSFLGKYLWLFIVGVAFFFIGFATLEPIMQSLASKFAKVHEKGKVLGQFTTFGYLGSFVGGVSGGLSYHHLGVSNTSLIVVALGLIWGLSLFLLNNPSKQKNVYFPLDAYNEEQFETLEDKIIEWYVNISEEIIIVKYNSDHISEEEIIHLAQNFRK"},"dna_sequence":{"accession":"NC_000915.1","fmin":"1249487","fmax":"1250819","strand":"+","sequence":"ATGTTTAAGAAAATTTTTCCATTAGCGTTAGTGTCATCGTTGCGGTTTTTGGGGCTTTTTATTGTTTTGCCGGTCATTAGTTTGTATGCGGATAGTTTCCATTCAAGCAGTCCCTTACTCGTGGGGTTGGCTGTGGGCGGAGCGTATCTTACGCAAATTGTTTTTCAAACCCCCATGGGCATTCTTAGCGATAAGATAGGCCGTAAAGTGGTGGTTATGGTGTGCTTGCTGTTGTTTTTAGCCGGCTCGTTAGTGTGCTTTATAGCGAATGATATTGTTTGGCTCGTTATAGGGCGCTTCATTCAAGGCATGGGGGCTTTAGGGGGGGTTATTAGTGCGATGGTGGCGGATGAAGTGAAAGAAGAAGAGCGCACCAAAGCCATGGCCATCATGGGAGCGTTTATTTTCATTAGCTTCACTATAAGCATGGCGATTGGCCCTGGGGTTGTAGCGTTTTTGGGGGGGGCAAAATGGCTCTTTTTACTCACGGCGATCTTAACTTTATTGAGTTTATTGATGCTTTTAAAAGTCAAAGACGCCCCTAAAATTTCTTACCAGATCAAAAACATAAAAGCTTACCAACCCAACTCTAAAGCCTTGTATCTTTTGTATCTAAGCTCTTTTTTTGAAAAAGCGTTCATGACGCTTATTTTTGTGCTGATCCCTTTAGCCTTAGTGAATGAATTTCATAAAGATGAAAGCTTTTTAATCTTGGTGTATGTGCCTGGAGCCTTATTAGGGGTCTTAAGCATGGGAATAGCGAGCGTTATGGCTGAAAAATACAACAAGCCTAAAGGAGTGATGCTTTCTGGCGTATTATTGTTTATTGTGAGTTATTTGTGCTTGTTTTTAGCCGACTCTAGCTTTTTAGGGAAATATTTATGGCTTTTTATTGTTGGGGTGGCGTTTTTCTTTATTGGTTTTGCCACCTTAGAGCCTATCATGCAATCTTTAGCGTCTAAATTCGCCAAAGTGCATGAAAAAGGCAAGGTTTTAGGGCAATTCACTACTTTTGGCTATTTAGGGAGCTTTGTTGGGGGCGTGAGCGGGGGGTTGAGCTACCATCATTTAGGCGTTTCTAACACAAGCTTGATCGTTGTAGCTTTAGGGCTTATTTGGGGGCTATCGCTCTTTTTACTCAACAACCCTTCCAAGCAAAAAAATGTCTATTTCCCCTTAGACGCTTACAATGAGGAACAATTTGAAACTTTAGAGGATAAAATCATTGAATGGTATGTTAATATTAGCGAAGAAATCATTATTGTGAAATATAATTCCGATCACATTAGCGAAGAAGAAATCATTCACTTAGCGCAAAACTTTAGAAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36758","NCBI_taxonomy_name":"Helicobacter pylori 26695","NCBI_taxonomy_id":"85962"}}}},"ARO_accession":"3003964","ARO_id":"40735","ARO_name":"hp1181","ARO_description":"hp1181 is a translocase that is part of the MFS efflux pump family. It is found in H. pylori and has role in the active efflux of antibiotics.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"37033":{"category_aro_accession":"3000689","category_aro_cvterm_id":"37033","category_aro_name":"metronidazole","category_aro_description":"Metronidazole is a nitroimidazole that is active against anaerobic bacteria and protozoa. It is not effective against aerobic bacteria. Nitroimidazoles act by oxidizing DNA causing strand breaks and cell death.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"41239":{"category_aro_accession":"3004115","category_aro_cvterm_id":"41239","category_aro_name":"nitroimidazole antibiotic","category_aro_description":"Nitroimidazoles are a group of drugs that have both antiprotozoal and antibacterial activity, classified with respect to the location of the nitro functional group.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2431":{"model_id":"2431","model_name":"hp1184","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"900"}},"model_sequences":{"sequence":{"3762":{"protein_sequence":{"accession":"NP_207975.1","sequence":"MLIKKIDLHKDPIRKLFFYYFIPLAFSMISLSTYSMIDGMFVGKKLGKEAIAAVNIAWPIFPGLIAYELLFGFGAASIVGYFLGQNKTHRARLVFSSVFYFVAISAFILSMALLPFSETIARFFGSNDALLSMSKRYIEIILMGAVFMVLHPLADVFVVNDKRPILAMVAMLIGSLANIFFNYLFIFVLKVGVQGSAIATVIGHAIGVLVLMQHFWRKKGQLYFIKRFSLSSVISSAKSGVPQSTAEFSASVMILLFNTAIMHTAGERFVSMYGIVMYNAIIFFTTLFAISQGIQPIASFSYGARNLERVKEVFVFGLKAAFCIGIVFYGAYYFLDEFLIKLYLQPSEQDPLFMQETKRAMNIYYVGYIFLGMTLLCAVFFQSIQRTKSSFIITLSHTLGFIVILLPILSHFYGINGVWVTYPIAQFLAFLVALGVTYYEIKKGVFTTYKEKNPIALKT"},"dna_sequence":{"accession":"NC_000915.1","fmin":"1252784","fmax":"1254164","strand":"-","sequence":"TTAAGTTTTCAAAGCGATAGGGTTTTTCTCTTTATAAGTGGTAAAAACCCCTTTTTTGATTTCGTAATAAGTTACCCCTAACGCTACTAAAAACGCTAAAAATTGCGCAATGGGGTAAGTTACCCAAACGCCATTAATCCCATAGAAATGACTTAAAATCGGCAATAGAATAACGATAAACCCCAGCGTGTGTGAAAGGGTGATGATAAACGAACTTTTGGTGCGTTGGATGGATTGGAAAAACACCGCGCACAACAAAGTCATGCCTAAGAAAATATAGCCCACATAATAAATATTCATCGCCCTTTTAGTCTCTTGCATAAAAAGGGGGTCTTGTTCGCTTGGCTGCAAATAAAGCTTGATTAAAAATTCATCTAAAAAATAATAAGCGCCATAGAAAACAATCCCTATACAAAACGCTGCTTTCAAACCAAAGACAAACACCTCTTTCACGCGCTCTAAATTTCTAGCCCCATAGCTAAAGCTCGCAATCGGTTGGATGCCTTGAGAAATCGCAAACAAAGTCGTAAAAAAGATAATCGCATTATACATAACGATCCCATACATGCTTACAAACCTTTCCCCAGCCGTGTGCATGATAGCGGTATTAAACAACAAAATCATAACAGAAGCACTAAATTCTGCCGTGCTTTGAGGCACGCCGCTTTTAGCTGAAGAAATGACTGAAGACAAGGAAAATCGTTTGATGAAATACAATTGCCCTTTTTTGCGCCAAAAATGCTGCATTAAGACTAAAACCCCTATCGCATGCCCTATCACGGTGGCTATCGCGCTGCCTTGAACCCCCACTTTTAAAACAAAAATAAACAAGTAGTTGAAAAAGATATTCGCTAACGAGCCAATCAGCATCGCTACCATCGCTAAAATGGGGCGTTTGTCATTCACCACAAAAACATCCGCCAAAGGGTGCAAAACCATAAAAACCGCGCCCATTAAAATGATTTCAATGTAGCGTTTGGACATGCTCAATAAAGCGTCATTGCTCCCAAAAAAACGCGCGATAGTTTCGCTAAAAGGCAATAACGCCATGCTCAAAATAAAGGCACTTATAGCGACAAAATAAAACACGCTGCTAAACACAAGCCTAGCCCTATGGGTTTTATTTTGACCCAAAAAATACCCCACAATACTCGCTGCCCCAAAACCAAAAAGCAATTCATACGCAATGAGCCCTGGAAAAATAGGCCATGCGATATTGACTGCAGCGATAGCTTCTTTACCCAGTTTCTTGCCCACAAACATGCCATCTATCATAGAGTAAGTGGAAAGTGAAATCATAGAAAAAGCTAAAGGGATAAAATAATAAAAAAAGAGCTTTCTTATCGGATCTTTATGCAAATCAATCTTTTTTATTAGCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36758","NCBI_taxonomy_name":"Helicobacter pylori 26695","NCBI_taxonomy_id":"85962"}}}},"ARO_accession":"3003965","ARO_id":"40736","ARO_name":"hp1184","ARO_description":"hp1184 is a translocase that belongs to the MATE efflux pump family. It is found in H. pylori and is involved in the active efflux of antibiotics.","ARO_category":{"36251":{"category_aro_accession":"3000112","category_aro_cvterm_id":"36251","category_aro_name":"multidrug and toxic compound extrusion (MATE) transporter","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Multidrug and toxic compound extrusion (MATE) transporters utilize the cationic gradient across the membrane as an energy source. Although there is a diverse substrate specificity, almost all MATE transporters recognize fluoroquinolones. Arciflavine, ethidium and aminoglycosides are also good substrates.","category_aro_class_name":"AMR Gene Family"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2433":{"model_id":"2433","model_name":"lrfA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"910"}},"model_sequences":{"sequence":{"3766":{"protein_sequence":{"accession":"AAC43550.1","sequence":"MSTCIEGTPSTTRTPTRAWVALAVLALPVLLIAIDNTVLAFALPLIAEDFRPSATTQLWIVDVYSLVLAALLVAMGSLGDRLGRRRVLLIGGAGFAVVSALAAFAPSTELLVGARALLGVFGAMLMPSTLSLIRNIFTDASARRLAIAIWASCFTAGSALGPIVGGALLEHFHWGAVFLVAVPILLPLLVLGPRLVPESRDPNPGPFDPVSIVLSFTTMLPIVWAVKTAAHDGLSAAAAAAFAVGIVSGALFVRRQNRSATPMLDIGLFKVMPFTSSILANFLSIIGLIGFIFFISQHLQLVLGLSPLTAGLVTLPGAVVSMIAGLAVVKAAKRFAPDTLMVTGLVFVAVGFLMILLFRHNLTVAAIIASFVVLELGVGVSQTVSNDTIVASVPAAKSGAASAVSETAYELGAVVGTATLGTIFTAFYRSNVDVPAGLTPEQTGAAAESIGGAAAVAADLPAATATQLLDSARAAFDSGIAPTAVIAAMLVLAAAAVVGVAFRR"},"dna_sequence":{"accession":"U40487.1","fmin":"170","fmax":"1685","strand":"+","sequence":"ATGTCCACCTGCATCGAGGGCACGCCGTCGACGACCAGGACGCCCACGCGCGCCTGGGTGGCGCTGGCCGTCCTCGCACTTCCGGTGCTGCTCATCGCGATCGACAACACCGTGCTGGCGTTCGCGTTGCCGCTGATCGCCGAGGACTTCCGCCCGTCGGCCACCACGCAGCTGTGGATCGTCGACGTGTACTCACTGGTGCTGGCCGCGCTGCTGGTCGCCATGGGCAGCCTCGGCGACCGACTGGGCCGCCGCAGGGTGCTGCTCATCGGCGGGGCCGGGTTCGCGGTGGTCTCGGCGCTGGCGGCCTTCGCCCCGAGCACCGAGTTGCTGGTGGGAGCGCGCGCACTTCTCGGTGTGTTCGGCGCGATGCTGATGCCTTCGACGCTGTCGTTGATCCGCAACATCTTCACCGACGCGTCGGCGCGGCGGTTGGCCATCGCGATCTGGGCGTCGTGTTTCACCGCGGGTTCCGCGCTGGGCCCGATCGTCGGCGGCGCGCTGCTGGAGCATTTCCACTGGGGCGCAGTGTTCCTGGTGGCGGTGCCGATCCTGTTGCCGCTGCTGGTCCTCGGCCCGCGTCTGGTGCCCGAATCGCGTGATCCCAATCCGGGCCCGTTCGATCCCGTGAGCATCGTGCTGTCGTTCACGACCATGCTGCCCATCGTGTGGGCGGTCAAAACCGCGGCGCACGACGGTCTGTCGGCGGCGGCCGCGGCCGCGTTCGCCGTGGGCATCGTCTCGGGTGCGTTGTTCGTGCGACGGCAGAACCGCAGTGCCACACCGATGCTCGACATCGGCCTGTTCAAGGTCATGCCGTTCACGTCGTCGATCCTGGCGAACTTCCTGTCGATCATCGGCCTGATCGGGTTCATCTTCTTCATCTCGCAGCACCTTCAGTTGGTGCTGGGCCTGTCCCCGCTCACCGCCGGCCTGGTGACGCTGCCGGGTGCCGTGGTGTCGATGATCGCGGGCCTGGCCGTGGTGAAGGCCGCCAAGCGCTTCGCACCCGACACCCTGATGGTCACGGGCCTGGTGTTCGTGGCGGTCGGGTTCCTGATGATCCTGTTGTTCCGCCACAACCTCACGGTGGCCGCGATCATCGCGTCGTTCGTGGTGCTCGAGCTCGGCGTCGGCGTCTCGCAGACCGTGTCCAACGACACCATCGTGGCGTCGGTTCCCGCCGCGAAATCCGGTGCGGCGTCCGCGGTTTCCGAGACGGCCTACGAGCTGGGCGCCGTGGTGGGGACAGCGACGCTGGGCACGATCTTCACGGCGTTCTACCGCAGCAACGTCGACGTGCCCGCGGGGCTGACGCCCGAGCAGACCGGTGCGGCGGCCGAGAGCATCGGCGGTGCGGCCGCGGTGGCAGCGGATCTGCCTGCCGCCACCGCCACGCAGCTTCTCGATTCGGCCCGTGCGGCGTTCGATTCGGGTATCGCCCCGACCGCGGTGATCGCCGCGATGCTGGTGCTGGCCGCCGCCGCGGTGGTGGGTGTGGCGTTCAGGCGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36769","NCBI_taxonomy_name":"Mycobacterium smegmatis str. MC2 155","NCBI_taxonomy_id":"246196"}}}},"ARO_accession":"3003967","ARO_id":"40738","ARO_name":"lrfA","ARO_description":"lfrA is involved in the active efflux of quinolones and is found in Mycobacterium smegmatis. lfrA corresponds to 2 loci in Pseudomonas aeruginosa PAO1 and 2 loci in Pseudomonas aeruginosa LESB58.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2435":{"model_id":"2435","model_name":"lmrP","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"3767":{"protein_sequence":{"accession":"ABF33001.1","sequence":"MQEFLNLPKQIQLRQLVRFVTITLGSSIFPFMAMYYTTYFGTFWTGLLMMITSLMGFVGTLYGGHLSDALGRKKVIMIGSVGTTLGWFLTILANLPNAAIPWLTFAGILLVEIASSFYGPAYEAMLIDLTDESNRRFVYTINYWFINIAVMFGAGLSGLFYDHHFLALLVALLLVNVLCFGVAYYYFDETRPETHAFDHGKGLLASFQNYRQVFQDRAFVLFTLGAIFSGSIWMQMDNYVPVHLKLYFQPTAVLGFQVTSSKMLSLMVLTNTLLIVLFMTVVNKLTEKWKLLPQLVVGSLLFTLGMLLAFTFTQFYAIWLSVVLLTFGEMINVPASQVLRADMMDHSQIGSYTGFVSMAQPLGAILASLLVSVSHFTGPLGVQCLFVVIALLGIYFTVVSAKMKKV"},"dna_sequence":{"accession":"CP000259.1","fmin":"1769089","fmax":"1770310","strand":"-","sequence":"CTACACCTTTTTCATTTTTGCAGAAACAACCGTAAAATAAATCCCTAGCAAAGCAATGACTACAAATAAGCATTGCACACCTAAAGGACCTGTAAAATGGCTGACAGATACTAGTAGACTAGCCAAAATAGCACCTAGGGGTTGTGCCATTGACACAAAACCTGTATAAGATCCTATTTGGGAATGATCCATCATATCAGCACGTAGGACTTGACTAGCAGGAACATTTATCATTTCCCCAAAAGTTAACAAAACAACTGATAGCCAAATAGCATAGAACTGCGTAAAGGTAAATGCCAAGAGCATCCCTAGAGTAAATAGTAAAGAACCAACCACAAGCTGAGGTAATAGTTTCCATTTTTCCGTTAATTTATTTACTACTGTCATGAAAAGGACAATCAGCAATGTATTAGTTAAAACCATTAATGATAACATTTTAGAACTAGTTACTTGGAAACCTAACACAGCCGTTGGCTGAAAATACAGTTTCAAATGGACTGGCACATAGTTATCCATCTGCATCCAGATACTACCAGAAAAGATGGCACCTAAGGTAAACAAGACAAAGGCACGATCCTGAAACACCTGACGGTAGTTCTGAAAACTCGCCAGTAATCCTTTACCATGATCAAAAGCGTGTGTTTCTGGTCTAGTCTCATCAAAATAGTAGTAAGCAACGCCAAAACAAAGTACATTAACGAGTAATAAGGCTACTAACAAGGCTAAAAAATGATGGTCATAAAAAAGCCCAGATAGCCCTGCACCAAACATGACGGCAATATTGATAAACCAATAATTGATGGTGTAAACAAATCGACGATTACTCTCATCAGTCAAATCAATCAACATAGCTTCATAGGCAGGACCATAAAAACTAGAAGCAATCTCTACCAATAAAATACCCGCAAAGGTTAACCAAGGAATAGCTGCATTAGGCAAATTAGCTAAAATAGTCAGAAACCAGCCTAGCGTTGTTCCTACTGACCCAATCATAATGACTTTTTTACGACCAAGAGCATCTGACAGATGCCCACCGTATAAAGTTCCAACAAATCCCATCAAACTGGTAATCATCATTAAGAGGCCTGTCCAAAACGTACCAAAGTAAGTCGTATAATACATGGCCATAAAGGGAAAGATACTACTGCCTAAGGTAATGGTCACAAAGCGTACCAGTTGCCTCAGCTGAATCTGCTTAGGAAGGTTTAAAAACTCTTGCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40741","NCBI_taxonomy_name":"Streptococcus pyogenes MGAS9429","NCBI_taxonomy_id":"370551"}}}},"ARO_accession":"3003969","ARO_id":"40740","ARO_name":"lmrP","ARO_description":"lmrP is a proton motive force-dependent drug transporter that is part of the MFS efflux pump family.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2436":{"model_id":"2436","model_name":"D-Ala-D-Ala ligase","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"4524":"E13G","4525":"G99R","4526":"V241D","4527":"D295G","4528":"P313L"},"clinical":{"4524":"E13G","4525":"G99R","4526":"V241D","4527":"D295G","4528":"P313L"}},"41342":{"param_type":"deletion mutation from peptide sequence","param_description":"A subtype of the deletion mutation detection model parameter. This parameter is used when a set of deletion mutations is reported in a peptide sequence format. These are specific to codon deletions, where a multiple of 3 nucleotides are deleted. Mutations of this type are reported in the CARD with the notation: [-][AAs][position range].","param_type_id":"41342","param_value":{"4529":"-DV244-245"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"650"},"41345":{"param_type":"insertion mutation from nucleotide sequence","param_description":"A subtype of the insertion mutation detection model parameter. This parameter is used when a set of insertion mutations is reported in a nucleotide sequence format. Such mutations may be of variable length - possibly causing a frameshift, but not causing premature termination or a functional knockout. Mutation parameters of this type are reported in CARD with the notation: [+]nt[position]:[nucleotides].","param_type_id":"41345","param_value":{"8151":"+nt41:GAGCA"}}},"model_sequences":{"sequence":{"3769":{"protein_sequence":{"accession":"AAN62561.1","sequence":"MKIILLYGGRSAEHDVSLLSAFSVVNAVYYNYYQVQLVMITRDGQWLKGSLLTEAPTSKEVLNLTDSAYQGTPIQPGEIKEEDAIVFPLLHGPNGEDGTIQGFLETIGMPYVGAGVLTSACGMDKIMTKYILQAAGIPQVPYVPVLKNYWKENPKKVFEQCEGSLLYPMFIKPANMGSSVGITKAENREELQNALQEAYRYDTRAIVEQGIEAREIEVAVLGNEDVRTTMPGEIVKDVAFYDYNSKYLDNKIEMQIPAQIPEETQAKAQEFAKKAYTMLGGSGLSRCDFFLTNKNELFLNELNTMPGFTEFSMYPLLWEKTGLPYGDLIEELIQLGVNRFKQRQAFLTDVE"},"dna_sequence":{"accession":"AY168442.1","fmin":"53","fmax":"1109","strand":"+","sequence":"TTGAAAATTATTTTATTATATGGCGGACGCAGTGCAGAGCATGATGTATCGCTTCTATCCGCTTTTTCAGTAGTCAATGCTGTATATTATAATTACTACCAAGTACAATTAGTAATGATCACGAGAGATGGCCAGTGGCTAAAAGGCTCTTTATTGACTGAAGCCCCTACATCCAAAGAAGTGTTGAATCTGACGGATTCGGCTTACCAAGGGACGCCGATCCAACCTGGTGAGATCAAGGAAGAGGATGCGATTGTTTTTCCGCTGCTCCACGGACCAAATGGAGAAGATGGAACGATCCAAGGTTTTCTAGAGACCATCGGCATGCCTTATGTAGGCGCAGGGGTTTTAACTAGTGCCTGTGGCATGGATAAGATTATGACCAAATATATCTTGCAGGCGGCGGGGATTCCGCAAGTTCCTTATGTACCCGTTCTTAAAAACTATTGGAAAGAAAATCCTAAAAAAGTATTTGAACAATGTGAAGGCAGTCTTTTGTATCCAATGTTTATCAAACCTGCCAATATGGGTTCAAGTGTTGGGATCACAAAAGCTGAAAATCGGGAAGAATTGCAAAATGCACTTCAAGAAGCCTACCGTTATGATACACGAGCGATCGTAGAACAAGGGATCGAAGCTCGCGAAATCGAAGTCGCTGTTCTTGGAAATGAAGATGTGCGTACAACAATGCCCGGCGAGATCGTTAAAGATGTAGCTTTTTATGATTACAATTCGAAGTATCTTGACAATAAGATTGAGATGCAGATCCCAGCTCAAATTCCTGAGGAGACACAAGCGAAAGCGCAAGAGTTTGCCAAAAAAGCTTATACGATGCTTGGAGGAAGCGGCCTCAGCCGCTGCGACTTTTTCTTGACGAACAAAAACGAATTATTCCTGAATGAATTGAACACGATGCCTGGTTTTACCGAGTTTAGTATGTACCCGCTGTTGTGGGAAAAAACCGGTCTGCCATATGGTGATTTGATTGAGGAATTGATTCAATTAGGAGTCAACCGTTTTAAACAGCGTCAAGCCTTTTTAACCGATGTCGAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36781","NCBI_taxonomy_name":"Enterococcus gallinarum","NCBI_taxonomy_id":"1353"}}}},"ARO_accession":"3003970","ARO_id":"40743","ARO_name":"D-Ala-D-Ala ligase","ARO_description":"Non-van ligases that synthesize D-Ala-D-Ala, the default cell wall precursor that makes a cell vulnerable to glycopeptide antibiotics. Mutations in the ddl gene can cause the production of nonfunctional\/inactivated D-Ala-D-Ala ligases, which can render bacteria glycopeptide dependent depending on the presence of vancomycin resistance clusters.","ARO_category":{"39340":{"category_aro_accession":"3002906","category_aro_cvterm_id":"39340","category_aro_name":"van ligase","category_aro_description":"van ligases synthesize alternative substrates for peptidoglycan synthesis that reduce vancomycin binding affinity.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2445":{"model_id":"2445","model_name":"erm(44)","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"3778":{"protein_sequence":{"accession":"CUU67654.1","sequence":"MINKEQNIMDNRNSKNSQNFITSRKYINDILKETSIGADDNIIEIGTGKGHFTKQLSNIARFVTGVEIDKSLYRNLKKDIELSNNVELVNKDILKYQFPKCKKYKVFGNIPYNISTEIVKKILYEGNAEYNYLIVEYGFAKRIMDKRRALGLLLLTKLDVEILKVIPNTYFHPKPRVESALILLKQHKSLIQKRDEKLYQFFVYKWVNKEYKQLFTKNQFNKALKNAKVKNINEMTNEQFISIFHSYKLFN"},"dna_sequence":{"accession":"LN623525.1","fmin":"13980","fmax":"14736","strand":"+","sequence":"ATGATAAATAAGGAGCAGAATATAATGGATAATAGAAATTCTAAAAACTCACAGAACTTTATAACATCCCGAAAATATATCAATGATATATTAAAAGAAACAAGCATAGGCGCTGATGATAATATAATTGAAATTGGAACTGGAAAAGGACATTTTACAAAGCAATTATCTAATATTGCTAGATTTGTAACTGGCGTAGAAATTGATAAGTCTTTATATCGTAATTTAAAAAAGGATATTGAATTGTCCAATAATGTCGAATTAGTGAACAAAGATATATTGAAGTATCAGTTCCCTAAATGTAAAAAGTATAAGGTTTTTGGTAATATACCATACAATATAAGTACTGAAATAGTTAAAAAAATCTTATATGAGGGGAATGCTGAATATAATTACCTTATTGTAGAATATGGTTTTGCTAAACGAATTATGGATAAACGAAGAGCACTAGGTCTATTACTTTTGACTAAATTAGATGTTGAAATATTAAAAGTAATTCCCAACACTTATTTTCATCCTAAACCTAGAGTAGAATCGGCATTAATCTTATTAAAGCAGCACAAATCTTTAATCCAAAAAAGAGACGAAAAATTATATCAATTTTTTGTGTATAAATGGGTAAATAAAGAGTATAAACAATTATTTACAAAAAATCAGTTTAATAAGGCGTTAAAAAATGCTAAAGTAAAAAATATAAATGAAATGACAAATGAACAATTTATATCAATTTTTCATAGTTATAAATTGTTTAATTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40387","NCBI_taxonomy_name":"Staphylococcus saprophyticus","NCBI_taxonomy_id":"29385"}}}},"ARO_accession":"3003971","ARO_id":"40752","ARO_name":"Erm(44)","ARO_description":"Variant of Erm(44) isolated from Staphylococcus saprophyticus, confers resistance to lincosamide and macrolide antibiotics but not streptogramins.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2424":{"model_id":"2424","model_name":"yojI","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1050"}},"model_sequences":{"sequence":{"4296":{"protein_sequence":{"accession":"NP_416715.1","sequence":"MELLVLVWRQYRWPFISVMALSLASAALGIGLIAFINQRLIETADTSLLVLPEFLGLLLLLMAVTLGSQLALTTLGHHFVYRLRSEFIKRILDTHVERIEQLGSASLLAGLTSDVRNITIAFVRLPELVQGIILTIGSAAYLWMLSGKMLLVTAIWMAITIWGGFVLVARVYKHMATLRETEDKLYTDFQTVLEGRKELTLNRERAEYVFNNLYIPDAQEYRHHIIRADTFHLSAVNWSNIMMLGAIGLVFWMANSLGWADTNVAATYSLTLLFLRTPLLSAVGALPTLLTAQVAFNKLNKFALAPFKAEFPRPQAFPNWQTLELRNVTFAYQDNAFSVGPINLTIKRGELLFLIGGNGSGKSTLAMLLTGLYQPQSGEILLDGKPVSGEQPEDYRKLFSAVFTDVWLFDQLLGPEGKPANPQLVEKWLAQLKMAHKLELSNGRIVNLKLSKGQKKRVALLLALAEERDIILLDEWAADQDPHFRREFYQVLLPLMQEMGKTIFAISHDDHYFIHADRLLEMRNGQLSELTGEERDAASRDAVARTA"},"dna_sequence":{"accession":"NC_000913.3","fmin":"2306971","fmax":"2308615","strand":"-","sequence":"TTATGCCGTCCGGGCAACGGCATCACGCGAAGCGGCATCGCGCTCTTCGCCCGTCAGCTCGCTAAGTTGCCCATTGCGCATTTCCAGCAGGCGGTCGGCGTGGATAAAGTAATGATCATCATGACTGATAGCGAAAATAGTTTTACCCATCTCCTGCATCAGCGGCAGCAACACCTGATAAAACTCACGACGGAAGTGTGGATCCTGATCCGCCGCCCATTCATCCAGCAGGATAATATCGCGTTCTTCTGCCAGCGCCAGCAACAGCGCCACGCGTTTTTTCTGCCCTTTTGATAACTTCAGGTTAACAATACGCCCGTTGCTTAACTCAAGCTTATGAGCCATTTTCAGCTGCGCCAGCCACTTCTCAACCAGTTGCGGGTTAGCGGGTTTACCCTCCGGCCCCAGCAGTTGATCAAACAGCCAGACATCGGTAAACACTGCCGAAAACAGTTTGCGATAATCTTCCGGTTGTTCGCCGCTGACAGGTTTGCCATCCAGCAAGATTTCGCCGCTTTGTGGCTGATACAAGCCCGTCAACAACATCGCCAGCGTCGATTTTCCGCTACCGTTGCCGCCAATCAGAAACAGCAGCTCGCCACGTTTGATGGTGAGATTAATCGGACCAACGGAAAACGCGTTATCCTGATAAGCAAACGTCACGTTACGCAGCTCCAGCGTTTGCCAGTTGGGAAACGCCTGCGGGCGCGGAAACTCTGCTTTGAAAGGCGCGAGCGCGAATTTGTTCAGCTTGTTAAACGCCACCTGCGCCGTCAGCAGCGTCGGCAATGCGCCAACCGCCGAAAGCAGCGGCGTACGCAGGAATAAAAGCGTCAACGAATAGGTCGCGGCAACGTTGGTATCAGCCCAACCGAGGCTGTTCGCCATCCAGAACACCAGGCCGATTGCGCCCAGCATCATGATGTTTGACCAGTTCACGGCACTAAGATGGAAGGTGTCTGCGCGAATAATATGGTGGCGATACTCTTGCGCATCAGGAATGTAGAGGTTGTTAAACACATACTCGGCGCGTTCCCGGTTCAGAGTCAGCTCTTTGCGCCCTTCAAGTACAGTTTGAAAATCCGTGTACAGCTTGTCTTCGGTTTCACGCAGGGTCGCCATATGTTTGTACACCCGCGCCACCAGCACAAAACCGCCCCAGATGGTGATCGCCATCCAGATAGCCGTTACCAGCAACATTTTGCCCGACAGCATCCACAGATACGCCGCTGAACCGATAGTGAGAATGATCCCCTGCACCAGTTCCGGCAGACGCACAAAAGCAATGGTGATATTGCGCACATCGCTGGTTAACCCCGCCAGCAACGAGGCGCTACCGAGTTGTTCAATGCGCTCGACGTGAGTATCCAGAATCCGCTTGATAAATTCACTACGCAGTCGGTAAACGAAGTGATGCCCCAAAGTGGTGAGCGCCAGTTGCGATCCGAGAGTGACTGCCATCAACAGCAGCAATAATCCCAGAAACTCCGGCAACACCAGCAGACTGGTATCCGCCGTTTCGATAAGGCGCTGATTGATAAAAGCAATTAAGCCAATGCCTAATGCCGCACTGGCGAGGCTTAGCGCCATCACACTGATAAATGGCCAGCGATACTGCCGCCAGACAAGTACAAGAAGTTCCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3003952","ARO_id":"40722","ARO_name":"YojI","ARO_description":"YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules.  The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"40721":{"category_aro_accession":"3003951","category_aro_cvterm_id":"40721","category_aro_name":"microcin J25","category_aro_description":"microcin J25 is a peptide antibiotic that inhibits transcription by bacterial RNA polymerase. MccJ25 is produced by Escherichia coli strains that harbor a plasmid-borne antibiotic-synthesis and antibiotic-export cassette, consisting of a gene for MccJ25 precursor (a 58 residue linear peptide), two genes for factors that process MccJ25 precursor into MccJ25, and one gene for export of MccJ25.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2432":{"model_id":"2432","model_name":"Klebsiella pneumoniae OmpK35","model_type":"protein knockout model","model_type_id":"40354","model_description":"An AMR detection model for instances where the absence of a protein - due to large-scale insertion elements, large deletions, or other methods of protein knockout - confers clinical resistance to a known antibiotic. These models include reference sequences. Protein knockout models are currently in development.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"3763":{"protein_sequence":{"accession":"YP_005226137.1","sequence":"MGGDGWNYTDNYMTGRTNGVATYRNSDFFGLVDGLSFALQYQGKNDHDRAIRKQNGDGFSTAATYAFDNGIALSAGYSSSNRSVDQKADGNGDKAEAWATSAKYDANNIYAAVMYSQTYNMTPEEDNHFAGKTQNFEAVVQYQFDFGLRPSIGYVQTKGKDLQSRAGFSGGDADLVKYIEVGTWYYFNKNMNVYAAYKFNQLDDNDYTKAAGVATDDQAAVGIVYQF"},"dna_sequence":{"accession":"NC_016845.1","fmin":"1904307","fmax":"1904991","strand":"-","sequence":"TTAGAACTGGTAAACGATACCCACGGCCGCCTGGTCGTCAGTGGCGACACCAGCCGCTTTGGTGTAATCGTTGTCGTCCAGCTGGTTGAATTTATACGCAGCGTAGACGTTCATGTTCTTGTTAAAGTAGTACCAGGTACCCACTTCGATGTATTTAACCAGATCCGCATCGCCGCCGGAGAAGCCAGCACGCGACTGCAGGTCCTTGCCTTTGGTCTGTACGTAGCCGATGGACGGACGCAGGCCGAAGTCAAACTGATACTGTACAACTGCTTCAAAGTTCTGAGTTTTACCAGCGAAGTGGTTATCTTCTTCCGGAGTCATGTTGTAAGTCTGGGAGTACATGACGGCCGCATAGATGTTGTTAGCGTCATATTTTGCAGAGGTCGCCCAGGCTTCGGCTTTGTCGCCATTGCCGTCAGCTTTCTGATCGACGCTACGGTTAGAGCTGGAGTAGCCTGCAGACAGTGCGATACCGTTGTCGAACGCGTAGGTGGCTGCGGTGCTGAAGCCGTCGCCATTCTGCTTGCGAATCGCACGGTCATGGTCGTTTTTACCCTGGTACTGCAGCGCGAAGCTCAGACCGTCAACCAGACCGAAGAAGTCGGAGTTACGGTAGGTTGCGACGCCGTTGGTACGACCGGTCATGTAGTTGTCGGTATAGTTCCAGCCGTCACCGCCCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40663","NCBI_taxonomy_name":"Klebsiella pneumoniae subsp. pneumoniae HS11286","NCBI_taxonomy_id":"1125630"}}}},"ARO_accession":"3003966","ARO_id":"40737","ARO_name":"Klebsiella pneumoniae OmpK35","ARO_description":"Klebsiella pneumoniae outer membrane porin protein. In beta-lactam-resistant Klebsiella, this porin is often deleted, limiting diffusion of the antibiotic into the cell. Klebsiella strains expressing OmpK35 are often beta-lactam sensitive even in the presence of beta-lactamases because of an inefficient mechanism.","ARO_category":{"41445":{"category_aro_accession":"3004281","category_aro_cvterm_id":"41445","category_aro_name":"General Bacterial Porin with reduced permeability to beta-lactams","category_aro_description":"These are GBPs that are associated with decreased susceptibility to beta-lactams either through mutations in the porin protein, absence of the porin protein, or expression of the porin protein.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36383":{"category_aro_accession":"3000244","category_aro_cvterm_id":"36383","category_aro_name":"reduced permeability to antibiotic","category_aro_description":"Reduction in permeability to antibiotic, generally through reduced production of porins, can provide resistance.","category_aro_class_name":"Resistance Mechanism"},"40429":{"category_aro_accession":"3003764","category_aro_cvterm_id":"40429","category_aro_name":"resistance by absence","category_aro_description":"Mechanism of antibiotic resistance conferred by deletion of gene (usually a porin)","category_aro_class_name":"Resistance Mechanism"}}},"2434":{"model_id":"2434","model_name":"Klebsiella pneumoniae OmpK36","model_type":"protein knockout model","model_type_id":"40354","model_description":"An AMR detection model for instances where the absence of a protein - due to large-scale insertion elements, large deletions, or other methods of protein knockout - confers clinical resistance to a known antibiotic. These models include reference sequences. Protein knockout models are currently in development.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"650"}},"model_sequences":{"sequence":{"3765":{"protein_sequence":{"accession":"YP_005228001.1","sequence":"MKVKVLSLLVPALLVAGAANAAEIYNKDGNKLDLYGKIDGLHYFSDDKSVDGDQTYMRVGVKGETQINDQLTGYGQWEYNVQANNTESSSDQAWTRLAFAGLKFGDAGSFDYGRNYGVVYDVTSWTDVLPEFGGDTYGSDNFLQSRANGVATYRNSDFFGLVDGLNFALQYQGKNGSVSGEGALSPTNNGRTALKQNGDGYGTSLTYDIYDGISAGFAYSNSKRLGDQNSKLALGRGDNAETYTGGLKYDANNIYLATQYTQTYNATRAGSLGFANKAQNFEVVAQYQFDFGLRPSVAYLQSKGKDLEGYGDQDILKYVDVGATYYFNKNMSTYVDYKINLLDDNSFTHNAGISTDDVVALGLVYQF"},"dna_sequence":{"accession":"NC_016845.1","fmin":"3727881","fmax":"3728985","strand":"-","sequence":"TTAGAACTGGTAAACCAGGCCCAGTGCAACCACGTCGTCGGTAGAGATACCGGCGTTGTGGGTGAAGCTATTGTCGTCCAGCAGGTTGATTTTGTAGTCAACATAGGTGGACATGTTTTTGTTGAAGTAGTAGGTCGCGCCAACGTCAACATATTTCAGGATGTCCTGGTCGCCGTAGCCTTCCAGATCCTTACCTTTAGACTGCAGGTAAGCCACGGACGGACGCAGACCGAAGTCGAACTGGTACTGAGCAACCACTTCGAAGTTCTGCGCTTTGTTAGCAAAGCCCAGGGAACCGGCGCGGGTCGCGTTGTAGGTCTGGGTGTACTGAGTGGCCAGGTAGATGTTGTTCGCGTCGTATTTCAGACCGCCGGTGTAGGTTTCAGCGTTGTCGCCACGACCCAGTGCCAGCTTGCTGTTCTGGTCGCCAAGACGTTTGGAGTTAGAGTATGCGAAACCAGCGCTGATGCCATCATAGATGTCATAGGTCAGAGAAGTACCGTAACCGTCGCCGTTCTGTTTCAAGGCGGTACGACCGTTGTTGGTAGGAGACAGAGCGCCTTCGCCGCTGACGCTGCCGTTTTTACCCTGATACTGCAGAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAATCAGAGTTACGGTAGGTTGCAACGCCGTTAGCACGGGACTGCAGGAAGTTGTCAGAACCGTAGGTGTCGCCGCCGAATTCCGGCAGAACGTCGGTCCAGGACGTTACGTCGTATACTACGCCGTAGTTACGACCGTAGTCGAAAGAGCCCGCGTCGCCAAATTTCAGGCCTGCGAATGCCAGACGAGTCCATGCCTGATCGCTGGAGCTTTCAGTGTTGTTCGCCTGAACGTTGTATTCCCACTGGCCGTAACCGGTCAGCTGGTCGTTGATCTGGGTTTCGCCTTTCACGCCTACACGCATGTAGGTCTGGTCGCCGTCGACGCTCTTGTCGTCAGAGAAGTAGTGCAGACCGTCAATTTTACCGTACAGGTCTAATTTGTTGCCGTCTTTGTTATAAATTTCAGCCGCATTTGCTGCGCCTGCTACCAGCAGAGCCGGTACCAGGAGGGACAGTACTTTAACTTTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40663","NCBI_taxonomy_name":"Klebsiella pneumoniae subsp. pneumoniae HS11286","NCBI_taxonomy_id":"1125630"}}}},"ARO_accession":"3003968","ARO_id":"40739","ARO_name":"Klebsiella pneumoniae OmpK36","ARO_description":"Klebsiella pneumoniae outer membrane porin protein. In beta-lactam-resistant Klebsiella, this porin is often deleted, limiting diffusion of the antibiotic into the cell. Klebsiella strains expressing OmpK36 are often beta-lactam sensitive even in the presence of beta-lactamases because of an inefficient mechanism.","ARO_category":{"41445":{"category_aro_accession":"3004281","category_aro_cvterm_id":"41445","category_aro_name":"General Bacterial Porin with reduced permeability to beta-lactams","category_aro_description":"These are GBPs that are associated with decreased susceptibility to beta-lactams either through mutations in the porin protein, absence of the porin protein, or expression of the porin protein.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36383":{"category_aro_accession":"3000244","category_aro_cvterm_id":"36383","category_aro_name":"reduced permeability to antibiotic","category_aro_description":"Reduction in permeability to antibiotic, generally through reduced production of porins, can provide resistance.","category_aro_class_name":"Resistance Mechanism"},"40429":{"category_aro_accession":"3003764","category_aro_cvterm_id":"40429","category_aro_name":"resistance by absence","category_aro_description":"Mechanism of antibiotic resistance conferred by deletion of gene (usually a porin)","category_aro_class_name":"Resistance Mechanism"}}},"2462":{"model_id":"2462","model_name":"Propionibacterium acnes gyrA conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"4555":"S101L","4556":"D105G"},"clinical":{"4555":"S101L","4556":"D105G"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1500"}},"model_sequences":{"sequence":{"4410":{"protein_sequence":{"accession":"WP_002530866.1","sequence":"MADDEKPDEQNQADRQGLVTGRHVGIQPVEIRDEIQNAYLDYAMSVIVGRALPDVRDGLKPVHRRVIYAMYDGGYRPDRGWNKCSRVVGDVMGKYHPHGDSAIYDTLVRLAQPWAMRYKLVQGQGNFGSQGNDGAAAMRYTECKMAPLAMEMVRDIDQDTVDFQPNYDNKETEPVVLPSRFPNLLVNGSSGIAVGMATNIPTHNLREVNEAVQWSLAHPNASHEELLEACMERIKGPDFPGGALIVGRQGIEDAYRTGRGSVTMRAVIDMEEDKKGRQCLVVTELPYMCNPDNLATKIADLVNSGRINGIADIRDDSSARTGQRLVIVLKRDAQPRVVMNNLYKHTALQDTFGCNMLALVDNVPRTLRLDQFISYWIDHQMEVIRRRTEYRLAQAEKDAHIQRALVKALDMLDEVIALIRRSPNTEAASTGLQELLDIDEIQARAILDMQLRRLAALERQKIIDRLEELERLIADYKAILASEDRQREIISTELAEIVDKYGDERRTRIIAADGDFSEEDFIPDDDVVVTITRGGYAKRTRTDLYRVQKRGGKGVRGASLRADDEMAQLFTTTNHQWILFFTNMGRVYRTKVWQLPEAGRDARGGHVAGLLSFLPDEKIAQVMTLRSYDGAEYLLLATRKGMVKKTALKAYDSSRQAGVIAVNFRTEDDELIGAEQCSAADDVLLISRKGQAIRFSAGDDQLRPMGRATSGVTGMKFRGDDELLSMSIIHSDMPEDDRFVFTATGGGYAKRTAVSEYRQQGRGGVGIKAMALSEERGSLVGGLVVSEADEIIAIKTSGQITRSAVSEVPAKGRSTMGVKFVSVRGGDAVSIIAVNPEHTVEEEVADESVETVEGDATQAQSGGVVRRSDTVDDDRAVDTAGNDMKPEDNGE"},"dna_sequence":{"accession":"NC_006085.1","fmin":"11846","fmax":"14522","strand":"+","sequence":"ATGGCTGACGACGAGAAGCCCGACGAGCAGAACCAGGCCGACCGTCAAGGATTGGTGACCGGCCGTCACGTCGGAATCCAGCCGGTCGAGATTCGTGACGAGATCCAGAACGCGTACCTCGACTACGCGATGAGCGTCATCGTCGGGCGTGCCCTGCCCGATGTGCGCGACGGCCTCAAACCGGTACACCGTCGGGTCATCTACGCGATGTACGACGGCGGTTACCGCCCCGACCGCGGCTGGAACAAGTGCTCCCGCGTCGTCGGTGACGTCATGGGTAAGTACCACCCTCACGGCGACTCGGCCATTTACGACACCTTGGTGCGTTTGGCTCAGCCATGGGCCATGCGATACAAGCTTGTCCAGGGTCAGGGTAACTTCGGGTCCCAGGGCAACGACGGTGCGGCTGCCATGCGATACACCGAGTGCAAGATGGCGCCGCTGGCCATGGAGATGGTGCGCGACATCGACCAGGACACTGTCGATTTCCAGCCCAACTATGACAACAAGGAGACCGAACCGGTCGTCTTGCCGTCGAGGTTCCCCAACCTGCTTGTCAATGGTTCTTCAGGTATCGCGGTGGGCATGGCCACCAACATCCCGACCCATAATCTGCGCGAGGTCAACGAGGCCGTGCAGTGGTCTTTGGCTCACCCCAATGCTTCCCACGAGGAACTGCTCGAGGCGTGCATGGAGCGCATTAAGGGTCCGGATTTCCCCGGCGGCGCCCTCATTGTGGGTCGGCAGGGCATCGAGGACGCCTACCGCACCGGCCGCGGTTCGGTGACGATGCGTGCCGTCATCGACATGGAAGAGGACAAGAAGGGACGCCAGTGCCTGGTCGTCACCGAGTTGCCTTATATGTGCAACCCGGACAACCTCGCCACCAAGATCGCCGACCTGGTGAACTCCGGTCGCATCAACGGTATCGCCGACATCCGTGACGACTCCTCAGCCCGTACTGGTCAGCGTTTAGTCATCGTCCTCAAGCGTGACGCTCAGCCGCGTGTCGTCATGAACAACCTGTACAAGCACACGGCTTTGCAGGACACCTTCGGCTGCAACATGCTGGCTCTGGTGGACAACGTGCCGCGCACCTTGCGTCTGGACCAATTTATCAGCTACTGGATTGACCACCAGATGGAGGTCATCCGCAGGCGTACCGAGTACCGCCTGGCTCAGGCCGAAAAAGACGCCCACATCCAGCGGGCTCTCGTCAAGGCCCTCGATATGCTCGACGAGGTCATCGCGCTCATCCGTCGCTCCCCGAACACTGAGGCCGCCAGCACCGGCCTACAGGAACTGCTTGATATCGACGAGATTCAGGCTCGCGCCATCCTCGATATGCAGTTGCGTCGTCTGGCTGCCCTGGAGCGTCAAAAGATCATCGACCGACTTGAAGAACTCGAGCGCCTCATCGCTGATTACAAAGCAATTCTGGCTAGCGAGGACCGCCAGCGCGAGATCATCTCTACCGAGCTTGCCGAGATCGTCGATAAGTATGGTGACGAGCGTCGCACCCGCATTATCGCCGCCGATGGGGACTTTTCCGAGGAAGACTTCATCCCCGACGATGACGTCGTCGTCACCATTACCCGGGGCGGCTACGCCAAGCGCACCCGCACTGACCTGTACCGGGTCCAGAAACGCGGTGGCAAGGGTGTTCGCGGCGCCAGCCTGCGCGCTGACGACGAGATGGCACAGCTATTCACTACCACGAACCACCAGTGGATCCTCTTCTTCACAAATATGGGTCGGGTGTATCGCACCAAGGTATGGCAGCTGCCGGAGGCTGGTCGTGACGCCAGGGGGGGTCACGTCGCTGGGTTGCTGAGCTTCCTGCCCGACGAGAAGATCGCCCAAGTCATGACCCTACGGTCCTACGACGGCGCCGAGTACCTCCTCCTGGCCACTCGTAAGGGTATGGTCAAGAAGACGGCGCTCAAGGCTTATGACTCGTCTCGTCAGGCCGGCGTTATCGCCGTTAATTTCCGTACCGAGGACGATGAGCTCATCGGCGCCGAGCAGTGCTCCGCCGCTGACGACGTGCTGCTTATCAGCCGTAAGGGGCAAGCGATCCGGTTCTCTGCCGGCGACGACCAGCTGCGCCCGATGGGGCGTGCGACTTCGGGCGTTACCGGCATGAAGTTCCGTGGTGATGACGAGTTGCTGTCAATGTCGATCATCCACTCCGACATGCCTGAGGATGATCGGTTCGTTTTCACAGCAACCGGTGGCGGCTACGCCAAGCGCACTGCTGTGTCGGAGTACCGTCAGCAGGGGCGTGGGGGAGTCGGCATCAAAGCGATGGCCCTCAGTGAGGAGCGCGGCTCCCTGGTTGGTGGCCTGGTGGTCAGCGAGGCTGACGAAATCATCGCGATTAAGACGTCAGGTCAGATCACCCGATCGGCCGTGTCTGAGGTGCCCGCCAAGGGACGCTCCACGATGGGGGTCAAGTTCGTCTCCGTACGAGGTGGCGACGCTGTCTCAATCATCGCTGTCAACCCCGAACATACCGTCGAGGAGGAAGTCGCTGACGAATCAGTGGAAACTGTTGAAGGCGATGCCACGCAGGCCCAATCGGGAGGTGTGGTTCGGCGAAGCGATACTGTGGACGACGACCGTGCCGTCGATACGGCGGGAAACGACATGAAGCCGGAGGACAACGGTGAGTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41661","NCBI_taxonomy_name":"Propionibacteriaceae","NCBI_taxonomy_id":"31957"}}}},"ARO_accession":"3003974","ARO_id":"40779","ARO_name":"Propionibacterium acnes gyrA conferring resistance to fluoroquinolones","ARO_description":"Point mutations in P. acnes gyrA protein known to confer resistance to fluoroquinolone antibiotics.","ARO_category":{"39876":{"category_aro_accession":"3003292","category_aro_cvterm_id":"39876","category_aro_name":"fluoroquinolone resistant gyrA","category_aro_description":"DNA gyrase is responsible for DNA supercoiling and consists of two alpha and two beta subunits. GyrA point mutations confer resistance by preventing fluoroquinolone antibiotics from binding the alpha-subunit.","category_aro_class_name":"AMR Gene Family"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"40463":{"category_aro_accession":"3003780","category_aro_cvterm_id":"40463","category_aro_name":"nybomycin","category_aro_description":"A  heterocyclic antibiotic that targets mutant gyrA (type II topoisomerase) containing an S84L substitution, counteracting acquired quinolone resistance. It is effective against quinolone-resistant Gram-positive bacteria including S. aureus and E. faecalis. Due to its ability to counteract quinolone resistance by targeting the mutant form of the gyrA protein, it is classified as a reverse antibiotic (RA).","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2476":{"model_id":"2476","model_name":"Halobacterium halobium 16S rRNA mutation conferring resistance to pactamycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"2600"},"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"7809":"A633G","7810":"C734U","7811":"C735U"},"clinical":{"7809":"A633G","7810":"C734U","7811":"C735U"}}},"model_sequences":{"sequence":{"3807":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"KY084523.1","fmin":"0","fmax":"1473","strand":"+","sequence":"ATTCCGGTTGATCCTGCCGGAGGCCATTGCTATCGGAGTCCGATTTAGCCATGCTAGTTGTGCGGGTTTAGACCCGCAGCGGAAAGCTCAGTAACACGTGGCCAAGCTACCCTGTGGACGGGAATACTCTCGGGAAACTGAGGCTAATCCCCGATAACGCTTTGCTCCTGGAAGGGGCAAAGCCGGAAACGCTCCGGCGCCACAGGATGCGGCTGCGGTCGCCTAGGTAGACGGTGGGGTAACGGCCCACCGTGCCCATAATCGGTACGGGCCGTGAGCCCAAGAGCCCGGAGACGGAATCTGAGACAAGATTCCGGGCCCTACGGGGCGCAGCAGGCGCGAAACCTTTACACTGTACGAAAGTGCGATAAGGGGACTCCGAGTGTGAAGGCATAGAGCCTTCACTTTTGTACACCGTAAGGTGGTGCACGAATAAGGACTGGGCAAGACCGGTGCCAGCCGCCGCGGTAATACCGGCAGTCCGAGTGATGGCCGATCTTATTGGGCCTAAAGCGTCCGTAGCTGGCTGAACAAGTCCGTTGGGAAATCTGTCCGCTTAACGGGCAGGCGTCCAGCGGCCACTGTTCAGCTTGGGACCCCCCGACCTGAGGGGTACGTCTGGGGTAGGAGTGAAATCCTGTAATCCTGGACGGACCGCCGGTGGCGAAAGCGCCTCAGGAGAACGGATCCGACAGTGAGGGACGAAAGCTAGGGTCTCGAACCGGATTAGATACCCGGGTAGTCCTAGCTGTAAACGATGTCCGCTAGGTGTGGCGCAGGCTACGAGCCTGCGCTGTGCCGTAGGGAAGCCGAGAAGCGGACCGCCTGGGAAGTACGTCTGCAAGGATGAAACTTAAAGGAATTGGCGGGGGAGCACTACAACCGGAGGAGCCTGCGGTTTAATTGGACTCAACGCCGGACATCTCACCAGCCCCGACAGTAGTAATGACGGTCAGGTTGATGACCTTACCCGAGGCTACTGAGAGGAGGTGCATGGCCGCCGTCAGCTCGTACCGTGAGGCGTCCTGTTAAGTCAGGCAACGAGCGAGACCCGCACTCCTACCTGCCAGCAGTACCCTTTGGGTAGCTGGGTACATTAGGTGGACTGCCGCTGCCAAAGCGGAGGAAGGAACGGGCAACGGTAGGTCAGTATGCCCCGAATGGGCTGGGCAACACGCGGGCTACAATGGTCGAGACAATGGGAAGCCACTCCGAGAGGAGGCGCTAATCTCCTAAACTCGATCGTAGTTCGGATTGAGGGCTGAAACTCGCCCTCATGAAGCTGGATTCGGTAGTAATCGCGTGTCAGCAGCGCGCGGTGAATACGTCCCTGCTCCTTGCACACACCGCCCGTCAAATCACCCGAGTGGGGTTCGGATGAGGCCGGCATGCGCTGGTCAAATCTGGGCTCCGCAAGGGGGATTAAGTCGTAACAAGGTAGCCGTAGGGGAATCTGCGGCTGGATCACCTCCT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40807","NCBI_taxonomy_name":"Halobacterium salinarum","NCBI_taxonomy_id":"2242"}}}},"ARO_accession":"3003977","ARO_id":"40806","ARO_name":"Halobacterium salinarum 16S rRNA mutation conferring resistance to pactamycin","ARO_description":"Point mutations in Halobacterium 16S rRNA that confer resistance to pactamycin antibiotic","ARO_category":{"40805":{"category_aro_accession":"3003976","category_aro_cvterm_id":"40805","category_aro_name":"16S rRNA with mutation conferring resistance to pactamycin","category_aro_description":"Point mutations in bacterial 16S rRNA that confer resistance to antibiotic pactamycin","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"40804":{"category_aro_accession":"3003975","category_aro_cvterm_id":"40804","category_aro_name":"pactamycin","category_aro_description":"Antibiotic produced by Streptomyces pactum, considered a universal translation inhibitor","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2478":{"model_id":"2478","model_name":"Helicobacter pylori 16S rRNA mutation conferring resistance to tetracycline","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"4758":"A965G","4759":"A967C"},"clinical":{"4758":"A965G","4759":"A967C"}},"40330":{"param_type":"multiple resistance variants","param_description":"A set of nucleotide or amino acid substitutions that are each required to confer resistance to an antibiotic drug or drug class by co-mutation. Compare to single resistance variant, where only one substitution is required. Multiple resistance variants parameters are indicated on appropriate models using the following notation: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2],...,[wild-type n][position n][mutation n]. When each included substitution is detected in a protein sequence, resistance is conferred. This parameter is not currently included in any detection algorithms.","param_type_id":"40330","param_value":{"4760":"A965G,G966U","4761":"A965G,A967C","4762":"A965U,G966U,A967C"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"4114":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"CP003904.1","fmin":"1511156","fmax":"1512657","strand":"-","sequence":"AGGAGGTGATCCAACCGCAGGTTCACTACGGTTACCTTGTTACGACTTCACCCCAGTCGCTGTGTGTGCCGTGGGCAGTAGCCAATTTAGCATCCTGACTTAAGGCAAACACAACTCCCATGGTGTGACGGGCGGTGAGTACAAGACCCGGGAACGTATTCACCGCAACATGGCTGATTTGCGATTACTAGCGATTCCAGCTTCATGCAGGCGAGTTGCAGCCTACAATCCGAACTGAGAGGTGTTTTGAAGATTGGCTCCATTCGCAGTATTGCTTCTCTTTGTGCACCCCATTGTAGCACGTGTGTAGCCCTAGGCGTAAGGGCCATGATGACTTGACGTCGTCCCCACCTTCCTNCCCTTACGGAGGCAGTATCCTTAGAGTTCTCAGCATAACCTGTTAGCAACTAAGAAAAGGGGTTGCGCTCGTTGCGGGACTTAACCCAACATCTCACGACACGAGCTGACGACAGCCGTGCAGCACCTGTTTTCAAGGTCTGGCAAGCCAGACACTCCACTATTTCTAGCGGATTCTCTCAATGTCAAGCCTAGGTAAGGTTCTTCGTGTATCTTCGAATTAAACCACATGCTCCACCGCTTGTGCGGGTCCCCGTCTATTCCTTTGAGTTTTAATCTTGCGACCGTACTCCCCAGGCGGGATGCTTAATGCGTTAGCTGCATTACTGGAGAGACTAAGCCCTCCAACAACTAGCATCCATCGTTTAGGGCGTGGACTACCAGGGTATCTAATCCTGTTTGCTCCCCAACMGCTTTCGCGCAATCAGCGTCAGTAATGTTCCAGCAGGTCGCCTTCGCAATGAGTATTCCTCTTGATCTCTACGGATTTTACCCCTACACCAAGAATTCCACCTACCTCTCCCACACTCTAGAATAGTAGTTTCAAATGCAGTTCTATGGTTAAGCCATAGGATTTCACACCTGACTGACTATCCCGCCTACGCGCTCTTTACGCCCAGTGATTCCGAGTAACGCTTGCACCCTCCGTATTACCGCGGCTGCTGGCACGGAGTTAGCCGGTGCTTATTCGTTAGATACCGTCATTATCTTCTCTAACAAAAGGAGTTTACAATCCTAAAACCTTCATCCTCCACGCGGCGTTGCTGCTTCAGGGTTTCCCCCATTGAGCAATATTCCCTACTGCTGCCTCCCGTAGGAGTCTGGACCGTGTCTCAGTTCCAGTGTGTCCGTTCACCCTCTCAGGCCGGATACCCGTCATAGCCTTGGTAAGCCATTACCTTACCAACAAGCTGATAGGACATAGGCTGATCTCTTAGCGATAAATCTTTCCCCCGTAGGAGTATCTGGTATTAATCATCGTTTCCAATGGCTATCCCAAACTAAGAGGCACATAACCTATGCGTTACTCACCCGTGCGCCACTAATCAGCACTCTAGCAAGCTAGAAGCTTCATCGTTCGACTTGCATGTATTAGGCACGCCGCCAGCGTTCACTCTGAGCCAGGATCAAACTCTCCATAAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36758","NCBI_taxonomy_name":"Helicobacter pylori 26695","NCBI_taxonomy_id":"85962"}}}},"ARO_accession":"3003510","ARO_id":"40112","ARO_name":"Helicobacter pylori 16S rRNA mutation conferring resistance to tetracycline","ARO_description":"Tetracycline binds tightly to the helix 34 domain in 16S rRNA, where it interferes sterically with the binding of aminoacyl-tRNA to the ribosome A site to block protein synthesis. Mutations in the nucleotide sequence in this domain of Helicobacter pylori can result in resistance against tetracycline.","ARO_category":{"40280":{"category_aro_accession":"3003669","category_aro_cvterm_id":"40280","category_aro_name":"16S rRNA with mutation conferring resistance to tetracycline derivatives","category_aro_description":"Point mutations in the bacterial 16S rRNA region shown clinically to confer resistance to tetracycline and tetracycline derivatives (polyketide antibiotics).","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2482":{"model_id":"2482","model_name":"Chlamydomonas reinhardtii 16S rRNA mutation in the rrnS gene conferring resistance to streptomycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"4748":"U14G","4749":"A474C","4750":"C856U","4751":"A858C","4752":"A859G","4753":"A1123G","4754":"A1123C","4755":"G1125A"},"clinical":{"4748":"U14G","4749":"A474C","4750":"C856U","4751":"A858C","4752":"A859G","4753":"A1123G","4754":"A1123C","4755":"G1125A"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"2500"}},"model_sequences":{"sequence":{"4108":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NC_005353.1","fmin":"38549","fmax":"40023","strand":"+","sequence":"ATCCATGGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCATGCTTAACACATGCAAGTCGAACGAGCAAAGCAATTTGTGTAGTGGCGAACGGGTGCGTAACGCGTAAGAACCTACCTATCGGAGGGGGATAACATTGGGAAACTGTTGCTAATACCCCATACAGCTGAGGAGTGAAAGGTGAAAAACCGCCGATAGAGGGGCTTGCGTCTGATTAGCTAGTTGGTGGGGGTAACGGCCTCCCAAGGCCACGAGCAGTAGCTGGTCTGAGAGGATGATCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGAGGAATTTTTCGCAATGGGCGCAAGCGACGGAGCAATGCCGCGTGCAGGAAGAAGGCCTGTGGGTCGTAAACTGCTTTTCTCAGAGAAGAAGTTCTGACGGTATCTGAGGAATAAGCACCGGCTAACTCTGTGCCAGCAGCCGCGGTAATACAGAGGGTGCAAGCGTTGTCCGCAATGATTGGGCGTAAAGCGTCTGTAGGTGGCTCGTAAAGTCTAATGTCAAATACCAGGGCTCAACCTTGGACCGGCATTGGAGTACTCACGAGCTTGAGTACGGTAGGGGCAGAGGGAATTCCATGTGGAGCGGTGAAATGCGTAGAGATATGGAGGAACACCAGTGGCGAAGGCGCTCTGCTGGGCCGAAACTGACACTGAGAGACGAAAGCTGGGGGAGCGAATAGGATTAGATACCCTAGTAGTCCCAGCCGTAAACTATGGAGACTAAGTGCTGCCGCAAGCAGTGCTGTAGCTAACGCGTTAAGTCTCCCGCCTGGGGAGTATGCTCGCAAGAGTGAAACTCAAAGGAATTGACGGGACCGCACAAGCGGTGGATTATGTGGATTAATTCGATACAACGCGAAGAACCTTACCAGGGTTTGACATGTCAAGAACCTCTCAGAAATGGGAGGGTGCCCTAACGGACTTGAACACAGGTGGTGCATGGCTGTCGTCAGCTCGTGCTGTGAAGTGTATAGTTAAGTCTCATAACGAGCGCAACCCTCGTCTTTAGTTGCCATTTGGTTCTCTAAAGAGACTGCCAGTGTAAGCTGGAGGAAGGTGAGGATGACGTCAAGTCAGCATGCCCCTTACATCCTGGGCTTCACACGTAATACAATGGTTGGGACAATCAGAAGCGACTCGTGAGAGCTAGCGGCTCTGTTAAACCCAACCTCAGTTCGGATTGTAGGCTGCAACTCGCCTACATGAAGCCGGAATCGCTAGTAATCGCCAGTCAGCTATATGGCGGTGAATACGTTCCCGGGTCTTGTACACACCGCCCGTCACACCATGGAAGCTGGTTCTGCTCCAAGTCGTTACCCTAACCTTCGGGAGGGGGGCGCCTAAAGCAGGGCTAGTGACTAGGGTGAAGTCGTAACAAGGTAGGGCTACTGGAAGGTGGCCCTGGCTCACCTCCTTC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40815","NCBI_taxonomy_name":"Chlamydomonas reinhardtii","NCBI_taxonomy_id":"3055"}}}},"ARO_accession":"3003978","ARO_id":"40814","ARO_name":"Chlamydomonas reinhardtii 16S rRNA (rrnS) mutation conferring resistance to streptomycin","ARO_description":"Point mutation in C. reinhardtii rrnS conferring resistance to streptomycin antibiotic.","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2517":{"model_id":"2517","model_name":"tetA(48)","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"650"}},"model_sequences":{"sequence":{"3853":{"protein_sequence":{"accession":"APB03214.1","sequence":"MEHAYKKKIEPKPGDLAVEAYGLIKTFGDNRAVDGVDLNVRTGTIYGVLGPNGAGKTTTIRMLATLLRPDAGSARIFGHDVQAESQIVRQLIGVTGQYASVDESLSATENLIIFSRLLGLGRKEARRKAEELLEEFGLSEAAKRPLKNFSGGMRRRLDLAASLIAQPPLIFLDEPTTGLDPRTRSQMWDTIRRLVNTGSTVLLTTQYLEEADQLADRIAVIDYGRVVAEGTADELKMSVGTSSLHLTVEDSVDMDRACHTVEQVLGVHANVSPEAGKITAPMANAGLVTDLLIELRTAGIGLSEMSVQKPTLDEVFLTITGHGVKEDAAQESYESNDREVARV"},"dna_sequence":{"accession":"KX531044.1","fmin":"0","fmax":"1032","strand":"+","sequence":"ATGGAGCATGCATACAAAAAGAAAATAGAACCAAAACCTGGCGACTTGGCCGTTGAGGCTTACGGACTGATCAAAACATTCGGAGATAACCGCGCCGTGGATGGGGTGGATCTGAACGTACGTACCGGAACGATCTACGGTGTACTTGGCCCGAATGGGGCAGGCAAGACGACCACCATCCGAATGCTGGCGACCTTGCTAAGACCGGATGCGGGTTCGGCCCGAATCTTCGGACATGATGTGCAGGCGGAATCGCAGATTGTCCGTCAGTTGATCGGGGTAACCGGCCAATACGCGTCGGTGGACGAATCGCTCAGCGCTACGGAGAATCTGATTATATTCTCACGTTTGCTTGGTTTGGGGCGTAAGGAGGCAAGGCGCAAGGCGGAAGAGCTGCTCGAGGAATTCGGTTTGTCGGAAGCCGCGAAGCGGCCGCTAAAAAATTTCTCGGGCGGCATGCGGAGAAGGCTGGATCTGGCGGCAAGCCTGATTGCCCAGCCGCCGCTTATCTTCCTGGATGAACCGACGACGGGGCTGGATCCAAGGACGCGTTCCCAGATGTGGGATACGATCCGCCGATTGGTGAATACCGGTTCAACGGTATTGCTGACCACGCAGTATCTCGAGGAGGCCGACCAGCTGGCAGACCGCATCGCCGTTATCGATTACGGCCGGGTTGTGGCCGAGGGGACGGCCGATGAACTGAAGATGTCGGTGGGCACTTCCTCGCTGCATTTGACTGTCGAGGATTCGGTTGACATGGATCGCGCCTGCCATACCGTGGAACAAGTGTTAGGCGTCCATGCCAATGTATCGCCGGAAGCCGGAAAGATAACGGCGCCGATGGCTAATGCGGGTCTTGTTACAGACCTGCTGATCGAGCTGCGAACAGCAGGAATCGGCTTGTCCGAGATGAGCGTGCAGAAGCCGACCCTGGATGAGGTGTTCCTAACGATCACCGGCCACGGCGTGAAGGAAGACGCTGCCCAAGAGTCTTATGAATCCAATGATCGGGAGGTGGCACGGGTATGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40862","NCBI_taxonomy_name":"Paenibacillus sp. LC231","NCBI_taxonomy_id":"1120679"}}}},"ARO_accession":"3003980","ARO_id":"40861","ARO_name":"tetA(48)","ARO_description":"TetA(48) is a Tetracycline efflux pump described in Paenibacillus sp. LC231, a strain of Paenibacillus isolated from Lechuguilla Cave, NM, USA. Described by Pawlowski et al. 2016.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2519":{"model_id":"2519","model_name":"LlmA 23S ribosomal RNA methyltransferase","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"3855":{"protein_sequence":{"accession":"APB03216.1","sequence":"MYVAQDWQDYEVIDTGGGEKLERWGDVILRRPDPQIIWPIEREDGQWRSVHGHYHRSSSGGGQWDMKKQLPDRWTISYDQLKFHIRPTNFKHTGLFPEQAANWRWMMDKIASAGRPVSVLNLFAYTGGATVAAASAGAQVVHVDAAKGMVQWAKENAALSGLADRPIRYITDDVFKFVQREQRRGNKYDAIIMDPPSYGRGPSGETWKLEQSLYPFLESCMSIVSDNPLFMLINSYTTGISPTVLNNMLTMTMKPKYGGTISAGEIGLPITRSGMNLPCGILGRWES"},"dna_sequence":{"accession":"KX531046.1","fmin":"0","fmax":"864","strand":"+","sequence":"ATGTATGTAGCTCAGGATTGGCAAGATTACGAGGTCATCGATACCGGAGGCGGAGAAAAGCTGGAACGCTGGGGCGACGTGATTCTCAGACGTCCGGATCCGCAGATCATATGGCCGATTGAACGTGAAGATGGACAGTGGCGCAGTGTGCACGGACACTATCATCGCAGCTCGTCGGGCGGCGGACAATGGGACATGAAAAAGCAGCTTCCGGACCGGTGGACCATCTCATACGACCAATTGAAATTTCATATTCGACCAACCAATTTTAAACATACCGGTTTGTTTCCGGAGCAGGCAGCCAACTGGCGCTGGATGATGGATAAGATCGCTTCTGCCGGACGTCCGGTCAGCGTGCTGAACCTGTTCGCCTATACCGGCGGAGCAACCGTGGCGGCCGCTTCGGCCGGAGCTCAGGTTGTTCATGTGGATGCTGCGAAGGGAATGGTTCAATGGGCCAAGGAAAACGCGGCATTGTCCGGACTTGCCGACCGTCCTATCCGTTATATCACGGATGATGTGTTTAAATTCGTACAACGGGAGCAGCGTCGGGGGAACAAATACGATGCGATCATTATGGACCCTCCATCTTATGGCCGCGGACCAAGTGGAGAAACGTGGAAGCTTGAGCAAAGCTTGTATCCCTTCCTCGAAAGCTGCATGAGCATCGTATCGGATAATCCGCTGTTCATGCTGATTAACTCCTATACAACCGGGATCTCCCCTACCGTTCTGAATAACATGCTGACCATGACCATGAAGCCGAAATACGGCGGTACCATCAGTGCGGGAGAGATCGGATTGCCGATTACCCGCTCCGGCATGAACCTGCCGTGCGGCATCCTAGGTCGATGGGAGTCCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40862","NCBI_taxonomy_name":"Paenibacillus sp. LC231","NCBI_taxonomy_id":"1120679"}}}},"ARO_accession":"3003982","ARO_id":"40864","ARO_name":"LlmA 23S ribosomal RNA methyltransferase","ARO_description":"Lincosamide (Clindamycin) resistant (putative) ribosomal methyltransferase related to the RlmK 23S rRNA methyltransferase COG family. Detected in Paenibacillus sp. LC231, an isolated strain of Paenibacillus found in Lechuguilla Cave, NM, USA. Described by Pawlowski et al. 2016.","ARO_category":{"41437":{"category_aro_accession":"3004273","category_aro_cvterm_id":"41437","category_aro_name":"Llm 23S ribosomal RNA methyltransferase","category_aro_description":"A family of lincosamide resistant 23S rRNA methyltransferases. The only member of the family discovered so far was isolated from Paenibacillus sp. LC231, a strain found in Lechuguilla Cave, NM, USA.","category_aro_class_name":"AMR Gene Family"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2520":{"model_id":"2520","model_name":"CatU","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"3856":{"protein_sequence":{"accession":"APB03217.1","sequence":"MKFHIINVEEWTRKPYYEHYLRSNKCTFSITVDIDITRLLYSLKANGFKLYPAFIYMVTRVVNDRVEFKTSFSPEGELGYWDRMTPSYTFFHNDDHTFSCLWTAFSNDFYRFHDHYEQDMEQYRDTKGLFVKENPPPNTFPISMIPWTSFSGFNLNIVNEADYLLPIITGGKYTEQGGRVLLPVSLQVHHAVCDGYHASMFFKELQSLADSFEDWLT"},"dna_sequence":{"accession":"KX531047.1","fmin":"0","fmax":"654","strand":"+","sequence":"ATGAAGTTTCACATTATTAATGTTGAAGAGTGGACGAGAAAGCCTTATTATGAGCATTATCTTCGATCGAATAAATGCACCTTCAGCATCACCGTGGATATCGACATTACTCGCTTGTTGTATTCGTTAAAAGCTAATGGATTCAAGCTTTATCCAGCTTTTATTTATATGGTTACAAGAGTTGTCAATGACCGGGTTGAATTCAAAACTTCCTTTAGTCCCGAAGGGGAATTGGGTTACTGGGATCGGATGACGCCGAGTTATACCTTTTTCCATAACGATGACCATACCTTCTCCTGTTTATGGACAGCATTTTCGAATGATTTCTATCGATTTCATGATCATTACGAGCAGGACATGGAGCAATATCGGGATACAAAAGGGCTGTTTGTTAAAGAGAATCCACCGCCGAACACGTTTCCCATATCCATGATACCCTGGACAAGCTTTAGCGGATTTAATCTAAACATTGTCAATGAAGCAGACTATCTTCTTCCCATCATAACCGGCGGAAAATATACCGAGCAGGGTGGCCGTGTTCTGCTTCCAGTCTCATTGCAGGTGCACCATGCTGTGTGTGATGGTTATCATGCCAGCATGTTCTTTAAGGAGTTGCAGAGCTTGGCGGATTCTTTTGAAGATTGGTTAACTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40862","NCBI_taxonomy_name":"Paenibacillus sp. LC231","NCBI_taxonomy_id":"1120679"}}}},"ARO_accession":"3003983","ARO_id":"40865","ARO_name":"CatU","ARO_description":"Chloramphenicol acetyltransferase conferring resistance to phenicol antibiotics detected in Paenibacillus sp. LC231, an isolated strain of Paenibacillus from Lechuguilla Cave, NM, USA. Described by Pawlowski et al. 2016.","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. cat is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Bacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini","category_aro_class_name":"AMR Gene Family"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2521":{"model_id":"2521","model_name":"BahA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1450"}},"model_sequences":{"sequence":{"3857":{"protein_sequence":{"accession":"APB03218.1","sequence":"MEIHKEKEKEKGVTFFRRIMANRKRRGPLSPGWKGASLGLGATGFILILIQANYLLTGHGVGKFIVGTFLFLFAAALISGLASMLLHGVKKLPSRYIWMLLYSLIMFLFCFIVQPGVSAVFIVSLAIVLSLFGALAYKFAAGSYKQVSKTRKIGAMACLSLITIAIGAGSFWLIRAGDDAAPDITLKQLKTSTRYEDSTMNNPAEQGTYPVQSLLYGSPDNYRTEFNQSGSLTTQTVDASRFVEKWSSLRTKSLGFGPEAMPLNGRVWYPEGEGTFPLVLIVHGNHLMNDYSDPGYEYLGRLLASKGYIFVSVDENFLNFSPYEDLFLISPLLSENPARGLLLLEHLQTWKDWNSDPDNPFYQKVDMERIALIGHSRGGEAVAIAAAYNKLGRHPDHGDIKFDYNFSIRSLISIAGTDGQYKPQGKPLPLQDVNYLSLHGAHDMDVNSLDGAKQYHRIRYTKGTNYMKSLVYIYGANHGQFNGGWGRGDGAGLGNQLFNLRQIMPRDEQETIAKVFISSFLDATLKDQRQYREVFKDLGYAKEWIPDNLYVGNYYDSQTTLIADFHEDIDLQSTTLPGGSLRGENLQQWKEEKVKTKWGEADYSAVRLGWNSNGSSEPASYTVTLPDNGVETGRDSSIVFSLADARKTEESGDPKELINFTITVEDRKGHQASLPLSHISKLPPVIEGKLLKWPFSNAGNTSEPVFQSYDFQLDDYYKMNPDFNPQQLSKIRIEFNLTKRGSILLRDVGIRS"},"dna_sequence":{"accession":"KX531048.1","fmin":"0","fmax":"2259","strand":"+","sequence":"TTGGAAATACACAAAGAGAAAGAAAAAGAAAAAGGCGTTACGTTTTTTCGAAGAATCATGGCAAACCGGAAGCGTAGGGGGCCGCTATCCCCTGGATGGAAGGGTGCGTCGCTTGGGCTCGGCGCCACCGGCTTTATTCTAATTCTGATACAGGCCAATTATCTATTGACGGGGCATGGTGTCGGTAAATTCATCGTGGGCACATTCCTGTTTCTCTTTGCGGCTGCCCTTATAAGCGGCCTAGCATCAATGTTGCTGCACGGGGTCAAGAAACTACCAAGCCGTTATATTTGGATGCTGCTGTATTCCCTGATCATGTTTTTATTCTGTTTTATTGTGCAGCCGGGCGTATCGGCAGTCTTCATCGTCTCTTTGGCCATTGTTTTATCTTTATTTGGTGCATTGGCTTATAAATTTGCAGCGGGAAGCTACAAGCAAGTGTCTAAAACCAGGAAAATCGGCGCGATGGCTTGTTTGTCCTTGATCACCATCGCGATCGGCGCTGGCAGCTTCTGGCTGATTCGGGCCGGAGATGATGCCGCTCCGGACATCACATTGAAACAGCTGAAAACCTCAACCCGATATGAAGACTCGACGATGAACAATCCGGCCGAACAAGGCACATATCCCGTCCAAAGCCTGTTATACGGAAGTCCTGACAACTATCGGACAGAATTTAATCAAAGCGGTTCCCTAACCACCCAAACGGTGGATGCGTCCAGGTTTGTTGAGAAGTGGTCGTCTTTGCGCACGAAGTCGCTTGGATTCGGACCCGAGGCCATGCCGTTAAACGGAAGAGTGTGGTATCCCGAAGGGGAAGGCACCTTTCCGCTTGTTTTGATTGTACATGGTAATCACTTGATGAATGATTATTCCGATCCGGGTTATGAATATCTCGGCAGGCTGCTCGCGAGCAAAGGGTATATATTTGTCTCCGTGGATGAAAATTTCCTCAATTTCTCCCCATATGAGGATCTATTCCTGATCAGCCCGCTGCTAAGTGAAAATCCGGCAAGGGGTCTGCTGCTGCTGGAGCATTTGCAAACCTGGAAGGACTGGAACAGCGATCCGGACAACCCGTTTTACCAAAAGGTCGATATGGAACGAATCGCCCTCATCGGTCATTCCCGGGGCGGCGAAGCGGTCGCGATCGCGGCAGCGTATAACAAGCTTGGCCGTCATCCGGACCATGGGGATATCAAGTTTGATTATAACTTTTCGATCCGCTCGCTCATTTCCATTGCGGGAACGGACGGGCAATATAAGCCCCAAGGCAAACCTCTGCCGCTGCAAGACGTAAATTATCTGTCTTTGCATGGAGCTCATGATATGGATGTCAACAGCCTGGACGGTGCGAAGCAATATCACCGGATTCGTTATACCAAGGGCACAAATTACATGAAATCGCTGGTCTATATTTATGGAGCCAACCACGGCCAGTTTAACGGAGGCTGGGGCAGAGGGGATGGGGCAGGGTTGGGGAACCAACTGTTTAACCTACGTCAAATTATGCCACGGGATGAGCAGGAAACCATCGCAAAAGTGTTCATATCTTCGTTCCTGGATGCCACGCTGAAGGACCAACGGCAATACAGGGAGGTGTTCAAGGATTTGGGTTACGCCAAGGAATGGATTCCCGACAATCTGTATGTGGGCAATTATTACGATTCGCAGACGACCTTGATCGCCGATTTTCATGAAGACATCGATCTGCAGAGCACCACGCTTCCTGGCGGCAGCCTGCGGGGCGAGAACCTGCAGCAATGGAAGGAAGAAAAGGTTAAGACAAAATGGGGCGAAGCGGATTACAGCGCGGTTCGCTTAGGCTGGAATTCGAACGGTTCGTCCGAGCCTGCCTCCTATACGGTTACTTTGCCGGATAACGGGGTGGAAACAGGAAGGGATAGCTCGATCGTATTTTCGCTGGCAGATGCACGCAAAACAGAAGAAAGCGGCGACCCGAAAGAGCTTATCAATTTTACGATTACGGTTGAAGATAGGAAGGGCCATCAGGCAAGTCTTCCCCTCAGCCACATATCCAAGTTGCCGCCTGTTATTGAAGGTAAACTTCTCAAATGGCCATTTTCGAATGCAGGCAATACTTCAGAACCCGTATTTCAAAGCTACGATTTCCAATTAGACGATTATTACAAAATGAATCCGGACTTCAACCCGCAGCAGTTGAGCAAGATTCGCATCGAGTTCAATCTAACCAAGCGGGGAAGCATTCTGCTTCGTGATGTTGGCATTCGATCTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40862","NCBI_taxonomy_name":"Paenibacillus sp. LC231","NCBI_taxonomy_id":"1120679"}}}},"ARO_accession":"3003984","ARO_id":"40866","ARO_name":"BahA","ARO_description":"Bacitracin amidohydrolase found in Paenibacillus sp. LC231, an isolated strain of Paenibacillus from Lechuguilla Cave, NM, USA. Confers resistance by bacitracin inactivation through amidohydrolysis. Described by Pawlowski et al. 2016.","ARO_category":{"41424":{"category_aro_accession":"3004260","category_aro_cvterm_id":"41424","category_aro_name":"Bah amidohydrolase","category_aro_description":"Bah amidohydrolases are membrane proteins that inactivate bacitracin.","category_aro_class_name":"AMR Gene Family"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2522":{"model_id":"2522","model_name":"TaeA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1200"}},"model_sequences":{"sequence":{"3858":{"protein_sequence":{"accession":"APB03219.1","sequence":"MNILTVEQVTKSYGDKILFQDASFGMEDQDKIGIIGVNGTGKSTFLRVIAGLEPPDSGKISMGNRIRVRYLAQNPEFDPDKTVLQQVFEGDLPEMKAVREYTETMELLELHPSHEELQQKLLKLNQTLETLQAWQLESDAKTILSKLGIRNYEAKMGTLSGGQRKRVALAAALIQPSDLLILDEPTNHIDNESVAWLEQYLQKRRGALLMITHDRYFLDRVANVMLELDHGRLFRYEANYSRFLELKAEREEREAASEQKRQNLLRSELAWIRRGAKARTTKQKARIERFEKLKDQEMVHSSGELDVSVASTRLGRKILEIEGLRMKIDDKTLIQDLSYIAVPEDRIGIVGPNGSGKSTLLNLIAGRIQPGGGEVVLGPTVKLGYFTQEHQEMDGSQRVIEYIKDEAEVVRTADGSAITAAQMLERFLFPPALQWTPIAKLSGGEKRRLYLLRVLMSAPNVLLLDEPTNDLDIQTLSVLEQYLDEFPGVCIVVSHDRFFLDRTVDKIMAFEGDGQIRVHVGSYSEYAEWMQRHGGEASGSKAEASIAKSASGSSDGTDSDSAKEAPRERLKFSYKEQREFDQIDGLIEDTESKLASIQSEMETAGSDAARLQELMKAQEETERELEHLMERWTYLNELAEKIEQSKKS"},"dna_sequence":{"accession":"KX531049.1","fmin":"0","fmax":"1947","strand":"+","sequence":"ATGAATATTTTGACCGTCGAACAGGTAACAAAAAGCTATGGAGACAAAATTCTGTTTCAAGATGCATCCTTCGGAATGGAGGATCAGGATAAAATCGGCATTATCGGCGTGAATGGCACGGGGAAATCCACATTTCTGCGGGTCATCGCGGGGCTCGAGCCGCCCGACTCCGGTAAAATATCGATGGGCAATCGCATCCGGGTTCGTTACCTCGCGCAAAATCCGGAGTTTGATCCGGACAAAACCGTCCTGCAGCAGGTGTTTGAGGGCGATCTTCCGGAGATGAAGGCCGTGCGGGAATACACCGAAACGATGGAACTGCTGGAGCTGCATCCAAGTCATGAGGAGCTCCAGCAGAAACTGCTGAAGCTCAATCAGACGCTGGAAACGCTGCAGGCATGGCAGCTTGAAAGCGATGCGAAAACCATCCTGTCCAAGCTGGGGATTCGGAATTATGAAGCGAAGATGGGAACGCTGTCGGGCGGCCAGCGTAAGCGGGTGGCATTAGCCGCCGCCTTGATTCAGCCTTCCGACTTGCTTATTTTGGACGAGCCGACCAACCACATTGACAATGAATCCGTTGCCTGGCTGGAGCAGTATTTGCAGAAGCGCCGCGGCGCGCTGCTCATGATTACGCATGACCGGTATTTTCTGGACCGGGTAGCCAATGTTATGCTGGAGCTGGATCACGGACGGCTGTTTCGATATGAGGCGAACTACAGCCGTTTTCTGGAGCTGAAGGCAGAACGCGAGGAGCGTGAAGCCGCTTCCGAGCAAAAGCGCCAAAATTTGCTGCGGAGCGAGCTTGCCTGGATCCGCAGAGGGGCCAAGGCCCGCACGACCAAGCAGAAGGCGAGGATTGAACGCTTCGAGAAACTCAAGGATCAGGAGATGGTGCACAGCTCCGGTGAACTGGACGTTTCGGTCGCTTCCACCCGCTTGGGACGCAAAATTCTGGAGATTGAAGGTCTCCGGATGAAGATCGACGACAAAACGTTAATTCAGGACCTTTCCTATATCGCCGTTCCCGAGGATCGGATAGGTATCGTAGGCCCGAACGGCAGCGGCAAATCCACGCTGCTCAATCTGATTGCCGGGCGGATTCAGCCGGGTGGCGGGGAAGTCGTGCTCGGACCGACGGTCAAGCTCGGTTATTTCACGCAGGAGCATCAGGAGATGGACGGCAGTCAGCGCGTGATTGAGTATATCAAGGATGAGGCCGAGGTTGTCCGCACGGCGGACGGTTCGGCGATTACCGCAGCCCAGATGCTGGAACGCTTTCTGTTCCCGCCCGCGCTGCAGTGGACGCCGATTGCGAAGCTGTCCGGAGGCGAGAAGCGCCGCTTGTATCTGCTGCGGGTGCTGATGAGCGCACCGAATGTGCTGCTGCTTGATGAACCGACCAATGATTTGGATATCCAGACATTGTCCGTCCTGGAGCAGTATTTGGATGAGTTCCCGGGCGTCTGTATCGTGGTATCCCATGATCGCTTTTTCCTGGATCGAACCGTGGACAAGATTATGGCTTTTGAGGGCGACGGTCAGATTCGTGTCCATGTCGGCTCTTACAGCGAATATGCGGAATGGATGCAGCGTCACGGCGGTGAAGCTTCCGGGAGCAAGGCGGAGGCATCCATAGCCAAATCTGCTTCGGGGAGCAGCGATGGCACGGACAGTGATTCAGCTAAAGAAGCGCCGCGTGAGCGCTTGAAATTCAGTTACAAAGAACAACGGGAGTTTGATCAGATTGACGGGCTCATCGAGGATACCGAGAGCAAGCTCGCTTCGATTCAATCCGAGATGGAGACCGCCGGCAGCGACGCAGCCAGGCTTCAGGAGCTGATGAAGGCTCAGGAGGAAACGGAACGTGAGCTGGAGCATCTGATGGAACGCTGGACCTATCTGAACGAGCTCGCGGAGAAGATTGAACAGAGCAAGAAATCGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40862","NCBI_taxonomy_name":"Paenibacillus sp. LC231","NCBI_taxonomy_id":"1120679"}}}},"ARO_accession":"3003986","ARO_id":"40868","ARO_name":"TaeA","ARO_description":"Pleuromutilin (Tiamulin) ABC efflux pump found in Paenibacillus sp. LC231, a strain of Paenibacillus isolated from Lechuguilla Cave, NM, USA. Confers resistance to pleuromutilin antibiotics. Described by Pawlowski et al. 2016.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"37716":{"category_aro_accession":"3001317","category_aro_cvterm_id":"37716","category_aro_name":"pleuromutilin","category_aro_description":"Pleuromutilin is a natural product antibiotic produced by Clitopilus passeckerianus. Related antibiotics of clinical significance, such as tiamulin and retapamulin, are semi-synthetic derivatives of this compound.","category_aro_class_name":"Antibiotic"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2523":{"model_id":"2523","model_name":"VatI","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"3859":{"protein_sequence":{"accession":"APB03220.1","sequence":"MTGPNPNERYPIPGDNNLQFIKNTITKPNIIAGDYSYYYALNGESFEDQVLYHYEFIGTKLMIGKFCSIASEVRFMMDGGNHRMDGSTFPFNIFGNGWEKFTPSLDQLPIKGDTIIGNDVWIGRRATIMSGVRIGDGAIIAAEAVVVKDVEPYTIVGGNPAKDIRKRYSTEVIQELLDIKWWDCDIEVINQYIGAIVSGDMDLLRKMRQN"},"dna_sequence":{"accession":"KX531050.1","fmin":"0","fmax":"633","strand":"+","sequence":"ATGACAGGACCGAATCCAAATGAGAGATATCCTATACCCGGAGATAACAATCTTCAGTTTATCAAGAACACGATTACAAAACCTAATATTATCGCAGGGGATTATTCATACTACTATGCCTTAAACGGAGAATCATTTGAGGATCAAGTATTGTATCATTATGAATTCATTGGAACTAAATTAATGATCGGCAAGTTTTGTTCCATTGCTTCCGAGGTCAGATTTATGATGGATGGAGGGAACCATCGGATGGACGGTTCAACCTTTCCATTTAATATCTTTGGAAACGGCTGGGAGAAATTCACTCCATCTTTGGATCAATTGCCGATCAAGGGAGATACGATCATTGGAAATGACGTGTGGATCGGAAGGCGTGCAACGATCATGTCGGGTGTAAGGATTGGCGATGGAGCTATCATTGCCGCTGAAGCTGTCGTTGTAAAGGATGTGGAGCCTTATACGATCGTTGGAGGCAATCCAGCGAAGGATATCCGCAAGCGATATTCCACCGAAGTCATTCAAGAGTTATTGGATATTAAATGGTGGGATTGCGATATCGAAGTCATCAATCAATATATTGGCGCAATTGTAAGCGGAGATATGGACTTGCTTAGAAAAATGAGACAAAATTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40862","NCBI_taxonomy_name":"Paenibacillus sp. LC231","NCBI_taxonomy_id":"1120679"}}}},"ARO_accession":"3003987","ARO_id":"40869","ARO_name":"VatI","ARO_description":"Streptogramin A acetyltransferase found in Paenibacillus sp. LC231, isolated from Lechuguilla Cave, NM, USA. Confers resistance to streptogramin A antibiotics. Described by Pawlowski et al. 2016.","ARO_category":{"36592":{"category_aro_accession":"3000453","category_aro_cvterm_id":"36592","category_aro_name":"streptogramin vat acetyltransferase","category_aro_description":"vat (Virginiamycin acetyltransferases) enzymes catalyze the transfer of an acetyl group from acetyl-CoA to the secondary alcohol of streptogramin A compounds, thus inactivating virginiamycin-like antibiotics and conferring resistance to these compounds.","category_aro_class_name":"AMR Gene Family"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2524":{"model_id":"2524","model_name":"AAC(2')-IIb","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"3860":{"protein_sequence":{"accession":"APB03221.1","sequence":"MNHRKGNEPTAAALMELHVLAMFTHDGNMQIRTINEPWPGEELAPRFFMGRTIDGSSICRFRHDVPEGIAGQLRALVEDEPIVTEEVLTRPKHFAAYMNLLRAEHYTSGPCYRIPDQTTQAKQTVRITPGNIREYSLTGFEWLTTEIDYDQPCVALIHENRVVSVCRSVRITERAHEAGLETSEEFRGRGYAAAVVAGWAIEVQKMGALALYSTLWGNSSSRRVANKLGLSYYGVNFTIS"},"dna_sequence":{"accession":"KX531051.1","fmin":"0","fmax":"723","strand":"+","sequence":"ATGAACCATAGGAAAGGTAACGAGCCAACCGCTGCGGCACTGATGGAATTGCATGTTCTGGCGATGTTTACGCATGACGGGAATATGCAAATTCGCACCATCAACGAGCCTTGGCCGGGAGAGGAGCTTGCCCCGAGGTTTTTCATGGGTCGAACGATAGACGGCTCTTCGATCTGCAGGTTTCGTCATGATGTTCCCGAAGGAATTGCCGGGCAATTGAGGGCTTTGGTTGAAGATGAGCCTATCGTTACTGAAGAGGTTCTGACGAGGCCTAAACATTTTGCAGCTTATATGAACCTCCTTCGCGCTGAGCACTATACGAGCGGACCTTGTTATCGGATACCTGATCAAACAACGCAGGCCAAACAGACGGTAAGGATCACACCGGGAAATATTCGCGAATATTCGCTCACCGGTTTTGAATGGCTGACCACGGAAATTGATTATGACCAGCCTTGTGTTGCGCTCATTCATGAGAATAGGGTGGTGTCGGTTTGCCGCAGCGTCCGGATTACTGAACGAGCTCACGAAGCTGGGCTTGAAACGTCAGAGGAATTTCGTGGAAGAGGTTATGCGGCTGCTGTTGTTGCCGGATGGGCCATAGAGGTGCAAAAAATGGGCGCGCTGGCGTTGTACAGTACTTTATGGGGAAATAGCTCTTCCCGGAGAGTAGCAAATAAATTAGGGTTGTCCTATTACGGAGTTAACTTCACGATCAGTTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40862","NCBI_taxonomy_name":"Paenibacillus sp. LC231","NCBI_taxonomy_id":"1120679"}}}},"ARO_accession":"3003988","ARO_id":"40870","ARO_name":"AAC(2')-IIb","ARO_description":"AAC(2')-IIb is an intrinsic Kasugamycin 2' acetyltransferase protein found in Paenibacillus sp. LC231, a strain of Paenibacillus isolated from Lechuguilla Cave, NM, USA. Confers resistance to aminoglycoside antibiotics, including kasugamycin. Described by Pawlowski et al. 2016.","ARO_category":{"36480":{"category_aro_accession":"3000341","category_aro_cvterm_id":"36480","category_aro_name":"AAC(2')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 2'.","category_aro_class_name":"AMR Gene Family"},"37695":{"category_aro_accession":"3001296","category_aro_cvterm_id":"37695","category_aro_name":"kasugamycin","category_aro_description":"An unusual aminoglycoside because the cyclitol ring is not amino substituted; it was discovered as a fermentation product of Streptomyces kasugaensis.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2525":{"model_id":"2525","model_name":"AAC(6')-34","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"3861":{"protein_sequence":{"accession":"APB03223.1","sequence":"MRIGDLIREDGGIAMLVYEAGPITVRELEEKDEISLASWLSNPDVLQYYEGRDNPHDVERVREHFYVDDDETRCIIKYEGKPIGYIQFYLLDEETLGEYGYNESDADCRTFATDQFIGEPDYWNRGIGTKLMTSMVEYLVFQRQADRIVMDPQAWNERAIACYEKCGFRKVRLLEKHEQHEGELRDCWIMEYRAERK"},"dna_sequence":{"accession":"KX531053.1","fmin":"0","fmax":"594","strand":"+","sequence":"ATGAGAATTGGGGATCTAATAAGGGAAGATGGGGGGATCGCGATGCTGGTGTACGAGGCTGGACCGATTACGGTTCGCGAGCTGGAGGAGAAGGATGAAATATCCTTAGCTTCTTGGCTGTCCAATCCGGATGTGCTGCAGTATTATGAGGGACGGGACAATCCTCACGACGTGGAGCGGGTGCGGGAGCATTTTTACGTGGATGATGATGAGACTCGCTGCATCATTAAATATGAGGGGAAACCGATCGGATATATTCAGTTTTATCTTCTGGATGAAGAGACGTTAGGCGAGTATGGATATAACGAGAGTGATGCAGACTGCAGAACCTTCGCCACGGATCAATTCATCGGGGAGCCGGATTATTGGAATCGAGGCATCGGTACGAAGCTCATGACTTCCATGGTGGAGTATCTCGTGTTTCAGAGGCAGGCTGATCGGATCGTAATGGACCCGCAGGCATGGAATGAACGGGCGATTGCTTGTTACGAAAAGTGCGGCTTCCGGAAGGTCAGACTGCTGGAGAAGCATGAACAGCATGAAGGTGAACTGCGGGACTGCTGGATTATGGAGTATCGGGCAGAGCGAAAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40862","NCBI_taxonomy_name":"Paenibacillus sp. LC231","NCBI_taxonomy_id":"1120679"}}}},"ARO_accession":"3003989","ARO_id":"40871","ARO_name":"AAC(6')-34","ARO_description":"AAC(6')-34 is an aminoglycoside 6'-phosphotransferase found in Paenibacillus sp. LC231, a strain of Paenibacillus from Lechuguilla Cave, NM, USA. Confers resistance to aminoglycoside antibiotics. Described by Pawlowski et al. 2016.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 6'.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2526":{"model_id":"2526","model_name":"VgbC","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"3862":{"protein_sequence":{"accession":"APB03225.1","sequence":"MQIAAQEYKTANRESGPYGITARQDRTIWFTEQKGNRIGRLTKDGDMRTFEVPTPDAGVMSILSAHTGDLWFTEYKANKIGRMTMEGTFAEFELPEANSSPYGLAEGPDGAIWFTELSGNRIGRITPAGIITEYDLPCEGSYPSYITAGPDGALWFTENQNNCIGRITVDGEITEYRIPTEQSGPVGITTGADGALWFVQINGNQIGRITTAGEITEFKLPSGNARPHAITAGVSGDLWFTEWGANQIGRITCTGDITEYPIPTPSAEPHGITVDSGGEVWFAEECDQIGRFTIQY"},"dna_sequence":{"accession":"KX531055.1","fmin":"0","fmax":"891","strand":"+","sequence":"ATGCAGATCGCCGCACAGGAGTACAAGACAGCGAATCGGGAATCGGGACCTTATGGTATTACGGCAAGACAAGATCGGACCATATGGTTCACGGAACAAAAAGGAAACCGGATCGGACGGCTCACCAAGGATGGGGATATGCGCACGTTCGAAGTGCCGACTCCAGATGCCGGGGTCATGTCTATCCTCTCTGCCCATACCGGTGACCTCTGGTTTACGGAGTACAAAGCAAATAAAATCGGAAGGATGACAATGGAAGGAACATTTGCGGAATTCGAGCTGCCTGAAGCCAATTCGTCTCCCTACGGCTTGGCTGAGGGTCCGGATGGAGCCATATGGTTCACCGAGCTAAGCGGCAACCGAATCGGAAGGATAACGCCGGCAGGCATTATCACGGAATATGACTTACCATGCGAAGGATCGTACCCTTCCTATATTACAGCCGGTCCGGACGGCGCGTTGTGGTTTACGGAAAACCAGAACAACTGCATCGGCCGAATTACGGTGGACGGGGAGATTACCGAGTACCGGATTCCAACAGAGCAATCCGGGCCGGTCGGCATCACGACAGGTGCCGATGGCGCTCTATGGTTTGTTCAAATCAACGGCAATCAAATCGGCCGGATCACAACGGCCGGGGAAATTACGGAATTCAAGCTCCCGTCCGGGAATGCCAGACCCCATGCCATCACGGCGGGCGTTTCCGGGGATCTATGGTTTACCGAATGGGGAGCCAATCAAATCGGACGAATTACCTGCACCGGGGACATTACCGAGTATCCAATCCCTACCCCCTCCGCAGAACCTCATGGCATAACCGTGGATTCGGGCGGCGAGGTCTGGTTCGCCGAGGAATGCGATCAGATCGGCCGGTTTACGATTCAGTATTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40862","NCBI_taxonomy_name":"Paenibacillus sp. LC231","NCBI_taxonomy_id":"1120679"}}}},"ARO_accession":"3003990","ARO_id":"40872","ARO_name":"vgbC","ARO_description":"VgbC is a streptogramin B-type lyase found in Paenibacillus sp. LC231, a strain of Paenibacillus isolated from Lechuguilla Cave, NM, USA. Confers resistance to streptogramin B-type antibiotics by linearization of the lactone ring on an ester bond, resulting in antibiotic inactivation. Described by Pawlowski et al. 2016.","ARO_category":{"36515":{"category_aro_accession":"3000376","category_aro_cvterm_id":"36515","category_aro_name":"streptogramin vgb lyase","category_aro_description":"vgb (Virginiamycin B) lyase inactivates type B streptogramin antibiotics by linearizing the streptogramin lactone ring at the ester linkage through an elimination mechanism, thus conferring resistance to these compounds.","category_aro_class_name":"AMR Gene Family"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin 1A is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"vernamycin B-gamma","category_aro_description":"Vernamycin B-gamma is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2527":{"model_id":"2527","model_name":"mphI","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"3863":{"protein_sequence":{"accession":"APB03226.1","sequence":"MTIAKPNDDYTQVIQEMLEIAGKHGVNLIPEGIEMNESGMDFLVGFAEEAGTGARWILRKPRRPDVLDRADNEARVLKLIQSHLSVDVPDWRIYTPELIAYPLLSGQPAASVSMEGYAWNMDHENPGDGFIRSLAEALVALHGVDHDAARAAGLRVKSPQEVRDETARNMEDIKSRLGVSDALWERWQKWLEEDSYWPTHSALIHGDLHPPHILIDERVQVTGLLDWTESEVASPAKDFVLYYAIYGEHNLRVLLDRYEQAGGKVWPRMFDHIVEQHAAYPVLIAQFALLTGQEEYMTMARNALGLTE"},"dna_sequence":{"accession":"KX531056.1","fmin":"0","fmax":"927","strand":"+","sequence":"ATGACAATAGCAAAACCAAATGATGATTATACACAAGTGATCCAAGAGATGCTGGAGATTGCCGGAAAACACGGGGTGAATTTGATTCCGGAGGGAATAGAGATGAATGAATCCGGCATGGATTTCCTTGTTGGATTCGCAGAGGAGGCAGGGACTGGAGCACGGTGGATTCTGCGGAAACCGAGACGACCGGATGTGCTGGATAGAGCAGATAACGAAGCTAGGGTCCTGAAGCTGATTCAATCCCATCTTTCGGTTGATGTACCGGATTGGCGGATTTACACGCCGGAGCTCATCGCCTATCCGCTGCTTAGCGGGCAGCCTGCCGCTTCCGTCAGCATGGAAGGATATGCATGGAATATGGATCATGAGAATCCGGGCGACGGGTTTATCCGCTCACTGGCTGAAGCGCTGGTTGCCTTGCATGGCGTCGATCATGATGCAGCCCGAGCAGCAGGTCTGCGGGTAAAGAGTCCCCAAGAGGTTCGTGATGAGACGGCGCGAAATATGGAAGACATCAAGAGCCGTCTGGGCGTTTCCGATGCGCTGTGGGAGAGATGGCAAAAATGGCTGGAGGAGGATTCCTATTGGCCGACGCATTCTGCCCTCATCCATGGCGATCTTCATCCCCCGCATATCCTGATTGATGAGCGCGTGCAGGTGACCGGACTTTTGGATTGGACGGAGTCCGAGGTAGCAAGTCCCGCCAAAGACTTCGTGTTATACTACGCTATTTATGGCGAGCATAATCTCCGTGTCCTGTTGGACCGGTATGAACAAGCCGGAGGGAAGGTATGGCCGCGCATGTTCGATCATATTGTCGAACAGCATGCCGCGTATCCCGTGCTGATCGCCCAGTTCGCTCTCCTGACAGGCCAGGAAGAGTATATGACGATGGCGCGGAATGCTCTGGGTTTGACGGAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40862","NCBI_taxonomy_name":"Paenibacillus sp. LC231","NCBI_taxonomy_id":"1120679"}}}},"ARO_accession":"3003991","ARO_id":"40873","ARO_name":"mphI","ARO_description":"mphI is a macrolide phosphotransferase protein found in Paenibacillus sp. LC231, a strain of Paenibacillus isolated from Lechuguilla Cave, NM, USA. Confers resistance to macrolide antibiotics. Described by Pawlowski et al. 2016.","ARO_category":{"36472":{"category_aro_accession":"3000333","category_aro_cvterm_id":"36472","category_aro_name":"macrolide phosphotransferase (MPH)","category_aro_description":"Macrolide phosphotransferases (MPH) are enzymes encoded by macrolide phosphotransferase genes (mph genes). These enzymes phosphorylate macrolides in GTP dependent manner at 2'-OH of desosamine sugar thereby inactivating them. Characterized MPH's are differentiated based on their substrate specificity.","category_aro_class_name":"AMR Gene Family"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2528":{"model_id":"2528","model_name":"rphB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1500"}},"model_sequences":{"sequence":{"3864":{"protein_sequence":{"accession":"APB03222.1","sequence":"MRSLVLDFQEMDKKQLGLVGGKGLHLGELSKIEGIRVPEGFCVTTIGYQRAIEQNETYQAMLNRLTMLSAEDRDQMVEISRKIRQTIMEVEIPSDVVTAVTRYLSRFGEEQAYAVRSSATAEDLPHASFAGQQDTYLNIIGVDAILQHISKCWASLFTDRAVIYRMQNGFDHRQVYLSVVVQRMVFPEASGILFTADPMTSNRKLLSIDAGFGLGEALVSGLVSADGYKVREGEIIEKRIAAKTLAIYGRKEGGTETKQIDPDQQKSQTLTDEQILQLARIGRQIEAHFGQPQDIEWCLAQDTFYIVQSRPITTLYPIPEANDQENHVYVSVGHQQMMTDPMKPLGLSFFLLTTPAPMRTAGGRLFVDTTAMLASPVSRENVLNTLGQSDPLIKDALMTILERGDFIKSLPIAENEQTPGKNNISSAGYQTPIDHDPTIVSDLMERTQSSIEVLKQNIQTKSGSDLFDFILEDIQELKKNLFDPQSSAVIMAAMNASTWINEKMNEWLGEKNAADTLSQSVPGNVTSEMGLALLDVADVIRPYPEIIDYLEQAKDDHFLDKLLTFDGGQQAQDAILDFLDKYGMRCAGEIDLTRTRWSEKPIALVPLILGNIKNFEPNASHRKFEQGRQEALKKEQELLDRLKQLPDGEGKAQETKRMIDLIRNFMGYREYPKYGMVNRYFIYKQALLKEAERLVQAGVIHHKEDIYYLTFEELDEVVRTNKLDNPGSMVEQQAKLAIRQMISKRKEEYNVFEKLTPPRVITSDGEIIAGEYKRENIPAEAIVGLPVSSGTVEGRARVILNMKDADLEEGDILVTAFTDPSWTPLFVSIKGLVTEVGGLMTHGAVIAREYGLPAVVGVENATKRIKDGQRIRVHGSEGYIEILS"},"dna_sequence":{"accession":"KX531052.1","fmin":"0","fmax":"2655","strand":"+","sequence":"ATGCGTTCGTTGGTTCTCGATTTTCAGGAAATGGACAAAAAGCAGCTTGGGCTCGTTGGTGGAAAAGGGCTCCATTTAGGGGAATTATCAAAAATTGAGGGAATACGAGTTCCCGAAGGATTTTGCGTGACAACCATAGGATATCAAAGAGCCATCGAACAAAACGAAACGTATCAAGCTATGCTCAATCGACTAACCATGCTATCAGCAGAGGATCGAGATCAAATGGTTGAAATCAGCAGGAAGATCAGACAAACCATTATGGAGGTAGAAATTCCATCCGATGTAGTGACAGCAGTAACTCGCTATCTCTCCCGGTTTGGCGAGGAACAGGCTTATGCCGTACGATCCAGTGCAACTGCTGAAGATTTACCGCATGCCTCTTTTGCGGGTCAACAAGACACCTATCTAAACATCATCGGCGTCGATGCCATCTTGCAGCATATCAGCAAATGCTGGGCTTCCTTGTTTACAGATCGCGCGGTGATCTATCGCATGCAAAATGGATTTGACCATCGTCAAGTTTATTTATCCGTAGTCGTTCAAAGGATGGTTTTCCCCGAGGCTTCAGGGATATTATTCACCGCTGATCCGATGACTTCTAATCGAAAGCTGCTATCCATCGATGCCGGTTTCGGACTTGGAGAAGCACTGGTCTCTGGCTTGGTATCTGCCGATGGTTACAAAGTACGGGAAGGAGAAATCATCGAGAAGCGGATAGCAGCCAAAACATTGGCGATCTACGGACGAAAAGAAGGCGGAACAGAAACAAAGCAAATCGATCCCGATCAGCAAAAGTCACAAACACTTACGGATGAGCAAATTTTACAACTGGCACGCATCGGGAGACAGATTGAGGCTCATTTTGGCCAACCCCAAGATATCGAGTGGTGTTTGGCCCAGGATACCTTTTATATTGTCCAGAGTCGGCCAATCACGACGCTATACCCGATACCTGAAGCGAATGATCAAGAAAATCACGTATACGTATCTGTCGGTCATCAACAAATGATGACGGATCCCATGAAACCGCTGGGATTGTCTTTTTTCCTGCTAACGACTCCTGCACCCATGCGTACAGCTGGCGGAAGGTTGTTTGTTGATACTACGGCTATGCTGGCTTCACCGGTTAGCAGAGAAAATGTATTAAATACCCTGGGACAATCCGATCCACTCATCAAAGACGCTCTTATGACCATCTTAGAGCGAGGAGATTTTATAAAATCGCTACCCATCGCTGAAAATGAACAGACTCCCGGAAAAAACAATATATCGTCTGCGGGTTATCAAACGCCAATCGACCACGATCCGACAATCGTTTCTGATTTAATGGAACGTACTCAATCATCGATCGAAGTGTTGAAACAAAACATCCAAACGAAATCCGGATCCGATTTATTTGATTTTATATTGGAAGATATCCAGGAACTGAAGAAGAATTTATTTGACCCACAAAGCTCGGCTGTCATCATGGCTGCAATGAATGCTTCAACCTGGATCAACGAAAAAATGAATGAATGGTTAGGCGAAAAAAACGCAGCCGACACGCTTTCTCAATCCGTACCGGGCAATGTTACTTCGGAAATGGGTCTGGCGCTGCTGGATGTTGCAGACGTCATTCGTCCTTATCCGGAAATCATTGATTATTTGGAGCAAGCAAAAGATGATCACTTTTTGGATAAGCTGCTTACATTTGATGGCGGGCAGCAAGCTCAAGACGCGATCCTAGATTTTCTTGACAAATATGGCATGCGATGTGCTGGAGAAATCGATTTAACAAGAACTCGTTGGAGTGAAAAACCAATTGCGCTTGTTCCGTTGATTCTGGGTAACATCAAAAACTTCGAGCCTAATGCCAGCCATCGGAAATTCGAGCAAGGGCGGCAGGAAGCTTTGAAAAAAGAACAAGAGCTATTAGATCGATTGAAACAATTGCCGGACGGTGAAGGAAAAGCCCAAGAAACCAAACGAATGATTGACCTCATTCGGAATTTCATGGGTTATCGGGAATACCCGAAATACGGTATGGTGAATCGTTACTTTATTTATAAGCAGGCTTTACTGAAAGAGGCTGAACGACTCGTACAAGCGGGCGTTATTCATCATAAGGAAGATATATATTATCTCACTTTTGAAGAGCTTGACGAGGTCGTACGCACAAATAAACTGGATAACCCGGGTTCCATGGTCGAGCAGCAAGCAAAGCTTGCGATCAGACAGATGATCAGCAAACGAAAAGAGGAGTACAACGTATTTGAAAAACTAACTCCTCCGCGCGTGATCACGTCGGATGGTGAAATCATCGCAGGGGAGTACAAACGAGAAAATATCCCAGCCGAAGCTATTGTCGGCCTGCCTGTTTCTTCCGGAACGGTCGAAGGACGAGCGCGTGTCATCTTAAACATGAAAGACGCCGATCTCGAGGAAGGAGATATATTAGTCACCGCTTTTACCGACCCTAGCTGGACGCCTCTGTTTGTATCCATTAAGGGCTTGGTCACCGAAGTGGGCGGACTGATGACCCATGGAGCCGTTATCGCGCGTGAATATGGCTTACCGGCCGTTGTCGGCGTTGAGAATGCTACCAAACGGATAAAGGACGGGCAGCGCATTCGCGTACATGGGTCCGAAGGCTATATTGAAATATTGTCATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40862","NCBI_taxonomy_name":"Paenibacillus sp. LC231","NCBI_taxonomy_id":"1120679"}}}},"ARO_accession":"3003992","ARO_id":"40874","ARO_name":"rphB","ARO_description":"rphB is a rifampin phosphotransferase protein found in Paenibacillus sp. LC231, a strain of Paenibacillus isolated from Lechuguilla Cave, NM, USA. Confers resistance to rifamycin antibiotics, specifically rifampin, through rifampin inactivation. Described by Pawlowski et al. 2016.","ARO_category":{"41087":{"category_aro_accession":"3004040","category_aro_cvterm_id":"41087","category_aro_name":"rifampin phosphotransferase","category_aro_description":"Enzymes, protein or other gene products that inactivate rifampin (rifamycin) antibiotics through phosphorylation of the antibiotic at the 21-OH position.","category_aro_class_name":"AMR Gene Family"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36656":{"category_aro_accession":"3000517","category_aro_cvterm_id":"36656","category_aro_name":"rifaximin","category_aro_description":"Rifaximin is a semi-synthetic rifamycin used to treat traveller's diarrhea. Rifaximin inhibits RNA synthesis by binding to the beta subunit of bacterial RNA polymerase.","category_aro_class_name":"Antibiotic"},"36669":{"category_aro_accession":"3000530","category_aro_cvterm_id":"36669","category_aro_name":"rifabutin","category_aro_description":"Rifabutin is a semisynthetic rifamycin used in tuberculosis therapy. It inhibits DNA-dependent RNA synthesis.","category_aro_class_name":"Antibiotic"},"36673":{"category_aro_accession":"3000534","category_aro_cvterm_id":"36673","category_aro_name":"rifapentine","category_aro_description":"Rifapentine is a semisynthetic rifamycin that inhibits DNA-dependent RNA synthesis. It is often used in the treatment of tuberculosis and leprosy.","category_aro_class_name":"Antibiotic"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2529":{"model_id":"2529","model_name":"cpaA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"3865":{"protein_sequence":{"accession":"APB03224.1","sequence":"MPLRITAMTETYADQIMQWSYEPPYDFYNSEPDEEFRKELLECSYYAILDKEGQLFGFCCTGSSAQIPIAIPLGAYDEDLLDFGLGMKPESTGQCRGKEFLSFVLASIAEFHKRQSFRLTVAKFNERAIRLYTQLGFSEVATFDYGGTTFITMIKKPGSGL"},"dna_sequence":{"accession":"KX531054.1","fmin":"0","fmax":"486","strand":"+","sequence":"ATGCCTCTTCGTATCACGGCCATGACCGAAACGTATGCCGATCAAATTATGCAATGGAGCTATGAACCTCCCTATGATTTCTACAACAGCGAACCGGATGAGGAGTTTCGGAAAGAACTTCTGGAGTGCTCGTATTACGCCATACTGGACAAGGAAGGGCAGCTCTTCGGCTTTTGCTGTACAGGCTCATCAGCCCAAATTCCGATCGCAATCCCGTTAGGTGCATATGACGAGGATCTGCTGGATTTCGGACTTGGGATGAAACCGGAATCGACCGGACAATGCCGGGGAAAAGAGTTTCTCTCGTTCGTGCTGGCATCCATCGCTGAATTTCACAAGCGCCAATCGTTTCGGCTGACCGTTGCCAAATTCAATGAACGAGCCATTCGCTTGTATACCCAGCTGGGCTTCTCGGAAGTTGCAACGTTTGATTATGGCGGCACTACGTTCATAACGATGATCAAGAAGCCGGGCTCCGGATTGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40862","NCBI_taxonomy_name":"Paenibacillus sp. LC231","NCBI_taxonomy_id":"1120679"}}}},"ARO_accession":"3003994","ARO_id":"40876","ARO_name":"cpaA","ARO_description":"cpaA is a capreomycin acetyltransferase protein found in Paenibacillus sp. LC231, an isolated strain of Paenibacillus in Lechuguilla Cave, NM, USA. Confers resistance to capreomycin, an aminoglycoside antibiotic. Described by Pawlowski et al. 2016.","ARO_category":{"41421":{"category_aro_accession":"3004257","category_aro_cvterm_id":"41421","category_aro_name":"cpa acetyltransferase","category_aro_description":"Acetyltransferases of the cpa family confer resistance to capreomycin, an aminoglycoside antibiotic","category_aro_class_name":"AMR Gene Family"},"40875":{"category_aro_accession":"3003993","category_aro_cvterm_id":"40875","category_aro_name":"capreomycin","category_aro_description":"Capreomycin is an aminoglycoside antibiotic, capable of treating a large number of infections but in particular used for killing bacteria causing tuberculosis.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2518":{"model_id":"2518","model_name":"tetB(48)","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"3854":{"protein_sequence":{"accession":"APB03215.1","sequence":"MSSSMIQPGTERQLKNRTSLGQTVRNSLTMAYRGLLKLRRTPEQLFDVTFQPIIFTLMFTYIFGGAISGDVASYLPVIIPGILVQTVITTSVVTGVQLREDMDKGVFDRFKSLPIARIAPLAGALLADTIRYTIATVLTFTMGYIMGYRPEGGLGYVALAGLVVILCSWAISWIFAFCGVIARSASGVQGISMIVLFPLTFLSNAFVPVDTMPGWLQWFVNMNPISHLVTAVRDLTNAGTVGWDLTISLVGAAVIVAIFAPITVRAYMRRT"},"dna_sequence":{"accession":"KX531045.1","fmin":"0","fmax":"816","strand":"+","sequence":"ATGAGCAGCTCCATGATTCAGCCTGGGACGGAACGTCAGCTTAAGAACCGCACGAGTTTGGGTCAGACGGTCCGAAATTCGTTGACGATGGCTTACCGCGGGCTGCTGAAGCTCCGGCGCACGCCCGAGCAGTTGTTTGACGTCACGTTTCAGCCCATTATTTTTACGCTGATGTTCACCTATATTTTTGGGGGCGCCATCTCGGGTGACGTGGCGAGTTATTTGCCCGTCATCATTCCCGGCATCCTCGTCCAGACCGTGATTACGACCTCCGTCGTCACAGGCGTTCAGCTGCGCGAGGATATGGATAAAGGCGTATTCGACCGATTCAAATCGCTGCCGATTGCACGCATCGCACCGCTGGCGGGTGCCCTGCTGGCAGACACGATTCGGTATACCATTGCGACAGTGCTTACCTTTACGATGGGATATATTATGGGGTATCGGCCCGAGGGCGGCTTGGGTTATGTTGCTCTTGCGGGGTTGGTCGTCATTTTGTGCTCATGGGCCATTAGCTGGATTTTTGCTTTCTGCGGCGTGATTGCAAGATCTGCCTCCGGCGTGCAGGGGATATCGATGATCGTGCTGTTTCCGCTCACGTTTCTCTCCAACGCGTTCGTGCCGGTGGATACGATGCCGGGCTGGCTGCAGTGGTTCGTCAATATGAATCCGATCTCGCATCTTGTGACAGCCGTTCGGGATCTCACCAACGCTGGCACCGTGGGCTGGGATCTCACGATATCCTTGGTTGGCGCCGCGGTTATCGTGGCGATCTTTGCTCCCATTACGGTTCGTGCGTACATGCGCCGCACTTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40862","NCBI_taxonomy_name":"Paenibacillus sp. LC231","NCBI_taxonomy_id":"1120679"}}}},"ARO_accession":"3003981","ARO_id":"40863","ARO_name":"tetB(48)","ARO_description":"Tetracycline resistant TetB(48) efflux pump found in Paenibacillus sp. LC231, a strain of Paenibacillus isolated from Lechuguilla Cave, NM, USA. Described by Pawlowski et al. 2016.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2550":{"model_id":"2550","model_name":"Clostridium difficile gyrA conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"4650":"A384D"},"clinical":{"4650":"A384D"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1500"}},"model_sequences":{"sequence":{"3887":{"protein_sequence":{"accession":"YP_001086469.1","sequence":"MEENNKILPIEIAEEMKKSYIDYSMSVIAGRALPDVRDGLKPVHRRILYSMSELNLTPDKPYRKSARIVGDVLGKYHPHGDTAVYYAMVRMAQDFSTRALLVDGHGNFGSVDGDSPAAMRYTEAKMSKLSLELLRDIEKETVDFKPNFDESLKEPSVLPARYPNLLVNGSNGIAVGMATSIPPHNLAEVIDATVYLIDNPECSVDDLIKFVQGPDFPTAAIIMGKESIAEAYRTGRGKVKVRSRAFIEELPKGKQQIIVTEIPYQVNKAKLVERIAELVKEKRIEGISDLRDESNRNGMRIVIELKRDANANIVLNNLYKHSQMEDTFSIIMLALVDGQPRVLNLKQILYHYIKHQEDVVTRRTKFELNKAEARAHILEGLKIALDNIDAVISLIRASKTGQEAKLGLIEKFKLTEIQAQAILDMRLQRLTGLERDKIEAEYEDLIKKINRLKEILADERLLLNVIKDEITIIKENYSDERRTEIRHAEGEIDMRDLISDEEIAITLTHFGYIKRLPSDTYKSQKRGGRGISALTTREEDFVRHLVTTTTHSRLLFFTNKGRVFKLNAYEIPEGKRQAKGTAIVNLLQLSADEKIATLIPIDGNDENEYLLLATKKGIVKKTKREEFKNINKSGLIAIGLRDDDELIGVELTDGKQEVLLVTKEGMSIRFDENDIRYMGRTAMGVKGITLSKEDFVVSMNLCSKGTDVLVVSKNGFGKRTNIEEYRSQIRAGKGIKTYNISEKTGTIVGADMVNEDDEIMIINSDGVLIRIRVNEISLFGRVTSGVKLMKTNDEVNVVSIAKINIEEE"},"dna_sequence":{"accession":"NC_009089.1","fmin":"6065","fmax":"8492","strand":"+","sequence":"ATGGAAGAAAATAACAAAATACTCCCTATTGAAATAGCGGAAGAAATGAAAAAATCGTATATTGATTATTCAATGAGTGTTATAGCTGGACGTGCTCTTCCTGATGTTAGAGATGGTTTAAAGCCAGTTCATAGAAGAATATTATATTCAATGAGTGAGTTAAATTTAACTCCAGATAAACCATACAGGAAGTCAGCTCGTATTGTTGGGGACGTTTTAGGTAAGTACCATCCTCATGGAGATACTGCTGTTTATTATGCTATGGTAAGAATGGCACAAGATTTTTCAACTAGAGCACTTTTAGTAGATGGTCATGGTAACTTTGGTTCTGTTGATGGGGATTCACCAGCTGCTATGCGTTATACAGAAGCTAAAATGAGTAAATTATCATTAGAACTACTGAGAGATATTGAAAAGGAAACTGTAGACTTTAAACCAAACTTTGATGAGTCGTTAAAAGAGCCTTCAGTATTGCCAGCTAGATATCCTAATTTATTAGTAAATGGCTCAAATGGTATAGCTGTTGGTATGGCAACTTCAATACCTCCACATAATTTAGCAGAAGTAATTGATGCAACTGTATATTTGATAGATAATCCAGAGTGTAGTGTAGATGATTTAATAAAATTTGTTCAAGGACCAGATTTCCCTACAGCTGCAATTATAATGGGAAAAGAAAGTATAGCAGAAGCATACAGAACTGGAAGAGGAAAAGTTAAAGTTAGGTCTAGAGCTTTTATAGAAGAGCTACCAAAAGGAAAACAGCAAATAATAGTTACAGAAATACCTTATCAAGTAAATAAGGCTAAACTGGTTGAAAGAATAGCAGAGTTAGTTAAAGAAAAGAGAATAGAAGGTATATCAGACCTAAGAGACGAAAGTAATAGAAATGGTATGAGAATTGTTATAGAATTAAAGAGGGATGCTAATGCTAATATAGTATTAAATAATTTGTATAAACATTCTCAAATGGAAGATACTTTTAGTATAATAATGCTTGCACTTGTAGATGGTCAGCCAAGAGTTTTAAATCTTAAACAAATATTATATCATTATATTAAACATCAAGAAGATGTTGTTACAAGAAGAACTAAATTTGAACTAAATAAAGCTGAAGCAAGAGCACATATTTTAGAAGGATTAAAGATTGCTTTAGATAATATAGATGCTGTTATAAGCTTGATAAGAGCTTCAAAGACTGGGCAAGAAGCTAAGCTAGGTTTAATAGAAAAATTCAAATTAACTGAAATCCAAGCACAAGCTATATTAGATATGAGACTTCAAAGACTTACAGGTTTAGAAAGAGATAAGATAGAAGCTGAATATGAAGATTTAATCAAGAAGATAAATAGATTAAAAGAGATTTTAGCTGATGAAAGATTACTTTTAAATGTAATAAAGGATGAAATTACAATAATAAAAGAAAATTACTCTGATGAGAGAAGAACAGAAATAAGACATGCTGAAGGCGAAATAGATATGAGAGATCTTATAAGTGATGAAGAAATAGCAATAACTCTTACTCACTTTGGATATATAAAAAGGCTTCCATCTGATACTTATAAGAGTCAAAAAAGGGGTGGAAGAGGTATTTCAGCACTTACAACTAGAGAAGAAGATTTTGTAAGGCACTTGGTAACTACAACTACTCATAGTAGACTATTATTCTTTACAAATAAAGGTAGAGTATTTAAATTAAATGCATATGAAATACCAGAAGGTAAGAGACAGGCTAAAGGTACTGCTATAGTGAATTTACTTCAATTGTCAGCAGATGAGAAAATTGCTACTCTAATACCTATTGATGGTAATGATGAAAATGAATATTTATTACTTGCAACGAAAAAAGGTATTGTTAAAAAGACTAAGAGAGAAGAGTTCAAAAATATAAATAAATCTGGTCTTATTGCAATAGGTTTAAGAGATGATGATGAGCTTATTGGAGTAGAACTTACAGATGGAAAACAAGAAGTACTTTTAGTAACTAAAGAAGGTATGTCTATAAGATTTGATGAAAATGATATAAGATATATGGGTAGAACAGCAATGGGTGTAAAAGGTATAACTTTAAGTAAAGAAGATTTTGTTGTGTCTATGAACCTTTGTAGTAAAGGTACAGATGTGTTAGTTGTAAGTAAGAATGGTTTTGGAAAGAGAACAAATATAGAAGAGTATAGAAGTCAAATAAGAGCTGGTAAAGGAATTAAAACTTATAATATATCTGAAAAAACTGGTACAATTGTAGGTGCAGATATGGTCAACGAAGATGATGAGATAATGATTATAAATTCTGATGGAGTTCTTATTAGAATAAGAGTCAATGAAATATCACTGTTTGGAAGAGTTACAAGTGGTGTTAAATTAATGAAGACGAATGATGAAGTCAATGTAGTTTCGATTGCCAAAATAAATATTGAAGAAGAATAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37603","NCBI_taxonomy_name":"Clostridium difficile 630","NCBI_taxonomy_id":"272563"}}}},"ARO_accession":"3003995","ARO_id":"40901","ARO_name":"Clostridium difficile gyrA conferring resistance to fluoroquinolones","ARO_description":"Amino acid substitutions in Clostridium difficile gyrase subunit A which when present confer functional resistance to fluoroquinolone antibiotics.","ARO_category":{"39876":{"category_aro_accession":"3003292","category_aro_cvterm_id":"39876","category_aro_name":"fluoroquinolone resistant gyrA","category_aro_description":"DNA gyrase is responsible for DNA supercoiling and consists of two alpha and two beta subunits. GyrA point mutations confer resistance by preventing fluoroquinolone antibiotics from binding the alpha-subunit.","category_aro_class_name":"AMR Gene Family"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"40463":{"category_aro_accession":"3003780","category_aro_cvterm_id":"40463","category_aro_name":"nybomycin","category_aro_description":"A  heterocyclic antibiotic that targets mutant gyrA (type II topoisomerase) containing an S84L substitution, counteracting acquired quinolone resistance. It is effective against quinolone-resistant Gram-positive bacteria including S. aureus and E. faecalis. Due to its ability to counteract quinolone resistance by targeting the mutant form of the gyrA protein, it is classified as a reverse antibiotic (RA).","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2551":{"model_id":"2551","model_name":"glycopeptide resistance gene cluster VanI","model_type":"gene cluster meta-model","model_type_id":"40298","model_description":"A meta-model to detect a defined gene cluster based on gene detection by other models.","model_param":{"40297":{"param_type":"gene order","param_description":"The gene order model parameter describes the relative order of a set of genes or other genetic elements on a chromosome, a plasmid or within an operon. Antibiotic resistance is only conferred when the detected set of genes appears in the indicated order; otherwise, no resistance phenotype is produced. This parameter is part of the gene cluster meta-model, and may be attached to detection models with the following notation: [[cvterm_id 1],[cvterm_id 2],...,[cvterm_id n]], where the cvterm_id denotes a gene-associated AMR term and an attached model id. This parameter currently (August 2017) lacks an algorithm for detection.","param_type_id":"40297","param_value":{"4683":"R:40383,R:40385,C:40377,A:40380,C:40384,C:40381"}}},"ARO_accession":"3003722","ARO_id":"40376","ARO_name":"glycopeptide resistance gene cluster VanI","ARO_description":"This inducible cluster confers high resistance to vancomycin and intermediate resistance to teicoplanin. It achieves this through peptidoglycan restructuring with its VanA ligase homologue, VanI, causing the precursurs to end in D-Ala-D-Lac. The cluster uniquely contains murF, the final enzyme in the synthesis of UDP-N-acetylmuramoyl-pentapeptide, the precursor of murein. The VanI gene cluster has been found in chromosomal DNA. Gene orientation: vanSRIWK-murFvanX","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2355":{"model_id":"2355","model_name":"ADC-31","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3648":{"protein_sequence":{"accession":"WP_001211223.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPLDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTSGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_050716.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTAGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAGCGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003870","ARO_id":"40569","ARO_name":"ADC-31","ARO_description":"ADC-31 is a beta-lactamase found in Acinetobacter baumannii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2356":{"model_id":"2356","model_name":"ADC-39","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3649":{"protein_sequence":{"accession":"WP_063857800.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNRSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_048654.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATCGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTGGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCATTTGGTTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCTGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCTGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCACCGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003871","ARO_id":"40570","ARO_name":"ADC-39","ARO_description":"ADC-39 is a beta-lactamase found in Acinetobacter baumannii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2717":{"model_id":"2717","model_name":"MuxA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"4042":{"protein_sequence":{"accession":"NP_251218.1","sequence":"MTPTTGKSKFRTLRPWLITALAFAAVIGLVMWLAAPASAPSSDGRPGRGGKPGAALPKANALTVGVARVEQGDLALHFNALGTVTAFNTVNVKPRVNGELVKVLFQEGQEVKAGDLLAVVDPRTYKAALAQAEGTLMQNQAQLKNAEIDLQRYKGLYAEDSIAKQTLDTQEAQVRQLQGTIRTNQGQVDDARLNLTFTEVRAPISGRLGLRQVDIGNLVTSGDTTPLVVITQVKPISVVFSLPQQQIGTVVEQMNGPGKLTVTALDRNQDKVLAEGTLTTLDNQIDTTTGTVKLKARFENADGKLFPNQFVNVRLLAQTLKGVLTIPANAVQRGTNGIYVYVVGADNKVSQRSVAIGTSENERVVVESGLKAGEQVVVEGTDRLRDGMEVRVAEASPQVLEGEPQKPQTGRPSGLQGDSVGSGSAE"},"dna_sequence":{"accession":"NC_002516.2","fmin":"2854010","fmax":"2855291","strand":"-","sequence":"TCATTCAGCGCTCCCGCTACCCACCGAGTCGCCCTGGAGGCCGCTGGGGCGGCCAGTCTGCGGTTTCTGCGGCTCGCCCTCGAGGACCTGCGGGGAGGCCTCGGCGACACGCACTTCCATACCGTCGCGCAGGCGGTCGGTGCCTTCCACCACCACCTGCTCGCCGGCCTTCAGGCCGCTTTCCACCACCACCCGCTCGTTCTCGCTGGTGCCGATGGCGACGCTGCGCTGGCTGACCTTGTTGTCGGCGCCGACCACGTAGACATAGATACCGTTGGTGCCGCGCTGCACGGCGTTGGCCGGAATGGTCAGCACGCCTTTGAGGGTCTGCGCCAGCAGGCGCACGTTGACGAACTGGTTGGGGAACAGCTTGCCGTCGGCGTTCTCGAAGCGCGCCTTGAGCTTGACCGTGCCGGTGGTGGTGTCGATCTGGTTGTCCAGGGTGGTCAGGGTGCCTTCGGCGAGAACCTTGTCCTGGTTGCGGTCCAGCGCGGTGACCGTCAGCTTGCCGGGGCCGTTCATCTGCTCGACGACGGTGCCGATCTGCTGCTGCGGCAGGCTGAACACCACCGAGATCGGCTTGACCTGGGTGATCACCACCAGCGGCGTGGTATCGCCGCTGGTGACCAGGTTGCCGATGTCCACCTGGCGCAGGCCGAGGCGCCCGGAAATCGGTGCGCGGACCTCGGTGAAGGTCAGGTTGAGGCGGGCGTCGTCGACCTGGCCCTGGTTGGTACGGATGGTGCCCTGCAACTGGCGGACCTGGGCTTCCTGGGTATCCAGGGTCTGCTTGGCTATCGAGTCCTCGGCATACAGCCCCTTGTAGCGCTGCAGGTCGATCTCGGCGTTCTTCAGTTGCGCCTGGTTCTGCATCAGCGTGCCCTCGGCCTGGGCCAGCGCCGCCTTGTAGGTGCGCGGGTCGACCACCGCCAGCAGGTCGCCGGCCTTGACCTCCTGCCCCTCCTGGAACAGCACCTTGACCAGCTCGCCGTTGACCCGCGGCTTGACGTTCACCGTGTTGAAGGCGGTGACGGTGCCAAGCGCGTTGAAATGCAGCGCCAGGTCGCCCTGCTCCACCCTGGCCACGCCGACGGTGAGCGCGTTGGCCTTGGGCAGCGCGGCGCCCGGCTTGCCGCCGCGACCGGGTCGCCCGTCGGAGGACGGTGCCGAGGCGGGCGCCGCCAGCCACATCACCAGGCCGATCACGGCGGCGAAGGCCAGGGCGGTGATCAGCCACGGGCGCAGGGTACGGAACTTGGATTTACCGGTCGTTGGAGTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3004073","ARO_id":"41155","ARO_name":"MuxA","ARO_description":"MuxA is a membrane fusion protein component of the efflux pump system MuxABC-OpmB in Pseudomonas aeruginosa.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36689":{"category_aro_accession":"3000550","category_aro_cvterm_id":"36689","category_aro_name":"aztreonam","category_aro_description":"Aztreonam was the first monobactam discovered, and is greatly effective against Gram-negative bacteria while inactive against Gram-positive bacteria. Artreonam is a poor substrate for beta-lactamases, and may even act as an inhibitor. In Gram-negative bacteria, Aztreonam interferes with filamentation, inhibiting cell division and leading to cell death.","category_aro_class_name":"Antibiotic"},"37626":{"category_aro_accession":"3001227","category_aro_cvterm_id":"37626","category_aro_name":"kitasamycin","category_aro_description":"Kitasamycin is a macrolide antibiotic and is produced by Streptoverticillium kitasatoense. The drug has antimicrobial activity against a wide spectrum of pathogens.","category_aro_class_name":"Antibiotic"},"40353":{"category_aro_accession":"3003701","category_aro_cvterm_id":"40353","category_aro_name":"rokitamycin","category_aro_description":"Rokitamycin is a macrolide antibiotic. Synthesized from strains of Streptomyces kitasatoensis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"515":{"model_id":"515","model_name":"mgtA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"311":{"protein_sequence":{"accession":"ABA28305.2","sequence":"MKRKELHETSRLAYGRRMTTRPAHIAMFSIALHGHVNPSLEVIRELVARGHRVTYAIPPLLADKVAEAGAEPKLWNSTLPGPDADPEAWGSTLLDNVEPFLADAIQSLPQLAQAYEGDEPDLVLHDIASYTARVLGRRWEVPVISLSPCMVAWEGYEQEVGEPMWEEPRKTERGQAYYARFHAWLEENGITDHPDPFIGRPDRSLVLIPKALQPHADRVDETTYTFVGACQGDRTAEGDWARPEGAEKVVLVSLGSAFTKQPAFYRECVRAFGELPGWHTVLQVGRHVDPAELGDVPDNVEVRTWVPQLAILQQADLFVTHAGAGGSQEGLATATPMIAVPQAADQFGNADMLQGLGVARTLPTEEATAKALRTAALALVDDPEVAARLKEIQARMAQEGGTRRAADLIEAELAAARG"},"dna_sequence":{"accession":"DQ185434","fmin":"0","fmax":"1257","strand":"+","sequence":"ATGAAGCGAAAAGAGTTGCACGAGACGTCTCGTCTCGCATACGGTCGTCGCATGACCACTCGCCCCGCGCACATCGCCATGTTCTCCATCGCCCTGCACGGCCACGTGAACCCCAGCCTGGAGGTCATCCGCGAGCTCGTCGCGCGGGGGCACCGGGTGACGTACGCGATCCCGCCGCTCCTCGCGGACAAGGTCGCCGAGGCGGGCGCCGAACCCAAGCTCTGGAACAGCACACTGCCCGGCCCCGACGCCGACCCGGAGGCCTGGGGGAGCACCCTCCTGGACAACGTGGAGCCCTTCCTCGCCGACGCGATCCAGTCGCTCCCGCAGCTCGCCCAGGCGTACGAGGGGGACGAGCCGGACCTGGTCCTGCACGACATCGCCTCCTACACCGCCCGCGTCCTGGGCCGCCGCTGGGAGGTGCCCGTGATCTCCCTGTCGCCCTGCATGGTCGCCTGGGAGGGGTACGAGCAGGAGGTCGGCGAGCCGATGTGGGAGGAGCCGCGGAAGACCGAGCGCGGGCAGGCGTACTACGCCCGCTTCCACGCCTGGCTGGAGGAGAACGGGATCACCGACCACCCCGACCCGTTCATCGGCCGCCCCGACCGCTCCCTGGTGCTGATCCCCAAGGCGCTCCAGCCCCACGCCGACCGGGTGGACGAGACGACGTACACCTTCGTCGGCGCCTGCCAGGGGGACCGCACCGCCGAGGGCGACTGGGCCCGTCCCGAGGGCGCGGAGAAGGTCGTCCTGGTCTCGCTCGGTTCGGCCTTCACCAAGCAGCCCGCGTTCTACCGGGAGTGCGTCCGGGCCTTCGGTGAGCTGCCCGGCTGGCACACCGTGCTCCAGGTCGGCCGGCACGTAGACCCGGCCGAGCTGGGCGACGTACCGGACAACGTGGAAGTCCGCACGTGGGTACCGCAGTTGGCGATCCTCCAGCAGGCCGACCTGTTCGTCACCCACGCGGGCGCGGGCGGCAGCCAGGAGGGTCTGGCCACCGCCACGCCGATGATCGCCGTACCGCAGGCCGCGGACCAGTTCGGCAACGCCGACATGCTCCAGGGCCTCGGCGTCGCCCGCACCCTCCCGACCGAGGAGGCCACCGCGAAGGCGCTGCGCACCGCCGCCCTCGCCCTGGTCGACGACCCGGAGGTGGCGGCGCGCCTGAAGGAGATCCAGGCGCGGATGGCCCAGGAGGGCGGCACCCGCCGGGCCGCCGACCTCATCGAGGCCGAACTGGCCGCCGCGCGCGGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39569","NCBI_taxonomy_name":"Streptomyces lividans","NCBI_taxonomy_id":"1916"}}}},"ARO_accession":"3000462","ARO_id":"36601","ARO_name":"mgtA","ARO_description":"A macrolide glycosyltransferase encoded by the mgtA gene in Streptomyces lividans. This enzyme inactivates macrolides using UDP-glucose as a cofactor. Its optimal substrates are lankamycin, calcomycin, rosaramicin, methymycin, and pikromycin, while interactions with erythomycin, oldeandomycin, azithromycin, and tylosin were weaker. It is inactive against spiramycin and carbomycin. Mechanism first described by Cundliffe, 1992.","ARO_category":{"41401":{"category_aro_accession":"3004237","category_aro_cvterm_id":"41401","category_aro_name":"mgt macrolide glycotransferase","category_aro_description":"The mgt family encompasses macrolide glycotransferases of the Streptomyces genus.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"37631":{"category_aro_accession":"3001232","category_aro_cvterm_id":"37631","category_aro_name":"methymycin","category_aro_description":"Produced by Streptomyces venezuelae ATCC 15439.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2614":{"model_id":"2614","model_name":"mphD","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"3951":{"protein_sequence":{"accession":"ANP63073.1","sequence":"MTIQDIQSLAEAHGLLLTDKMNFNEMGIDFKVVFALDTKGQQWLLRIPRRDGMREQIKKEKRILELVKKHLSVEVPDWRISSTELVAYPILKDNPVLNLDAETYEIIWNMDKDSPKYITSLAKTLFEIHSIPEKEVRENDLKIMKPSDLRPEIANNLQLVKSEIGISEQLETRYRKWLDNDVLWADFTQFIHGDLYAGHVLASKDGAVSGVIDWSTAHIDDPAIDFAGHVTLFGEESLKTLIIEYEKLGGKVWNKLYEQTLERAAASPLMYGLFALETQNESLIVGAKAQLGVI"},"dna_sequence":{"accession":"CP016215.1","fmin":"74426","fmax":"75311","strand":"+","sequence":"ATGACAATTCAAGATATTCAATCACTTGCTGAAGCACACGGCTTGTTGCTTACGGACAAAATGAATTTCAATGAAATGGGCATTGATTTTAAGGTCGTTTTTGCTCTTGATACAAAGGGGCAACAATGGTTGCTGCGTATTCCTCGTCGTGATGGCATGAGGGAACAAATCAAGAAAGAAAAACGCATTTTAGAATTGGTAAAAAAACATCTTTCTGTAGAGGTTCCTGATTGGAGAATTTCATCTACAGAATTAGTGGCTTATCCCATACTTAAAGATAATCCTGTTTTAAATTTGGATGCTGAAACCTATGAAATAATTTGGAATATGGACAAAGATAGCCCGAAATACATAACATCTTTGGCAAAAACCTTATTTGAAATCCATAGTATTCCTGAAAAAGAAGTTCGGGAAAATGATTTGAAAATTATGAAACCTTCAGATTTAAGACCTGAAATAGCAAACAATTTGCAGTTAGTAAAATCTGAAATTGGTATAAGTGAGCAATTGGAAACCCGCTACAGAAAATGGTTGGATAATGATGTTCTATGGGCAGATTTCACCCAATTTATACATGGCGATTTATATGCTGGGCATGTACTAGCTTCAAAGGATGGAGCTGTTTCAGGCGTTATTGATTGGTCAACAGCCCATATAGATGACCCAGCGATTGATTTTGCTGGGCATGTAACTTTGTTTGGAGAAGAAAGCCTCAAAACTCTAATCATCGAGTATGAAAAACTAGGGGGTAAAGTTTGGAATAAACTATATGAACAGACTTTAGAAAGAGCAGCGGCCTCTCCTTTGATGTATGGTTTATTTGCCTTAGAAACTCAAAATGAAAGCCTTATCGTTGGAGCAAAAGCTCAGTTGGGAGTTATATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3003741","ARO_id":"40396","ARO_name":"mphD","ARO_description":"The mphD gene codes for a macrolide 2'-phosphotransferase partial sequence detected in Pseudomonas aeruginosa that provides a high level of resistance to all 14- and 15-membered-ring macrolides.","ARO_category":{"36472":{"category_aro_accession":"3000333","category_aro_cvterm_id":"36472","category_aro_name":"macrolide phosphotransferase (MPH)","category_aro_description":"Macrolide phosphotransferases (MPH) are enzymes encoded by macrolide phosphotransferase genes (mph genes). These enzymes phosphorylate macrolides in GTP dependent manner at 2'-OH of desosamine sugar thereby inactivating them. Characterized MPH's are differentiated based on their substrate specificity.","category_aro_class_name":"AMR Gene Family"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2685":{"model_id":"2685","model_name":"Pseudomonas aeruginosa CpxR","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"4018":{"protein_sequence":{"accession":"SIP52035.1","sequence":"MSELLLIDDDRELCELLGTWLVQEGFSVRASHDGAQARRALAEQTPDAVVLDVMLPDGSGLELLKQLRGDHPDLPVLMLSARGEPLDRILGLELGADDYLAKPCDPRELTARLRAVLRRTHPAQPSAQMQLGDLSLNLTRGVAQIDGQEISLTLSESRILEALLRQPGEPLDKQALAQLALGRKLTLYDRSLDMHVSNLRKKLGSHPDGSPRILALRGRGYYYSH"},"dna_sequence":{"accession":"LT673656.1","fmin":"1884344","fmax":"1885022","strand":"-","sequence":"TCAGTGGCTGTAGTAGTAGCCGCGGCCGCGCAGGGCGAGGATGCGCGGGCTGCCGTCGGGGTGGCTGCCGAGCTTCTTGCGCAGGTTGCTGACGTGCATGTCCAGGCTGCGGTCGTAGAGGGTCAGCTTGCGGCCCAGCGCCAGTTGCGCCAGGGCCTGCTTGTCCAGCGGCTCGCCGGGCTGGCGCAGGAGCGCTTCGAGGATGCGGCTTTCGGAAAGGGTCAGGCTGATCTCCTGGCCGTCGATCTGCGCCACGCCGCGCGTCAGGTTCAGCGACAGGTCGCCCAGTTGCATCTGCGCGCTGGGTTGCGCCGGGTGGGTTCGCCGCAGCACGGCGCGCAGCCGTGCGGTGAGTTCGCGCGGGTCGCAGGGCTTGGCCAGGTAGTCGTCGGCGCCCAGTTCCAGACCGAGGATGCGGTCCAGCGGCTCGCCGCGGGCGGACAGCATCAGCACCGGCAGGTCGGGATGGTCGCCGCGCAGTTGCTTGAGCAGTTCCAGGCCGCTACCGTCCGGCAGCATCACGTCGAGCACCACGGCATCCGGTGTCTGCTCGGCGAGGGCGCGACGGGCCTGGGCGCCGTCGTGGCTGGCACGCACGGAGAAACCTTCCTGGACCAGCCAGGTACCGAGCAGCTCGCAGAGCTCCCGGTCATCGTCGATCAACAGCAGTTCGCTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004054","ARO_id":"41119","ARO_name":"Pseudomonas aeruginosa CpxR","ARO_description":"CpxR is directly involved in activation of expression of RND efflux pump MexAB-OprM in P. aeruginosa. CpxR is required to enhance mexAB-oprM expression and drug resistance, in the absence of repressor MexR.","ARO_category":{"35996":{"category_aro_accession":"0000079","category_aro_cvterm_id":"35996","category_aro_name":"clavulanate","category_aro_description":"Clavulanic acid is a beta-lactamase inhibitor (marketed by GlaxoSmithKline, formerly Beecham) combined with penicillin group antibiotics to overcome certain types of antibiotic resistance. It is used to overcome resistance in bacteria that secrete beta-lactamase, which otherwise inactivates most penicillins.","category_aro_class_name":"Adjuvant"},"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35979":{"category_aro_accession":"0000062","category_aro_cvterm_id":"35979","category_aro_name":"ceftriaxone","category_aro_description":"Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36468":{"category_aro_accession":"3000329","category_aro_cvterm_id":"36468","category_aro_name":"sulfamethoxazole","category_aro_description":"Sulfamethoxazole is a sulfonamide antibiotic usually taken with trimethoprim, a diaminopyrimidine antibiotic. Sulfamethoxazole inhibits dihydropteroate synthase, essential to tetrahydrofolic acid biosynthesis. This pathway generates compounds used in the synthesis of many amino acids and nucleotides.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36689":{"category_aro_accession":"3000550","category_aro_cvterm_id":"36689","category_aro_name":"aztreonam","category_aro_description":"Aztreonam was the first monobactam discovered, and is greatly effective against Gram-negative bacteria while inactive against Gram-positive bacteria. Artreonam is a poor substrate for beta-lactamases, and may even act as an inhibitor. In Gram-negative bacteria, Aztreonam interferes with filamentation, inhibiting cell division and leading to cell death.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"40362":{"category_aro_accession":"3003708","category_aro_cvterm_id":"40362","category_aro_name":"panipenem","category_aro_description":"Panipenem is a carbapenem antibacterial agent with a broad spectrum of in vitro activity covering a wide range of Gram-negative and Gram-positive aerobic and anaerobic bacterial.  It is used in combination with betamipron to inhibit panipenem uptake into the renal tubule and prevent nephrotoxicity.","category_aro_class_name":"Antibiotic"},"40957":{"category_aro_accession":"3004024","category_aro_cvterm_id":"40957","category_aro_name":"trimethoprim-sulfamethoxazole","category_aro_description":"An antibiotic cocktail containing the diaminopyrimidine antibiotic Trimethoprim and the sulfonamide antibiotic sulfamethoxazole (1 TMP:5 SMX).","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36421":{"category_aro_accession":"3000282","category_aro_cvterm_id":"36421","category_aro_name":"sulfonamide antibiotic","category_aro_description":"Sulfonamides are broad spectrum, synthetic antibiotics that contain the sulfonamide group. Sulfonamides inhibit dihydropteroate synthase, which catalyzes the conversion of p-aminobenzoic acid to dihydropteroic acid as part of the tetrahydrofolic acid biosynthetic pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor of many nucleotides and amino acids. Many sulfamides are taken with trimethoprim, an inhibitor of dihydrofolate reductase, also disturbing the trihydrofolic acid synthesis pathway.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2646":{"model_id":"2646","model_name":"tetB(60)","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1100"}},"model_sequences":{"sequence":{"3979":{"protein_sequence":{"accession":"ANZ79241.1","sequence":"MRTMKRLLSYLRYEKKGVLIGLFCLLLSTGATLTGPLVAKHIIDNVITPMGQAHDFKAGGLLLWVGIYVTVNLVGVAGAYLNRVYMKTLSNRIAKRIRDEVFEHVQTLPVSYFDHLPAGKVVSRITSDTESVRANFYVSGISTLFSTIVMLVGVYITIFLLNATLGLVLLFLVPVMILWQRTVATKQKKYYSENRELYSQLSGQLNESIQGAGIVQAFQQEEKIVAEYDATATSWVEVGRKELILESYFSWSLVGMLRNITHFGVIYYFSMQFIGGTLGISAGLLYAFIDYINRIYEPIQTFMNVVSGFQQSMAAGDRVFELMDTPSEESGEELFTFDEGCIEFKDVSFEYTAGVPVLKHLNFTVEPGQTVAFVGHTGSGKSSIMNLLFRFYDPTSGAIFIDGKNTRDFNRRSVRSEMGIVLQDPYLFTGTIASNVGLNNESIEPETIKEAIIKVGGGHLLTKSDKGLDYEVKEKGMDFSSGERQLISFARAIVFDPKILILDEATSHIDTETEEIIQNAINVVKEGRTTFMIAHRLSTIAHADQIFVLDKGEIVERGTHDELLQLQGQYAEMVALQKG"},"dna_sequence":{"accession":"KX000273.1","fmin":"0","fmax":"1740","strand":"+","sequence":"ATGAGAACGATGAAGCGATTATTAAGCTACCTCCGTTATGAGAAAAAAGGAGTTCTGATTGGACTCTTCTGCCTGTTACTCTCAACAGGAGCAACCTTAACAGGGCCACTCGTTGCGAAACACATTATCGATAATGTGATTACTCCGATGGGGCAGGCGCATGATTTCAAAGCAGGTGGCCTACTTTTATGGGTTGGTATTTACGTGACAGTGAACTTAGTGGGAGTTGCTGGGGCCTATTTAAACCGTGTATATATGAAGACTCTCTCAAACCGTATTGCAAAACGCATTCGTGACGAAGTGTTCGAGCATGTACAAACCTTGCCGGTATCGTACTTCGACCATTTACCAGCTGGGAAAGTGGTTTCTAGAATTACAAGTGATACAGAATCAGTGCGTGCAAACTTCTACGTGAGTGGGATTTCGACGCTTTTCAGTACGATTGTGATGTTGGTAGGTGTTTATATAACCATTTTCTTATTAAACGCAACGCTAGGACTCGTATTATTATTCCTAGTTCCTGTGATGATTCTATGGCAGAGAACCGTTGCTACGAAGCAGAAAAAATACTATTCCGAAAATCGTGAACTCTATAGTCAGTTGAGTGGACAATTAAACGAAAGCATTCAAGGAGCAGGCATCGTTCAAGCCTTCCAGCAAGAAGAAAAAATTGTTGCAGAATATGATGCCACGGCAACTTCTTGGGTAGAAGTTGGTCGTAAGGAATTAATTCTTGAGTCGTACTTCTCGTGGAGTCTTGTCGGCATGCTTCGAAACATTACTCATTTTGGAGTTATCTATTATTTCAGTATGCAGTTTATCGGTGGAACACTCGGGATTTCAGCAGGTCTTTTATATGCATTTATTGACTACATTAATCGTATATATGAGCCGATTCAAACTTTTATGAATGTCGTGTCTGGCTTCCAGCAATCAATGGCTGCTGGTGACCGTGTGTTTGAACTAATGGATACACCGAGCGAGGAATCGGGAGAAGAGCTCTTCACGTTTGATGAAGGATGTATCGAATTTAAAGATGTGAGTTTTGAGTACACAGCGGGAGTTCCTGTGTTGAAACACTTGAATTTCACGGTAGAACCAGGACAGACGGTTGCTTTTGTCGGACATACTGGTTCAGGGAAATCATCCATTATGAACTTACTGTTTCGCTTCTACGACCCAACGAGTGGTGCTATCTTCATCGATGGCAAAAACACACGCGACTTTAACAGACGTAGTGTTCGAAGCGAGATGGGAATCGTTCTTCAAGATCCGTACCTCTTTACAGGAACGATTGCTTCAAACGTAGGGCTCAACAATGAATCGATTGAGCCTGAGACGATAAAAGAGGCGATTATTAAAGTGGGTGGAGGACATCTACTTACGAAGAGTGACAAGGGCTTGGACTACGAGGTGAAAGAAAAAGGAATGGATTTCTCTTCAGGAGAACGCCAACTGATTTCATTTGCTCGTGCGATCGTCTTTGACCCGAAAATCTTAATTTTAGACGAGGCAACTTCGCATATCGATACCGAGACAGAAGAGATTATTCAGAATGCAATTAATGTCGTCAAAGAAGGGCGTACAACCTTTATGATTGCTCACCGACTTTCCACAATTGCTCATGCTGACCAAATTTTTGTGTTGGATAAAGGAGAAATTGTAGAACGTGGAACGCATGATGAATTGCTTCAACTGCAAGGTCAATATGCCGAAATGGTCGCCCTACAAAAAGGATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3004036","ARO_id":"41069","ARO_name":"tetB(60)","ARO_description":"tetB(60) is a subunit of tetAB(60), an ABC transporter that confers resistance to tetracycline and tigercycline identified by screening a human saliva metagenomic library in Escherichia coli, which is required for resistance.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2643":{"model_id":"2643","model_name":"tetA(46)","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1100"}},"model_sequences":{"sequence":{"3976":{"protein_sequence":{"accession":"AET10444.1","sequence":"MIRAIWEYIRERKWRYVKIAMVLILYDYTLLIPTQVIQRLVDHLSQQTLTQSNFVWDMVLLVGSAILNYLTAFYWQLRLFQSSVHFKATLQGQAFRKLVAMRRPFFEKFRSGDLLTRFTTDVDGMADMAGYGMMVLLFGGGLFAFIIPTMFFISWQLTLISFIPMIFLVVSTYFLSRKQEEYVEQNREAVAQLNDEVLESIEGIRVMRAYSRRDQQVKQFQKKTASLSKTGDKIASIQYSFGPLALLFIGFSTVLLLLFGGQSLASGQLSLGKLLALQLYLVFLIEPMWMMTDLILVYQTGQMSYKKLKEVIDETDDLEPDGTHYLEQIDSVEFKDYSFSYPGAERKSLSGIDWTIQRGQTVGIVGRTGAGKTTLVRQFLRQYPVGEGEFLVNQQPIVDYNRHSIEEKIGYVSQEHILFSKSIRENIALGKKGASQEDLMEAVAQAAFADDLERMSHGMDTLIGEKGVSVSGGQKQRISLARAFLRDADLLLLDDSLSAVDAKTEQAIIDTIQKERKDKTTIIVSHRLSAVHQADWIIVLDQGQIVEEGRASDLLAQEGWYYEQYQRQQKQEGE"},"dna_sequence":{"accession":"HQ652506.1","fmin":"373","fmax":"2098","strand":"+","sequence":"ATGATCAGAGCTATTTGGGAGTATATCAGGGAGCGCAAGTGGCGATATGTGAAGATCGCTATGGTACTGATTCTTTATGATTACACTTTATTGATCCCGACGCAAGTCATTCAGCGCTTAGTGGATCATTTGAGTCAGCAGACGCTGACGCAATCGAACTTTGTATGGGATATGGTCCTCTTGGTGGGATCAGCCATCCTCAATTACCTGACGGCTTTTTATTGGCAGTTGCGACTCTTTCAGTCGTCAGTCCATTTCAAGGCGACCCTTCAGGGACAAGCTTTTCGTAAGCTAGTAGCTATGCGGCGTCCCTTTTTTGAGAAATTTCGCTCAGGGGACCTCTTGACGCGCTTTACGACGGATGTGGATGGCATGGCCGATATGGCTGGTTACGGGATGATGGTGCTCCTGTTTGGCGGTGGCTTGTTTGCCTTTATTATTCCGACCATGTTTTTCATTTCTTGGCAATTAACCTTGATTTCCTTTATTCCCATGATCTTCCTTGTCGTCTCTACCTATTTTTTGAGTAGAAAGCAGGAGGAGTATGTTGAGCAAAACCGGGAAGCGGTTGCTCAGTTGAACGATGAAGTCTTGGAGTCCATCGAAGGGATCCGGGTCATGCGGGCCTATAGTAGACGGGATCAGCAGGTCAAACAGTTTCAGAAGAAAACGGCTAGTCTATCCAAAACAGGGGACAAAATTGCTTCTATCCAATATTCTTTTGGCCCCTTAGCCCTGTTGTTTATTGGATTCTCGACAGTCTTGCTCCTGCTATTTGGAGGACAGTCCCTAGCAAGTGGGCAGTTGAGCCTTGGCAAGCTATTGGCCTTGCAACTGTATTTGGTCTTTTTAATTGAGCCTATGTGGATGATGACGGACCTGATCTTGGTCTATCAGACAGGGCAAATGTCCTATAAAAAACTAAAAGAAGTGATTGATGAGACAGATGATCTTGAGCCAGATGGTACACACTATTTAGAGCAGATCGATTCGGTAGAGTTTAAGGATTATTCCTTCAGTTATCCTGGTGCTGAGCGAAAGAGCCTATCAGGCATTGATTGGACTATCCAGCGAGGACAGACGGTTGGAATTGTTGGTCGTACCGGTGCAGGAAAGACTACCCTGGTTCGACAATTCTTGCGGCAATACCCAGTTGGTGAGGGAGAATTCTTGGTCAACCAGCAACCGATCGTGGACTACAACCGACACTCGATTGAAGAAAAAATTGGTTATGTTTCCCAAGAACATATTTTATTTTCTAAGTCTATCCGTGAGAATATAGCGCTTGGTAAAAAAGGAGCCAGCCAAGAAGACTTGATGGAAGCAGTAGCCCAAGCTGCTTTTGCGGATGATCTCGAGCGGATGTCTCATGGAATGGACACCCTGATCGGTGAGAAAGGGGTCTCTGTATCAGGAGGTCAAAAACAGCGGATCTCTTTGGCGCGTGCCTTCTTAAGAGATGCAGATCTCTTGTTGTTAGATGATTCCCTTTCGGCAGTGGATGCGAAGACCGAACAGGCCATTATTGACACCATTCAAAAAGAACGAAAAGACAAGACGACCATCATTGTTTCTCATCGCTTGTCGGCTGTCCATCAGGCTGATTGGATCATCGTCTTGGATCAAGGACAGATTGTTGAAGAAGGCAGGGCTAGTGATTTATTAGCTCAAGAGGGCTGGTATTATGAACAATACCAACGGCAACAAAAACAGGAAGGAGAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41065","NCBI_taxonomy_name":"Streptococcus australis","NCBI_taxonomy_id":"113107"}}}},"ARO_accession":"3004032","ARO_id":"41064","ARO_name":"tetA(46)","ARO_description":"tetA(46) is a subunit of tetAB(46), a heterodimeric ABC transporter, that is required for conferring tetracycline resistance in Streptococcus australis isolated from the oral cavity.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2644":{"model_id":"2644","model_name":"tetB(46)","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1180"}},"model_sequences":{"sequence":{"3977":{"protein_sequence":{"accession":"AET10445.1","sequence":"MKVLKRLLSRITLYPTVFLAGFICLLLATIFSELSPFLLQKMIDGPLTALTHGGGQGDLLQMGGFYLLVLSLGQLISYMGNRILLHGSNQVTASLRDQAFQVMQGLPISYFDDKPAGKIATRIVNDTETLRTQFYNSCMILVIYLVRFLFILGILFYLSPMMGLLLCLVFPIFYGIQYLYKVMTDQPMKDFFDARSEVNTQVNELLHGASMIQLYHQEPGVVEEFEATTQKMLGANDRILLADSIASWTLTELLKFLVIAGILTIAGISFLQGNIGVTAGFLFININYVINLFDLMANLSRQFPNIRRSLETGSRVLAFLDQPLEADGALELKIEKAEVVFDDVQFAYEEGKPVLKDISIQAHPGQTLALVGHTGSGKSSIMNLLYRFYDPQEGEIRIDGQNIRHFSRESLRSHMGIVLQDPYLFTGTIASNVAMSQEHIDRNAVKDALKKVGAWPFVERLEKGIDHPVVEKGSAFSSGERQLISFARTLYMNPQILILDEATSHIDTETEEIIQKAMAVLQKGRTTFIIAHRLSTIQDADQILVLSEGRIVERGQHADLVAHGGIYAQMQAIQQTVE"},"dna_sequence":{"accession":"HQ652506.1","fmin":"2099","fmax":"3836","strand":"+","sequence":"ATGAAAGTATTGAAACGATTATTATCTAGGATCACGCTTTATCCAACTGTCTTTCTTGCTGGCTTCATTTGCCTCTTACTAGCCACCATTTTTTCTGAATTGTCTCCCTTTCTTCTCCAAAAGATGATCGATGGGCCTTTGACTGCATTGACCCACGGTGGAGGACAAGGGGACTTGCTTCAGATGGGAGGATTCTATCTCTTGGTCTTGAGCCTGGGGCAGCTGATTAGCTACATGGGCAATCGGATCTTGCTACATGGAAGTAATCAAGTAACCGCTAGTCTGAGAGACCAAGCCTTTCAAGTCATGCAAGGGCTGCCTATTTCTTATTTTGATGATAAGCCGGCTGGGAAGATCGCGACAAGAATTGTCAATGATACGGAGACCTTGAGGACCCAGTTTTATAACTCTTGTATGATTTTAGTCATCTATTTGGTACGCTTTCTCTTTATCCTAGGGATTCTCTTTTACCTGAGTCCTATGATGGGCCTTCTCTTGTGTTTGGTCTTTCCGATTTTCTATGGGATCCAGTATCTCTACAAGGTCATGACGGACCAGCCTATGAAGGATTTCTTTGATGCGCGAAGCGAGGTCAATACCCAGGTCAATGAACTCTTGCACGGTGCTAGTATGATTCAGCTCTATCATCAAGAGCCTGGTGTGGTGGAGGAGTTTGAAGCCACTACCCAGAAGATGTTAGGAGCAAATGATCGAATCCTCTTAGCCGATTCTATCGCTTCTTGGACCTTGACGGAATTGCTCAAGTTTTTAGTGATTGCAGGCATTTTGACTATCGCTGGGATTTCTTTCCTACAGGGTAATATCGGTGTGACGGCTGGTTTCTTATTTATCAATATTAACTATGTGATTAATCTATTTGATCTCATGGCCAATCTTAGTCGTCAATTCCCAAATATTCGGCGATCCTTAGAAACGGGGAGCCGCGTCCTTGCCTTCTTAGACCAACCGTTAGAGGCCGATGGTGCATTGGAACTGAAGATAGAAAAGGCAGAGGTCGTGTTTGACGACGTTCAATTTGCCTATGAAGAAGGTAAGCCAGTTCTGAAGGATATTTCCATCCAAGCCCATCCAGGTCAAACCCTTGCCTTGGTTGGCCATACTGGTTCGGGTAAATCCTCCATTATGAACTTGCTCTATCGTTTCTATGATCCGCAGGAGGGAGAAATTCGGATCGACGGCCAGAATATTCGCCATTTCTCTAGAGAGAGTCTTCGCTCCCACATGGGCATTGTTCTACAAGATCCTTATCTATTTACAGGAACCATTGCTAGTAATGTGGCCATGAGTCAGGAACACATTGATCGGAATGCGGTCAAAGATGCCTTGAAAAAAGTCGGAGCATGGCCCTTTGTAGAGCGTCTTGAAAAGGGAATCGACCATCCAGTTGTAGAAAAAGGATCGGCCTTTTCAAGTGGCGAACGCCAGTTGATTTCCTTTGCGAGGACGCTCTATATGAATCCGCAAATTCTGATTTTGGATGAGGCAACCTCTCACATCGATACGGAAACAGAAGAAATCATCCAGAAAGCTATGGCTGTCCTGCAAAAGGGCCGGACCACCTTTATCATTGCCCATCGCTTGTCGACTATCCAAGATGCGGATCAGATCTTGGTTCTATCAGAAGGGCGCATTGTCGAACGTGGGCAACATGCAGACTTAGTTGCCCATGGTGGCATCTACGCCCAGATGCAAGCTATCCAACAGACGGTTGAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41065","NCBI_taxonomy_name":"Streptococcus australis","NCBI_taxonomy_id":"113107"}}}},"ARO_accession":"3004033","ARO_id":"41066","ARO_name":"tetB(46)","ARO_description":"tetB(46) is a subunit of tetAB(46), a heterodimeric ABC transporter, that is required for conferring tetracycline resistance in Streptococcus australis isolated from the oral cavity.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2645":{"model_id":"2645","model_name":"tetA(60)","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1100"}},"model_sequences":{"sequence":{"3978":{"protein_sequence":{"accession":"ANZ79240.1","sequence":"MNDLLKVIINFIKKHPMRYLVSFILMIGSSIAAVYPARIIGQVVDKIVASELNAEWLGTQLVILVGIILVAYITESIWTYFIFIGYYEIQKELRVKLLRNNLRKKIPFYAHFRTGEIITRSSEDVTTIGDMMGFGMFALMNSTLLMSVSIYMMVTTISLPLTIAAILPLPILSYLVYKWGFDLEEEYNKAQNAVSQLNNEVLEMIDGTYVIRAYGQEDAMMDEFRAKTKKAMKQNIIVTEIESRFIPLAQLFMMISFTIALFYGGYLVSTGAILVGDVIAFQVYMGAIMWPMFMIGDIITNYKRGKVATERINEVLKHDDEIERGGTKTLETIESIEFKDFHFMYPGEEAPLLKEINLTLRKGETLGIVGKTGSGKTTLLMQLLHQFPYRGEKLLINGEPLIDYDTQSVAGHLAYVPQEHTLFSRTIRENMLFGKEDATDDEIWEALTLASFEGDVKRMPDELDTMVGEKGVSLSGGQKQRLSIARAFLRNRECLILDDALSAVDAKTEREIISHLQQERGGCMNIISAHRLSAIRHADEIIVMNEGRISERGTHEELLEQRGWYYEQYLTQEMEEEIE"},"dna_sequence":{"accession":"KX000272.1","fmin":"0","fmax":"1740","strand":"+","sequence":"ATGAACGATTTATTAAAAGTCATTATTAATTTTATAAAGAAACATCCGATGCGCTACCTTGTTAGTTTTATTTTGATGATCGGAAGTAGTATTGCGGCGGTGTACCCAGCGCGTATTATCGGACAAGTTGTTGATAAAATCGTAGCGAGCGAACTGAATGCCGAGTGGCTTGGGACACAACTCGTGATTTTAGTCGGGATTATTCTTGTGGCGTATATTACGGAGAGTATTTGGACATATTTTATTTTTATTGGGTATTATGAAATTCAAAAAGAATTACGTGTGAAGTTACTACGTAATAATTTACGGAAGAAAATTCCGTTTTATGCGCATTTTAGAACGGGCGAAATTATTACGCGTAGCAGTGAAGACGTTACAACGATTGGCGATATGATGGGGTTTGGGATGTTTGCATTGATGAACTCTACATTGCTGATGAGCGTATCGATTTATATGATGGTCACAACGATTTCATTGCCACTGACCATCGCAGCGATTTTGCCACTGCCAATCCTTTCGTATCTTGTATATAAATGGGGATTCGATTTAGAAGAAGAGTACAACAAGGCGCAAAATGCAGTTTCACAATTAAATAATGAAGTGCTTGAGATGATTGACGGGACGTATGTGATTCGTGCTTACGGGCAAGAAGATGCGATGATGGATGAGTTCAGGGCGAAAACGAAAAAGGCCATGAAACAAAATATTATCGTGACTGAAATTGAATCGCGCTTTATTCCACTGGCGCAATTATTTATGATGATTAGCTTTACCATTGCCCTTTTCTACGGTGGGTATCTAGTATCGACTGGGGCTATTCTAGTCGGGGATGTCATTGCCTTCCAAGTCTATATGGGGGCGATTATGTGGCCGATGTTTATGATTGGCGATATTATTACGAACTATAAACGCGGAAAAGTGGCGACGGAGCGTATTAATGAAGTGTTGAAACATGACGATGAAATTGAACGCGGCGGTACAAAAACGCTCGAGACGATTGAATCCATTGAGTTTAAGGACTTCCATTTTATGTATCCAGGCGAAGAGGCACCATTATTAAAAGAGATTAACCTTACGTTACGTAAAGGCGAGACGCTTGGAATCGTTGGAAAAACGGGTTCTGGGAAGACGACGCTCTTGATGCAATTATTACATCAATTTCCGTACCGAGGAGAGAAGCTGCTCATTAACGGAGAGCCATTGATTGATTACGACACTCAATCGGTGGCAGGGCATCTAGCCTATGTGCCACAAGAACACACCCTTTTCTCACGCACGATTCGCGAGAATATGTTATTCGGAAAAGAGGATGCAACGGATGATGAAATTTGGGAAGCGTTGACGCTAGCCTCTTTTGAAGGAGACGTGAAACGAATGCCAGACGAGCTCGATACGATGGTCGGAGAAAAAGGGGTATCGCTCAGTGGAGGTCAAAAACAACGCTTATCGATTGCTCGTGCTTTCTTACGCAACCGTGAATGCTTAATTTTGGATGATGCGTTATCTGCAGTTGATGCGAAAACGGAAAGGGAAATTATCTCGCACTTGCAACAAGAACGCGGAGGTTGTATGAATATCATTTCTGCGCACAGACTTTCTGCAATTCGTCATGCGGATGAAATTATTGTGATGAATGAAGGACGTATTAGTGAGAGGGGTACCCACGAGGAGCTGCTCGAACAACGAGGATGGTACTATGAACAGTATCTCACACAAGAAATGGAGGAGGAAATCGAATGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3004035","ARO_id":"41068","ARO_name":"tetA(60)","ARO_description":"tetA(60) is a subunit of tetAB(60), an ABC transporter that confers resistance to tetracycline and tigercycline identified by screening a human saliva metagenomic library in Escherichia coli, which is required for resistance.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"522":{"model_id":"522","model_name":"floR","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"101":{"protein_sequence":{"accession":"AAG16656.1","sequence":"MTTTRPAWAYTLPAALLLMAPFDILASLAMDIYLPVVPAMPGILNTTPAMIQLTLSLYMVMLGVGQVIFGPLSDRIGRRPILLAGATAFVIASLGAAWSSTAPAFVAFRLLQAVGASAMLVATFATVRDVYANRPEGVVIYGLFSSVLAFVPALGPIAGALIGEFLGWQAIFITLAILAMLALLNAGFRWHETRPLDQVKTRRSVLPIFASPAFWVYTVGFSAGMGTFFVFFSTAPRVLIGQAEYSEIGFSFAFATVALVMIVTTRFAKSFVARWGIAGCVARGMALLVCGAVLLGIGELYGSPSFLTFILPMWVVAVGIVFTVSVTANGALAEFDDIAGSAVAFYFCVQSLIVSIVGTLAVALLNGDTAWPVICYATAMAVLVSLGLVLLRLRGAATEKSPVV"},"dna_sequence":{"accession":"AF231986","fmin":"3307","fmax":"4522","strand":"+","sequence":"ATGACCACCACACGCCCCGCGTGGGCCTATACGCTGCCGGCAGCACTGCTGCTGATGGCTCCTTTCGACATCCTCGCTTCACTGGCGATGGATATTTATCTCCCTGTCGTTCCAGCGATGCCCGGCATCCTGAACACGACGCCCGCTATGATCCAACTCACGTTGAGCCTCTATATGGTGATGCTCGGCGTGGGCCAGGTGATTTTTGGTCCGCTCTCAGACAGAATCGGGCGACGGCCAATTCTACTTGCGGGCGCAACGGCTTTCGTCATTGCGTCTCTGGGAGCAGCTTGGTCTTCAACTGCACCGGCCTTTGTCGCTTTCCGTCTACTTCAAGCAGTGGGCGCGTCGGCCATGCTGGTGGCGACGTTCGCGACGGTTCGCGACGTTTATGCCAACCGTCCTGAGGGTGTCGTCATCTACGGCCTTTTCAGTTCGGTGCTGGCGTTCGTGCCTGCGCTCGGCCCTATCGCCGGAGCATTGATCGGCGAGTTCTTGGGATGGCAGGCGATATTCATTACTTTGGCTATACTGGCGATGCTCGCACTCCTAAATGCGGGTTTCAGGTGGCACGAAACCCGCCCTCTGGATCAAGTCAAGACGCGCCGATCTGTCTTGCCGATCTTCGCGAGTCCGGCTTTTTGGGTTTACACTGTCGGCTTTAGCGCCGGTATGGGCACCTTCTTCGTCTTCTTCTCGACGGCTCCCCGTGTGCTCATAGGCCAAGCGGAATATTCCGAGATCGGATTCAGCTTTGCCTTCGCCACTGTCGCGCTTGTAATGATCGTGACAACCCGTTTCGCGAAGTCCTTTGTCGCCAGATGGGGCATCGCAGGATGCGTGGCGCGTGGGATGGCGTTGCTTGTTTGCGGAGCGGTCCTGTTGGGGATCGGCGAACTTTACGGCTCGCCGTCATTCCTCACCTTCATCCTACCGATGTGGGTTGTCGCGGTCGGTATTGTCTTCACGGTGTCCGTTACCGCGAACGGCGCTTTGGCAGAGTTCGACGACATCGCGGGATCAGCGGTCGCGTTCTACTTCTGCGTTCAAAGCCTGATAGTCAGCATTGTCGGGACATTGGCGGTGGCACTTTTAAACGGTGACACAGCGTGGCCCGTGATCTGTTACGCCACGGCGATGGCGGTACTGGTTTCGTTGGGGCTGGTGCTCCTTCGGCTCCGTGGGGCTGCCACCGAGAAGTCGCCAGTCGTCTAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002705","ARO_id":"39139","ARO_name":"floR","ARO_description":"floR is a plasmid or chromosome-encoded chloramphenicol exporter that is found in Bordetella bronchiseptica, Escherichia coli, Klebsiella pneumoniae,Salmonella typhimurium DT104 and Vibrio cholerae","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36600":{"category_aro_accession":"3000461","category_aro_cvterm_id":"36600","category_aro_name":"florfenicol","category_aro_description":"Florfenicol is a fluorine derivative of chloramphenicol, where the nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3) and the hydroxyl group (-OH), by a fluorine group (-F). The action mechanism is the same as chloramphenicol's, where the antibiotic binds to the 23S RNA of the 50S subunit of bacterial ribosomes to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2713":{"model_id":"2713","model_name":"MexXY","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)","model_param":{"41141":{"param_type":"efflux pump components","param_description":"This detection model parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305.","param_type_id":"41141","param_value":{"7590":"2223,334,1786"}}},"ARO_accession":"3003032","ARO_id":"39466","ARO_name":"MexXY-OprM","ARO_description":"MexXY-OprM is a multidrug efflux protein expressed in Pseudomonas aeruginosa. MexY is the membrane fusion protein; MexX is the RND-type membrane protein; and OprM is the outer membrane channel. MexXY-OprM is associated with resistance to acriflavine, erythromycin, norfloxacin and ofloxacin. The efflux system may also be involved in acquisition of higher resistance, in particular when bacteria are repeatedly exposed to subinhibitory doses of AGs.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavin","category_aro_description":"Acriflavin is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36193":{"category_aro_accession":"3000054","category_aro_cvterm_id":"36193","category_aro_name":"acridine dye","category_aro_description":"Acridine dyes are cell permeable, basic molecules with an acridine chromophore. These compounds intercalate DNA. The image shown represents the core structure of the acridine family, with specific dyes containing varying substituents.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2716":{"model_id":"2716","model_name":"OpmB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"850"}},"model_sequences":{"sequence":{"4041":{"protein_sequence":{"accession":"NP_251215.1","sequence":"MKHTPSLLALALVAALGGCAIGPDYQRPDLAVPAEFKEAEGWRRAEPRDVFQRGAWWELYGDQTLNDLQMHLERSNQTLAQSVAQFRQAEALVRGARAAFFPSITGNVGKTRSGQGGGDSTVLLPGGSTVSSGGSGAISTSYSTNLSVSWEVDLWGKLRRQLEANQASLHASAADLAAVRLSQQSQLAQNYLQLRVMDEQIRLLNDTVTAYERSLKVAENKYRAGIVTRADVAQARTQLKSTQAQAIDLKYQRAQLEHAIAVLVGLPPAQFNLPPVASVPKLPDLPAVVPSQLLERRPDIASAERKVISANAQIGVAKAAYFPDLTLSAAGGYRSGSLSNWISTPNRFWSIGPQFAMTLFDGGLIGSQVDQAEATYDQTVATYRQTVLDGFREVEDYLVQLSVLDEESGVQREALESAREALRLAENQYKAGTVDYTDVVTNQATALSNERTVLTLLGSRLTASVQLIAAMGGGWDSADIERTDERLGRVEEGLPPSP"},"dna_sequence":{"accession":"NC_002516.2","fmin":"2846282","fmax":"2847779","strand":"-","sequence":"TCAGGGCGAAGGCGGCAGGCCCTCTTCGACCCGGCCGAGCCGCTCGTCGGTCCGCTCGATGTCGGCGCTGTCCCAGCCGCCGCCCATTGCCGCGATCAACTGGACGCTGGCGGTCAGGCGGCTGCCGAGCAGGGTCAGCACGGTGCGTTCGTTGCTCAGCGCGGTGGCCTGGTTGGTGACCACGTCGGTGTAGTCGACGGTGCCGGCCTTGTACTGGTTCTCGGCCAGGCGCAGTGCCTCGCGGGCCGACTCCAGGGCTTCGCGCTGCACCCCGCTCTCCTCGTCGAGGACGCTCAATTGCACCAGGTAGTCCTCCACCTCGCGGAAACCGTCGAGCACGGTCTGCCGGTAGGTCGCCACGGTCTGGTCGTAGGTAGCCTCGGCCTGGTCCACCTGGGAGCCGATCAGGCCGCCGTCAAACAGGGTCATGGCGAACTGCGGGCCGATCGACCAGAAGCGGTTCGGCGTGCTGATCCAGTTGCTCAGGCTGCCGCTGCGGTAGCCGCCGGCGGCGCTCAGGGTGAGGTCGGGGAAATAGGCGGCCTTGGCCACGCCGATCTGGGCGTTGGCGGAAATCACCTTGCGTTCCGCCGAGGCGATGTCCGGCCGTCGTTCGAGCAATTGCGACGGCACCACTGCCGGCAGGTCCGGCAGCTTCGGCACGCTCGCCACCGGCGGCAGGTTGAATTGCGCCGGCGGCAGGCCGACCAGCACGGCGATGGCGTGCTCCAGCTGGGCACGCTGGTACTTCAGGTCGATGGCCTGGGCCTGGGTGCTTTTCAACTGGGTGCGGGCCTGGGCCACGTCGGCCCTGGTGACGATGCCGGCGCGGTATTTGTTCTCGGCCACCTTCAGCGAACGCTCGTAGGCCGTCACCGTGTCGTTGAGCAGGCGGATCTGTTCGTCCATCACCCGCAGTTGCAGGTAGTTCTGCGCCAGTTGCGACTGCTGGCTGAGGCGCACCGCGGCGAGGTCGGCGGCGCTGGCATGCAGGCTCGCCTGGTTGGCCTCCAGTTGCCGGCGCAGCTTGCCCCAGAGGTCGACCTCCCAGCTGACACTGAGGTTGGTCGAGTAGCTGGTGCTGATCGCGCCAGAGCCGCCGCTGCTCACCGTCGAGCCTCCCGGCAGCAACACGGTGCTGTCGCCGCCGCCCTGGCCGCTGCGGGTCTTGCCCACGTTGCCGGTGATCGACGGGAAGAACGCCGCCCGCGCGCCGCGCACCAGCGCCTCGGCCTGGCGGAACTGCGCCACCGACTGGGCCAGGGTCTGGTTGGAACGTTCCAGGTGCATCTGCAGGTCGTTCAGGGTCTGGTCGCCGTACAGCTCCCACCAGGCGCCGCGCTGGAACACGTCGCGCGGCTCGGCGCGGCGCCAGCCTTCGGCTTCCTTGAATTCGGCGGGCACCGCCAGGTCCGGTCGCTGGTAGTCGGGGCCGATGGCGCAGCCGCCGAGGGCGGCGACCAGGGCCAGGGCGAGCAACGAGGGGGTGTGTTTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3004072","ARO_id":"41154","ARO_name":"OpmB","ARO_description":"OpmB is an outer membrane efflux protein in Pseudomonas aeruginosa that shows functional cooperation with MuxABC, to form the efflux pump system MuxABC-OpmB.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36689":{"category_aro_accession":"3000550","category_aro_cvterm_id":"36689","category_aro_name":"aztreonam","category_aro_description":"Aztreonam was the first monobactam discovered, and is greatly effective against Gram-negative bacteria while inactive against Gram-positive bacteria. Artreonam is a poor substrate for beta-lactamases, and may even act as an inhibitor. In Gram-negative bacteria, Aztreonam interferes with filamentation, inhibiting cell division and leading to cell death.","category_aro_class_name":"Antibiotic"},"37626":{"category_aro_accession":"3001227","category_aro_cvterm_id":"37626","category_aro_name":"kitasamycin","category_aro_description":"Kitasamycin is a macrolide antibiotic and is produced by Streptoverticillium kitasatoense. The drug has antimicrobial activity against a wide spectrum of pathogens.","category_aro_class_name":"Antibiotic"},"40353":{"category_aro_accession":"3003701","category_aro_cvterm_id":"40353","category_aro_name":"rokitamycin","category_aro_description":"Rokitamycin is a macrolide antibiotic. Synthesized from strains of Streptomyces kitasatoensis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"347":{"model_id":"347","model_name":"SFH-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1878":{"protein_sequence":{"accession":"AAF09244.1","sequence":"MASEKNLTLTHFKGPLYIVEDKEYVQENSMVYIGTDGITIIGATWTPETAETLYKEIRKVSPLPINEVINTNYHTDRAGGNAYWKTLGAKIVATQMTYDLQKSQWGSIVNFTRQGNNKYPNLEKSLPDTVFPGDFNLQNGSIRAMYLGEAHTKDGIFVYFPAERVLYGNCILKENLGNMSFANRTEYPKTLEKLKGLIEQGELKVDSIIAGHDTPIHDVGLIDHYLTLLEKAPK"},"dna_sequence":{"accession":"AF197943","fmin":"0","fmax":"705","strand":"+","sequence":"ATGGCTTCTGAAAAAAACTTAACGCTTACCCATTTCAAAGGTCCGCTCTATATTGTAGAAGATAAGGAGTATGTACAGGAAAACTCAATGGTTTACATCGGCACCGATGGTATAACCATCATTGGTGCGACATGGACTCCTGAGACTGCTGAAACTCTTTATAAAGAAATACGGAAGGTCAGCCCCCTCCCCATAAACGAAGTCATTAATACCAATTACCATACTGATCGAGCTGGTGGAAATGCTTATTGGAAAACGCTTGGGGCAAAGATCGTGGCCACACAGATGACCTACGACCTGCAGAAAAGCCAGTGGGGAAGTATTGTAAACTTCACTCGACAAGGTAATAATAAATACCCAAATCTGGAGAAAAGTCTGCCGGATACTGTTTTTCCTGGAGACTTTAACTTGCAAAATGGCAGCATCCGCGCCATGTATTTAGGCGAAGCACATACTAAGGATGGTATCTTTGTGTACTTCCCAGCAGAGCGCGTTTTGTATGGGAACTGCATTCTCAAAGAAAATCTGGGTAATATGAGTTTTGCCAACAGAACTGAGTACCCAAAAACCTTGGAAAAACTTAAAGGACTTATCGAGCAGGGGGAGCTTAAAGTCGACTCGATCATTGCAGGGCATGATACTCCGATACATGACGTAGGCCTGATCGATCACTACCTTACACTGCTTGAGAAGGCGCCTAAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39675","NCBI_taxonomy_name":"Serratia fonticola","NCBI_taxonomy_id":"47917"}}}},"ARO_accession":"3000849","ARO_id":"37229","ARO_name":"SFH-1","ARO_description":"SFH-1 confers resistance to carbapenems in Serratia fonticola.","ARO_category":{"41374":{"category_aro_accession":"3004210","category_aro_cvterm_id":"41374","category_aro_name":"SFH beta-lactamase","category_aro_description":"This type of Subclass B2 beta-lactamases was first identified from a Serratia fonticola environmental isolate.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2654":{"model_id":"2654","model_name":"adeL","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"650"}},"model_sequences":{"sequence":{"3988":{"protein_sequence":{"accession":"ALH22601.1","sequence":"MRVFNKVVETNSFSLAADSLGLPRASVTTTIQALEKHLQVRLLNRTTRKISLTPDGAVYYDRTARILADVADIESSFHDAERGPRGQLRIDVPVSIGRLILIPRLRDFHARYPDIDLVIGLNDRPVDLVGEAVDCAIRVGELKDSSLIARRIGTFQCATAASPIYLEKYGEPTSIEDLQKNHKAIHFFSSRTGRNFDWDFVVDDLIKSVSVRGRVSVNDGDAYIDLALQGFGIIQGPRYMLTNHLESGLLKEVLPQWTPAPMPISAVYLQNRHLSLKVKVFVDWVAELFAGCPLLGGTALPFDQKCEFACDKETGHEYTIRTLVEQHNIAEAYTLKT"},"dna_sequence":{"accession":"KR297239.1","fmin":"414","fmax":"1428","strand":"-","sequence":"TTAAGTTTTGAGCGTATAAGCTTCAGCAATATTATGCTGCTCGACCAAAGTACGAATTGTATATTCATGACCAGTTTCTTTATCACAGGCAAATTCACATTTCTGGTCGAAAGGTAAAGCTGTACCGCCAAGTAATGGACAGCCTGCAAAAAGTTCAGCGACCCAATCTACAAACACTTTTACTTTAAGCGATAAATGACGATTTTGAAGATAAACTGCTGAAATCGGCATCGGTGCTGGCGTCCACTGAGGCAATACCTCTTTTAACAAACCTGATTCTAAATGGTTGGTGAGCATATAACGTGGGCCTTGAATTATACCAAAACCTTGCAAAGCCAAGTCGATATAAGCATCACCGTCATTTACCGAAACACGTCCACGTACTGACACACTTTTAATTAAATCATCAACCACAAAGTCCCAATCGAAGTTGCGTCCGGTACGGCTTGAAAAGAAGTGAATCGCTTTATGATTTTTTTGCAAATCTTCAATTGAGGTAGGTTCGCCATATTTTTCTAAATAAATCGGTGAAGCAGCTGTTGCACACTGGAAAGTTCCGATACGACGCGCAATTAAGCTTGAATCTTTTAATTCACCCACCCGAATTGCACAATCAACCGCTTCTCCAACCAAGTCTACAGGTCGGTCGTTCAGACCAATCACTAAATCAATATCAGGATAGCGTGCATGAAAATCACGGAGCCTTGGAATTAAAATTAAACGTCCAATCGATACAGGCACATCAATACGAAGCTGACCTCTTGGCCCCCGCTCTGCATCATGAAAAGAAGATTCAATATCGGCAACATCCGCTAAAATACGGGCTGTCCGATCATAATATACGGCGCCATCCGGTGTGAGACTAATTTTTCGTGTTGTCCGATTAAGCAATCGAACTTGTAAATGCTTCTCTAAAGCCTGAATGGTTGTAGTCACAGAAGCACGCGGTAAACCCAAACTATCAGCTGCTAAACTGAAACTATTTGTTTCAACAACTTTGTTGAATACTCTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3000620","ARO_id":"36962","ARO_name":"adeL","ARO_description":"AdeL is a regulator of AdeFGH in Acinetobacter baumannii. AdeL mutations are associated with AdeFGH overexpression and multidrug resistance.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1745":{"model_id":"1745","model_name":"KPC-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1032":{"protein_sequence":{"accession":"AAK70220.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"AY034847","fmin":"5","fmax":"887","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002312","ARO_id":"38712","ARO_name":"KPC-2","ARO_description":"KPC-2 is a beta-lactamase found in Klebsiella pneumoniae and Pseudomonas aeruginosa.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2655":{"model_id":"2655","model_name":"Pseudomonas aeruginosa emrE","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"170"}},"model_sequences":{"sequence":{"4411":{"protein_sequence":{"accession":"NP_253677.1","sequence":"MTNYLYLAIAIAAEVVATTSLKAVAGFSKPLPLLLVVGGYVLAFSMLVLVMRTLPVGVVYAIWSGLGIVLVSLVAMFVYGQRLDPAALLGIGLIIAGVLVIQLFSRASGH"},"dna_sequence":{"accession":"NC_002516.2","fmin":"5606102","fmax":"5606435","strand":"+","sequence":"ATGACCAACTATCTCTACCTCGCCATCGCCATCGCCGCCGAAGTGGTCGCCACCACCTCGCTGAAAGCCGTCGCCGGATTCAGCAAGCCACTGCCGCTGCTGCTGGTGGTGGGCGGCTACGTGCTCGCCTTCAGCATGCTCGTGCTGGTCATGCGCACCCTGCCGGTCGGCGTGGTCTACGCCATCTGGTCCGGACTCGGCATCGTCCTGGTCAGCCTGGTGGCGATGTTCGTCTACGGCCAGCGCCTGGACCCCGCCGCCCTCCTCGGCATCGGCCTGATCATCGCCGGCGTGCTGGTGATCCAGTTGTTCTCCCGCGCTTCGGGGCACTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3004038","ARO_id":"41082","ARO_name":"Pseudomonas aeruginosa emrE","ARO_description":"EmrE is a small multidrug transporter that functions as a homodimer and that couples the efflux of small polyaromatic cations from the cell with the import of protons down an electrochemical gradient. Confers resistance to tetraphenylphosphonium, methyl viologen, gentamicin, kanamycin, and neomycin.","ARO_category":{"36004":{"category_aro_accession":"0010003","category_aro_cvterm_id":"36004","category_aro_name":"small multidrug resistance (SMR) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Small multidrug resistance (SMR) proteins are a relatively small family of transporters, restricted to prokaryotic cells. They are also the smallest multidrug transporters, with only four transmembrane alpha-helices and no significant extramembrane domain.","category_aro_class_name":"AMR Gene Family"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2656":{"model_id":"2656","model_name":"Escherichia coli emrE","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"190"}},"model_sequences":{"sequence":{"4413":{"protein_sequence":{"accession":"CAA77936.1","sequence":"MNPYIYLGGAILAEVIGTTLMKFSEGFTRLWPSVGTIICYCASFWLLAQTLAYIPTGIAYAIWSGVGIVLISLLSWGFFGQRLDLPAIIGMMLICAGVLIINLLSRSTPH"},"dna_sequence":{"accession":"Z11877.1","fmin":"485","fmax":"818","strand":"+","sequence":"ATGAACCCTTATATTTATCTTGGTGGTGCAATACTTGCAGAGGTCATTGGTACAACCTTAATGAAGTTTTCAGAAGGTTTTACACGGTTATGGCCATCTGTTGGTACAATTATTTGTTATTGTGCATCATTCTGGTTATTAGCTCAGACGCTGGCTTATATTCCTACAGGGATTGCTTATGCTATCTGGTCAGGAGTCGGTATTGTCCTGATTAGCTTACTGTCATGGGGATTTTTCGGCCAACGGCTGGACCTGCCAGCCATTATAGGCATGATGTTGATTTGTGCCGGTGTGTTGATTATTAATTTATTGTCACGAAGCACACCACATTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004039","ARO_id":"41083","ARO_name":"Escherichia coli emrE","ARO_description":"Member of the small MDR (multidrug resistance) family of transporters; in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin; proton-dependent secondary transporter which exchanges protons for compound translocation","ARO_category":{"36004":{"category_aro_accession":"0010003","category_aro_cvterm_id":"36004","category_aro_name":"small multidrug resistance (SMR) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Small multidrug resistance (SMR) proteins are a relatively small family of transporters, restricted to prokaryotic cells. They are also the smallest multidrug transporters, with only four transmembrane alpha-helices and no significant extramembrane domain.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2659":{"model_id":"2659","model_name":"Klebsiella pneumoniae acrA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"770"}},"model_sequences":{"sequence":{"3994":{"protein_sequence":{"accession":"CAC41008.1","sequence":"MNKNRGLTPLAVVLMLSGSLALTGCDDKPAQQGAQHMPEVGIVTLKSAPLQITTELPGRTSAYRIAEVRPQVSGIILKRNFVEGSDIQAGVFLYQIDPATYQGSYDSAKGDLAKAQAAANMDQLTVKRYQKLLGTQYISQQDYDPAVATAQQNNAAVVAAKTAVETARINLAYTQKSPLRSAAGSGKSPVTEGALVQNGQTTALATVQQVDPIYVDVTQSSNDFLRLKQELADARLKQENGKAKVELVTNDGLKYPQSGTLEFSDVTVDQTTGSITLRAIFPNPDHTLLPGMFVRARLEEGINPDALLVPQQGVTRTPRGDASVMVVGEGDKVEVRQVTASQAIGDKWLVTDGLKSGDRVIVTGLQKIKPGVQVKAQEVASDDKQQAAGNAPSEQTKS"},"dna_sequence":{"accession":"AJ318073.1","fmin":"793","fmax":"1990","strand":"+","sequence":"ATGAACAAAAACAGAGGGTTAACGCCTCTGGCGGTCGTTCTGATGCTCTCAGGCAGCTTAGCGCTAACAGGATGTGACGATAAACCGGCTCAACAGGGAGCCCAGCACATGCCGGAAGTCGGTATTGTGACGCTCAAATCCGCACCTCTACAAATAACCACCGAACTGCCAGGCCGCACCAGCGCCTATCGCATTGCGGAAGTCCGTCCTCAGGTCAGTGGCATTATTTTAAAACGTAACTTCGTGGAAGGTAGCGATATCCAGGCCGGCGTCTTCCTGTATCAGATCGATCCAGCCACCTATCAAGGCAGCTATGACAGCGCCAAAGGCGACCTGGCAAAAGCCCAGGCGGCGGCAAACATGGATCAACTGACGGTCAAGCGTTATCAGAAACTGTTGGGCACCCAATATATTAGTCAACAAGACTACGATCCCGCCGTTGCGACGGCGCAACAAAACAATGCCGCCGTGGTCGCGGCGAAAACTGCCGTTGAAACCGCGCGCATCAATTTGGCCTACACCCAAAAGTCACCTCTCCGATCAGCGGCCGGATCGGGTAAATCCCCCGTGACCGAAGGGGCGTTGGTACAGAATGGTCAAACGACCGCCTTGGCAACCGTTCAGCAAGTGGATCCGATCTATGTTGACGTCACCCAGTCGAGCAATGATTTCCTGCGCCTGAAGCAGGAGCTAGCCGACGCCCGCCTGAAACAGGAAAACGGCAAAGCGAAAGTGGAGCTGGTGACTAATGACGGGCTTAAGTATCCGCAGTCCGGCACGCTGGAATTCTCGGATGTCACCGTCGATCAGACCACCGGCTCAATCACGCTACGCGCTATTTTCCCGAACCCGGATCACACCCTGCTTCCGGGGATGTTCGTCCGTGCCCGTCTGGAAGAAGGGATTAACCCTGACGCCCTGCTGGTACCGCAACAGGGTGTTACCCGTACGCCGCGCGGCGACGCCAGCGTCATGGTAGTGGGTGAAGGCGATAAAGTCGAAGTCCGCCAGGTCACTGCTTCTCAGGCGATCGGCGATAAATGGCTGGTCACTGACGGTCTGAAATCCGGCGATCGCGTTATCGTCACCGGCCTGCAAAAAATCAAACCAGGTGTGCAGGTAAAAGCGCAGGAAGTAGCTTCTGATGATAAACAGCAAGCCGCAGGCAACGCGCCATCAGAACAAACCAAGTCTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3004041","ARO_id":"41088","ARO_name":"Klebsiella pneumoniae acrA","ARO_description":"AcrA is a subunit of the AcrAB multidrug efflux system that in K. pneumoniae, which is encoded by the acrRAB operon.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2660":{"model_id":"2660","model_name":"Enterobacter cloacae acrA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"760"}},"model_sequences":{"sequence":{"3995":{"protein_sequence":{"accession":"ABG77965.1","sequence":"MNKNRGLTPLAVVLMLSGSLALTGCDDKPAQQGAQQAPEVGVVTLKSEPLQITTELPGRTNAYRIAEVRPQVSGIILKRNFTEGGDVQAGESLYQIDPATYQASYESAKGDLAKAQAAAKIAQLTLNRYQKLLGTKYISQQDYDTALADAQQANAAVVAAKAAVETARINLAYTKVTSPISGRIGKSSVTEGALVQNGQTTALATVQQLDPIYVDVTQSSNDFLRLKQELANGTLKQENGKAKVELITNDGIKFPQEGTLEFSDVTVDQTTGSITLRAIFPNPDKNLLPGMFVRARLEEGTNPTALLVPQQGVTRTPRGDASALVVGADNKVEMRNITATQAIGDKWLVTEGLKDGDRVIVTGLQKVRPGAQVKAQEVKSDDKQQASAAGQSEQTKS"},"dna_sequence":{"accession":"DQ679966","fmin":"299","fmax":"1493","strand":"+","sequence":"ATGAACAAAAACAGAGGGTTAACGCCTCTGGCGGTCGTTCTGATGCTTTCAGGCAGCTTAGCGCTAACAGGATGTGACGACAAACCGGCTCAACAAGGAGCTCAGCAGGCGCCAGAAGTAGGCGTTGTGACGCTCAAATCTGAACCTCTACAAATCACCACCGAATTACCCGGCCGTACAAATGCTTACCGCATTGCGGAAGTGCGTCCTCAGGTTAGCGGCATTATCCTGAAACGCAACTTCACCGAAGGCGGTGATGTGCAGGCCGGTGAGTCTCTGTATCAGATTGATCCCGCAACCTATCAGGCGTCTTATGAAAGCGCGAAAGGCGATCTGGCTAAAGCGCAGGCCGCGGCTAAAATTGCCCAGCTGACGCTGAACCGCTATCAAAAACTGCTCGGTACCAAGTACATCAGTCAGCAGGATTACGATACCGCCCTGGCGGATGCCCAGCAGGCTAACGCCGCCGTGGTGGCAGCCAAAGCGGCCGTCGAAACCGCGCGCATTAACCTGGCCTATACCAAAGTGACCTCCCCTATCAGCGGTCGTATTGGTAAATCTTCCGTCACGGAAGGGGCTCTGGTGCAAAACGGTCAGACCACTGCGCTGGCGACCGTGCAGCAGCTCGATCCGATCTATGTTGACGTCACGCAGTCCAGCAATGATTTCCTGCGCCTGAAACAGGAGTTGGCTAACGGCACCCTGAAACAGGAAAACGGCAAAGCCAAAGTGGAGCTGATTACCAACGACGGTATCAAGTTCCCGCAGGAAGGGACGCTGGAATTCTCTGACGTGACGGTCGACCAGACCACCGGTTCCATCACCTTACGTGCGATTTTCCCGAACCCTGACAAAAATCTGCTGCCAGGTATGTTCGTTCGCGCACGTCTGGAAGAAGGAACGAATCCAACCGCCCTTCTGGTTCCACAGCAGGGTGTGACCCGTACGCCACGCGGCGATGCGAGCGCACTGGTTGTTGGGGCTGATAACAAAGTCGAAATGCGCAACATCACCGCCACCCAGGCGATTGGGGATAAATGGCTGGTGACGGAAGGTCTGAAAGATGGCGATCGCGTGATTGTTACTGGTTTGCAAAAAGTTCGTCCTGGCGCGCAGGTTAAAGCACAGGAAGTGAAATCTGACGATAAACAACAAGCTTCGGCCGCTGGCCAGTCAGAACAAACCAAGTCTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3004042","ARO_id":"41089","ARO_name":"Enterobacter cloacae acrA","ARO_description":"AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. cloacae.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2661":{"model_id":"2661","model_name":"Escherichia coli acrA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"670"}},"model_sequences":{"sequence":{"3996":{"protein_sequence":{"accession":"NP_414996.1","sequence":"MNKNRGFTPLAVVLMLSGSLALTGCDDKQAQQGGQQMPAVGVVTVKTEPLQITTELPGRTSAYRIAEVRPQVSGIILKRNFKEGSDIEAGVSLYQIDPATYQATYDSAKGDLAKAQAAANIAQLTVNRYQKLLGTQYISKQEYDQALADAQQANAAVTAAKAAVETARINLAYTKVTSPISGRIGKSNVTEGALVQNGQATALATVQQLDPIYVDVTQSSNDFLRLKQELANGTLKQENGKAKVSLITSDGIKFPQDGTLEFSDVTVDQTTGSITLRAIFPNPDHTLLPGMFVRARLEEGLNPNAILVPQQGVTRTPRGDATVLVVGADDKVETRPIVASQAIGDKWLVTEGLKAGDRVVISGLQKVRPGVQVKAQEVTADNNQQAASGAQPEQSKS"},"dna_sequence":{"accession":"NC_000913.3","fmin":"484425","fmax":"485619","strand":"-","sequence":"TTAAGACTTGGACTGTTCAGGCTGAGCACCGCTTGCGGCTTGCTGGTTATTATCAGCGGTAACTTCTTGTGCTTTTACCTGGACACCAGGACGCACTTTCTGCAGCCCACTTATTACTACGCGATCGCCTGCTTTCAGACCTTCTGTCACCAGCCACTTATCGCCAATAGCCTGGCTTGCAACGATCGGACGGGTTTCCACTTTGTCATCCGCGCCAACTACCAGTACGGTGGCATCGCCACGCGGCGTACGGGTTACGCCCTGTTGCGGGACTAAAATAGCGTTTGGATTAAGCCCTTCTTCCAGACGTGCGCGCACGAACATACCCGGCAGCAGAGTGTGATCCGGGTTCGGGAAGATAGCGCGTAGGGTGATAGACCCAGTGGTCTGATCAACGGTAACGTCAGAGAATTCCAGCGTACCGTCCTGCGGGAACTTAATGCCGTCACTGGTGATCAGTGACACTTTGGCTTTGCCGTTCTCTTGTTTCAGCGTGCCATTCGCCAGTTCCTGTTTCAGGCGCAGGAAGTCGTTGCTGGACTGGGTCACATCAACGTAGATCGGATCAAGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGACCGTTCTGTACCAATGCGCCTTCCGTCACGTTCGACTTACCAATGCGACCGCTAATCGGAGAGGTGACTTTGGTGTAAGCCAGATTGATCCGCGCAGTTTCAACGGCAGCTTTCGCCGCAGTTACCGCAGCATTCGCCTGTTGCGCATCAGCCAGAGCCTGATCGTACTCTTGCTTACTGATGTACTGAGTACCGAGCAGTTTCTGATAACGATTCACCGTCAATTGCGCGATATTGGCTGCAGCCTGGGCTTTCGCCAGATCACCTTTCGCACTGTCGTATGTCGCCTGATAGGTCGCAGGATCAATCTGATAGAGAGAGACACCTGCTTCGATGTCGCTACCTTCTTTGAAATTACGCTTCAGGATAATCCCGCTAACTTGAGGACGAACTTCTGCGATCCGGTAGGCACTGGTGCGACCCGGAAGCTCGGTTGTGATCTGCAGAGGTTCAGTTTTGACTGTTACTACGCCAACGGCGGGCATCTGCTGGCCACCTTGTTGGGCCTGTTTGTCGTCACATCCTGTTAGGGCTAAGCTGCCTGAGAGCATCAGAACGACCGCCAGAGGCGTAAACCCTCTGTTTTTGTTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3004043","ARO_id":"41090","ARO_name":"Escherichia coli acrA","ARO_description":"AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2666":{"model_id":"2666","model_name":"antibiotic resistant fabI","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"7383":"G93A","7384":"G93S","7385":"G93V","7386":"M159T","7387":"F203L","7388":"F203C","7389":"F203A","7390":"F203V"},"clinical":{"7383":"G93A","7384":"G93S","7385":"G93V","7386":"M159T","7387":"F203L","7388":"F203C","7389":"F203A","7390":"F203V"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"4000":{"protein_sequence":{"accession":"NP_415804.1","sequence":"MGFLSGKRILVTGVASKLSIAYGIAQAMHREGAELAFTYQNDKLKGRVEEFAAQLGSDIVLQCDVAEDASIDTMFAELGKVWPKFDGFVHSIGFAPGDQLDGDYVNAVTREGFKIAHDISSYSFVAMAKACRSMLNPGSALLTLSYLGAERAIPNYNVMGLAKASLEANVRYMANAMGPEGVRVNAISAGPIRTLAASGIKDFRKMLAHCEAVTPIRRTVTIEDVGNSAAFLCSDLSAGISGEVVHVDGGFSIAAMNELELK"},"dna_sequence":{"accession":"NC_000913.3","fmin":"1350250","fmax":"1351039","strand":"-","sequence":"TTATTTCAGTTCGAGTTCGTTCATTGCAGCAATGCTGAAACCGCCGTCAACGTGGACCACTTCACCGGAGATACCGGCAGAGAGATCGGAGCACAGGAATGCCGCAGAGTTACCCACATCTTCAATAGTAACGGTACGGCGAATCGGGGTAACGGCTTCGCAATGAGCCAGCATTTTGCGGAAGTCTTTGATACCGGAGGCCGCCAGAGTACGGATCGGACCAGCAGAGATGGCGTTAACACGCACACCTTCCGGACCCATCGCGTTCGCCATATAGCGCACGTTCGCTTCCAGAGACGCTTTTGCCAGACCCATAACGTTGTAGTTCGGGATAGCGCGCTCAGCGCCAAGGTAGGAAAGGGTCAGCAGGGCAGAACCCGGATTCAGCATGGAGCGGCAAGCTTTTGCCATTGCAACGAAGCTGTAGGAGCTGATGTCGTGGGCAATTTTGAAGCCTTCACGGGTAACGGCGTTAACATAGTCACCATCCAGCTGATCGCCAGGTGCAAAACCAATAGAGTGTACGAAACCGTCAAATTTCGGCCAAACTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGCATCTTCTGCAACATCGCACTGCAGAACGATGTCAGAACCCAATTGAGCGGCAAATTCTTCTACGCGGCCTTTCAGTTTGTCGTTCTGGTAGGTGAATGCCAGTTCAGCTCCTTCGCGGTGCATCGCCTGAGCGATACCGTAGGCGATGGATAGTTTGCTGGCAACACCGGTTACCAGAATGCGCTTACCGGAAAGAAAACCCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3004045","ARO_id":"41097","ARO_name":"Escherichia coli fabI mutations conferring resistance to isoniazid and triclosan","ARO_description":"fabI is a enoyl-acyl carrier reductase used in lipid metabolism and fatty acid biosynthesis. The bacterial biocide Triclosan blocks the final reduction step in fatty acid elongation, inhibiting biosynthesis. Point mutations in fabI can confer resistance to Triclosan and Isoniazid","ARO_category":{"41434":{"category_aro_accession":"3004270","category_aro_cvterm_id":"41434","category_aro_name":"antibiotic resistant fabI","category_aro_description":"fabI is a enoyl-acyl carrier reductase used in lipid metabolism and fatty acid biosynthesis. The bacterial biocide Triclosan blocks the final reduction step in fatty acid elongation, inhibiting biosynthesis. Point mutations in fabI can confer resistance to Triclosan and Isoniazid.","category_aro_class_name":"AMR Gene Family"},"36659":{"category_aro_accession":"3000520","category_aro_cvterm_id":"36659","category_aro_name":"isoniazid","category_aro_description":"Isoniazid is an organic compound that is the first-line anti tuberculosis medication in prevention and treatment. As a prodrug, it is activated by mycobacterial catalase-peroxidases such as M. tuberculosis KatG. Isoniazid inhibits mycolic acid synthesis, which prevents cell wall synthesis in mycobacteria.","category_aro_class_name":"Drug Class"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2303":{"model_id":"2303","model_name":"bcr-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"3570":{"protein_sequence":{"accession":"ALV80601.1","sequence":"MPASASRIQVGSGERRLLLLLSALVAFGPLSIDMYLPSLPAIAADLGASDAQVQRSISGFLVGFCVGMLFYGPLSDRFGRRPVLLAGIALYLFSSLACALADSAGQLVLLRVLQALGGGAASVLARAMVRDLYPLGEAARMLALMHMVTMLAPLAAPLLGGYLMLWAGWRALFVVLALFAGLCLLAVWRVAESHPPERRGGSLAQAFLAYGRLLGDRRALGYVLCMGLAFAGMFAYISAAPFVFIEHFGVRAERFGWFFGLNILGVMLATWCSARLVRRHGPRPLLRAGSLLACVSGLFLLGYAALGERGGLWALVPGLLCFVSVTGLLGANCIASLLALYPGQAGAASAVAVSGQFGLGCLASLAVGWLALPGVLPMALVMAVCGVGSLLALGLALHGGNR"},"dna_sequence":{"accession":"CP012901.1","fmin":"5979156","fmax":"5980365","strand":"-","sequence":"TCAACGGTTTCCGCCGTGCAGGGCCAAGCCCAGCGCGAGCAGGCTGCCGACGCCGCAGACGGCCATCACCAGCGCCATCGGCAGCACGCCGGGCAGCGCCAGCCAGCCGACCGCCAGGCTGGCCAGGCAGCCGAGGCCGAACTGCCCGGACACCGCCACCGCCGAAGCCGCCCCGGCCTGTCCGGGATACAACGCCAGCAGGCTGGCGATGCAGTTGGCGCCGAGCAGGCCGGTGACGCTGACGAAGCACAGCAGGCCGGGCACCAGCGCCCACAACCCGCCCCGCTCGCCGAGCGCCGCATAGCCGAGGAGGAACAGCCCGGACACGCAGGCCAGCAGGCTGCCGGCCCGCAGCAGCGGCCGCGGACCGTGGCGGCGCACCAGGCGCGCGCTGCACCAGGTGGCGAGCATCACGCCGAGGATGTTCAGGCCGAAGAACCAGCCGAAGCGCTCCGCGCGCACGCCGAAATGCTCGATGAACACGAAGGGCGCGGCGCTGATGTAGGCGAACATCCCGGCGAACGCCAGCCCCATGCACAGCACGTAGCCCAGCGCGCGACGGTCGCCGAGCAGCCGCCCATAGGCGAGAAAGGCCTGGGCCAGGCTGCCGCCGCGGCGCTCCGGCGGGTGGCTTTCGGCGACCCGCCAGACCGCCAGCAGGCAGAGCCCGGCGAACAGCGCCAGGACCACGAACAACGCGCGCCAGCCGGCCCAGAGCATCAGGTAGCCGCCGAGCAGCGGCGCGGCCAGCGGTGCCAGCATGGTCACCATGTGCATCAATGCCAGCATCCGGGCGGCCTCGCCCAACGGATAGAGGTCGCGCACCATGGCCCGCGCCAGCACCGACGCGGCGCCGCCGCCGAGGGCCTGGAGCACCCTCAGCAGGACCAGTTGCCCCGCGCTGTCGGCCAGCGCGCAGGCCAGGCTGCTGAACAGGTACAAGGCGATACCGGCCAGCAGCACCGGGCGCCGGCCGAAACGGTCGGACAAGGGGCCGTAGAACAGCATGCCGACGCAGAAGCCGACCAGGAAGCCGCTGATGCTCCGCTGCACCTGGGCATCGCTGGCGCCGAGATCGGCGGCGATCGCCGGCAGGCTCGGCAGGTACATGTCGATCGACAGCGGGCCGAACGCCACCAGCGCCGACAACAGCAGCAACAGGCGTCGTTCGCCGCTTCCGACCTGAATCCTCGATGCACTCGCAGGCAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3003801","ARO_id":"40486","ARO_name":"bcr-1","ARO_description":"Transmembrane protein which expels bicyclomycin from the cell, leading to bicyclomycin resistance. Identified in Pseudomonas aeruginosa strains responsible for outbreaks in Brazil, often appearing with blaSPM-1, another bicyclomycin resistance gene","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35972":{"category_aro_accession":"0000055","category_aro_cvterm_id":"35972","category_aro_name":"bicyclomycin","category_aro_description":"Bicyclomycin represents a unique class of antibiotics, discovered in 1972. It is obtained by the fermentation of Streptomyces sapporonensis. In the crystalline form bicyclomycin is observed to be rhombic or monoclinic, depending on the solvent used. This antibiotic kills bacteria by inhibiting the Rho transcription terminator factor, halting ribonucleic acid (RNA) synthesis.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1474":{"model_id":"1474","model_name":"mexR","model_type":"protein overexpression model","model_type_id":"41091","model_description":"This model detects protein overexpression based on the presence of mutations.The detection of the protein without an associated mutation indicates that the protein is likely to be expressed at low or basal levels. The detection of the protein with the mutation indicates that the protein is likely overexpressed. This model reflects how certain proteins are functional with and without mutations. For example, efflux pump subunits and regulators are functional with mutations and without mutations. Without mutations, efflux pump subunits and regulators are usually expressed at a low level. When an efflux pump regulator has a mutation, it can cause the overexpression of the efflux pump it is responsible for regulating, leading to resistance to specific drugs. Protein overexpression models have two parameters: a curated BLASTP cutoff, and a curated set of mutations (single resistance variants, frameshift mutations, indels, etc.) shown clinically to confer resistance. This model type is a combination of the protein homolog and protein variant model. A detected hit can be categorized as Perfect, Strict, or Loose with no mutation(s) or as Strict or Loose with mutation(s).","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2760":"I72N","2761":"L75P","2762":"L75R","2763":"R83C","2825":"R91C","2826":"R91H","2888":"L45P","2889":"I46N","2890":"L57R","2891":"T69I","6704":"L57P","7614":"N53D","7615":"H107P"},"clinical":{"2760":"I72N","2761":"L75P","2762":"L75R","2763":"R83C","2825":"R91C","2826":"R91H","2888":"L45P","2889":"I46N","2890":"L57R","2891":"T69I","6704":"L57P","7614":"N53D","7615":"H107P"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"270"}},"model_sequences":{"sequence":{"4368":{"protein_sequence":{"accession":"NP_249115.1","sequence":"MNYPVNPDLMPALMAVFQHVRTRIQSELDCQRLDLTPPDVHVLKLIDEQRGLNLQDLGRQMCRDKALITRKIRELEGRNLVRRERNPSDQRSFQLFLTDEGLAIHQHAEAIMSRVHDELFAPLTPVEQATLVHLLDQCLAAQPLEDI"},"dna_sequence":{"accession":"NC_002516","fmin":"471305","fmax":"471749","strand":"-","sequence":"TTAAATATCCTCAAGCGGTTGCGCGGCCAGGCACTGGTCGAGGAGATGCACCAGGGTGGCCTGTTCCACCGGGGTGAGCGGGGCAAACAACTCGTCATGCACGCGTGACATGATGGCCTCCGCATGCTGGTGGATGGCCAGCCCCTCGTCGGTGAGGAAGAGCTGGAAGCTGCGCTGGTCGCTGGGGTTGCGCTCGCGGCGGACCAGGTTTCTTCCCTCCAGCTCGCGGATCTTCCGGGTGATCAGTGCCTTGTCGCGGCACATCTGGCGTCCCAGGTCCTGCAGGTTCAGCCCGCGTTGTTCGTCGATAAGCTTCAATACATGGACGTCGGGCGGGGTCAGGTCGAGTCGCTGGCAATCGAGCTCGCTCTGGATGCGCGTCCGCACATGCTGGAAGACCGCCATCAGCGCGGGCATCAGGTCGGGATTCACGGGGTAGTTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3000506","ARO_id":"36645","ARO_name":"MexR","ARO_description":"MexR is the repressor of the MexRAB-OprM operon. Mutant forms of mexR result in up-regulation of efflux pump system MexAB-OprM.","ARO_category":{"35996":{"category_aro_accession":"0000079","category_aro_cvterm_id":"35996","category_aro_name":"clavulanate","category_aro_description":"Clavulanic acid is a beta-lactamase inhibitor (marketed by GlaxoSmithKline, formerly Beecham) combined with penicillin group antibiotics to overcome certain types of antibiotic resistance. It is used to overcome resistance in bacteria that secrete beta-lactamase, which otherwise inactivates most penicillins.","category_aro_class_name":"Adjuvant"},"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35979":{"category_aro_accession":"0000062","category_aro_cvterm_id":"35979","category_aro_name":"ceftriaxone","category_aro_description":"Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36468":{"category_aro_accession":"3000329","category_aro_cvterm_id":"36468","category_aro_name":"sulfamethoxazole","category_aro_description":"Sulfamethoxazole is a sulfonamide antibiotic usually taken with trimethoprim, a diaminopyrimidine antibiotic. Sulfamethoxazole inhibits dihydropteroate synthase, essential to tetrahydrofolic acid biosynthesis. This pathway generates compounds used in the synthesis of many amino acids and nucleotides.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36689":{"category_aro_accession":"3000550","category_aro_cvterm_id":"36689","category_aro_name":"aztreonam","category_aro_description":"Aztreonam was the first monobactam discovered, and is greatly effective against Gram-negative bacteria while inactive against Gram-positive bacteria. Artreonam is a poor substrate for beta-lactamases, and may even act as an inhibitor. In Gram-negative bacteria, Aztreonam interferes with filamentation, inhibiting cell division and leading to cell death.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"40362":{"category_aro_accession":"3003708","category_aro_cvterm_id":"40362","category_aro_name":"panipenem","category_aro_description":"Panipenem is a carbapenem antibacterial agent with a broad spectrum of in vitro activity covering a wide range of Gram-negative and Gram-positive aerobic and anaerobic bacterial.  It is used in combination with betamipron to inhibit panipenem uptake into the renal tubule and prevent nephrotoxicity.","category_aro_class_name":"Antibiotic"},"40957":{"category_aro_accession":"3004024","category_aro_cvterm_id":"40957","category_aro_name":"trimethoprim-sulfamethoxazole","category_aro_description":"An antibiotic cocktail containing the diaminopyrimidine antibiotic Trimethoprim and the sulfonamide antibiotic sulfamethoxazole (1 TMP:5 SMX).","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36421":{"category_aro_accession":"3000282","category_aro_cvterm_id":"36421","category_aro_name":"sulfonamide antibiotic","category_aro_description":"Sulfonamides are broad spectrum, synthetic antibiotics that contain the sulfonamide group. Sulfonamides inhibit dihydropteroate synthase, which catalyzes the conversion of p-aminobenzoic acid to dihydropteroic acid as part of the tetrahydrofolic acid biosynthetic pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor of many nucleotides and amino acids. Many sulfamides are taken with trimethoprim, an inhibitor of dihydrofolate reductase, also disturbing the trihydrofolic acid synthesis pathway.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2682":{"model_id":"2682","model_name":"MexAB-OprM with NalC mutations conferring resistance to aztreonam","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)","model_param":{"41141":{"param_type":"efflux pump components","param_description":"This detection model parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305.","param_type_id":"41141","param_value":{"7531":"1670,440,1925,1305"}}},"ARO_accession":"3004051","ARO_id":"41116","ARO_name":"MexAB-OprM with NalC mutations conferring resistance to aztreonam","ARO_description":"MexAB-OprM efflux pump system with NalC mutations conferring resistance to aztreonam. While efflux gene hyperexpression typically results from mutations in the linked mexR repressor gene, it also occurs independently of mexR mutations in so-called nalC mutants that demonstrate more modest mexAB-oprM expression and, thus, more modest multidrug resistance than do mexR strains.","ARO_category":{"35996":{"category_aro_accession":"0000079","category_aro_cvterm_id":"35996","category_aro_name":"clavulanate","category_aro_description":"Clavulanic acid is a beta-lactamase inhibitor (marketed by GlaxoSmithKline, formerly Beecham) combined with penicillin group antibiotics to overcome certain types of antibiotic resistance. It is used to overcome resistance in bacteria that secrete beta-lactamase, which otherwise inactivates most penicillins.","category_aro_class_name":"Adjuvant"},"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35979":{"category_aro_accession":"0000062","category_aro_cvterm_id":"35979","category_aro_name":"ceftriaxone","category_aro_description":"Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36468":{"category_aro_accession":"3000329","category_aro_cvterm_id":"36468","category_aro_name":"sulfamethoxazole","category_aro_description":"Sulfamethoxazole is a sulfonamide antibiotic usually taken with trimethoprim, a diaminopyrimidine antibiotic. Sulfamethoxazole inhibits dihydropteroate synthase, essential to tetrahydrofolic acid biosynthesis. This pathway generates compounds used in the synthesis of many amino acids and nucleotides.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36689":{"category_aro_accession":"3000550","category_aro_cvterm_id":"36689","category_aro_name":"aztreonam","category_aro_description":"Aztreonam was the first monobactam discovered, and is greatly effective against Gram-negative bacteria while inactive against Gram-positive bacteria. Artreonam is a poor substrate for beta-lactamases, and may even act as an inhibitor. In Gram-negative bacteria, Aztreonam interferes with filamentation, inhibiting cell division and leading to cell death.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"40362":{"category_aro_accession":"3003708","category_aro_cvterm_id":"40362","category_aro_name":"panipenem","category_aro_description":"Panipenem is a carbapenem antibacterial agent with a broad spectrum of in vitro activity covering a wide range of Gram-negative and Gram-positive aerobic and anaerobic bacterial.  It is used in combination with betamipron to inhibit panipenem uptake into the renal tubule and prevent nephrotoxicity.","category_aro_class_name":"Antibiotic"},"40957":{"category_aro_accession":"3004024","category_aro_cvterm_id":"40957","category_aro_name":"trimethoprim-sulfamethoxazole","category_aro_description":"An antibiotic cocktail containing the diaminopyrimidine antibiotic Trimethoprim and the sulfonamide antibiotic sulfamethoxazole (1 TMP:5 SMX).","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36421":{"category_aro_accession":"3000282","category_aro_cvterm_id":"36421","category_aro_name":"sulfonamide antibiotic","category_aro_description":"Sulfonamides are broad spectrum, synthetic antibiotics that contain the sulfonamide group. Sulfonamides inhibit dihydropteroate synthase, which catalyzes the conversion of p-aminobenzoic acid to dihydropteroic acid as part of the tetrahydrofolic acid biosynthetic pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor of many nucleotides and amino acids. Many sulfamides are taken with trimethoprim, an inhibitor of dihydrofolate reductase, also disturbing the trihydrofolic acid synthesis pathway.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2683":{"model_id":"2683","model_name":"MexAB-OprM with NalD mutation conferring resistance to multiple antibiotics","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)","model_param":{"41141":{"param_type":"efflux pump components","param_description":"This detection model parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305.","param_type_id":"41141","param_value":{"7532":"1213,440,1925,1305"}}},"ARO_accession":"3004052","ARO_id":"41117","ARO_name":"MexAB-OprM with NalD mutations conferring resistance to multiple antibiotics","ARO_description":"MexAB-OprM efflux pump system with a NalD mutation conferring resistance to multiple antibiotics. This NalD mutation was found in multidrug-resistant clinical strains lacking mutations in MexR or NalC.","ARO_category":{"35996":{"category_aro_accession":"0000079","category_aro_cvterm_id":"35996","category_aro_name":"clavulanate","category_aro_description":"Clavulanic acid is a beta-lactamase inhibitor (marketed by GlaxoSmithKline, formerly Beecham) combined with penicillin group antibiotics to overcome certain types of antibiotic resistance. It is used to overcome resistance in bacteria that secrete beta-lactamase, which otherwise inactivates most penicillins.","category_aro_class_name":"Adjuvant"},"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35979":{"category_aro_accession":"0000062","category_aro_cvterm_id":"35979","category_aro_name":"ceftriaxone","category_aro_description":"Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36468":{"category_aro_accession":"3000329","category_aro_cvterm_id":"36468","category_aro_name":"sulfamethoxazole","category_aro_description":"Sulfamethoxazole is a sulfonamide antibiotic usually taken with trimethoprim, a diaminopyrimidine antibiotic. Sulfamethoxazole inhibits dihydropteroate synthase, essential to tetrahydrofolic acid biosynthesis. This pathway generates compounds used in the synthesis of many amino acids and nucleotides.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36689":{"category_aro_accession":"3000550","category_aro_cvterm_id":"36689","category_aro_name":"aztreonam","category_aro_description":"Aztreonam was the first monobactam discovered, and is greatly effective against Gram-negative bacteria while inactive against Gram-positive bacteria. Artreonam is a poor substrate for beta-lactamases, and may even act as an inhibitor. In Gram-negative bacteria, Aztreonam interferes with filamentation, inhibiting cell division and leading to cell death.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"40362":{"category_aro_accession":"3003708","category_aro_cvterm_id":"40362","category_aro_name":"panipenem","category_aro_description":"Panipenem is a carbapenem antibacterial agent with a broad spectrum of in vitro activity covering a wide range of Gram-negative and Gram-positive aerobic and anaerobic bacterial.  It is used in combination with betamipron to inhibit panipenem uptake into the renal tubule and prevent nephrotoxicity.","category_aro_class_name":"Antibiotic"},"40523":{"category_aro_accession":"3003832","category_aro_cvterm_id":"40523","category_aro_name":"ticarcillin","category_aro_description":"Ticarcillin is a carboxypenicillin used for the treatment of Gram-negative bacteria, particularly P. aeruginosa. Ticarcillin's antibiotic properties arise from its ability to prevent cross-linking of peptidoglycan during cell wall synthesis, when the bacteria try to divide, causing cell death.","category_aro_class_name":"Antibiotic"},"40957":{"category_aro_accession":"3004024","category_aro_cvterm_id":"40957","category_aro_name":"trimethoprim-sulfamethoxazole","category_aro_description":"An antibiotic cocktail containing the diaminopyrimidine antibiotic Trimethoprim and the sulfonamide antibiotic sulfamethoxazole (1 TMP:5 SMX).","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36421":{"category_aro_accession":"3000282","category_aro_cvterm_id":"36421","category_aro_name":"sulfonamide antibiotic","category_aro_description":"Sulfonamides are broad spectrum, synthetic antibiotics that contain the sulfonamide group. Sulfonamides inhibit dihydropteroate synthase, which catalyzes the conversion of p-aminobenzoic acid to dihydropteroic acid as part of the tetrahydrofolic acid biosynthetic pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor of many nucleotides and amino acids. Many sulfamides are taken with trimethoprim, an inhibitor of dihydrofolate reductase, also disturbing the trihydrofolic acid synthesis pathway.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2679":{"model_id":"2679","model_name":"MexAB-OprM with MexR mutations conferring resistance to multiple antibiotics","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)","model_param":{"41141":{"param_type":"efflux pump components","param_description":"This detection model parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305.","param_type_id":"41141","param_value":{"7528":"1474,440,1925,1305"}}},"ARO_accession":"3004080","ARO_id":"41182","ARO_name":"MexAB-OprM with MexR mutations confers resistance to multiple antibiotics","ARO_description":"MexAB-OprM efflux pump system with MexR mutations confers resistance to multiple antibiotics in P. aeruginosa.","ARO_category":{"35996":{"category_aro_accession":"0000079","category_aro_cvterm_id":"35996","category_aro_name":"clavulanate","category_aro_description":"Clavulanic acid is a beta-lactamase inhibitor (marketed by GlaxoSmithKline, formerly Beecham) combined with penicillin group antibiotics to overcome certain types of antibiotic resistance. It is used to overcome resistance in bacteria that secrete beta-lactamase, which otherwise inactivates most penicillins.","category_aro_class_name":"Adjuvant"},"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35979":{"category_aro_accession":"0000062","category_aro_cvterm_id":"35979","category_aro_name":"ceftriaxone","category_aro_description":"Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36468":{"category_aro_accession":"3000329","category_aro_cvterm_id":"36468","category_aro_name":"sulfamethoxazole","category_aro_description":"Sulfamethoxazole is a sulfonamide antibiotic usually taken with trimethoprim, a diaminopyrimidine antibiotic. Sulfamethoxazole inhibits dihydropteroate synthase, essential to tetrahydrofolic acid biosynthesis. This pathway generates compounds used in the synthesis of many amino acids and nucleotides.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36689":{"category_aro_accession":"3000550","category_aro_cvterm_id":"36689","category_aro_name":"aztreonam","category_aro_description":"Aztreonam was the first monobactam discovered, and is greatly effective against Gram-negative bacteria while inactive against Gram-positive bacteria. Artreonam is a poor substrate for beta-lactamases, and may even act as an inhibitor. In Gram-negative bacteria, Aztreonam interferes with filamentation, inhibiting cell division and leading to cell death.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"40362":{"category_aro_accession":"3003708","category_aro_cvterm_id":"40362","category_aro_name":"panipenem","category_aro_description":"Panipenem is a carbapenem antibacterial agent with a broad spectrum of in vitro activity covering a wide range of Gram-negative and Gram-positive aerobic and anaerobic bacterial.  It is used in combination with betamipron to inhibit panipenem uptake into the renal tubule and prevent nephrotoxicity.","category_aro_class_name":"Antibiotic"},"40957":{"category_aro_accession":"3004024","category_aro_cvterm_id":"40957","category_aro_name":"trimethoprim-sulfamethoxazole","category_aro_description":"An antibiotic cocktail containing the diaminopyrimidine antibiotic Trimethoprim and the sulfonamide antibiotic sulfamethoxazole (1 TMP:5 SMX).","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36421":{"category_aro_accession":"3000282","category_aro_cvterm_id":"36421","category_aro_name":"sulfonamide antibiotic","category_aro_description":"Sulfonamides are broad spectrum, synthetic antibiotics that contain the sulfonamide group. Sulfonamides inhibit dihydropteroate synthase, which catalyzes the conversion of p-aminobenzoic acid to dihydropteroic acid as part of the tetrahydrofolic acid biosynthetic pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor of many nucleotides and amino acids. Many sulfamides are taken with trimethoprim, an inhibitor of dihydrofolate reductase, also disturbing the trihydrofolic acid synthesis pathway.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2680":{"model_id":"2680","model_name":"MexAB-OprM with prematurely terminated MexR conferring resistance to meropenem and ciprofloxacin","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)","model_param":{"41141":{"param_type":"efflux pump components","param_description":"This detection model parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305.","param_type_id":"41141","param_value":{"7529":"2678,440,1925,1305"}}},"ARO_accession":"3004048","ARO_id":"41113","ARO_name":"MexAB-OprM with prematurely terminated MexR conferring resistance to meropenem and ciprofloxacin","ARO_description":"MexAB-OprM efflux pump system with a prematurely terminated MexR confers resistance to meropenem and ciprofloxacin.","ARO_category":{"35996":{"category_aro_accession":"0000079","category_aro_cvterm_id":"35996","category_aro_name":"clavulanate","category_aro_description":"Clavulanic acid is a beta-lactamase inhibitor (marketed by GlaxoSmithKline, formerly Beecham) combined with penicillin group antibiotics to overcome certain types of antibiotic resistance. It is used to overcome resistance in bacteria that secrete beta-lactamase, which otherwise inactivates most penicillins.","category_aro_class_name":"Adjuvant"},"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35979":{"category_aro_accession":"0000062","category_aro_cvterm_id":"35979","category_aro_name":"ceftriaxone","category_aro_description":"Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36468":{"category_aro_accession":"3000329","category_aro_cvterm_id":"36468","category_aro_name":"sulfamethoxazole","category_aro_description":"Sulfamethoxazole is a sulfonamide antibiotic usually taken with trimethoprim, a diaminopyrimidine antibiotic. Sulfamethoxazole inhibits dihydropteroate synthase, essential to tetrahydrofolic acid biosynthesis. This pathway generates compounds used in the synthesis of many amino acids and nucleotides.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36689":{"category_aro_accession":"3000550","category_aro_cvterm_id":"36689","category_aro_name":"aztreonam","category_aro_description":"Aztreonam was the first monobactam discovered, and is greatly effective against Gram-negative bacteria while inactive against Gram-positive bacteria. Artreonam is a poor substrate for beta-lactamases, and may even act as an inhibitor. In Gram-negative bacteria, Aztreonam interferes with filamentation, inhibiting cell division and leading to cell death.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"40362":{"category_aro_accession":"3003708","category_aro_cvterm_id":"40362","category_aro_name":"panipenem","category_aro_description":"Panipenem is a carbapenem antibacterial agent with a broad spectrum of in vitro activity covering a wide range of Gram-negative and Gram-positive aerobic and anaerobic bacterial.  It is used in combination with betamipron to inhibit panipenem uptake into the renal tubule and prevent nephrotoxicity.","category_aro_class_name":"Antibiotic"},"40957":{"category_aro_accession":"3004024","category_aro_cvterm_id":"40957","category_aro_name":"trimethoprim-sulfamethoxazole","category_aro_description":"An antibiotic cocktail containing the diaminopyrimidine antibiotic Trimethoprim and the sulfonamide antibiotic sulfamethoxazole (1 TMP:5 SMX).","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36421":{"category_aro_accession":"3000282","category_aro_cvterm_id":"36421","category_aro_name":"sulfonamide antibiotic","category_aro_description":"Sulfonamides are broad spectrum, synthetic antibiotics that contain the sulfonamide group. Sulfonamides inhibit dihydropteroate synthase, which catalyzes the conversion of p-aminobenzoic acid to dihydropteroic acid as part of the tetrahydrofolic acid biosynthetic pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor of many nucleotides and amino acids. Many sulfamides are taken with trimethoprim, an inhibitor of dihydrofolate reductase, also disturbing the trihydrofolic acid synthesis pathway.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2681":{"model_id":"2681","model_name":"antibiotic resistant fabG","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"7530":"Y151V"},"clinical":{"7530":"Y151V"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"4014":{"protein_sequence":{"accession":"NP_415611.1","sequence":"MNFEGKIALVTGASRGIGRAIAETLAARGAKVIGTATSENGAQAISDYLGANGKGLMLNVTDPASIESVLEKIRAEFGEVDILVNNAGITRDNLLMRMKDEEWNDIIETNLSSVFRLSKAVMRAMMKKRHGRIITIGSVVGTMGNGGQANYAAAKAGLIGFSKSLAREVASRGITVNVVAPGFIETDMTRALSDDQRAGILAQVPAGRLGGAQEIANAVAFLASDEAAYITGETLHVNGGMYMV"},"dna_sequence":{"accession":"NC_000913.3","fmin":"1150669","fmax":"1151404","strand":"+","sequence":"ATGAATTTTGAAGGAAAAATCGCACTGGTAACCGGTGCAAGCCGCGGAATTGGCCGCGCAATTGCTGAAACGCTCGCAGCCCGTGGCGCGAAAGTTATTGGCACTGCGACCAGTGAAAATGGCGCTCAGGCGATCAGTGATTATTTAGGTGCCAACGGCAAAGGTCTGATGTTGAATGTGACCGACCCGGCATCTATCGAATCTGTTCTGGAAAAAATTCGCGCAGAATTTGGTGAAGTGGATATCCTGGTCAATAATGCCGGTATCACTCGTGATAACCTGTTAATGCGAATGAAAGATGAAGAGTGGAACGATATTATCGAAACCAACCTTTCATCTGTTTTCCGTCTGTCAAAAGCGGTAATGCGCGCTATGATGAAAAAGCGTCATGGTCGTATTATCACTATCGGTTCTGTGGTTGGTACCATGGGAAATGGCGGTCAGGCCAACTACGCTGCGGCGAAAGCGGGCTTGATCGGCTTCAGTAAATCACTGGCGCGCGAAGTTGCGTCACGCGGTATTACTGTAAACGTTGTTGCTCCGGGCTTTATTGAAACGGACATGACACGTGCGCTGAGCGATGACCAGCGTGCGGGTATCCTGGCGCAGGTTCCTGCGGGTCGCCTCGGCGGCGCACAGGAAATCGCCAACGCGGTTGCATTCCTGGCATCCGACGAAGCAGCTTACATCACGGGTGAAACTTTGCATGTGAACGGCGGGATGTACATGGTCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3004049","ARO_id":"41114","ARO_name":"Escherichia coli fabG mutations conferring resistance to triclosan","ARO_description":"fabG is a 3-oxoacyl-acyl carrier protein reductase involved in lipid metabolism and fatty acid biosynthesis.The bacterial biocide Triclosan blocks the final reduction step in fatty acid elongation, inhibiting biosynthesis. Point mutations in fabG can confer resistance to Triclosan.","ARO_category":{"41448":{"category_aro_accession":"3004284","category_aro_cvterm_id":"41448","category_aro_name":"antibiotic resistance fabG","category_aro_description":"fabG is a 3-oxoacyl-acyl carrier protein reductase involved in lipid metabolism and fatty acid biosynthesis. The bacterial biocide Triclosan blocks the final reduction step in fatty acid elongation, inhibiting biosynthesis. Point mutations in fabG can confer resistance to Triclosan.","category_aro_class_name":"AMR Gene Family"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1213":{"model_id":"1213","model_name":"nalD","model_type":"protein overexpression model","model_type_id":"41091","model_description":"This model detects protein overexpression based on the presence of mutations.The detection of the protein without an associated mutation indicates that the protein is likely to be expressed at low or basal levels. The detection of the protein with the mutation indicates that the protein is likely overexpressed. This model reflects how certain proteins are functional with and without mutations. For example, efflux pump subunits and regulators are functional with mutations and without mutations. Without mutations, efflux pump subunits and regulators are usually expressed at a low level. When an efflux pump regulator has a mutation, it can cause the overexpression of the efflux pump it is responsible for regulating, leading to resistance to specific drugs. Protein overexpression models have two parameters: a curated BLASTP cutoff, and a curated set of mutations (single resistance variants, frameshift mutations, indels, etc.) shown clinically to confer resistance. This model type is a combination of the protein homolog and protein variant model. A detected hit can be categorized as Perfect, Strict, or Loose with no mutation(s) or as Strict or Loose with mutation(s).","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"6750":"S32N"},"clinical":{"6750":"S32N"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"375"},"41345":{"param_type":"insertion mutation from nucleotide sequence","param_description":"A subtype of the insertion mutation detection model parameter. This parameter is used when a set of insertion mutations is reported in a nucleotide sequence format. Such mutations may be of variable length - possibly causing a frameshift, but not causing premature termination or a functional knockout. Mutation parameters of this type are reported in CARD with the notation: [+]nt[position]:[nucleotides].","param_type_id":"41345","param_value":{"8153":"+nt410:TGTTCATCGAACTCTGCGAGCAG"}}},"model_sequences":{"sequence":{"232":{"protein_sequence":{"accession":"NP_252264.1","sequence":"MRRTKEDSEKTRTAILLAAEELFLEKGVSHTSLEQIARAAGVTRGAVYWHFQNKAHLFNEMLNQVRLPPEQLTERLSGCDGSDPLRSLYDLCLEAVQSLLTQEKKRRILTILMQRCEFTEELREAQERNNAFVQMFIELCEQLFARDECRVRLHPGMTPRIASRALHALILGLFNDWLRDPRLFDPDTDAEHLLEPMFRGLVRDWGQASSAP"},"dna_sequence":{"accession":"NC_002516","fmin":"4006509","fmax":"4007148","strand":"+","sequence":"ATGCGACGCACAAAGGAAGATTCTGAAAAAACCCGTACGGCCATCCTCCTGGCCGCCGAGGAACTGTTCCTGGAAAAGGGCGTGTCCCATACCAGCCTGGAACAGATCGCCAGGGCCGCCGGGGTGACCCGTGGCGCCGTCTACTGGCACTTCCAGAACAAGGCCCACCTGTTCAACGAGATGCTCAACCAGGTACGCCTGCCGCCGGAGCAACTCACCGAGCGCCTGTCCGGCTGCGATGGCAGCGACCCGCTGCGCTCGCTCTACGACCTCTGCCTGGAGGCCGTGCAATCGTTGCTGACGCAGGAGAAGAAGCGCCGCATCCTGACCATCCTGATGCAACGTTGCGAATTCACCGAGGAACTGCGCGAGGCGCAGGAACGCAACAACGCCTTCGTGCAGATGTTCATCGAACTCTGCGAGCAGTTGTTCGCCCGCGACGAATGCCGTGTGCGGCTGCATCCGGGCATGACCCCGAGGATCGCCTCGCGCGCCTTGCACGCGCTGATCCTGGGCCTGTTCAACGACTGGTTGCGCGACCCGCGCCTGTTCGATCCGGATACGGACGCGGAACACCTGCTGGAGCCGATGTTCCGTGGCCTGGTGCGCGACTGGGGTCAGGCCAGCTCGGCGCCGTAGC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3000819","ARO_id":"37199","ARO_name":"nalD","ARO_description":"NalD is a repressor of MexAB-OprM. Mutations lead to multidrug resistance and MexAB-OprM overexpression.","ARO_category":{"35996":{"category_aro_accession":"0000079","category_aro_cvterm_id":"35996","category_aro_name":"clavulanate","category_aro_description":"Clavulanic acid is a beta-lactamase inhibitor (marketed by GlaxoSmithKline, formerly Beecham) combined with penicillin group antibiotics to overcome certain types of antibiotic resistance. It is used to overcome resistance in bacteria that secrete beta-lactamase, which otherwise inactivates most penicillins.","category_aro_class_name":"Adjuvant"},"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35979":{"category_aro_accession":"0000062","category_aro_cvterm_id":"35979","category_aro_name":"ceftriaxone","category_aro_description":"Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36468":{"category_aro_accession":"3000329","category_aro_cvterm_id":"36468","category_aro_name":"sulfamethoxazole","category_aro_description":"Sulfamethoxazole is a sulfonamide antibiotic usually taken with trimethoprim, a diaminopyrimidine antibiotic. Sulfamethoxazole inhibits dihydropteroate synthase, essential to tetrahydrofolic acid biosynthesis. This pathway generates compounds used in the synthesis of many amino acids and nucleotides.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36689":{"category_aro_accession":"3000550","category_aro_cvterm_id":"36689","category_aro_name":"aztreonam","category_aro_description":"Aztreonam was the first monobactam discovered, and is greatly effective against Gram-negative bacteria while inactive against Gram-positive bacteria. Artreonam is a poor substrate for beta-lactamases, and may even act as an inhibitor. In Gram-negative bacteria, Aztreonam interferes with filamentation, inhibiting cell division and leading to cell death.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"40362":{"category_aro_accession":"3003708","category_aro_cvterm_id":"40362","category_aro_name":"panipenem","category_aro_description":"Panipenem is a carbapenem antibacterial agent with a broad spectrum of in vitro activity covering a wide range of Gram-negative and Gram-positive aerobic and anaerobic bacterial.  It is used in combination with betamipron to inhibit panipenem uptake into the renal tubule and prevent nephrotoxicity.","category_aro_class_name":"Antibiotic"},"40523":{"category_aro_accession":"3003832","category_aro_cvterm_id":"40523","category_aro_name":"ticarcillin","category_aro_description":"Ticarcillin is a carboxypenicillin used for the treatment of Gram-negative bacteria, particularly P. aeruginosa. Ticarcillin's antibiotic properties arise from its ability to prevent cross-linking of peptidoglycan during cell wall synthesis, when the bacteria try to divide, causing cell death.","category_aro_class_name":"Antibiotic"},"40957":{"category_aro_accession":"3004024","category_aro_cvterm_id":"40957","category_aro_name":"trimethoprim-sulfamethoxazole","category_aro_description":"An antibiotic cocktail containing the diaminopyrimidine antibiotic Trimethoprim and the sulfonamide antibiotic sulfamethoxazole (1 TMP:5 SMX).","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36421":{"category_aro_accession":"3000282","category_aro_cvterm_id":"36421","category_aro_name":"sulfonamide antibiotic","category_aro_description":"Sulfonamides are broad spectrum, synthetic antibiotics that contain the sulfonamide group. Sulfonamides inhibit dihydropteroate synthase, which catalyzes the conversion of p-aminobenzoic acid to dihydropteroic acid as part of the tetrahydrofolic acid biosynthetic pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor of many nucleotides and amino acids. Many sulfamides are taken with trimethoprim, an inhibitor of dihydrofolate reductase, also disturbing the trihydrofolic acid synthesis pathway.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2686":{"model_id":"2686","model_name":"MexAB-OprM with CpxR regulator conferring resistance to ciprofloxacin, ceftazidime, and aztreonam","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)","model_param":{"41141":{"param_type":"efflux pump components","param_description":"This detection model parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305.","param_type_id":"41141","param_value":{"7534":"2685,440,1925,1305"}}},"ARO_accession":"3004053","ARO_id":"41118","ARO_name":"MexAB-OprM with CpxR regulator conferring resistance to ciprofloxacin, ceftazidime, and aztreonam","ARO_description":"CpxR is directly involved in activation of expression of RND efflux pump MexAB-OprM in P. aeruginosa. CpxR is required to enhance mexAB-oprM expression and drug resistance, in the absence of repressor MexR.","ARO_category":{"35996":{"category_aro_accession":"0000079","category_aro_cvterm_id":"35996","category_aro_name":"clavulanate","category_aro_description":"Clavulanic acid is a beta-lactamase inhibitor (marketed by GlaxoSmithKline, formerly Beecham) combined with penicillin group antibiotics to overcome certain types of antibiotic resistance. It is used to overcome resistance in bacteria that secrete beta-lactamase, which otherwise inactivates most penicillins.","category_aro_class_name":"Adjuvant"},"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35979":{"category_aro_accession":"0000062","category_aro_cvterm_id":"35979","category_aro_name":"ceftriaxone","category_aro_description":"Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36468":{"category_aro_accession":"3000329","category_aro_cvterm_id":"36468","category_aro_name":"sulfamethoxazole","category_aro_description":"Sulfamethoxazole is a sulfonamide antibiotic usually taken with trimethoprim, a diaminopyrimidine antibiotic. Sulfamethoxazole inhibits dihydropteroate synthase, essential to tetrahydrofolic acid biosynthesis. This pathway generates compounds used in the synthesis of many amino acids and nucleotides.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36689":{"category_aro_accession":"3000550","category_aro_cvterm_id":"36689","category_aro_name":"aztreonam","category_aro_description":"Aztreonam was the first monobactam discovered, and is greatly effective against Gram-negative bacteria while inactive against Gram-positive bacteria. Artreonam is a poor substrate for beta-lactamases, and may even act as an inhibitor. In Gram-negative bacteria, Aztreonam interferes with filamentation, inhibiting cell division and leading to cell death.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"40362":{"category_aro_accession":"3003708","category_aro_cvterm_id":"40362","category_aro_name":"panipenem","category_aro_description":"Panipenem is a carbapenem antibacterial agent with a broad spectrum of in vitro activity covering a wide range of Gram-negative and Gram-positive aerobic and anaerobic bacterial.  It is used in combination with betamipron to inhibit panipenem uptake into the renal tubule and prevent nephrotoxicity.","category_aro_class_name":"Antibiotic"},"40957":{"category_aro_accession":"3004024","category_aro_cvterm_id":"40957","category_aro_name":"trimethoprim-sulfamethoxazole","category_aro_description":"An antibiotic cocktail containing the diaminopyrimidine antibiotic Trimethoprim and the sulfonamide antibiotic sulfamethoxazole (1 TMP:5 SMX).","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36421":{"category_aro_accession":"3000282","category_aro_cvterm_id":"36421","category_aro_name":"sulfonamide antibiotic","category_aro_description":"Sulfonamides are broad spectrum, synthetic antibiotics that contain the sulfonamide group. Sulfonamides inhibit dihydropteroate synthase, which catalyzes the conversion of p-aminobenzoic acid to dihydropteroic acid as part of the tetrahydrofolic acid biosynthetic pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor of many nucleotides and amino acids. Many sulfamides are taken with trimethoprim, an inhibitor of dihydrofolate reductase, also disturbing the trihydrofolic acid synthesis pathway.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2688":{"model_id":"2688","model_name":"ArmR","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"100"}},"model_sequences":{"sequence":{"4019":{"protein_sequence":{"accession":"NP_252408.1","sequence":"MSLNTPRNKPSRTETEAVAASSGRSAVGRRDYTEQLRRAARRNAWDLYGEHFY"},"dna_sequence":{"accession":"NC_002516.2","fmin":"4165718","fmax":"4165880","strand":"-","sequence":"TCAGTAGAAGTGCTCGCCGTAGAGGTCCCAGGCATTGCGCCGGGCTGCCCGGCGCAGCTGCTCGGTGTAATCCCGCCGGCCGACGGCGGATCGTCCCGAGCTGGCAGCGACAGCTTCGGTCTCGGTGCGGGACGGTTTGTTGCGCGGAGTGTTCAGGGACAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3004056","ARO_id":"41121","ARO_name":"ArmR","ARO_description":"ArmR, a 53-amino-acid antirepressor, allosterically inhibits MexR dimer-DNA binding by occupying a hydrophobic binding cavity within the center of the MexR dimer. ArmR up-regulation and MexR-ArmR complex formation have previously been shown to upregulate MexAB-OprM.","ARO_category":{"35996":{"category_aro_accession":"0000079","category_aro_cvterm_id":"35996","category_aro_name":"clavulanate","category_aro_description":"Clavulanic acid is a beta-lactamase inhibitor (marketed by GlaxoSmithKline, formerly Beecham) combined with penicillin group antibiotics to overcome certain types of antibiotic resistance. It is used to overcome resistance in bacteria that secrete beta-lactamase, which otherwise inactivates most penicillins.","category_aro_class_name":"Adjuvant"},"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35979":{"category_aro_accession":"0000062","category_aro_cvterm_id":"35979","category_aro_name":"ceftriaxone","category_aro_description":"Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36468":{"category_aro_accession":"3000329","category_aro_cvterm_id":"36468","category_aro_name":"sulfamethoxazole","category_aro_description":"Sulfamethoxazole is a sulfonamide antibiotic usually taken with trimethoprim, a diaminopyrimidine antibiotic. Sulfamethoxazole inhibits dihydropteroate synthase, essential to tetrahydrofolic acid biosynthesis. This pathway generates compounds used in the synthesis of many amino acids and nucleotides.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36689":{"category_aro_accession":"3000550","category_aro_cvterm_id":"36689","category_aro_name":"aztreonam","category_aro_description":"Aztreonam was the first monobactam discovered, and is greatly effective against Gram-negative bacteria while inactive against Gram-positive bacteria. Artreonam is a poor substrate for beta-lactamases, and may even act as an inhibitor. In Gram-negative bacteria, Aztreonam interferes with filamentation, inhibiting cell division and leading to cell death.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"40362":{"category_aro_accession":"3003708","category_aro_cvterm_id":"40362","category_aro_name":"panipenem","category_aro_description":"Panipenem is a carbapenem antibacterial agent with a broad spectrum of in vitro activity covering a wide range of Gram-negative and Gram-positive aerobic and anaerobic bacterial.  It is used in combination with betamipron to inhibit panipenem uptake into the renal tubule and prevent nephrotoxicity.","category_aro_class_name":"Antibiotic"},"40957":{"category_aro_accession":"3004024","category_aro_cvterm_id":"40957","category_aro_name":"trimethoprim-sulfamethoxazole","category_aro_description":"An antibiotic cocktail containing the diaminopyrimidine antibiotic Trimethoprim and the sulfonamide antibiotic sulfamethoxazole (1 TMP:5 SMX).","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36421":{"category_aro_accession":"3000282","category_aro_cvterm_id":"36421","category_aro_name":"sulfonamide antibiotic","category_aro_description":"Sulfonamides are broad spectrum, synthetic antibiotics that contain the sulfonamide group. Sulfonamides inhibit dihydropteroate synthase, which catalyzes the conversion of p-aminobenzoic acid to dihydropteroic acid as part of the tetrahydrofolic acid biosynthetic pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor of many nucleotides and amino acids. Many sulfamides are taken with trimethoprim, an inhibitor of dihydrofolate reductase, also disturbing the trihydrofolic acid synthesis pathway.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2689":{"model_id":"2689","model_name":"Staphylococcus aureus 23S rRNA with mutation conferring resistance to linezolid","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"5000"},"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"7940":"C2579T","7941":"G2604T"},"clinical":{"7940":"C2579T","7941":"G2604T"}}},"model_sequences":{"sequence":{"4128":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NZ_CP009828.1","fmin":"497113","fmax":"500039","strand":"+","sequence":"AGATTAAGTTATTAAGGGCGCACGGTGGATGCCTTGGCACTAGAAGCCGATGAAGGACGTTACTAACGACGATATGCTTTGGGGAGCTGTAAGTAAGCTTTGATCCAGAGATTTCCGAATGGGGAAACCCAGCATGAGTTATGTCATGTTATCGATATGTGAATACATAGCATATCAGAAGGCACACCCGGAGAACTGAAACATCTTAGTACCCGGAGGAAGAGAAAGAAAATTCGATTCCCTTAGTAGCGGCGAGCGAAACGGGAAGAGCCCAAACCAACAAGCTTGCTTGTTGGGGTTGTAGGACACTCTATACGGAGTTACAAAGGACGACATTAGACGAATCATCTGGAAAGATGAATCAAAGAAGGTAATAATCCTGTAGTCGAAAATGTTGTCTCTCTTGAGTGGATCCTGAGTACGACGGAGCACGTGAAATTCCGTCGGAATCTGGGAGGACCATCTCCTAAGGCTAAATACTCTCTAGTGACCGATAGTGAACCAGTACCGTGAGGGAAAGGTGAAAAGCACCCCGGAAGGGGAGTGAAATAGAACCTGAAACCGTGTGCTTACAAGTAGTCAGAGCCCGTTAATGGGTGATGGCGTGCCTTTTGTAGAATGAACCGGCGAGTTACGATTTGATGCAAGGTTAAGCAGTAAATGTGGAGCCGTAGCGAAAGCGAGTCTGAATAGGGCGTTTAGTATTTGGTCGTAGACCCGAAACCAGGTGATCTACCCTTGGTCAGGTTGAAGTTCAGGTAACACTGAATGGAGGACCGAACCGACTTACGTTGAAAAGTGAGCGGATGAACTGAGGGTAGCGGAGAAATTCCAATCGAACCTGGAGATAGCTGGTTCTCTCCGAAATAGCTTTAGGGCTAGCCTCAAGTGATGATTATTGGAGGTAGAGCACTGTTTGGACGAGGGGCCCCTCTCGGGTTACCGAATTCAGACAAACTCCGAATGCCAATTAATTTAACTTGGGAGTCAGAACATGGGTGATAAGGTCCGTGTTCGAAAGGGAAACAGCCCAGACCACCAGCTAAGGTCCCAAAATATATGTTAAGTGGAAAAGGATGTGGCGTTGCCCAGACAACTAGGATGTTGGCTTAGAAGCAGCCATCATTTAAAGAGTGCGTAATAGCTCACTAGTCGAGTGACACTGCGCCGAAAATGTACCGGGGCTAAACATATTACCGAAGCTGTGGATTGTCCTTTGGACAATGGTAGGAGAGCGTTCTAAGGGCGTTGAAGCATGATCGTAAGGACATGTGGAGCGCTTAGAAGTGAGAATGCCGGTGTGAGTAGCGAAAGACGGGTGAGAATCCCGTCCACCGATTGACTAAGGTTTCCAGAGGAAGGCTCGTCCGCTCTGGGTTAGTCGGGTCCTAAGCTGAGGCCGACAGGCGTAGGCGATGGATAACAGGTTGATATTCCTGTACCACCTATAATCGTTTTAATCGATGGGGGGACGCAGTAGGATAGGCGAAGCGTGCGATTGGATTGCACGTCTAAGCAGTAAGGCTGAGTATTAGGCAAATCCGGTACTCGTTAAGGCTGAGCTGTGATGGGGAGAAGACATTGTGTCTTCGAGTCGTTGATTTCACACTGCCGAGAAAAGCCTCTAGATAGAAAATAGGTGCCCGTACCGCAAACCGACACAGGTAGTCAAGATGAGAATTCTAAGGTGAGCGAGCGAACTCTCGTTAAGGAACTCGGCAAAATGACCCCGTAACTTCGGGAGAAGGGGTGCTCTTTAGGGTTAACGCCCAGAAGAGCCGCAGTGAATAGGCCCAAGCGACTGTTTATCAAAAACACAGGTCTCTGCTAAACCGTAAGGTGATGTATAGGGGCTGACGCCTGCCCGGTGCTGGAAGGTTAAGAGGAGTGGTTAGCTTCTGCGAAGCTACGAATCGAAGCCCCAGTAAACGGCGGCCGTAACTATAACGGTCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCCGCACGAAAGGCGTAACGATTTGGGCACTGTCTCAACGAGAGACTCGGTGAAATCATAGTACCTGTGAAGATGCAGGTTACCCGCGACAGGACGGAAAGACCCCGTGGAGCTTTACTGTAGCCTGATATTGAAATTCGGCACAGCTTGTACAGGATAGGTAGGAGCCTTTGAAACGTGAGCGCTAGCTTACGTGGAGGCGCTGGTGGGATACTACCCTAGCTGTGTTGGCTTTCTAACCCGCACCACTTATCGTGGTGGGAGACAGTGTCAGGCGGGCAGTTTGACTGGGGCGGTCGCCTCCTAAAAGGTAACGGAGGCGCTCAAAGGTTCCCTCAGAATGGTTGGAAATCATTCATAGAGTGTAAAGGCATAAGGGAGCTTGACTGCGAGACCTACAAGTCGAGCAGGGTCGAAAGACGGACTTAGTGATCCGGTGGTTCCGCATGGAAGGGCCATCGCTCAACGGATAAAAGCTACCCCGGGGATAACAGGCTTATCTCCCCCAAGAGTTCACATCGACGGGGAGGTTTGGCACCTCGATGTCGGCTCATCGCATCCTGGGGCTGTAGTCGGTCCCAAGGGTTGGGCTGTTCGCCCATTAAAGCGGTACGCGAGCTGGGTTCAGAACGTCGTGAGACAGTTCGGTCCCTATCCGTCGTGGGCGTAGGAAATTTGAGAGGAGCTGTCCTTAGTACGAGAGGACCGGGATGGACATACCTCTGGTGTACCAGTTGTCGTGCCAACGGCATAGCTGGGTAGCTATGTGTGGACGGGATAAGTGCTGAAAGCATCTAAGCATGAAGCCCCCCTCAAGATGAGATTTCCCAACTTCGGTTATAAGATCCCTCAAAGATGATGAGGTTAATAGGTTCGAGGTGGAAGCATGGTGACATGTGGAGCTGACGAATACTAATCGATCGAAGACTTAATCAAAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3004058","ARO_id":"41124","ARO_name":"Staphylococcus aureus 23S rRNA with mutation conferring resistance to linezolid","ARO_description":"Point mutations in the 23S rRNA subunit of the large ribosomal bacterial subunit in Staphylococcus aureus, which confer resistance to linezolid by disrupting antibiotic target binding","ARO_category":{"41123":{"category_aro_accession":"3004057","category_aro_cvterm_id":"41123","category_aro_name":"23S rRNA with mutation conferring resistance to linezolid antibiotics","category_aro_description":"Point mutations in the 23S rRNA subunit may confer resistance to linezolid and other oxazolidinone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"35989":{"category_aro_accession":"0000072","category_aro_cvterm_id":"35989","category_aro_name":"linezolid","category_aro_description":"Linezolid is a synthetic antibiotic used for the treatment of serious infections caused by Gram-positive bacteria that are resistant to several other antibiotics. It inhibits protein synthesis by binding to domain V of the 23S rRNA of the 50S subunit of bacterial ribosomes.","category_aro_class_name":"Antibiotic"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36600":{"category_aro_accession":"3000461","category_aro_cvterm_id":"36600","category_aro_name":"florfenicol","category_aro_description":"Florfenicol is a fluorine derivative of chloramphenicol, where the nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3) and the hydroxyl group (-OH), by a fluorine group (-F). The action mechanism is the same as chloramphenicol's, where the antibiotic binds to the 23S RNA of the 50S subunit of bacterial ribosomes to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin 1A is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"vernamycin B-gamma","category_aro_description":"Vernamycin B-gamma is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"36218":{"category_aro_accession":"3000079","category_aro_cvterm_id":"36218","category_aro_name":"oxazolidinone antibiotic","category_aro_description":"Oxazolidinones are a class of synthetic antibiotics discovered the the 1980's.  They inhibit protein synthesis by binding to domain V of the 23S rRNA of the 50S subunit of bacterial ribosomes.  Linezolid is the only member of this class currently in clinical use.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2691":{"model_id":"2691","model_name":"Type A NfxB","model_type":"protein overexpression model","model_type_id":"41091","model_description":"This model detects protein overexpression based on the presence of mutations.The detection of the protein without an associated mutation indicates that the protein is likely to be expressed at low or basal levels. The detection of the protein with the mutation indicates that the protein is likely overexpressed. This model reflects how certain proteins are functional with and without mutations. For example, efflux pump subunits and regulators are functional with mutations and without mutations. Without mutations, efflux pump subunits and regulators are usually expressed at a low level. When an efflux pump regulator has a mutation, it can cause the overexpression of the efflux pump it is responsible for regulating, leading to resistance to specific drugs. Protein overexpression models have two parameters: a curated BLASTP cutoff, and a curated set of mutations (single resistance variants, frameshift mutations, indels, etc.) shown clinically to confer resistance. This model type is a combination of the protein homolog and protein variant model. A detected hit can be categorized as Perfect, Strict, or Loose with no mutation(s) or as Strict or Loose with mutation(s).","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"7548":"R42G"},"clinical":{"7548":"R42G"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"310"}},"model_sequences":{"sequence":{"4022":{"protein_sequence":{"accession":"NP_253290.1","sequence":"MTLISHDERLIKALAVAIVDRPRATLKELAEAAGVSKATLHRFCGTRDNLVQMLEDHGETVLNQIIQACDLEHAEPLEALQRLIKEHLTHRELLVFLVFQYRPDFLDPHGEGARWQSYLEALDAFFLRGQQKGVFRIDITAAVFTELFITLVYGMVDAERRGRAASSNSAHTLEQMFLHGASNPARS"},"dna_sequence":{"accession":"NC_002516.2","fmin":"5155560","fmax":"5156124","strand":"+","sequence":"ATGACCCTGATTTCCCATGACGAGCGACTCATCAAGGCGCTGGCAGTCGCTATCGTCGACCGCCCGCGAGCGACGCTGAAGGAACTGGCCGAGGCGGCCGGCGTAAGCAAGGCCACCCTGCACCGCTTCTGCGGCACGCGGGACAACCTGGTGCAGATGCTCGAGGACCACGGAGAGACCGTACTGAACCAGATCATCCAGGCCTGCGACCTGGAGCATGCCGAGCCTCTGGAGGCGTTGCAGCGCCTGATCAAGGAACACCTCACCCACCGCGAGCTGCTGGTATTCCTGGTATTCCAGTACCGCCCGGACTTCCTCGACCCGCACGGCGAAGGCGCACGCTGGCAGTCCTACCTGGAAGCGCTGGACGCCTTCTTCCTGCGCGGACAGCAGAAAGGCGTGTTTCGCATCGACATCACGGCGGCCGTGTTCACCGAACTGTTCATCACCCTGGTCTACGGCATGGTCGATGCGGAACGTCGCGGACGGGCGGCCAGCTCCAATTCCGCGCATACCCTGGAGCAGATGTTCCTCCATGGCGCCTCCAATCCGGCTCGCTCCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3004059","ARO_id":"41125","ARO_name":"Type A NfxB","ARO_description":"Type A NfxB mutants are four to eight times more resistant to ofloxacin, erythromycin, and new zwitterionic cephems, i.e., cefpirome, cefclidin, cefozopran, and cefoselis, than the parent strain, PAO1. nfxB corresponds to 2 loci in Pseudomonas aeruginosa PAO1 (gene name: esrC\/nfxB) and 2 loci in Pseudomonas aeruginosa LESB58 (gene name: nfxB).","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2693":{"model_id":"2693","model_name":"Type B NfxB","model_type":"protein overexpression model","model_type_id":"41091","model_description":"This model detects protein overexpression based on the presence of mutations.The detection of the protein without an associated mutation indicates that the protein is likely to be expressed at low or basal levels. The detection of the protein with the mutation indicates that the protein is likely overexpressed. This model reflects how certain proteins are functional with and without mutations. For example, efflux pump subunits and regulators are functional with mutations and without mutations. Without mutations, efflux pump subunits and regulators are usually expressed at a low level. When an efflux pump regulator has a mutation, it can cause the overexpression of the efflux pump it is responsible for regulating, leading to resistance to specific drugs. Protein overexpression models have two parameters: a curated BLASTP cutoff, and a curated set of mutations (single resistance variants, frameshift mutations, indels, etc.) shown clinically to confer resistance. This model type is a combination of the protein homolog and protein variant model. A detected hit can be categorized as Perfect, Strict, or Loose with no mutation(s) or as Strict or Loose with mutation(s).","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"7549":"H87R"},"clinical":{"7549":"H87R"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"310"}},"model_sequences":{"sequence":{"4023":{"protein_sequence":{"accession":"NP_253290.1","sequence":"MTLISHDERLIKALAVAIVDRPRATLKELAEAAGVSKATLHRFCGTRDNLVQMLEDHGETVLNQIIQACDLEHAEPLEALQRLIKEHLTHRELLVFLVFQYRPDFLDPHGEGARWQSYLEALDAFFLRGQQKGVFRIDITAAVFTELFITLVYGMVDAERRGRAASSNSAHTLEQMFLHGASNPARS"},"dna_sequence":{"accession":"NC_002516.2","fmin":"5155560","fmax":"5156124","strand":"+","sequence":"ATGACCCTGATTTCCCATGACGAGCGACTCATCAAGGCGCTGGCAGTCGCTATCGTCGACCGCCCGCGAGCGACGCTGAAGGAACTGGCCGAGGCGGCCGGCGTAAGCAAGGCCACCCTGCACCGCTTCTGCGGCACGCGGGACAACCTGGTGCAGATGCTCGAGGACCACGGAGAGACCGTACTGAACCAGATCATCCAGGCCTGCGACCTGGAGCATGCCGAGCCTCTGGAGGCGTTGCAGCGCCTGATCAAGGAACACCTCACCCACCGCGAGCTGCTGGTATTCCTGGTATTCCAGTACCGCCCGGACTTCCTCGACCCGCACGGCGAAGGCGCACGCTGGCAGTCCTACCTGGAAGCGCTGGACGCCTTCTTCCTGCGCGGACAGCAGAAAGGCGTGTTTCGCATCGACATCACGGCGGCCGTGTTCACCGAACTGTTCATCACCCTGGTCTACGGCATGGTCGATGCGGAACGTCGCGGACGGGCGGCCAGCTCCAATTCCGCGCATACCCTGGAGCAGATGTTCCTCCATGGCGCCTCCAATCCGGCTCGCTCCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3004060","ARO_id":"41127","ARO_name":"Type B NfxB","ARO_description":"Type B NfxB mutants are more resistant to tetracycline and chloramphenicol, as well as ofloxacin, erythromycin, and the new zwitterionic cephems, than was PAO1, and they are four to eight times more susceptible to carbenicillin, sulbenicillin, imipenem, panipenem, biapenem, moxalactam, aztreonam, gentamicin, and kanamycin than PAO1. The mutation at the 46th amino acid position is sufficient for overproduction of OprJ and the multidrug resistance. nfxB corresponds to 2 loci in Pseudomonas aeruginosa PAO1 (gene name: esrC\/nfxB) and 2 loci in Pseudomonas aeruginosa LESB58 (gene name: nfxB).","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2695":{"model_id":"2695","model_name":"MexCD\u2013OprJ with type B NfxB mutation","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)","model_param":{"41141":{"param_type":"efflux pump components","param_description":"This detection model parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305.","param_type_id":"41141","param_value":{"7552":"2693,805,1523,704"}}},"ARO_accession":"3004062","ARO_id":"41129","ARO_name":"MexCD-OprJ with type B NfxB mutation","ARO_description":"MexCD-OprJ with Type B NfxB mutions are more resistant to tetracycline and chloramphenicol, as well as ofloxacin, erythromycin, and the new zwitterionic cephems, than was PAO1, and they are four to eight times more susceptible to carbenicillin, sulbenicillin, imipenem, panipenem, biapenem, moxalactam, aztreonam, gentamicin, and kanamycin than PAO1.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2697":{"model_id":"2697","model_name":"EdeQ","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"250"}},"model_sequences":{"sequence":{"4026":{"protein_sequence":{"accession":"AHH86051.1","sequence":"MSVTLREVTLENWEECIELEPTPEQSEFVAPNLYSIAESKFQTTFVPLAIYHDDTMVGFVMYGLDPDDGNYWIYRLLIDAKYQRLGYGRTAISQVIEILKAKEDCQKIVIGYAPANVAAENLYASLGFQKNGMVLFGETIAELNF"},"dna_sequence":{"accession":"KC771276.1","fmin":"44894","fmax":"45332","strand":"+","sequence":"ATGTCTGTGACACTTCGTGAAGTAACTTTGGAAAACTGGGAAGAGTGTATTGAACTGGAACCTACTCCCGAACAGAGCGAGTTTGTTGCCCCAAACCTTTACTCCATCGCTGAATCAAAGTTTCAAACTACATTTGTTCCTTTGGCCATATACCATGATGACACGATGGTTGGCTTTGTCATGTATGGGCTTGACCCTGACGATGGGAATTACTGGATTTACAGACTCTTAATTGATGCGAAGTACCAACGACTAGGCTATGGACGTACTGCCATTTCACAAGTCATTGAGATCCTGAAAGCAAAGGAAGATTGTCAAAAAATTGTCATTGGCTATGCCCCAGCCAATGTCGCAGCCGAAAACCTTTACGCTTCGCTCGGATTTCAAAAGAATGGAATGGTTTTGTTCGGCGAGACGATTGCAGAATTGAACTTTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41133","NCBI_taxonomy_name":"Brevibacillus brevis","NCBI_taxonomy_id":"1393"}}}},"ARO_accession":"3004063","ARO_id":"41130","ARO_name":"EdeQ","ARO_description":"EdeQ is an N-acetyltransferase enzyme that confers high-level self-resistance to edeine in Brevibacillus brevis, a natural edeine producer. EdeQ converts active edeine to N-acetyledeine, which is ineffective in vivo.","ARO_category":{"41131":{"category_aro_accession":"3004064","category_aro_cvterm_id":"41131","category_aro_name":"Edeine acetyltransferase","category_aro_description":"Edeine acetyltransferase enzymes catalyze the transfer of an acetyl group to active edeine, converting it to an inactive form in vivo. This mechanism is used for high-level self-resistance in edeine-producing Brevibacillus spp.","category_aro_class_name":"AMR Gene Family"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36666":{"category_aro_accession":"3000527","category_aro_cvterm_id":"36666","category_aro_name":"polyamine antibiotic","category_aro_description":"Polyamine antibiotics are organic compounds having two or more primary amino groups.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2706":{"model_id":"2706","model_name":"MvaT","model_type":"protein knockout model","model_type_id":"40354","model_description":"An AMR detection model for instances where the absence of a protein - due to large-scale insertion elements, large deletions, or other methods of protein knockout - confers clinical resistance to a known antibiotic. These models include reference sequences. Protein knockout models are currently in development.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"4034":{"protein_sequence":{"accession":"NP_253005.1","sequence":"MSLINEYRATEEAIKELQERLKSLEQDDKLKKELEFEEKLRTLMGTYQKSLRDVISLLDPDAKIGKSTRTAKAPAGKRARKVKQYKNPHTGEVIETKGGNHKTLKEWKAKWGPEAVESWATLLG"},"dna_sequence":{"accession":"NC_002516.2","fmin":"4843811","fmax":"4844186","strand":"+","sequence":"ATGTCCCTGATCAACGAATATCGCGCCACGGAAGAAGCCATCAAGGAACTTCAGGAGCGCCTGAAGTCCCTGGAACAAGACGACAAACTGAAAAAAGAACTGGAATTCGAAGAGAAGCTGCGCACGCTGATGGGCACTTACCAGAAGTCCCTGCGTGACGTGATTTCCCTGCTCGATCCGGACGCCAAGATCGGCAAGAGCACCCGCACCGCCAAGGCACCTGCCGGCAAGCGCGCGCGCAAGGTCAAGCAGTACAAGAACCCGCACACCGGCGAAGTCATCGAGACCAAGGGCGGCAACCACAAGACTTTGAAAGAGTGGAAAGCCAAGTGGGGCCCCGAGGCCGTCGAGAGCTGGGCCACCCTGCTCGGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3004069","ARO_id":"41146","ARO_name":"MvaT","ARO_description":"MvaT, a global regulator of virulence genes in P. aeruginosa, has also shown to be able to repress the expression of the MexEF-OprN pump.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2707":{"model_id":"2707","model_name":"MexEF-OprN with MvaT deletion conferring resistance to chloramphenicol and norfloxacin","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)","model_param":{"41141":{"param_type":"efflux pump components","param_description":"This detection model parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305.","param_type_id":"41141","param_value":{"7585":"2706,1067,1300,172"}}},"ARO_accession":"3004070","ARO_id":"41147","ARO_name":"MexEF-OprN with MvaT deletion conferring resistance to chloramphenicol and norfloxacin","ARO_description":"A deletion of MvaT results in the overexpression of MexEF-OprN conferring resistance to chloramphenicol and norfloxacin.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"255":{"model_id":"255","model_name":"determinant of bleomycin resistance","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"3682":{"protein_sequence":{"accession":"YP_007652797.1","sequence":"MADHVTPNLPSRDFDVTEAFYAKLGFATSWKDRGWMILQRGGLQLEFFPYPDLDPATSSFGCCLRLDDLDAMVALVNAAGAEEKSTGWPRFKAPQLEASGLRIGYLIDPDCTLVRLIQNPD"},"dna_sequence":{"accession":"NC_020818.1","fmin":"9883","fmax":"10249","strand":"+","sequence":"ATGGCTGACCACGTCACCCCCAATCTGCCATCGCGCGATTTCGATGTGACAGAGGCGTTTTATGCGAAGCTGGGCTTTGCGACGAGTTGGAAGGATCGCGGCTGGATGATCCTGCAGCGCGGCGGTTTGCAGCTCGAATTCTTCCCCTATCCTGACCTCGACCCAGCTACGAGCTCGTTCGGCTGTTGCCTGCGGTTGGATGATCTCGATGCCATGGTGGCATTGGTGAACGCGGCGGGAGCCGAGGAAAAAAGCACCGGCTGGCCGCGCTTCAAAGCTCCGCAACTGGAGGCGAGCGGCCTGAGGATCGGCTACCTGATCGATCCCGACTGCACGCTGGTGCGGCTGATCCAGAACCCCGACTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001205","ARO_id":"37586","ARO_name":"BRP(MBL)","ARO_description":"A novel bleomycin resistance protein encoded by a metallo-beta-lactamase-associated ble gene. Expression of BRP(MBL) confers resistance to bleomycin and bleomycin-like antibiotics in Enterobacteriaceae and Acinetobacter, where it is co-expressed with an MBL and controlled by the same promoter region.","ARO_category":{"41420":{"category_aro_accession":"3004256","category_aro_cvterm_id":"41420","category_aro_name":"Bleomycin resistant protein","category_aro_description":"Bleomycin resistant proteins (BRP) confer resistance to bleomycin and to bleomycin-like molecules.","category_aro_class_name":"AMR Gene Family"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2267":{"model_id":"2267","model_name":"Escherichia coli nfsA mutations conferring resistance to nitrofurantoin","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3467":"R15C","3468":"Y45C","3469":"R203L","3470":"R203C","3471":"G131D","3472":"S33R","8195":"R133S"},"clinical":{"3467":"R15C","3468":"Y45C","3469":"R203L","3470":"R203C","3471":"G131D","3472":"S33R","8195":"R133S"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"425"},"41342":{"param_type":"deletion mutation from peptide sequence","param_description":"A subtype of the deletion mutation detection model parameter. This parameter is used when a set of deletion mutations is reported in a peptide sequence format. These are specific to codon deletions, where a multiple of 3 nucleotides are deleted. Mutations of this type are reported in the CARD with the notation: [-][AAs][position range].","param_type_id":"41342","param_value":{"8187":"-MTPTIELICGHRSIRHFTDEPISEAQ1-26","8188":"-QYDEQLA191-197"}},"41343":{"param_type":"deletion mutation from nucleotide sequence","param_description":"A subtype of the deletion mutation detection model parameter. This parameter is used when a set of deletion mutations is reported in a nucleotide sequence format. Such mutations may be of variable length - possibly causing a frameshift, but not premature termination of functional knockout. Mutation parameters of this type are reported in the CARD with the notation: [-]nt[position]:[nucleotides].","param_type_id":"41343","param_value":{"8189":"-nt25:T","8190":"-nt603:C"}},"40394":{"param_type":"nonsense mutation","param_description":"A nucleotide substitution resulting in a change from an amino acid codon to a STOP codon. Nonsense mutations truncate protein translation prematurely, resulting in a defective or completely inactive protein. In CARD, nonsense mutations may be attached to models using the notation: [wild type amino acid][position][STOP] (e.g. Q42STOP). This parameter is not currently used in detection algorithms.","param_type_id":"40394","param_value":{"8192":"Q44STOP","8193":"K141STOP","8194":"E233STOP"}}},"model_sequences":{"sequence":{"3520":{"protein_sequence":{"accession":"NP_415372.1","sequence":"MTPTIELICGHRSIRHFTDEPISEAQREAIINSARATSSSSFLQCSSIIRITDKALREELVTLTGGQKHVAQAAEFWVFCADFNRHLQICPDAQLGLAEQLLLGVVDTAMMAQNALIAAESLGLGGVYIGGLRNNIEAVTKLLKLPQHVLPLFGLCLGWPADNPDLKPRLPASILVHENSYQPLDKGALAQYDEQLAEYYLTRGSNNRRDTWSDHIRRTIIKESRPFILDYLHKQGWATR"},"dna_sequence":{"accession":"NC_000913.3","fmin":"891183","fmax":"891906","strand":"+","sequence":"ATGACGCCAACCATTGAACTTATTTGTGGCCATCGCTCCATTCGCCATTTCACTGATGAACCCATTTCCGAAGCGCAGCGTGAGGCGATTATTAACAGCGCCCGTGCGACGTCCAGTTCCAGTTTTTTGCAGTGCAGTAGCATTATTCGCATTACCGACAAAGCGTTACGTGAAGAACTGGTGACGCTGACCGGCGGGCAAAAACACGTAGCGCAAGCGGCGGAGTTCTGGGTGTTCTGTGCCGACTTTAACCGCCATTTACAGATCTGTCCGGATGCTCAGCTCGGCCTGGCGGAACAACTGTTGCTCGGTGTCGTTGATACGGCAATGATGGCGCAGAATGCATTAATCGCAGCGGAATCGCTGGGATTGGGCGGGGTATATATCGGCGGCCTGCGCAATAATATTGAAGCGGTGACGAAACTGCTTAAATTACCGCAGCATGTTCTGCCGCTGTTTGGGCTGTGCCTTGGCTGGCCTGCGGATAATCCGGATCTTAAGCCGCGTTTACCGGCCTCCATTTTGGTGCATGAAAACAGCTATCAACCGCTGGATAAAGGCGCACTGGCGCAGTATGACGAGCAACTGGCGGAATATTACCTCACCCGTGGCAGCAATAATCGCCGGGATACCTGGAGCGATCATATCCGCCGAACAATCATTAAAGAAAGCCGCCCATTTATTCTGGATTATTTGCACAAACAGGGTTGGGCGACGCGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3003751","ARO_id":"40407","ARO_name":"Escherichia coli nfsA mutations conferring resistance to nitrofurantoin","ARO_description":"nfsA encodes the major oxygen-insesitive nitroreductase in E. coli. The first step of resistance to nitrofurazone is mutation of nfsA.","ARO_category":{"40411":{"category_aro_accession":"3003754","category_aro_cvterm_id":"40411","category_aro_name":"antibiotic resistant nfsA","category_aro_description":"The nfsA-encoded nitroreductase is the major oxygen-insensitive nitroreductase present in E. coli. NfsA uses only NADPH and has broad electron acceptor specificity. Mutations in nfsA cause resistance to nitrofurazone and furazolidone. Resistance to nitrofurantoin via mutation of nfsA reduces the fitness of clinical isolates of E. coli.","category_aro_class_name":"AMR Gene Family"},"35992":{"category_aro_accession":"0000075","category_aro_cvterm_id":"35992","category_aro_name":"nitrofurantoin","category_aro_description":"Nitrofurantoin is an antibiotic used to treat urinary tract infections. It inhibits enzyme synthesis by inhibiting essential enzymes involved in the citric acid cycle, as well as those involved in DNA, RNA, and protein synthesis. It is marketed under the following brand names: Furadantin, Macrobid, Macrodantin, Nitro Macro and Urantoin.","category_aro_class_name":"Antibiotic"},"41240":{"category_aro_accession":"3004116","category_aro_cvterm_id":"41240","category_aro_name":"nitrofuran antibiotic","category_aro_description":"Nitrofurans are chemotherapeutic agents with antibacterial and antiprotozoal activity.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1897":{"model_id":"1897","model_name":"tet(L)","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"880"}},"model_sequences":{"sequence":{"518":{"protein_sequence":{"accession":"AAA22851.1","sequence":"MNTSYSQSNLRHNQILIWLCILSFFSVLNEMVLNVSLPDIANDFNKPPASTNWVNTAFMLTFSIGTAVYGKLSDQLGIKRLLLFGIIINCFGSVIGFVGHSFFSLLIMARFIQGAGAAAFPALVMVVVARYIPKENRGKAFGLIGSIVAMGEGVGPAIGGMIAHYIHWSYLLLIPMITIITVPFLMKLLKKEVRIKGHFDIKGIILMSVGIVFFMLFTTSYSISFLIVSVLSFLIFVKHIRKVTDPFVDPGLGKNIPFMIGVLCGGIIFGTVAGFVSMVPYMMKDVHQLSTAEIGSVIIFPGTMSVIIFGYIGGILVDRRGPLYVLNIGVTFLSVSFLTASFLLETTSWFMTIIIVFVLGGLLFTKTVISTIVSSSLKQQEAGAGMSLLNFTSFLSEGTGIAIVGGLLSIPLLDQRLLPMEVDQSTYLYSNLLLLFSGIIVISWLVTLNVYKHSQRDF"},"dna_sequence":{"accession":"M11036","fmin":"0","fmax":"1377","strand":"+","sequence":"GTGAATACATCCTATTCACAATCGAATTTACGACACAACCAAATTTTAATTTGGCTTTGCATTTTATCTTTTTTTAGCGTATTAAATGAAATGGTTTTGAACGTCTCATTACCTGATATTGCAAATGATTTTAATAAACCACCTGCGAGTACAAACTGGGTGAACACAGCCTTTATGTTAACCTTTTCCATTGGAACAGCTGTATATGGAAAGCTATCTGATCAATTAGGCATCAAAAGGTTACTCCTATTTGGAATTATAATAAATTGTTTCGGGTCGGTAATTGGGTTTGTTGGCCATTCTTTCTTTTCCTTACTTATTATGGCTCGTTTTATTCAAGGGGCTGGTGCAGCTGCATTTCCAGCACTCGTAATGGTTGTAGTTGCGCGCTATATTCCAAAGGAAAATAGGGGTAAAGCATTTGGTCTTATTGGATCGATAGTAGCCATGGGAGAAGGAGTCGGTCCAGCGATTGGTGGAATGATAGCCCATTATATTCATTGGTCCTATCTTCTACTCATTCCTATGATAACAATTATCACTGTTCCGTTTCTTATGAAATTATTAAAGAAAGAAGTAAGGATAAAAGGTCATTTTGATATCAAAGGAATTATACTAATGTCTGTAGGCATTGTATTTTTTATGTTGTTTACAACATCATATAGCATTTCTTTTCTTATCGTTAGCGTGCTGTCATTCCTGATATTTGTAAAACATATCAGGAAAGTAACAGATCCTTTTGTTGATCCCGGATTAGGGAAAAATATACCTTTTATGATTGGAGTTCTTTGTGGGGGAATTATATTTGGAACAGTAGCAGGGTTTGTCTCTATGGTTCCTTATATGATGAAAGATGTTCACCAGCTAAGTACTGCCGAAATCGGAAGTGTAATTATTTTCCCTGGAACAATGAGTGTCATTATTTTCGGCTACATTGGTGGGATACTTGTTGATAGAAGAGGTCCTTTATACGTGTTAAACATCGGAGTTACATTTCTTTCTGTTAGCTTTTTAACTGCTTCCTTTCTTTTAGAAACAACATCATGGTTCATGACAATTATAATCGTATTTGTTTTAGGTGGGCTTCTGTTCACCAAAACAGTTATATCAACAATTGTTTCAAGTAGCTTGAAACAGCAGGAAGCTGGTGCTGGAATGAGTTTGCTTAACTTTACCAGCTTTTTATCAGAGGGAACAGGTATTGCAATTGTAGGTGGTTTATTATCCATACCCTTACTTGATCAAAGGTTATTACCTATGGAAGTTGATCAGTCAACTTATCTGTATAGTAATTTGTTATTACTTTTTTCAGGAATCATTGTCATTAGTTGGCTGGTTACCTTGAATGTATATAAACATTCTCAAAGGGATTTCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36826","NCBI_taxonomy_name":"Geobacillus stearothermophilus","NCBI_taxonomy_id":"1422"}}}},"ARO_accession":"3000179","ARO_id":"36318","ARO_name":"tet(L)","ARO_description":"TetL is a tetracycline efflux protein found in many species of Gram-negative and Gram-positive bacteria.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1240":{"model_id":"1240","model_name":"Bacillus Cluster A intrinsic mph","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4389":{"protein_sequence":{"accession":"EEL41021.1","sequence":"MEEIKMNTLKIKQLATKEGLNILEDSIKINESGVDFQVAHAKEQNGDKWILRIPRRPESMRHVLQEKKALEIIKNHAGFQVPDWSIFTEDLIAYKQLSGVPAATIDIEQQGYIWSFNEKNAPSEYHISLGKVLANLHSLPQQEFNNIGIEILTANELRASMEQRMNRVKEQYYVNQKLWDRWQAWLTEDSFWPSHVGVTHGDIHPGHILIDKKNNVTGLIDWTEVGIADVSIDFTSHYLLFGKDGLTKLISSYDNAGGKTWSRMDEHIIELLTTSSITVAEYAQVSGLKEMHEAAVHMLATES"},"dna_sequence":{"accession":"ACMJ01000036","fmin":"72074","fmax":"72986","strand":"-","sequence":"TTAACTTTCAGTTGCTAGCATGTGTACAGCTGCTTCATGCATCTCTTTCAAACCTGACACTTGAGCATATTCAGCAACAGTGATACTACTTGTTGTTAGAAGTTCGATAATATGTTCATCCATTCTTGACCAAGTTTTACCACCAGCATTGTCATAAGAGCTAATTAACTTTGTTAGTCCATCTTTCCCAAAGAGCAGATAATGTGATGTGAAATCTATAGAAACATCAGCTATCCCTACTTCTGTCCAATCGATTAAGCCAGTTACATTATTTTTCTTATCAATCAGGATATGACCTGGATGTATATCCCCATGCGTTACTCCTACATGAGATGGCCAAAAAGAATCTTCAGTTAGCCATGCTTGCCAACGATCCCATAATTTTTGATTGACATAGTATTGTTCCTTCACTCGATTCATCCTTTGTTCCATAGAAGCTCTTAATTCATTAGCAGTAAGAATTTCAATACCGATATTATTAAATTCTTGTTGAGGTAATGAGTGTAAATTCGCTAGAACTTTTCCTAATGAAATATGGTATTCAGATGGTGCGTTTTTTTCATTAAAGCTCCATATATATCCTTGTTGTTCTATATCAATAGTGGCGGCAGGAACGCCACTTAGTTGCTTATAGGCAATTAAGTCTTCAGTGAATATAGACCAATCAGGAACTTGGAATCCTGCATGGTTTTTTATGATTTCCAATGCCTTTTTTTCTTGTAGGACATGTCTCATAGATTCTGGTCTACGAGGAATTCTTAGTATCCATTTATCTCCGTTTTGTTCTTTAGCGTGTGCTACTTGAAAGTCAACACCAGATTCATTGATTTTTATTGAATCTTCTAAGATATTTAGGCCTTCCTTAGTTGCTAATTGTTTAATTTTAAGTGTGTTCATTTTTATTTCCTCCAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39617","NCBI_taxonomy_name":"Bacillus cereus Rock3-29","NCBI_taxonomy_id":"526984"}}}},"ARO_accession":"3003072","ARO_id":"39614","ARO_name":"Bacillus Cluster A intrinsic mph","ARO_description":"Bacillus Cluster A mph are chromosomally-encoded macrolide phosphotransferases that inactivate 14- and 15-membered macrolides such as erythromycin, clarithromycin, azithromycin.","ARO_category":{"36472":{"category_aro_accession":"3000333","category_aro_cvterm_id":"36472","category_aro_name":"macrolide phosphotransferase (MPH)","category_aro_description":"Macrolide phosphotransferases (MPH) are enzymes encoded by macrolide phosphotransferase genes (mph genes). These enzymes phosphorylate macrolides in GTP dependent manner at 2'-OH of desosamine sugar thereby inactivating them. Characterized MPH's are differentiated based on their substrate specificity.","category_aro_class_name":"AMR Gene Family"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"249":{"model_id":"249","model_name":"basS","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"900"}},"model_sequences":{"sequence":{"3375":{"protein_sequence":{"accession":"AEX49906.1","sequence":"MSRAAVPSVRRRLLVNLLVGFVLCWLSVAALTYHLSLKQVNRLFDDDMVDFGEAALRLLDLATEDQAGEDGSITEIIERSREAIQGLPLLRRESALGYALWRDGQPLLSSLNLPPEITAQGPGFSTVEAQGTHWRVLQLNIDGFQIWISENLIYRQHTMNLLLFYSLFPLLLALPLLGGLVWFGVARGLAPLREVQAEVQQRSARHLQPIAVEAVPLEIRGLIDELNLLLERLRTALEAERRLTSDAAHEIRTPLASLRTHAQVALRSEDPKAHARGLLQVSRSVERISTLMEQILLLARLDGDALLEQFHPVNLATLAEDVLSELARQAIDKDIELSLHQETVHVMGIDLWLKAMVGNLVGNALRYTPAGGQVEIRVENRAQHAVLRVRDNGPGVALEEQQAIFTRFYRSPATSSGEGSGLGLPIVKRIVELHFGSIGLGKGLEGKGLEVQVFLPKTQPDATRPPARGPDSGRSHI"},"dna_sequence":{"accession":"JQ340365","fmin":"0","fmax":"1434","strand":"+","sequence":"ATGTCCCGTGCCGCCGTCCCCTCCGTCCGCCGGCGCCTGCTGGTCAACCTGCTGGTCGGCTTCGTGCTGTGCTGGCTGAGCGTGGCGGCGCTGACCTACCACCTCTCGCTGAAGCAGGTGAACCGCCTGTTCGACGACGACATGGTGGACTTCGGCGAAGCCGCCCTGCGCCTGCTCGACCTTGCCACCGAAGACCAGGCCGGCGAGGACGGCTCCATCACCGAGATCATCGAACGCAGCCGCGAAGCGATCCAGGGTCTGCCCCTGCTGCGCCGCGAAAGCGCCCTCGGCTACGCCCTGTGGCGCGACGGCCAGCCGCTGCTGTCGAGCCTCAACCTGCCGCCGGAGATCACGGCCCAGGGCCCCGGCTTCAGCACCGTGGAAGCCCAGGGCACCCACTGGCGGGTGCTCCAGCTGAACATCGACGGCTTCCAGATCTGGATCAGCGAAAACCTGATCTACCGCCAGCACACCATGAACCTGCTGCTGTTCTACTCGCTGTTCCCACTGCTGCTGGCGCTGCCGTTGCTCGGCGGCCTGGTCTGGTTCGGCGTTGCCCGCGGCCTGGCGCCGCTACGCGAAGTGCAGGCCGAGGTCCAGCAGCGCTCCGCGCGACACCTGCAGCCGATCGCGGTGGAAGCGGTGCCGCTGGAGATCCGCGGCCTCATCGACGAACTCAACCTCCTGCTGGAGCGTCTGCGCACCGCCCTCGAGGCCGAACGCCGACTGACCAGCGACGCCGCCCATGAAATCCGCACGCCACTGGCCAGCCTGCGCACCCATGCCCAGGTCGCGCTGCGTTCGGAAGACCCCAAGGCCCACGCCCGCGGCCTGCTGCAAGTCAGTCGCAGCGTCGAGCGGATCAGCACCTTGATGGAGCAGATCCTGCTCCTCGCCCGCCTCGACGGCGACGCCCTGCTGGAGCAATTCCACCCGGTCAACCTCGCCACCCTGGCCGAAGACGTACTCTCCGAACTGGCGCGCCAGGCCATCGACAAGGACATCGAGCTGTCGTTGCACCAGGAGACCGTGCACGTGATGGGCATCGACCTGTGGCTGAAGGCGATGGTCGGCAACCTGGTGGGCAACGCCCTGCGCTACACACCGGCCGGGGGCCAGGTCGAGATCCGCGTCGAGAATCGCGCCCAGCACGCCGTGCTGCGGGTGCGCGACAACGGCCCCGGGGTCGCCCTGGAAGAGCAGCAGGCGATCTTCACCCGCTTCTACCGCAGCCCCGCCACCAGCAGCGGCGAGGGCAGCGGCCTGGGCCTGCCGATCGTCAAGCGCATCGTCGAACTGCACTTCGGCAGTATCGGCCTGGGCAAGGGACTGGAGGGCAAAGGGCTGGAAGTGCAGGTGTTCCTGCCGAAGACCCAGCCGGACGCGACGCGGCCGCCGGCCAGAGGTCCGGACAGCGGGCGGTCACATATCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3003583","ARO_id":"40193","ARO_name":"basS","ARO_description":"Histidine protein kinase sensor Lipid A modification gene; part of a two-component system involved in polymyxin resistance that senses high extracellular Fe(2+)","ARO_category":{"41433":{"category_aro_accession":"3004269","category_aro_cvterm_id":"41433","category_aro_name":"pmr phosphoethanolamine transferase","category_aro_description":"This family of phosphoethanolamine transferase catalyze the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine to lipid A, which impedes the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2291":{"model_id":"2291","model_name":"Chlamydia trachomatis intrinsic murA conferring resistance to fosfomycin","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"3556":{"protein_sequence":{"accession":"AAN28945","sequence":"MPGIKVFGETVLRGSVRVSGAKNATTKLLVASLLSDQRTILKNVPNIEDVRQTVDLCRVLGAIVEWDQQAQVIEIHTPRILLSKVPPQFSCVNRIPILLLGALLRRCPYGIFVPILGGDAIGPRTLHFHLEGWKKLGAEIVISDEGYWASAPNGLVGAHITLPYPSVGATENLILASVGAQGRTIIKNAALEVEIIDLIVFLQKAGVEITTDNDKTIEIFGCQDFYSVEHFIIPDKIEAASFGMAAVVSQGRIFVEQARHEHMIPFLKVLRSIGGGFSVHENGIEFFYDKPLKGGVLLETDVHPGFITDWQQPFAVLLSQSEGCSVIHETVHENRLGYLKGLVKMGAHCDLFHECLSAKSCRYSTGNHPHSAVIHGPTPLQATDLVIPDLRAGFAYVMAALIAEGGASWIENTEMLDRGYTDWRGKLERLGAKVLARDAVSVYV"},"dna_sequence":{"accession":"AY152390","fmin":"0","fmax":"1335","strand":"+","sequence":"ATGCCTGGTATCAAGGTTTTTGGAGAAACGGTCTTAAGAGGATCTGTGCGCGTGTCAGGAGCTAAAAATGCTACAACTAAATTACTTGTAGCCTCCTTACTTTCGGATCAGCGAACGATTTTAAAGAACGTCCCTAATATTGAAGATGTTCGGCAAACGGTAGATCTTTGTCGGGTTTTAGGGGCGATTGTAGAGTGGGATCAGCAAGCGCAAGTGATTGAAATTCACACTCCGCGCATTTTATTGTCCAAGGTTCCTCCGCAATTTTCTTGTGTTAATCGGATTCCTATTTTGCTGTTAGGAGCGTTGTTACGTCGTTGTCCTTATGGGATTTTTGTTCCTATTTTGGGAGGGGATGCTATAGGACCTCGTACGCTACATTTCCATTTAGAAGGATGGAAGAAGCTTGGAGCAGAGATAGTAATTAGTGATGAAGGCTATTGGGCTTCAGCTCCAAATGGTCTTGTTGGAGCACACATCACGTTACCCTACCCTTCTGTGGGAGCCACAGAAAACCTCATCCTTGCTTCTGTAGGGGCTCAAGGACGAACGATTATTAAGAATGCTGCTCTTGAAGTGGAAATCATTGATTTGATTGTCTTTTTACAGAAAGCAGGCGTGGAGATTACAACAGATAATGATAAGACCATCGAAATTTTTGGATGTCAGGATTTCTATTCTGTTGAGCACTTCATTATTCCAGATAAAATCGAGGCTGCTTCTTTCGGTATGGCTGCGGTAGTTTCTCAGGGAAGGATCTTCGTAGAACAAGCGCGCCATGAGCATATGATCCCTTTTTTAAAGGTATTAAGATCGATAGGAGGGGGATTCTCTGTACATGAGAATGGGATCGAATTTTTCTACGATAAGCCTTTGAAAGGGGGTGTTCTTCTAGAAACGGATGTGCATCCAGGGTTTATTACAGATTGGCAACAACCTTTTGCCGTATTGCTCTCTCAGTCAGAAGGTTGTTCGGTGATCCATGAGACAGTGCATGAGAATCGTCTTGGGTATTTGAAAGGTTTGGTAAAAATGGGAGCGCATTGTGATTTATTTCACGAGTGTTTGAGTGCTAAGTCGTGTCGCTATTCTACAGGGAATCATCCTCATAGCGCAGTCATTCATGGTCCGACTCCTTTGCAGGCAACAGACTTAGTGATTCCTGATTTGCGCGCAGGATTTGCTTATGTCATGGCCGCACTCATTGCAGAAGGCGGAGCCTCATGGATTGAGAATACCGAGATGCTGGATCGAGGGTACACTGATTGGCGAGGGAAATTAGAAAGATTAGGAGCTAAGGTTTTAGCGCGAGACGCAGTATCTGTGTATGTTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40470","NCBI_taxonomy_name":"Chlamydia trachomatis","NCBI_taxonomy_id":"813"}}}},"ARO_accession":"3003785","ARO_id":"40469","ARO_name":"Chlamydia trachomatis intrinsic murA conferring resistance to fosfomycin","ARO_description":"Chlamydia murA confers intrinsic resistance to fosfomycin. The presence of an aspartic acid residue in place of the critical cysteine at position 119 that enables fosfomycin binding is believed to be responsible for this intrinsic resistance.","ARO_category":{"39245":{"category_aro_accession":"3002811","category_aro_cvterm_id":"39245","category_aro_name":"murA transferase","category_aro_description":"murA or UDP-N-acetylglucosamine enolpyruvyl transferase catalyses the initial step in peptidoglycan biosynthesis and is inhibited by fosfomycin. Overexpression of murA through mutations confers fosfomycin resistance.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2108":{"model_id":"2108","model_name":"Enterococcus faecium EF-Tu mutants conferring resistance to GE2270A","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3055":"G258A","4119":"G275A"},"clinical":{"3055":"G258A","4119":"G275A"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3656":{"protein_sequence":{"accession":"YP_006374661.1","sequence":"MGMWCTLCTSYTYQTNKKYIVFLGGHFKMAKEKFDRSKPHVNIGTIGHVDHGKTTLTAAITTVLSKKNGGQAMAYDQIDGAPEERERGITISTAHVEYETDTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSAADGPMPQTREHILLSRQVGVPYIVVFLNKVDMVDDEELLELVEMEVRDLLTEYEFPGDDVPVVAGSALKALEGDASYEEKILELMAAVDEYIPTPERDNDKPFMMPVEDVFSITGRGTVATGRVERGQVRVGDEVEVVGIAEETSKTTVTGVEMFRKLLDYAEAGDNIGALLRGVAREDIQRGQVLAKPGTITPHTKFSAEVYVLTKEEGGRHTPFFTNYRPQFYFRTTDVTGVVELPEGTEMVMPGDNVTMEVELIHPIAIENGTKFSIREGGRTVGAGVVTEIKA"},"dna_sequence":{"accession":"NC_017960.1","fmin":"60337","fmax":"61609","strand":"+","sequence":"ATGGGCATGTGGTGTACCTTGTGTACATCATATACCTATCAGACAAATAAAAAATATATTGTATTTTTAGGAGGACATTTTAAAATGGCAAAAGAAAAATTTGACCGTTCTAAACCACACGTTAACATTGGTACTATCGGACACGTTGACCATGGTAAAACTACATTAACAGCTGCAATCACAACTGTACTATCTAAGAAAAACGGCGGCCAAGCTATGGCTTACGATCAAATCGATGGTGCTCCAGAAGAACGCGAACGCGGAATCACAATCTCAACAGCTCACGTTGAGTATGAAACAGATACACGCCACTACGCTCACGTTGACTGCCCAGGACACGCGGATTACGTTAAAAACATGATCACTGGTGCTGCTCAAATGGACGGAGCTATCTTGGTAGTTTCTGCTGCTGACGGCCCAATGCCTCAAACTCGTGAACACATCCTATTGTCTCGTCAAGTTGGTGTTCCTTACATCGTTGTATTCTTGAACAAAGTAGACATGGTTGATGACGAAGAATTACTAGAATTAGTTGAAATGGAAGTTCGTGACCTATTAACAGAATACGAATTCCCTGGTGACGATGTTCCTGTAGTTGCTGGATCAGCTTTGAAAGCTCTAGAAGGCGACGCTTCATACGAAGAAAAAATTCTTGAATTAATGGCTGCAGTTGACGAATACATCCCAACTCCAGAACGTGACAACGACAAACCATTCATGATGCCAGTTGAAGACGTGTTCTCAATTACTGGACGTGGTACTGTTGCTACAGGTCGTGTTGAACGTGGACAAGTTCGCGTTGGTGACGAAGTTGAAGTTGTTGGTATTGCTGAAGAAACTTCAAAAACAACAGTTACTGGTGTTGAAATGTTCCGTAAATTGTTAGACTACGCTGAAGCTGGAGACAACATTGGTGCTTTACTACGTGGTGTTGCACGTGAAGACATCCAACGTGGACAAGTTTTAGCTAAACCAGGTACAATCACACCTCATACAAAATTCTCTGCAGAAGTATACGTGTTGACAAAAGAAGAAGGTGGACGTCATACTCCATTCTTCACTAACTACCGTCCACAATTCTACTTCCGTACAACTGACGTAACAGGTGTTGTTGAATTACCAGAAGGAACTGAAATGGTTATGCCTGGCGACAACGTAACAATGGAAGTTGAATTAATCCACCCAATCGCTATCGAAAACGGTACTAAATTCTCAATCCGTGAAGGCGGACGTACAGTTGGTGCCGGTGTCGTTACAGAAATCAAAGCTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37599","NCBI_taxonomy_name":"Enterococcus faecium DO","NCBI_taxonomy_id":"333849"}}}},"ARO_accession":"3003438","ARO_id":"40022","ARO_name":"Enterococcus faecium EF-Tu mutants conferring resistance to GE2270A","ARO_description":"Sequence variants of Enterococcus faecium elongation factor Tu that confer resistance to GE2270A","ARO_category":{"37711":{"category_aro_accession":"3001312","category_aro_cvterm_id":"37711","category_aro_name":"elfamycin resistant EF-Tu","category_aro_description":"Sequence variants of elongation factor Tu that confer resistance to elfamycin antibiotics.","category_aro_class_name":"AMR Gene Family"},"36725":{"category_aro_accession":"3000586","category_aro_cvterm_id":"36725","category_aro_name":"pulvomycin","category_aro_description":"Pulvomycin is a polyketide antibiotic that binds elongation factor Tu (EF-Tu) to inhibit protein biosynthesis by preventing the formation of the ternary complex (EF-Tu*GTP*aa-tRNA). Phenotypically, it was shown that pulvomycin sensitivity is dominant over resistance.","category_aro_class_name":"Antibiotic"},"37636":{"category_aro_accession":"3001237","category_aro_cvterm_id":"37636","category_aro_name":"GE2270A","category_aro_description":"GE2270A is the model molecule of cyclic thiazolyl peptide elfamycins. GE2270A is produced by Planobispora rosea. Biosynthesis of the molecule has been shown to originate as a ribosomally synthesized peptide that undergoes significant post-translational modification. Clinical use of cyclic thiazolyl peptides is hindered by their low water solubility and bioavailability.","category_aro_class_name":"Antibiotic"},"37641":{"category_aro_accession":"3001242","category_aro_cvterm_id":"37641","category_aro_name":"enacyloxin IIa","category_aro_description":"Enacyloxin IIa is structurally distinct but acts in a similar mechanism to kirromycin-like elfamycins. It prohibits the transfer of the amino acid at the A site to the elongating peptide chain. It is most likely that the mechanism of action is that EF-Tu*GDP is locked in the EF-Tu*GTP form, and EF-Tu*GDP*aa-tRNA is immobilized on the ribosome. It is an open question whether enacyloxin IIa actually belongs to the kirromycin-like group of elfamycins due to their high similarity.","category_aro_class_name":"Antibiotic"},"39998":{"category_aro_accession":"3003414","category_aro_cvterm_id":"39998","category_aro_name":"LFF571","category_aro_description":"LFF571 is a novel semi-synthetic thiopeptide antibiotic derived from GE2270. It has been shown to possess potent in vitro and in vivo activity against Gram-positive bacteria. It is hypothesized that it a translation inhibitor leading to cell death.","category_aro_class_name":"Antibiotic"},"37618":{"category_aro_accession":"3001219","category_aro_cvterm_id":"37618","category_aro_name":"elfamycin antibiotic","category_aro_description":"Elfamycins are molecules that inhibit bacterial elongation factor Tu (EF-Tu), a key protein which brings aminoacyl-tRNA (aa-tRNA) to the ribosome during protein synthesis. Elfamycins defined by their target (EF-Tu), rather than a conserved chemical backbone. Elfamycins follow two mechanisms to disrupt protein synthesis: 1. kirromycins and enacyloxin fix EF-Tu in the GTP bound conformation and lock EF-Tu onto the ribosome, and 2. pulvomycin and GE2270 cover the binding site of aa-tRNA disallowing EF-Tu from being charged with aa-tRNA. All elfamycins cause increased the affinity of EF-Tu for GTP.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1300":{"model_id":"1300","model_name":"MexF","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"2110"}},"model_sequences":{"sequence":{"378":{"protein_sequence":{"accession":"NP_251184.1","sequence":"MNFSQFFIQRPIFAAVLSLLILIGGAISLFQLPISEYPEVVPPTVVVRANFPGANPKVIGETVASPLEQAITGVENMLYMSSQSTSDGKLTLTITFALGTDLDNAQVQVQNRVTRTEPKLPEEVTRLGITVDKASPDLTMVVHLTSPDNRYDMLYLSNYAVLNVKDELARLDGVGDVQLFGLGDYSLRVWLDPNKVASRNLTATDVVNAIREQNRQVAAGTLGAPPAPSDTSFQLSINTQGRLVTEEEFENIIIRAGANGEITRLRDIARVELGSNQYALRSLLNNKPAVAIPIFQRPGSNAIEISNLVREKMAELKHSFPQGMDYSIVYDPTIFVRGSIEAVVHTLFEALVLVVLVVILFLQTWRASIIPLAAVPVSLIGTFAVMHMLGFSLNALSLFGLVLAIGIVVDDAIVVVENVERNIGLGLKPVEATKRAMREVTGPIIATALVLCAVFIPTAFISGLTGQFYRQFALTIAISTVISAFNSLTLSPALAAVLLKGHHEPKDRFSVFLDKLLGSWLFRPFNRFFDRASHGYVGTVNRVLRGSSIALLVYGGLMVLTYFGFSSTPTGFVPQQDKQYLVAFAQLPDAASLDRTEAVIKQMSEIALAQPGVADSVAFPGLSINGFTNSPNSGIVFTPLKPFDERKDPSQSAGAIAAALNAKYADIQDAYIAIFPPPPVQGLGTIGGFRLQIEDRGNQGYEELFKQTQNIITKARALPELEPSSVFSSYQVNVPQIDADIDREKAKTHGVAISDIFDTLQVYLGSLYANDFNRFGRTYQVNVQAEQQFRLEPEQIGQLKVRNNLGEMVPLASFIKVSDTSGPDRVMHYNGFITAELNGAPAAGYSSGQAQAAIEKLLKEELPNGMTYEWTELTYQQILAGNTALFVFPLCVLLAFLVLAAQYESWSLPLAVILIVPMTLLSAITGVILAGSDNNIFTQIGLIVLVGLACKNAILIVEFAKDKQEEGMDRVAAVLEACRLRLRPILMTSIAFIMGVVPLVISTGAGAEMRHAMGVAVFSGMIGVTFFGLLLTPVFYVLIRRFVENREARRAANDKGLPEVHA"},"dna_sequence":{"accession":"NC_002516","fmin":"2810008","fmax":"2813197","strand":"+","sequence":"ATGAATTTCTCCCAATTCTTCATCCAGCGGCCGATCTTCGCCGCGGTGCTGTCGCTGCTGATCCTGATTGGCGGCGCCATCTCCCTGTTCCAGCTACCCATCAGCGAATACCCGGAAGTGGTGCCGCCGACCGTCGTGGTCCGCGCCAACTTCCCCGGCGCCAACCCGAAAGTCATCGGCGAGACCGTCGCCTCTCCCCTTGAACAGGCGATCACCGGGGTGGAGAACATGCTCTACATGTCCTCCCAGTCGACCTCCGACGGCAAGCTGACCCTGACCATCACCTTCGCCCTCGGCACCGACCTGGACAACGCCCAGGTGCAGGTGCAGAACCGCGTCACCCGGACCGAGCCGAAGCTCCCGGAAGAAGTGACCCGGCTCGGCATCACCGTCGACAAGGCCTCGCCCGACCTGACCATGGTCGTGCACCTGACCTCGCCGGATAACCGCTACGACATGCTCTACCTGTCGAACTACGCGGTGCTCAACGTGAAGGACGAACTGGCCCGCCTCGACGGCGTCGGCGACGTCCAGTTGTTCGGCCTCGGCGACTATTCGCTGCGCGTCTGGCTGGACCCGAACAAGGTCGCCTCGCGCAACCTCACCGCCACCGACGTGGTCAACGCCATCCGCGAGCAGAACCGCCAGGTCGCCGCCGGCACCCTGGGCGCGCCGCCGGCGCCGAGCGATACCAGCTTCCAGTTGTCGATCAACACCCAGGGTCGCCTGGTCACCGAGGAAGAGTTCGAGAACATCATCATCCGCGCCGGCGCCAACGGCGAGATCACCCGTCTGCGCGACATCGCCCGGGTCGAGCTGGGCTCCAACCAGTACGCCCTGCGTTCGCTGCTGAACAACAAGCCGGCGGTGGCGATCCCGATCTTCCAGCGTCCCGGCTCGAACGCCATCGAGATCTCCAACCTGGTGCGGGAGAAGATGGCCGAGCTGAAGCACAGCTTCCCGCAAGGCATGGACTACTCCATCGTCTACGACCCGACCATCTTCGTCCGCGGCTCCATCGAGGCGGTGGTGCACACCCTGTTCGAAGCCCTGGTGCTGGTGGTGCTGGTGGTGATCCTGTTCCTGCAGACCTGGCGCGCCTCGATCATCCCGCTGGCCGCGGTGCCGGTGTCGCTGATCGGCACCTTCGCGGTGATGCACATGCTCGGCTTCTCGCTCAACGCGCTGTCGCTGTTCGGCCTGGTGCTGGCCATCGGCATCGTGGTGGACGACGCCATCGTGGTGGTGGAGAACGTCGAGCGCAACATCGGCCTCGGCCTCAAGCCGGTGGAAGCCACCAAGCGTGCCATGCGCGAGGTGACCGGGCCGATCATCGCCACGGCGCTGGTGCTCTGCGCGGTGTTCATCCCGACCGCGTTCATCTCCGGCCTCACCGGGCAGTTCTACCGCCAGTTCGCCCTGACCATCGCGATCTCCACGGTGATCTCGGCGTTCAACTCGCTGACCCTGTCGCCAGCGCTGGCGGCGGTCCTGCTCAAGGGCCACCACGAGCCGAAGGACCGCTTCTCGGTGTTCCTCGACAAGCTCCTCGGCAGTTGGCTGTTCCGTCCGTTCAACCGTTTCTTCGACCGCGCCAGCCATGGCTACGTCGGCACGGTGAACCGGGTCCTGCGCGGCAGCTCGATCGCCCTGCTGGTCTACGGCGGACTGATGGTGCTGACCTACTTCGGCTTCTCCAGCACGCCGACCGGTTTCGTCCCGCAGCAGGACAAGCAGTACCTGGTGGCCTTCGCCCAGTTGCCCGACGCGGCCAGCCTGGACCGTACCGAGGCGGTGATCAAGCAGATGTCCGAGATCGCCCTGGCGCAGCCCGGCGTGGCGGACTCGGTGGCCTTCCCCGGCCTGTCGATCAACGGCTTCACCAACAGCCCGAACAGCGGCATCGTGTTCACCCCGCTGAAGCCGTTCGACGAGCGCAAGGACCCGAGCCAGTCGGCCGGGGCCATCGCCGCCGCGCTGAACGCCAAGTACGCCGACATTCAGGACGCCTACATCGCGATCTTCCCGCCGCCGCCGGTACAGGGGCTGGGGACCATCGGCGGCTTCCGCCTGCAGATCGAGGACCGTGGCAACCAGGGCTACGAGGAGCTGTTCAAGCAGACCCAGAACATCATCACCAAGGCCCGTGCGCTGCCTGAGCTGGAACCCAGCTCGGTGTTCTCCAGCTACCAGGTCAACGTGCCGCAGATCGACGCCGACATCGACCGCGAGAAGGCCAAGACCCACGGCGTGGCGATCAGCGACATCTTCGACACCCTGCAGGTCTACCTCGGCTCGCTGTACGCGAACGACTTCAACCGCTTCGGCCGTACCTATCAGGTCAACGTCCAGGCCGAGCAGCAGTTCCGCCTCGAACCCGAGCAGATCGGCCAGCTGAAGGTGCGCAACAACCTCGGCGAGATGGTCCCGCTGGCGTCCTTCATCAAGGTCAGCGACACCTCCGGTCCGGACCGTGTGATGCACTACAACGGCTTCATCACCGCCGAACTCAACGGCGCCCCGGCCGCGGGCTACAGCTCCGGCCAGGCGCAGGCGGCGATCGAGAAGCTGCTGAAGGAGGAACTGCCCAACGGCATGACCTACGAGTGGACCGAGCTGACCTACCAGCAGATCCTCGCCGGCAATACCGCGCTGTTCGTCTTCCCGCTCTGCGTGCTGCTGGCCTTCCTCGTGCTGGCCGCCCAGTACGAGAGCTGGAGCCTACCGCTGGCGGTGATCCTGATCGTGCCGATGACCCTGCTGTCGGCGATCACCGGGGTGATCCTGGCCGGCAGCGACAACAACATCTTTACCCAGATCGGCCTGATCGTTCTGGTGGGGCTGGCGTGCAAGAACGCGATCCTGATCGTCGAGTTCGCCAAGGACAAGCAGGAGGAAGGCATGGACCGCGTCGCCGCGGTGCTGGAAGCCTGCCGCCTGCGCCTGCGGCCGATCCTGATGACGTCCATCGCCTTCATCATGGGTGTGGTGCCGCTGGTGATCTCCACCGGCGCCGGCGCCGAGATGCGCCATGCGATGGGCGTGGCGGTGTTCTCCGGGATGATCGGGGTGACCTTCTTCGGCCTGCTGCTGACGCCGGTGTTCTACGTCCTCATCCGCCGCTTCGTGGAGAACCGCGAAGCGCGCCGCGCCGCCAACGACAAAGGCCTGCCAGAGGTGCATGCATGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3000804","ARO_id":"37184","ARO_name":"MexF","ARO_description":"MexF is the multidrug inner membrane transporter of the MexEF-OprN complex. mexF corresponds to 2 loci in Pseudomonas aeruginosa PAO1 (gene name: mexF\/mexB) and 4 loci in Pseudomonas aeruginosa LESB58 (gene name: mexD\/mexB).","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"624":{"model_id":"624","model_name":"Mycobacterium leprae rpoB mutations conferring resistance to rifampicin","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"2040":"V472I","2041":"S456L"},"clinical":{"2040":"V472I","2041":"S456L"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"2300"}},"model_sequences":{"sequence":{"4334":{"protein_sequence":{"accession":"CAC30845.1","sequence":"MLEGCILPDFGQSKTDVSPSQSRPQSSPNNSVPGAPNRISFAKLREPLEVPGLLDVQTDSFEWLIGSPCWRAAAASRGDLKPVGGLEEVLYELSPIEDFSGSMSLSFSDPRFDEVKAPVEECKDKDMTYAAPLFVTAEFINNNTGEIKSQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDETIDKSTEKTLHSVKVIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTSEQITERFGFSEIMRSTLEKDNTVGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLHAGELITSSTLTEEDVVATIEYLVRLHEGQSTMTVPGGVEVPVETDDIDHFGNRRLRTVGELIQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVSDEIEYLTADEEDRHVVAQANSPIDEAGRFLEPRVLVRRKAGEVEYVASSEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAIDAGHVVVAEKSGVIEEVSADYITVMADDGTRRTYRMRKFARSNHGTCANQSPIVDAGDRVEAGQVIADGPCTENGEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSHEDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPAEDMPFLPDGTPVDIILNTHGVPRRMNVGQILETHLGWVAKSGWKIDVAGGIPDWAVNLPEELLHAAPNQIVSTPVFDGAKEEELQGLLSSTLPNRDGDVMVGGDGKAVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLCLNVEVLSSDGAAIELREGEDEDLERAAANLGINLSRNESASIEDLA"},"dna_sequence":{"accession":"AL450380","fmin":"2273268","fmax":"2276805","strand":"-","sequence":"CTAAGCCAGATCTTCTATGGACGCCGATTCGTTGCGGGACAAGTTGATACCGAGGTTGGCCGCAGCCCGCTCGAGGTCCTCATCCTCACCTTCGCGCAACTCGATCGCCGCACCGTCGGACGACAGCACCTCGACGTTGAGACACAGCGACTGTAACTCCTTGAGCAGCACCTTGAACGACTCGGGGATGCCCGGCTCGGGGATGTTCTCACCCTTAACGATAGCCTCGTAAACCTTGACCCGACCGACGGTGTCGTCGGACTTGATGGTCAACAGCTCCTGCAGCGTGTAGGCCGCACCGTAGGCCTGCATGGCCCAGCACTCCATCTCACCGAATCGCTGGCCACCGAACTGTGCCTTACCACCCAACGGCTGCTGGGTAATCATCGAGTACGGGCCGGTGGAGCGGGCGTGGATCTTGTCGTCCACCAAGTGGTGCAGCTTCATGATGTACATGTAGCCAACCGTCACCGGATAAGGGAACGGCTCACCGCTGCGCCCATCGAAGAGCACCGCCTTGCCGTCGCCGCCCACCATCACATCGCCGTCGCGGTTGGGCAACGTGGAGGACAACAGGCCCTGTAGTTCCTCTTCCTTGGCGCCGTCGAACACCGGGGTCGACACGATCTGGTTGGGCGCAGCGTGCAACAACTCCTCAGGCAAGTTGACCGCCCAATCCGGTATACCGCCGGCCACGTCGATCTTCCAGCCGGACTTGGCTACCCACCCAAGGTGGGTTTCCAAGATCTGACCGACGTTCATCCGCCGCGGCACCCCGTGAGTGTTGAGGATGATGTCCACCGGGGTGCCGTCTGGCAGAAACGGCATATCCTCGGCAGGCAGGATCTTGCCGATCACGCCCTTGTTGCCGTGCCGCCCAGCCAGCTTGTCACCGTCAGAGATCTTGCGCTTCTGGGCTACGTAGACACGGACCAGCTCGTTGACGCCGGCGGGCAGCTCGTCGTCATCCTCATGGGAGAACACCCGAATGCCGATCACCTTGCCGGATTCGCCGTGTGGCACCTTCAGCGACGTGTCACGGACCTCGCGGGCCTTTTCGCCGAAGATCGCCCGCAGCAACCGCTCTTCCGGTGTCAGCTCAGTTTCCCCCTTCGGGGTGACCTTGCCAACCAGGATATCACCGTCACGAACCTCCGCGCCAATCCGCACGATGCCCCGCTCGTCCAAGTCGGCTAGCACCTCATCGGAGACGTTGGGAATGTCCCGGGTGATCTCCTCAGCACCCAGCTTGGTGTCACGGGCGTCGATCTCATGCTCCTCAATGTGAATCGAAGTAAGCACGTCCTCTTCGACCAGTCGGTTAGACAGGATGATCGCATCCTCGTAGTTGTGACCCTCCCACGGCATGATCGCCACCAGCAAGTTCTTGCCCAACGCCATCTCGCCGTTCTCAGTGCACGGACCGTCAGCAATCACTTGGCCGGCCTCGACCCGATCCCCCGCATCCACGATCGGGGACTGGTTGGCGCAGGTGCCGTGGTTGGAGCGCGCGAACTTACGCATCCGATAAGTCCGCCGGGTGCCGTCATCGGCCATCACGGTGATGTAGTCGGCGGAAACCTCCTCGATCACCCCGGACTTCTCCGCAACGACGACGTGGCCAGCGTCGATGGCCGCGCGCAACTCCATACCGGTACCCACCAACGGTGCTTCGCTGCGCACCAACGGAACCGCTTGGCGCTGCATGTTAGCGCCCATCAGGGCACGGTTGGCGTCGTCGTGCTCAAGGAACGGAATCATCGCTGTGGCCACCGACACCATCTGGCGTGGCGAGACATCCATGTAATCCACCTCGGACGAGGCCACGTACTCCACCTCGCCCGCCTTGCGGCGCACCAACACGCGCGGCTCGAGGAAGCGGCCGGCCTCGTCGATCGGCGAGTTGGCCTGCGCCACGACATGGCGGTCTTCCTCGTCAGCGGTCAAGTATTCGATCTCGTCGCTGACCACACCGTCAACCACTTTGCGGTACGGTGTTTCGATGAACCCGAAGGGGTTGACCCGCGCGTACACCGACAATGAACCGATCAGACCTATGTTCGGGCCCTCCGGAGTCTCGATCGGGCACATCCGGCCGTAGTGCGAAGGGTGCACGTCACGGACCTCTAGCCCGGCACGCTCACGCGACAAACCACCCGGGCCCAGCGCCGACAGCCGGCGCTTGTGGGTCAGGCCCGACAGAGGGTTGTTCTGATCCATGAACTGCGACAGCTGGCTGGTGCCGAAGAATTCCTTGATAGCGGCGACCACCGGACGGATATTGATCAGCGTCTGCGGCGTGATCGCCTCGACGTCCTGGGTGGTCATCCGCTCCCGGACCACCCGCTCCATCCGCGACATACCGACCCGGATCTGGTTCTGGATCAATTCGCCGACCGTGCGCAGCCGGCGGTTGCCGAAGTGGTCGATATCGTCAGTTTCCACTGGCACTTCTACCCCACCTGGGACAGTCATTGTCGACTGACCCTCATGCAGACGAACCAGGTACTCTATGGTGGCGACGACATCCTCTTCGGTCAGCGTGGACGACGTGATCAACTCACCGGCGTGCAACCCGAGCTTCTTGTTGACCTTGTAACGACCAACCCTGGCCAGGTCGTAGCGTTTCTCCTTGAAGAACAGGTTCTCCAACAGCGTCTGCGCGGACTCCTTAGTCGGCGGCTCACCTGGGCGCAACTTACGATAGATGTCTAGCAGCGCCTCGTCGGTGCCAACTGTGTTGTCCTTCTCCAGCGTCGAGCGCATGATCTCGGAGAAACCGAAACGCTCGGTGATCTGCTCACTGGTCCAACCTAGCGCTTTGAGAAGCACCGTGACGGGTTGCCGGCGCTTCCGGTCAATGCGGACACCGACGGTGTCGCGTTTATCGACATCGAATTCCAACCAGGCACCGCGGCTGGGAATCACCTTGACACTATGCAGCGTCTTTTCTGTGGACTTGTCGATCGTCTCGTCGAAGTATACTCCAGGGGAGCGCACCAGCTGGCTAACGACGACACGCTCGGTCCCGTTGATGATGAAGGTTCCCTTCTCAGTCATCATAGGGAAGTCGCCCATAAACACCGTCTGGCTCTTGATCTCCCCGGTGTTGTTGTTGATGAACTCGGCCGTGACGAACAGCGGGGCCGCGTACGTCATGTCCTTGTCTTTGCACTCTTCGACGGGCGCCTTGACTTCGTCAAAACGGGGATCGGAGAAAGACAATGACATTGAGCCGGAGAAATCCTCGATCGGCGACAGCTCGTAGAGCACCTCTTCGAGACCACCCACCGGCTTGAGATCGCCGCGGCTTGCGGCCGCTGCACGCCAGCACGGCGATCCGATCAACCACTCAAATGAATCAGTCTGCACATCAAGTAGCCCCGGAACCTCAAGCGGTTCGCGGAGCTTGGCAAATGAAATTCGGTTGGGCGCGCCGGGCACGGAGTTGTTGGGCGAACTTTGGGGGCGACTCTGGCTAGGACTAACGTCTGTCTTGCTCTGGCCGAAATCTGGCAAGATGCATCCTTCCAGCAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40074","NCBI_taxonomy_name":"Mycobacterium leprae","NCBI_taxonomy_id":"1769"}}}},"ARO_accession":"3003284","ARO_id":"39868","ARO_name":"Mycobacterium leprae rpoB mutations conferring resistance to rifampicin","ARO_description":"Point mutations that occurs in Mycobacterium leprae rpoB resulting in resistance to rifampicin","ARO_category":{"36349":{"category_aro_accession":"3000210","category_aro_cvterm_id":"36349","category_aro_name":"rifamycin-resistant beta-subunit of RNA polymerase (rpoB)","category_aro_description":"Rifampin resistant RNA polymerases include amino acids substitutions which disrupt the affinity of rifampin for its binding site. These mutations are frequently concentrated in the rif I region of the beta-subunit and most often involve amino acids which make direct interactions with rifampin. However, mutations which also confer resistance can occur outside this region and may involve amino acids which do not directly make contact with rifampin.","category_aro_class_name":"AMR Gene Family"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36656":{"category_aro_accession":"3000517","category_aro_cvterm_id":"36656","category_aro_name":"rifaximin","category_aro_description":"Rifaximin is a semi-synthetic rifamycin used to treat traveller's diarrhea. Rifaximin inhibits RNA synthesis by binding to the beta subunit of bacterial RNA polymerase.","category_aro_class_name":"Antibiotic"},"36669":{"category_aro_accession":"3000530","category_aro_cvterm_id":"36669","category_aro_name":"rifabutin","category_aro_description":"Rifabutin is a semisynthetic rifamycin used in tuberculosis therapy. It inhibits DNA-dependent RNA synthesis.","category_aro_class_name":"Antibiotic"},"36673":{"category_aro_accession":"3000534","category_aro_cvterm_id":"36673","category_aro_name":"rifapentine","category_aro_description":"Rifapentine is a semisynthetic rifamycin that inhibits DNA-dependent RNA synthesis. It is often used in the treatment of tuberculosis and leprosy.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1305":{"model_id":"1305","model_name":"OprM","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"850"}},"model_sequences":{"sequence":{"427":{"protein_sequence":{"accession":"NP_249118.1","sequence":"MKRSFLSLAVAAVVLSGCSLIPDYQRPEAPVAAAYPQGQAYGQNTGAAAVPAADIGWREFFRDPQLQQLIGVALENNRDLRVAALNVEAFRAQYRIQRADLFPRIGVDGSGTRQRLPGDLSTTGSPAISSQYGVTLGTTAWELDLFGRLRSLRDQALEQYLATEQAQRSAQTTLVASVATAYLTLKADQAQLQLTKDTLGTYQKSFDLTQRSYDVGVASALDLRQAQTAVEGARATLAQYTRLVAQDQNALVLLLGSGIPANLPQGLGLDQTLLTEVPAGLPSDLLQRRPDILEAEHQLMAANASIGAARAAFFPSISLTANAGTMSRQLSGLFDAGSGSWLFQPSINLPIFTAGSLRASLDYAKIQKDINVAQYEKAIQTAFQEVADGLAARGTFTEQLQAQRDLVKASDEYYQLADKRYRTGVDNYLTLLDAQRSLFTAQQQLITDRLNQLTSEVNLYKALGGGWNQQTVTQQQTAKKEDPQA"},"dna_sequence":{"accession":"NC_002516","fmin":"476332","fmax":"477790","strand":"+","sequence":"ATGAAACGGTCCTTCCTTTCCCTGGCGGTAGCCGCTGTCGTTCTGTCCGGCTGCTCGCTGATCCCCGACTACCAGCGCCCCGAGGCGCCGGTAGCCGCGGCCTACCCGCAAGGGCAGGCCTACGGGCAGAACACCGGCGCGGCGGCCGTTCCGGCCGCCGACATCGGCTGGCGCGAGTTCTTCCGCGACCCGCAGTTGCAGCAACTGATCGGCGTGGCGCTGGAAAACAACCGCGACCTGCGGGTCGCCGCGCTGAACGTCGAGGCCTTCCGGGCGCAGTACCGCATCCAGCGGGCCGACCTGTTCCCGCGGATCGGCGTGGACGGTAGCGGCACCCGCCAGCGTTTGCCGGGCGACCTGTCGACCACCGGCAGTCCGGCGATTTCCAGCCAGTACGGGGTGACCCTGGGCACTACCGCCTGGGAACTCGATCTCTTCGGCCGCCTGCGCAGCCTGCGCGACCAGGCCCTGGAGCAGTACCTGGCGACCGAACAGGCGCAGCGCAGCGCGCAGACCACCCTGGTGGCCAGCGTGGCGACCGCCTACCTGACGCTGAAGGCCGACCAGGCGCAGTTGCAGCTGACCAAGGACACCCTGGGCACCTACCAGAAGAGTTTCGACCTGACCCAGCGCAGCTACGACGTCGGCGTCGCCTCCGCGCTCGACCTGCGCCAGGCGCAGACCGCCGTGGAAGGCGCCCGCGCGACCCTGGCGCAGTACACCCGCCTGGTAGCCCAGGACCAGAATGCGCTGGTCCTGCTGCTGGGCTCCGGGATCCCGGCGAACCTGCCGCAAGGCCTGGGCCTGGACCAGACCCTGCTGACCGAAGTGCCGGCGGGTCTGCCGTCGGACCTGCTGCAACGGCGCCCGGACATCCTCGAGGCCGAGCACCAGCTCATGGCTGCCAACGCCAGCATCGGCGCCGCGCGCGCGGCGTTCTTCCCGAGCATCAGCCTGACCGCCAACGCCGGCACCATGAGCCGCCAACTGTCCGGCCTGTTCGACGCCGGTTCGGGTTCCTGGTTGTTCCAGCCGTCGATCAACCTGCCGATCTTCACCGCCGGCAGCCTGCGTGCCAGCCTGGACTACGCGAAGATCCAGAAGGACATCAACGTCGCGCAGTACGAGAAGGCGATCCAGACGGCGTTCCAGGAAGTCGCCGACGGCCTGGCCGCGCGCGGTACCTTCACCGAGCAGTTGCAGGCGCAGCGCGATCTGGTCAAGGCCAGCGACGAGTACTACCAGCTCGCCGACAAGCGCTATCGCACGGGGGTGGACAACTACCTGACCCTGCTCGACGCGCAACGCTCGCTGTTCACCGCGCAGCAGCAACTGATCACCGACCGCCTCAATCAGCTGACCAGCGAGGTCAACCTGTACAAGGCCCTCGGCGGCGGCTGGAACCAGCAGACCGTGACCCAGCAGCAGACCGCGAAGAAGGAAGATCCCCAGGCTTGAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3000379","ARO_id":"36518","ARO_name":"OprM","ARO_description":"OprM is an outer membrane factor protein found in Pseudomonas aeruginosa and Burkholderia vietnamiensis. It is part of the MexAB-OprM, MexVW-OprM, MexXY-OprM and the AmrAB-OprM complex.","ARO_category":{"35996":{"category_aro_accession":"0000079","category_aro_cvterm_id":"35996","category_aro_name":"clavulanate","category_aro_description":"Clavulanic acid is a beta-lactamase inhibitor (marketed by GlaxoSmithKline, formerly Beecham) combined with penicillin group antibiotics to overcome certain types of antibiotic resistance. It is used to overcome resistance in bacteria that secrete beta-lactamase, which otherwise inactivates most penicillins.","category_aro_class_name":"Adjuvant"},"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavin","category_aro_description":"Acriflavin is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35979":{"category_aro_accession":"0000062","category_aro_cvterm_id":"35979","category_aro_name":"ceftriaxone","category_aro_description":"Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36468":{"category_aro_accession":"3000329","category_aro_cvterm_id":"36468","category_aro_name":"sulfamethoxazole","category_aro_description":"Sulfamethoxazole is a sulfonamide antibiotic usually taken with trimethoprim, a diaminopyrimidine antibiotic. Sulfamethoxazole inhibits dihydropteroate synthase, essential to tetrahydrofolic acid biosynthesis. This pathway generates compounds used in the synthesis of many amino acids and nucleotides.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36689":{"category_aro_accession":"3000550","category_aro_cvterm_id":"36689","category_aro_name":"aztreonam","category_aro_description":"Aztreonam was the first monobactam discovered, and is greatly effective against Gram-negative bacteria while inactive against Gram-positive bacteria. Artreonam is a poor substrate for beta-lactamases, and may even act as an inhibitor. In Gram-negative bacteria, Aztreonam interferes with filamentation, inhibiting cell division and leading to cell death.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"40362":{"category_aro_accession":"3003708","category_aro_cvterm_id":"40362","category_aro_name":"panipenem","category_aro_description":"Panipenem is a carbapenem antibacterial agent with a broad spectrum of in vitro activity covering a wide range of Gram-negative and Gram-positive aerobic and anaerobic bacterial.  It is used in combination with betamipron to inhibit panipenem uptake into the renal tubule and prevent nephrotoxicity.","category_aro_class_name":"Antibiotic"},"40523":{"category_aro_accession":"3003832","category_aro_cvterm_id":"40523","category_aro_name":"ticarcillin","category_aro_description":"Ticarcillin is a carboxypenicillin used for the treatment of Gram-negative bacteria, particularly P. aeruginosa. Ticarcillin's antibiotic properties arise from its ability to prevent cross-linking of peptidoglycan during cell wall synthesis, when the bacteria try to divide, causing cell death.","category_aro_class_name":"Antibiotic"},"40957":{"category_aro_accession":"3004024","category_aro_cvterm_id":"40957","category_aro_name":"trimethoprim-sulfamethoxazole","category_aro_description":"An antibiotic cocktail containing the diaminopyrimidine antibiotic Trimethoprim and the sulfonamide antibiotic sulfamethoxazole (1 TMP:5 SMX).","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36193":{"category_aro_accession":"3000054","category_aro_cvterm_id":"36193","category_aro_name":"acridine dye","category_aro_description":"Acridine dyes are cell permeable, basic molecules with an acridine chromophore. These compounds intercalate DNA. The image shown represents the core structure of the acridine family, with specific dyes containing varying substituents.","category_aro_class_name":"Drug Class"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36421":{"category_aro_accession":"3000282","category_aro_cvterm_id":"36421","category_aro_name":"sulfonamide antibiotic","category_aro_description":"Sulfonamides are broad spectrum, synthetic antibiotics that contain the sulfonamide group. Sulfonamides inhibit dihydropteroate synthase, which catalyzes the conversion of p-aminobenzoic acid to dihydropteroic acid as part of the tetrahydrofolic acid biosynthetic pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor of many nucleotides and amino acids. Many sulfamides are taken with trimethoprim, an inhibitor of dihydrofolate reductase, also disturbing the trihydrofolic acid synthesis pathway.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1600":{"model_id":"1600","model_name":"Pseudomonas mutant PhoP conferring resistance to colistin","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"4367":"R117L","4368":"A110V"},"experimental":{"4367":"R117L","4368":"A110V"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"3670":{"protein_sequence":{"accession":"NP_249870.1","sequence":"MKLLVVEDEALLRHHLYTRLGEQGHVVDAVPDAEEALYRVSEYHHDLAVIDLGLPGMSGLDLIRELRSQGKSFPILILTARGNWQDKVEGLAAGADDYVVKPFQFEELEARLNALLRRSSGFVQSTIEAGPLVLDLNRKQALVEEQPVALTAYEYRILEYLMRHHQQVVAKERLMEQLYPDDEERDANVIEVLVGRLRRKLEACGGFKPIDTVRGQGYLFTERCR"},"dna_sequence":{"accession":"NC_002516.2","fmin":"1277687","fmax":"1278365","strand":"+","sequence":"ATGAAACTGCTGGTAGTGGAAGACGAGGCGCTGTTGCGCCACCACCTCTATACCCGCCTGGGTGAACAGGGGCACGTGGTGGACGCGGTACCGGATGCCGAGGAAGCCCTCTACCGGGTCAGCGAATACCACCACGACCTGGCGGTGATCGACCTCGGCCTGCCGGGCATGAGCGGCCTGGACCTGATCCGCGAGCTGCGTTCGCAGGGCAAGTCCTTCCCGATCCTGATCCTCACCGCCCGCGGCAACTGGCAGGACAAGGTCGAAGGCCTGGCCGCCGGGGCCGACGACTACGTGGTCAAGCCGTTCCAGTTCGAGGAACTGGAAGCGCGCCTGAACGCGTTGCTGCGACGCTCCTCGGGGTTCGTCCAGTCGACCATCGAGGCCGGCCCCCTGGTCCTCGACCTGAACCGCAAGCAGGCGCTGGTCGAGGAGCAACCGGTGGCGCTGACCGCCTACGAATACCGCATCCTCGAATACCTCATGCGGCATCACCAGCAGGTGGTGGCCAAGGAACGCCTGATGGAACAGCTCTATCCCGACGACGAGGAGCGCGACGCCAACGTCATCGAGGTGCTGGTCGGCCGCCTGCGGCGCAAGCTGGAGGCCTGCGGCGGCTTCAAGCCGATCGATACGGTGCGCGGCCAGGGCTACCTGTTCACCGAGCGCTGCCGGTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3003895","ARO_id":"40597","ARO_name":"Pseudomonas mutant PhoP conferring resistance to colistin","ARO_description":"Mutations in Pseudomonas aeruginosa PhoP of the two-component PhoPQ regulatory system. Presence of mutation confers resistance to colistin.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"41433":{"category_aro_accession":"3004269","category_aro_cvterm_id":"41433","category_aro_name":"pmr phosphoethanolamine transferase","category_aro_description":"This family of phosphoethanolamine transferase catalyze the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine to lipid A, which impedes the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"320":{"model_id":"320","model_name":"Streptococcus pneumoniae PBP2x conferring resistance to amoxicillin","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"4473":"I371T","4474":"R384G","4475":"N514H","4476":"L546V","4477":"N605T","4478":"M400T","4479":"M339F"},"clinical":{"4473":"I371T","4474":"R384G","4475":"N514H","4476":"L546V","4477":"N605T","4478":"M400T","4479":"M339F"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1450"}},"model_sequences":{"sequence":{"331":{"protein_sequence":{"accession":"AFC91898.1","sequence":"MKWTKRVIRYATKNRKSPAENRRRVGKSLSLLSVFVFAIFLVNFAVIIGTGTRFGTDLAKEAKKVHQTTRTVPAKRGTIYDRNGVPIAEDATSYNVYAVIDENYKSATGKILYVEKTQFNKVAEVFHKYLDMEESYVREQLSQPNLKQVSFGAKGNGITYANMMSIKKELETAEVKGIDFTTSPNRSYPNGQFASSFIGLAQLHENEDGSKSLLGTSGMESSLNSILAGKDGIITYEKDRLGNVVPGTEQVSQQTVDGKDVYTTISSTLQSFMETQMNAFQEKVKGKYMTATLVSAKTGEILATTQRPTFDADTKEGLTKDFVWRDILYQSNYEPGSPMKVMTLAASIDNNTFPGGEYFNSSELKIADVTIRDWDVNESLTGGGMMTFSQGFAHSSNVGMTLLEQKMGDATWLDYLNRFKFGVPTRFGLTDEYAGQLPADNIVNIAQSSFGQGISVTQTQMIRAFTAIANDGVMLEPKFISAIYDPNDQTARKSQKEVVGNPVSKDAASLTRTNMILVGTDPVYGTMYNHSTGKPTVTVPGQNVALKSGTAQIADEKNGGYLVGLTNYIFSAVSMNPAENPDFILYVTVQQPEHYSGIQLGEFANPILERASAMKDSLNLQTTAKALEQVSQQSPYPMPSVKDISPGDLAEELRRNLVQPIVVGTGTKIKESSVEEGTNLAPNQQVILLSDKVEEIPDMYGWKKETAEAFAKWLDIELEFEGSGSVVQKQDVRTNTAIKNIKKITLTLGD"},"dna_sequence":{"accession":"JN645706","fmin":"0","fmax":"2253","strand":"+","sequence":"ATGAAGTGGACAAAAAGAGTAATCCGTTATGCGACCAAAAATCGGAAATCGCCGGCTGAAAACAGACGCAGAGTTGGAAAAAGTCTGAGTTTATTATCTGTCTTTGTTTTTGCCATTTTTTTAGTCAATTTTGCGGTCATTATTGGGACAGGCACTCGCTTTGGAACAGATTTAGCGAAGGAAGCTAAGAAGGTTCATCAAACCACCCGTACAGTTCCTGCCAAACGTGGGACTATTTATGACCGAAATGGAGTCCCGATTGCTGAGGATGCAACCTCCTATAATGTCTATGCGGTCATTGATGAGAACTATAAGTCAGCAACGGGTAAGATTCTTTACGTAGAAAAAACACAATTTAACAAGGTTGCAGAGGTCTTTCATAAGTATCTGGACATGGAAGAATCCTATGTAAGAGAGCAACTCTCGCAACCTAATCTCAAGCAAGTTTCCTTTGGAGCAAAGGGCAATGGGATTACCTATGCCAATATGATGTCTATCAAAAAAGAGTTGGAAACTGCAGAGGTCAAGGGGATTGATTTTACAACCAGTCCTAATCGTAGTTACCCAAACGGACAATTTGCTTCTAGTTTTATCGGACTAGCTCAGCTCCATGAAAATGAAGATGGGAGCAAGAGTTTGCTGGGAACTTCTGGGATGGAGAGTTCCTTGAACAGTATTCTCGCAGGGAAAGATGGCATTATTACTTATGAAAAGGATCGTCTAGGTAATGTTGTACCCGGAACAGAACAAGTTTCCCAACAAACGGTAGATGGCAAGGATGTTTATACAACGATTTCCAGCACCCTTCAGTCCTTCATGGAGACCCAGATGAATGCCTTTCAAGAAAAAGTAAAAGGTAAGTATATGACGGCGACCTTGGTCAGTGCTAAAACAGGGGAAATTCTTGCAACAACGCAGAGACCAACCTTTGATGCCGATACTAAGGAAGGACTTACCAAGGACTTTGTTTGGCGTGATATCCTCTATCAAAGTAACTATGAGCCGGGGTCACCCATGAAGGTCATGACGCTAGCAGCTTCTATTGATAACAATACCTTCCCAGGTGGAGAATACTTCAATAGCAGTGAATTAAAAATAGCGGATGTGACAATTCGAGATTGGGACGTTAATGAAAGTTTGACCGGTGGTGGTATGATGACATTTTCTCAAGGATTTGCTCACTCAAGTAACGTTGGGATGACCCTCCTTGAGCAAAAGATGGGAGATGCTACCTGGCTTGATTATCTTAATCGTTTTAAATTTGGTGTTCCGACCCGTTTCGGTTTGACGGATGAGTATGCTGGTCAGCTTCCTGCGGATAATATCGTTAACATTGCGCAAAGCTCATTTGGGCAAGGGATTTCAGTGACCCAGACGCAAATGATTCGTGCCTTTACAGCTATTGCTAATGACGGTGTCATGCTGGAACCTAAATTTATTAGTGCCATTTATGATCCAAATGATCAAACTGCTCGGAAATCTCAAAAAGAAGTTGTGGGAAATCCTGTTTCCAAAGATGCAGCTAGTCTAACTCGGACTAACATGATTTTGGTAGGGACGGATCCGGTTTATGGAACCATGTATAACCACAGCACAGGCAAGCCAACTGTAACTGTTCCTGGGCAAAATGTAGCCCTCAAGTCTGGTACGGCTCAGATTGCTGACGAGAAAAATGGTGGTTATCTAGTCGGGTTAACCAACTATATTTTCTCGGCTGTATCAATGAACCCTGCTGAAAATCCTGATTTTATCTTGTATGTGACGGTCCAACAACCTGAACATTATTCAGGTATTCAGTTGGGAGAATTTGCCAATCCTATCTTGGAGCGGGCTTCAGCTATGAAAGACTCTCTCAATCTTCAAACAACAGCTAAAGCTTTGGAGCAAGTAAGTCAACAAAGTCCTTATCCTATGCCTAGTGTCAAGGATATTTCACCTGGTGATTTAGCAGAAGAATTGCGTCGCAATCTTGTACAACCCATCGTTGTGGGAACAGGAACAAAGATTAAAGAATCATCTGTAGAAGAAGGGACCAATCTTGCACCAAACCAACAAGTTATCCTTTTATCGGATAAGGTAGAAGAAATTCCAGACATGTATGGCTGGAAAAAAGAGACTGCTGAGGCCTTTGCTAAATGGTTGGATATCGAGCTGGAATTTGAAGGTTCAGGTTCCGTCGTTCAGAAGCAGGATGTTCGGACTAATACAGCTATCAAAAACATTAAAAAAATTACATTAACTTTAGGAGACTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35917","NCBI_taxonomy_name":"Streptococcus pneumoniae","NCBI_taxonomy_id":"1313"}}}},"ARO_accession":"3003043","ARO_id":"39477","ARO_name":"Streptococcus pneumoniae PBP2x conferring resistance to amoxicillin","ARO_description":"PBP2x is a penicillin-binding protein found in Streptococcus pneumoniae","ARO_category":{"40661":{"category_aro_accession":"3003938","category_aro_cvterm_id":"40661","category_aro_name":"Penicillin-binding protein mutations conferring resistance to beta-lactam antibiotics","category_aro_description":"Mutations in PBP transpeptidases that change the affinity for penicillin thereby conferring resistance to penicillin antibiotics","category_aro_class_name":"AMR Gene Family"},"35927":{"category_aro_accession":"0000008","category_aro_cvterm_id":"35927","category_aro_name":"cefoxitin","category_aro_description":"Cefoxitin is a cephamycin antibiotic often grouped with the second generation cephalosporins. Cefoxitin is bactericidal and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. Cefoxitin's 7-alpha-methoxy group and 3' leaving group make it a poor substrate for most beta-lactamases.","category_aro_class_name":"Antibiotic"},"35930":{"category_aro_accession":"0000011","category_aro_cvterm_id":"35930","category_aro_name":"cloxacillin","category_aro_description":"Cloxacillin is a semisynthetic, isoxazolyl penicillin derivative in the beta-lactam class of antibiotics. It interferes with peptidogylcan synthesis and is commonly used for treating penicillin-resistant Staphylococcus aureus infections.","category_aro_class_name":"Antibiotic"},"35934":{"category_aro_accession":"0000015","category_aro_cvterm_id":"35934","category_aro_name":"methicillin","category_aro_description":"Derived from penicillin to combat penicillin-resistance, methicillin is insensitive to beta-lactamases (also known as penicillinases) secreted by many penicillin-resistant bacteria. Methicillin is bactericidal, and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Antibiotic"},"35961":{"category_aro_accession":"0000043","category_aro_cvterm_id":"35961","category_aro_name":"carbenicillin","category_aro_description":"Carbenicillin is a semi-synthetic antibiotic belonging to the carboxypenicillin subgroup of the penicillins. It has gram-negative coverage which includes Pseudomonas aeruginosa but limited gram-positive coverage. The carboxypenicillins are susceptible to degradation by beta-lactamase enzymes. Carbenicillin antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Antibiotic"},"35971":{"category_aro_accession":"0000054","category_aro_cvterm_id":"35971","category_aro_name":"penicillin","category_aro_description":"Penicillin (sometimes abbreviated PCN) is a beta-lactam antibiotic used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms. It works by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Antibiotic"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35975":{"category_aro_accession":"0000058","category_aro_cvterm_id":"35975","category_aro_name":"cefazolin","category_aro_description":"Cefazolin (INN), also known as cefazoline or cephazolin, is a first generation cephalosporin antibiotic. It is administered parenterally, and is active against a broad spectrum of bacteria.","category_aro_class_name":"Antibiotic"},"35976":{"category_aro_accession":"0000059","category_aro_cvterm_id":"35976","category_aro_name":"cefepime","category_aro_description":"Cefepime (INN) is a fourth-generation cephalosporin antibiotic developed in 1994. It contains an aminothiazolyl group that decreases its affinity with beta-lactamases. Cefepime shows high binding affinity with penicillin-binding proteins and has an extended spectrum of activity against Gram-positive and Gram-negative bacteria, with greater activity against both Gram-negative and Gram-positive organisms than third-generation agents.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35978":{"category_aro_accession":"0000061","category_aro_cvterm_id":"35978","category_aro_name":"ceftobiprole","category_aro_description":"Ceftobiprole (Zeftera\/Zevtera) is a next generation (5th generation) cephalosporin antibiotic with activity against methicillin-resistant Staphylococcus aureus, penicillin-resistant Streptococcus pneumoniae, Pseudomonas aeruginosa, and Enterococci. Ceftobiprole inhibits transpeptidases essential to building cell walls, and is a poor substrate for most beta-lactamases.","category_aro_class_name":"Antibiotic"},"35979":{"category_aro_accession":"0000062","category_aro_cvterm_id":"35979","category_aro_name":"ceftriaxone","category_aro_description":"Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"35980":{"category_aro_accession":"0000063","category_aro_cvterm_id":"35980","category_aro_name":"cefuroxime","category_aro_description":"Cefuroxime is a second-generation cephalosporin antibiotic with increased stability with beta-lactamases than first-generation cephalosporins. Cefuroxime is active against Gram-positive organisms but less active against methicillin-resistant strains.","category_aro_class_name":"Antibiotic"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"35987":{"category_aro_accession":"0000070","category_aro_cvterm_id":"35987","category_aro_name":"ertapenem","category_aro_description":"Ertapenem is a carbapenem antibiotic and is highly resistant to beta-lactamases like other carbapenems. It inhibits bacterial cell wall synthesis.","category_aro_class_name":"Antibiotic"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"35995":{"category_aro_accession":"0000078","category_aro_cvterm_id":"35995","category_aro_name":"piperacillin","category_aro_description":"Piperacillin is an acetylureidopenicillin and has an extended spectrum of targets relative to other beta-lactam antibiotics. It inhibits cell wall synthesis in bacteria, and is usually taken with the beta-lactamase inhibitor tazobactam to overcome penicillin-resistant bacteria.","category_aro_class_name":"Antibiotic"},"36309":{"category_aro_accession":"3000170","category_aro_cvterm_id":"36309","category_aro_name":"imipenem","category_aro_description":"Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.","category_aro_class_name":"Antibiotic"},"36689":{"category_aro_accession":"3000550","category_aro_cvterm_id":"36689","category_aro_name":"aztreonam","category_aro_description":"Aztreonam was the first monobactam discovered, and is greatly effective against Gram-negative bacteria while inactive against Gram-positive bacteria. Artreonam is a poor substrate for beta-lactamases, and may even act as an inhibitor. In Gram-negative bacteria, Aztreonam interferes with filamentation, inhibiting cell division and leading to cell death.","category_aro_class_name":"Antibiotic"},"36976":{"category_aro_accession":"3000632","category_aro_cvterm_id":"36976","category_aro_name":"benzylpenicillin","category_aro_description":"Benzylpenicillin, commonly referred to as penicillin G, is effective against both Gram-positive and Gram-negative bacteria. It is unstable in acid.","category_aro_class_name":"Antibiotic"},"36977":{"category_aro_accession":"3000633","category_aro_cvterm_id":"36977","category_aro_name":"phenoxymethylpenicillin","category_aro_description":"Phenoxymethylpenicillin, or penicillin V, is a penicillin derivative that is acid stable but less active than benzylpenicillin (penicillin G).","category_aro_class_name":"Antibiotic"},"36978":{"category_aro_accession":"3000634","category_aro_cvterm_id":"36978","category_aro_name":"propicillin","category_aro_description":"Propicillin is an orally taken penicillin derivative that has high absorption but poor activity.","category_aro_class_name":"Antibiotic"},"36979":{"category_aro_accession":"3000635","category_aro_cvterm_id":"36979","category_aro_name":"dicloxacillin","category_aro_description":"Dicloxacillin is a penicillin derivative that has an extra chlorine atom in comparison to cloxacillin. While more active than cloxacillin, its high affinity for serum protein reduces its activity in human serum in vitro.","category_aro_class_name":"Antibiotic"},"36980":{"category_aro_accession":"3000636","category_aro_cvterm_id":"36980","category_aro_name":"flucloxacillin","category_aro_description":"Flucloxacillin is similar to cloxacillin, with an extra additional fluorine atom.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"36982":{"category_aro_accession":"3000638","category_aro_cvterm_id":"36982","category_aro_name":"azlocillin","category_aro_description":"Azlocillin is a semisynthetic derivative of penicillin that is notably active against Ps. aeruginosa and other Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36983":{"category_aro_accession":"3000639","category_aro_cvterm_id":"36983","category_aro_name":"mezlocillin","category_aro_description":"Mezlocillin is a penicillin derivative taken parenterally.","category_aro_class_name":"Antibiotic"},"36984":{"category_aro_accession":"3000640","category_aro_cvterm_id":"36984","category_aro_name":"doripenem","category_aro_description":"Doripenem is a carbapenem with a broad range of activity against Gram-positive and Gram-negative bacteria, and along with meropenem, it is the most active beta-lactam antibiotic against Pseudomonas aeruginosa. It inhibits bacterial cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36985":{"category_aro_accession":"3000641","category_aro_cvterm_id":"36985","category_aro_name":"cefalexin","category_aro_description":"Cefalexin is a cephalosporin antibiotic that causes filamentation. It is resistant to staphylococcal beta-lactamase, but degraded by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"36986":{"category_aro_accession":"3000642","category_aro_cvterm_id":"36986","category_aro_name":"cefadroxil","category_aro_description":"Cefadroxil, or p-hydroxycephalexin, is an cephalosporin antibiotic similar to cefalexin.","category_aro_class_name":"Antibiotic"},"36987":{"category_aro_accession":"3000643","category_aro_cvterm_id":"36987","category_aro_name":"cefotiam","category_aro_description":"Cefotiam is a cephalosporin antibiotic with similar activity to cefuroxime but more active against enterobacteria. It is consumed orally as the prodrug cefotiam hexetil.","category_aro_class_name":"Antibiotic"},"36988":{"category_aro_accession":"3000644","category_aro_cvterm_id":"36988","category_aro_name":"cefaclor","category_aro_description":"Cefaclor is a semisynthetic cephalosporin derived from cephalexin. It has broad-spectrum antibiotic activity.","category_aro_class_name":"Antibiotic"},"36989":{"category_aro_accession":"3000645","category_aro_cvterm_id":"36989","category_aro_name":"cefotaxime","category_aro_description":"Cefotaxime is a semisynthetic cephalosporin taken parenterally. It is resistant to most beta-lactamases and active against Gram-negative rods and cocci due to its aminothiazoyl and methoximino functional groups.","category_aro_class_name":"Antibiotic"},"36990":{"category_aro_accession":"3000646","category_aro_cvterm_id":"36990","category_aro_name":"cefixime","category_aro_description":"Cefixime is a cephalosporin resistant to most beta-lactamases. It is active against many enterobacteria, but activity against staphylococci is poor.","category_aro_class_name":"Antibiotic"},"36991":{"category_aro_accession":"3000647","category_aro_cvterm_id":"36991","category_aro_name":"cefpodoxime","category_aro_description":"Cefpodoxime is a semisynthetic cephalosporin that acts similarly to cefotaxime with broad-spectrum activity. It is stable to many plasmid-mediated beta-lactamses. Cefpodoxime is consumed as the prodrug cefpodoxime proxetil.","category_aro_class_name":"Antibiotic"},"36992":{"category_aro_accession":"3000648","category_aro_cvterm_id":"36992","category_aro_name":"ceftibuten","category_aro_description":"Ceftibuten is a semisynthetic cephalosporin active against Gram-negative bacilli. It is resistant against many plasmid-mediated beta-lactamases.","category_aro_class_name":"Antibiotic"},"36993":{"category_aro_accession":"3000649","category_aro_cvterm_id":"36993","category_aro_name":"cefditoren","category_aro_description":"Cefditoren is a semisynthetic cephalosporin active against staphylococci, streptococci, and and most enterobacteria. It is resistant to staphylococcal and most enterobacterial beta-lactamases, and is usually taken as the prodrug cefditoren pivoxil.","category_aro_class_name":"Antibiotic"},"36994":{"category_aro_accession":"3000650","category_aro_cvterm_id":"36994","category_aro_name":"cefdinir","category_aro_description":"Cefdinir is similar to cefixime with a modified side-chain at its 7-amino position. It also shares similar activity with cefixime but is more active against staphylococci. It has also be shown to enhance phagocytosis.","category_aro_class_name":"Antibiotic"},"36995":{"category_aro_accession":"3000651","category_aro_cvterm_id":"36995","category_aro_name":"ceftaroline","category_aro_description":"Ceftaroline is a novel cephalosporin active against methicillin resistant Staphylococcus aureus. Like other cephalosporins it binds penicillin-binding proteins to inhibit cell wall synthesis. It strongly binds with PBP2a, associated with methicillin resistance. It is taken orally as the prodrug ceftaroline fosamil.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"37085":{"category_aro_accession":"3000705","category_aro_cvterm_id":"37085","category_aro_name":"isopenicillin N","category_aro_description":"Isopenicillin N is a natural penicillin derivative produced by Penicillium chrysogenum with activity similar to penicillin N.","category_aro_class_name":"Antibiotic"},"37086":{"category_aro_accession":"3000706","category_aro_cvterm_id":"37086","category_aro_name":"penicillin N","category_aro_description":"Penicillin N is a penicillin derivative produced by Cephalosporium acremonium.","category_aro_class_name":"Antibiotic"},"37141":{"category_aro_accession":"3000761","category_aro_cvterm_id":"37141","category_aro_name":"mecillinam","category_aro_description":"Mecillinam is a broad-spectrum beta-lactam antibiotic that was semi-synthetically derived to have a different drug centre, being a 6-alpha-amidinopenicillanate instead of a 6-alpha-acylaminopenicillanate. Contrasting most beta-lactam drugs, mecillinam is most active against Gram-negative bacteria. It binds specifically to penicillin binding protein 2 (PBP2).","category_aro_class_name":"Antibiotic"},"40928":{"category_aro_accession":"3004001","category_aro_cvterm_id":"40928","category_aro_name":"cefmetazole","category_aro_description":"Cefmetazole is a semi-synthetic cephamycin antibiotic with broad spectrum antibiotic activity against both gram-positive and gram-negative bacteria, that disrupt cell wall synthesis through binding to PBPs causing cell lysis.","category_aro_class_name":"Antibiotic"},"40929":{"category_aro_accession":"3004002","category_aro_cvterm_id":"40929","category_aro_name":"cefonicid","category_aro_description":"Cefonicid is a second-generation cephalosporin-class beta-lactam antibiotic with broad spectrum activity. Particularly used against urinary tract infections and lower respiratory infections. Causes cell lysis by inactivation of PBPs through binding, inhibiting peptidoglycan synthesis.","category_aro_class_name":"Antibiotic"},"40932":{"category_aro_accession":"3004005","category_aro_cvterm_id":"40932","category_aro_name":"cefprozil","category_aro_description":"Cefprozil is a cephalosporin and beta-lactam antibiotic with bactericidal activity. It selectively binds to PBPs and inhibits peptidoglycan synthesis, a major cell wall component, resulting in cell lysis.","category_aro_class_name":"Antibiotic"},"40933":{"category_aro_accession":"3004006","category_aro_cvterm_id":"40933","category_aro_name":"ceftiofur","category_aro_description":"Ceftiofur is a third-generation broad spectrum cephalosporin and beta-lactam antibiotic. It causes cell lysis by disrupting peptidoglycan cross-linkage and cell wall formation by binding to PBPs.","category_aro_class_name":"Antibiotic"},"40934":{"category_aro_accession":"3004007","category_aro_cvterm_id":"40934","category_aro_name":"ceftizoxime","category_aro_description":"Ceftizoxime is a third-generation cephalosporin and broad spectrum beta-lactam antibiotic. Ceftizoxime causes bacterial cell lysis through peptidoglycan cross-linking inhibition by binding to PBPs.","category_aro_class_name":"Antibiotic"},"40935":{"category_aro_accession":"3004008","category_aro_cvterm_id":"40935","category_aro_name":"cephapirin","category_aro_description":"Cephapirin is a first-generation cephalosporin and broad spectrum beta-lactam antibiotic. Inactivation of penicillin-binding proteins through cephapirin binding disrupts peptidoglycan cross-linking, resulting in cell lysis.","category_aro_class_name":"Antibiotic"},"40936":{"category_aro_accession":"3004009","category_aro_cvterm_id":"40936","category_aro_name":"cefradine","category_aro_description":"Cefradine is a first-generation cephalosporin and broad spectrum beta-lactam antibiotic. Cefradine binding to penicillin-binding proteins disrupts cell wall peptidoglycan cross-linkage, resulting in cell lysis.","category_aro_class_name":"Antibiotic"},"40943":{"category_aro_accession":"3004016","category_aro_cvterm_id":"40943","category_aro_name":"loracarbef","category_aro_description":"Loracarbef is a second-generation cephalosporin (carbacephem) and broad spectrum beta-lactam antibiotic. Loracarbef inhibits PBPs through binding, disrupting peptidoglycan cell wall cross-linkage and resulting in cell death.","category_aro_class_name":"Antibiotic"},"40944":{"category_aro_accession":"3004017","category_aro_cvterm_id":"40944","category_aro_name":"moxalactam","category_aro_description":"Moxalactam (Latamoxef) is a broad spectrum cephalosporin (oxacephem) and beta-lactam antibiotic. Moxalactam binding to PBPs inhibits peptidoglycan cross-linkage in the cell wall, resulting in cell death. Moxalactam is proposed to be effective against meningitides as it passes the blood-brain barrier.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2104":{"model_id":"2104","model_name":"Ureaplasma urealyticum parC conferring resistance to fluoroquinolone","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"3974":"S83L","3975":"S83W","3976":"S84P","4636":"E87Q"},"clinical":{"3974":"S83L","3975":"S83W","3976":"S84P","4636":"E87Q"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1400"}},"model_sequences":{"sequence":{"3529":{"protein_sequence":{"accession":"WP_010891786.1","sequence":"MSVNHQKIINTPLDNIVGESYAKYAKYIIQDRALPDIRDGLKPVQRRILYAMSELGIFYDKPYKKSARTVGEVIGKYHPHGDSSIYEAMVRMSQDWKNNLCLLDMHGNKGSIDGDNAAAMRYTEARLSKIASVMLANLKKDVVKFSPNFDDSEKEPSILPSLFPNLLINGATGIASGYATNIPPHNPNEVFDALIYRIDHPDCSVEKLIEICPAPDFPTGGEIHDLNGCANAHKTGEGKFIIRACIDFKINDNKINQIIISSIPYETNKALIIKEIEDIIYNKEVAGLIEVRDESDAKGISIIIDTKKDINLENVKNYLYKKTNLEISYNTKFIAIVHRTPTLVNLSTYLDAQINHSLDVINKVDLYDLNKILLRIEIVEGLIKCVDLIDEIIKIIRASESRQDAKNTLIQVFNFTNNQAEAIIMMRLHNLTRTDIFDLKNEWQTLQDEAKTLQERINSLQVRKNYLKQKMIEFKKTFGFERKTKLFDELVKVEINEDQMIEKQNLNLVISRDGYIKTVSKKSFESSKYDELGLKTNDILFYHNIINSHDKILIITSKAKLINLVAHKITSMRWKDVGEHLNNYVKFDANEKVIAVYIWNEQFKIDEYQLVLASRLNLIKRIELSELDINKNSKQISIMKLNDNDNLISANLIKKGHNQFIIAISKLGLALLFLVHEINCLNRLAKGIKIMKLKPNDEVSAILITPNNGYNVQLFLERGSKCFNISELKLSKRAATPTNLYPITKKVQNVLAAFLVAHENVFYLLDQQQKINPYYLSNPKPTKLDTKISIYENDQMITDVVKDCFLSDEAISDFKKINMYANEFDNEMLKINKNHDDSQLELIDEEEEKK"},"dna_sequence":{"accession":"NC_002162.1","fmin":"531446","fmax":"533999","strand":"+","sequence":"ATGAGTGTAAATCATCAAAAAATTATTAATACACCTTTAGACAACATTGTTGGTGAAAGTTATGCAAAATATGCAAAATACATTATTCAAGATCGTGCTTTACCTGATATTCGTGATGGTTTAAAACCTGTTCAACGACGAATTTTATACGCAATGAGTGAATTAGGAATCTTTTATGATAAACCTTATAAAAAATCTGCACGTACAGTAGGAGAAGTAATTGGTAAATATCATCCACATGGAGATTCATCAATTTATGAAGCAATGGTGAGAATGAGTCAAGATTGAAAAAATAATCTATGTTTATTAGATATGCATGGTAATAAAGGTTCAATTGATGGTGATAATGCTGCTGCAATGCGTTATACAGAAGCTCGATTATCAAAAATTGCTAGTGTAATGTTAGCCAACTTAAAAAAAGATGTTGTTAAATTTAGTCCAAACTTTGATGATAGTGAAAAAGAGCCATCAATTTTACCATCTCTTTTTCCTAATTTGTTAATCAATGGAGCAACAGGAATTGCTTCTGGTTATGCAACAAATATTCCTCCTCATAACCCTAATGAAGTTTTTGATGCTTTAATTTATCGTATTGATCATCCAGATTGTAGTGTAGAAAAACTAATTGAAATCTGTCCTGCGCCAGATTTTCCCACAGGTGGGGAAATCCACGATTTAAATGGATGTGCTAATGCTCACAAAACTGGTGAAGGTAAATTTATAATTCGTGCTTGCATTGATTTTAAAATCAATGATAATAAGATTAATCAAATTATTATTAGTTCAATCCCTTATGAAACAAACAAGGCTTTAATCATTAAAGAAATTGAAGATATTATTTATAATAAAGAAGTTGCTGGATTAATCGAAGTTCGTGATGAATCTGATGCTAAGGGAATTAGTATAATTATTGATACTAAAAAAGATATTAATTTAGAAAATGTTAAAAACTATTTATATAAAAAAACCAACTTGGAAATCAGCTATAATACAAAATTTATTGCAATTGTTCACCGAACTCCTACACTTGTAAATCTATCTACATATTTAGATGCTCAAATTAATCATAGTTTAGATGTAATTAATAAAGTCGATTTATATGATCTAAACAAAATTTTGTTACGTATTGAAATTGTTGAAGGCTTAATTAAATGCGTTGATTTAATTGATGAAATTATTAAAATTATTCGTGCTAGTGAATCGCGTCAAGATGCAAAAAATACTTTAATTCAAGTTTTTAATTTTACAAATAATCAAGCTGAAGCGATTATTATGATGCGTTTACATAATTTGACACGTACTGATATATTTGATTTAAAAAATGAATGACAAACGCTACAAGACGAAGCTAAAACGCTACAAGAACGAATAAATTCACTTCAAGTTCGCAAAAATTATTTAAAACAAAAAATGATTGAATTTAAAAAAACTTTTGGTTTTGAACGCAAAACAAAATTATTTGATGAATTAGTAAAAGTTGAAATAAACGAAGATCAAATGATCGAAAAACAAAATTTGAATTTAGTAATAAGTCGTGATGGATACATTAAAACTGTTTCTAAAAAGTCATTTGAGTCATCTAAATATGATGAATTAGGATTAAAAACTAATGATATTCTTTTTTATCATAATATCATTAATTCTCATGATAAAATCCTAATCATTACATCAAAAGCTAAATTAATTAATTTAGTTGCTCATAAAATCACTTCTATGCGGTGAAAAGATGTTGGTGAACACTTAAATAATTATGTGAAATTTGATGCTAATGAAAAAGTTATAGCTGTTTATATATGGAACGAACAATTTAAAATTGATGAATATCAATTAGTTTTGGCTTCTAGATTAAATCTAATTAAAAGAATTGAATTAAGCGAGTTGGATATAAATAAAAATAGTAAACAAATTAGCATTATGAAATTAAATGATAATGATAATTTAATCAGTGCTAATTTAATCAAAAAAGGTCATAATCAATTTATTATTGCAATTTCTAAATTAGGATTAGCCCTGCTATTTTTAGTTCATGAAATTAATTGCTTAAATCGTTTAGCTAAAGGAATTAAAATTATGAAATTAAAACCAAATGATGAGGTTAGTGCTATTTTAATTACTCCTAATAATGGTTATAATGTTCAACTTTTTTTAGAACGGGGAAGTAAGTGTTTTAATATTAGTGAATTAAAATTATCAAAACGTGCGGCCACACCAACAAATTTATATCCAATAACAAAAAAAGTGCAAAATGTTTTAGCAGCTTTTTTAGTTGCTCATGAAAATGTTTTTTATCTTTTAGATCAACAACAAAAAATAAATCCATATTACTTATCAAACCCCAAACCAACAAAACTAGATACTAAAATTAGTATCTATGAAAACGATCAAATGATCACTGATGTAGTTAAAGATTGCTTTTTAAGTGATGAAGCAATTAGTGATTTTAAAAAAATTAATATGTACGCAAATGAATTTGATAATGAAATGCTAAAAATTAATAAAAATCACGATGATTCACAATTAGAATTAATTGATGAAGAGGAAGAAAAAAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40416","NCBI_taxonomy_name":"Ureaplasma parvum","NCBI_taxonomy_id":"134821"}}}},"ARO_accession":"3003309","ARO_id":"39893","ARO_name":"Ureaplasma urealyticum parC conferring resistance to fluoroquinolone","ARO_description":"Point mutation in Ureaplasma urealyticum parC resulting in fluoroquinolone resistance","ARO_category":{"36913":{"category_aro_accession":"3000619","category_aro_cvterm_id":"36913","category_aro_name":"fluoroquinolone resistant parC","category_aro_description":"ParC is a subunit of topoisomerase IV, which decatenates and relaxes DNA to allow access to genes for transcription or translation. Point mutations in ParC prevent fluoroquinolone antibiotics from inhibiting DNA synthesis, and confer low-level resistance. Higher-level resistance results from both gyrA and parC mutations.","category_aro_class_name":"AMR Gene Family"},"40471":{"category_aro_accession":"3003786","category_aro_cvterm_id":"40471","category_aro_name":"fluoroquinolone self resistant parC","category_aro_description":"Inherent parC resistance to fluoroquinolone from an antibiotic producer. The presence of these genes confers self-resistance to the antibiotic it produces.","category_aro_class_name":"AMR Gene Family"},"35942":{"category_aro_accession":"0000023","category_aro_cvterm_id":"35942","category_aro_name":"enoxacin","category_aro_description":"Enoxacin belongs to a group called fluoroquinolones. Its mode of action depends upon blocking bacterial DNA replication by binding itself to DNA gyrase and causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37004":{"category_aro_accession":"3000660","category_aro_cvterm_id":"37004","category_aro_name":"lomefloxacin","category_aro_description":"Lomefloxacin is a difluoropiperazinyl quinolone, sharing similar activities with other fluoroquinolones. It is used to treat urinary tract infections. Relative to other fluoroquinolones, it has a longer half life and has higher serum concentrations.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"37008":{"category_aro_accession":"3000664","category_aro_cvterm_id":"37008","category_aro_name":"trovafloxacin","category_aro_description":"Trovafloxacin is a trifluoroquinalone with a broad spectrum of activity that acts by inhibiting the uncoiling of supercoiled DNA. While potent against many Gram-positive and Gram-negative bacteria, it is less active against pseudomonads and Cl. difficile. It is usually taken as the prodrug trovafloxacin mesylate or alatrofloxacin mesylate for oral or intravenous administration, respectively.","category_aro_class_name":"Antibiotic"},"37009":{"category_aro_accession":"3000665","category_aro_cvterm_id":"37009","category_aro_name":"grepafloxacin","category_aro_description":"Grepafloxacin is a broad-spectrum antibacterial quinoline. It is no longer taken due to its high toxicity.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"37142":{"category_aro_accession":"3000762","category_aro_cvterm_id":"37142","category_aro_name":"pefloxacin","category_aro_description":"Pefloxacin is structurally and functionally similar to norfloxacin. It is poorly active against mycobacteria, while anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2711":{"model_id":"2711","model_name":"MexXY-OprM","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)","model_param":{"41141":{"param_type":"efflux pump components","param_description":"This detection model parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305.","param_type_id":"41141","param_value":{"7588":"2223,334,1786,1305"}}},"ARO_accession":"3003032","ARO_id":"39466","ARO_name":"MexXY-OprM","ARO_description":"MexXY-OprM is a multidrug efflux protein expressed in Pseudomonas aeruginosa. MexY is the membrane fusion protein; MexX is the RND-type membrane protein; and OprM is the outer membrane channel. MexXY-OprM is associated with resistance to acriflavine, erythromycin, norfloxacin and ofloxacin. The efflux system may also be involved in acquisition of higher resistance, in particular when bacteria are repeatedly exposed to subinhibitory doses of AGs.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavin","category_aro_description":"Acriflavin is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36193":{"category_aro_accession":"3000054","category_aro_cvterm_id":"36193","category_aro_name":"acridine dye","category_aro_description":"Acridine dyes are cell permeable, basic molecules with an acridine chromophore. These compounds intercalate DNA. The image shown represents the core structure of the acridine family, with specific dyes containing varying substituents.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2712":{"model_id":"2712","model_name":"MexXY-OprA","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)","model_param":{"41141":{"param_type":"efflux pump components","param_description":"This detection model parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305.","param_type_id":"41141","param_value":{"7589":"2223,334,1786,1570"}}},"ARO_accession":"3003038","ARO_id":"39472","ARO_name":"MexXY-OprA","ARO_description":"MexXY-OprA is a multidrug efflux protein expressed in Pseudomonas aeruginosa. MexY is the membrane fusion protein; MexX is the RND-type membrane protein; and OprA is the outer membrane channel. MexXY-OprA is associated with resistance to aminoglycosides","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2705":{"model_id":"2705","model_name":"MexEF-OprN with MexS mutations conferring resistance to chloramphenicol, ciprofloxacin, and trimethoprim","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)","model_param":{"41141":{"param_type":"efflux pump components","param_description":"This detection model parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305.","param_type_id":"41141","param_value":{"7584":"1041,1608,1067,1300,172"}}},"ARO_accession":"3004068","ARO_id":"41145","ARO_name":"MexEF-OprN with MexS mutations conferring resistance to chloramphenicol, ciprofloxacin, and trimethoprim","ARO_description":"The MexEF\u2013OprN efflux pump with MexS mutations conferring resistance to chloramphenicol and ciprofloxacin. The model includes the MexT regulator, as MexS is suggested to inactivate MexT.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2694":{"model_id":"2694","model_name":"MexCD\u2013OprJ with type A NfxB mutation","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)","model_param":{"41141":{"param_type":"efflux pump components","param_description":"This detection model parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305.","param_type_id":"41141","param_value":{"7551":"2691,805,1523,704"}}},"ARO_accession":"3004061","ARO_id":"41128","ARO_name":"MexCD-OprJ with type A NfxB mutation","ARO_description":"MexCD\u2013OprJ with type A NfxB phenotype are four to eight times more resistant to ofloxacin, erythromycin, and new zwitterionic cephems, i.e., cefpirome, cefclidin, cefozopran, and cefoselis, than the parent strain, PAO1.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2348":{"model_id":"2348","model_name":"ADC-18","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3641":{"protein_sequence":{"accession":"WP_002118772.1","sequence":"MRFKKISCLLLPPLFIFSTSIYAGNTPKEQEVKKLVDQNFKPLLDKYDVPGMAVGVIQNNKKYEIYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKAKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKTKNAIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPPLHLKNSYVNVPKTQMQNYAYGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLTFINANLNPQKYPKDIQRAISETHQGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGSYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_048642","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGCTTACTTTTACCGCCTCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGAACAAGAAGTTAAAAAACTGGTAGATCAAAATTTTAAGCCTTTATTAGATAAATATGATGTGCCTGGTATGGCCGTGGGGGTCATTCAAAATAATAAAAAATATGAAATATATTATGGCCTACAATCCGTTCAGGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAACTAGGTTCGGTCAGTAAATTATTTACCGCTACAGCTGGTGGATATGCAAAAGCAAAAGGAAAAATCTCTTTTGATGACACACCCGGAAAATATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAATCTTCTTCAACTTGCGACGTATACAAGTGGCAATCTCGCCTTACAATTTCCAGATGAAGTTCAAACAGACCAACAAGTTTTAACTTTTTTCAAAGATTGGAAAACTAAAAACGCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCTTATTTGGAAAAGTTGTGGCTTTGTCTATGAATAAACCTTTTGACCAAGTCTTAGAAAAAACAATTTTTCCACCTCTCCATTTAAAAAATAGCTATGTAAATGTACCCAAAACTCAAATGCAAAATTATGCATATGGCTATAACCAAGAAAATCAGCCGATCCGAGTTAACCCTGGCCCGCTAGATGCTCCAGCATACGGCGTTAAATCGACACTACCAGATATGCTGACTTTTATTAATGCCAACCTCAACCCACAGAAATATCCGAAAGATATTCAACGTGCAATTAGTGAAACACATCAAGGTTTCTATCAAGTCGGTACGATGTATCAAGCATTGGGTTGGGAAGAATTTTCTTATCCAGCACCTTTACAAACTTTATTAGACAGTAATTCAGAGCAAATCGTGATGAAGCCTAATAAAGTGACTGCCATTTCCAAAGAACCTTCAGTTAAGATGTTCCACAAAACTGGCTCAACAAATGGCTTTGGATCTTATGTGGTGTTTATTCCAAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCAGTATTGAATGCAATAAAGAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40550","NCBI_taxonomy_name":"Acinetobacter calcoaceticus\/baumannii complex","NCBI_taxonomy_id":"909768"}}}},"ARO_accession":"3003862","ARO_id":"40561","ARO_name":"ADC-18","ARO_description":"ADC-18 is a beta-lactamase found in Acinetobacter pittii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2349":{"model_id":"2349","model_name":"ADC-19","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3642":{"protein_sequence":{"accession":"WP_063857793.1","sequence":"MRFKKISCLLLSPLFIFNTSIYAGNTSKEQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKKLKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPDLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLKFINANLNPQKYPKDIQRAINETHQGFYQVGTMYQALGWEEFSYPALLQTLLDSNSEQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_048643.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGCTTACTTTTATCTCCTCTTTTTATTTTTAATACATCAATTTATGCGGGCAATACATCAAAAGAACAAGAAATTAAAAAACTGGTAGATCAGAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCTGTAAATAGCAGTACCATTTTTGAGCTAGGTTCAGTTAGTAAATTATTTACCGCAACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAAAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCAACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATAGACAATATTCAAATCCAAGCATTGGTTTATTTGGAAAAGTTGTGGCATTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCAGATCTTGGCTTAAAACATAGCTATGTAAATGTTCCTAAAACTCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCAATTCGTGTTAACCCTGGTCCACTAGATGCTCCAGCATATGGGGTTAAATCGACGCTACCCGATATGCTTAAGTTTATTAATGCCAACCTCAACCCACAGAAATATCCGAAAGATATTCAACGTGCAATTAATGAAACACATCAAGGTTTCTACCAAGTCGGCACGATGTATCAGGCACTTGGTTGGGAAGAATTTTCTTATCCAGCGCTTTTACAAACTTTATTAGACAGTAATTCAGAACAAATTGTGATGAAGCCTAATAAAGTGACTGCCATTTCAAAAGAACCTTCAGTTAAGATGTTCCACAAAACTGGTTCAACCAATGGTTTCGGAACTTATGTCGTGTTCATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCAGTATTAAATGCAATAAAGAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3003863","ARO_id":"40562","ARO_name":"ADC-19","ARO_description":"ADC-19 is a beta-lactamase found in Acinetobacter pittii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2350":{"model_id":"2350","model_name":"ADC-20","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3643":{"protein_sequence":{"accession":"WP_063857794.1","sequence":"MRFKKISCLLLSPLFIFSTSIYADNTPKDQEIKKLVDQNFKPLLDKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKTVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTSGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPGLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLKFINANLNPQKYPKDIQRAINETHQGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_048645","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGACAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCTTTATTAGATAAATATGATGTGCCGGGTATGGCCGTGGGTGTTATTCAGAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAACCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGTCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCAACGTATACAAGTGGTAACCTTGCCTTGCAATTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGCATTGGTTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGGCCTTGGCTTAAAACATAGCTATGTAAATGTTCCTAAAACTCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCAATTCGTGTTAACCCTGGTCCGCTAGATGCTCCAGCATATGGGGTTAAATCGACGCTACCCGATATGCTTAAGTTTATTAATGCCAACCTCAACCCACAGAAATATCCGAAAGATATTCAACGTGCAATTAATGAAACACATCAGGGTTTCTATCAAGTCGGCACCATGTATCAGGCACTTGGTTGGGAAGAATTTTCTTATCCAGCGCCTTTACAAACTTTATTAGACAGTAATTCAGAACAAATTGTGATGAAGCCTAATAAAGTGACTGCCATTTCAAAAGAACCTTCAGTTAAGATGTTCCACAAAACTGGTTCAACCAATGGTTTCGGAACTTATGTCGTGTTCATTCCTAAAGAAAATATTGGCCTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAAGCAGCGTATGCCGTGTTAAATGCAATAAAGAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3003864","ARO_id":"40563","ARO_name":"ADC-20","ARO_description":"ADC-20 is a beta-lactamase found in Acinetobacter pittii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2351":{"model_id":"2351","model_name":"ADC-21","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3644":{"protein_sequence":{"accession":"WP_063857795.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLDKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVSSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKLKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPDLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFINANINPQKYPADIQRAINETHQGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSIKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_048646","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCTTTATTAGATAAATATGATGTGCCGGGTATGGCCGTGGGTGTTATTCAGAATAATAAAAAGTATGAAATGTATTATGGTCTACAATCTGTTCAAGATAAAAAAGCCGTAAGTAGCAGTACCATTTTTGAACTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCAACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACTTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCAGATCTGGGATTAAAACATAGTTATGTAAATGTGCCTAAAACTCAGATGCAAAACTATGCTTTTGGCTATAATCAAGAAAATCAGCCAATTCGTGTTAACCCCGGTCCGCTAGATGCTCCAGCATACGGCGTTAAATCGACCCTACCTGATATGCTGAGTTTCATTAATGCCAATATAAATCCACAAAAATATCCAGCAGATATTCAACGTGCAATTAATGAAACACATCAAGGTTTCTATCAAGTCGGCACCATGTATCAGGCACTTGGTTGGGAAGAATTTTCTTATCCAGCGCCTTTACAAACTTTATTAGACAGTAATTCAGAACAAATTGTGATGAAGCCTAATAAAGTGACTGCCATTTCCAAAGAACCTTCAATTAAGATGTTCCACAAAACTGGTTCGACTAACGGTTTTGGAACATATGTCGTGTTCATTCCTAAAGAAAATATTGGCTTAGTCATGTTGACCAATAAACGTATTCCGAATGAAGAACGCATTAAAGCAGCTTATGCTGTGTTAAATGCAATAAAGAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3003865","ARO_id":"40564","ARO_name":"ADC-21","ARO_description":"ADC-21 is a beta-lactamase found in Acinetobacter pittii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2352":{"model_id":"2352","model_name":"ADC-22","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3645":{"protein_sequence":{"accession":"WP_063857796.1","sequence":"MRFKKISCLLLPPLFIFSTSIYAGNTPKDREIKKLVDQNFKPLLDKYDVPGMAVGVIQNNKKYETYYGLQSVQDKKAVSSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPDLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLKFINANLNTQKYPKDIQRAINETHQGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_048647.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGCTTACTTTTACCTCCTCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCGAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCTTTATTAGATAAATATGATGTGCCGGGTATGGCCGTGGGCGTTATTCAGAATAATAAAAAATATGAAACGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAGTAGCAGCACCATTTTTGAACTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATTTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCAACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATAGACAATATTCAAATCCAAGCATTGGTTTATTTGGAAAAGTTGTGGCATTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCAGATCTTGGCTTAAAACATAGCTATGTAAATGTTCCTAAAACTCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCAATTCGTGTTAACCCTGGTCCGCTAGATGCTCCAGCATATGGGGTTAAATCGACGCTACCCGATATGCTTAAGTTTATTAATGCCAACCTCAACACACAGAAATATCCGAAAGATATTCAACGTGCAATTAATGAAACACATCAGGGTTTCTATCAAGTCGGCACCATGTATCAGGCACTTGGTTGGGAAGAATTTTCTTATCCAGCGCCTTTACAAACTTTATTAGACAGTAATTCAGAACAAATTGTGATGAAGCCTAATAAAGTGACTGCCATTTCAAAAGAACCTTCAGTTAAGATGTTCCACAAAACTGGTTCAACCAATGGTTTCGGAACTTATGTCGTGTTCATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCCGTGTTAAATGCAATAAAGAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3003866","ARO_id":"40565","ARO_name":"ADC-22","ARO_description":"ADC-22 is a beta-lactamase found in Acinetobacter pittii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2353":{"model_id":"2353","model_name":"ADC-23","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3646":{"protein_sequence":{"accession":"WP_063857797.1","sequence":"MRFKKISCLLLPPLFIFSTSIYAGNTPKEQEVKKLVDQNFKPLLDKYDVPGMAVGVIQNNKKYEIYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKAKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKTKNAIGEYRQYSNPSIGLFGKIVALSMNKPFDQVLEKTIFPPLHLKNSYVNVPKTQMQNYAYGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLTFINANLNPQKYPKDIQRAINETHQGFYQVGTMYQALGWEEFSYPASLQTLLDSNSEQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_048648.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGCTTACTTTTACCGCCTCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGAACAAGAAGTTAAAAAACTGGTAGATCAAAATTTTAAGCCTTTATTAGATAAATATGATGTGCCTGGTATGGCCGTGGGGGTCATTCAAAATAATAAAAAATATGAAATATATTATGGCCTACAATCCGTTCAGGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAACTAGGTTCGGTCAGTAAATTATTTACCGCTACAGCTGGTGGATATGCAAAAGCAAAAGGAAAAATCTCTTTTGATGACACACCCGGAAAATATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAATCTTCTTCAACTTGCGACGTATACAAGTGGCAATCTCGCCTTACAATTTCCAGATGAAGTTCAAACAGACCAACAAGTTTTAACTTTTTTCAAAGATTGGAAAACTAAAAACGCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCTTATTTGGAAAAATTGTGGCTTTGTCTATGAATAAACCTTTTGACCAAGTCTTAGAAAAAACAATTTTTCCACCTCTCCATTTAAAAAATAGCTATGTAAATGTACCTAAAACTCAAATGCAAAATTATGCATATGGCTATAACCAAGAAAATCAGCCGATCCGAGTTAACCCTGGTCCGCTAGATGCCCCTGCGTACGGCGTTAAATCGACACTACCAGATATGCTGACTTTTATTAATGCCAACCTCAACCCACAGAAATATCCGAAAGATATTCAACGTGCAATTAATGAAACACATCAAGGTTTCTATCAAGTCGGTACGATGTATCAAGCATTGGGTTGGGAAGAATTTTCTTATCCAGCGTCTTTACAAACTTTATTAGACAGTAATTCAGAGCAAATCGTGATGAAGCCTAATAAAGTGACTGCCATTTCAAAAGAACCTTCAGTTAAGATGTTCCACAAAACTGGCTCAACAAATGGCTTTGGAACTTATGTGGTGTTTATTCCAAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCAGTATTAAATGCAATAAAGAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3003867","ARO_id":"40566","ARO_name":"ADC-23","ARO_description":"ADC-23 is a beta-lactamase found in Acinetobacter pittii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2718":{"model_id":"2718","model_name":"MuxB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1900"}},"model_sequences":{"sequence":{"4043":{"protein_sequence":{"accession":"NP_251217.1","sequence":"MNPSRPFILRPVATTLLMVAILLSGLIAYRFLPISALPEVDYPTIQVVTLYPGASPEIMTSSITAPLENQLGQIPGLNEMSSSSSGGASVITLQFSLQSNLDVAEQEVQAAINAAQSLLPNDLPNQPVFSKVNPADAPILTLAVMSDGMPLPQIQDLVDTRLAQKISQISGVGLVSISGGQRPAVRVRANPTALAAAGLSLEDLRSTVTSNNLNGPKGSFDGPTRASTLDANDQLRSADAYRDLIIAYKNGSPLRIRDVASVEDDAENVRLAAWANNLPAVVLNIQRQPGANVIEVVDRIKALLPQLQSTLPGNLDVQVLTDRTTTIRASVKDVQFELALAVALVVMVTFLFLRNVYATLIPSFAVPLSLIGTFGVMYLSGFSINNLTLMALTIATGFVVDDAIVMVENIARYLEQGDSPLEAALKGSKQIGFTIISLTFSLIAVLIPLLFMGDVAGRLFREFAITLAVAILISGFVSLTLTPMLSAKLLRHIDEDQQGRFARAAGRVIDGLIAQYAKALRVVLRHQPLTLLVAIATLALTALLYLAMPKGFFPVQDTGVIQGVAEAPQSISFQAMSERQRALAEVVLKDPAVASLSSYIGVDGSNPTLNTGRLLINLKPHSERDVTASEVIQRLQPELDHLPGIKLYMQPVQDLTIEDRVARTQYQFTLQDADPDVLAEWVPKLVARLQELPQLADVASDWQDKGLQAYLNIDRDTASRLGVKLSDIDSVLYNAFGQRLISTIFTQATQYRVVLEVAPQFQLGPQALEQLYVPSSDGTQVRLSSLAKVEERHTLLAINHIAQFPSATLSFNLAKGYSLGEAVEAIRGVEASLELPLSMQGSFRGAALAFEASLSNTLLLILASVVTMYIVLGILYESFIHPVTILSTLPSAGVGALLALMLAGQEIGIVAIIGIILLIGIVKKNAIMMIDFALDAERNEGKPPHEAIYQACLLRFRPILMTTMAALLGALPLMLAGGAGAELRQPLGITMVGGLLLSQVLTLFTTPVIYLYFDRLARRWAAWRKQRGLDLNTEAGFDGDAGR"},"dna_sequence":{"accession":"NC_002516.2","fmin":"2850882","fmax":"2854014","strand":"-","sequence":"TCATCGCCCGGCGTCCCCGTCGAACCCGGCCTCGGTGTTCAGGTCCAGCCCGCGCTGCTTGCGCCAGGCCGCCCAGCGACGGGCCAGGCGGTCGAAGTAGAGATAGATCACCGGGGTGGTGAACAGGGTCAGGACCTGGCTCAGCAGCAGGCCACCGACCATGGTGATGCCCAGCGGCTGGCGCAGCTCGGCGCCGGCGCCGCCGGCGAGCATCAGCGGCAGCGCGCCGAGCAGCGCGGCCATGGTGGTCATCAGGATCGGCCGGAAGCGCAGCAGGCAGGCCTGGTAGATCGCCTCATGGGGCGGCTTGCCTTCGTTGCGCTCGGCGTCGAGGGCGAAATCGATCATCATGATCGCGTTCTTCTTGACGATGCCGATCAGCAGGATGATGCCGATGATCGCCACGATGCCGATCTCCTGCCCCGCCAGCATCAGCGCCAGCAGCGCGCCGACCCCGGCCGAGGGCAGGGTCGAGAGGATGGTCACCGGATGGATGAAGCTCTCGTAGAGGATGCCCAGGACGATGTACATGGTCACCACCGAGGCGAGGATCAGCAGCAGCGTGTTCGACAGCGAGGCCTCGAAGGCCAGCGCCGCGCCGCGGAAGCTGCCCTGCATGCTCAGCGGCAGCTCCAGGCTGGCCTCGACGCCACGGATCGCCTCGACCGCCTCGCCCAGGGAGTAACCCTTGGCCAGGTTGAACGACAGGGTCGCCGAGGGGAACTGGGCGATATGGTTGATCGCCAGCAGGGTATGCCGCTCCTCCACCTTCGCCAGGCTCGACAGGCGCACCTGGGTGCCGTCGCTGGACGGCACGTAGAGCTGCTCCAGGGCCTGCGGGCCGAGCTGGAACTGCGGCGCCACCTCCAGCACCACGCGGTACTGGGTGGCCTGGGTGAAGATGGTCGAGATCAGCCGCTGGCCGAAGGCGTTGTAGAGCACGCTGTCGATGTCGGAGAGCTTCACGCCGAGGCGCGAGGCGGTGTCGCGGTCGATGTTCAGGTAGGCCTGCAAGCCCTTGTCCTGCCAGTCGCTGGCGACGTCGGCGAGCTGCGGCAACTCCTGCAGCCGCGCCACCAGCTTCGGCACCCACTCGGCGAGCACGTCCGGGTCGGCGTCCTGCAAGGTGAACTGGTACTGGGTGCGGGCGACCCGGTCCTCGATGGTCAGGTCCTGCACCGGCTGCATGTACAGCTTGATCCCGGGCAGGTGGTCGAGTTCGGGCTGCAGGCGCTGGATCACTTCGCTGGCGGTGACGTCGCGCTCGCTGTGCGGCTTGAGGTTGATCAGCAGGCGGCCGGTGTTGAGGGTCGGGTTGCTGCCGTCGACGCCGATGTAGGAGGACAGGCTGGCCACCGCCGGGTCCTTCAGCACCACCTCGGCAAGGGCGCGCTGGCGCTCGGACATGGCCTGGAAGGAGATCGACTGCGGCGCTTCGGCGACGCCCTGGATCACCCCGGTGTCCTGCACCGGGAAGAAGCCCTTGGGCATGGCCAGGTAGAGTAGCGCGGTCAGCGCCAGGGTGGCGATGGCCACCAGCAGGGTCAGCGGCTGGTGCCGCAGGACCACCCGCAGGGCCTTGGCGTACTGTGCGATCAGGCCATCGATGACCCGCCCCGCGGCGCGCGCGAAGCGGCCCTGCTGGTCCTCGTCGATGTGGCGCAGCAGCTTGGCGCTGAGCATCGGCGTAAGGGTCAGGGAGACGAAGCCGGAAATCAGGATCGCCACCGCCAGGGTGATGGCGAACTCGCGGAACAGCCGCCCGGCGACGTCGCCCATGAACAGCAGCGGGATCAGCACGGCGATCAGCGAGAAAGTCAGCGAGATGATGGTGAAGCCGATCTGCTTCGAGCCCTTGAGCGCCGCTTCCAGCGGCGAGTCGCCCTGCTCCAGGTAGCGGGCGATGTTCTCCACCATGACGATCGCGTCGTCGACCACGAAGCCGGTGGCGATGGTCAGCGCCATCAGGGTCAGGTTGTTGATCGAGAAGCCGGACAGGTACATCACGCCGAAGGTACCGATCAGCGACAGCGGCACGGCGAAGCTGGGAATCAGGGTGGCGTAGACGTTGCGCAGGAACAGGAAGGTGACCATCACCACCAGCGCCACCGCCAGCGCCAGCTCGAACTGCACGTCCTTGACCGAGGCGCGGATGGTGGTGGTGCGGTCGGTCAGCACCTGCACGTCGAGATTGCCCGGCAGGGTCGATTGCAGCTGCGGCAGCAGCGCCTTGATCCGGTCGACCACCTCGATCACGTTGGCCCCCGGCTGGCGCTGGATGTTCAGCACCACCGCCGGCAGGTTGTTGGCCCAGGCGGCCAGGCGCACGTTCTCGGCGTCGTCCTCGACGCTGGCGACGTCGCGGATGCGCAGCGGCGAGCCGTTCTTGTAGGCGATGATCAGGTCGCGGTAGGCGTCGGCCGAGCGCAACTGGTCGTTGGCGTCCAGGGTCGAGGCACGGGTCGGGCCGTCGAAGCTGCCCTTGGGGCCGTTGAGGTTGTTGCTGGTCACCGTGCTGCGCAGGTCCTCCAGGCTCAGCCCCGCCGCCGCCAGCGCCGTCGGGTTGGCGCGCACCCGCACCGCCGGGCGCTGGCCGCCGCTGATGCTGACCAGGCCGACCCCGGAGATCTGCGAGATCTTCTGTGCCAGGCGGGTATCCACCAGGTCCTGGATCTGCGGCAGCGGCATGCCGTCGGACATCACCGCCAGGGTCAGGATCGGTGCGTCCGCCGGATTCACCTTGCTGAACACCGGCTGGTTCGGCAGGTCGTTGGGCAGCAGGCTCTGCGCGGCGTTGATCGCCGCCTGGACTTCCTGCTCGGCGACATCGAGGTTGCTCTGCAGGCTGAATTGCAGGGTGATCACCGAGGCGCCGCCGGAACTGCTGGAAGACATCTCGTTGAGCCCCGGAATCTGCCCGAGCTGGTTCTCCAGCGGCGCGGTGATCGACGAGGTCATGATCTCCGGGCTGGCGCCGGGGTACAGGGTGACCACCTGGATGGTCGGGTAGTCCACTTCCGGCAACGCCGAGATCGGCAGGAAGCGGTAGGCGATCAGGCCCGAGAGCAGGATCGCCACCATCAGCAGGGTGGTCGCGACCGGCCGCAGGATGAACGGGCGGGACGGGTTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3004074","ARO_id":"41156","ARO_name":"MuxB","ARO_description":"MuxB is one of the two necessary RND components in the Pseudomonas aeruginosa efflux pump system MuxABC-OpmB.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36689":{"category_aro_accession":"3000550","category_aro_cvterm_id":"36689","category_aro_name":"aztreonam","category_aro_description":"Aztreonam was the first monobactam discovered, and is greatly effective against Gram-negative bacteria while inactive against Gram-positive bacteria. Artreonam is a poor substrate for beta-lactamases, and may even act as an inhibitor. In Gram-negative bacteria, Aztreonam interferes with filamentation, inhibiting cell division and leading to cell death.","category_aro_class_name":"Antibiotic"},"37626":{"category_aro_accession":"3001227","category_aro_cvterm_id":"37626","category_aro_name":"kitasamycin","category_aro_description":"Kitasamycin is a macrolide antibiotic and is produced by Streptoverticillium kitasatoense. The drug has antimicrobial activity against a wide spectrum of pathogens.","category_aro_class_name":"Antibiotic"},"40353":{"category_aro_accession":"3003701","category_aro_cvterm_id":"40353","category_aro_name":"rokitamycin","category_aro_description":"Rokitamycin is a macrolide antibiotic. Synthesized from strains of Streptomyces kitasatoensis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2720":{"model_id":"2720","model_name":"MuxC","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1900"}},"model_sequences":{"sequence":{"4045":{"protein_sequence":{"accession":"NP_251216.1","sequence":"MSLSTPFIRRPVATTLLTLALLLAGTLSFGLLPVAPLPNVDFPAIVVSASLPGASPETMASSVATPLERSLGRIAGISEMTSSSSLGSTTVVLVFDLEKDIDGAAREVQAAINGAMSLLPSGMPNNPSYRKANPSDMPIMVLTLTSETQSRGEMYDLASTVLAPKLSQVQGVGQVSIGGSSLPAVRVDLNPDAMSQYGLSLDSVRTAIAAANSNGPKGAVEKDDKHWQVDANDQLRKAREYEPLVIHYNADNGAAVRLGDVAKVSDSVEDVRNAGFSDDLPAVLLIVTRQPGANIIEATDAIHAQLPVLQELLGPQVKLNVMDDRSPSIRASLEEAELTLLISVALVILVVFLFLRNGRATLIPSLAVPVSLIGTFAVMYLCDFSLNNLSLMALIIATGFVVDDAIVVVENIARRIEEGDPPIQAAITGARQVGFTVLSMTLSLVAVFIPLLLMGGLTGRLFREFAVTLSAAILVSLVVSLTLTPMLCARLLRPLKRPEGASLARRSDRFFAAFMLRYRASLGWALEHSRLMVVIMLACIAMNLWLFVVVPKGFLPQQDSGRLRGYAVADQSISFQSLSAKMGEYRKILSSDPAVENVVGFIGGGRWQSSNTGSFFVTLKPIGERDPVEKVLTRLRERIAKVPGAALYLNAGQDVRLGGRDSNAQYEFTLRSDDLTLLREWAPKVEAAMRKLPQLVDVNSDSQDKGVQTRLVIDRDRAATLGINVEMVDAVLNDSFGQRQVSTIFNPLNQYRVVMEVDQQYQQSPEILRQVQVIGNDGQRVPLSAFSHYEPSRAPLEVNHQGQFAATTLSFNLAPGAQIGPTREAIMQALEPLHIPVDVQTSFEGNAGAVQDTQNQMPWLILLALLAVYIVLGILYESYVHPLTILSTLPSAGVGALLALILCRSELSLIALIGIILLIGIVKKNAIMMIDFALEAERNHGLSPREAILEACMMRFRPIMMTTLAALLGALPLIFGIGGDAALRRPLGITIVGGLIGSQLLTLYTTPVVYLYLDRLRHWVNQKRGVRTDGALETPL"},"dna_sequence":{"accession":"NC_002516.2","fmin":"2847775","fmax":"2850886","strand":"-","sequence":"TCATAGGGGTGTCTCCAGCGCACCGTCCGTGCGTACGCCGCGTTTCTGGTTGACCCAGTGGCGCAGGCGGTCGAGATAGAGGTAGACCACCGGGGTGGTGTACAGGGTCAGCAACTGGCTGCCGATCAGCCCGCCGACGATGGTGATGCCCAGCGGCCGGCGCAGCGCGGCGTCGCCGCCGATGCCGAAGATCAGCGGCAAGGCGCCGAGCAAGGCGGCCAGGGTGGTCATCATGATCGGCCGGAAGCGCATCATGCAGGCCTCGAGGATCGCCTCGCGCGGGCTCAGGCCGTGGTTGCGCTCGGCCTCCAGGGCGAAGTCGATCATCATGATCGCGTTCTTCTTGACGATGCCGATCAGCAGGATGATGCCGATCAGCGCGATCAGGCTCAGCTCGCTGCGGCAGAGGATCAGCGCGAGCAGCGCGCCGACCCCGGCCGAAGGCAGGGTCGAGAGGATGGTCAGCGGGTGCACGTAGCTCTCGTAGAGGATGCCGAGGACGATGTACACCGCCAGCAGCGCCAGGAGGATCAGCCAGGGCATCTGGTTCTGCGTGTCCTGCACCGCGCCGGCGTTGCCCTCGAAGCTGGTCTGCACGTCCACCGGGATGTGCAGCGGCTCCAGGGCCTGCATGATGGCCTCGCGGGTCGGGCCGATCTGCGCGCCCGGTGCCAGGTTGAAGGACAGCGTGGTGGCGGCGAACTGGCCCTGGTGGTTGACCTCCAGCGGTGCCCGGCTCGGTTCGTAGTGGCTGAACGCGGACAGCGGCACGCGCTGGCCGTCGTTGCCGATCACCTGGACCTGGCGGAGGATCTCCGGGCTCTGCTGGTACTGCTGGTCGACCTCCATCACCACCCGGTACTGGTTCAGCGGGTTGAAGATGGTCGACACCTGGCGCTGGCCGAAAGAGTCGTTGAGCACCGCGTCGACCATTTCCACGTTGATCCCCAGGGTCGCCGCGCGGTCGCGGTCGATCACCAGGCGGGTCTGCACGCCCTTGTCCTGGGAGTCGCTGTTGACGTCCACCAGCTGCGGCAGCTTGCGCATCGCCGCCTCGACCTTCGGCGCCCATTCGCGGAGCAGGGTCAGGTCGTCGCTGCGCAGGGTGAATTCGTACTGCGCGTTGCTGTCGCGGCCGCCCAGGCGCACGTCCTGGCCGGCGTTGAGATAGAGCGCCGCGCCGGGCACCTTGGCGATCCGCTCGCGCAGCCGGGTGAGGACCTTCTCCACCGGGTCGCGCTCGCCGATCGGCTTGAGAGTGACGAAGAACGAACCGGTGTTGCTCGACTGCCAACGGCCGCCACCGATGAAGCCGACCACGTTTTCCACCGCCGGATCGGAAGAGAGGATCTTGCGGTACTCGCCCATCTTCGCGCTCAGGGACTGGAACGAGATGCTCTGGTCGGCCACCGCGTAGCCGCGCAGGCGCCCGGAGTCCTGCTGCGGGAGGAAGCCCTTGGGCACCACCACGAACAACCAGAGGTTCATGGCGATGCAGGCCAGCATGATCACCACCATCAGCCGCGAGTGCTCCAGCGCCCAGCCCAGGCTGGCGCGGTAGCGCAGCATGAAGGCGGCGAAGAAGCGATCGCTGCGCCGCGCCAGGGAAGCGCCTTCGGGCCGTTTCAGCGGACGCAGCAGACGCGCGCAGAGCATCGGCGTGAGGGTCAGGGATACCACCAGGGACACCAGGATCGCCGCCGAGAGAGTCACCGCGAACTCGCGGAACAGCCGTCCGGTGAGGCCACCCATGAGCAGCAGCGGGATGAACACCGCGACCAGCGAGAGCGTCATCGACAGCACGGTGAAACCGACCTGGCGGGCGCCGGTGATCGCCGCCTGGATCGGCGGATCGCCCTCCTCGATGCGTCGGGCGATGTTCTCCACCACCACTATGGCGTCATCCACCACGAAGCCGGTGGCGATGATCAGCGCCATCAGCGACAGGTTGTTCAGGCTGAAGTCGCACAGGTACATGACCGCGAAGGTGCCGATCAGCGAGACCGGCACCGCCAGGCTGGGGATCAGCGTGGCGCGGCCGTTGCGCAGGAACAGGAAGACCACCAGGATCACCAGCGCCACCGAGATCAGCAGGGTCAGCTCGGCCTCTTCCAGCGACGCACGGATCGACGGGCTGCGATCGTCCATCACGTTCAGCTTGACCTGCGGCCCGAGCAGTTCCTGCAACACCGGCAGTTGCGCGTGGATGGCGTCGGTGGCCTCGATGATGTTGGCGCCGGGCTGGCGGGTGACGATTAGCAGCACAGCCGGCAGGTCGTCGGAAAAGCCGGCGTTGCGCACGTCCTCCACCGAGTCGCTGACCTTGGCCACGTCGCCGAGGCGCACCGCGGCGCCGTTGTCGGCGTTGTAGTGGATCACCAGCGGCTCGTACTCGCGGGCCTTGCGCAACTGGTCGTTGGCGTCCACCTGCCAGTGCTTGTCGTCCTTCTCGACGGCGCCCTTGGGGCCGTTGCTGTTGGCCGCGGCGATGGCCGTGCGCACGCTGTCCAGGGACAGCCCGTACTGGCTCATGGCATCCGGGTTGAGGTCGACCCGCACCGCCGGCAGCGAGCTGCCGCCGATGCTCACCTGCCCTACCCCCTGCACCTGCGACAGCTTGGGCGCCAGCACGGTCGAGGCGAGGTCGTACATCTCGCCGCGACTCTGGGTCTCCGAGGTCAGGGTGAGGACCATGATCGGCATGTCCGAGGGGTTGGCCTTGCGGTAGCTGGGATTGTTCGGCATACCGCTGGGCAGCAGGCTCATCGCGCCGTTGATCGCCGCCTGCACCTCGCGGGCGGCGCCGTCGATGTCCTTCTCCAGGTCGAACACGAGCACCACGGTGGTCGAGCCCAGCGAACTGCTGGAGGTCATCTCGCTGATCCCGGCGATCCGTCCCAGCGAGCGCTCCAGCGGCGTGGCCACCGACGAGGCCATGGTTTCCGGGCTGGCGCCCGGCAGGCTGGCGCTGACCACGATGGCCGGAAAATCGACGTTGGGCAGCGGCGCCACCGGCAGCAGGCCGAACGACAGGGTGCCGGCCAGCAGCAACGCCAGGGTCAGCAGCGTGGTGGCGACCGGGCGGCGGATGAAGGGCGTGGACAGACTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3004075","ARO_id":"41158","ARO_name":"MuxC","ARO_description":"MuxC is one of the two necessary RND components of the MuxABC-OpmB efflux pumps system in Pseudomonas aeruginosa.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36689":{"category_aro_accession":"3000550","category_aro_cvterm_id":"36689","category_aro_name":"aztreonam","category_aro_description":"Aztreonam was the first monobactam discovered, and is greatly effective against Gram-negative bacteria while inactive against Gram-positive bacteria. Artreonam is a poor substrate for beta-lactamases, and may even act as an inhibitor. In Gram-negative bacteria, Aztreonam interferes with filamentation, inhibiting cell division and leading to cell death.","category_aro_class_name":"Antibiotic"},"37626":{"category_aro_accession":"3001227","category_aro_cvterm_id":"37626","category_aro_name":"kitasamycin","category_aro_description":"Kitasamycin is a macrolide antibiotic and is produced by Streptoverticillium kitasatoense. The drug has antimicrobial activity against a wide spectrum of pathogens.","category_aro_class_name":"Antibiotic"},"40353":{"category_aro_accession":"3003701","category_aro_cvterm_id":"40353","category_aro_name":"rokitamycin","category_aro_description":"Rokitamycin is a macrolide antibiotic. Synthesized from strains of Streptomyces kitasatoensis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2724":{"model_id":"2724","model_name":"MuxABC-OpmB","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)","model_param":{"41141":{"param_type":"efflux pump components","param_description":"This detection model parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305.","param_type_id":"41141","param_value":{"7597":"2717,2718,2720,2716"}}},"ARO_accession":"3004076","ARO_id":"41159","ARO_name":"MuxABC-OpmB","ARO_description":"MuxABC-OpmB is an RND-type multidrug efflux pump in Pseudomonas aeruginosa. This efflux pump confers resistance to aztreonam, novobiocin, tetracycline, erythromycin, kitasamycin and rokitamycin.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36689":{"category_aro_accession":"3000550","category_aro_cvterm_id":"36689","category_aro_name":"aztreonam","category_aro_description":"Aztreonam was the first monobactam discovered, and is greatly effective against Gram-negative bacteria while inactive against Gram-positive bacteria. Artreonam is a poor substrate for beta-lactamases, and may even act as an inhibitor. In Gram-negative bacteria, Aztreonam interferes with filamentation, inhibiting cell division and leading to cell death.","category_aro_class_name":"Antibiotic"},"37626":{"category_aro_accession":"3001227","category_aro_cvterm_id":"37626","category_aro_name":"kitasamycin","category_aro_description":"Kitasamycin is a macrolide antibiotic and is produced by Streptoverticillium kitasatoense. The drug has antimicrobial activity against a wide spectrum of pathogens.","category_aro_class_name":"Antibiotic"},"40353":{"category_aro_accession":"3003701","category_aro_cvterm_id":"40353","category_aro_name":"rokitamycin","category_aro_description":"Rokitamycin is a macrolide antibiotic. Synthesized from strains of Streptomyces kitasatoensis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2729":{"model_id":"2729","model_name":"MexJK-OprM","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)","model_param":{"41141":{"param_type":"efflux pump components","param_description":"This detection model parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305.","param_type_id":"41141","param_value":{"7606":"2205,2206,2219,1305"}}},"ARO_accession":"3003694","ARO_id":"40346","ARO_name":"MexJK-OprM","ARO_description":"MexJK-OprM is a multidrug efflux protein expressed in the Gram-negative Pseudomonas aeruginosa. MexJ is the membrane fusion protein, MexK is the inner membrane resistance-nodulation-cell division (RND) transporter, and OprM is the outer membrane factor protein.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2731":{"model_id":"2731","model_name":"MexJK-OpmH","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)","model_param":{"41141":{"param_type":"efflux pump components","param_description":"This detection model parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305.","param_type_id":"41141","param_value":{"7607":"2205,2206,2219,2195"}}},"ARO_accession":"3003691","ARO_id":"40339","ARO_name":"MexJK-OpmH","ARO_description":"MexJK-OpmH is a triclosan efflux protein expressed in the Gram-negative Pseudomonas aeruginosa. MexJ is the membrane fusion protein, MexK is the inner membrane resistance-nodulation-cell division (RND) transporter, and OpmH is the outer membrane efflux protein. MexJK is constitutively expressed in mexL mutants.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2732":{"model_id":"2732","model_name":"MexVW-OprM","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)","model_param":{"41141":{"param_type":"efflux pump components","param_description":"This detection model parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305.","param_type_id":"41141","param_value":{"7705":"2207,2208,1305"}}},"ARO_accession":"3003029","ARO_id":"39463","ARO_name":"MexVW-OprM","ARO_description":"MexVW-OprM is a multidrug efflux protein expressed in Pseudomonas aeruginosa. MexV is the membrane fusion protein; MexW is the RND-type membrane protein; and OprM is the outer membrane channel. MexVW-OprM is associated with resistance to fluoroquinolones, tetracycline, chloramphenicol, erythromycin and acriflavine.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavin","category_aro_description":"Acriflavin is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36193":{"category_aro_accession":"3000054","category_aro_cvterm_id":"36193","category_aro_name":"acridine dye","category_aro_description":"Acridine dyes are cell permeable, basic molecules with an acridine chromophore. These compounds intercalate DNA. The image shown represents the core structure of the acridine family, with specific dyes containing varying substituents.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2733":{"model_id":"2733","model_name":"TriABC-OpmH","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)","model_param":{"41141":{"param_type":"efflux pump components","param_description":"This detection model parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305.","param_type_id":"41141","param_value":{"7609":"2192,2193,2194,2195"}}},"ARO_accession":"3003678","ARO_id":"40313","ARO_name":"TriABC-OpmH","ARO_description":"TriABC-OpmH is a triclosan-specific efflux pump expressed in the Gram-negative Pseudomonas aeruginosa. TriABC is the only P. aeruginosa resistance nodulation cell division (RND) pump which contains two membrane fusion proteins, TriA and TriB, and both are required for efflux pump function. TriABC associated with OpmH assemble a functional triclosan efflux pump.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2734":{"model_id":"2734","model_name":"PmpM","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"900"}},"model_sequences":{"sequence":{"4054":{"protein_sequence":{"accession":"NP_250052.1","sequence":"MNSPALPLSRGLRIRAELKELLTLAAPIMIAQLATTAMGFVDAVMAGRASPHDLAAVALGNSIWIPMFLLMTGTLLATTAKVAQRHGAGDQPGTGPLVRQALWLALLIGPLSGAVLWWLSEPILGLMKVRPELIGPSLLYLKGIALGFPAAALYHVLRCYTNGLGRTRPSMVLGIGGLLLNIPINYALIYGHFGMPKMGGPGCGWATGSVMWFMFLGMLFWVNKASIYRASQLFSRWEWPDRATIGPLVAVGLPIGIAVFAESSIFSVIALLIGGLDENVVAGHQIALNFSALVFMIPYSLGMAVTVRVGHNLGAGLPRDARFAAGVGMAAALGYACVSASLMLLLREQIAAMYSPDPAVIAIAASLIVFSALFQFSDALQVTAAGALRGYQDTRVTMIMTLFAYWGIGLPVGYSLGLTDWFQEPTGPRGLWQGLVVGLTGAAIMLCIRLARSARRFIRQHERLQREDAEAASVLGR"},"dna_sequence":{"accession":"NC_002516.2","fmin":"1472546","fmax":"1473980","strand":"-","sequence":"CTACCGGCCAAGGACTGAGGCGGCCTCCGCGTCCTCCCGCTGCAGGCGCTCGTGCTGGCGGATGAAGCGCCGCGCGCTGCGCGCCAGGCGGATGCAGAGCATGATCGCCGCGCCGGTCAGGCCCACCACCAGGCCTTGCCACAGACCGCGCGGTCCGGTGGGTTCCTGGAACCAGTCGGTGAGGCCGAGGCTGTAGCCCACCGGCAGGCCGATGCCCCAGTAGGCGAACAGGGTCATGATCATCGTCACCCGGGTGTCCTGGTAGCCGCGCAGGGCCCCGGCGGCGGTGACCTGCAGGGCGTCGGAGAACTGGAACAGCGCGGAGAACACGATCAGCGAGGCGGCGATGGCGATCACCGCCGGGTCCGGCGAATACATCGCGGCGATCTGCTCGCGCAGCAACAACATCAGGCTCGCCGAGACGCAGGCGTAGCCCAGCGCCGCGGCCATCCCCACGCCGGCGGCGAAGCGCGCGTCGCGCGGCAGGCCGGCGCCGAGGTTGTGGCCGACCCGCACGGTCACCGCCATCCCCAGCGAATAGGGAATCATGAACACCAGCGCGCTGAAGTTCAGGGCGATCTGGTGGCCGGCCACCACGTTCTCGTCGAGCCCGCCGATCAGCAGGGCGATCACCGAGAAGATGCTCGACTCGGCGAACACCGCGATGCCGATCGGCAGGCCGACCGCCACCAGCGGGCCGATGGTCGCGCGATCCGGCCACTCCCAGCGCGAGAACAACTGGCTGGCGCGGTAGATCGAGGCCTTGTTCACCCAGAACAGCATGCCGAGGAACATGAACCACATCACCGAGCCGGTGGCCCAGCCGCAGCCGGGGCCACCCATCTTCGGCATGCCGAAGTGGCCGTAGATCAGCGCGTAGTTGATCGGGATGTTCAGCAGCAGCCCGCCGATCCCCAGCACCATGCTCGGCCGGGTCCGTCCCAGGCCGTTGGTGTAGCAGCGCAGTACGTGGTACAGCGCCGCCGCCGGGAAGCCCAGGGCGATGCCCTTGAGGTACAGCAGGCTCGGCCCGATCAGTTCCGGGCGCACTTTCATCAAGCCGAGGATCGGCTCCGACAACCACCACAGCACCGCCCCCGACAGCGGTCCGATCAGCAGCGCCAGCCACAGCGCCTGGCGCACCAGCGGCCCGGTGCCGGGCTGGTCGCCGGCGCCATGGCGCTGGGCGACCTTGGCCGTGGTGGCGAGCAGGGTGCCGGTCATCAGCAGGAACATCGGGATCCAGATGGAGTTGCCCAGCGCCACCGCTGCCAGGTCGTGCGGACTGGCGCGCCCGGCCATCACCGCATCGACGAAGCCCATGGCGGTGGTCGCCAGTTGCGCGATCATGATCGGCGCGGCGAGGGTCAGCAGTTCCTTGAGTTCGGCGCGGATGCGCAAGCCACGGGAAAGGGGCAGGGCGGGGCTGTTCAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3004077","ARO_id":"41170","ARO_name":"PmpM","ARO_description":"PmpM is a multidrug efflux pump belonging to the MATE family of Pseudomonas aeruginosa. PmpM is an H+ drug antiporter and is the first reported case of an H+ coupled efflux pump in the MATE family. PmpM confers resistance to fluoroquinolones, fradiomycin, benzalkonium chloride, chlorhexidine gluconate, ethidium bromide, tetraphenylphosphonium chloride (TPPCl), and rhodamine 6G.","ARO_category":{"36251":{"category_aro_accession":"3000112","category_aro_cvterm_id":"36251","category_aro_name":"multidrug and toxic compound extrusion (MATE) transporter","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Multidrug and toxic compound extrusion (MATE) transporters utilize the cationic gradient across the membrane as an energy source. Although there is a diverse substrate specificity, almost all MATE transporters recognize fluoroquinolones. Arciflavine, ethidium and aminoglycosides are also good substrates.","category_aro_class_name":"AMR Gene Family"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2743":{"model_id":"2743","model_name":"E. coli AcrAB-TolC with AcrR mutation conferring resistance to cirpofloxacin","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)","model_param":{"41141":{"param_type":"efflux pump components","param_description":"This detection model parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305.","param_type_id":"41141","param_value":{"7636":"2306,2661,1104,826"}}},"ARO_accession":"3004078","ARO_id":"41180","ARO_name":"Escherichia coli AcrAB-TolC with AcrR mutation conferring resistance to ciprofloxacin, tetracycline, and ceftazidime","ARO_description":"AcrR is the repressor of the AcrAB operon, where a mutation in AcrR allows AcrAB-TolC to confer resistance to ciprofloxacin, tetracycline, and ceftazidime.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2744":{"model_id":"2744","model_name":"Escherichia coli AcrAB-TolC with MarR mutations conferring resistance to ciprofloxacin and tetracycline","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)","model_param":{"41141":{"param_type":"efflux pump components","param_description":"This detection model parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305.","param_type_id":"41141","param_value":{"7637":"2661,1104,826,431"}}},"ARO_accession":"3004079","ARO_id":"41181","ARO_name":"Escherichia coli AcrAB-TolC with MarR mutations conferring resistance to ciprofloxacin and tetracycline","ARO_description":"The Escherichia coli AcrAB-TolC with MarR mutation (Y137H) conferring resistance to ciprofloxacin and tetracycline.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2750":{"model_id":"2750","model_name":"APH(3')-VIII","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"4437":{"protein_sequence":{"accession":"EPF73263","sequence":"MKLPQKIRNFIGNNRLIVNKVGQSPSDVYCFERNRETFFLKVSSVQYATTTYSVAREAQMMLWLADKINVPELVFSEIDQNFEYMLSKSIDAQPISDLSLAQSELIMLYQDVLSQLRSVPVQNCPFNSDINSRLQESQYFMEIGLLNQVDDENIDIELWGEHQSYLELWTELNNHRVKENLVFTHGDITDSNIFVDQSNKIYFLDLGRAGLADEFVDIAFVERCLREDGSEESAQKFLKQLSFDDLSKRQYFLKLDELN"},"dna_sequence":{"accession":"ATGI01000028.1","fmin":"7477","fmax":"8257","strand":"-","sequence":"TCAATTTAACTCATCAAGTTTTAGAAAATATTGACGTTTGGATAGGTCATCAAAACTTAATTGTTTGAGAAACTTCTGAGCACTCTCTTCAGAACCATCTTCACGAAGACAACGTTCAACAAAGGCAATATCTACAAACTCATCTGCCAAGCCAGCGCGTCCTAAGTCCAAAAAATAAATCTTATTTGACTGATCAACGAAAATATTACTGTCAGTAATATCTCCATGTGTAAACACTAAATTTTCTTTCACACGATGATTGTTTAACTCTGTCCACAGTTCTAGATAACTCTGATGCTCACCCCATAGCTCTATATCAATATTTTCATCATCAACCTGATTTAACAACCCAATCTCCATAAAGTATTGGGATTCTTGTAAACGGCTATTGATATCTGAATTAAATGGACAATTTTGTACAGGTACTGATCGTAACTGGCTTAATACATCTTGATAAAGCATGATTAATTCGGATTGAGCTAAGGACAAATCTGATATAGGTTGAGCATCAATAGACTTGCTTAACATATACTCAAAATTTTGATCTATTTCACTGAATACTAACTCAGGTACGTTAATCTTATCAGCTAACCAAAGCATCATCTGTGCTTCACGCGCAACACTATAAGTTGTTGTTGCATATTGCACACTAGACACTTTTAAGAAGAACGTTTCCCGATTTCGTTCAAAGCAATATACATCAGAAGGTGATTGACCAACTTTGTTAACGATTAATCGATTATTTCCAATAAAATTTCTAATTTTCTGAGGTAGTTTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41191","NCBI_taxonomy_name":"Acinetobacter rudis CIP 110305","NCBI_taxonomy_id":"421052"}}}},"ARO_accession":"3004086","ARO_id":"41190","ARO_name":"APH(3')-VIII","ARO_description":"APH(3')-VIII is an aminoglycoside phosphoryltransferase that acts on the 3-OH target of aminoglycosides.","ARO_category":{"36265":{"category_aro_accession":"3000126","category_aro_cvterm_id":"36265","category_aro_name":"APH(3')","category_aro_description":"Phosphorylation of 2-deoxystreptamine aminoglycosides on the hydroxyl group at position 3'","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2751":{"model_id":"2751","model_name":"APH(3')-IX","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"4068":{"protein_sequence":{"accession":"ENV34035","sequence":"MINDMKISLPQSLKSFIGNQPLQKDKVGQSPSDVYSFTKNNEKYYLKTTELIYAQTTYSIIREAKILDWLDGKLNVPELVLMDTDHENEYMISKAVPAKPLQDFTGKSDQFFIDIYTDALAQLQSISIKNCPFISNKKFRLAEAEFFIENGLLDELDDDEKDLKLWSSYQNFAEFLDDLKQQNFQEEYVFSHGDLTDSNVFLSHDAQIYFLDVGRAGIADRFVDIAFIERSLREDCSEDAALQFLNHLAEDDSFKRNYFLKLDELN"},"dna_sequence":{"accession":"APPN01000061.1","fmin":"80497","fmax":"81298","strand":"+","sequence":"ATGATCAATGATATGAAAATTTCACTTCCGCAAAGTCTTAAAAGTTTTATTGGAAATCAACCATTACAAAAAGATAAAGTGGGACAATCCCCTTCTGATGTGTATTCTTTTACCAAAAATAATGAAAAATACTATTTAAAAACCACTGAGCTAATTTATGCTCAAACAACTTATAGTATCATACGTGAAGCAAAAATACTCGACTGGCTAGATGGAAAGCTCAATGTTCCAGAGCTAGTTTTAATGGATACCGACCATGAAAATGAGTACATGATCAGCAAGGCAGTCCCCGCAAAACCCTTACAAGATTTCACAGGAAAAAGTGATCAATTTTTCATAGATATTTATACAGATGCTTTGGCACAATTACAGTCTATTTCAATAAAAAACTGTCCATTTATATCCAATAAAAAATTTCGATTAGCTGAGGCGGAATTCTTTATTGAAAATGGCTTACTTGATGAATTGGATGATGATGAAAAAGATCTAAAGCTTTGGTCCAGTTATCAAAATTTTGCTGAATTCTTAGATGATCTAAAACAGCAAAATTTCCAAGAAGAATATGTATTTAGTCATGGTGACCTAACCGACAGCAATGTATTTTTAAGTCATGATGCACAAATCTACTTTTTAGATGTCGGACGTGCTGGTATCGCAGATCGATTTGTAGATATTGCCTTTATTGAACGTAGTCTACGAGAAGATTGCTCTGAGGATGCTGCACTTCAATTTTTAAATCATTTAGCAGAAGACGATTCTTTTAAACGGAATTATTTTCTAAAATTGGATGAGTTAAATTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41193","NCBI_taxonomy_name":"Acinetobacter gerneri DSM 14967 = CIP 107464","NCBI_taxonomy_id":"1120926"}}}},"ARO_accession":"3004087","ARO_id":"41192","ARO_name":"APH(3')-IX","ARO_description":"APH(3')-IX is an aminoglycoside phosphoryltransferase that acts on the 3-OH target of aminoglycosides.","ARO_category":{"36265":{"category_aro_accession":"3000126","category_aro_cvterm_id":"36265","category_aro_name":"APH(3')","category_aro_description":"Phosphorylation of 2-deoxystreptamine aminoglycosides on the hydroxyl group at position 3'","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2745":{"model_id":"2745","model_name":"E. coli AcrAB-TolC","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"2661,1104,826,2306,431,1922,2776,228,2066,520"}},"ARO_accession":"3000384","ARO_id":"36523","ARO_name":"AcrAB-TolC","ARO_description":"AcrAB-TolC is a tripartite RND efflux system that confers resistance to tetracycline, chloramphenicol, ampicillin, nalidixic acid, and rifampin  in Gram-negative bacteria. The system spans the cell membrane (AcrB) and the outer-membrane (TolC), and is linked together in the periplasm by AcrA.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2746":{"model_id":"2746","model_name":"AcrAD-TolC confers resistance to amikacin, gentamicin, and tobramycin","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"2661,1427,826,1337,986,152,2764"}},"ARO_accession":"3004081","ARO_id":"41183","ARO_name":"AcrAD-TolC confers resistance to amikacin, gentamicin, and tobramycin","ARO_description":"The AcrAD-TolC efflux pump system in E. coli confers resistance to amikacin, gentamicin, and tobramycin.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2747":{"model_id":"2747","model_name":"AcrEF-TolC confers resistance to ciprofloxacin and tetracycline","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)","model_param":{"41141":{"param_type":"efflux pump components","param_description":"This detection model parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305.","param_type_id":"41141","param_value":{"7771":"520,1445,1437,826,1248"}}},"ARO_accession":"3004083","ARO_id":"41185","ARO_name":"AcrEF-TolC confers resistance to ciprofloxacin","ARO_description":"AcrEF-TolC efflux pump system of E. coli confers resistance to fluoroquinolones (ciprofloxacin).","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2748":{"model_id":"2748","model_name":"oqxAB","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)","model_param":{"41141":{"param_type":"efflux pump components","param_description":"This detection model parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305.","param_type_id":"41141","param_value":{"7704":"2399,2400"}}},"ARO_accession":"3003921","ARO_id":"40630","ARO_name":"oqxAB","ARO_description":"oqxAB encodes for OqxAB, a plasmid-encoded efflux pump, which confer resistance to multiple agents including fluoroquinolones.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35992":{"category_aro_accession":"0000075","category_aro_cvterm_id":"35992","category_aro_name":"nitrofurantoin","category_aro_description":"Nitrofurantoin is an antibiotic used to treat urinary tract infections. It inhibits enzyme synthesis by inhibiting essential enzymes involved in the citric acid cycle, as well as those involved in DNA, RNA, and protein synthesis. It is marketed under the following brand names: Furadantin, Macrobid, Macrodantin, Nitro Macro and Urantoin.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"41240":{"category_aro_accession":"3004116","category_aro_cvterm_id":"41240","category_aro_name":"nitrofuran antibiotic","category_aro_description":"Nitrofurans are chemotherapeutic agents with antibacterial and antiprotozoal activity.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2749":{"model_id":"2749","model_name":"lnuG","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"4181":{"protein_sequence":{"accession":"APU52409.1","sequence":"MLKQKELMARVKELVQSDERISACMMYGSFTKGEGDQYSDIEYYVFLKDDTISTFDSAKWLNEVASYTLLYQNEYGTEVVIFENLIRGEFHFLSENEMNIIPSFKESGYIPDTKAMFIYDETGQLELYLSELEGPGPNRLTEENVNFLLNNFSNLWLMGINVLKRGENARSLELLSQLQKNILQLIRIAEENADNWFNMTKNLEKEISPENYEKFKKTTARLNELELYEAYKNSLLLVMELRNLVEKQYQLTISDDFLGKLFNYMNE"},"dna_sequence":{"accession":"KX470419.1","fmin":"3811","fmax":"4615","strand":"+","sequence":"TTGTTAAAACAAAAGGAACTAATGGCAAGGGTTAAGGAACTTGTCCAGTCAGATGAACGAATATCTGCTTGTATGATGTATGGCTCTTTTACAAAAGGAGAGGGAGATCAATACTCTGATATAGAATATTACGTTTTTCTAAAAGATGATACAATTTCCACCTTTGATTCAGCAAAATGGCTAAATGAAGTCGCTTCCTACACTTTACTCTATCAAAATGAGTACGGTACGGAAGTAGTAATTTTTGAAAATCTAATACGTGGTGAATTTCATTTCCTTTCCGAAAACGAAATGAATATTATTCCTTCATTCAAAGAATCAGGCTACATTCCTGACACAAAAGCAATGTTTATTTATGATGAAACAGGACAACTAGAATTGTATTTATCAGAGTTGGAAGGTCCGGGACCAAATAGACTTACAGAAGAAAACGTAAATTTTTTATTGAATAATTTTTCCAACCTATGGTTAATGGGGATTAATGTTCTTAAAAGAGGGGAAAATGCACGTTCACTGGAACTTTTATCTCAATTACAAAAAAATATACTACAACTCATTCGAATTGCGGAAGAAAATGCCGATAATTGGTTTAATATGACAAAGAATCTTGAAAAAGAAATTAGTCCTGAAAACTATGAAAAGTTTAAAAAGACTACTGCCCGATTAAATGAATTAGAACTATATGAAGCCTATAAGAACTCTTTGCTTCTCGTTATGGAACTTCGAAATCTCGTTGAAAAACAGTATCAATTAACCATTAGCGATGATTTTTTAGGCAAACTGTTTAATTATATGAACGAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3004085","ARO_id":"41189","ARO_name":"lnuG","ARO_description":"lnuG is a transposon-mediated lincosamide nucleotidyltransferase found in Enterococcus faecalis on Tn6260.","ARO_category":{"36360":{"category_aro_accession":"3000221","category_aro_cvterm_id":"36360","category_aro_name":"lincosamide nucleotidyltransferase (LNU)","category_aro_description":"Resistance to the lincosamide antibiotic by ATP-dependent modification of the 3' and\/or 4'-hydroxyl groups of the methylthiolincosamide sugar.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2753":{"model_id":"2753","model_name":"HMB-1 beta-lactamase","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"4072":{"protein_sequence":{"accession":"AMY61250.1","sequence":"MKIHLWISLGLLLLTNIVLAEEPLPELEVKKIDEGVYLHTSYENYPSWGLVASHGLVFVDGKDAYIIDTPATVKDTEVLVQWINDQGFKPKASISTHFHDDSTIGIAYLNSKSIPTYASEQTNELLNKEVAAQATHSFKKNPYWLLKNKIEAFYPGAGHTPDNLVVWLPKQKILFGGCFVKPEGLGNLSHAVVSEWPASAEKLINRYSDAKIVVPGHGTMGDASLLEKTKQRALEAVAKKK"},"dna_sequence":{"accession":"KU961660","fmin":"2031","fmax":"2757","strand":"+","sequence":"ATGAAAATACATTTATGGATATCATTGGGTCTTTTGCTGCTGACAAACATCGTTCTTGCAGAAGAACCGCTACCCGAACTGGAAGTTAAAAAAATCGATGAGGGTGTTTATCTGCATACGTCCTATGAAAATTATCCAAGCTGGGGCTTGGTTGCATCCCACGGTTTGGTTTTTGTGGATGGTAAAGACGCTTACATTATTGATACACCCGCTACTGTTAAAGACACAGAAGTGTTAGTGCAATGGATTAACGATCAAGGCTTCAAACCCAAGGCCAGCATTTCTACGCACTTTCACGATGACAGCACCATCGGCATTGCCTACTTAAATTCCAAATCCATTCCGACCTACGCATCAGAACAAACTAATGAATTGCTTAATAAAGAAGTCGCTGCACAGGCAACGCATTCGTTTAAGAAAAATCCTTATTGGCTGTTAAAAAATAAAATCGAAGCTTTTTATCCGGGCGCTGGCCACACGCCTGACAATTTAGTGGTGTGGTTGCCGAAGCAGAAAATTCTATTCGGTGGCTGTTTTGTAAAACCCGAAGGGCTGGGAAATTTAAGCCATGCGGTAGTTTCTGAATGGCCTGCTTCTGCAGAAAAACTTATCAATCGCTATAGCGACGCAAAAATCGTAGTACCGGGTCATGGAACAATGGGCGATGCATCGCTGCTGGAAAAAACCAAACAGCGTGCGCTTGAGGCGGTTGCAAAGAAGAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004092","ARO_id":"41198","ARO_name":"HMB-1","ARO_description":"Shotgun cloning of beta-lactam resistant P. aeruginosa NRZ-03096 yielded a clone producing a novel subclass B1 enzyme with only 74.3% identity to the next nearest relative, KHM-1. The novel MBL was named HMB-1 (for Hamburg MBL). HMB-1 gene was chromosomally located as part of a Tn 3 family transposon that was named Tn 6345, where expression of bla HMB-1 in E. coli TOP10 led to increased resistance to \u03b2-lactams.","ARO_category":{"41373":{"category_aro_accession":"3004209","category_aro_cvterm_id":"41373","category_aro_name":"HMB beta-lactamase","category_aro_description":"First identified from a multi-drug resistant Pseudomonas aeruginosa clinical isolate in 2012, HMB type beta-lactamases can be encoded in transposons and hydrolyze carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2752":{"model_id":"2752","model_name":"ANT(3'')-IIa","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"4069":{"protein_sequence":{"accession":"EEX02086","sequence":"MPDFIQLEYLQEKLQQLLAESLFAIYLYGSAVDGGLGPESDLDVLVVVTQPLTSALREQLAQELLKISQPVGELQRPLEVTILLKDEIQAGNYPLSYEMQFGEWLREELKEGGTLSSQKDPDISILLRKARFHHTVLFGPALDQWAPEISDQELWQAMSDTYPEIVAHWDEDADERNQILALCRIYFSLVMKDIASKDNAARWVMPQLPPEQKFVLQRLIQEYRGEIGKQNWQEEHYALQPIVNFLSSKIEEQFEQKRNLIT"},"dna_sequence":{"accession":"GG704579.1","fmin":"34580","fmax":"35269","strand":"-","sequence":"TTATGTGATCAAATTTCTTTTCTGCTCAAACTGCTCTTCAATTTTTGAACTCAGAAAATTAACAATAGGCTGCAAAGCATAATGTTCCTCTTGCCAATTTTGTTTGCCTATTTCCCCTCTATATTCCTGTATAAGCCGCTGCAATACGAATTTCTGCTCAGGAGGAAGCTGAGGCATAACCCATCGAGCTGCATTGTCTTTTGAAGCAATATCCTTCATGACTAAACTAAAATAGATCCGGCATAAAGCTAAAATCTGGTTTCTTTCATCTGCATCCTCATCCCAATGAGCTACAATTTCGGGATAAGTATCAGACATTGCTTGCCATAGTTCTTGATCAGAAATTTCAGGTGCCCATTGGTCCAAAGCTGGACCAAATAAAACTGTATGATGAAATCTCGCTTTTCTAAGCAATATACTAATATCTGGGTCTTTCTGCGAACTTAATGTTCCACCTTCTTTAAGTTCTTCACGTAGCCATTCACCAAACTGCATTTCATAACTTAAAGGATAATTTCCAGCCTGAATCTCATCTTTTAATAAAATAGTAACTTCTAATGGTCTTTGTAATTCCCCAACAGGCTGTGAAATTTTTAGTAATTCTTGTGCAAGCTGCTCGCGTAAAGCAGATGTTAATGGTTGAGTAACCACGACCAGAACATCAAGGTCACTTTCTGGCCCTAAGCCAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35598","NCBI_taxonomy_name":"Acinetobacter baumannii ATCC 19606","NCBI_taxonomy_id":"575584"}}}},"ARO_accession":"3004089","ARO_id":"41195","ARO_name":"ANT(3'')-IIa","ARO_description":"ANT(3'')-IIa is a aminoglycoside nucleotidyltransferase identified in Acinetobacter spp. via horizontal gene transfer mechanisms.","ARO_category":{"41439":{"category_aro_accession":"3004275","category_aro_cvterm_id":"41439","category_aro_name":"ANT(3'')","category_aro_description":"Nucleotidylylation of streptomycin at the hydroxyl group at position 3''","category_aro_class_name":"AMR Gene Family"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2754":{"model_id":"2754","model_name":"ANT(3'')-IIb","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"4070":{"protein_sequence":{"accession":"ENU91137","sequence":"MSEQFQLQQLQEYLHALFAESLFAIYLYGSAVDGGLGPESDLDLLVVVTQPLTHVQRQQLAQALLTLSHPIGGLQRALEVTILLKEEVISGRYPLNYELQFGEWLREELVDGGELSAQNDPDISILLKKAHMHHRTLFGPDLTSWLDEIPDQQLWQAMADLYPSIVAHWDEDGDERNQILALCRIYFSLSLGEIVSKSHAAQWVIAQLEEKDQPVLQRMVQEYKGEMTKQDWPSQHQVLQPIVNFLSQHIETFFDKKGLKIKQ"},"dna_sequence":{"accession":"APPC01000022.1","fmin":"55968","fmax":"56760","strand":"-","sequence":"TTATTGTTTTATTTTCAGGCCCTTTTTATCAAAAAAAGTCTCTATGTGCTGACTCAGAAAATTAACGATAGGCTGTAAAACCTGATGCTGACTTGGCCAGTCCTGTTTTGTCATCTCGCCTTTATACTCTTGCACCATTCGTTGTAAAACAGGCTGATCTTTTTCCTCAAGTTGAGCGATCACCCATTGGGCAGCATGCGACTTAGAAACAATCTCACCTAGACTCAAACTAAAATAGATTCGGCATAACGCTAAAATCTGATTACGTTCATCACCATCTTCATCCCAATGTGCCACTATTGATGGATAAAGGTCTGCCATCGCTTGCCAAAGTTGCTGATCTGGAATCTCATCTAACCAACTTGTTAAATCTGGCCCAAACAATGTTCGGTGATGCATGTGCGCTTTCTTTAACAAGATACTGATGTCTGGATCATTTTGTGCTGACAGCTCCCCTCCATCGACGAGTTCCTCACGCAACCATTCCCCAAACTGTAATTCATAATTTAAAGGATATCTGCCTGAAATCACTTCTTCTTTGAGCAAGATAGTTACTTCAAGTGCTCGTTGCAATCCACCAATTGGATGTGAAAGCGTTAATAAGGCTTGTGCAAGCTGCTGTCGCTGAACGTGTGTTAGAGGTTGAGTCACAACGACCAGAAGATCCAGATCACTTTCCGGGCCTAAACCGCCATCCACAGCAGAACCATACAAGTAAATCGCAAATAATGATTCTGCAAATAAAGCATGTAAATATTCTTGTAACTGCTGAAGCTGAAATTGTTCTGACAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41199","NCBI_taxonomy_name":"Acinetobacter sp. NIPH 758","NCBI_taxonomy_id":"1217712"}}}},"ARO_accession":"3004090","ARO_id":"41196","ARO_name":"ANT(3'')-IIb","ARO_description":"ANT(3'')-IIb is a aminoglycoside nucleotidyltransferase identified in Acinetobacter spp. via horizontal gene transfer mechanisms.","ARO_category":{"41439":{"category_aro_accession":"3004275","category_aro_cvterm_id":"41439","category_aro_name":"ANT(3'')","category_aro_description":"Nucleotidylylation of streptomycin at the hydroxyl group at position 3''","category_aro_class_name":"AMR Gene Family"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2755":{"model_id":"2755","model_name":"ANT(3'')-IIc","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"4071":{"protein_sequence":{"accession":"ENU37733","sequence":"MSETLQLEQLTGYLQQLLGESLFAIYLYGSAVDGGLGPESDLDILVVVSQALTLPQRQQLAETLLQISHPIGAAQRALEVTIVRKDHILSGSYPLSYELQFGEWLRDELSQGDMLSEHADPDLSILLKKAQLHHRSLFGPSLTQWSVEIPDQQLWQAMADTYPSIVAHWDEDADERNQILALCRIYFSLVTNEIAPKDQAAQWVIAQLQPQHQPVLQRMVQEYKGEIEKQNWQQQHHALQPVVDFLSSKIDERFKQKKV"},"dna_sequence":{"accession":"APOM01000001.1","fmin":"40253","fmax":"41033","strand":"-","sequence":"TCAAACTTTTTTCTGTTTAAACCGTTCATCAATTTTTGAAGACAGGAAATCAACAACAGGCTGTAAAGCATGATGCTGTTGTTGCCAGTTTTGCTTTTCAATCTCACCTTTATATTCTTGCACCATTCGCTGCAAAACAGGCTGATGTTGCGGTTGTAACTGAGCAATCACCCATTGCGCAGCCTGATCTTTAGGCGCAATCTCATTCGTCACCAAACTAAAATAAATACGGCATAAGGCCAGAATCTGGTTACGCTCATCCGCATCTTCATCCCAATGTGCCACTATCGATGGATAGGTATCTGCCATCGCCTGCCAGAGTTGCTGATCCGGAATTTCAACTGACCACTGCGTCAAACTTGGTCCAAACAAGCTACGATGATGTAGTTGTGCTTTCTTCAGTAAAATACTCAGATCTGGGTCTGCATGTTCGCTAAGCATATCGCCTTGGCTTAACTCATCCCGCAACCATTCCCCAAACTGTAGTTCATAGCTGAGTGGATAACTTCCCGAAAGAATATGGTCTTTGCGTACGATGGTGACTTCAAGTGCACGTTGCGCAGCACCAATCGGATGCGAAATTTGTAATAAGGTTTCTGCCAGTTGCTGTCGTTGCGGAAGTGTCAGTGCTTGACTCACCACAACCAAAATATCCAGATCACTTTCTGGACCTAGCCCGCCATCAACAGCTGATCCATATAGATAAATGGCAAAGAGAGATTCACCCAAAAGCTGCTGTAAATATCCTGTTAACTGTTCCAGTTGCAAGGTTTCGGACAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41200","NCBI_taxonomy_name":"Acinetobacter parvus DSM 16617 = CIP 108168","NCBI_taxonomy_id":"981333"}}}},"ARO_accession":"3004091","ARO_id":"41197","ARO_name":"ANT(3'')-IIc","ARO_description":"ANT(3'')-IIc is a aminoglycoside nucleotidyltransferase identified in Acinetobacter spp. via horizontal gene transfer mechanisms.","ARO_category":{"41439":{"category_aro_accession":"3004275","category_aro_cvterm_id":"41439","category_aro_name":"ANT(3'')","category_aro_description":"Nucleotidylylation of streptomycin at the hydroxyl group at position 3''","category_aro_class_name":"AMR Gene Family"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2756":{"model_id":"2756","model_name":"NDM-17","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4073":{"protein_sequence":{"accession":"AOT73359.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLLVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGLVAAQHSLTFAANGWVKPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"KX812714","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGTTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGCTGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCAAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004093","ARO_id":"41201","ARO_name":"NDM-17","ARO_description":"NDM-17 is a metallo-beta-lactamase isolated from Escherichia coli with enhanced carbapenemase activity compared to NDM-1.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2354":{"model_id":"2354","model_name":"ADC-25","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3647":{"protein_sequence":{"accession":"WP_001211217.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_048649.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003868","ARO_id":"40567","ARO_name":"ADC-25","ARO_description":"ADC-25 is a beta-lactamase found in Acinetobacter baumannii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2758":{"model_id":"2758","model_name":"LpeA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"680"}},"model_sequences":{"sequence":{"4077":{"protein_sequence":{"accession":"CAH14032.1","sequence":"MLGIQFNRGQWRSNYYWQIPVLIIAVISILFFISKKLFYSKVTPESIPNKLVEVEPIKSHNLQQTIHLLGTIHPKHATTLIAKESGMLDTLIPTGQKVTKGTLIAKINNPDLEKNLQLSLSAVELAKAQYERITPLIKSGYVSTKEVEEKKQAWIDAQKELSKTRIELDNLRFYAPFDGIIGAYKKREGAQVNAGESVVSIYDPSALVVDFDIPCSNLATLNEGQPVYVLGKRYSLSHLQKMLDEDTHMCPADVDIQCDDCLIGATTSVELLVAEKNNTIVIPFQAIFLRNSKPFVYLVKKGKIVLASVKTGLQQEDKIEIVEGLKAGQQLVTKGQERLYPEMTVDIYHPATSSS"},"dna_sequence":{"accession":"CR628336.1","fmin":"3280793","fmax":"3281861","strand":"+","sequence":"GTGTTAGGAATTCAATTCAATAGAGGTCAATGGCGGTCAAACTATTATTGGCAAATACCTGTGCTGATAATAGCTGTTATTAGCATTCTGTTTTTCATCAGTAAAAAATTATTCTACTCAAAAGTTACGCCAGAAAGCATACCTAATAAACTGGTGGAAGTTGAGCCCATTAAAAGCCACAACTTACAACAAACAATCCATTTATTAGGTACCATTCATCCAAAACACGCAACGACATTAATTGCTAAAGAATCAGGTATGTTGGACACCCTTATCCCAACTGGTCAAAAAGTCACAAAAGGGACACTTATTGCAAAAATCAACAACCCTGATCTTGAAAAAAATCTACAGCTTTCATTAAGTGCGGTAGAATTGGCAAAAGCACAATATGAACGTATCACCCCTTTAATTAAATCAGGATATGTCAGTACAAAGGAAGTCGAAGAAAAAAAACAAGCCTGGATTGATGCCCAAAAAGAATTATCAAAAACAAGGATTGAATTAGATAACCTCCGCTTTTACGCTCCTTTCGACGGAATAATTGGAGCATACAAAAAGAGAGAAGGAGCACAAGTCAATGCAGGTGAATCTGTTGTAAGTATTTACGACCCTTCTGCTTTAGTTGTCGATTTTGATATTCCTTGCAGTAATTTGGCAACTCTTAATGAAGGTCAGCCGGTTTATGTGCTGGGTAAACGGTATTCATTAAGTCATTTACAAAAAATGCTCGACGAAGACACCCACATGTGCCCTGCTGATGTTGATATTCAATGTGATGATTGTCTTATTGGTGCGACCACAAGTGTTGAGCTCCTTGTTGCGGAAAAAAATAACACTATTGTCATCCCCTTCCAGGCAATATTTTTGAGAAATAGTAAACCTTTTGTATATCTTGTAAAAAAGGGAAAGATTGTGCTTGCTTCAGTGAAAACTGGGTTGCAACAAGAGGATAAAATTGAAATTGTCGAGGGATTAAAAGCTGGGCAACAACTGGTTACAAAAGGCCAGGAACGCTTATATCCTGAAATGACCGTTGATATTTATCATCCAGCGACAAGTAGCAGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41208","NCBI_taxonomy_name":"Legionella pneumophila str. Paris","NCBI_taxonomy_id":"297246"}}}},"ARO_accession":"3004099","ARO_id":"41207","ARO_name":"LpeA","ARO_description":"LpeA is a subunit of the LpeAB efflux pump in Legionella pneumophila, which is homologous to AcrA in E. coli.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2759":{"model_id":"2759","model_name":"LpeB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1700"}},"model_sequences":{"sequence":{"4076":{"protein_sequence":{"accession":"CAH14033.1","sequence":"MKLTSYFIKHPVITIILNAMIVVLGLLCLYNLSVREYPDINFPTITVSASYPNASPDLVETAITNVLEDRLAGIEGLETITSQSSAGYAQITLMFRSGTSMDRALSTTQDAVGVAKALLPPEVRSPTVERQRKSNGLPFIGISLESTSKDFGELTHYANLNLKNVFRSVQGVASVEVWGQPYTYNITLQPEKLFSFGVNVDEIVNALAKNRISLPAGNYRNKIPSTLNSELKTREDYENLLIKANSKHPILLKSLANVALETDNSQMRVRVNGHAGVVLSINKANEANPIEVSKEIRKVIKGLQQGLPKDLKINTIIDQSDFINASIKNIRSAIGEAIFLVLIIVFLFLRNIKATIIPLITIPISLLGSLLFLKLFGFSINLMTLLAMVLAIGLVVDDAIIVLENIWRHIESGLSPLDAALKGAREIGFAIIAMTFTLSSVYLPIAFIQGMLGQLFVEFAVALAGSVFISGIVALTLSPLMCANLLSASSKNWWPQFDNALEKLTKHYSNILQFILKHQKITLLTALISVVACFGFYNLISHETAPKEDRGLIGIYIPPVAGEDIGMLDNKTGKLEKKLDAIPEANNRLTFIGDWGGSIVLPLKPHAQRHRSANQIVEKLRPSFNHFPSMDPHVWSWDTGLPGVDDAGSGSELTLVISTPDHFRQLFDETEKLKSVLDKSKLFAAVNYDLRLDTMGYNIDLDYNQLAKLGLTANQVAKTIEVFFSGDKSQTFEKDGVVYNISIKGDSSPWTLNELYLTTNEGKSVSLGAITKMQPKAQPATLDHYQQMRSTTLHVQLHKGDSMAKAIEKLWGTTKEVMPQHYKLTWIGAAKAFHESSNSMLFLFFLSLAFIYAILCTQFENFTDPFIILFTVPLACSGALLFTYLFGQSLNIYTQVGLITLIGLISKHGILIVEFANKLHKDGASLPEAIQKSAALRLRPILMTTGAMVFGAIPLVLSHDAGSESRHAIGTVLISGLGLGTLFTLFVLPAVYNIIKSKLIDMQKTGGKKRCSKE"},"dna_sequence":{"accession":"CR628336.1","fmin":"3281865","fmax":"3284910","strand":"+","sequence":"ATGAAACTCACCAGCTATTTCATCAAACATCCTGTAATCACCATCATCTTAAACGCCATGATTGTTGTTCTGGGGTTATTATGTCTCTATAATTTATCCGTTAGGGAATATCCTGATATCAATTTTCCTACAATAACTGTTTCAGCAAGCTACCCCAACGCCAGTCCCGATTTAGTTGAAACCGCAATAACCAATGTTCTGGAGGACCGTCTTGCAGGTATAGAAGGGTTAGAAACAATTACGTCGCAATCAAGTGCAGGCTATGCGCAAATCACCTTGATGTTTCGTTCCGGAACATCCATGGATAGAGCACTGAGTACCACTCAAGACGCCGTAGGAGTAGCCAAAGCACTTCTGCCACCGGAGGTAAGATCGCCAACAGTTGAACGCCAACGCAAATCCAATGGCCTTCCTTTTATTGGGATTTCATTGGAATCAACATCCAAAGACTTTGGTGAGCTGACTCATTACGCTAATCTTAATTTAAAAAATGTCTTTCGCAGTGTGCAAGGTGTTGCTTCCGTTGAAGTATGGGGGCAACCCTATACATACAACATTACCCTTCAACCTGAAAAATTATTTTCTTTTGGAGTTAATGTTGATGAAATAGTGAATGCGCTCGCAAAAAATCGTATTTCGTTGCCCGCAGGTAATTATAGAAATAAAATTCCCAGTACTCTTAATTCTGAGCTGAAAACCCGGGAAGATTATGAGAATCTTTTAATCAAGGCAAATTCCAAACATCCCATTTTACTCAAATCACTGGCTAATGTCGCATTGGAAACCGATAACTCACAAATGCGAGTTCGCGTTAATGGGCACGCTGGTGTTGTGCTTTCTATCAATAAAGCGAATGAAGCCAATCCTATTGAAGTCTCTAAAGAAATTAGAAAAGTGATTAAAGGATTACAACAAGGGTTGCCCAAGGATCTGAAAATAAACACTATTATTGATCAATCGGATTTTATTAATGCCTCCATTAAAAACATTAGATCCGCGATTGGTGAAGCCATTTTTTTAGTCTTAATCATAGTCTTCCTTTTTTTACGTAATATTAAAGCCACCATCATCCCTCTAATTACCATTCCAATTTCATTATTGGGGTCCTTGCTTTTCCTTAAATTGTTTGGTTTTTCAATCAATTTAATGACCTTACTGGCTATGGTATTGGCAATCGGTTTGGTTGTAGACGATGCGATTATTGTCTTGGAAAACATTTGGCGTCATATTGAAAGCGGATTATCTCCTTTGGATGCTGCGCTTAAAGGAGCACGTGAAATTGGCTTCGCCATTATAGCGATGACATTTACCCTTAGCAGTGTTTATTTGCCTATAGCCTTTATCCAGGGGATGCTGGGACAGCTCTTCGTTGAATTTGCTGTTGCTCTGGCAGGCAGTGTTTTCATTTCGGGGATTGTTGCCCTGACACTTTCACCATTGATGTGTGCCAACCTTTTGAGTGCATCTTCTAAAAACTGGTGGCCACAATTCGATAATGCTCTTGAAAAGTTAACTAAACATTACTCCAATATTTTACAATTCATTCTGAAACACCAAAAGATTACTTTGCTAACAGCTCTAATTTCTGTCGTTGCTTGCTTTGGATTTTATAATTTAATTAGCCATGAAACCGCTCCTAAAGAAGATCGAGGTTTAATAGGTATTTATATCCCTCCTGTAGCAGGAGAAGACATAGGGATGTTGGACAACAAAACAGGAAAACTTGAAAAAAAACTAGATGCCATCCCCGAGGCAAATAATCGCCTGACTTTTATTGGTGACTGGGGCGGGTCAATAGTACTGCCATTAAAACCTCATGCTCAACGTCATCGAAGTGCGAACCAGATTGTTGAGAAATTAAGACCTTCTTTTAACCACTTCCCCTCCATGGATCCTCATGTATGGAGTTGGGATACAGGCTTACCAGGAGTTGATGATGCCGGGAGTGGATCTGAATTGACTCTGGTTATTTCTACCCCAGACCATTTCAGGCAATTATTTGATGAAACTGAAAAATTAAAAAGTGTTCTAGACAAGAGCAAATTATTTGCAGCAGTGAACTATGACCTTCGCCTTGATACCATGGGATACAATATAGACCTTGATTATAACCAACTGGCGAAACTTGGACTGACAGCAAATCAGGTGGCAAAGACGATTGAGGTATTTTTCAGTGGCGACAAGTCACAAACCTTTGAAAAAGATGGGGTCGTTTATAATATATCGATTAAAGGAGATTCCTCCCCCTGGACTTTGAATGAACTTTATTTAACTACAAATGAAGGGAAGTCTGTTTCATTGGGAGCTATTACCAAAATGCAGCCCAAGGCTCAACCGGCAACTCTTGATCATTATCAGCAAATGCGTTCGACCACTCTCCATGTCCAATTACATAAGGGAGACTCTATGGCAAAGGCTATTGAAAAATTATGGGGCACTACCAAAGAAGTGATGCCTCAACACTATAAACTGACCTGGATTGGTGCGGCCAAAGCATTCCATGAATCTTCCAATTCCATGTTATTTTTGTTTTTCTTATCTTTGGCTTTCATCTATGCCATTTTATGCACACAATTCGAGAATTTTACTGACCCCTTCATTATTCTATTCACTGTACCACTAGCCTGCTCGGGCGCCTTATTATTCACTTATTTATTTGGACAATCCTTAAACATTTATACTCAGGTAGGTTTGATTACTTTAATCGGGCTCATTAGCAAACACGGTATTTTAATAGTGGAATTTGCTAATAAACTTCATAAAGATGGTGCTTCGTTGCCAGAAGCTATACAGAAATCAGCTGCATTGCGTTTACGGCCTATATTAATGACAACTGGCGCCATGGTTTTTGGCGCCATCCCTTTGGTATTATCGCATGATGCGGGTTCTGAATCCCGGCATGCCATAGGAACTGTATTGATTAGCGGGCTCGGTCTTGGAACACTATTTACCCTATTTGTTTTGCCTGCGGTTTACAACATCATCAAATCCAAACTAATTGATATGCAAAAAACAGGGGGCAAAAAACGGTGCAGCAAAGAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41208","NCBI_taxonomy_name":"Legionella pneumophila str. Paris","NCBI_taxonomy_id":"297246"}}}},"ARO_accession":"3004100","ARO_id":"41209","ARO_name":"LpeB","ARO_description":"LpeB is a subunit of the LpeAB efflux pump in Legionella pneumophila, which is homologous to AcrB in E. coli.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2760":{"model_id":"2760","model_name":"MexGHI-OpmD","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)","model_param":{"41141":{"param_type":"efflux pump components","param_description":"This detection model parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305.","param_type_id":"41141","param_value":{"7742":"995,1344,1647,442"}}},"ARO_accession":"3000799","ARO_id":"37179","ARO_name":"MexGHI-OpmD","ARO_description":"MexGHI-OpmD is an efflux complex expressed in Pseudomonas aeruginosa. MexG is a membrane protein required for drug export; MexH is the membrane fusion protein; MexI is the inner membrane transporter; and MexJ is the outer membrane channel protein. MexGHI-OpmD confers resistance to vanadium, norfloxacin, and acriflavin.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavin","category_aro_description":"Acriflavin is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36193":{"category_aro_accession":"3000054","category_aro_cvterm_id":"36193","category_aro_name":"acridine dye","category_aro_description":"Acridine dyes are cell permeable, basic molecules with an acridine chromophore. These compounds intercalate DNA. The image shown represents the core structure of the acridine family, with specific dyes containing varying substituents.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2761":{"model_id":"2761","model_name":"MexPQ-OpmE","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)","model_param":{"41141":{"param_type":"efflux pump components","param_description":"This detection model parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305.","param_type_id":"41141","param_value":{"7743":"2211,2212,2213"}}},"ARO_accession":"3003697","ARO_id":"40349","ARO_name":"MexPQ-OpmE","ARO_description":"MexPQ-OpmE multidrug efflux pump expressed in Pseudomonas aeruginosa. MexP is the membrane fusion protein; MexQ is the inner membrane transporter; and OpmE is the outer membrane channel.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavin","category_aro_description":"Acriflavin is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36309":{"category_aro_accession":"3000170","category_aro_cvterm_id":"36309","category_aro_name":"imipenem","category_aro_description":"Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"37626":{"category_aro_accession":"3001227","category_aro_cvterm_id":"37626","category_aro_name":"kitasamycin","category_aro_description":"Kitasamycin is a macrolide antibiotic and is produced by Streptoverticillium kitasatoense. The drug has antimicrobial activity against a wide spectrum of pathogens.","category_aro_class_name":"Antibiotic"},"40353":{"category_aro_accession":"3003701","category_aro_cvterm_id":"40353","category_aro_name":"rokitamycin","category_aro_description":"Rokitamycin is a macrolide antibiotic. Synthesized from strains of Streptomyces kitasatoensis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36193":{"category_aro_accession":"3000054","category_aro_cvterm_id":"36193","category_aro_name":"acridine dye","category_aro_description":"Acridine dyes are cell permeable, basic molecules with an acridine chromophore. These compounds intercalate DNA. The image shown represents the core structure of the acridine family, with specific dyes containing varying substituents.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2762":{"model_id":"2762","model_name":"MexMN-OprM","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)","model_param":{"41141":{"param_type":"efflux pump components","param_description":"This detection model parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305.","param_type_id":"41141","param_value":{"7744":"2216,2217,1305"}}},"ARO_accession":"3003703","ARO_id":"40357","ARO_name":"MexMN-OprM","ARO_description":"MexMN-OprM is a multidrug efflux pump expressed in Pseudomonas aeruginosa. MexM is the membrane fusion protein; MexN is the inner membrane transporter; and OprM is the outer membrane channel.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2763":{"model_id":"2763","model_name":"MdtABC-TolC","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)","model_param":{"41141":{"param_type":"efflux pump components","param_description":"This detection model parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305.","param_type_id":"41141","param_value":{"7745":"387,820,1315,826,986,1337,152,2764"}}},"ARO_accession":"3000787","ARO_id":"37167","ARO_name":"MdtABC-TolC","ARO_description":"MdtABC-TolC is a multidrug efflux system in Gram-negative bacteria, including E. coli and Salmonella. MdtA is a membrane fusion protein; TolC is the outer membrane channel; MdtBC form a drug transporter. In the absence of MdtB, the MdtAC-TolC has narrower drug specificity, leading to the loss of novobiocin resistance, for example.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2765":{"model_id":"2765","model_name":"EmrAB-TolC","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)","model_param":{"41141":{"param_type":"efflux pump components","param_description":"This detection model parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305.","param_type_id":"41141","param_value":{"7747":"1757,1847,826,1330"}}},"ARO_accession":"3000344","ARO_id":"36483","ARO_name":"EmrAB-TolC","ARO_description":"EmrAB-TolC is a multidrug efflux system found in E. coli. EmrB is the electrochemical-gradient powered transporter; EmrA is the linker; and TolC is the outer membrane channel. It confers resistance to nalidixic acid and thiolactomycin.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2766":{"model_id":"2766","model_name":"EmrKY-TolC","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)","model_param":{"41141":{"param_type":"efflux pump components","param_description":"This detection model parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305.","param_type_id":"41141","param_value":{"7748":"609,540,826,1318,1015,1248"}}},"ARO_accession":"3000373","ARO_id":"36512","ARO_name":"EmrKY-TolC","ARO_description":"EmrKY is a homolog of EmrAB found in E. coli. Together with TolC, it is a tripartite multidrug transporter.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2768":{"model_id":"2768","model_name":"MdtEF-TolC","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)","model_param":{"41141":{"param_type":"efflux pump components","param_description":"This detection model parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305.","param_type_id":"41141","param_value":{"7750":"1903,121,826,869,1015,1318,91,1248,2324"}}},"ARO_accession":"3000788","ARO_id":"37168","ARO_name":"MdtEF-TolC","ARO_description":"MdtEF-TolC is a multidrug efflux complex in Gram-negative bacteria, including E. coli. MdtE is the membrane fusion protein, MdtF is the inner membrane transporter, while TolC is the outer membrane channel.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35930":{"category_aro_accession":"0000011","category_aro_cvterm_id":"35930","category_aro_name":"cloxacillin","category_aro_description":"Cloxacillin is a semisynthetic, isoxazolyl penicillin derivative in the beta-lactam class of antibiotics. It interferes with peptidogylcan synthesis and is commonly used for treating penicillin-resistant Staphylococcus aureus infections.","category_aro_class_name":"Antibiotic"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2769":{"model_id":"2769","model_name":"MdtNOP","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1442,2056,45,2330"}},"ARO_accession":"3004101","ARO_id":"41212","ARO_name":"MdtNOP","ARO_description":"MdtNOP is a MFS efflux pump protein found in E. coli. The deletion of mdtP from strain W3110 resulted in increased susceptibility to acriflavin, puromycin, and tetraphenylarsonium chloride. An E. coli mdtN null mutant is more sensitive to sulfur drugs than wild type","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavin","category_aro_description":"Acriflavin is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35965":{"category_aro_accession":"0000047","category_aro_cvterm_id":"35965","category_aro_name":"puromycin","category_aro_description":"Puromycin is an aminonucleoside antibiotic, derived from Streptomyces alboniger, that causes premature chain termination during ribosomal protein translation.","category_aro_class_name":"Antibiotic"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36193":{"category_aro_accession":"3000054","category_aro_cvterm_id":"36193","category_aro_name":"acridine dye","category_aro_description":"Acridine dyes are cell permeable, basic molecules with an acridine chromophore. These compounds intercalate DNA. The image shown represents the core structure of the acridine family, with specific dyes containing varying substituents.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2770":{"model_id":"2770","model_name":"kamB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"4082":{"protein_sequence":{"accession":"WP_063964000.1","sequence":"MRRVVGKRVQEFSDAEFEQLRSQYDDVVLDVGTGDGKHPYKVARQNPSRLVVALDADKSRMEKISAKAAAKPAKGGLPNLLYLWATAERLPPLSGVGELHVLMPWGSLLRGVLGSSPEMLRGMAAVCRPGASFLVALNLHAWRPSVPEVGEHPEPTPDSADEWLAPRYAEAGWKLADCRYLEPEEVAGLETSWTRRLHSSRDRFDVLALTGTISP"},"dna_sequence":{"accession":"NG_050561.1","fmin":"100","fmax":"748","strand":"+","sequence":"ATGCGCCGCGTGGTGGGCAAGCGGGTCCAGGAGTTCTCCGACGCCGAGTTCGAGCAGCTACGGAGTCAGTACGACGACGTGGTGCTCGACGTCGGCACCGGCGACGGGAAGCATCCGTACAAGGTCGCCCGCCAGAACCCCTCCCGGCTGGTGGTGGCGCTCGACGCCGACAAGAGCCGGATGGAGAAGATCTCGGCGAAGGCGGCGGCCAAGCCCGCGAAGGGCGGCCTGCCCAACCTGCTGTACCTGTGGGCCACCGCCGAGCGGCTCCCCCCGTTGTCGGGGGTGGGCGAGCTGCACGTCCTCATGCCGTGGGGCAGCCTGCTGCGCGGGGTCCTCGGCTCCTCGCCGGAGATGCTGCGCGGGATGGCGGCGGTGTGCCGGCCGGGCGCGTCCTTCCTGGTCGCGCTGAACCTGCACGCCTGGCGGCCCTCGGTGCCGGAGGTGGGCGAGCACCCCGAGCCCACCCCGGACTCCGCCGACGAGTGGCTGGCGCCCCGCTACGCCGAGGCCGGGTGGAAGCTCGCCGACTGCCGCTACCTGGAGCCGGAGGAGGTGGCGGGTCTGGAGACCTCCTGGACCCGCCGTCTGCACTCCTCCCGCGACCGGTTCGACGTGCTCGCGCTCACCGGCACGATCAGTCCGTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41214","NCBI_taxonomy_name":"Streptoalloteichus tenebrarius","NCBI_taxonomy_id":"1933"}}}},"ARO_accession":"3004102","ARO_id":"41213","ARO_name":"kamB","ARO_description":"Methyltransferase enzyme first described in Streptoalloteichus tenebrarius. Confers resistance to aminoglycoside antibiotics (esp. apramycin) through methylation of the 16S rRNA at A1408, thereby modifying the antibiotic target.","ARO_category":{"41436":{"category_aro_accession":"3004272","category_aro_cvterm_id":"41436","category_aro_name":"16S rRNA methyltransferase (A1408)","category_aro_description":"Methyltransferases that methylate the A1408 position of 16S rRNA, which is part of an aminoglycoside binding site.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2771":{"model_id":"2771","model_name":"QepA2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"850"}},"model_sequences":{"sequence":{"4083":{"protein_sequence":{"accession":"WP_032492277.1","sequence":"MSATLHDTAADRRKATRREWIGLAVVALPCLVYAMDLTVLNLALPVLSRELQPSSAQLLWILDIYGFFVAGFLITMGTLGDRIGRRRLLLIGAAFFAFGSVLAALADTAALLIAARALLGLAGATIAPSTMALIRNMFHDPRQRQFAIGVWIAAFSLGSAIGPLVGGVLLEFFHWGAVFWLNVPVMLLTLALGPRFLPEYRDPDAGHLDLASVLLSLAAVLLTIYGLKQLAEHGAGLASMAALLAGLAVGALFLRRQGHIAYPLLDLRLFAHAPFRAALAAYALAALAMFGVYIFMTQYLQLVLGLSPLQAGLATLPWSLCFVIGSLLSPQLAARWPAARILVVGLSAAAFGFAVLGLGQGLWWLVPATIVMGLGLAPVFTIGNEIIITSAPSERAGAASALSETVSEFSGALGIALFGSVGLVVYRQALTSAALPGLPADALQAAGASLGGAVHLADTLPAWQGAALLAAARAGFTDALQATAWAGAVLVLVAAGLVARLLRKRPALASG"},"dna_sequence":{"accession":"NG_050460.1","fmin":"100","fmax":"1636","strand":"+","sequence":"ATGTCCGCCACGCTCCACGACACCGCAGCGGATCGTCGGAAGGCCACCCGCCGCGAATGGATCGGCCTGGCCGTGGTCGCCCTGCCGTGCCTGGTCTACGCCATGGACCTCACGGTGCTGAACCTGGCGCTGCCGGTGCTCAGCCGTGAACTGCAGCCCTCCAGCGCCCAGCTTCTCTGGATCCTGGACATCTACGGCTTCTTCGTCGCCGGCTTCCTGATCACCATGGGCACGCTGGGCGACCGCATCGGCCGGCGCCGGCTGTTGTTGATCGGCGCGGCGTTCTTCGCATTCGGCTCGGTGCTCGCGGCGCTGGCCGATACCGCCGCGCTGTTGATCGCGGCGCGCGCCTTGCTCGGCCTGGCCGGCGCCACCATCGCGCCGTCCACCATGGCGCTGATCCGCAACATGTTCCACGACCCGCGCCAGCGCCAGTTCGCCATCGGCGTGTGGATCGCCGCGTTTTCGCTGGGCAGCGCGATCGGTCCGCTGGTCGGCGGCGTGTTGCTGGAGTTCTTCCACTGGGGCGCCGTGTTCTGGCTCAACGTGCCGGTGATGCTGCTGACGCTGGCGCTCGGCCCTCGCTTCCTGCCCGAGTATCGTGATCCGGACGCGGGGCACCTGGACCTGGCCAGCGTGCTGCTGTCGCTGGCGGCGGTGCTGCTGACGATCTACGGGCTCAAGCAGTTGGCCGAGCATGGAGCGGGCCTCGCCTCGATGGCTGCGCTGCTGGCCGGGCTGGCGGTCGGGGCGCTGTTCCTGCGCCGCCAGGGCCACATCGCCTACCCGCTGCTGGACCTGCGGCTGTTCGCGCACGCGCCGTTCCGCGCGGCGCTGGCGGCGTATGCGCTGGCCGCGCTGGCCATGTTCGGCGTCTACATCTTCATGACGCAGTACCTGCAGCTCGTGCTGGGGCTGTCGCCGCTGCAGGCCGGGCTGGCCACGCTGCCCTGGTCCCTGTGCTTCGTCATCGGTTCGCTGTTGTCGCCGCAGCTCGCGGCGCGCTGGCCGGCGGCGCGCATCCTCGTCGTGGGCCTGTCGGCAGCGGCGTTCGGCTTCGCCGTGCTGGGGCTGGGGCAGGGCCTGTGGTGGCTGGTGCCGGCCACGATCGTCATGGGCCTGGGCCTGGCGCCGGTGTTCACCATCGGCAACGAGATCATCATCACCAGCGCGCCGTCCGAGCGCGCGGGCGCGGCCTCGGCCTTGTCGGAGACGGTGTCCGAATTCAGCGGCGCGCTGGGCATCGCGCTGTTCGGCAGCGTCGGCCTGGTGGTCTACCGGCAGGCGCTGACCAGCGCGGCGCTGCCCGGCCTGCCGGCCGATGCGCTGCAGGCGGCCGGTGCCTCGCTCGGGGGCGCCGTGCACCTGGCCGACACCCTGCCGGCGTGGCAGGGCGCGGCCTTGCTGGCGGCCGCACGCGCGGGCTTCACCGATGCGCTGCAGGCCACGGCCTGGGCCGGCGCGGTGCTGGTGCTGGTGGCCGCTGGGCTGGTGGCGCGCCTGCTGCGCAAGCGCCCAGCGCTCGCATCTGGTTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004103","ARO_id":"41215","ARO_name":"QepA2","ARO_description":"QepA2 is a plasmid-mediated quinolone resistance pump found in an Escherichia coli isolate from France","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2773":{"model_id":"2773","model_name":"TMB-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"4085":{"protein_sequence":{"accession":"WP_063865147.1","sequence":"MRPFLFLIIFISHFAFANEEIPGLEVEEIDNGVFLHKSYSRVEGWGLVSSNGLVVISGGKAFIIDTPWSESDTEKLVDWIRSKKYELAGSISTHSHEDKTAGIKWLNGKSITTYASALTNEILKREGKEQARSSFKGNEFSLMDGFLEVYYPGGGHTIDNLVVWIPSSKILYGGCFIRSLESSGLGYTGEAKIDQWPQSARNTISKYPEAKIVVPGHGKIGDFELLKHTKVLAEKASNKANHGDR"},"dna_sequence":{"accession":"NG_050313","fmin":"15","fmax":"753","strand":"+","sequence":"ATGCGACCATTTTTATTTTTAATAATTTTTATCAGTCATTTCGCTTTTGCCAACGAAGAAATACCCGGATTGGAAGTTGAGGAAATTGACAACGGCGTTTTTTTGCACAAGTCATACAGCCGGGTGGAAGGCTGGGGCCTGGTAAGTTCAAACGGACTTGTTGTCATCAGCGGCGGAAAAGCATTCATTATTGACACTCCATGGTCGGAATCAGATACAGAAAAGCTTGTAGATTGGATACGATCAAAAAAGTATGAGCTGGCGGGAAGCATTTCTACACATTCACACGAAGACAAGACTGCCGGTATAAAATGGCTAAACGGCAAATCCATTACTACATATGCCTCAGCGCTGACTAATGAAATTCTAAAAAGAGAGGGTAAGGAGCAGGCAAGGAGCTCATTCAAAGGTAATGAATTTTCGCTGATGGACGGTTTTCTAGAAGTCTATTATCCCGGAGGCGGCCATACTATTGATAACTTAGTGGTATGGATCCCTAGTTCAAAAATATTGTATGGCGGCTGTTTCATACGTAGCTTGGAATCCAGTGGGCTAGGTTACACTGGTGAAGCTAAAATTGATCAGTGGCCACAATCCGCTAGAAATACAATTTCGAAGTATCCTGAAGCTAAGATTGTGGTGCCTGGTCATGGAAAAATTGGCGATTTCGAGTTGTTAAAACATACCAAGGTCCTTGCAGAAAAGGCCTCTAACAAGGCCAATCACGGCGACCGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40546","NCBI_taxonomy_name":"Proteobacteria","NCBI_taxonomy_id":"1224"}}}},"ARO_accession":"3004105","ARO_id":"41217","ARO_name":"TMB-1","ARO_description":"TMB-1 is a TMB metallo-beta-lactamase found in Achromobacter sp.","ARO_category":{"41216":{"category_aro_accession":"3004104","category_aro_cvterm_id":"41216","category_aro_name":"TMB beta-lactamase","category_aro_description":"TMB-1, the first known member of the Tripoli metallo-beta-lactamase family (TMB) was isolated from Achromobacter xylosoxidans in a Tripoli central hospital. TMB-1 was located on a class 1 integron and is a chromosomally-encoded beta-lactamase capable of hydrolyzing multiple antibiotics.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2774":{"model_id":"2774","model_name":"TMB-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"4086":{"protein_sequence":{"accession":"BAM73613.1","sequence":"MRPFLFLIIFISHFAFANEEIPGLEVEEIDNGVFLHKSYSRVEGWGLVSSNGLVVISGGKAFIIDTPWSESDTEKLVDWIRSKKYELAGSISTHSHEDKTAGIKWLNGKSITTYASALTNEILKREGKEQARSSFKGNEFSLMDGFLEVYYPGGGHTIDNLVVWIPSSKILYGGCFIRSLEPSGLGYTGEAKIDQWPQSARNTISKYPEAKIVVPGHGKIGDFELLKHTKVLAEKASNKANHGDR"},"dna_sequence":{"accession":"AB758278","fmin":"98","fmax":"836","strand":"+","sequence":"ATGCGACCATTTTTATTTTTAATAATTTTTATCAGTCATTTCGCTTTTGCCAACGAAGAAATACCCGGATTGGAAGTTGAGGAAATTGACAACGGCGTTTTTTTGCACAAGTCATACAGCCGGGTGGAAGGCTGGGGCCTGGTAAGTTCAAACGGACTTGTTGTCATCAGCGGCGGAAAAGCATTCATTATTGACACTCCATGGTCGGAATCAGATACAGAAAAGCTTGTAGATTGGATACGATCAAAAAAGTATGAGCTGGCGGGAAGCATTTCTACACATTCACACGAAGACAAGACTGCCGGTATAAAATGGCTAAACGGCAAATCCATTACTACATATGCCTCAGCGCTGACTAATGAAATTCTAAAAAGAGAGGGTAAGGAGCAGGCAAGGAGCTCATTCAAAGGTAATGAATTTTCGCTGATGGACGGTTTTCTAGAAGTCTATTATCCCGGAGGCGGCCATACTATTGATAACTTAGTGGTATGGATCCCTAGTTCAAAAATATTGTATGGCGGCTGTTTCATACGTAGCTTGGAACCCAGTGGGCTAGGTTACACTGGTGAAGCTAAAATTGATCAGTGGCCACAATCCGCTAGAAATACAATTTCGAAGTATCCTGAAGCTAAGATTGTGGTGCCTGGTCATGGAAAAATTGGCGATTTCGAGTTGTTAAAACATACCAAGGTCCTTGCAGAAAAGGCCTCTAACAAGGCCAATCACGGCGACCGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41219","NCBI_taxonomy_name":"Acinetobacter courvalinii","NCBI_taxonomy_id":"280147"}}}},"ARO_accession":"3004106","ARO_id":"41218","ARO_name":"TMB-2","ARO_description":"TMB-2 is a TMB metallo-beta-lactamase found in Acinetobacter sp.","ARO_category":{"41216":{"category_aro_accession":"3004104","category_aro_cvterm_id":"41216","category_aro_name":"TMB beta-lactamase","category_aro_description":"TMB-1, the first known member of the Tripoli metallo-beta-lactamase family (TMB) was isolated from Achromobacter xylosoxidans in a Tripoli central hospital. TMB-1 was located on a class 1 integron and is a chromosomally-encoded beta-lactamase capable of hydrolyzing multiple antibiotics.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2775":{"model_id":"2775","model_name":"Pseudomonas aeruginosa soxR","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"4087":{"protein_sequence":{"accession":"NP_250963.1","sequence":"MKNSCASRELSVGELARRAGVAVSALHFYETKGLISSQRNAGNQRRFSRETLRRVVVIKVAQRVGIPLAEIARALQTLPAGRSPSAADWARLSAQWKEDLTERIDKLLLLRDQLDGCIGCGCLSLQACPLRNPGDQLSAEGPGAHWLDAEGREHDG"},"dna_sequence":{"accession":"NC_002516.2","fmin":"2503424","fmax":"2503895","strand":"-","sequence":"CTAGCCGTCGTGCTCGCGGCCCTCGGCGTCCAGCCAGTGCGCTCCCGGCCCCTCGGCGGAAAGCTGGTCGCCGGGGTTGCGCAACGGGCAGGCCTGGAGCGACAGGCAGCCGCAACCGATGCAGCCGTCCAGTTGGTCGCGCAACAGCAGCAGCTTGTCGATGCGCTCGGTGAGATCCTCCTTCCACTGCGCCGACAGGCGCGCCCAGTCCGCCGCGCTAGGGCTGCGCCCCGCCGGCAGGGTCTGCAGGGCGCGAGCGATCTCCGCGAGGGGAATGCCGACCCGCTGGGCGACCTTGATCACCACCACCCGGCGTAGCGTCTCGCGACTGAAGCGCCGCTGGTTGCCGGCGTTGCGCTGGCTGCTGATCAGCCCCTTGGTTTCGTAGAAATGCAGGGCGGAGACCGCCACGCCGGCACGCCTGGCCAGTTCGCCGACGCTCAGTTCACGAGATGCGCAGGAATTCTTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3004107","ARO_id":"41228","ARO_name":"Pseudomonas aeruginosa soxR","ARO_description":"SoxR is a redox-sensitive transcriptional activator that induces expression of a small regulon that includes the RND efflux pump-encoding operon mexGHI-opmD. SoxR was shown to be activated by pyocyanin.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavin","category_aro_description":"Acriflavin is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36193":{"category_aro_accession":"3000054","category_aro_cvterm_id":"36193","category_aro_name":"acridine dye","category_aro_description":"Acridine dyes are cell permeable, basic molecules with an acridine chromophore. These compounds intercalate DNA. The image shown represents the core structure of the acridine family, with specific dyes containing varying substituents.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2778":{"model_id":"2778","model_name":"MCR-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"4094":{"protein_sequence":{"accession":"WP_065419574.1","sequence":"MTSHHSWYRYSINPFVLMGLVALFLAATANLTFFEKAMAVYPVSDNLGFIISMAVAVMGAMLLIVVLLSYRYVLKPVLILLLIMGAVTSYFTDTYGTVYDTTMLQNAMQTDQAESKDLMNLAFFVRIIGLGVLPSVLVAVAKVNYPTWGKGLIQRAMTWGVSLVLLLVPIGLFSSQYASFFRVHKPVRFYINPITPIYSVGKLASIEYKKATAPTDTIYHAKDAVQTTKPSERKPRLVVFVVGETARADHVQFNGYGRETFPQLAKVDGLANFSQVTSCGTSTAYSVPCMFSYLGQDDYDVDTAKYQENVLDTLDRLGVGILWRDNNSDSKGVMDKLPATQYFDYKSATNNTICNTNPYNECRDVGMLVGLDDYVSANNGKDMLIMLHQMGNHGPAYFKRYDEQFAKFTPVCEGNELAKCEHQSLINAYDNALLATDDFIAKSIDWLKTHEANYDVAMLYVSDHGESLGENGVYLHGMPNAFAPKEQRAVPAFFWSNNTTFKPTASDTVLTHDAITPTLLKLFDVTAGKVKDRAAFIQ"},"dna_sequence":{"accession":"NG_051171.1","fmin":"100","fmax":"1717","strand":"+","sequence":"ATGACATCACATCACTCTTGGTATCGCTATTCTATCAATCCTTTTGTGCTGATGGGTTTGGTGGCGTTATTTTTGGCAGCGACAGCGAACCTGACATTTTTTGAAAAAGCGATGGCGGTCTATCCTGTATCGGATAACTTAGGCTTTATCATCTCAATGGCGGTGGCGGTGATGGGTGCTATGCTACTGATTGTCGTGCTGTTATCCTATCGCTATGTGCTAAAGCCTGTCCTGATTTTGCTACTGATTATGGGTGCGGTGACGAGCTATTTTACCGATACTTATGGCACGGTCTATGACACCACCATGCTCCAAAATGCCATGCAAACCGACCAAGCCGAGTCTAAGGACTTGATGAATTTGGCGTTTTTTGTGCGAATTATCGGGCTTGGCGTGTTGCCAAGTGTGTTGGTCGCAGTTGCCAAAGTCAATTATCCAACATGGGGCAAAGGTCTGATTCAGCGTGCGATGACATGGGGTGTCAGCCTTGTGCTGTTGCTTGTGCCGATTGGACTATTTAGCAGTCAGTATGCGAGTTTCTTTCGGGTGCATAAGCCAGTGCGTTTTTATATCAACCCGATTACGCCGATTTATTCGGTGGGTAAGCTTGCCAGTATCGAGTACAAAAAAGCCACTGCGCCAACAGACACCATCTATCATGCCAAAGACGCCGTGCAGACCACCAAGCCGAGCGAGCGTAAGCCACGCCTAGTGGTGTTCGTCGTCGGTGAGACGGCGCGTGCTGACCATGTGCAGTTCAATGGCTATGGCCGTGAGACTTTCCCGCAGCTTGCCAAAGTTGATGGCTTGGCGAATTTTAGCCAAGTGACATCGTGTGGCACATCGACGGCGTATTCTGTGCCGTGTATGTTCAGCTATTTGGGTCAAGATGACTATGATGTCGATACCGCCAAATACCAAGAAAATGTGCTAGATACGCTTGACCGCTTGGGTGTGGGTATCTTGTGGCGTGATAATAATTCAGACTCAAAAGGCGTGATGGATAAGCTACCTGCCACGCAGTATTTTGATTATAAATCAGCAACCAACAATACCATCTGTAACACCAATCCCTATAACGAATGCCGTGATGTCGGTATGCTTGTCGGGCTAGATGACTATGTCAGCGCCAATAATGGCAAAGATATGCTCATCATGCTACACCAAATGGGCAATCATGGGCCGGCGTACTTTAAGCGTTATGATGAGCAATTTGCCAAATTCACCCCCGTGTGCGAAGGCAACGAGCTTGCCAAATGCGAACACCAATCACTCATCAATGCCTATGACAATGCGCTACTTGCGACTGATGATTTTATCGCCAAAAGCATCGATTGGCTAAAAACGCATGAAGCGAACTACGATGTCGCCATGCTCTATGTCAGTGACCACGGCGAGAGCTTGGGCGAAAATGGTGTCTATCTGCATGGTATGCCAAATGCCTTTGCACCAAAAGAACAGCGAGCTGTGCCTGCGTTTTTTTGGTCAAATAATACGACATTCAAGCCAACTGCCAGCGATACTGTGCTGACGCATGATGCGATTACGCCAACACTGCTTAAGCTGTTTGATGTCACAGCGGGCAAGGTCAAAGACCGCGCGGCATTTATCCAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004110","ARO_id":"41231","ARO_name":"MCR-2","ARO_description":"MCR-2 is a plasmid-borne phosphoethanolamine transferase that interferes with binding of colistin to the cell membrane via addition of phosphoethanolamine to lipid A, resulting in reduction of the negative charge of the cell membrane. Originally identified in a Belgian sample of Escherichia coli by Xavier et al, (2016).","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2779":{"model_id":"2779","model_name":"FosA6","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"280"}},"model_sequences":{"sequence":{"4095":{"protein_sequence":{"accession":"WP_069174570.1","sequence":"MLSGLNHLTLAVSQLAPSVAFYQQLLGMTLHARWDSGAYLSCGDLWLCLSLDPQRRVTPPEESDYTHYAFSISEADFASFAARLEAAGVAIWKLNRSEGASHYFLDPDGHKLELHVGSLAQRLAACREQQYKGMVFFDQ"},"dna_sequence":{"accession":"NG_051497.1","fmin":"0","fmax":"620","strand":"+","sequence":"CCGGCTTTGAGATGCTGATGCTGTGGCACGAGCGCTGGCACCGCGACCCGGCGCATCAATGGCTGCGTCAGTTCATTGTGAATTCACTGGAGGAACAGACATGCTGAGTGGACTGAATCACCTGACCCTGGCAGTCAGCCAGCTGGCGCCGAGCGTGGCGTTTTATCAGCAGCTGCTGGGCATGACGCTGCATGCCCGCTGGGACAGCGGGGCTTATCTCTCCTGCGGCGATTTGTGGCTGTGCCTGTCGCTGGATCCGCAGCGGCGCGTTACTCCGCCGGAAGAGAGCGACTACACCCATTATGCGTTTAGTATTAGCGAAGCCGATTTTGCTAGCTTCGCCGCCCGCCTTGAGGCTGCCGGCGTGGCGATCTGGAAGCTGAACCGTAGCGAAGGTGCCTCGCACTATTTCCTCGATCCCGATGGCCATAAGCTGGAGCTGCACGTCGGCAGTCTCGCCCAGCGTCTGGCCGCCTGCCGCGAACAGCAGTATAAGGGGATGGTGTTTTTTGATCAGTGAAGCTGCTTCGCAGACGCTAGATCACCCGTAGCCCCGGTAAGCGCAGCTCCACCGGGGAGAACAGGTTAAATTCACTCCATCGCCACCTTCACCGCTTCTC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004111","ARO_id":"41232","ARO_name":"FosA6","ARO_description":"fosA6 is a plasmid-encoded enzyme that confers resistance to fosfomycin in Escherichia coli by breaking the epoxide ring of the molecule.","ARO_category":{"36272":{"category_aro_accession":"3000133","category_aro_cvterm_id":"36272","category_aro_name":"fosfomycin thiol transferase","category_aro_description":"Catalyzes the addition of a thiol group from a nucleophilic molecule to fosfomycin.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2780":{"model_id":"2780","model_name":"FosA7","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"250"}},"model_sequences":{"sequence":{"4093":{"protein_sequence":{"accession":"KKE03230.1","sequence":"MLQSLNHLTLAVSNLQTSLTFWRDLLGLQLHAEWDTGAYLTCGDLWVCLSYDVSCNYVAPQECDYTHYAFSIAPEDFEPFSYKLKQAGVTVWKDNKSEGQSFYFLDPDGHKLELHVGDLASRLAQCREKPYSGMRFGPGK"},"dna_sequence":{"accession":"LAPJ01000014.1","fmin":"36822","fmax":"37245","strand":"+","sequence":"ATGCTTCAATCTCTGAACCACTTAACGCTTGCTGTCAGTAATTTGCAAACTAGCCTGACCTTCTGGCGCGATTTGCTGGGGTTGCAGCTACATGCTGAGTGGGATACTGGCGCTTACCTTACCTGTGGCGACCTTTGGGTCTGTCTTTCTTACGACGTATCCTGTAACTACGTGGCCCCGCAGGAATGTGACTATACCCACTACGCATTCAGCATCGCGCCAGAAGATTTTGAACCGTTCTCGTATAAGCTGAAACAGGCGGGAGTGACGGTCTGGAAAGACAATAAAAGCGAAGGGCAATCTTTCTATTTTCTTGACCCCGATGGCCACAAGCTGGAACTGCATGTGGGAGATTTAGCATCTCGACTGGCGCAGTGCCGGGAGAAGCCTTACTCTGGAATGCGTTTCGGGCCTGGAAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35663","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Heidelberg","NCBI_taxonomy_id":"611"}}}},"ARO_accession":"3004113","ARO_id":"41234","ARO_name":"FosA7","ARO_description":"fosA7 is an enzyme that confers resistance to fosfomycin in Escherichia coli by breaking the epoxide ring of the molecule.","ARO_category":{"36272":{"category_aro_accession":"3000133","category_aro_cvterm_id":"36272","category_aro_name":"fosfomycin thiol transferase","category_aro_description":"Catalyzes the addition of a thiol group from a nucleophilic molecule to fosfomycin.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2787":{"model_id":"2787","model_name":"Moraxella catarrhalis M35","model_type":"protein knockout model","model_type_id":"40354","model_description":"An AMR detection model for instances where the absence of a protein - due to large-scale insertion elements, large deletions, or other methods of protein knockout - confers clinical resistance to a known antibiotic. These models include reference sequences. Protein knockout models are currently in development.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"650"}},"model_sequences":{"sequence":{"4101":{"protein_sequence":{"accession":"AAX99225","sequence":"MKKLALATAVAALSVSAAQATPTVYGKAFLTVDANNTDTTYNSGLVQLSEDTNESGLNSNTSRIGFKGSEALNANTDVVYQLEYKIDIDADRGDNFKSRDTYLGLAHKQYGTLLAGRLTTIDDSVDFASMLEDNNVADIGPTFNAPRANNAFAYVSPEYNGTQFLAMYAFDSDTDKGGLAKDDQFGVGATYSTGPINAGATYIHYGDDSHIRLSGNYAVSPALTVGALYQISEFGVAAKNQKASPLSEGKVGDKKENTLIVSGEMKTATPWTAYGQATLIKNVAGNDGDESVGVGIGGKYAFNKATTGHVYTGYVNSERKNVKYEGSNETHKNAHKDTKFDGYKNSGFGIGAGLEYKF"},"dna_sequence":{"accession":"AY905613","fmin":"0","fmax":"1077","strand":"+","sequence":"ATGAAAAAACTTGCTCTAGCAACCGCTGTCGCTGCTTTATCTGTATCTGCTGCACAAGCAACACCGACTGTTTACGGTAAAGCGTTTTTAACTGTTGATGCCAACAATACTGATACAACTTATAATTCAGGTCTTGTACAATTATCTGAAGATACCAATGAAAGCGGGCTTAACTCAAATACCTCACGCATTGGTTTTAAAGGTTCTGAAGCTTTAAATGCTAATACTGATGTTGTGTATCAACTTGAATATAAGATTGACATTGATGCTGATCGTGGCGATAACTTTAAATCTCGTGATACTTACCTAGGTCTTGCTCATAAACAATACGGCACATTGTTGGCTGGTCGCTTAACGACTATTGATGACAGTGTTGATTTTGCCAGCATGTTGGAAGATAATAATGTCGCTGACATCGGTCCTACTTTTAATGCCCCTCGTGCCAACAATGCCTTTGCTTATGTATCACCTGAGTATAATGGTACTCAGTTCTTAGCTATGTATGCATTTGACTCAGATACTGACAAGGGCGGTCTTGCCAAAGATGACCAGTTTGGTGTGGGTGCAACTTATAGCACAGGCCCTATCAATGCAGGTGCGACTTATATTCACTACGGTGATGACAGTCACATTCGCCTATCTGGCAACTATGCGGTTTCTCCAGCATTGACTGTAGGTGCTTTATATCAAATCTCAGAATTTGGTGTCGCTGCCAAAAATCAAAAAGCCAGTCCTTTGTCTGAGGGCAAGGTAGGCGATAAAAAAGAAAACACCCTTATCGTGAGTGGCGAGATGAAAACTGCCACGCCATGGACAGCCTATGGTCAGGCAACTTTGATTAAAAATGTTGCTGGTAATGATGGCGATGAGTCAGTGGGTGTTGGTATTGGTGGTAAATATGCCTTTAATAAAGCCACCACAGGTCATGTCTACACTGGCTATGTCAACAGCGAGCGTAAAAATGTCAAGTATGAGGGCAGTAATGAAACACATAAAAATGCACACAAAGATACAAAGTTTGATGGTTATAAGAACAGTGGCTTTGGTATCGGCGCAGGTTTAGAATATAAATTCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41250","NCBI_taxonomy_name":"Moraxella catarrhalis","NCBI_taxonomy_id":"480"}}}},"ARO_accession":"3004124","ARO_id":"41249","ARO_name":"Moraxella catarrhalis M35","ARO_description":"The outer membrane protein M35 of Moraxella catarrhalis is an antigenically conserved porin. Down-regulation of M35 significantly increases the MICs of aminopenicillins, specifically amoxicillin.","ARO_category":{"41445":{"category_aro_accession":"3004281","category_aro_cvterm_id":"41445","category_aro_name":"General Bacterial Porin with reduced permeability to beta-lactams","category_aro_description":"These are GBPs that are associated with decreased susceptibility to beta-lactams either through mutations in the porin protein, absence of the porin protein, or expression of the porin protein.","category_aro_class_name":"AMR Gene Family"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36383":{"category_aro_accession":"3000244","category_aro_cvterm_id":"36383","category_aro_name":"reduced permeability to antibiotic","category_aro_description":"Reduction in permeability to antibiotic, generally through reduced production of porins, can provide resistance.","category_aro_class_name":"Resistance Mechanism"},"40429":{"category_aro_accession":"3003764","category_aro_cvterm_id":"40429","category_aro_name":"resistance by absence","category_aro_description":"Mechanism of antibiotic resistance conferred by deletion of gene (usually a porin)","category_aro_class_name":"Resistance Mechanism"}}},"2781":{"model_id":"2781","model_name":"porin OmpC","model_type":"protein knockout model","model_type_id":"40354","model_description":"An AMR detection model for instances where the absence of a protein - due to large-scale insertion elements, large deletions, or other methods of protein knockout - confers clinical resistance to a known antibiotic. These models include reference sequences. Protein knockout models are currently in development.","model_sequences":{"sequence":{"4096":{"protein_sequence":{"accession":"APB87301","sequence":"MKVKVLSLLVPALLVAGAANAAEVYNKDGNKLDLYGKVDGLHYFSDNKDVDGDQTYMRLGFKGETQVTDQLTGYGQWEYQIQGNSAENENNSWTRVAFAGLKFQDVGSFDYGRNYGVVYDVTSWTDVLPEFGGDTYGSDNFMQQRGNGFATYRNTDFFGLVDGLNFAVQYQGKNGSVSGEGMTNNGRDALRQNGDGVGGSITYDYEGFGIGAAVSSSKRTDAQNTAAYIGNGDRAETYTGGLKYDANNIYLAAQYTQTYNATRVGSLGWANKAQNFEAVAQYQFDFGLRPSVAYLQSKGKNLGVINGRNYDDEDILKYVDVGATYYFNKNMSTYVDYKINLLDDNQFTRDAGINTDNIVALGLVYQF"},"dna_sequence":{"accession":"KY086517","fmin":"0","fmax":"1104","strand":"+","sequence":"ATGAAAGTTAAAGTACTGTCCCTCCTGGTCCCAGCTCTGCTGGTAGCAGGCGCAGCAAACGCTGCTGAAGTTTACAACAAAGACGGCAACAAATTAGATCTGTACGGTAAAGTAGACGGCCTGCACTATTTCTCTGACAACAAAGATGTAGATGGCGACCAGACCTACATGCGTCTTGGCTTCAAAGGTGAAACTCAGGTTACTGACCAGCTGACCGGTTACGGCCAGTGGGAATATCAGATCCAGGGCAACAGCGCTGAAAACGAAAACAACTCCTGGACCCGTGTGGCATTCGCAGGTCTGAAATTCCAGGATGTGGGTTCTTTCGACTACGGTCGTAACTACGGCGTTGTTTACGACGTAACTTCCTGGACCGACGTACTGCCAGAATTCGGTGGCGACACCTACGGTTCTGACAACTTCATGCAGCAGCGTGGTAACGGCTTTGCGACCTACCGTAACACTGACTTCTTCGGTCTGGTTGACGGCCTGAACTTTGCTGTTCAGTACCAGGGCAAAAACGGTAGCGTAAGCGGCGAAGGCATGACCAACAATGGTCGCGATGCTCTGCGTCAGAACGGCGACGGCGTTGGCGGTTCTATCACTTATGATTACGAAGGCTTCGGTATCGGTGCTGCAGTTTCCAGCTCCAAACGTACTGATGCTCAGAACACCGCTGCTTACATCGGTAACGGCGACCGTGCTGAAACCTACACCGGTGGTCTGAAATACGACGCTAACAACATCTACCTGGCTGCTCAGTACACCCAGACCTACAACGCAACTCGCGTAGGTTCCCTGGGTTGGGCGAACAAAGCACAGAACTTCGAAGCTGTTGCTCAGTACCAGTTCGACTTCGGTCTGCGTCCGTCTGTAGCATACCTGCAGTCTAAAGGTAAAAACCTGGGTGTCATCAATGGTCGTAACTACGACGACGAAGATATCCTGAAATATGTTGATGTTGGCGCGACCTACTACTTCAACAAAAACATGTCCACCTACGTTGACTACAAAATCAACCTGCTGGACGACAACCAGTTCACTCGTGACGCTGGCATCAACACTGATAACATCGTAGCTCTGGGTCTGGTTTACCAGTTCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004114","ARO_id":"41238","ARO_name":"porin OmpC","ARO_description":"In the presence of antibiotic stress, there is a coupled down-regulation of the porin OmpC with the OmpF.  Mutants both lacking both OmpC and OmpF proteins are resistant to cephaloridine and cefazolin. Analyses of genes involved in the increased resistance to tetracycline suggest that the up-regulation of efflux pump genes is accompanied by a decrease of OmpF and OmpC synthesis. Homologs of OmpC have been identified in Escherichia coli, Salmonella enterica, Enterobacter aerogenes and Serratia marcescens.","ARO_category":{"41445":{"category_aro_accession":"3004281","category_aro_cvterm_id":"41445","category_aro_name":"General Bacterial Porin with reduced permeability to beta-lactams","category_aro_description":"These are GBPs that are associated with decreased susceptibility to beta-lactams either through mutations in the porin protein, absence of the porin protein, or expression of the porin protein.","category_aro_class_name":"AMR Gene Family"},"35975":{"category_aro_accession":"0000058","category_aro_cvterm_id":"35975","category_aro_name":"cefazolin","category_aro_description":"Cefazolin (INN), also known as cefazoline or cephazolin, is a first generation cephalosporin antibiotic. It is administered parenterally, and is active against a broad spectrum of bacteria.","category_aro_class_name":"Antibiotic"},"41256":{"category_aro_accession":"3004129","category_aro_cvterm_id":"41256","category_aro_name":"cephaloridine","category_aro_description":"Cephaloridine is a semisynthetic, broad-spectrum, first-generation cephalosporin with antibacterial activity. Cephaloridine binds to and inactivates penicillin-binding proteins (PBPs) located on the inner membrane of the bacterial cell wall. PBPs are enzymes involved in the terminal stages of assembling the bacterial cell wall and in reshaping the cell wall during growth and division. Inactivation of PBPs interferes with the cross-linkage of peptidoglycan chains necessary for bacterial cell wall strength and rigidity. This results in the weakening of the bacterial cell wall and causes cell lysis.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36383":{"category_aro_accession":"3000244","category_aro_cvterm_id":"36383","category_aro_name":"reduced permeability to antibiotic","category_aro_description":"Reduction in permeability to antibiotic, generally through reduced production of porins, can provide resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2782":{"model_id":"2782","model_name":"Vibrio cholerae OmpU","model_type":"protein knockout model","model_type_id":"40354","model_description":"An AMR detection model for instances where the absence of a protein - due to large-scale insertion elements, large deletions, or other methods of protein knockout - confers clinical resistance to a known antibiotic. These models include reference sequences. Protein knockout models are currently in development.","model_sequences":{"sequence":{"4097":{"protein_sequence":{"accession":"AID70696","sequence":"MNKTLIALAVSAAAVATGAYADGINQSGDKAGSTVYSAKGTSLEIGGRAEARLSLKDGKAEDKSRVRLNFLGKAEINDSLYGIGFYEGEFTTADNADGSELDNRYTYAGIGGTYGEVTYGKNDGALGVITDFTDIMSYHGNSAADKIAVADRTDNMLAYKGQFGDLGVKASYRFADRDTSTGEFTDNKKEDGYSLSAIYAFGDTGFNIGAGYADQNDNNEYMLAASYRMENVYFGALFTDGEKNFNSKSNGNNSVVKGKFTGVQDYTGYELAAGYKLGQAAFTTTYNNAETANDTSANNVAIDATYYFKPNFRTYISYNFNLLDSGDKLGNSSVSKIDAEDELAIGLRYDF"},"dna_sequence":{"accession":"KJ699300","fmin":"0","fmax":"1056","strand":"+","sequence":"ATGAACAAGACTCTGATTGCTCTTGCTGTATCAGCTGCTGCAGTGGCTACTGGCGCTTACGCTGACGGAATCAACCAAAGCGGTGACAAAGCAGGTTCAACCGTTTACAGCGCGAAAGGTACTTCTCTAGAAATCGGTGGCCGTGCTGAAGCGCGCCTATCTCTGAAAGATGGCAAAGCTGAAGATAAATCTCGCGTACGCCTGAATTTCCTAGGTAAAGCAGAAATCAATGACAGCCTATACGGCATCGGTTTCTACGAAGGTGAATTCACTACTGCAGATAACGCTGACGGCTCAGAATTAGATAACCGTTACACCTACGCTGGTATCGGTGGCACTTACGGTGAAGTGACTTATGGTAAAAACGATGGTGCATTGGGCGTAATCACTGACTTCACCGATATCATGTCTTACCACGGTAACTCAGCCGCAGACAAAATCGCTGTAGCTGACCGTACAGACAACATGTTGGCTTACAAAGGCCAATTTGGTGACCTGGGCGTAAAAGCAAGCTACCGTTTTGCAGATCGTGATACTTCAACGGGTGAATTCACTGACAATAAAAAAGAAGACGGTTACTCACTATCTGCTATCTACGCCTTTGGTGACACTGGTTTCAACATCGGTGCAGGCTATGCAGATCAAAACGATAACAACGAGTACATGCTAGCCGCTTCTTACCGTATGGAAAATGTGTACTTCGGTGCTCTATTTACTGACGGTGAAAAGAATTTCAATAGTAAAAGCAACGGTAATAACTCTGTTGTGAAGGGCAAATTTACAGGTGTCCAAGATTATACTGGTTACGAATTAGCTGCTGGTTACAAGCTAGGTCAAGCTGCATTTACGACTACGTACAACAACGCAGAGACTGCAAACGATACATCAGCAAACAACGTAGCTATTGATGCTACTTACTACTTTAAGCCAAACTTCCGCACTTATATCTCTTACAACTTCAACCTACTTGACTCTGGTGACAAGCTAGGTAACAGCTCTGTATCTAAGATCGACGCTGAAGACGAACTGGCTATCGGTCTACGTTACGACTTCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36789","NCBI_taxonomy_name":"Vibrio cholerae","NCBI_taxonomy_id":"666"}}}},"ARO_accession":"3004117","ARO_id":"41241","ARO_name":"Vibrio cholerae OmpU","ARO_description":"A ToxR-Regulated outer membrane porin. In Vibrio cholerae, ToxR controls resistance to P2 (a BPI-derived antimicrobial peptide) by regulating the production of OmpU. OmpU also confers resistance to polymyxin B sulfate.","ARO_category":{"41446":{"category_aro_accession":"3004282","category_aro_cvterm_id":"41446","category_aro_name":"General Bacterial Porin with reduced permeability to peptide antibiotics","category_aro_description":"These are GBPs that are associated with decreased susceptibility to peptide antibiotics either through mutations in the porin protein, absence of the porin protein, or expression of the porin protein.","category_aro_class_name":"AMR Gene Family"},"41245":{"category_aro_accession":"3004121","category_aro_cvterm_id":"41245","category_aro_name":"BPI","category_aro_description":"Bactericidal\/permeability-increasing (BPI) protein is a member of a new generation of proteins known as super-antibiotics that are implicated as endotoxin neutralising agents. The potent (nM) cytotoxicity of BPI is limited to gram-negative bacteria (GNB), reflecting the high affinity (<10 nM) of BPI for bacterial lipopolysaccharides (LPS). Binding of BPI to live bacteria via LPS causes immediate growth arrest, actual killing coincides with later damage to the inner membrane.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36383":{"category_aro_accession":"3000244","category_aro_cvterm_id":"36383","category_aro_name":"reduced permeability to antibiotic","category_aro_description":"Reduction in permeability to antibiotic, generally through reduced production of porins, can provide resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2788":{"model_id":"2788","model_name":"Escherichia coli LamB","model_type":"protein knockout model","model_type_id":"40354","model_description":"An AMR detection model for instances where the absence of a protein - due to large-scale insertion elements, large deletions, or other methods of protein knockout - confers clinical resistance to a known antibiotic. These models include reference sequences. Protein knockout models are currently in development.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"850"}},"model_sequences":{"sequence":{"4102":{"protein_sequence":{"accession":"BAB38442","sequence":"MMITLRKLPLAVAVAAGVMSAQAMAVDFHGYARSGIGWTGSGGEQQCFQTTGAQSKYRLGNECETYAELKLGQEVWKEGDKSFYFDTNVAYSVAQQNDWEATDPAFREANVQGKNLIEWLPGSTIWAGKRFYQRHDVHMIDFYYWDISGPGAGLENIDVGFGKLSLAATRSSEAGGSSSFASNNIYDYTNETANDVFDVRLAQMEVNPGGTLELGVDYGRANLRDNYRLVDGASKDGWLFTAEHTQSVLKGFNKFVVQYATDSMTSQGKGLSQGSGVAFDNEKFAYNINNNGHMLRILDHGAISMGDNWDMMYVGMYQDINWDNDNGTKWWTVGIRPMYKWTPIMSTVMEIGYDNVESQRTGDKNNQYKITLAQQWQAGDSIWSRPAIRVFATYAKWDEKWGYDYNGDSKVNPNYGKAVPADFNGGSFGRGDSDEWTFGAQMEIWW"},"dna_sequence":{"accession":"BA000007","fmin":"5101244","fmax":"5102585","strand":"+","sequence":"ATGATGATTACTCTGCGCAAACTTCCTCTGGCGGTTGCCGTCGCAGCGGGCGTAATGTCTGCTCAGGCAATGGCTGTTGATTTCCACGGCTATGCACGTTCCGGTATTGGCTGGACAGGTAGCGGCGGTGAACAACAGTGTTTCCAGACTACCGGTGCTCAAAGTAAATACCGTCTTGGCAACGAATGTGAAACTTATGCTGAATTAAAATTGGGTCAGGAAGTGTGGAAAGAGGGCGATAAGAGCTTCTATTTCGACACTAACGTGGCCTATTCCGTCGCGCAACAGAATGACTGGGAAGCTACCGACCCGGCCTTCCGTGAAGCAAACGTGCAGGGTAAAAACCTGATCGAATGGCTGCCAGGCTCCACCATCTGGGCAGGTAAGCGCTTCTACCAACGTCATGACGTTCATATGATCGACTTCTACTACTGGGATATTTCTGGTCCTGGTGCCGGTCTGGAAAACATCGATGTTGGCTTCGGTAAACTCTCTCTGGCAGCAACCCGCTCCTCTGAAGCAGGTGGTTCTTCCTCTTTCGCCAGCAACAATATTTATGACTATACCAACGAAACCGCGAACGACGTTTTCGATGTGCGTTTAGCGCAGATGGAAGTCAACCCGGGCGGCACATTAGAACTGGGTGTCGACTACGGTCGTGCCAACCTGCGTGATAACTATCGTCTGGTTGATGGCGCATCGAAAGACGGCTGGTTATTCACTGCTGAACATACTCAGAGTGTCCTGAAGGGCTTTAACAAGTTTGTTGTTCAGTACGCTACTGACTCGATGACCTCGCAGGGTAAAGGTCTGTCGCAGGGTTCTGGCGTTGCATTTGATAACGAAAAATTTGCCTACAATATCAACAACAACGGTCACATGCTGCGTATCCTCGACCACGGTGCGATCTCCATGGGCGACAACTGGGACATGATGTACGTGGGTATGTACCAGGATATCAACTGGGATAACGACAACGGCACCAAGTGGTGGACCGTCGGTATTCGCCCGATGTACAAGTGGACGCCAATCATGAGCACCGTGATGGAAATCGGCTACGACAACGTCGAATCCCAGCGCACCGGCGACAAGAACAATCAGTACAAAATTACCCTCGCACAACAATGGCAGGCTGGCGACAGCATCTGGTCACGCCCGGCTATTCGTGTCTTCGCAACCTACGCCAAGTGGGATGAGAAATGGGGTTACGACTACAACGGCGATAGCAAGGTTAACCCGAACTACGGCAAAGCCGTTCCTGCTGATTTCAACGGCGGCAGCTTCGGTCGTGGCGACAGCGACGAGTGGACCTTCGGTGCCCAGATGGAAATCTGGTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36747","NCBI_taxonomy_name":"Escherichia coli O157:H7 str. Sakai","NCBI_taxonomy_id":"386585"}}}},"ARO_accession":"3004126","ARO_id":"41252","ARO_name":"Escherichia coli LamB","ARO_description":"LamB is a negative regulator for antibiotic resistance, it serves as a porin to influx antibiotic. When down-regulated, it increases resistance to chlortetracycline, ciprofloxacin, balofloxacin and nalidixic acid. It also interacts with Odp1, an energy metabolic enzyme, creating a complex that decreases in antibiotic-resistant strains.","ARO_category":{"41443":{"category_aro_accession":"3004279","category_aro_cvterm_id":"41443","category_aro_name":"Sugar Porin (SP)","category_aro_description":"Members of the Sugar Porin family tend to facilitate the transport of maltodextrins and other sugars across the outer membrane of Gram-negative bacteria. These porins form a homotrimeric structure.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"41257":{"category_aro_accession":"3004130","category_aro_cvterm_id":"41257","category_aro_name":"balofloxacin","category_aro_description":"Balofloxacin is an 8-methoxy fluoroquinolone antibiotic. It shows potent bactericidal activity and inhibits the supercoiling activity of DNA gyrase of S. aureus, E. coli, and P. aeruginosa.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36383":{"category_aro_accession":"3000244","category_aro_cvterm_id":"36383","category_aro_name":"reduced permeability to antibiotic","category_aro_description":"Reduction in permeability to antibiotic, generally through reduced production of porins, can provide resistance.","category_aro_class_name":"Resistance Mechanism"},"40429":{"category_aro_accession":"3003764","category_aro_cvterm_id":"40429","category_aro_name":"resistance by absence","category_aro_description":"Mechanism of antibiotic resistance conferred by deletion of gene (usually a porin)","category_aro_class_name":"Resistance Mechanism"}}},"2786":{"model_id":"2786","model_name":"Burkholderia pseudomallei Omp38","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"4100":{"protein_sequence":{"accession":"AAP82271","sequence":"MNKTLIVAAVAASFATVAHAQSSVTLYGVLDAGITYQSNVATPSGSGKSLWSVGAGVDQSRFGLRGSEDLGGGLKAIFTLESGFNIGNGRFNNGGGMFNRQAFVGLSSNYGTVTLGRQYDATQDYLSPLSATGTWGGTYFAHPLNNDRLNTNGDVAVNNTVKFTSANYAGLQFGGTYSFSNNSQFANNRAYSAGASYQFQGLKVGAAYSQANNAGANTTGATDPLTGFNIGGTNAASIQGRSRVYGAGASYAYGPLQGGLLWTQSRLDNLANGAPTIRADNYEANVKYNLTPALGLGVAYTYTNAKANGESTHWNQVGVQADYALSKRTDVYAQAVYQRSSKNANASIYNGDLSTPFSTSINQTAATVGLRHRF"},"dna_sequence":{"accession":"AY312416","fmin":"0","fmax":"1122","strand":"+","sequence":"ATGAACAAGACTCTGATTGTTGCAGCAGTTGCTGCATCGTTCGCAACCGTCGCTCACGCGCAAAGCAGCGTCACGCTGTACGGTGTGCTCGACGCGGGCATCACGTACCAAAGCAACGTCGCGACGCCGTCGGGCTCGGGCAAGTCGCTGTGGTCGGTCGGCGCCGGCGTCGACCAAAGCCGTTTCGGTCTGCGCGGCTCGGAAGACCTGGGTGGCGGCCTGAAGGCGATCTTCACGTTGGAAAGCGGCTTCAACATCGGTAACGGCCGCTTCAACAACGGTGGCGGCATGTTCAACCGTCAAGCGTTCGTCGGTCTGTCGAGCAACTACGGCACCGTCACGCTGGGCCGTCAGTACGACGCAACCCAAGACTACCTGTCGCCGCTGTCGGCAACGGGCACCTGGGGCGGCACGTACTTCGCGCACCCGCTCAACAACGACCGCCTGAACACGAACGGCGACGTCGCGGTGAACAATACGGTCAAGTTCACGAGCGCGAACTACGCCGGCCTGCAATTCGGCGGCACGTACTCGTTCTCGAACAACTCGCAATTCGCGAACAACCGTGCATACAGCGCGGGCGCTTCGTACCAGTTCCAAGGCCTGAAGGTCGGTGCGGCGTACTCGCAAGCTAACAACGCTGGCGCGAATACCACGGGCGCAACGGATCCGCTGACCGGCTTCAACATCGGCGGCACGAACGCAGCAAGCATCCAAGGCCGTTCGCGCGTGTACGGCGCCGGCGCAAGCTACGCTTACGGCCCGCTGCAAGGCGGCCTGCTCTGGACGCAATCGCGTCTCGACAACCTGGCAAACGGCGCGCCGACCATCCGTGCCGACAACTACGAAGCAAACGTGAAGTACAACCTGACGCCGGCTCTGGGTCTGGGTGTTGCTTACACGTACACGAACGCGAAGGCGAACGGCGAAAGCACTCACTGGAACCAAGTTGGCGTCCAGGCCGACTACGCGCTGTCGAAGCGCACCGACGTGTACGCACAAGCCGTGTACCAGCGTTCGTCGAAGAACGCGAATGCGTCGATCTACAACGGCGACCTCAGCACGCCGTTCAGCACGTCGATCAACCAAACCGCAGCGACGGTTGGTCTGCGTCACCGCTTC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36923","NCBI_taxonomy_name":"Burkholderia pseudomallei","NCBI_taxonomy_id":"28450"}}}},"ARO_accession":"3004123","ARO_id":"41248","ARO_name":"Burkholderia pseudomallei Omp38","ARO_description":"Heterologous expression of Burkholderia pseudomallei Omp38 (BpsOmp38) in Omp-deficient E. coli host cells lowers their permeability and in consequence, their antimicrobial susceptibility to penicillin G, cefoxitin, ceftazidime and imipenem.","ARO_category":{"41445":{"category_aro_accession":"3004281","category_aro_cvterm_id":"41445","category_aro_name":"General Bacterial Porin with reduced permeability to beta-lactams","category_aro_description":"These are GBPs that are associated with decreased susceptibility to beta-lactams either through mutations in the porin protein, absence of the porin protein, or expression of the porin protein.","category_aro_class_name":"AMR Gene Family"},"35927":{"category_aro_accession":"0000008","category_aro_cvterm_id":"35927","category_aro_name":"cefoxitin","category_aro_description":"Cefoxitin is a cephamycin antibiotic often grouped with the second generation cephalosporins. Cefoxitin is bactericidal and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. Cefoxitin's 7-alpha-methoxy group and 3' leaving group make it a poor substrate for most beta-lactamases.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36309":{"category_aro_accession":"3000170","category_aro_cvterm_id":"36309","category_aro_name":"imipenem","category_aro_description":"Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.","category_aro_class_name":"Antibiotic"},"36976":{"category_aro_accession":"3000632","category_aro_cvterm_id":"36976","category_aro_name":"benzylpenicillin","category_aro_description":"Benzylpenicillin, commonly referred to as penicillin G, is effective against both Gram-positive and Gram-negative bacteria. It is unstable in acid.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36383":{"category_aro_accession":"3000244","category_aro_cvterm_id":"36383","category_aro_name":"reduced permeability to antibiotic","category_aro_description":"Reduction in permeability to antibiotic, generally through reduced production of porins, can provide resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2783":{"model_id":"2783","model_name":"Vibrio cholerae OmpT","model_type":"protein knockout model","model_type_id":"40354","model_description":"An AMR detection model for instances where the absence of a protein - due to large-scale insertion elements, large deletions, or other methods of protein knockout - confers clinical resistance to a known antibiotic. These models include reference sequences. Protein knockout models are currently in development.","model_sequences":{"sequence":{"4105":{"protein_sequence":{"accession":"AAC28105","sequence":"MKKTLLALAVLAAAGSVNAAEILKSDAGTVDFYGQLRTELKFLEDKDPTIGSGSSRAGVDANYTVNDSLALQGKVEFALKDSGDMYVRNHILGVKTNFGKFSFGKQWTTSDDVYGADYSYFFGGTGLRYGTLSDALHDSQVKYVYEADSFWVKAGYGFPEDNAKQELAELYVGATFGDLAVHAGGGQNRDKAFKVGSNTVGTTTTDIKADVTNSYFEVTGEYTIGDALIGVTYYNAELDVENNPLVIDEDAISVAGTYKVADKTKLYAGYEYVMQEANTGADEDGTLVYLGVEYKFASWARVYAEYGYGDGTTLGYTNKGSDAEVKATKVDSANNFGIGARIYW"},"dna_sequence":{"accession":"AF079766","fmin":"786","fmax":"1821","strand":"+","sequence":"ATGAAAAAAACTCTATTAGCACTCGCAGTGCTTGCAGCCGCAGGCTCTGTAAACGCAGCTGAAATTCTAAAATCAGATGCTGGCACTGTTGATTTTTACGGTCAGCTACGTACAGAATTGAAATTCTTAGAAGATAAAGATCCAACAATTGGTTCTGGTTCTTCGCGCGCTGGTGTTGATGCAAACTACACCGTTAACGATAGCTTAGCGTTACAAGGTAAAGTGGAATTCGCACTAAAAGACAGTGGCGATATGTATGTTCGTAACCACATTCTTGGTGTAAAAACTAATTTTGGTAAGTTTAGCTTTGGTAAACAATGGACTACATCTGACGATGTATACGGTGCTGACTACTCTTATTTCTTTGGTGGTACAGGTCTTCGTTACGGCACACTGTCTGATGCACTACACGATTCTCAAGTCAAGTATGTTTACGAAGCTGACAGCTTCTGGGTTAAAGCTGGTTACGGTTTTCCAGAAGATAATGCAAAGCAAGAGCTAGCAGAACTGTATGTAGGTGCAACATTTGGTGATTTGGCTGTGCACGCTGGTGGTGGTCAAAACCGTGATAAAGCATTCAAAGTTGGTAGTAATACGGTTGGCACAACAACCACAGATATTAAAGCTGACGTAACAAATAGTTACTTTGAAGTGACAGGTGAGTACACTATTGGTGATGCACTGATTGGTGTTACTTACTACAACGCAGAACTAGATGTAGAAAATAACCCACTAGTGATCGATGAAGACGCTATTTCTGTTGCTGGTACATACAAAGTTGCTGACAAGACAAAATTGTATGCTGGCTATGAGTATGTAATGCAAGAAGCGAACACTGGCGCAGATGAAGATGGTACTCTTGTTTACCTAGGTGTTGAATACAAATTTGCAAGCTGGGCTCGTGTATATGCTGAGTATGGCTACGGCGATGGTACAACTCTGGGTTACACCAACAAGGGTTCTGACGCAGAAGTTAAAGCAACGAAAGTCGACAGCGCTAATAACTTTGGTATCGGCGCTCGTATCTACTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36789","NCBI_taxonomy_name":"Vibrio cholerae","NCBI_taxonomy_id":"666"}}}},"ARO_accession":"3004118","ARO_id":"41242","ARO_name":"Vibrio cholerae OmpT","ARO_description":"A ToxR negatively regulated outer membrane porin. In Vibrio cholerae, ToxR controls resistance to P2 (a BPI-derived antimicrobial peptide) by regulating the production of OmpT, especially in the absence of OmpU.","ARO_category":{"41446":{"category_aro_accession":"3004282","category_aro_cvterm_id":"41446","category_aro_name":"General Bacterial Porin with reduced permeability to peptide antibiotics","category_aro_description":"These are GBPs that are associated with decreased susceptibility to peptide antibiotics either through mutations in the porin protein, absence of the porin protein, or expression of the porin protein.","category_aro_class_name":"AMR Gene Family"},"41245":{"category_aro_accession":"3004121","category_aro_cvterm_id":"41245","category_aro_name":"BPI","category_aro_description":"Bactericidal\/permeability-increasing (BPI) protein is a member of a new generation of proteins known as super-antibiotics that are implicated as endotoxin neutralising agents. The potent (nM) cytotoxicity of BPI is limited to gram-negative bacteria (GNB), reflecting the high affinity (<10 nM) of BPI for bacterial lipopolysaccharides (LPS). Binding of BPI to live bacteria via LPS causes immediate growth arrest, actual killing coincides with later damage to the inner membrane.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36383":{"category_aro_accession":"3000244","category_aro_cvterm_id":"36383","category_aro_name":"reduced permeability to antibiotic","category_aro_description":"Reduction in permeability to antibiotic, generally through reduced production of porins, can provide resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2790":{"model_id":"2790","model_name":"Serratia marcescens Omp1","model_type":"protein knockout model","model_type_id":"40354","model_description":"An AMR detection model for instances where the absence of a protein - due to large-scale insertion elements, large deletions, or other methods of protein knockout - confers clinical resistance to a known antibiotic. These models include reference sequences. Protein knockout models are currently in development.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"4104":{"protein_sequence":{"accession":"AIA49384.1","sequence":"MKRNILAVVIPALLAAGAANAAEIYNKDGNKLDLYGKVDGLHYFSDDKGNDGDQTYVRFGFKGETQITDQLTGYGQWEYNVQANHSESQGTEGTKTRLGFAGLKFADYGSFDYGRNYGVLYDVEGWTDMLPEFGGDTYTYTDNFMTGRTNGVATYRNNNFFGLVDGLNFAVQYQGKNQNDGRNVKKQNGDGWGISSTYDIGEGVSFGAAYASSNRTDDQKLRSNERGDKADAWTVGAKYDANNVYLAAMYAETRNMTPFGGGNFGAGCAATDDKCGGFASKTQNFEVTAQYQFDFGLRPEVSYLQSKGKNLNVPGVGSDQDLVKYVSVGTTYYFNKNMSTYVDYKINLLDDNEFTKATGTATDDIVAVGLVYQF"},"dna_sequence":{"accession":"CP005927.1","fmin":"4320303","fmax":"4321494","strand":"+","sequence":"ATGTTTGAAAAAATCACCGCCGCACCCGCCGACCCGATCCTGGGCCTGACCGACATTTTCCGCGCCGACGCCCGCCCGAATAAAATCAATTTAGGCATTGGCGTTTATAAAGATGAAACCGGCAAAACCCCGGTGCTGACCAGCGTAAAAAAAGCTGAACAGTATCTGCTGGAAAACGAGACCACCAAAAACTATCTCGGCATTGAAGGCATCCCGGCGTTTGCCAGCTGCACGCAAGAGCTGCTGTTCGGTAAAGAGAGCCCGATCGTCACCGATCGTCGCGCACGCACCGCACAGACGCCAGGCGGCACCGGCGGCTTGCGCGTAGCGGCAGACTTTATCGCCAACCAGACCAGCGCCAAGCGCATCTGGATCAGCAACCCAAGCTGGCCGAACCACAAGAACGTCTTTAGCGCCGTTGGCCTGGAAGTGCTGGAGTACGCCTACTACGACGCAGCCAACCACGCGCTGGATTTTGACGGCCTGCTGAACAGCCTGAAACAGGCTCAGGCCGGTGATGTCGTGTTGTTCCACGGCTGCTGCCATAACCCGACCGGTATCGATCCAACGGCGGAACAGTGGGCGCAGCTGGCTGAGCTTTCCGCCGCCAATGGCTGGCTGCCGCTGTTCGACTTCGCCTACCAGGGCTTCGCCAACGGTCTGGAAGAGGATGCGCAGGGTCTGCGTATTTTCGCCGCCAAACATCAAGAGCTGATCGTCGCCAGCTCCTACTCGAAAAACTTCGGCCTGTACAATGAGCGCGTCGGCGCTTGCACCCTTGTAGCTGCCGATGCCGAAACCGCCGATCGCGCCTTCAGCCAGGTGAAGGCGGCCATTCGTGCCAACTACTCTAACCCGCCGTCGCACGGCGCGGCCGTTGTCGCCACCATTCTGGGCAACGACGCCCTGCGCGCGATGTGGGAGCAGGAGCTGACCGACATGCGCCAGCGCATTCACCGCATGCGTCAGCTGTTCGTGAACACCCTGCAGGAGAAAGGCGCACAACAGGACTTCAGCTTTATCATCCAGCAGAACGGCATGTTCTCATTCAGCGGCCTGACCAAAGAACAGGTGCTGCGTCTGCGTGAAGAGTTCGGCGTATACGCCGTAAACTCGGGCCGGGTGAACGTGGCCGGCATGACGCCGGACAACATGGCACCGCTGTGTGAAGCCATCGTCGCCGTGCTCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41255","NCBI_taxonomy_name":"Serratia sp. FS14","NCBI_taxonomy_id":"1327989"}}}},"ARO_accession":"3004128","ARO_id":"41254","ARO_name":"Serratia marcescens Omp1","ARO_description":"Omp1 is an outer membrane porin that confers resistance by absence in S. marcescens.  Knockout, deletion or other inhibition of the omp1 gene confers resistance to certain beta-lactamase antibiotics - including Cefoxitin, Ceftriaxone, Cefotaxime, and Moxalactam - as well as Ciprofloxacin, Tetracycline, and Chloramphenicol, by preventing passage of the antibiotic into the cell.","ARO_category":{"41445":{"category_aro_accession":"3004281","category_aro_cvterm_id":"41445","category_aro_name":"General Bacterial Porin with reduced permeability to beta-lactams","category_aro_description":"These are GBPs that are associated with decreased susceptibility to beta-lactams either through mutations in the porin protein, absence of the porin protein, or expression of the porin protein.","category_aro_class_name":"AMR Gene Family"},"35927":{"category_aro_accession":"0000008","category_aro_cvterm_id":"35927","category_aro_name":"cefoxitin","category_aro_description":"Cefoxitin is a cephamycin antibiotic often grouped with the second generation cephalosporins. Cefoxitin is bactericidal and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. Cefoxitin's 7-alpha-methoxy group and 3' leaving group make it a poor substrate for most beta-lactamases.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35979":{"category_aro_accession":"0000062","category_aro_cvterm_id":"35979","category_aro_name":"ceftriaxone","category_aro_description":"Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36989":{"category_aro_accession":"3000645","category_aro_cvterm_id":"36989","category_aro_name":"cefotaxime","category_aro_description":"Cefotaxime is a semisynthetic cephalosporin taken parenterally. It is resistant to most beta-lactamases and active against Gram-negative rods and cocci due to its aminothiazoyl and methoximino functional groups.","category_aro_class_name":"Antibiotic"},"40944":{"category_aro_accession":"3004017","category_aro_cvterm_id":"40944","category_aro_name":"moxalactam","category_aro_description":"Moxalactam (Latamoxef) is a broad spectrum cephalosporin (oxacephem) and beta-lactam antibiotic. Moxalactam binding to PBPs inhibits peptidoglycan cross-linkage in the cell wall, resulting in cell death. Moxalactam is proposed to be effective against meningitides as it passes the blood-brain barrier.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36383":{"category_aro_accession":"3000244","category_aro_cvterm_id":"36383","category_aro_name":"reduced permeability to antibiotic","category_aro_description":"Reduction in permeability to antibiotic, generally through reduced production of porins, can provide resistance.","category_aro_class_name":"Resistance Mechanism"},"40429":{"category_aro_accession":"3003764","category_aro_cvterm_id":"40429","category_aro_name":"resistance by absence","category_aro_description":"Mechanism of antibiotic resistance conferred by deletion of gene (usually a porin)","category_aro_class_name":"Resistance Mechanism"}}},"2805":{"model_id":"2805","model_name":"Mycoplasma gallisepticum 23S rRNA mutation conferring resistance to pleuromutilin antibiotics","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"7889":"A2072G","7890":"A2073G","7891":"G2075U","7892":"G2461A","7893":"A2517U","7894":"C2069A","7895":"G2461U","7896":"U2518G","7897":"A2586U"},"clinical":{"7889":"A2072G","7890":"A2073G","7891":"G2075U","7892":"G2461A","7893":"A2517U","7894":"C2069A","7895":"G2461U","7896":"U2518G","7897":"A2586U"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"5000"}},"model_sequences":{"sequence":{"4152":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NC_004829.2","fmin":"80510","fmax":"83423","strand":"+","sequence":"ATACATAAGTTACTAAGGGCTTATGGTGGATGCCTTGGCACTAGAAGGCGATGAAGGACGTGCAAACCTGCGAAATGCTACGGGGAGCTGGTTGGAAGCGATAATCCGTAGATGTCCGAATGGGGGAACCTGATTAATAGTGATATTAATTATTTAGATCTGAATACATAGGGTCTAAAAGCAATACGTTGTGAAGTGAAACATCTCAGTAGCAACAGGAAAAGAAATCGAAAGAGATTCCGTGTGTAGTGGCGAGCGAAAGCGGAACAGGCCAAACCAAGATTTATCTTGGGGTTATAGGACTGCAATGTGGACTTTGAACTGATAGGAGAAGTAGTTGAAAAGCTACGCGATAAAGGGTTATAGCCCCGTATCTTAAATTGGTTTAATACCTAGCAGGATCCTGAGTACATCGAGAAACGTTATCTTGATGGAAGTCGCCCAGACCATTGGGCAAGCCTAAATACTAACTAGTGACCGATAGCGTATAGTACCGTGAGGGAAAGGTGAAAAGAACCCAGGGATGGGAGTGAAATAGATTCTGAAGCCATATGCCTACAACGTGTCAGAGCACATTAATGTGTGATGGCGTGCGTTTTGAAGTATGAGCCGGCGAGTTATGATAGCAAGCAGGTTAACCTTTAGAAGGGAAGCCGAAGCGAAAGCGAGTTTGAATAGAGCGAATTAAAGTGTTTGTTATTATAGACCCGAAACGGGTTGAGCTAGTCATGGGCAGGTTGAAGTTAGAGTAACATCTAATGGAGGACCGAACCGACTTTCGTTGAAACGACAGCGGATGACCTGTGACTAGGGGTGAAATTCCAATCGAAATCCGTGATAGCTGGTTCTCGTCGAAATAGTTTTAAGACTAGCGTAAGATCATGATCAACTGGAGGTAGAGCTACTGAATGTATGATGGCGCCGCCTTGGTGTACTGAATACAATTAAACTCCGAATGCCAATTGATTTATTCTTGCAGTCAGACAGTGGGGGATAAGCTTCATTGTCACAAGGGGAAGAGCCCAGATCATTAAATAAGGTCCCTAAAATATGCTAAGTGGAAAAGGTTGTTAAAATACTTAAACAGCAAGGATGTTGGCTTAGAAGCAGCCATCGTTTAAAGAGTGCGTAACAGCTCACTTGTCGAGTGTTTTTGCGCCGAAGATGTAACGGGGCTAAGCATATTACCGAATTTATGGATTATTATTCGTAAGAATGATAGTGGTAGACGAGCGTTGTATATGGGATGAAGTCAAACCGTGAGGATTGGTGGACTGTATACAAGTGAGAATGCCGGTGTAAGTAACGCTTGAGAGTGAGAATCTCTCAAACCGATTGACTAAGGTTTCCTGGACGAGGGTCGTCCTTCCAGGGTTAGTCTGGACCTAAGGCGAGGCAGAAATACGTAGTCGATGGAAGAACAGGTTAATATTCCTGTACAAACAAATAGCTGATGGAGTGACGGAGAAGGTTAATGCATCCCCATTATCGGATTTGGGGTTAAATAAGAAGTCTTAAGGGTTGGCAAATCCGCCTTTTTTAAGGACAACTTATGAATACGAGTGAACGCTTTGCAAGTAGCGAAGATGCATACATCACGCTTCCAAGAAAAGCTTCTAGGGTTAACTATTTGTTTCCAGTACCGAGAACGAACACACGTGGTCAAGGAGAAGATCCTAAGGTTAGCGAGTGAACTATAGCTAAGGAACTCTGCAAATTCATCCCGTAAGTTCGCAAGAAGGGATGCTCAATGTAACAGTTGAGCCGCAGTGAAGAACGAGGGGGGACTGTTTAACTAAAACACAGCTCTATGCTAAATCGCAAGATGATGTATATGGGGTGACACCTGCCCAGTGCTGGAAGGTTAAAGAAGGGTGTTAGAGCAATCAAAGCTCCCGACTGAAGCCCCAGTGAACGGCGGCCGTAACTATAACGGTCCTAAGGTAGCGAAATTCCTTGTCGGGTAAATTCCGTCCCGCTTGAATGGTGTAACCATCTCTTGACTGTCTCGGCTATAGACTCGGTGAAATCCAGGTACGGGTGAAGACACCCGTTAGGCGCAACGGGACGGAAAGACCCCATGAAGCTTTACTGTAACTTAATATTGGGCAGAGTTTAGACATATAGAGAATAGGTGGGAGACTTTGAAGCAACTTCGCTAGGAGTTGTGGAGTCACCAGTGGAATACCACCTTTGTTTAAATTCTTCTCTAACTAGTTGCTGTTATCCAGCAATAGGACAGTGTTAGGCGGGCAGTTTGACTGGGGCGGTCGCCTCCCAAAAGGTAACGGAGGCGTGCAAAGGTACCCTCAGCACGGTTGGAAATCGTGTTAAGAGTGTAATGGTATAAGGGTGCTTGACTGTGAGACTAACAGGTCGAACAGGTAAGAAATTAGGTCATAGTGATCCGGTGGTTCAGTATGGAATGGCCATCGCTCAACGGATAAAAGCTACTCTGGGGATAACAGGCTGATACTGCCCAAGAGTTCACATCGACGGCAGTGTTTGGCACCTCGATGTCGACTCATCTCATCCTCGAGCTGAAGCAGGTTCGAAGGGTTCGGCTGTTCGCCGATTAAAGAGATACGTGAGTTGGGTTCAAACCGTCGCGAGACAGGTTGGTCCCTATCTATTGTGCCCGCAGGAAGATTGAAAAGATTTACTCTTAGTACGAGAGGACCGGAGTGAAGACACCTCTTGTGCTCCAGTTGTAGTGCCAACTGCACCGCTGGGTAGCAACGTGTCGAACGGATAAACGCTGAAAGCATCTAAGTGTGAAACCGACTTTAAGAATAATCTTCCCTTCCAGCAATGGAGTAAGAATCGTTGTAGACTACGACGTTGATAGGCTAAAGGTGTAAGTGCCGCGAGGTATTTAGCTGATTAGTACTAATAATTCGAGGACTTAGATTT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41282","NCBI_taxonomy_name":"Mycoplasma gallisepticum str. R(low)","NCBI_taxonomy_id":"710127"}}}},"ARO_accession":"3004159","ARO_id":"41306","ARO_name":"Mycoplasma gallisepticum 23S rRNA mutation conferring resistance to pleuromutilin antibiotics","ARO_description":"Point mutations in the 23S rRNA (domain V) of Mycoplasma gallisepticum can confer resistance to pleuromutilin antibiotics (tiamulin and valnemulin). The mutants also show cross-resistance to lincomycin, chloramphenicol and florfenicol.","ARO_category":{"41330":{"category_aro_accession":"3004178","category_aro_cvterm_id":"41330","category_aro_name":"23S rRNA with mutation conferring resistance to pleuromutilin antibiotics","category_aro_description":"Point mutations in the 23S rRNA subunit may confer resistance to pleuromutilin antibiotics","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36600":{"category_aro_accession":"3000461","category_aro_cvterm_id":"36600","category_aro_name":"florfenicol","category_aro_description":"Florfenicol is a fluorine derivative of chloramphenicol, where the nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3) and the hydroxyl group (-OH), by a fluorine group (-F). The action mechanism is the same as chloramphenicol's, where the antibiotic binds to the 23S RNA of the 50S subunit of bacterial ribosomes to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin 1A is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"vernamycin B-gamma","category_aro_description":"Vernamycin B-gamma is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37716":{"category_aro_accession":"3001317","category_aro_cvterm_id":"37716","category_aro_name":"pleuromutilin","category_aro_description":"Pleuromutilin is a natural product antibiotic produced by Clitopilus passeckerianus. Related antibiotics of clinical significance, such as tiamulin and retapamulin, are semi-synthetic derivatives of this compound.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2789":{"model_id":"2789","model_name":"Escherichia coli MipA","model_type":"protein knockout model","model_type_id":"40354","model_description":"An AMR detection model for instances where the absence of a protein - due to large-scale insertion elements, large deletions, or other methods of protein knockout - confers clinical resistance to a known antibiotic. These models include reference sequences. Protein knockout models are currently in development.","model_sequences":{"sequence":{"4103":{"protein_sequence":{"accession":"NP_310518","sequence":"MTKLKLLALGVLIATSAGVAHAEGKFSLGAGVGVVEHPYKDYDTDVYPVPVINYEGDNFWFRGLGGGYYLWNDATDKLSITAYWSPLYFKAKDSGDHQMRHLDDRKSTMMAGLSYAHFTQYGYLRTTLAGDTLDNSNGIVWDMAWLYRYTNGGLTVTPGIGVQWNSENQNEYYYGVSRKESARSGLRGYNSNDSWSPYLELSASYNFLGDWSVYGTARYTRLSDEVTDSPIVDKSWTGLISTGITYKF"},"dna_sequence":{"accession":"NC_002695","fmin":"2467330","fmax":"2468077","strand":"+","sequence":"TCAGAATTTGTAGGTGATCCCGGTAGAAATCAGGCCAGTCCAGGATTTATCCACAATCGGGCTGTCAGTAACTTCATCAGACAGACGGGTGTAGCGCGCGGTACCGTAAACACTCCAGTCGCCGAGGAAGTTGTAGCTGGCGCTCAGCTCCAGGTAAGGGCTCCAGCTGTCGTTCGAGTTATAGCCACGCAGACCGCTGCGAGCGGACTCTTTGCGCGATACGCCATAATAGTATTCGTTCTGGTTTTCGCTGTTCCACTGCACACCAATACCCGGAGTCACGGTCAGGCCACCGTTGGTGTAACGATACAACCAGGCCATATCCCAGACGATGCCGTTGCTGTTATCCAGGGTATCGCCAGCCAGGGTGGTACGCAGGTAACCGTACTGGGTAAAGTGAGCATAAGACAGACCAGCCATCATGGTGCTCTTACGGTCATCCAGGTGACGCATTTGGTGATCGCCACTGTCTTTAGCTTTGAAGTAAAGCGGCGACCAGTAAGCGGTAATTGAAAGTTTATCCGTTGCGTCATTCCACAGGTAGTAACCACCACCTAAGCCACGGAACCAGAAGTTATCGCCTTCATAGTTGATTACCGGTACTGGGTAAACATCGGTATCGTAATCTTTATATGGGTGTTCAACGACACCTACGCCTGCGCCCAGGGAAAATTTACCTTCAGCGTGCGCTACGCCTGCAGACGTTGCGATAAGCACTCCAAGTGCCAGAAGTTTGAGTTTGGTCAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36747","NCBI_taxonomy_name":"Escherichia coli O157:H7 str. Sakai","NCBI_taxonomy_id":"386585"}}}},"ARO_accession":"3004127","ARO_id":"41253","ARO_name":"Escherichia coli mipA","ARO_description":"MltA-interacting protein (mipA), is an antibiotic resistance-related outer membrane protein. Deletion of mipA increases kanamycin, nalidixic acid and streptomycin resistance.","ARO_category":{"41444":{"category_aro_accession":"3004280","category_aro_cvterm_id":"41444","category_aro_name":"MipA-interacting Protein","category_aro_description":"The MltA-interacting Protein (MipA) family consists mainly of homologs to MipA and OmpV proteins. Proteins of this family, are predicted to form a \u00df-barrel.","category_aro_class_name":"AMR Gene Family"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36383":{"category_aro_accession":"3000244","category_aro_cvterm_id":"36383","category_aro_name":"reduced permeability to antibiotic","category_aro_description":"Reduction in permeability to antibiotic, generally through reduced production of porins, can provide resistance.","category_aro_class_name":"Resistance Mechanism"},"40429":{"category_aro_accession":"3003764","category_aro_cvterm_id":"40429","category_aro_name":"resistance by absence","category_aro_description":"Mechanism of antibiotic resistance conferred by deletion of gene (usually a porin)","category_aro_class_name":"Resistance Mechanism"}}},"2785":{"model_id":"2785","model_name":"Klebsiella pneumoniae OmpK37","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"4406":{"protein_sequence":{"accession":"CAA09666.1","sequence":"MKRKVLALVIPALLAAGAAHAAEIYNKDGNKLDLYGKVDGLHYFSSDSKKDGDQTYLRFGFKGETQINDILTGYGQWEYNVQANNTETSSDQAWTRLAFAGIKVGDYGSFDYGRNYGVLYDVEGWTDILPEFGGDSYTYADNFMAGRANGVATYRNSDFFGLVEGLNFALQYQGKNEGQNAQDINVGTNNRSSDSDVRFDNGDGFGLSTSYDFGMGISAAAAYTSSDRTNDQMTQTNARGDKAEAWTAGLKYDANDIYLATMYSETRNMTPYGNDGVANKTQNFEVTAQYQFDFGLRPAISYLQSKGKDLYNNGRYADKDLVKYMDVGATYYFNRNMSTYVDYKINLLDGNDKFYEDNGISTDNIVALGLVYQF"},"dna_sequence":{"accession":"AJ011502.1","fmin":"300","fmax":"1425","strand":"+","sequence":"ATGAAAAGAAAAGTACTGGCCCTCGTTATTCCGGCTTTATTAGCCGCCGGTGCCGCGCATGCGGCGGAAATTTATAATAAAGACGGGAATAAATTAGATCTCTATGGCAAGGTAGATGGTCTGCATTATTTCTCCAGCGACTCGAAAAAAGACGGCGATCAAACTTATTTACGTTTTGGCTTTAAAGGCGAAACCCAGATCAACGATATTCTTACCGGCTATGGCCAGTGGGAATATAACGTTCAGGCCAACAACACCGAGACCTCCAGCGATCAGGCGTGGACCCGTCTGGCATTCGCCGGTATCAAAGTGGGCGATTACGGCTCCTTCGACTACGGTCGTAACTACGGCGTGCTGTACGACGTTGAAGGCTGGACCGATATTCTGCCGGAGTTCGGCGGCGACTCCTACACCTATGCGGATAACTTTATGGCAGGCCGCGCCAACGGCGTCGCAACCTACCGCAACAGCGATTTTTTCGGTCTGGTGGAGGGTCTGAACTTCGCCCTGCAGTATCAGGGTAAAAACGAAGGCCAGAACGCGCAGGATATCAACGTCGGCACCAATAACCGCAGCAGCGACAGCGATGTTCGCTTCGACAATGGCGATGGTTTCGGCCTCTCTACTTCCTACGACTTCGGCATGGGCATCAGCGCGGCGGCAGCTTACACCTCGTCTGACCGTACTAACGATCAGATGACCCAGACCAACGCGCGCGGCGATAAAGCGGAAGCCTGGACCGCCGGCCTGAAGTACGACGCCAACGATATCTACCTGGCGACCATGTACTCTGAAACCCGCAATATGACCCCGTACGGCAATGACGGCGTGGCCAATAAAACACAAAACTTCGAAGTCACCGCGCAGTATCAGTTCGACTTCGGCCTGCGTCCGGCCATCTCCTACCTGCAGTCCAAAGGCAAAGATCTGTACAATAACGGCCGCTATGCCGATAAAGATCTGGTCAAATATATGGACGTTGGCGCGACCTATTACTTCAACCGTAATATGTCCACCTATGTTGATTACAAAATCAACCTGCTGGATGGTAACGACAAATTCTACGAAGACAACGGTATCTCTACCGATAACATCGTCGCCCTGGGCCTGGTTTACCAGTTCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3004122","ARO_id":"41247","ARO_name":"Klebsiella pneumoniae OmpK37","ARO_description":"Klebsiella pneumoniae outer membrane porin protein. Is preferentially detected in porin-deficient strains. Functional characterization of this new porin revealed a narrower pore than those of porins OmpK35 and OmpK36, which did not allow penetration by certain \u03b2-lactams. Also, when a resistant strain expresses porin OmpK37 is less susceptible to cefotaxime and cefoxitin than when it is expressing either OmpK36 or OmpK35.","ARO_category":{"41445":{"category_aro_accession":"3004281","category_aro_cvterm_id":"41445","category_aro_name":"General Bacterial Porin with reduced permeability to beta-lactams","category_aro_description":"These are GBPs that are associated with decreased susceptibility to beta-lactams either through mutations in the porin protein, absence of the porin protein, or expression of the porin protein.","category_aro_class_name":"AMR Gene Family"},"35927":{"category_aro_accession":"0000008","category_aro_cvterm_id":"35927","category_aro_name":"cefoxitin","category_aro_description":"Cefoxitin is a cephamycin antibiotic often grouped with the second generation cephalosporins. Cefoxitin is bactericidal and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. Cefoxitin's 7-alpha-methoxy group and 3' leaving group make it a poor substrate for most beta-lactamases.","category_aro_class_name":"Antibiotic"},"36989":{"category_aro_accession":"3000645","category_aro_cvterm_id":"36989","category_aro_name":"cefotaxime","category_aro_description":"Cefotaxime is a semisynthetic cephalosporin taken parenterally. It is resistant to most beta-lactamases and active against Gram-negative rods and cocci due to its aminothiazoyl and methoximino functional groups.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"40360":{"category_aro_accession":"3003706","category_aro_cvterm_id":"40360","category_aro_name":"penem","category_aro_description":"Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur.","category_aro_class_name":"Drug Class"},"36383":{"category_aro_accession":"3000244","category_aro_cvterm_id":"36383","category_aro_name":"reduced permeability to antibiotic","category_aro_description":"Reduction in permeability to antibiotic, generally through reduced production of porins, can provide resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2791":{"model_id":"2791","model_name":"Streptococcus mitis CdsA with mutation conferring daptomycin resistance","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"7791":"D222N"},"clinical":{"7791":"D222N"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"475"}},"model_sequences":{"sequence":{"4106":{"protein_sequence":{"accession":"AQA08261.1","sequence":"MTKDLQKRTLFAVLALAIFLPVLFAGGLLLQIGIGLLAMLGVHELLHMKGLKTMTIEGALTLFATFALTVPLENYLTFLPVDGNVVAYSVLITIMLGTTVFSKNYTIEDAAFPIAVSFYVGFGFNALLDARVAGFDKVLLALFIVWATDSAAYLTGMNFGKHKLAPRVSPNKSIEGFVGGILGAVLITVIFMLVDSTVALPYGIYRMSLFAAFFSVAGQFGDLIESAMKRHFGVKDSGKFIPGHGGVLDRFDSMLIVFPMMHLFGLF"},"dna_sequence":{"accession":"CP019562.1","fmin":"220125","fmax":"220929","strand":"+","sequence":"ATGACCAAGGATTTACAAAAGAGAACATTGTTTGCGGTATTGGCCCTGGCGATTTTCCTTCCAGTCTTGTTTGCGGGAGGGCTCTTGTTGCAGATAGGGATTGGCTTGTTAGCGATGCTAGGCGTCCATGAACTCTTGCATATGAAGGGACTAAAGACTATGACCATTGAGGGTGCTTTGACTCTTTTTGCGACCTTCGCTCTCACAGTTCCTTTAGAAAATTACCTAACTTTTTTGCCTGTTGATGGAAATGTGGTTGCCTATAGTGTTCTGATTACCATAATGCTAGGGACGACCGTTTTCAGTAAAAACTATACGATTGAAGATGCCGCTTTTCCAATTGCTGTGAGTTTTTATGTTGGTTTTGGCTTCAATGCCTTACTAGATGCTCGGGTGGCAGGTTTTGACAAGGTACTTTTGGCCCTTTTTATCGTTTGGGCGACAGATAGCGCAGCCTACCTGACAGGGATGAATTTTGGTAAACATAAGTTGGCTCCGAGAGTTTCTCCTAATAAGAGTATTGAGGGCTTTGTCGGTGGTATTCTAGGTGCGGTACTGATAACAGTGATTTTCATGTTAGTGGACAGCACAGTTGCTCTTCCTTATGGGATTTATAGAATGAGTCTCTTTGCTGCCTTCTTCAGTGTGGCCGGTCAGTTTGGTGACTTGATTGAAAGTGCCATGAAACGCCATTTCGGTGTCAAGGATTCTGGCAAATTTATCCCTGGACATGGCGGTGTGTTGGATCGCTTTGACAGCATGCTGATTGTGTTTCCAATGATGCACTTATTTGGCCTGTTTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39527","NCBI_taxonomy_name":"Streptococcus oralis","NCBI_taxonomy_id":"1303"}}}},"ARO_accession":"3004097","ARO_id":"41205","ARO_name":"Streptococcus mitis CdsA with mutation conferring daptomycin resistance","ARO_description":"CdsA is a phosphatidate cytidylyltransferase which plays a role in the production of membrane phosphatidylglycerol and cardiolipin.","ARO_category":{"41204":{"category_aro_accession":"3004096","category_aro_cvterm_id":"41204","category_aro_name":"daptomycin resistant CdsA","category_aro_description":"Mutations to the CdsA phosphatidate cytidylyltransferase conferring resistance to daptomycin.","category_aro_class_name":"AMR Gene Family"},"35985":{"category_aro_accession":"0000068","category_aro_cvterm_id":"35985","category_aro_name":"daptomycin","category_aro_description":"Daptomycin is a novel lipopeptide antibiotic used in the treatment of certain infections caused by Gram-positive organisms. Daptomycin interferes with the bacterial cell membrane, reducing membrane potential and inhibiting cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2792":{"model_id":"2792","model_name":"Moraxella catarrhalis 23S rRNA with mutation conferring resistance to macrolide antibiotics","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"7794":"A2330T"},"clinical":{"7794":"A2330T"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"5000"}},"model_sequences":{"sequence":{"4107":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NG_041971.1","fmin":"0","fmax":"3156","strand":"+","sequence":"TCAAGTAATGAAGTGCACATGGTGGATGCCTTGGCAGTCAGAGGCGATGAAAGACGTGATAGCCTGCGATAAGCGTCGGTGAGGTGGCAATATCCTGTGACCCGGCGATTTCTGAATGGGGAAACCCAACCAACATAAGTTGGTTATTACACAGTTTACTGTGTAAGGCAAACCGGGAGAAGTGAAACATCTCAGTACCCCGAGGAAAAGACATCAAATGAGATTCCGTAAGTAGCGGCGAGCGAACACGGAGGAGCCGATCAATTTTACAGTAGCAAAATGGCGTGGGAAAGCCAACCATAGTAGGTGATAGTCCTGTATGCGAAACTGTTTAAGCGACATATTAAGTAGGGCGGAACACGAGAAATTCTGTCTGAAGATGGGGGGACCATCCTCCAAGGCTAAATACTCCTGACTGACCGATAGTGAACCAGTACCGTGAGGGAAAGGCGAAAAGAACCCCTGTTAGGGGAGTGAAATAGAACCTGAAACCGTGTGCATACAAGCAGTCGGAGCCCGACCACTTAATCGTTTTGAGGATAACAATGAATTTTTACTACGTCTATGTCATACAAAACGTGGATAATCATGATGAGTTTTATGTTGGTTTTACCACCAGTTTAAAACAAAGAATTGATGACCATAATAATGGCACAACTTACTCAACCAGAGCAAGAACATGGCGTATTGTTTATTGTGAAGCCTACATTAATGAACAAGTGGCAAGAAAACGAGAGCGAACCATAAAAAATAATGGTCGTATGAGAACTTTCTTGATGAATCGTGTCAAATCACAATTTGACAATCAGAACGATTAAGTGGTCGGGTGACGGCGTACCTTTTGTATAATGGGTCAGCGACTTATATTCTGTAGCAAGGTTAACCGAATAGGGGAGCCGTAGGGAAACCGAGTCTTAATAGGGCGAATGAGTTGCAGGGTATAGACCCGAAACCGAGTGATCTATCCATGAGCAGGTTGAAAGTGCCGTAACAGGCACCGGAGGACCGAACCCACTGTCGTTGAAAAGCCAGGGGATGACTTGTGGATAGGGGTGAAAGGCTAATCAAACTCGGTGATAGCTGGTTCTCCCCGAAAGCTATTTAGGTAGCGCCTCGGACGAATACCATTGGGGGTAGAGCACTGTTTCGGCTAGGGGGTCACACCGACTTACCAAACCGATGCAAACTCCGAATACCGATGAGTAATATCCGGGAGACAGACGGCGGGTGCTAACGTCCGTCGTCAAGAGGGAAACAACCCAGACCGCCAGCTAAGGCCCCAAATTCCTAGTTAAGTGGGAAACGATGTGGGAAGGCACAGACAGCTAGGAGGTTGGCTTAGAAGCAGCCACCCTTTAAAGAAAGCGTAATAGCTCACTAGTCGAGTCGGCCTGCGCGGAAGATGTAACGGGGCTCAAACTAGGAGCCGAAGCTGCGGATTTAATTGTTTCAATTAAGTGGTAGGGGAGCGTTGTGTAAGCCTGTGAAGGTGCACTGTAAGGTGTGCTGGAGGTATCACAAGAGCGAATGCTGACGTGAGTAACGACAAAACGGGTGAAAAGCCCGTTCGCCGGAAGACCAAGGGTTCCAGTCCAACGTTAATCGGGGCTGGGTGAGTCGACCCCTAAGGCGAGGCCGAAAGGCGTAGTCGATGGGAAATCGGTTAATATTCCGATACTTGTTTATGATGCGATGGAGGGACGGAGAAGGTTATGCCAGCCTGGCGATGGTTGTCCAGGTGGAAGGATGTAGTTAGACTGAGTAGGCAAATCCGCTCGGTTATTAATGAGATCTGATAGCAAGCCAGTTTACTGGCAAAGTGGCAAATACCCTGCTTCCAGGAAAAGCTTCTAAGCGATAGTCATAAACGAATCGTACCCGAAACCGACACAGGTGGTCAGGTAGAGAATACCAAGGCGCTTGAGAGAACTCTGCTGAAGGAACTAGGCAAAATGGTACCGTAACTTCGGGAGAAGGTACGCTGCCGATGGTGATAAGACTTGCTCTTTGAGCTGTTGGCAGTCGCAGATACCAGGCTGCTGCAACTGTTTATTAAAAACACAGCACTCTGCAAACACGAAAGTGGACGTATAGGGTGTGATGCCTGCCCGGTGCTGGAAGGTTAATTGATGGGGTTAGCGTAAGCGAAGCTCTTGATCGAAGCCCCAGTAAACGGCGGCCGTAACTATAACGGTCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCATAATGATGGCAGCGCTGTCTCCAGCAGAGACTCAGTGAAATCGAAATCGCAGTGAAGATGCTGTGTACCCGCGGCTAGACGGAAAGACCCCGTGAACCTTTACTACAGCTTTACATTGAACTTTGACCTAACTTGTGTAGGATAGGTGGGAGGCTTTGAAGCAGATACGCCAGTATTTGTGGAGCCAACCTTGAAATACCACCCTGGTTATGTTGGGGTTCTAACTTAGGATCAACAAATCCAAGGACAATGTATGGTGGGTAGTTTGACTGGGGCGGTCTCCTCCTAAAGAGTAACGGAGGAGTACGAAGGTGCGCTCAGAACGGTCGGAAATCGTTCAAAGAGTATAAAGGCAAAAGCGCGCTTAACTGCGAGACCCACAAGTCGAGCAGGTACGAAAGTAGGTCTTAGTGATCCGGTGGTTCTGTATGGAAGGGCCATCGCTCAACGGATAAAAGGTACTCTGGGGATAACAGGCTGATACCGCCCAAGAGTTCATATCGACGGCGGTGTTTGGCACCTCGATGTCGGCTCATCTCATCCTGGGGCTGAAGCAGGTCCCAAGGGTATGGCTGTTCGCCATTTAAAGAGGTACGCGAGCTGGGTTTAGAACGTCGTGAGACAGTTCGGTCCCTATCTACCGTGGGCGTTGGAAATTTGAGAGGATCTGCTCCTAGTACGAGAGGACCAGAGTGGACGAACCTCTGGTGTTTCGGTTGTCACGCCAGTGGCATTGCCGAGTAGCTATGTTCGGATGGGATAACCGCTGAAAGCATCTAAGCGGGAAGCCCACCTCAAGATAAGATTTCCCTAAAGAGCCGTTGTAGACGACGACGTTGATAGGTTGGGTGTGGAAGTGTAGTGATACATGTAGCTAACCAATACTAATTGCTCGTTTGGCTTGACCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41250","NCBI_taxonomy_name":"Moraxella catarrhalis","NCBI_taxonomy_id":"480"}}}},"ARO_accession":"3004138","ARO_id":"41265","ARO_name":"Moraxella catarrhalis 23S rRNA with mutation conferring resistance to macrolide antibiotics","ARO_description":"Point mutations in the 23S ribosomal RNA subunit of M. catarrhalis shown clinically to confer resistance to macrolide class antibiotics.","ARO_category":{"41251":{"category_aro_accession":"3004125","category_aro_cvterm_id":"41251","category_aro_name":"23S rRNA with mutation conferring resistance to macrolide antibiotics","category_aro_description":"Nucleotide point mutations in the 23S rRNA subunit may confer resistance to macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36600":{"category_aro_accession":"3000461","category_aro_cvterm_id":"36600","category_aro_name":"florfenicol","category_aro_description":"Florfenicol is a fluorine derivative of chloramphenicol, where the nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3) and the hydroxyl group (-OH), by a fluorine group (-F). The action mechanism is the same as chloramphenicol's, where the antibiotic binds to the 23S RNA of the 50S subunit of bacterial ribosomes to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin 1A is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"vernamycin B-gamma","category_aro_description":"Vernamycin B-gamma is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2793":{"model_id":"2793","model_name":"Chlamydomonas reinhardtii 23S rRNA with mutation conferring resistance to Erythromycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"2000"},"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"7817":"G1628G","7818":"G1627A"},"clinical":{"7817":"G1628G","7818":"G1627A"}}},"model_sequences":{"sequence":{"4139":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NC_005353.1","fmin":"148590","fmax":"151993","strand":"-","sequence":"AAGGTCAAAATCAAACGGCCTTTAGTATATCTCGGCTAAAGCCATTGCTGACTGTACACCTGATACCTATATAACGGCTTGTCTAGCCGCGGCCTTAGAGAGCACTCATCTTGAGTTTAGCTTCCTACTTAGATGCTTTCAGCAGTTATCTATCCATGCGTAGCTACCCAGCGTTTCCCATTGGAATGAGAACTGGTACACAATTGGCATGTCCTTTCAGGTCCTCTCGTACTATGAAAGGCTACTCTCAATGCTCTAACGCCTACACCGGATATGGACCAAACTGTCTCACGCATGAAATTTTAAAGCCGAATAAAACTTGCGGTCTTTAAAACTAACCCCTTTACTTTCGTAAAGGCATGGACTATGTCTTCATCCTGCTACTGTTAATGGCAGGAGTCGGCGTATTATACTTTCCCACTCTCGAGAAAATATCCTATAAATCGAGCAACAATAAATAAATTGTATGTAAACATTCTTTTAGAGATTGGCTAAATTTATAAAGTCTCTACGGGGACGATTTCTTTTTTTCACTTAAACTGTCTAGCACAGCACGAACGGTTTCAGAAGTTGTTTTACGCGTCTTCGAATCATTCAGAGCTGCAATTTGATCCACCCATGTACAAACTTCTAAGAATTTGTCCGGGGATTCTTTTGCTGACGGAAGCCGCCAAATAATTTTTAAAACTAAATTTGCTTGTTTTTGTTTTAGTTTTAGAAAAGGTTGTAGTTGTGTTAAAAAATTATGCAAAGGCTTGATTTCGCTTAGAATATAATCCGAAACGCTACCCCTATCTCTTACATAACCAACCCCAATTTCATCCACTAATTTGTCTAAAAACCAACGTCTCTGTGTCTTTTGCGTGACTTGGAACGCGAGTGATAGCTGATGCTTAAATTTATAAGACTGATTAGGCTTAATTTGAGCGATTATGCTACCGTCACCGTCTACAAACCCTGCTAAGTAGAGTAAGAACTCTTTATTATATTTTGTATTCATAAGATGTTTTATTTAATTTATTGAATTATTAAACCAAAAAGAAATGGTCTTCCCTCGGCGTTGCCATCTATTGCCCACGAATGTGGTTTATGCGACAGTTTGTACTTAAAACAATAGGAAGGTTTCACCGATATAAGCCGATACTTTGCTTACATTACTGCAAGCACACGCAGTGTTATTTACGTTTTGAACCCAGCTCACGTACCACTTTAATGGGCGAACAGCCCAACCCTTCGGACCTACTACAGACCGAGGATGTGATGAGCCGACATCGAGGTGCCAAACCTTCCCGTCGATGTGAACTCTTGGGGAAGATCAGCCTGTTATCCCTAGAGTAACTTTTATCCGTTGAGCGACGGCCCTTCCACGCGGCACCGTCGGATCACTAAGGCCGGCTTTCGCCCCTGCTCGACTTGTAGGTCTTGCAGTCAAGCTCCCTTTTGCCTTTACACTCAATGTCTGATTTCCGTCCAGACTGAGGGAACCTTTGCACGCCTCCGTTACCTTTTAGGAGGCATTCGCCCCAAATAAACTGCCCACCTGAAACTGTCAAGGGTCCTGATTCAAGGATCCCCATTAGGATTCTAGCTCTTCCAGAGTGGTCTCTCAATGACGGCTCTAATTACCCCGGAAGGTAATCTTCATAGCCTCCCACCTAGGCTGCGCAAGAAAAGCCCAAACCCAATTCCAAGATACAGTCAAGCTTCATAGGGTCTTTCTGTCCAGGTGTAGGTAGTCCGCATCTTCACGGGACAAGTCTATTTCACCGAGCCTCTCTCCGAGACAGCGCCCAGATCGTTACGCCTTTCGTGCAGGTCGAAACTTACTCGACAATGAATTTCGCTACCTTAGGATCGTTATAGTTACGACCGCCGTTCACCGGGGCTTCGGTCGTCAGCTTTTTTCTTACGAAATAACCAACTTCCTTAACCTTCCGGCACTGGGCAGGCGTCAGCCCCCATATATTGTCTTACGACTTTGCGGAGACCTGTGTTTTTGGTAAACAGTCGCCTGGGCCTGGTCACTGCGACCCACCTTGTTACGGATGGGTGCCCCTTCTTCCGAAGTTACGGGGCCAGTTTGCCGAGTTCCTTAGAGAGAGTTCTCTCGCGCCCCTTGGTATTCTCTACCAACCTACCTGTGTCGGTTTCAGGTACAGGTCATTAAATTATAAAGATGTATGAGCTTTTCTTGGAAGTATGACATCACTAGCTACTCGACGGCGAACCATCAAATAGGGATCACGTCTCCACTCAAGATAGCTTTTTTTCTATCTCTCAACGTCTAAACGCTTCCACTGCAATCCAAAAACAGTTCTAGCTTAGCCTCCTTCGTCCCTCAGATCATAATTTAACTCGTACAGGAATATTAACCTGTTTTCCATCGACGACGCCGTTTGGCCTAGTCTTAGGTCCTGACTAACCCCCCATGGACGAACCTAGTGGAGGAACCCTTAGGTTTTCGGGGCATTGGATTCTCACCAATGTTTTCGTTACTCAAGCCGACATTCTCACTTCCGCTTCGTCCATCCCCACTTACGTGAAAACTTCACCCGAGAGCGGAACGCTCCCCTACCTATAATTTATATAATAAATTATATCACAGCTTCGGCAGGTCACTTAGTCCCGGCCATTATCGGCGCAAGAACGCTTTACCAGTGAGCTATTACGCACTCTTTGAAGGGTGGCTGCTTCTAAGCAAACCTCCTGGTTGTTTCAGCATTCTCACATCCTTTTCCACTTAGTGACCATTTAGGGGCCTTAGCTGGTGATCTGGGCTGTTTCCCTCTTGACAATGAAGCTTATCCCCCACTGTCTCACTGGTTTACGGAAGACATGTCTTGTATTCTGAGTTTGCCACGACTTGGTACCGCTTTCGCAGCCCGCATCGAAACAGTAGCTTTACCCCAAGACAGTTCATCGTTACCGCTGCGCCTCAACGCATTTCGGGGAGATCCAGCTAGCTCCGAGTTCGATTGGAATTTCTCCCCTATTCACAGCTCATCCGCCGATTTTTCAACATCGGTCGGTTCGGACCTCCACTTGGTGTTACCCAAGCTTCATCCTGGCCATGAATAGATCACCCGGGTTCGGGTCCATAAGAAGTGACCATTTGCGCCCTATTCAGACTCGCTTTCGCTTGGGCTCCGGATTTTACTCCTTAACCCAGCCACTCCCTATAAGTCGCCGGCTCATTCTTCAACAGGCACGCGGTCACAAGCATTCTTGCTCCCACTGCTTGTCAGCATACGGTTTCATGTTCTATTTCACTCCCCAACAGGGGTTCTTTTCACCTTTCCCTCGTGGTACTATTTCGCTATCGGTCACTCAGGAGTATTTAGCCTTACGAGGTGGTCCTCGCTGATTCACACGGGATTTCACGTGCCCCATGCTACTCGGGATT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40815","NCBI_taxonomy_name":"Chlamydomonas reinhardtii","NCBI_taxonomy_id":"3055"}}}},"ARO_accession":"3004132","ARO_id":"41259","ARO_name":"Chlamydomonas reinhardtii 23S rRNA with mutation conferring resistance to erythromycin","ARO_description":"Point mutation in 23S rRNA of C. reinhardtii chloroplast shown clinically to confer resistance to Erythromycin, a macrolide antibiotic.","ARO_category":{"41251":{"category_aro_accession":"3004125","category_aro_cvterm_id":"41251","category_aro_name":"23S rRNA with mutation conferring resistance to macrolide antibiotics","category_aro_description":"Nucleotide point mutations in the 23S rRNA subunit may confer resistance to macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36600":{"category_aro_accession":"3000461","category_aro_cvterm_id":"36600","category_aro_name":"florfenicol","category_aro_description":"Florfenicol is a fluorine derivative of chloramphenicol, where the nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3) and the hydroxyl group (-OH), by a fluorine group (-F). The action mechanism is the same as chloramphenicol's, where the antibiotic binds to the 23S RNA of the 50S subunit of bacterial ribosomes to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin 1A is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"vernamycin B-gamma","category_aro_description":"Vernamycin B-gamma is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2794":{"model_id":"2794","model_name":"Helicobacter pylori 23S rRNA with mutation conferring resistance to clarithromycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"2000"},"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"7905":"A2146C","7906":"A2146G","7907":"A2146U","7908":"A2147G","7909":"A2147C"},"clinical":{"7905":"A2146C","7906":"A2146G","7907":"A2146U","7908":"A2147G","7909":"A2147C"}}},"model_sequences":{"sequence":{"4113":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"AB162858.1","fmin":"0","fmax":"2975","strand":"+","sequence":"AAGGCAGTGGTAGCGCTGAAGAATATTCGTGCAATTGTCGTTATTCATTATAAAAGGGCAGGTTTTAAAGGATATTTTAAAATTTAAAACAAGCTTTTAAGAGCAGATGGCGGATGCCTTGCCAAAGAGAGGCGATGAAGGACGTACTAGACTGCGATAAGCTATGCGGAGCTGTCAAGGAGCTTTGATGCGTAGATGTCCGAATGGGGCAACCCAACTAATAGAGATATTAGTTACTCTAATTTAGAGAGCGAACCTAGTGAAGTGAAACATCTCAGTAACTAGAGGAAAAGAAATCAACGAGATTCCCTAAGTAGTGGCGAGCGAACGGGGAAAAGGGCAAACCGAGTGCTTGCATTCGGGGTTGAGGACTGCAACATCCAAGAGAACGCTTTAGCAGAGTTACCTGGAAAGGTAAGCCATAGAAAGTGATAGCCTTGTATGCGACAAGGCGTTCTTAGGTAGCAGGATCCAGAGTAGGCCAGGACACGAGAAATCCAGGTTGAAGCTGGGGAGACCACTCTCCAACCCTAAATACTACTCTTTGAGCGATAGCGAACAAGTACCGTGAGGGAAAGGTGAAAAGAACCGCAGTGAGCGGAGTGAAATAGAACCTGAAACCATCTGCTTACAATCATTCAGAGCCCTATGATTTATCAGGGTGATGGACTGCCTTTTGCATAATGATCCTGCGAGTTGTGGTATCTGGCAAGGTTAAGCGGATGCGAAGCCGTAGCGAAAGCGAGTCTTAATAGGGCGGTTTAAGTCAGATGCTGCAGACCCGAAGCTAAGTGATCTATCCATGGCCAAGTTGAAACGCGTGTAATAGCGCGTGGAGGACTGAACTCGTACCCATTGAAACGGGTTGGGATGAGCTGTGGATAGGGGTGAAAGGTCAAACAAACTTAGTGATAGCTGGTTCTCTTCGAAATATATTTAGGTATAGCCTCAAGTGATAATAAAAGGGGGTAGAGCTCTGATTGGGCTAGGGCTGCTCGCCGCGGTACCAAACCCTATCAAACTTCGAATACCTTTTATCGTATCTTGGGAGTCAGGCGGTGGGTGATAAAATCAATCGTCAAAAGGGGAACAACCCAGACTACCAAATAAGGTCCCTAAGTTCTATTCTGAGTGGAAAAAGATGTGTGGCTACTCAAACAACCAGGAGGTTGGCTTAGAAGCAGCCATCCTTTAAAGAAAGCGTAACAGCTCACTGGTCTAGTGGTCATGCGCTGAAAATATAACGGGGCTAAGATAGACACCGAATTTGTAGATTGTGTTAAACACAGTGGTAGAAGAGCGTTCATACCAGCGTTGAAGGTATACCGGTAAGGAGTGCTGGAGCGGTATGAAGTGAGCATGCAGGAATGAGTAACGATAAGATATATGAGAATTGTATCCGCCGTAAATCTAAGGTTTCCTACGCGATGGTCGTCATCGTAGGGTTAGTCGGGTCCTAAGCCGAGTCCGAAAGGGGTAGGTGATGGCAAATTGGTTAATATTCCAATACCGACTCATGGAGCGTGATGGGGGGACGCATAGGGTTAAGCGAGCTAGCTGATGGAAGTGCTAGTCTAAGGGCGTAGATTGGAGGGAAGGCAAATCCACCTCTGTATTTGAAACCCAAACAGGCTCTTTGAGTCCTTTCAGGACAAAGGGAGAATCGCTGATACCGTCGTGCCAAGAAAAGCCTCTAAGCATATCCATAGTCGTCCGTACCGCAAACCGACACAGGTAGATGAGATGAGTATTCTAAGGCGCGTGAAAGAACTCTGGTTAAGGAACTCTGCAAACTAGCACCGTAAGTTCGCGATAAGGTGTGCCGCAGCAATGCGGTCTCAGCAAAGAGTCCCTCCCGACTGTTTACCAAAAACACAGCACTTTGCCAACTCGTAAGAGGAAGTATAAGGTGTGACGCCTGCCCGGTGCTCGAAGGTTAAGAGGATGCGTCAGTCGCAAGATGAAGCGTTGAATTGAAGCCCGAGTAAACGGCGGCCGTAACTATAACGGTCCTAAGGTAGCGAAATTCCTTGTCGGTTAAATACCGACCTGCATGAATGGCGTAACGAGATGGGAGCTGTCTCAACCAGAGATTCAGTGAAATTGTAGTGGAGGTGAAAATTCCTCCTACCCGCGGCAAGACGGAAAGACCCCGTGGACCTTTACTACAACTTAGCACTGCTAACGGGAATATCATGTGCAGGATAGGTGGGAGGCTTTGAAGTAAGGGCTTTGGCTCTTATGGAGCCATCCTTGAGATACCACCCTTGATGTTTCTGTTAGCTAACTGGCCTGTGTTATCCACAGGCAGGACAATGCTTGGTGGGTAGTTTGACTGGGGCGGTCGCCTCCTAAAAAGTAACGGAGGCTTGCAAAGGTTGGCTCATTGCGGTTGGAAATCGCAAGTTGAGTGTAATGGCACAAGCCAGCCTGACTGTAAGACATACAAGTCAAGCAGAGACGAAAGTCGGTCATAGTGATCCGGTGGTTCTGTGTGGAAGGGCCATCGCTCAAAGGATAAAAGGTACCCCGGGGATAACAGGCTGATCTCCCCCAAGAGCTCACATCGACGGGGAGGTTTGGCACCTCGATGTCGGCTCATCGCATCCTGGGGCTGGAGCAGGTCCCAAGGGTATGGCTGTTCGCCATTTAAAGCGGTACGCGAGCTGGGTTCAGAACGTCGTGAGACAGTTCGGTCCCTATCTGCCGTGGGCGTAGGAAAGTTGAGGAGAGCTGTCCCTAGTACGAGAGGACCGGGATGGACGTGTCACTGGTGCACCAGTTGTTCTGCCAAGAGCATCGCTGGGTAGCTACACACGGATGTGATAACTGCTGAAAGCATCTAAGCAGGAAGCCAACTCCAAGATAAACTTTCCCTGAAGCTCGCACAAAGACTATGTGCTTGATAGGGTAGATGTGTAAGCGCAGTAATGCGTTTAGCTGACTACTACTAATAGAGCGTTTGGCTTGTTTTT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36906","NCBI_taxonomy_name":"Helicobacter pylori","NCBI_taxonomy_id":"210"}}}},"ARO_accession":"3004134","ARO_id":"41261","ARO_name":"Helicobacter pylori 23S rRNA with mutation conferring resistance to clarithromycin","ARO_description":"Point mutations in Helicobacter pylori shown to confer resistance to clarithromycin, a macrolide antibiotic","ARO_category":{"41251":{"category_aro_accession":"3004125","category_aro_cvterm_id":"41251","category_aro_name":"23S rRNA with mutation conferring resistance to macrolide antibiotics","category_aro_description":"Nucleotide point mutations in the 23S rRNA subunit may confer resistance to macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36600":{"category_aro_accession":"3000461","category_aro_cvterm_id":"36600","category_aro_name":"florfenicol","category_aro_description":"Florfenicol is a fluorine derivative of chloramphenicol, where the nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3) and the hydroxyl group (-OH), by a fluorine group (-F). The action mechanism is the same as chloramphenicol's, where the antibiotic binds to the 23S RNA of the 50S subunit of bacterial ribosomes to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin 1A is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"vernamycin B-gamma","category_aro_description":"Vernamycin B-gamma is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2795":{"model_id":"2795","model_name":"MCR-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"4121":{"protein_sequence":{"accession":"ASF81896.1","sequence":"MPSLIKIKIVPLMFFLALYFAFMLNWRGVLHFYEILYKLEDFKFGFAISLPILLVAALNFVFVPFSIRYLIKPFFALLIALSAIVSYTMMKYRVLFDQNMIQNIFETNQNEALAYLSLPIIVWVTIAGFIPAILLFFVEIEYEEKWFKGILTRALSMFASLIVIAVIAALYYQDYVSVGRNNSNLQREIVPANFVNSTVKYVYNRYLAEPIPFTTLGDDAKRDTNQSKPTLMFLVVGETARGKNFSMNGYEKDTNPFTSKSGGVISFNDVRSCGTATAVSVPCMFSNMGRKEFDDNRARNSEGLLDVLQKTGISIFWKENDGGCKGVCDRVPNIEIEPKDHPKFCDKNTCYDEVVLQDLDSEIAQMKGDKLVGFHLIGSHGPTYYKRYPDAHRQFTPDCPRSDIENCTDEELTNTYDNTIRYTDFVIGEMIAKLKTYEDKYNTALLYVSDHGESLGALGLYLHGTPYQFAPDDQTRVPMQVWMSPGFTKEKGVDMACLQQKAADTRYSHDNIFSSVLGIWDVKTSVYEKGLDIFSQCRNVQ"},"dna_sequence":{"accession":"KY924928.1","fmin":"161133","fmax":"162759","strand":"+","sequence":"ATGCCTTCCCTTATAAAAATAAAAATTGTTCCGCTTATGTTCTTTTTGGCACTGTATTTTGCATTTATGCTGAACTGGCGTGGAGTTCTCCATTTTTACGAAATCCTTTACAAATTAGAAGATTTTAAGTTTGGTTTCGCCATTTCATTACCAATATTGCTTGTTGCAGCGCTTAACTTTGTATTTGTTCCATTTTCGATACGGTATTTAATAAAGCCTTTTTTTGCACTTCTTATCGCACTTAGTGCAATCGTTAGTTACACAATGATGAAGTATAGAGTCTTGTTTGATCAAAACATGATTCAGAATATTTTTGAAACCAATCAAAATGAGGCGTTAGCATATTTAAGCTTACCAATTATAGTATGGGTTACTATTGCTGGTTTTATCCCTGCCATTTTACTTTTCTTTGTTGAAATTGAATATGAGGAAAAATGGTTCAAAGGGATTCTAACTCGTGCCCTATCGATGTTTGCATCACTTATAGTGATTGCGGTTATTGCAGCACTATACTATCAAGATTATGTGTCAGTGGGGCGCAACAATTCAAACCTCCAGCGTGAGATTGTTCCAGCCAATTTCGTTAATAGTACCGTTAAATACGTTTACAATCGTTATCTTGCTGAACCAATCCCATTTACAACTTTAGGTGATGATGCAAAACGGGATACTAATCAAAGTAAGCCCACGTTGATGTTTCTGGTCGTTGGTGAAACCGCTCGTGGTAAAAATTTCTCGATGAATGGCTATGAGAAAGACACCAATCCATTTACCAGTAAATCTGGTGGCGTGATCTCCTTTAATGATGTTCGTTCGTGTGGGACTGCAACCGCTGTATCCGTCCCCTGCATGTTCTCCAATATGGGGAGAAAGGAGTTTGATGATAATCGCGCTCGCAATAGCGAGGGCCTGCTAGATGTGTTGCAAAAAACGGGGATCTCCATTTTTTGGAAGGAGAACGATGGAGGCTGCAAAGGCGTCTGCGACCGAGTACCTAACATCGAAATCGAACCAAAGGATCACCCTAAGTTCTGCGATAAAAACACATGCTATGACGAGGTTGTCCTTCAAGACCTCGATAGTGAAATTGCTCAAATGAAAGGGGATAAGCTGGTTGGCTTCCACCTGATAGGTAGCCATGGCCCAACCTACTACAAGCGCTACCCTGATGCTCATCGTCAGTTCACCCCTGACTGTCCACGCAGTGATATTGAAAACTGCACAGATGAAGAGCTCACCAACACCTATGACAACACCATCCGCTACACCGATTTCGTGATTGGAGAGATGATTGCCAAGTTGAAAACCTACGAAGATAAGTACAACACCGCGTTGCTCTACGTCTCCGATCATGGTGAATCACTGGGAGCATTAGGGCTTTACCTACACGGTACACCGTACCAGTTTGCACCGGATGATCAGACCCGTGTTCCTATGCAGGTGTGGATGTCACCTGGATTTACCAAAGAGAAAGGCGTTGATATGGCGTGTTTGCAGCAGAAAGCCGCTGATACTCGTTACTCACACGATAATATTTTCTCATCTGTATTGGGTATCTGGGACGTCAAAACATCAGTTTACGAAAAGGGTCTAGATATTTTCAGTCAATGTCGTAATGTTCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004139","ARO_id":"41267","ARO_name":"MCR-3","ARO_description":"MCR-3 is a plasmid-borne phosphoethanolamine transferase that interferes with binding of colistin to the cell membrane via addition of phosphoethanolamine to lipid A, resulting reduction in negative charge of the cell membrane. Originally described by Yin et al. 2017, from a porcine Escherichia coli plasmid pWJ1.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2796":{"model_id":"2796","model_name":"OprZ","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"4132":{"protein_sequence":{"accession":"EGP45230","sequence":"MKPVAMTLLALALSGCSLAPTHERPAAPVPAQYDTPAQPGQAAAPQDWRAYFNDPALQAWIAAALANNRDLRVAALRIEEARALYGVQQSERLPAIDASGEFSRGRATEPGQPRTPVSNRYRAAVGITAFELDFFGRVRSLSDAALARYLASEEAHRAATLALVAETATAYFNQRSLAEQLRLTDDTLALRETTLKLTQRRYDAGLETAIGLRTAQMLVESSRATRAELTREASLARHALGLLAGDFALPLGVDPTPLESQSLTPLAAGLPSELLTRRPDLRQAEQALRAANADIGAARAAFFPSVQLTTDIGTTADRFSDLFSGGTGGWSFAPRLTLPIFNAGRNRANLSLAETRKHIAVAQYEGSIQAAFRDVADALSARDALRDQIEAQRKVRDADRERQRLAERRYARGVANYLEMLEAQRSLFESEQEFIRLQQRRLVNAVDLYKALGGWDDGSSPAS"},"dna_sequence":{"accession":"AFRQ01000061.1","fmin":"22598","fmax":"23990","strand":"-","sequence":"TCAGGACGCCGGCGATGAGCCGTCGTCCCAGCCGCCCAGCGCCTTGTACAGATCCACCGCGTTGACCAGCCGGCGCTGCTGCAGCCGGATGAATTCCTGTTCCGACTCGAACAGGCTGCGCTGGGCCTCCAGCATCTCCAGGTAGTTCGCCACCCCGCGCGCATAACGCCGCTCGGCCAGCCGCTGGCGTTCGCGGTCGGCGTCGCGCACCTTGCGCTGGGCCTCGATCTGGTCGCGCAGCGCGTCGCGCGCCGACAGCGCGTCGGCCACGTCGCGGAACGCGGCCTGGATGCTGCCTTCGTACTGGGCCACCGCGATGTGCTTGCGGGTCTCGGCCAGCGACAGGTTGGCGCGGTTGCGGCCGGCGTTGAAGATCGGCAGCGTCAGGCGCGGCGCGAAGCTCCAGCCGCCGGTGCCGCCGCTGAACAGATCCGAGAAGCGGTCGGCGGTGGTGCCGATGTCCGTGGTCAGCTGCACCGACGGGAAGAACGCCGCGCGCGCCGCGCCGATGTCGGCGTTGGCCGCGCGCAGCGCCTGCTCTGCCTGGCGCAGGTCGGGGCGGCGCGTCAGCAGTTCGGACGGCAGCCCCGCCGCCAGCGGCGTCAGGCTCTGGCTTTCCAGCGGCGTAGGGTCGACGCCGAGCGGCAGCGCGAAATCGCCGGCCAGCAGGCCCAGCGCGTGCCGCGCCAGGCTGGCCTCGCGGGTCAGCTCGGCGCGCGTGGCGCGCGAGCTTTCCACCAGCATCTGCGCGGTGCGCAGGCCGATGGCGGTTTCCAGCCCGGCGTCGTAGCGGCGCTGGGTCAGCTTGAGCGTGGTCTCGCGCAGCGCCAGCGTGTCGTCGGTCAGGCGCAGTTGCTCGGCCAGCGAACGCTGGTTGAAGTAGGCCGTCGCCGTCTCCGCCACCAGCGCCAGCGTGGCGGCGCGGTGCGCTTCCTCGCTGGCCAGGTAGCGCGCCAGCGCGGCGTCCGACAGGCTCCGCACCCGGCCGAAGAAGTCCAGCTCGAACGCGGTGATGCCGACGGCCGCGCGGTAGCGGTTGGACACCGGCGTGCGCGGCTGGCCCGGCTCGGTCGCGCGGCCGCGGCTGAATTCGCCGCTGGCGTCGATGGCCGGCAGGCGTTCGGATTGCTGCACGCCGTACAGCGCGCGCGCTTCCTCGATGCGCAGCGCCGCCACGCGCAGGTCGCGGTTGTTGGCCAGCGCGGCCGCGATCCAGGCCTGCAGCGCCGGATCGTTGAAATAGGCGCGCCAGTCCTGCGGCGCGGCGGCCTGGCCGGGCTGCGCCGGCGTGTCGTACTGCGCCGGCACCGGCGCCGCGGGGCGCTCATGGGTGGGCGCCAGCGAGCAGCCGGACAATGCCAGCGCCAGCAGGGTCATTGCCACGGGTTTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41271","NCBI_taxonomy_name":"Achromobacter insuavis AXX-A","NCBI_taxonomy_id":"1003200"}}}},"ARO_accession":"3004142","ARO_id":"41270","ARO_name":"OprZ","ARO_description":"OprZ is the outer membrane component of the AxyXY-OprZ efflux pump system in Achromobacter spp.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35976":{"category_aro_accession":"0000059","category_aro_cvterm_id":"35976","category_aro_name":"cefepime","category_aro_description":"Cefepime (INN) is a fourth-generation cephalosporin antibiotic developed in 1994. It contains an aminothiazolyl group that decreases its affinity with beta-lactamases. Cefepime shows high binding affinity with penicillin-binding proteins and has an extended spectrum of activity against Gram-positive and Gram-negative bacteria, with greater activity against both Gram-negative and Gram-positive organisms than third-generation agents.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2797":{"model_id":"2797","model_name":"AxyX","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4133":{"protein_sequence":{"accession":"EGP45232.2","sequence":"MTHRVPFRTLAFASVLVLVSACSKQEAPEAAKAPAEVGVIVARATPTAVASELPGRLEPYREAEVRARVAGIVTRRLYEEGQEVTRGTPLFQIDPAPLQAAYDSEAAALARAQANLSAAADKLRRYADLVSDRAISERDHAESVAQERQARAEVALAKANLQSARLRLEYARVTSPIDGRARRALVTEGALVGEGQATPLTVVQQLDPIYVNFSQPAAEVMQLQKQIRAGALQGVAPDKMRVRLLLPDGSEYGQGGTLSFADLAVDPGTDNVTMRALFANPGRELLPGMYVRVRLEQAVNRDTFLVPRNALLRNADGAHVLVAGDDGELRSVAVTAHRLLGPNWVVTEGLAGGERVVVENAAQLAPGQKIKPVERTAPSAPVATAGNNEKR"},"dna_sequence":{"accession":"AFRQ01000061.1","fmin":"27130","fmax":"28306","strand":"-","sequence":"TTACCTTTTTTCGTTATTTCCCGCGGTCGCCACGGGCGCGCTCGGCGCGGTCCGCTCGACCGGTTTGATTTTCTGGCCGGGGGCCAGCTGCGCGGCGTTTTCCACCACCACGCGTTCGCCGCCCGCCAGGCCCTCGGTGACGACCCAGTTCGGGCCCAGCAGCCGGTGCGCGGTCACCGCCACGCTGCGCAGCTCGCCGTCGTCGCCGGCCACCAGCACGTGCGCGCCGTCGGCGTTGCGCAGCAGGGCGTTGCGCGGCACCAGGAAGGTGTCGCGGTTGACCGCCTGCTCCAGCCGCACCCGCACGTACATGCCCGGCAACAGTTCGCGGCCCGGGTTGGCGAACAGCGCGCGCATGGTCACGTTGTCGGTGCCGGGGTCGACCGCCAGGTCGGCGAACGACAGCGTGCCGCCCTGGCCATACTCGGAGCCGTCCGGCAGCAGCAGGCGCACCCGCATCTTGTCGGGCGCGACGCCTTGCAGGGCGCCGGCGCGGATCTGCTTCTGCAACTGCATGACCTCGGCCGCGGGTTGCGAGAAGTTGACGTAGATCGGGTCGAGTTGCTGCACCACCGTCAGCGGCGTGGCCTGGCCTTCGCCCACCAGCGCGCCCTCGGTGACCAGCGCGCGGCGCGCGCGGCCGTCGATCGGCGAGGTGACGCGGGCGTATTCCAGCCGCAGCCTGGCGCTCTGCAGGTTGGCCTTGGCCAACGCCACTTCGGCGCGGGCCTGGCGTTCCTGGGCCACGCTCTCGGCGTGGTCGCGTTCGCTGATGGCGCGGTCCGACACCAGGTCGGCGTAGCGGCGCAGCTTGTCGGCGGCGGCCGACAGGTTGGCCTGGGCACGCGCCAACGCGGCCGCCTCGGAATCGTAGGCCGCCTGCAGCGGCGCCGGATCGATCTGGAACAGCGGCGTGCCGCGCGTCACTTCCTGGCCTTCTTCATACAGGCGGCGGGTGACGATGCCGGCCACGCGGGCGCGGACCTCGGCCTCGCGATAGGGCTCCAGCCGGCCGGGCAGCTCGCTGGCGACGGCGGTGGGCGTGGCCCTGGCCACGATGACGCCGACTTCGGCGGGGGCCTTGGCGGCTTCGGGGGCTTCCTGCTTCGAGCATGCGGAAACGAGAACCAGTACGGATGCGAATGCGAGCGTTCTGAAGGGAACTCGGTGCGTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41271","NCBI_taxonomy_name":"Achromobacter insuavis AXX-A","NCBI_taxonomy_id":"1003200"}}}},"ARO_accession":"3004143","ARO_id":"41272","ARO_name":"AxyX","ARO_description":"AxyX is the inner membrane transporter of the AxyXY-OprZ efflux pump system in Achromobacter spp.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35976":{"category_aro_accession":"0000059","category_aro_cvterm_id":"35976","category_aro_name":"cefepime","category_aro_description":"Cefepime (INN) is a fourth-generation cephalosporin antibiotic developed in 1994. It contains an aminothiazolyl group that decreases its affinity with beta-lactamases. Cefepime shows high binding affinity with penicillin-binding proteins and has an extended spectrum of activity against Gram-positive and Gram-negative bacteria, with greater activity against both Gram-negative and Gram-positive organisms than third-generation agents.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2798":{"model_id":"2798","model_name":"AxyZ","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"7819":"V29G"},"clinical":{"7819":"V29G"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"4134":{"protein_sequence":{"accession":"EGP45233.1","sequence":"MARKTKEESQRTRDRILDAAEHVFLSKGVASTTMSDIADFAGVSRGAVYGHYKNKIDVCIAMCDRALGEAVSLTRVSTDGEALEALYASMRQYVQIYAEEGSVQRVLEILYLKCERSDENAPLLRRRDLWERHALRTSEKLLRAAVSREDLPPALDVRLSNVYLHSLVEGVFGTICWSDRLKGDIWPRVERMLRAAIDTLRLSPQLRLPQAA"},"dna_sequence":{"accession":"AFRQ01000061.1","fmin":"28538","fmax":"29177","strand":"+","sequence":"ATGGCCCGCAAGACGAAAGAAGAATCCCAACGCACCCGCGACCGCATCCTGGACGCCGCCGAACACGTGTTCCTGTCCAAGGGCGTGGCCAGCACCACCATGAGCGATATCGCTGATTTCGCGGGCGTGTCCCGGGGCGCCGTCTACGGCCATTACAAGAACAAGATCGATGTCTGCATCGCCATGTGCGACCGGGCCCTGGGGGAAGCGGTGTCGCTGACCCGCGTGTCGACCGACGGCGAGGCGCTGGAAGCGCTCTACGCGTCGATGCGCCAGTACGTGCAGATCTACGCCGAGGAAGGCTCGGTGCAGCGTGTGCTGGAAATCCTCTACCTGAAATGCGAGCGCAGCGACGAGAACGCGCCGCTCCTGCGCCGCCGCGACCTGTGGGAGCGCCACGCCCTGCGCACTTCCGAAAAGTTGCTGCGCGCCGCCGTCAGCCGCGAGGACCTGCCGCCCGCGCTGGACGTGCGTCTGTCCAATGTCTACCTGCACTCCCTGGTCGAGGGCGTGTTTGGCACCATCTGCTGGTCCGATCGCCTCAAGGGCGATATCTGGCCGCGCGTCGAGCGCATGCTCCGCGCCGCCATCGACACGCTGCGCCTGTCGCCGCAACTGCGGTTGCCACAGGCCGCCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41271","NCBI_taxonomy_name":"Achromobacter insuavis AXX-A","NCBI_taxonomy_id":"1003200"}}}},"ARO_accession":"3004145","ARO_id":"41274","ARO_name":"AxyZ","ARO_description":"AxyZ is a transcriptional regulator of the AxyXY-OprZ efflux pump system.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35976":{"category_aro_accession":"0000059","category_aro_cvterm_id":"35976","category_aro_name":"cefepime","category_aro_description":"Cefepime (INN) is a fourth-generation cephalosporin antibiotic developed in 1994. It contains an aminothiazolyl group that decreases its affinity with beta-lactamases. Cefepime shows high binding affinity with penicillin-binding proteins and has an extended spectrum of activity against Gram-positive and Gram-negative bacteria, with greater activity against both Gram-negative and Gram-positive organisms than third-generation agents.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2799":{"model_id":"2799","model_name":"AxyY","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1700"}},"model_sequences":{"sequence":{"4135":{"protein_sequence":{"accession":"EGP45231.1","sequence":"MARFFIDRPVFAWVISLLIALVGLLSIRALPVAQYPDIAPPVVNIGASYPGASAKVVEEAVTAIIEREMNGAPGLMYTSSSSDSTGWASINLTFKQGTNPDIAAVEVQNRLKAVEPRLPESVRRDGVRVEKAADNIQLVVSLKSDGSLDDMQLGELAASNVLQALRRVEGVGKVQSFGAEAAMRIWPDPAKLTALSLTPGDIVSALRSHNARVTIGELGNQAVPKDAPLNASIVAGESLHTPEQFANIPLRALPDGATLRLKDVARVELGGTDYMYLSRVNGLTGTGLGIKLAPGSNAVETTRRIRETMRELAQYFPPGVTWDIPYETSTFVEISIKKVLMTLLEAVALVFCVMYLFMQNLRATLIPTLVVPVALLGTLGVMLGLGYSINVLTMFGMVLAIGILVDDAIVVVENVERIMAEEGLSPHDATVKAMGQISGAIVGITVVLVSVFVPMAFFDGAVGNIYRQFAVTLAVSIAFSAFLALSLTPALCASLLKPVPAGHHEKRGFFGWFNRAFARLTTRYTARVAGVLARPVRFGLAYALVIGVAALLFARLPSSFLPDEDQGSFMAMVILPQGSPQAETMAVVKDVERYMMEHEPVQYVYSVNGFSQYGSGPNSAMFFVTLKDWKERRDASQHVDAVVKRINKAFADRKNLMVFALNSPPLPDLGSTSGFDFRLQDRGGLGYEALTQARQKLLAKAAEHPALTDVVFAGQEEAPQLQLRVDRDKAQAMGVPIDEINTALAVMYGSDYIGDFMLNGQVRRVMVQADGKRRVDVDDISRLHVRNLQGQMVPLSAFATLTWSMGPPQLNRYNGFPSFTINGSAARGHSSGEAMRAMETLAAELPRGIGFDWSGQSYEERLSGNQAPVLFALSVLIVFLALAALYESWSIPLAVILVVPLGVIGALLGVTVRGMPNDIYFKVGLIATIGLSAKNAILIVEVAKDLVRDGQGILSATLEAARLRLRPIVMTSLAFGVGVLPLALATGAASGAQAAIGTGVLGGIITATVLAVFLVPLFFLIVGRMVGMRARPARPDGREPLETTP"},"dna_sequence":{"accession":"AFRQ01000061.1","fmin":"23986","fmax":"27124","strand":"-","sequence":"TCATGGCGTCGTCTCCAGCGGTTCGCGGCCGTCGGGGCGCGCGGGGCGGGCGCGCATGCCGACCATGCGTCCCACGATGAGAAAGAACAGCGGCACCAGGAACACCGCCAGCACGGTCGCCGTGATGATCCCGCCCAGCACGCCGGTGCCGATGGCGGCCTGCGCGCCCGAGGCGGCGCCAGTGGCCAGCGCCAGCGGCAGCACGCCCACGCCAAAGGCCAGCGAGGTCATCACGATCGGCCGCAGCCGCAGCCGCGCCGCTTCCAGCGTGGCGGACAGGATGCCCTGGCCGTCGCGCACCAGGTCCTTGGCCACTTCCACGATCAGGATCGCGTTCTTGGCGGACAGGCCGATGGTGGCGATCAGGCCGACCTTGAAGTAGATGTCGTTGGGCATGCCGCGCACGGTCACCCCCAGCAGCGCGCCGATCACGCCCAGCGGCACCACCAGGATCACCGCCAGCGGAATCGACCAGCTTTCATACAGCGCCGCCAGCGCCAGGAACACGATCAGCACCGACAGCGCGAACAGCACCGGCGCCTGGTTGCCGGACAGCCGCTCTTCGTACGATTGGCCCGACCAGTCGAAGCCGATGCCGCGCGGCAGCTCGGCCGCCAGCGTCTCCATGGCGCGCATGGCCTCGCCGCTGCTGTGGCCGCGCGCCGCCGAGCCGTTGATGGTGAACGACGGGAAGCCGTTGTAGCGGTTCAGCTGCGGCGGCCCCATCGACCACGTCAGCGTGGCGAACGCCGACAGCGGCACCATCTGGCCCTGCAGGTTGCGCACGTGCAGGCGCGAGATGTCGTCCACGTCCACGCGGCGCTTGCCGTCGGCCTGCACCATCACGCGCCGAACCTGGCCGTTGAGCATGAAGTCGCCGATGTAGTCCGAGCCGTACATCACAGCCAGCGCGGTGTTGATCTCGTCGATCGGCACGCCCATGGCCTGCGCCTTGTCGCGGTCGACGCGCAGTTGCAGCTGCGGCGCCTCTTCCTGGCCGGCGAACACCACGTCCGTCAGCGCGGGATGCTCGGCCGCCTTGGCCAGCAGCTTCTGGCGCGCCTGCGTCAGGGCTTCGTAGCCGAGGCCGCCGCGATCCTGCAGCCGGAAGTCGAAGCCCGAGGTCGAGCCCAGGTCAGGCAGCGGCGGCGAGTTCAGCGCGAACACCATCAGGTTCTTGCGATCCGCGAACGCCTTGTTGATGCGCTTGACCACCGCGTCCACGTGTTGCGAGGCATCGCGGCGTTCCTTCCAGTCCTTCAGCGTGACGAAGAACATGGCGGAGTTCGGGCCGCTGCCGTACTGGCTGAAGCCGTTGACCGAATACACGTACTGCACCGGCTCGTGCTCCATCATGTAGCGTTCGACGTCCTTGACCACCGCCATGGTCTCGGCCTGCGGCGAGCCCTGCGGCAGGATCACCATGGCCATGAAGCTGCCCTGGTCCTCGTCCGGCAGGAACGACGATGGCAGCCGCGCGAACAGCAACGCCGCCACGCCGATCACCAGCGCATAGGCCAGGCCGAAGCGTACCGGCCGCGCCAGCACGCCGGCCACCCGCGCCGTATAGCGCGTGGTCAGGCGCGCGAAGGCGCGGTTGAACCAGCCGAAGAAGCCGCGCTTCTCGTGGTGGCCGGCCGGGACGGGTTTGAGCAGGCTGGCGCACAGCGCCGGCGTCAGCGACAGCGCCAGGAAGGCCGAGAAGGCGATCGACACCGCCAGCGTCACGGCGAACTGGCGGTAGATGTTGCCCACCGCGCCGTCGAAGAACGCCATCGGCACGAACACCGACACCAGCACCACGGTGATGCCGACGATGGCGCCGCTGATCTGGCCCATGGCCTTGACCGTGGCGTCATGCGGCGACAGGCCTTCCTCGGCCATGATGCGCTCGACGTTCTCGACCACCACGATGGCGTCGTCCACCAGGATGCCGATGGCCAGCACCATGCCGAACATCGTCAGCACGTTGATCGAATAGCCCAGCCCCAGCATCACCCCCAGCGTGCCCAGCAGCGCCACCGGCACCACCAGGGTCGGGATCAGCGTGGCGCGCAGGTTCTGCATGAACAGGTACATCACGCAGAACACCAGCGCCACCGCCTCCAGCAGCGTCATCAGGACCTTCTTGATCGAGATCTCGACGAAGGTGGAGGTCTCGTACGGAATGTCCCAGGTCACGCCCGGCGGGAAGTATTGCGCCAGCTCGCGCATGGTCTCGCGGATGCGGCGGGTGGTTTCGACGGCGTTGGAGCCGGGCGCCAGCTTGATGCCCAGGCCGGTGCCGGTCAGGCCGTTGACGCGCGACAGGTACATGTAGTCGGTGCCGCCCAGCTCCACCCGCGCCACGTCCTTCAGGCGCAGCGTGGCGCCGTCCGGCAGCGCCCGCAGCGGGATGTTGGCGAACTGTTCCGGCGTGTGCAGCGATTCGCCCGCCACGATGCTGGCGTTCAGCGGCGCGTCCTTGGGCACGGCCTGGTTGCCCAGTTCGCCGATGGTGACGCGCGCGTTGTGGCTGCGCAGCGCCGAGACGATGTCGCCCGGCGTCAGCGACAGGGCGGTGAGCTTGGCCGGGTCCGGCCAGATGCGCATCGCCGCTTCCGCGCCGAACGACTGCACCTTGCCCACGCCTTCGACCCGCCGCAGCGCCTGCAGCACATTGGAGGCGGCCAGCTCGCCCAGTTGCATGTCGTCCAGGCTGCCGTCCGACTTCAACGACACCACCAGCTGGATGTTGTCGGCCGCCTTTTCCACGCGCACGCCATCGCGCCGCACCGATTCGGGCAGGCGAGGCTCGACCGCCTTCAGGCGGTTCTGCACTTCCACCGCCGCGATGTCGGGGTTGGTGCCCTGCTTGAAGGTCAGGTTGATGCTGGCCCAGCCGGTCGAATCGCTGCTGGACGAGGTGTACATCAGGCCCGGGGCGCCGTTCATCTCGCGTTCGATGATGGCGGTGACGGCTTCCTCGACCACCTTGGCCGAGGCGCCGGGATAGCTGGCGCCGATGTTGACGACGGGCGGAGCGATGTCCGGATACTGCGCCACCGGCAGCGCGCGGATCGACAACAGGCCGACCAGCGCGATGAGCAGCGAGATCACCCACGCGAAAACGGGGCGATCGATAAAGAAACGCGCCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41271","NCBI_taxonomy_name":"Achromobacter insuavis AXX-A","NCBI_taxonomy_id":"1003200"}}}},"ARO_accession":"3004144","ARO_id":"41273","ARO_name":"AxyY","ARO_description":"AxyY is the periplasmic adaptor protein of the AxyXY-OprZ efflux pump system in Achromobacter spp.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35976":{"category_aro_accession":"0000059","category_aro_cvterm_id":"35976","category_aro_name":"cefepime","category_aro_description":"Cefepime (INN) is a fourth-generation cephalosporin antibiotic developed in 1994. It contains an aminothiazolyl group that decreases its affinity with beta-lactamases. Cefepime shows high binding affinity with penicillin-binding proteins and has an extended spectrum of activity against Gram-positive and Gram-negative bacteria, with greater activity against both Gram-negative and Gram-positive organisms than third-generation agents.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2800":{"model_id":"2800","model_name":"cfrC","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4138":{"protein_sequence":{"accession":"YP_001255356.1","sequence":"MKQTKTKYGKMKQIASNLKLPDYRYEQLTKAIFHQRIDNFHDMHILPKALRIALVNEFGKNVSSVTPIFSQDSKQAQKLLFELTDGERIEAVGLKYKQGWESFCISSQCGCSFGCRFCATGSAGFKRNLTADEITDQLLYFYFNDHRLNSISFMGMGEAFANPELFDAVKILTDQNLFGLSQRRITISTIGIIPGIQRLTKEFPQVNLAFSLHSPFESQRSDLMPINKRFPLNEVMKTLDEHIIHTGRRVFIAYIMLEGINDSKEHAEAIIGLLRNRGSWEHLYHIDLIPYNSTDKTTFKFQSSSAIKQFCSTLKKASISATVRTQFGSEISAACGQLCYENEL"},"dna_sequence":{"accession":"NC_009495.1","fmin":"3035492","fmax":"3036527","strand":"-","sequence":"TCATAATTCATTTTCATAACACAATTGTCCGCAAGCAGCACTAATTTCAGAACCAAATTGTGTTCTAACAGTTGCACTAATACTAGCTTTCTTTAGTGTACTGCAAAATTGCTTGATAGCACTTGAAGATTGAAATTTAAAAGTTGTTTTGTCCGTAGAATTATAAGGTATCAAATCAATGTGATATAAATGCTCCCATGAACCACGATTTCTCAATAAACCTATAATTGCCTCTGCATGTTCTTTCGAATCATTAATTCCTTCAAGCATAATATAAGCAATAAACACTCGTCGTCCCGTATGAATGATATGTTCATCTAATGTCTTCATTACCTCATTCAATGGAAATCTTTTATTTATAGGCATTAAATCGCTTCGTTGACTTTCAAATGGTGAATGAAGTGAAAAAGCCAGATTCACTTGTGGAAATTCTTTAGTCAGTCTTTGAATTCCTGGTATAATGCCAATTGTTGAAATAGTAATTCTTCGTTGACTTAACCCAAATAAATTTTGATCAGTTAAAATTTTTACTGCATCAAATAACTCTGGATTTGCAAAAGCCTCACCCATTCCCATAAATGAAATACTATTCAATCTATGGTCATTAAAATAGAAATAAAGTAATTGGTCAGTTATCTCATCAGCAGTAAGATTGCGTTTAAATCCAGCACTTCCCGTTGCACAAAAACGACATCCAAAACTACAACCACATTGGGAAGAAATACAAAACGATTCCCACCCCTGTTTATACTTTAGTCCAACGGCTTCTATTCTTTCTCCATCAGTCAATTCAAATAACAACTTTTGAGCTTGTTTAGAATCTTGTGAAAAAATAGGTGTTACACTAGATACATTCTTTCCAAACTCATTTACTAAAGCTATCCTTAACGCTTTTGGTAGTATATGCATATCATGAAAATTATCTATTCTTTGATGAAAAATAGCTTTTGTAAGCTGTTCGTATCTATAATCAGGTAATTTTAAATTCGATGCTATTTGTTTCATTTTTCCATATTTCGTTTTTGTCTGTTTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41276","NCBI_taxonomy_name":"Clostridium botulinum A str. ATCC 3502","NCBI_taxonomy_id":"413999"}}}},"ARO_accession":"3004146","ARO_id":"41275","ARO_name":"cfrC","ARO_description":"Acfr-like 23S rRNA methyltransferase shown to confer resistance to linezolid and phenicol antibiotics, including florfenicol and chloramphenicol, in Clostridium.","ARO_category":{"36341":{"category_aro_accession":"3000202","category_aro_cvterm_id":"36341","category_aro_name":"Cfr 23S ribosomal RNA methyltransferase","category_aro_description":"Cfr genes produce enzymes which catalyze the methylation of the 23S rRNA subunit at position 8 of adenine-2503. Methylation of 23S rRNA at this site confers resistance to some classes of antibiotics, including streptogramins, chloramphenicols, florfenicols, linezolids and clindamycin.","category_aro_class_name":"AMR Gene Family"},"35989":{"category_aro_accession":"0000072","category_aro_cvterm_id":"35989","category_aro_name":"linezolid","category_aro_description":"Linezolid is a synthetic antibiotic used for the treatment of serious infections caused by Gram-positive bacteria that are resistant to several other antibiotics. It inhibits protein synthesis by binding to domain V of the 23S rRNA of the 50S subunit of bacterial ribosomes.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36600":{"category_aro_accession":"3000461","category_aro_cvterm_id":"36600","category_aro_name":"florfenicol","category_aro_description":"Florfenicol is a fluorine derivative of chloramphenicol, where the nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3) and the hydroxyl group (-OH), by a fluorine group (-F). The action mechanism is the same as chloramphenicol's, where the antibiotic binds to the 23S RNA of the 50S subunit of bacterial ribosomes to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"36218":{"category_aro_accession":"3000079","category_aro_cvterm_id":"36218","category_aro_name":"oxazolidinone antibiotic","category_aro_description":"Oxazolidinones are a class of synthetic antibiotics discovered the the 1980's.  They inhibit protein synthesis by binding to domain V of the 23S rRNA of the 50S subunit of bacterial ribosomes.  Linezolid is the only member of this class currently in clinical use.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2806":{"model_id":"2806","model_name":"Escherichia coli 23S rRNA with mutation conferring resistance to clindamycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"7898":"G2032A"},"clinical":{"7898":"G2032A"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"5000"}},"model_sequences":{"sequence":{"4153":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"AE014075.1","fmin":"237159","fmax":"240063","strand":"+","sequence":"GGTTAAGCGACTAAGCGTACACGGTGGATGCCCTGGCAGTCAGAGGCGATGAAGGACGTGCTAATCTGCGATAAGCGTCGGTAAGGTGATATGAACCGTTATAACCGGCGATTTCCGAATGGGGAAACCCAGTGTGTTTCGACACACTATCATTAACTGAATCCATAGGTTAATGAGGCGAACCGGGGGAACTGAAACATCTAAGTACCCCGAGGAAAAGAAATCAACCGAGATTCCCCCAGTAGCGGCGAGCGAACGGGGAGGAGCCCAGAGCCTGAATCAGTGTGTGTGTTAGTGGAAGCGTCTGGAAAGGCGCGCGATACAGGGTGACAGCCCCGTACACAAAAATGCACATGCTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGGGGGACCATCCTCCAAGGCTAAATACTCCTGACTGACCGATAGTGAACCAGTACCGTGAGGGAAAGGCGAAAAGAACCCCGGCGAGGGGAGTGAAAAAGAACCTGAAACCGTGTACGTACAAGCAGTGGGAGCATGCTTAGGCGTGTGACTGCGTACCTTTTGTATAATGGGTCAGCGACTTATATTCTGTAGCAAGGTTAACCGAATAGGGGAGCCGAAGGGAAACCGAGTCTTAACTGGGCGTTAAGTTGCAGGGTATAGACCCGAAACCCGGTGATCTAGCCATGGGCAGGTTGAAGGTTGGGTAACACTAACTGGAGGACCGAACCGACTAATGTTGAAAAATTAGCGGATGACTTGTGGCTGGGGGTGAAAGGCCAATCAAACCGGGAGATAGCTGGTTCTCCCCGAAAGCTATTTAGGTAGCGCCTCGTGAACTCATCTCCGGGGGTAGAGCACTGTTTCGGCAAGGGGGTCATCCCGACTTACCAACCCGATGCAAACTGCGAATACCGGAGAATGTTATCACGGGAGACACACGGCGGGTGCTAACGTCCGTCGNGAAGAGGGAAACAACCCAGACCGCCAGCTAAGGTCCCAAAGTCATGGTTAAGTGGGAAACGATGTGGGAAGGCCCAGACAGCCAGGATGTTGGCTTAGAAGCAGCCATCATTTAAAGAAAGCGTAATAGCTCACTGGTCGAGTCGGCCTGCGCGGAAGATGTAACGGGGCTAAACCATGCACCGAAGCTGCGGCAGCGACGCTTATGCGTTGTTGGGTAGGGGAGCGTTCTGTAAGCCTGTGAAGGTGTACTGTGAGGTATGCTGGAGGTATCAGAAGTGCGAATGCTGACATAAGTAACGATAAAGCGGGTGAAAAGCCCGCTCGCCGGAAGACCAAGGGTTCCTGTCCAACGTTAATCGGGGCAGGGTGAGTCGACCCCTAAGGCGAGGCCGAAAGGCGTAGTCGATGGGAAACAGGTTAATATTCCTGTACTTGGTGTTACTGCGAAGGGGGGACGGAGAAGGCTATGTTGGCCGGGCGACGGTTGTCCCGGTTTAAGCGTGTAGGCTGGTTTTCCAGGCAAATCCGGAAAATCAAGGCTGAGGCGTGATGACGAGGCACTACGGTGCTGAAGCAACAAATGCCCTGCTTCCAGGAAAAGCCTCTAAGCATCAGGTAACATCAAATCGTACCCCAAACCGACACAGGTGGTCAGGTAGAGAATACCAAGGCGCTTGAGAGAACTCGGGTGAAGGAACTAGGCAAAATGGTGCCGTAACTTCGGGAGAAGGCACGCTGATATGTAGGTGAAGCGACTTGCTCGTGGAGCTGAAATCAGTCGAAGATACCAGCTGGCTGCAACTGTTTATTAAAAACACAGCACTGTGCAAACACGAAAGTGGACGTATACGGTGTGACGCCTGCCCGGTGCCGGAAGGTTAATTGATGGGGTTAGCGCAAGCGAAGCTCTTGATCGAAGCCCCGGTAAACGGCGGCCGTAACTATAACGGTCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAATGATGGCCAGGCTGTCTCCACCCGAGACTCAGTGAAATTGAACTCGCTGTGAAGATGCAGTGTACCCGCGGCAAGACGGAAAGACCCCGTGAACCTTTACTATAGCTTGACACTGAACATTGAGCCTTGATGTGTAGGATAGGTGGGAGGCTTTGAAGTGTGGACGCCAGTCTGCATGGAGCCGACCTTGAAATACCACCCTTTAATGTTTGATGTTCTAACGTTGACCCGTAATCCGGGTTGCGGACAGTGTCTGGTGGGTAGTTTGACTGGGGCGGTCTCCTCCTAAAGAGTAACGGAGGAGCACGAAGGTTGGCTAATCCTGGTCGGACATCAGGAGGTTAGTGCAATGGCATAAGCCAGCTTGACTGCGAGCGTGACGGCGCGAGCAGGTGCGAAAGCAGGTCATAGTGATCCGGTGGTTCTGAATGGAAGGGCCATCGCTCAACGGATAAAAGGTACTCCGGGGATAACAGGCTGATACCGCCCAAGAGTTCATATCGACGGCGGTGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGGGCTGAAGTAGGTCCCAAGGGTATGGCTGTTCGCCATTTAAAGTGGTACGCGAGCTGGGTTTAGAACGTCGTGAGACAGTTCGGTCCCTATCTGCCGTGGGCGCTGGAGAACTGAGGGGGGCTGCTCCTAGTACGAGAGGACCGGAGTGGACGCATCACTGGTGTTCGGGTTGTCATGCCAATGGCACTGCCCGGTAGCTAAATGCGGAAGAGATAAGTGCTGAAAGCATCTAAGCACGAAACTTGCCCCGAGATGAGTTCTCCCTGACTCCTTGAGGGTCCTGAAGGAACGTTGAAGACGACGACGTTGATAGGCCGGGTGTGTAAGCGCAGCGATGCGTTGAGCTAACCGGTACTAATGAACCGTGAGGCTTAACCTT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36763","NCBI_taxonomy_name":"Escherichia coli CFT073","NCBI_taxonomy_id":"199310"}}}},"ARO_accession":"3004149","ARO_id":"41296","ARO_name":"Escherichia coli 23S rRNA with mutation conferring resistance to clindamycin","ARO_description":"Point mutation in the 23S rRNA of Escherichia coli shown clinically to confer resistance to clindamycin, a lincosamide antibiotic","ARO_category":{"41349":{"category_aro_accession":"3004187","category_aro_cvterm_id":"41349","category_aro_name":"23S rRNA with mutation conferring resistance to lincosamide antibiotics","category_aro_description":"Point mutations in the 23S rRNA subunit may confer resistance to lincosamide antibiotics by reducing antibiotic binding-site affinity.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36600":{"category_aro_accession":"3000461","category_aro_cvterm_id":"36600","category_aro_name":"florfenicol","category_aro_description":"Florfenicol is a fluorine derivative of chloramphenicol, where the nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3) and the hydroxyl group (-OH), by a fluorine group (-F). The action mechanism is the same as chloramphenicol's, where the antibiotic binds to the 23S RNA of the 50S subunit of bacterial ribosomes to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin 1A is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"vernamycin B-gamma","category_aro_description":"Vernamycin B-gamma is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2807":{"model_id":"2807","model_name":"Escherichia coli 23S rRNA with mutation conferring resistance to clarithromycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"7899":"G2032U"},"clinical":{"7899":"G2032U"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"5000"}},"model_sequences":{"sequence":{"4154":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"AE014075.1","fmin":"237159","fmax":"240063","strand":"+","sequence":"GGTTAAGCGACTAAGCGTACACGGTGGATGCCCTGGCAGTCAGAGGCGATGAAGGACGTGCTAATCTGCGATAAGCGTCGGTAAGGTGATATGAACCGTTATAACCGGCGATTTCCGAATGGGGAAACCCAGTGTGTTTCGACACACTATCATTAACTGAATCCATAGGTTAATGAGGCGAACCGGGGGAACTGAAACATCTAAGTACCCCGAGGAAAAGAAATCAACCGAGATTCCCCCAGTAGCGGCGAGCGAACGGGGAGGAGCCCAGAGCCTGAATCAGTGTGTGTGTTAGTGGAAGCGTCTGGAAAGGCGCGCGATACAGGGTGACAGCCCCGTACACAAAAATGCACATGCTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGGGGGACCATCCTCCAAGGCTAAATACTCCTGACTGACCGATAGTGAACCAGTACCGTGAGGGAAAGGCGAAAAGAACCCCGGCGAGGGGAGTGAAAAAGAACCTGAAACCGTGTACGTACAAGCAGTGGGAGCATGCTTAGGCGTGTGACTGCGTACCTTTTGTATAATGGGTCAGCGACTTATATTCTGTAGCAAGGTTAACCGAATAGGGGAGCCGAAGGGAAACCGAGTCTTAACTGGGCGTTAAGTTGCAGGGTATAGACCCGAAACCCGGTGATCTAGCCATGGGCAGGTTGAAGGTTGGGTAACACTAACTGGAGGACCGAACCGACTAATGTTGAAAAATTAGCGGATGACTTGTGGCTGGGGGTGAAAGGCCAATCAAACCGGGAGATAGCTGGTTCTCCCCGAAAGCTATTTAGGTAGCGCCTCGTGAACTCATCTCCGGGGGTAGAGCACTGTTTCGGCAAGGGGGTCATCCCGACTTACCAACCCGATGCAAACTGCGAATACCGGAGAATGTTATCACGGGAGACACACGGCGGGTGCTAACGTCCGTCGNGAAGAGGGAAACAACCCAGACCGCCAGCTAAGGTCCCAAAGTCATGGTTAAGTGGGAAACGATGTGGGAAGGCCCAGACAGCCAGGATGTTGGCTTAGAAGCAGCCATCATTTAAAGAAAGCGTAATAGCTCACTGGTCGAGTCGGCCTGCGCGGAAGATGTAACGGGGCTAAACCATGCACCGAAGCTGCGGCAGCGACGCTTATGCGTTGTTGGGTAGGGGAGCGTTCTGTAAGCCTGTGAAGGTGTACTGTGAGGTATGCTGGAGGTATCAGAAGTGCGAATGCTGACATAAGTAACGATAAAGCGGGTGAAAAGCCCGCTCGCCGGAAGACCAAGGGTTCCTGTCCAACGTTAATCGGGGCAGGGTGAGTCGACCCCTAAGGCGAGGCCGAAAGGCGTAGTCGATGGGAAACAGGTTAATATTCCTGTACTTGGTGTTACTGCGAAGGGGGGACGGAGAAGGCTATGTTGGCCGGGCGACGGTTGTCCCGGTTTAAGCGTGTAGGCTGGTTTTCCAGGCAAATCCGGAAAATCAAGGCTGAGGCGTGATGACGAGGCACTACGGTGCTGAAGCAACAAATGCCCTGCTTCCAGGAAAAGCCTCTAAGCATCAGGTAACATCAAATCGTACCCCAAACCGACACAGGTGGTCAGGTAGAGAATACCAAGGCGCTTGAGAGAACTCGGGTGAAGGAACTAGGCAAAATGGTGCCGTAACTTCGGGAGAAGGCACGCTGATATGTAGGTGAAGCGACTTGCTCGTGGAGCTGAAATCAGTCGAAGATACCAGCTGGCTGCAACTGTTTATTAAAAACACAGCACTGTGCAAACACGAAAGTGGACGTATACGGTGTGACGCCTGCCCGGTGCCGGAAGGTTAATTGATGGGGTTAGCGCAAGCGAAGCTCTTGATCGAAGCCCCGGTAAACGGCGGCCGTAACTATAACGGTCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAATGATGGCCAGGCTGTCTCCACCCGAGACTCAGTGAAATTGAACTCGCTGTGAAGATGCAGTGTACCCGCGGCAAGACGGAAAGACCCCGTGAACCTTTACTATAGCTTGACACTGAACATTGAGCCTTGATGTGTAGGATAGGTGGGAGGCTTTGAAGTGTGGACGCCAGTCTGCATGGAGCCGACCTTGAAATACCACCCTTTAATGTTTGATGTTCTAACGTTGACCCGTAATCCGGGTTGCGGACAGTGTCTGGTGGGTAGTTTGACTGGGGCGGTCTCCTCCTAAAGAGTAACGGAGGAGCACGAAGGTTGGCTAATCCTGGTCGGACATCAGGAGGTTAGTGCAATGGCATAAGCCAGCTTGACTGCGAGCGTGACGGCGCGAGCAGGTGCGAAAGCAGGTCATAGTGATCCGGTGGTTCTGAATGGAAGGGCCATCGCTCAACGGATAAAAGGTACTCCGGGGATAACAGGCTGATACCGCCCAAGAGTTCATATCGACGGCGGTGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGGGCTGAAGTAGGTCCCAAGGGTATGGCTGTTCGCCATTTAAAGTGGTACGCGAGCTGGGTTTAGAACGTCGTGAGACAGTTCGGTCCCTATCTGCCGTGGGCGCTGGAGAACTGAGGGGGGCTGCTCCTAGTACGAGAGGACCGGAGTGGACGCATCACTGGTGTTCGGGTTGTCATGCCAATGGCACTGCCCGGTAGCTAAATGCGGAAGAGATAAGTGCTGAAAGCATCTAAGCACGAAACTTGCCCCGAGATGAGTTCTCCCTGACTCCTTGAGGGTCCTGAAGGAACGTTGAAGACGACGACGTTGATAGGCCGGGTGTGTAAGCGCAGCGATGCGTTGAGCTAACCGGTACTAATGAACCGTGAGGCTTAACCTT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36763","NCBI_taxonomy_name":"Escherichia coli CFT073","NCBI_taxonomy_id":"199310"}}}},"ARO_accession":"3004160","ARO_id":"41307","ARO_name":"Escherichia coli 23S rRNA with mutation conferring resistance to clarithromycin","ARO_description":"Point mutation in the 23S rRNA of Escherichia coli shown clinically to confer resistance to clarithromycin, a macrolide antibiotic","ARO_category":{"41251":{"category_aro_accession":"3004125","category_aro_cvterm_id":"41251","category_aro_name":"23S rRNA with mutation conferring resistance to macrolide antibiotics","category_aro_description":"Nucleotide point mutations in the 23S rRNA subunit may confer resistance to macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36600":{"category_aro_accession":"3000461","category_aro_cvterm_id":"36600","category_aro_name":"florfenicol","category_aro_description":"Florfenicol is a fluorine derivative of chloramphenicol, where the nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3) and the hydroxyl group (-OH), by a fluorine group (-F). The action mechanism is the same as chloramphenicol's, where the antibiotic binds to the 23S RNA of the 50S subunit of bacterial ribosomes to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin 1A is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"vernamycin B-gamma","category_aro_description":"Vernamycin B-gamma is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2808":{"model_id":"2808","model_name":"Propionibacteria 23S rRNA with mutation conferring resistance to macrolide antibiotics","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"7900":"G2281A","7901":"G2294A","7902":"G2295A"},"clinical":{"7900":"G2281A","7901":"G2294A","7902":"G2295A"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"5000"}},"model_sequences":{"sequence":{"4155":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"Y10819.1","fmin":"1849","fmax":"4984","strand":"+","sequence":"GTGACAAGCTACTAAGTGCGATCGGTGGATGCCTAGGCACCAAGAGCCGATGAAGGACGTTGTAACCTGCGATAAGCCCTGGGGAGCTGGTAAACGAGCTTTGATCCGGGGATGTCCGAATGGGGAAACCTCGAAGGTGACCAGTTTAGCTACTGGCGACCGCCGCCTGAATGTATAGGGCGGTTGGAGGGAACGTGGGGAAGTGAAACATCTTAGTACCCACAGGAAGAGRAAACAACCGTGAWTCCGTGAATATTGGCGAGCGAAAGCGGAAGAGGCCAAACCGGAGTGTGTGATAGCCGGCAGGTGTTGCATGTGCGGGGTTGTGGGAAGCGTTTTGACTGAACTGCCGTGAGGTCGGAGAGTGATAAAGGATTGATGAAGCAGAAGCGTCTGGGAAGGCGCGGCATAGATGGTGATACCCCTGTATGCGTAAGTTGATCTCTCTCTTAATGTTTTCCCAAGTAGTACGGAACCCCTGAAATYCCGTACGAATCTGGCGGACCACCCGTTAAGCCTAAATACBCCTTGGTGACCGATMGCGGACAAGTACCCGTGAGGGAAAGGGTGAAAATGTACCCCCGGGAGGGGAGTGAAATAGTMCCTGAAACCGATCGCATACAATCCGTCGGAGCCTGCCCTTGTGGTGGGTGACGGCGTGCCTTTTGRAAGAATGAGCCTGCGAGTTAGTGGTGTGTGGCGAGGTTAACCCGTGTGGGGAAGCCGTAGCGAAAGCGAGTCCGAATAGGGCGTTTGAGTCGCATGCTCTAGACCCGAAGCGGTGTGATCTATCCATGGCCAGGGTGAAGCGACGGTAAGACGTCGTGGAGGCCCGAACCCACCAGGGTTGCAAACCTGGGGGATGAGCTGTGGATAGGGGTGAAAGGCCAATCAAACACCGTGATAGCTGGTTCTCCCCGAAATGCATTTAGGTGCAGCGTCATGTGTTTCTTGTCGGAGGTAGAGCACTGGATGGTCTAGGGGGCTTACCAGCTTACCGAAATCAGCCAAACTCCGAATGCCGACAAGTGAGAGCATGGCAGTGAGACGGCGGGGGATAAGCTTCGTCGTCGAGAGGGAAACAGCCCAGATCATCAGCTAAGGCCCCTAAGTGGTGACTAAGTGGAAAAGGACGTGGAGTTGCGGAGACAACCAGGAGGTTGGCTTGGAAGCAGCCATCCTTGAAAGAGTGCGTAATAGCTCACTGGTCAAGTGATTCTGCACCGACAATTTAGCGGGGCTCAAGTCATCCGCCGAAGCTGTGGCATCTACGCGTGTATCCGGCATCCTTTGGGGTGTCCAGGTGCGTGGATGGGTAGGGGAGCGTTGTGTGTGCGTTGAAGCGGCGGGGTGACCCGGTCGTGGAGTGCACGCAAGTGAGAATGCAGGCATGAGTAGCGTATGACGGGTGAGAAACCCGTCCGCCGAATATCCAAGGGTTCCAGGGTCAAGCTAATCTGCCCTGGGTGAGTCGGGTCCTAAGGCGAGGCCGACAGGCGTAGTCGATGGACAACGGGTTGATATTCCCGTACCGGCGCGAGAACGATCCTGCCGAGGTGAGTGATGCTAAGCATGCAAGGCGGTCGTGGGGGCTTCGGTTCCCTGATCGTTGAGTCTGTAACCCGATCTTGTAGTAGGCAAGCTGCGGAGGGACGCAGGAAGGTAGTCTGGCACCGTATTGGTTTGCGGTGTTAAGCCTGTAGGGTGTCTGGCCAGGTAAATCCGGTCGGACGTGTGCCTGAGAGGTGATGAGTGGTGCCACTTTTGTGGTACGTATCCGGATGATCCTATGCTGCCTAGAAAATCTTCGTGAGCGAGTTCTCGAGCTGCCCGTACCCCAAACCGACACTGGTGGATAGGTAGAGAATACCAAGGCGATCGAGATAATCATGGTGAAGGAACTCGGCAAAATCCTCCCGTAACTTCGGAATAAGGGAGACTGGAGGCGTGACGGCAGTTTACTTGTCGGTGCGTCGATAGTCGCAGAGAATAGGCCCAAGCGACTGCTTACTAAAAGCACAGGTCCGTGCTAAGTCGAAAGACGATGTATACGGACTGACTCCTGCCCGGTGCTCKGAAGGTTAAGGGGACGTGTTAGCACTTTTGTGCGAGGCACTGAACTTAAGCCCCAGTAAACGGCGGTGGTAACTATAACCATCCTAAGGKAGCGAAATTCCTTGTCGGGKAAGTTCCGRCCTGSACGAATGGAGTAACGACTTGGGCGCTGTCTCCACCATGAACTCGGCGAAATTGCATTACGAGTAAAGATGCTCGTTACGCGCACAGGGACGGAAAGVNCCCGGGACCTTTACTATAGTTTGGTATTGGTGATCGGTACGACTTGTGTAGGATAGGTGGGAGACTTTGAAGCGGTCACGCTAGTGATTGTGGAGTCATTGTTGAAATACCACTCTGGTCGTTCTGGTTATCTAACCTAGGTCCGTGATCCGGATCAGGGACAGTGCCTGATGGGTAGTTTGACTGGGGCGGTCGCCTCCMAAAAGGTAACGGAGGCGCCCAAAGGTTCCCTCAGCCTGGTTGGTAATCAGGTGTTGAGTGTAAGTGCACAAGGGAGCTTGACTGTGAGACAGACATGTCGAGCAGGGACGAAAGTCGGGACTAGTGATCYTCTGGTGGATTGTGGAATCGCCAGAACTCAACGGATAAAAGGTACCCCGGGGATAACAGGCTGATCTTTCCCGAGCGCTCACAGCGACGGAATGGNTTGGCACCTCGATGTCGGCTCGTCGCATCCTGGGGCTGGAGTCGGTCCCAAGGGTTGGGCTGTTCGCCCATTAAAGCGGCACGCGARGCTGGGGKTAAGAACGTCGTGAGACAGTTCCGGKCCCTATACCGCTGCSCGTMGKATCTTGAGAGGGCTGTCCTTAGTACGCAAGGACCGGGACGGACCAACCTCTGGTGTGCCAGTTGTTCCACCAGGAGCATGGCTGGTTGGCTACGTTGGGGAGTGATAACCGCTGAAAGCATCTAAGTGGGAAGCACGCTTCAAGATGAGGGTTCCTGCACAGTTAATGTGGTAAGGCCCCCGGTAGACCACCGGGTGATAGGTCGGATGTGGAAGCATGGTGACATGTGGAGCTGACCGATACTAAGTGGCCGAGGGCTTGTCCCACA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41309","NCBI_taxonomy_name":"Propionibacterium freudenreichii","NCBI_taxonomy_id":"1744"}}}},"ARO_accession":"3004161","ARO_id":"41308","ARO_name":"Propionibacteria 23S rRNA with mutation conferring resistance to macrolide antibiotics","ARO_description":"Point mutation in the 23S rRNA of Propionibacteria shown clinically to confer resistance to macrolides","ARO_category":{"41251":{"category_aro_accession":"3004125","category_aro_cvterm_id":"41251","category_aro_name":"23S rRNA with mutation conferring resistance to macrolide antibiotics","category_aro_description":"Nucleotide point mutations in the 23S rRNA subunit may confer resistance to macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36600":{"category_aro_accession":"3000461","category_aro_cvterm_id":"36600","category_aro_name":"florfenicol","category_aro_description":"Florfenicol is a fluorine derivative of chloramphenicol, where the nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3) and the hydroxyl group (-OH), by a fluorine group (-F). The action mechanism is the same as chloramphenicol's, where the antibiotic binds to the 23S RNA of the 50S subunit of bacterial ribosomes to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin 1A is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"vernamycin B-gamma","category_aro_description":"Vernamycin B-gamma is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2802":{"model_id":"2802","model_name":"Escherichia coli 23S rRNA with mutation conferring resistance to macrolide antibiotics","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"7845":"U754A","7847":"G2057A","7848":"A2058G","7849":"A2058U","7850":"C2611U"},"clinical":{"7845":"U754A","7847":"G2057A","7848":"A2058G","7849":"A2058U","7850":"C2611U"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"5000"}},"model_sequences":{"sequence":{"4149":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"AE014075.1","fmin":"237159","fmax":"240063","strand":"+","sequence":"GGTTAAGCGACTAAGCGTACACGGTGGATGCCCTGGCAGTCAGAGGCGATGAAGGACGTGCTAATCTGCGATAAGCGTCGGTAAGGTGATATGAACCGTTATAACCGGCGATTTCCGAATGGGGAAACCCAGTGTGTTTCGACACACTATCATTAACTGAATCCATAGGTTAATGAGGCGAACCGGGGGAACTGAAACATCTAAGTACCCCGAGGAAAAGAAATCAACCGAGATTCCCCCAGTAGCGGCGAGCGAACGGGGAGGAGCCCAGAGCCTGAATCAGTGTGTGTGTTAGTGGAAGCGTCTGGAAAGGCGCGCGATACAGGGTGACAGCCCCGTACACAAAAATGCACATGCTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGGGGGACCATCCTCCAAGGCTAAATACTCCTGACTGACCGATAGTGAACCAGTACCGTGAGGGAAAGGCGAAAAGAACCCCGGCGAGGGGAGTGAAAAAGAACCTGAAACCGTGTACGTACAAGCAGTGGGAGCATGCTTAGGCGTGTGACTGCGTACCTTTTGTATAATGGGTCAGCGACTTATATTCTGTAGCAAGGTTAACCGAATAGGGGAGCCGAAGGGAAACCGAGTCTTAACTGGGCGTTAAGTTGCAGGGTATAGACCCGAAACCCGGTGATCTAGCCATGGGCAGGTTGAAGGTTGGGTAACACTAACTGGAGGACCGAACCGACTAATGTTGAAAAATTAGCGGATGACTTGTGGCTGGGGGTGAAAGGCCAATCAAACCGGGAGATAGCTGGTTCTCCCCGAAAGCTATTTAGGTAGCGCCTCGTGAACTCATCTCCGGGGGTAGAGCACTGTTTCGGCAAGGGGGTCATCCCGACTTACCAACCCGATGCAAACTGCGAATACCGGAGAATGTTATCACGGGAGACACACGGCGGGTGCTAACGTCCGTCGNGAAGAGGGAAACAACCCAGACCGCCAGCTAAGGTCCCAAAGTCATGGTTAAGTGGGAAACGATGTGGGAAGGCCCAGACAGCCAGGATGTTGGCTTAGAAGCAGCCATCATTTAAAGAAAGCGTAATAGCTCACTGGTCGAGTCGGCCTGCGCGGAAGATGTAACGGGGCTAAACCATGCACCGAAGCTGCGGCAGCGACGCTTATGCGTTGTTGGGTAGGGGAGCGTTCTGTAAGCCTGTGAAGGTGTACTGTGAGGTATGCTGGAGGTATCAGAAGTGCGAATGCTGACATAAGTAACGATAAAGCGGGTGAAAAGCCCGCTCGCCGGAAGACCAAGGGTTCCTGTCCAACGTTAATCGGGGCAGGGTGAGTCGACCCCTAAGGCGAGGCCGAAAGGCGTAGTCGATGGGAAACAGGTTAATATTCCTGTACTTGGTGTTACTGCGAAGGGGGGACGGAGAAGGCTATGTTGGCCGGGCGACGGTTGTCCCGGTTTAAGCGTGTAGGCTGGTTTTCCAGGCAAATCCGGAAAATCAAGGCTGAGGCGTGATGACGAGGCACTACGGTGCTGAAGCAACAAATGCCCTGCTTCCAGGAAAAGCCTCTAAGCATCAGGTAACATCAAATCGTACCCCAAACCGACACAGGTGGTCAGGTAGAGAATACCAAGGCGCTTGAGAGAACTCGGGTGAAGGAACTAGGCAAAATGGTGCCGTAACTTCGGGAGAAGGCACGCTGATATGTAGGTGAAGCGACTTGCTCGTGGAGCTGAAATCAGTCGAAGATACCAGCTGGCTGCAACTGTTTATTAAAAACACAGCACTGTGCAAACACGAAAGTGGACGTATACGGTGTGACGCCTGCCCGGTGCCGGAAGGTTAATTGATGGGGTTAGCGCAAGCGAAGCTCTTGATCGAAGCCCCGGTAAACGGCGGCCGTAACTATAACGGTCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAATGATGGCCAGGCTGTCTCCACCCGAGACTCAGTGAAATTGAACTCGCTGTGAAGATGCAGTGTACCCGCGGCAAGACGGAAAGACCCCGTGAACCTTTACTATAGCTTGACACTGAACATTGAGCCTTGATGTGTAGGATAGGTGGGAGGCTTTGAAGTGTGGACGCCAGTCTGCATGGAGCCGACCTTGAAATACCACCCTTTAATGTTTGATGTTCTAACGTTGACCCGTAATCCGGGTTGCGGACAGTGTCTGGTGGGTAGTTTGACTGGGGCGGTCTCCTCCTAAAGAGTAACGGAGGAGCACGAAGGTTGGCTAATCCTGGTCGGACATCAGGAGGTTAGTGCAATGGCATAAGCCAGCTTGACTGCGAGCGTGACGGCGCGAGCAGGTGCGAAAGCAGGTCATAGTGATCCGGTGGTTCTGAATGGAAGGGCCATCGCTCAACGGATAAAAGGTACTCCGGGGATAACAGGCTGATACCGCCCAAGAGTTCATATCGACGGCGGTGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGGGCTGAAGTAGGTCCCAAGGGTATGGCTGTTCGCCATTTAAAGTGGTACGCGAGCTGGGTTTAGAACGTCGTGAGACAGTTCGGTCCCTATCTGCCGTGGGCGCTGGAGAACTGAGGGGGGCTGCTCCTAGTACGAGAGGACCGGAGTGGACGCATCACTGGTGTTCGGGTTGTCATGCCAATGGCACTGCCCGGTAGCTAAATGCGGAAGAGATAAGTGCTGAAAGCATCTAAGCACGAAACTTGCCCCGAGATGAGTTCTCCCTGACTCCTTGAGGGTCCTGAAGGAACGTTGAAGACGACGACGTTGATAGGCCGGGTGTGTAAGCGCAGCGATGCGTTGAGCTAACCGGTACTAATGAACCGTGAGGCTTAACCTT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36763","NCBI_taxonomy_name":"Escherichia coli CFT073","NCBI_taxonomy_id":"199310"}}}},"ARO_accession":"3004131","ARO_id":"41258","ARO_name":"Escherichia coli 23S rRNA with mutation conferring resistance to erythromycin and telithromycin","ARO_description":"Point mutation in the 23S rRNA of Escherichia coli shown clinically to confer resistance to the macrolide-class antibiotics erythromycin and telithromycin.","ARO_category":{"41251":{"category_aro_accession":"3004125","category_aro_cvterm_id":"41251","category_aro_name":"23S rRNA with mutation conferring resistance to macrolide antibiotics","category_aro_description":"Nucleotide point mutations in the 23S rRNA subunit may confer resistance to macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35974":{"category_aro_accession":"0000057","category_aro_cvterm_id":"35974","category_aro_name":"telithromycin","category_aro_description":"Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36600":{"category_aro_accession":"3000461","category_aro_cvterm_id":"36600","category_aro_name":"florfenicol","category_aro_description":"Florfenicol is a fluorine derivative of chloramphenicol, where the nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3) and the hydroxyl group (-OH), by a fluorine group (-F). The action mechanism is the same as chloramphenicol's, where the antibiotic binds to the 23S RNA of the 50S subunit of bacterial ribosomes to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin 1A is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"vernamycin B-gamma","category_aro_description":"Vernamycin B-gamma is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2803":{"model_id":"2803","model_name":"Mycobacterium tuberculosis thyA with mutation conferring resistance to para-aminosalicylic acid","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"7851":"W101R","7852":"H75N","7853":"T22A","7854":"T202A","7855":"Y36C","7857":"V77F","7858":"W83C","7860":"G91R","7862":"S105P","7863":"R126Q","7864":"F152V","7865":"C161T","7866":"H207R","7867":"I211V","7868":"P224L","7869":"R235P"},"clinical":{"7851":"W101R","7852":"H75N","7853":"T22A","7854":"T202A","7855":"Y36C","7857":"V77F","7858":"W83C","7860":"G91R","7862":"S105P","7863":"R126Q","7864":"F152V","7865":"C161T","7866":"H207R","7867":"I211V","7868":"P224L","7869":"R235P"}},"40394":{"param_type":"nonsense mutation","param_description":"A nucleotide substitution resulting in a change from an amino acid codon to a STOP codon. Nonsense mutations truncate protein translation prematurely, resulting in a defective or completely inactive protein. In CARD, nonsense mutations may be attached to models using the notation: [wild type amino acid][position][STOP] (e.g. Q42STOP). This parameter is not currently used in detection algorithms.","param_type_id":"40394","param_value":{"7856":"G76STOP","7859":"W83STOP","7861":"W98STOP"}},"41343":{"param_type":"deletion mutation from nucleotide sequence","param_description":"A subtype of the deletion mutation detection model parameter. This parameter is used when a set of deletion mutations is reported in a nucleotide sequence format. Such mutations may be of variable length - possibly causing a frameshift, but not premature termination of functional knockout. Mutation parameters of this type are reported in the CARD with the notation: [-]nt[position]:[nucleotides].","param_type_id":"41343","param_value":{"8076":"-nt260:C","8077":"-nt111:T","8082":"-nt472:C"}},"41345":{"param_type":"insertion mutation from nucleotide sequence","param_description":"A subtype of the insertion mutation detection model parameter. This parameter is used when a set of insertion mutations is reported in a nucleotide sequence format. Such mutations may be of variable length - possibly causing a frameshift, but not causing premature termination or a functional knockout. Mutation parameters of this type are reported in CARD with the notation: [+]nt[position]:[nucleotides].","param_type_id":"41345","param_value":{"8079":"+nt217:CACGAGCAC","8080":"+nt372:T"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4150":{"protein_sequence":{"accession":"NP_217280.1","sequence":"MTPYEDLLRFVLETGTPKSDRTGTGTRSLFGQQMRYDLSAGFPLLTTKKVHFKSVAYELLWFLRGDSNIGWLHEHGVTIWDEWASDTGELGPIYGVQWRSWPAPSGEHIDQISAALDLLRTDPDSRRIIVSAWNVGEIERMALPPCHAFFQFYVADGRLSCQLYQRSADLFLGVPFNIASYALLTHMMAAQAGLSVGEFIWTGGDCHIYDNHVEQVRLQLSREPRPYPKLLLADRDSIFEYTYEDIVVKNYDPHPAIKAPVAV"},"dna_sequence":{"accession":"NC_000962.3","fmin":"3073679","fmax":"3074471","strand":"-","sequence":"TCATACCGCGACTGGAGCTTTGATCGCCGGATGCGGATCGTAGTTCTTCACAACGATGTCTTCATAGGTGTACTCGAAGATTGAATCCCGGTCGGCTAGAAGTAGTTTCGGATATGGCCGCGGCTCGCGGCTGAGCTGCAGCCGTACTTGCTCGACGTGATTGTCGTAGATGTGGCAGTCGCCACCGGTCCAGATGAACTCGCCGACCGACAAGCCGGCCTGGGCGGCCATCATGTGGGTGAGCAACGCATAGCTGGCGATGTTGAACGGCACACCCAGAAACAGGTCGGCGCTGCGTTGGTAGAGCTGACAGCTCAGCCGGCCATCGGCGACGTAGAACTGGAAGAACGCATGACAGGGCGGCAGCGCCATCCGCTCGATTTCGCCGACGTTCCAGGCCGACACGATGATGCGCCGGGAATCGGGATCGGTGCGCAGCAAATCCAGCGCCGCGCTGATCTGGTCGATGTGCTCACCGGATGGAGCCGGCCACGATCGCCATTGTACACCGTAGATCGGCCCGAGTTCGCCTGTATCACTTGCCCATTCGTCCCAGATGGTGACTCCGTGCTCGTGCAGCCAACCGATATTGGAATCGCCGCGCAAAAACCACAGCAGCTCGTAGGCTACCGATTTGAAATGGACTTTCTTGGTAGTGAGCAGCGGGAAACCGGCCGACAAATCATAGCGCATCTGCTGGCCGAACAGGCTGCGGGTTCCGGTGCCGGTGCGGTCGGATTTGGGCGTACCCGTTTCGAGCACGAAGCGCAGCAGGTCCTCGTATGGCGTCAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3004153","ARO_id":"41300","ARO_name":"Mycobacterium tuberculosis thyA with mutation conferring resistance to para-aminosalicylic acid","ARO_description":"Point mutations in the thymidylate synthetase thyA gene shown clinically to confer resistance to para-aminosalicylic acid. Loss-of-function mutations in thyA disrupt the catalytic activity and substrate-binding affinity, thus conferring resistance.","ARO_category":{"41299":{"category_aro_accession":"3004152","category_aro_cvterm_id":"41299","category_aro_name":"aminosalicylate resistant thymidylate synthase","category_aro_description":"Antibiotic resistant form of thymidylate synthase (synthetase), an enzyme that catalyzes the conversion of dUMP to dTMP in nucleotide biosynthesis. Loss-of-function mutations in thymidylate synthase confer resistance to p-aminosalicylic acid by disrupting the substrate-binding affinity and catalytic activity.","category_aro_class_name":"AMR Gene Family"},"40948":{"category_aro_accession":"3004019","category_aro_cvterm_id":"40948","category_aro_name":"para-aminosalicylic acid","category_aro_description":"para-aminosalicylic acid (PAS) is an anti-tubercular antibiotic agent, often used in conjunction with Isoniazid for treatment of M. tuberculosis infections. PAS diminishes bacterial cell growth by limiting folic acid production.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2804":{"model_id":"2804","model_name":"Mycobacterium tuberculosis folC with mutation conferring resistance to para-aminosalicylic acid","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"7874":"E40Q","7875":"E40G","7873":"T20P","7876":"I43T","7877":"I43S","7878":"I43A","7879":"R49P","7880":"R49W","7881":"L56V","7882":"R91W","7883":"S150G","7884":"S150C","7885":"E153A","7886":"E153G","7887":"A420V"},"clinical":{"7874":"E40Q","7875":"E40G","7873":"T20P","7876":"I43T","7877":"I43S","7878":"I43A","7879":"R49P","7880":"R49W","7881":"L56V","7882":"R91W","7883":"S150G","7884":"S150C","7885":"E153A","7886":"E153G","7887":"A420V"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4151":{"protein_sequence":{"accession":"NP_216963.1","sequence":"MNSTNSGPPDSGSATGVVPTPDEIASLLQVEHLLDQRWPETRIDPSLTRISALMDLLGSPQRSYPSIHIAGTNGKTSVARMVDALVTALHRRTGRTTSPHLQSPVERISIDGKPISPAQYVATYREIEPLVALIDQQSQASAGKGGPAMSKFEVLTAMAFAAFADAPVDVAVVEVGMGGRWDATNVINAPVAVITPISIDHVDYLGADIAGIAGEKAGIITRAPDGSPDTVAVIGRQVPKVMEVLLAESVRADASVAREDSEFAVLRRQIAVGGQVLQLQGLGGVYSDIYLPLHGEHQAHNAVLALASVEAFFGAGAQRQLDGDAVRAGFAAVTSPGRLERMRSAPTVFIDAAHNPAGASALAQTLAHEFDFRFLVGVLSVLGDKDVDGILAALEPVFDSVVVTHNGSPRALDVEALALAAGERFGPDRVRTAENLRDAIDVATSLVDDAAADPDVAGDAFSRTGIVITGSVVTAGAARTLFGRDPQ"},"dna_sequence":{"accession":"NC_000962.3","fmin":"2746134","fmax":"2747598","strand":"-","sequence":"TCATTGCGGATCACGACCGAACAAGGTCCGAGCCGCCCCTGCGGTGACAACCGAGCCGGTGATGACGATCCCGGTTCTCGAGAATGCGTCCCCGGCCACATCCGGGTCGGCGGCGGCGTCGTCGACCAGTGAGGTGGCAACGTCGATAGCATCGCGCAGGTTCTCGGCGGTGCGCACCCGGTCGGGTCCGAACCGCTCGCCGGCCGCCAGCGCCAGGGCCTCGACATCCAGCGCCCGCGGCGACCCGTTGTGGGTCACGACGACGGAATCGAACACCGGCTCCAGTGCGGCCAGGATGCCGTCCACGTCCTTGTCGCCCAGCACGCTGAGCACCCCGACCAGAAATCGGAAGTCGAACTCATGCGCCAGCGTTTGTGCCAGAGCACTCGCCCCGGCCGGATTGTGCGCGGCGTCGATGAACACCGTGGGTGCGCTGCGCATGCGCTCCAACCGGCCGGGACTGGTGACGGCGGCAAAGCCGGCCCGGACGGCGTCGCCGTCGAGCTGACGCTGCGCACCGGCACCGAAAAAGGCCTCGACGGAAGCGAGGGCGAGCACCGCGTTGTGCGCCTGGTGTTCACCGTGCAGCGGCAAGTAGATGTCGGAGTAAACCCCGCCGAGGCCCTGCAGTTGCAGTACCTGACCGCCGACCGCGATCTGTCGCCGTAGCACCGCGAATTCGGAATCCTCCCGGGCCACCGACGCGTCGGCGCGCACCGATTCGGCCAGCAGCACCTCCATGACCTTCGGGACCTGACGCCCGATGACCGCGACGGTGTCCGGCGAACCGTCGGGGGCCCGAGTGATGATGCCCGCCTTCTCCCCGGCGATCCCGGCGATATCGGCACCGAGATAGTCGACGTGATCAATGCTGATCGGGGTGATGACGGCGACCGGTGCGTTGATCACGTTGGTGGCGTCCCAACGTCCGCCCATGCCCACCTCGACCACTGCCACGTCGACGGGCGCGTCCGCAAAGGCCGCGAACGCCATCGCGGTGAGCACCTCGAACTTGCTCATCGCCGGGCCACCCTTACCCGCAGAAGCCTGCGACTGCTGGTCGATCAGCGCCACCAACGGCTCGATCTCCCGGTAGGTCGCCACATACTGCGCCGGGCTGATCGGCTTGCCGTCGATCGAAATGCGTTCCACCGGTGACTGCAGGTGTGGGCTGGTGGTTCGGCCGGTGCGCCGGTGCAGCGCGGTGACCAGCGCGTCGACCATGCGCGCCACCGAGGTCTTGCCGTTGGTGCCCGCGATATGGATCGACGGATAGCTGCGTTGGGGCGAGCCCAGCAGGTCCATCAACGCGCTGATCCGGGTCAGGCTCGGATCGATGCGGGTCTCCGGCCAGCGTTGGTCGAGTAGATGCTCAACCTGCAGCAGGGACGCGATCTCGTCCGGAGTGGGCACGACGCCGGTGGCCGATCCCGAGTCAGGCGGGCCGGAATTCGTCGAATTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3004157","ARO_id":"41304","ARO_name":"Mycobacterium tuberculosis folC with mutation conferring resistance to para-aminosalicylic acid","ARO_description":"Point mutations in the dihydrofolate synthetase folC gene shown clinically to confer resistance to p-aminosalicylic acid or other aminosalicylates. Mutations in folC inhibit bioactivation of PAS and thus confer resistance.","ARO_category":{"41302":{"category_aro_accession":"3004155","category_aro_cvterm_id":"41302","category_aro_name":"aminosalicylate resistant dihydrofolate synthase","category_aro_description":"Dihydrofolate synthase (synthetase) enzymes resistant to aminosalicylates (inc. para-aminosalicylic acid) caused by mutation. Dihydrofolate synthase is required for bioactivation of p-aminosalicylic acid, and mutation in dihydrofolate synthase inhibits production of the dihydrofolate analog hydroxyl-dihydrofolate, thus preventing activation and conferring resistance.","category_aro_class_name":"AMR Gene Family"},"40948":{"category_aro_accession":"3004019","category_aro_cvterm_id":"40948","category_aro_name":"para-aminosalicylic acid","category_aro_description":"para-aminosalicylic acid (PAS) is an anti-tubercular antibiotic agent, often used in conjunction with Isoniazid for treatment of M. tuberculosis infections. PAS diminishes bacterial cell growth by limiting folic acid production.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2810":{"model_id":"2810","model_name":"Mycobaccterium abscessus 23S rRNA with mutation conferring resistance to clarithromycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"7910":"A2271G","7911":"A2272G","7912":"A2272C"},"clinical":{"7910":"A2271G","7911":"A2272G","7912":"A2272C"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"5700"}},"model_sequences":{"sequence":{"4156":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NC_010397.1","fmin":"1464207","fmax":"1467319","strand":"+","sequence":"CTAAGTTCTTAAGGGCGCATGGTGAATGCCTTGGCACTAGAAGCCGAAGAAGGACGTAGGAGGCTGCGATAAGCCTCGGGGAGCTGCCAACCGAGCTTTGATCCGAGGATCTCCGAATGGGGAAACCCAGCACGAGTGATGTCGTGTTACCCACTGCTGAATATATAGGCTTTGGGAGGAAACGCGGGGAAGTGAAACATCTCAGTACCCGTAGGAAGAGAAAACAACCGTGATTCCGTGAGTAGTGGCGAGCGAAAGCGGAAGATGGCTAAACCGCATGCATGTGATACCTGGTAGGGGTTGTGTGTGCGGGGTTGTGGGAGTTGTACTTGCCGGTTCTACCAGGCCGGCGGACAGTAAAAAAGTGTCGTGATTAGCGGAAGTGGTCTGGGACGGCCCGCCGCAGACGGTGAGAGTCCGGTACGCGAAAATCCGACACCTGTCTCGTACTTCATCCCGAGTAGCAGCGGGCTCGTGGAATCTGCTGTGAATCTGCCGGGACCACCCGGTAAGCCTAAATACTCTCTAGTGACCGATAGCGGATTAGTACCGTGAGGGAATGGTGAAAAGTACCCCGGGAGGGGAGTGAAATAGTACCTGAAACCATGTGCCTACAATCCGTCAAAGCCTCCTCGTGGGGTGATGGCGTGCCTTTTGAAGAATGAGCCTGCGAGTCAGGGACACGTCGCGAGGTTAACCCGTGTGGGGTAGCCGTAGCGAAAGCGAGTCTGAATAGGGCGCCCATAGTGGCGTGTTCTGGACCCGAAGCGGAGTGATCTACCCATGGCCAGGGTGAAGCGGCGGTAAGACGCCGTGGAGGCCCGAACCCACTTAGGTTGAAGACTGAGGGGATGAGCTGTGGGTAGGGGTGAAAGGCCAATCAAACTCCGTGATAGCTGGTTCTCCCCGAAATGCATTTAGGTGCAGCGTCGCGTGTTTCTTGTTGGAGGTAGAGCTACTGGATGGCCGATGGGCCCTACTAGGTTACTGACGTCAGCCAAACTCCGAATGCCAATAAGTTAGAGCGCGGCAGTGAGACGGCGGGGGAGAAGCTCCGTACGTCGAGAGGGAAACAGCCCAGATCGCCGGCTAAGGCCCCTAAGCGTGTACTAAGTGGAAAAGGATGTGCAGTCGCGAAGACAACCAGGAGGTTGGCTTAGAAGCAGCCACCCTTGAAAGAGTGCGTAATAGCTCACTGGTCAAGTGATTGTGCGCCGACAATGTAGCGGGGCTCAAGTACACCGCCGAAGCCGCGGCATTCATGCAATACATTCCCTTCGGGGCAGTGGCATGGATGGGTAGGGGAGCGTCCTGCACCCAGCGAAGCTGCGAAGTAATTCAGCAGTGGAGGGTGCGGGAGTGAGAATGCAGGCATGAGTAGCGACAGGCAAGTGAGAAACTTGCCCGCCGAATGACCAAGGGTTCCTGGGCCAGGCTAGTCCTCCCAGGGTAAGTCGGGACCTAAGGCGAGGCCGACAGGCGTAGTCGATGGACAACGGGTTGATATTCCCGTACCCGTGTGTGCGCGCCCATGATGAATCATCGGTACTAACCACCCAAAAGGTTCTAGATCAATCTCTTCGGAGTGCGACGTGAACCCGCTGCGTGGGACCTTCGGTGGTAGTAGTCAAGCGATGGGGTGACGCAGGAAGGTAGCTGTACCGGTTAGTGGTTATACCGGAGCAAGCCCGTAGGACGACATCTAGGCAAATCCGGATGTCATACGTCTGAGAGGTGACGCATAGCCGATTGAGGCGAATTCAGTGATCCTATGCTGCCAAGAAAAGCCTCTAGTGAGTTCACACACGGCCCGTACCCCAAACCAACACAGGTGGTCAGGTAGAGAATACTAAGGCGTACGAGATAACTATGGTTAAGGAACTCGGCAAAATACCCCCGTAACTTCGGGAGAAGGGGGACCTCGCTTGGTGACCGGACTTGCTCCGTGAGCTGAACGAGGTCGCAGAGACCAGTGAGAAGCGACTGTTTACTAAAAACACAGGTCCGTGCGAAGTCGCAAGACGATGTATACGGACTGACGCCTGCCCGGTGCTGGAAGGTTAAGAGGACCCGTTAACCCTTGGGTGAAGCGGAGAATTTAAGCCCCAGTAAACGGCGGTGGTAACTATAACCATCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAACGACTTCTCAACTGTCTCAACCATAGACTCGGCGAAATTGCACTACGAGTAAAGATGCTCGTTACGCGCGGCAGGACGAAAAGACCCCGGGACCTTCACTATAGCTTGGTATTGGCGTTTGGTTCGGTTTGTGTAGGATAGGTGGGAGACTGTGAAGCAGGCACGCCAGTGTTTGTGGAGTCATCGTTGAAATACCACTCTGATCGTATTGAACCTCTAACCTCGGACCGTATATCCGGTCCAGGGACAGTGCCTGGTGGGTAGTTTAACTGGGGCGGTTGCCTCCCAAAATGTAACGGAGGCGCCCAAAGGTTCCCTCAACCTGGACGGCAATCAGGTGTTGAGTGCAAGTGCACAAGGGAGCTTGACTGCGAGACCTACAAGTCAAGCAGGGACGAAAGTCGGGACTAGTGATCCGGCACCTCTGAGTGGAAGGGGTGTCGCTCAACGGATAAAAGGTACCCCGGGGATAACAGGCTGATCTTCCCCAAGAGTCCATATCGACGGGATGGTTTGGCACCTCGATGTCGGCTCGTCGCATCCTGGGGCTGGAGCAGGTCCCAAGGGTTGGGCTGTTCGCCCATTAAAGCGGCACGCGAGCTGGGTTTAGAACGTCGTGAGACAGTTCGGTCTCTATCCGCCGCGCGCGTCAGAAACTTGAGGAAACCTGTCCCTAGTACGAGAGGACCGGGACGGACGAACCTCTGGTGTACCAGTTGTTCCACCAGGAGCACGGCTGGATAGCTACGTTCGGACAGGATAACCGCTGAAAGCATCTAAGCGGGAAACCTATTCCAAGACCAGGTTTCTTACCCTTTTAGAGGGATAAGGTCACCCACAGACTATGGGTTCAATAGGCCAGACCTGCAAGCGTAGTAATACGTTCAGGGAACTGGCACTAATCGACCGAAAACTTACTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36888","NCBI_taxonomy_name":"Mycobacterium abscessus","NCBI_taxonomy_id":"36809"}}}},"ARO_accession":"3004163","ARO_id":"41311","ARO_name":"Mycobacterium abscessus 23S rRNA with mutation conferring resistance to clarithromycin","ARO_description":"Point mutation in the 23S rRNA of Mycobacterium abscessus shown to confer resistance to clarithromycin, a macrolide type antibiotic.","ARO_category":{"41251":{"category_aro_accession":"3004125","category_aro_cvterm_id":"41251","category_aro_name":"23S rRNA with mutation conferring resistance to macrolide antibiotics","category_aro_description":"Nucleotide point mutations in the 23S rRNA subunit may confer resistance to macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36600":{"category_aro_accession":"3000461","category_aro_cvterm_id":"36600","category_aro_name":"florfenicol","category_aro_description":"Florfenicol is a fluorine derivative of chloramphenicol, where the nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3) and the hydroxyl group (-OH), by a fluorine group (-F). The action mechanism is the same as chloramphenicol's, where the antibiotic binds to the 23S RNA of the 50S subunit of bacterial ribosomes to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin 1A is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"vernamycin B-gamma","category_aro_description":"Vernamycin B-gamma is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2811":{"model_id":"2811","model_name":"Mycobacterium avium 23S rRNA with mutation conferring resistance to clarithromycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"7913":"A2272C","7914":"A2274G","7915":"A2274U"},"clinical":{"7913":"A2272C","7914":"A2274G","7915":"A2274U"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"5700"}},"model_sequences":{"sequence":{"4157":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NG_041979.1","fmin":"0","fmax":"3112","strand":"+","sequence":"TGTGTGTAAGTAAGTGTTTAAGGGCGCATGGTGGATGCCTTGGCATCGAGAGCCGATGAAGGACGTGGGAGGCTGCGATATGCCTCGGGGAGCTGTCAACCGAGCATTGATCCGAGGATTTCCGAATGGGGAAACCCAGCACGAGTGATGTCGTGTTACCCGTATCTGAATATATAGGGTGCGGGAGGTAACGCGGGGAAGTGAAACATCTCAGTACCCGTAGGAGAAGAAAACAATTGTGATTCCGTCAGTAGTGGCGAGCGAACGCGGAACAGGCTAAACCGCATGCATGGACAACCGGGTAGGGGTTGTGTGTGCGGGGTTGTGGGATTGATATGTCTCAGCTCTACCTGGCTGAGGGGTAGTCAGAAAGTGTCGTGGTTAGCGGAAGTGGCCTGGGACGGCCCGCCGTAGACGGTGAGAGCCCGGTACGCGAAAACCCGGCACCTGCCTTATATCAACACCCGAGTAGCAGCGGGCCCGTGGAATCTGCTGTGAATCTGCCGGGACCACCCGGTAAGCCTAAATACTTCTCGATGACCGATAGCGGATTAGTACCGTGAGGGAATGGTGAAAAGTACCCCGGGAGGGGAGTGAAATAGTACCTGAAACCGTGTGCCTACAATCCGTCAGAGCCTCCTCGTGGGGTGATGGCGTGCCTTTTGAAGAATGAGCCTGCGAGTCAGGGACACGTCGCGAGGTTAACCCGTGCGGGGTAGCCGCAGCGAAAGCGAGTCTGAATAGGGCGCATCCCCTTTGGGGTGTAGTGGCGTGTTCTGGACCCGAAGCGGAGTGATCTACCCATGGCCAGGGTGAAGCGCGGGTAAGACCGCGTGGAGGCCCGAACCCACTTAGGTTGAAGACTGAGGGGATGAGCTGTGGGTAGGGGTGAAAGGCCAATCAAACTCCGTGATAGCTGGTTCTCCCCGAAATGCATTTAGGTGCAGCGTTGCGTGGTTCACCACGGAGGTAGAGCTACTGGATGGCCGATGGGCCCTACTAGGTTACTGACGTCAGCCAAACTCCGAATGCCGTGGTGTAAAGCGTGGCAGTGAGACGGCGGGGGATAAGCTCCGTACGTCGAAAGGGAAACAGCCCAGATCGCCGGCTAAGGCCCCTAAGCGTGTGCTAAGTGGAAAAGGATGTGTAGTCGCAGAGACAACCAGGAGGTTGGCTTAGAAGCAGCCACCCTTGAAAGAGTGCGTAATAGCTCACTGGTCAAGTGATTATGCGCCGATAATGTAGCGGGGCTCAAGCACACCGCCGAAGCCGCGGCACATTCATCTTTACGGTGGATGTGGGTAGGGGAGCGTCCCCCATTCAGCGAAGCCTCCGGGTGACCGGTGGTGGAGGGTGGGGGAGTGAGAATGCAGGCATGAGTAGCGATAAGGCAAGTGAGAACCTTGCCCGCCGTAAGACCAAGGGTTCCTGGGCCAGGCCAGTCCGCCCAGGGTGAGTCGGGACCTAAGGCGAGGCCGACAGGCGTAGTCGATGGACAACGGGTTGATATTCCCGTACCCGTGTATGGGCGTCCCTGATGAATCAGCGGTACTAACCACCCAAAACCGGATCGACCATTCCCCTTCGGGGGCGTGGCGATTCGGGGCTGCGTGGGACCTTCGCTGGTAGTAGTCAAGCAATGGGGTGACGCAGGAAGGCAGCCGTACCAGTCAGTGGTAATACTGGGGCAAGCCCGTAGGGAGAGCGATAGGCAAATCCGTCGCTCACTAATCCTGAGAGGTGATGCATAGCCGGTTGAGGCGAATTCGGTGATCCTCTGCTGCCAAGAAAAGCCTCTAGCGAGCACATACACGGCCCGTACCCCAAACCAACACAGGTGGTCAGGTAGAGAATACCAAGGCGTACGAGATAACTATGGTTAAGGAACTCGGCAAAATGCCCCCGTAACTTCGGGAGAAGGGGGGCCGGAATACCGTGAACACCCTTGCGGTGGGAGCGGGATTCGGCCGCAGAAACCAGTGGGTAGCGACTGTTTACTAAAAACACAGGTCCGTGCGAAGTCGCAAGACGATGTATACGGACTGACGCCTGCCCGGTGCTGGAAGGTTAAGAGGACCCGTTAACCCGTAAGGGTGAAGCGGAGAATTTAAGCCCCAGTAAACGGCGGTGGTAACTATAACCATCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAACGACTTCCCAACTGTCTCAACCATAGACTCGGCGAAATTGCACTACGAGTAAAGATGCTCGTTACGCGCGGCAGGACGAAAAGACCCCGGGACCTTCACTACAACTTGGTATTGGTGTTCGGTACGGTTTGTGTAGGATAGGTGGGAGACTTTGAAGCACAGACGCCAGTTTGTGTGGAGTCGTTGTTGAAATACCACTCTGATCGTATTGGACACCTAACGTCGAACCCTTATCGGGTTCACGGACAGTGCCTGGCGGGTAGTTTAACTGGGGCGGTTGCCTCCTAAAATGTAACGGAGGCGCCCAAAGGTTCCCTCAACCTGGACGGCAATCAGGTGGCGAGTGTAAGTGCACAAGGGAGCTTGACTGCGAGACTTACAAGTCAAGCAGGGACGAAAGTCGGGACTAGTGATCCGGCACCCCCGAGTGGAAGGGGTGTCGCTCAACGGATAAAAGGTACCCCGGGGATAACAGGCTGATCTTCCCCAAGAGTCCATATCGACGGGATGGTTTGGCACCTCGATGTCGGCTCGTCGCATCCTGGGGCTGGAGCAGGTCCCAAGGGTTGGGCTGTTCGCCCATTAAAGCGGCACGCGAGCTGGGTTTAGAACGTCGTGAGACAGTTCGGTCTCTATCCGCCGCGCGCGTCAGAAACTTGAGGAAACCTGTCCCTAGTACGAGAGGACCGGGACGGACGAACCTCTGGTATACCAGTTGTCCCACCAGGGGCACGGCTGGATAGCCACGTTCGGACAGGATAACCGCTGAAAGCATCTAAGCGGGAAACCTTCTCCAAGATCAGGTTTCTCACCCTTTTAGAGGGATAAGGCCCCCCGCAGACCACGGGATTGATAGGCCAGACCTGGAAGCTCAGTAATGAGTGCAGGGAACTGGCACTAACCGGCCGAAAAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39582","NCBI_taxonomy_name":"Mycobacterium avium","NCBI_taxonomy_id":"1764"}}}},"ARO_accession":"3004164","ARO_id":"41312","ARO_name":"Mycobacterium avium 23S rRNA with mutation conferring resistance to clarithromycin","ARO_description":"Point mutation in the 23S rRNA of Mycobacterium avium shown to confer resistance to clarithromycin, a macrolide type antibiotic.","ARO_category":{"41251":{"category_aro_accession":"3004125","category_aro_cvterm_id":"41251","category_aro_name":"23S rRNA with mutation conferring resistance to macrolide antibiotics","category_aro_description":"Nucleotide point mutations in the 23S rRNA subunit may confer resistance to macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36600":{"category_aro_accession":"3000461","category_aro_cvterm_id":"36600","category_aro_name":"florfenicol","category_aro_description":"Florfenicol is a fluorine derivative of chloramphenicol, where the nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3) and the hydroxyl group (-OH), by a fluorine group (-F). The action mechanism is the same as chloramphenicol's, where the antibiotic binds to the 23S RNA of the 50S subunit of bacterial ribosomes to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin 1A is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"vernamycin B-gamma","category_aro_description":"Vernamycin B-gamma is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2812":{"model_id":"2812","model_name":"Mycobacterium chelonae 23S rRNA with mutation conferring resistance to clarithromycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"7916":"A2272C","7917":"A2272G","7918":"A2273C","7919":"A2273G"},"clinical":{"7916":"A2272C","7917":"A2272G","7918":"A2273C","7919":"A2273G"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"5700"}},"model_sequences":{"sequence":{"4158":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"GU143889.1","fmin":"0","fmax":"3113","strand":"+","sequence":"CTAAGTTCTTAAGGGCACATGGTGAATGCCTTGGCACTAGAAGCCGAAGAAGGACGTAGGAGGCTGCGATAAGCCTCGGGGAGCTGCCAACCGAGCTTTGATCCGAGGATGTCCGAATGGGGAAACCCAGCACGAGTGATGTCGTGTTACCCACTGCTGAATATATAGGCTTTGGGAGGAAACGCGGGGAAGTGAAACATCTCAGTACCCGTAGGAAGAGAAAACAACCGTGATTCCGTGAGTAGTGGCGAGCGAAAGCGGAAGATGGCTAAACCGCATGCATGTGATACCTGGTAGGGGTTGTGTGTGCGGGGTTGTGGGAGTTGTACTTGCCGGTTCTACCAGGCCGGCGGACAGTAAAAAAGTGTCGTGATTAGCGGAAGTGGTCTGGGACGGCCCGCCGCAGACGGTGAGAGTCCGGTACGCGAAAATCCGACACCTGTCTCGTACTTCATCCCGAGTAGCAGCGGGCTCGTGGAATCTGCTGTGAATCTGCCGGGACCACCCGGTAAGCCTAAATACTCTCTAGTGACCGATAGCGGATTAGTACCGTGAGGGAATGGTGAAAAGTACCCCGGGAGGGGAGTGAAATAGTACCTGAAACCATGTGCCTACAATCCGTCAAAGCCTCCTTGTGGGGTGATGGCGTGCCTTTTGAAGAATGAGCCTGCGAGTCAGGGACACGTCGCGAGGTTAACCCGTGAGGGGTAGCCGTAGCGAAAGCGAGTCTGAATAGGGCGCCCATAGTGGCGTGTTCTGGACCCGAAGCGGAGTGATCTACCCATGGCCAGGGTGAAGCGGCGGTAAGACGCCGTGGAGGCCCGAACCCACTTAGGTTGAAGACTGAGGGGATGAGCTGTGGGTAGGGGTGAAAGGCCAATCAAACTCCGTGATAGCTGGTTCTCCCCGAAATGCATTTAGGTGCAGCGTCGCGTGTTTCTTATTGGAGGTAGAGCTACTGGATGGCCGATGGGCCCTACTAGGTTACTGACGTCAGCCAAACTCCGAATGCCAATAAGTTAGAGCGCGGCAGTGAGACGGCGGGGGAGAAGCTCCGTACGTCGAGAGGGAAACAGCCCAGATCGCCGGCTAAGGCCCCTAAGCGTGTACTAAGTGGAAAAGGATGTGCAGTCGCAAAGACAACCAGGAGGTTGGCTTAGAAGCAGCCACCCTTGAAAGAGTGCGTAATAGCTCACTGGTCAAGTGATTGTGCGCCGACAATGTAGCGGGGCTCAAGTACACCGCCGAAGCCGCGGCATTCATGCAATACATTCCCTTCGGGGCAGTGGCATGGATGGGTAGGGGAGCGTCCTGCACCCAGCGAAGCTGCGGAGTAATCCAGCAGTGGAGGGTGCGGGAGTGAGAATGCAGGCATGAGTAGCGACAGGCAAGTGAGAAACTTGCCCGCCGAATGACCAAGGGTTCCTGGGCCAGGCTAGTCCTCCCAGGGTAAGTCGGGACCTAAGGCGAGGCCGACAGGCGTAGTCGATGGACAACGGGTTGATATTCCCGTACCCGTGTGTGCGCGCCCATGATGAATCATCGGTACTAACCACCCAAAAGGTTCTAGATCAATCTCTTCGGAGTGCGACGTGAACCCGCTGCGTGGGACCTTCGGTGGTAGTAGTCAAGCGATGGGGTGACGCAGGAAGGTAGCTGTACCGGTTAGTGGTTATACCGGAGCAAGCCCGTAGGGCGACGTCTAGGTAAATCCGGATGTCATTAAGCCTGAGAGGTGACGCATAGCCGATTGAGGCGAATTCAGTGATCCTATGCTGCCAAGAAAAGCCTCTAGTGAGTTCACACACGGCCCGTACCCCAAACCAACACAGGTGGTCAGGTAGAGAATACTAAGGCGTACGAGATAACTATGGTTAAGGAACTCGGCAAAATACCCCCGTAACTTCGGGAGAAGGGGGACCTCGCTTGGTGACCGGACTTGCTCCGTGAGCTGAACGAGGTCGCAGAGACCAGTGAGAAGCGACTGTTTACTAAAAACACAGGTCCGTGCGAAGTCGCAAGACGATGTATACGGACTGACGCCTGCCCGGTGCTGGAAGGTTAAGAGGACCCGTTAACCCTTGGGTGAAGCGGAGAATTTAAGCCCCAGTAAACGGCGGTGGTAACTATAACCATCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAACGACTTCTCAACTGTCTCAACCATAGACTCGGCGAAATTGCACTACGAGTAAAGATGCTCGTTACGCGCGGCAGGACGAAAAGACCCCGGGACCTTCACTATAGCTTGGTATTGGCGTTTGGTTCGGTTTGTGTAGGATAGGTGGGAGACTGTGAAGCAGGCACGCCAGTGTTTGTGGAGTCATCGTTGAAATACCACTCTGATCGTATTGAACCTCTAACCTCGGACCGTATATCCGGTCCAGGGACAGTGCCTGGTGGGTAGTTTAACTGGGGCGGTTGCCTCCCAAAATGTAACGGAGGCGCCCAAAGGTTCCCTCAACCTGGACGGCAATCAGGTGTTGAGTGCAAGTGCACAAGGGAGCTTGACTGCGAGACTTACAAGTCGAGCAGGGACGAAAGTCGGGACTAGTGATCCGGCATCTCTGAGTGGAAGGGATGTCGCTCAACGGATAAAAGGTACCCCGGGGATAACAGGCTGATCTTCCCCAAGAGTCCATATCGACGGGATGGTTTGGCACCTCGATGTCGGCTCGTCGCATCCTGGGGCTGGAGCAGGTCCCAAGGGTTGGGCTGTTCGCCCATTAAAGCGGCACGCGAGCTGGGTTTAGAACGTCGTGAGACAGTTCGGTCTCTATCCGCCGCGCGCGTCAGAAACTTGAGGAAACCTGTCCCTAGTACGAGAGGACCGGGACGGACGAACCTCTGGTGTACCAGTTGTTCCACCAGGAGCACGGCTGGATAGCTACGTTCGGACAGGATAACCGCTGAAAGCATCTAAGCGGGAAACCTATTCCAAGACCAGGTTTCTTACCCTTTTAGAGGGATAAGGTCACCCACAGACTATGGGTTCAATAGGCCAGACCTGTAAGCGTAGTAATACGTTCAGGGAACTGGCACTAATCGACCGAAAACTTACTAAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41314","NCBI_taxonomy_name":"Mycobacterium chelonae","NCBI_taxonomy_id":"1774"}}}},"ARO_accession":"3004165","ARO_id":"41313","ARO_name":"Mycobacterium chelonae 23S rRNA with mutation conferring resistance to clarithromycin","ARO_description":"Point mutation in the 23S rRNA of Mycobacterium chelonae shown to confer resistance to clarithromycin, a macrolide type antibiotic.","ARO_category":{"41251":{"category_aro_accession":"3004125","category_aro_cvterm_id":"41251","category_aro_name":"23S rRNA with mutation conferring resistance to macrolide antibiotics","category_aro_description":"Nucleotide point mutations in the 23S rRNA subunit may confer resistance to macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36600":{"category_aro_accession":"3000461","category_aro_cvterm_id":"36600","category_aro_name":"florfenicol","category_aro_description":"Florfenicol is a fluorine derivative of chloramphenicol, where the nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3) and the hydroxyl group (-OH), by a fluorine group (-F). The action mechanism is the same as chloramphenicol's, where the antibiotic binds to the 23S RNA of the 50S subunit of bacterial ribosomes to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin 1A is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"vernamycin B-gamma","category_aro_description":"Vernamycin B-gamma is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2813":{"model_id":"2813","model_name":"Mycobacterium intracellulare 23S rRNA with mutation conferring resistance to clarithromycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"8172":"A2266U","8173":"A2266C","8174":"A2266G"},"clinical":{"8172":"A2266U","8173":"A2266C","8174":"A2266G"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"5700"}},"model_sequences":{"sequence":{"4177":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NR_076151.1","fmin":"0","fmax":"3103","strand":"+","sequence":"TAAGTGTTTAAGGGCGCATGGTGGATGCCTTGGCATCGAGAGCCGATGAAGGACGTGGGAGGCTGCGATATGCCTCGGGGAGCTGTCAACCGAGCATTGATCCGAGGATTTCCGAATGGGGAAACCCAGCACGAGTGATGTCGTGTTACCCGCATCTGAATATATAGGGTGCGGGAGGGAACGCGGGGAAGTGAAACATCTCAGTACCCGTAGGAGAAGAAAACAATTGTGATTCCGTAAGTAGTGGCGAGCGAACGCGGAACAGGCTAAACCGCACGCATGTGATACCGGGTAGGGGTTGTGTGTGCGGGGTTGTGGGAGGATACATCTCAGCTCTACCTGGCTGAGGGGTAGTCAGAAAGTGTCGTGGTTAGCGGAAGTGGCCTGGGATGGTCTGCCGTAGACGGTGAGAGCCCGGTACGCGAAAACCCGTCACCTACCTTGTATCAATTCCCGAGTAGCAGCGGGCCCGTGGAATCTGCTGTGAATCTGCCGGGACCACCCGGTAAGCCTAAATACTTCTCGATGACCGATAGCGGATTAGTACCGTGAGGGAATGGTGAAAAGTACCCCGGGAGGGGAGTGAAATAGTACCTGAAACCGTGTGCCTACAATCCGTCAGAGCCTCCTTGTGGGGTGATGGCGTGCCTTTTGAAGAATGAGCCTGCGAGTCAGGGACACGTCGCGAGGTTAACCCGTGCGGGGTAGCCGCAGCGAAAGCGAGTCTGAATAGGGCGCATCCCCTTTGGGGTGTAGTGGCGTGTTCTGGACCCGAAGCGGAGTGATCTACCCATGGCCAGGGTGAAGCGCGGGTAAGACCGCGTGGAGGCCCGAACCCACTTAGGTTGAAGACTGAGGGGATGAGCTGTGGGTAGGGGTGAAAGGCCAATCAAACTCCGTGATAGCTGGTTCTCCCCGAAATGCATTTAGGTGCAGCGTTGCGTGGTTCACCACGGAGGTAGAGCTACTGGATGGCCGATGGGCCCTACTAGGTTACTGACGTCAGCCAAACTCCGAATGCCGTGGTGTAAAGCGTGGCAGTGAGACGGCGGGGGATAAGCTCCGTACGTCGAAAGGGAAACAGCCCAGATCGCCGGCTAAGGCCCCTAAGCGTGTGCTAAGTGGAAAAGGATGTGTAGTCGCAGAGACAACCAGGAGGTTGGCTTAGAAGCAGCCACCCTTGAAAGAGTGCGTAATAGCTCACTGGTCAAGTGATTATGCGCCGATAATGTAGCGGGGCTCAAGCACACCGCCGAAGCCGCGGCACATTCACGTTTACGTGGATGTGGGTAGGGGGAGCGTCCCTCATTCAGCGAAGCCTCCGGGTGACCGGTGGTGGAGGGTGGGGGAGTGAGAATGCAGGCATGAGTAGCGATAAGGCAAGTGAGAACCTTGCCCGCCGTAAGACCAAGGGTTCCTGGGCCAGGCCAGTCCGCCCAGGGTGAGTCGGGACCTAAGGCGAGGCCGACAGGCGTAGTCGATGGACAACGGGTTGATATTCCCGTACCCGTGTATGGGCGTCCCTGATGAATCAGCGGTACTAACCACCCAAAACCGGATCGACCATTCCCCTTCGGGGGCATGGAGTTTCGGGGCTGCGTGGGACCTTCGCTGGTAGTAGTCAAGCAATGGGGTGACGCAGGAAGGTAGCCGTACCAGTCAGTGGTAATACTGGGGCAAGCCTGTAGGGAGAGCGATAGGCAAATCCGTCGCTCATTAATCCTGAGAGGTGATGCATAGCCGATTGAGGTGAATTCGGTGATCCTCTGCTGCCAAGAAAAGCCTCTAGCGAGCACATACACGGCCCGTACCCCAAACCAACACAGGTGGTCAGGTAGAGAATACCAAGGCGTACGAGATAACTATGGTTAAGGAACTCGGCAAAATGCCCCCGTAACTTCGGGAGAAGGGGGGCCGGAATACCGTGAACACCCTTGCGGTGGGAGCGGGATCCGGCCGCAGAAACCAGTGGGTAGCGACTGTTTACTAAAAACACAGGTCCGTGCGAAGTCGCAAGACGATGTATACGGACTGACGCCTGCCCGGTGCTGGAAGGTTAAGAGGACCCGTTAACCGTAAGGTGAAGCGGAGAATTTAAGCCCCAGTAAACGGCGGTGGTAACTATAACCATCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAACGACTTCCCAACTGTCTCAACCATAGACTCGGCGAAATTGCACTACGAGTAAAGATGCTCGTTACGCGCGGCAGGACGAAAAGACCCCGGGACCTTCACTACAACTTGGTATTGGTGTTCGGTACGGTTTGTGTAGGATAGGTGGGAGACTGTGAAATACAGACGCCAGTTTGTATGGAGTCGTTGTTGAAATACCACTCTGATCGTATTGGACACCTAACGTCGAACCCTTATCGGGTTCACGGACAGTGCCTGGCGGGTAGTTTAACTGGGGCGGTTGCCTCCTAAAATGTAACGGAGGCGCCCAAAGGTTCCCTCAACCTGGACGGCAATCAGGTGACGAGTGTAAGTGCACAAGGGAGCTTGACTGCGAGACTTACAAGTCAAGCAGGGACGAAAGTCGGGACTAGTGATCCGGCACCCCCGAGTGGAAGGGGTGTCGCTCAACGGATAAAAGGTACCCCGGGGATAACAGGCTGATCTTCCCCAAGAGTCCATATCGACGGGATGGTTTGGCACCTCGATGTCGGCTCGTCGCATCCTGGGGCTGGAGCAGGTCCCAAGGGTTGGGCTGTTCGCCCATTAAAGCGGCACGCGAGCTGGGTTTAGAACGTCGTGAGACAGTTCGGTCTCTATCCGCCGCGCGCGTCAGAAACTTGAGGAAACCTGTCCCTAGTACGAGAGGACCGGGACGGACGAACCTCTGGTATACCAGTTGTTCCACCAGGAGCACGGCTGGATAGCCACGTTCGGACAGGATAACCGCTGAAAGCATCTAAGCGGGAAACCTTCTCCAAGATCAGGTTTCTCACCCTTTTAGAGGGATAAGGCCCCCCGCAGACCACGGGTTCGATAGGCTAGACCTGGAAGCTCAGCAATGAGTGCAGGGAACTGGCACTAACCGGCCGAAAACTTAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41317","NCBI_taxonomy_name":"Mycobacterium intracellulare","NCBI_taxonomy_id":"1767"}}}},"ARO_accession":"3004166","ARO_id":"41315","ARO_name":"Mycobacterium intracellulare 23S rRNA with mutation conferring resistance to clarithromycin","ARO_description":"Point mutation in the 23S rRNA of Mycobacterium intracellulare shown to confer resistance to clarithromycin, a macrolide type antibiotic.","ARO_category":{"41251":{"category_aro_accession":"3004125","category_aro_cvterm_id":"41251","category_aro_name":"23S rRNA with mutation conferring resistance to macrolide antibiotics","category_aro_description":"Nucleotide point mutations in the 23S rRNA subunit may confer resistance to macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36600":{"category_aro_accession":"3000461","category_aro_cvterm_id":"36600","category_aro_name":"florfenicol","category_aro_description":"Florfenicol is a fluorine derivative of chloramphenicol, where the nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3) and the hydroxyl group (-OH), by a fluorine group (-F). The action mechanism is the same as chloramphenicol's, where the antibiotic binds to the 23S RNA of the 50S subunit of bacterial ribosomes to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin 1A is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"vernamycin B-gamma","category_aro_description":"Vernamycin B-gamma is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2814":{"model_id":"2814","model_name":"Mycobacterium intracellulare 23S rRNA with mutation conferring resistance to azithromycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"7923":"A2268C"},"clinical":{"7923":"A2268C"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"5700"}},"model_sequences":{"sequence":{"4159":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NR_076151.1","fmin":"0","fmax":"3103","strand":"+","sequence":"TAAGTGTTTAAGGGCGCATGGTGGATGCCTTGGCATCGAGAGCCGATGAAGGACGTGGGAGGCTGCGATATGCCTCGGGGAGCTGTCAACCGAGCATTGATCCGAGGATTTCCGAATGGGGAAACCCAGCACGAGTGATGTCGTGTTACCCGCATCTGAATATATAGGGTGCGGGAGGGAACGCGGGGAAGTGAAACATCTCAGTACCCGTAGGAGAAGAAAACAATTGTGATTCCGTAAGTAGTGGCGAGCGAACGCGGAACAGGCTAAACCGCACGCATGTGATACCGGGTAGGGGTTGTGTGTGCGGGGTTGTGGGAGGATACATCTCAGCTCTACCTGGCTGAGGGGTAGTCAGAAAGTGTCGTGGTTAGCGGAAGTGGCCTGGGATGGTCTGCCGTAGACGGTGAGAGCCCGGTACGCGAAAACCCGTCACCTACCTTGTATCAATTCCCGAGTAGCAGCGGGCCCGTGGAATCTGCTGTGAATCTGCCGGGACCACCCGGTAAGCCTAAATACTTCTCGATGACCGATAGCGGATTAGTACCGTGAGGGAATGGTGAAAAGTACCCCGGGAGGGGAGTGAAATAGTACCTGAAACCGTGTGCCTACAATCCGTCAGAGCCTCCTTGTGGGGTGATGGCGTGCCTTTTGAAGAATGAGCCTGCGAGTCAGGGACACGTCGCGAGGTTAACCCGTGCGGGGTAGCCGCAGCGAAAGCGAGTCTGAATAGGGCGCATCCCCTTTGGGGTGTAGTGGCGTGTTCTGGACCCGAAGCGGAGTGATCTACCCATGGCCAGGGTGAAGCGCGGGTAAGACCGCGTGGAGGCCCGAACCCACTTAGGTTGAAGACTGAGGGGATGAGCTGTGGGTAGGGGTGAAAGGCCAATCAAACTCCGTGATAGCTGGTTCTCCCCGAAATGCATTTAGGTGCAGCGTTGCGTGGTTCACCACGGAGGTAGAGCTACTGGATGGCCGATGGGCCCTACTAGGTTACTGACGTCAGCCAAACTCCGAATGCCGTGGTGTAAAGCGTGGCAGTGAGACGGCGGGGGATAAGCTCCGTACGTCGAAAGGGAAACAGCCCAGATCGCCGGCTAAGGCCCCTAAGCGTGTGCTAAGTGGAAAAGGATGTGTAGTCGCAGAGACAACCAGGAGGTTGGCTTAGAAGCAGCCACCCTTGAAAGAGTGCGTAATAGCTCACTGGTCAAGTGATTATGCGCCGATAATGTAGCGGGGCTCAAGCACACCGCCGAAGCCGCGGCACATTCACGTTTACGTGGATGTGGGTAGGGGGAGCGTCCCTCATTCAGCGAAGCCTCCGGGTGACCGGTGGTGGAGGGTGGGGGAGTGAGAATGCAGGCATGAGTAGCGATAAGGCAAGTGAGAACCTTGCCCGCCGTAAGACCAAGGGTTCCTGGGCCAGGCCAGTCCGCCCAGGGTGAGTCGGGACCTAAGGCGAGGCCGACAGGCGTAGTCGATGGACAACGGGTTGATATTCCCGTACCCGTGTATGGGCGTCCCTGATGAATCAGCGGTACTAACCACCCAAAACCGGATCGACCATTCCCCTTCGGGGGCATGGAGTTTCGGGGCTGCGTGGGACCTTCGCTGGTAGTAGTCAAGCAATGGGGTGACGCAGGAAGGTAGCCGTACCAGTCAGTGGTAATACTGGGGCAAGCCTGTAGGGAGAGCGATAGGCAAATCCGTCGCTCATTAATCCTGAGAGGTGATGCATAGCCGATTGAGGTGAATTCGGTGATCCTCTGCTGCCAAGAAAAGCCTCTAGCGAGCACATACACGGCCCGTACCCCAAACCAACACAGGTGGTCAGGTAGAGAATACCAAGGCGTACGAGATAACTATGGTTAAGGAACTCGGCAAAATGCCCCCGTAACTTCGGGAGAAGGGGGGCCGGAATACCGTGAACACCCTTGCGGTGGGAGCGGGATCCGGCCGCAGAAACCAGTGGGTAGCGACTGTTTACTAAAAACACAGGTCCGTGCGAAGTCGCAAGACGATGTATACGGACTGACGCCTGCCCGGTGCTGGAAGGTTAAGAGGACCCGTTAACCGTAAGGTGAAGCGGAGAATTTAAGCCCCAGTAAACGGCGGTGGTAACTATAACCATCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAACGACTTCCCAACTGTCTCAACCATAGACTCGGCGAAATTGCACTACGAGTAAAGATGCTCGTTACGCGCGGCAGGACGAAAAGACCCCGGGACCTTCACTACAACTTGGTATTGGTGTTCGGTACGGTTTGTGTAGGATAGGTGGGAGACTGTGAAATACAGACGCCAGTTTGTATGGAGTCGTTGTTGAAATACCACTCTGATCGTATTGGACACCTAACGTCGAACCCTTATCGGGTTCACGGACAGTGCCTGGCGGGTAGTTTAACTGGGGCGGTTGCCTCCTAAAATGTAACGGAGGCGCCCAAAGGTTCCCTCAACCTGGACGGCAATCAGGTGACGAGTGTAAGTGCACAAGGGAGCTTGACTGCGAGACTTACAAGTCAAGCAGGGACGAAAGTCGGGACTAGTGATCCGGCACCCCCGAGTGGAAGGGGTGTCGCTCAACGGATAAAAGGTACCCCGGGGATAACAGGCTGATCTTCCCCAAGAGTCCATATCGACGGGATGGTTTGGCACCTCGATGTCGGCTCGTCGCATCCTGGGGCTGGAGCAGGTCCCAAGGGTTGGGCTGTTCGCCCATTAAAGCGGCACGCGAGCTGGGTTTAGAACGTCGTGAGACAGTTCGGTCTCTATCCGCCGCGCGCGTCAGAAACTTGAGGAAACCTGTCCCTAGTACGAGAGGACCGGGACGGACGAACCTCTGGTATACCAGTTGTTCCACCAGGAGCACGGCTGGATAGCCACGTTCGGACAGGATAACCGCTGAAAGCATCTAAGCGGGAAACCTTCTCCAAGATCAGGTTTCTCACCCTTTTAGAGGGATAAGGCCCCCCGCAGACCACGGGTTCGATAGGCTAGACCTGGAAGCTCAGCAATGAGTGCAGGGAACTGGCACTAACCGGCCGAAAACTTAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41317","NCBI_taxonomy_name":"Mycobacterium intracellulare","NCBI_taxonomy_id":"1767"}}}},"ARO_accession":"3004167","ARO_id":"41316","ARO_name":"Mycobacterium intracellulare 23S rRNA with mutation conferring resistance to azithromycin","ARO_description":"Point mutation in the 23S rRNA of Mycobaccterium avium shown to confer resistance to azithromycin, a macrolide type antibiotic.","ARO_category":{"41251":{"category_aro_accession":"3004125","category_aro_cvterm_id":"41251","category_aro_name":"23S rRNA with mutation conferring resistance to macrolide antibiotics","category_aro_description":"Nucleotide point mutations in the 23S rRNA subunit may confer resistance to macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36600":{"category_aro_accession":"3000461","category_aro_cvterm_id":"36600","category_aro_name":"florfenicol","category_aro_description":"Florfenicol is a fluorine derivative of chloramphenicol, where the nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3) and the hydroxyl group (-OH), by a fluorine group (-F). The action mechanism is the same as chloramphenicol's, where the antibiotic binds to the 23S RNA of the 50S subunit of bacterial ribosomes to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin 1A is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"vernamycin B-gamma","category_aro_description":"Vernamycin B-gamma is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2815":{"model_id":"2815","model_name":"Mycobacterium kansasii 23S rRNA with mutation conferring resistance to clarithromycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"8171":"A2265U"},"clinical":{"8171":"A2265U"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"5700"}},"model_sequences":{"sequence":{"4178":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NZ_CP019883.1","fmin":"5018387","fmax":"5021505","strand":"+","sequence":"TTGTAAGTGTCTAAGGGCGCATGGTGGATGCCTTGGCATCGAGAGCCGATGAAGGACGTGGGAGGCTGCGATAAGCCTCGGGGAGCTGTCAACCGAGCGTGGATCCGAGGATTTCCGAATGGGGAAACCCAGCACGAGTGATGTCGTGTTACCCGCATCTGAATATATAGGGTGCGGGAGGGAACGCGGGGAAGTGAAACATCTCAGTACCCGTAGGAGAAGAAAACAAAAGTGATTCCGTAAGTAGTGGCGAGCGAACGCGGAACATGGCTAAACCGCACGCATGGGTAACCGGGTAGGGGTTGTGTGTGCGGGGTTGTGGGATCGATACGTCTCAGCTCTACCCGGCTGAGGGGCAGTCAGAAAGTGTCGTGGTTAACGGAAGTGGCCTGGGATGGTCTGCCGTAGACGGTGAGAGCCCGGTACGTGAAAACCCGGCACCTGCCTTGTATCAATTCCCGAGTAGCAGCGGGCCCGTGGAATCTGCTGTGAATCTGCCGGGACCACCCGGTAAGCCTAAATACTCCTCGATGACCGATAGCGGAATAGTACCGTGAGGGAATGGTGAAAAGTACCCCGGGAGGGGAGTGAAAGAGTACCTGAAACCGTGTGCCTACAATCCGTCAGAGCCCTTTCGTGGGGTGATGGCGTGCCTTTTGAAGAATGAGCCTGCGAGTCAGGGACATGTCGCGAGGTTAACCCGTGCGGGGTAGCCGCAGCGAAAGCGAGTCTGAATAGGGCGTATCGCGCGCGAGCGTGTGTAGTGGCGTGTTCTGGACCCGAAGCGGAGTGATCTACCCATGGCCAGGGTGAAGCGCGGGTAAGACCGCGTGGAGGCCCGAACCCACTTAGGTTGAAGACTGAGGGGATGAGCTGTGGGTAGGGGTGAAAGGCCAATCAAACTCCGTGATAGCTGGTTCTCCCCGAAATGCATTTAGGTGCAGCGTTGCGTGTTTCACCACGGAGGTAGAGCTACTGGATGGCCGATGGGCCCCACTAGGTTACTGACGTCAGCCAAACTCCGAATGCCGTGGTGTATAGCGTGGCAGTGAGACGGCGGGGGATAAGCTCCGTACGTCGAAAGGGAAACAGCCCAGATCGCCGGCTAAGGCCCCAAAGCGTGTGCTAAGTGGGAAAGGATGTGCAGTCGCAGAGACAACCAGGAGGTTGGCTTAGAAGCAGCCACCCTTGAAAGAGTGCGTAATAGCTCACTGGTCAAGTGATTGTGCGCCGATAATGTAGCGGGGCTCAAGCACACCGCCGAAGCCGCGACAACCGCAAGGTTGGGTAGGGGAGCGTCCCTCATTCAGCGAAGCTGCCGGGTGACCGGTGGTGGAGGATGGGGGAGTGAGAATGCAGGCATGAGTAGCGATAAGGCAAGTGAGAACCTTGCCCGCCGAAAGACCAAGGGTTCCTGGGCCAGGCCAGTCCGCCCAGGGTGAGTCGGGACCTAAGGCGAGGCCGACAGGCGTAGTCGATGGACAACGGGTTGATATTCCCGTACCCGTGTGTGGGCGCCCGTGATGAATCAGCGGTACTAACCACCCAAAACCGGATCGATCACTCCCCTTCGGGGGCGTGGAGGTCTGGGGCTGCGTGGAGCCTTCGCTGGTAGTAGTCAAGCGATGGGGTGACGCAGGAAGGCAGCCGTACCAGTCAGTGGTAATACTGGGGCAAGCCAGTAGGGAGAGCGATAGGCAAATCCGTCGCTCACAAATCCTGAGAGGTGACGCATAGCCGATTGAGGCGAATTCGGTGATCCTCTGCTGCCAAGAAAAGCCTCTAGCGAGCACACACACGGCCCGTACCCCAAACCGACACAGGTGGTCAGGTAGAGAATACCAAGGCGTACGAGATAACTATGGTTAAGGAACTCGGCAAAATGCCCCCGTAACTTCGGGAGAAGGGGGACCGGAATACCGTGAACACCCTTGCGGTGGGAGCGGGATTCGGTCGCAGAAACCAGTGAGAAGCGACTGTTTACTAAAAACACAGGTCCGTGCGAAGTCGCAAGACGATGTATACGGACTGACGCCTGCCCGGTGCTGGAAGGTTAAGAGGACCCGTTAACCCGCAAGGGTGAAGCGGAGAATTTAAGCCCCAGTAAACGGCGGTGGTAACTATAACCATCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAACGACTTCTCAACTGTCTCAACCATAGACTCGGCGAAATTGCACTACGAGTAAAGATGCTCGTTACGCGCGGCAGGACGAAAAGACCCCGGGACCTTCACTACAACTTGGTATTGGTGTTCGGTACGGTTTGTGTAGGATAGGTGGGAGACTGTGAAACCTCAACGCCAGTTGGGGTGGAGTCGTTGTTGAAATACCACTCTGATCGTATTGGACACCTAACGTCGAACCCTGAATCGGGTTCACGGACAGTGCCTGGCGGGTAGTTTAACTGGGGCGGTTGCCTCCTAAAATGTAACGGAGGCGCCCAAAGGTTCCCTCAACCTGGACGGCAATCAGGTGGCGAGTGTAAGTGCACAAGGGAGCTTGACTGCGAGACCTACAAGTCAAGCAGGGACGAAAGTCGGGACTAGTGATCCGGCACCTCTGAGTGGAAGGGGTGTCGCTCAACGGATAAAAGGTACCCCGGGGATAACAGGCTGATCTTCCCCAAGAGTCCATATCGACGGGATGGTTTGGCACCTCGATGTCGGCTCGTCGCATCCTGGGGCTGGAGCAGGTCCCAAGGGTTGGGCTGTTCGCCCATTAAAGCGGCACGCGAGCTGGGTTTAGAACGTCGTGAGACAGTTCGGTCTCTATCCGCCGCGCGCGTCAGAAGCTTGAGGAAACCTGTCCCTAGTACGAGAGGACCGGGACGGACGAACCTCTAGTGCACCAGTTGTCCCACCAGGGGCACCGCTGGATAGCTACGTTCGGACAGGATAACCGCTGAAAGCATCTAAGCGGGAAACCTTCTCCAAGATCAGGCTTCTCACCCACTTGGTGGGATAAGGCCCCCCGCAGAACACGGGTTCGATAGGCCAGACCTGGAAGCTCAGTAATGAGTGAAGGGAACTGGCACTAACCGGCCGAAAACTTACCAACACAAATAATCG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41347","NCBI_taxonomy_name":"Mycobacterium kansasii","NCBI_taxonomy_id":"1768"}}}},"ARO_accession":"3004168","ARO_id":"41318","ARO_name":"Mycobacterium kansasii 23S rRNA with mutation conferring resistance to clarithromycin","ARO_description":"Point mutation in the 23S rRNA of Mycobacterium kansasii shown to confer resistance to clarithromycin, a macrolide type antibiotic.","ARO_category":{"41251":{"category_aro_accession":"3004125","category_aro_cvterm_id":"41251","category_aro_name":"23S rRNA with mutation conferring resistance to macrolide antibiotics","category_aro_description":"Nucleotide point mutations in the 23S rRNA subunit may confer resistance to macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36600":{"category_aro_accession":"3000461","category_aro_cvterm_id":"36600","category_aro_name":"florfenicol","category_aro_description":"Florfenicol is a fluorine derivative of chloramphenicol, where the nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3) and the hydroxyl group (-OH), by a fluorine group (-F). The action mechanism is the same as chloramphenicol's, where the antibiotic binds to the 23S RNA of the 50S subunit of bacterial ribosomes to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin 1A is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"vernamycin B-gamma","category_aro_description":"Vernamycin B-gamma is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2816":{"model_id":"2816","model_name":"Mycobacterium smegmatis 23S rRNA with mutation conferring resistance to clarithromycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"7925":"A2266G","7926":"A2267G"},"clinical":{"7925":"A2266G","7926":"A2267G"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"5000"}},"model_sequences":{"sequence":{"4161":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"AB011184.1","fmin":"0","fmax":"3162","strand":"+","sequence":"TTGTAAGTGTTTAAGGGCGCATGGTGGATGCCTTGGCACTGGGAGCCGATGAAGGACGTAGGAGGCTGCGATAAGCCTCGGGGAGCTGTCAACCGAGCGTTGATCCGAGGATGTCCGAATGGGGAAACCCGGCACGAGTGATGTCGTGTCACCAGGCGCTGAATATATAGGCGTCTGGGGGGAACGCGGGGAAGTGAAACATCTCAGTACCCGTAGGAAGAGAAAACAAAATGTGATTCCGTGAGTAGTGGCGAGCGAAAGCGGAGGATGGCTAAACCGTATGCATGTGATACCGGGTAGGGGTTGTGTGTGCGGGGTTGTGGGACCTATCTTTCCGGCTCTACCTGGCTGGAGGGCAGTGAGAAAATGTTGTGGTTAGCGGAAATGGCTTGGGATGGCCTGCCGTAGACGGTGAGAGCCCGGTACGTGAAAACCCGACGTCTGTCTTGATGGTGTTCCCGAGTAGCAGCGGGCCCGTGGAATCTGCTGTGAATCTGCCGGGACCACCCGGTAAGCCTGAATACTTCCCAGTGACCGATAGCGGATTAGTACCGTGAGGGAATGGTGAAAAGTACCCCGGGAGGGGAGTGAAAGAGTACCTGAAACCGTGCGCTTACAATCCGTCAGAGCCCTCGACGTGTCGTGGGGTGATGGCGTGCCTTTTGAAGAATGAGCCTGCGAGTCAGGGACATGTCGCGAGGTTAACCCGGGTGGGGTAGCCGCAGCGAAAGCGAGTCTGAATAGGGCGTATCCACGCAACAGTGTGTGGTGTAGTGGTGTGTTCTGGACCCGAAGCGGAGTGATCTACCCATGGCCAGGGTGAAGCGCGGGTAAGACCGCGTGGAGGCCCGAACCCACTTAGGTTGAAGACTGAGGGGATGAGCTGTGGGTAGGGGTGAAAGGCCAATCAAACTCCGTGATAGCTGGTTCTCCCCGAAATGCATTTAGGTGCAGCGTTGCGTGTTTCTTGCCGGAGGTAGAGCTACTGGATGGCCGATGGGCCCCACAGGGTTACTGACGTCAGCCAAACTCCGAATGCCGGTAAGTCCAAGAGTGCGGCAGTGAGACGGCGGGGGATAAGCTCCGTGCGTCGAGAGGGAAACAGCCCAGATCGCCGGCTAAGGCCCCTAAGCGTGTGCTAAGTGGAAAAGGATGTGCAGTCGCGAAGACAACCAGGAGGTTGGCTTAGAAGCAGCCACCCTTGAAAGAGTGCGTAATAGCTCACTGGTCAAGTGATTGTGCGCCGATAATGTAGCGGGGCTCAAGCACACCGCCGAAGCCGCGGCAACGACCTTGTGTCGTTGGGTAGGGGAGCGTCCTGCATCCGGTGAAGCCGCCGAGTGATCGAGTGGTGGAGGGTGTGGGAGTGAGAATGCAGGCATGAGTAGCGATTAGGCAAGTGAGAACCTTGCCCGCCGAAAGACCAAGGGTTCCTGGGCCAGGCCAGTCCGCCCAGGGTGAGTCGGGACCTAAGGCGAGGCCGACAGGCGTAGTCGATGGACAACGGGTTGATATTCCCGTACCCGTGTATGTGCGTCCATGATGAATCAGCGGTACTAACCATCCAAAACCACCGTGACTGCACCTTTCGGGGTGTGGCGTTGGTGGGGCTGCATGGGACCTTCGTTGGTAGTAGTCAAGCGATGGGGTGACGCAGGAAGGTAGCCGTACCGGTCAGTGGTAATACCGGGGTAAGCCTGTAGGGAGTCAGATAGGTAAATCCGTCTGGCATATATCCTGAGAGGTGATGCATAGCCGAGTGAGGCGAATTCGGTGATCCTATGCTGCCGAGAAAAGCCTCTAGCGAGGACATACACGGCCCGTACCCCAAACCAACACAGGTGGTCAGGTAGAGAATACTAAGGCGTACGAGTGAACTATGGTTAAGGAACTCGGCAAAATGCCCCCGTAACTTCGGGAGAAGGGGGACCCACATGGCGTGTAAGCCTTTACGGCCCAAGCGTGAGTGGGTGGCACAAACCAGTGAGAAGCGACTGTTTACTAAAAACACAGGTCCGTGCGAAGTCGCAAGACGATGTATACGGACTGACGCCTGCCCGGTGCTGGAAGGTTAAGAGGACCCGTTAACCCTTCGGGGTGAAGCGGAGAATTTAAGCCCCAGTAAACGGCGGTGGTAACTATAACCATCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAACGACTTCTCAACTGTCTCAACCATAGACTCGGCGAAATTGCACTACGAGTAAAGATGCTCGTTACGCGCGGCAGGACGAAAAGACCCCGGGACCTTCACTACAACTTGGTATTGGTGCTCGATACGGTTTGTGTAGGATAGGTGGGAGACTGTGAAGCTCACACGCCAGTGTGGGTGGAGTCGTTGTTGAAATACCACTCTGATCGTATTGGGCCTCTAACCTCGGACCGTATATCCGGTTCAGGGACAGTGCCTGGTGGGTAGTTTAACTGGGGCGGTTGCCTCCTAAAATGTAACGGAGGCGCCCAAAGGTTCCCTCAACCTGGACGGCAATCAGGTGTTGAGTGTAAGTGCACAAGGGAGCTTGACTGCGAGACGGACATGTCGAGCAGGGACGAAAGTCGGGACTAGTGATCCGGCACCTCTGAGTGGAAGGGGTGTCGCTCAACGGATAAAAGGTACCCCGGGGATAACAGGCTGATCTTCCCCAAGAGTCCATATCGACGGGATGGTTTGGCACCTCGATGTCGGCTCGTCGCATCCTGGGGCTGGAGCAGGTCCCAAGGGTTGGGCTGTTCGCCCATTAAAGCGGCACGCGAGCTGGGTTTAGAACGTCGTGAGACAGTTCGGTCTCTATCCGCCGCGCGCGTCAGAAGCTTGAGGAAACCTGTCCCTAGTACGAGAGGACCGGGACGGACGAACCTCTGGTATACCAGTTGTCCCACCAGGGGCACGGCTGGATAGCCACGTTCGGACAGGATAACCGCTGAAAGCATCTAAGCGGGAAACCTCTTCCAAGACCAGGCTTCTCACCCTCTAGGAGGGATAAGGCCCCCCGCAGACCACGGGATTGATAGACCAGACCTGGAAGCCTAGTAATAGGTGCAGGGAACTGGCACTAACCGGCCGAAAACTTACAACACCCCATAATCGTTGTAAGAAGAAAACATTGACGCACC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36871","NCBI_taxonomy_name":"Mycobacterium smegmatis","NCBI_taxonomy_id":"1772"}}}},"ARO_accession":"3004169","ARO_id":"41319","ARO_name":"Mycobacterium smegmatis 23S rRNA with mutation conferring resistance to clarithromycin","ARO_description":"Point mutation in the 23S rRNA of Mycobaccterium smegmatis shown to confer resistance to clarithromycin, a macrolide type antibiotic.","ARO_category":{"41251":{"category_aro_accession":"3004125","category_aro_cvterm_id":"41251","category_aro_name":"23S rRNA with mutation conferring resistance to macrolide antibiotics","category_aro_description":"Nucleotide point mutations in the 23S rRNA subunit may confer resistance to macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36600":{"category_aro_accession":"3000461","category_aro_cvterm_id":"36600","category_aro_name":"florfenicol","category_aro_description":"Florfenicol is a fluorine derivative of chloramphenicol, where the nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3) and the hydroxyl group (-OH), by a fluorine group (-F). The action mechanism is the same as chloramphenicol's, where the antibiotic binds to the 23S RNA of the 50S subunit of bacterial ribosomes to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin 1A is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"vernamycin B-gamma","category_aro_description":"Vernamycin B-gamma is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2817":{"model_id":"2817","model_name":"Streptococcus pneumoniae 23S rRNA with mutation conferring resistance to macrolide antibiotics","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"8175":"A2125G","8176":"A2126G","8177":"C2641A","8178":"C2641G"},"clinical":{"8175":"A2125G","8176":"A2126G","8177":"C2641A","8178":"C2641G"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"5000"}},"model_sequences":{"sequence":{"4179":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NZ_CP018138.1","fmin":"1692408","fmax":"1695312","strand":"+","sequence":"TTTGGATAAGTCCTCGAGCTATTAGTATTAGTCCGCTACATGTGTCGCCACACTTCCACTTCTAACCTATCTACCTGATCATCTCTCAGGGCTCTTACTGATATATAATCATGGGAAATCTCATCTTGAGGTGGGTTTCACACTTAGATGCTTTCAGCGTTTATCCCTTCCCTACATAGCTACCCAGCGATGCCTTTGGCAAGACAACTGGTACACCAGCGGTAAGTCCACTCTGGTCCTCTCGTACTAGGAGCAGATCCTCTCAAATTTCCTACGCCCGCGACGGATAGGGACCGAACTGTCTCACGACGTTCTGAACCCAGCTCGCGTGCCGCTTTAATGGGCGAACAGCCCAACCCTTGGGACCGACTACAGCCCCAGGATGCGACGAGCCGACATCGAGGTGCCAAACCTCCCCGTCGATGTGAACTCTTGGGGGAGATAAGCCTGTTATCCCCAGGGTAGCTTTTATCCGTTGAGCGATGGCCCTTCCATACGGAACCACCGGATCACTAAGCCCGACTTTCGTCCCTGCTCGAGTTGTAGCTCTCGCAGTCAAGCTCCCTTATACCTTTATACTCTGCGAATGATTTCCAACCATTCTGAGGGAACCTTTGGGCGCCTCCGTTACCTTTTAGGAGGCGACCGCCCCAGTCAAACTGCCCGTCAGACACTGTCTCCGATAGGGATCACCTATCTGGGTTAGAGTGGCCATAACACAAGGGTAGTATCCCAACAGCGTCTCCTTCGAAACTGGCGTCCCGATCTCTTAGACTCCTACCTATCCTGTACATGTGGTACAGACACTCAATATCAAACTGCAGTAAAGCTCCATGGGGTCTTTCCGTCCTGTCGCGGGTAACCTGCATCTTCACAGGTACTAAAATTTCACCGAGTCTCTCGTTGAGACAGTGCCCAAATCATTACGCCTTTCGTGCGGGTCGGAACTTACCCGACAAGGAATTTCGCTACCTTAGGACCGTTATAGTTACGGCCGCCGTTTACTGGGGCTTCAATTCATACCTTCGCTTACGCTAAGCACTCCTCTTAACCTTCCAGCACCGGGCAGGCGTCACCCCCTATACATCATCTTACGATTTAGCAGAGAGCTGTGTTTTTGATAAACAGTTGCTTGGGCCTATTCACTGCGGCTGACCTAAAGTCAGCACCCCTTCTCCCGAAGTTACGGGGTCATTTTGCCGAGTTCCTTAACGAGAGTTCTCTCGCTCACCTGAGGCTACTCGCCTCGACTACCTGTGTCGGTTTGCGGTACGGGTAGAGTATGTTTAAACGCTAGAAGCTTTTCTTGGCAGTGTGACGTCACTAACTTCGCTACTAAACTTCGCTCCCCATCACAGCTCAATGTTATAGAATTAAGCATTTGACTCAATTCACACCTCACTGCTTAGACAGACTCTTCCAATCGTCTGCTTTAGTTAGCCTACTGCGTCCCTCCATCACTACATACTCTAGTACAGGAATATCAACCTGTTGTCCATCGGATACACCTTTCGGTCTCTCCTTAGGTCCCGACTAACCCAGGGCGGACGAGCCTTCCCCTGGAAACCTTAGTCTTACGGTGGACAGGATTCTCACCTGTCTTTCGCTACTCATACCGGCATTCTCACTTCTATGCGTTCCAGCACTCCTCACGGTATACCTTCATCACACATAGAACGCTCTCCTACCATACCTATAAAGGTATCCACAGCTTCGGTAAATTGTTTTAGCCCCGGTACATTTTCGGCGCAGGGTCACTCGACTAGTGAGCTATTACGCACTCTTTGAATGAATAGCTGCTTCTAAGCTAACATCCTAGTTGTCTGTGCAACCCCACATCCTTTTCCACTTAACAATTATTTTGGGACCTTAGCTGGTGGTCTGGGCTGTTTCCCTTTCGACTACGGATCTTAGCACTCGCAGTCTGACTGCCGACCATAATTCATTGGCATTCGGAGTTTATCTGAGATTGGTAATCCGGGATGGACCCCTCACCCAAACAGTGCTCTACCTCCAAGAATCTCTAATGTCGACGCTAGCCCTAAAGCTATTTCGGAGAGAACCAGCTATCTCCAAGTTCGTTTGGAATTTCTCCGCTACCCACAAGTCATCCAAGCACTTTTCAACGTGCCCTGGTTCGGTCCTCCAGTGCGTCTTACCGCACCTTCAACCTGCTCATGGGTAGGTCACATGGTTTCGGGTCTACGTCATGATACTAATTCGCCCTGTTCAGACTCGGTTTCCCTACGGCTCCGTCTCTTCAACTTAACCTCGCATCATAACGTAACTCGCCGGTTCATTCTACAAAAGGCACGCTCTCACCCATTAACGGGCTCGAACTTGTTGTAGGCACACGGTTTCAGGTTCTATTTCACTCCCCTCCCGGGGTGCTTTTCACCTTTCCCTCACGGTACTGGTTCACTATCGGTCACTAGGGAGTATTTAGGGTTGGGAGATGGTCCTCCCAGATTCCGACGGGATTTCACGTGTCCCGCCGTACTCAGGATACTGCTAGGTACAAAGACTATTTTAAATACGAGGCTATTACTCTCTTTGGCTGATCTTCCCAAATCATTCTTCTATAATCTTTGAGTCCACATTGCAGTCCTACAACCCCGAAGAGTAAACTCTTCGGTTTGCCCTTCTGCCGTTTCGCTCGCCGCTACTAAGGCAATCGCTTTTGCTTTCTCTTCCTGCAGCTACTTAGATGTTTCAGTTCACTGCGTCTTCCTCCTCACATCCTTAACAGATGTGGGTAACAGGTATTACCTGTTGGGTTCCCCCATTCGGAAATCCCTGGATCATCGCTTACTTACAGCTACCCAAGGTATATCGTCGTTTGTCACGTCCTTCGTCGGCTCCTAGTGCCAAGGCATCCACCGTGCGCCCTTATTAACTTAACCT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35917","NCBI_taxonomy_name":"Streptococcus pneumoniae","NCBI_taxonomy_id":"1313"}}}},"ARO_accession":"3004170","ARO_id":"41320","ARO_name":"Streptococcus pneumoniae 23S rRNA with mutation conferring resistance to macrolide antibiotics","ARO_description":"Point mutation in the 23S rRNA of Streptococcus pneumoniae shown to confer resistance to macrolide type antibiotics","ARO_category":{"41251":{"category_aro_accession":"3004125","category_aro_cvterm_id":"41251","category_aro_name":"23S rRNA with mutation conferring resistance to macrolide antibiotics","category_aro_description":"Nucleotide point mutations in the 23S rRNA subunit may confer resistance to macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36600":{"category_aro_accession":"3000461","category_aro_cvterm_id":"36600","category_aro_name":"florfenicol","category_aro_description":"Florfenicol is a fluorine derivative of chloramphenicol, where the nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3) and the hydroxyl group (-OH), by a fluorine group (-F). The action mechanism is the same as chloramphenicol's, where the antibiotic binds to the 23S RNA of the 50S subunit of bacterial ribosomes to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin 1A is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"vernamycin B-gamma","category_aro_description":"Vernamycin B-gamma is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2818":{"model_id":"2818","model_name":"Streptomyces ambofaciens 23S rRNA with mutation conferring resistance to macrolides","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"7931":"A2305G"},"clinical":{"7931":"A2305G"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"5000"}},"model_sequences":{"sequence":{"4163":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NZ_CP012949.1","fmin":"4334992","fmax":"4338141","strand":"+","sequence":"ACAGTGGACGCGAGCATCTGTGGCCAAGTTTTTAAGGGCGCACGGTGGATGCCTTGGCACCAGGAACCGATGAAGGACGTGGGAGGCCACGATAGTCCCCGGGGAGCCGTCAACCAGGCTTTGATCCGGGGGTTTCCGAATGGGGAAACCCGGCAGTCGTCATGGGCTGTCACCCGCTGCTGAACACATAGGCAGTGTGGAGGGAACGCGGGGAAGTGAAACATCTCAGTACCCGCAGGAAGAGAAAACAACCGTGATTCCGGGAGTAGTGGCGAGCGAAACCGGATGAGGCCAAACCGTATACGTGTGAGACCCGGCAGGGGTTGCGTGTGCGGGGTTGTGGGATCTCTCTTTCACAGTCTGCCGGCTGTGAGGCGAGTCAGAAACCGTTGATGTAGGCGAAGGACATGCGAAAGGTCCGGCGTAGAGGGTAAGACCCCCGTAGTCGAAACATCAGCGGCTCGTTTGAGAGACACCCAAGTAGCACGGGGCCCGAGAAATCCCGTGTGAATCTGGCGGGACCACCCGCTAAGCCTAAATATTCCCTGGTGACCGATAGCGGATAGTACCGTGAGGGAATGGTGAAAAGTACCGCGGGAGCGGAGTGAAATAGTACCTGAAACCGTGTGCCTACAAGCCGTGGGAGCGTCGGACATCAAGCTTGCTTGGTGTCTCGTGACTGCGTGCCTTTTGAAGAATGAGCCTGCGAGTTTGCGGTGTGTTGCGAGGTTAACCCGAGTGGGGAAGCCGTAGCGAAAGCGAGTCCGAATAGGGCGTTTCAGTAGCACGCTCAAGACCCGAAGCGGAGTGATCTAGCCATGGGCAGGTTGAAGCGGAGGTAAGACTTCGTGGAGGACCGAACCCACCAGGGTTGAAAACCTGGGGGATGACCTGTGGTTAGGGGTGAAAGGCCAATCAAACTCCGTGATAGCTGGTTCTCCCCGAAATGCATTTAGGTGCAGCGTCGTGTGTTTCTTGCCGGAGGTAGAGCACTGGATAGGCGATGGGCCCTACCGGGTTACTGACCTTAGCCAAACTCCGAATGCCGGTAAGTGAGAGCGCGGCAGTGAGACTGTGGGGGATAAGCTCCATGGTCGAGAGGGAAACAGCCCAGAGCATCGACTAAGGCCCCTAAGCGTACGCTAAGTGGGAAAGGATGTGGAGTCGCACAGACAACCAGGAGGTTGGCTTAGAAGCAGCCACCCTTGAAAGAGTGCGTAATAGCTCACTGGTCTAGTGATTCCGCGCCGACAATGTAGCGGGGCTCAAGCGTACCGCCGAAGTCGTGTCATTCATACAATAGGGCCAACGCCTGTATGGATGGGTAGGGGAGCGTCGTGTGCCGGGTGAAGCAGCCGCGGAAGCGAGTTGTGGACGGTTCACGAGTGAGAATGCAGGCATGAGTAGCGATACAAACGTGAGAAACGTTTGCGCCGATTGACTAAGGGTTCCTGGGTCAAGCTGATCTGCCCAGGGTAAGTCGGGACCTAAGGCGAGGCCGACAGGCGTAGTCGATGGATAACCGGTTGATATTCCGGTACCCGCTGTGAAGCGTCAAACATCGAGCATCGTGATGCTAAGGCCGTGAAGCCGCCCTGATCTCTTCGGAGTTGAGGGGAGTGGTGGAGCCGCCGGACCAAGCGGTTAGTAGGTGAGTGATGGGGTGACGCAGGAAGGTAGTCCATCCCGGGCGGTGGTTGTCCCGGGGTAAGGGTGTAGGACGTCAGGTAGGTAAATCCGCCTGGCAATAGTCTGAGACCTGATGCCGAGCCGATTGTGGTGAAGTGGATGATCCTATGCTGTCGAGAAAAGCCTCTAGCGAGTTTCATGGCGGCCCGTACCCTAAACCGACTCAGGTGGTCAGGTAGAGAATACCGAGGCGTTCGGGTGAACTATGGTTAAGGAACTCGGCAAAATGCCCCCGTAACTTCGGGAGAAGGGGGGCCACACCTGGTGATGATCTTTACGGTCTGAGCTGGGGGTGGCCGCAGAGACCAGCGAGAAGCGACTGTTTACTAAAAACACAGGTCCGTGCGAAGCCGTAAGGCGATGTATACGGACTGACGCCTGCCCGGTGCTGGAACGTTAAGGGGACCGGTTAGCTCCATTTCGGTGGGGCGAAGCTGAGAACTTAAGCGCCAGTAAACGGCGGTGGTAACTATAACCATCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAACGACTTCTCGACTGTCTCAACCATAGGCCCGGTGAAATTGCACTACGAGTAAAGATGCTCGTTTCGCGCAGCAGGACGGAAAGACCCCGGGACCTTTACTACAGTTTGATATTGGTGTTCGGTTCGGCTTGTGTAGGATAGCTGGGAGACTTTGAAGCTCGCACGCCAGTGTGGGTGGAGTCGTCGTTGAAATACCAGTCTGGTCGTGCTGGATGTCTAACCTGGGTCCGTGATCCGGATCAGGGACAGTGTCTGATGGGTAGTTTAACTGGGGCGGTTGCCTCCTAAAGAGTAACGGAGGCGCCCAAAGGTTCCCTCAGCCTGGTTGGCAATCAGGTGTTGAGTGTAAGTGCACAAGGGAGCTTGACTGTGAGACCGACGGGTCGAGCAGGGACGAAAGTCGGGACTAGTGATCCGGCGGTGGCTTGTGGAAGCGCCGTCGCTCAACGGATAAAAGGTACCCCGGGGATAACAGGCTGATCTTCCCCAAGAGTCCATATCGACGGGATGGTTTGGCACCTCGATGTCGGCTCGTCGCATCCTGGGGCTGGAGTCGGTCCCAAGGGTTGGGCTGTTCGCCCATTAAAGCGGTACGCGAGCTGGGTTTAGAACGTCGTGAGACAGTTCGGTCCCTATCCGCTGTGCGCGTAGGAGTCTTGAGAAGGGCTGTCCCTAGTACGAGAGGACCGGGACGGACGAACCTCTGGTGTGCCAGTTGTCCTGCCAAGGGCATGGCTGGTTGGCTACGTTCGGGAGGGATAACCGCTGAAAGCATCTAAGCGGGAAGCCTGCTTCGAGATGAGGACTCCCACCCCCTTGAGGGGTTAAGGCTCCCAGTAGACGACTGGGTTGATAGGCCGGATCTGGAAGCACCGCAAGGTGTGGAGGTGACCGGTACTAATAGGCCGAGGGCTTGTCCTCAGTTG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36864","NCBI_taxonomy_name":"Streptomyces ambofaciens","NCBI_taxonomy_id":"1889"}}}},"ARO_accession":"3004171","ARO_id":"41322","ARO_name":"Streptomyces ambofaciens 23S rRNA with mutation conferring resistance to macrolide antibiotics","ARO_description":"Point mutation in the 23S rRNA of Streptomyces ambofaciens shown to confer resistance to macrolide type antibiotics","ARO_category":{"41251":{"category_aro_accession":"3004125","category_aro_cvterm_id":"41251","category_aro_name":"23S rRNA with mutation conferring resistance to macrolide antibiotics","category_aro_description":"Nucleotide point mutations in the 23S rRNA subunit may confer resistance to macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36600":{"category_aro_accession":"3000461","category_aro_cvterm_id":"36600","category_aro_name":"florfenicol","category_aro_description":"Florfenicol is a fluorine derivative of chloramphenicol, where the nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3) and the hydroxyl group (-OH), by a fluorine group (-F). The action mechanism is the same as chloramphenicol's, where the antibiotic binds to the 23S RNA of the 50S subunit of bacterial ribosomes to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin 1A is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"vernamycin B-gamma","category_aro_description":"Vernamycin B-gamma is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2819":{"model_id":"2819","model_name":"Escherichia coli 23S rRNA with mutation conferring resistance to oxazolidinone antibiotics","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"7932":"G2032A","7933":"G2032U","7934":"G2032C","7935":"G2447U"},"clinical":{"7932":"G2032A","7933":"G2032U","7934":"G2032C","7935":"G2447U"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"5000"}},"model_sequences":{"sequence":{"4164":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"AE014075.1","fmin":"237159","fmax":"240063","strand":"+","sequence":"GGTTAAGCGACTAAGCGTACACGGTGGATGCCCTGGCAGTCAGAGGCGATGAAGGACGTGCTAATCTGCGATAAGCGTCGGTAAGGTGATATGAACCGTTATAACCGGCGATTTCCGAATGGGGAAACCCAGTGTGTTTCGACACACTATCATTAACTGAATCCATAGGTTAATGAGGCGAACCGGGGGAACTGAAACATCTAAGTACCCCGAGGAAAAGAAATCAACCGAGATTCCCCCAGTAGCGGCGAGCGAACGGGGAGGAGCCCAGAGCCTGAATCAGTGTGTGTGTTAGTGGAAGCGTCTGGAAAGGCGCGCGATACAGGGTGACAGCCCCGTACACAAAAATGCACATGCTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGGGGGACCATCCTCCAAGGCTAAATACTCCTGACTGACCGATAGTGAACCAGTACCGTGAGGGAAAGGCGAAAAGAACCCCGGCGAGGGGAGTGAAAAAGAACCTGAAACCGTGTACGTACAAGCAGTGGGAGCATGCTTAGGCGTGTGACTGCGTACCTTTTGTATAATGGGTCAGCGACTTATATTCTGTAGCAAGGTTAACCGAATAGGGGAGCCGAAGGGAAACCGAGTCTTAACTGGGCGTTAAGTTGCAGGGTATAGACCCGAAACCCGGTGATCTAGCCATGGGCAGGTTGAAGGTTGGGTAACACTAACTGGAGGACCGAACCGACTAATGTTGAAAAATTAGCGGATGACTTGTGGCTGGGGGTGAAAGGCCAATCAAACCGGGAGATAGCTGGTTCTCCCCGAAAGCTATTTAGGTAGCGCCTCGTGAACTCATCTCCGGGGGTAGAGCACTGTTTCGGCAAGGGGGTCATCCCGACTTACCAACCCGATGCAAACTGCGAATACCGGAGAATGTTATCACGGGAGACACACGGCGGGTGCTAACGTCCGTCGNGAAGAGGGAAACAACCCAGACCGCCAGCTAAGGTCCCAAAGTCATGGTTAAGTGGGAAACGATGTGGGAAGGCCCAGACAGCCAGGATGTTGGCTTAGAAGCAGCCATCATTTAAAGAAAGCGTAATAGCTCACTGGTCGAGTCGGCCTGCGCGGAAGATGTAACGGGGCTAAACCATGCACCGAAGCTGCGGCAGCGACGCTTATGCGTTGTTGGGTAGGGGAGCGTTCTGTAAGCCTGTGAAGGTGTACTGTGAGGTATGCTGGAGGTATCAGAAGTGCGAATGCTGACATAAGTAACGATAAAGCGGGTGAAAAGCCCGCTCGCCGGAAGACCAAGGGTTCCTGTCCAACGTTAATCGGGGCAGGGTGAGTCGACCCCTAAGGCGAGGCCGAAAGGCGTAGTCGATGGGAAACAGGTTAATATTCCTGTACTTGGTGTTACTGCGAAGGGGGGACGGAGAAGGCTATGTTGGCCGGGCGACGGTTGTCCCGGTTTAAGCGTGTAGGCTGGTTTTCCAGGCAAATCCGGAAAATCAAGGCTGAGGCGTGATGACGAGGCACTACGGTGCTGAAGCAACAAATGCCCTGCTTCCAGGAAAAGCCTCTAAGCATCAGGTAACATCAAATCGTACCCCAAACCGACACAGGTGGTCAGGTAGAGAATACCAAGGCGCTTGAGAGAACTCGGGTGAAGGAACTAGGCAAAATGGTGCCGTAACTTCGGGAGAAGGCACGCTGATATGTAGGTGAAGCGACTTGCTCGTGGAGCTGAAATCAGTCGAAGATACCAGCTGGCTGCAACTGTTTATTAAAAACACAGCACTGTGCAAACACGAAAGTGGACGTATACGGTGTGACGCCTGCCCGGTGCCGGAAGGTTAATTGATGGGGTTAGCGCAAGCGAAGCTCTTGATCGAAGCCCCGGTAAACGGCGGCCGTAACTATAACGGTCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAATGATGGCCAGGCTGTCTCCACCCGAGACTCAGTGAAATTGAACTCGCTGTGAAGATGCAGTGTACCCGCGGCAAGACGGAAAGACCCCGTGAACCTTTACTATAGCTTGACACTGAACATTGAGCCTTGATGTGTAGGATAGGTGGGAGGCTTTGAAGTGTGGACGCCAGTCTGCATGGAGCCGACCTTGAAATACCACCCTTTAATGTTTGATGTTCTAACGTTGACCCGTAATCCGGGTTGCGGACAGTGTCTGGTGGGTAGTTTGACTGGGGCGGTCTCCTCCTAAAGAGTAACGGAGGAGCACGAAGGTTGGCTAATCCTGGTCGGACATCAGGAGGTTAGTGCAATGGCATAAGCCAGCTTGACTGCGAGCGTGACGGCGCGAGCAGGTGCGAAAGCAGGTCATAGTGATCCGGTGGTTCTGAATGGAAGGGCCATCGCTCAACGGATAAAAGGTACTCCGGGGATAACAGGCTGATACCGCCCAAGAGTTCATATCGACGGCGGTGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGGGCTGAAGTAGGTCCCAAGGGTATGGCTGTTCGCCATTTAAAGTGGTACGCGAGCTGGGTTTAGAACGTCGTGAGACAGTTCGGTCCCTATCTGCCGTGGGCGCTGGAGAACTGAGGGGGGCTGCTCCTAGTACGAGAGGACCGGAGTGGACGCATCACTGGTGTTCGGGTTGTCATGCCAATGGCACTGCCCGGTAGCTAAATGCGGAAGAGATAAGTGCTGAAAGCATCTAAGCACGAAACTTGCCCCGAGATGAGTTCTCCCTGACTCCTTGAGGGTCCTGAAGGAACGTTGAAGACGACGACGTTGATAGGCCGGGTGTGTAAGCGCAGCGATGCGTTGAGCTAACCGGTACTAATGAACCGTGAGGCTTAACCTT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36763","NCBI_taxonomy_name":"Escherichia coli CFT073","NCBI_taxonomy_id":"199310"}}}},"ARO_accession":"3004173","ARO_id":"41324","ARO_name":"Escherichia coli 23S rRNA with mutation conferring resistance to oxazolidinone antibiotics","ARO_description":"Point mutation in the 23S rRNA of Escherichia coli shown to confer resistance to oxazolidinone type antibiotics","ARO_category":{"41323":{"category_aro_accession":"3004172","category_aro_cvterm_id":"41323","category_aro_name":"23S rRNA with mutation conferring resistance to oxazolidinone antibiotics","category_aro_description":"Point mutations in the 23S rRNA subunit may confer resistance to oxazolidinone antibiotics","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36600":{"category_aro_accession":"3000461","category_aro_cvterm_id":"36600","category_aro_name":"florfenicol","category_aro_description":"Florfenicol is a fluorine derivative of chloramphenicol, where the nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3) and the hydroxyl group (-OH), by a fluorine group (-F). The action mechanism is the same as chloramphenicol's, where the antibiotic binds to the 23S RNA of the 50S subunit of bacterial ribosomes to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin 1A is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"vernamycin B-gamma","category_aro_description":"Vernamycin B-gamma is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"36218":{"category_aro_accession":"3000079","category_aro_cvterm_id":"36218","category_aro_name":"oxazolidinone antibiotic","category_aro_description":"Oxazolidinones are a class of synthetic antibiotics discovered the the 1980's.  They inhibit protein synthesis by binding to domain V of the 23S rRNA of the 50S subunit of bacterial ribosomes.  Linezolid is the only member of this class currently in clinical use.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2820":{"model_id":"2820","model_name":"Chlamydia trachomatis 23S rRNA with mutation conferring resistance to macrolide antibiotics","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"7938":"A2109C","7939":"A2663C"},"clinical":{"7938":"A2109C","7939":"A2663C"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"5000"}},"model_sequences":{"sequence":{"4165":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NR_076160.1","fmin":"0","fmax":"2940","strand":"+","sequence":"CAGACCAAGTTAATAAGAGCTATTGGTGGATGCCTTGGCATTGACAGGCGAAGAAGGACGCGAATACCTGCGAAAAGCTCCGGCGAGCTGGTGATAAGCAAAGACCCGGAGGTATCCGAATGGGGAAACCCGGTAGAGTAATAGACTACCATTGCATGCTGAATACATAGGTATGCAAAGCGACACCTGCCGAACTGAAACATCTTAGTAAGCAGAGGAAAAGAAATCGAAGAGATTCCCTGTGTAGCGGCGAGCGAAAGGGGAATAGCCTAAACCGAGCTGATAAGGCTCGGGGTTGTAGGATTGAGGATAAAGGATCAGGACTCCTAGTTGAACACATCTGGAAAGATGGATGATACAGGGTGATAGTCCCGTAGACGAAAGGAGAGAAAGACCGACCTCAACACCTGAGTAGGACTAGACACGTGAAACCTAGTCTGAATCTGGGGAGACCACTCTCCAAGGCTAAATACTAGTCAATGACCGATAGTGAACCAGTACTGTGAAGGAAAGGCGAAAAGAACCCTTGTTAAGGGAGTGAAATAGAACCTGAAACCAGTAGCTTACAAGCGGTCGGAGACCAATGGCCCGTAAGGGTCAAGGTTGACGGCGTGCCTTTTGCATGATGAGCCAGGGAGTTAAGCTAAACGGCGAGGTTAAGGGATATACATTCCGGAGCCGGAGCGAAAGCGAGTTTTAAAAGAGCGAAGAGTCGTTTGGTTTAGACACGAAACCAAGTGAGCTATTTATGACCAGGTTGAAGCATGGGTAAAACTATGTGGAGGACCGAACTAGTACCTGTTGAAAAAGGTTTGGATGAGTTGTGAATAGGGGTGAAAGGCCAATCAAACTTGGAGATATCTTGTTCTCTCCGAAATAACTTTAGGGTTAGCCTCGGATAATAAGCTTTTGGGGGTAGAGCACTGAATTCTAGCGGGGGCCTACCGGCTTACCAACGGAAATCAAACTCCGAATACCAGAAGCGAGTCCGGGAGATAGACAGCGGGGGCTAAGCTTCGTTGTCGAGAGGGGAACAGCCCAGACCGCCGATTAAGGTCCCTAATTTTATGCTAAGTGGGTAAGGAAGTGATGATTCGAAGACAGTTGGAATGTTGGCTTAGAGGCAGCAATCATTTAAAGAGTGCGTAACAGCTCACCAATCGAGAATCATTGCGCCGATAATAAACGGGACTAAGCATAAAACCGACATCGCGGGTGTGTCGATAAGACACGCGGTAGGAGAGCGTAGTATTCAGCAGAGAAGGTGTACCGGAAGGAGCGCTGGAGCGGATACTAGTGAAGATCCATGGCATAAGTAACGATAAAGGGAGTGAAAATCTCCCTCGCCGTAAGCCCAAGGTTTCCAGGGTCAAGCTCGTCTTCCCTGGGTTAGTCGGCCCCTAAGTTGAGGCGTAACTGCGTAGACGATGGAGCAGCAGGTTAAATATTCCTGCACCACCTAAAACTATAGCGAAGGAATGACGGAGTAAGTTAAGCACGCGGACGATTGGAAGAGTCCGTAGAGCGATGAGAACGGTTAGTAGGCAAATCCGCTAACATAAGATCAGGTCGCGATCAAGGGGAATCTTCGGGGGAACCGATGGTGTGGAGCGAGGCTTTCAAGAAATAATTTCTAGCTGTTGATGGTGACCGTACCAAAACCGACACAGGTGGGCGAGATGAATATTCTAAGGCGCGCGAGATAACTTTCGTTAAGGAACTCGGCAAATTATCCCCGTAACTTCGGAATAAGGGGAGCCTTTTAGGGTGACTATGGAACGATAGGAGCCCCGGGGGGCCGCAGAGAAATGGCCCAGGCGACTGTTTAGCAAAAACACAGCACTATGCAAACCTCTAAGGGGAAGTATATGGTGTGACGCCTGCCCAATGCCAAAAGGTTAAAGGGATATGTCAGCTGCAAAGCGAAGCATTGAACCTAAGCCCTGGTGAATGGCCGCCGTAACTATAACGGTGCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGTGTAACGATCTGGGCACTGTCTCAACGAAAGACTCGGTGAAATTGTAGTAGCAGTGAAGATGCTGTTTACCCGCGAAAGGACGAAAAGACCCCGTGAACCTTTACTGTACTTTGGTATTGATTTTTGGTTTGTTATGTGTAGGATAGCCAGGAGACTAAGAACACTCTTCTTCAGGAGAGTGGGAGTCAACGTTGAAATACTGGTCTTAACAAGCTGGGAATCTAACATTATTCCATGAATCTGGAAGATGGACATTGCCAGACGGGCAGTTTTACTGGGGCGGTATCCTCCTAAAAAGTAACGGAGGAGCCCAAAGCTTATTTCATCGTGGTTGGCAATCACGAGTAGAGCGTAAAGGTATAAGATAGGTTGACTGCAAGACCAACAAGTCGAGCAGAGACGAAAGTCGGGCTTAGTGATCCGGCGGTGGAAAGTGGAATCGCCGTCGCTTAACGGATAAAAGGTACTCCGGGGATAACAGGCTGATCGCCACCAAGAGTTCATATCGACGTGGCGGTTTGGCACCTCGATGTCGGCTCATCGCATCCTGGGGCTGGAGAAGGTCCCAAGGGTTTGGCTGTTCGCCAATTAAAGCGGTACGCGAGCTGGGTTCAAAACGTCGTGAGACAGTTTGGTCTCTATCCTTCGTGGGCGCAGGATACTTGAGAGGAGCTGTTCCTAGTACGAGAGGACCGGAATGGACGAACCAATGGTGTGTCGGTTGTTTTGCCAAGGGCATAGCCGGGTGGCTCACGTTCGGAAAGGATAAGCATTGAAAGCATCTAAATGCCAAGCCTCCCTCAAGATAAGGTATCCCAATGAGACTCCATGTAGACTACGTGGTTGATAGGTTGGAGGTGTAAGCACAGTAATGTGTTCAGCTAACCAATACTAATAAGTCCAAAGACTTGGTCTT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40470","NCBI_taxonomy_name":"Chlamydia trachomatis","NCBI_taxonomy_id":"813"}}}},"ARO_accession":"3004174","ARO_id":"41325","ARO_name":"Chlamydia trachomatis 23S rRNA with mutation conferring resistance to macrolide antibiotics","ARO_description":"Point mutation in the 23S rRNA of Chlamydia trachomatis shown to confer resistance to macrolide type antibiotics","ARO_category":{"41251":{"category_aro_accession":"3004125","category_aro_cvterm_id":"41251","category_aro_name":"23S rRNA with mutation conferring resistance to macrolide antibiotics","category_aro_description":"Nucleotide point mutations in the 23S rRNA subunit may confer resistance to macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36600":{"category_aro_accession":"3000461","category_aro_cvterm_id":"36600","category_aro_name":"florfenicol","category_aro_description":"Florfenicol is a fluorine derivative of chloramphenicol, where the nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3) and the hydroxyl group (-OH), by a fluorine group (-F). The action mechanism is the same as chloramphenicol's, where the antibiotic binds to the 23S RNA of the 50S subunit of bacterial ribosomes to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin 1A is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"vernamycin B-gamma","category_aro_description":"Vernamycin B-gamma is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2822":{"model_id":"2822","model_name":"Mycoplasma hominis 23S rRNA with mutation conferring resistance to macrolide antibiotic","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"7942":"G2087A","7943":"A2578U"},"clinical":{"7942":"G2087A","7943":"A2578U"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"5000"}},"model_sequences":{"sequence":{"4166":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"CP011538.1","fmin":"333282","fmax":"336166","strand":"-","sequence":"ACCAATAAATTTATTAGTACTGGTCAGCTGAATGCATTGCTGCACTTACACCTCCAGCCTATCAACCTCATAGTCTATAAGGAATTTTAAAGGGAATACTAATCTTTGAGGGGGCTTCCCGCTTAGATGCTTTCAGCGGTTATCCCTGCCGCACTTGGCTACCCAGCTATGCTTCTGGCGAAACAACTGGCACACCATCGGTGCGTCCACTCCGGTCCTCTCGTACTAAGAGTAGCTCTCATCAATATTCCAACGCCCACATCAGATAGGAACCAAACTGTCTCACGACGTTTTGAACCCAGCTCGCGTACCGCTTTAATGGGCGAACAGCCCAACCCTTGGAACCGACTCCAGCTCCAGGATGCGATGAGCCGACATCGAGGTGCCAAACCTTCCCGTCGATGTGATCTCTTGGGAAAGATAAGCCTGTTATCCCCGGGGTAGCTTTTATCCGTTGAGCGACGGCCTTTCCACGAAGAACCGCCGGATCACTAAGTCCTGCTTTCGCACCTGCTCGACTTGTAGGTCTCACAGTCAATCACACTTCTACCTTTATGCTCTTAGATACGGTTTCTGACCGTATTGAGTGTAACTTTGAACGCCTCCGTTACCCTTTAGGAGGCGACCGCCCCAGTCAAACTACCCACCACACACTGTCCTCTTCCCGGATAACGGGAACAAGTTAGAAGTTCAATGTAACAAGGGTGGTATTTCAACGGCGACTACTCTTAAACTAGCGTTCAAGCATCAACGTCTCCCACCTATCCTACACATGTTAAATCAAACTCCAATATGAAGTTATAGTAAAGCTCCACGGGGTCTTTTCGTCTAGATGCGGGTCTCCGGCGTCTTCGCCGGAACCATAATTTCACCGAGTCTATTGTCGAGACAGTTAAGAGATAATTACTCCTTTCGTGCAGGTCAGTATTTAGCCGACAAGGAATTTCGCTACCTTAGGACCGTTATAGTTACGGCCGCCGTTCACCCGGGCTTCACATTAATGCTTCGCTAATGCTAACACCTCTGCTTAACCTTCGGGCACTGGGCAGGAGTCACCCCATATACATCATCTTACGACTTAGCATAGAGCTGTGTTTTTGATAAACAGTTCCCCCTTACTATTCACTGCGGCCCACATTTTATTGTGGGCATCCCTTCTTGCGAACTTACGGGATGAATTTGCAGAGTTCCTTGACAATAGTTTTCTCGCTCGCCTTAGAATACTCATCTTGGGGACGTGTGTCCGTTCTCGGTACGGGTTTCCTAACACTTAATGTTAGAAGCTTTTTTAAGAGGCATGAAATCATCTAATTCGCTACTCAGTTGCCCTTTTGCTATGCGTCGTAACTCCCAGTTAAGTTATGCGGATTTGCCTACATAACCCAGTTGTTACTTACCCCACAATCCAATTAGTGGTAAAATTATCCTTCCCCGTCACTCCATCACATGTTAAGAAAGTACAGGAATATTAACCTGTTGTCCATCGGCTACGCCTTTCGGCCTCGTCTTAGGACCCGACTAACCCTGGGTGGACGAACCTTGCCCAGGAAACCTTCCCCAATAGGCGTCAGAGATTCTCACTCTGAATCGTTACTCATACCGGCATTCTCACTTGTAAGCGCTCCACCAGTCCTCACGGTCTGGCTTCTAAGCCCTTACAACGCTCTCCTAACGCATTTCTGCCCGTAGCTTCGGTATTGTGTTTTAGTCCCGTTGAATTATCGGCACAAAGTCTCTCGACTAGTGAGCTATTACGCACTCTTTAAACGGTGGCTGCTTCTAAGCCAACATCCTAGCTGTTTAAGAAACTTCACAACCTTTCTCACTTAACACAATTTTGGGACCTTAGCTGACGATCTGGGTTGTTCCCCTCGCGTGCATCGACGTTATCACCGATGTACCGACTGCATAGTAATACATGATAGTATTCGGAGTTTGATTATAGTCAGTACGGCTAGGCGCCGCCATTCCATATTCAGTGCTCTACCCCCATCATTTAACACTACACGCTAGCCCTAAAGCTATTTCGGAGAGAACCAGCTATCTCCAAGTTCGATTGGAATTTCACCCCTACCCACAAGTCATCCGGGCACTTTTTAGCGTACTGCGGTTCGGTCCTCCACTTAGTGTTACCTAAGTTTCAACCTGCTCATGGGTAGATCACCTGGTTTCGGGTCTATATCAACATACTAAATCGCCCTATTCAGACTCGATTTCTCTACGGCTTCGCTTTATTCTACTTAACCTCGCATGTTGACATAACTCGCCGGTCCATTCTGCAAGATGTACGCCATCACCCATTAACGGGCTCTGACTAACTGTAAGTAATTGGTTTCAGAATCTATTTCACTCCCCTCCCGGGGTTCTTTTCACCTTTCCCTCACGGTACTAGTTCACTATCGGTGTCTGGTTAGTATTTAGCCTTACCGGGTGGTCCCGGCAAATTCAGACAGGGTTTCACGTGCCCCGCCCTACTCAGGATACTGCTAGGAGATTTATACATTTCGCTTACGGGAATTTCACCCTCTATGTTTAAGCGTTCCAACTTATTCTGCTATGTACAAATTCATTAATCCATGTCGCAGTCCTACAACCCCAACAACATGTGTTGGTTTGGGCTCTTCCCCGTTCGCTCGCCACTACTTAGGGAATCATTCTTTATTTTCTCTTCCTGCTGCTACTGAGATGTTTCAATTCACAGCGTGTCTCTTCATTCGACTATGAATTCATCGATATGATAATTGAGGATTAGCTCAATTAGGTTTCCCCATTCGGAAATCCCCGGATAACAGCTTATTTCCAGCTAACCGAGGCTTATCGCAGGTAATCACGTCCTTCATCGACTTCCAGACCCAAGGCATCCACCAAAAACTCTTGCTTGTTT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40311","NCBI_taxonomy_name":"Mycoplasma hominis","NCBI_taxonomy_id":"2098"}}}},"ARO_accession":"3004176","ARO_id":"41327","ARO_name":"Mycoplasma hominis 23S rRNA with mutation conferring resistance to macrolide antibiotics","ARO_description":"Point mutation in the 23S rRNA of Mycoplasma hominis shown to confer resistance to macrolide type antibiotics","ARO_category":{"41251":{"category_aro_accession":"3004125","category_aro_cvterm_id":"41251","category_aro_name":"23S rRNA with mutation conferring resistance to macrolide antibiotics","category_aro_description":"Nucleotide point mutations in the 23S rRNA subunit may confer resistance to macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36600":{"category_aro_accession":"3000461","category_aro_cvterm_id":"36600","category_aro_name":"florfenicol","category_aro_description":"Florfenicol is a fluorine derivative of chloramphenicol, where the nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3) and the hydroxyl group (-OH), by a fluorine group (-F). The action mechanism is the same as chloramphenicol's, where the antibiotic binds to the 23S RNA of the 50S subunit of bacterial ribosomes to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin 1A is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"vernamycin B-gamma","category_aro_description":"Vernamycin B-gamma is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2823":{"model_id":"2823","model_name":"Mycoplasma fermentans 23S rRNA with mutation conferring resistance to macrolide antibiotics","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"5000"},"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"8308":"G2057A"},"clinical":{"8308":"G2057A"}}},"model_sequences":{"sequence":{"4167":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NC_021002.1","fmin":"901870","fmax":"904756","strand":"-","sequence":"CTTTTAAACCGATCGATTTATTAGTATTGGTCAGCTCAACGTATTACTACGCTTACACCTCCAACCTATCAACCTCATAGTCTATAAGGAATCTCAAGGGAATACTTATCTCTGAGGAGGCTTCCCACTTAGATGCTTTCAGCGGTTATCCTTTCCGTACTTAGCTACCCAGCTATGCTCCTGGCGGAACAACTGGAACACCAGTGGTACGTCCACTCCGGTCCTCTCGTACTAAGAGCGGCTCTCATCAATATTCCAACGCCCACATCAGATAGGGACCAAACTGTCTCACGACGTTTTGAACCCAGCTCGCGTACCGCTTTAATGGGCGAACAGCCCAACCCTTGGAACCGACTCCAGCTCCAGGATGCGATGAGCCGACATCGAGGTGCCAAACCTTGCCGTCGATGTGATCTCTTGGGCAAGATAAGCCTGTTATCCCCAGGGTAACTTTTATCCGTTGAGCGACTGCCATTCCACAATGTACAGCCGGATCACTAAGTCCTGCTTTCGCACCTGCTCGACTTGTAAGTCTCACAGTCAAGCACACTTCTACCTTTGCGCTCTACATACGGTTTCTGACCGTACTGAGTGTACCTTTGAACGCCTCCGTTACTCTTTAGGAGGCGACCGCCCCAGTCAAACTACCCGTCACGCACTGTCCACCCACCTGATGATGATGGCATGTTAGAAACTCAATATACCAAGGGTGGTATTTCAAGGATGACTCCACGAGAACTAGCGTCCTCGCTTCAAAGTCTCCCACCTATCCTACACATGTTAGACCAAGTTCCAATACGAAACTGTAGTAAAGCTCCATGGGGTCTTTTCGTCTTGATGCGGGTACCCAGCGTTTTCACTGGGACCATAATTTCACCGAGTCTAGTGTTGAGACAGTTGAGAGATCATTGCGCCTTTCGTGCAGGTCAGTATTTAGCCGACAAGGAATTTCGCTACCTTAGGACCGTTATAGTTACGGCCGCCGTTCACCCGGGCTTCATTTCAACGCTTCGCAAATGCTAACGCATCCACTTAACCTTCGGGCACTGGGCAGGCTTCACCCCCTATACATCACCTTGCGGTTTAGCAGAGAGCTGTGTTTTTGATAAACAGTTGCCCCTCATAATTTACTGTGGCCTAAGTGTTACCTTAGGCGCCCCTTCTTGCGAACTTACGGGGTCATTTTGCAGAGTTCCTTAACACTAGTTTTCTCGCTCGCCTTAGAATACTCATCTCGGGGACGTGTGTCCGTTCTCGGTACAGGTTTCCATAATATTAAGTTTAGAAGCTTTTCTTGGAAGTGTGGAATCATCTAATTCGGTTTGACCCTATGCATCACGCCTCCCGGTTATAGACTGCGGATTTGCCTACAGTCACCAGTGAACGCTTACCCCACAATCCAGTAAGTGGTAAGATTATCCTCCTCCGTCACTCCATCACTATTATAGAAAGTACAGGAATATTAACCTGTTGTCCATCGGCTACGCTTTTCAGCCTCGTCTTAGGTCCTGACTAACCCTGGGTGGACGAACCTTGCCCAGGAAACCTTCCCCAATAGGCGTCGTAGATTCTCACTACGAATCGTTACTCATACCGGCATTCTCACTTCCTAGCGCTCCACCAGTCCTCACGGTCTGACTTCATTGCCCTAGGAACGCTCCTCTAACGTAAATATAATTACCCGCGGCTTCGGTATCGTGTTTTAGTCCCGTTAAATTGTTGGCGCAAGGTCTCTTGACTAGTGAGCTATTACGCACTCTTTAAAAGGTGGCTGCTTCTGAGCCAACTTCCTAGTTGTTTATGAAACCTCACAACCTTTCTCACTTAACACGATTTTGGGACCTTAGCCGGCGATCTGGGTTGTTGCCCTCGCGAGCCGGGACGTTAGCACCCCGGTTCCGACTGCATAGCAATACATAGCGGTATTCGGAGTTTGATTATAGTCAGTACCCCTAGGCGAGGCCATTCCATATTCAGTGCTCTACCACCACTACTTAACACTACACGCTAGCCCTAAAGCTATTTCGAGGAGAACCAGCTATCTCCAAGTTCGATTGGAATTTCTCCACTATTCACAAGTCATCCGGGCACTTTTCAGCGTACTACGGTTCGGCCCTCCGCTTGGGGTTAGCCAAGTTTCAGCCTGCTCATGAATAGATCACATGGTTTCGGGTATATGACAACATACTAAGACGCCCTATTAAGACTCGATTTCTCTACGGCTCCGCTTTTTTCTGCTTAACCTCGCATGCTGTCATAACTCGCCGGTCCATACTGCAAGATGTACGCCATCACCCATAAACGGGCTCTGACTAATTGTAAGTAAGTGGTTTCAGAATCTATTTCACTCCCCTCTCGGGGTTCTTTTCACCTTTCCCTCACGGTACTAGTTCACTATCGGTGTCTGATTAGTATTTAGCCTTACCGGGTGGTCCCGGCAGATTCAGACAGGGTTCCACGTGCCCCGCCCTACTCAGGATACGATCAGAAGACTTAACAATTTCACATACGGGGGTATCACCCTCTATGCCGCTTCTTCCCAAAAGCTTCTGCTATCATTAAGTTTTGTAACTTCATGTAGATCGTCCTACAACCCCCATTGCTGGGTTTGGGCTCTTTCTCGTTCGCTCGCCGCTACTAAAGAAATCATTGTTTATTTTCTCTTCCTCTTGCTACTAAGATGTTTCAGTTCACAAGGTGTCTCACTCAAGTTCCTATGAATTCAGAACAAGGCAACTAGGCATTACCCTAGTTAGGTTTCCCCATTCGGAAATCCCCGTTTCATAGCATATTTCCGGCTCCACGAGGCTTATCGCAGGTAATCACGTCCTTCATCGACTTTCAGACCCAAGGCATCCACCACAAACTCTTCCTTATTTAAAAGTA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41329","NCBI_taxonomy_name":"Mycoplasma fermentans PG18","NCBI_taxonomy_id":"496833"}}}},"ARO_accession":"3004177","ARO_id":"41328","ARO_name":"Mycoplasma fermentans 23S rRNA with mutation conferring resistance to macrolide antibiotics","ARO_description":"Point mutation in the 23S rRNA of Mycoplasma fermentans shown to confer resistance to macrolide type antibiotics","ARO_category":{"41251":{"category_aro_accession":"3004125","category_aro_cvterm_id":"41251","category_aro_name":"23S rRNA with mutation conferring resistance to macrolide antibiotics","category_aro_description":"Nucleotide point mutations in the 23S rRNA subunit may confer resistance to macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36600":{"category_aro_accession":"3000461","category_aro_cvterm_id":"36600","category_aro_name":"florfenicol","category_aro_description":"Florfenicol is a fluorine derivative of chloramphenicol, where the nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3) and the hydroxyl group (-OH), by a fluorine group (-F). The action mechanism is the same as chloramphenicol's, where the antibiotic binds to the 23S RNA of the 50S subunit of bacterial ribosomes to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin 1A is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"vernamycin B-gamma","category_aro_description":"Vernamycin B-gamma is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2824":{"model_id":"2824","model_name":"Mycoplasma pneumoniae 23S rRNA mutation conferring resistance to erythromycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"7945":"A2063G","7946":"A2064G"},"clinical":{"7945":"A2063G","7946":"A2064G"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"5000"}},"model_sequences":{"sequence":{"4169":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NR_077056.1","fmin":"0","fmax":"2905","strand":"+","sequence":"CAATAAGTTACTAAGGGCTTATGGTGGATGCCTTGGCACTAATAGGCGATGAAGGACGTGTTAACCTGCGATAAGCTTCGGGTAGGTGGTAAGAACCTCAGATCCGGAGATTTCCGAATGGAGCAATCCGGTAGTTGGAAACAGCTATCATTAATTGATGAATAAATAGTCAATTAAAGCAATACGTGGTGAAGTGAAACATCTCAGTAGCCACAGGAAAAGAAAACGAATGTGATTCCGTGTGTAGTGGCGAGCGAAAGCGGAACAGGCCAAACTTATCATTAGATAGGGGTTGTAGGGCTTGCAATGTGGACTTGAAAACGATAGAAGAAGCTGTTGGAAAGCAGCGCGCAAAAGGGTGATAGCCCCGTATTTGAAATTGTTTTCATACCTAGCGAGATCCCTGAGTAGCTCGGAAAACGTTATTTTGAGTGAATCTGCCCAGACCATTGGGTAAGCCTAAATACTAATTAGTGACCGATAGCGAAACAGTACCGTGAGGGAAAGGTGAAAAGAACCCAGAGATGGGAGTGAAATAGATTCTGAAACCATATGCCTACAACGTGTCAGAGCACATTAATGTGTGATGGCGTGCGTTTTGAAGTATGAGCCGGCGAGTTATGATAGCAAGCGTTAGTTAACCAGGAGATGGGGAGCTGTAGCGAAAGCGAGTTTTAAAAGAGCGTTTGTTTGTTATTATAGACCCGAAACGGGTTGAGCTAGTCATGAGCAGGTTGAAGGTTGAGTAACATCAACTGGAGGACCGAACCGACTCTCGTTGAAACGATAGCGGATGACTTGTGATTAGGGGTGAAATTCCAATCGAAATCCGTGATAGCTGGTTCTCGTCGAAATAGCTTTAAGGCTAGCGTGAGATCACAAATAAGTGGAGGTAAAGCTACTGAATGTATGATGGCGCCACCTAGGCGTACTGAATACAATTAAACTCTGAATGCCATTTATTTTATTCTCGCAGTCAGACAGTGGGGGATAAGCTTCATTGTCAAGAGGGGAAGAGCCCAGATCATTAAATAAGGTCCCCAAAATATACTAAGTGGAAAAGGATGTGAAAGTGCTAAAACAGCAAGGATGTTGGCTTAGAAGCAGCCATCGTTTAAAGAGTGCGTAACAGCTCACTTGTCGAGTGTTTTTGCGCCGAAGATGTAACGGGGCTAAGTATATTACCGAATTTATGGATAAGATTTATATCTTGTGGTAGACGAGCGTTGTATTGGAGTTGAAGTCAAAGCGTGAGCATTGGTGGATCCAATACAAGTGAGAATGCCGGCATGAGTAACGCTTGGGAGTGAGAATCTCCCAAACCGATTGACTAAGGTTTCCTGGACCAGGGTCGTCCTTCCAGGGTTAGTCTGGACCTAAGCTGAGGCTGAAAAGCGTAGGCGATGGACAACAGGTTAATATTCCTGTACTTACAGTTAGACTGATGGAGTGACAAAGAAGGTTTTCCACCCCCATAATTGGATTTGGGGATAAATCATAAGGTGGTACAATAGGCAAATCCGTTGTGCATAACATTGAGTGATGATGTCGAGTGAATGAGTGATCAAGTAGCGAAGGTGGTATTAATCATGCTTTCAAGAAAAGCTTCTAGGGTTAATCTAGCTGTAACCAGTACCGAGAACGAACACACGTAGTCAAGGAGAGGATCCTAAGGTTAGCGAGTGAACTATAGCCAAGGAACTCTGCAAATTAACCCCGTAAGTTAGCGAGAAGGGGTGCTTATGTAAAAGTAAGCCGCAGTGAAGAACGAGGGGGGACTGTTTAACTAAAACACAACTCTATGCCAAACCGTAAGGTGATGTATATGGGGTGACACCTGCCCAGTGCTGGAAGGTTAAAGAAGGAGGTTAGCGCAAGCGAAGCTTTTAACTGAAGCCCCAGTGAACGGCGGCCGTAACTATAACGGTCCTAAGGTAGCGAAATTCCTAGTCGGGTAAATTCCGTCCCGCTTGAATGGTGTAACCATCTCTTGACTGTCTCGGCTATAGACTCGGTGAAATCCAGGTACGGGTGAAGACACCCGTTAGGCGCAACGGGACGGAAAGACCCCGTGAAGCTTTACTGTAGCTTAATATTGATCAGGACATTATCATGTAGAGAATAGGTAGGAGCAATCGATGCAAGTTCGCTAGGACTTGTTGATGCGAAAGGTGGAATACTACCCTTGGTTGTGTGCTGTTCTAATTGGTAACTGTTATCCAGTTTCAAGACAGTGTTAGGTGGGCAGTTTGACTGGGGCGGTCGCCTCCTAAAAGGTAACGGAGGCGTACAAAGGTACCTTCAGTACGGTTGGAAATCGTATGTAGAGTGTAATGGTGTAAGGGTGCTTGACTGTGAGACATACAGGTCGAACAGGTGAGAAATCAGGTCATAGTGATCCGGTGGTCCAGTATGGAATGGCCATCGCTCAACGGATAAAAGCTACTCCGGGGATAACAGGCTGATACTGCCCAAGAGTTCATATCGACGGCAGTGTTTGGCACCTCGATGTCGACTCATCTCATCCTCGAGCTGAAGCAGGTTCGAAGGGTTCGGCTGTTCGCCGATTAAAGAGATACGTGAGTTGGGTTCAAACCGTCGTGAGACAGGTTGGTCCCTATCTATTGTGCCCGTAGGAAGATTGAAGAGTGTTGCTTCTAGTACGAGAGGACCGAAGCGAGGACACCTCTTATGCTCCAGTTGTAGCGCCAGCTGCACCGCTGGGTAGTAACGTGTCTATTAGATAAACGCTGAAAGCATCTAAGTGTGAAACTATCTCAAAGATTAATCTTCCCATTTCGCAAGAAAGTAAGAGCCGTCAAAGACGATGACGTTGATAGGTTACAGGTGTAAGCATAGTGATATGTTGAGCTGAGTAATACTAATTGCTCGAGGACTTATTGGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41332","NCBI_taxonomy_name":"Mycoplasma pneumoniae","NCBI_taxonomy_id":"2104"}}}},"ARO_accession":"3004179","ARO_id":"41331","ARO_name":"Mycoplasma pneumoniae 23S rRNA mutation conferring resistance to erythromycin","ARO_description":"Point mutation in the 23S rRNA of Mycoplasma pneumoniae shown to confer resistance to erythromycin","ARO_category":{"41251":{"category_aro_accession":"3004125","category_aro_cvterm_id":"41251","category_aro_name":"23S rRNA with mutation conferring resistance to macrolide antibiotics","category_aro_description":"Nucleotide point mutations in the 23S rRNA subunit may confer resistance to macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36600":{"category_aro_accession":"3000461","category_aro_cvterm_id":"36600","category_aro_name":"florfenicol","category_aro_description":"Florfenicol is a fluorine derivative of chloramphenicol, where the nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3) and the hydroxyl group (-OH), by a fluorine group (-F). The action mechanism is the same as chloramphenicol's, where the antibiotic binds to the 23S RNA of the 50S subunit of bacterial ribosomes to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin 1A is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"vernamycin B-gamma","category_aro_description":"Vernamycin B-gamma is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2825":{"model_id":"2825","model_name":"Halobacterium halobium 23S rRNA mutation conferring resistance to chloramphenicol","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"7947":"A2088C","7948":"C2471U"},"clinical":{"7947":"A2088C","7948":"C2471U"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"5300"}},"model_sequences":{"sequence":{"4170":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"X03407.1","fmin":"2910","fmax":"5815","strand":"+","sequence":"GTGGCTACTGTGCCACCTGGTGGATAGCTCGGCTCGGATGCCGACGAAGGACGTGCCAAGCTGCGATAAGCCTGAGGGAGCCGCACGGAGGCTAAGAACTCAGGATCTCCTAATGGGAATCCCTATAACAATTGCCTTGCGCAATGGGGAACGGCCGGAATTGAAGCATCTCAGTACGGCCAGGAAGAGAAATCGAATGAGACGCCGTTAGTAATGGCGAATGAACGCGGCACAGTCCAAACCGAAGCCTTCGGGCAATGTGGTGTTCGGACTGACTTTCATCGTTTGACCGTTCGTGTGAAGTCTCCTGAAACGGAGCGCGATACAGGGTGACAGCCCCGTATCACGGACCAGTACGACGTGCGTCAGCTCCAGAGTAGCGGGGGTTGGAAATCCCTCGTGAATTGTGGCAGGCATCGACTGCCAAGACTAAGTACTCTCCGAGACCGATAGTGAACAAGTAGTGTGAACGAACGCTGAAAAGCACCCCACAAAGGGGGGTGAAATAGGGCTTGAAATCAGGTGGCGATGGAGCGACGGGGCATAAAAGGCCTCTCTGGGAACGACTTGAGTGCAAACTCATGGTAGGACCTGAGAGGAGCCGATGTTCCGTCGTACGTTTTGAAAAACGAGCTAGGGAGTGTGCCTGTTTGACGAGTCTAACCGGAGTATCCGGGAAGGCGTAGGGAAACCAATATGGCCGCGGCATTGCGAGGGCCACCGTGTTCAAGCGCGGGGAGTCAAACGGGCACGACCCGAAACCCGGTGATCTACGCGTGGGCAAGGTGAAGCATGGCGAAAGCCATGTGGAGGCCTGTTAGGGTTGGTGTCTTTCAACACCCTCCCGTGACCTACGTGTAGGGGTGAAAGGCCCATCGAACCGGGCAACAGCTGGTTCCAACCGAAACATGTCGAAGCATGACCTCTGCCGAGGTAGTTCGTGGGGTAGAGCGACCGATTGGGGAGTTCAACTCCGAGAGGAGTTGTCTCCCCTGTCAAACTCCAAACCTACGGACGCCGTCGACGCAGGGAATCCGGTGTGCGGGGTAAGCCTGTGCACCGTGAGGGAGACAACCCAGAGTTAGGTTAAGGTCCCAAAGTGCGAGCTAAGTGCGATTGAAGGTGGTCTCGAGCCCTAGACAGCCGGGAGGTGAGCTTAGAAGCAGCTACCCTCTAAGAAAAGCGTAACAGCTTACCGGCCGAGGTTCGAGGCGCCCAAAATGATCGGGGCTTAAGTTCGCCACCGAGACCTAACGGCACGGGTAACACCGTGATCCAGTAGGTTGGCATTCTGTTCGGGTGGAAGCTCGGGTGAGAACTCGAGTGGACCGAGTGGAAAAGAAAATCCTGGCCATAGTAGCAGCGTTAGTCGGGTAAGAATCCCGATGGCCGAAAGAGCAAGGGTTCCTCGGCAATGCTTATCAGCCGAGGGTTAGCCGATCCTAAGGCCCGTCGTAATTCGAGCGGGTCAAAAGGGAAACTGGTTAATATTCCAGTGCCACCGTACATTGAAAGTCGACGCCTCGGAGCAGCTTGAGCCGGGCATTCGCCCGGTCGAACCGTCGAAGTTCGTGGAAGCCGTAATGGCAGGAAGCGAACGAACGTCGGAACAGGGAAACTCAAGTCAATCTGGGGCCCGTGAAAAGGCGAGTACGGTGTTCGTACCGAGATCCGACACAGGTGCTCTGGCAGAGGAAGCCAAGGCCTGTCGGGAATAACCGACGTTAGGGAATTCGGCAAGTTAGTCCCGTAAGTTCGCGATAAGGGATGCCTGCCACGCAATGAGGCAGGTCGCAGTGACTCGGAGGCTCCGACTGTCTAATAACAACATAGGTGACCGCAAATCCGCAAGGACGCGTACGGTCACTGAATCCTGCCCAGTGCGGGTATCTGAACACCCAGTACAATGGGGCGAAGGACCCGTTAACGGCGGGGGTAACTATGACCCTCTTAAGGTAGCGTAGTACCTTGCCGCTTCAGTAGCGGCTTGCATGAATGGATCAACGAGAGCCTCACTGTCCCAACGTTGGGCCCGGTGAACTGTACGTTCCAGTGCGGAGTCTGGAGACCCCCAAGGGGAAGCGAAGACCCTATAGAGCTTTACTGCAGGCTGTCGCTGGGACACGGTCGCTGATGTGCAGAGTAGGTAGGAGACGTTACACAGGTACGTGCGCTAGCACGCCACCGAGTCACACATGAAACACTACCCGTCAGTGACTGTGACCCTCACTCCGGGAGGAGGACACCGGTAGCCGGGCAGTTTGACTGGGGCGGTACGCGCTTGAAAAGATATCGAGCGCGCCCTAAGCCTATCTCAGCCGAGTCAGAGACTCGGCGAAGAGTGCAAGAGCATAAGATAGGCTGACAGTGTCCTACACAACGAGGGACGCTGACGCGAAAGCTGGTCTAGCGAACCAATTAGGCTGCTTGATGCGGCCAATTGCTGACAGAAAAGCTACCTTAGGGATAACAGAGTCGTCACTCGCAAGAGCACATATCGACCGAGTGGCTGCTACCTCGATGTCGGTTCCCTCCATCCTGCCCGTGCAGAAGCGGGCAAGGGTGAGGTTGTTCGCCTATTAAAGGAGGTCGTGAGCTGGGTTTAGACCGTCGTGAGACAGGTCGGCTGCTATCTATTGGGGGTGTTTTGGTGCTTGACAGGAACGTTCGTATAGTACGAGAGGAACTACGAACGGGTGCCACTGGTGTATCGGTTGTCCGAGAGGGCATGTGCCGAGCAGCTACGCACCACGGGGTAAGAGCTGAATGCATCTAAGCTCGAAACCCACCTGGAAAAGAAGCACCACTGAGACCGCTCGTAGAAGACGAGTTCGATAGACTTGGGGTGTACGCGTCGAGGCAACGAGACGTTTAGCCCGCGAGTACTAACAGGTCAATGCCACAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40807","NCBI_taxonomy_name":"Halobacterium salinarum","NCBI_taxonomy_id":"2242"}}}},"ARO_accession":"3004180","ARO_id":"41333","ARO_name":"Halobacterium halobium 23S rRNA mutation conferring resistance to chloramphenicol","ARO_description":"Point mutation in the 23S rRNA of Halobacterium halobium shown to confer resistance to chloramphenicol","ARO_category":{"41350":{"category_aro_accession":"3004188","category_aro_cvterm_id":"41350","category_aro_name":"23S rRNA with mutation conferring resistance to phenicol antibiotics","category_aro_description":"Point mutations in the 23S rRNA subunit shown clinically to confer resistance to phenicol class antibiotics, including chloramphenicol and florfenicol, by disrupting antibiotic binding-site affinity","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36600":{"category_aro_accession":"3000461","category_aro_cvterm_id":"36600","category_aro_name":"florfenicol","category_aro_description":"Florfenicol is a fluorine derivative of chloramphenicol, where the nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3) and the hydroxyl group (-OH), by a fluorine group (-F). The action mechanism is the same as chloramphenicol's, where the antibiotic binds to the 23S RNA of the 50S subunit of bacterial ribosomes to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin 1A is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"vernamycin B-gamma","category_aro_description":"Vernamycin B-gamma is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2826":{"model_id":"2826","model_name":"Streptococcus pneumoniae 23S rRNA mutation conferring resistance to macrolides and streptogramins antibiotics","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"7949":"A2129C"},"clinical":{"7949":"A2129C"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"5000"}},"model_sequences":{"sequence":{"4171":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NZ_CP018138.1","fmin":"1692408","fmax":"1695312","strand":"-","sequence":"TTTGGATAAGTCCTCGAGCTATTAGTATTAGTCCGCTACATGTGTCGCCACACTTCCACTTCTAACCTATCTACCTGATCATCTCTCAGGGCTCTTACTGATATATAATCATGGGAAATCTCATCTTGAGGTGGGTTTCACACTTAGATGCTTTCAGCGTTTATCCCTTCCCTACATAGCTACCCAGCGATGCCTTTGGCAAGACAACTGGTACACCAGCGGTAAGTCCACTCTGGTCCTCTCGTACTAGGAGCAGATCCTCTCAAATTTCCTACGCCCGCGACGGATAGGGACCGAACTGTCTCACGACGTTCTGAACCCAGCTCGCGTGCCGCTTTAATGGGCGAACAGCCCAACCCTTGGGACCGACTACAGCCCCAGGATGCGACGAGCCGACATCGAGGTGCCAAACCTCCCCGTCGATGTGAACTCTTGGGGGAGATAAGCCTGTTATCCCCAGGGTAGCTTTTATCCGTTGAGCGATGGCCCTTCCATACGGAACCACCGGATCACTAAGCCCGACTTTCGTCCCTGCTCGAGTTGTAGCTCTCGCAGTCAAGCTCCCTTATACCTTTATACTCTGCGAATGATTTCCAACCATTCTGAGGGAACCTTTGGGCGCCTCCGTTACCTTTTAGGAGGCGACCGCCCCAGTCAAACTGCCCGTCAGACACTGTCTCCGATAGGGATCACCTATCTGGGTTAGAGTGGCCATAACACAAGGGTAGTATCCCAACAGCGTCTCCTTCGAAACTGGCGTCCCGATCTCTTAGACTCCTACCTATCCTGTACATGTGGTACAGACACTCAATATCAAACTGCAGTAAAGCTCCATGGGGTCTTTCCGTCCTGTCGCGGGTAACCTGCATCTTCACAGGTACTAAAATTTCACCGAGTCTCTCGTTGAGACAGTGCCCAAATCATTACGCCTTTCGTGCGGGTCGGAACTTACCCGACAAGGAATTTCGCTACCTTAGGACCGTTATAGTTACGGCCGCCGTTTACTGGGGCTTCAATTCATACCTTCGCTTACGCTAAGCACTCCTCTTAACCTTCCAGCACCGGGCAGGCGTCACCCCCTATACATCATCTTACGATTTAGCAGAGAGCTGTGTTTTTGATAAACAGTTGCTTGGGCCTATTCACTGCGGCTGACCTAAAGTCAGCACCCCTTCTCCCGAAGTTACGGGGTCATTTTGCCGAGTTCCTTAACGAGAGTTCTCTCGCTCACCTGAGGCTACTCGCCTCGACTACCTGTGTCGGTTTGCGGTACGGGTAGAGTATGTTTAAACGCTAGAAGCTTTTCTTGGCAGTGTGACGTCACTAACTTCGCTACTAAACTTCGCTCCCCATCACAGCTCAATGTTATAGAATTAAGCATTTGACTCAATTCACACCTCACTGCTTAGACAGACTCTTCCAATCGTCTGCTTTAGTTAGCCTACTGCGTCCCTCCATCACTACATACTCTAGTACAGGAATATCAACCTGTTGTCCATCGGATACACCTTTCGGTCTCTCCTTAGGTCCCGACTAACCCAGGGCGGACGAGCCTTCCCCTGGAAACCTTAGTCTTACGGTGGACAGGATTCTCACCTGTCTTTCGCTACTCATACCGGCATTCTCACTTCTATGCGTTCCAGCACTCCTCACGGTATACCTTCATCACACATAGAACGCTCTCCTACCATACCTATAAAGGTATCCACAGCTTCGGTAAATTGTTTTAGCCCCGGTACATTTTCGGCGCAGGGTCACTCGACTAGTGAGCTATTACGCACTCTTTGAATGAATAGCTGCTTCTAAGCTAACATCCTAGTTGTCTGTGCAACCCCACATCCTTTTCCACTTAACAATTATTTTGGGACCTTAGCTGGTGGTCTGGGCTGTTTCCCTTTCGACTACGGATCTTAGCACTCGCAGTCTGACTGCCGACCATAATTCATTGGCATTCGGAGTTTATCTGAGATTGGTAATCCGGGATGGACCCCTCACCCAAACAGTGCTCTACCTCCAAGAATCTCTAATGTCGACGCTAGCCCTAAAGCTATTTCGGAGAGAACCAGCTATCTCCAAGTTCGTTTGGAATTTCTCCGCTACCCACAAGTCATCCAAGCACTTTTCAACGTGCCCTGGTTCGGTCCTCCAGTGCGTCTTACCGCACCTTCAACCTGCTCATGGGTAGGTCACATGGTTTCGGGTCTACGTCATGATACTAATTCGCCCTGTTCAGACTCGGTTTCCCTACGGCTCCGTCTCTTCAACTTAACCTCGCATCATAACGTAACTCGCCGGTTCATTCTACAAAAGGCACGCTCTCACCCATTAACGGGCTCGAACTTGTTGTAGGCACACGGTTTCAGGTTCTATTTCACTCCCCTCCCGGGGTGCTTTTCACCTTTCCCTCACGGTACTGGTTCACTATCGGTCACTAGGGAGTATTTAGGGTTGGGAGATGGTCCTCCCAGATTCCGACGGGATTTCACGTGTCCCGCCGTACTCAGGATACTGCTAGGTACAAAGACTATTTTAAATACGAGGCTATTACTCTCTTTGGCTGATCTTCCCAAATCATTCTTCTATAATCTTTGAGTCCACATTGCAGTCCTACAACCCCGAAGAGTAAACTCTTCGGTTTGCCCTTCTGCCGTTTCGCTCGCCGCTACTAAGGCAATCGCTTTTGCTTTCTCTTCCTGCAGCTACTTAGATGTTTCAGTTCACTGCGTCTTCCTCCTCACATCCTTAACAGATGTGGGTAACAGGTATTACCTGTTGGGTTCCCCCATTCGGAAATCCCTGGATCATCGCTTACTTACAGCTACCCAAGGTATATCGTCGTTTGTCACGTCCTTCGTCGGCTCCTAGTGCCAAGGCATCCACCGTGCGCCCTTATTAACTTAACCT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35917","NCBI_taxonomy_name":"Streptococcus pneumoniae","NCBI_taxonomy_id":"1313"}}}},"ARO_accession":"3004181","ARO_id":"41334","ARO_name":"Streptococcus pneumoniae 23S rRNA mutation conferring resistance to macrolides and streptogramins antibiotics","ARO_description":"Point mutation in the 23S rRNA of Streptococcus pneumoniae shown to confer resistance to macrolides and streptogramins types of antibiotics","ARO_category":{"41251":{"category_aro_accession":"3004125","category_aro_cvterm_id":"41251","category_aro_name":"23S rRNA with mutation conferring resistance to macrolide antibiotics","category_aro_description":"Nucleotide point mutations in the 23S rRNA subunit may confer resistance to macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"41335":{"category_aro_accession":"3004182","category_aro_cvterm_id":"41335","category_aro_name":"23S rRNA with mutation conferring resistance to streptogramins antibiotics","category_aro_description":"Nucleotide point mutations in the 23S rRNA subunit may confer resistance to streptogramins antibiotics.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36600":{"category_aro_accession":"3000461","category_aro_cvterm_id":"36600","category_aro_name":"florfenicol","category_aro_description":"Florfenicol is a fluorine derivative of chloramphenicol, where the nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3) and the hydroxyl group (-OH), by a fluorine group (-F). The action mechanism is the same as chloramphenicol's, where the antibiotic binds to the 23S RNA of the 50S subunit of bacterial ribosomes to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin 1A is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"vernamycin B-gamma","category_aro_description":"Vernamycin B-gamma is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37620":{"category_aro_accession":"3001221","category_aro_cvterm_id":"37620","category_aro_name":"josamycin","category_aro_description":"A macrolide antibiotic from Streptomyces narbonensis\u00a0subsp.\u00a0josamyceticus. The drug has antimicrobial activity against a wide spectrum of pathogens.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2827":{"model_id":"2827","model_name":"Mycobacterium tuberculosis ribD with mutation conferring resistance to para-aminosalicylic acid","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"},"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"7951":"G8R"},"clinical":{"7951":"G8R"}},"41339":{"param_type":"mutation in regulatory element","param_description":"An AMR detection model parameter to describe mutations in regulatory elements upstream of a coding DNA region shown to confer resistance to an antibiotic drug or drug class. Regulatory element mutations in CARD use the following notation: nt[wild-type][-][position][mutation].","param_type_id":"41339","param_value":{"8013":"ntG-11A"}}},"model_sequences":{"sequence":{"4172":{"protein_sequence":{"accession":"NP_217187.1","sequence":"MPDSGQLGAADTPLRLLSSVHYLTDGELPQLYDYPDDGTWLRANFISSLDGGATVDGTSGAMAGPGDRFVFNLLRELADVIVVGVGTVRIEGYSGVRMGVVQRQHRQARGQSEVPQLAIVTRSGRLDRDMAVFTRTEMAPLVLTTTAVADDTRQRLAGLAEVIACSGDDPGTVDEAVLVSQLAARGLRRILTEGGPTLLGTFVERDVLDELCLTIAPYVVGGLARRIVTGPGQVLTRMRCAHVLTDDSGYLYTRYVKT"},"dna_sequence":{"accession":"NC_000962.3","fmin":"2986838","fmax":"2987615","strand":"+","sequence":"ATGCCCGACTCTGGTCAGCTCGGAGCCGCTGACACCCCGCTAAGGCTGCTCAGCTCGGTGCATTACCTCACCGACGGCGAACTCCCCCAGCTTTACGACTATCCGGATGACGGCACCTGGTTGCGGGCGAACTTCATCAGCAGCTTGGACGGCGGCGCTACCGTCGATGGCACCAGCGGGGCGATGGCCGGGCCCGGCGACCGATTCGTCTTCAACCTGTTGCGTGAACTTGCCGACGTCATCGTGGTCGGCGTGGGCACCGTGCGCATTGAGGGCTACTCCGGCGTCCGGATGGGTGTCGTCCAGCGCCAGCACCGGCAGGCCCGAGGCCAAAGCGAAGTTCCGCAACTGGCAATCGTCACCAGGTCCGGTCGCCTTGACCGTGACATGGCGGTATTCACCCGGACCGAGATGGCACCGTTGGTGCTCACCACCACGGCGGTCGCCGATGACACGCGCCAGCGGCTCGCGGGCCTCGCCGAGGTGATCGCGTGCTCCGGCGACGATCCGGGCACGGTCGATGAGGCAGTGCTCGTGTCCCAGCTCGCGGCTCGCGGTCTGCGCCGGATCCTTACCGAAGGCGGGCCGACGTTGCTCGGGACATTCGTCGAGCGTGACGTGCTCGACGAGCTGTGTCTGACGATCGCCCCCTACGTCGTCGGCGGCCTGGCGCGCCGCATAGTGACGGGACCCGGGCAGGTGCTGACCCGGATGCGCTGTGCCCATGTCCTCACCGACGACTCCGGCTACCTGTACACCCGCTACGTCAAGACCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3004184","ARO_id":"41337","ARO_name":"Mycobacterium tuberculosis ribD with mutation conferring resistance to para-aminosalicylic acid","ARO_description":"ribD is a Mycobacterium tuberculosis riboflavin biosynthesis enzyme. Point mutations in ribD cause enzyme overexpression, which allows the C-terminal reductase domain to act as an alternative dihydrofolate reductase. Thus, mutations in ribD confer resistance to DHFR inhibitors such as para-aminosalicylic acid.","ARO_category":{"41336":{"category_aro_accession":"3004183","category_aro_cvterm_id":"41336","category_aro_name":"aminosalicylate resistant dihydrofolate reductase","category_aro_description":"Antibiotic target replacement dihydrofolate reductase enzymes or domains with catalytic activity that confer resistance to aminosalicylates, esp. p-aminosalicylic acid.","category_aro_class_name":"AMR Gene Family"},"40948":{"category_aro_accession":"3004019","category_aro_cvterm_id":"40948","category_aro_name":"para-aminosalicylic acid","category_aro_description":"para-aminosalicylic acid (PAS) is an anti-tubercular antibiotic agent, often used in conjunction with Isoniazid for treatment of M. tuberculosis infections. PAS diminishes bacterial cell growth by limiting folic acid production.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2828":{"model_id":"2828","model_name":"mecD","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"4173":{"protein_sequence":{"accession":"AQX82857.1","sequence":"MKNIKVKILIVCSLCLISFFLYNLLKENEIDKIFSSIENRNVDEINENITFLSRNTFSKKQRYDRMNHIDNSLGIKKVNITDIKLLEEIVDTRKYSANMHYDSKFGKFTKKGYFEFEKNGESKRWELNWTPEVIIPGLTATNEVRVEELKSSRGEIVDRNGIPLAIDGEHYQVGIDPKNYNKKDSKQIAKLLNINESTLKNKLKQSWVKDGVFVPIKSYVELSDEIKNKIPEYGLSVNKIKGRTYPLKEASAHLLGYIGEINADELNDPKFKGYDSHSIVGKTGIEYMYDKELQNRDGLIVYITDDDGLTDSKEILVHKKPKNGKKIVLSIDSRVQNSIYNHLKDDNGSGTAMNPKTGELLALVSYPSFNPYDFMFGISNKKYQALLNDKKAPLLNKFQELTSPGSTQKLLTSIIGLNNGVINESKSYEINGKGWRKDGSWGGYKVTRFEVVNGRIDLEKAIAHSDNIFFARTTLEMGGKKFVRGMKDLGVGEETPSDYPVRTGQIANKINLERNLNNDILLADSGYGQGEILVNPIHILSIYSSLVNEGNMMAPKLNMEHKSKVWKKHITSQKNIDILTSSMRKVVTGTHKLDTERNYANFAGKTGTAELKMTQNEGLGTQIGWFVGYDQQNPNMMLAINVKNVEDKGMSSYNAQKFAQVMDDLYEHGARTYEPDSE"},"dna_sequence":{"accession":"KY013611.1","fmin":"15437","fmax":"17474","strand":"+","sequence":"ATGAAGAATATAAAAGTTAAAATATTAATAGTTTGTAGCCTATGTCTTATATCATTTTTCTTATATAATTTATTGAAAGAAAATGAAATTGATAAAATATTTTCTTCAATTGAAAATCGAAATGTAGATGAAATAAATGAGAATATTACTTTTTTATCAAGAAATACTTTTAGTAAAAAACAAAGATACGATAGAATGAATCATATTGATAATTCTCTAGGCATAAAAAAAGTAAATATAACTGATATAAAGTTATTAGAAGAAATTGTAGACACTCGAAAATATAGTGCTAATATGCACTATGATTCTAAATTCGGTAAATTCACAAAAAAAGGTTATTTTGAGTTTGAAAAAAATGGTGAGAGTAAACGTTGGGAATTGAACTGGACACCAGAGGTTATAATTCCAGGACTTACAGCAACTAATGAAGTACGAGTAGAAGAATTGAAATCAAGTAGAGGTGAAATTGTAGATAGAAATGGAATTCCTTTAGCGATAGATGGTGAACATTATCAGGTAGGAATTGATCCTAAAAATTATAATAAGAAGGATAGTAAACAAATAGCTAAGTTATTAAATATAAATGAGAGTACTTTAAAGAACAAATTAAAACAATCATGGGTTAAAGATGGAGTATTTGTTCCAATCAAATCATATGTAGAATTAAGTGATGAAATTAAAAATAAAATACCTGAATACGGATTATCTGTGAATAAAATAAAAGGTAGAACTTACCCATTAAAAGAAGCAAGTGCTCATTTGTTAGGTTATATTGGTGAAATAAATGCAGATGAGCTTAATGATCCAAAATTTAAAGGATATGATTCTCATTCAATTGTTGGTAAAACTGGTATTGAATATATGTACGATAAAGAATTACAAAACAGAGATGGTTTAATAGTATATATTACTGATGATGATGGTTTAACAGATTCAAAAGAAATATTAGTTCATAAGAAACCTAAAAATGGAAAAAAGATAGTTTTATCGATAGATAGTAGAGTTCAAAATAGTATTTACAATCATTTAAAAGATGATAATGGATCTGGTACTGCTATGAATCCCAAAACAGGAGAATTATTAGCTTTAGTAAGCTATCCATCATTTAATCCTTATGATTTTATGTTTGGTATTTCAAATAAAAAATATCAGGCCTTATTAAATGATAAAAAGGCTCCGCTTTTAAATAAATTTCAAGAATTAACTTCTCCAGGTTCTACTCAAAAATTGCTAACTTCTATAATAGGTTTAAATAATGGGGTTATAAATGAAAGCAAAAGTTATGAAATAAATGGTAAAGGATGGAGAAAAGATGGGAGCTGGGGAGGATATAAAGTAACAAGATTTGAAGTTGTCAATGGACGAATTGATTTAGAGAAAGCTATAGCACATTCAGACAATATCTTTTTTGCTAGAACAACCCTAGAAATGGGTGGGAAAAAATTTGTAAGGGGAATGAAGGATTTAGGTGTAGGAGAGGAAACGCCTTCTGATTACCCTGTTCGGACTGGCCAAATAGCGAATAAAATTAATCTAGAAAGAAATTTGAATAATGATATATTGTTAGCAGACTCAGGTTATGGACAAGGTGAAATATTGGTGAATCCAATTCATATTTTATCTATATATAGTTCATTAGTAAATGAAGGGAATATGATGGCACCTAAATTAAATATGGAACATAAAAGCAAAGTATGGAAAAAACATATTACATCACAAAAAAATATTGATATATTAACAAGTAGTATGAGAAAAGTTGTTACAGGCACTCATAAATTAGATACCGAAAGAAATTATGCTAACTTTGCTGGAAAAACTGGTACAGCAGAATTAAAAATGACTCAGAATGAAGGATTAGGTACACAAATTGGATGGTTTGTGGGTTATGATCAACAAAATCCAAATATGATGTTAGCTATAAATGTTAAAAATGTTGAAGACAAAGGTATGTCTAGCTATAATGCACAAAAATTTGCGCAAGTAATGGATGATTTATATGAACATGGAGCTAGGACTTATGAACCAGACTCAGAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40025","NCBI_taxonomy_name":"Macrococcus caseolyticus","NCBI_taxonomy_id":"69966"}}}},"ARO_accession":"3004185","ARO_id":"41338","ARO_name":"mecD","ARO_description":"mecD is a PBP2a variant identified on a genomic resistance island in Macrococcus caseolyticus. MecD confers resistance to methicillin and other beta-lactam antibiotics through the production of an alternative low-affinity PBP. First described by Schwendener et al. 2017 and identified from canine and bovine sources.","ARO_category":{"37589":{"category_aro_accession":"3001208","category_aro_cvterm_id":"37589","category_aro_name":"methicillin resistant PBP2","category_aro_description":"In methicillin sensitive S. aureus (MSSA), beta-lactams bind to native penicillin-binding proteins (PBPs) and disrupt synthesis of the cell membrane's peptidoglycan layer. In methicillin resistant S. aureus (MRSA), foreign PBP2a acquired by lateral gene transfer is able to perform peptidoglycan synthesis in the presence of beta-lactams.","category_aro_class_name":"AMR Gene Family"},"35927":{"category_aro_accession":"0000008","category_aro_cvterm_id":"35927","category_aro_name":"cefoxitin","category_aro_description":"Cefoxitin is a cephamycin antibiotic often grouped with the second generation cephalosporins. Cefoxitin is bactericidal and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. Cefoxitin's 7-alpha-methoxy group and 3' leaving group make it a poor substrate for most beta-lactamases.","category_aro_class_name":"Antibiotic"},"35930":{"category_aro_accession":"0000011","category_aro_cvterm_id":"35930","category_aro_name":"cloxacillin","category_aro_description":"Cloxacillin is a semisynthetic, isoxazolyl penicillin derivative in the beta-lactam class of antibiotics. It interferes with peptidogylcan synthesis and is commonly used for treating penicillin-resistant Staphylococcus aureus infections.","category_aro_class_name":"Antibiotic"},"35934":{"category_aro_accession":"0000015","category_aro_cvterm_id":"35934","category_aro_name":"methicillin","category_aro_description":"Derived from penicillin to combat penicillin-resistance, methicillin is insensitive to beta-lactamases (also known as penicillinases) secreted by many penicillin-resistant bacteria. Methicillin is bactericidal, and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Antibiotic"},"35961":{"category_aro_accession":"0000043","category_aro_cvterm_id":"35961","category_aro_name":"carbenicillin","category_aro_description":"Carbenicillin is a semi-synthetic antibiotic belonging to the carboxypenicillin subgroup of the penicillins. It has gram-negative coverage which includes Pseudomonas aeruginosa but limited gram-positive coverage. The carboxypenicillins are susceptible to degradation by beta-lactamase enzymes. Carbenicillin antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Antibiotic"},"35971":{"category_aro_accession":"0000054","category_aro_cvterm_id":"35971","category_aro_name":"penicillin","category_aro_description":"Penicillin (sometimes abbreviated PCN) is a beta-lactam antibiotic used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms. It works by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Antibiotic"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35975":{"category_aro_accession":"0000058","category_aro_cvterm_id":"35975","category_aro_name":"cefazolin","category_aro_description":"Cefazolin (INN), also known as cefazoline or cephazolin, is a first generation cephalosporin antibiotic. It is administered parenterally, and is active against a broad spectrum of bacteria.","category_aro_class_name":"Antibiotic"},"35976":{"category_aro_accession":"0000059","category_aro_cvterm_id":"35976","category_aro_name":"cefepime","category_aro_description":"Cefepime (INN) is a fourth-generation cephalosporin antibiotic developed in 1994. It contains an aminothiazolyl group that decreases its affinity with beta-lactamases. Cefepime shows high binding affinity with penicillin-binding proteins and has an extended spectrum of activity against Gram-positive and Gram-negative bacteria, with greater activity against both Gram-negative and Gram-positive organisms than third-generation agents.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35978":{"category_aro_accession":"0000061","category_aro_cvterm_id":"35978","category_aro_name":"ceftobiprole","category_aro_description":"Ceftobiprole (Zeftera\/Zevtera) is a next generation (5th generation) cephalosporin antibiotic with activity against methicillin-resistant Staphylococcus aureus, penicillin-resistant Streptococcus pneumoniae, Pseudomonas aeruginosa, and Enterococci. Ceftobiprole inhibits transpeptidases essential to building cell walls, and is a poor substrate for most beta-lactamases.","category_aro_class_name":"Antibiotic"},"35979":{"category_aro_accession":"0000062","category_aro_cvterm_id":"35979","category_aro_name":"ceftriaxone","category_aro_description":"Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"35980":{"category_aro_accession":"0000063","category_aro_cvterm_id":"35980","category_aro_name":"cefuroxime","category_aro_description":"Cefuroxime is a second-generation cephalosporin antibiotic with increased stability with beta-lactamases than first-generation cephalosporins. Cefuroxime is active against Gram-positive organisms but less active against methicillin-resistant strains.","category_aro_class_name":"Antibiotic"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"35987":{"category_aro_accession":"0000070","category_aro_cvterm_id":"35987","category_aro_name":"ertapenem","category_aro_description":"Ertapenem is a carbapenem antibiotic and is highly resistant to beta-lactamases like other carbapenems. It inhibits bacterial cell wall synthesis.","category_aro_class_name":"Antibiotic"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"35995":{"category_aro_accession":"0000078","category_aro_cvterm_id":"35995","category_aro_name":"piperacillin","category_aro_description":"Piperacillin is an acetylureidopenicillin and has an extended spectrum of targets relative to other beta-lactam antibiotics. It inhibits cell wall synthesis in bacteria, and is usually taken with the beta-lactamase inhibitor tazobactam to overcome penicillin-resistant bacteria.","category_aro_class_name":"Antibiotic"},"36309":{"category_aro_accession":"3000170","category_aro_cvterm_id":"36309","category_aro_name":"imipenem","category_aro_description":"Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.","category_aro_class_name":"Antibiotic"},"36689":{"category_aro_accession":"3000550","category_aro_cvterm_id":"36689","category_aro_name":"aztreonam","category_aro_description":"Aztreonam was the first monobactam discovered, and is greatly effective against Gram-negative bacteria while inactive against Gram-positive bacteria. Artreonam is a poor substrate for beta-lactamases, and may even act as an inhibitor. In Gram-negative bacteria, Aztreonam interferes with filamentation, inhibiting cell division and leading to cell death.","category_aro_class_name":"Antibiotic"},"36976":{"category_aro_accession":"3000632","category_aro_cvterm_id":"36976","category_aro_name":"benzylpenicillin","category_aro_description":"Benzylpenicillin, commonly referred to as penicillin G, is effective against both Gram-positive and Gram-negative bacteria. It is unstable in acid.","category_aro_class_name":"Antibiotic"},"36977":{"category_aro_accession":"3000633","category_aro_cvterm_id":"36977","category_aro_name":"phenoxymethylpenicillin","category_aro_description":"Phenoxymethylpenicillin, or penicillin V, is a penicillin derivative that is acid stable but less active than benzylpenicillin (penicillin G).","category_aro_class_name":"Antibiotic"},"36978":{"category_aro_accession":"3000634","category_aro_cvterm_id":"36978","category_aro_name":"propicillin","category_aro_description":"Propicillin is an orally taken penicillin derivative that has high absorption but poor activity.","category_aro_class_name":"Antibiotic"},"36979":{"category_aro_accession":"3000635","category_aro_cvterm_id":"36979","category_aro_name":"dicloxacillin","category_aro_description":"Dicloxacillin is a penicillin derivative that has an extra chlorine atom in comparison to cloxacillin. While more active than cloxacillin, its high affinity for serum protein reduces its activity in human serum in vitro.","category_aro_class_name":"Antibiotic"},"36980":{"category_aro_accession":"3000636","category_aro_cvterm_id":"36980","category_aro_name":"flucloxacillin","category_aro_description":"Flucloxacillin is similar to cloxacillin, with an extra additional fluorine atom.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"36982":{"category_aro_accession":"3000638","category_aro_cvterm_id":"36982","category_aro_name":"azlocillin","category_aro_description":"Azlocillin is a semisynthetic derivative of penicillin that is notably active against Ps. aeruginosa and other Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36983":{"category_aro_accession":"3000639","category_aro_cvterm_id":"36983","category_aro_name":"mezlocillin","category_aro_description":"Mezlocillin is a penicillin derivative taken parenterally.","category_aro_class_name":"Antibiotic"},"36984":{"category_aro_accession":"3000640","category_aro_cvterm_id":"36984","category_aro_name":"doripenem","category_aro_description":"Doripenem is a carbapenem with a broad range of activity against Gram-positive and Gram-negative bacteria, and along with meropenem, it is the most active beta-lactam antibiotic against Pseudomonas aeruginosa. It inhibits bacterial cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36985":{"category_aro_accession":"3000641","category_aro_cvterm_id":"36985","category_aro_name":"cefalexin","category_aro_description":"Cefalexin is a cephalosporin antibiotic that causes filamentation. It is resistant to staphylococcal beta-lactamase, but degraded by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"36986":{"category_aro_accession":"3000642","category_aro_cvterm_id":"36986","category_aro_name":"cefadroxil","category_aro_description":"Cefadroxil, or p-hydroxycephalexin, is an cephalosporin antibiotic similar to cefalexin.","category_aro_class_name":"Antibiotic"},"36987":{"category_aro_accession":"3000643","category_aro_cvterm_id":"36987","category_aro_name":"cefotiam","category_aro_description":"Cefotiam is a cephalosporin antibiotic with similar activity to cefuroxime but more active against enterobacteria. It is consumed orally as the prodrug cefotiam hexetil.","category_aro_class_name":"Antibiotic"},"36988":{"category_aro_accession":"3000644","category_aro_cvterm_id":"36988","category_aro_name":"cefaclor","category_aro_description":"Cefaclor is a semisynthetic cephalosporin derived from cephalexin. It has broad-spectrum antibiotic activity.","category_aro_class_name":"Antibiotic"},"36989":{"category_aro_accession":"3000645","category_aro_cvterm_id":"36989","category_aro_name":"cefotaxime","category_aro_description":"Cefotaxime is a semisynthetic cephalosporin taken parenterally. It is resistant to most beta-lactamases and active against Gram-negative rods and cocci due to its aminothiazoyl and methoximino functional groups.","category_aro_class_name":"Antibiotic"},"36990":{"category_aro_accession":"3000646","category_aro_cvterm_id":"36990","category_aro_name":"cefixime","category_aro_description":"Cefixime is a cephalosporin resistant to most beta-lactamases. It is active against many enterobacteria, but activity against staphylococci is poor.","category_aro_class_name":"Antibiotic"},"36991":{"category_aro_accession":"3000647","category_aro_cvterm_id":"36991","category_aro_name":"cefpodoxime","category_aro_description":"Cefpodoxime is a semisynthetic cephalosporin that acts similarly to cefotaxime with broad-spectrum activity. It is stable to many plasmid-mediated beta-lactamses. Cefpodoxime is consumed as the prodrug cefpodoxime proxetil.","category_aro_class_name":"Antibiotic"},"36992":{"category_aro_accession":"3000648","category_aro_cvterm_id":"36992","category_aro_name":"ceftibuten","category_aro_description":"Ceftibuten is a semisynthetic cephalosporin active against Gram-negative bacilli. It is resistant against many plasmid-mediated beta-lactamases.","category_aro_class_name":"Antibiotic"},"36993":{"category_aro_accession":"3000649","category_aro_cvterm_id":"36993","category_aro_name":"cefditoren","category_aro_description":"Cefditoren is a semisynthetic cephalosporin active against staphylococci, streptococci, and and most enterobacteria. It is resistant to staphylococcal and most enterobacterial beta-lactamases, and is usually taken as the prodrug cefditoren pivoxil.","category_aro_class_name":"Antibiotic"},"36994":{"category_aro_accession":"3000650","category_aro_cvterm_id":"36994","category_aro_name":"cefdinir","category_aro_description":"Cefdinir is similar to cefixime with a modified side-chain at its 7-amino position. It also shares similar activity with cefixime but is more active against staphylococci. It has also be shown to enhance phagocytosis.","category_aro_class_name":"Antibiotic"},"36995":{"category_aro_accession":"3000651","category_aro_cvterm_id":"36995","category_aro_name":"ceftaroline","category_aro_description":"Ceftaroline is a novel cephalosporin active against methicillin resistant Staphylococcus aureus. Like other cephalosporins it binds penicillin-binding proteins to inhibit cell wall synthesis. It strongly binds with PBP2a, associated with methicillin resistance. It is taken orally as the prodrug ceftaroline fosamil.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"37085":{"category_aro_accession":"3000705","category_aro_cvterm_id":"37085","category_aro_name":"isopenicillin N","category_aro_description":"Isopenicillin N is a natural penicillin derivative produced by Penicillium chrysogenum with activity similar to penicillin N.","category_aro_class_name":"Antibiotic"},"37086":{"category_aro_accession":"3000706","category_aro_cvterm_id":"37086","category_aro_name":"penicillin N","category_aro_description":"Penicillin N is a penicillin derivative produced by Cephalosporium acremonium.","category_aro_class_name":"Antibiotic"},"37141":{"category_aro_accession":"3000761","category_aro_cvterm_id":"37141","category_aro_name":"mecillinam","category_aro_description":"Mecillinam is a broad-spectrum beta-lactam antibiotic that was semi-synthetically derived to have a different drug centre, being a 6-alpha-amidinopenicillanate instead of a 6-alpha-acylaminopenicillanate. Contrasting most beta-lactam drugs, mecillinam is most active against Gram-negative bacteria. It binds specifically to penicillin binding protein 2 (PBP2).","category_aro_class_name":"Antibiotic"},"40928":{"category_aro_accession":"3004001","category_aro_cvterm_id":"40928","category_aro_name":"cefmetazole","category_aro_description":"Cefmetazole is a semi-synthetic cephamycin antibiotic with broad spectrum antibiotic activity against both gram-positive and gram-negative bacteria, that disrupt cell wall synthesis through binding to PBPs causing cell lysis.","category_aro_class_name":"Antibiotic"},"40929":{"category_aro_accession":"3004002","category_aro_cvterm_id":"40929","category_aro_name":"cefonicid","category_aro_description":"Cefonicid is a second-generation cephalosporin-class beta-lactam antibiotic with broad spectrum activity. Particularly used against urinary tract infections and lower respiratory infections. Causes cell lysis by inactivation of PBPs through binding, inhibiting peptidoglycan synthesis.","category_aro_class_name":"Antibiotic"},"40932":{"category_aro_accession":"3004005","category_aro_cvterm_id":"40932","category_aro_name":"cefprozil","category_aro_description":"Cefprozil is a cephalosporin and beta-lactam antibiotic with bactericidal activity. It selectively binds to PBPs and inhibits peptidoglycan synthesis, a major cell wall component, resulting in cell lysis.","category_aro_class_name":"Antibiotic"},"40933":{"category_aro_accession":"3004006","category_aro_cvterm_id":"40933","category_aro_name":"ceftiofur","category_aro_description":"Ceftiofur is a third-generation broad spectrum cephalosporin and beta-lactam antibiotic. It causes cell lysis by disrupting peptidoglycan cross-linkage and cell wall formation by binding to PBPs.","category_aro_class_name":"Antibiotic"},"40934":{"category_aro_accession":"3004007","category_aro_cvterm_id":"40934","category_aro_name":"ceftizoxime","category_aro_description":"Ceftizoxime is a third-generation cephalosporin and broad spectrum beta-lactam antibiotic. Ceftizoxime causes bacterial cell lysis through peptidoglycan cross-linking inhibition by binding to PBPs.","category_aro_class_name":"Antibiotic"},"40935":{"category_aro_accession":"3004008","category_aro_cvterm_id":"40935","category_aro_name":"cephapirin","category_aro_description":"Cephapirin is a first-generation cephalosporin and broad spectrum beta-lactam antibiotic. Inactivation of penicillin-binding proteins through cephapirin binding disrupts peptidoglycan cross-linking, resulting in cell lysis.","category_aro_class_name":"Antibiotic"},"40936":{"category_aro_accession":"3004009","category_aro_cvterm_id":"40936","category_aro_name":"cefradine","category_aro_description":"Cefradine is a first-generation cephalosporin and broad spectrum beta-lactam antibiotic. Cefradine binding to penicillin-binding proteins disrupts cell wall peptidoglycan cross-linkage, resulting in cell lysis.","category_aro_class_name":"Antibiotic"},"40943":{"category_aro_accession":"3004016","category_aro_cvterm_id":"40943","category_aro_name":"loracarbef","category_aro_description":"Loracarbef is a second-generation cephalosporin (carbacephem) and broad spectrum beta-lactam antibiotic. Loracarbef inhibits PBPs through binding, disrupting peptidoglycan cell wall cross-linkage and resulting in cell death.","category_aro_class_name":"Antibiotic"},"40944":{"category_aro_accession":"3004017","category_aro_cvterm_id":"40944","category_aro_name":"moxalactam","category_aro_description":"Moxalactam (Latamoxef) is a broad spectrum cephalosporin (oxacephem) and beta-lactam antibiotic. Moxalactam binding to PBPs inhibits peptidoglycan cross-linkage in the cell wall, resulting in cell death. Moxalactam is proposed to be effective against meningitides as it passes the blood-brain barrier.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2829":{"model_id":"2829","model_name":"dfrA2d","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"4174":{"protein_sequence":{"accession":"AAX84553.1","sequence":"MNEGKNEVSTSAAGRFAFPSNATFALGDRVRKKSGAAWQGRIVGWYCTTLTPEGYAVESESHPGSVQIYPMTALERVA"},"dna_sequence":{"accession":"AY973253.1","fmin":"125","fmax":"362","strand":"+","sequence":"ATGAATGAAGGAAAAAATGAGGTCAGTACTTCAGCTGCTGGCCGGTTCGCATTCCCATCAAACGCCACGTTTGCCTTGGGGGATCGCGTACGCAAGAAGTCTGGCGCTGCTTGGCAGGGGCGCATTGTCGGGTGGTACTGCACAACACTTACCCCTGAAGGCTACGCCGTCGAGTCCGAATCTCACCCAGGCTCAGTCCAGATTTATCCCATGACTGCGCTTGAACGGGTGGCCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002855","ARO_id":"39289","ARO_name":"dfrA2d","ARO_description":"dfrA2d is an integron-encoded dihydrofolate reductase found in Enterobacteriaceae","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36408":{"category_aro_accession":"3000269","category_aro_cvterm_id":"36408","category_aro_name":"brodimoprim","category_aro_description":"Brodimoprim is a structural derivative of trimethoprim and an inhibitor of bacterial dihydrofolate reductase. The 4-methoxy group of trimethoprim is replaced with a bromine atom.","category_aro_class_name":"Antibiotic"},"36423":{"category_aro_accession":"3000284","category_aro_cvterm_id":"36423","category_aro_name":"tetroxoprim","category_aro_description":"Tetroxoprim is a trimethoprim derivative that inhibits bacterial dihydrofolate reductase.","category_aro_class_name":"Antibiotic"},"36476":{"category_aro_accession":"3000337","category_aro_cvterm_id":"36476","category_aro_name":"iclaprim","category_aro_description":"Iclaprim is a bactericidal compound that inhibits dihydrofolate reductase. It is used against clinically important Gram-positive pathogens, including methicillin-sensitive Staphylococcus aureus and methicillin-resistant S. aureus.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2831":{"model_id":"2831","model_name":"Nocardia rifampin resistant beta-subunit of RNA polymerase (rpoB2)","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"2200"}},"model_sequences":{"sequence":{"4176":{"protein_sequence":{"accession":"BAD59497.1","sequence":"MLEGRIVTVSSRTESPLAAPGVPGAPRRLSFARIREPLAVPGLLDIQTESFGWLIGAPDWCARAAARGTEPVAGLAEVLAEISPIEDFAGTMSLTLSDPRFEEVKASVEECKDKDLTYAAPWFVTAEFVNNNTGEIKSQTVFMGDFPMMTAHGTFVVNGTERVVVSQLVRSPGVYFDHAIDKGSEKDVHSARVIPSRGAWLEFDVDKRDTLGVRIDRKRRQPVTVLLKALGWSAERIAERFGFAPLIMASLAKDNVAGTDDALLEIHRKLRPGEPPTKESAQNLLANLFFTEKRYDLARVGRYKIDKKLGLRAPGAPRVLTEDDIAATIEYLVRLHAGERTMIAPGGVEVPVEVDDIDHFGNRRVRTVGELIQNQIRVGLSRMERVVRERMTTQDVEAITPQSLMNIRPVVAAMKEFFGTSQLSQFMDQRNPLASLTNKRRLSALGPGGLSRERAGLEVRDVHYSHYGRMCPIETPEGPNIGLMGYLSVYARVNPFGFVETPYRRVVDGRVTDEVDYLTADEEDRHVVAQANEPLDAEGRFLAARIPVRRKNSEVELVDSAAVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLIRSEAPIVGTGMELRAAVDAGDVVVNEKAGVVEEVSADYVTVMADDGTRKSYRMRKFNRSNQGTCSNQRPIVDEGQRVEAGQVLADGPCTENGEMALGKNLLVAIMPWEGHNYEDAIILSQRLVEQDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDDDLPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVIGKILPTEDMPFLPDGTPVDIILNTHGVPRRMNIGQILETHLGWIGKAGWKVEGNPEWAKDLPEEMWEAPADSNIATPVFDGAREEELTGLLGSTLPNRDGERMVDDNGKAVLFDGRSGEPFPYPVAVGYMYILKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGDNIPEPGVPESFKVLLKELQALCLNVEVLSAGAAVELAHGVDDDHERTAANLGINLSRAESITETELSG"},"dna_sequence":{"accession":"AP006618.1","fmin":"4835199","fmax":"4838688","strand":"+","sequence":"GTGCTGGAAGGACGCATCGTGACAGTCTCGAGTCGGACCGAGTCCCCGCTCGCCGCGCCCGGAGTCCCGGGTGCGCCCCGGCGGCTCTCGTTCGCCAGAATCCGCGAGCCCCTGGCGGTTCCGGGCCTGCTGGACATTCAGACCGAATCGTTCGGGTGGCTGATCGGCGCACCCGACTGGTGCGCCCGCGCGGCAGCCCGCGGGACGGAACCGGTCGCCGGGCTGGCCGAGGTGCTCGCCGAGATCAGCCCCATCGAGGACTTCGCGGGCACGATGTCGCTGACGTTGTCCGATCCGCGGTTCGAGGAGGTCAAGGCCTCCGTCGAGGAGTGCAAGGACAAGGATCTGACCTATGCCGCGCCGTGGTTCGTCACGGCGGAATTCGTGAACAACAACACCGGCGAGATCAAGAGCCAGACCGTTTTCATGGGTGATTTCCCCATGATGACCGCGCACGGGACATTCGTCGTCAACGGCACCGAACGGGTGGTCGTGTCGCAACTGGTGCGCTCGCCGGGCGTGTACTTCGACCACGCGATCGACAAGGGTTCGGAGAAGGACGTGCACAGCGCGCGGGTGATCCCGTCGCGCGGTGCCTGGCTGGAGTTCGACGTCGACAAGCGCGACACCCTGGGCGTGCGCATCGACCGCAAGCGCCGTCAGCCGGTAACGGTGCTGCTCAAGGCGCTGGGCTGGAGTGCGGAGCGAATCGCCGAGCGATTCGGGTTCGCCCCGCTGATCATGGCCTCGCTGGCCAAGGACAACGTGGCGGGCACCGACGACGCTTTGCTCGAGATCCATCGCAAGCTGCGTCCGGGCGAGCCGCCGACCAAGGAGTCGGCACAGAACCTGCTGGCAAATCTGTTCTTCACCGAGAAGCGCTACGACCTGGCGCGGGTGGGCCGTTACAAGATCGACAAGAAGCTCGGGCTGCGCGCTCCGGGGGCACCGCGGGTGCTCACCGAGGACGACATCGCGGCCACCATCGAGTACCTGGTGCGCCTGCACGCCGGGGAGAGGACGATGATCGCGCCCGGCGGGGTCGAGGTGCCGGTGGAGGTCGACGACATCGACCATTTCGGTAACCGCCGGGTGCGCACCGTGGGTGAGCTGATCCAGAACCAGATCCGCGTGGGTCTGTCCCGGATGGAACGGGTGGTGCGGGAGCGCATGACCACCCAGGACGTCGAGGCGATCACGCCGCAGTCGCTGATGAACATCCGCCCGGTGGTCGCGGCGATGAAGGAGTTCTTCGGCACCTCGCAGCTGTCGCAGTTCATGGACCAGCGCAACCCGCTGGCGAGCCTGACCAACAAGCGGCGGCTGTCCGCGCTCGGGCCGGGCGGGCTCTCGCGCGAACGGGCCGGCTTGGAGGTCCGCGACGTGCACTACAGCCACTACGGCCGGATGTGCCCGATCGAGACGCCGGAGGGGCCGAACATCGGCCTGATGGGGTACCTGTCGGTGTACGCGCGGGTCAACCCGTTCGGTTTCGTCGAGACCCCCTACCGGCGGGTGGTGGACGGCCGGGTCACCGACGAGGTCGATTACCTCACCGCCGACGAGGAGGACCGGCACGTGGTGGCCCAGGCGAACGAACCGCTGGACGCCGAGGGCCGCTTCCTGGCCGCGCGAATCCCGGTGCGCCGGAAGAACTCCGAGGTGGAACTCGTCGATTCCGCCGCGGTGGATTACATGGATGTGTCGCCGCGGCAGATGGTGTCGGTGGCGACGGCGATGATTCCGTTCCTCGAGCATGATGATGCCAACCGTGCGCTGATGGGTGCGAATATGCAGCGTCAGGCGGTGCCGTTGATTCGGTCGGAGGCGCCGATCGTGGGTACCGGTATGGAGCTGCGTGCGGCGGTGGATGCCGGTGATGTGGTGGTGAACGAGAAGGCCGGTGTGGTCGAGGAGGTTTCGGCCGATTACGTCACGGTGATGGCCGATGACGGGACTCGTAAGTCGTATCGGATGCGGAAGTTCAACCGGTCGAATCAGGGGACGTGTTCGAATCAGCGGCCGATCGTGGACGAGGGTCAGCGGGTCGAGGCCGGGCAGGTGTTGGCTGATGGGCCGTGCACCGAGAACGGTGAGATGGCGCTGGGTAAGAACCTGTTGGTGGCGATCATGCCGTGGGAGGGGCACAACTACGAGGACGCGATCATCCTGTCGCAGCGGTTGGTGGAGCAGGATGTGTTGACCTCGATCCATATCGAGGAGCACGAGATCGATGCTCGTGACACCAAGCTCGGTGCCGAGGAGATCACTCGCGACATTCCGAATGTCTCCGATGAGGTGTTGGCGGATCTGGACGAGCGTGGCATCGTGCGGATCGGTGCGGAGGTGCGTGATGGTGACATCCTGGTCGGTAAGGTCACGCCCAAGGGTGAGACCGAGCTGACGCCGGAGGAGCGGTTGCTGCGGGCGATCTTCGGGGAGAAGGCGCGTGAGGTGCGTGATACCTCGTTGAAGGTGCCCCACGGTGAGTCGGGCAAGGTCATCGGGATCCGGGTGTTCTCTCGGGAGGACGATGACGATCTGCCGCCCGGTGTCAACGAGTTGGTGCGGGTGTATGTGGCGCAGAAGCGCAAGATCCAAGACGGTGACAAGCTGGCCGGTCGGCACGGGAACAAGGGTGTGATCGGCAAGATCCTGCCCACCGAGGACATGCCGTTCCTGCCCGATGGCACCCCGGTCGACATCATCCTCAACACCCACGGTGTGCCGCGGCGTATGAACATCGGCCAGATCCTGGAAACCCACCTCGGCTGGATCGGCAAAGCCGGCTGGAAGGTCGAGGGCAACCCCGAGTGGGCCAAGGATCTGCCGGAGGAGATGTGGGAGGCCCCCGCGGACTCCAACATCGCGACTCCGGTGTTCGACGGTGCCCGCGAGGAGGAGCTGACGGGTCTGCTGGGCTCGACGCTGCCCAACCGTGACGGTGAGCGGATGGTCGACGACAACGGCAAGGCCGTGCTGTTCGACGGTCGTTCCGGTGAGCCGTTCCCGTACCCGGTGGCGGTGGGCTACATGTACATCCTGAAGCTGCACCACCTGGTCGACGACAAGATCCACGCTCGCTCCACCGGCCCGTACTCGATGATCACCCAGCAGCCGCTCGGTGGTAAGGCCCAGTTCGGTGGCCAGCGCTTCGGTGAGATGGAGTGCTGGGCGATGCAGGCCTACGGCGCGGCCTACACCCTGCAGGAACTGCTCACGATCAAGTCCGACGACGTCGTCGGCCGCGTGAAGGTCTACGAGGCGATCGTCAAGGGCGACAACATCCCGGAACCCGGTGTGCCGGAATCGTTCAAGGTGTTGTTGAAGGAACTCCAGGCACTGTGCCTCAACGTCGAGGTGCTGTCCGCCGGTGCCGCGGTCGAACTGGCGCACGGGGTCGACGACGATCACGAGCGGACGGCCGCGAACCTCGGCATCAACCTGTCCCGCGCCGAATCCATCACGGAGACCGAGCTGTCCGGGTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41346","NCBI_taxonomy_name":"Nocardia farcinica IFM 10152","NCBI_taxonomy_id":"247156"}}}},"ARO_accession":"3000501","ARO_id":"36640","ARO_name":"rpoB2","ARO_description":"Due to gene duplication, the genomes of Nocardia species include both rifampin-sensitive beta-subunit of RNA polymerase (rpoB) and rifampin-resistant beta-subunit of RNA polymerase (rpoB2) genes, with ~88% similarity between the two gene products. Expression of the rpoB2 variant results in replacement of rifampin sensitivity with rifampin resistance.","ARO_category":{"36349":{"category_aro_accession":"3000210","category_aro_cvterm_id":"36349","category_aro_name":"rifamycin-resistant beta-subunit of RNA polymerase (rpoB)","category_aro_description":"Rifampin resistant RNA polymerases include amino acids substitutions which disrupt the affinity of rifampin for its binding site. These mutations are frequently concentrated in the rif I region of the beta-subunit and most often involve amino acids which make direct interactions with rifampin. However, mutations which also confer resistance can occur outside this region and may involve amino acids which do not directly make contact with rifampin.","category_aro_class_name":"AMR Gene Family"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36656":{"category_aro_accession":"3000517","category_aro_cvterm_id":"36656","category_aro_name":"rifaximin","category_aro_description":"Rifaximin is a semi-synthetic rifamycin used to treat traveller's diarrhea. Rifaximin inhibits RNA synthesis by binding to the beta subunit of bacterial RNA polymerase.","category_aro_class_name":"Antibiotic"},"36669":{"category_aro_accession":"3000530","category_aro_cvterm_id":"36669","category_aro_name":"rifabutin","category_aro_description":"Rifabutin is a semisynthetic rifamycin used in tuberculosis therapy. It inhibits DNA-dependent RNA synthesis.","category_aro_class_name":"Antibiotic"},"36673":{"category_aro_accession":"3000534","category_aro_cvterm_id":"36673","category_aro_name":"rifapentine","category_aro_description":"Rifapentine is a semisynthetic rifamycin that inhibits DNA-dependent RNA synthesis. It is often used in the treatment of tuberculosis and leprosy.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"37":{"model_id":"37","model_name":"Escherichia coli mdfA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"561":{"protein_sequence":{"accession":"AFH35853.1","sequence":"MQNKLASGARLGRQALLFPLCLVLYEFSTYIGNDMRQPGMLENVEQYQAGIEWVPTSMNAYLAGGMFIQWLLGPLSDRIGRRPVMLAGVVWFIVTCLAILLAQNIEQFTLLRFLHGISLCFIGAVGYDAIQESFEEAVCIKITALMANVALIAPLLGPLVGASWIHVLPWEGMFVLFAALAAISFFGLQRAMPETATRIGEKLSLKELGRDYKLVLKNGRFVAGALALGFLSLPLLAWIAQSPIIIITGEQLSSYEYGLLQVPIFGALIAGNLLLARLTSRRTVRSLIIMGGWPIMIGLLVAAAATVISSHAYLWMTAGLSIYAFGIGLANAGLVRLTLFASVMSKGTVSAAMGMLQMLIFTVGIEISKHAWLNGGNGLFNLFNLVNGILLLSLMVIFLKDKQMGNSHEG"},"dna_sequence":{"accession":"JQ394987","fmin":"0","fmax":"1233","strand":"+","sequence":"ATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGCGTTACTTTTTCCTCTCTGTCTGGTGCTTTACGAATTTTCAACCTATATCGGCAACGATATGAGGCAACCCGGTATGTTGGAAAATGTGGAACAATATCAGGCGGGCATTGAGTGGGTTCCTACTTCGATGAACGCGTATCTGGCGGGCGGGATGTTTATACAATGGCTGCTGGGGCCGCTGTCGGATCGTATTGGTCGTCGTCCGGTGATGCTGGCGGGAGTGGTGTGGTTTATCGTCACATGTCTGGCAATATTGCTGGCGCAAAACATTGAACAATTCACCCTGTTGCGCTTCTTGCACGGCATAAGCCTCTGTTTCATTGGCGCTGTGGGATACGACGCAATTCAGGAATCCTTCGAAGAGGCGGTTTGTATCAAGATCACCGCGCTGATGGCGAACGTGGCGCTGATTGCTCCGCTACTTGGTCCGCTGGTGGGCGCGTCGTGGATCCATGTGCTGCCCTGGGAGGGGATGTTTGTTTTGTTTGCCGCATTGGCAGCGATCTCCTTTTTCGGTCTGCAACGGGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGCGCTGGCGCTGGGATTCCTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATTACCGGCGAGCAGTTGAGCAGCTATGAATATGGCTTGCTGCAAGTGCCTATTTTCGGGGCGTTAATTGCGGGTAACTTGCTGTTAGCGCGTCTGACCTCGCGCCGCACCGTACGTTCGCTGATTATTATGGGCGGCTGGCCGATTATGATTGGTCTATTGGTCGCTGCTGCGGCAACGGTTATCTCATCGCACGCGTATTTATGGATGACTGCCGGGTTAAGTATTTATGCTTTCGGTATTGGTCTGGCGAATGCGGGACTGGTGCGATTAACCCTGTTTGCCAGCGTTATGAGTAAAGGTACGGTTTCTGCCGCGATGGGAATGCTGCAAATGCTGATCTTTACCGTTGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACTGTTTAATCTCTTCAACCTTGTCAACGGAATTTTGTTGCTGTCGCTGATGGTTATCTTTTTAAAAGATAAACAGATGGGAAATTCTCACGAAGGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001328","ARO_id":"37727","ARO_name":"Escherichia coli mdfA","ARO_description":"Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr\/CmlA chloramphenicol exporter.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"40514":{"category_aro_accession":"3003823","category_aro_cvterm_id":"40514","category_aro_name":"benzalkonium chloride","category_aro_description":"Benzalkonium chloride is a type of cationic surfactant. It is an organic salt called a quaternary ammonium compound. It has three main categories of use: as a biocide, a cationic surfactant, and as a phase transfer agent.","category_aro_class_name":"Drug Class"},"40518":{"category_aro_accession":"3003827","category_aro_cvterm_id":"40518","category_aro_name":"rhodamine","category_aro_description":"Rhodamine is a flurone dye that is often used as a tracer due to determine the rate and direction of flow and transport. It permeates the cell membrane of gram negative organisms E. coli and P. aeruginosa.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"328":{"model_id":"328","model_name":"Salmonella enterica cmlA","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"623":{"protein_sequence":{"accession":"CAD31707.1","sequence":"MDMYLPAVPFMPNALGTTASTIQLTLTTYLVMIGAGQLLFGPLSDRLGRRPVLLGGGLANVVASMGLALTSSAEVFLGLRILQACGASACLVSTFATVRDIYAGREESNVIYGILGSMLAMVPAVGPLLGALVDMWLGWRAIFAFLGLGMIAASAAAWRFWPETRVQRVAGLQWSQLLLPVKCLNFWLYTLCYAAGMGSFFVFFSIAPGLMMGRQGVSQLGFSLLFATVAIAMVFTARFMGRVIPKWGSPSVLRMGMGCLIAGAVLLAITEIWALQSVLGFIAPMWLVGIGVATAVSVAPNGALRGFDHVAGTVTAVYFCLGGVLLGSIGTLIISLLPRNTAWPVVVYCLTLATVVLGLSCVSRVKGSRGQGEHDVVALQSAGSTSNPNR"},"dna_sequence":{"accession":"AJ487033","fmin":"1685","fmax":"2858","strand":"+","sequence":"ATGGACATGTACTTGCCAGCAGTGCCGTTTATGCCAAACGCGCTTGGTACGACAGCGAGCACAATTCAGCTTACGCTGACAACGTACTTGGTCATGATTGGTGCCGGTCAGCTCTTGTTTGGACCGCTATCGGACCGACTGGGGCGCCGCCCCGTTCTACTGGGAGGTGGCCTCGCAAACGTTGTGGCGTCAATGGGCCTCGCTCTTACGTCATCGGCTGAAGTCTTTCTGGGGCTTCGGATTCTTCAGGCTTGTGGTGCCTCGGCGTGCCTTGTTTCCACATTTGCAACAGTACGTGACATTTACGCAGGTCGCGAGGAAAGTAATGTCATTTACGGCATACTCGGATCCATGCTGGCCATGGTCCCGGCGGTAGGCCCATTGCTCGGAGCGCTCGTCGACATGTGGCTTGGGTGGCGGGCTATCTTTGCGTTTCTAGGTTTGGGCATGATCGCTGCATCTGCAGCAGCGTGGCGATTCTGGCCTGAAACCCGGGTGCAACGAGTTGCGGGCTTGCAATGGTCGCAGCTGCTACTCCCCGTTAAGTGCCTGAACTTCTGGTTGTACACGTTGTGTTACGCCGCTGGAATGGGTAGCTTCTTCGTCTTTTTCTCCATTGCGCCCGGACTAATGATGGGCAGGCAAGGTGTGTCTCAGCTTGGCTTCAGCCTGCTGTTCGCCACAGTGGCAATTGCCATGGTGTTTACGGCTCGTTTTATGGGGCGTGTGATACCCAAGTGGGGCAGCCCAAGTGTCTTGCGAATGGGAATGGGATGCCTGATAGCTGGAGCAGTATTGCTTGCCATCACCGAAATATGGGCTTTGCAGTCCGTGTTAGGCTTTATTGCTCCAATGTGGCTAGTGGGTATTGGTGTCGCCACAGCGGTATCTGTGGCGCCCAATGGCGCTCTTCGAGGATTCGACCATGTTGCTGGAACGGTCACGGCAGTCTACTTCTGCTTGGGCGGTGTACTGCTAGGAAGCATCGGAACGTTGATCATTTCGCTGTTGCCGCGCAACACGGCTTGGCCGGTTGTCGTGTACTGTTTGACCCTTGCAACAGTCGTGCTCGGTCTGTCTTGTGTTTCCCGAGTGAAGGGCTCTCGCGGCCAGGGGGAGCATGATGTGGTCGCGCTACAAAGTGCGGGAAGTACATCAAATCCCAATCGTTGAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35732","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium","NCBI_taxonomy_id":"90371"}}}},"ARO_accession":"3002691","ARO_id":"39125","ARO_name":"Salmonella enterica cmlA","ARO_description":"cmlA is a plasmid-encoded chloramphenicol exporter that is found in Salmonella typhimurium","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2704":{"model_id":"2704","model_name":"MexEF-OprN with MexT mutation conferring resistance to chloramphenicol, ciprofloxacin, and trimethoprim","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)","model_param":{"41141":{"param_type":"efflux pump components","param_description":"This detection model parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305.","param_type_id":"41141","param_value":{"7572":"1608,1067,1300,172"}}},"ARO_accession":"3004066","ARO_id":"41142","ARO_name":"MexEF-OprN with MexT mutation conferring resistance to chloramphenicol, ciprofloxacin, and trimethoprim","ARO_description":"The MexEF\u2013OprN efflux pump in P. aeruginosa is overexpressed with MexT mutation conferring resistance to chloramphenicol and ciprofloxacin","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2832":{"model_id":"2832","model_name":"AAC(2')-Ie","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"4182":{"protein_sequence":{"accession":"NP_302635.1","sequence":"MDTHHVHTARLVHTADLDGETLRRLQQMVTDAFAGDFDETDWEHALGGMHALIWRHGTIIAHAAVVQRRLFYHGNALRCGYLEGVAVRKDCRGRGLVHALLDAIEQVIRGAYQFGALSSSDRARRVYMSRGWLPWLGPTSVLAPTGVIRTPDDDGSVFVLPVGINPDTSSGLMCDWRAGNVW"},"dna_sequence":{"accession":"NC_002677.1","fmin":"3039191","fmax":"3039740","strand":"+","sequence":"ATGGATACCCACCACGTACATACCGCCCGCCTGGTTCATACCGCCGATCTCGACGGCGAGACTCTCCGGCGCCTCCAGCAGATGGTCACCGACGCTTTCGCCGGAGACTTCGACGAGACCGACTGGGAACACGCATTGGGCGGGATGCACGCCCTGATCTGGCGGCACGGCACAATCATTGCGCACGCCGCGGTCGTTCAGCGGCGACTATTCTACCACGGCAACGCGTTGCGTTGCGGTTACCTCGAAGGTGTCGCGGTACGGAAGGACTGCCGGGGCCGCGGACTTGTACATGCGCTGCTGGACGCTATCGAGCAAGTGATACGCGGCGCCTATCAATTCGGTGCCTTGAGTTCCTCGGACCGAGCCCGTCGGGTGTATATGTCGCGCGGGTGGTTACCATGGCTCGGCCCGACGTCAGTGCTGGCTCCTACCGGTGTGATCCGTACGCCCGATGATGACGGCTCGGTGTTTGTCCTTCCGGTCGGCATCAACCCGGACACCTCCTCGGGGTTGATGTGCGATTGGCGCGCAGGCAACGTGTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40083","NCBI_taxonomy_name":"Mycobacterium leprae TN","NCBI_taxonomy_id":"272631"}}}},"ARO_accession":"3002527","ARO_id":"38927","ARO_name":"AAC(2')-Ie","ARO_description":"AAC(2')-Ie is a chromosomal-encoded aminoglycoside acetyltransferase in M. leprae","ARO_category":{"36480":{"category_aro_accession":"3000341","category_aro_cvterm_id":"36480","category_aro_name":"AAC(2')","category_aro_description":"Acetylation of the aminoglycoside antibiotic on the amino group at position 2'.","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2833":{"model_id":"2833","model_name":"Brachyspira hyodysenteriae 23S rRNA with mutation conferring resistance to tylosin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"2000"},"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"8198":"A2058G","8199":"A2058U"},"clinical":{"8198":"A2058G","8199":"A2058U"}}},"model_sequences":{"sequence":{"4183":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NZ_CP015910.2","fmin":"2512812","fmax":"2515808","strand":"-","sequence":"ATATGGTCAAGTCATTGGTCTGATTAGTGCTGCTCAGCTGAACAGGTATTTCTTCCCTGCTTACACTTGCAGTCTATCAACGTCGTAGTCTCCAACGAAACTCATAGGGAAAGTTAATCTTGAAGGAGGCTTCCCACTTAGATGCTTTCAGCGGTTATCCCGTCCGCACATAGCTACTCTGCGATGCTCTTGGCAGAACAACAGATACACCAGCGGTGCGTTCATTCCGGTCCTCTCGTACTAAGAATGACTCTTCTCAACTTTCCAACGCCCACAACGGATAGGGACCAAACTGTCTCACGACGTTCTGAACCCAGCTCGCGTACCGCTTTAATTGGCGAACAGCCAAACCCTTGGGACCTGCTCCAGCCCCAGGATGCGATGAGCCGACATCGAGGTGCCAAACCTCCCCGTCGATATGAACTCTTGGGGGAGATAAGCCTGTTATCCCCGGAGTACCTTTTGTCCGTTTAGCGATGGCCCTTCCACTCGGGACCACCGGATCACTAAAACCTACTTTCGTACCTGCTCGAGATGTCTCTCTCGCAGTCAAGCCACCTTATGCCTTTATACTCTACTACCGATTTCTATTCGGTTTGAGGTGACCTTTGCACGCCTCCGTTACTCTTTAGGAGGCGACCGCCCCAGTCAAACTACCCGCCTGACAATGTCCGACTGCCGGATAACGGCTAATCGTTAGAATCCCATTTTGCGAAGGATGGTATTTCAACGATGGCTCCATGAAAGCTGGCGCTCCCACTTCAAAGCCTCCCATCTATCCTACACATCACAAAACAAAACTCAATGTCAAGTTATAGTAAAGGTTCACGGGGTCTTTCCGTCCTGTTGCGGGTAATCAGCATCTTCACTGATAATTCAATTTCACCGAGTTCTTCCCCGAGACAGTGCCCGGATCGTTACACCATTCGTGCAGGTCGGAACTTACCCGACAAGGAATTTCGCTACCTTAGGACCGTCATAGTTACGGCCGCCGTTTACTGGGGCTTCAATTCGAAGCTTCGCTTACGCTAACCTCTCCTTTTAACCTTCCAGCACTGGGCAGGTGTCAATCCCTATACATCCATTTACATGTTTGCAGAGATCTGTGTTTTTGTTAAACAGTCGGCCAGGCCTTTTCACTGCGACTCTCCTCTCAATATTGCTACCAAGATTCAAGCGTCTCTTTTTCCGAAGTTACAAGACTAATTTGCAGAGTTCCTTAGGGAAGATTATCTCGAGCGCCTTAGAATACTCATCTCACCCACCTGTGTCGGTTTGCGGTACGATTATGACATGCCTAACCTTAGAAATTATTTCTCGACAGCCTAGCTCATGCAACTTCCTGAACCCGAAAGCCCAGTCACTATCCAGCCTCAACCTTAAAGAAGCAAGCATTTGACTCACCTCAAGTCTAAACTGTTTGACGTTATCTACCAATCTAACGCGTACATAAACAATCTGTGTCATTCCATCGAAACATATCATAGTACAGGAATATTTACCTGTTTCCCATCGACTACGCTTTTCAGCCTCATCTTAGGGGTCGACTAACCCTAGGCAGATTAGCTTTACCTAGGAAACCTTGGGTTTGCGGCGAACGGGTTTCTCACCCGTTTTCTCGTTACTCATGCCTGCATCCTCACTTCTTATACCTCCAGCCCACCTCACGATGAACCTTCGACGGCTTAAAGAACGCTCTCCTACCAATTATAGATTAACTCTATAATTCCCTAGCTTCGGTACTATGTTTGAGCCCCGTTACATTTTCGGCGCAAGAACACTCGACCAGTGAGCTGTTACGCACTCTTTAAAGGAATGGCTGCTTCTAAGCCAACCTCCTGGCTGTTTAAGTATTCTCACATCCTTTCCCACTTAACATAGATTTTGGGACCTTAGCTGAGGATCTGGGCTGTTTCCCTTTTGACAATGACGCTTATCCGCCGCTGTCTAACTGCCATGTTCTTAACTTACGGTATTCGGAGTTTAGTTGGGTTTGGTACTCGGTTAGGAGCCCTAGTCCATTTAGTGCTCTACCCCCGCAAGTAAACACATAACGCTGCCCCTAAAGACATTTCGGAGAGAACCAGCTATCTCCAAGTTTGATTAGCCTTTCACTCCTACCCACAAGTCATCCAAAGCCTTTTCACGGCCACTGGTTCGCACCTCCATTCGATGTTACTCGAGTTTCGCGCTGCTCATAGGTAGATCACTTGGCTTCGGGTCGTATAGCATGCAACTAATTTCGCCCTATTAAGGCTCGCTTTCACTACGACTACAAGGCTATTACCTCTTAATCTTGCTACATACTATAAGTCGCAGGCTCATTCTACAAAAGGCACGCCATCAGGCCATCTACTATTGCTAGCAGGGTACCCTCTGACTACTTGTAAGCTTAAGGTTTCAGGTTCTATTTAATAACCCTCAACGGGAGACTTTTCACCTTTCCCTCACGGTACTCTACACTATTGGTCACTGGTTAGTATTTTGCCTTGGATAGTGGTCTACCCAGATTCAAACAGGGTTTCACGTGCCCCGCCCTACTCAGGAACGATAAAACCTTGTCTATATGATTTCGTGTACAGGACTATCACCCACTATGGTCTGCTTTTCCAAAACAGTTCCACTATCATATAAAGCAAAGTCGATGCATGCAAGTACATCGCTTACCGCCCTACAACACCATAATAACAACGCCTTGCAGCTTGACATTATTAAGGTTTAGGCTCTTCCCCTTTCGCTCGCCACTACTTAGGGAATCTCAATTTTGATTACTCTTCCTCCAGGTACTTAGATGTTTCAGTTCCCTGGGTGTCGCCTCATACACCTATGGATTCAGTGTATGATATAGAAGGTTTACTTCTATAGGTTTTCCCATTCGGTGATCTACGGATCATAGAATATTTGCTTCTCCCCGTAGCTTATCGCAGCTTGTCACGACCTTCATCGCCTTCCAGTGCCTAGGCATCCACCTTAAGCCCTTACTTACTTGACCATAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41351","NCBI_taxonomy_name":"Brachyspira hyodysenteriae ATCC 27164","NCBI_taxonomy_id":"1266923"}}}},"ARO_accession":"3004133","ARO_id":"41260","ARO_name":"Brachyspira hyodysenteriae 23S rRNA with mutation conferring resistance to tylosin","ARO_description":"Point mutation in B. hyodysenteriae 23S rRNA shown to confer resistance to tylosin and erythromycin","ARO_category":{"41251":{"category_aro_accession":"3004125","category_aro_cvterm_id":"41251","category_aro_name":"23S rRNA with mutation conferring resistance to macrolide antibiotics","category_aro_description":"Nucleotide point mutations in the 23S rRNA subunit may confer resistance to macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36600":{"category_aro_accession":"3000461","category_aro_cvterm_id":"36600","category_aro_name":"florfenicol","category_aro_description":"Florfenicol is a fluorine derivative of chloramphenicol, where the nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3) and the hydroxyl group (-OH), by a fluorine group (-F). The action mechanism is the same as chloramphenicol's, where the antibiotic binds to the 23S RNA of the 50S subunit of bacterial ribosomes to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin 1A is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"vernamycin B-gamma","category_aro_description":"Vernamycin B-gamma is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2834":{"model_id":"2834","model_name":"Mycobacterium tuberculosis iniB with mutation conferring resistance to ethambutol","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"8200":"A47T"},"clinical":{"8200":"A47T"}},"41339":{"param_type":"mutation in regulatory element","param_description":"An AMR detection model parameter to describe mutations in regulatory elements upstream of a coding DNA region shown to confer resistance to an antibiotic drug or drug class. Regulatory element mutations in CARD use the following notation: nt[wild-type][-][position][mutation].","param_type_id":"41339","param_value":{"8201":"ntC-89T"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"4184":{"protein_sequence":{"accession":"NP_214855.1","sequence":"MTSLIDYILSLFRSEDAARSFVAAPGRAMTSAGLIDIAPHQISSVAANVVPGLNLGAGDPMSGLRQAVAARHGFAQDVANVGFAGDAGAGVASVITTDVGAGLASGLGAGFLGQGGLALAASSGGFGGQVGLAAQVGLGFTAVIEAEVGAQVGAGLGIGTGLGAQAGMGFGGGVGLGLGGQAGGVIGGSAAGAIGAGVGGRLGGNGQIGVAGQGAVGAGVGAGVGGQAGIASQIGVSAGGGLGGVGNVSGLTGVSSNAVLASNASGQAGLIASEGAALNGAAMPHLSGPLAGVGVGGQAGAAGGAGLGFGAVGHPTPQPAALGAAGVVAKTEAAAGVVGGVGGATAAGVGGAHGDILGHEGAALGSVDTVNAGVTPVEHGLVLPSGPLIHGGTGGYGGMNPPVTDAPAPQVPARAQPMTTAAEHTPAVTQPQHTPVEPPVHDKPPSHSVFDVGHEPPVTHTPPAPIELPSYGLFGLPGF"},"dna_sequence":{"accession":"NC_000962.3","fmin":"409361","fmax":"410801","strand":"+","sequence":"ATGACCTCGCTTATCGATTACATCCTGAGCCTGTTCCGCAGCGAAGACGCCGCCCGGTCGTTCGTTGCCGCTCCGGGACGGGCCATGACCAGTGCCGGGCTGATCGATATCGCGCCGCACCAAATCTCATCGGTGGCGGCCAATGTGGTGCCGGGTCTGAATCTGGGTGCCGGCGACCCCATGAGCGGATTGCGGCAGGCCGTCGCCGCTCGGCATGGCTTTGCGCAGGACGTCGCCAATGTCGGCTTCGCCGGTGACGCGGGCGCGGGGGTGGCAAGCGTCATCACGACCGATGTCGGTGCGGGCCTGGCTAGCGGACTGGGTGCTGGGTTCCTGGGTCAGGGTGGCCTGGCTCTCGCCGCGTCAAGCGGTGGTTTCGGCGGTCAGGTCGGCTTGGCTGCCCAGGTCGGTCTGGGTTTTACTGCCGTGATTGAGGCCGAGGTCGGCGCTCAGGTTGGTGCTGGGTTAGGTATTGGGACGGGTCTGGGTGCTCAGGCCGGTATGGGCTTTGGCGGCGGGGTTGGCCTGGGTCTGGGTGGTCAGGCCGGCGGTGTGATCGGTGGGAGCGCGGCCGGGGCTATCGGTGCCGGCGTCGGCGGTCGCCTAGGCGGCAATGGCCAGATCGGAGTTGCCGGCCAGGGTGCCGTTGGCGCTGGTGTCGGCGCTGGTGTCGGCGGCCAGGCGGGCATCGCTAGCCAGATCGGTGTCTCAGCCGGTGGTGGGCTCGGCGGCGTCGGCAATGTCAGCGGCCTGACCGGGGTCAGCAGCAACGCAGTGTTGGCTTCCAACGCAAGCGGCCAGGCGGGGTTGATCGCCAGTGAAGGCGCTGCCTTGAACGGCGCTGCTATGCCTCATCTGTCGGGCCCGTTAGCCGGTGTCGGTGTGGGTGGTCAGGCCGGCGCCGCTGGCGGCGCCGGGTTGGGCTTCGGAGCGGTCGGGCACCCGACTCCTCAGCCGGCGGCCCTGGGCGCGGCTGGCGTGGTGGCCAAGACCGAGGCGGCTGCTGGAGTGGTTGGCGGGGTCGGCGGGGCAACCGCGGCCGGGGTCGGCGGGGCACACGGCGACATCCTGGGCCACGAGGGAGCCGCACTGGGCAGTGTCGACACGGTCAACGCCGGTGTCACGCCCGTCGAGCATGGCTTGGTCCTGCCCAGTGGCCCCCTGATCCACGGCGGTACCGGCGGCTATGGCGGCATGAACCCGCCAGTGACCGATGCGCCGGCACCGCAAGTTCCGGCGCGGGCCCAGCCGATGACCACGGCGGCCGAGCACACGCCGGCGGTTACCCAACCGCAGCACACGCCGGTCGAGCCGCCGGTCCACGATAAGCCGCCGAGCCATTCGGTGTTTGACGTCGGTCACGAGCCGCCGGTGACGCACACGCCGCCGGCGCCCATCGAACTGCCGTCGTACGGCCTTTTCGGACTACCCGGGTTCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3004135","ARO_id":"41262","ARO_name":"Mycobacterium tuberculosis iniB with mutation conferring resistance to ethambutol","ARO_description":"Point mutations in M. tuberculosis iniB shown to confer resistance to ethambutol.","ARO_category":{"41263":{"category_aro_accession":"3004136","category_aro_cvterm_id":"41263","category_aro_name":"Ethambutol resistant iniB","category_aro_description":"Point mutations occurring in the iniB region of the iniBAC operon shown to confer resistance to ethambutol","category_aro_class_name":"AMR Gene Family"},"36636":{"category_aro_accession":"3000497","category_aro_cvterm_id":"36636","category_aro_name":"ethambutol","category_aro_description":"Ethambutol is an antimycobacterial drug prescribed to treat tuberculosis. It is usually given in combination with other tuberculosis drugs, such as isoniazid, rifampicin, and pyrazinamide. Ethambutol inhibits arabinosyl biosynthesis, disrupting mycobacterial cell wall formation.","category_aro_class_name":"Antibiotic"},"36666":{"category_aro_accession":"3000527","category_aro_cvterm_id":"36666","category_aro_name":"polyamine antibiotic","category_aro_description":"Polyamine antibiotics are organic compounds having two or more primary amino groups.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2835":{"model_id":"2835","model_name":"PatA-PatB","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)","model_param":{"41141":{"param_type":"efflux pump components","param_description":"This detection model parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305.","param_type_id":"41141","param_value":{"8203":"2081,2112"}}},"ARO_accession":"3000769","ARO_id":"37149","ARO_name":"PatA-PatB","ARO_description":"PatA-PatB is an efflux protein complex that is associated with fluoroquinolone resistance in Streptococcus pneumoniae. Experiments indicate that PatA and PatB form a heterodimeric transporter.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2836":{"model_id":"2836","model_name":"Bla2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"475"}},"model_sequences":{"sequence":{"4187":{"protein_sequence":{"accession":"AAR20596.1","sequence":"MKNTLLKLGVCVSLLGITPFVSTISSVQAERKVEHKVIKNETGTISISQLNKNVWVHTELGCFNGEAVPSNGLILNTSKGLVLVDSSWDDKLTKELIEMAEKKFKKSVTDVIITHAHADRIGGIKTLKERGIKAHSTTLTAELAKKNGYEEPLGDLQAITKLKFGNMKVETFYPGKGHTEDNIVVWLPQYNMLVGGCLVKSASAKDLGNITDAYVNEWSTSIENVLKRYENINFVVPGHGEVGDKGLLLHTLDLLK"},"dna_sequence":{"accession":"AY453162","fmin":"500","fmax":"1271","strand":"+","sequence":"ATGAAAAATACATTATTAAAATTAGGGGTATGTGTTAGTTTACTAGGAATAACTCCATTTGTTAGTACAATTTCTTCTGTACAAGCAGAACGAAAGGTAGAGCATAAAGTAATAAAAAATGAGACAGGAACTATTTCAATTTCTCAGTTAAACAAAAATGTTTGGGTTCATACGGAGTTAGGTTGTTTTAACGGAGAAGCAGTTCCTTCGAACGGTTTAATCCTTAATACTTCTAAAGGATTAGTACTTGTCGATTCTTCTTGGGATGATAAGTTAACGAAGGAATTAATAGAGATGGCAGAAAAGAAATTTAAGAAGAGTGTAACGGATGTTATTATTACACATGCACACGCTGATCGGATTGGTGGAATAAAAACGTTGAAAGAAAGAGGCATTAAAGCGCATAGTACAACGTTAACTGCGGAACTAGCAAAGAAAAATGGATATGAAGAACCACTTGGAGACTTACAAGCAATTACGAAATTGAAGTTTGGAAATATGAAAGTAGAAACGTTTTATCCAGGGAAAGGACATACAGAAGATAATATCGTCGTATGGTTACCACAATACAACATGTTAGTTGGAGGCTGTTTAGTGAAGTCTGCGTCCGCGAAAGATTTAGGAAATATTACTGATGCTTATGTAAATGAATGGTCTACATCGATTGAGAATGTGCTGAAGCGATATGAAAATATAAATTTTGTAGTACCTGGTCATGGAGAAGTAGGGGACAAAGGATTACTTTTACATACATTGGATTTGTTAAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36786","NCBI_taxonomy_name":"Bacillus anthracis","NCBI_taxonomy_id":"1392"}}}},"ARO_accession":"3004189","ARO_id":"41353","ARO_name":"Bla2","ARO_description":"Bla2 is a chromosomal-encoded beta-lactamase, found in Bacillus anthracis, which has penicillin, cephalosporin, and carbapenem-hydrolizing abilities.","ARO_category":{"41394":{"category_aro_accession":"3004230","category_aro_cvterm_id":"41394","category_aro_name":"subclass B1 Bacillus anthracis Bla beta-lactamase","category_aro_description":"Beta-lactamases belonging to the Bla genes from Bacillus anthracis that are classified as subclass B1 beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2837":{"model_id":"2837","model_name":"APH(2'')-If","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4188":{"protein_sequence":{"accession":"AAW34150.1","sequence":"MDIKKIIEEKCNIVVDSIKLIGEGYDSKAYIVNNEYVFKIKFSANKKKGYEKEKAIYDFLNKKLNTNIKIPNIEYSYISEELSILGYKEIKGTFLTPEIYFALSKEKQELLKQDIAMFLRQMHDLDYSEISSYTIDNKQNVLEEYQLLKETIYDSLTDIEKQYVEEFMQRLNSTTIFDGKKCLCHNDFSCNHLLLDDENRLCGVIDFGDSGIIDEYCDFIYLLEDSEEEIGVSFGEDILRLYGNIDISKAKEYQDVVEQYYPIETIVYGIKNNRPDFIEKGRKEIYIRTRKDEKLRK"},"dna_sequence":{"accession":"AY701528.1","fmin":"9695","fmax":"10589","strand":"+","sequence":"ATGGATATAAAAAAGATAATAGAAGAAAAATGCAATATAGTTGTTGATAGTATAAAGTTGATTGGTGAGGGTTATGACAGCAAAGCATACATTGTAAATAATGAATATGTTTTCAAAATCAAATTTAGTGCTAATAAGAAAAAAGGGTATGAAAAAGAAAAAGCAATATATGATTTTCTAAACAAAAAATTAAATACAAATATTAAAATACCAAATATAGAATATTCATATATAAGTGAAGAATTATCTATTTTAGGATATAAAGAAATTAAAGGAACTTTTTTAACACCAGAAATATATTTTGCCTTATCAAAAGAAAAGCAAGAATTATTAAAGCAAGATATTGCTATGTTTTTAAGACAAATGCACGATTTAGATTATAGTGAAATAAGTTCATATACGATAGACAATAAACAAAATGTTTTAGAAGAATATCAATTACTTAAAGAAACAATATATGATAGTCTTACTGATATTGAAAAACAATATGTAGAAGAATTTATGCAAAGATTAAATAGTACAACTATATTTGATGGTAAAAAATGCTTATGCCATAATGATTTTAGTTGTAATCATTTATTACTTGATGATGAAAATAGATTATGTGGTGTAATAGATTTTGGAGATTCTGGAATTATAGATGAATACTGTGATTTCATATATTTGCTAGAAGATAGTGAAGAAGAAATTGGCGTGTCTTTTGGAGAAGATATATTAAGATTATACGGAAATATTGATATTTCAAAAGCAAAGGAATATCAAGATGTTGTAGAACAATATTATCCAATAGAAACTATTGTATATGGTATTAAAAATAATAGACCTGATTTTATAGAAAAAGGTAGAAAAGAGATTTATATAAGAACTCGCAAAGATGAAAAATTAAGGAAGTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3004191","ARO_id":"41355","ARO_name":"APH(2'')-If","ARO_description":"Aminoglycoside 2''-phosphotransferase identified from the gram-negative pathogen Campylobacter jejuni. APH(2'')-If was shown to confer resistance to 4,6-disubstituted antibiotics kanamycin, tobramycin, dibekacin, gentamicin and sisomicin through antibiotic phosphorylation. Described by Toth et al. 2013.","ARO_category":{"36267":{"category_aro_accession":"3000128","category_aro_cvterm_id":"36267","category_aro_name":"APH(2'')","category_aro_description":"Phosphorylation of 2-deoxystreptamine aminoglycosides on the hydroxyl group at position 2''","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"40942":{"category_aro_accession":"3004015","category_aro_cvterm_id":"40942","category_aro_name":"gentamicin A","category_aro_description":"Gentamicin A is part of a complex of broad spectrum aminoglycoside antibiotics. Gentamicin inhibits protein synthesis, resulting in bacterial cell death.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2838":{"model_id":"2838","model_name":"MCR-1.2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"4189":{"protein_sequence":{"accession":"ANR95875.1","sequence":"MMLHTSVWYRRSVSPFVLVASVAVFLTATANLTFFDKISQTYPIADNLGFVLTIAVVLFGAMLLITTLLSSYRYVLKPVLILLLIMGAVTSYFTDTYGTVYDTTMLQNALQTDQAETKDLLNAAFIMRIIGLGVLPSLLVAFVKVDYPTWGKGLMRRLGLIVASLALILLPVVAFSSHYASFFRVHKPLRSYVNPIMPIYSVGKLASIEYKKASAPKDTIYHAKDAVQATKPDMRKPRLVVFVVGETARADHVSFNGYERDTFPQLAKIDGVTNFSNVTSCGTSTAYSVPCMFSYLGADEYDVDTAKYQENVLDTLDRLGVSILWRDNNSDSKGVMDKLPKAQFADYKSATNNAICNTNPYNECRDVGMLVGLDDFVAANNGKDMLIMLHQMGNHGPAYFKRYDEKFAKFTPVCEGNELAKCEHQSLINAYDNALLATDDFIAQSIQWLQTHSNAYDVSMLYVSDHGESLGENGVYLHGMPNAFAPKEQRSVPAFFWTDKQTGITPMATDTVLTHDAITPTLLKLFDVTADKVKDRTAFIR"},"dna_sequence":{"accession":"KX236309.1","fmin":"3136","fmax":"4762","strand":"-","sequence":"TCAGCGGATGAATGCGGTGCGGTCTTTGACTTTGTCCGCGGTGACATCAAACAGCTTTAATAATGTCGGCGTGATCGCGTCATGGGTCAGGACGGTATCGGTTGCCATTGGCGTGATGCCAGTTTGCTTATCCGTCCAGAAAAATGCAGGCACACTGCGCTGTTCTTTTGGTGCAAAGGCATTTGGCATACCATGTAGATAGACACCGTTCTCACCCAGACTTTCGCCATGATCGCTGACATACAGCATTGAGACATCATAGGCATTGCTGTGCGTCTGCAGCCACTGGATACTTTGAGCGATGAAATCATCGGTGGCAAGCAAGGCATTGTCATAAGCATTGATCAAGGACTGATGTTCGCACTTGGCAAGCTCATTACCTTCACACACTGGCGTGAATTTGGCAAACTTTTCATCATATCGCTTAAAATACGCAGGCCCGTGATTGCCCATTTGGTGCAGCATGATCAGCATATCTTTGCCGTTATTGGCAGCGACAAAGTCATCTAAGCCAACGAGCATACCGACATCGCGGCATTCGTTATAAGGATTGGTGTTGCAGATGGCGTTGTTGGTCGCGGATTTATAATCGGCAAATTGCGCTTTTGGCAGCTTATCCATCACGCCTTTTGAGTCCGAATTATTATCACGCCACAAGATACTTACGCCCAAGCGATCCAGCGTATCCAGCACATTTTCTTGGTATTTGGCGGTATCGACATCATACTCATCCGCGCCCAGATAGCTGAACATACACGGCACAGAATACGCCGTCGATGTGCCGCACGATGTGACATTGCTAAAATTGGTCACGCCATCGATCTTGGCAAGCTGTGGGAAAGTATCGCGCTCATAGCCATTGAAGCTGACATGATCGGCGCGTGCCGTCTCACCGACGACGAACACCACTAGGCGTGGCTTACGCATATCAGGCTTGGTTGCTTGTACCGCGTCTTTGGCGTGATAAATGGTATCTTTTGGCGCACTGGCTTTTTTATACTCAATACTGGCAAGCTTACCCACCGAGTAGATTGGCATGATCGGATTGACATAGCTACGCAGCGGCTTATGCACGCGAAAGAAACTGGCATAATGACTGCTGAACGCCACCACAGGCAGTAAAATCAGCGCAAGACTTGCCACGATCAAGCCCAATCGGCGCATCAAACCCTTGCCCCAAGTCGGATAATCCACCTTAACAAAAGCCACAAGCAAACTTGGTAGCACACCCAAACCAATGATACGCATGATAAACGCTGCGTTTAATAGATCCTTGGTCTCGGCTTGGTCGGTCTGTAGGGCATTTTGGAGCATGGTCGTATCATAGACCGTGCCATAAGTGTCAGTAAAATAACTGGTCACCGCGCCCATGATTAATAGCAAAATCAACACAGGCTTTAGCACATAGCGATACGATGATAACAGCGTGGTGATCAGTAGCATCGCGCCAAAGAGCACGACAGCGATCGTCAGCACAAAGCCGAGATTGTCCGCGATGGGATAGGTTTGGCTGATTTTATCAAAAAAGGTAAGATTGGCGGTCGCGGTCAAGAAAACGGCAACACTCGCCACAAGAACAAACGGACTGACCGAGCGTCGGTACCACACAGAAGTATGCAGCATCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3004194","ARO_id":"41358","ARO_name":"MCR-1.2","ARO_description":"A plasmid-borne novel MCR-1 functional variant detected in a Klebsiella pneumoniae isolate collected from a rectal swab in Italy. MCR-1.2 differs from MCR-1 by a single amino acid substitution from Glutamine to Leucine at position 3 in the N-terminal region. Described by DiPilato et al. 2016","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2839":{"model_id":"2839","model_name":"GOB-18","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4190":{"protein_sequence":{"accession":"AAY53478.1","sequence":"MRNFATLFFMFICLGLSAQVVKEPENMPKEWNQAYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGTAESFPIIKANIQKLGFNYKDIKILLLTQAHYDHTGALQDFKTETAAKFYVDKADVDVLRTGGKSDYEMGKYGVTFKPVTPDKTLKDQDKIKLGNITLTLLHHPGHTKGSCSFIFETKDEKRKYRVLIANMPSVIVDKKFSEVTAYPNIQSDYAYTFGVMKKLDFDIWVASHASQFDLHEKRKEGDPYNPQLFMDKQSYFQNLNDLEKSYLNKIKKDSQDK"},"dna_sequence":{"accession":"DQ004496.1","fmin":"0","fmax":"290","strand":"+","sequence":"ATGAGAAATTTTGCTACACTGTTTTTCATGTTCATTTGCTTGGGCTTGAGTGCTCAGGTAGTAAAAGAACCTGAAAATATGCCCAAAGAATGGAATCAGGCTTATGAACCATTCAGAATTGCAGGTAATTTATATTACGTAGGAACCTATGATTTGGCTTCTTACCTTATTGTGACAGACAAAGGCAATATTCTCATTAATACAGGAACGGCAGAATCGTTTCCAATAATAAAAGCAAATATCCAAAAGCTCGGGTTTAATTATAAAGACATTAAGATCTTGCTGCTTAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36960","NCBI_taxonomy_name":"Elizabethkingia meningoseptica","NCBI_taxonomy_id":"238"}}}},"ARO_accession":"3004213","ARO_id":"41377","ARO_name":"GOB-18","ARO_description":"GOB-18 is a member of subclass B3 GOB family of beta-lactamases isolated from Elizabethkingia meningoseptica. GOB-18 is unlike other subclass B3 beta-lactamases as it is fully active against a broad range of beta-lactam substrates using a single Zn(II) ion in its active site.","ARO_category":{"41376":{"category_aro_accession":"3004212","category_aro_cvterm_id":"41376","category_aro_name":"GOB beta-lactamase","category_aro_description":"The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2840":{"model_id":"2840","model_name":"NPS-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"4191":{"protein_sequence":{"accession":"AAK14791","sequence":"MLKSTLLAFGLFIALSARAENQAIAQLFQRAGVDGTIVIESLTTRQRLVHNDPRAQQRYPAASTFKVLNTLIALEEGAISGENQIFHWNGTQYSIANWNQDQTLDSAFKVSCVWCYQQIALRVGALKYPAYIQQTNYGHLLEPFNGTEFWLDGSLTISAEEQVAFLRRVVERKLPFKASSYDSLKKVMFADENAQYRLYAKTGWATRITPSVGWYVGYVEAQDDVWLFALNLATRDANDLPLRTQIAKDALKAIGAFHAK"},"dna_sequence":{"accession":"AY027589","fmin":"45","fmax":"828","strand":"+","sequence":"ATGCTGAAGAGCACCCTTCTGGCCTTTGGTCTCTTTATCGCACTCTCAGCGCGTGCAGAGAACCAGGCAATCGCCCAGCTTTTCCAGAGGGCAGGAGTCGATGGGACCATCGTCATCGAGTCTCTAACCACCAGACAGCGCTTGGTTCACAACGATCCTCGTGCGCAACAACGATACCCGGCAGCTTCCACGTTCAAGGTACTCAATACCTTGATTGCTCTCGAAGAGGGCGCCATTTCAGGTGAGAACCAGATCTTTCACTGGAACGGTACCCAGTATTCGATTGCGAATTGGAACCAGGACCAGACTCTAGACAGTGCGTTTAAAGTGAGTTGTGTCTGGTGCTACCAGCAGATTGCCCTTCGAGTGGGGGCACTCAAGTACCCAGCCTATATTCAACAGACAAACTATGGTCATTTACTGGAACCCTTCAATGGAACGGAGTTTTGGCTGGATGGCTCTTTGACGATCAGCGCGGAAGAACAGGTTGCCTTTCTCCGACGGGTTGTTGAGCGAAAACTACCGTTCAAAGCGAGCAGCTATGATTCCCTGAAGAAAGTCATGTTCGCCGATGAGAATGCCCAGTATCGCCTTTATGCAAAAACGGGTTGGGCGACCCGCATCACTCCCTCGGTGGGTTGGTATGTTGGCTATGTTGAAGCACAGGACGATGTTTGGCTGTTTGCCCTGAATCTTGCTACCCGCGACGCAAATGACCTGCCCCTACGAACGCAGATAGCCAAAGACGCGCTGAAGGCGATAGGTGCGTTTCATGCGAAGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004239","ARO_id":"41403","ARO_name":"NPS-1","ARO_description":"NPS-1 is a plasmid-encoded class D beta-lactamases identified from two Pseudomonas aeruginosa isolates in 1986.","ARO_category":{"41404":{"category_aro_accession":"3004240","category_aro_cvterm_id":"41404","category_aro_name":"NPS beta-lactamase","category_aro_description":"NPS beta-lactamases are class D beta-lactamases that have partial hydrolyzing abilities against penicillins and cephalosporin.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2841":{"model_id":"2841","model_name":"Escherichia coli 23S rRNA with mutation conferring resistance to chloramphenicol","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"The rRNA gene variant model is an AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown clinically to confer resistance to known antibiotic(s) relative to the wild-type rRNA sequence. Like the protein variant model, rRNA gene variant models detect the presence of an rRNA sequence based on its homolog, and then secondarily search submitted query sequences for a curated mutation. This model includes an rRNA gene reference sequence, a BLASTN bitscore cutoff, and a set of mapped resistance variants. A submitted sequence must have both high homolog to the reference sequence and include a known resistance variant to be detected.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"8226":"G2057A"},"clinical":{"8226":"G2057A"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models without a protein reference sequence but including a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of a specific gene amongst a batch of submitted sequences.","param_type_id":"41093","param_value":"5000"}},"model_sequences":{"sequence":{"4193":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"AE014075","fmin":"237159","fmax":"240063","strand":"+","sequence":"GGTTAAGCGACTAAGCGTACACGGTGGATGCCCTGGCAGTCAGAGGCGATGAAGGACGTGCTAATCTGCGATAAGCGTCGGTAAGGTGATATGAACCGTTATAACCGGCGATTTCCGAATGGGGAAACCCAGTGTGTTTCGACACACTATCATTAACTGAATCCATAGGTTAATGAGGCGAACCGGGGGAACTGAAACATCTAAGTACCCCGAGGAAAAGAAATCAACCGAGATTCCCCCAGTAGCGGCGAGCGAACGGGGAGGAGCCCAGAGCCTGAATCAGTGTGTGTGTTAGTGGAAGCGTCTGGAAAGGCGCGCGATACAGGGTGACAGCCCCGTACACAAAAATGCACATGCTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGGGGGACCATCCTCCAAGGCTAAATACTCCTGACTGACCGATAGTGAACCAGTACCGTGAGGGAAAGGCGAAAAGAACCCCGGCGAGGGGAGTGAAAAAGAACCTGAAACCGTGTACGTACAAGCAGTGGGAGCATGCTTAGGCGTGTGACTGCGTACCTTTTGTATAATGGGTCAGCGACTTATATTCTGTAGCAAGGTTAACCGAATAGGGGAGCCGAAGGGAAACCGAGTCTTAACTGGGCGTTAAGTTGCAGGGTATAGACCCGAAACCCGGTGATCTAGCCATGGGCAGGTTGAAGGTTGGGTAACACTAACTGGAGGACCGAACCGACTAATGTTGAAAAATTAGCGGATGACTTGTGGCTGGGGGTGAAAGGCCAATCAAACCGGGAGATAGCTGGTTCTCCCCGAAAGCTATTTAGGTAGCGCCTCGTGAACTCATCTCCGGGGGTAGAGCACTGTTTCGGCAAGGGGGTCATCCCGACTTACCAACCCGATGCAAACTGCGAATACCGGAGAATGTTATCACGGGAGACACACGGCGGGTGCTAACGTCCGTCGNGAAGAGGGAAACAACCCAGACCGCCAGCTAAGGTCCCAAAGTCATGGTTAAGTGGGAAACGATGTGGGAAGGCCCAGACAGCCAGGATGTTGGCTTAGAAGCAGCCATCATTTAAAGAAAGCGTAATAGCTCACTGGTCGAGTCGGCCTGCGCGGAAGATGTAACGGGGCTAAACCATGCACCGAAGCTGCGGCAGCGACGCTTATGCGTTGTTGGGTAGGGGAGCGTTCTGTAAGCCTGTGAAGGTGTACTGTGAGGTATGCTGGAGGTATCAGAAGTGCGAATGCTGACATAAGTAACGATAAAGCGGGTGAAAAGCCCGCTCGCCGGAAGACCAAGGGTTCCTGTCCAACGTTAATCGGGGCAGGGTGAGTCGACCCCTAAGGCGAGGCCGAAAGGCGTAGTCGATGGGAAACAGGTTAATATTCCTGTACTTGGTGTTACTGCGAAGGGGGGACGGAGAAGGCTATGTTGGCCGGGCGACGGTTGTCCCGGTTTAAGCGTGTAGGCTGGTTTTCCAGGCAAATCCGGAAAATCAAGGCTGAGGCGTGATGACGAGGCACTACGGTGCTGAAGCAACAAATGCCCTGCTTCCAGGAAAAGCCTCTAAGCATCAGGTAACATCAAATCGTACCCCAAACCGACACAGGTGGTCAGGTAGAGAATACCAAGGCGCTTGAGAGAACTCGGGTGAAGGAACTAGGCAAAATGGTGCCGTAACTTCGGGAGAAGGCACGCTGATATGTAGGTGAAGCGACTTGCTCGTGGAGCTGAAATCAGTCGAAGATACCAGCTGGCTGCAACTGTTTATTAAAAACACAGCACTGTGCAAACACGAAAGTGGACGTATACGGTGTGACGCCTGCCCGGTGCCGGAAGGTTAATTGATGGGGTTAGCGCAAGCGAAGCTCTTGATCGAAGCCCCGGTAAACGGCGGCCGTAACTATAACGGTCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAATGATGGCCAGGCTGTCTCCACCCGAGACTCAGTGAAATTGAACTCGCTGTGAAGATGCAGTGTACCCGCGGCAAGACGGAAAGACCCCGTGAACCTTTACTATAGCTTGACACTGAACATTGAGCCTTGATGTGTAGGATAGGTGGGAGGCTTTGAAGTGTGGACGCCAGTCTGCATGGAGCCGACCTTGAAATACCACCCTTTAATGTTTGATGTTCTAACGTTGACCCGTAATCCGGGTTGCGGACAGTGTCTGGTGGGTAGTTTGACTGGGGCGGTCTCCTCCTAAAGAGTAACGGAGGAGCACGAAGGTTGGCTAATCCTGGTCGGACATCAGGAGGTTAGTGCAATGGCATAAGCCAGCTTGACTGCGAGCGTGACGGCGCGAGCAGGTGCGAAAGCAGGTCATAGTGATCCGGTGGTTCTGAATGGAAGGGCCATCGCTCAACGGATAAAAGGTACTCCGGGGATAACAGGCTGATACCGCCCAAGAGTTCATATCGACGGCGGTGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGGGCTGAAGTAGGTCCCAAGGGTATGGCTGTTCGCCATTTAAAGTGGTACGCGAGCTGGGTTTAGAACGTCGTGAGACAGTTCGGTCCCTATCTGCCGTGGGCGCTGGAGAACTGAGGGGGGCTGCTCCTAGTACGAGAGGACCGGAGTGGACGCATCACTGGTGTTCGGGTTGTCATGCCAATGGCACTGCCCGGTAGCTAAATGCGGAAGAGATAAGTGCTGAAAGCATCTAAGCACGAAACTTGCCCCGAGATGAGTTCTCCCTGACTCCTTGAGGGTCCTGAAGGAACGTTGAAGACGACGACGTTGATAGGCCGGGTGTGTAAGCGCAGCGATGCGTTGAGCTAACCGGTACTAATGAACCGTGAGGCTTAACCTT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36763","NCBI_taxonomy_name":"Escherichia coli CFT073","NCBI_taxonomy_id":"199310"}}}},"ARO_accession":"3004150","ARO_id":"41297","ARO_name":"Escherichia coli 23S rRNA with mutation conferring resistance to chloramphenicol","ARO_description":"Point mutation in the 23S rRNA of Escherichia coli shown clinically to confer resistance to chloramphenicol","ARO_category":{"41350":{"category_aro_accession":"3004188","category_aro_cvterm_id":"41350","category_aro_name":"23S rRNA with mutation conferring resistance to phenicol antibiotics","category_aro_description":"Point mutations in the 23S rRNA subunit shown clinically to confer resistance to phenicol class antibiotics, including chloramphenicol and florfenicol, by disrupting antibiotic binding-site affinity","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36600":{"category_aro_accession":"3000461","category_aro_cvterm_id":"36600","category_aro_name":"florfenicol","category_aro_description":"Florfenicol is a fluorine derivative of chloramphenicol, where the nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3) and the hydroxyl group (-OH), by a fluorine group (-F). The action mechanism is the same as chloramphenicol's, where the antibiotic binds to the 23S RNA of the 50S subunit of bacterial ribosomes to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin 1A is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"pristinamycin IIA","category_aro_description":"Pristinamycin IIA is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"vernamycin B-gamma","category_aro_description":"Vernamycin B-gamma is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2842":{"model_id":"2842","model_name":"Vibrio cholerae varG","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4194":{"protein_sequence":{"accession":"AAF94716.1","sequence":"MFVSHLSFPHLIEERKMKLSTLALAPITAALLTFNASAKGHDHDNQRAIFFPGETVQDTVKVEVEPSATQSLKLGQKINNLYERQFDNSQATVQKLGKNTYWIGVNYYNATVVVNEDSVLLIDPLGDGRIDALFKGVQSITNKPITTIMYSHYHLDHLGGGNQLVDLIKKNYPKVDKIRVIASQTVADKINQHAEVGENGVKTPKVPAPNDIYDLTKPQTVQFGSMKIKMMAPKGSGHTPDNTMILIPSDRVLHFADMINPDQLPFYNFAGAEHFHGYEEDLQSLLSKPLSKQWDFINGGHGNIGSKQDVKDLLEYIADIRTEVGKQLEVAPYTPVLSDGNHFVWFKRWQDEITNNVHTALANKYGHMYGFDSGVVETHAAMILADMIDH"},"dna_sequence":{"accession":"AE003852.1","fmin":"1674272","fmax":"1675445","strand":"+","sequence":"ATGTTTGTTTCTCATTTATCTTTTCCCCACCTGATTGAGGAGAGAAAAATGAAACTATCCACCTTAGCTTTAGCCCCTATTACTGCAGCACTACTTACTTTTAATGCAAGTGCTAAAGGCCATGACCACGACAATCAACGCGCGATTTTTTTCCCTGGTGAAACTGTTCAAGACACTGTGAAAGTCGAAGTTGAGCCTTCTGCGACTCAGTCTCTGAAACTGGGACAAAAAATTAATAATCTGTATGAGCGCCAGTTTGATAACAGCCAAGCCACCGTTCAAAAATTGGGCAAGAATACCTACTGGATAGGGGTCAATTATTACAACGCTACCGTTGTGGTTAACGAAGACTCTGTCTTGCTGATTGACCCACTAGGCGATGGTCGTATTGATGCGCTTTTTAAAGGGGTGCAATCCATCACGAATAAACCGATCACTACGATTATGTATTCTCACTACCACTTAGATCATTTAGGTGGTGGCAACCAACTGGTTGACTTAATTAAGAAAAATTATCCAAAAGTAGATAAAATCCGCGTTATTGCTAGCCAAACCGTTGCGGACAAGATCAACCAACACGCCGAAGTAGGCGAAAACGGTGTGAAAACCCCGAAAGTTCCAGCGCCGAATGACATATACGACCTGACGAAGCCTCAAACGGTTCAATTTGGCTCAATGAAAATCAAGATGATGGCACCAAAAGGCTCTGGCCATACACCTGATAACACCATGATTCTGATCCCAAGCGATCGCGTGTTGCATTTCGCGGACATGATTAATCCCGATCAACTACCGTTTTACAATTTCGCGGGAGCAGAACATTTCCACGGTTACGAAGAAGATCTACAAAGCCTTCTGAGCAAACCGCTGAGCAAACAGTGGGACTTTATTAACGGTGGCCATGGCAATATAGGTTCGAAACAGGATGTAAAAGATCTGCTTGAGTATATTGCGGACATCAGAACTGAAGTGGGCAAGCAGCTAGAAGTCGCCCCCTACACTCCAGTGTTGAGTGACGGTAACCACTTTGTTTGGTTCAAACGCTGGCAAGATGAGATCACTAACAATGTACATACCGCACTGGCAAACAAGTATGGCCACATGTACGGTTTCGATTCAGGCGTGGTTGAAACACACGCGGCAATGATTCTCGCAGATATGATTGATCACTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39595","NCBI_taxonomy_name":"Vibrio cholerae O1 biovar El Tor str. N16961","NCBI_taxonomy_id":"243277"}}}},"ARO_accession":"3004289","ARO_id":"41453","ARO_name":"Vibrio cholerae varG","ARO_description":"varG is an Ambler class B metallo-beta-lactamase found on the antibiotic resistance var regulon in Vibrio cholerae, along with an antibiotic efflux pump varABCDEF. These genes are organized as a regulon under the control of VarR transcriptional activator. VarG was shown to have beta-lactamase activity against penicillins, carbapenems and cephalosporins in-vitro. Described by Lin HV et al. 2017.","ARO_category":{"41452":{"category_aro_accession":"3004288","category_aro_cvterm_id":"41452","category_aro_name":"subclass B1 Vibrio cholerae varG beta-lactamase","category_aro_description":"varG is an Ambler class B metallo-beta-lactamase found on the antibiotic resistance var regulon in Vibrio cholerae, along with an antibiotic efflux pump varABCDEF. These genes are organized as a regulon under the control of VarR transcriptional activator. VarG was shown to have beta-lactamase activity against penicillins, carbapenems and cephalosporins in-vitro.","category_aro_class_name":"AMR Gene Family"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2843":{"model_id":"2843","model_name":"Escherichia coli ampC","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"4195":{"protein_sequence":{"accession":"NP_418574.1","sequence":"MFKTTLCALLITASCSTFAAPQQINDIVHRTITPLIEQQKIPGMAVAVIYQGKPYYFTWGYADIAKKQPVTQQTLFELGSVSKTFTGVLGGDAIARGEIKLSDPTTKYWPELTAKQWNGITLLHLATYTAGGLPLQVPDEVKSSSDLLRFYQNWQPAWAPGTQRLYANSSIGLFGALAVKPSGLSFEQAMQTRVFQPLKLNHTWINVPPAEEKNYAWGYREGKAVHVSPGALDAEAYGVKSTIEDMARWVQSNLKPLDINEKTLQQGIQLAQSRYWQTGDMYQGLGWEMLDWPVNPDSIINGSDNKIALAARPVKAITPPTPAVRASWVHKTGATGGFGSYVAFIPEKELGIVMLANKNYPNPARVDAAWQILNALQ"},"dna_sequence":{"accession":"NC_000913.3","fmin":"4377810","fmax":"4378944","strand":"-","sequence":"TTACTGTAGAGCGTTAAGAATCTGCCAGGCGGCGTCGACTCTCGCTGGATTGGGATAGTTTTTGTTTGCCAGCATCACGATACCCAGCTCTTTTTCTGGAATAAACGCGACATAGCTACCAAATCCGCCGGTCGCCCCTGTTTTATGTACCCATGATGCGCGTACTGCAGGAGTTGGGGGCGTAATCGCTTTTACGGGGCGTGCTGCCAGTGCAATTTTATTGTCACTGCCGTTAATGATGCTGTCAGGATTTACCGGCCAGTCCAGCATTTCCCAGCCCAGGCCCTGATACATATCGCCGGTTTGCCAGTAGCGAGATTGTGCCAGTTGTATCCCTTGTTGAAGCGTTTTCTCATTGATATCAAGGGGTTTTAAATTGCTTTGCACCCAGCGGGCCATATCTTCAATGGTCGACTTCACACCATAAGCTTCAGCATCTAACGCCCCAGGCGAAACATGCACTGCCTTACCTTCGCGATATCCCCAGGCGTAATTCTTTTCTTCTGCGGGCGGTACATTAATCCACGTATGGTTGAGTTTGAGTGGCTGGAAGACACGAGTTTGCATCGCCTGCTCAAAACTCAAACCAGACGGCTTCACAGCCAGTGCGCCGAACAAACCGATACTGGAGTTGGCATACAGACGTTGTGTTCCTGGAGCCCATGCAGGCTGCCAGTTTTGATAGAAGCGCAGCAAGTCGCTTGAGGATTTCACCTCATCCGGCACCTGCAATGGCAGGCCGCCAGCAGTGTAGGTTGCGAGATGTAATAGTGTGATCCCATTCCACTGTTTAGCGGTAAGTTCAGGCCAGTATTTTGTTGTGGGATCGCTTAACTTGATTTCCCCTCGAGCAATAGCGTCGCCACCAAGCACGCCAGTAAATGTTTTGCTGACCGAACCTAACTCAAACAACGTTTGCTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCCTGATAAATTACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAGGCGCAGAGCGTCGTTTTGAACAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3004290","ARO_id":"41454","ARO_name":"Escherichia coli ampC beta-lactamase","ARO_description":"A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.","ARO_category":{"41396":{"category_aro_accession":"3004232","category_aro_cvterm_id":"41396","category_aro_name":"ampC-type beta-lactamase","category_aro_description":"AmpC beta-lactamases are clinically important class C beta-lactamase enzymes which confer resistance to cephalosporins and penicillin-like antibiotics. AmpC beta-lactamases are typically found in Enterobacteriaceae, and were described in Escherichia coli in 1940 as the first reported enzymatic deactivation of penicillin. The name AmpC connects these enzymes functionally across many species, however these enzymes are generally unnamed and not phylogenetically related.","category_aro_class_name":"AMR Gene Family"},"35971":{"category_aro_accession":"0000054","category_aro_cvterm_id":"35971","category_aro_name":"penicillin","category_aro_description":"Penicillin (sometimes abbreviated PCN) is a beta-lactam antibiotic used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms. It works by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2844":{"model_id":"2844","model_name":"Rhodobacter sphaeroides ampC beta-lactamase","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4196":{"protein_sequence":{"accession":"YP_355256.1","sequence":"MKHLSPLSILLMVGALTPALAQDTTPSFESAAAAAFESVIEEHDIPGLVVGVTHGGRHSFYQTGLASREDQQPVTPDTLFELGSISKIFNVTLAALAEERGALSLDAPVADYLPSLRGSPAGELTLIDLATHHTGGLPLQVPDEVADVDRLVDWLRSWRPPEPGTRSYSNISIGLLGHITAGVLGMSYADASQTVIFPALGLKSTWIDVPTDAMGRYAFGYDRKTDAPTRVTPGVLDDEAYGVKSSARDMLTLLDLELGTGTASPEVQTAVATTQEGRFQTRLYTQAMIWEAYPWPVDPERLVEGNGYDFILQPQPVDEVDTTPDRRVILNKTGSTNGFGGYIAIVPSEDLGVVVLANRNYPNEARVRATYDLITHILAE"},"dna_sequence":{"accession":"NC_007494.2","fmin":"874560","fmax":"875703","strand":"+","sequence":"ATGAAGCACCTTTCCCCCCTCTCCATCCTGCTCATGGTGGGCGCGCTGACGCCCGCGCTTGCGCAAGACACCACGCCGTCGTTCGAGAGCGCCGCCGCCGCGGCCTTCGAGAGCGTCATCGAGGAGCATGACATTCCCGGTCTGGTGGTGGGCGTGACCCACGGCGGACGGCACAGTTTCTATCAGACAGGCTTGGCCTCACGGGAAGATCAGCAGCCGGTAACCCCTGACACGCTTTTTGAGCTCGGTTCGATCAGCAAGATCTTCAACGTGACGCTGGCGGCCTTGGCAGAGGAGCGGGGCGCGCTGTCGCTCGATGCGCCGGTCGCCGACTATCTTCCCTCCCTGCGAGGTTCTCCTGCAGGAGAGCTGACGCTGATCGATCTGGCGACGCACCATACCGGCGGCCTCCCGTTGCAGGTGCCGGACGAAGTTGCAGATGTAGATCGCCTGGTCGACTGGCTACGGAGTTGGCGACCGCCCGAGCCCGGTACGCGCAGCTATTCCAACATCAGCATCGGCCTATTGGGGCACATCACCGCGGGCGTGCTGGGCATGAGCTATGCTGATGCGTCCCAGACGGTTATCTTCCCGGCGCTCGGATTGAAGAGCACGTGGATCGACGTCCCCACCGATGCGATGGGACGCTACGCCTTCGGCTATGACCGCAAGACAGACGCGCCAACCCGGGTTACGCCCGGCGTGCTGGACGATGAAGCGTACGGGGTAAAATCCTCCGCTCGCGACATGCTGACGCTGCTCGACCTCGAGCTTGGAACCGGCACTGCCTCGCCCGAAGTTCAAACGGCGGTGGCCACCACGCAGGAGGGCCGGTTCCAGACCCGCCTGTACACGCAGGCCATGATATGGGAGGCCTATCCTTGGCCTGTCGACCCAGAGCGTCTGGTGGAGGGGAACGGGTATGACTTCATCCTCCAGCCTCAGCCTGTGGACGAGGTGGACACGACACCCGATCGGAGGGTCATCCTGAACAAGACAGGTTCCACGAACGGCTTCGGTGGGTACATCGCGATCGTGCCAAGCGAGGATCTGGGCGTCGTCGTCCTTGCCAACCGCAACTACCCCAACGAGGCGCGGGTTCGAGCCACTTACGACCTGATCACTCACATCTTGGCCGAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41456","NCBI_taxonomy_name":"Rhodobacter sphaeroides 2.4.1","NCBI_taxonomy_id":"272943"}}}},"ARO_accession":"3004291","ARO_id":"41455","ARO_name":"Rhodobacter sphaeroides ampC beta-lactamase","ARO_description":"A periplasmic cephalosporinase described in Rhodobacter sphaeroides shown to contribute to resistance of beta-lactam antibiotics.","ARO_category":{"41396":{"category_aro_accession":"3004232","category_aro_cvterm_id":"41396","category_aro_name":"ampC-type beta-lactamase","category_aro_description":"AmpC beta-lactamases are clinically important class C beta-lactamase enzymes which confer resistance to cephalosporins and penicillin-like antibiotics. AmpC beta-lactamases are typically found in Enterobacteriaceae, and were described in Escherichia coli in 1940 as the first reported enzymatic deactivation of penicillin. The name AmpC connects these enzymes functionally across many species, however these enzymes are generally unnamed and not phylogenetically related.","category_aro_class_name":"AMR Gene Family"},"36976":{"category_aro_accession":"3000632","category_aro_cvterm_id":"36976","category_aro_name":"benzylpenicillin","category_aro_description":"Benzylpenicillin, commonly referred to as penicillin G, is effective against both Gram-positive and Gram-negative bacteria. It is unstable in acid.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2845":{"model_id":"2845","model_name":"Laribacter hongkongensis ampC beta-lactamase","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4197":{"protein_sequence":{"accession":"AAT46346.1","sequence":"MKKRITPFSRFASKGLFACSAGMLLVTVAHAANTAAAPAGMDAMVQTVMQAHQIPGMAIAIIQPGKTTYHNYGVASRETGQPVRETTLFEIGSLSKPFTALVAQRAETEGRIDLSAPASRYVAALRGSAFDRITLRQLGTYSAGGLPLQFPDNVTTPADVLAYYQHWQPVHPAGTTRLYSNPSIGLMGLAASQATGESFAGLLGTTVLHPLGMNSTYLQVPPEARSRYAMGYTAAGKAVRVSPGPLDEETYGVKSTTADMAGFLLAHMDPARSKGALQSALQQTRVPVYCAGQTRQGLGWESYQDWKNLDVLLAGNSNQMVFEPQPVKACPAGTMNDPDVWVNKTGSTAGFGAYAVFLPARQTGIVILANRNFPIADRIRLAHGILTALH"},"dna_sequence":{"accession":"AY632076.1","fmin":"0","fmax":"1173","strand":"+","sequence":"ATGAAAAAACGGATTACCCCATTTTCCCGCTTTGCATCAAAAGGCCTTTTCGCCTGTAGCGCAGGCATGTTGCTGGTGACGGTGGCACATGCTGCCAATACGGCAGCAGCACCAGCCGGCATGGATGCCATGGTACAAACCGTGATGCAGGCACACCAGATTCCGGGCATGGCCATTGCCATCATCCAGCCAGGAAAGACCACTTATCACAATTATGGTGTCGCCTCCCGCGAAACCGGCCAGCCGGTCCGGGAAACCACCCTGTTTGAAATCGGGTCCCTTTCCAAACCGTTTACTGCACTGGTCGCCCAGCGGGCTGAAACCGAAGGCCGGATTGACCTGTCTGCACCGGCCAGCCGCTACGTTGCCGCCCTGCGAGGCAGTGCATTCGACCGGATCACCCTCAGGCAGCTCGGTACTTATAGCGCAGGCGGATTACCGCTCCAGTTTCCTGACAATGTCACCACCCCGGCAGACGTGCTGGCTTATTACCAGCATTGGCAACCTGTCCATCCGGCAGGTACCACCCGGCTGTATTCCAATCCGAGCATTGGCCTGATGGGGCTGGCTGCCAGTCAGGCAACCGGAGAGTCCTTTGCCGGCCTGCTCGGGACAACGGTGCTGCACCCCCTCGGCATGAACTCGACCTATCTGCAAGTGCCCCCGGAGGCCCGTTCACGTTATGCCATGGGATATACCGCCGCCGGAAAAGCGGTCAGGGTCAGCCCCGGTCCGCTGGATGAGGAAACCTACGGCGTCAAGTCCACAACCGCAGACATGGCCGGATTTTTATTGGCGCATATGGACCCTGCGCGCAGCAAAGGTGCATTGCAGTCGGCATTACAGCAAACACGTGTACCGGTTTATTGCGCCGGACAGACCCGGCAAGGACTGGGCTGGGAAAGTTATCAAGACTGGAAAAACCTAGACGTGCTGCTGGCGGGAAATTCAAATCAAATGGTGTTTGAGCCGCAGCCGGTAAAAGCCTGTCCTGCCGGCACCATGAATGATCCTGATGTGTGGGTCAACAAGACCGGTTCTACTGCGGGATTCGGCGCTTATGCCGTATTCCTGCCTGCCCGACAGACCGGCATTGTCATCCTGGCCAACCGTAATTTCCCGATTGCAGACCGTATCCGGCTCGCTCACGGGATTTTGACCGCATTGCACTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41458","NCBI_taxonomy_name":"Laribacter hongkongensis","NCBI_taxonomy_id":"168471"}}}},"ARO_accession":"3004292","ARO_id":"41457","ARO_name":"Laribacter hongkongensis ampC beta-lactamase","ARO_description":"A chromosome-encoded class C beta-lactamase described in the pathogen Laribacter hongkongensis, often associated with gastroenteritis. Laribacter ampC has been shown to confer resistance to non-carbapenem beta-lactamases, as described by Lau et al. 2005.","ARO_category":{"41396":{"category_aro_accession":"3004232","category_aro_cvterm_id":"41396","category_aro_name":"ampC-type beta-lactamase","category_aro_description":"AmpC beta-lactamases are clinically important class C beta-lactamase enzymes which confer resistance to cephalosporins and penicillin-like antibiotics. AmpC beta-lactamases are typically found in Enterobacteriaceae, and were described in Escherichia coli in 1940 as the first reported enzymatic deactivation of penicillin. The name AmpC connects these enzymes functionally across many species, however these enzymes are generally unnamed and not phylogenetically related.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2846":{"model_id":"2846","model_name":"BUT-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4198":{"protein_sequence":{"accession":"AAN17791.1","sequence":"MCRTLCHVTYGRFSMMKKTLCCALVLSASFSAFAAQKTLSDKQLEEAVNQTLKPMITAQAIPGMAVAVIYQGKPHYFTYGVADIAKNQPVTTQTIFELGSVSKTFTGVLGGDIVARGEVKLSDPAMKYWPELTGKQWQGITLLDLATYTAGGLPLQVPDEVDNQAALLKFYQNWQPDWAPGTRRQYANSSIGLFGALAVKPSGMTFNDAMRQRVLQPLNLKHTWLTVPASEENHYAWGYRDGKAMHVGPGMLDTEAYGVKSTIEDMASWVQYNMNPQQVKQPTLQKGLEIAQSRYWRSGSMYQGLGWEMLNWPVAAATVINGSDNKVALAASPVTAIEPPVAPVKASLVHKTGSTNGFGAYVAFIPEKQIGIVMLANKMYPNTERVKAANTLLNTLQ"},"dna_sequence":{"accession":"AF440406.1","fmin":"959","fmax":"2153","strand":"+","sequence":"ATGTGCCGGACCCTCTGTCATGTTACTTATGGAAGATTTTCAATGATGAAAAAAACACTCTGCTGCGCGCTGGTTCTGAGCGCCTCTTTCTCCGCCTTTGCTGCACAAAAAACATTGAGTGACAAACAGTTAGAAGAGGCTGTCAATCAAACGCTTAAACCGATGATTACAGCCCAGGCCATTCCCGGCATGGCGGTGGCGGTGATTTATCAGGGCAAGCCGCACTACTTTACCTACGGCGTGGCCGACATCGCGAAAAATCAGCCGGTGACGACACAGACGATTTTTGAGCTGGGCTCCGTGAGTAAAACTTTCACCGGCGTGCTGGGCGGCGATATCGTGGCGCGCGGGGAAGTGAAGCTGAGTGACCCGGCGATGAAATACTGGCCAGAACTGACGGGCAAGCAGTGGCAGGGCATCACGTTGCTGGATCTGGCGACCTACACCGCCGGCGGCTTGCCGTTGCAGGTGCCGGATGAGGTCGATAATCAGGCCGCGCTGCTGAAGTTTTACCAGAACTGGCAGCCGGACTGGGCGCCGGGAACCCGTCGTCAGTACGCCAACTCGAGCATTGGCCTGTTTGGTGCGTTGGCAGTGAAACCGTCCGGGATGACGTTTAACGATGCGATGCGCCAGCGCGTTCTGCAACCGCTGAACCTGAAACATACCTGGCTCACCGTTCCGGCCAGTGAAGAAAATCATTACGCCTGGGGCTATCGTGACGGCAAAGCCATGCACGTCGGGCCGGGCATGCTGGATACCGAAGCCTACGGTGTCAAATCCACCATCGAAGATATGGCGAGCTGGGTGCAATACAACATGAACCCGCAGCAGGTGAAACAGCCGACGCTGCAAAAAGGGCTGGAGATTGCGCAGTCGCGCTACTGGCGCAGCGGCAGTATGTATCAGGGCTTAGGCTGGGAAATGCTGAACTGGCCGGTTGCGGCGGCGACCGTCATTAACGGCAGCGATAACAAAGTGGCGCTGGCGGCTTCGCCCGTGACGGCCATTGAACCGCCGGTTGCGCCGGTGAAAGCTTCTCTGGTGCATAAAACCGGGTCGACCAACGGCTTCGGCGCGTACGTGGCGTTCATTCCTGAAAAACAAATCGGCATCGTGATGCTGGCTAACAAAATGTATCCGAATACCGAGCGGGTTAAAGCGGCAAATACTCTTCTCAACACGCTGCAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41461","NCBI_taxonomy_name":"Buttiauxella agrestis","NCBI_taxonomy_id":"82977"}}}},"ARO_accession":"3004294","ARO_id":"41460","ARO_name":"BUT-1","ARO_description":"A chromosome-encoded  class C cephalosporinase and penicillinase from Buttiauxella spp. shown clinically to confer resistance to beta-lactam antibiotics. Described by Fihman et al. 2002.","ARO_category":{"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2343":{"model_id":"2343","model_name":"ADC-13","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3636":{"protein_sequence":{"accession":"WP_063857788.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEIYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKTKGTISFKDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPGLSLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLKFINANLNPQKYPADIQRAINETHQGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_048637.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTTGTAGATCAAAATTTTAAACCGTTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATTTATTATGGTCTACAATCCGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCAGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAACAAAAGGAACAATCTCTTTTAAAGACACACCCGGAAAATATTGGAAAGAGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTTGCTACCTATACAAGTGGGAACCTTGCTTTGCAATTTCCAGATGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGATTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGGCCTTAGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAATCAAGAAAATCAGCCAATTCGTGTTAACCCTGGTCCGCTAGATGCTCCAGCATACGGCGTTAAATCGACACTACCAGACATGCTTAAGTTTATTAATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGTGCAATTAATGAAACACATCAAGGTTTCTATCAAGTCGGCACCATGTATCAAGCATTAGGTTGGGAAGAATTTTCTTATCCAGCGCCTTTACAAACTTTATTAGACAGTAATTCAGAACAAATTGTGATGAAGCCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTTCCACAAAACTGGCTCAACCAATGGTTTCGGAACATATGTCGTGTTCATTCCTAAAGAAAATATTGGCTTAGTCATGTTGACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCAGTGTTAAACGCAATAAAGAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3003857","ARO_id":"40556","ARO_name":"ADC-13","ARO_description":"ADC-13 is a beta-lactamase found in Acinetobacter pittii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2344":{"model_id":"2344","model_name":"ADC-14","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3637":{"protein_sequence":{"accession":"WP_063857789.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEIYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKTKGTISFKDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPGLSLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLKFINANLNPQKYPADIQRAINETHQGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERFKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_048638","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTTGTAGATCAAAATTTTAAACCGTTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATTTATTATGGTCTACAATCCGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCAGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAACAAAAGGAACAATCTCTTTTAAAGACACACCCGGAAAATATTGGAAAGAGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAGCTTGCTACCTATACAAGTGGGAACCTTGCTTTGCAATTTCCAGATGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGATTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGGCCTTAGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAATCAAGAAAATCAGCCAATTCGTGTTAACCCTGGTCCGCTAGATGCTCCAGCATACGGCGTTAAATCGACACTACCAGACATGCTTAAGTTTATTAATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGTGCAATTAATGAAACACATCAAGGTTTCTATCAAGTCGGCACCATGTATCAAGCATTAGGTTGGGAAGAATTTTCTTATCCAGCGCCTTTACAAACTTTATTAGACAGTAATTCAGAACAAATTGTGATGAAGCCTAATAAAGTGACCGCTATTTCAAAAGAACCTTCAGTTAAGATGTTCCACAAAACTGGCTCAACCAATGGTTTCGGAACATATGTCGTGTTCATTCCTAAAGAAAATATTGGCTTAGTCATGTTGACCAATAAACGTATTCCAAATGAAGAACGCTTTAAGGCAGCGTATGCAGTGTTAAACGCAATAAAGAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3003858","ARO_id":"40557","ARO_name":"ADC-14","ARO_description":"ADC-14 is a beta-lactamase found in Acinetobacter pittii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2345":{"model_id":"2345","model_name":"ADC-15","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3638":{"protein_sequence":{"accession":"WP_063857790.1","sequence":"MRFKKISCLLLSPLFIFNTSIYAGNTPKDQEIKKLVDQNFKPLLDKYDVPGMAVGVIQNNKKYETYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKTKGTISFKDTTGKYWKELKNTPIDQVNLFQLATYTSGNLGLQFPDEVQTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQLLEKTIFPDLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLKFINANLNPQKYPKDIQRAINETHQGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSVKIFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_048639","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAATACCTCAATTTATGCAGGGAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCTTTATTAGATAAATATGATGTGCCGGGTATGGCCGTGGGCGTTATTCAGAATAATAAAAAATATGAAACGTATTACGGCCTACAATCCGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTCGGTTCAGTTAGTAAATTATTTACCGCTACAGCAGGTGGATATGCCAAAACAAAAGGAACAATTTCTTTTAAAGACACAACCGGAAAATATTGGAAAGAATTAAAAAACACACCAATTGACCAAGTTAACTTATTTCAACTTGCTACTTATACGAGTGGCAACCTTGGCTTACAGTTTCCAGATGAAGTCCAAACAGATCAGCAAGTTTTAACTTTTTTCAAAGACTGGAAGCCTAAAAACTCAATCGGTGAATATCGACAATATTCAAATCCAAGCATTGGTTTATTTGGAAAAGTTGTTGCATTGTCTATGAATAAACCTTTCGACCAACTCTTAGAAAAAACAATTTTTCCAGATCTTGGCTTAAAACATAGCTATGTAAATGTACCGAAGACCCAGATGCAAAACTATGCTTTTGGCTATAATCAAGAAAATCAGCCAATTCGTGTTAACCCTGGTCCGTTAGATGCACCTGCGTACGGCGTCAAATCGACACTACCCGATATGCTTAAGTTTATTAATGCCAACCTCAACCCACAGAAATATCCGAAAGATATTCAACGTGCAATTAATGAAACACATCAGGGTTTCTATCAAGTCGGCACCATGTATCAGGCACTTGGTTGGGAAGAATTTTCTTATCCAGCGCCTTTACAAACTTTATTAGACAGTAATTCAGAACAAATTGTGATGAAGCCTAATAAAGTGACTGCCATTTCAAAAGAACCTTCAGTTAAGATATTCCACAAAACTGGTTCAACCAATGGTTTCGGAACTTATGTCGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTGACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCGGTGTTAAATGCAATAAAAAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3003859","ARO_id":"40558","ARO_name":"ADC-15","ARO_description":"ADC-15 is a beta-lactamase found in Acinetobacter pittii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2347":{"model_id":"2347","model_name":"ADC-17","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3640":{"protein_sequence":{"accession":"WP_063857792.1","sequence":"MRFKKISCLLLPPLFIFSTSIYAGNTPKDREIKKLVDQNFKPLLDKYDVPGMAVGVIQNNKKYETYYGLQSVQDKKAVSSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDRQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPDLGLKHSYVNVPKTQMQNYAFGYNRENQPIRVNPGPLDAPAYGVKSTLPDMLKFINANLNTQKYPKDIQRAINETHQGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_048641.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGCTTACTTTTACCTCCTCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCGAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCTTTGTTAGATAAATATGATGTGCCGGGTATGGCCGTGGGCGTTATTCAGAATAATAAAAAATATGAAACGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAGTAGCAGTACCATTTTTGAACTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATTTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACGCCGATTGACCAAGTTAACTTACTTCAACTCGCAACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCGACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATAGACAATATTCAAATCCAAGCATTGGTTTATTTGGAAAAGTTGTGGCATTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCAGATCTTGGCCTAAAACATAGCTATGTAAATGTTCCTAAAACTCAGATGCAAAACTATGCTTTTGGCTATAACCGAGAAAATCAGCCAATTCGTGTTAACCCTGGTCCGCTAGATGCTCCAGCATATGGGGTTAAATCGACGCTACCCGATATGCTTAAGTTTATTAATGCCAACCTCAACACACAGAAATATCCGAAAGATATTCAACGTGCAATTAATGAAACACATCAGGGTTTCTATCAAGTCGGCACCATGTATCAGGCACTTGGTTGGGAAGAATTTTCTTATCCAGCGCCTTTACAAACTTTATTAGACAGTAATTCAGAACAAATTGTGATGAAGCCTAATAAAGTGACTGCCATTTCAAAAGAACCTTCAGTTAAGATGTTCCACAAAACTGGTTCAACCAATGGTTTCGGAACTTATGTCGTGTTCATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCCGTGTTGAATGCAATAAAGAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3003861","ARO_id":"40560","ARO_name":"ADC-17","ARO_description":"ADC-17 is a beta-lactamase found in Acinetobacter pittii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2346":{"model_id":"2346","model_name":"ADC-16","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3639":{"protein_sequence":{"accession":"WP_063857791.1","sequence":"MRFKKISCLLLPPLFIFSSSIYAGNTPKEQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSNTIFELGSVSKLFTATAGGYAKTKGTISFNDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKEWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPDLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFINANLNPQKYPANIQRAINETHQGFYQVGTMYQALGWEEFSYPALLQTLLDSNSEQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_048640.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGCTTACTTTTACCGCCTCTTTTTATTTTTAGTAGCTCAATTTATGCGGGTAATACACCAAAAGAGCAAGAGATCAAAAAACTGGTTGATCAAAATTTTAAGCCTTTATTAGAAAAATATGATGTGCCCGGTATGGCTGTGGGCGTTATTCAAAATAACAAAAAGTATGAAATGTATTATGGTCTACAATCCGTTCAAGATAAAAAAGCCGTTAATAGCAATACCATTTTTGAGCTAGGCTCGGTCAGTAAATTATTTACCGCTACAGCAGGCGGATATGCCAAAACAAAAGGAACAATCTCTTTTAATGACACGCCTGGAAAATATTGGAAAGAACTAAAAAATACACCGATTGATCAAGTGAATTTACTTCAACTTGCGACATATACCAGTGGCAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACGTTTTTCAAAGAATGGAAACCTAAAAACCCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTTGACCAAGTCTTGGAAAAAACCATTTTTCCAGATCTTGGCTTAAAACATAGCTATGTAAATGTGCCTAAAACTCAAATGCAAAACTATGCATTTGGCTATAACCAAGAAAATCAGCCGATTCGCGTCAATCCTGGTCCACTCGATGCACCAGCATACGGCGTTAAATCTACCCTACCGGATATGCTGAGTTTTATTAATGCAAACCTAAATCCACAAAAATATCCAGCAAATATTCAACGTGCAATTAATGAAACACATCAAGGTTTCTACCAAGTCGGCACCATGTATCAAGCACTAGGTTGGGAAGAGTTCTCTTATCCAGCACTTTTACAAACTTTATTAGACAGTAATTCAGAACAAATCGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCCGTTAAGATGTTCCACAAAACTGGATCGACTAACGGTTTTGGAACATATGTCGTGTTCATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACTAATAAACGTATTCCCAATGAAGAACGCATTAAAGCAGCTTATGCTGTGTTAAATGCAATAAAGAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3003860","ARO_id":"40559","ARO_name":"ADC-16","ARO_description":"ADC-16 is a beta-lactamase found in Acinetobacter pittii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2357":{"model_id":"2357","model_name":"ADC-41","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3650":{"protein_sequence":{"accession":"WP_063857802.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLDKYDVPGMAVGVIQNNKKYETYYGLQSVQDKKAVSSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPGLGLKHSYVNVPKNQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLKFINANLNPQKYPADIQRAINETHQGFYQVGIMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_048656.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCTTTATTAGATAAATATGATGTGCCGGGTATGGCCGTGGGCGTTATTCAGAATAATAAAAAATATGAAACGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAGTAGCAGTACCATTTTTGAACTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCAACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGGCCTTGGCTTAAAACATAGCTATGTAAATGTACCGAAGAACCAGATGCAAAACTATGCTTTTGGCTATAATCAAGAAAATCAGCCAATTCGTGTTAACCCTGGTCCGCTAGATGCTCCAGCATACGGCGTCAAATCGACACTACCCGATATGCTTAAGTTTATTAATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGTGCAATTAATGAAACACATCAAGGTTTCTATCAAGTCGGCATCATGTATCAAGCATTAGGTTGGGAAGAATTTTCTTATCCAGCGCCTTTACAAACTTTATTAGACAGTAATTCAGAACAAATTGTGATGAAGCCTAATAAAGTGACTGCCATTTCAAAAGAACCTTCAGTTAAGATGTTCCACAAAACTGGTTCAACCAATGGTTTCGGAACTTATGTCGTGTTCATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCCGTGCTGAATGCAATAAAGAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3003872","ARO_id":"40571","ARO_name":"ADC-41","ARO_description":"ADC-41 is a beta-lactamase found in Acinetobacter pittii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2358":{"model_id":"2358","model_name":"ADC-42","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3651":{"protein_sequence":{"accession":"WP_063857803.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDREIKKLVDQNFKPLLDKYDVPGMAVGVIQNNKKYETYYGLQSVQDKKSVSSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTSGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKEWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPGLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFINANINPQKYPKDTQRAINETHQGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGSYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_048657.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCGAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCTTTATTAGATAAATATGATGTGCCGGGTATGGCCGTGGGCGTTATTCAGAATAATAAAAAATATGAAACGTATTATGGTCTTCAATCTGTTCAAGATAAAAAATCCGTAAGTAGCAGTACCATTTTTGAACTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGTCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCAACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGAATGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGGCCTTGGCTTAAAACATAGCTATGTAAATGTACCGAAGACCCAGATGCAAAACTATGCTTTTGGCTATAATCAAGAAAATCAGCCAATTCGTGTTAACCCCGGTCCGCTAGATGCTCCAGCATACGGTGTTAAATCGACCTTACCTGATATGCTGAGTTTCATTAATGCCAATATAAATCCACAAAAATATCCGAAAGATACTCAACGTGCAATTAATGAAACACATCAAGGTTTCTACCAAGTCGGCACGATGTATCAGGCACTTGGTTGGGAAGAATTTTCTTATCCAGCGCCTTTACAAACTTTATTAGACAGTAATTCAGAGCAAATCGTGATGAAGCCTAATAAAGTGACTGCCATTTCCAAAGAACCTTCAGTTAAGATGTTCCACAAAACTGGCTCAACAAATGGCTTTGGATCTTATGTGGTGTTTATTCCAAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCAGTGCTGAATGCAATAAAGAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3003873","ARO_id":"40572","ARO_name":"ADC-42","ARO_description":"ADC-42 is a beta-lactamase found in Acinetobacter pittii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2359":{"model_id":"2359","model_name":"ADC-43","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3652":{"protein_sequence":{"accession":"WP_032055358.1","sequence":"MRFKKISCLLLPPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLDKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPGLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFINANLNPLKYPKDIQRAINETHKGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_048658.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGCTTACTTTTACCCCCTCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCTTTATTAGATAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTCGGTTCAGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAATTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCAACGTATACAAGTGGTAACCTTGCCTTGCAATTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGGCCTTGGCTTAAAACATAGCTATGTAAATGTTCCTAAAACTCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCAATTCGTGTTAACCCTGGTCCGCTAGATGCTCCTGCATACGGCGTTAAATCGACACTACCAGACATGCTGAGTTTTATTAATGCCAACCTCAACCCACTGAAATATCCGAAAGATATTCAACGTGCAATTAATGAAACACATAAAGGTTTCTATCAAGTCGGCACCATGTATCAAGCCTTGGGTTGGGAAGAATTTTCTTATCCAGCGCCTTTACAAACTTTATTAGACAGTAATTCAGAGCAAATCGTGATGAAGCCTAATAAAGTGACTGCCATTTCCAAAGAACCTTCAGTTAAGATGTTCCACAAAACTGGCTCAACAAATGGCTTTGGAACTTATGTGGTGTTTATTCCAAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCAGTATTGAATGCTATAAAAAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40550","NCBI_taxonomy_name":"Acinetobacter calcoaceticus\/baumannii complex","NCBI_taxonomy_id":"909768"}}}},"ARO_accession":"3003874","ARO_id":"40573","ARO_name":"ADC-43","ARO_description":"ADC-43 is a beta-lactamase found in Acinetobacter pittii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2360":{"model_id":"2360","model_name":"ADC-44","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3653":{"protein_sequence":{"accession":"WP_063857804.1","sequence":"MRFKKISCLLLPPLFIFSTSIYAGNTSKEQEIKKLVDQNFKPLLDKYNVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKTKGTISFKDTPGKYWKELKNTPIDQVNLLQLATYTSGNLGLQFPDEVQTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPGLSLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLKFINANLNPQKYPKDIQRAINETHQGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSIKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_048659.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGCTTACTTTTACCCCCTCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACATCAAAAGAACAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCTTTATTAGATAAATATAATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCAGTTAGTAAATTATTTACCGCGACAGCAGGTGGATATGCCAAAACAAAAGGAACAATCTCTTTTAAAGACACACCCGGAAAATATTGGAAAGAGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTTGCTACCTATACAAGTGGCAACCTTGGCTTACAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAGCCTAAAAACTCAATCGGTGAATATCGACAATATTCAAATCCAAGCATTGGTTTATTTGGAAAAGTTGTTGCATTGTCTATGAATAAACCTTTCGATCAAGTCTTAGAAAAAACAATTTTTCCGGGCCTTAGCTTAAAACATAGCTATGTAAATGTTCCTAAAACTCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCAATTCGTGTTAACCCTGGTCCGTTAGATGCACCTGCGTACGGCGTCAAATCGACACTACCCGATATGCTTAAGTTTATTAATGCCAACCTCAACCCACAGAAATATCCGAAAGATATTCAACGTGCAATTAATGAAACACATCAGGGTTTCTACCAAGTCGGCACGATGTATCAGGCACTTGGTTGGGAAGAATTTTCTTATCCAGCGCCTTTACAAACTTTATTAGACAGTAATTCAGAGCAAATCGTGATGAAGCCTAATAAAGTGACTGCCATTTCAAAAGAACCTTCAATTAAGATGTTCCACAAAACTGGCTCAACAAATGGCTTTGGAACTTATGTGGTGTTTATTCCAAAAGAAAATATTGGCTTAGTCATGTTGACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCATATGCGGTGCTGAATGCAATAAAGAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3003876","ARO_id":"40575","ARO_name":"ADC-44","ARO_description":"ADC-44 is a beta-lactamase found in Acinetobacter pittii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2361":{"model_id":"2361","model_name":"ADC-56","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3654":{"protein_sequence":{"accession":"WP_031973850.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYQQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_048666.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCAACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTACCGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003878","ARO_id":"40577","ARO_name":"ADC-56","ARO_description":"ADC-56 is a beta-lactamase found in Acinetobacter baumannii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2362":{"model_id":"2362","model_name":"ADC-61","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3655":{"protein_sequence":{"accession":"WP_033503051.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPLDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_048671.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTCTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTACCGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003879","ARO_id":"40578","ARO_name":"ADC-61","ARO_description":"ADC-61 is a beta-lactamase found in Acinetobacter baumannii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2363":{"model_id":"2363","model_name":"ADC-74","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3657":{"protein_sequence":{"accession":"WP_001211203.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNRSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRANPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLDAIKK"},"dna_sequence":{"accession":"NG_048679.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATCGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTGGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCATTTGGTTATAACCAAGAAAATCAGCCGATTCGAGCTAACCCCGGCCCACTCGATGCCCCTGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCTGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCACCGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGGATGCAATAAAGAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003880","ARO_id":"40579","ARO_name":"ADC-74","ARO_description":"ADC-74 is a beta-lactamase found in Acinetobacter baumannii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2364":{"model_id":"2364","model_name":"ADC-75","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3658":{"protein_sequence":{"accession":"WP_063857817.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_048680.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTACCGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003881","ARO_id":"40580","ARO_name":"ADC-75","ARO_description":"ADC-75 is a beta-lactamase found in Acinetobacter baumannii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2365":{"model_id":"2365","model_name":"ADC-76","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3659":{"protein_sequence":{"accession":"WP_001211237.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKVLKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGESRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPTDIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_048681.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACCCCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCGTTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGTGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATCCAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATACGGTGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGTATTAAGGCAGCGTATGCAGTTTTAAATGCAATAAAAAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003882","ARO_id":"40581","ARO_name":"ADC-76","ARO_description":"ADC-76 is a beta-lactamase found in Acinetobacter baumannii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2366":{"model_id":"2366","model_name":"ADC-77","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3660":{"protein_sequence":{"accession":"WP_063857818.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFINANLNPQKYPTDIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_048682.1","fmin":"53","fmax":"1205","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCTCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCCACCTTACCGGATATGTTGAGTTTTATTAATGCCAACCTTAACCCACAAAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAGCCTAATAAAGTGACTGCTATTTCAAAAGAGCCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTACCGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003883","ARO_id":"40582","ARO_name":"ADC-77","ARO_description":"ADC-77 is a beta-lactamase found in Acinetobacter baumannii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2367":{"model_id":"2367","model_name":"ADC-78","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3661":{"protein_sequence":{"accession":"WP_057691006.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLDAIKK"},"dna_sequence":{"accession":"NG_048683.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTACCGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGGATGCAATAAAGAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003884","ARO_id":"40583","ARO_name":"ADC-78","ARO_description":"ADC-78 is a beta-lactamase found in Acinetobacter baumannii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2368":{"model_id":"2368","model_name":"ADC-79","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3662":{"protein_sequence":{"accession":"WP_001159760.1","sequence":"MQFKKISCLLLSPLFIFSTSIYADNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_048684.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCAATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGACAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTGTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCAGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003885","ARO_id":"40584","ARO_name":"ADC-79","ARO_description":"ADC-79 is a beta-lactamase found in Acinetobacter baumannii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2369":{"model_id":"2369","model_name":"ADC-80","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3663":{"protein_sequence":{"accession":"WP_029424536.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKVLKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPTDIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYIVFIPKENIGLVMLTNKRIPNEERIKAAYAVLSAIKK"},"dna_sequence":{"accession":"NG_048686.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACCCCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGTGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGATCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCCACCTTACCGGATATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAGCCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATATAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAGTGCAATAAAGAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003886","ARO_id":"40585","ARO_name":"ADC-80","ARO_description":"ADC-80 is a beta-lactamase found in Acinetobacter baumannii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2370":{"model_id":"2370","model_name":"ADC-81","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3664":{"protein_sequence":{"accession":"WP_059262723.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNRSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLDAIKK"},"dna_sequence":{"accession":"NG_048687.1","fmin":"0","fmax":"1167","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATCGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTGGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCATTTGGTTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCTGCATATGGCGCCCCTGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCTGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGGATGCAATAAAGAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003887","ARO_id":"40586","ARO_name":"ADC-81","ARO_description":"ADC-81 is a beta-lactamase found in Acinetobacter baumannii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2371":{"model_id":"2371","model_name":"ADC-82","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3665":{"protein_sequence":{"accession":"WP_001211216.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDALAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_050718.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCTAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTACCGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003888","ARO_id":"40587","ARO_name":"ADC-82","ARO_description":"ADC-82 is a beta-lactamase found in Acinetobacter baumannii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2377":{"model_id":"2377","model_name":"Escherichia coli PtsI with mutation conferring resistance to fosfomycin","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"4379":"V25I"},"clinical":{"4379":"V25I"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1100"}},"model_sequences":{"sequence":{"3675":{"protein_sequence":{"accession":"CDJ72759","sequence":"MISGILASPGIAFGKALLLKEDEIVIDRKKISADQVDQEVERFLSGRAKASAQLETIKTKAGETFGEEKEAIFEGHIMLLEDEELEQEIIALIKDKHMTADAAAHEVIEGQASALEELDDEYLKERAADVRDIGKRLLRNILGLKIIDLSAIQDEVILVAADLTPSETAQLNLKKVLGFITDAGGRTSHTSIMARSLELPAIVGTGSVTSQVKNDDYLILDAVNNQVYVNPTNEVIDKMRAVQEQVASEKAELAKLKDLPAITLDGHQVEVCANIGTVRDVEGAERNGAEGVGLYRTEFLFMDRDALPTEEEQFAAYKAVAEACGSQAVIVRTMDIGGDKELPYMNFPKEENPFLGWRAIRIAMDRREILRDQLRAILRASAFGKLRIMFPMIISVEEVRALRKEIEIYKQELRDEGKAFDESIEIGVMVETPAAATIARHLAKEVDFFSIGTNDLTQYTLAVDRGNDMISHLYQPMSPSVLNLIKQVIDASHAEGKWTGMCGELAGDERATLLLLGMGLDEFSMSAISIPRIKKIIRNTNFEDAKVLAEQALAQPTTDELMTLVNKFIEEKTIC"},"dna_sequence":{"accession":"HG738867","fmin":"2416338","fmax":"2418066","strand":"+","sequence":"ATGATTTCAGGCATTTTAGCATCCCCGGGTATCGCTTTCGGTAAAGCTCTGCTTCTGAAAGAAGACGAAATTGTCATTGACCGGAAAAAAATTTCTGCCGACCAGGTTGATCAGGAAGTTGAACGTTTTCTGAGCGGTCGTGCCAAGGCATCAGCCCAGCTGGAAACGATCAAAACGAAAGCTGGTGAAACGTTCGGTGAAGAAAAAGAAGCCATCTTTGAAGGGCATATTATGCTGCTCGAAGATGAGGAGCTGGAGCAGGAAATCATAGCCCTGATTAAAGATAAGCACATGACAGCTGACGCAGCTGCTCATGAAGTTATCGAAGGTCAGGCTTCTGCCCTGGAAGAGCTGGATGATGAATACCTGAAAGAACGTGCGGCTGACGTACGTGATATCGGTAAGCGCCTGCTGCGCAACATCCTGGGCCTGAAGATTATCGACCTGAGCGCCATTCAGGATGAAGTCATTCTGGTTGCCGCTGACCTGACGCCGTCCGAAACCGCACAGCTGAACCTGAAGAAGGTGCTGGGTTTCATCACCGACGCGGGTGGCCGTACTTCCCACACCTCTATCATGGCGCGTTCTCTGGAACTACCTGCTATCGTGGGTACCGGTAGCGTCACCTCTCAGGTGAAAAATGACGACTATCTGATTCTGGATGCCGTAAATAATCAGGTTTACGTCAATCCAACCAACGAAGTTATTGATAAAATGCGCGCTGTTCAGGAGCAAGTGGCTTCTGAAAAAGCAGAGCTTGCTAAACTGAAAGATCTGCCAGCTATTACGCTGGACGGTCACCAGGTAGAAGTATGCGCTAACATTGGTACGGTTCGTGACGTTGAAGGTGCAGAGCGTAACGGCGCTGAAGGCGTTGGTCTGTATCGTACTGAGTTCCTGTTCATGGACCGCGACGCACTGCCCACTGAAGAAGAACAGTTTGCTGCTTACAAAGCAGTGGCTGAAGCGTGTGGCTCGCAAGCGGTTATCGTTCGTACCATGGACATCGGCGGCGACAAAGAGCTGCCATACATGAACTTCCCGAAAGAAGAGAACCCGTTCCTCGGCTGGCGCGCTATCCGTATCGCGATGGATCGTAGAGAGATCCTGCGCGATCAGCTCCGCGCTATCCTGCGTGCCTCGGCTTTCGGTAAATTGCGCATTATGTTCCCGATGATCATCTCTGTTGAAGAAGTGCGTGCACTGCGCAAAGAGATCGAAATCTACAAACAGGAACTGCGCGACGAAGGTAAAGCGTTTGACGAGTCAATTGAAATCGGCGTAATGGTGGAAACACCGGCTGCCGCAACAATTGCACGTCATTTAGCCAAAGAAGTTGATTTCTTTAGTATCGGCACCAATGATTTAACGCAGTACACTCTGGCAGTTGACCGTGGTAATGATATGATTTCACACCTTTACCAGCCAATGTCACCGTCCGTGCTGAACTTGATCAAGCAAGTTATTGATGCTTCTCATGCTGAAGGCAAATGGACTGGCATGTGTGGTGAGCTTGCTGGCGATGAACGTGCTACACTTCTGTTGCTGGGGATGGGTCTGGACGAATTCTCTATGAGCGCCATTTCTATCCCGCGCATTAAGAAGATTATCCGTAACACGAACTTCGAAGATGCGAAGGTGTTAGCAGAGCAGGCTCTTGCTCAACCGACAACGGACGAGTTAATGACGCTGGTTAACAAGTTCATTGAAGAAAAAACAATCTGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40589","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MC4100","NCBI_taxonomy_id":"1403831"}}}},"ARO_accession":"3003899","ARO_id":"40601","ARO_name":"Escherichia coli PtsI with mutation conferring resistance to fosfomycin","ARO_description":"PtsI (phosphoenolpyruvate-protein phosphotransferase) is involved in cyclic AMP synthesis, which regulates glpT expression. As a result, mutations to ptsI confer resistance to fosfomycin by affecting the regulation of fosfomycin import.","ARO_category":{"41414":{"category_aro_accession":"3004250","category_aro_cvterm_id":"41414","category_aro_name":"PtsI phosphotransferase","category_aro_description":"PtsI family phosphotransferases are involved in cyclic AMP synthesis, which regulates glpT expression. Mutations in PtsI family genes can negatively affect expression of UhpT, which is needed for fosfomycin import.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2848":{"model_id":"2848","model_name":"MCR-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"4202":{"protein_sequence":{"accession":"ASR73329.1","sequence":"MISRFKTLSVNQFTFITALFYVAIFNLPLFGIVRKGIEKQPEVDPLFIASMPLFLTFALSFLFSIFTVKYLLKPFFIVLTLLSSSVFFAAYQYNVVFDYGMIENTFQTHPAEALMYVNLASITNLLLTGLLPSYLIYKADIHYQPFFKELLHKLAFMLLMFVGIGIVAFFYYQDYAAFVRNNSELRRYIVPTYFVSSASKYLNEHYLQTPMEYQQLGLDAKNASRNPNTKPNLLVVVVGETARSMSYQYYGYNKPTNAHTQNQGLIAFNDTSSCGTATAVSLPCMFSRMGRADYDPRRANAQDTVIDVLSHSGIKVQWFDNDSGCKGVCDQVENLTIDLKSDPKLCSGQYCFDQVLLNKLDKILAVAPSQDTVIFLHIIGSHGPTYYLRYPPEHRKFIPDCPRSDIQNCSQEELINTYDNTILYTDFILSEVVNKLKGKQDMFDTAMLYLSDHGESLGEKGMYLHGAPYSIAPKEQTSVPMLAWVSNDFSQDNQLNMTCVAQRAEQGGFSHDNLFDSLLGLMNVKTTVYQSQLDIFAPCRY"},"dna_sequence":{"accession":"MF543359.1","fmin":"5807","fmax":"7433","strand":"-","sequence":"CTAATACCTGCAAGGTGCAAAAATATCGAGTTGGCTCTGATAGACGGTGGTTTTTACATTCATAAGTCCTAGCAAACTGTCGAACAAATTGTCGTGGGAAAAGCCGCCCTGTTCTGCTCGCTGTGCAACACAAGTCATGTTCAACTGATTATCTTGGCTAAAGTCATTAGATACCCAAGCCAGCATTGGTACGCTAGTTTGTTCTTTCGGTGCAATACTATAGGGCGCACCATGTAAATACATGCCCTTTTCACCCAAAGACTCACCATGGTCAGAGAGATACAGCATTGCAGTATCGAACATATCCTGCTTACCTTTTAATTTATTCACCACTTCACTGAGAATAAAATCCGTATATAGAATAGTGTTGTCGTAGGTGTTAATCAGTTCTTCTTGACTGCAATTTTGAATATCACTGCGCGGACAATCCGGTATAAATTTACGATGCTCTGGCGGGTATCTAAGATAATAAGTTGGTCCATGACTACCAATGATATGCAAAAAAATTACTGTATCTTGACTTGGTGCTACTGCCAGAATTTTATCTAATTTGTTGAGCAATACTTGGTCAAAACAATATTGGCCAGAACACAGCTTCGGATCACTCTTCAAATCTATCGTGAGATTTTCAACCTGATCACACACACCTTTACAGCCAGAATCATTATCAAACCACTGTACTTTTATACCACTATGACTTAACACATCAATCACTGTGTCTTGAGCATTAGCACGGCGAGGATCATAGTCTGCCCGCCCCATTCGTGAAAACATACAGGGTAGAGACACCGCCGTGGCCGTGCCGCATGAGCTAGTATCGTTAAACGCAATCAGCCCCTGATTTTGGGTATGAGCATTGGTTGGCTTGTTATATCCATAATATTGATAGCTCATTGAGCGCGCAGTTTCACCCACAACAACCACTAATAAGTTAGGTTTAGTGTTCGGGTTACGACTGGCATTCTTCGCATCTAGGCCAAGTTGTTGGTATTCCATGGGCGTCTGCAAATAGTGCTCATTGAGATATTTAGATGCACTACTGACAAAATAGGTAGGGACAATGTAACGCCTTAACTCACTGTTGTTTCGAACAAATGCAGCATAATCTTGATAGTAAAAAAAGGCGACTATCCCAATGCCAACGAACATTAGCAGCATAAAGGCTAATTTATGCAATAACTCCTTAAAAAAGGGCTGATAATGAATATCGGCCTTATAAATAAGATATGACGGTAATAGCCCAGTCAGCAGTAGATTGGTAATTGATGCAAGATTTACATACATCAATGCTTCAGCAGGATGTGTTTGAAACGTGTTTTCTATCATGCCGTAGTCAAACACGACATTGTATTGATAGGCTGCAAAAAATACACTTGAGGAAAGTAACGTCAATACGATAAAAAAGGGCTTCAGCAGGTATTTGACGGTAAAAATTGAAAACAAAAAACTCAGCGCAAATGTTAAAAATAGCGGCATAGATGCGATGAAAAGGGGATCAACTTCTGGTTGTTTTTCAATTCCTTTTCGCACTATACCAAAGAGCGGTAGATTGAAAATGGCAACATAAAACAACGCAGTGATGAAAGTGAATTGGTTAACCGATAACGTCTTAAATCTAGAAATCAC"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41493","NCBI_taxonomy_name":"Salmonella sp.","NCBI_taxonomy_id":"599"}}}},"ARO_accession":"3004325","ARO_id":"41492","ARO_name":"MCR-4","ARO_description":"MCR-4 is a plasmid-borne phosphoethanolamine transferase variant of MCR-1, isolated from Salmonella enterica serovar Typhimurium of porcine origin in Italy, Spain and Belgium through 2013 and 2015-2016. MCR-4 confers resistance to collistin via addition of a phosphoethanolamine group to lipid A, reducing the negative charge of the cell membrane. Described by Carattoli et al. 2017.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2849":{"model_id":"2849","model_name":"MCR-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"4295":{"protein_sequence":{"accession":"ATU90148.1","sequence":"MRLSAFITFLKMRPQVRTEFLTLFISLVFTLLCNGVFWNALLAGRDSLTSGTWLMLLCTGLLITGLQWLLLLLVATRWSVKPLLILLAVMTPAAVYFMRNYGVYLDKAMLRNLMETDVREASELLQWRMLPYLLVAAVSVWWIARVRVLRTGWKQAVMMRSACLAGALAMISMGLWPVMDVLIPTLRENKPLRYLITPANYVISGIRVLTEQASSSADEAREVVAADAHRGPQEQGRRPRALVLVVGETVRAANWGLSGYERQTTPELAARDVINFSDVTSCGTDTATSLPCMFSLNGRRDYDERQIRRRESVLHVLNRSDVNILWRDNQSGCKGVCDGLPFENLSSAGHPTLCHGERCLDEILLEGLAEKITTSRSDMLIVLHMLGNHGPAYFQRYPASYRRWSPTCDTTDLASCSHEALVNTYDNAVLYTDHVLARTIDLLSGIRSHDTALLYVSDHGESLGEKGLYLHGIPYVIAPDEQIKVPMIWWQSSQVYADQACMQTHASRAPVSHDHLFHTLLGMFDVKTAAYTPELDLLATCRKGQPQ"},"dna_sequence":{"accession":"MG241339.1","fmin":"0","fmax":"1644","strand":"+","sequence":"ATGCGGTTGTCTGCATTTATCACTTTCTTGAAAATGCGCCCGCAAGTGCGCACTGAATTTTTGACTCTGTTCATCAGCCTTGTGTTCACCCTGCTGTGCAATGGCGTGTTTTGGAATGCCCTTCTTGCTGGACGCGACTCCCTAACTTCTGGAACATGGCTAATGCTCCTTTGCACTGGGTTGCTGATCACCGGGCTGCAATGGTTGTTGCTCCTTCTGGTGGCCACGCGCTGGAGTGTCAAGCCACTACTGATTCTGCTTGCTGTCATGACGCCCGCCGCCGTTTATTTCATGCGCAACTACGGGGTTTATCTCGACAAGGCCATGCTGCGGAATCTGATGGAGACGGACGTCAGGGAAGCCAGTGAGCTGTTGCAATGGAGAATGCTGCCCTACTTGTTGGTTGCAGCCGTATCCGTGTGGTGGATTGCGAGAGTCAGGGTTTTACGAACGGGCTGGAAACAAGCGGTAATGATGCGCAGCGCTTGTCTGGCTGGCGCTCTCGCCATGATTTCCATGGGTCTGTGGCCAGTCATGGATGTGCTGATACCCACGCTTCGTGAAAACAAGCCGCTTCGCTATTTGATCACTCCTGCAAACTACGTCATCTCGGGCATTCGGGTTTTGACTGAACAGGCGTCATCGTCAGCAGACGAAGCAAGGGAAGTCGTTGCAGCCGATGCGCATCGAGGGCCTCAAGAACAAGGCCGCCGTCCTCGTGCTCTCGTACTGGTTGTCGGGGAAACCGTCAGGGCGGCTAATTGGGGGTTGAGCGGCTATGAACGACAAACCACCCCTGAGTTGGCCGCACGCGACGTGATCAATTTTTCCGATGTCACCAGTTGCGGGACGGATACGGCTACATCCCTTCCCTGCATGTTTTCCCTCAATGGTCGGCGCGACTACGACGAACGCCAGATTCGTCGGCGCGAGTCCGTGCTGCACGTTTTAAACCGTAGTGACGTCAACATTCTCTGGCGCGATAACCAGTCGGGCTGTAAAGGCGTCTGTGATGGACTGCCCTTTGAAAACCTGTCTTCGGCAGGCCATCCCACACTGTGCCATGGCGAGCGCTGCCTGGATGAAATTCTGCTCGAAGGGTTGGCCGAGAAGATAACAACAAGCCGCAGCGATATGCTGATCGTTCTGCATATGCTGGGCAATCACGGCCCAGCGTATTTCCAGCGCTATCCCGCAAGCTACCGACGCTGGTCGCCAACCTGCGACACCACCGATCTGGCCAGCTGTTCGCATGAAGCCTTGGTGAACACCTACGACAACGCCGTGCTTTACACCGATCATGTGCTTGCCCGTACCATTGACCTGCTGTCCGGCATCCGCTCACACGACACGGCGCTGCTGTACGTTTCCGATCATGGGGAATCGCTCGGCGAGAAAGGCCTGTATCTCCATGGCATACCTTACGTCATCGCGCCGGATGAGCAGATCAAGGTGCCGATGATCTGGTGGCAGTCGAGTCAGGTTTATGCCGACCAAGCCTGTATGCAAACTCATGCCTCTCGGGCACCGGTAAGTCACGATCACCTGTTTCACACCTTGCTCGGGATGTTCGACGTGAAAACCGCTGCCTACACGCCAGAGTTGGACCTTCTGGCAACATGCAGAAAAGGACAACCACAATGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41660","NCBI_taxonomy_name":"Aeromonas hydrophila subsp. hydrophila","NCBI_taxonomy_id":"196023"}}}},"ARO_accession":"3004332","ARO_id":"41500","ARO_name":"MCR-5","ARO_description":"MCR-5 is a transposon-associated phosphoethanolamine transferase gene, identified in Salmonella Paratyphi B dTa+ (d-tartrate fermenting Salmonella enterica subsp. enterica serovar Paratyphi B) isolates from food-producing animals. The isolates were collected between 2011 and 2013, and retrieved from the German National Reference Laboratory for Salmonella. MCR-5 confers resistance to collistin through the addition of a phosphoethanolamine group to lipid A, causing a reduction in negative charge of the cell membrane. Described by Borowiak et al, 2017.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2850":{"model_id":"2850","model_name":"Salmonella enterica gyrA with mutation conferring resistance to triclosan","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1500"},"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"8272":"S83F","8273":"D87G"},"clinical":{"8272":"S83F","8273":"D87G"}}},"model_sequences":{"sequence":{"4207":{"protein_sequence":{"accession":"NP_461214.1","sequence":"MSDLAREITPVNIEEELKSSYLDYAMSVIVGRALPDVRDGLKPVHRRVLYAMNVLGNDWNKAYKKSARVVGDVIGKYHPHGDSAVYDTIVRMAQPFSLRYMLVDGQGNFGSIDGDSAAAMRYTEIRLAKIAHELMADLEKETVDFVDNYDGTEKIPDVMPTKIPNLLVNGSSGIAVGMATNIPPHNLTEVINGCLAYIDNEDISIEGLMEHIPGPDFPTAAIINGRRGIEEAYRTGRGKVYIRARAEVEADAKTGRETIIVHEIPYQVNKARLIEKIAELVKDKRVEGISALRDESDKDGMRIVIEVKRDAVGEVVLNNLYSQTQLQVSFGINMVALHHGQPKIMNLKDIISAFVRHRREVVTRRTIFELRKARDRAHILEALAIALANIDPIIELIRRAPTPAEAKAALISRPWDLGNVAAMLERAGDDAARPEWLEPEFGVRDGQYYLTEQQAQAILDLRLQKLTGLEHEKLLDEYKELLEQIAELLHILGSADRLMEVIREEMELIRDQFGDERRTEITANSADINIEDLISQEDVVVTLSHQGYVKYQPLTDYEAQRRGGKGKSAARIKEEDFIDRLLVANTHDTILCFSSRGRLYWMKVYQLPEASRGARGRPIVNLLPLEANERITAILPVREYEEGVNVFMATASGTVKKTALTEFSRPRSAGIIAVNLNDGDELIGVDLTSGSDEVMLFSAAGKVVRFKEDAVRAMGRTATGVRGIKLAGDDKVVSLIIPRGEGAILTVTQNGYGKRTAADEYPTKSRATQGVISIKVTERNGSVVGAVQVDDCDQIMMITDAGTLVRTRVSEISVVGRNTQGVILIRTAEDENVVGLQRVAEPVDDEELDAIDGSVAEGDEDIAPEAESDDDVADDADE"},"dna_sequence":{"accession":"NC_003197.2","fmin":"2373709","fmax":"2376346","strand":"-","sequence":"TTACTCGTCAGCGTCATCCGCAACGTCGTCATCGCTTTCCGCTTCCGGGGCGATATCCTCATCCCCTTCCGCCACGCTGCCGTCGATAGCGTCGAGTTCTTCGTCATCTACCGGTTCAGCAACGCGTTGCAGACCCACCACGTTTTCATCTTCCGCCGTGCGGATAAGGATAACGCCCTGGGTATTACGTCCCACTACGCTGATCTCGGACACACGGGTACGCACCAGAGTACCGGCATCCGTGATCATCATGATCTGGTCGCAATCGTCTACCTGTACCGCACCGACAACGGAACCGTTGCGCTCGGTCACTTTGATAGAGATAACGCCCTGCGTCGCACGAGACTTGGTCGGGTACTCGTCCGCTGCGGTACGCTTCCCGTAGCCGTTTTGCGTTACGGTCAGAATAGCGCCTTCGCCGCGTGGGATGATCAGAGAGACGACTTTATCGTCTCCCGCCAGCTTAATACCGCGCACACCGGTCGCGGTACGCCCCATCGCACGGACGGCGTCTTCTTTGAAGCGCACCACTTTACCCGCGGCCGAGAACAGCATGACTTCGTCAGAACCAGAAGTCAGGTCAACGCCAATCAGCTCGTCGCCGTCGTTGAGGTTCACCGCGATAATACCGGCGGAACGCGGACGGCTGAATTCGGTCAGCGCCGTTTTCTTCACGGTACCGCTGGCGGTCGCCATAAAGACGTTGACGCCTTCTTCATACTCACGAACCGGCAGAATCGCGGTGATACGTTCGTTGGCTTCCAGCGGCAGCAGGTTGACGATCGGACGACCGCGCGCGCCGCGGCTGGCTTCCGGCAGCTGATAGACCTTCATCCAGTACAGACGGCCCCGGCTGGAGAAGCAGAGGATGGTGTCATGGGTGTTAGCCACCAGCAGGCGGTCGATAAAGTCTTCTTCTTTAATACGCGCGGCAGATTTACCTTTCCCACCACGACGTTGCGCTTCGTAATCTGTCAGCGGTTGATATTTGACGTAACCCTGGTGAGACAGCGTCACGACAACATCTTCCTGGCTAATCAGATCTTCGATATTAATATCGGCGCTGTTGGCGGTGATTTCGGTACGACGCTCATCGCCGAACTGATCGCGAATTAACTCCATCTCTTCGCGGATCACTTCCATCAGGCGATCGGCGCTGCCCAGAATGTGCAGCAATTCAGCAATCTGCTCCAGCAGCTCTTTGTATTCGTCGAGCAGTTTTTCATGCTCCAGGCCGGTCAGTTTCTGCAAACGCAGATCCAGAATCGCCTGCGCCTGCTGTTCAGTCAGGTAGTACTGACCGTCACGCACGCCAAATTCTGGCTCCAGCCATTCCGGACGCGCGGCGTCATCACCAGCGCGCTCCAGCATCGCAGCAACGTTGCCCAGATCCCACGGACGCGAAATCAGCGCCGCTTTTGCTTCCGCCGGCGTTGGCGCGCGGCGAATCAGTTCGATAATCGGGTCGATGTTGGCCAGCGCAATCGCCAGAGCTTCAAGGATATGCGCACGGTCACGGGCTTTACGCAGTTCAAAAATAGTCCGACGCGTCACCACTTCACGGCGGTGGCGCACGAACGCTGAAATGATATCTTTCAGGTTCATGATCTTCGGCTGGCCGTGATGCAGCGCCACCATGTTAATACCGAAGGAAACCTGTAGCTGGGTCTGGGAGTAGAGATTATTAAGCACCACCTCGCCCACCGCATCGCGTTTCACTTCAATCACGATGCGCATCCCGTCTTTGTCGGATTCGTCACGCAGCGCGCTGATGCCTTCCACGCGTTTATCTTTCACCAGCTCGGCGATTTTCTCGATCAGGCGCGCTTTGTTCACCTGATAGGGAATTTCATGGACGATGATGGTTTCACGGCCCGTTTTGGCGTCAGCTTCAACTTCCGCGCGGGCGCGAATGTACACTTTGCCACGACCGGTGCGGTAGGCTTCTTCGATACCACGACGACCGTTGATGATCGCGGCGGTCGGGAAGTCCGGCCCCGGAATATGTTCCATCAGCCCTTCAATGCTGATGTCTTCGTTGTCGATATACGCCAGGCAGCCGTTAATCACTTCCGTCAGGTTGTGCGGCGGGATATTCGTCGCCATACCTACTGCGATACCGGAAGAACCGTTCACCAGCAGATTCGGAATTTTGGTCGGCATGACGTCCGGAATTTTTTCCGTACCGTCATAGTTATCCACGAAATCCACCGTCTCTTTTTCGAGATCGGCCATCAGTTCGTGGGCGATTTTCGCCAGACGGATCTCCGTATAACGCATTGCCGCCGCGGAGTCGCCGTCAATAGAACCGAAGTTACCCTGACCATCCACCAGCATGTAACGCAGCGAGAATGGCTGCGCCATACGAACGATGGTGTCATACACTGCGGAATCGCCGTGGGGATGGTATTTACCGATTACGTCACCAACGACACGGGCAGATTTTTTATAGGCTTTGTTCCAGTCATTGCCCAATACGTTCATGGCGTAAAGTACGCGACGGTGTACCGGCTTCAGGCCATCTCGGACATCCGGCAGCGCACGGCCAACAATGACCGACATCGCATAATCCAGATAGGAGCTCTTCAGCTCCTCCTCAATGTTGACCGGTGTAATTTCTCTCGCAAGGTCGCTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35734","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium str. LT2","NCBI_taxonomy_id":"99287"}}}},"ARO_accession":"3004334","ARO_id":"41502","ARO_name":"Salmonella enterica gyrA with mutation conferring resistance to triclosan","ARO_description":"Point mutations in Salmonella enterica serovar Typhimurium which have been shown to increase the minimum inhibitory concentration of the antibiotic triclosan. It is hypothesized that decreased susceptibility to triclosan in Salmonella gyrA mutants occurs indirectly due to alterations in the stress response pathways.","ARO_category":{"41501":{"category_aro_accession":"3004333","category_aro_cvterm_id":"41501","category_aro_name":"triclosan resistant gyrA","category_aro_description":"DNA gyrase is responsible for DNA supercoiling and consists of two alpha and two beta subunits. Point mutations in gyrA have been shown to decrease susceptibility to the antibiotic triclosan. Although the mechanism is unclear, it is hypothesized that changes in supercoiling activity of mutant DNA gyrase proteins alters expression of stress response pathways thereby indirectly decreasing triclosan susceptibility. It has been shown that triclosan does not interact directly with gyrA.","category_aro_class_name":"AMR Gene Family"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2851":{"model_id":"2851","model_name":"Escherichia coli gyrA with mutation conferring resistance to triclosan","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"1500"},"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"8275":"S83F","8276":"D87G"},"clinical":{"8275":"S83F","8276":"D87G"}}},"model_sequences":{"sequence":{"4208":{"protein_sequence":{"accession":"AAC75291.1","sequence":"MSDLAREITPVNIEEELKSSYLDYAMSVIVGRALPDVRDGLKPVHRRVLYAMNVLGNDWNKAYKKSARVVGDVIGKYHPHGDSAVYDTIVRMAQPFSLRYMLVDGQGNFGSIDGDSAAAMRYTEIRLAKIAHELMADLEKETVDFVDNYDGTEKIPDVMPTKIPNLLVNGSSGIAVGMATNIPPHNLTEVINGCLAYIDDEDISIEGLMEHIPGPDFPTAAIINGRRGIEEAYRTGRGKVYIRARAEVEVDAKTGRETIIVHEIPYQVNKARLIEKIAELVKEKRVEGISALRDESDKDGMRIVIEVKRDAVGEVVLNNLYSQTQLQVSFGINMVALHHGQPKIMNLKDIIAAFVRHRREVVTRRTIFELRKARDRAHILEALAVALANIDPIIELIRHAPTPAEAKTALVANPWQLGNVAAMLERAGDDAARPEWLEPEFGVRDGLYYLTEQQAQAILDLRLQKLTGLEHEKLLDEYKELLDQIAELLRILGSADRLMEVIREELELVREQFGDKRRTEITANSADINLEDLITQEDVVVTLSHQGYVKYQPLSEYEAQRRGGKGKSAARIKEEDFIDRLLVANTHDHILCFSSRGRVYSMKVYQLPEATRGARGRPIVNLLPLEQDERITAILPVTEFEEGVKVFMATANGTVKKTVLTEFNRLRTAGKVAIKLVDGDELIGVDLTSGEDEVMLFSAEGKVVRFKESSVRAMGCNTTGVRGIRLGEGDKVVSLIVPRGDGAILTATQNGYGKRTAVAEYPTKSRATKGVISIKVTERNGLVVGAVQVDDCDQIMMITDAGTLVRTRVSEISIVGRNTQGVILIRTAEDENVVGLQRVAEPVDEEDLDTIDGSAAEGDDEIAPEVDVDDEPEEE"},"dna_sequence":{"accession":"U00096.3","fmin":"2336792","fmax":"2339420","strand":"-","sequence":"TTATTCTTCTTCTGGCTCGTCGTCAACGTCCACTTCCGGAGCGATTTCATCGTCCCCTTCCGCGGCACTGCCGTCGATGGTATCCAGATCTTCCTCGTCAACCGGTTCAGCAACACGTTGCAGACCCACTACGTTTTCATCTTCCGCAGTACGGATGAGGATCACGCCCTGGGTGTTACGGCCCACGATGCTGATTTCCGAAACGCGAGTACGTACCAGCGTACCGGCATCGGTGATCATCATGATCTGGTCGCAGTCATCTACCTGTACCGCGCCAACAACTAAACCGTTACGTTCGGTAACCTTGATGGAGATAACCCCTTTCGTCGCACGCGACTTGGTTGGGTATTCCGCCACTGCGGTACGTTTACCGTAACCGTTTTGCGTTGCGGTGAGGATTGCGCCATCGCCACGAGGCACGATCAGAGAGACGACTTTATCGCCTTCACCTAAGCGAATACCGCGAACACCGGTGGTGTTGCAGCCCATCGCACGGACAGAAGACTCTTTAAAGCGCACCACTTTACCTTCAGCGGAGAACAGCATTACTTCGTCTTCGCCGCTGGTCAGGTCAACGCCGATCAGCTCATCGCCGTCAACCAGTTTGATCGCCACTTTACCGGCGGTACGCAGACGGTTGAACTCGGTGAGGACAGTTTTCTTCACGGTACCGTTAGCGGTCGCCATGAAGACTTTCACGCCTTCTTCAAACTCGGTCACTGGCAGGATCGCAGTGATACGTTCGTCCTGCTCCAGCGGCAGCAGGTTGACGATCGGACGACCGCGCGCGCCACGAGTGGCTTCCGGCAACTGATAAACTTTCATCGAATAGACGCGACCACGGCTGGAGAAGCACAGAATATGGTCGTGAGTGTTCGCCACCAGCAGTCGGTCGATAAAGTCTTCTTCTTTAATACGTGCGGCAGATTTACCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTGAGAGAGCGTCACGACCACATCTTCCTGGGTGATCAGATCTTCCAGGTTGATGTCTGCGCTGTTGGCGGTGATTTCAGTACGACGTTTGTCACCGAACTGTTCACGAACCAGCTCCAGCTCTTCACGGATCACTTCCATCAGACGATCGGCGCTACCAAGAATACGCAACAGTTCCGCGATCTGATCCAGCAGCTCTTTGTATTCGTCGAGCAGTTTTTCGTGCTCAAGACCGGTCAGTTTCTGCAAACGCAGATCCAGAATCGCCTGAGCTTGCTGTTCGGTCAGGTAGTACAGACCATCACGCACGCCGAACTCTGGCTCCAGCCATTCCGGACGCGCAGCATCGTCGCCAGCACGTTCGAGCATCGCGGCAACGTTGCCCAGCTGCCACGGATTAGCAACCAGCGCAGTTTTCGCTTCTGCAGGCGTCGGCGCATGACGGATCAGTTCGATGATCGGGTCGATGTTCGCCAGCGCCACGGCTAATGCTTCAAGGATATGAGCACGATCGCGAGCTTTACGCAGTTCGAAAATAGTACGACGGGTCACCACTTCACGGCGGTGACGAACAAACGCCGCGATGATGTCTTTCAGGTTCATGATCTTCGGCTGACCATGGTGCAATGCCACCATGTTGATACCGAAAGAAACCTGCAACTGGGTCTGGGAGTAGAGGTTGTTGAGCACAACTTCACCGACCGCATCGCGTTTCACTTCAATCACGATGCGCATACCGTCTTTGTCAGACTCGTCACGCAGCGCGCTGATGCCTTCCACGCGTTTTTCTTTTACCAGTTCCGCAATCTTCTCGATCAGGCGCGCTTTGTTTACCTGATACGGAATTTCGTGGACGATAATGGTTTCACGACCGGTTTTGGCGTCAACTTCCACTTCTGCGCGAGCGCGGATATACACCTTGCCGCGACCGGTACGGTAAGCTTCTTCAATACCGCGACGACCGTTAATGATTGCCGCCGTCGGGAAGTCCGGCCCCGGGATGTGTTCCATCAGCCCTTCAATGCTGATGTCTTCATCATCAATATACGCCAGACAACCGTTGATGACTTCCGTCAGGTTGTGCGGCGGGATGTTGGTTGCCATACCTACGGCGATACCGGAAGAACCGTTCACCAGCAGGTTAGGAATTTTGGTTGGCATGACGTCCGGAATTTTTTCCGTGCCGTCATAGTTATCAACGAAATCGACCGTCTCTTTTTCGAGATCGGCCATCAGTTCATGGGCAATTTTCGCCAGACGGATTTCCGTATAACGCATTGCCGCCGCAGAGTCGCCGTCGATAGAACCGAAGTTACCCTGACCGTCTACCAGCATATAACGCAGCGAGAATGGCTGCGCCATGCGGACGATCGTGTCATAGACCGCCGAGTCACCATGGGGATGGTATTTACCGATTACGTCACCAACGACACGGGCAGATTTTTTATAGGCTTTGTTCCAGTCATTGCCTAGTACGTTCATGGCGTAAAGTACGCGACGGTGTACCGGCTTCAGGCCATCTCGGACATCTGGCAGCGCACGGCCAACAATGACCGACATCGCATAATCCAGATAGGAGCTCTTCAGCTCTTCCTCAATGTTGACCGGTGTAATTTCTCTCGCAAGGTCGCTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3004335","ARO_id":"41503","ARO_name":"Escherichia coli gyrA with mutation conferring resistance to triclosan","ARO_description":"Point mutations in Escherichia coli which have been shown to increase the minimum inhibitory concentration of the antibiotic triclosan. It is hypothesized that decreased susceptibility to triclosan in E. coli gyrA mutants occurs indirectly due to alterations in the stress response pathways.","ARO_category":{"41501":{"category_aro_accession":"3004333","category_aro_cvterm_id":"41501","category_aro_name":"triclosan resistant gyrA","category_aro_description":"DNA gyrase is responsible for DNA supercoiling and consists of two alpha and two beta subunits. Point mutations in gyrA have been shown to decrease susceptibility to the antibiotic triclosan. Although the mechanism is unclear, it is hypothesized that changes in supercoiling activity of mutant DNA gyrase proteins alters expression of stress response pathways thereby indirectly decreasing triclosan susceptibility. It has been shown that triclosan does not interact directly with gyrA.","category_aro_class_name":"AMR Gene Family"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2852":{"model_id":"2852","model_name":"PDC-73","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"4209":{"protein_sequence":{"accession":"AKR18013.1","sequence":"GEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNLSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"KR057742.1","fmin":"0","fmax":"1116","strand":"+","sequence":"GGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCTGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004336","ARO_id":"41504","ARO_name":"PDC-73","ARO_description":"An AmpC-like beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2853":{"model_id":"2853","model_name":"PDC-74","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"4210":{"protein_sequence":{"accession":"AKR18014.1","sequence":"GEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPRPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"KR057743.1","fmin":"0","fmax":"1116","strand":"+","sequence":"GGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCCGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004337","ARO_id":"41505","ARO_name":"PDC-74","ARO_description":"An AmpC-like beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2854":{"model_id":"2854","model_name":"PDC-75","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"4211":{"protein_sequence":{"accession":"AKR18015.1","sequence":"GEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPRPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"KR057744.1","fmin":"0","fmax":"1116","strand":"+","sequence":"GGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCCCTACGGGTCGGTCCCCGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCATGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004338","ARO_id":"41506","ARO_name":"PDC-75","ARO_description":"An AmpC-like beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2855":{"model_id":"2855","model_name":"PDC-76","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"4212":{"protein_sequence":{"accession":"AKR18016.1","sequence":"GEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPIAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"KR057745.1","fmin":"0","fmax":"1116","strand":"+","sequence":"GGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCCCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCATTGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004339","ARO_id":"41507","ARO_name":"PDC-76","ARO_description":"An AmpC-like beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2856":{"model_id":"2856","model_name":"PDC-77","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"4213":{"protein_sequence":{"accession":"AKR18017.1","sequence":"GEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPRPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"KR057746.1","fmin":"0","fmax":"1116","strand":"+","sequence":"GGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTTCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCCGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004340","ARO_id":"41508","ARO_name":"PDC-77","ARO_description":"An AmpC-like beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2857":{"model_id":"2857","model_name":"PDC-78","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"4214":{"protein_sequence":{"accession":"AKR18018.1","sequence":"GEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSHFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPRPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"KR057747.1","fmin":"0","fmax":"1116","strand":"+","sequence":"GGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCACTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTTCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCCGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004341","ARO_id":"41509","ARO_name":"PDC-78","ARO_description":"An AmpC-like beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2858":{"model_id":"2858","model_name":"PDC-79","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"4215":{"protein_sequence":{"accession":"AKR18019.1","sequence":"GEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAKGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"KR057748.1","fmin":"0","fmax":"1116","strand":"+","sequence":"GGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTTCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCAAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004342","ARO_id":"41510","ARO_name":"PDC-79","ARO_description":"An AmpC-like beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2859":{"model_id":"2859","model_name":"PDC-80","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"4216":{"protein_sequence":{"accession":"AKR18020.1","sequence":"GEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAGGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"KR057749.1","fmin":"0","fmax":"1116","strand":"+","sequence":"GGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGGAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCACTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004343","ARO_id":"41511","ARO_name":"PDC-80","ARO_description":"An AmpC-like beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2860":{"model_id":"2860","model_name":"PDC-81","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"4217":{"protein_sequence":{"accession":"AKR18021.1","sequence":"GEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNLSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"KR057750.1","fmin":"0","fmax":"1116","strand":"+","sequence":"GGCGAGGCCCCGGCGGATCGCCTGAAGGCATTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCTGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCTAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTATGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004344","ARO_id":"41512","ARO_name":"PDC-81","ARO_description":"An AmpC-like beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2861":{"model_id":"2861","model_name":"PDC-82","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"4218":{"protein_sequence":{"accession":"AKR18022.1","sequence":"GEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQLPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLLEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"KR057751.1","fmin":"0","fmax":"1116","strand":"+","sequence":"GGCGAGGCCCCGGCGGATCGCCTGAAGGCATTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGCTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCCTGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCTAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTATGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004345","ARO_id":"41513","ARO_name":"PDC-82","ARO_description":"An AmpC-like beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2862":{"model_id":"2862","model_name":"PDC-83","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"4219":{"protein_sequence":{"accession":"AKR18023.1","sequence":"GEAPADRLKALVDAAVQPAMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"KR057752.1","fmin":"0","fmax":"1116","strand":"+","sequence":"GGCGAGGCCCCGGCGGATCGCCTGAAGGCATTGGTCGACGCCGCCGTACAACCGGCGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCTAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTATGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004346","ARO_id":"41514","ARO_name":"PDC-83","ARO_description":"An AmpC-like beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2863":{"model_id":"2863","model_name":"PDC-84","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"4220":{"protein_sequence":{"accession":"AKR18024.1","sequence":"GEAPADRLKALVDAAVQPAMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPIAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"KR057753.1","fmin":"0","fmax":"1116","strand":"+","sequence":"GGCGAGGCCCCGGCGGATCGCCTGAAGGCATTGGTCGACGCCGCCGTACAACCGGCGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCTAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCATTGCCGAGCGGGTGAAGATCGCCTATGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004347","ARO_id":"41515","ARO_name":"PDC-84","ARO_description":"An AmpC-like beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2864":{"model_id":"2864","model_name":"PDC-85","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"4221":{"protein_sequence":{"accession":"AKR18025.1","sequence":"GEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGHGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"KR057754.1","fmin":"0","fmax":"1116","strand":"+","sequence":"GGCGAGGCCCCGGCGGATCGCCTGAAGGCATTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCCATGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCTAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTATGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004348","ARO_id":"41516","ARO_name":"PDC-85","ARO_description":"An AmpC-like beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2865":{"model_id":"2865","model_name":"PDC-86","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"4222":{"protein_sequence":{"accession":"AKR18026.1","sequence":"DEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAKGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"KR057755.1","fmin":"0","fmax":"1116","strand":"+","sequence":"GATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCAAAGGCTACGGGGTGAAGACCAGCGCCGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACTCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004349","ARO_id":"41517","ARO_name":"PDC-86","ARO_description":"An AmpC-like beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2866":{"model_id":"2866","model_name":"PDC-87","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"4223":{"protein_sequence":{"accession":"AKR18027.1","sequence":"DEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPIAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"KR057756.1","fmin":"0","fmax":"1116","strand":"+","sequence":"GATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCTTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCATTGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004350","ARO_id":"41518","ARO_name":"PDC-87","ARO_description":"An AmpC-like beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2867":{"model_id":"2867","model_name":"PDC-88","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"4224":{"protein_sequence":{"accession":"AKR18028.1","sequence":"DEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"KR057757.1","fmin":"0","fmax":"1110","strand":"+","sequence":"GATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCTTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004351","ARO_id":"41519","ARO_name":"PDC-88","ARO_description":"An AmpC-like beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2868":{"model_id":"2868","model_name":"PDC-89","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"4225":{"protein_sequence":{"accession":"AKR18029.1","sequence":"DEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"KR057758.1","fmin":"0","fmax":"1107","strand":"+","sequence":"GATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCAATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGGCGCTGCAGCCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004352","ARO_id":"41520","ARO_name":"PDC-89","ARO_description":"An AmpC-like beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2869":{"model_id":"2869","model_name":"PDC-90","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"4226":{"protein_sequence":{"accession":"AKR18030.1","sequence":"DEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"KR057759.1","fmin":"0","fmax":"1107","strand":"+","sequence":"GATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCCGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACTCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004353","ARO_id":"41521","ARO_name":"PDC-90","ARO_description":"An AmpC-like beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2870":{"model_id":"2870","model_name":"PDC-91","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"4227":{"protein_sequence":{"accession":"AKR18031.1","sequence":"DEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSLQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"KR057760.1","fmin":"0","fmax":"1104","strand":"+","sequence":"GATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCTTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004354","ARO_id":"41522","ARO_name":"PDC-91","ARO_description":"An AmpC-like beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2871":{"model_id":"2871","model_name":"PDC-92","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"4228":{"protein_sequence":{"accession":"AKR18032.1","sequence":"DEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMAPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"KR057761.1","fmin":"0","fmax":"1110","strand":"+","sequence":"GATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004355","ARO_id":"41523","ARO_name":"PDC-92","ARO_description":"An AmpC-like beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2872":{"model_id":"2872","model_name":"PDC-93","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"4229":{"protein_sequence":{"accession":"AKR18033.1","sequence":"DEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMAPQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"KR057762.1","fmin":"0","fmax":"1116","strand":"+","sequence":"GATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCCGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004356","ARO_id":"41524","ARO_name":"PDC-93","ARO_description":"An AmpC-like beta-lactamase found in Pseudomonas aeruginosa","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2873":{"model_id":"2873","model_name":"catV","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"4232":{"protein_sequence":{"accession":"ATL63235.1","sequence":"MKFQRIDLDNWSRRSYFEHYLNRVNCTFSMTANIDITELLPALRQKEMKLYPAFLYMVTNAVNAHREFRTSFHADGELGYWESMIPSYTFFHQDDQTFSTMWTEFADEFPVFYQNYVADMKKYGDNKGLVAKELEPPYTFPVSCIPWVSFSGFNLNISGDGRYLLPIITSGKYFGQEGKTLLPVSLQVHHAVCDGYHASLFIHDLQKWATNYKEWLGVE"},"dna_sequence":{"accession":"KY753886.1","fmin":"0","fmax":"660","strand":"+","sequence":"ATGAAATTTCAGCGAATCGATCTAGATAATTGGAGCAGAAGGTCTTATTTCGAGCATTATCTGAACCGAGTGAATTGCACCTTCAGTATGACTGCCAACATAGATATAACGGAATTGCTGCCCGCTCTACGGCAAAAGGAGATGAAGCTGTACCCGGCTTTTCTGTATATGGTGACAAACGCTGTCAATGCGCATCGTGAATTTCGGACTTCCTTCCATGCGGATGGCGAGTTGGGCTATTGGGAGAGCATGATACCCAGCTATACTTTTTTTCACCAGGATGATCAAACTTTTTCTACGATGTGGACGGAATTCGCTGACGAGTTCCCTGTGTTTTATCAAAATTACGTAGCGGATATGAAAAAGTATGGGGACAACAAAGGTCTTGTGGCAAAAGAGTTGGAACCGCCTTACACTTTCCCTGTCTCGTGTATTCCCTGGGTGAGCTTCAGTGGGTTTAATCTGAATATTTCGGGAGATGGGCGATATTTGCTGCCAATCATTACGAGCGGAAAGTATTTCGGGCAAGAAGGCAAAACGTTATTGCCTGTTTCTTTGCAGGTCCATCATGCGGTTTGTGATGGCTATCACGCGAGCCTGTTCATCCATGATCTGCAAAAATGGGCAACAAACTATAAGGAATGGTTAGGTGTCGAGTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41526","NCBI_taxonomy_name":"Brevibacillus brevis Vm4","NCBI_taxonomy_id":"1289602"}}}},"ARO_accession":"3004357","ARO_id":"41525","ARO_name":"catV","ARO_description":"A chloramphenicol acetyltransferase identified in Brevibacillus brevis and shown to confer resistance to chloramphenicol antibiotics. Described by Pawlowski et al. 2017.","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. cat is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Bacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2874":{"model_id":"2874","model_name":"ACI-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"4259":{"protein_sequence":{"accession":"CAB51471.1","sequence":"MKKFCFLFLIICGLMVFCLQDCQARQKLNLADLENKYNAVIGVYAVDMENGKKICYKPDTRFSYCSTHKVFTAAELLRQKNTSDLNEIRKFSAEDILSYAPITKDHVADGMTLAEICSASLRWSDNTAANLILQEIGGVENFKVALKNIGDKTTKPARNEPELNLFNPKDNRDTSTPRQMVKNLQVYIFGDILSDDKKKLLIDWMSDNSITDTLIKAETPQGWKVIDKSGSGDYGARNDIAVIYPPNRKPIVMAIMSRRTEKNAKSDDAMIAEAAKRIFDNLVF"},"dna_sequence":{"accession":"AJ007350.1","fmin":"239","fmax":"1094","strand":"+","sequence":"ATGAAGAAATTTTGTTTTTTGTTTTTGATAATCTGTGGCTTGATGGTTTTCTGCCTTCAGGATTGTCAAGCGCGGCAGAAATTAAATCTTGCTGATCTGGAAAATAAATATAACGCCGTGATTGGTGTTTACGCCGTTGACATGGAGAATGGAAAAAAAATTTGCTACAAACCTGATACGCGTTTTTCCTACTGCTCGACACACAAAGTTTTTACGGCTGCAGAATTGCTAAGACAAAAAAATACCTCCGATTTGAATGAAATTCGTAAGTTTTCGGCGGAAGATATTTTGTCCTACGCGCCAATCACCAAAGACCATGTTGCTGATGGCATGACGCTGGCGGAAATTTGTTCGGCATCGCTCAGGTGGAGTGACAACACGGCGGCAAATTTAATTTTGCAGGAGATCGGCGGCGTGGAAAATTTCAAGGTGGCACTTAAAAATATTGGCGACAAAACTACCAAACCTGCGCGAAATGAACCTGAACTTAATCTTTTCAATCCAAAAGATAATCGTGATACTAGCACGCCGAGACAGATGGTAAAAAATTTGCAAGTCTATATATTCGGCGATATTTTGAGCGACGACAAGAAAAAACTGCTGATTGATTGGATGAGCGACAATTCCATAACCGACACGCTTATCAAGGCAGAAACTCCGCAAGGTTGGAAAGTTATCGACAAGAGCGGTTCAGGCGATTATGGGGCGCGGAATGATATTGCCGTGATTTATCCGCCCAATCGCAAACCCATTGTCATGGCGATAATGTCGCGCCGCACGGAAAAAAATGCAAAATCTGACGACGCTATGATTGCGGAGGCGGCAAAACGAATTTTTGATAATTTAGTATTTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41532","NCBI_taxonomy_name":"Acidaminococcus fermentans","NCBI_taxonomy_id":"905"}}}},"ARO_accession":"3004359","ARO_id":"41531","ARO_name":"ACI-1","ARO_description":"A class A beta-lactamase described in Acidaminococcus fermentans. ACI-1 was the first description of a beta-lactamase enzyme in a gram-negative anaerobic cocci. Described by Galan et al 2000.","ARO_category":{"41530":{"category_aro_accession":"3004358","category_aro_cvterm_id":"41530","category_aro_name":"ACI beta-lactamase","category_aro_description":"A family of class A beta-lactamase enzymes described in the gram-negative cocci Acidaminococcus fermentans.","category_aro_class_name":"AMR Gene Family"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2875":{"model_id":"2875","model_name":"sul4","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4260":{"protein_sequence":{"accession":"WP_102607457.1","sequence":"MSTTLTSFKWGERTYIMGILNVTPDSFSGDGVMVEEDVIAKAVAQAKQFVADGADIIDIGGESTRPGSSPISAEEELARVLPVVQAVRQAVDVVISIDSYRASVAEAALAAGASWLNDVWGLRMDPDMAGLAAQAGCPIVLMHNRSKPKNIAQEKKLGGRFIGVKYDDLITDVKRELQESIDIALKAGVKESQIILDPGIGFGKTVEQSLQLLDQINQFKTMGFPILIGPSRKSFIGYTLDLPPDQRIEGTAATVAIGIDRGADVVRVHDVKAIVRVARMTDAIVRR"},"dna_sequence":{"accession":"NG_056174.1","fmin":"100","fmax":"964","strand":"+","sequence":"ATGTCAACCACACTAACCAGCTTCAAATGGGGTGAACGCACCTACATCATGGGCATCCTCAACGTCACTCCAGACAGCTTTTCTGGAGATGGCGTTATGGTTGAAGAAGATGTCATCGCCAAAGCGGTAGCCCAGGCCAAACAATTTGTAGCCGACGGCGCAGACATCATCGACATTGGCGGCGAGAGTACCCGCCCTGGCAGCTCACCTATAAGCGCAGAGGAAGAACTGGCGCGGGTGCTGCCGGTGGTGCAGGCCGTACGCCAGGCTGTGGACGTCGTTATTTCCATCGACAGCTACCGCGCTTCCGTGGCCGAAGCGGCCCTGGCGGCAGGCGCCAGCTGGCTCAACGACGTCTGGGGGCTGCGCATGGACCCGGACATGGCCGGCCTGGCAGCACAAGCCGGCTGCCCCATCGTCCTTATGCACAACCGCAGCAAACCAAAGAACATAGCGCAAGAAAAAAAGCTGGGCGGGCGCTTCATCGGGGTAAAATACGACGACCTCATCACCGACGTTAAACGTGAATTACAAGAAAGCATCGACATCGCCTTAAAAGCCGGCGTAAAAGAGTCCCAAATTATCCTGGATCCCGGCATCGGCTTCGGTAAAACCGTCGAGCAAAGTTTGCAACTGCTCGACCAGATTAATCAGTTCAAAACAATGGGATTTCCCATCTTAATAGGTCCGTCGCGCAAATCATTTATTGGCTATACGCTCGATTTGCCGCCAGACCAGCGCATAGAAGGAACGGCGGCCACCGTCGCCATTGGCATTGACCGAGGAGCCGACGTTGTGCGCGTCCATGACGTCAAAGCAATCGTTCGGGTCGCCCGTATGACAGATGCAATCGTGAGACGTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3004361","ARO_id":"41534","ARO_name":"sul4","ARO_description":"sul4 is a dihydropteroate synthase gene and mobile sulfonamide resistance gene shown to confer resistance when expressed in E. coli.","ARO_category":{"41402":{"category_aro_accession":"3004238","category_aro_cvterm_id":"41402","category_aro_name":"sulfonamide resistant sul","category_aro_description":"The sul genes encode forms of dihydropteroate synthase that confer resistance to sulfonamide.","category_aro_class_name":"AMR Gene Family"},"36421":{"category_aro_accession":"3000282","category_aro_cvterm_id":"36421","category_aro_name":"sulfonamide antibiotic","category_aro_description":"Sulfonamides are broad spectrum, synthetic antibiotics that contain the sulfonamide group. Sulfonamides inhibit dihydropteroate synthase, which catalyzes the conversion of p-aminobenzoic acid to dihydropteroic acid as part of the tetrahydrofolic acid biosynthetic pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor of many nucleotides and amino acids. Many sulfamides are taken with trimethoprim, an inhibitor of dihydrofolate reductase, also disturbing the trihydrofolic acid synthesis pathway.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2876":{"model_id":"2876","model_name":"OXA-436","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4261":{"protein_sequence":{"accession":"ARX76025.1","sequence":"MRALALSAVLMVTTMIGMPAVAKEWQENKSWNAHFSEHKTQGVVVLWNENTQQGFTNDLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIAAWNRDHDLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNLDSFWLDGGIRISATQQIAFLRKLYHNKLHVSERSQRIVKQAMLTEANADYIIRAKTGYSVRIEPKIGWWVGWIELDDNVWFFATNMDMPTAEGLGLRQTITKAVLKQEKIIP"},"dna_sequence":{"accession":"KY863418.1","fmin":"140925","fmax":"141723","strand":"+","sequence":"ATGCGTGCGTTAGCCTTATCGGCTGTGTTGATGGTGACAACGATGATTGGCATGCCTGCGGTGGCAAAGGAGTGGCAAGAGAACAAGAGTTGGAATGCTCACTTTAGCGAACATAAAACCCAAGGCGTGGTTGTGCTCTGGAACGAGAATACACAGCAGGGTTTTACCAACGATCTTAAACGGGCAAACCAAGCATTTTTACCTGCATCGACCTTTAAGATCCCAAACAGTTTAATTGCCTTGGACTTAGGTGTGGTTAAGGATGAGCATCAAGTCTTTAAATGGGATGGACAGACGCGAGATATCGCCGCGTGGAATCGCGACCATGACTTAATCACCGCGATGAAGTATTCGGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCCCGTATGAGTAAAATGTTGCACGCCTTCGATTATGGTAATGAGGATATCTCGGGCAATTTGGACAGTTTTTGGCTCGATGGTGGTATTCGCATTTCGGCTACCCAGCAAATCGCTTTTTTACGCAAGCTGTACCACAACAAGTTGCACGTTTCTGAGCGTAGTCAGCGCATCGTTAAACAAGCCATGCTGACCGAGGCAAATGCCGACTATATCATCCGGGCGAAAACTGGCTATTCGGTCAGAATTGAACCGAAAATCGGTTGGTGGGTTGGCTGGATCGAACTGGATGACAATGTGTGGTTCTTCGCGACAAATATGGATATGCCCACCGCTGAGGGCTTAGGGTTGCGTCAAACCATTACGAAAGCAGTGCTGAAACAGGAAAAAATTATTCCTTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36926","NCBI_taxonomy_name":"Enterobacter asburiae","NCBI_taxonomy_id":"61645"}}}},"ARO_accession":"3003128","ARO_id":"39705","ARO_name":"OXA-436","ARO_description":"An OXA-48-like plasmid-encoded beta-lactamase shown to confer resistance to carbapenems through hydrolysis. Identified in multiple Enterobacteriaceae isolates from several patients in Denmark. Beta-lactamase activity against carbapenems and penicillins but little to no activity against cephalosporin antibiotics. Described by Samuelsen et al. 2017.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2877":{"model_id":"2877","model_name":"OXA-535","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4262":{"protein_sequence":{"accession":"AOQ26572.1","sequence":"MRALALSAVLMVTTMIGMPAVAKEWQENKSWNAHFSEHKTQGVVVLWNENTQQGFTNDLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIAAWNRDHDLITAMKYSVVPVYQGFARQIGEARMSKMLHAFDYGNEDISGNLDSFWLDGGIRISATQQIAFLRKLYHNKLHVSERSQRIVKQAMLTEANADYIIRAKTGYSVRIEPKIGWWVGWVELDDNVWFFATNMDMPTAEGLGLRQSITKAVLKQEKIIP"},"dna_sequence":{"accession":"KX828709.1","fmin":"0","fmax":"798","strand":"+","sequence":"ATGCGTGCGTTAGCCTTATCGGCTGTGTTGATGGTGACAACGATGATTGGCATGCCTGCGGTAGCGAAGGAGTGGCAAGAGAACAAGAGCTGGAATGCTCACTTTAGCGAACATAAAACCCAAGGCGTGGTTGTGCTCTGGAACGAGAATACACAGCAGGGTTTTACTAACGATCTTAAACGGGCAAACCAAGCATTTTTACCAGCATCGACCTTTAAGATCCCAAACAGTTTAATTGCCTTGGACTTAGGCGTGGTTAAGGATGAACATCAAGTCTTTAAATGGGATGGACAGACGCGTGATATCGCCGCGTGGAATCGTGACCATGATTTAATCACCGCGATGAAGTATTCGGTTGTGCCTGTTTATCAAGGATTTGCCCGCCAAATTGGCGAGGCACGTATGAGTAAAATGCTGCATGCCTTCGATTATGGCAATGAGGATATCTCGGGCAATTTAGACAGCTTTTGGCTCGATGGTGGTATTCGCATTTCGGCTACCCAGCAAATCGCTTTTTTACGCAAGCTCTACCACAACAAGCTGCACGTTTCTGAGCGTAGTCAGCGCATTGTCAAACAAGCCATGCTGACCGAGGCAAATGCTGACTATATCATCCGGGCGAAAACTGGCTATTCGGTCAGAATTGAACCGAAAATTGGTTGGTGGGTTGGCTGGGTCGAACTCGATGACAATGTGTGGTTCTTCGCGACTAATATGGATATGCCCACCGCTGAGGGCTTAGGGTTGCGTCAAAGCATTACGAAAGCAGTGCTGAAACAGGAAAAAATTATTCCTTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41536","NCBI_taxonomy_name":"Shewanella sp.","NCBI_taxonomy_id":"50422"}}}},"ARO_accession":"3004362","ARO_id":"41535","ARO_name":"OXA-535","ARO_description":"A chromosome-carried OXA-48-like beta-lactamase, OXA-535, identified in Shewanella spp. JAB-1. Likely the progenitor to the plasmid-carried OXA-436. Expression of OXA-535 in E. coli demonstrated carbapenem-hydrolyzing activity. Described by Jousset et al. 2017.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2879":{"model_id":"2879","model_name":"QepA3","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"900"}},"model_sequences":{"sequence":{"4267":{"protein_sequence":{"accession":"AEZ36150.1","sequence":"MSATLHDTAADRRKATRREWIGLAVVALPCLVYAMDLTVLNLALPVLSRELQPSSAQLLWILDIYGFFVAGFLITMGTLGDRIGRRRLLLIGAAFFAFASVLAALADTAALLIAARALLGLAGATIAPSTMALVRNMFHDPRQRQFAIGVWIAAFSLGSAIGPLVGGVLLEFFHWGAVFWLNVPVMLLTLALGPRFLPEYRDPDAGHLDLASVLLSLAAVLLTIYGLKQLAEHGEGLASMAALLAGLAVGALFLRRQGHIAYPLLDLRLFAHALFRAALAAYALAALAMFGVYIFMTQYLQLVLGLSPLQAGLATLPCSLCFVIGSLLSPQLAARWPAARILVVGLSAAAFGFAVLGLGQGLWWLVPATIVKGLGLAPVFTIGNEIIITSAPSERAGAASALSETVSEFSGALGIALFGSVGLVVYRQALTSAALPGLPADALQTAGASLGGAVHLADTLPAWQGAALLAAARAGFTDALQATAWAGAVLVLVAAGLVARLLRKRPALASG"},"dna_sequence":{"accession":"JQ064560.1","fmin":"0","fmax":"1536","strand":"+","sequence":"ATGTCCGCCACGCTCCACGACACCGCAGCGGATCGTCGGAAGGCCACCCGCCGCGAATGGATCGGCCTGGCCGTGGTCGCCCTGCCGTGCCTGGTCTACGCCATGGACCTCACGGTGCTGAACCTGGCGCTGCCGGTGCTCAGCCGTGAACTGCAGCCCTCCAGCGCCCAGCTTCTCTGGATCCTGGACATCTACGGCTTCTTCGTCGCCGGCTTCCTGATCACCATGGGCACGCTGGGCGACCGCATCGGCCGGCGCCGGCTGTTGTTGATCGGCGCGGCGTTCTTCGCATTCGCCTCGGTGCTCGCGGCGCTGGCCGATACCGCCGCGCTGTTGATCGCGGCGCGCGCCTTGCTCGGCCTGGCCGGCGCCACCATCGCGCCGTCCACCATGGCGCTGGTCCGCAACATGTTCCACGACCCGCGCCAGCGCCAGTTCGCCATCGGCGTGTGGATCGCCGCGTTTTCGCTGGGCAGCGCGATCGGTCCGCTGGTCGGCGGCGTGTTGCTGGAGTTCTTCCACTGGGGCGCCGTGTTCTGGCTCAACGTGCCGGTGATGCTGCTGACGCTGGCGCTCGGCCCTCGCTTCCTGCCCGAGTATCGTGATCCGGACGCGGGGCACCTGGACCTGGCCAGCGTGCTGCTGTCGCTGGCGGCGGTGCTGCTGACGATCTACGGGCTCAAGCAGTTGGCCGAGCATGGAGAGGGCCTCGCCTCGATGGCTGCGCTGCTGGCCGGGCTGGCGGTCGGGGCGCTGTTCCTGCGCCGCCAGGGCCACATCGCCTACCCGCTGCTGGACCTGCGGCTGTTCGCGCACGCGCTGTTCCGCGCGGCGCTGGCGGCGTATGCGCTGGCCGCGCTGGCCATGTTCGGCGTCTACATCTTCATGACGCAGTACCTGCAGCTCGTGCTGGGGCTGTCGCCGCTGCAGGCCGGGCTGGCCACGCTGCCCTGCTCCCTGTGCTTCGTCATCGGTTCGCTGTTGTCGCCGCAGCTCGCGGCGCGCTGGCCGGCGGCGCGCATCCTCGTCGTGGGCCTGTCGGCAGCGGCGTTCGGCTTCGCCGTGCTGGGGCTGGGGCAGGGCCTGTGGTGGCTGGTGCCGGCCACGATCGTCAAGGGCCTGGGCCTGGCGCCGGTGTTCACCATCGGCAACGAGATCATCATCACCAGCGCGCCGTCCGAGCGCGCGGGCGCGGCCTCGGCCTTGTCGGAGACGGTGTCCGAATTCAGCGGCGCGCTGGGCATCGCGCTGTTCGGCAGCGTCGGCCTGGTGGTCTACCGGCAGGCGCTGACCAGCGCGGCGCTGCCCGGCCTGCCGGCCGATGCGCTGCAGACGGCCGGTGCCTCGCTCGGGGGCGCCGTGCACCTGGCCGACACCCTGCCGGCGTGGCAGGGCGCGGCCTTGCTGGCGGCCGCACGCGCGGGCTTCACCGATGCGCTGCAGGCCACGGCCTGGGCCGGCGCGGTGCTGGTGCTGGTGGCCGCTGGGCTGGTGGCGCGCCTGCTGCGCAAGCGCCCAGCGCTCGCATCTGGTTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36770","NCBI_taxonomy_name":"Enterobacter aerogenes","NCBI_taxonomy_id":"548"}}}},"ARO_accession":"3004378","ARO_id":"41552","ARO_name":"QepA3","ARO_description":"A plasmid-mediate quinolone efflux pump described in Enterobacter aerogenes and Escherichia coli. QepA3 confers resistance to fluoroquinolone antibiotics by expelling the antibiotic molecules from the cell. This is distinct from the usual chromosomal mutation mechanism of quinolone resistance. Described by Wang et al. 2017.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2880":{"model_id":"2880","model_name":"QepA4","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"900"}},"model_sequences":{"sequence":{"4268":{"protein_sequence":{"accession":"AQX36338.1","sequence":"MSATLHDTAADRRKATRREWIGLAVVALPCLVYAMDLTVLNLALPVLSRELQPSSAQLLWILDIYGFFVAGFLITMGTLGDRIGRRRLLLIGAALFAFASVLAALADTAALLIAARALLGLAGATIAPSTMALIRNMFHDPRQRQFAIGVWIAAFSLGSAIGPLVGGVLLEFFHWGAVFWLNVPVMLLTLALGPRFLPEYRDPDAGHLDLASVLLSLAAVLLTIYGLKQLAEHGAGLASMAALLAGLAVGALFLRRQGHIAYPLLDLRLFAHAPFRAALAAYALAALAMFGVYIFMTQYLQLVLGLSPLQAGLATLPWSLCFVIGSLLSPQLAARWPAARILVVGLSAAAFGFAVLGLGQGLWWLVPATIVMGLGLAPVFTIGNEIIITSAPSERAGAASALSETVSEFSGALGIALFGSVGLVVYRQALTSAALPGLPADALQAAGASLGGAVHLADTLPAWQGAALLAAARAGFTDALQATAWAGAVLVLVAAGLVARLLRKRPALASG"},"dna_sequence":{"accession":"KX686116.1","fmin":"0","fmax":"1536","strand":"+","sequence":"ATGTCCGCCACGCTCCACGACACCGCAGCGGATCGTCGGAAGGCCACCCGCCGCGAATGGATCGGCCTGGCCGTGGTCGCCCTGCCGTGCCTGGTCTACGCCATGGACCTCACGGTGCTGAACCTGGCGCTGCCGGTGCTCAGCCGTGAACTGCAGCCCTCCAGCGCCCAGCTTCTCTGGATCCTGGACATCTACGGCTTCTTCGTCGCCGGCTTCCTGATCACCATGGGCACGCTGGGCGACCGCATCGGCCGGCGCCGGCTGTTGTTGATCGGCGCGGCGTTATTCGCATTCGCCTCGGTGCTCGCGGCGCTGGCCGATACCGCCGCGCTGTTGATCGCGGCGCGCGCCTTGCTCGGCCTGGCCGGCGCCACCATCGCGCCGTCCACCATGGCGCTGATCCGCAACATGTTCCACGACCCGCGCCAGCGCCAGTTCGCCATCGGCGTGTGGATCGCCGCGTTTTCGCTGGGCAGCGCGATCGGTCCGCTGGTCGGCGGCGTGTTGCTGGAGTTCTTCCACTGGGGCGCCGTGTTCTGGCTCAACGTGCCGGTGATGCTGCTGACGCTGGCGCTCGGCCCTCGCTTCCTGCCCGAGTATCGTGATCCGGACGCGGGGCACCTGGACCTGGCCAGCGTGCTGCTGTCGCTGGCGGCGGTGCTGCTGACGATCTACGGGCTCAAGCAGTTGGCCGAGCATGGAGCGGGCCTCGCCTCGATGGCTGCGCTGCTGGCCGGGCTGGCGGTCGGGGCGCTGTTCCTGCGCCGCCAGGGCCACATCGCCTACCCGCTGCTGGACCTGCGGCTGTTCGCGCACGCGCCGTTCCGCGCGGCGCTGGCGGCGTATGCGCTGGCCGCGCTGGCCATGTTCGGCGTCTACATCTTCATGACGCAGTACCTGCAGCTCGTGCTGGGGCTGTCGCCGCTGCAGGCCGGGCTGGCCACGCTGCCCTGGTCCCTGTGCTTCGTCATCGGTTCGCTGTTGTCGCCGCAGCTCGCGGCGCGCTGGCCGGCGGCGCGCATCCTCGTCGTGGGCCTGTCGGCAGCGGCGTTCGGCTTCGCCGTGCTGGGGCTGGGGCAGGGCCTGTGGTGGCTGGTGCCGGCCACGATCGTCATGGGCCTGGGCCTGGCGCCGGTGTTCACCATCGGCAACGAGATCATCATCACCAGCGCGCCGTCCGAGCGCGCGGGCGCGGCCTCGGCCTTGTCGGAGACGGTGTCCGAATTCAGCGGCGCGCTGGGCATCGCGCTGTTCGGCAGCGTCGGCCTGGTGGTCTACCGGCAGGCGCTGACCAGCGCGGCGCTGCCCGGCCTGCCGGCCGATGCGCTGCAGGCGGCCGGTGCCTCGCTCGGGGGCGCCGTGCACCTGGCCGACACCCTGCCGGCGTGGCAGGGCGCGGCCTTGCTGGCGGCCGCACGCGCGGGCTTCACCGATGCGCTGCAGGCCACGGCCTGGGCCGGCGCGGTGCTGGTGCTGGTGGCCGCTGGGCTGGTGGCGCGCCTGCTGCGCAAGCGCCCAGCGCTCGCATCTGGTTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004379","ARO_id":"41553","ARO_name":"QepA4","ARO_description":"A plasmid-mediate quinolone efflux pump variant described in Escherichia coli. QepA4 confers resistance to quinolone and fluoroquinolone antibiotics by expulsion from the cell. Described by Manageiro et al. 2017.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2881":{"model_id":"2881","model_name":"tet(59)","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4269":{"protein_sequence":{"accession":"AMP42492.1","sequence":"MNKFAITALTITALDAMGIGLIMPVLPTLLREYVSAENLANHYGILLALYAIMQVFFAPLLGKWSDKFGRRPILLLSLAGAAVDYTLLALSSSLWMLYVGRLISGVTGATGAVAASVIADNTASQERTKWFGRLGAAFGIGLIAGPAIGGFTGQFSAHLPFIIAAILNALSFLVIMLIFKDNKIKNTEKNTTETAENSRPFLQVIKPVILLLFIFFMTQMIGQIPATTWVLFTEHRFQWGSMEVGLSLAGLGIMHALFQAFVAGAIAKKFNEKVTIIVGFVVDGAAFIILSLLTKGWMIYPTLILLAGGSIALPALQGLMSAQVNQTNQGKLQGVLVSLTNTTGVIGPLLFSFIFGQTLASWDGWIWMIGAIMYVLLIVFILSFYRSTKKIVKIAKLPAS"},"dna_sequence":{"accession":"KU736879.1","fmin":"22312","fmax":"23515","strand":"+","sequence":"ATGAATAAATTTGCGATCACCGCTTTAACGATCACCGCCCTAGATGCTATGGGGATCGGCTTGATCATGCCTGTATTGCCTACATTGTTACGTGAATACGTGTCGGCTGAAAATTTAGCAAATCATTACGGTATCCTGCTGGCACTGTATGCCATCATGCAGGTTTTTTTTGCTCCTCTACTTGGCAAATGGTCTGATAAATTCGGGCGCCGACCAATATTACTACTATCTCTTGCAGGCGCTGCTGTGGATTACACTTTGCTTGCATTATCTAGCTCACTTTGGATGCTATACGTTGGGCGATTAATTTCTGGAGTTACTGGCGCAACAGGTGCGGTCGCCGCTTCTGTTATTGCTGACAATACTGCTTCACAAGAGCGTACTAAGTGGTTTGGACGCTTAGGGGCGGCTTTTGGTATCGGGTTAATCGCTGGCCCTGCAATTGGCGGCTTTACAGGGCAATTCTCAGCTCACCTTCCTTTTATTATTGCTGCCATTTTAAATGCGCTCTCTTTTTTAGTTATTATGTTGATATTTAAAGATAATAAAATCAAAAATACTGAAAAAAACACCACAGAAACAGCAGAAAATTCGCGACCTTTCCTGCAAGTGATCAAGCCAGTCATACTATTGTTATTTATCTTTTTTATGACTCAAATGATAGGGCAAATTCCAGCAACGACATGGGTGTTATTTACGGAACATCGTTTTCAATGGGGCAGTATGGAGGTCGGCCTATCTTTAGCGGGGTTAGGCATCATGCATGCCTTGTTCCAAGCATTTGTAGCGGGCGCAATCGCCAAGAAATTCAATGAAAAAGTGACGATTATTGTGGGCTTTGTTGTTGATGGAGCAGCATTCATTATTTTGTCATTATTGACAAAGGGTTGGATGATTTACCCTACATTAATCTTACTCGCCGGCGGCAGTATTGCGCTACCAGCCTTACAGGGGTTAATGTCAGCTCAAGTCAATCAAACTAACCAAGGTAAGCTACAAGGCGTTCTAGTCAGCTTAACCAATACGACGGGGGTGATCGGCCCATTATTATTTAGCTTTATTTTTGGTCAAACACTGGCAAGTTGGGATGGCTGGATATGGATGATTGGTGCGATAATGTATGTTTTATTGATTGTATTTATTTTATCTTTTTATAGAAGCACCAAAAAGATAGTTAAAATAGCGAAGCTACCAGCGAGCTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41633","NCBI_taxonomy_name":"uncultured bacterium IN-14","NCBI_taxonomy_id":"1805592"}}}},"ARO_accession":"3004441","ARO_id":"41632","ARO_name":"tet(59)","ARO_description":"Tet(59) is a chromosome-encoded tetracycline efflux pump described from a Chinese pig manure sample.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2882":{"model_id":"2882","model_name":"tet(W\/N\/W)","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4270":{"protein_sequence":{"accession":"AMP42147.1","sequence":"MKIINIGILAHVDAGKTTLTESLLYASGAISEPGSVEKGTTRTDTMFLERQRGITIQAAVTSFQWHRCKVNIVDTPGHMDFLAEVYRSLAVLDGAILVISAKDGVQAQTRILFHALRKMNIPTVIFINKIDQAGVDLQSVYQSVRDKLSADIIIKQTVSLSPEIVLEENTDIEAWDAVIENNDELLEKYIAGEPISREKLAREEQQRVQDASLFPVYHGSAKNGLGIQPLMDAVTGLFQPIGEQGGAALCGSVFKVEYTDCGQRLVYLRLYSGTLRLRDTVALAGREKLKITEMRIPSKGEIVRTDTAHKGEIVILPSDSLRLNDILGDKTQLPREMWSDVPFPMLRTTITPKTAEQRDRLLDALTQIADTDPLLHYEVDSITHEIILSFLGRVQLEVVSALLSEKYKLETVVKEPTVIYMERPLKAASHTIHIEVPPNPFWASIGLSVTPLPLGSGVQYESRVSLGYLNQSFQNAVRDGIRYGLEQGLFGWNVTDCKICFEYGLYYSPVSTPADFRSLAPIVLEQALKESGTQLLEPYLSFTLYAPREYLSRAYHDAPKYCATIETVQVKKDEVVFTGEIPARCIQAYRTDLAFYTNGRSVCLTELKGYQATVGEPIIQPRRPNSRLDKVRHMFSKIP"},"dna_sequence":{"accession":"KU736867.1","fmin":"19653","fmax":"21573","strand":"+","sequence":"ATGAAAATAATCAATATTGGAATTCTTGCCCATGTAGACGCTGGAAAGACGACCTTGACGGAGAGCCTGCTATATGCCAGCGGAGCCATTTCAGAACCGGGGAGCGTCGAAAAAGGGACAACGAGGACGGACACCATGTTTTTGGAGCGGCAGCGTGGGATTACCATTCAAGCGGCAGTCACTTCCTTCCAGTGGCACAGATGTAAAGTTAACATTGTGGATACGCCCGGCCACATGGATTTTTTGGCGGAGGTGTACCGCTCTTTGGCTGTTTTAGATGGGGCCATCTTGGTGATCTCCGCTAAAGATGGCGTGCAGGCCCAGACCCGTATTCTGTTCCATGCCCTGCGGAAAATGAACATTCCCACCGTTATCTTTATCAACAAGATCGACCAGGCTGGCGTTGATTTGCAGAGCGTATATCAGTCTGTTCGGGATAAGCTCTCCGCCGATATTATCATCAAGCAGACGGTGTCGCTGTCCCCGGAAATAGTCCTGGAGGAAAATACCGACATAGAAGCATGGGATGCGGTCATCGAAAATAACGATGAATTATTGGAAAAGTATATCGCAGGAGAACCAATCAGCCGGGAAAAACTTGCGCGGGAGGAACAGCAGCGGGTTCAAGACGCCTCCCTGTTCCCAGTCTATCATGGCAGCGCCAAAAATGGCCTTGGCATTCAACCGTTGATGGATGCGGTGACAGGGCTGTTCCAACCGATTGGGGAACAGGGGGGCGCCGCCCTATGCGGCAGCGTTTTCAAGGTGGAGTATACAGATTGCGGCCAGAGGCTTGTCTATCTGCGGCTATACAGCGGAACGCTGCGTCTGCGGGATACGGTGGCCCTAGCCGGGAGAGAAAAGCTGAAAATCACAGAGATGCGTATTCCATCCAAAGGGGAGATTGTTCGGACAGATACCGCCCATAAGGGCGAAATTGTCATCCTTCCCAGCGACAGCTTGAGATTAAACGATATATTGGGGGACAAAACCCAACTTCCTCGTGAAATGTGGAGTGATGTTCCCTTCCCTATGCTGCGGACGACGATTACGCCAAAAACGGCAGAGCAAAGAGACCGGTTGCTGGACGCTCTTACGCAAATTGCGGATACTGACCCGCTTTTGCACTACGAGGTGGATTCCATCACCCATGAGATCATTCTTTCTTTTTTGGGCCGGGTGCAGTTGGAGGTTGTTTCCGCTTTGCTGTCGGAAAAATACAAGCTTGAAACAGTGGTAAAGGAACCCACCGTCATTTATATGGAGCGGCCGCTCAAAGCAGCCAGCCACACCATCCATATCGAGGTGCCGCCCAACCCGTTTTGGGCATCCATCGGACTGTCTGTTACACCACTCCCGCTTGGCTCCGGTGTACAATACGAGAGCCGGGTTTCGCTGGGATACTTGAACCAGAGTTTTCAAAACGCTGTCAGGGATGGTATCCGTTACGGGCTGGAGCAGGGCTTGTTCGGCTGGAACGTAACGGACTGTAAGATTTGCTTTGAATACGGGCTTTATTACAGTCCGGTCAGCACGCCGGCGGACTTCCGCTCATTGGCCCCGATTGTATTGGAACAGGCATTGAAGGAATCAGGGACGCAACTGCTGGAACCTTATCTCTCCTTCACCCTCTATGCGCCCCGGGAATATCTTTCCAGGGCTTATCATGATGCACCGAAATACTGTGCCACCATCGAAACGGTCCAGGTAAAAAAGGATGAAGTTGTCTTTACTGGCGAGATTCCCGCCCGTTGCATACAGGCATACCGTACTGATTTGGCCTTTTACACCAACGGGCGGAGTGTGTGCCTGACGGAACTGAAAGGGTATCAGGCCACTGTCGGCGAGCCAATCATCCAGCCCCGTCGTCCAAACAGCCGTTTGGATAAGGTGCGCCATATGTTCAGTAAGATTCCTTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41635","NCBI_taxonomy_name":"uncultured bacterium IN-02","NCBI_taxonomy_id":"1805580"}}}},"ARO_accession":"3004442","ARO_id":"41634","ARO_name":"tet(W\/N\/W)","ARO_description":"tet(W\/N\/W) is a mosaic tetracycline resistance gene and ribosomal protection protein.","ARO_category":{"35921":{"category_aro_accession":"0000002","category_aro_cvterm_id":"35921","category_aro_name":"tetracycline-resistant ribosomal protection protein","category_aro_description":"A family of proteins known to bind to the 30S ribosomal subunit. This interaction prevents tetracycline and tetracycline derivatives from inhibiting ribosomal function. Thus, these proteins confer elevated resistance to tetracycline derivatives as a ribosomal protection protein.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2884":{"model_id":"2884","model_name":"RSA-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4271":{"protein_sequence":{"accession":"AUW34365.1","sequence":"MGMQLARSTILTVLLCLPIAVTATTKEEIQKIERQRNLTVGIALVDDGGTLLFGHRETQRFAMCSTFKLPLAAATLKQIESGKWSAAERLSYSAGQLDAYAPAAKRYLPTGYITVAEANQASVQLSDNTAANLLLDKLGGPSQLTSMFRSLGDSVSRLDRREPDLNTNVSGDPRDTTTPGAMARIVAKLVYGNYLSTAGREQLQRLLIGNNTGDSRIRAGIASGWTTGDKTGSCPNGGRNDAAFLVSPDGRRFALTVYLNAPSLDDKARNEVVATVARLAVESIR"},"dna_sequence":{"accession":"MG739510.1","fmin":"0","fmax":"858","strand":"+","sequence":"ATGGGAATGCAACTAGCTAGGTCGACGATCCTCACTGTTTTGCTCTGTCTGCCGATTGCTGTAACGGCTACGACTAAGGAGGAGATCCAAAAGATTGAGCGTCAGCGCAACCTCACGGTTGGCATCGCTCTTGTAGACGACGGGGGAACACTCCTGTTCGGTCATCGCGAAACGCAGCGCTTCGCCATGTGCTCGACATTTAAGTTGCCGCTGGCGGCTGCAACGCTTAAGCAAATCGAGAGCGGAAAGTGGTCTGCCGCCGAGCGGCTGAGCTATAGCGCTGGCCAATTAGATGCCTACGCGCCAGCTGCCAAGAGATATCTACCTACAGGCTACATCACGGTAGCTGAGGCTAACCAAGCCTCGGTCCAGCTCAGCGATAATACTGCTGCCAACTTGCTGCTTGACAAACTCGGAGGGCCATCGCAGCTCACATCCATGTTTCGCTCCCTCGGCGATTCCGTGAGTCGCCTGGATAGAAGAGAACCCGATTTGAACACCAACGTTTCGGGTGACCCGCGCGACACGACTACGCCGGGCGCGATGGCACGCATTGTCGCAAAGCTGGTATATGGAAACTATCTAAGTACAGCAGGCCGAGAGCAATTGCAGCGGCTTCTCATTGGCAATAACACAGGCGACTCGAGGATTCGCGCTGGAATCGCATCTGGCTGGACGACTGGCGACAAAACGGGTTCCTGCCCCAATGGCGGACGAAATGACGCTGCGTTCCTGGTAAGCCCTGATGGCCGCAGATTTGCGCTGACAGTGTACCTGAACGCCCCATCGCTTGACGACAAGGCACGGAACGAGGTGGTCGCTACGGTAGCTCGCTTGGCGGTTGAGAGTATCCGCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3004444","ARO_id":"41637","ARO_name":"RSA-1","ARO_description":"RSA-1 is a class A beta-lactamase resistance enzyme identified from a functional metagenomic study of contaminated river sediments.","ARO_category":{"41636":{"category_aro_accession":"3004443","category_aro_cvterm_id":"41636","category_aro_name":"RSA beta-lactamase","category_aro_description":"A family of class A beta-lactamase enzymes, RSA beta-lactamases show carbapenemase and cephalosporinase activity","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2885":{"model_id":"2885","model_name":"RSA-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4272":{"protein_sequence":{"accession":"AUW34359.1","sequence":"MIKKIISGACLVLLAGCVLGVKPAGKETGFMIDSGRFAGMDGCAIVFDARMGKIAGVYGEKRCKERVTACSTFKVPLALMAFDSGVLSDESTVLKWDGVQWPFDSWNQDQTAASWLRNSVVWYSQRLTPMLGLEKIKAYLKAFDYGNQDFSSGLTSAWLTITKSDTNPDKGSLKISAYEELEFFRRFWRGALPVSGAAVEKTKKMIYLETSPGGYALHGKTGSGYLDGLTGDFGWFAGHVEGKGREYFVVTAVTRNGNAADARIPGLVAKELAKNILKDNSVW"},"dna_sequence":{"accession":"MG739504.1","fmin":"0","fmax":"852","strand":"+","sequence":"ATGATTAAAAAGATTATTTCTGGAGCTTGCTTGGTTTTGCTGGCTGGGTGCGTGTTGGGTGTGAAGCCGGCGGGGAAAGAGACGGGGTTTATGATTGATTCTGGACGTTTTGCCGGGATGGATGGCTGCGCTATTGTTTTTGATGCGCGGATGGGAAAAATTGCGGGGGTTTATGGGGAGAAGCGGTGCAAGGAACGGGTTACGGCTTGTTCTACGTTCAAGGTGCCGCTGGCTTTGATGGCTTTTGATTCTGGGGTGCTGAGCGACGAGAGCACGGTGCTGAAGTGGGATGGAGTGCAGTGGCCGTTCGACTCCTGGAACCAGGACCAGACGGCGGCCTCGTGGCTGCGCAATTCGGTGGTGTGGTATTCGCAGCGGCTGACTCCAATGCTGGGCTTGGAAAAGATAAAGGCTTACCTAAAGGCTTTCGATTACGGGAATCAGGACTTTTCTTCCGGCCTGACCAGCGCTTGGCTTACCATCACCAAGAGCGATACGAATCCGGATAAGGGCAGTCTTAAAATCTCAGCCTACGAGGAACTGGAGTTCTTTAGACGGTTTTGGCGTGGCGCGCTCCCGGTGAGCGGGGCCGCGGTGGAGAAGACTAAAAAAATGATTTACCTGGAGACCTCTCCCGGCGGTTATGCGCTGCACGGCAAGACCGGCTCCGGCTATCTCGACGGATTGACCGGGGATTTCGGCTGGTTCGCCGGCCACGTAGAGGGCAAAGGCCGGGAGTATTTTGTTGTAACGGCCGTCACGCGGAATGGGAATGCCGCCGACGCACGCATCCCCGGCCTGGTGGCGAAGGAACTCGCCAAGAACATCCTTAAAGATAATTCGGTCTGGTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3004445","ARO_id":"41638","ARO_name":"RSA-2","ARO_description":"RSA-2 is a class A beta-lactamase enzyme identified from a functional metagenomics study of contaminated river sediments in India.","ARO_category":{"41636":{"category_aro_accession":"3004443","category_aro_cvterm_id":"41636","category_aro_name":"RSA beta-lactamase","category_aro_description":"A family of class A beta-lactamase enzymes, RSA beta-lactamases show carbapenemase and cephalosporinase activity","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2886":{"model_id":"2886","model_name":"Haemophilus influenzae PBP3 conferring resistance to beta-lactam antibiotics","model_type":"protein variant model","model_type_id":"40293","model_description":"The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and\/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: \"strict\" and \"loose\". A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"},"snp":{"param_type":"single resistance variant","param_description":"A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences.","param_type_id":"36301","param_value":{"8321":"D350N","8322":"S357N","8323":"S385T","8324":"L389F","8325":"V562L"},"clinical":{"8321":"D350N","8322":"S357N","8323":"S385T","8324":"L389F","8325":"V562L"}}},"model_sequences":{"sequence":{"4273":{"protein_sequence":{"accession":"NP_439290","sequence":"MVKFNSSRKSGKSKKTIRKLTAPETVKQNKPQKVFEKCFMRGRYMLSTVLILLGLCALVARAAYVQSINADTLSNEADKRSLRKDEVLSVRGSILDRNGQLLSVSVPMSAIVADPKTMLKENSLADKERIAALAEELGMTENDLVKKIEKNSKSGYLYLARQVELSKANYIRRLKIKGIILETEHRRFYPRVEEAAHVVGYTDIDGNGIEGIEKSFNSLLVGKDGSRTVRKDKRGNIVAHISDEKKYDAQDVTLSIDEKLQSMVYREIKKAVSENNAESGTAVLVDVRTGEVLAMATAPSYNPNNRVGVKSELMRNRAITDTFEPGSTVKPFVVLTALQRGVVKRDEIIDTTSFKLSGKEIVDVAPRAQQTLDEILMNSSNRGVSRLALRMPPSALMETYQNAGLSKPTDLGLIGEQVGILNANRKRWADIERATVAYGYGITATPLQIARAYATLGSFGVYRPLSITKVDPPVIGKRVFSEKITKDIVGILEKVAIKNKRAMVEGYRVGVKTGTARKIENGHYVNKYVAFTAGIAPISDPRYALVVLINDPKAGEYYGGAVSAPVFSNIMGYALRANAIPQDAEAAENTTTKSAKRIVYIGEHKNQKVN"},"dna_sequence":{"accession":"NC_000907.1","fmin":"1197839","fmax":"1199672","strand":"+","sequence":"ATGGTGAAATTTAATTCCTCGCGTAAATCAGGTAAGTCAAAAAAAACAATTAGAAAATTGACCGCACCTGAAACTGTAAAGCAAAACAAGCCTCAAAAGGTGTTTGAAAAATGCTTTATGCGTGGACGTTATATGCTTTCTACGGTTCTTATTTTACTTGGCCTGTGTGCTTTAGTCGCACGAGCAGCTTATGTTCAATCTATTAATGCCGATACGTTATCGAATGAAGCGGATAAGCGTTCTTTGCGTAAAGATGAAGTATTATCGGTGCGTGGTTCTATTTTAGATCGTAATGGTCAGCTTTTATCTGTAAGCGTGCCGATGAGCGCGATTGTGGCAGATCCAAAAACGATGTTGAAGGAAAATTCGCTTGCGGATAAAGAACGAATTGCAGCTTTAGCCGAAGAATTAGGTATGACTGAAAATGATTTAGTGAAAAAAATTGAGAAAAATTCTAAATCTGGTTATTTGTATTTAGCACGTCAAGTTGAATTAAGTAAAGCTAACTATATTCGTAGATTAAAAATTAAGGGTATTATTTTAGAAACAGAGCATCGCCGTTTTTATCCTCGTGTAGAAGAAGCTGCACACGTGGTGGGTTATACGGATATTGATGGAAATGGTATTGAAGGCATTGAGAAAAGTTTTAATTCCCTGCTTGTTGGTAAAGACGGTTCACGTACTGTTCGTAAAGATAAACGTGGGAATATTGTTGCACATATCTCCGATGAGAAAAAATATGATGCACAAGATGTTACCTTAAGTATCGATGAAAAATTGCAATCTATGGTGTATCGTGAGATTAAAAAGGCGGTGTCTGAGAATAATGCTGAGTCTGGTACTGCGGTGTTAGTTGATGTTCGAACAGGGGAAGTGTTAGCTATGGCGACTGCGCCCTCTTATAATCCAAACAACCGTGTCGGCGTGAAATCAGAGTTAATGCGTAACCGTGCAATTACCGATACTTTTGAGCCAGGTTCTACGGTAAAACCTTTCGTTGTTTTAACCGCACTTCAACGAGGTGTAGTTAAACGAGATGAAATTATTGATACTACGTCCTTTAAATTAAGCGGTAAAGAAATTGTGGACGTTGCACCACGTGCTCAGCAAACTTTAGACGAGATTTTAATGAACTCTAGTAACCGTGGTGTAAGTCGTCTTGCATTACGTATGCCACCTAGTGCATTAATGGAAACTTATCAAAATGCAGGTTTAAGTAAACCGACAGATTTAGGCTTGATCGGAGAGCAAGTTGGGATTTTGAATGCAAATCGTAAACGCTGGGCAGATATTGAGCGTGCAACAGTCGCTTATGGTTATGGTATTACTGCGACACCTTTACAAATTGCTCGTGCCTATGCAACCCTTGGTAGTTTCGGTGTTTATCGTCCGCTTTCTATCACTAAAGTTGATCCGCCAGTTATTGGGAAACGGGTTTTCTCTGAAAAAATAACTAAAGATATTGTGGGAATTTTAGAGAAAGTAGCAATTAAAAATAAACGCGCAATGGTGGAAGGCTACCGTGTCGGCGTAAAAACAGGTACGGCACGTAAGATTGAAAATGGACATTATGTAAATAAGTATGTGGCATTTACTGCGGGTATTGCACCAATTAGTGATCCTCGTTATGCATTAGTGGTTTTGATCAATGATCCAAAAGCAGGAGAATATTATGGTGGTGCGGTTTCTGCCCCTGTATTCTCTAACATTATGGGCTATGCGTTACGTGCAAATGCTATTCCGCAAGATGCTGAAGCAGCTGAAAACACAACAACGAAAAGTGCAAAACGTATTGTTTATATTGGCGAACACAAGAATCAAAAAGTGAATTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41640","NCBI_taxonomy_name":"Haemophilus influenzae Rd KW20","NCBI_taxonomy_id":"71421"}}}},"ARO_accession":"3004446","ARO_id":"41639","ARO_name":"Haemophilus influenzae PBP3 conferring resistance to beta-lactam antibiotics","ARO_description":"PBP3 is a penicillin-binding protein and beta-lactam resistance enzyme encoded by the ftsI gene in Haemophilus influenzae. Mutations in ftsI confer resistance to beta-lactam antibiotics.","ARO_category":{"40661":{"category_aro_accession":"3003938","category_aro_cvterm_id":"40661","category_aro_name":"Penicillin-binding protein mutations conferring resistance to beta-lactam antibiotics","category_aro_description":"Mutations in PBP transpeptidases that change the affinity for penicillin thereby conferring resistance to penicillin antibiotics","category_aro_class_name":"AMR Gene Family"},"35927":{"category_aro_accession":"0000008","category_aro_cvterm_id":"35927","category_aro_name":"cefoxitin","category_aro_description":"Cefoxitin is a cephamycin antibiotic often grouped with the second generation cephalosporins. Cefoxitin is bactericidal and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. Cefoxitin's 7-alpha-methoxy group and 3' leaving group make it a poor substrate for most beta-lactamases.","category_aro_class_name":"Antibiotic"},"35930":{"category_aro_accession":"0000011","category_aro_cvterm_id":"35930","category_aro_name":"cloxacillin","category_aro_description":"Cloxacillin is a semisynthetic, isoxazolyl penicillin derivative in the beta-lactam class of antibiotics. It interferes with peptidogylcan synthesis and is commonly used for treating penicillin-resistant Staphylococcus aureus infections.","category_aro_class_name":"Antibiotic"},"35934":{"category_aro_accession":"0000015","category_aro_cvterm_id":"35934","category_aro_name":"methicillin","category_aro_description":"Derived from penicillin to combat penicillin-resistance, methicillin is insensitive to beta-lactamases (also known as penicillinases) secreted by many penicillin-resistant bacteria. Methicillin is bactericidal, and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Antibiotic"},"35961":{"category_aro_accession":"0000043","category_aro_cvterm_id":"35961","category_aro_name":"carbenicillin","category_aro_description":"Carbenicillin is a semi-synthetic antibiotic belonging to the carboxypenicillin subgroup of the penicillins. It has gram-negative coverage which includes Pseudomonas aeruginosa but limited gram-positive coverage. The carboxypenicillins are susceptible to degradation by beta-lactamase enzymes. Carbenicillin antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Antibiotic"},"35971":{"category_aro_accession":"0000054","category_aro_cvterm_id":"35971","category_aro_name":"penicillin","category_aro_description":"Penicillin (sometimes abbreviated PCN) is a beta-lactam antibiotic used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms. It works by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Antibiotic"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35975":{"category_aro_accession":"0000058","category_aro_cvterm_id":"35975","category_aro_name":"cefazolin","category_aro_description":"Cefazolin (INN), also known as cefazoline or cephazolin, is a first generation cephalosporin antibiotic. It is administered parenterally, and is active against a broad spectrum of bacteria.","category_aro_class_name":"Antibiotic"},"35976":{"category_aro_accession":"0000059","category_aro_cvterm_id":"35976","category_aro_name":"cefepime","category_aro_description":"Cefepime (INN) is a fourth-generation cephalosporin antibiotic developed in 1994. It contains an aminothiazolyl group that decreases its affinity with beta-lactamases. Cefepime shows high binding affinity with penicillin-binding proteins and has an extended spectrum of activity against Gram-positive and Gram-negative bacteria, with greater activity against both Gram-negative and Gram-positive organisms than third-generation agents.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35978":{"category_aro_accession":"0000061","category_aro_cvterm_id":"35978","category_aro_name":"ceftobiprole","category_aro_description":"Ceftobiprole (Zeftera\/Zevtera) is a next generation (5th generation) cephalosporin antibiotic with activity against methicillin-resistant Staphylococcus aureus, penicillin-resistant Streptococcus pneumoniae, Pseudomonas aeruginosa, and Enterococci. Ceftobiprole inhibits transpeptidases essential to building cell walls, and is a poor substrate for most beta-lactamases.","category_aro_class_name":"Antibiotic"},"35979":{"category_aro_accession":"0000062","category_aro_cvterm_id":"35979","category_aro_name":"ceftriaxone","category_aro_description":"Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"35980":{"category_aro_accession":"0000063","category_aro_cvterm_id":"35980","category_aro_name":"cefuroxime","category_aro_description":"Cefuroxime is a second-generation cephalosporin antibiotic with increased stability with beta-lactamases than first-generation cephalosporins. Cefuroxime is active against Gram-positive organisms but less active against methicillin-resistant strains.","category_aro_class_name":"Antibiotic"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"35987":{"category_aro_accession":"0000070","category_aro_cvterm_id":"35987","category_aro_name":"ertapenem","category_aro_description":"Ertapenem is a carbapenem antibiotic and is highly resistant to beta-lactamases like other carbapenems. It inhibits bacterial cell wall synthesis.","category_aro_class_name":"Antibiotic"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"35995":{"category_aro_accession":"0000078","category_aro_cvterm_id":"35995","category_aro_name":"piperacillin","category_aro_description":"Piperacillin is an acetylureidopenicillin and has an extended spectrum of targets relative to other beta-lactam antibiotics. It inhibits cell wall synthesis in bacteria, and is usually taken with the beta-lactamase inhibitor tazobactam to overcome penicillin-resistant bacteria.","category_aro_class_name":"Antibiotic"},"36309":{"category_aro_accession":"3000170","category_aro_cvterm_id":"36309","category_aro_name":"imipenem","category_aro_description":"Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.","category_aro_class_name":"Antibiotic"},"36689":{"category_aro_accession":"3000550","category_aro_cvterm_id":"36689","category_aro_name":"aztreonam","category_aro_description":"Aztreonam was the first monobactam discovered, and is greatly effective against Gram-negative bacteria while inactive against Gram-positive bacteria. Artreonam is a poor substrate for beta-lactamases, and may even act as an inhibitor. In Gram-negative bacteria, Aztreonam interferes with filamentation, inhibiting cell division and leading to cell death.","category_aro_class_name":"Antibiotic"},"36976":{"category_aro_accession":"3000632","category_aro_cvterm_id":"36976","category_aro_name":"benzylpenicillin","category_aro_description":"Benzylpenicillin, commonly referred to as penicillin G, is effective against both Gram-positive and Gram-negative bacteria. It is unstable in acid.","category_aro_class_name":"Antibiotic"},"36977":{"category_aro_accession":"3000633","category_aro_cvterm_id":"36977","category_aro_name":"phenoxymethylpenicillin","category_aro_description":"Phenoxymethylpenicillin, or penicillin V, is a penicillin derivative that is acid stable but less active than benzylpenicillin (penicillin G).","category_aro_class_name":"Antibiotic"},"36978":{"category_aro_accession":"3000634","category_aro_cvterm_id":"36978","category_aro_name":"propicillin","category_aro_description":"Propicillin is an orally taken penicillin derivative that has high absorption but poor activity.","category_aro_class_name":"Antibiotic"},"36979":{"category_aro_accession":"3000635","category_aro_cvterm_id":"36979","category_aro_name":"dicloxacillin","category_aro_description":"Dicloxacillin is a penicillin derivative that has an extra chlorine atom in comparison to cloxacillin. While more active than cloxacillin, its high affinity for serum protein reduces its activity in human serum in vitro.","category_aro_class_name":"Antibiotic"},"36980":{"category_aro_accession":"3000636","category_aro_cvterm_id":"36980","category_aro_name":"flucloxacillin","category_aro_description":"Flucloxacillin is similar to cloxacillin, with an extra additional fluorine atom.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"36982":{"category_aro_accession":"3000638","category_aro_cvterm_id":"36982","category_aro_name":"azlocillin","category_aro_description":"Azlocillin is a semisynthetic derivative of penicillin that is notably active against Ps. aeruginosa and other Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36983":{"category_aro_accession":"3000639","category_aro_cvterm_id":"36983","category_aro_name":"mezlocillin","category_aro_description":"Mezlocillin is a penicillin derivative taken parenterally.","category_aro_class_name":"Antibiotic"},"36984":{"category_aro_accession":"3000640","category_aro_cvterm_id":"36984","category_aro_name":"doripenem","category_aro_description":"Doripenem is a carbapenem with a broad range of activity against Gram-positive and Gram-negative bacteria, and along with meropenem, it is the most active beta-lactam antibiotic against Pseudomonas aeruginosa. It inhibits bacterial cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36985":{"category_aro_accession":"3000641","category_aro_cvterm_id":"36985","category_aro_name":"cefalexin","category_aro_description":"Cefalexin is a cephalosporin antibiotic that causes filamentation. It is resistant to staphylococcal beta-lactamase, but degraded by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"36986":{"category_aro_accession":"3000642","category_aro_cvterm_id":"36986","category_aro_name":"cefadroxil","category_aro_description":"Cefadroxil, or p-hydroxycephalexin, is an cephalosporin antibiotic similar to cefalexin.","category_aro_class_name":"Antibiotic"},"36987":{"category_aro_accession":"3000643","category_aro_cvterm_id":"36987","category_aro_name":"cefotiam","category_aro_description":"Cefotiam is a cephalosporin antibiotic with similar activity to cefuroxime but more active against enterobacteria. It is consumed orally as the prodrug cefotiam hexetil.","category_aro_class_name":"Antibiotic"},"36988":{"category_aro_accession":"3000644","category_aro_cvterm_id":"36988","category_aro_name":"cefaclor","category_aro_description":"Cefaclor is a semisynthetic cephalosporin derived from cephalexin. It has broad-spectrum antibiotic activity.","category_aro_class_name":"Antibiotic"},"36989":{"category_aro_accession":"3000645","category_aro_cvterm_id":"36989","category_aro_name":"cefotaxime","category_aro_description":"Cefotaxime is a semisynthetic cephalosporin taken parenterally. It is resistant to most beta-lactamases and active against Gram-negative rods and cocci due to its aminothiazoyl and methoximino functional groups.","category_aro_class_name":"Antibiotic"},"36990":{"category_aro_accession":"3000646","category_aro_cvterm_id":"36990","category_aro_name":"cefixime","category_aro_description":"Cefixime is a cephalosporin resistant to most beta-lactamases. It is active against many enterobacteria, but activity against staphylococci is poor.","category_aro_class_name":"Antibiotic"},"36991":{"category_aro_accession":"3000647","category_aro_cvterm_id":"36991","category_aro_name":"cefpodoxime","category_aro_description":"Cefpodoxime is a semisynthetic cephalosporin that acts similarly to cefotaxime with broad-spectrum activity. It is stable to many plasmid-mediated beta-lactamses. Cefpodoxime is consumed as the prodrug cefpodoxime proxetil.","category_aro_class_name":"Antibiotic"},"36992":{"category_aro_accession":"3000648","category_aro_cvterm_id":"36992","category_aro_name":"ceftibuten","category_aro_description":"Ceftibuten is a semisynthetic cephalosporin active against Gram-negative bacilli. It is resistant against many plasmid-mediated beta-lactamases.","category_aro_class_name":"Antibiotic"},"36993":{"category_aro_accession":"3000649","category_aro_cvterm_id":"36993","category_aro_name":"cefditoren","category_aro_description":"Cefditoren is a semisynthetic cephalosporin active against staphylococci, streptococci, and and most enterobacteria. It is resistant to staphylococcal and most enterobacterial beta-lactamases, and is usually taken as the prodrug cefditoren pivoxil.","category_aro_class_name":"Antibiotic"},"36994":{"category_aro_accession":"3000650","category_aro_cvterm_id":"36994","category_aro_name":"cefdinir","category_aro_description":"Cefdinir is similar to cefixime with a modified side-chain at its 7-amino position. It also shares similar activity with cefixime but is more active against staphylococci. It has also be shown to enhance phagocytosis.","category_aro_class_name":"Antibiotic"},"36995":{"category_aro_accession":"3000651","category_aro_cvterm_id":"36995","category_aro_name":"ceftaroline","category_aro_description":"Ceftaroline is a novel cephalosporin active against methicillin resistant Staphylococcus aureus. Like other cephalosporins it binds penicillin-binding proteins to inhibit cell wall synthesis. It strongly binds with PBP2a, associated with methicillin resistance. It is taken orally as the prodrug ceftaroline fosamil.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"37085":{"category_aro_accession":"3000705","category_aro_cvterm_id":"37085","category_aro_name":"isopenicillin N","category_aro_description":"Isopenicillin N is a natural penicillin derivative produced by Penicillium chrysogenum with activity similar to penicillin N.","category_aro_class_name":"Antibiotic"},"37086":{"category_aro_accession":"3000706","category_aro_cvterm_id":"37086","category_aro_name":"penicillin N","category_aro_description":"Penicillin N is a penicillin derivative produced by Cephalosporium acremonium.","category_aro_class_name":"Antibiotic"},"37141":{"category_aro_accession":"3000761","category_aro_cvterm_id":"37141","category_aro_name":"mecillinam","category_aro_description":"Mecillinam is a broad-spectrum beta-lactam antibiotic that was semi-synthetically derived to have a different drug centre, being a 6-alpha-amidinopenicillanate instead of a 6-alpha-acylaminopenicillanate. Contrasting most beta-lactam drugs, mecillinam is most active against Gram-negative bacteria. It binds specifically to penicillin binding protein 2 (PBP2).","category_aro_class_name":"Antibiotic"},"40928":{"category_aro_accession":"3004001","category_aro_cvterm_id":"40928","category_aro_name":"cefmetazole","category_aro_description":"Cefmetazole is a semi-synthetic cephamycin antibiotic with broad spectrum antibiotic activity against both gram-positive and gram-negative bacteria, that disrupt cell wall synthesis through binding to PBPs causing cell lysis.","category_aro_class_name":"Antibiotic"},"40929":{"category_aro_accession":"3004002","category_aro_cvterm_id":"40929","category_aro_name":"cefonicid","category_aro_description":"Cefonicid is a second-generation cephalosporin-class beta-lactam antibiotic with broad spectrum activity. Particularly used against urinary tract infections and lower respiratory infections. Causes cell lysis by inactivation of PBPs through binding, inhibiting peptidoglycan synthesis.","category_aro_class_name":"Antibiotic"},"40932":{"category_aro_accession":"3004005","category_aro_cvterm_id":"40932","category_aro_name":"cefprozil","category_aro_description":"Cefprozil is a cephalosporin and beta-lactam antibiotic with bactericidal activity. It selectively binds to PBPs and inhibits peptidoglycan synthesis, a major cell wall component, resulting in cell lysis.","category_aro_class_name":"Antibiotic"},"40933":{"category_aro_accession":"3004006","category_aro_cvterm_id":"40933","category_aro_name":"ceftiofur","category_aro_description":"Ceftiofur is a third-generation broad spectrum cephalosporin and beta-lactam antibiotic. It causes cell lysis by disrupting peptidoglycan cross-linkage and cell wall formation by binding to PBPs.","category_aro_class_name":"Antibiotic"},"40934":{"category_aro_accession":"3004007","category_aro_cvterm_id":"40934","category_aro_name":"ceftizoxime","category_aro_description":"Ceftizoxime is a third-generation cephalosporin and broad spectrum beta-lactam antibiotic. Ceftizoxime causes bacterial cell lysis through peptidoglycan cross-linking inhibition by binding to PBPs.","category_aro_class_name":"Antibiotic"},"40935":{"category_aro_accession":"3004008","category_aro_cvterm_id":"40935","category_aro_name":"cephapirin","category_aro_description":"Cephapirin is a first-generation cephalosporin and broad spectrum beta-lactam antibiotic. Inactivation of penicillin-binding proteins through cephapirin binding disrupts peptidoglycan cross-linking, resulting in cell lysis.","category_aro_class_name":"Antibiotic"},"40936":{"category_aro_accession":"3004009","category_aro_cvterm_id":"40936","category_aro_name":"cefradine","category_aro_description":"Cefradine is a first-generation cephalosporin and broad spectrum beta-lactam antibiotic. Cefradine binding to penicillin-binding proteins disrupts cell wall peptidoglycan cross-linkage, resulting in cell lysis.","category_aro_class_name":"Antibiotic"},"40943":{"category_aro_accession":"3004016","category_aro_cvterm_id":"40943","category_aro_name":"loracarbef","category_aro_description":"Loracarbef is a second-generation cephalosporin (carbacephem) and broad spectrum beta-lactam antibiotic. Loracarbef inhibits PBPs through binding, disrupting peptidoglycan cell wall cross-linkage and resulting in cell death.","category_aro_class_name":"Antibiotic"},"40944":{"category_aro_accession":"3004017","category_aro_cvterm_id":"40944","category_aro_name":"moxalactam","category_aro_description":"Moxalactam (Latamoxef) is a broad spectrum cephalosporin (oxacephem) and beta-lactam antibiotic. Moxalactam binding to PBPs inhibits peptidoglycan cross-linkage in the cell wall, resulting in cell death. Moxalactam is proposed to be effective against meningitides as it passes the blood-brain barrier.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35962":{"category_aro_accession":"0000044","category_aro_cvterm_id":"35962","category_aro_name":"cephamycin","category_aro_description":"Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2888":{"model_id":"2888","model_name":"HERA-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4274":{"protein_sequence":{"accession":"AAL26797.1","sequence":"MKKITPLFVIAFLTLIALLAPAQASVTPDMTDFLRQQEQRLHARIGMAVVNAQGETVFGYRQDERFPLTSTFKTLACAALLERLQKNGGSLDEQVTIPPDALLDYAPVTKNYLAPATISLRMLCAAAVSYSDNTAGNRILTYLGGPDAVTQFMRGIGDHVTRLDRTEPTLNEATPGDARDTSSPQKMAAGLQKILTSPPLISANRATLAQWMRDDKVGDALLRAALPKGWAIADKTGAGGYGSRAIIAAVYPPERPPFYVAIFITQTEASMKMANETIAEIGKQLFAGQP"},"dna_sequence":{"accession":"AF311385.1","fmin":"0","fmax":"873","strand":"+","sequence":"ATGAAAAAAATCACCCCGCTCTTTGTCATCGCATTTCTGACTCTGATCGCGTTACTGGCCCCGGCGCAGGCCTCCGTCACGCCAGATATGACGGACTTTTTACGCCAGCAGGAGCAACGGCTTCACGCCAGAATTGGCATGGCGGTTGTCAACGCGCAAGGCGAAACGGTGTTCGGTTATCGGCAGGACGAGCGTTTCCCGCTGACCAGCACCTTTAAAACCCTGGCCTGCGCCGCGTTGCTTGAGCGGTTGCAGAAAAACGGCGGTTCGCTGGATGAACAGGTGACTATTCCGCCAGACGCCTTGCTGGACTATGCGCCAGTGACTAAAAACTACCTCGCCCCTGCCACCATCTCTTTACGCATGCTGTGCGCGGCGGCGGTGAGCTACAGCGACAACACGGCGGGCAACCGCATTCTGACTTACCTTGGCGGCCCTGATGCCGTCACGCAGTTTATGCGCGGGATCGGCGACCATGTGACCCGTCTGGATCGAACGGAGCCCACGCTGAATGAAGCCACGCCAGGCGATGCGCGCGATACCTCTTCGCCGCAGAAGATGGCGGCAGGGCTGCAAAAAATCCTCACCTCCCCTCCCCTGATATCGGCTAACCGGGCGACGCTGGCGCAGTGGATGCGTGACGATAAAGTGGGAGATGCGCTGCTACGCGCCGCGCTGCCGAAAGGCTGGGCAATTGCCGATAAAACCGGGGCGGGCGGCTACGGCTCGCGGGCGATTATCGCGGCGGTCTATCCGCCGGAACGCCCGCCGTTTTATGTCGCGATTTTTATTACGCAAACGGAAGCCTCGATGAAAATGGCAAATGAAACCATTGCTGAAATCGGCAAGCAGTTGTTTGCCGGGCAGCCCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41643","NCBI_taxonomy_name":"Atlantibacter hermannii","NCBI_taxonomy_id":"565"}}}},"ARO_accession":"3004448","ARO_id":"41642","ARO_name":"HERA-1","ARO_description":"A class A beta-lactamase with penicillinase activity described in Atlantibacter (Escherichia) hermannii","ARO_category":{"41641":{"category_aro_accession":"3004447","category_aro_cvterm_id":"41641","category_aro_name":"HERA beta-lactamase","category_aro_description":"A class A beta-lactamase family shown to hydrolyze penicillin but without cephalosporinase activity.","category_aro_class_name":"AMR Gene Family"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2889":{"model_id":"2889","model_name":"TRU-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4275":{"protein_sequence":{"accession":"WP_042027926.1","sequence":"MKQRIALSLLALGPLLLVPRVYAAADEPMANIVEKAVQPLLEEYRIPGMAVAVLKEGKPHYFNYGVANRESGRRISERTLFEIGSVSKTFTATLGTYAVVKGGFRLDDKVSQHAPWLQNSAFDRVTMAQLATYSAGGLPLQFPDAVDSNERMRQYYRQWSPLYAAGTHREYSNPSIGLFGHLAASTLGQPFRQLMSQTLLPKLDLQHTYLEVPDAAMVDYAYGYSKEDKPVRVNPGVLADEAYGIKTSAADLIKFVGANMTGSGDKAVQQALAMTRTGFYSVGEMTQGLGWESYAYPVTEQALLAGNSPAVSFKANPVKPFVAPRVMGNERLYNKTGSTNGFGAYVVFVPARGVGIVMLANRNYPIEARVKAAYAIMRHLAP"},"dna_sequence":{"accession":"NG_047550.1","fmin":"0","fmax":"1149","strand":"+","sequence":"ATGAAACAACGAATCGCGCTATCACTGCTGGCATTGGGGCCCCTGTTGCTCGTCCCACGCGTTTATGCCGCGGCAGATGAGCCCATGGCGAACATAGTGGAAAAGGCTGTCCAGCCGCTGCTGGAGGAGTACCGGATCCCGGGCATGGCGGTCGCCGTGCTGAAGGAGGGCAAGCCTCACTACTTCAATTATGGCGTCGCCAATCGGGAGAGCGGCCGGCGCATCAGCGAGCGGACCCTGTTCGAGATTGGTTCGGTCAGCAAGACCTTTACTGCGACCTTGGGCACCTACGCGGTCGTCAAAGGGGGCTTTCGGCTGGATGACAAGGTGAGCCAGCACGCGCCTTGGTTGCAGAATTCGGCGTTTGATCGCGTCACCATGGCCCAGCTGGCGACCTACAGCGCAGGGGGCTTGCCGTTGCAGTTTCCCGATGCGGTCGACTCAAACGAGAGAATGCGCCAGTACTACCGGCAGTGGTCACCGCTTTATGCGGCAGGCACTCATCGCGAGTACTCCAACCCCAGCATAGGTCTGTTCGGCCATCTGGCGGCGAGCACCCTGGGCCAACCATTCAGACAACTGATGAGCCAGACTCTGCTGCCCAAGCTCGATTTGCAGCACACCTATCTCGAGGTGCCAGACGCAGCCATGGTTGACTACGCCTATGGCTATTCGAAGGAAGACAAACCCGTCAGGGTCAATCCCGGAGTGCTGGCGGACGAAGCCTATGGCATCAAGACCAGCGCGGCGGATCTCATCAAGTTTGTGGGCGCCAACATGACAGGCAGTGGCGACAAGGCGGTGCAGCAAGCGCTGGCCATGACCCGTACCGGTTTCTACTCGGTGGGAGAGATGACCCAGGGGCTGGGGTGGGAGAGCTACGCCTATCCCGTGACCGAACAGGCGCTGCTGGCGGGCAATTCACCGGCGGTGAGCTTCAAGGCCAATCCGGTCAAACCCTTTGTGGCTCCCAGAGTGATGGGGAACGAGCGACTCTACAACAAGACAGGCTCGACCAACGGCTTTGGTGCCTATGTGGTGTTTGTCCCGGCCAGAGGCGTGGGCATCGTCATGCTGGCCAATCGCAACTACCCCATCGAGGCCAGGGTCAAGGCTGCCTATGCCATCATGCGCCATCTGGCACCCTGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41646","NCBI_taxonomy_name":"Aeromonas enteropelogenes","NCBI_taxonomy_id":"29489"}}}},"ARO_accession":"3004450","ARO_id":"41645","ARO_name":"TRU-1","ARO_description":"A class C beta-lactamase enzyme identified from Aeromonas enteropelogenes. TRU-1 confers resistance to penicillin and cephalosporin antibiotics.","ARO_category":{"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"237":{"model_id":"237","model_name":"Chryseobacterium meningosepticum BlaB","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"4414":{"protein_sequence":{"accession":"WP_029728367.1","sequence":"MLKKIKISLILALGLTSLKAFGQENPDVKIEKLKDNLYVYTTYNTFNGTKYAANAVYLVTDKGVVVIDCPWGEDKFKSFTDEIYKKHGKKVIMNIATHSHDDRAGGLEYFGKIGAKTYSTKMTDSILAKENKPRAQYTFDNNKSFKVGKSEFQVYYPGKGHTADNVVVWFPKEKVLVGGCIIKSADSKDLGYIGEAYVNDWTQSVHNIQQKFSGAQYVVAGHDDWKDQRSIQHTLDLINEYQQKQKASN"},"dna_sequence":{"accession":"NZ_CP007547.1","fmin":"3053571","fmax":"3054321","strand":"-","sequence":"TTAATTTGAAGCCTTTTGTTTTTGTTGATATTCATTGATTAAGTCTAGTGTATGTTGTATTGATCTTTGATCTTTCCAATCATCATGCCCTGCAACAACGTACTGAGCACCGGAAAACTTTTGTTGAATATTGTGTACAGACTGCGTCCAGTCGTTTACATATGCTTCTCCAATATACCCCAGGTCCTTTGAATCAGCACTTTTTATAATACAACCTCCAACCAATACTTTTTCTTTTGGAAACCATACCACCACATTATCTGCTGTGTGCCCTTTTCCGGGATAGTAAACCTGAAACTCGGATTTTCCTACTTTGAAAGATTTATTATTGTCAAAAGTATATTGTGCTCTTGGCTTATTCTCTTTTGCTAAAATAGAATCTGTCATTTTAGTAGAATAAGTTTTTGCACCTATTTTACCAAAATATTCAAGACCTCCGGCACGATCATCATGAGAATGTGTTGCAATATTCATAATAACTTTCTTTCCGTGTTTTTTATAAATCTCGTCCGTAAAGCTTTTAAATTTGTCTTCTCCCCACGGACAGTCTATAACCACAACACCCTTATCAGTTACCAGATATACTGCATTTGCGGCATATTTAGTCCCGTTAAATGTATTGTAGGTTGTGTATACATACAGATTATCTTTTAGCTTTTCAATTTTGACATCAGGATTCTCCTGTCCAAATGCCTTCAAACTGGTAAGCCCAAGAGCAAGAATCAAGCTTATTTTTATTTTTTTCAACAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41081","NCBI_taxonomy_name":"Elizabethkingia anophelis","NCBI_taxonomy_id":"1117645"}}}},"ARO_accession":"3000579","ARO_id":"36718","ARO_name":"Chryseobacterium meningosepticum BlaB","ARO_description":"This BlaB specific to Chryseobacterium meningosepticum mediates resistance against many beta-lactam antibiotics, notably penams and carbapenems.","ARO_category":{"41365":{"category_aro_accession":"3004201","category_aro_cvterm_id":"41365","category_aro_name":"BlaB beta-lactamase","category_aro_description":"BlaB beta-lactamases are class B beta-lactamases that are found in a variety of species and have the ability to hydrolyze penams and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2890":{"model_id":"2890","model_name":"Agrobacterium fabrum chloramphenicol acetyltransferase","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"4423":{"protein_sequence":{"accession":"AAA22081.1","sequence":"MENYFESPFRGITLDKQVKSPNLVVGKYSYYSGYYHGHSFEDCARYLLPDEGADRLVIGSFCSIGSGAAFIMAGNQGHRNEWISTFPFFFMPEVPEFENAANGYLPAGDTVIGNDVWIGSEAIIMPGITVGDGAVIGTRALVTKDVEPYAIVGGNPAKTIRKRFDDDSIALLLEMKWWGWPAERLKAAMPLMTSGNVAALYRFWRSDSL"},"dna_sequence":{"accession":"M58472.1","fmin":"147","fmax":"777","strand":"+","sequence":"ATGGAAAACTATTTCGAAAGCCCATTCCGGGGCATTACACTCGACAAGCAGGTGAAGAGCCCGAACCTGGTGGTCGGAAAATACAGCTATTATTCCGGCTATTACCACGGCCACAGTTTCGAGGATTGCGCCCGGTACCTGCTGCCCGATGAGGGCGCGGACAGGCTGGTGATCGGAAGCTTCTGCTCGATCGGTTCGGGCGCCGCCTTCATCATGGCGGGCAATCAGGGGCACCGCAACGAATGGATCAGTACCTTCCCGTTCTTCTTCATGCCGGAGGTGCCGGAATTCGAGAATGCCGCCAACGGTTATCTGCCGGCGGGCGACACCGTCATCGGCAACGATGTCTGGATCGGTTCGGAAGCGATCATCATGCCCGGCATCACCGTCGGTGATGGCGCGGTGATCGGAACGCGGGCGCTGGTGACGAAGGACGTCGAGCCCTACGCCATCGTCGGCGGCAACCCCGCAAAAACGATCCGCAAGCGGTTTGACGACGATAGCATCGCCCTGCTGCTCGAGATGAAATGGTGGGGCTGGCCGGCGGAGCGGCTGAAAGCTGCAATGCCGCTGATGACCAGCGGCAATGTCGCGGCGCTCTATCGTTTCTGGCGGTCCGATAGCCTCTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36775","NCBI_taxonomy_name":"Agrobacterium tumefaciens str. C58","NCBI_taxonomy_id":"176299"}}}},"ARO_accession":"3004451","ARO_id":"41662","ARO_name":"Agrobacterium fabrum chloramphenicol acetyltransferase","ARO_description":"A chloramphenicol resistance determinant described in the Gram-negative bacterium Agrobacterium fabrum.","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. cat is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Bacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2891":{"model_id":"2891","model_name":"Bacillus clausii chloramphenicol acetyltransferase","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"4424":{"protein_sequence":{"accession":"AAQ63644.1","sequence":"MEILTLLIRDTMGSKRIFLNPYFQQQPTFSLTNEINITILMKNLKKKHYKLYPAFIFMVTKIVNAHREFRINFNSEGNLGYWTEICPLYTIFDNKSHTFSGIWSPNLTIFSEFHSKYENDAERYNGTRRLFPKKPIPDNPIPISMIPWSSFTAFNLNINNGGDFLLPIITGGKYSQVNDELFLPVSIQNASCLFVMATMQSVFINDLQNLVDESEDWIYLVVSDEWYY"},"dna_sequence":{"accession":"AY238971.1","fmin":"1054","fmax":"1741","strand":"+","sequence":"ATGGAAATTTTAACACTATTAATTCGTGATACCATGGGATCGAAAAGAATATTTTTGAACCCCTATTTCCAGCAGCAGCCAACATTCAGTCTGACGAATGAAATTAATATAACTATACTTATGAAGAACTTAAAGAAAAAGCATTATAAGTTATATCCTGCGTTTATTTTTATGGTGACAAAAATCGTGAACGCCCATAGAGAATTTAGAATAAATTTTAACTCAGAAGGAAATTTAGGTTACTGGACGGAGATTTGCCCACTCTATACCATTTTTGATAACAAATCACACACATTTTCTGGCATCTGGTCACCAAACTTAACTATTTTTTCTGAGTTTCATTCTAAATATGAAAATGATGCAGAAAGATACAATGGCACGAGGAGATTATTTCCAAAAAAACCAATACCAGATAACCCTATTCCGATTTCTATGATTCCTTGGAGTTCTTTTACAGCATTTAATCTAAATATAAATAATGGCGGAGATTTTCTCTTACCCATAATAACTGGAGGGAAGTATTCACAAGTAAATGATGAATTATTCCTGCCTGTCTCTATCCAAAATGCATCATGCCTATTTGTGATGGCTACCATGCAAAGTGTTTTTATCAATGACTTACAAAACCTTGTTGATGAAAGTGAAGACTGGATTTACCTGGTCGTTAGTGATGAATGGTATTATTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36882","NCBI_taxonomy_name":"Bacillus clausii","NCBI_taxonomy_id":"79880"}}}},"ARO_accession":"3004452","ARO_id":"41663","ARO_name":"Bacillus clausii chloramphenicol acetyltransferase","ARO_description":"A chloramphenicol resistance determinant described in Bacillus clausii.","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. cat is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Bacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2892":{"model_id":"2892","model_name":"Proteus mirabilis chloramphenicol acetyltransferase","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"4425":{"protein_sequence":{"accession":"AAQ63644.1","sequence":"MEILTLLIRDTMGSKRIFLNPYFQQQPTFSLTNEINITILMKNLKKKHYKLYPAFIFMVTKIVNAHREFRINFNSEGNLGYWTEICPLYTIFDNKSHTFSGIWSPNLTIFSEFHSKYENDAERYNGTRRLFPKKPIPDNPIPISMIPWSSFTAFNLNINNGGDFLLPIITGGKYSQVNDELFLPVSIQNASCLFVMATMQSVFINDLQNLVDESEDWIYLVVSDEWYY"},"dna_sequence":{"accession":"M11587.1","fmin":"879","fmax":"1533","strand":"+","sequence":"ATGGACACAAAGCGCGTGGGTATATTGGTTGTTGATCTATCCCAATGGGGACGAAAAGAACACTTTGAAGCATTTCAGTCTTTTGCTCAATGCACCTTTAGCCAGACCGTTCAACTGGATATTACTTCATTATTAAAAACCGTAAAGCAAAATGGGTACAAATTCTATCCGACATTTATATACATCATTAGCCTATTGGTAAATAAACATGCAGAATTCCGCATGGCAATGAAAGACGGGGAATTGGTGATATGGGATAGTGTTAACCCTGGGTACAATATCTTTCATGAACAGACCGAAACATTTTCATCTTTATGGAGTTACTACCACAAAGATATCAATCGTTTTTTGAAAACTTATTCAGAAGATATAGCACAATACGGCGACGATCTAGCCTATTTTCCAAAAGAATTTATCGAAAATATGTTTTTTGTGTCAGCAAATCCTTGGGTAAGTTTCACCAGTTTTAACTTGAATATGGCGAATATAAACAATTTCTTTGCCCCTGTATTTACAATAGGTAAATATTATACGCAAGGAGATAAAGTTCTGATGCCACTAGCAATTCAAGTGCATCATGCCGTATGTGATGGCTTCCATGTAGGCAGATTACTCAATGAAATACAGCAATACTGCGATGAGGGATGTAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36882","NCBI_taxonomy_name":"Bacillus clausii","NCBI_taxonomy_id":"79880"}}}},"ARO_accession":"3004453","ARO_id":"41664","ARO_name":"Proteus mirabilis chloramphenicol acetyltransferase","ARO_description":"A chloramphenicol resistance determinant described in Proteus mirabilis.","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. cat is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Bacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2893":{"model_id":"2893","model_name":"Campylobacter coli chloramphenicol acetyltransferase","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"4426":{"protein_sequence":{"accession":"AAA23018.1","sequence":"MQFTKIDINNWTRKEYFDHYFGNTPCTYSMTVKLDISKLKKDGKKLYPTLLYGVTTIINRHEEFRTALDENGQVGVFSEMLPCYTVFHKETETFSSIWTEFTADYTEFLQNYQKDIDAFGERMGMSAKPNPPENTFPVSMIPWTSFEGFNLNLKKGYDYLLPIFTFGKYYEEGGKYYIPLSIQVHHAVCDGFHVCRFLDELQDLLNK"},"dna_sequence":{"accession":"M35190.1","fmin":"308","fmax":"932","strand":"+","sequence":"ATGCAATTCACAAAGATTGATATAAATAATTGGACACGAAAAGAGTATTTCGACCACTATTTTGGCAATACGCCCTGCACATATAGTATGACGGTAAAACTCGATATTTCTAAGTTGAAAAAGGATGGAAAAAAGTTATACCCAACTCTTTTATATGGAGTTACAACGATCATCAATCGACATGAAGAGTTCAGGACCGCATTAGATGAAAACGGACAGGTAGGCGTTTTTTCAGAAATGCTGCCTTGCTACACAGTTTTTCATAAGGAAACTGAAACCTTTTCGAGTATTTGGACTGAGTTTACAGCAGACTATACTGAGTTTCTTCAGAACTATCAAAAGGATATAGACGCTTTTGGTGAACGAATGGGAATGTCCGCAAAGCCTAATCCTCCGGAAAACACTTTCCCTGTTTCTATGATACCGTGGACAAGCTTTGAAGGCTTTAACTTAAATCTAAAAAAAGGATATGACTATCTACTGCCGATATTTACGTTTGGGAAGTATTATGAGGAGGGCGGAAAATACTATATTCCCTTATCGATTCAAGTGCATCATGCCGTTTGTGACGGCTTTCATGTTTGCCGTTTTTTGGATGAATTACAAGACTTGCTGAATAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36835","NCBI_taxonomy_name":"Campylobacter coli","NCBI_taxonomy_id":"195"}}}},"ARO_accession":"3004454","ARO_id":"41665","ARO_name":"Campylobacter coli chloramphenicol acetyltransferase","ARO_description":"A chloramphenicol resistance determinant described in Campylobacter coli.","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. cat is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Bacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2894":{"model_id":"2894","model_name":"Streptococcus suis chloramphenicol acetyltransferase","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"4427":{"protein_sequence":{"accession":"BAC11901.1","sequence":"MNFNKIDLDNWKRKEIFNHYLNQQTTFSITTEIDISVLYRNIKQKRYKFYPAFVFLVTRVINSNTAFRTGYNSEGELGYWDKLDPLYTIFDSVSKTFSGIWTPARNDFKEFYDLYLSDVEKYNGSGKLFPKTPIPENAFSISIIPWTSFTGFNLNINNNSNYLLPIITAGKFINKGNSIYLPLSLQVHHSVCDGYHAGLFMNSIQELADRPNDWLF"},"dna_sequence":{"accession":"AB080798.1","fmin":"2658","fmax":"3309","strand":"+","sequence":"ATGAACTTTAATAAAATTGATTTAGACAATTGGAAGAGAAAAGAGATATTTAATCATTATTTGAACCAACAAACGACTTTTAGTATAACCACAGAAATTGATATTAGTGTTTTATACCGAAACATAAAACAAAAAAGATATAAATTTTATCCTGCATTTGTTTTCTTAGTGACAAGGGTGATAAACTCAAATACAGCTTTTAGAACTGGTTACAATAGCGAGGGAGAGTTAGGCTATTGGGATAAGTTAGACCCACTATACACAATTTTTGATAGTGTATCTAAAACATTCTCTGGTATTTGGACTCCTGCAAGGAATGACTTCAAAGAGTTTTATGATTTATACCTTTCTGATGTAGAGAAATATAATGGTTCGGGGAAATTGTTTCCCAAAACACCTATACCCGAAAATGCTTTTTCTATTTCTATTATTCCATGGACTTCATTTACTGGGTTTAACTTAAATATCAATAATAATAGTAATTATCTTCTACCCATTATTACAGCAGGAAAATTCATTAATAAAGGTAATTCAATATATTTACCGCTATCTTTACAGGTACATCATTCTGTTTGTGATGGTTATCATGCAGGATTGTTTATGAACTCTATTCAGGAATTGGCAGATAGGCCTAATGACTGGCTTTTTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39534","NCBI_taxonomy_name":"Streptococcus suis","NCBI_taxonomy_id":"1307"}}}},"ARO_accession":"3004455","ARO_id":"41666","ARO_name":"Streptococcus suis chloramphenicol acetyltransferase","ARO_description":"A chloramphenicol resistance determinant described in Streptococcus suis.","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. cat is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Bacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2895":{"model_id":"2895","model_name":"Enterococcus faecium chloramphenicol acetyltransferase","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"4428":{"protein_sequence":{"accession":"NP_863168.1","sequence":"MTFNIINLETWDRKEYFNHYFNQQTTYSVTKELDITLLKSMIKDKGYELYPALIHAIVSVINRNKVFRTGINSEGNLGYWDKLEPLYTVFNKETEKFSNIWTESNASFNSFYNSYKNDLFKYKDKNEMFPKKPIPENTVPISMIPWIDFSSFNLNIGNNSRFLLPIITIGKFYSKDDKIYLPFSLQVHHAVCDGYHVSLFMNEFQNIIDNVNEWI"},"dna_sequence":{"accession":"NC_005000.1","fmin":"17463","fmax":"18111","strand":"+","sequence":"ATGACTTTTAATATTATTAATTTAGAAACTTGGGATAGAAAAGAATATTTCAATCATTATTTTAATCAACAAACAACTTATAGTGTTACTAAAGAATTAGATATTACCTTGTTAAAAAGTATGATAAAAGATAAAGGATATGAACTGTATCCTGCTTTGATTCATGCAATTGTAAGTGTTATAAATCGAAATAAAGTATTTAGAACAGGGATTAATAGTGAGGGGAATTTGGGTTATTGGGATAAATTAGAACCTTTATATACAGTCTTTAATAAAGAAACTGAAAAATTTTCTAATATTTGGACAGAATCAAATGCTAGTTTTAACTCTTTTTATAATAGTTATAAGAATGATTTATTTAAATATAAAGATAAAAATGAAATGTTTCCTAAAAAGCCGATACCTGAAAACACAGTTCCTATCTCGATGATTCCTTGGATTGATTTTAGTTCATTTAATTTAAATATTGGTAATAATAGTAGATTTTTATTGCCAATTATTACAATAGGTAAATTTTATAGTAAGGATGATAAGATCTATTTACCATTTTCATTGCAAGTTCATCATGCAGTATGTGATGGTTACCATGTTTCATTATTTATGAATGAATTTCAAAATATAATTGATAATGTAAATGAATGGATTTAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3004456","ARO_id":"41667","ARO_name":"Enterococcus faecium chloramphenicol acetyltransferase","ARO_description":"A chloramphenicol resistance determinant described in an Enterococcus faecium plasmid","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. cat is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Bacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2896":{"model_id":"2896","model_name":"Staphylococcus intermedius chloramphenicol acetyltransferase","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"4429":{"protein_sequence":{"accession":"AAA26615.1","sequence":"MTFNIIKLENWDRKEYFEHYFNQQTTYSITKEIDITLFKDMIKKKGYEIYPSLIYAIMEVVNKNKVFRTGINSENKLGYWDKLNPLYTVFNKQTEKFTNIWTESDNNFTSFYNNYKNDLFEYKDKEEMFPKKPIPENTIPISMIPWIDFSSFNLNIGNNSSFLLPIITIGKFYSENNKIYIPVALQLHHAVCDGYHASLFINEFQDIIKKVDDWI"},"dna_sequence":{"accession":"M64281.1","fmin":"207","fmax":"855","strand":"+","sequence":"ATGACTTTTAATATTATCAAATTAGAAAATTGGGATAGAAAAGAATATTTTGAACACTATTTTAACCAGCAAACTACGTATAGCATTACTAAAGAAATTGATATTACTTTGTTTAAAGATATGATAAAAAAGAAAGGATATGAAATTTATCCTTCTTTGATTTATGCAATTATGGAAGTTGTAAATAAAAATAAAGTGTTTAGAACAGGAATTAATAGTGAGAATAAATTAGGCTATTGGGATAAGTTAAATCCTTTGTATACAGTTTTTAATAAGCAAACTGAAAAATTTACTAACATTTGGACTGAATCTGATAACAACTTCACTTCTTTTTATAATAATTATAAAAATGACTTGTTTGAATATAAAGATAAAGAAGAAATGTTTCCTAAAAAACCGATACCTGAAAACACCATACCGATTTCAATGATTCCTTGGATTGATTTTAGTTCATTTAATTTAAACATTGGTAACAATAGCAGCTTTTTATTGCCTATTATTACGATAGGTAAATTTTATAGTGAGAATAATAAAATTTATATACCAGTTGCCTTACAGCTTCATCATGCTGTATGTGATGGTTACCATGCTTCATTATTTATAAATGAATTTCAAGATATAATTAAGAAGGTAGATGATTGGATTTAG"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36842","NCBI_taxonomy_name":"Staphylococcus intermedius","NCBI_taxonomy_id":"1285"}}}},"ARO_accession":"3004457","ARO_id":"41668","ARO_name":"Staphylococcus intermedius chloramphenicol acetyltransferase","ARO_description":"A chloramphenicol resistance determinant described in Staphylococcus intermedius","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. cat is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Bacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2897":{"model_id":"2897","model_name":"Enterococcus faecalis chloramphenicol acetyltransferase","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"4430":{"protein_sequence":{"accession":"CAA63498.2","sequence":"MTFNIIELENWDRKEYFEHYFNQQTTYSITKEIDITLFKDMIKKKGYEIYPSLIYAIMEVVNKNKVFRTGINSENKLGYWDKLNPLYTVFNKQTEKFTNIWTESDKNFISFYNNYKNDLLEYKDKEEMFPKKPIPENTIPISMIPWIDFSSFNLNIGNNSSFLLPIITIGKFYSENNKIYIPVALQLHHSVCDGYHASLFMNEFQDIIHRVDDWI"},"dna_sequence":{"accession":"X92945.2","fmin":"8934","fmax":"9582","strand":"-","sequence":"CTAAATCCAATCATCTACCCTATGAATTATATCTTGAAATTCATTCATAAATAGTGAAGCATGGTAACCATCACATACAGAATGATGAAGTTGCAGAGCAACTGGTATATAAATTTTATTATTCTCACTATAAAATTTACCTATCGTAATAATAGGCAATAAAAAGCTGCTATTGTTACCAATATTTAAATTAAATGAACTAAAATCAATCCAAGGAATCATTGAAATCGGTATGGTGTTTTCAGGTATCGGTTTTTTAGGAAACATTTCTTCTTTATCTTTATATTCAAGCAAGTCATTTTTATAATTATTATAAAAAGAAATGAAGTTTTTATCAGATTCAGTCCAAATGTTAGTAAATTTTTCAGTTTGCTTATTAAAAACTGTATACAAAGGATTTAACTTATCCCAATAACCTAATTTATTCTCACTATTAATTCCTGTTCTAAACACTTTATTTTTATTTACAACTTCCATAATTGCATAAATTAAAGAGGGATAAATTTCATATCCTTTCTTTTTTATCATATCTTTAAACAAAGTAATATCAATTTCTTTAGTAATGCTATAAGTAGTTTGCTGATTAAAATAGTGTTCAAAATATTCTTTTCTATCCCAATTTTCTAATTCAATAATATTAAAAGTCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3004458","ARO_id":"41669","ARO_name":"Enterococcus faecalis chloramphenicol acetyltransferase","ARO_description":"A chloramphenicol acetyltransferase and resistance determinant described in Enterococcus faecalis","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. cat is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Bacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2898":{"model_id":"2898","model_name":"Shigella flexneri chloramphenicol acetyltransferase","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"4431":{"protein_sequence":{"accession":"AAL08441.1","sequence":"MEKKITGYTTVDISQWHRKEHFEAFQSVAQCTYNQTVQLDITAFLKTVKKNKHKFYPAFIHILARLMNAHPEFRMAMKDGELVIWDSVHPCYTVFHEQTETFSSLWSEYHDDFRQFLHIYSXDVACYGENLAYFPKXFXENMXFVSANPWVSFTSFDLNVANMDNFFAPVFTMGKYYTQGDKVLMPLAIQVHHAVCDGFHVGRMLNELQQYCDEWQGGA"},"dna_sequence":{"accession":"AF326777.3","fmin":"23980","fmax":"24640","strand":"-","sequence":"TTACGCCCCGCCCTGCCACTCATCGCAGTACTGTTGTAATTCATTAAGCATTCTGCCGACATGGAAGCCATCACAAACGGCATGATGAACCTGAATCGCCAGCGGCATCAGCACCTTGTCGCCTTGCGTATAATATTTGCCCATGGTGAAAACGGGGGCGAAGAAGTTGTCCATATTGGCCACGTTTAAATCAAAACTGGTGAAACTCACCCAGGGATTGGCTGAGACGAAANACATATTCTCNATAAACCNTTTAGGGAAATAGGCCAGGTTTTCACCGTAACACGCCACATCTNGCGAATATATGTGTAGAAACTGCCGGAAATCGTCGTGGTATTCACTCCAGAGCGATGAAAACGTTTCAGTTTGCTCATGGAAAACGGTGTAACAAGGGTGAACACTATCCCATATCACCAGCTCACCGTCTTTCATTGCCATACGGAATTCCGGATGAGCATTCATCAGGCGGGCAAGAATGTGAATAAAGGCCGGATAAAACTTGTGCTTATTTTTCTTTACGGTCTTTAAAAAGGCCGTAATATCCAGCTGAACGGTCTGGTTATAGGTACATTGAGCAACTGACTGAAATGCCTCAAAATGTTCTTTACGATGCCATTGGGATATATCAACGGTGGTATATCCAGTGATTTTTTTCTCCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39537","NCBI_taxonomy_name":"Shigella flexneri 2a","NCBI_taxonomy_id":"42897"}}}},"ARO_accession":"3004459","ARO_id":"41670","ARO_name":"Shigella flexneri chloramphenicol acetyltransferase","ARO_description":"A chloramphenicol acetyltransferase and chloramphenicol resistance determinant described in Shigella flexneri","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. cat is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Bacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2899":{"model_id":"2899","model_name":"Vibrio anguillarum chloramphenicol acetyltransferase","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"4432":{"protein_sequence":{"accession":"AAB23649.1","sequence":"MEFRLVDLKTWKRKEYFTHYFESVPCTYSMTVKLDITTIKTGKAKLYPALLYAVSTVVNRHEEFRMTVDDEGQIGIFSEMMPCYTIFQKDTEMFSNIWTEYIGDYTEFCKQYEKDMQQYGENKGMMAKPNPPVNTFPVSMIPWTTFEGFNLNLQKGYGYLLPIFTFGRYYEENGKYWIPLSIQVHHAVCDGFHTCRFINELQDVIQSLQNHGGDEE"},"dna_sequence":{"accession":"S48276.1","fmin":"478","fmax":"1129","strand":"+","sequence":"ATGGAGTTTCGTTTGGTTGATCTGAAAACATGGAAAAGAAAAGAGTACTTTACGCATTATTTTGAATCTGTGCCTTGCACATATAGCATGACCGTAAAGCTGGATATTACTACGATAAAAACCGGTAAAGCGAAATTGTATCCCGCCCTTTTGTATGCCGTTTCAACAGTAGTTAACCGGCATGAAGAATTCCGTATGACTGTGGACGATGAAGGTCAAATCGGGATATTTAGTGAAATGATGCCGTGCTATACAATTTTCCAAAAGGACACGGAGATGTTTTCAAATATCTGGACCGAGTATATCGGTGATTATACGGAGTTCTGCAAACAGTATGAAAAAGATATGCAGCAATACGGTGAAAACAAGGGCATGATGGCAAAGCCAAATCCGCCTGTGAATACTTTCCCAGTCTCTATGATTCCATGGACAACCTTTGAAGGATTTAATTTAAATTTGCAAAAGGGATATGGGTATCTGCTTCCCATTTTTACGTTTGGACGATATTATGAAGAAAACGGGAAATATTGGATTCCGTTATCTATTCAGGTACATCATGCGGTATGCGATGGATTTCATACCTGCCGTTTTATCAATGAATTACAGGATGTAATCCAAAGTTTACAAAACCATGGAGGTGACGAAGAATGA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39536","NCBI_taxonomy_name":"Vibrio anguillarum","NCBI_taxonomy_id":"55601"}}}},"ARO_accession":"3004460","ARO_id":"41671","ARO_name":"Vibrio anguillarum chloramphenicol acetyltransferase","ARO_description":"A chloramphenicol resistance determinant described in a Vibrio anguillarum plasmid sequence","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. cat is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Bacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1042":{"model_id":"1042","model_name":"Pseudomonas aeruginosa catB7","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"4375":{"protein_sequence":{"accession":"NP_249397.1","sequence":"MGNYFESPFRGKLLSEQVSNPNIRVGRYSYYSGYYHGHSFDDCARYLMPDRDDVDKLVIGSFCSIGSGAAFIMAGNQGHRAEWASTFPFHFMHEEPVFAGAVNGYQPAGDTLIGHDVWIGTEAMFMPGVRVGHGAIIGSRALVTGDVEPYAIVGGNPARTIRKRFSDGDIQNLLEMAWWDWPLADIEAAMPLLCTGDIPALYRHWKQRQATA"},"dna_sequence":{"accession":"NC_002516","fmin":"779462","fmax":"780101","strand":"-","sequence":"TCAGGCCGTGGCCTGGCGCTGTTTCCAGTGCCGGTACAAGGCGGGGATATCCCCAGTACACAGCAGTGGCATGGCTGCCTCGATATCGGCCAGTGGCCAGTCCCACCAGGCCATTTCCAGCAGGTTCTGGATATCGCCATCGGAAAAGCGCTTACGAATGGTCCGGGCCGGGTTACCGCCGACGATGGCATAGGGCTCGACATCGCCGGTCACCAGCGCGCGGCTGCCGATGATGGCTCCGTGGCCGACCCGTACGCCGGGCATGAACATCGCCTCGGTACCGATCCAGACGTCATGGCCGATCAGCGTGTCGCCGGCTGGCTGATAGCCGTTCACGGCGCCGGCGAAGACAGGCTCTTCGTGCATGAAGTGGAAGGGGAAGGTCGACGCCCATTCGGCGCGGTGTCCCTGGTTGCCGGCCATGATGAAGGCGGCGCCACTGCCGATCGAGCAGAAACTGCCGATGACCAGCTTGTCCACGTCGTCGCGGTCCGGCATCAGGTAGCGGGCGCAGTCGTCGAAGGAATGCCCGTGATAGTAGCCGGAGTAGTAGCTGTAGCGCCCCACCCGTATGTTCGGGTTGCTGACCTGTTCCGAGAGCAGCTTGCCCCTGAAGGGGCTCTCGAAATAGTTGCCCAT"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3002679","ARO_id":"39113","ARO_name":"Pseudomonas aeruginosa catB7","ARO_description":"catB7 is a chromosome-encoded variant of the cat gene found in Pseudomonas aeruginosa","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. cat is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Bacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini","category_aro_class_name":"AMR Gene Family"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2900":{"model_id":"2900","model_name":"EBR-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: \"perfect\", \"strict\" and \"loose\". A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences.","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"4438":{"protein_sequence":{"accession":"ALG03771.1","sequence":"MKKIFSLIALIGSFAFGQIKPIQIDPINNNLFVYQTFNSFNDVEYNANGMYLVTNKGIVLFDVPWQKSQYQELNDILQEKYNLPVIAVFATHSHDDRAGDLSFYNELNIPTYATSLTNSKLKKEGKATSKFEIELGKTYKFGNEKFVVEYFGEGHTSDNVVVWFPKYKVLNGGCLIKGADAVNLGYTGEANVVEWPKTVHKLVAKHPTIKQVIPGHDNWKATGHIENTFKLLEKK"},"dna_sequence":{"accession":"KR131616.1","fmin":"0","fmax":"708","strand":"+","sequence":"ATGAAAAAAATATTTTCACTTATTGCATTGATAGGAAGTTTTGCATTTGGTCAAATAAAACCAATTCAAATTGATCCAATTAATAATAATCTATTTGTTTATCAAACATTTAATTCGTTTAATGATGTTGAATATAATGCAAATGGAATGTATTTGGTAACGAATAAAGGAATCGTTTTGTTTGATGTTCCTTGGCAGAAATCGCAGTATCAAGAGTTAAATGATATATTGCAAGAAAAGTATAATTTGCCAGTTATCGCTGTCTTTGCAACACATTCGCATGATGATAGAGCAGGAGATTTGAGTTTTTATAATGAGTTGAATATTCCTACTTATGCAACTTCTTTAACCAATTCTAAATTAAAAAAAGAAGGAAAAGCAACTTCTAAATTTGAGATTGAATTAGGTAAAACATACAAGTTTGGTAATGAAAAGTTTGTTGTTGAATATTTTGGAGAAGGACATACTTCTGATAATGTTGTGGTTTGGTTTCCGAAATATAAAGTGTTGAATGGAGGTTGTTTGATAAAGGGTGCTGATGCTGTAAATTTAGGTTACACAGGCGAAGCTAATGTTGTTGAATGGCCAAAAACAGTACACAAACTAGTTGCAAAACATCCAACGATTAAACAAGTTATTCCAGGTCATGATAATTGGAAAGCTACTGGACACATCGAAAATACGTTTAAACTTTTAGAAAAGAAATAA"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41679","NCBI_taxonomy_name":"Empedobacter falsenii","NCBI_taxonomy_id":"343874"}}}},"ARO_accession":"3004463","ARO_id":"41678","ARO_name":"EBR-2","ARO_description":"EBR-2 is a novel EBR-like class B beta-lactamase isolated from an extensively drug-resistant strain of Empedobacter falsenii","ARO_category":{"41368":{"category_aro_accession":"3004204","category_aro_cvterm_id":"41368","category_aro_name":"EBR beta-lactamase","category_aro_description":"EBR beta-lactamases are Class B beta-lactamases first isolated from Empedobacter brevis and are able to hydrolyze penicillins, cephalosporins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penam","category_aro_description":"Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"_version":"2.0.2","_comment":{"description":"This file contains the complete data for all of CARD's AMR detection models, including reference sequences, SNP mapping data, model parameters, and ARO classification.","access":"public"},"_timestamp":"2018-06-28T13:14:14+00:00"}